47 CFR 52.34 - Obligations regarding local number porting to and from interconnected VoIP or Internet-based TRS...

Code of Federal Regulations, 2010 CFR

2010-10-01

... and from interconnected VoIP or Internet-based TRS providers. 52.34 Section 52.34 Telecommunication... Portability § 52.34 Obligations regarding local number porting to and from interconnected VoIP or Internet-based TRS providers. (a) An interconnected VoIP or VRS or IP Relay provider must facilitate an end-user...

47 CFR 52.34 - Obligations regarding local number porting to and from interconnected VoIP or Internet-based TRS...

Code of Federal Regulations, 2011 CFR

2011-10-01

... and from interconnected VoIP or Internet-based TRS providers. 52.34 Section 52.34 Telecommunication... Portability § 52.34 Obligations regarding local number porting to and from interconnected VoIP or Internet-based TRS providers. (a) An interconnected VoIP or VRS or IP Relay provider must facilitate an end-user...

ChIP-seq.

PubMed

Kim, Tae Hoon; Dekker, Job

2018-05-01

Owing to its digital nature, ChIP-seq has become the standard method for genome-wide ChIP analysis. Using next-generation sequencing platforms (notably the Illumina Genome Analyzer), millions of short sequence reads can be obtained. The densities of recovered ChIP sequence reads along the genome are used to determine the binding sites of the protein. Although a relatively small amount of ChIP DNA is required for ChIP-seq, the current sequencing platforms still require amplification of the ChIP DNA by ligation-mediated PCR (LM-PCR). This protocol, which involves linker ligation followed by size selection, is the standard ChIP-seq protocol using an Illumina Genome Analyzer. The size-selected ChIP DNA is amplified by LM-PCR and size-selected for the second time. The purified ChIP DNA is then loaded into the Genome Analyzer. The ChIP DNA can also be processed in parallel for ChIP-chip results. © 2018 Cold Spring Harbor Laboratory Press.

ChIP and ChIP-Related Techniques: Expanding the Fields of Application and Improving ChIP Performance.

PubMed

Visa, Neus; Jordán-Pla, Antonio

2018-01-01

Protein-DNA interactions in vivo can be detected and quantified by chromatin immunoprecipitation (ChIP). ChIP has been instrumental for the advancement of epigenetics and has set the groundwork for the development of a number of ChIP-related techniques that have provided valuable information about the organization and function of genomes. Here, we provide an introduction to ChIP and discuss the applications of ChIP in different research areas. We also review some of the strategies that have been devised to improve ChIP performance.

Compact Modbus TCP/IP protocol for data acquisition systems based on limited hardware resources

NASA Astrophysics Data System (ADS)

Bai, Q.; Jin, B.; Wang, D.; Wang, Y.; Liu, X.

2018-04-01

The Modbus TCP/IP has been a standard industry communication protocol and widely utilized for establishing sensor-cloud platforms on the Internet. However, numerous existing data acquisition systems built on traditional single-chip microcontrollers without sufficient resources cannot support it, because the complete Modbus TCP/IP protocol always works dependent on a full operating system which occupies abundant hardware resources. Hence, a compact Modbus TCP/IP protocol is proposed in this work to make it run efficiently and stably even on a resource-limited hardware platform. Firstly, the Modbus TCP/IP protocol stack is analyzed and the refined protocol suite is rebuilt by streamlining the typical TCP/IP suite. Then, specific implementation of every hierarchical layer is respectively presented in detail according to the protocol structure. Besides, the compact protocol is implemented in a traditional microprocessor to validate the feasibility of the scheme. Finally, the performance of the proposed scenario is assessed. The experimental results demonstrate that message packets match the frame format of Modbus TCP/IP protocol and the average bandwidth reaches to 1.15 Mbps. The compact protocol operates stably even based on a traditional microcontroller with only 4-kB RAM and 12-MHz system clock, and no communication congestion or frequent packet loss occurs.

Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

PubMed Central

Euskirchen, Ghia M.; Rozowsky, Joel S.; Wei, Chia-Lin; Lee, Wah Heng; Zhang, Zhengdong D.; Hartman, Stephen; Emanuelsson, Olof; Stolc, Viktor; Weissman, Sherman; Gerstein, Mark B.; Ruan, Yijun; Snyder, Michael

2007-01-01

Recent progress in mapping transcription factor (TF) binding regions can largely be credited to chromatin immunoprecipitation (ChIP) technologies. We compared strategies for mapping TF binding regions in mammalian cells using two different ChIP schemes: ChIP with DNA microarray analysis (ChIP-chip) and ChIP with DNA sequencing (ChIP-PET). We first investigated parameters central to obtaining robust ChIP-chip data sets by analyzing STAT1 targets in the ENCODE regions of the human genome, and then compared ChIP-chip to ChIP-PET. We devised methods for scoring and comparing results among various tiling arrays and examined parameters such as DNA microarray format, oligonucleotide length, hybridization conditions, and the use of competitor Cot-1 DNA. The best performance was achieved with high-density oligonucleotide arrays, oligonucleotides ≥50 bases (b), the presence of competitor Cot-1 DNA and hybridizations conducted in microfluidics stations. When target identification was evaluated as a function of array number, 80%–86% of targets were identified with three or more arrays. Comparison of ChIP-chip with ChIP-PET revealed strong agreement for the highest ranked targets with less overlap for the low ranked targets. With advantages and disadvantages unique to each approach, we found that ChIP-chip and ChIP-PET are frequently complementary in their relative abilities to detect STAT1 targets for the lower ranked targets; each method detected validated targets that were missed by the other method. The most comprehensive list of STAT1 binding regions is obtained by merging results from ChIP-chip and ChIP-sequencing. Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies. PMID:17568005

Security Research on VoIP with Watermarking

NASA Astrophysics Data System (ADS)

Hu, Dong; Lee, Ping

2008-11-01

With the wide application of VoIP, many problems have occurred. One of the problems is security. The problems with securing VoIP systems, insufficient standardization and lack of security mechanisms emerged the need for new approaches and solutions. In this paper, we propose a new security architecture for VoIP which is based on digital watermarking which is a new, flexible and powerful technology that is increasingly gaining more and more attentions. Besides known applications e.g. to solve copyright protection problems, we propose to use digital watermarking to secure not only transmitted audio but also signaling protocol that VoIP is based on.

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

PubMed Central

Carroll, Thomas S.; Liang, Ziwei; Salama, Rafik; Stark, Rory; de Santiago, Ines

2014-01-01

With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention. The ENCODE consortium's large scale analysis of transcription factor binding and epigenetic marks as well as concordant work on ChIP-seq by other laboratories has established a new generation of ChIP-seq quality control measures. The use of these metrics alongside common processing steps has however not been evaluated. In this study, we investigate the effects of blacklisting and removal of duplicated reads on established metrics of ChIP-seq quality and show that the interpretation of these metrics is highly dependent on the ChIP-seq preprocessing steps applied. Further to this we perform the first investigation of the use of these metrics for ChIP-exo data and make recommendations for the adaptation of the NSC statistic to allow for the assessment of ChIP-exo efficiency. PMID:24782889

VoIP attacks detection engine based on neural network

NASA Astrophysics Data System (ADS)

Safarik, Jakub; Slachta, Jiri

2015-05-01

The security is crucial for any system nowadays, especially communications. One of the most successful protocols in the field of communication over IP networks is Session Initiation Protocol. It is an open-source project used by different kinds of applications, both open-source and proprietary. High penetration and text-based principle made SIP number one target in IP telephony infrastructure, so security of SIP server is essential. To keep up with hackers and to detect potential malicious attacks, security administrator needs to monitor and evaluate SIP traffic in the network. But monitoring and following evaluation could easily overwhelm the security administrator in networks, typically in networks with a number of SIP servers, users and logically or geographically separated networks. The proposed solution lies in automatic attack detection systems. The article covers detection of VoIP attacks through a distributed network of nodes. Then the gathered data analyze aggregation server with artificial neural network. Artificial neural network means multilayer perceptron network trained with a set of collected attacks. Attack data could also be preprocessed and verified with a self-organizing map. The source data is detected by distributed network of detection nodes. Each node contains a honeypot application and traffic monitoring mechanism. Aggregation of data from each node creates an input for neural networks. The automatic classification on a centralized server with low false positive detection reduce the cost of attack detection resources. The detection system uses modular design for easy deployment in final infrastructure. The centralized server collects and process detected traffic. It also maintains all detection nodes.

Regulation of IP 3 Receptors by IP 3 and Ca 2+

NASA Astrophysics Data System (ADS)

Taylor, Colin W.; Swatton, Jane E.

Inositol 1,4,5-trisphosphate ( IP 3) receptors are intracellular Ca 2+ channels that mediate release of Ca 2+ from intracellular stores. The channels are oligomeric assemblies of four subunits, each of which has an N-terminal IP 3-binding domain and each of which contributes to formation of the Ca 2+ channel. In mammals, three different genes encode IP 3 receptors subunits and the type 1 receptor (and perhaps the type 2 receptor) is also expressed as splice variants. Further diversity arises from assembly of the receptor in hetero- and homo-tetrameric channels. The subtypes differ in their expression and regulation, but they share the key property of being regulated by both IP3 and cytosolic Ca 2+. All three mammalian IP 3 subtypes, and probably also the IP 3 receptors expressed in invertebrates, are biphasically regulated by cytosolic Ca2+, although the underlying mechanisms appear to differ between subtypes. The interactions between IP 3 and Ca 2+ in controlling IP 3 receptor gating, and the physiological significance of such regulation will be reviewed.

IP-Based Video Modem Extender Requirements

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

Pierson, L G; Boorman, T M; Howe, R E

2003-12-16

Visualization is one of the keys to understanding large complex data sets such as those generated by the large computing resources purchased and developed by the Advanced Simulation and Computing program (aka ASCI). In order to be convenient to researchers, visualization data must be distributed to offices and large complex visualization theaters. Currently, local distribution of the visual data is accomplished by distance limited modems and RGB switches that simply do not scale to hundreds of users across the local, metropolitan, and WAN distances without incurring large costs in fiber plant installation and maintenance. Wide Area application over the DOEmore » Complex is infeasible using these limited distance RGB extenders. On the other hand, Internet Protocols (IP) over Ethernet is a scalable well-proven technology that can distribute large volumes of data over these distances. Visual data has been distributed at lower resolutions over IP in industrial applications. This document describes requirements of the ASCI program in visual signal distribution for the purpose of identifying industrial partners willing to develop products to meet ASCI's needs.« less

Role of Ipsdienol, Ipsenol, and cis-Verbenol in chemical ecology of Ips avulsus, Ips calligraphus, and Ips grandicollis (Coleoptera: Curculionidae: Scolytinae)

Treesearch

Jeremy D. Allison; Jessica I. McKenney; Daniel R. Miller; Matthew L. Gimmel

2012-01-01

ABSTRACT Stressed or damaged pine (Pinus sp.) trees in the southeastern United States are often colonized simultaneously by three southern Ips species (Coleoptera: Curculionidae: Scolytinae): small southern pine engraver, Ips avulsus (Eichhoff); sixspined ips, Ips calligraphus (Germar); and...

ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition.

PubMed

Zhu, Lin; Guo, Wei-Li; Deng, Su-Ping; Huang, De-Shuang

2016-01-01

In recent years, thanks to the efforts of individual scientists and research consortiums, a huge amount of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experimental data have been accumulated. Instead of investigating them independently, several recent studies have convincingly demonstrated that a wealth of scientific insights can be gained by integrative analysis of these ChIP-seq data. However, when used for the purpose of integrative analysis, a serious drawback of current ChIP-seq technique is that it is still expensive and time-consuming to generate ChIP-seq datasets of high standard. Most researchers are therefore unable to obtain complete ChIP-seq data for several TFs in a wide variety of cell lines, which considerably limits the understanding of transcriptional regulation pattern. In this paper, we propose a novel method called ChIP-PIT to overcome the aforementioned limitation. In ChIP-PIT, ChIP-seq data corresponding to a diverse collection of cell types, TFs and genes are fused together using the three-mode pair-wise interaction tensor (PIT) model, and the prediction of unperformed ChIP-seq experimental results is formulated as a tensor completion problem. Computationally, we propose efficient first-order method based on extensions of coordinate descent method to learn the optimal solution of ChIP-PIT, which makes it particularly suitable for the analysis of massive scale ChIP-seq data. Experimental evaluation the ENCODE data illustrate the usefulness of the proposed model.

47 CFR 52.34 - Obligations regarding local number porting to and from interconnected VoIP or Internet-based TRS...

Code of Federal Regulations, 2012 CFR

2012-10-01

... and from interconnected VoIP or Internet-based TRS providers. 52.34 Section 52.34 Telecommunication... Portability § 52.34 Obligations regarding local number porting to and from interconnected VoIP or Internet... customer's or a Registered Internet-based TRS User's valid number portability request, as it is defined in...

47 CFR 52.34 - Obligations regarding local number porting to and from interconnected VoIP or Internet-based TRS...

Code of Federal Regulations, 2013 CFR

2013-10-01

... and from interconnected VoIP or Internet-based TRS providers. 52.34 Section 52.34 Telecommunication... Portability § 52.34 Obligations regarding local number porting to and from interconnected VoIP or Internet... customer's or a Registered Internet-based TRS User's valid number portability request, as it is defined in...

47 CFR 52.34 - Obligations regarding local number porting to and from interconnected VoIP or Internet-based TRS...

Code of Federal Regulations, 2014 CFR

2014-10-01

... and from interconnected VoIP or Internet-based TRS providers. 52.34 Section 52.34 Telecommunication... Portability § 52.34 Obligations regarding local number porting to and from interconnected VoIP or Internet... customer's or a Registered Internet-based TRS User's valid number portability request, as it is defined in...

ChIP-re-ChIP: Co-occupancy Analysis by Sequential Chromatin Immunoprecipitation.

PubMed

Beischlag, Timothy V; Prefontaine, Gratien G; Hankinson, Oliver

2018-01-01

Chromatin immunoprecipitation (ChIP) exploits the specific interactions between DNA and DNA-associated proteins. It can be used to examine a wide range of experimental parameters. A number of proteins bound at the same genomic location can identify a multi-protein chromatin complex where several proteins work together to regulate gene transcription or chromatin configuration. In many instances, this can be achieved using sequential ChIP; or simply, ChIP-re-ChIP. Whether it is for the examination of specific transcriptional or epigenetic regulators, or for the identification of cistromes, the ability to perform a sequential ChIP adds a higher level of power and definition to these analyses. In this chapter, we describe a simple and reliable method for the sequential ChIP assay.

Vertical displacement of Ips Latidens and Ips Pini

Treesearch

Daniel R. Miller

2000-01-01

The effect of semiochemical interruptants was examined for Ips latidens (LeConte) and Ips pini (Say) using artificial trees (tall-traps) consisting of an array of seven Lindgren multiple-funnel traps suspended vertically on a rope ladder. S-(+)- Ipsdienol reduced the numbers of I. latidens captured in (±)-ipsenol...

A Real-time Spectrum Handoff Algorithm for VoIP based Cognitive Radio Networks: Design and Performance Analysis

NASA Astrophysics Data System (ADS)

Chakraborty, Tamal; Saha Misra, Iti

2016-03-01

Secondary Users (SUs) in a Cognitive Radio Network (CRN) face unpredictable interruptions in transmission due to the random arrival of Primary Users (PUs), leading to spectrum handoff or dropping instances. An efficient spectrum handoff algorithm, thus, becomes one of the indispensable components in CRN, especially for real-time communication like Voice over IP (VoIP). In this regard, this paper investigates the effects of spectrum handoff on the Quality of Service (QoS) for VoIP traffic in CRN, and proposes a real-time spectrum handoff algorithm in two phases. The first phase (VAST-VoIP based Adaptive Sensing and Transmission) adaptively varies the channel sensing and transmission durations to perform intelligent dropping decisions. The second phase (ProReact-Proactive and Reactive Handoff) deploys efficient channel selection mechanisms during spectrum handoff for resuming communication. Extensive performance analysis in analytical and simulation models confirms a decrease in spectrum handoff delay for VoIP SUs by more than 40% and 60%, compared to existing proactive and reactive algorithms, respectively and ensures a minimum 10% reduction in call-dropping probability with respect to the previous works in this domain. The effective SU transmission duration is also maximized under the proposed algorithm, thereby making it suitable for successful VoIP communication.

[Modulation of Kv4 channels by KChIPs clamping].

PubMed

Cui, Yuan-Yuan; Wang, Ke-Wei

2009-01-01

The rapidly inactivating (A-type) potassium channels regulate membrane excitability that defines the fundamental mechanism of neuronal functions such as pain signaling. Cytosolic Kv channel-interacting proteins KChIPs co-assemble with Kv4 (Shal) alpha subunits to form a native complex. The specific binding of auxiliary KChIPs to the Kv4 N-terminus results in modulation of gating properties, surface expression and subunit assembly of Kv4 channels. Based on recent structural efforts, here we attempt to emphasize the interaction between KChIPs and Kv4 channel complex in which a single KChIP1 molecule laterally clamps two neighboring Kv4.3 N-termini in a 4:4 manner. Greater insights into molecular mechanism between KChIPs and Kv4 interaction may provide therapeutic potentials by structure-based design of chemical compounds aimed at disrupting the protein-protein interaction for treatment of membrane excitability-related disorders.

All-IP-Ethernet architecture for real-time sensor-fusion processing

NASA Astrophysics Data System (ADS)

Hiraki, Kei; Inaba, Mary; Tezuka, Hiroshi; Tomari, Hisanobu; Koizumi, Kenichi; Kondo, Shuya

2016-03-01

Serendipter is a device that distinguishes and selects very rare particles and cells from huge amount of population. We are currently designing and constructing information processing system for a Serendipter. The information processing system for Serendipter is a kind of sensor-fusion system but with much more difficulties: To fulfill these requirements, we adopt All IP based architecture: All IP-Ethernet based data processing system consists of (1) sensor/detector directly output data as IP-Ethernet packet stream, (2) single Ethernet/TCP/IP streams by a L2 100Gbps Ethernet switch, (3) An FPGA board with 100Gbps Ethernet I/F connected to the switch and a Xeon based server. Circuits in the FPGA include 100Gbps Ethernet MAC, buffers and preprocessing, and real-time Deep learning circuits using multi-layer neural networks. Proposed All-IP architecture solves existing problem to construct large-scale sensor-fusion systems.

ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data.

PubMed

Wu, Song; Wang, Jianmin; Zhao, Wei; Pounds, Stanley; Cheng, Cheng

2010-06-03

ChIP-Seq is a powerful tool for identifying the interaction between genomic regulators and their bound DNAs, especially for locating transcription factor binding sites. However, high cost and high rate of false discovery of transcription factor binding sites identified from ChIP-Seq data significantly limit its application. Here we report a new algorithm, ChIP-PaM, for identifying transcription factor target regions in ChIP-Seq datasets. This algorithm makes full use of a protein-DNA binding pattern by capitalizing on three lines of evidence: 1) the tag count modelling at the peak position, 2) pattern matching of a specific tag count distribution, and 3) motif searching along the genome. A novel data-based two-step eFDR procedure is proposed to integrate the three lines of evidence to determine significantly enriched regions. Our algorithm requires no technical controls and efficiently discriminates falsely enriched regions from regions enriched by true transcription factor (TF) binding on the basis of ChIP-Seq data only. An analysis of real genomic data is presented to demonstrate our method. In a comparison with other existing methods, we found that our algorithm provides more accurate binding site discovery while maintaining comparable statistical power.

Attributes associated with probability of infestation by the pinon ips, Ips confusus, (Coleoptera: Scolytidae) in pinon pine, Pinus edulis

Treesearch

Jose E. Negron; Jill L. Wilson

2003-01-01

We examined attributes of pinon pine (Pinus edulis) associated with the probability of infestation by pinon ips (Ips confusus) in an outbreak in the Coconino National Forest, Arizona. We used data collected from 87 plots, 59 infested and 28 uninfested, and a logistic regression approach to estimate the probability ofinfestation based on plotand tree-level attributes....

Research of future network with multi-layer IP address

NASA Astrophysics Data System (ADS)

Li, Guoling; Long, Zhaohua; Wei, Ziqiang

2018-04-01

The shortage of IP addresses and the scalability of routing systems [1] are challenges for the Internet. The idea of dividing existing IP addresses between identities and locations is one of the important research directions. This paper proposed a new decimal network architecture based on IPv9 [11], and decimal network IP address from E.164 principle of traditional telecommunication network, the IP address level, which helps to achieve separation and identification and location of IP address, IP address form a multilayer network structure, routing scalability problem in remission at the same time, to solve the problem of IPv4 address depletion. On the basis of IPv9, a new decimal network architecture is proposed, and the IP address of the decimal network draws on the E.164 principle of the traditional telecommunication network, and the IP addresses are hierarchically divided, which helps to realize the identification and location separation of IP addresses, the formation of multi-layer IP address network structure, while easing the scalability of the routing system to find a way out of IPv4 address exhausted. In addition to modifying DNS [10] simply and adding the function of digital domain, a DDNS [12] is formed. At the same time, a gateway device is added, that is, IPV9 gateway. The original backbone network and user network are unchanged.

Integrating QoS and security functions in an IP-VPN gateway

NASA Astrophysics Data System (ADS)

Fan, Kuo-Pao; Chang, Shu-Hsin; Lin, Kuan-Ming; Pen, Mau-Jy

2001-10-01

IP-based Virtual Private Network becomes more and more popular. It can not only reduce the enterprise communication cost but also increase the revenue of the service provider. The common IP-VPN application types include Intranet VPN, Extranet VPN, and remote access VPN. For the large IP-VPN market, some vendors develop dedicated IP-VPN devices; while some vendors add the VPN functions into their existing network equipment such as router, access gateway, etc. The functions in the IP-VPN device include security, QoS, and management. The common security functions supported are IPSec (IP Security), IKE (Internet Key Exchange), and Firewall. The QoS functions include bandwidth control and packet scheduling. In the management component, policy-based network management is under standardization in IETF. In this paper, we discuss issues on how to integrate the QoS and security functions in an IP-VPN Gateway. We propose three approaches to do this. They are (1) perform Qos first (2) perform IPSec first and (3) reserve fixed bandwidth for IPSec. We also compare the advantages and disadvantages of the three proposed approaches.

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.

PubMed

Guertin, Michael J; Cullen, Amy E; Markowetz, Florian; Holding, Andrew N

2018-04-17

A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide changes in occupancy. Analysis-based normalization methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor (TF) binding, these assumptions do not hold true. The challenges in normalization are confounded by experimental variability during sample preparation, processing and recovery. We present a novel normalization strategy utilizing an internal standard of unchanged peaks for reference. Our method can be readily applied to monitor genome-wide changes by ChIP-seq that are otherwise lost or misrepresented through analytical normalization. We compare our approach to normalization by total read depth and two alternative methods that utilize external experimental controls to study TF binding. We successfully resolve the key challenges in quantitative ChIP-seq analysis and demonstrate its application by monitoring the loss of Estrogen Receptor-alpha (ER) binding upon fulvestrant treatment, ER binding in response to estrodiol, ER mediated change in H4K12 acetylation and profiling ER binding in patient-derived xenographs. This is supported by an adaptable pipeline to normalize and quantify differential TF binding genome-wide and generate metrics for differential binding at individual sites.

Cross-layer restoration with software defined networking based on IP over optical transport networks

NASA Astrophysics Data System (ADS)

Yang, Hui; Cheng, Lei; Deng, Junni; Zhao, Yongli; Zhang, Jie; Lee, Young

2015-10-01

The IP over optical transport network is a very promising networking architecture applied to the interconnection of geographically distributed data centers due to the performance guarantee of low delay, huge bandwidth and high reliability at a low cost. It can enable efficient resource utilization and support heterogeneous bandwidth demands in highly-available, cost-effective and energy-effective manner. In case of cross-layer link failure, to ensure a high-level quality of service (QoS) for user request after the failure becomes a research focus. In this paper, we propose a novel cross-layer restoration scheme for data center services with software defined networking based on IP over optical network. The cross-layer restoration scheme can enable joint optimization of IP network and optical network resources, and enhance the data center service restoration responsiveness to the dynamic end-to-end service demands. We quantitatively evaluate the feasibility and performances through the simulation under heavy traffic load scenario in terms of path blocking probability and path restoration latency. Numeric results show that the cross-layer restoration scheme improves the recovery success rate and minimizes the overall recovery time.

IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography.

PubMed

Hamada, Kozo; Miyatake, Hideyuki; Terauchi, Akiko; Mikoshiba, Katsuhiko

2017-05-02

The inositol 1,4,5-trisphosphate (IP 3 ) receptor (IP 3 R) is an IP 3 -gated ion channel that releases calcium ions (Ca 2+ ) from the endoplasmic reticulum. The IP 3 -binding sites in the large cytosolic domain are distant from the Ca 2+ conducting pore, and the allosteric mechanism of how IP 3 opens the Ca 2+ channel remains elusive. Here, we identify a long-range gating mechanism uncovered by channel mutagenesis and X-ray crystallography of the large cytosolic domain of mouse type 1 IP 3 R in the absence and presence of IP 3 Analyses of two distinct space group crystals uncovered an IP 3 -dependent global translocation of the curvature α-helical domain interfacing with the cytosolic and channel domains. Mutagenesis of the IP 3 R channel revealed an essential role of a leaflet structure in the α-helical domain. These results suggest that the curvature α-helical domain relays IP 3 -controlled global conformational dynamics to the channel through the leaflet, conferring long-range allosteric coupling from IP 3 binding to the Ca 2+ channel.

IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography

PubMed Central

Hamada, Kozo; Miyatake, Hideyuki; Terauchi, Akiko; Mikoshiba, Katsuhiko

2017-01-01

The inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) is an IP3-gated ion channel that releases calcium ions (Ca2+) from the endoplasmic reticulum. The IP3-binding sites in the large cytosolic domain are distant from the Ca2+ conducting pore, and the allosteric mechanism of how IP3 opens the Ca2+ channel remains elusive. Here, we identify a long-range gating mechanism uncovered by channel mutagenesis and X-ray crystallography of the large cytosolic domain of mouse type 1 IP3R in the absence and presence of IP3. Analyses of two distinct space group crystals uncovered an IP3-dependent global translocation of the curvature α-helical domain interfacing with the cytosolic and channel domains. Mutagenesis of the IP3R channel revealed an essential role of a leaflet structure in the α-helical domain. These results suggest that the curvature α-helical domain relays IP3-controlled global conformational dynamics to the channel through the leaflet, conferring long-range allosteric coupling from IP3 binding to the Ca2+ channel. PMID:28416699

Space Network IP Services (SNIS): An Architecture for Supporting Low Earth Orbiting IP Satellite Missions

NASA Technical Reports Server (NTRS)

Israel, David J.

2005-01-01

The NASA Space Network (SN) supports a variety of missions using the Tracking and Data Relay Satellite System (TDRSS), which includes ground stations in White Sands, New Mexico and Guam. A Space Network IP Services (SNIS) architecture is being developed to support future users with requirements for end-to-end Internet Protocol (IP) communications. This architecture will support all IP protocols, including Mobile IP, over TDRSS Single Access, Multiple Access, and Demand Access Radio Frequency (RF) links. This paper will describe this architecture and how it can enable Low Earth Orbiting IP satellite missions.

ChIP-seq: advantages and challenges of a maturing technology.

PubMed

Park, Peter J

2009-10-01

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a technique for genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes. Owing to the tremendous progress in next-generation sequencing technology, ChIP-seq offers higher resolution, less noise and greater coverage than its array-based predecessor ChIP-chip. With the decreasing cost of sequencing, ChIP-seq has become an indispensable tool for studying gene regulation and epigenetic mechanisms. In this Review, I describe the benefits and challenges in harnessing this technique with an emphasis on issues related to experimental design and data analysis. ChIP-seq experiments generate large quantities of data, and effective computational analysis will be crucial for uncovering biological mechanisms.

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

PubMed

Ambrosini, Giovanna; Dreos, René; Kumar, Sunil; Bucher, Philipp

2016-11-18

ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data. Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade. The various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/ .

A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages.

PubMed

Park, Seung-Jin; Kim, Jong-Hwan; Yoon, Byung-Ha; Kim, Seon-Young

2017-03-01

Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, 'ChIPseeker' performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.

ChIP-seq and ChIP-exo profiling of Pol II, H2A.Z, and H3K4me3 in human K562 cells.

PubMed

Mchaourab, Zenab F; Perreault, Andrea A; Venters, Bryan J

2018-03-06

The human K562 chronic myeloid leukemia cell line has long served as an experimental paradigm for functional genomic studies. To systematically and functionally annotate the human genome, the ENCODE consortium generated hundreds of functional genomic data sets, such as chromatin immunoprecipitation coupled to sequencing (ChIP-seq). While ChIP-seq analyses have provided tremendous insights into gene regulation, spatiotemporal insights were limited by a resolution of several hundred base pairs. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq that overcomes this limitation by providing higher precision mapping of protein-DNA interactions. To study the interplay of transcription initiation and chromatin, we profiled the genome-wide locations for RNA polymerase II (Pol II), the histone variant H2A.Z, and the histone modification H3K4me3 using ChIP-seq and ChIP-exo. In this Data Descriptor, we present detailed information on parallel experimental design, data generation, quality control analysis, and data validation. We discuss how these data lay the foundation for future analysis to understand the relationship between the occupancy of Pol II and nucleosome positions at near base pair resolution.

A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages

PubMed Central

Park, Seung-Jin; Kim, Jong-Hwan; Yoon, Byung-Ha; Kim, Seon-Young

2017-01-01

Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. ‘dada2’ performs trimming of the high-throughput sequencing data. ‘QuasR’ and ‘mosaics’ perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, ‘ChIPseeker’ performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git. PMID:28416945

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

PubMed Central

2011-01-01

Background Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster. Results Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis. Conclusions Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis. PMID:21356108

77 FR 33227 - Assessment Questionnaire-IP Sector Specific Agency Risk Self Assessment Tool (IP-SSARSAT)

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-05

... DEPARTMENT OF HOMELAND SECURITY [Docket No. DHS-2011-0069] Assessment Questionnaire--IP Sector Specific Agency Risk Self Assessment Tool (IP-SSARSAT) AGENCY: National Protection and Programs Directorate...), Office of Infrastructure Protection (IP), Sector Outreach and Programs Division (SOPD), previously named...

76 FR 81955 - Assessment Questionnaire-IP Sector Specific Agency Risk Self Assessment Tool (IP-SSARSAT)

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-29

... DEPARTMENT OF HOMELAND SECURITY [Docket No. DHS-2011-0069] Assessment Questionnaire--IP Sector Specific Agency Risk Self Assessment Tool (IP-SSARSAT) AGENCY: National Protection and Programs Directorate...), Office of Infrastructure Protection (IP), Sector Specific Agency Executive Management Office (SSA EMO...

Running TCP/IP over ATM Networks.

ERIC Educational Resources Information Center

Witt, Michael

1995-01-01

Discusses Internet protocol (IP) and subnets and describes how IP may operate over asynchronous transfer mode (ATM). Topics include TCP (transmission control protocol), ATM cells and adaptation layers, a basic architectural model for IP over ATM, address resolution, mapping IP to a subnet technology, and connection management strategy. (LRW)

Traffic shaping and scheduling for OBS-based IP/WDM backbones

NASA Astrophysics Data System (ADS)

Elhaddad, Mahmoud S.; Melhem, Rami G.; Znati, Taieb; Basak, Debashis

2003-10-01

We introduce Proactive Reservation-based Switching (PRS) -- a switching architecture for IP/WDM networks based on Labeled Optical Burst Switching. PRS achieves packet delay and loss performance comparable to that of packet-switched networks, without requiring large buffering capacity, or burst scheduling across a large number of wavelengths at the core routers. PRS combines proactive channel reservation with periodic shaping of ingress-egress traffic aggregates to hide the offset latency and approximate the utilization/buffering characteristics of discrete-time queues with periodic arrival streams. A channel scheduling algorithm imposes constraints on burst departure times to ensure efficient utilization of wavelength channels and to maintain the distance between consecutive bursts through the network. Results obtained from simulation using TCP traffic over carefully designed topologies indicate that PRS consistently achieves channel utilization above 90% with modest buffering requirements.

VoIP Accessibility: A Usability Study of Voice over Internet Protocol (VoIP) Systems and A Survey of VoIP Users with Vision Loss

ERIC Educational Resources Information Center

Packer, Jaclyn; Reuschel, William

2018-01-01

Introduction: Accessibility of Voice over Internet Protocol (VoIP) systems was tested with a hands-on usability study and an online survey of VoIP users who are visually impaired. The survey examined the importance of common VoIP features, and both methods assessed difficulty in using those features. Methods: The usability test included four paid…

A review of the integration of traditional, complementary and alternative medicine into the curriculum of South African medical schools

PubMed Central

2014-01-01

Background Traditional, complementary and alternative (TCAM) medicine is consumed by a large majority of the South African population. In the context of increasing overall demand for healthcare this paper investigates the extent to which South African medical schools have incorporated TCAM into their curriculum because of the increased legislative and policy interest in formally incorporating TCAM into the health care system since democracy in 1994. Methods Heads of School from seven South African medical schools were surveyed telephonically. Results One school was teaching both Traditional African Medicine (TM) and CAM, five were teaching either TM or CAM and another was not teaching any aspect of TCAM. Conclusions In conclusion, there is a paucity of curricula which incorporate TCAM. Medical schools have not responded to government policies or the contextual realities by incorporating TCAM into the curriculum for their students. South African medical schools need to review their curricula to increase their students’ knowledge of TCAM given the demands of the population and the legislative realities. PMID:24575843

Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP).

PubMed

Desvoyes, Bénédicte; Sequeira-Mendes, Joana; Vergara, Zaida; Madeira, Sofia; Gutierrez, Crisanto

2018-01-01

Identification of chromatin modifications, e.g., histone acetylation and methylation, among others, is widely carried out by using a chromatin immunoprecipitation (ChIP) strategy. The information obtained with these procedures is useful to gain an overall picture of modifications present in all cells of the population under study. It also serves as a basis to figure out the mechanisms of chromatin organization and gene regulation at the population level. However, the ultimate goal is to understand gene regulation at the level of single chromatin fibers. This requires the identification of chromatin modifications that occur at a given genomic location and within the same chromatin fiber. This is achieved by following a sequential ChIP strategy using two antibodies to distinguish different chromatin modifications. Here, we describe a sequential ChIP protocol (Re-ChIP), paying special attention to the controls needed and the required steps to obtain meaningful and reproducible results. The protocol is developed for young Arabidopsis seedlings but could be adapted to other plant materials.

VoIP for Telerehabilitation: A Pilot Usability Study for HIPAA Compliance

PubMed Central

Watzlaf, Valerie R.; Ondich, Briana

2012-01-01

Consumer-based, free Voice and video over the Internet Protocol (VoIP) software systems such as Skype and others are used by health care providers to deliver telerehabilitation and other health-related services to clients. Privacy and security applications as well as HIPAA compliance within these protocols have been questioned by practitioners, health information managers, and other healthcare entities. This pilot usability study examined whether four respondents who used the top three, free consumer-based, VoIP software systems perceived these VoIP technologies to be private, secure, and HIPAA compliant; most did not. While the pilot study limitations include the number of respondents and systems assessed, the protocol can be applied to future research and replicated for instructional purposes. Recommendations are provided for VoIP companies, providers, and clients/consumers. PMID:25945194

Challenges Regarding IP Core Functional Reliability

NASA Technical Reports Server (NTRS)

Berg, Melanie D.; LaBel, Kenneth A.

2017-01-01

For many years, intellectual property (IP) cores have been incorporated into field programmable gate array (FPGA) and application specific integrated circuit (ASIC) design flows. However, the usage of large complex IP cores were limited within products that required a high level of reliability. This is no longer the case. IP core insertion has become mainstream including their use in highly reliable products. Due to limited visibility and control, challenges exist when using IP cores and subsequently compromise product reliability. We discuss challenges and suggest potential solutions to critical application IP insertion.

A TCP/IP framework for ethernet-based measurement, control and experiment data distribution

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Minny, J.

2010-11-01

A complete modular but scalable TCP/IP based scientific instrument control and data distribution system has been designed and realized. The system features an IEEE 802.3 compliant 10 Mbps Medium Access Controller (MAC) and Physical Layer Device that is suitable for the full-duplex monitoring and control of various physically widespread measurement transducers in the presence of a local network infrastructure. The cumbersomeness of exchanging and synchronizing data between the various transducer units using physical storage media led to the choice of TCP/IP as a logical alternative. The system and methods developed are scalable for broader usage over the Internet. The system comprises a PIC18f2620 and ENC28j60 based hardware and a software component written in C, Java/Javascript and Visual Basic.NET programming languages for event-level monitoring and browser user-interfaces respectively. The system exchanges data with the host network through IPv4 packets requested and received on a HTTP page. It also responds to ICMP echo, UDP and ARP requests through a user selectable integrated DHCP and static IPv4 address allocation scheme. The round-trip time, throughput and polling frequency are estimated and reported. A typical application to temperature monitoring and logging is also presented.

A native IP satellite communications system

NASA Astrophysics Data System (ADS)

Koudelka, O.; Schmidt, M.; Ebert, J.; Schlemmer, H.; Kastner-Puschl, S.; Riedler, W.

2004-08-01

≪ In the framework of ESA's ARTES-5 program the Institute of Applied Systems Technology (Joanneum Research) in cooperation with the Department of Communications and Wave Propagation has developed a novel meshed satellite communications system which is optimised for Internet traffic and applications (L*IP—Local Network Interconnection via Satellite Systems Using the IP Protocol Suite). Both symmetrical and asymmetrical connections are supported. Bandwidth on demand and guaranteed quality of service are key features of the system. A novel multi-frequency TDMA access scheme utilises efficient methods of IP encapsulation. In contrast to other solutions it avoids legacy transport network techniques. While the DVB-RCS standard is based on ATM or MPEG transport cells, the solution of the L*IP system uses variable-length cells which reduces the overhead significantly. A flexible and programmable platform based on Linux machines was chosen to allow the easy implementation and adaptation to different standards. This offers the possibility to apply the system not only to satellite communications, but provides seamless integration with terrestrial fixed broadcast wireless access systems. The platform is also an ideal test-bed for a variety of interactive broadband communications systems. The paper describes the system architecture and the key features of the system.

Design and measurement of fully digital ternary content addressable memory using ratioless static random access memory cells and hierarchical-AND matching comparator

NASA Astrophysics Data System (ADS)

Nishikata, Daisuke; Ali, Mohammad Alimudin Bin Mohd; Hosoda, Kento; Matsumoto, Hiroshi; Nakamura, Kazuyuki

2018-04-01

A 36-bit × 32-entry fully digital ternary content addressable memory (TCAM) using the ratioless static random access memory (RL-SRAM) technology and fully complementary hierarchical-AND matching comparators (HAMCs) was developed. Since its fully complementary and digital operation enables the effect of device variabilities to be avoided, it can operate with a quite low supply voltage. A test chip incorporating a conventional TCAM and a proposed 24-transistor ratioless TCAM (RL-TCAM) cells and HAMCs was developed using a 0.18 µm CMOS process. The minimum operating voltage of 0.25 V of the developed RL-TCAM, which is less than half of that of the conventional TCAM, was measured via the conventional CMOS push–pull output buffers with the level-shifting and flipping technique using optimized pull-up voltage and resistors.

Mobile-ip Aeronautical Network Simulation Study

NASA Technical Reports Server (NTRS)

Ivancic, William D.; Tran, Diepchi T.

2001-01-01

NASA is interested in applying mobile Internet protocol (mobile-ip) technologies to its space and aeronautics programs. In particular, mobile-ip will play a major role in the Advanced Aeronautic Transportation Technology (AATT), the Weather Information Communication (WINCOMM), and the Small Aircraft Transportation System (SATS) aeronautics programs. This report presents the results of a simulation study of mobile-ip for an aeronautical network. The study was performed to determine the performance of the transmission control protocol (TCP) in a mobile-ip environment and to gain an understanding of how long delays, handoffs, and noisy channels affect mobile-ip performance.

Subtype-selective regulation of IP(3) receptors by thimerosal via cysteine residues within the IP(3)-binding core and suppressor domain.

PubMed

Khan, Samir A; Rossi, Ana M; Riley, Andrew M; Potter, Barry V L; Taylor, Colin W

2013-04-15

IP(3)R (IP(3) [inositol 1,4,5-trisphosphate] receptors) and ryanodine receptors are the most widely expressed intracellular Ca(2+) channels and both are regulated by thiol reagents. In DT40 cells stably expressing single subtypes of mammalian IP(3)R, low concentrations of thimerosal (also known as thiomersal), which oxidizes thiols to form a thiomercurylethyl complex, increased the sensitivity of IP(3)-evoked Ca(2+) release via IP(3)R1 and IP(3)R2, but inhibited IP(3)R3. Activation of IP(3)R is initiated by IP(3) binding to the IBC (IP(3)-binding core; residues 224-604) and proceeds via re-arrangement of an interface between the IBC and SD (suppressor domain; residues 1-223). Thimerosal (100 μM) stimulated IP(3) binding to the isolated NT (N-terminal; residues 1-604) of IP(3)R1 and IP(3)R2, but not to that of IP(3)R3. Binding of a competitive antagonist (heparin) or partial agonist (dimeric-IP(3)) to NT1 was unaffected by thiomersal, suggesting that the effect of thimerosal is specifically related to IP(3)R activation. IP(3) binding to NT1 in which all cysteine residues were replaced by alanine was insensitive to thimerosal, so too were NT1 in which cysteine residues were replaced in either the SD or IBC. This demonstrates that thimerosal interacts directly with cysteine in both the SD and IBC. Chimaeric proteins in which the SD of the IP(3)R was replaced by the structurally related A domain of a ryanodine receptor were functional, but thimerosal inhibited both IP(3) binding to the chimaeric NT and IP(3)-evoked Ca(2+) release from the chimaeric IP(3)R. This is the first systematic analysis of the effects of a thiol reagent on each IP(3)R subtype. We conclude that thimerosal selectively sensitizes IP(3)R1 and IP(3)R2 to IP(3) by modifying cysteine residues within both the SD and IBC and thereby stabilizing an active conformation of the receptor.

Subtype-selective regulation of IP3 receptors by thimerosal via cysteine residues within the IP3-binding core and suppressor domain

PubMed Central

Khan, Samir A.; Rossi, Ana M.; Riley, Andrew M.; Potter, Barry V. L.; Taylor, Colin W.

2013-01-01

IP3R (IP3 [inositol 1,4,5-trisphosphate] receptors) and ryanodine receptors are the most widely expressed intracellular Ca2+ channels and both are regulated by thiol reagents. In DT40 cells stably expressing single subtypes of mammalian IP3R, low concentrations of thimerosal (also known as thiomersal), which oxidizes thiols to form a thiomercurylethyl complex, increased the sensitivity of IP3-evoked Ca2+ release via IP3R1 and IP3R2, but inhibited IP3R3. Activation of IP3R is initiated by IP3 binding to the IBC (IP3-binding core; residues 224–604) and proceeds via re-arrangement of an interface between the IBC and SD (suppressor domain; residues 1–223). Thimerosal (100 μM) stimulated IP3 binding to the isolated NT (N-terminal; residues 1–604) of IP3R1 and IP3R2, but not to that of IP3R3. Binding of a competitive antagonist (heparin) or partial agonist (dimeric-IP3) to NT1 was unaffected by thiomersal, suggesting that the effect of thimerosal is specifically related to IP3R activation. IP3 binding to NT1 in which all cysteine residues were replaced by alanine was insensitive to thimerosal, so too were NT1 in which cysteine residues were replaced in either the SD or IBC. This demonstrates that thimerosal interacts directly with cysteine in both the SD and IBC. Chimaeric proteins in which the SD of the IP3R was replaced by the structurally related A domain of a ryanodine receptor were functional, but thimerosal inhibited both IP3 binding to the chimaeric NT and IP3-evoked Ca2+ release from the chimaeric IP3R. This is the first systematic analysis of the effects of a thiol reagent on each IP3R subtype. We conclude that thimerosal selectively sensitizes IP3R1 and IP3R2 to IP3 by modifying cysteine residues within both the SD and IBC and thereby stabilizing an active conformation of the receptor. PMID:23282150

Applying a gaming approach to IP strategy.

PubMed

Gasnier, Arnaud; Vandamme, Luc

2010-02-01

Adopting an appropriate IP strategy is an important but complex area, particularly in the pharmaceutical and biotechnology sectors, in which aspects such as regulatory submissions, high competitive activity, and public health and safety information requirements limit the amount of information that can be protected effectively through secrecy. As a result, and considering the existing time limits for patent protection, decisions on how to approach IP in these sectors must be made with knowledge of the options and consequences of IP positioning. Because of the specialized nature of IP, it is necessary to impart knowledge regarding the options and impact of IP to decision-makers, whether at the level of inventors, marketers or strategic business managers. This feature review provides some insight on IP strategy, with a focus on the use of a new 'gaming' approach for transferring the skills and understanding needed to make informed IP-related decisions; the game Patentopolis is discussed as an example of such an approach. Patentopolis involves interactive activities with IP-related business decisions, including the exploitation and enforcement of IP rights, and can be used to gain knowledge on the impact of adopting different IP strategies.

Vaccines and IP Rights: A Multifaceted Relationship.

PubMed

Durell, Karen

2016-01-01

Just as there are many forms of vaccines and components to vaccines-particular compositions, delivery systems, components, and distribution networks-there are a variety of intellectual property (IP) protections applicable for vaccines. IP rights such as patent, copyright, trademarks, plant breeders' rights, and trade secrets may all be applicable to vaccines. Thus, discussion of IP rights and vaccines should not begin and end with the application of one IP right to a vaccine. The discussion should engage considerations of multiple IP rights applicable to a vaccine and how these can be utilized in an integrated manner in a strategy aimed at supporting the development and distribution of the vaccine. Such an approach to IP rights to vaccines allows for the integrated rights to be considered in light of the justifications for protecting vaccines with IP rights, as well as the issues relating to specific IP rights for vaccines, such as compulsory license regimes, available humanitarian purpose IP credits, etc. To view vaccines as the subject of multiple IP protections involves a refocusing, but the outcome can provide significant benefits for vaccine development and distribution.

An ethernet/IP security review with intrusion detection applications

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

Laughter, S. A.; Williams, R. D.

2006-07-01

Supervisory Control and Data Acquisition (SCADA) and automation networks, used throughout utility and manufacturing applications, have their own specific set of operational and security requirements when compared to corporate networks. The modern climate of heightened national security and awareness of terrorist threats has made the security of these systems of prime concern. There is a need to understand the vulnerabilities of these systems and how to monitor and protect them. Ethernet/IP is a member of a family of protocols based on the Control and Information Protocol (CIP). Ethernet/IP allows automation systems to be utilized on and integrated with traditional TCP/IPmore » networks, facilitating integration of these networks with corporate systems and even the Internet. A review of the CIP protocol and the additions Ethernet/IP makes to it has been done to reveal the kind of attacks made possible through the protocol. A set of rules for the SNORT Intrusion Detection software is developed based on the results of the security review. These can be used to monitor, and possibly actively protect, a SCADA or automation network that utilizes Ethernet/IP in its infrastructure. (authors)« less

Extending Tactical Fleet Communications Through VoIP

DTIC Science & Technology

2014-09-01

corporate world , the military is leveraging VoIP communication solutions as well. Shore commands like Tactical Training Group Pacific use VoIP for...VoIP fuzzing (e.g., Asteroid , PROTOS, Sip-Proxy)  VoIP signaling manipulation (e.g., IAXAuthJack, IAXHangup, SIP-Kill)  VoIP media...as well, but instead of just matching the information to rules, it compares synchronization information between the protocols to determine if the

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

PubMed Central

2010-01-01

Background Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome. Results We have developed ChIPpeakAnno as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. In addition, we have implemented functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, the package includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes. Conclusions ChIPpeakAnno enables batch annotation of the binding sites identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R. Allowing users to pass their own annotation data such

Historical data learning based dynamic LSP routing for overlay IP/MPLS over WDM networks

NASA Astrophysics Data System (ADS)

Yu, Xiaojun; Xiao, Gaoxi; Cheng, Tee Hiang

2013-08-01

Overlay IP/MPLS over WDM network is a promising network architecture starting to gain wide deployments recently. A desirable feature of such a network is to achieve efficient routing with limited information exchanges between the IP/MPLS and the WDM layers. This paper studies dynamic label switched path (LSP) routing in the overlay IP/MPLS over WDM networks. To enhance network performance while maintaining its simplicity, we propose to learn from the historical data of lightpath setup costs maintained by the IP-layer integrated service provider (ISP) when making routing decisions. Using a novel historical data learning scheme for logical link cost estimation, we develop a new dynamic LSP routing method named Existing Link First (ELF) algorithm. Simulation results show that the proposed algorithm significantly outperforms the existing ones under different traffic loads, with either limited or unlimited numbers of optical ports. Effects of the number of candidate routes, add/drop ratio and the amount of historical data are also evaluated.

A study on efficient detection of network-based IP spoofing DDoS and malware-infected Systems.

PubMed

Seo, Jung Woo; Lee, Sang Jin

2016-01-01

Large-scale network environments require effective detection and response methods against DDoS attacks. Depending on the advancement of IT infrastructure such as the server or network equipment, DDoS attack traffic arising from a few malware-infected systems capable of crippling the organization's internal network has become a significant threat. This study calculates the frequency of network-based packet attributes and analyzes the anomalies of the attributes in order to detect IP-spoofed DDoS attacks. Also, a method is proposed for the effective detection of malware infection systems triggering IP-spoofed DDoS attacks on an edge network. Detection accuracy and performance of the collected real-time traffic on a core network is analyzed thru the use of the proposed algorithm, and a prototype was developed to evaluate the performance of the algorithm. As a result, DDoS attacks on the internal network were detected in real-time and whether or not IP addresses were spoofed was confirmed. Detecting hosts infected by malware in real-time allowed the execution of intrusion responses before stoppage of the internal network caused by large-scale attack traffic.

Measuring the impostor phenomenon: a comparison of Clance's IP Scale and Harvey's I-P Scale.

PubMed

Holmes, S W; Kertay, L; Adamson, L B; Holland, C L; Clance, P R

1993-02-01

Many of the discrepancies reported to date in empirical investigations of the impostor phenomenon (IP) may be due in part to (a) the use of different methods for identifying individuals suffering from this syndrome (impostors), (b) the common use of a median split procedure to classify subjects and (c) the fact that subjects in many studies were drawn from impostor-prone samples. In this study, we compared the scores of independently identified impostors and nonimpostors on two instruments designed to measure the IP: Harvey's I-P Scale and Clance's IP Scale. The results suggest that Clance's scale may be the more sensitive and reliable instrument. Cutoff score suggestions for both instruments are offered.

A comparison of the microstructure and properties of the IPS Empress 2 and the IPS Empress glass-ceramics.

PubMed

Höland, W; Schweiger, M; Frank, M; Rheinberger, V

2000-01-01

The aim of this report is to analyze the microstructures of glass-ceramics of the IPS Empress 2 and IPS Empress systems by scanning electron microscopy. The main properties of the glass-ceramics were determined and compared to each other. The flexural strength of the pressed glass-ceramic (core material) was improved by a factor of more than three for IPS Empress 2 (lithium disilicate glass-ceramic) in comparison with IPS Empress (leucite glass-ceramic). For the fracture toughness, the K(IC) value was measured as 3.3 +/- 0.3 MPa. m(0.5) for IPS Empress 2 and 1.3 +/- 0.1 MPa. m(0.5) for IPS Empress. Abrasion behavior, chemical durability, and optical properties such as translucency of all glass-ceramics fulfill the dental standards. The authors concluded that IPS Empress 2 can be used to fabricate 3-unit bridges up to the second premolar. Copyright 2000 John Wiley & Sons, Inc.

Changing the Global Health Care Landscape—Proceedings of a “Glocal” Symposium*

PubMed Central

Porcino, Antony Joseph; Candidate, PhD; Hollenberg, Daniel; Graff, Tom; Hymel, Glenn M.

2011-01-01

Background This glocal (global knowledge with local action) symposium was convened by a professional therapeutic massage bodywork professional organization to bring together the fields of economics, politics, and traditional and complementary and alternative medicine (TCAM) to begin development of effective TCAM advocacy worldwide. The symposium addressed the core question, “What information will be needed to address issues that will arise as TCAM practitioners advocate for a respectful and equalfooting access to health care provision, public and private, worldwide?” Participants and Setting The 35 international participants convened in a Victoria, Canada hotel. They were selectively invited to provide expertise in: advocacy, politics, public policy, economics, TCAM practice, integrative practice, sociology and TCAM research, education, media and language framing, psychology, and mediation. Methods The two-day symposium used a facilitated dialogue and knowledge-sharing design process geared to achieving group-supported recommendations. Invited panelists discussed each agenda topic, followed by facilitated discussion with the entire group. Results In general, participants agreed that advocacy from a TCAM perspective is needed. Additionally, more research should use methods with more relevance to everyday health care provision and health care costs such as effectiveness comparative trials and cost effectiveness studies. A number of specific advocacy steps were recommended. Most focused on developing local support for better access and equity regarding TCAM within local health care systems and advocacy work, which needs to both understand and engage the local TCAM practitioners and those using the TCAM services. Conclusions The increasing awareness of TCAM and advancement toward integrative medicine—including traditional medicines and perspectives—are themes currently in development worldwide. Now is a good time for TCAM practitioners to open dialogue to

Modulation by clamping: Kv4 and KChIP interactions.

PubMed

Wang, Kewei

2008-10-01

The rapidly inactivating (A-type) potassium channels regulate membrane excitability that defines the fundamental mechanism of neuronal functions such as pain signaling. Cytosolic Kv channel-interacting proteins KChIPs that belong to neuronal calcium sensor (NCS) family of calcium binding EF-hand proteins co-assemble with Kv4 (Shal) alpha subunits to form a native complex that encodes major components of neuronal somatodendritic A-type K+ current, I(SA), in neurons and transient outward current, I(TO), in cardiac myocytes. The specific binding of auxiliary KChIPs to the Kv4 N-terminus results in modulation of gating properties, surface expression and subunit assembly of Kv4 channels. Here, I attempt to emphasize the interaction between KChIPs and Kv4 based on recent progress made in understanding the structure complex in which a single KChIP1 molecule laterally clamps two neighboring Kv4.3 N-termini in a 4:4 manner. Greater insights into molecular mechanism between KChIPs and Kv4 interaction may provide therapeutic potentials of designing compounds aimed at disrupting the protein-protein interaction for treatment of membrane excitability-related disorders.

All-optical 10Gb/s ternary-CAM cell for routing look-up table applications.

PubMed

Mourgias-Alexandris, George; Vagionas, Christos; Tsakyridis, Apostolos; Maniotis, Pavlos; Pleros, Nikos

2018-03-19

We experimentally demonstrate the first all-optical Ternary-Content Addressable Memory (T-CAM) cell that operates at 10Gb/s and comprises two monolithically integrated InP Flip-Flops (FF) and a SOA-MZI optical XOR gate. The two FFs are responsible for storing the data bit and the ternary state 'X', respectively, with the XOR gate used for comparing the stored FF-data and the search bit. The experimental results reveal error-free operation at 10Gb/s for both Write and Ternary Content Addressing of the T-CAM cell, indicating that the proposed optical T-CAM cell could in principle lead to all-optical T-CAM-based Address Look-up memory architectures for high-end routing applications.

Strategy for Developing Expert-System-Based Internet Protocols (TCP/IP)

NASA Technical Reports Server (NTRS)

Ivancic, William D.

1997-01-01

The Satellite Networks and Architectures Branch of NASA's Lewis Research is addressing the issue of seamless interoperability of satellite networks with terrestrial networks. One of the major issues is improving reliable transmission protocols such as TCP over long latency and error-prone links. Many tuning parameters are available to enhance the performance of TCP including segment size, timers and window sizes. There are also numerous congestion avoidance algorithms such as slow start, selective retransmission and selective acknowledgment that are utilized to improve performance. This paper provides a strategy to characterize the performance of TCP relative to various parameter settings in a variety of network environments (i.e. LAN, WAN, wireless, satellite, and IP over ATM). This information can then be utilized to develop expert-system-based Internet protocols.

40-Gbps optical backbone network deep packet inspection based on FPGA

NASA Astrophysics Data System (ADS)

Zuo, Yuan; Huang, Zhiping; Su, Shaojing

2014-11-01

In the era of information, the big data, which contains huge information, brings about some problems, such as high speed transmission, storage and real-time analysis and process. As the important media for data transmission, the Internet is the significant part for big data processing research. With the large-scale usage of the Internet, the data streaming of network is increasing rapidly. The speed level in the main fiber optic communication of the present has reached 40Gbps, even 100Gbps, therefore data on the optical backbone network shows some features of massive data. Generally, data services are provided via IP packets on the optical backbone network, which is constituted with SDH (Synchronous Digital Hierarchy). Hence this method that IP packets are directly mapped into SDH payload is named POS (Packet over SDH) technology. Aiming at the problems of real time process of high speed massive data, this paper designs a process system platform based on ATCA for 40Gbps POS signal data stream recognition and packet content capture, which employs the FPGA as the CPU. This platform offers pre-processing of clustering algorithms, service traffic identification and data mining for the following big data storage and analysis with high efficiency. Also, the operational procedure is proposed in this paper. Four channels of 10Gbps POS signal decomposed by the analysis module, which chooses FPGA as the kernel, are inputted to the flow classification module and the pattern matching component based on TCAM. Based on the properties of the length of payload and net flows, buffer management is added to the platform to keep the key flow information. According to data stream analysis, DPI (deep packet inspection) and flow balance distribute, the signal is transmitted to the backend machine through the giga Ethernet ports on back board. Practice shows that the proposed platform is superior to the traditional applications based on ASIC and NP.

Ips Bark Beetles in the South

Treesearch

Michael D. Conner; Robert C. Wilkinson

1983-01-01

Ips beetles usually attack weakened, dying, or recently felled trees and fresh logging debris. Large numbers Ips may build up when natural events such as lightning storms, ice storms, tornadoes, wildfires, and droughts create large amounts of pine suitable for the breeding of these beetles. Ips populations may also build up following forestry activities, such as...

VoIP in a Campus Environment

ERIC Educational Resources Information Center

Young, Dan

2005-01-01

Internet Protocol (IP) Telephony, or voice-over IP (VoIP), has proved to be a wise decision for many organizations. This technology crosses the boundaries of public and private networks, enterprise and residential markets, voice and data technologies, as well as local and long-distance services. The convergence of voice and data into a single,…

Protocol for the Individual Placement and Support (IPS) in Pain Trial: A randomized controlled trial investigating the effectiveness of IPS for patients with chronic pain.

PubMed

Linnemørken, Lene Therese B; Sveinsdottir, Vigdis; Knutzen, Thomas; Rødevand, Linn; Hernæs, Kjersti Helene; Reme, Silje Endresen

2018-02-13

Work disability involves large costs to the society as well as to the individual. Work disability is common among people with chronic pain conditions, yet few effective interventions exist. Individual Placement and Support (IPS) is an evidence-based work rehabilitation model originally developed to help people with severe mental illness obtain and maintain employment. The effectiveness of IPS for patients with severe mental illness is well documented, but the model has never before been tested for patients with chronic pain. The aim of the IPS in Pain trial is to investigate the effectiveness of IPS as an integrated part of the interdisciplinary treatment for patients with chronic pain in a hospital outpatient clinic. The study is a randomized controlled trial comparing pain treatment with integrated IPS to treatment as usual in unemployed patients suffering from various chronic pain conditions. The primary outcome of the study is labor market participation during 12 months after enrollment, and secondary outcomes include physical and mental health and well-being, collected at baseline, 6, and 12 months. Finally, there will be an additional long-term follow-up for the primary outcome, which will be collected through a brief phone interview at 24 months. The IPS in Pain trial will be the first report of the effectiveness of the IPS model of supported employment applied in an outpatient setting for chronic pain patients. It will thus provide important information about the effectiveness of repurposing IPS to a new patient group in great need of job support. Clinicaltrials.gov: NCT02697656 . Registered January 15th, 2016.

Encrypted IP video communication system

NASA Astrophysics Data System (ADS)

Bogdan, Apetrechioaie; Luminiţa, Mateescu

2010-11-01

Digital video transmission is a permanent subject of development, research and improvement. This field of research has an exponentially growing market in civil, surveillance, security and military aplications. A lot of solutions: FPGA, ASIC, DSP have been used for this purpose. The paper presents the implementation of an encrypted, IP based, video communication system having a competitive performance/cost ratio .

The extended TRIP supporting VoIP routing reservation with distributed QoS

NASA Astrophysics Data System (ADS)

Wang, Furong; Wu, Ye

2004-04-01

In this paper, an existing protocol, i.e. TRIP (Telephony Routing over IP) is developed to provide distributed QoS when making resource reservations for VoIP services such as H.323, SIP. Enhanced LSs (location servers) are deployed in ITADs (IP Telephony Administrative Domains) to take in charge of intra-domain routing policy because of small propagation price. It is an easy way to find an IP telephone route for intra-domain VoIP media association and simultaneously possess intra-domain load balancing features. For those routing reservations bridging domains, inter-domain routing policy is responsible for finding the shortest inter-domain route with enough resources. I propose the routing preference policy based on QoS price when the session traffic is shaped by a token bucket, related QoS messages, and message cooperation.

Apiaceous vegetable consumption decreases PhIP-induced DNA adducts and increases methylated PhIP metabolites in the urine metabolome in rats.

PubMed

Kim, Jae Kyeom; Gallaher, Daniel D; Chen, Chi; Yao, Dan; Trudo, Sabrina P

2015-03-01

Heterocyclic aromatic amines, such as 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), are carcinogenic compounds produced during heating of protein-containing foods. Apiaceous vegetables inhibit PhIP-activating enzymes, whereas cruciferous vegetables induce both PhIP-activating and -detoxifying enzymes. We investigated the effects of these vegetables, either alone or combined, on PhIP metabolism and colonic DNA adduct formation in rats. Male Wistar rats were fed cruciferous vegetables (21%, wt:wt), apiaceous vegetables (21%, wt:wt), or a combination of both vegetables (10.5% wt:wt of each). Negative and positive control groups were fed an AIN-93G diet. After 6 d, all groups received an intraperitoneal injection of PhIP (10 mg · kg body weight(-1)) except for the negative control group, which received only vehicle. Urine was collected for 24 h after the injection for LC-tandem mass spectrometry metabolomic analyses. On day 7, rats were killed and tissues processed. Compared with the positive control, cruciferous vegetables increased the activity of hepatic PhIP-activating enzymes [39.5% and 45.1% for cytochrome P450 (CYP) 1A1 (P = 0.0006) and CYP1A2 (P < 0.0001), respectively] and of uridine 5'-diphospho-glucuronosyltransferase 1A (PhIP-detoxifying) by 24.5% (P = 0.0267). Apiaceous vegetables did not inhibit PhIP-activating enzymes, yet reduced colonic PhIP-DNA adducts by 20.4% (P = 0.0496). Metabolomic analyses indicated that apiaceous vegetables increased the relative abundance of urinary methylated PhIP metabolites. The sum of these methylated metabolites inversely correlated with colonic PhIP-DNA adducts (r = -0.43, P = 0.01). We detected a novel methylated urinary PhIP metabolite and demonstrated that methylated metabolites are produced in the human liver S9 fraction. Apiaceous vegetables did not inhibit the activity of PhIP-activating enzymes in rats, suggesting that the reduction in PhIP-DNA adducts may involve other pathways. Further investigation

Induced pluripotent stem (iPS) cells: a new source for cell-based therapeutics?

PubMed

de Lázaro, Irene; Yilmazer, Açelya; Kostarelos, Kostas

2014-07-10

The generation of induced pluripotent stem (iPS) cells from somatic cells by the ectopic expression of defined transcription factors has provided the regenerative medicine field with a new tool for cell replacement strategies. The advantages that these pluripotent cells can offer in comparison to other sources of stem cells include the generation of patient-derived cells and the lack of embryonic tissue while maintaining a versatile differentiation potential. The promise of iPS cell derivatives for therapeutic applications is encouraging albeit very early in development, with the first clinical study currently ongoing in Japan. Many challenges are yet to be circumvented before this technology can be clinically translated widely though. The delivery and expression of the reprogramming factors, the genomic instability, epigenetic memory and impact of cell propagation in culture are only some of the concerns. This article aims to critically discuss the potential of iPS cells as a new source of cell therapeutics. Copyright © 2014 Elsevier B.V. All rights reserved.

A Protocol Specification-Based Intrusion Detection System for VoIP and Its Evaluation

NASA Astrophysics Data System (ADS)

Phit, Thyda; Abe, Kôki

We propose an architecture of Intrusion Detection System (IDS) for VoIP using a protocol specification-based detection method to monitor the network traffics and alert administrator for further analysis of and response to suspicious activities. The protocol behaviors and their interactions are described by state machines. Traffic that behaves differently from the standard specifications are considered to be suspicious. The IDS has been implemented and simulated using OPNET Modeler, and verified to detect attacks. It was found that our system can detect typical attacks within a reasonable amount of delay time.

Multi-service terminal adapter based on IP technology applications in rural area

NASA Astrophysics Data System (ADS)

Gao, Li; Li, Xiaobo; Yan, Juntao; Ren, Xupeng

Take advantage of ample modern existing telecom network resources to rural areas may achieve it's information society gradually. This includes the establishment of integrated rural information service platform, modern remote education center and electronic administration management platform for rural areas. The geographical and economic constraints must be overcome for structuring the rural service support system, in order to provide technical support, information products and information services to modern rural information service system. It is important that development an access platform based IP technology, which supports multi-service access in order to implement a variety of types of mobile terminal equipment adapter access and to reduce restrictions on mobile terminal equipment.

Inositol hexakisphosphate (IP6) generated by IP5K mediates cullin-COP9 signalosome interactions and CRL function.

PubMed

Scherer, Paul C; Ding, Yan; Liu, Zhiqing; Xu, Jing; Mao, Haibin; Barrow, James C; Wei, Ning; Zheng, Ning; Snyder, Solomon H; Rao, Feng

2016-03-29

The family of cullin-RING E3 Ligases (CRLs) and the constitutive photomorphogenesis 9 (COP9) signalosome (CSN) form dynamic complexes that mediate ubiquitylation of 20% of the proteome, yet regulation of their assembly/disassembly remains poorly understood. Inositol polyphosphates are highly conserved signaling molecules implicated in diverse cellular processes. We now report that inositol hexakisphosphate (IP6) is a major physiologic determinant of the CRL-CSN interface, which includes a hitherto unidentified electrostatic interaction between the N-terminal acidic tail of CSN subunit 2 (CSN2) and a conserved basic canyon on cullins. IP6, with an EC50 of 20 nM, acts as an intermolecular "glue," increasing cullin-CSN2 binding affinity by 30-fold, thereby promoting assembly of the inactive CRL-CSN complexes. The IP6 synthase, Ins(1,3,4,5,6)P5 2-kinase (IPPK/IP5K) binds to cullins. Depleting IP5K increases the percentage of neddylated, active Cul1 and Cul4A, and decreases levels of the Cul1/4A substrates p27 and p21. Besides dysregulating CRL-mediated cell proliferation and UV-induced apoptosis, IP5K depletion potentiates by 28-fold the cytotoxic effect of the neddylation inhibitor MLN4924. Thus, IP5K and IP6 are evolutionarily conserved components of the CRL-CSN system and are potential targets for cancer therapy in conjunction with MLN4924.

Induced Pluripotent Stem (iPS) Cells in Dentistry: A Review

PubMed Central

Malhotra, Neeraj

2016-01-01

iPS cells are derived from somatic cells via transduction and expression of selective transcription factors. Both viral-integrating (like retroviral) and non-integrating (like, mRNA or protein-based) techniques are available for the production of iPS cells. In the field of dentistry, iPS cells have been derived from stem cells of apical papilla, dental pulp stem cells, and stem cells from exfoliated deciduous teeth, gingival and periodontal ligament fibroblasts, and buccal mucosa fibroblasts. iPS cells have the potential to differentiate into all derivatives of the 3 primary germ layers i.e. ectoderm, endoderm, and mesoderm. They are autogeneically accessible, and can produce patient-specific or disease-specific cell lines without the issue of ethical controversy. They have been successfully tested to produce mesenchymal stem cells-like cells, neural crest-like cells, ameloblasts-like cells, odontoblasts-like cells, and osteoprogenitor cells. These cells can aid in regeneration of periodontal ligament, alveolar bone, cementum, dentin-pulp complex, as well as possible Biotooth formation. However certain key issues like, epigenetic memory of iPS cells, viral-transduction, tumorgenesis and teratoma formation need to be overcome, before they can be successfully used in clinical practice. The article discusses the sources, pros and cons, and current applications of iPS cells in dentistry with an emphasis on encountered challenges and their solutions. PMID:27572712

All-IP wireless sensor networks for real-time patient monitoring.

PubMed

Wang, Xiaonan; Le, Deguang; Cheng, Hongbin; Xie, Conghua

2014-12-01

This paper proposes the all-IP WSNs (wireless sensor networks) for real-time patient monitoring. In this paper, the all-IP WSN architecture based on gateway trees is proposed and the hierarchical address structure is presented. Based on this architecture, the all-IP WSN can perform routing without route discovery. Moreover, a mobile node is always identified by a home address and it does not need to be configured with a care-of address during the mobility process, so the communication disruption caused by the address change is avoided. Through the proposed scheme, a physician can monitor the vital signs of a patient at any time and at any places, and according to the IPv6 address he can also obtain the location information of the patient in order to perform effective and timely treatment. Finally, the proposed scheme is evaluated based on the simulation, and the simulation data indicate that the proposed scheme might effectively reduce the communication delay and control cost, and lower the packet loss rate. Copyright © 2014 Elsevier Inc. All rights reserved.

HPC Access Using KVM over IP

DTIC Science & Technology

2007-06-01

these devices coupled with the difficulties- working with IP Video Systems (formerly Teraburst and cost-of installing dedicated long-distance fiber optic...dedicated fiber is best revealed that the IP Video Systems solutions seem to be suited for installation for point-to-point communications. the best...Research completion of the SBIR Phase II effort is planned for late (SBIR) effort with IP Video Systems (formerly known as FY 07. This paper will discuss

Analysis of Handoff Mechanisms in Mobile IP

NASA Astrophysics Data System (ADS)

Jayaraj, Maria Nadine Simonel; Issac, Biju; Haldar, Manas Kumar

2011-06-01

One of the most important challenges in mobile Internet Protocol (IP) is to provide service for a mobile node to maintain its connectivity to network when it moves from one domain to another. IP is responsible for routing packets across network. The first major version of IP is the Internet Protocol version 4 (IPv4). It is one of the dominant protocols relevant to wireless network. Later a newer version of IP called the IPv6 was proposed. Mobile IPv6 is mainly introduced for the purpose of mobility. Mobility management enables network to locate roaming nodes in order to deliver packets and maintain connections with them when moving into new domains. Handoff occurs when a mobile node moves from one network to another. It is a key factor of mobility because a mobile node can trigger several handoffs during a session. This paper briefly explains on mobile IP and its handoff issues, along with the drawbacks of mobile IP.

Apiaceous Vegetable Consumption Decreases PhIP-Induced DNA Adducts and Increases Methylated PhIP Metabolites in the Urine Metabolome in Rats123

PubMed Central

Kim, Jae Kyeom; Gallaher, Daniel D; Chen, Chi; Yao, Dan; Trudo, Sabrina P

2015-01-01

Background: Heterocyclic aromatic amines, such as 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), are carcinogenic compounds produced during heating of protein-containing foods. Apiaceous vegetables inhibit PhIP-activating enzymes, whereas cruciferous vegetables induce both PhIP-activating and -detoxifying enzymes. Objective: We investigated the effects of these vegetables, either alone or combined, on PhIP metabolism and colonic DNA adduct formation in rats. Methods: Male Wistar rats were fed cruciferous vegetables (21%, wt:wt), apiaceous vegetables (21%, wt:wt), or a combination of both vegetables (10.5% wt:wt of each). Negative and positive control groups were fed an AIN-93G diet. After 6 d, all groups received an intraperitoneal injection of PhIP (10 mg · kg body weight−1) except for the negative control group, which received only vehicle. Urine was collected for 24 h after the injection for LC–tandem mass spectrometry metabolomic analyses. On day 7, rats were killed and tissues processed. Results: Compared with the positive control, cruciferous vegetables increased the activity of hepatic PhIP-activating enzymes [39.5% and 45.1% for cytochrome P450 (CYP) 1A1 (P = 0.0006) and CYP1A2 (P < 0.0001), respectively] and of uridine 5′-diphospho-glucuronosyltransferase 1A (PhIP-detoxifying) by 24.5% (P = 0.0267). Apiaceous vegetables did not inhibit PhIP-activating enzymes, yet reduced colonic PhIP-DNA adducts by 20.4% (P = 0.0496). Metabolomic analyses indicated that apiaceous vegetables increased the relative abundance of urinary methylated PhIP metabolites. The sum of these methylated metabolites inversely correlated with colonic PhIP-DNA adducts (r = −0.43, P = 0.01). We detected a novel methylated urinary PhIP metabolite and demonstrated that methylated metabolites are produced in the human liver S9 fraction. Conclusions: Apiaceous vegetables did not inhibit the activity of PhIP-activating enzymes in rats, suggesting that the reduction in PhIP

Improving Air Pollution Modeling Over The Po Valley Using Saharan Dust Transport Forecasts

NASA Astrophysics Data System (ADS)

Kishcha, P.; Carnevale, C.; Finzi, G.; Pisoni, E.; Volta, M.; Nickovic, S.; Alpert, P.

2012-04-01

more accurate PM10 concentrations than the base TCAM model. Then, a comparison between modeled concentrations and PM10 measurements was carried out at 230 PM10 monitoring sites, distributed within the model domain. This model-vs.-measurement comparison showed that the integrated TCAM -DREAM model more accurately reproduced PM10 concentrations than the base TCAM model, both in term of correlation and mean error. Our results are of importance to countries which have to pay a penalty for exceeding the pollution limit. By extracting dust contribution from PM10 measurements, these countries could show lower rates of man-made pollution.

GMI-IPS: Python Processing Software for Aircraft Campaigns

NASA Technical Reports Server (NTRS)

Damon, M. R.; Strode, S. A.; Steenrod, S. D.; Prather, M. J.

2018-01-01

NASA's Atmospheric Tomography Mission (ATom) seeks to understand the impact of anthropogenic air pollution on gases in the Earth's atmosphere. Four flight campaigns are being deployed on a seasonal basis to establish a continuous global-scale data set intended to improve the representation of chemically reactive gases in global atmospheric chemistry models. The Global Modeling Initiative (GMI), is creating chemical transport simulations on a global scale for each of the ATom flight campaigns. To meet the computational demands required to translate the GMI simulation data to grids associated with the flights from the ATom campaigns, the GMI ICARTT Processing Software (GMI-IPS) has been developed and is providing key functionality for data processing and analysis in this ongoing effort. The GMI-IPS is written in Python and provides computational kernels for data interpolation and visualization tasks on GMI simulation data. A key feature of the GMI-IPS, is its ability to read ICARTT files, a text-based file format for airborne instrument data, and extract the required flight information that defines regional and temporal grid parameters associated with an ATom flight. Perhaps most importantly, the GMI-IPS creates ICARTT files containing GMI simulated data, which are used in collaboration with ATom instrument teams and other modeling groups. The initial main task of the GMI-IPS is to interpolate GMI model data to the finer temporal resolution (1-10 seconds) of a given flight. The model data includes basic fields such as temperature and pressure, but the main focus of this effort is to provide species concentrations of chemical gases for ATom flights. The software, which uses parallel computation techniques for data intensive tasks, linearly interpolates each of the model fields to the time resolution of the flight. The temporally interpolated data is then saved to disk, and is used to create additional derived quantities. In order to translate the GMI model data to the

Sensor proxy mobile IPv6 (SPMIPv6)--a novel scheme for mobility supported IP-WSNs.

PubMed

Islam, Md Motaharul; Huh, Eui-Nam

2011-01-01

IP based Wireless Sensor Networks (IP-WSNs) are gaining importance for their broad range of applications in health-care, home automation, environmental monitoring, industrial control, vehicle telematics and agricultural monitoring. In all these applications, mobility in the sensor network with special attention to energy efficiency is a major issue to be addressed. Host-based mobility management protocols are not suitable for IP-WSNs because of their energy inefficiency, so network based mobility management protocols can be an alternative for the mobility supported IP-WSNs. In this paper we propose a network based mobility supported IP-WSN protocol called Sensor Proxy Mobile IPv6 (SPMIPv6). We present its architecture, message formats and also evaluate its performance considering signaling cost, mobility cost and energy consumption. Our analysis shows that with respect to the number of IP-WSN nodes, the proposed scheme reduces the signaling cost by 60% and 56%, as well as the mobility cost by 62% and 57%, compared to MIPv6 and PMIPv6, respectively. The simulation results also show that in terms of the number of hops, SPMIPv6 decreases the signaling cost by 56% and 53% as well as mobility cost by 60% and 67% as compared to MIPv6 and PMIPv6 respectively. It also indicates that proposed scheme reduces the level of energy consumption significantly.

Comparative calibration of IP scanning equipment

NASA Astrophysics Data System (ADS)

Ingenito, F.; Andreoli, P.; Batani, D.; Boutoux, G.; Cipriani, M.; Consoli, F.; Cristofari, G.; Curcio, A.; De Angelis, R.; Di Giorgio, G.; Ducret, J.; Forestier-Colleoni, P.; Hulin, S.; Jakubowska, K.; Rabhi, N.

2016-05-01

Imaging Plates (IP) are diagnostic devices which contain a photostimulable phosphor layer that stores the incident radiation dose as a latent image. The image is read with a scanner which stimulates the decay of electrons, previously excited by the incident radiation, by exposition to a laser beam. This results in emitted light, which is detected by photomultiplier tubes; so the latent image is reconstructed. IPs have the interesting feature that can be reused many times, after erasing stored information. Algorithms to convert signals stored in the detector to Photostimulated luminescence (PSL) counts depend on the scanner and are not available on every model. A comparative cross-calibration of the IP scanner Dürr CR35 BIO, used in ABC laboratory, was performed, using the Fujifilm FLA 7000 scanner as a reference, to find the equivalence between grey-scale values given by the Dürr scanner to PSL counts. Using an IP and a 55Fe β-source, we produced pairs of samples with the same exposition times, which were analysed by both scanners, placing particular attention to fading times of the image stored on IPs. Data analysis led us to the determine a conversion formula which can be used to compare data of experiments obtained in different laboratories and to use IP calibrations available, till now, only for Fujifilm scanners.

Predictive IP controller for robust position control of linear servo system.

PubMed

Lu, Shaowu; Zhou, Fengxing; Ma, Yajie; Tang, Xiaoqi

2016-07-01

Position control is a typical application of linear servo system. In this paper, to reduce the system overshoot, an integral plus proportional (IP) controller is used in the position control implementation. To further improve the control performance, a gain-tuning IP controller based on a generalized predictive control (GPC) law is proposed. Firstly, to represent the dynamics of the position loop, a second-order linear model is used and its model parameters are estimated on-line by using a recursive least squares method. Secondly, based on the GPC law, an optimal control sequence is obtained by using receding horizon, then directly supplies the IP controller with the corresponding control parameters in the real operations. Finally, simulation and experimental results are presented to show the efficiency of proposed scheme. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Analysis of ChIP-seq Data in R/Bioconductor.

PubMed

de Santiago, Ines; Carroll, Thomas

2018-01-01

The development of novel high-throughput sequencing methods for ChIP (chromatin immunoprecipitation) has provided a very powerful tool to study gene regulation in multiple conditions at unprecedented resolution and scale. Proactive quality-control and appropriate data analysis techniques are of critical importance to extract the most meaningful results from the data. Over the last years, an array of R/Bioconductor tools has been developed allowing researchers to process and analyze ChIP-seq data. This chapter provides an overview of the methods available to analyze ChIP-seq data based primarily on software packages from the open-source Bioconductor project. Protocols described in this chapter cover basic steps including data alignment, peak calling, quality control and data visualization, as well as more complex methods such as the identification of differentially bound regions and functional analyses to annotate regulatory regions. The steps in the data analysis process were demonstrated on publicly available data sets and will serve as a demonstration of the computational procedures routinely used for the analysis of ChIP-seq data in R/Bioconductor, from which readers can construct their own analysis pipelines.

VoIP to the Rescue

ERIC Educational Resources Information Center

Milner, Jacob

2005-01-01

Voice over Internet Protocol (VoIP) is everywhere. The technology lets users make and receive phone calls over the Internet, transporting voice traffic alongside data traffic such as instant messages (IMs) and e-mail. While the number of consumer customers using VoIP increases every week, the technology is finding its way into K-12 education as…

ChIP-nexus: a novel ChIP-exo protocol for improved detection of in vivo transcription factor binding footprints

PubMed Central

He, Qiye; Johnston, Jeff; Zeitlinger, Julia

2014-01-01

Understanding how eukaryotic enhancers are bound and regulated by specific combinations of transcription factors is still a major challenge. To better map transcription factor binding genome-wide at nucleotide resolution in vivo, we have developed a robust ChIP-exo protocol called ChIP experiments with nucleotide resolution through exonuclease, unique barcode and single ligation (ChIP-nexus), which utilizes an efficient DNA self-circularization step during library preparation. Application of ChIP-nexus to four proteins—human TBP and Drosophila NFkB, Twist and Max— demonstrates that it outperforms existing ChIP protocols in resolution and specificity, pinpoints relevant binding sites within enhancers containing multiple binding motifs and allows the analysis of in vivo binding specificities. Notably, we show that Max frequently interacts with DNA sequences next to its motif, and that this binding pattern correlates with local DNA sequence features such as DNA shape. ChIP-nexus will be broadly applicable to studying in vivo transcription factor binding specificity and its relationship to cis-regulatory changes in humans and model organisms. PMID:25751057

Achieving quality of service in IP networks

NASA Astrophysics Data System (ADS)

Hays, Tim

2001-07-01

The Internet Protocol (IP) has served global networks well, providing a standardized method to transmit data among many disparate systems. But IP is designed for simplicity, and only enables a `best effort' service that can be subject to delays and loss of data. For data networks, this is an acceptable trade-off. In the emerging world of convergence, driven by new applications such as video streaming and IP telephony, minimizing latency and packet loss as well as jitter can be critical. Simply increasing the size of the IP network `pipe' to meet those demands is not always sufficient. In this environment, vendors and standards bodies are endeavoring to create technologies and techniques to enable IP to improve the quality of service it can provide, while retaining the characteristics that has enabled it to become the dominant networking protocol.

Solar Type II Radio Bursts and IP Type II Events

NASA Technical Reports Server (NTRS)

Cane, H. V.; Erickson, W. C.

2005-01-01

We have examined radio data from the WAVES experiment on the Wind spacecraft in conjunction with ground-based data in order to investigate the relationship between the shocks responsible for metric type II radio bursts and the shocks in front of coronal mass ejections (CMEs). The bow shocks of fast, large CMEs are strong interplanetary (IP) shocks, and the associated radio emissions often consist of single broad bands starting below approx. 4 MHz; such emissions were previously called IP type II events. In contrast, metric type II bursts are usually narrowbanded and display two harmonically related bands. In addition to displaying complete dynamic spectra for a number of events, we also analyze the 135 WAVES 1 - 14 MHz slow-drift time periods in 2001-2003. We find that most of the periods contain multiple phenomena, which we divide into three groups: metric type II extensions, IP type II events, and blobs and bands. About half of the WAVES listings include probable extensions of metric type II radio bursts, but in more than half of these events, there were also other slow-drift features. In the 3 yr study period, there were 31 IP type II events; these were associated with the very fastest CMEs. The most common form of activity in the WAVES events, blobs and bands in the frequency range between 1 and 8 MHz, fall below an envelope consistent with the early signatures of an IP type II event. However, most of this activity lasts only a few tens of minutes, whereas IP type II events last for many hours. In this study we find many examples in the radio data of two shock-like phenomena with different characteristics that occur simultaneously in the metric and decametric/hectometric bands, and no clear example of a metric type II burst that extends continuously down in frequency to become an IP type II event. The simplest interpretation is that metric type II bursts, unlike IP type II events, are not caused by shocks driven in front of CMEs.

Continuously Connected With Mobile IP

NASA Technical Reports Server (NTRS)

2002-01-01

Cisco Systems developed Cisco Mobile Networks, making IP devices mobile. With this innovation, a Cisco router and its connected IP devices can roam across network boundaries and connection types. Because a mobile user is able to keep the same IP address while roaming, a live IP connection can be maintained without interruption. Glenn Research Center jointly tested the technology with Cisco, and is working to use it on low-earth-orbiting research craft. With Cisco's Mobile Networks functionality now available in Cisco IOS Software release 12.2(4)T, the commercial advantages and benefits are numerous. The technology can be applied to public safety, military/homeland security, emergency management services, railroad and shipping systems, and the automotive industry. It will allow ambulances, police, firemen, and the U.S. Coast Guard to stay connected to their networks while on the move. In the wireless battlefield, the technology will provide rapid infrastructure deployment for U.S. national defense. Airline, train, and cruise passengers utilizing Cisco Mobile Networks can fly all around the world with a continuous Internet connection. Cisco IOS(R) Software is a registered trademark of Cisco Systems.

Pre-equilibrium Longitudinal Flow in the IP-Glasma Framework for Pb+Pb Collisions at the LHC

NASA Astrophysics Data System (ADS)

McDonald, Scott; Shen, Chun; Fillion-Gourdeau, François; Jeon, Sangyong; Gale, Charles

2017-08-01

In this work, we debut a new implementation of IP-Glasma and quantify the pre-equilibrium longitudinal flow in the IP-Glasma framework. The saturation physics based IP-Glasma model naturally provides a non-zero initial longitudinal flow through its pre-equilibrium Yang-Mills evolution. A hybrid IP-Glasma+MUSIC+UrQMD frame-work is employed to test this new implementation against experimental data and to make further predictions about hadronic flow observables in Pb+Pb collisions at 5.02 TeV. Finally, the non-zero pre-equilibrium longitudinal flow of the IP-Glasma model is quantified, and its origin is briefly discussed.

IPS - a vision aided navigation system

NASA Astrophysics Data System (ADS)

Börner, Anko; Baumbach, Dirk; Buder, Maximilian; Choinowski, Andre; Ernst, Ines; Funk, Eugen; Grießbach, Denis; Schischmanow, Adrian; Wohlfeil, Jürgen; Zuev, Sergey

2017-04-01

Ego localization is an important prerequisite for several scientific, commercial, and statutory tasks. Only by knowing one's own position, can guidance be provided, inspections be executed, and autonomous vehicles be operated. Localization becomes challenging if satellite-based navigation systems are not available, or data quality is not sufficient. To overcome this problem, a team of the German Aerospace Center (DLR) developed a multi-sensor system based on the human head and its navigation sensors - the eyes and the vestibular system. This system is called integrated positioning system (IPS) and contains a stereo camera and an inertial measurement unit for determining an ego pose in six degrees of freedom in a local coordinate system. IPS is able to operate in real time and can be applied for indoor and outdoor scenarios without any external reference or prior knowledge. In this paper, the system and its key hardware and software components are introduced. The main issues during the development of such complex multi-sensor measurement systems are identified and discussed, and the performance of this technology is demonstrated. The developer team started from scratch and transfers this technology into a commercial product right now. The paper finishes with an outlook.

75 FR 13235 - IP-Enabled Services

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-19

... FEDERAL COMMUNICATIONS COMMISSION 47 CFR Part 63 [WC Docket No. 04-36; FCC 09-40] IP-Enabled Services AGENCY: Federal Communications Commission ACTION: Final rule; announcement of effective date... Internet Protocol (VoIP) service the discontinuance obligations that apply to domestic non-dominant...

Sensor Proxy Mobile IPv6 (SPMIPv6)—A Novel Scheme for Mobility Supported IP-WSNs

PubMed Central

Islam, Md. Motaharul; Huh, Eui-Nam

2011-01-01

IP based Wireless Sensor Networks (IP-WSNs) are gaining importance for their broad range of applications in health-care, home automation, environmental monitoring, industrial control, vehicle telematics and agricultural monitoring. In all these applications, mobility in the sensor network with special attention to energy efficiency is a major issue to be addressed. Host-based mobility management protocols are not suitable for IP-WSNs because of their energy inefficiency, so network based mobility management protocols can be an alternative for the mobility supported IP-WSNs. In this paper we propose a network based mobility supported IP-WSN protocol called Sensor Proxy Mobile IPv6 (SPMIPv6). We present its architecture, message formats and also evaluate its performance considering signaling cost, mobility cost and energy consumption. Our analysis shows that with respect to the number of IP-WSN nodes, the proposed scheme reduces the signaling cost by 60% and 56%, as well as the mobility cost by 62% and 57%, compared to MIPv6 and PMIPv6, respectively. The simulation results also show that in terms of the number of hops, SPMIPv6 decreases the signaling cost by 56% and 53% as well as mobility cost by 60% and 67% as compared to MIPv6 and PMIPv6 respectively. It also indicates that proposed scheme reduces the level of energy consumption significantly. PMID:22319386

Validation of a Brief Structured Interview: The Children's Interview for Psychiatric Syndromes (ChIPS).

PubMed

Young, Matthew E; Bell, Ziv E; Fristad, Mary A

2016-12-01

Evidence-based assessment is important in the treatment of childhood psychopathology. While researchers and clinicians frequently use structured diagnostic interviews to ensure reliability, the most commonly used instrument, the Schedule for Affective Disorders and Schizophrenia for School Aged Children (K-SADS) is too long for most clinical applications. The Children's Interview for Psychiatric Syndromes (ChIPS/P-ChIPS) is a highly-structured brief diagnostic interview. The present study compared K-SADS and ChIPS/P-ChIPS diagnoses in an outpatient clinical sample of 50 parent-child pairs aged 7-14. Agreement between most diagnoses was moderate to high between the instruments and with consensus clinical diagnoses. ChIPS was significantly briefer to administer than the K-SADS. Interviewer experience level and participant demographics did not appear to affect agreement. Results provide further evidence for the validity of the ChIPS and support its use in clinical and research settings.

Crosslayer Survivability in Overlay-IP-WDM Networks

ERIC Educational Resources Information Center

Pacharintanakul, Peera

2010-01-01

As the Internet moves towards a three-layer architecture consisting of overlay networks on top of the IP network layer on top of WDM-based physical networks, incorporating the interaction between and among network layers is crucial for efficient and effective implementation of survivability. This dissertation has four major foci as follows:…

Operational Space Weather Products at IPS

NASA Astrophysics Data System (ADS)

Neudegg, D.; Steward, G.; Marshall, R.; Terkildsen, M.; Kennewell, J.; Patterson, G.; Panwar, R.

2008-12-01

IPS Radio and Space Services operates an extensive network (IPSNET) of monitoring stations and observatories within the Australasian and Antarctic regions to gather information on the space environment. This includes ionosondes, magnetometers, GPS-ISM, oblique HF sounding, riometers, and solar radio and optical telescopes. IPS exchanges this information with similar organisations world-wide. The Regional Warning Centre (RWC) is the Australian Space Forecast Centre (ASFC) and it utilizes this data to provide products and services to support customer operations. A wide range of customers use IPS services including; defence force and emergency services using HF radio communications and surveillance systems, organisations involved in geophysical exploration and pipeline cathodic protection, GPS users in aviation. Subscriptions to the alerts, warnings, forecasts and reports regarding the solar, geophysical and ionospheric conditions are distributed by email and Special Message Service (SMS). IPS also develops and markets widely used PC software prediction tools for HF radio skywave and surface wave (ASAPS/GWPS) and provides consultancy services for system planning.

A Conjoint Analysis of Voice Over IP Attributes.

ERIC Educational Resources Information Center

Zubey, Michael L.; Wagner, William; Otto, James R.

2002-01-01

Managers need to understand the tradeoffs associated with voice over Internet protocol (VoIP) networks as compared to the Public Switched Telephone Network (PSTN). This article measures the preference structures between IP telephony and PSTN services using conjoint analysis. The purpose is to suggest VoIP technology attributes that best meet…

Adaptation technology between IP layer and optical layer in optical Internet

NASA Astrophysics Data System (ADS)

Ji, Yuefeng; Li, Hua; Sun, Yongmei

2001-10-01

Wavelength division multiplexing (WDM) optical network provides a platform with high bandwidth capacity and is supposed to be the backbone infrastructure supporting the next-generation high-speed multi-service networks (ATM, IP, etc.). In the foreseeable future, IP will be the predominant data traffic, to make fully use of the bandwidth of the WDM optical network, many attentions have been focused on IP over WDM, which has been proposed as the most promising technology for new kind of network, so-called Optical Internet. According to OSI model, IP is in the 3rd layer (network layer) and optical network is in the 1st layer (physical layer), so the key issue is what adaptation technology should be used in the 2nd layer (data link layer). In this paper, firstly, we analyze and compare the current adaptation technologies used in backbone network nowadays. Secondly, aiming at the drawbacks of above technologies, we present a novel adaptation protocol (DONA) between IP layer and optical layer in Optical Internet and describe it in details. Thirdly, the gigabit transmission adapter (GTA) we accomplished based on the novel protocol is described. Finally, we set up an experiment platform to apply and verify the DONA and GTA, the results and conclusions of the experiment are given.

ROVER: A DNS-Based Method to Detect and Prevent IP Hijacks

ERIC Educational Resources Information Center

Gersch, Joseph E.

2013-01-01

The Border Gateway Protocol (BGP) is critical to the global internet infrastructure. Unfortunately BGP routing was designed with limited regard for security. As a result, IP route hijacking has been observed for more than 16 years. Well known incidents include a 2008 hijack of YouTube, loss of connectivity for Australia in February 2012, and an…

FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes.

PubMed

Parodi, Alice C L; Sangalli, Laura M; Vantini, Simone; Amati, Bruno; Secchi, Piercesare; Morelli, Marco J

2017-08-15

Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) generates local accumulations of sequencing reads on the genome ("peaks"), which correspond to specific protein-DNA interactions or chromatin modifications. Peaks are detected by considering their total area above a background signal, usually neglecting their shapes, which instead may convey additional biological information. We present FunChIP, an R/Bioconductor package for clustering peaks according to a functional representation of their shapes: after approximating their profiles with cubic B-splines, FunChIP minimizes their functional distance and classifies the peaks applying a k-mean alignment and clustering algorithm. The whole pipeline is user-friendly and provides visualization functions for a quick inspection of the results. An application to the transcription factor Myc in 3T9 murine fibroblasts shows that clusters of peaks with different shapes are associated with different genomic locations and different transcriptional regulatory activity. The package is implemented in R and is available under Artistic Licence 2.0 from the Bioconductor website (http://bioconductor.org/packages/FunChIP). marco.morelli@iit.it. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Protection against cancer by dietary IP6 and inositol.

PubMed

Vucenik, Ivana; Shamsuddin, AbulKalam M

2006-01-01

Inositol hexaphosphate (IP(6)) is a naturally occurring polyphosphorylated carbohydrate, abundantly present in many plant sources and in certain high-fiber diets, such as cereals and legumes. In addition to being found in plants, IP(6) is contained in almost all mammalian cells, although in much smaller amounts, where it is important in regulating vital cellular functions such as signal transduction, cell proliferation, and differentiation. For a long time IP(6) has been recognized as a natural antioxidant. Recently IP(6) has received much attention for its role in cancer prevention and control of experimental tumor growth, progression, and metastasis. In addition, IP(6) possesses other significant benefits for human health, such as the ability to enhance immune system, prevent pathological calcification and kidney stone formation, lower elevated serum cholesterol, and reduce pathological platelet activity. In this review we show the efficacy and discuss some of the molecular mechanisms that govern the action of this dietary agent. Exogenously administered IP(6) is rapidly taken up into cells and dephosphorylated to lower inositol phosphates, which further affect signal transduction pathways resulting in cell cycle arrest. A striking anticancer action of IP(6) was demonstrated in different experimental models. In addition to reducing cell proliferation, IP(6) also induces differentiation of malignant cells. Enhanced immunity and antioxidant properties also contribute to tumor cell destruction. Preliminary studies in humans show that IP(6) and inositol, the precursor molecule of IP(6), appear to enhance the anticancer effect of conventional chemotherapy, control cancer metastases, and improve quality of life. Because it is abundantly present in regular diet, efficiently absorbed from the gastrointestinal tract, and safe, IP(6) + inositol holds great promise in our strategies for cancer prevention and therapy. There is clearly enough evidence to justify the

Pattern of Traditional Medicine Utilization among HIV/AIDS Patients on Antiretroviral Therapy at a University Hospital in Northwestern Ethiopia: A Cross-Sectional Study

PubMed Central

Tadesse, Wondmagegn Tamiru

2017-01-01

The objective of this study was to assess traditional, complementary, and alternative medicine (TCAM) utilization pattern among HIV/AIDS patients on antiretroviral therapy at University of Gondar Comprehensive Specialized Hospital. Materials and Methods. Data on sociodemographic profile and clinical and TCAM utilization were collected using a structured, pretested questionnaire from April 01 to May 28, 2014, through interviews with patients. Data on CD4 count, HIV stage, and ART regimen were collected from patient records. Analysis was conducted descriptively using SPSS version 20. Results. Of the 300 participants, 43.7% reported using TCAM, with the largest proportion of them from religious institutions (churches/mosques) (41.22%), followed by home prepared (32.82%) and traditional healers (16.03%). The leading forms of TCAM used were spiritual and herbal therapies constituting 56.49% and 36.64% of the patients, respectively. The most frequently used herbal products included Nigella sativa (22.92%) and Moringa oleifera (20.83%). Most of the patients (73.30%) using TCAM reported improvement in their conditions. Conclusions. TCAM utilization among HIV/AIDS patients on ART was common and different sources and types were used alongside ART, with improvement reported by most. Further research is needed to identify CAM therapies which may be used as adjunct treatments among these patients. PMID:28421118

Pattern of Traditional Medicine Utilization among HIV/AIDS Patients on Antiretroviral Therapy at a University Hospital in Northwestern Ethiopia: A Cross-Sectional Study.

PubMed

Endale Gurmu, Abyot; Teni, Fitsum Sebsibe; Tadesse, Wondmagegn Tamiru

2017-01-01

The objective of this study was to assess traditional, complementary, and alternative medicine (TCAM) utilization pattern among HIV/AIDS patients on antiretroviral therapy at University of Gondar Comprehensive Specialized Hospital. Materials and Methods . Data on sociodemographic profile and clinical and TCAM utilization were collected using a structured, pretested questionnaire from April 01 to May 28, 2014, through interviews with patients. Data on CD4 count, HIV stage, and ART regimen were collected from patient records. Analysis was conducted descriptively using SPSS version 20. Results . Of the 300 participants, 43.7% reported using TCAM, with the largest proportion of them from religious institutions (churches/mosques) (41.22%), followed by home prepared (32.82%) and traditional healers (16.03%). The leading forms of TCAM used were spiritual and herbal therapies constituting 56.49% and 36.64% of the patients, respectively. The most frequently used herbal products included Nigella sativa (22.92%) and Moringa oleifera (20.83%). Most of the patients (73.30%) using TCAM reported improvement in their conditions. Conclusions . TCAM utilization among HIV/AIDS patients on ART was common and different sources and types were used alongside ART, with improvement reported by most. Further research is needed to identify CAM therapies which may be used as adjunct treatments among these patients.

Efficient genomic correction methods in human iPS cells using CRISPR-Cas9 system.

PubMed

Li, Hongmei Lisa; Gee, Peter; Ishida, Kentaro; Hotta, Akitsu

2016-05-15

Precise gene correction using the CRISPR-Cas9 system in human iPS cells holds great promise for various applications, such as the study of gene functions, disease modeling, and gene therapy. In this review article, we summarize methods for effective editing of genomic sequences of iPS cells based on our experiences correcting dystrophin gene mutations with the CRISPR-Cas9 system. Designing specific sgRNAs as well as having efficient transfection methods and proper detection assays to assess genomic cleavage activities are critical for successful genome editing in iPS cells. In addition, because iPS cells are fragile by nature when dissociated into single cells, a step-by-step confirmation during the cell recovery process is recommended to obtain an adequate number of genome-edited iPS cell clones. We hope that the techniques described here will be useful for researchers from diverse backgrounds who would like to perform genome editing in iPS cells. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

ERP44 inhibits human lung cancer cell migration mainly via IP3R2.

PubMed

Huang, Xue; Jin, Meng; Chen, Ying-Xiao; Wang, Jun; Zhai, Kui; Chang, Yan; Yuan, Qi; Yao, Kai-Tai; Ji, Guangju

2016-06-01

Cancer cell migration is involved in tumour metastasis. However, the relationship between calcium signalling and cancer migration is not well elucidated. In this study, we used the human lung adenocarcinoma A549 cell line to examine the role of endoplasmic reticulum protein 44 (ERP44), which has been reported to regulate calcium release inside of the endoplasmic reticulum (ER), in cell migration. We found that the inositol 1,4,5-trisphosphate receptors (IP3Rs/ITPRs) inhibitor 2-APB significantly inhibited A549 cell migration by inhibiting cell polarization and pseudopodium protrusion, which suggests that Ca2+ is necessary for A549 cell migration. Similarly, the overexpression of ERP44 reduced intracellular Ca2+ release via IP3Rs, altered cell morphology and significantly inhibited the migration of A549 cells. These phenomena were primarily dependent on IP3R2 because wound healing in A549 cells with IP3R2 rather than IP3R1 or IP3R3 siRNA was markedly inhibited. Moreover, the overexpression of ERP44 did not affect the migration of the human neuroblastoma cell line SH-SY5Y, which mainly expresses IP3R1. Based on the above observations, we conclude that ERP44 regulates A549 cell migration mainly via an IP3R2-dependent pathway.

ERP44 inhibits human lung cancer cell migration mainly via IP3R2

PubMed Central

Zhai, Kui; Chang, Yan; Yuan, Qi; Yao, Kai-Tai; Ji, Guangju

2016-01-01

Cancer cell migration is involved in tumour metastasis. However, the relationship between calcium signalling and cancer migration is not well elucidated. In this study, we used the human lung adenocarcinoma A549 cell line to examine the role of endoplasmic reticulum protein 44 (ERP44), which has been reported to regulate calcium release inside of the endoplasmic reticulum (ER), in cell migration. We found that the inositol 1,4,5-trisphosphate receptors (IP3Rs/ITPRs) inhibitor 2-APB significantly inhibited A549 cell migration by inhibiting cell polarization and pseudopodium protrusion, which suggests that Ca2+ is necessary for A549 cell migration. Similarly, the overexpression of ERP44 reduced intracellular Ca2+ release via IP3Rs, altered cell morphology and significantly inhibited the migration of A549 cells. These phenomena were primarily dependent on IP3R2 because wound healing in A549 cells with IP3R2 rather than IP3R1 or IP3R3 siRNA was markedly inhibited. Moreover, the overexpression of ERP44 did not affect the migration of the human neuroblastoma cell line SH-SY5Y, which mainly expresses IP3R1. Based on the above observations, we conclude that ERP44 regulates A549 cell migration mainly via an IP3R2-dependent pathway. PMID:27347718

Sustained signalling by PTH modulates IP3 accumulation and IP3 receptors through cyclic AMP junctions

PubMed Central

Meena, Abha; Tovey, Stephen C.; Taylor, Colin W.

2015-01-01

ABSTRACT Parathyroid hormone (PTH) stimulates adenylyl cyclase through type 1 PTH receptors (PTH1R) and potentiates the Ca2+ signals evoked by carbachol, which stimulates formation of inositol 1,4,5-trisphosphate (IP3). We confirmed that in HEK cells expressing PTH1R, acute stimulation with PTH(1-34) potentiated carbachol-evoked Ca2+ release. This was mediated by locally delivered cyclic AMP (cAMP), but unaffected by inhibition of protein kinase A (PKA), exchange proteins activated by cAMP, cAMP phosphodiesterases (PDEs) or substantial inhibition of adenylyl cyclase. Sustained stimulation with PTH(1-34) causes internalization of PTH1R–adenylyl cyclase signalling complexes, but the consequences for delivery of cAMP to IP3R within cAMP signalling junctions are unknown. Here, we show that sustained stimulation with PTH(1-34) or with PTH analogues that do not evoke receptor internalization reduced the potentiated Ca2+ signals and attenuated carbachol-evoked increases in cytosolic IP3. Similar results were obtained after sustained stimulation with NKH477 to directly activate adenylyl cyclase, or with the membrane-permeant analogue of cAMP, 8-Br-cAMP. These responses were independent of PKA and unaffected by substantial inhibition of adenylyl cyclase. During prolonged stimulation with PTH(1-34), hyperactive cAMP signalling junctions, within which cAMP is delivered directly and at saturating concentrations to its targets, mediate sensitization of IP3R and a more slowly developing inhibition of IP3 accumulation. PMID:25431134

Lessons Learned in the Design and Use of IP1 / IP2 Flexible Packaging - 13621

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

Sanchez, Mike; Reeves, Wendall; Smart, Bill

2013-07-01

For many years in the USA, Low Level Radioactive Waste (LLW), contaminated soils and construction debris, have been transported, interim stored, and disposed of, using IP1 / IP2 metal containers. The performance of these containers has been more than adequate, with few safety occurrences. The containers are used under the regulatory oversight of the US Department of Transportation (DOT), 49 Code of Federal Regulations (CFR). In the late 90's the introduction of flexible packaging for the transport, storage, and disposal of low level contaminated soils and construction debris was introduced. The development of flexible packaging came out of a needmore » for a more cost effective package, for the large volumes of waste generated by the decommissioning of many of the US Department of Energy (DOE) legacy sites across the US. Flexible packaging had to be designed to handle a wide array of waste streams, including soil, gravel, construction debris, and fine particulate dust migration. The design also had to meet all of the IP1 requirements under 49CFR 173.410, and be robust enough to pass the IP2 testing 49 CFR 173.465 required for many LLW shipments. Tens of thousands of flexible packages have been safely deployed and used across the US nuclear industry as well as for hazardous non-radioactive applications, with no recorded release of radioactive materials. To ensure that flexible packages are designed properly, the manufacturer must use lessons learned over the years, and the tests performed to provide evidence that these packages are suitable for transporting low level radioactive wastes. The design and testing of flexible packaging for LLW, VLLW and other hazardous waste streams must be as strict and stringent as the design and testing of metal containers. The design should take into consideration the materials being loaded into the package, and should incorporate the right materials, and manufacturing methods, to provide a quality, safe product. Flexible packaging

Covert Channels in SIP for VoIP Signalling

NASA Astrophysics Data System (ADS)

Mazurczyk, Wojciech; Szczypiorski, Krzysztof

In this paper, we evaluate available steganographic techniques for SIP (Session Initiation Protocol) that can be used for creating covert channels during signaling phase of VoIP (Voice over IP) call. Apart from characterizing existing steganographic methods we provide new insights by introducing new techniques. We also estimate amount of data that can be transferred in signalling messages for typical IP telephony call.

IP access networks with QoS support

NASA Astrophysics Data System (ADS)

Sargento, Susana; Valadas, Rui J. M. T.; Goncalves, Jorge; Sousa, Henrique

2001-07-01

The increasing demand of new services and applications is pushing for drastic changes on the design of access networks targeted mainly for residential and SOHO users. Future access networks will provide full service integration (including multimedia), resource sharing at the packet level and QoS support. It is expected that using IP as the base technology, the ideal plug-and-play scenario, where the management actions of the access network operator are kept to a minimum, will be achieved easily. This paper proposes an architecture for access networks based on layer 2 or layer 3 multiplexers that allows a number of simplifications in the network elements and protocols (e.g. in the routing and addressing functions). We discuss two possible steps in the evolution of access networks towards a more efficient support of IP based services. The first one still provides no QoS support and was designed with the goal of reusing as much as possible current technologies; it is based on tunneling to transport PPP sessions. The second one introduces QoS support through the use of emerging technologies and protocols. We illustrate the different phases of a multimedia Internet access session, when using SIP for session initiation, COPS for the management of QoS policies including the AAA functions and RSVP for resource reservation.

IPS guidestar selection for stellar mode (ASTRO)

NASA Technical Reports Server (NTRS)

Mullins, Larry; Wooten, Lewis

1988-01-01

This report describes how guide stars are selected for the Optical Sensor Package (OSP) for the Instrument Pointing System (IPS) when it is operating in the stellar mode on the ASTRO missions. It also describes how the objective loads are written and how the various roll angles are related; i.e., the celestial roll or position angle, the objective load roll angles, and the IPS gimbal angles. There is a brief description of how the IPS operates and its various modes of operation; i.e., IDOP, IDIN, and OSPCAL.

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

PubMed

Yang, Chia-Chun; Andrews, Erik H; Chen, Min-Hsuan; Wang, Wan-Yu; Chen, Jeremy J W; Gerstein, Mark; Liu, Chun-Chi; Cheng, Chao

2016-08-12

Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP's output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired. To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server ( http://syslab3.nchu.edu.tw/iTAR/ ) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF. The iTAR web server provides a user-friendly interface and supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the web server generates the chart of the

Heterogeneous IP Ecosystem enabling Reuse (HIER)

DTIC Science & Technology

2017-03-22

Technical Approach and Justification IP reuse is a cornerstone of the commercial electronics market particularly in the digital domain...even in the digital domain. Significant investments in custom ASIC designs have been made by the government, but the IP resulting from such... approach to address requirements for that program. Research Plan The original vision for the HIER activity involved the evaluation

Global Analysis of Transcription Factor-Binding Sites in Yeast Using ChIP-Seq

PubMed Central

Lefrançois, Philippe; Gallagher, Jennifer E. G.; Snyder, Michael

2016-01-01

Transcription factors influence gene expression through their ability to bind DNA at specific regulatory elements. Specific DNA-protein interactions can be isolated through the chromatin immunoprecipitation (ChIP) procedure, in which DNA fragments bound by the protein of interest are recovered. ChIP is followed by high-throughput DNA sequencing (Seq) to determine the genomic provenance of ChIP DNA fragments and their relative abundance in the sample. This chapter describes a ChIP-Seq strategy adapted for budding yeast to enable the genome-wide characterization of binding sites of transcription factors (TFs) and other DNA-binding proteins in an efficient and cost-effective way. Yeast strains with epitope-tagged TFs are most commonly used for ChIP-Seq, along with their matching untagged control strains. The initial step of ChIP involves the cross-linking of DNA and proteins. Next, yeast cells are lysed and sonicated to shear chromatin into smaller fragments. An antibody against an epitope-tagged TF is used to pull down chromatin complexes containing DNA and the TF of interest. DNA is then purified and proteins degraded. Specific barcoded adapters for multiplex DNA sequencing are ligated to ChIP DNA. Short DNA sequence reads (28–36 base pairs) are parsed according to the barcode and aligned against the yeast reference genome, thus generating a nucleotide-resolution map of transcription factor-binding sites and their occupancy. PMID:25213249

A short-term clinical evaluation of IPS Empress 2 crowns.

PubMed

Toksavul, Suna; Toman, Muhittin

2007-01-01

The aim of this study was to evaluate the clinical performance of all-ceramic crowns made with the IPS Empress 2 system after an observation period of 12 to 60 months. Seventy-nine IPS Empress 2 crowns were placed in 21 patients. The all-ceramic crowns were evaluated clinically, radiographically, and using clinical photographs. The evaluations took place at baseline (2 days after cementation) and at 6-month intervals for 12 to 60 months. Survival rate of the crowns was determined using Kaplan-Meier statistical analysis. Based on the US Public Health Service criteria, 95.24% of the crowns were rated satisfactory after a mean follow-up period of 58 months. Fracture was registered in only 1 crown. One endodontically treated tooth failed as a result of fracture at the cervical margin area. In this in vivo study, IPS Empress 2 crowns exhibited a satisfactory clinical performance during an observation period ranging from 12 to 60 months.

Research and Simulation on Application of the Mobile IP Network

NASA Astrophysics Data System (ADS)

Yibing, Deng; Wei, Hu; Minghui, Li; Feng, Gao; Junyi, Shen

The paper analysed the mobile node, home agent, and foreign agent of mobile IP network firstly, some key technique, such as mobile IP network basical principle, protocol work principle, agent discovery, registration, and IP packet transmission, were discussed. Then a network simulation model was designed, validating the characteristic of mobile IP network, and some advantages, which were brought by mobile network, were testified. Finally, the conclusion is gained: mobile IP network could realize the expectation of consumer that they can communicate with others anywhere.

How to Combine ChIP with qPCR.

PubMed

Asp, Patrik

2018-01-01

Chromatin immunoprecipitation (ChIP) coupled with quantitative PCR (qPCR) has in the last 15 years become a basic mainstream tool in genomic research. Numerous commercially available ChIP kits, qPCR kits, and real-time PCR systems allow for quick and easy analysis of virtually anything chromatin-related as long as there is an available antibody. However, the highly accurate quantitative dimension added by using qPCR to analyze ChIP samples significantly raises the bar in terms of experimental accuracy, appropriate controls, data analysis, and data presentation. This chapter will address these potential pitfalls by providing protocols and procedures that address the difficulties inherent in ChIP-qPCR assays.

First IPS Radio Sources Detected By MEXART

NASA Astrophysics Data System (ADS)

Mejia-Ambriz, J.; Gonzalez-Esparza, A.; Carrillo-Vargas, A.; Villanueva-Hernandez, P.; Aguilar-Rodriguez, E.; Andrade-Mascote, E.; Vazquez-Hernandez, S.; Sierra-Figueredo, P.; Ananthakrishnan, S.; Manoharan, P.

2008-12-01

We present a first study of strong radio sources that are known to exhibit interplanetary scintillations (IPS) detected by the Mexican Array Radio Telescope (MEXART). These observations were made using one quarter of the total antenna (16 rows of 64 dipoles each) and a Butler Matrix (BM) of 16X16 ports. The BM displays 16 beams at different declinations (from -48 to +88 degrees). We report the directionality and efficiency of the beams. These first observations of radio IPS sources and the calibration of the BM is the first step to initiate MEXART IPS maps in the near future.

Triazolophostins: a library of novel and potent agonists of IP3 receptors.

PubMed

Vibhute, Amol M; Konieczny, Vera; Taylor, Colin W; Sureshan, Kana M

2015-06-28

IP3 receptors are channels that mediate the release of Ca(2+) from the intracellular stores of cells stimulated by hormones or neurotransmitters. Adenophostin A (AdA) is the most potent agonist of IP3 receptors, with the β-anomeric adenine contributing to the increased potency. The potency of AdA and its stability towards the enzymes that degrade IP3 have aroused interest in AdA analogs for biological studies. The complex structure of AdA poses problems that have necessitated optimization of synthetic conditions for each analog. Such lengthy one-at-a-time syntheses limit access to AdA analogs. We have addressed this problem by synthesizing a library of triazole-based AdA analogs, triazolophostins, by employing click chemistry. An advanced intermediate having all the necessary phosphates and a β-azide at the anomeric position was reacted with various alkynes under Cu(i) catalysis to yield triazoles, which upon deprotection gave triazolophostins. All eleven triazolophostins synthesized are more potent than IP3 and some are equipotent with AdA in functional analyses of IP3 receptors. We show that a triazole ring can replace adenine without compromising the potency of AdA and provide facile routes to novel AdA analogs.

Validation of a Brief Structured Interview: The Children’s Interview for Psychiatric Syndromes (ChIPS)

PubMed Central

Young, Matthew E.; Bell, Ziv E.; Fristad, Mary A.

2016-01-01

Evidence-based assessment is important in the treatment of childhood psychopathology (Jensen-Doss, 2011). While researchers and clinicians frequently use structured diagnostic interviews to ensure reliability, the most commonly used instrument, the Schedule for Affective Disorders and Schizophrenia for School Aged Children (K-SADS; Kaufman et al., 1997), is too long for most clinical applications. The Children’s Interview for Psychiatric Syndromes, (ChIPS/P-ChIPS; Weller, Weller, Rooney, & Fristad, 1999a; 1999b) is a highly-structured brief diagnostic interview. The present study compared K-SADS and ChIPS/P-ChIPS diagnoses in an outpatient clinical sample of 50 parent-child pairs aged 7–14. Agreement between most diagnoses was moderate to high between instruments and with consensus clinical diagnoses. ChIPS was significantly briefer to administer than the K-SADS. Interviewer experience level and participant demographics did not appear to affect agreement. Results provide further evidence for the validity of the ChIPS and support its use in clinical and research settings. PMID:27761777

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments

PubMed Central

Micsinai, Mariann; Parisi, Fabio; Strino, Francesco; Asp, Patrik; Dynlacht, Brian D.; Kluger, Yuval

2012-01-01

Numerous algorithms have been developed to analyze ChIP-Seq data. However, the complexity of analyzing diverse patterns of ChIP-Seq signals, especially for epigenetic marks, still calls for the development of new algorithms and objective comparisons of existing methods. We developed Qeseq, an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length. To objectively assess its performance relative to other 14 ChIP-Seq peak finders, we designed a novel protocol based on Validation Discriminant Analysis (VDA) to optimally select validation sites and generated two validation datasets, which are the most comprehensive to date for algorithmic benchmarking of key epigenetic marks. In addition, we systematically explored a total of 315 diverse parameter configurations from these algorithms and found that typically optimal parameters in one dataset do not generalize to other datasets. Nevertheless, default parameters show the most stable performance, suggesting that they should be used. This study also provides a reproducible and generalizable methodology for unbiased comparative analysis of high-throughput sequencing tools that can facilitate future algorithmic development. PMID:22307239

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments.

PubMed

Micsinai, Mariann; Parisi, Fabio; Strino, Francesco; Asp, Patrik; Dynlacht, Brian D; Kluger, Yuval

2012-05-01

Numerous algorithms have been developed to analyze ChIP-Seq data. However, the complexity of analyzing diverse patterns of ChIP-Seq signals, especially for epigenetic marks, still calls for the development of new algorithms and objective comparisons of existing methods. We developed Qeseq, an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length. To objectively assess its performance relative to other 14 ChIP-Seq peak finders, we designed a novel protocol based on Validation Discriminant Analysis (VDA) to optimally select validation sites and generated two validation datasets, which are the most comprehensive to date for algorithmic benchmarking of key epigenetic marks. In addition, we systematically explored a total of 315 diverse parameter configurations from these algorithms and found that typically optimal parameters in one dataset do not generalize to other datasets. Nevertheless, default parameters show the most stable performance, suggesting that they should be used. This study also provides a reproducible and generalizable methodology for unbiased comparative analysis of high-throughput sequencing tools that can facilitate future algorithmic development.

Using VoIP to compete.

PubMed

Werbach, Kevin

2005-09-01

Internet telephony, or VoIP, is rapidly replacing the conventional kind. This year, for the first time, U.S. companies bought more new Internet-phone connections than standard lines. The major driver behind this change is cost. But VoIP isn't just a new technology for making old-fashioned calls cheaper, says consultant Kevin Werbach. It is fundamentally changing how companies use voice communications. What makes VoIP so powerful is that it turns voice into digital data packets that can be stored, copied, combined with other data, and distributed to virtually any device that connects to the Internet. And it makes it simple to provide all the functionality of a corporate phone-call features, directories, security-to anyone anywhere there's broadband access. That fosters new kinds of businesses such as virtual call centers, where widely dispersed agents work at all hours from their homes. The most successful early adopters, says Werbach, will focus more on achieving business objectives than on saving money. They will also consider how to push VoIP capabilities out to the extended organization, making use of everyone as a resource. Deployment may be incremental, but companies should be thinking about where VoIP could take them. Executives should ask what they could do if, on demand, they could bring all their employees, customers, suppliers, and partners together in a virtual room, with shared access to every modern communications and computing channel. They should take a fresh look at their business processes to find points at which richer and more customizable communications could eliminate bottlenecks and enhance quality. The important dividing line won't be between those who deploy Vol P and those who don't, or even between early adopters and laggards. It will be between those who see Vol P as just a new way to do the same old things and those who use itto rethink their entire businesses.

Software for rapid time dependent ChIP-sequencing analysis (TDCA).

PubMed

Myschyshyn, Mike; Farren-Dai, Marco; Chuang, Tien-Jui; Vocadlo, David

2017-11-25

Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) and associated methods are widely used to define the genome wide distribution of chromatin associated proteins, post-translational epigenetic marks, and modifications found on DNA bases. An area of emerging interest is to study time dependent changes in the distribution of such proteins and marks by using serial ChIP-seq experiments performed in a time resolved manner. Despite such time resolved studies becoming increasingly common, software to facilitate analysis of such data in a robust automated manner is limited. We have designed software called Time-Dependent ChIP-Sequencing Analyser (TDCA), which is the first program to automate analysis of time-dependent ChIP-seq data by fitting to sigmoidal curves. We provide users with guidance for experimental design of TDCA for modeling of time course (TC) ChIP-seq data using two simulated data sets. Furthermore, we demonstrate that this fitting strategy is widely applicable by showing that automated analysis of three previously published TC data sets accurately recapitulates key findings reported in these studies. Using each of these data sets, we highlight how biologically relevant findings can be readily obtained by exploiting TDCA to yield intuitive parameters that describe behavior at either a single locus or sets of loci. TDCA enables customizable analysis of user input aligned DNA sequencing data, coupled with graphical outputs in the form of publication-ready figures that describe behavior at either individual loci or sets of loci sharing common traits defined by the user. TDCA accepts sequencing data as standard binary alignment map (BAM) files and loci of interest in browser extensible data (BED) file format. TDCA accurately models the number of sequencing reads, or coverage, at loci from TC ChIP-seq studies or conceptually related TC sequencing experiments. TC experiments are reduced to intuitive parametric values that facilitate biologically

Near surface IP investigations: Four case studies

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

Hearst, R.B.; Morris, W.A.; Clark, M.A.

1995-12-31

The use of the Induced Polarisation (IP) method of geophysical surveying for near surface site investigations is gaining acceptance within the geophysical community. In this study the IP method is evaluated as a tool for the delineation of ground water resources; contamination plume detection in a lateritic horizon; and acid mine drainage leak detection from decommissioned mine tailings. A time domain IP system was selected for this study primarily for the flexibility in the selection and setting of receiver time windows and diagnostic characteristics attributed to submitting the data to Cole-Cole analysis. Analysis of the acquired data in conjunction withmore » available borehole and geological information illustrates the effectiveness and usefulness of the survey method for solving near surface problems. In all of the locations tested, it was found that with a properly designed IP survey it was possible to resolve the target and/or related structures.« less

HPC Access Using KVM over IP

DTIC Science & Technology

2007-06-08

Lightwave VDE /200 KVM-over-Fiber (Keyboard, Video and Mouse) devices installed throughout the TARDEC campus. Implementation of this system required...development effort through the pursuit of an Army-funded Phase-II Small Business Innovative Research (SBIR) effort with IP Video Systems (formerly known as...visualization capabilities of a DoD High- Performance Computing facility, many advanced features are necessary. TARDEC-HPC’s SBIR with IP Video Systems

Standard Spacecraft Interfaces and IP Network Architectures: Prototyping Activities at the GSFC

NASA Technical Reports Server (NTRS)

Schnurr, Richard; Marquart, Jane; Lin, Michael

2003-01-01

Advancements in fright semiconductor technology have opened the door for IP-based networking in spacecraft architectures. The GSFC believes the same signlJicant cost savings gained using MIL-STD-1553/1773 as a standard low rate interface for spacecraft busses cun be realized for highspeed network interfaces. To that end, GSFC is developing hardware and software to support a seamless, space mission IP network based on Ethernet and MIL-STD-1553. The Ethernet network shall connect all fright computers and communications systems using interface standards defined by the CCSDS Standard Onboard InterFace (SOIF) Panel. This paper shall discuss the prototyping effort underway at GSFC and expected results.

A Simple Method to Quantitate IP-10 in Dried Blood and Plasma Spots

PubMed Central

Aabye, Martine G.; Eugen-Olsen, Jesper; Werlinrud, Anne Marie; Holm, Line Lindebo; Tuuminen, Tamara; Ravn, Pernille; Ruhwald, Morten

2012-01-01

Background Antigen specific release of IP-10 is an established marker for infection with M.tuberculosis. Compared to IFN-γ, IP-10 is released in 100-fold higher concentrations enabling the development of novel assays for detection. Dried blood spots are a convenient sample for high throughput newborn screening. Aim To develop a robust and sensitive ELISA-based assay for IP-10 detection in plasma, dried blood spots (DBS) and dried plasma spots (DPS); to validate the ELISA in clinically relevant samples; and to assess the performance of the assay for detection of Cytomegalovirus (CMV) and M.tuberculosis specific immune responses. Method We raised mice and rat monoclonal antibodies against human IP-10 and developed an ELISA. The assay was validated and applied to the detection of CMV and M.tuberculosis specific responses in 18 patients with immune reactivity towards M.tuberculosis and 32 healthy controls of which 22 had immune reactivity towards CMV and none towards M.tuberculosis. We compared the performance of this new assay to IFN-γ. Results The ELISA was reliable for IP-10 detection in both plasma and filter paper samples. The linear range of the ELISA was 2.5–600 pg/ml. IFN-γ was not readily detectable in DPS samples. IP-10 was stabile in filter paper samples for at least 4 weeks at 37°C. The correlation between IP-10 detected in plasma, DPS and DBS samples was excellent (r2>0.97). Conclusions This newly developed assay is reliable for IP-10 quantification in plasma, DBS and DPS samples from antigen stimulated and non-stimulated whole blood. The filter paper assays enable easy sample acquisition and transport at ambient temperature e.g. via the postal system. The system can potentially simplify diagnostic assays for M.tuberculosis and CMV infection. PMID:22761744

Modeling Alzheimer's disease with human induced pluripotent stem (iPS) cells.

PubMed

Mungenast, Alison E; Siegert, Sandra; Tsai, Li-Huei

2016-06-01

In the last decade, induced pluripotent stem (iPS) cells have revolutionized the utility of human in vitro models of neurological disease. The iPS-derived and differentiated cells allow researchers to study the impact of a distinct cell type in health and disease as well as performing therapeutic drug screens on a human genetic background. In particular, clinical trials for Alzheimer's disease (AD) have been failing. Two of the potential reasons are first, the species gap involved in proceeding from initial discoveries in rodent models to human studies, and second, an unsatisfying patient stratification, meaning subgrouping patients based on the disease severity due to the lack of phenotypic and genetic markers. iPS cells overcome this obstacles and will improve our understanding of disease subtypes in AD. They allow researchers conducting in depth characterization of neural cells from both familial and sporadic AD patients as well as preclinical screens on human cells. In this review, we briefly outline the status quo of iPS cell research in neurological diseases along with the general advantages and pitfalls of these models. We summarize how genome-editing techniques such as CRISPR/Cas9 will allow researchers to reduce the problem of genomic variability inherent to human studies, followed by recent iPS cell studies relevant to AD. We then focus on current techniques for the differentiation of iPS cells into neural cell types that are relevant to AD research. Finally, we discuss how the generation of three-dimensional cell culture systems will be important for understanding AD phenotypes in a complex cellular milieu, and how both two- and three-dimensional iPS cell models can provide platforms for drug discovery and translational studies into the treatment of AD. Copyright © 2015 Elsevier Inc. All rights reserved.

Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples.

PubMed

Rehimi, Rizwan; Bartusel, Michaela; Solinas, Francesca; Altmüller, Janine; Rada-Iglesias, Alvaro

2017-08-29

Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, transcription factors, or chromatin-modifying enzymes at a given locus or on a genome-wide scale. The combination of ChIP assays with next-generation sequencing (i.e., ChIP-Seq) is a powerful approach to globally uncover gene regulatory networks and to improve the functional annotation of genomes, especially of non-coding regulatory sequences. ChIP protocols normally require large amounts of cellular material, thus precluding the applicability of this method to investigating rare cell types or small tissue biopsies. In order to make the ChIP assay compatible with the amount of biological material that can typically be obtained in vivo during early vertebrate embryogenesis, we describe here a simplified ChIP protocol in which the number of steps required to complete the assay were reduced to minimize sample loss. This ChIP protocol has been successfully used to investigate different histone modifications in various embryonic chicken and adult mouse tissues using low to medium cell numbers (5 x 10 4 - 5 x 10 5 cells). Importantly, this protocol is compatible with ChIP-seq technology using standard library preparation methods, thus providing global epigenomic maps in highly relevant embryonic tissues.

Electric conductivity for laboratory and field monitoring of induced partial saturation (IPS) in sands

NASA Astrophysics Data System (ADS)

Kazemiroodsari, Hadi

Liquefaction is loss of shear strength in fully saturated loose sands caused by build-up of excess pore water pressure, during moderate to large earthquakes, leading to catastrophic failures of structures. Currently used liquefaction mitigation measures are often costly and cannot be applied at sites with existing structures. An innovative, practical, and cost effective liquefaction mitigation technique titled "Induced Partial Saturation" (IPS) was developed by researchers at Northeastern University. The IPS technique is based on injection of sodium percarbonate solution into fully saturated liquefaction susceptible sand. Sodium percarbonate dissolves in water and breaks down into sodium and carbonate ions and hydrogen peroxide which generates oxygen gas bubbles. Oxygen gas bubbles become trapped in sand pores and therefore decrease the degree of saturation of the sand, increase the compressibility of the soil, thus reduce its potential for liquefaction. The implementation of IPS required the development and validation of a monitoring and evaluation technique that would help ensure that the sands are indeed partially saturated. This dissertation focuses on this aspect of the IPS research. The monitoring system developed was based on using electric conductivity fundamentals and probes to detect the transport of chemical solution, calculate degree of saturation of sand, and determine the final zone of partial saturation created by IPS. To understand the fundamentals of electric conductivity, laboratory bench-top tests were conducted using electric conductivity probes and small specimens of Ottawa sand. Bench-top tests were used to study rate of generation of gas bubbles due to reaction of sodium percarbonate solution in sand, and to confirm a theory based on which degree of saturation were calculated. In addition to bench-top tests, electric conductivity probes were used in a relatively large sand specimen prepared in a specially manufactured glass tank. IPS was

Building of communication system for nuclear accident emergency disposal based on IP multimedia subsystem

NASA Astrophysics Data System (ADS)

Wang, Kang; Gao, Guiqing; Qin, Yuanli; He, Xiangyong

2018-05-01

The nuclear accident emergency disposal must be supported by an efficient, real-time modularization and standardization communication system. Based on the analysis of communication system for nuclear accident emergency disposal which included many functions such as the internal and external communication, multiply access supporting and command center. Some difficult problems of the communication system were discussed such as variety access device type, complex composition, high mobility, set up quickly, multiply business support, and so on. Taking full advantages of the IP Multimedia Subsystem (IMS), a nuclear accident emergency communication system was build based on the IMS. It was studied and implemented that some key unit and module functions of communication system were included the system framework implementation, satellite access, short-wave access, load/vehicle-mounted communication units. The application tests showed that the system could provide effective communication support for the nuclear accident emergency disposal, which was of great practical value.

Call progress time measurement in IP telephony

NASA Astrophysics Data System (ADS)

Khasnabish, Bhumip

1999-11-01

Usually a voice call is established through multiple stages in IP telephony. In the first stage, a phone number is dialed to reach a near-end or call-originating IP-telephony gateway. The next stages involve user identification through delivering an m-digit user-id to the authentication and/or billing server, and then user authentication by using an n- digit PIN. After that, the caller is allowed (last stage dial tone is provided) to dial a destination phone number provided that authentication is successful. In this paper, we present a very flexible method for measuring call progress time in IP telephony. The proposed technique can be used to measure the system response time at every stage. It is flexible, so that it can be easily modified to include new `tone' or a set of tones, or `voice begin' can be used in every stage to detect the system's response. The proposed method has been implemented using scripts written in Hammer visual basic language for testing with a few commercially available IP telephony gateways.

Use of traditional complementary and alternative medicine for HIV patients in KwaZulu-Natal, South Africa.

PubMed

Peltzer, Karl; Preez, Natalie Friend-du; Ramlagan, Shandir; Fomundam, Henry

2008-07-24

Traditional medicine use has been reported is common among individuals with moderate and advanced HIV disease. The aim of this cross-sectional study was to assess the use of Traditional Complementary and Alternative Medicine (TCAM) for HIV patients prior to initiating antiretroviral therapy in three public hospitals in KwaZulu-Natal, South Africa. Using systematic sampling, 618 HIV-positive patients were selected from outpatient departments from three hospitals and interviewed with a questionnaire. TCAM was commonly used for HIV in the past six months by study participants (317, 51.3%) and herbal therapies alone (183, 29.6%). The use of micronutrients (42.9%) was excluded from TCAM since mostly vitamins were provided by the health facility. Herbal therapies were the most expensive, costing on average 128 Rand (US$16) per patient per month. Most participants (90%) indicated that their health care provider was not aware that they were taking herbal therapies for HIV (90%). Herbal therapies were mainly used for pain relief (87.1%) and spiritual practices or prayer for stress relief (77.6%). Multivariate logistic regression with use of herbs for HIV as the dependent variable identified being on a disability grant and fewer clinic visits to be associated with use of herbs, and TCAM use for HIV identified being on a disability grant, number of HIV symptoms and family members not contributing to main source of household income to be associated with TCAM use. Traditional herbal therapies and TCAM are commonly used by HIV treatment naïve outpatients of public health facilities in South Africa. Health care providers should routinely screen patients on TCAM use when initiating ART and also during follow-up and monitoring keeping in mind that these patients may not fully disclose other therapies.

Use of traditional complementary and alternative medicine for HIV patients in KwaZulu-Natal, South Africa

PubMed Central

Peltzer, Karl; Preez, Natalie Friend-du; Ramlagan, Shandir; Fomundam, Henry

2008-01-01

Background Traditional medicine use has been reported is common among individuals with moderate and advanced HIV disease. The aim of this cross-sectional study was to assess the use of Traditional Complementary and Alternative Medicine (TCAM) for HIV patients prior to initiating antiretroviral therapy in three public hospitals in KwaZulu-Natal, South Africa. Methods Using systematic sampling, 618 HIV-positive patients were selected from outpatient departments from three hospitals and interviewed with a questionnaire. Results TCAM was commonly used for HIV in the past six months by study participants (317, 51.3%) and herbal therapies alone (183, 29.6%). The use of micronutrients (42.9%) was excluded from TCAM since mostly vitamins were provided by the health facility. Herbal therapies were the most expensive, costing on average 128 Rand (US$16) per patient per month. Most participants (90%) indicated that their health care provider was not aware that they were taking herbal therapies for HIV (90%). Herbal therapies were mainly used for pain relief (87.1%) and spiritual practices or prayer for stress relief (77.6%). Multivariate logistic regression with use of herbs for HIV as the dependent variable identified being on a disability grant and fewer clinic visits to be associated with use of herbs, and TCAM use for HIV identified being on a disability grant, number of HIV symptoms and family members not contributing to main source of household income to be associated with TCAM use. Conclusion Traditional herbal therapies and TCAM are commonly used by HIV treatment naïve outpatients of public health facilities in South Africa. Health care providers should routinely screen patients on TCAM use when initiating ART and also during follow-up and monitoring keeping in mind that these patients may not fully disclose other therapies. PMID:18652666

Combining multiple ChIP-seq peak detection systems using combinatorial fusion.

PubMed

Schweikert, Christina; Brown, Stuart; Tang, Zuojian; Smith, Phillip R; Hsu, D Frank

2012-01-01

Due to the recent rapid development in ChIP-seq technologies, which uses high-throughput next-generation DNA sequencing to identify the targets of Chromatin Immunoprecipitation, there is an increasing amount of sequencing data being generated that provides us with greater opportunity to analyze genome-wide protein-DNA interactions. In particular, we are interested in evaluating and enhancing computational and statistical techniques for locating protein binding sites. Many peak detection systems have been developed; in this study, we utilize the following six: CisGenome, MACS, PeakSeq, QuEST, SISSRs, and TRLocator. We define two methods to merge and rescore the regions of two peak detection systems and analyze the performance based on average precision and coverage of transcription start sites. The results indicate that ChIP-seq peak detection can be improved by fusion using score or rank combination. Our method of combination and fusion analysis would provide a means for generic assessment of available technologies and systems and assist researchers in choosing an appropriate system (or fusion method) for analyzing ChIP-seq data. This analysis offers an alternate approach for increasing true positive rates, while decreasing false positive rates and hence improving the ChIP-seq peak identification process.

Evaluation of AL-FEC performance for IP television services QoS

NASA Astrophysics Data System (ADS)

Mammi, E.; Russo, G.; Neri, A.

2010-01-01

The IP television services quality is a critical issue because of the nature of transport infrastructure. Packet loss is the main cause of service degradation in such kind of network platforms. The use of forward error correction (FEC) techniques in the application layer (AL-FEC), between the source of TV service (video server) and the user terminal, seams to be an efficient strategy to counteract packet losses alternatively or in addiction to suitable traffic management policies (only feasible in "managed networks"). A number of AL-FEC techniques have been discussed in literature and proposed for inclusion in TV over IP international standards. In this paper a performance evaluation of the AL-FEC defined in SMPTE 2022-1 standard is presented. Different typical events occurring in IP networks causing different types (in terms of statistic distribution) of IP packet losses have been studied and AL-FEC performance to counteract these kind of losses have been evaluated. The performed analysis has been carried out in view of fulfilling the TV services QoS requirements that are usually very demanding. For managed networks, this paper envisages a strategy to combine the use of AL-FEC with the set-up of a transport quality based on FEC packets prioritization. Promising results regard this kind of strategy have been obtained.

Integrating Saharan dust forecasts into a regional chemical transport model: a case study over Northern Italy.

PubMed

Carnevale, C; Finzi, G; Pisoni, E; Volta, M; Kishcha, P; Alpert, P

2012-02-15

The Po Valley in Northern Italy is frequently affected by high PM10 concentrations, where both natural and anthropogenic sources play a significant role. To improve air pollution modeling, 3D dust fields, produced by means of the DREAM dust forecasts, were integrated as boundary conditions into the mesoscale 3D deterministic Transport Chemical Aerosol Model (TCAM). A case study of the TCAM and DREAM integration was implemented over Northern Italy for the period May 15-June 30, 2007. First, the Saharan dust impact on PM10 concentration was analyzed for eleven remote PM10 sites with the lowest level of air pollution. These remote sites are the most sensitive to Saharan dust intrusions into Northern Italy, because of the absence of intensive industrial pollution. At these remote sites, the observed maxima in PM10 concentration during dust events is evidence of dust aerosol near the surface in Northern Italy. Comparisons between modeled PM10 concentrations and measurements at 230 PM10 sites in Northern Italy, showed that the integrated TCAM-DREAM model more accurately reproduced PM10 concentration than the base TCAM model, both in terms of correlation and mean error. Specifically, the correlation median increased from 0.40 to 0.65, while the normalized mean absolute error median dropped from 0.5 to 0.4. Copyright © 2011 Elsevier B.V. All rights reserved.

Negative regulation of DAB2IP by Akt and SCFFbw7 pathways.

PubMed

Dai, Xiangping; North, Brian J; Inuzuka, Hiroyuki

2014-05-30

Deletion of ovarian carcinoma 2/disabled homolog 2 (DOC-2/DAB2) interacting protein (DAB2IP), is a tumor suppressor that serves as a scaffold protein involved in coordinately regulating cell proliferation, survival and apoptotic pathways. DAB2IP is epigenetically down-regulated in a variety of tumors through the action of the histone methyltransferase EZH2. Although DAB2IP is transcriptionally down-regulated in a variety of tumors, it remains unclear if other mechanisms contribute to functional inactivation of DAB2IP. Here we demonstrate that DAB2IP can be functionally down-regulated by two independent mechanisms. First, we identified that Akt1 can phosphorylate DAB2IP on S847, which regulates the interaction between DAB2IP and its effector molecules H-Ras and TRAF2. Second, we demonstrated that DAB2IP can be degraded in part through ubiquitin-proteasome pathway by SCF(Fbw7). DAB2IP harbors two Fbw7 phosho-degron motifs, which can be regulated by the kinase, CK1δ. Our data hence indicate that in addition to epigenetic down-regulation, two additional pathways can functional inactivate DAB2IP. Given that DAB2IP has previously been identified to possess direct causal role in tumorigenesis and metastasis, our data indicate that a variety of pathways may pass through DAB2IP to govern cancer development, and therefore highlight DAB2IP agonists as potential therapeutic approaches for future anti-cancer drug development.

Functional myogenic engraftment from mouse iPS cells.

PubMed

Darabi, Radbod; Pan, Weihong; Bosnakovski, Darko; Baik, June; Kyba, Michael; Perlingeiro, Rita C R

2011-11-01

Direct reprogramming of adult fibroblasts to a pluripotent state has opened new possibilities for the generation of patient- and disease-specific stem cells. However the ability of induced pluripotent stem (iPS) cells to generate tissue that mediates functional repair has been demonstrated in very few animal models of disease to date. Here we present the proof of principle that iPS cells may be used effectively for the treatment of muscle disorders. We combine the generation of iPS cells with conditional expression of Pax7, a robust approach to derive myogenic progenitors. Transplantation of Pax7-induced iPS-derived myogenic progenitors into dystrophic mice results in extensive engraftment, which is accompanied by improved contractility of treated muscles. These findings demonstrate the myogenic regenerative potential of iPS cells and provide rationale for their future therapeutic application for muscular dystrophies.

Attributes associated with probability of infestation by the pinon Ips, Ips confusus, (Coleoptera: Scolytidae) in pinon pine, Pinus edulis

Treesearch

Jose F. Negron; Jill L. Wilson

2008-01-01

(Please note, this is an abstract only) We examined attributes associated with the probability of infestation by pinon ips (Ips confusus), in pinon pine (Pinus edulis), in an outbreak in the Coconino National Forest, Arizona. We used data collected from 87 plots, 59 infested and 28 uninfested, and a logistic regression approach to estimate the probability of...

Inhibition of pulmonary fibrosis by the chemokine IP-10/CXCL10.

PubMed

Tager, Andrew M; Kradin, Richard L; LaCamera, Peter; Bercury, Scott D; Campanella, Gabriele S V; Leary, Carol P; Polosukhin, Vasiliy; Zhao, Long-Hai; Sakamoto, Hideo; Blackwell, Timothy S; Luster, Andrew D

2004-10-01

Pulmonary fibrosis is an enigmatic and devastating disease with few treatment options, now thought to result from abnormal wound healing in the lung in response to injury. We have previously noted a role for the chemokine interferon gamma-inducible protein of 10 kD (IP-10)/CXC chemokine ligand 10 in the regulation of cutaneous wound healing, and consequently investigated whether IP-10 regulates pulmonary fibrosis. We found that IP-10 is highly expressed in a mouse model of pulmonary fibrosis induced by bleomycin. IP-10-deficient mice exhibited increased pulmonary fibrosis after administration of bleomycin, suggesting that IP-10 limits the development of fibrosis in this model. Substantial fibroblast chemoattractant and proliferative activities were generated in the lung after bleomycin exposure. IP-10 significantly inhibited fibroblast responses to the chemotactic, but not the proliferative activity generated, suggesting that IP-10 may attenuate fibroblast accumulation in bleomycin-induced pulmonary fibrosis by limiting fibroblast migration. Consistent with this inhibitory activity of IP-10 on fibroblast migration, fibroblast accumulation in the lung after bleomycin exposure was dramatically increased in IP-10-deficient mice compared with wild-type mice. Conversely, transgenic mice overexpressing IP-10 were protected from mortality after bleomycin exposure, and demonstrated decreased fibroblast accumulation in the lung after challenge compared with wild-type mice. Our findings suggest that interruption of fibroblast recruitment may represent a novel therapeutic strategy for pulmonary fibrosis, which could have applicability to a wide range of fibrotic illnesses.

Cultural consonance, constructions of science and co-existence: a review of the integration of traditional, complementary and alternative medicine in low- and middle-income countries

PubMed Central

Lakshmi, Josyula K; Nambiar, Devaki; Narayan, Venkatesh; Sathyanarayana, Tamysetty N; Porter, John; Sheikh, Kabir

2015-01-01

This review examined the determinants, patterns and imports of official recognition, and incorporation of different traditional, complementary and alternative systems of medicine (TCAM) in the public health establishment of low- and middle-income countries, with a particular focus on India. Public health systems in most countries have tended to establish health facilities centred on allopathy, and then to recognize or derecognize different TCAM based on evidence or judgement, to arrive at health-care configurations that include several systems of medicine with disparate levels of authority, jurisdiction and government support. The rationale for the inclusion of TCAM providers in the public health workforce ranges from the need for personnel to address the disease burden borne by the public health system, to the desirability of providing patients with a choice of therapeutic modalities, and the nurturing of local culture. Integration, mostly described as a juxtaposition of different systems of medical practice, is often implemented as a system of establishing personnel with certification in different medical systems, in predominantly allopathic health-care facilities, to practise allopathic medicine. A hierarchy of systems of medicine, often unacknowledged, is exercised in most societies, with allopathy at the top, certain TCAM systems next and local healing traditions last. The tools employed by TCAM practitioners in diagnosis, research, pharmacy, marketing and education and training, which are seen to increasingly emulate those of allopathy, are sometimes inappropriate for use in therapeutic systems with widely divergent epistemologies, which call for distinct research paradigms. The coexistence of numerous systems of medicine, while offering the population greater choice, and presumably enhancing geographical access to health care as well, is often fraught with tensions related to the coexistence of philosophically disparate, even opposed, disciplines, with

Redox routes to substitution of aluminum(III): synthesis and characterization of (IP-)2AlX (IP = α-iminopyridine, X = Cl, Me, SMe, S2CNMe2, C≡CPh, N3, SPh, NHPh).

PubMed

Myers, Thomas W; Holmes, Alexandra L; Berben, Louise A

2012-08-20

Redox active ligands are shown to facilitate a variety of group transfer reactions at redox inert aluminum(III). Disulfides can be used as a two-electron group transfer reagent, and we show that (IP(-))(2)AlSR can be formed by reaction of [(THF)(6)Na][(IP(2-))(2)Al] (1c) with disulfides RSSR (where X = C(S)NMe(2), 4; SMe, 5). In a more general redox route to substitution of aluminum bis(iminopyridine) complexes, we report zinc(II) salts as a group transfer reagent. Reaction of [((R)IP(2-))(2)Al](-) (R = H, 1c; Me, 1d) with ZnX(2) affords ((R)IP(-))(2)AlX (where IP = iminopyridine, R = H, and X = Cl, 2; CCPh, 6; N(3), 7; SPh, 8; or R = Me and X = NHPh, 9). Single crystal X-ray diffraction analysis of the complexes reveal that each of the five coordinate complexes reported here has a trigonal bipyramidal geometry with τ = 0.668 - 0.858. We observed a correlation between the greatest deviations from ideal trigonal bipyramidal symmetry (lowest τ values), the bond lengths consistent with smallest degree of ligand reduction, and the least polarizable X ligand in (IP(-))(2)AlX. Complex 4 is six-coordinate and is best described as distorted octahedral. Variable temperature magnetic susceptibility measurements indicate that each of the complexes 3-9 has a biradical electronic structure similar to previously reported 2. Magnetic exchange coupling constants in the range J = -94 to -212 cm(-1) were fit to the data for 2-9 to describe the energy of antiferromagnetic interaction between ligand radicals assuming a spin Hamiltonian of the form Ĥ = -2JŜ(L(1))·Ŝ(L(2)). The strongest coupling occurs when the angle between the ligand planes is smallest, presumably to afford good overlap with the Al-X σ* orbital. Electrochemical properties of the complexes were probed using cyclic voltammetry and each of 3-9 displayed a reversible two-electron reduction and two quasi-reversible one-electron oxidation processes. The energy of the ligand based redox processes for 2-9 differ by

Effective distance adaptation traffic dispatching in software defined IP over optical network

NASA Astrophysics Data System (ADS)

Duan, Zhiwei; Li, Hui; Liu, Yuze; Ji, Yuefeng; Li, Hongfa; Lin, Yi

2017-10-01

The rapid growth of IP traffic has contributed to the wide deployment of optical devices (ROADM/OXC, etc.). Meanwhile, with the emergence and application of high-performance network services such as ultra-high video transmission, people are increasingly becoming more and more particular about the quality of service (QoS) of network. However, the pass-band shape of WSSs which is utilized in the ROADM/OXC is not ideal, causing narrowing of spectrum. Spectral narrowing can lead to signal impairment. Therefore, guard-bands need to be inserted between adjacent paths. In order to minimize the bandwidth waste due to guard bands, we propose an effective distance-adaptation traffic dispatching algorithm in IP over optical network based on SDON architecture. We use virtualization technology to set up virtual resources direct links by extracting part of the resources on paths which meet certain specific constraints. We also assign different bandwidth to each IP request based on path length. There is no need for guard-bands between the adjacent paths on the virtual link, which can effectively reduce the number of guard-bands and save the spectrum.

Limitations and possibilities of low cell number ChIP-seq

PubMed Central

2012-01-01

Background Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant starting material in the range of 1–20 million cells per immunoprecipitation, and remain a bottleneck to the acquisition of biologically relevant epigenetic data. Using a ChIP-seq protocol optimised for low cell numbers (down to 100,000 cells / IP), we examined the performance of the ChIP-seq technique on a series of decreasing cell numbers. Results We present an enhanced native ChIP-seq method tailored to low cell numbers that represents a 200-fold reduction in input requirements over existing protocols. The protocol was tested over a range of starting cell numbers covering three orders of magnitude, enabling determination of the lower limit of the technique. At low input cell numbers, increased levels of unmapped and duplicate reads reduce the number of unique reads generated, and can drive up sequencing costs and affect sensitivity if ChIP is attempted from too few cells. Conclusions The optimised method presented here considerably reduces the input requirements for performing native ChIP-seq. It extends the applicability of the technique to isolated primary cells and rare cell populations (e.g. biobank samples, stem cells), and in many cases will alleviate the need for cell culture and any associated alteration of epigenetic marks. However, this study highlights a challenge inherent to ChIP-seq from low cell numbers: as cell input numbers fall, levels of unmapped sequence reads and PCR-generated duplicate reads rise. We discuss a number of solutions to overcome the effects of reducing cell number that may aid further improvements to ChIP performance. PMID:23171294

Dietary Chemoprevention of PhIP Induced Carcinogenesis in Male Fischer 344 Rats with Tomato and Broccoli

PubMed Central

Canene-Adams, Kirstie; Sfanos, Karen S.; Liang, Chung-Tiang; Yegnasubramanian, Srinivasan; Nelson, William G.; Brayton, Cory; De Marzo, Angelo M.

2013-01-01

The heterocyclic amine, 2-amino-1-methyl-6-phenylimidazo[4,5-B]pyridine (PhIP), found in meats cooked at high temperatures, has been implicated in epidemiological and rodent studies for causing breast, prostate, and colorectal cancers. A previous animal study using a xenograft model has shown that whole tomato and broccoli, when eaten in combination, exhibit a marked effect on tumor reduction compared to when eaten alone. Our aim was to determine if PhIP-induced carcinogenesis can be prevented by dietary consumption of whole tomato + broccoli powders. Male Fischer 344 rats (n = 45) were randomized into the following treatment groups: control (AIN93G diet), PhIP (200 ppm in AIN93G diet for the first 20 weeks of the study), or tomato + broccoli + PhIP (mixed in AIN93G diet at 10% each and fed with PhIP for 20 weeks, and then without PhIP for 32 weeks). Study animals were monitored for 52 weeks and were euthanized as necessary based on a set of criteria for health status and tumor burden. Although there appeared to be some hepatic and intestinal toxicity due to the combination of PhIP and tomato + broccoli, these rodents had improved survival and reduced incidence and/or severity of PhIP-induced neoplastic lesions compared to the PhIP-alone treated group. Rats eating tomato + broccoli exhibited a marked decrease in the number and size of cribiform prostatic intraepitheilial neoplasia/carcinoma in situ (cribiform PIN/CIS) lesions and in the incidence of invasive intestinal adenocarcinomas and skin carcinomas. Although the apparent toxic effects of combined PhIP and tomato + broccoli need additional study, the results of this study support the hypothesis that a diet rich in tomato and broccoli can reduce or prevent dietary carcinogen-induced cancers. PMID:24312188

Using the MDCT thick slab MinIP method for the follow-up of pulmonary emphysema.

PubMed

Lan, Hai; Nishitani, Hiromu; Nishihara, Sadamitsu; Ueno, Junji; Takao, Shoichiro; Iwamoto, Seiji; Kawanaka, Takashi; Mahmut, Mawlan; Qingge, Si

2011-08-01

The purpose of this study was to evaluate the usefulness of thick slab minimum intensity projection (MinIP) as a follow-up method in patients with pulmonary emphysema. This method was used to determine the presence or absence of changes over time in the lung field based on multi-detector-row CT (MDCT) data. Among patients diagnosed with pulmonary emphysema who underwent 16-MDCT (slice thickness, 1 mm) twice at an interval of 6 months or more, 12 patients without changes in the lung field and 14 with clear changes in the lung field were selected as subjects. An image interpretation experiment was performed by five image interpreters. Pulmonary emphysema was followed up using two types of thick slab MinIP (thick slab MinIP 1 and 2) and multi-planar reformation (MPR), and the results of image interpretation were evaluated by receiver operating characteristic (ROC) analysis. In addition, the time required for image interpretation was compared among the three follow-up methods. The area under the ROC curve (Az) was 0.794 for thick slab MinIP 1, 0.778 for the thick slab MinIP 2, and 0.759 for MPR, showing no significant differences among the three methods. Individual differences in each item were significantly more marked for MPR than for thick slab MinIP. The time required for image interpretation was around 18 seconds for thick slab MinIP 1, 11 seconds for thick slab MinIP 2, and approximately 127 seconds for MPR, showing significant differences among the three methods. There were no significant differences in the results of image interpretation regarding the presence or absence of changes in the lung fields between thick slab MinIP and MPR. However, thick slab MinIP showed a shorter image interpretation time and smaller individual differences in the results among image interpreters than MPR, suggesting the usefulness of this method for determining the presence or absence of changes with time in the lung fields of patients with pulmonary emphysema.

Different KChIPs compete for heteromultimeric assembly with pore-forming Kv4 subunits.

PubMed

Zhou, Jingheng; Tang, Yiquan; Zheng, Qin; Li, Meng; Yuan, Tianyi; Chen, Liangyi; Huang, Zhuo; Wang, KeWei

2015-06-02

Auxiliary Kv channel-interacting proteins 1-4 (KChIPs1-4) coassemble with pore-forming Kv4 α-subunits to form channel complexes underlying somatodendritic subthreshold A-type current that regulates neuronal excitability. It has been hypothesized that different KChIPs can competitively bind to Kv4 α-subunit to form variable channel complexes that can exhibit distinct biophysical properties for modulation of neural function. In this study, we use single-molecule subunit counting by total internal reflection fluorescence microscopy in combinations with electrophysiology and biochemistry to investigate whether different isoforms of auxiliary KChIPs, KChIP4a, and KChIP4bl, can compete for binding of Kv4.3 to coassemble heteromultimeric channel complexes for modulation of channel function. To count the number of photobleaching steps solely from cell membrane, we take advantage of a membrane tethered k-ras-CAAX peptide that anchors cytosolic KChIP4 proteins to the surface for reduction of background noise. Single-molecule subunit counting reveals that the number of KChIP4 isoforms in Kv4.3-KChIP4 complexes can vary depending on the KChIP4 expression level. Increasing the amount of KChIP4bl gradually reduces bleaching steps of KChIP4a isoform proteins, and vice versa. Further analysis of channel gating kinetics from different Kv4-KChIP4 subunit compositions confirms that both KChIP4a and KChIP4bl can modulate the channel complex function upon coassembly. Taken together, our findings show that auxiliary KChIPs can heteroassemble with Kv4 in a competitive manner to form heteromultimeric Kv4-KChIP4 channel complexes that are biophysically distinct and regulated under physiological or pathological conditions. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Modeling Alzheimer’s disease with human induced pluripotent stem (iPS) cells

PubMed Central

Mungenast, Alison E.; Siegert, Sandra; Tsai, Li-Huei

2018-01-01

In the last decade, induced pluripotent stem (iPS) cells have revolutionized the utility of human in vitro models of neurological disease. The iPS-derived and differentiated cells allow researchers to study the impact of a distinct cell type in health and disease as well as performing therapeutic drug screens on a human genetic background. In particular, clinical trials for Alzheimer’s disease (AD) have been often failing. Two of the potential reasons are first, the species gap involved in proceeding from initial discoveries in rodent models to human studies, and second, an unsatisfying patient stratification, meaning subgrouping patients based on the disease severity due to the lack of phenotypic and genetic markers. iPS cells overcome this obstacles and will improve our understanding of disease subtypes in AD. They allow researchers conducting in depth characterization of neural cells from both familial and sporadic AD patients as well as preclinical screens on human cells. In this review, we briefly outline the status quo of iPS cell research in neurological diseases along with the general advantages and pitfalls of these models. We summarize how genome-editing techniques such as CRISPR/Cas will allow researchers to reduce the problem of genomic variability inherent to human studies, followed by recent iPS cell studies relevant to AD. We then focus on current techniques for the differentiation of iPS cells into neural cell types that are relevant to AD research. Finally, we discuss how the generation of three-dimensional cell culture systems will be important for understanding AD phenotypes in a complex cellular milieu, and how both two- and three-dimensional iPS cell models can provide platforms for drug discovery and translational studies into the treatment of AD. PMID:26657644

The Spacelab IPS Star Simulator

NASA Astrophysics Data System (ADS)

Wessling, Francis C., III

The cost of doing business in space is very high. If errors occur while in orbit the costs grow and desired scientific data may be corrupted or even lost. The Spacelab Instrument Pointing System (IPS) Star Simulator is a unique test bed that allows star trackers to interface with simulated stars in a laboratory before going into orbit. This hardware-in-the-loop testing of equipment on earth increases the probability of success while in space. The IPS Star Simulator provides three fields of view 2.55 x 2.55 deg each for input into star trackers. The fields of view are produced on three separate monitors. Each monitor has 4096 x 4096 addressable points and can display 50 stars (pixels) maximum at a given time. The pixel refresh rate is 1000 Hz. The spectral output is approximately 550 nm. The available relative visual magnitude range is two to eight visual magnitudes. The star size is less than 100 arcsec. The minimum star movement is less than 5 arcsec and the relative position accuracy is approximately 40 arcsec. The purpose of this paper is to describe the IPS Star Simulator design and to provide an operational scenario so others may gain from the approach and possible use of the system.

Intellectual Property and Strategic Agreements (IP/SA) | FNLCR Staging

Cancer.gov

IP/SA handles all invention issues including patents and copyrights. All employee inventionreports are filed through the IP/SA office for all activities under the OTS contract.Additionally,request for assignment ofcopyri

Prognostic value of CtIP/RBBP8 expression in breast cancer.

PubMed

Soria-Bretones, Isabel; Sáez, Carmen; Ruíz-Borrego, Manuel; Japón, Miguel A; Huertas, Pablo

2013-12-01

CtIP/RBBP8 is a multifunctional protein involved in transcription, DNA replication, DNA repair by homologous recombination and the G1 and G2 checkpoints. Its multiple roles are controlled by its interaction with several specific factors, including the tumor suppressor proteins BRCA1 and retinoblastoma. Both its functions and interactors point to a putative oncogenic potential of CtIP/RBBP8 loss. However, CtIP/RBBP8 relevance in breast tumor appearance, development, and prognosis has yet to be established. We performed a retrospective analysis of CtIP/RBBP8 and RB1 levels by immunohistochemistry using 384 paraffin-embedded breast cancer biopsies obtained during tumor removal surgery. We have observed that low or no expression of CtIP/RBBP8 correlates with high-grade breast cancer and with nodal metastasis. Reduction on CtIP/RBBP8 is most common in hormone receptor (HR)-negative, HER2-positive, and basal-like tumors. We observed lower levels of RB1 on those tumors with reduced CtIP/RBBP8 levels. On luminal tumors, decreased but not absence of CtIP/RBBP8 levels correlate with increased disease-free survival when treated with a combination of hormone, radio, and chemo therapies. © 2013 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Prognostic value of CtIP/RBBP8 expression in breast cancer

PubMed Central

Soria-Bretones, Isabel; Sáez, Carmen; Ruíz-Borrego, Manuel; Japón, Miguel A; Huertas, Pablo

2013-01-01

CtIP/RBBP8 is a multifunctional protein involved in transcription, DNA replication, DNA repair by homologous recombination and the G1 and G2 checkpoints. Its multiple roles are controlled by its interaction with several specific factors, including the tumor suppressor proteins BRCA1 and retinoblastoma. Both its functions and interactors point to a putative oncogenic potential of CtIP/RBBP8 loss. However, CtIP/RBBP8 relevance in breast tumor appearance, development, and prognosis has yet to be established. We performed a retrospective analysis of CtIP/RBBP8 and RB1 levels by immunohistochemistry using 384 paraffin-embedded breast cancer biopsies obtained during tumor removal surgery. We have observed that low or no expression of CtIP/RBBP8 correlates with high-grade breast cancer and with nodal metastasis. Reduction on CtIP/RBBP8 is most common in hormone receptor (HR)-negative, HER2-positive, and basal-like tumors. We observed lower levels of RB1 on those tumors with reduced CtIP/RBBP8 levels. On luminal tumors, decreased but not absence of CtIP/RBBP8 levels correlate with increased disease-free survival when treated with a combination of hormone, radio, and chemo therapies. PMID:24403251

Actuator development for the Instrument Pointing System (IPS)

NASA Technical Reports Server (NTRS)

Suttner, K.

1984-01-01

The mechanisms of the instrument pointing system (IPS) are described. Particular emphasis is placed on the actuators which are necessary for operating the IPS. The actuators are described as follows: (1) two linear actuators that clamp the gimbals down during ascent and descent; (2) two linear actuators that attach the payload to the IPS during the mission, and release it into the payload clamps; (3) one rotational actuator that opens and closes the payload clamps; and (4) three identical drive units that represent the three orthogonal gimbal axes and are the prime movers for pointing. Design features, manufacturing problems, test performance, and results are presented.

Development and Evaluation of a Computerized Engagement Intervention for IPS Supported Employment

ERIC Educational Resources Information Center

Haslett, William R.

2013-01-01

Background: Current information technology offers the promise of innovative approaches to engagement for mental health. Specific psychosocial services may also benefit from technology-based engagement interventions. Individual Placement and Support (IPS) is an evidence-based service that helps people who have a severe mental illness to gain…

Voice Over Internet Protocol (VoIP) in a Control Center Environment

NASA Technical Reports Server (NTRS)

Pirani, Joseph; Calvelage, Steven

2010-01-01

The technology of transmitting voice over data networks has been available for over 10 years. Mass market VoIP services for consumers to make and receive standard telephone calls over broadband Internet networks have grown in the last 5 years. While operational costs are less with VoIP implementations as opposed to time division multiplexing (TDM) based voice switches, is it still advantageous to convert a mission control center s voice system to this newer technology? Marshall Space Flight Center (MSFC) Huntsville Operations Support Center (HOSC) has converted its mission voice services to a commercial product that utilizes VoIP technology. Results from this testing, design, and installation have shown unique considerations that must be addressed before user operations. There are many factors to consider for a control center voice design. Technology advantages and disadvantages were investigated as they refer to cost. There were integration concerns which could lead to complex failure scenarios but simpler integration for the mission infrastructure. MSFC HOSC will benefit from this voice conversion with less product replacement cost, less operations cost and a more integrated mission services environment.

Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application.

PubMed

Zhong, Jian; Ye, Zhenqing; Lenz, Samuel W; Clark, Chad R; Bharucha, Adil; Farrugia, Gianrico; Robertson, Keith D; Zhang, Zhiguo; Ordog, Tamas; Lee, Jeong-Heon

2017-12-21

Chromatin immunoprecipitation-sequencing (ChIP-seq) is a widely used epigenetic approach for investigating genome-wide protein-DNA interactions in cells and tissues. The approach has been relatively well established but several key steps still require further improvement. As a part of the procedure, immnoprecipitated DNA must undergo purification and library preparation for subsequent high-throughput sequencing. Current ChIP protocols typically yield nanogram quantities of immunoprecipitated DNA mainly depending on the target of interest and starting chromatin input amount. However, little information exists on the performance of reagents used for the purification of such minute amounts of immunoprecipitated DNA in ChIP elution buffer and their effects on ChIP-seq data. Here, we compared DNA recovery, library preparation efficiency, and ChIP-seq results obtained with several commercial DNA purification reagents applied to 1 ng ChIP DNA and also investigated the impact of conditions under which ChIP DNA is stored. We compared DNA recovery of ten commercial DNA purification reagents and phenol/chloroform extraction from 1 to 50 ng of immunopreciptated DNA in ChIP elution buffer. The recovery yield was significantly different with 1 ng of DNA while similar in higher DNA amounts. We also observed that the low nanogram range of purified DNA is prone to loss during storage depending on the type of polypropylene tube used. The immunoprecipitated DNA equivalent to 1 ng of purified DNA was subject to DNA purification and library preparation to evaluate the performance of four better performing purification reagents in ChIP-seq applications. Quantification of library DNAs indicated the selected purification kits have a negligible impact on the efficiency of library preparation. The resulting ChIP-seq data were comparable with the dataset generated by ENCODE consortium and were highly correlated between the data from different purification reagents. This study provides

IP voice over ATM satellite: experimental results over satellite channels

NASA Astrophysics Data System (ADS)

Saraf, Koroush A.; Butts, Norman P.

1999-01-01

IP telephony, a new technology to provide voice communication over traditional data networks, has the potential to revolutionize telephone communication within the modern enterprise. This innovation uses packetization techniques to carry voice conversations over IP networks. This packet switched technology promises new integrated services, and lower cost long-distance communication compared to traditional circuit switched telephone networks. Future satellites will need to carry IP traffic efficiently in order to stay competitive in servicing the global data- networking and global telephony infrastructure. However, the effects of Voice over IP over switched satellite channels have not been investigated in detail. To fully understand the effects of satellite channels on Voice over IP quality; several experiments were conducted at Lockheed Martin Telecommunications' Satellite Integration Lab. The result of those experiments along with suggested improvements for voice communication over satellite are presented in this document. First, a detailed introduction of IP telephony as a suitable technology for voice communication over future satellites is presented. This is followed by procedures for the experiments, along with results and strategies. In conclusion we hope that these capability demonstrations will alleviate any uncertainty regarding the applicability of this technology to satellite networks.

Validation of the Spanish version of the Irrational Procrastination Scale (IPS).

PubMed

Guilera, Georgina; Barrios, Maite; Penelo, Eva; Morin, Christopher; Steel, Piers; Gómez-Benito, Juana

2018-01-01

The present study is centered in adapting and validating a Spanish version of the Irrational Procrastination Scale (IPS). The sample consists of 365 adults aged 18-77 years (M = 37.70, SD = 12.64). Participants were administered two measures of procrastination, the IPS and the Decisional Procrastination Questionnaire, as well as the Big Five Inventory, and the Satisfaction With Life Scale. First, the factor and replication analysis revealed that the internal structure of the scale is clearly one-dimensional, supporting the idea that IPS seems to measure general procrastination as a single trait. Second, the internal consistency is satisfactory as is the temporal stability of the IPS scores. Third, the correlations encountered between the IPS scores and other measures of procrastination, personality traits and satisfaction with life are all in the expected direction and magnitude. Finally, consistent with previous research, procrastination is related to age, with the youngest being the most procrastinating group. This study represents the first attempt in adapting and validating the IPS measure of procrastination into Spanish. Results suggest that the Spanish version of the IPS offers valid and reliable scores when applied to adult population.

Validation of the Spanish version of the Irrational Procrastination Scale (IPS)

PubMed Central

Guilera, Georgina; Penelo, Eva; Morin, Christopher; Steel, Piers; Gómez-Benito, Juana

2018-01-01

The present study is centered in adapting and validating a Spanish version of the Irrational Procrastination Scale (IPS). The sample consists of 365 adults aged 18–77 years (M = 37.70, SD = 12.64). Participants were administered two measures of procrastination, the IPS and the Decisional Procrastination Questionnaire, as well as the Big Five Inventory, and the Satisfaction With Life Scale. First, the factor and replication analysis revealed that the internal structure of the scale is clearly one-dimensional, supporting the idea that IPS seems to measure general procrastination as a single trait. Second, the internal consistency is satisfactory as is the temporal stability of the IPS scores. Third, the correlations encountered between the IPS scores and other measures of procrastination, personality traits and satisfaction with life are all in the expected direction and magnitude. Finally, consistent with previous research, procrastination is related to age, with the youngest being the most procrastinating group. This study represents the first attempt in adapting and validating the IPS measure of procrastination into Spanish. Results suggest that the Spanish version of the IPS offers valid and reliable scores when applied to adult population. PMID:29304119

Application of Mobile-ip to Space and Aeronautical Networks

NASA Technical Reports Server (NTRS)

Leung, Kent; Shell, Dan; Ivancic, William D.; Stewart, David H.; Bell, Terry L.; Kachmar, Brian A.

2001-01-01

The National Aeronautics and Space Administration (NASA) is interested in applying mobile Internet protocol (mobile-ip) technologies to its space and aeronautics programs. In particular, mobile-ip will play a major role in the Advanced Aeronautic Transportation Technology (AAT-F), the Weather Information Communication (WINCOMM), and the Small Aircraft Transportation System (SATS) aeronautics programs. This paper describes mobile-ip and mobile routers--in particular, the features, capabilities, and initial performance of the mobile router are presented. The application of mobile-router technology to NASA's space and aeronautics programs is also discussed.

TCAMS lessons learned

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

Harris, D.

1997-11-01

This report contains viewgraphs on the CINC mobile alternate headquarters and the tech control automation, maintenance and support facility. A discussion on software cost reduction by reuse is given as well as managing risk by assessment and mitigation.

Quantification of histone modification ChIP-seq enrichment for data mining and machine learning applications

PubMed Central

2011-01-01

Background The advent of ChIP-seq technology has made the investigation of epigenetic regulatory networks a computationally tractable problem. Several groups have applied statistical computing methods to ChIP-seq datasets to gain insight into the epigenetic regulation of transcription. However, methods for estimating enrichment levels in ChIP-seq data for these computational studies are understudied and variable. Since the conclusions drawn from these data mining and machine learning applications strongly depend on the enrichment level inputs, a comparison of estimation methods with respect to the performance of statistical models should be made. Results Various methods were used to estimate the gene-wise ChIP-seq enrichment levels for 20 histone methylations and the histone variant H2A.Z. The Multivariate Adaptive Regression Splines (MARS) algorithm was applied for each estimation method using the estimation of enrichment levels as predictors and gene expression levels as responses. The methods used to estimate enrichment levels included tag counting and model-based methods that were applied to whole genes and specific gene regions. These methods were also applied to various sizes of estimation windows. The MARS model performance was assessed with the Generalized Cross-Validation Score (GCV). We determined that model-based methods of enrichment estimation that spatially weight enrichment based on average patterns provided an improvement over tag counting methods. Also, methods that included information across the entire gene body provided improvement over methods that focus on a specific sub-region of the gene (e.g., the 5' or 3' region). Conclusion The performance of data mining and machine learning methods when applied to histone modification ChIP-seq data can be improved by using data across the entire gene body, and incorporating the spatial distribution of enrichment. Refinement of enrichment estimation ultimately improved accuracy of model predictions. PMID

On recovering distributed IP information from inductive source time domain electromagnetic data

NASA Astrophysics Data System (ADS)

Kang, Seogi; Oldenburg, Douglas W.

2016-10-01

We develop a procedure to invert time domain induced polarization (IP) data for inductive sources. Our approach is based upon the inversion methodology in conventional electrical IP (EIP), which uses a sensitivity function that is independent of time. However, significant modifications are required for inductive source IP (ISIP) because electric fields in the ground do not achieve a steady state. The time-history for these fields needs to be evaluated and then used to define approximate IP currents. The resultant data, either a magnetic field or its derivative, are evaluated through the Biot-Savart law. This forms the desired linear relationship between data and pseudo-chargeability. Our inversion procedure has three steps: (1) Obtain a 3-D background conductivity model. We advocate, where possible, that this be obtained by inverting early-time data that do not suffer significantly from IP effects. (2) Decouple IP responses embedded in the observations by forward modelling the TEM data due to a background conductivity and subtracting these from the observations. (3) Use the linearized sensitivity function to invert data at each time channel and recover pseudo-chargeability. Post-interpretation of the recovered pseudo-chargeabilities at multiple times allows recovery of intrinsic Cole-Cole parameters such as time constant and chargeability. The procedure is applicable to all inductive source survey geometries but we focus upon airborne time domain EM (ATEM) data with a coincident-loop configuration because of the distinctive negative IP signal that is observed over a chargeable body. Several assumptions are adopted to generate our linearized modelling but we systematically test the capability and accuracy of the linearization for ISIP responses arising from different conductivity structures. On test examples we show: (1) our decoupling procedure enhances the ability to extract information about existence and location of chargeable targets directly from the data maps

Localization and socialization: Experimental insights into the functional architecture of IP3 receptors

NASA Astrophysics Data System (ADS)

Diambra, Luis; Marchant, Jonathan S.

2009-09-01

Inositol 1,4,5-trisphosphate (IP3)-evoked Ca2+ signals display great spatiotemporal malleability. This malleability depends on diversity in both the cellular organization and in situ functionality of IP3 receptors (IP3Rs) that regulate Ca2+ release from the endoplasmic reticulum (ER). Recent experimental data imply that these considerations are not independent, such that—as with other ion channels—the local organization of IP3Rs impacts their functionality, and reciprocally IP3R activity impacts their organization within native ER membranes. Here, we (i) review experimental data that lead to our understanding of the "functional architecture" of IP3Rs within the ER, (ii) propose an updated terminology to span the organizational hierarchy of IP3Rs observed in intact cells, and (iii) speculate on the physiological significance of IP3R socialization in Ca2+ dynamics, and consequently the emerging need for modeling studies to move beyond gridded, planar, and static simulations of IP3R clustering even over short experimental timescales.

Standardization efforts in IP telephony

NASA Astrophysics Data System (ADS)

Sengodan, Senthil; Bansal, Raj

1999-11-01

The recent interest in IP telephony has led to a tremendous increase of standardization activities in the area. The three main standards bodies in the area of IP telephony are the International Telecommunication Union's (ITU-T) Study Group (SG) 16, the Internet Engineering Task Force (IETF) and the European Telecommunication Standards Institute's (ETSI) TIPHON project. In addition, forums such as the International Multimedia Teleconferencing Consortium (IMTC), the Intelligent Network Forum (INF), the International Softswitch Consortium (ISC), the Electronic Computer Telephony Forum (ECTF), and the MIT's Internet Telephony Consortium (ITC) are looking into various other aspects that aim at the growth of this industry. This paper describes the main tasks (completed and in progress) undertaken by these organizations. In describing such work, an overview of the underlying technology is also provided.

Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection

PubMed Central

Sun, Hong; Guns, Tias; Fierro, Ana Carolina; Thorrez, Lieven; Nijssen, Siegfried; Marchal, Kathleen

2012-01-01

Computationally retrieving biologically relevant cis-regulatory modules (CRMs) is not straightforward. Because of the large number of candidates and the imperfection of the screening methods, many spurious CRMs are detected that are as high scoring as the biologically true ones. Using ChIP-information allows not only to reduce the regions in which the binding sites of the assayed transcription factor (TF) should be located, but also allows restricting the valid CRMs to those that contain the assayed TF (here referred to as applying CRM detection in a query-based mode). In this study, we show that exploiting ChIP-information in a query-based way makes in silico CRM detection a much more feasible endeavor. To be able to handle the large datasets, the query-based setting and other specificities proper to CRM detection on ChIP-Seq based data, we developed a novel powerful CRM detection method ‘CPModule’. By applying it on a well-studied ChIP-Seq data set involved in self-renewal of mouse embryonic stem cells, we demonstrate how our tool can recover combinatorial regulation of five known TFs that are key in the self-renewal of mouse embryonic stem cells. Additionally, we make a number of new predictions on combinatorial regulation of these five key TFs with other TFs documented in TRANSFAC. PMID:22422841

Antibody performance in ChIP-sequencing assays: From quality scores of public data sets to quantitative certification.

PubMed

Mendoza-Parra, Marco-Antonio; Saravaki, Vincent; Cholley, Pierre-Etienne; Blum, Matthias; Billoré, Benjamin; Gronemeyer, Hinrich

2016-01-01

We have established a certification system for antibodies to be used in chromatin immunoprecipitation assays coupled to massive parallel sequencing (ChIP-seq). This certification comprises a standardized ChIP procedure and the attribution of a numerical quality control indicator (QCi) to biological replicate experiments. The QCi computation is based on a universally applicable quality assessment that quantitates the global deviation of randomly sampled subsets of ChIP-seq dataset with the original genome-aligned sequence reads. Comparison with a QCi database for >28,000 ChIP-seq assays were used to attribute quality grades (ranging from 'AAA' to 'DDD') to a given dataset. In the present report we used the numerical QC system to assess the factors influencing the quality of ChIP-seq assays, including the nature of the target, the sequencing depth and the commercial source of the antibody.  We have used this approach specifically to certify mono and polyclonal antibodies obtained from Active Motif directed against the histone modification marks H3K4me3, H3K27ac and H3K9ac for ChIP-seq. The antibodies received the grades AAA to BBC ( www.ngs-qc.org). We propose to attribute such quantitative grading of all antibodies attributed with the label "ChIP-seq grade".

Proposal of Secure VoIP System Using Attribute Certificate

NASA Astrophysics Data System (ADS)

Kim, Jin-Mook; Jeong, Young-Ae; Hong, Seong-Sik

VoIP is a service that changes the analogue audio signal into a digital signal and then transfers the audio information to the users after configuring it as a packet; and it has an advantage of lower price than the existing voice call service and better extensibility. However, VoIP service has a system structure that, compared to the existing PSTN (Public Switched Telephone Network), has poor call quality and is vulnerable in the security aspect. To make up these problems, TLS service was introduced to enhance the security. In practical system, however, since QoS problem occurs, it is necessary to develop the VoIP security system that can satisfy QoS at the same time in the security aspect. In this paper, a user authentication VoIP system that can provide a service according to the security and the user through providing a differential service according to the approach of the users by adding AA server at the step of configuring the existing VoIP session is suggested. It was found that the proposed system of this study provides a quicker QoS than the TLS-added system at a similar level of security. Also, it is able to provide a variety of additional services by the different users.

Photometric studies of δ Scuti stars. I. IP Virginis

USGS Publications Warehouse

Joner, Michael D.; Hintz, Eric G.; Collier, Matthew W.

1998-01-01

We report 15 new times of maximum light for the δ Scuti star IP Virginis (formerly known as SA 106‐1024). An analysis of all times of maximum light indicates that IP Vir has been decreasing in period at a constant rate of − days day−1. Evidence is also presented that IP Vir is a double‐mode variable with a period ratio of . This period ratio predicts a [Fe/H] value of −0.3. From photometric (uvbyβ) observations, we find a foreground reddening of .008 mag and a metallicity of [Fe/H] = +0.05. It is shown that [Fe/H] = −0.3 is most likely the correct value. Intrinsic ‐ and c1‐values, plotted in a model atmosphere grid, indicate a mean effective temperature, K, and a mean surface gravity, . All of these physical parameters support Landolt's initial conclusion that IP Vir is an ordinary δ Sct star.

Enabling IP Header Compression in COTS Routers via Frame Relay on a Simplex Link

NASA Technical Reports Server (NTRS)

Nguyen, Sam P.; Pang, Jackson; Clare, Loren P.; Cheng, Michael K.

2010-01-01

NASA is moving toward a networkcentric communications architecture and, in particular, is building toward use of Internet Protocol (IP) in space. The use of IP is motivated by its ubiquitous application in many communications networks and in available commercial off-the-shelf (COTS) technology. The Constellation Program intends to fit two or more voice (over IP) channels on both the forward link to, and the return link from, the Orion Crew Exploration Vehicle (CEV) during all mission phases. Efficient bandwidth utilization of the links is key for voice applications. In Voice over IP (VoIP), the IP packets are limited to small sizes to keep voice latency at a minimum. The common voice codec used in VoIP is G.729. This new algorithm produces voice audio at 8 kbps and in packets of 10-milliseconds duration. Constellation has designed the VoIP communications stack to use the combination of IP/UDP/RTP protocols where IP carries a 20-byte header, UDP (User Datagram Protocol) carries an 8-byte header, and RTP (Real Time Transport Protocol) carries a 12-byte header. The protocol headers total 40 bytes and are equal in length to a 40-byte G.729 payload, doubling the VoIP latency. Since much of the IP/UDP/RTP header information does not change from IP packet to IP packet, IP/UDP/RTP header compression can avoid transmission of much redundant data as well as reduce VoIP latency. The benefits of IP header compression are more pronounced at low data rate links such as the forward and return links during CEV launch. IP/UDP/RTP header compression codecs are well supported by many COTS routers. A common interface to the COTS routers is through frame relay. However, enabling IP header compression over frame relay, according to industry standard (Frame Relay IP Header Compression Agreement FRF.20), requires a duplex link and negotiations between the compressor router and the decompressor router. In Constellation, each forward to and return link from the CEV in space is treated

Optimization of OSPF Routing in IP Networks

NASA Astrophysics Data System (ADS)

Bley, Andreas; Fortz, Bernard; Gourdin, Eric; Holmberg, Kaj; Klopfenstein, Olivier; Pióro, Michał; Tomaszewski, Artur; Ümit, Hakan

The Internet is a huge world-wide packet switching network comprised of more than 13,000 distinct subnetworks, referred to as Autonomous Systems (ASs) autonomous system AS . They all rely on the Internet Protocol (IP) internet protocol IP for transport of packets across the network. And most of them use shortest path routing protocols shortest path routing!protocols , such as OSPF or IS-IS, to control the routing of IP packets routing!of IP packets within an AS. The idea of the routing is extremely simple — every packet is forwarded on IP links along the shortest route between its source and destination nodes of the AS. The AS network administrator can manage the routing of packets in the AS by supplying the so-called administrative weights of IP links, which specify the link lengths that are used by the routing protocols for their shortest path computations. The main advantage of the shortest path routing policy is its simplicity, allowing for little administrative overhead. From the network engineering perspective, however, shortest path routing can pose problems in achieving satisfactory traffic handling efficiency. As all routing paths depend on the same routing metric routing!metric , it is not possible to configure the routing paths for the communication demands between different pairs of nodes explicitly or individually; the routing can be controlled only indirectly and only as a whole by modifying the routing metric. Thus, one of the main tasks when planning such networks is to find administrative link weights that induce a globally efficient traffic routing

Factors affecting human heterocyclic amine intake and the metabolism of PhIP.

PubMed

Knize, Mark G; Kulp, Kristen S; Salmon, Cynthia P; Keating, Garrett A; Felton, James S

2002-09-30

We are working to understand possible human health effects from exposure to heterocyclic amines that are formed in meat during cooking. Laboratory-cooked beef, pork, and chicken are capable of producing tens of nanograms of MeIQx, IFP, and PhIP per gram of meat and smaller amounts of other heteroyclic amines. Well-done restaurant-cooked beef, pork, and chicken may contain PhIP and IFP at concentrations as high as tens of nanograms per gram and MeIQx at levels up to 3 ng/g. Although well-done chicken breast prepared in the laboratory may contain large amounts of PhIP, a survey of flame-grilled meat samples cooked in private homes showed PhIP levels in beef steak and chicken breast are not significantly different (P=0.36). The extremely high PhIP levels reported in some studies of grilled chicken are not seen in home-cooked samples.Many studies suggest individuals may have varying susceptibility to carcinogens and that diet may influence metabolism, thus affecting cancer susceptibility. To understand the human metabolism of PhIP, we examined urinary metabolites of PhIP in volunteers following a single well-done meat exposure. Using solid-phase extraction and LC/MS/MS, we quantified four major PhIP metabolites in human urine. In addition to investigating individual variation, we examined the interaction of PhIP with a potentially chemopreventive food. In a preliminary study of the effect of broccoli on PhIP metabolism, we fed chicken to six volunteers before and after eating steamed broccoli daily for 3 days. Preliminary results suggest that broccoli, which contains isothiocyanates shown to induce Phases I and II metabolism in vitro, may affect both the rate of metabolite excretion and the metabolic products of a dietary carcinogen. This newly developed methodology will allow us to assess prevention strategies that reduce the possible risks associated with PhIP exposure.

The role of calsenilin/DREAM/KChIP3 in contextual fear conditioning.

PubMed

Alexander, Jon C; McDermott, Carmel M; Tunur, Tumay; Rands, Vicky; Stelly, Claire; Karhson, Debra; Bowlby, Mark R; An, W Frank; Sweatt, J David; Schrader, Laura A

2009-03-01

Potassium channel interacting proteins (KChIPs) are members of a family of calcium binding proteins that interact with Kv4 potassium (K(+)) channel primary subunits and also act as transcription factors. The Kv4 subunit is a primary K(+) channel pore-forming subunit, which contributes to the somatic and dendritic A-type currents throughout the nervous system. These A-type currents play a key role in the regulation of neuronal excitability and dendritic processing of incoming synaptic information. KChIP3 is also known as calsenilin and as the transcription factor, downstream regulatory element antagonist modulator (DREAM), which regulates a number of genes including prodynorphin. KChIP3 and Kv4 primary channel subunits are highly expressed in hippocampus, an area of the brain important for learning and memory. Through its various functions, KChIP3 may play a role in the regulation of synaptic plasticity and learning and memory. We evaluated the role of KChIP3 in a hippocampus-dependent memory task, contextual fear conditioning. Male KChIP3 knockout (KO) mice showed significantly enhanced memory 24 hours after training as measured by percent freezing. In addition, we found that membrane association and interaction with Kv4.2 of KChIP3 protein was significantly decreased and nuclear KChIP3 expression was increased six hours after the fear conditioning training paradigm with no significant change in KChIP3 mRNA. In addition, prodynorphin mRNA expression was significantly decreased six hours after fear conditioning training in wild-type (WT) but not in KO animals. These data suggest a role for regulation of gene expression by KChIP3/DREAM/calsenilin in consolidation of contextual fear conditioning memories.

Study on improved Ip-iq APF control algorithm and its application in micro grid

NASA Astrophysics Data System (ADS)

Xie, Xifeng; Shi, Hua; Deng, Haiyingv

2018-01-01

In order to enhance the tracking velocity and accuracy of harmonic detection by ip-iq algorithm, a novel ip-iq control algorithm based on the Instantaneous reactive power theory is presented, the improved algorithm adds the lead correction link to adjust the zero point of the detection system, the Fuzzy Self-Tuning Adaptive PI control is introduced to dynamically adjust the DC-link Voltage, which meets the requirement of the harmonic compensation of the micro grid. Simulation and experimental results verify the proposed method is feasible and effective in micro grid.

Calibration and application of the IP25 biomarker for Arctic sea ice reconstructions

NASA Astrophysics Data System (ADS)

Cabedo Sanz, P.; Navarro Rodriguez, A.; Belt, S. T.; Brown, T. A.; Knies, J.; Husum, K.; Giraudeau, J.; Andrews, J.

2012-04-01

The presence of the sea ice diatom biomarker IP25 in Arctic marine sediments has been used in previous studies as a proxy for past spring sea ice occurrence and as an indicator of wider palaeoenvironmental conditions for different regions of the Arctic over various timescales [e.g. 1, 3]. In addition, measurement of IP25 has also been applied as a sea ice origin tracer for studying the transfer of organic carbon through Arctic food-webs [2]. The current study focuses on three main areas: (1) In order to improve on the quantitative analytical aspects of IP25 based research, we present here the results of a large scale extraction, purification and identification procedure for IP25 from marine sediments. This has confirmed the structure of IP25 in sediments and enabled more robust quantitative measurements by gas chromatography - mass spectrometry (GC-MS) to be established. (2) Quantitative measurements of IP25 from a sediment core from Andfjord (continental shelf, Tromsø, Norway) have been determined for the period 6.3 to 14.3 ka BP. The results of this study add significant further information to that reported previously from other biomarker studies for this core (e.g. brassicasterol) [4]. (3) Analytical detection issues (GC-MS) regarding the occurrence of IP25 in other sub-Arctic regions (e.g. East Greenland - North Iceland area) will be presented and discussed with relation to other proxy data (e.g. IRD). Belt, S. T., Vare, L. L., Massé, G., Manners, H. R., Price, J. C., MacLachlan, S. E., Andrews, J. T. & Schmidt, S. (2010) 'Striking similarities in temporal changes to spring sea ice occurrence across the central Canadian Arctic Archipelago over the last 7000 years', Quaternary Science Reviews, 29 (25-26), pp. 3489-3504. Brown, T. A. & Belt, S. T. (2012) 'Identification of the sea ice diatom biomarker IP25 in Arctic benthic macrofauna: direct evidence for a sea ice diatom diet in Arctic heterotrophs', Polar Biology, 35, pp. 131-137. Müller, J., Massé, G

Generation of Isogenic Human iPS Cell Line Precisely Corrected by Genome Editing Using the CRISPR/Cas9 System.

PubMed

Grobarczyk, Benjamin; Franco, Bénédicte; Hanon, Kevin; Malgrange, Brigitte

2015-10-01

Genome engineering and human iPS cells are two powerful technologies, which can be combined to highlight phenotypic differences and identify pathological mechanisms of complex diseases by providing isogenic cellular material. However, very few data are available regarding precise gene correction in human iPS cells. Here, we describe an optimized stepwise protocol to deliver CRISPR/Cas9 plasmids in human iPS cells. We highlight technical issues especially those associated to human stem cell culture and to the correction of a point mutation to obtain isogenic iPS cell line, without inserting any resistance cassette. Based on a two-steps clonal isolation protocol (mechanical picking followed by enzymatic dissociation), we succeed to select and expand corrected human iPS cell line with a great efficiency (more than 2% of the sequenced colonies). This protocol can also be used to obtain knock-out cell line from healthy iPS cell line by the NHEJ pathway (with about 15% efficiency) and reproduce disease phenotype. In addition, we also provide protocols for functional validation tests after every critical step.

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.

PubMed

Qin, Qian; Mei, Shenglin; Wu, Qiu; Sun, Hanfei; Li, Lewyn; Taing, Len; Chen, Sujun; Li, Fugen; Liu, Tao; Zang, Chongzhi; Xu, Han; Chen, Yiwen; Meyer, Clifford A; Zhang, Yong; Brown, Myles; Long, Henry W; Liu, X Shirley

2016-10-03

Transcription factor binding, histone modification, and chromatin accessibility studies are important approaches to understanding the biology of gene regulation. ChIP-seq and DNase-seq have become the standard techniques for studying protein-DNA interactions and chromatin accessibility respectively, and comprehensive quality control (QC) and analysis tools are critical to extracting the most value from these assay types. Although many analysis and QC tools have been reported, few combine ChIP-seq and DNase-seq data analysis and quality control in a unified framework with a comprehensive and unbiased reference of data quality metrics. ChiLin is a computational pipeline that automates the quality control and data analyses of ChIP-seq and DNase-seq data. It is developed using a flexible and modular software framework that can be easily extended and modified. ChiLin is ideal for batch processing of many datasets and is well suited for large collaborative projects involving ChIP-seq and DNase-seq from different designs. ChiLin generates comprehensive quality control reports that include comparisons with historical data derived from over 23,677 public ChIP-seq and DNase-seq samples (11,265 datasets) from eight literature-based classified categories. To the best of our knowledge, this atlas represents the most comprehensive ChIP-seq and DNase-seq related quality metric resource currently available. These historical metrics provide useful heuristic quality references for experiment across all commonly used assay types. Using representative datasets, we demonstrate the versatility of the pipeline by applying it to different assay types of ChIP-seq data. The pipeline software is available open source at https://github.com/cfce/chilin . ChiLin is a scalable and powerful tool to process large batches of ChIP-seq and DNase-seq datasets. The analysis output and quality metrics have been structured into user-friendly directories and reports. We have successfully compiled 23

Macrophages induce differentiation of plasma cells through CXCL10/IP-10

PubMed Central

Joo, HyeMee; Clayton, Sandra; Dullaers, Melissa; Herve, Marie-Cecile; Blankenship, Derek; De La Morena, Maria Teresa; Balderas, Robert; Picard, Capucine; Casanova, Jean-Laurent; Pascual, Virginia; Oh, SangKon; Banchereau, Jacques

2012-01-01

In tonsils, CD138+ plasma cells (PCs) are surrounded by CD163+ resident macrophages (Mϕs). We show here that human Mϕs (isolated from tonsils or generated from monocytes in vitro) drive activated B cells to differentiate into CD138+CD38++ PCs through secreted CXCL10/IP-10 and VCAM-1 contact. IP-10 production by Mϕs is induced by B cell–derived IL-6 and depends on STAT3 phosphorylation. Furthermore, IP-10 amplifies the production of IL-6 by B cells, which sustains the STAT3 signals that lead to PC differentiation. IP-10–deficient mice challenged with NP-Ficoll show a decreased frequency of NP-specific PCs and lower titers of antibodies. Thus, our results reveal a novel dialog between Mϕs and B cells, in which IP-10 acts as a PC differentiation factor. PMID:22987802

Protocol for the effect evaluation of Individual Placement and Support (IPS): a randomized controlled multicenter trial of IPS versus treatment as usual for patients with moderate to severe mental illness in Norway.

PubMed

Sveinsdottir, Vigdis; Løvvik, Camilla; Fyhn, Tonje; Monstad, Karin; Ludvigsen, Kari; Øverland, Simon; Reme, Silje Endresen

2014-11-18

Roughly one third of disability pensions in Norway are issued for mental and behavioral disorders, and vocational rehabilitation offered to this group has traditionally been dominated by train-and-place approaches with assisted or sheltered employment. Based on a more innovative place-and-train approach, Individual Placement and Support (IPS) involves supported employment in real-life competitive work settings, and has shown great promise for patients with severe mental illness. The study is a multicenter Randomized Controlled Trial (RCT) of IPS in a Norwegian context, involving an effect evaluation, a process evaluation, and a cost/benefit analysis. IPS will be compared to high quality treatment as usual (TAU), with labor market participation and educational activity at 12 months post inclusion as the primary outcome. The primary outcome will be measured using register data, and the project will also include complete follow-up up to 4 years after inclusion for long-term outcome data. Secondary outcomes include mental health status, disability and quality of life, collected through survey questionnaires at baseline, and after 6 and 12 months. Participants will include patients undergoing treatment for moderate to severe mental illness who are either unemployed or on sickness or social benefits. The estimated total sample size of 400-500 will be randomly assigned to the interventions. To be eligible, participants must have an expressed desire to work, and sufficient Norwegian reading and writing skills to fill out the questionnaires. The Effect Evaluation of Individual Placement and Support (IPS) will be one of the largest randomized controlled trials to date investigating the effectiveness of IPS on competitive employment, and the first study to evaluate the effectiveness of IPS for patients with moderate to severe mental illness within a Norwegian context. Clinicaltrials.gov: NCT01964092 . Registered October 16th, 2013.

Cultural consonance, constructions of science and co-existence: a review of the integration of traditional, complementary and alternative medicine in low- and middle-income countries.

PubMed

Lakshmi, Josyula K; Nambiar, Devaki; Narayan, Venkatesh; Sathyanarayana, Tamysetty N; Porter, John; Sheikh, Kabir

2015-10-01

This review examined the determinants, patterns and imports of official recognition, and incorporation of different traditional, complementary and alternative systems of medicine (TCAM) in the public health establishment of low- and middle-income countries, with a particular focus on India. Public health systems in most countries have tended to establish health facilities centred on allopathy, and then to recognize or derecognize different TCAM based on evidence or judgement, to arrive at health-care configurations that include several systems of medicine with disparate levels of authority, jurisdiction and government support. The rationale for the inclusion of TCAM providers in the public health workforce ranges from the need for personnel to address the disease burden borne by the public health system, to the desirability of providing patients with a choice of therapeutic modalities, and the nurturing of local culture. Integration, mostly described as a juxtaposition of different systems of medical practice, is often implemented as a system of establishing personnel with certification in different medical systems, in predominantly allopathic health-care facilities, to practise allopathic medicine. A hierarchy of systems of medicine, often unacknowledged, is exercised in most societies, with allopathy at the top, certain TCAM systems next and local healing traditions last. The tools employed by TCAM practitioners in diagnosis, research, pharmacy, marketing and education and training, which are seen to increasingly emulate those of allopathy, are sometimes inappropriate for use in therapeutic systems with widely divergent epistemologies, which call for distinct research paradigms. The coexistence of numerous systems of medicine, while offering the population greater choice, and presumably enhancing geographical access to health care as well, is often fraught with tensions related to the coexistence of philosophically disparate, even opposed, disciplines, with

Measuring Sister Chromatid Cohesion Protein Genome Occupancy in Drosophila melanogaster by ChIP-seq.

PubMed

Dorsett, Dale; Misulovin, Ziva

2017-01-01

This chapter presents methods to conduct and analyze genome-wide chromatin immunoprecipitation of the cohesin complex and the Nipped-B cohesin loading factor in Drosophila cells using high-throughput DNA sequencing (ChIP-seq). Procedures for isolation of chromatin, immunoprecipitation, and construction of sequencing libraries for the Ion Torrent Proton high throughput sequencer are detailed, and computational methods to calculate occupancy as input-normalized fold-enrichment are described. The results obtained by ChIP-seq are compared to those obtained by ChIP-chip (genomic ChIP using tiling microarrays), and the effects of sequencing depth on the accuracy are analyzed. ChIP-seq provides similar sensitivity and reproducibility as ChIP-chip, and identifies the same broad regions of occupancy. The locations of enrichment peaks, however, can differ between ChIP-chip and ChIP-seq, and low sequencing depth can splinter broad regions of occupancy into distinct peaks.

Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments

PubMed Central

Welch, Rene; Chung, Dongjun; Grass, Jeffrey; Landick, Robert

2017-01-01

Abstract ChIP-exo/nexus experiments rely on innovative modifications of the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a novel statistical quality control pipeline and accompanying R/Bioconductor package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments. ChIPexoQual evaluates a number of key issues including strand imbalance, library complexity, and signal enrichment of data. Assessment of these features are facilitated through diagnostic plots and summary statistics computed over regions of the genome with varying levels of coverage. We evaluated our QC pipeline with both large collections of public ChIP-exo/nexus data and multiple, new ChIP-exo datasets from Escherichia coli. ChIPexoQual analysis of these datasets resulted in guidelines for using these QC metrics across a wide range of sequencing depths and provided further insights for modelling ChIP-exo data. PMID:28911122

OSI and TCP/IP

NASA Technical Reports Server (NTRS)

Randolph, Lynwood P.

1994-01-01

The Open Systems Interconnection Transmission Control Protocol/Internet Protocol (OSI TCP/IP) and the Government Open Systems Interconnection Profile (GOSIP) are compared and described in terms of Federal internetworking. The organization and functions of the Federal Internetworking Requirements Panel (FIRP) are discussed and the panel's conclusions and recommendations with respect to the standards and implementation of the National Information Infrastructure (NII) are presented.

Intellectual Property and Strategic Agreements (IP/SA) | Frederick National Laboratory for Cancer Research

Cancer.gov

What does IP/SA handle? IP/SA handles all invention issues including patents and copyrights. All employee inventionreports are filed through the IP/SA office for all activities under the OTS contract.Additionally,&nbs

Real-time services in IP network architectures

NASA Astrophysics Data System (ADS)

Gilardi, Antonella

1996-12-01

The worldwide internet system seems to be the success key for the provision of real time multimedia services to both residential and business users and someone says that in such a way broadband networks will have a reason to exist. This new class of applications that use multiple media (voice, video and data) impose constraints to the global network nowadays consisting of subnets with various data links. The attention will be focused on the interconnection of IP non ATM and ATM networks. IETF and ATM forum are currently involved in the developing specifications suited to adapt the connectionless IP protocol to the connection oriented ATM protocol. First of all the link between the ATM and the IP service model has to be set in order to match the QoS and traffic requirements defined in the relative environment. A further significant topic is represented by the mapping of IP resource reservation model onto the ATM signalling and in the end it is necessary to define how the routing works when there are QoS parameters associated. This paper, considering only unicast applications, will examine the above issues taking as a starting point the situation where an host launches as call set up request with the relevant QoS and traffic descriptor and at some point a router at the edge of the ATM network has to decide how forwarding and request in order to establish an end to end link with the right capabilities. The aim is to compare the proposals emerging from different standard bodies to point out convergency or incompatibility.

The Incredibly Long-Lived SN 2005ip

NASA Astrophysics Data System (ADS)

Fox, Ori

2016-10-01

Type IIn supernovae (SNe IIn) are defined by their relatively narrow spectral line features associated with a dense circumstellar medium (CSM) formed by the progenitor star. The nature of the progenitor and mass loss remains relatively unknown. Shock interaction with the dense CSM can often result in significant UV emission for several years post-explosion, thereby probing the CSM characteristics, progenitor mass loss history and, ultimately, the progenitor itself. The Type IIn SN 2005ip proves to be one of the most interesting and well-studied targets within this subclass. Compared to all other supernovae, SN 2005ip is the most luminous for its age. Now more than 11 years post-explosion, the SN has released >10^51 erg throughout its lifetime as the forward shock continues to collide with a dense CSM. Here we propose HST/STIS-MAMA UV observations of SN 2005ip to investigate the massive CSM. When accounting for the shock travel time, these observations will probe material lost from the progenitor more than 1000 years prior to the explosion. We already have a single HST/STIS spectrum of SN 2005ip from 2014, which was obtained while the shock was still within a higher mass regime. With just 5 orbits, a second spectrum will allow us to directly trace the evolution of the CSM and produce new constraints on the pre-SN mass-loss history. Coinciding with Cycle 24's UV Initiative, this program offers new insight regarding both the progenitor and explosion characteristics of the SN IIn subclass.

LMIP/AAA: Local Authentication, Authorization and Accounting (AAA) Protocol for Mobile IP

NASA Astrophysics Data System (ADS)

Chenait, Manel

Mobile IP represents a simple and scalable global mobility solution. However, it inhibits various vulnerabilities to malicious attacks and, therefore, requires the integration of appropriate security services. In this paper, we discuss two authentication schemes suggested for Mobile IP: standard authentication and Mobile IP/AAA authentication. In order to provide Mobile IP roaming services including identity verication, we propose an improvement to Mobile/AAA authentication scheme by applying a local politic key management in each domain, hence we reduce hando latency by avoiding the involvement of AAA infrastructure during mobile node roaming.

IP/sub 3/ stimulates CA/sup + +/ efflux from fusogenic carrot protoplasts

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

Rincon, M.; Boss, W.F.

1986-04-01

Polyphosphoinositide breakdown plays an important role in signal transduction in animal cells (Berridge and Irvine, 1984, Nature, 312:315). Upon stimulation, phospholipase C hydrolyzes phosphatidylinositol 4,5-bisphosphate to inositol 1,4,5-trisphosphate (IP/sub 3/) and diacylglycerol both of which act as cellular second messengers. IP/sub 3/ mobilizes Ca/sup + +/ from internal stores, hence the cytosolic free Ca/sup + +/ concentration increases and those physiological activities regulated by Ca/sup + +/ are stimulated. To test if plant cells also responded to IP/sub 3/, Ca/sup + +/ efflux studies were done with fusogenic carrot protoplasts released in EGTA. The protoplasts were preloaded with /sup 45/Ca/supmore » + +/ placed in a Ca/sup + +/-free medium, and efflux determined as /sup 45/Ca/sup + +/ loss from the protoplasts. IP/sub 3/ (10-20..mu..M) caused enhanced /sup 45/Ca/sup + +/ efflux and the response was sustained for at least 15 min. In plants, as in animals, the observed IP/sub 3/-enhanced /sup 45/Ca/sup + +/ efflux suggested that IP/sub 3/ released Ca/sup + +/ from internal stores, and the increased free cytosolic Ca/sup + +/ activated Ca/sup + +/ pumping mechanisms which restored the Ca/sup + +/ concentration in the cytosol to the normal level.« less

Interfacing the Controllogics PLC over Ethernet/IP.

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

Kasemir, K. U.; Dalesio, L. R.

2001-01-01

The Allen-Bradley ControlLogix [1] line of programmable logic controllers (PLCs) offers several interfaces: Ethernet, ControlNet, DeviceNet, RS-232 and others. The ControlLogix Ethernet interface module 1756-ENET uses EtherNet/IP, the ControlNet protocol [2], encapsulated in Ethernet packages, with specific service codes [3]. A driver for the Experimental Physics and Industrial Control System (EPICS) has been developed that utilizes this EtherNet/IP protocol for controllers running the vxWorks RTOS as well as a Win32 and Unix/Linux test program. Features, performance and limitations of this interface are presented.

Preparation of pancreatic β-cells from human iPS cells with small molecules

PubMed Central

2012-01-01

Human induced pluripotent stem (iPS) cells obtained from patients are expected to be a useful source for cell transplantation therapy, because many patients (including those with type 1 diabetes and severe type 2 diabetes) are on waiting lists for transplantation for a long time due to the shortage of donors. At present, many concerns related to clinical application of human iPS cells have been raised, but rapid development of methods for the establishment, culture, and standardization of iPS cells will lead autologous cell therapy to be realistic sooner or later. However, establishment of a method for preparing some of desired cell types is still challenging. Regarding pancreatic β-cells, there have been many reports about differentiation of these cells from human embryonic stem (ES)/iPS cells, but a protocol for clinical application has still not been established. Since there is clear proof that cell transplantation therapy is effective for diabetes based on the results of clinical islet transplantation, pancreatic β-cells prepared from human iPS cells are considered likely to be effective for reducing the burden on patients. In this article, the current status of procedures for preparing pancreatic β-cells from human ES/iPS cells, including effective use of small molecules, is summarized, and some of the problems that still need to be overcome are discussed. PMID:22722666

Longevity and clinical performance of IPS-Empress ceramic restorations--a literature review.

PubMed

El-Mowafy, Omar; Brochu, Jean-François

2002-04-01

A literature review of longevity and clinical performance of IPS-Empress restorations is presented. A MEDLINE search was conducted in fall 2000. Selection criteria were set so as to identify suitable clinical trials that were published in full and that had lasted more than 2 years. A total of 6 clinical trials on the performance of IPS-Empress inlays and onlays and a total of 3 clinical trials on the performance of IPS-Empress crowns were identified. Survival rates for IPS-Empress inlays and onlays ranged from 96% at 4.5 years to 91% at 7 years; most failures were due to bulk fracture. IPS-Empress crowns had a survival rate ranging from 92% to 99% at 3 to 3.5 years; crown failure was also mainly due to fracture. Dentists should inform their patients about these survival rates when offering such treatment. The use of IPS-Empress crowns in the posterior of the mouth is not recommended until the results of more long-term clinical trials are available.

Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments.

PubMed

Welch, Rene; Chung, Dongjun; Grass, Jeffrey; Landick, Robert; Keles, Sündüz

2017-09-06

ChIP-exo/nexus experiments rely on innovative modifications of the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a novel statistical quality control pipeline and accompanying R/Bioconductor package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments. ChIPexoQual evaluates a number of key issues including strand imbalance, library complexity, and signal enrichment of data. Assessment of these features are facilitated through diagnostic plots and summary statistics computed over regions of the genome with varying levels of coverage. We evaluated our QC pipeline with both large collections of public ChIP-exo/nexus data and multiple, new ChIP-exo datasets from Escherichia coli. ChIPexoQual analysis of these datasets resulted in guidelines for using these QC metrics across a wide range of sequencing depths and provided further insights for modelling ChIP-exo data. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

PubMed

Landt, Stephen G; Marinov, Georgi K; Kundaje, Anshul; Kheradpour, Pouya; Pauli, Florencia; Batzoglou, Serafim; Bernstein, Bradley E; Bickel, Peter; Brown, James B; Cayting, Philip; Chen, Yiwen; DeSalvo, Gilberto; Epstein, Charles; Fisher-Aylor, Katherine I; Euskirchen, Ghia; Gerstein, Mark; Gertz, Jason; Hartemink, Alexander J; Hoffman, Michael M; Iyer, Vishwanath R; Jung, Youngsook L; Karmakar, Subhradip; Kellis, Manolis; Kharchenko, Peter V; Li, Qunhua; Liu, Tao; Liu, X Shirley; Ma, Lijia; Milosavljevic, Aleksandar; Myers, Richard M; Park, Peter J; Pazin, Michael J; Perry, Marc D; Raha, Debasish; Reddy, Timothy E; Rozowsky, Joel; Shoresh, Noam; Sidow, Arend; Slattery, Matthew; Stamatoyannopoulos, John A; Tolstorukov, Michael Y; White, Kevin P; Xi, Simon; Farnham, Peggy J; Lieb, Jason D; Wold, Barbara J; Snyder, Michael

2012-09-01

Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

PubMed Central

Landt, Stephen G.; Marinov, Georgi K.; Kundaje, Anshul; Kheradpour, Pouya; Pauli, Florencia; Batzoglou, Serafim; Bernstein, Bradley E.; Bickel, Peter; Brown, James B.; Cayting, Philip; Chen, Yiwen; DeSalvo, Gilberto; Epstein, Charles; Fisher-Aylor, Katherine I.; Euskirchen, Ghia; Gerstein, Mark; Gertz, Jason; Hartemink, Alexander J.; Hoffman, Michael M.; Iyer, Vishwanath R.; Jung, Youngsook L.; Karmakar, Subhradip; Kellis, Manolis; Kharchenko, Peter V.; Li, Qunhua; Liu, Tao; Liu, X. Shirley; Ma, Lijia; Milosavljevic, Aleksandar; Myers, Richard M.; Park, Peter J.; Pazin, Michael J.; Perry, Marc D.; Raha, Debasish; Reddy, Timothy E.; Rozowsky, Joel; Shoresh, Noam; Sidow, Arend; Slattery, Matthew; Stamatoyannopoulos, John A.; Tolstorukov, Michael Y.; White, Kevin P.; Xi, Simon; Farnham, Peggy J.; Lieb, Jason D.; Wold, Barbara J.; Snyder, Michael

2012-01-01

Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals. PMID:22955991

Consideration of IP Telephony Quality on the IEEE802.11a Wireless LAN

NASA Astrophysics Data System (ADS)

Miyashita, Michifumi; Takamatsu, Hideyuki; Kurono, Masahiro

Recently, IP telephony services in wired network are started, and paid attention for its charge-free nature due to IP technology. On the other hand, the Hot-Spot service, which provides one to access the Internet at the public space such as cafe, using the IEEE wireless LAN has been evolved, and it is expected that the IP telephony service on the Hot-Spot network will be developed. However, the IP telephony quality on the IEEE802.11a wireless LAN has not been fully studied yet. In this paper, we discuss about the quality of IP telephony service on the IEEE802.11a wireless LAN from the aspect of R-value, and show ability to improve the IP telephony quality on the Hot-Spot network employing PLC function defined in the ITU-T Recommendation G.711 Appendix I.

Non-Viral Generation of Marmoset Monkey iPS Cells by a Six-Factor-in-One-Vector Approach

PubMed Central

Debowski, Katharina; Warthemann, Rita; Lentes, Jana; Salinas-Riester, Gabriela; Dressel, Ralf; Langenstroth, Daniel; Gromoll, Jörg; Sasaki, Erika; Behr, Rüdiger

2015-01-01

Groundbreaking studies showed that differentiated somatic cells of mouse and human origin could be reverted to a stable pluripotent state by the ectopic expression of only four proteins. The resulting pluripotent cells, called induced pluripotent stem (iPS) cells, could be an alternative to embryonic stem cells, which are under continuous ethical debate. Hence, iPS cell-derived functional cells such as neurons may become the key for an effective treatment of currently incurable degenerative diseases. However, besides the requirement of efficacy testing of the therapy also its long-term safety needs to be carefully evaluated in settings mirroring the clinical situation in an optimal way. In this context, we chose the long-lived common marmoset monkey (Callithrix jacchus) as a non-human primate species to generate iPS cells. The marmoset monkey is frequently used in biomedical research and is gaining more and more preclinical relevance due to the increasing number of disease models. Here, we describe, to our knowledge, the first-time generation of marmoset monkey iPS cells from postnatal skin fibroblasts by non-viral means. We used the transposon-based, fully reversible piggyback system. We cloned the marmoset monkey reprogramming factors and established robust and reproducible reprogramming protocols with a six-factor-in-one-construct approach. We generated six individual iPS cell lines and characterized them in comparison with marmoset monkey embryonic stem cells. The generated iPS cells are morphologically indistinguishable from marmoset ES cells. The iPS cells are fully reprogrammed as demonstrated by differentiation assays, pluripotency marker expression and transcriptome analysis. They are stable for numerous passages (more than 80) and exhibit euploidy. In summary, we have established efficient non-viral reprogramming protocols for the derivation of stable marmoset monkey iPS cells, which can be used to develop and test cell replacement therapies in

Non-viral generation of marmoset monkey iPS cells by a six-factor-in-one-vector approach.

PubMed

Debowski, Katharina; Warthemann, Rita; Lentes, Jana; Salinas-Riester, Gabriela; Dressel, Ralf; Langenstroth, Daniel; Gromoll, Jörg; Sasaki, Erika; Behr, Rüdiger

2015-01-01

Groundbreaking studies showed that differentiated somatic cells of mouse and human origin could be reverted to a stable pluripotent state by the ectopic expression of only four proteins. The resulting pluripotent cells, called induced pluripotent stem (iPS) cells, could be an alternative to embryonic stem cells, which are under continuous ethical debate. Hence, iPS cell-derived functional cells such as neurons may become the key for an effective treatment of currently incurable degenerative diseases. However, besides the requirement of efficacy testing of the therapy also its long-term safety needs to be carefully evaluated in settings mirroring the clinical situation in an optimal way. In this context, we chose the long-lived common marmoset monkey (Callithrix jacchus) as a non-human primate species to generate iPS cells. The marmoset monkey is frequently used in biomedical research and is gaining more and more preclinical relevance due to the increasing number of disease models. Here, we describe, to our knowledge, the first-time generation of marmoset monkey iPS cells from postnatal skin fibroblasts by non-viral means. We used the transposon-based, fully reversible piggyback system. We cloned the marmoset monkey reprogramming factors and established robust and reproducible reprogramming protocols with a six-factor-in-one-construct approach. We generated six individual iPS cell lines and characterized them in comparison with marmoset monkey embryonic stem cells. The generated iPS cells are morphologically indistinguishable from marmoset ES cells. The iPS cells are fully reprogrammed as demonstrated by differentiation assays, pluripotency marker expression and transcriptome analysis. They are stable for numerous passages (more than 80) and exhibit euploidy. In summary, we have established efficient non-viral reprogramming protocols for the derivation of stable marmoset monkey iPS cells, which can be used to develop and test cell replacement therapies in

Efficient recovery of the functional IP10-scFv fusion protein from inclusion bodies with an on-column refolding system.

PubMed

Guo, Jun-Qing; Li, Qing-Mei; Zhou, Ji-Yong; Zhang, Gai-Ping; Yang, Yan-Yan; Xing, Guang-Xu; Zhao, Dong; You, Shang-You; Zhang, Chu-Yu

2006-01-01

A functional IP10-scFv fusion protein retaining the antibody specificity for acidic isoferritin and chemokine function was produced at high level in Esherichia coli (E. coli). IP10-scFv gene from the recombinant plasmid pc3IP104c9 was subcloned into pET28a fused to N-terminal His-tag sequence in frame and overexpressed in E. coli BL21(DE3). With an on-column refolding procedure based on Ni-chelating chromatography, the active fusion protein was recovered efficiently from inclusion bodies with a refolding yield of approximate 45% confirmed by spectrophotometer. The activity of refolded IP10-scFv was determined through sodium dodecyl sulfate-polyacrylamide gel electrophoresis, Western blotting and enzyme-linked immunosorbent assay. The results showed the fusion protein retains the specific binding activity to AIF with an affinity constant of 4.48x10(-8) M as well as the chemokine function of IP-10. The overall yield of IP10-scFv with bioactivity in E. coli flask culture was more than 40 mg/L.

Briefer assessment of social network drinking: A test of the Important People Instrument-5 (IP-5).

PubMed

Hallgren, Kevin A; Barnett, Nancy P

2016-12-01

The Important People instrument (IP; Longabaugh et al., 2010) is one of the most commonly used measures of social network drinking. Although its reliability and validity are well-supported, the length of the instrument may limit its use in many settings. The present study evaluated whether a briefer, 5-person version of the IP (IP-5) adequately reproduces scores from the full IP. College freshmen (N = 1,053) reported their own past-month drinking, alcohol-related consequences, and information about drinking in their close social networks at baseline and 1 year later. From this we derived network members' drinking frequency, percentage of drinkers, and percentage of heavy drinkers, assessed for up to 10 (full IP) or 5 (IP-5) network members. We first modeled the expected concordance between full-IP scores and scores from simulated shorter IP instruments by sampling smaller subsets of network members from full IP data. Then, using quasi-experimental methods, we administered the full IP and IP-5 and compared the 2 instruments' score distributions and concurrent and year-lagged associations with participants' alcohol consumption and consequences. Most of the full-IP variance was reproduced from simulated shorter versions of the IP (ICCs ≥ 0.80). The full IP and IP-5 yielded similar score distributions, concurrent associations with drinking (r = 0.22 to 0.52), and year-lagged associations with drinking. The IP-5 retains most of the information about social network drinking from the full IP. The shorter instrument may be useful in clinical and research settings that require frequent measure administration, yielding greater temporal resolution for monitoring social network drinking. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

[Unresolved issues in the evaluation of research projects involving induced pluripotent stem cells (iPS)].

PubMed

Casado, María; de Lecuona, Itziar

2013-01-01

This paper identifies problems and analyzes those conflicts posed by the evaluation of research projects involving the collection and use of human induced pluripotent stem cells (iPS) in Spain. Current legislation is causing problems of interpretation, circular and unnecessary referrals, legal uncertainty and undue delays. Actually, this situation may cause a lack of control and monitoring, and even some paralysis in regenerative medicine and cell therapy research, that is a priority nowadays. The analysis of the current legislation and its bioethical implications, led us to conclude that the review of iPS research projects cannot be assimilated to the evaluation of research projects that involve human embryonic stem cell (hESC). In this context, our proposal is based on the review by the Research Ethics Committees and the checkout by the Spanish Comission of Guarantees for Donation and Use of Human Cells and Tissues (CGDUCTH) of human iPS cells research projects. Moreover, this article claims for a more transparent research system, by effectively articulating the Registry on Research Projects. Finally, a model of verification protocol (checklist) for checking out biomedical research projects involving human iPS cells is suggested.

The Worldwide Interplanetary Scintillation (IPS) Stations (WIPSS) Network October 2016 Observing Campaign: Initial WIPSS Data Analyses

NASA Astrophysics Data System (ADS)

Bisi, M. M.; Fallows, R. A.; Jackson, B. V.; Tokumaru, M.; Gonzalez-Esparza, A.; Morgan, J.; Chashei, I. V.; Mejia-Ambriz, J.; Tyul'bashev, S. A.; Manoharan, P. K.; De la Luz, V.; Aguilar-Rodriguez, E.; Yu, H. S.; Barnes, D.; Chang, O.; Odstrcil, D.; Fujiki, K.; Shishov, V.

2017-12-01

Interplanetary Scintillation (IPS) allows for the determination of velocity and a proxy for plasma density to be made throughout the corona and inner heliosphere. Where sufficient observations are undertaken, the results can be used as input to the University of California, San Diego (UCSD) three-dimensional (3-D) time-dependent tomography suite to allow for the full 3-D reconstruction of both velocity and density throughout the inner heliosphere. By combining IPS results from multiple observing locations around the planet, we can increase both the temporal and spatial coverage across the whole of the inner heliosphere and hence improve forecast capability. During October 2016, a unique opportunity arose whereby the European-based LOw Frequency ARray (LOFAR) radio telescope was used to make nearly four weeks of continuous observations of IPS as a heliospheric space-weather trial campaign. This was expanded into a global effort to include observations of IPS from the Murchison Widefield Array (MWA) in Western Australia and many more observations from various IPS-dedicated WIPSS Network systems. LOFAR is a next-generation low-frequency radio interferometer capable of observing in the radio frequency range 10-250 MHz, nominally with up to 80 MHz bandwidth at a time. MWA in Western Australia is capable of observing in the 80-300 MHz frequency range nominally using up to 32 MHz of bandwidth. IPS data from LOFAR, ISEE, the MEXican Array Radio Telescope (MEXART), and, where possible, other WIPSS Network systems (such as LPI-BSA and Ooty), will be used in this study and we will present some initial findings for these data sets. We also make a first attempt at the 3-D reconstruction of multiple pertinent WIPSS results in the UCSD tomography. We will also try to highlight some of the potential future tools that make LOFAR a very unique system to be able to test and validate a whole plethora of IPS analysis methods with the same set of IPS data.

Modeling hypertrophic IP3 transients in the cardiac myocyte.

PubMed

Cooling, Michael; Hunter, Peter; Crampin, Edmund J

2007-11-15

Cardiac hypertrophy is a known risk factor for heart disease, and at the cellular level is caused by a complex interaction of signal transduction pathways. The IP3-calcineurin pathway plays an important role in stimulating the transcription factor NFAT which binds to DNA cooperatively with other hypertrophic transcription factors. Using available kinetic data, we construct a mathematical model of the IP3 signal production system after stimulation by a hypertrophic alpha-adrenergic agonist (endothelin-1) in the mouse atrial cardiac myocyte. We use a global sensitivity analysis to identify key controlling parameters with respect to the resultant IP3 transient, including the phosphorylation of cell-membrane receptors, the ligand strength and binding kinetics to precoupled (with G(alpha)GDP) receptor, and the kinetics associated with precoupling the receptors. We show that the kinetics associated with the receptor system contribute to the behavior of the system to a great extent, with precoupled receptors driving the response to extracellular ligand. Finally, by reparameterizing for a second hypertrophic alpha-adrenergic agonist, angiotensin-II, we show that differences in key receptor kinetic and membrane density parameters are sufficient to explain different observed IP3 transients in essentially the same pathway.

Impact of VoIP and QoS on Open and Distance Learning

ERIC Educational Resources Information Center

Saxena, P. C.; Jasola, Sanjay; Sharma, Ramesh C.

2006-01-01

Voice over Internet Protocol (VoIP) is becoming a reality in many organizations. The potential for mobility in voice over wi-fi networks will derive demand for the technology. Wireless VoIP is poised to rival VoIP as an alternative telephony tool. Internet has been used to transport data in the form of packet. In the past, Internet did not support…

Optimal use of tandem biotin and V5 tags in ChIP assays

PubMed Central

Kolodziej, Katarzyna E; Pourfarzad, Farzin; de Boer, Ernie; Krpic, Sanja; Grosveld, Frank; Strouboulis, John

2009-01-01

Background Chromatin immunoprecipitation (ChIP) assays coupled to genome arrays (Chip-on-chip) or massive parallel sequencing (ChIP-seq) lead to the genome wide identification of binding sites of chromatin associated proteins. However, the highly variable quality of antibodies and the availability of epitopes in crosslinked chromatin can compromise genomic ChIP outcomes. Epitope tags have often been used as more reliable alternatives. In addition, we have employed protein in vivo biotinylation tagging as a very high affinity alternative to antibodies. In this paper we describe the optimization of biotinylation tagging for ChIP and its coupling to a known epitope tag in providing a reliable and efficient alternative to antibodies. Results Using the biotin tagged erythroid transcription factor GATA-1 as example, we describe several optimization steps for the application of the high affinity biotin streptavidin system in ChIP. We find that the omission of SDS during sonication, the use of fish skin gelatin as blocking agent and choice of streptavidin beads can lead to significantly improved ChIP enrichments and lower background compared to antibodies. We also show that the V5 epitope tag performs equally well under the conditions worked out for streptavidin ChIP and that it may suffer less from the effects of formaldehyde crosslinking. Conclusion The combined use of the very high affinity biotin tag with the less sensitive to crosslinking V5 tag provides for a flexible ChIP platform with potential implications in ChIP sequencing outcomes. PMID:19196479

GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis.

PubMed

Stricker, Georg; Engelhardt, Alexander; Schulz, Daniel; Schmid, Matthias; Tresch, Achim; Gagneur, Julien

2017-08-01

Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a widely used approach to study protein-DNA interactions. Often, the quantities of interest are the differential occupancies relative to controls, between genetic backgrounds, treatments, or combinations thereof. Current methods for differential occupancy of ChIP-Seq data rely however on binning or sliding window techniques, for which the choice of the window and bin sizes are subjective. Here, we present GenoGAM (Genome-wide Generalized Additive Model), which brings the well-established and flexible generalized additive models framework to genomic applications using a data parallelism strategy. We model ChIP-Seq read count frequencies as products of smooth functions along chromosomes. Smoothing parameters are objectively estimated from the data by cross-validation, eliminating ad hoc binning and windowing needed by current approaches. GenoGAM provides base-level and region-level significance testing for full factorial designs. Application to a ChIP-Seq dataset in yeast showed increased sensitivity over existing differential occupancy methods while controlling for type I error rate. By analyzing a set of DNA methylation data and illustrating an extension to a peak caller, we further demonstrate the potential of GenoGAM as a generic statistical modeling tool for genome-wide assays. Software is available from Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/GenoGAM.html . gagneur@in.tum.de. Supplementary information is available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Traffic-engineering-aware shortest-path routing and its application in IP-over-WDM networks [Invited

NASA Astrophysics Data System (ADS)

Lee, Youngseok; Mukherjee, Biswanath

2004-03-01

Single shortest-path routing is known to perform poorly for Internet traffic engineering (TE) where the typical optimization objective is to minimize the maximum link load. Splitting traffic uniformly over equal-cost multiple shortest paths in open shortest path first and intermediate system-intermediate system protocols does not always minimize the maximum link load when multiple paths are not carefully selected for the global traffic demand matrix. However, a TE-aware shortest path among all the equal-cost multiple shortest paths between each ingress-egress pair can be selected such that the maximum link load is significantly reduced. IP routers can use the globally optimal TE-aware shortest path without any change to existing routing protocols and without any serious configuration overhead. While calculating TE-aware shortest paths, the destination-based forwarding constraint at a node should be satisfied, because an IP router will forward a packet to the next hop toward the destination by looking up the destination prefix. We present a mathematical problem formulation for finding a set of TE-aware shortest paths for the given network as an integer linear program, and we propose a simple heuristic for solving large instances of the problem. Then we explore the usage of our proposed algorithm for the integrated TE method in IP-over-WDM networks. The proposed algorithm is evaluated through simulations in IP networks as well as in IP-over-WDM networks.

Calcium waves in a grid of clustered channels with synchronous IP3 binding and unbinding.

PubMed

Rückl, M; Rüdiger, S

2016-11-01

Calcium signals in cells occur at multiple spatial scales and variable temporal duration. However, a physical explanation for transitions between long-lasting global oscillations and localized short-term elevations (puffs) of cytoplasmic Ca 2+ is still lacking. Here we introduce a phenomenological, coarse-grained model for the calcium variable, which is represented by ordinary differential equations. Due to its small number of parameters, and its simplicity, this model allows us to numerically study the interplay of multi-scale calcium concentrations with stochastic ion channel gating dynamics even in larger systems. We apply this model to a single cluster of inositol trisphosphate (IP 3 ) receptor channels and find further evidence for the results presented in earlier work: a single cluster may be capable of producing different calcium release types, where long-lasting events are accompanied by unbinding of IP 3 from the receptor (Rückl et al., PLoS Comput. Biol. 11, e1003965 (2015)). Finally, we show the practicability of the model in a grid of 64 clusters which is computationally intractable with previous high-resolution models. Here long-lasting events can lead to synchronized oscillations and waves, while short events stay localized. The frequency of calcium releases as well as their coherence can thereby be regulated by the amplitude of IP 3 stimulation. Finally the model allows for a new explanation of oscillating [IP 3 ], which is not based on metabolic production and degradation of IP 3 .

EQuIP-ped for Success

ERIC Educational Resources Information Center

Ewing, Molly

2015-01-01

The Educators Evaluating the Quality of Instructional Products (EQuIP) Rubric for science is a new tool for science educators that provides criteria by which to examine the alignment and overall quality of lessons and units with respect to the "Next Generation Science Standards" ("NGSS"). The rubric criteria are divided into…

(S)-(+)-Ipsdienol: Interspecific Inhibition of Ips latidens (LeConte) by Ips pini (Say) (Coleoptera: Scolytidae)

Treesearch

Daniel R. Miller; John H. Borden

1992-01-01

In south-central British Columbia, the attraction of Ips latidens (LeConte) to its pheromone, ipsenol, was inhibited by (S)-(+)-ipsdienol, a pheromone for I. pini (Say). (R)-(-)-Ipsdienol had no effect on I. latidens. (S)-(+)-lpsdienol probably plays a role in interspecific communication between the two species...

Migration features of Ips typographus in the Tatra Mountains: using a genetic method

Treesearch

Ferenc Lakatos

2003-01-01

The genetic structure of Ips typographus populations in the Tatra Mountains was studied based on the observed differences of gene flow and migration rate. It was a highlighted question as to what extent different natural barriers influence the migration potential of the species.

A Public Health Agenda for Traditional, Complementary, and Alternative Medicine

PubMed Central

Bodeker, Gerard; Kronenberg, Fredi

2002-01-01

Traditional medicine (a term used here to denote the indigenous health traditions of the world) and complementary and alternative medicine (T/CAM) have, in the past 10 years, claimed an increasing share of the public’s awareness and the agenda of medical researchers. Studies have documented that about half the population of many industrialized countries now use T/CAM, and the proportion is as high as 80% in many developing countries. Most research has focused on clinical and experimental medicine (safety, efficacy, and mechanism of action) and regulatory issues, to the general neglect of public health dimensions. Public health research must consider social, cultural, political, and economic contexts to maximize the contribution of T/CAM to health care systems globally. PMID:12356597

78 FR 49693 - Speech-to-Speech and Internet Protocol (IP) Speech-to-Speech Telecommunications Relay Services...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-15

...] Speech-to-Speech and Internet Protocol (IP) Speech-to-Speech Telecommunications Relay Services...: This is a summary of the Commission's Speech-to-Speech and Internet Protocol (IP) Speech-to-Speech...), Internet Protocol Relay (IP Relay), and IP captioned telephone service (IP CTS) as compensable forms of TRS...

A hierarchical clustering scheme approach to assessment of IP-network traffic using detrended fluctuation analysis

NASA Astrophysics Data System (ADS)

Takuma, Takehisa; Masugi, Masao

2009-03-01

This paper presents an approach to the assessment of IP-network traffic in terms of the time variation of self-similarity. To get a comprehensive view in analyzing the degree of long-range dependence (LRD) of IP-network traffic, we use a hierarchical clustering scheme, which provides a way to classify high-dimensional data with a tree-like structure. Also, in the LRD-based analysis, we employ detrended fluctuation analysis (DFA), which is applicable to the analysis of long-range power-law correlations or LRD in non-stationary time-series signals. Based on sequential measurements of IP-network traffic at two locations, this paper derives corresponding values for the LRD-related parameter α that reflects the degree of LRD of measured data. In performing the hierarchical clustering scheme, we use three parameters: the α value, average throughput, and the proportion of network traffic that exceeds 80% of network bandwidth for each measured data set. We visually confirm that the traffic data can be classified in accordance with the network traffic properties, resulting in that the combined depiction of the LRD and other factors can give us an effective assessment of network conditions at different times.

IP-1 Certification of Cargo Containers

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

Hagler, Lisle

The purpose and scope of this engineering note is to demonstrate that the structural design of the cargo container complies with the IP-1 container requirements of 49 CFR 173.410 as required by CFR 173.411.

Is VoIP Worth It?

ERIC Educational Resources Information Center

Schaffhauser, Dian

2008-01-01

School districts have by and large had great results implementing VoIP, which has become the conduit for delivering expanded functionality, achieving greater internal control, and gaining freedom from onerous monthly phone bills. But demonstrating a financial return on what is a substantial investment can be an elusive effort. The goal of…

47 CFR 64.606 - VRS and IP Relay provider and TRS program certification.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false VRS and IP Relay provider and TRS program... Services and Related Customer Premises Equipment for Persons With Disabilities § 64.606 VRS and IP Relay... including notification in the Federal Register. (2) VRS and IP Relay provider. Any entity desiring to...

Spike-In Normalization of ChIP Data Using DNA-DIG-Antibody Complex.

PubMed

Eberle, Andrea B

2018-01-01

Chromatin immunoprecipitation (ChIP) is a widely used method to determine the occupancy of specific proteins within the genome, helping to unravel the function and activity of specific genomic regions. In ChIP experiments, normalization of the obtained data by a suitable internal reference is crucial. However, particularly when comparing differently treated samples, such a reference is difficult to identify. Here, a simple method to improve the accuracy and reliability of ChIP experiments by the help of an external reference is described. An artificial molecule, composed of a well-defined digoxigenin (DIG) labeled DNA fragment in complex with an anti-DIG antibody, is synthesized and added to each chromatin sample before immunoprecipitation. During the ChIP procedure, the DNA-DIG-antibody complex undergoes the same treatments as the chromatin and is therefore purified and quantified together with the chromatin of interest. This external reference compensates for variability during the ChIP routine and improves the similarity between replicates, thereby emphasizing the biological differences between samples.

Temperature Dependence of IP3-Mediated Local and Global Ca2+ Signals

PubMed Central

Dickinson, George D.; Parker, Ian

2013-01-01

We examined the effect of temperature (12–40°C) on local and global Ca2+ signals mediated by inositol trisphosphate receptor/channels (IP3R) in human neuroblastoma (SH-SY5Y) cells. The amplitudes and spatial spread of local signals arising from single IP3R (blips) and clusters of IP3R (puffs) showed little temperature dependence, whereas their kinetics (durations and latencies) were markedly accelerated by increasing temperature. In contrast, the amplitude of global Ca2+ waves increased appreciably at lower temperatures, probably as a result of the longer duration of IP3R channel opening. Several parameters, including puff and blip durations, puff latency and frequency, and frequency of repetitive Ca2+ waves, showed a biphasic temperature dependence on Arrhenius plots. In all cases the transition temperature occurred at ∼25°C, possibly reflecting a phase transition in the lipids of the endoplasmic reticulum membrane. Although the IP3-evoked Ca2+ signals were qualitatively similar at 25°C and 36°C, one should consider the temperature sensitivity of IP3-mediated signal amplitudes when extrapolating from room temperature to physiological temperature. Conversely, further cooling may be advantageous to improve the optical resolution of channel gating kinetics. PMID:23442860

The role of DAB2IP in androgen receptor activation during prostate cancer progression.

PubMed

Wu, K; Liu, J; Tseng, S-F; Gore, C; Ning, Z; Sharifi, N; Fazli, L; Gleave, M; Kapur, P; Xiao, G; Sun, X; Oz, O K; Min, W; Alexandrakis, G; Yang, C-R; Hsieh, C-L; Wu, H-C; He, D; Xie, D; Hsieh, J-T

2014-04-10

Altered androgen-receptor (AR) expression and/or constitutively active AR are commonly associated with prostate cancer (PCa) progression. Targeting AR remains a focal point for designing new strategy of PCa therapy. Here, we have shown that DAB2IP, a novel tumor suppressor in PCa, can inhibit AR-mediated cell growth and gene activation in PCa cells via distinct mechanisms. DAB2IP inhibits the genomic pathway by preventing AR nuclear translocation or phosphorylation and suppresses the non-genomic pathway via its unique functional domain to inactivate c-Src. Also, DAB2IP is capable of suppressing AR activation in an androgen-independent manner. In addition, DAB2IP can inhibit several AR splice variants showing constitutive activity in PCa cells. In DAB2IP(-/-) mice, the prostate gland exhibits hyperplastic epithelia, in which AR becomes more active. Consistently, DAB2IP expression inversely correlates with AR activation status particularly in recurrent or metastatic PCa patients. Taken together, DAB2IP is a unique intrinsic AR modulator in normal cells, and likely can be further developed into a therapeutic agent for PCa.

Evidence for Holocene centennial variability in sea ice cover based on IP25 biomarker reconstruction in the southern Kara Sea (Arctic Ocean)

NASA Astrophysics Data System (ADS)

Hörner, Tanja; Stein, Rüdiger; Fahl, Kirsten

2017-10-01

The Holocene is characterized by the late Holocene cooling trend as well as by internal short-term centennial fluctuations. Because Arctic sea ice acts as a significant component (amplifier) within the climate system, investigating its past long- and short-term variability and controlling processes is beneficial for future climate predictions. This study presents the first biomarker-based (IP25 and PIP25) sea ice reconstruction from the Kara Sea (core BP00-07/7), covering the last 8 ka. These biomarker proxies reflect conspicuous short-term sea ice variability during the last 6.5 ka that is identified unprecedentedly in the source region of Arctic sea ice by means of a direct sea ice indicator. Prominent peaks of extensive sea ice cover occurred at 3, 2, 1.3 and 0.3 ka. Spectral analysis of the IP25 record revealed 400- and 950-year cycles. These periodicities may be related to the Arctic/North Atlantic Oscillation, but probably also to internal climate system fluctuations. This demonstrates that sea ice belongs to a complex system that more likely depends on multiple internal forcing.

NHE isoform switching and KChIP2 upregulation in aging porcine atria.

PubMed

Kant, Ritu; Hu, Zhaoyang; Malhotra, Jaideep K; Krogh-Madsen, Trine; Christini, David J; Heerdt, Paul M; Abbott, Geoffrey W

2013-01-01

Aging increases the risk of cardiac pathologies including atrial fibrillation and can alter myocardial responsiveness to therapeutic agents. Here, seeking molecular correlates of myocardial aging processes, we performed global "whole transcript" analysis of 25,388 genes using 572,667 probes to compare the left atrial (LA) transcriptomes of young adult (9 months old) versus elderly (10 years old) female swine. NHE2 (>9-fold) and KChIP2 (3.8-fold) exhibited the highest aging-related expression increases. Real-time qPCR recapitulated these findings and indicated a 50% decrease in LA NHE1, a twofold increase in right atrial KChIP2, but no significant changes for these transcripts in either ventricle. Notably, even in young adult pigs, NHE2 transcript was detectable and enriched in the atria over the ventricles. NHE1, the recognized cardiac isoform of the sodium hydrogen exchanger, has proven a compelling but clinically disappointing therapeutic target with respect to reperfusion arrhythmias. Our data challenge the dogma that NHE1 is alone in the myocardium and suggest that NHE2 could negatively impact the pharmacological responsiveness of atrial tissue to NHE1-specific inhibitors. KChIP2 is a cytosolic β subunit essential for generation of I to. The increased KChIP2 expression we observed with aging substantially shortened in silico atrial myocyte action potential duration, a predisposing factor in atrial fibrillation. Consistent with this, 4/5 elderly swine sustained pacing-induced AF≥15 s after cessation of stimulation, compared to 0/3 young swine. Our findings uncover potential molecular bases for increased arrhythmogenicity and reduced pharmacologic efficacy in the aging atrium, in a large animal model of human cardiac physiology.

78 FR 14701 - Misuse of Internet Protocol (IP) Captioned Telephone Service; Telecommunications Relay Services...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-07

...] Misuse of Internet Protocol (IP) Captioned Telephone Service; Telecommunications Relay Services and..., the information collection associated with the Commission's Misuse of Internet Protocol (IP) Captioned... Registration and Documentation of Disability for Eligibility to Use IP Captioned Telephone Service, CG Docket...

Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data.

PubMed

Bao, Yanchun; Vinciotti, Veronica; Wit, Ernst; 't Hoen, Peter A C

2013-05-30

ImmunoPrecipitation (IP) efficiencies may vary largely between different antibodies and between repeated experiments with the same antibody. These differences have a large impact on the quality of ChIP-seq data: a more efficient experiment will necessarily lead to a higher signal to background ratio, and therefore to an apparent larger number of enriched regions, compared to a less efficient experiment. In this paper, we show how IP efficiencies can be explicitly accounted for in the joint statistical modelling of ChIP-seq data. We fit a latent mixture model to eight experiments on two proteins, from two laboratories where different antibodies are used for the two proteins. We use the model parameters to estimate the efficiencies of individual experiments, and find that these are clearly different for the different laboratories, and amongst technical replicates from the same lab. When we account for ChIP efficiency, we find more regions bound in the more efficient experiments than in the less efficient ones, at the same false discovery rate. A priori knowledge of the same number of binding sites across experiments can also be included in the model for a more robust detection of differentially bound regions among two different proteins. We propose a statistical model for the detection of enriched and differentially bound regions from multiple ChIP-seq data sets. The framework that we present accounts explicitly for IP efficiencies in ChIP-seq data, and allows to model jointly, rather than individually, replicates and experiments from different proteins, leading to more robust biological conclusions.

HRCT findings of collagen vascular disease-related interstitial pneumonia (CVD-IP): a comparative study among individual underlying diseases.

PubMed

Tanaka, N; Kunihiro, Y; Kubo, M; Kawano, R; Oishi, K; Ueda, K; Gondo, T

2018-05-29

To identify characteristic high-resolution computed tomography (CT) findings for individual collagen vascular disease (CVD)-related interstitial pneumonias (IPs). The HRCT findings of 187 patients with CVD, including 55 patients with rheumatoid arthritis (RA), 50 with systemic sclerosis (SSc), 46 with polymyositis/dermatomyositis (PM/DM), 15 with mixed connective tissue disease, 11 with primary Sjögren's syndrome, and 10 with systemic lupus erythematosus, were evaluated. Lung parenchymal abnormalities were compared among CVDs using χ 2 test, Kruskal-Wallis test, and multiple logistic regression analysis. A CT-pathology correlation was performed in 23 patients. In RA-IP, honeycombing was identified as the significant indicator based on multiple logistic regression analyses. Traction bronchiectasis (81.8%) was further identified as the most frequent finding based on χ 2 test. In SSc IP, lymph node enlargement and oesophageal dilatation were identified as the indicators based on multiple logistic regression analyses, and ground-glass opacity (GGO) was the most extensive based on Kruskal-Wallis test, which reflects the higher frequency of the pathological nonspecific interstitial pneumonia (NSIP) pattern present in the CT-pathology correlation. In PM/DM IP, airspace consolidation and the absence of honeycombing were identified as the indicators based on multiple logistic regression analyses, and predominance of consolidation over GGO (32.6%) and predominant subpleural distribution of GGO/consolidation (41.3%) were further identified as the most frequent findings based on χ 2 test, which reflects the higher frequency of the pathological NSIP and/or the organising pneumonia patterns present in the CT-pathology correlation. Several characteristic high-resolution CT findings with utility for estimating underlying CVD were identified. Copyright © 2018 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Potassium Channel Interacting Protein 2 (KChIP2) is not a transcriptional regulator of cardiac electrical remodeling

PubMed Central

Winther, Sine V.; Tuomainen, Tomi; Borup, Rehannah; Tavi, Pasi; Antoons, Gudrun; Thomsen, Morten B.

2016-01-01

The heart-failure relevant Potassium Channel Interacting Protein 2 (KChIP2) augments CaV1.2 and KV4.3. KChIP3 represses CaV1.2 transcription in cardiomyocytes via interaction with regulatory DNA elements. Hence, we tested nuclear presence of KChIP2 and if KChIP2 translocates into the nucleus in a Ca2+ dependent manner. Cardiac biopsies from human heart-failure patients and healthy donor controls showed that nuclear KChIP2 abundance was significantly increased in heart failure; however, this was secondary to a large variation of total KChIP2 content. Administration of ouabain did not increase KChIP2 content in nuclear protein fractions in anesthetized mice. KChIP2 was expressed in cell lines, and Ca2+ ionophores were applied in a concentration- and time-dependent manner. The cell lines had KChIP2-immunoreactive protein in the nucleus in the absence of treatments to modulate intracellular Ca2+ concentration. Neither increasing nor decreasing intracellular Ca2+ concentrations caused translocation of KChIP2. Microarray analysis did not identify relief of transcriptional repression in murine KChIP2−/− heart samples. We conclude that although there is a baseline presence of KChIP2 in the nucleus both in vivo and in vitro, KChIP2 does not directly regulate transcriptional activity. Moreover, the nuclear transport of KChIP2 is not dependent on Ca2+. Thus, KChIP2 does not function as a conventional transcription factor in the heart. PMID:27349185

Comparison of gating dynamics of different IP3R channels with immune algorithm searching for channel parameter distributions

NASA Astrophysics Data System (ADS)

Cai, Xiuhong; Li, Xiang; Qi, Hong; Wei, Fang; Chen, Jianyong; Shuai, Jianwei

2016-10-01

The gating properties of the inositol 1, 4, 5-trisphosphate (IP3) receptor (IP3R) are determined by the binding and unbinding capability of Ca2+ ions and IP3 messengers. With the patch clamp experiments, the stationary properties have been discussed for Xenopus oocyte type-1 IP3R (Oo-IP3R1), type-3 IP3R (Oo-IP3R3) and Spodoptera frugiperda IP3R (Sf-IP3R). In this paper, in order to provide insights about the relation between the observed gating characteristics and the gating parameters in different IP3Rs, we apply the immune algorithm to fit the parameters of a modified DeYoung-Keizer model. By comparing the fitting parameter distributions of three IP3Rs, we suggest that the three types of IP3Rs have the similar open sensitivity in responding to IP3. The Oo-IP3R3 channel is easy to open in responding to low Ca2+ concentration, while Sf-IP3R channel is easily inhibited in responding to high Ca2+ concentration. We also show that the IP3 binding rate is not a sensitive parameter for stationary gating dynamics for three IP3Rs, but the inhibitory Ca2+ binding/unbinding rates are sensitive parameters for gating dynamics for both Oo-IP3R1 and Oo-IP3R3 channels. Such differences may be important in generating the spatially and temporally complex Ca2+ oscillations in cells. Our study also demonstrates that the immune algorithm can be applied for model parameter searching in biological systems.

78 FR 54201 - Misuse of Internet Protocol (IP) Captioned Telephone Service; Telecommunications Relay Services...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-03

...] Misuse of Internet Protocol (IP) Captioned Telephone Service; Telecommunications Relay Services and... further possible actions necessary to improve internet protocol captioned telephone relay service (IP CTS... for calculating the compensation rate paid to IP CTS providers. This action is necessary to ensure...

[Two years clinical observation of a kind of castable ceramic--IPS Empress].

PubMed

Liu, Y; Li, Y; Nie, Y

1999-03-01

We used this material in clinic since 1995. Discussion on the prosthetic effects of the above-mentioned material to spreat it clinically. Through half to two years clinical observations to evaluate the effect of IPS Empress crowns in anterior teeth and inlays in posteriors. and Prosthesis made of this kind of material IPS Empress is one kind of excellent all-ceramic prosthetic material. IPS Empress also could be used in post crowns and the clinical effect was satisfactory.

Investigation of the pathogenesis of autoimmune diseases by iPS cells.

PubMed

Natsumoto, Bunki; Shoda, Hirofumi; Fujio, Keishi; Otsu, Makoto; Yamamoto, Kazuhiko

2017-01-01

The pluripotent stem cells have a self-renewal ability and can be differentiated into theoretically all of cell types. The induced pluripotent stem (iPS) cells overcame the ethical problems of the human embryonic stem (ES) cell, and enable pathologic analysis of intractable diseases and drug discovery. The in vitro disease model using disease-specific iPS cells enables repeated analyses of human cells without influence of environment factors. Even though autoimmune diseases are polygenic diseases, autoimmune disease-specific iPS cells are thought to be a promising tool for analyzing the pathogenesis of the diseases and drug discovery in future.

The ROI of VoIP: Everybody Says VoIP Saves Big Bucks. But Does It?

ERIC Educational Resources Information Center

Villano, Matt

2006-01-01

Advocates of Voice over Internet Protocol (VoIP) say it saves money on long distance calls by sending them over the Internet, improves communication by eliminating the Private Branch Exchange (PBX), and offers a host of neat features such as call forwarding, e-mail accessible voicemail, and more. When it comes to measuring the dollars-and-cents…

Demonstrating a Realistic IP Mission Prototype

NASA Technical Reports Server (NTRS)

Rash, James; Ferrer, Arturo B.; Goodman, Nancy; Ghazi-Tehrani, Samira; Polk, Joe; Johnson, Lorin; Menke, Greg; Miller, Bill; Criscuolo, Ed; Hogie, Keith

2003-01-01

Flight software and hardware and realistic space communications environments were elements of recent demonstrations of the Internet Protocol (IP) mission concept in the lab. The Operating Missions as Nodes on the Internet (OMNI) Project and the Flight Software Branch at NASA/GSFC collaborated to build the prototype of a representative space mission that employed unmodified off-the-shelf Internet protocols and technologies for end-to-end communications between the spacecraft/instruments and the ground system/users. The realistic elements used in the prototype included an RF communications link simulator and components of the TRIANA mission flight software and ground support system. A web-enabled camera connected to the spacecraft computer via an Ethernet LAN represented an on-board instrument creating image data. In addition to the protocols at the link layer (HDLC), transport layer (UDP, TCP), and network (IP) layer, a reliable file delivery protocol (MDP) at the application layer enabled reliable data delivery both to and from the spacecraft. The standard Network Time Protocol (NTP) performed on-board clock synchronization with a ground time standard. The demonstrations of the prototype mission illustrated some of the advantages of using Internet standards and technologies for space missions, but also helped identify issues that must be addressed. These issues include applicability to embedded real-time systems on flight-qualified hardware, range of applicability of TCP, and liability for and maintenance of commercial off-the-shelf (COTS) products. The NASA Earth Science Technology Office (ESTO) funded the collaboration to build and demonstrate the prototype IP mission.

Blocking adenylyl cyclase inhibits olfactory generator currents induced by "IP(3)-odors".

PubMed

Chen, S; Lane, A P; Bock, R; Leinders-Zufall, T; Zufall, F

2000-07-01

Vertebrate olfactory receptor neurons (ORNs) transduce odor stimuli into electrical signals by means of an adenylyl cyclase/cAMP second messenger cascade, but it remains widely debated whether this cAMP cascade mediates transduction for all odorants or only certain odor classes. To address this problem, we have analyzed the generator currents induced by odors that failed to produce cAMP in previous biochemical assays but instead produced IP(3) ("IP(3)-odors"). We show that in single salamander ORNs, sensory responses to "cAMP-odors" and IP(3)-odors are not mutually exclusive but coexist in the same cells. The currents induced by IP(3)-odors exhibit identical biophysical properties as those induced by cAMP odors or direct activation of the cAMP cascade. By disrupting adenylyl cyclase to block cAMP formation using two potent antagonists of adenylyl cyclase, SQ22536 and MDL12330A, we show that this molecular step is necessary for the transduction of both odor classes. To assess whether these results are also applicable to mammals, we examine the electrophysiological responses to IP(3)-odors in intact mouse main olfactory epithelium (MOE) by recording field potentials. The results show that inhibition of adenylyl cyclase prevents EOG responses to both odor classes in mouse MOE, even when "hot spots" with heightened sensitivity to IP(3)-odors are examined.

IP over fiber technologies: ATM/POS/SDL

NASA Astrophysics Data System (ADS)

Jin, Depeng; Zeng, Lieguang

2001-10-01

The explosive growth of Internet traffic has created the need to transport IP over high-speed links such as fiber. Three main IP over fiber technologies have been developed: ATM, POS and SDL. As ATM has been widely researched and developed, this paper mainly discusses the POS and SDL. POS is a traditional mapping method of packets, and this paper presents the realization state machine of POS and analyzes the Probability of Packet Loss. SDL is a new framing protocol for variable/fixed length of packet, which extends the HEC-liking framing mechanism used in ATM. This paper analyzes this new protocol and gives the performance results such as MTTF and PFP. Finally, the comparison of POS and SDL is provided.

Serum IFN-γ-induced protein 10 (IP-10) as a biomarker for severity of acute respiratory infection in healthy adults.

PubMed

Hayney, Mary S; Henriquez, Kelsey M; Barnet, Jodi H; Ewers, Tola; Champion, Heather M; Flannery, Sean; Barrett, Bruce

2017-05-01

The inflammatory chemokine, interferon-gamma inducible protein of 10kDa (IP-10), is a biomarker associated with several conditions. This study investigated serum concentrations of IP-10 in healthy individuals who developed acute respiratory infection (ARI). The hypothesis is that serum IP-10 concentrations correlate with ARI severity and detection of viral pathogens. Data come from a randomized controlled trial measuring the effects of mindfulness meditation or exercise on ARI (Clinical Trials ID: NCT01654289). Healthy adults ages 30-69 were followed for a single season for ARI incidence and severity. This trial is ongoing, and the investigators are still blinded. When a participant reported ARI symptoms, nasal swab and lavage for PCR-based viral identification and blood samples were collected within the first 72h of ARI symptoms. Serum IP-10 concentrations were measured by ELISA (R&D Systems, Inc., Quantikine ELISA, Minneapolis, MN). ARI severity was measured using the validated Wisconsin Upper Respiratory Symptom Survey (WURSS-24) until the ARI episode resolved. Serum IP-10 concentrations from 225 ARI episodes correlated with ARI global severity (rho 0.28 [95% CI: 0.15-0.39]; p<0.001). IP-10 concentrations were higher with an ARI in which a viral pathogen was detected compared to no viral pathogen detected (median 366pg/ml [IQR: 227-486] vs 163pg/ml [IQR: 127-295], p<0.0001). Influenza infections had higher IP-10 concentrations than coronavirus, enterovirus or rhinovirus, and paramyxovirus. Serum IP-10 concentration correlates with ARI global severity. Also, IP-10 concentration measured early in the course of the ARI correlates with the daily severity, duration, and illness symptoms. Copyright © 2017 Elsevier B.V. All rights reserved.

Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain.

PubMed

Potter, Jane A; Randall, Richard E; Taylor, Garry L

2008-02-28

IPS-1/MAVS/VISA/Cardif is an adaptor protein that plays a crucial role in the induction of interferons in response to viral infection. In the initial stage of the intracellular antiviral response two RNA helicases, retinoic acid inducible gene-I (RIG-I) and melanoma differentiation-association gene 5 (MDA5), are independently able to bind viral RNA in the cytoplasm. The 62 kDa protein IPS-1/MAVS/VISA/Cardif contains an N-terminal caspase activation and recruitment (CARD) domain that associates with the CARD regions of RIG-I and MDA5, ultimately leading to the induction of type I interferons. As a first step towards understanding the molecular basis of this important adaptor protein we have undertaken structural studies of the IPS-1 MAVS/VISA/Cardif CARD region. The crystal structure of human IPS-1/MAVS/VISA/Cardif CARD has been determined to 2.1A resolution. The protein was expressed and crystallized as a maltose-binding protein (MBP) fusion protein. The MBP and IPS-1 components each form a distinct domain within the structure. IPS-1/MAVS/VISA/Cardif CARD adopts a characteristic six-helix bundle with a Greek-key topology and, in common with a number of other known CARD structures, contains two major polar surfaces on opposite sides of the molecule. One face has a surface-exposed, disordered tryptophan residue that may explain the poor solubility of untagged expression constructs. The IPS-1/MAVS/VISA/Cardif CARD domain adopts the classic CARD fold with an asymmetric surface charge distribution that is typical of CARD domains involved in homotypic protein-protein interactions. The location of the two polar areas on IPS-1/MAVS/VISA/Cardif CARD suggest possible types of associations that this domain makes with the two CARD domains of MDA5 or RIG-I. The N-terminal CARD domains of RIG-I and MDA5 share greatest sequence similarity with IPS-1/MAVS/VISA/Cardif CARD and this has allowed modelling of their structures. These models show a very different charge profile for the

Stimulation of Inositol 1,4,5-Trisphosphate (IP3) Receptor Subtypes by Adenophostin A and Its Analogues

PubMed Central

Saleem, Huma; Tovey, Stephen C.; Riley, Andrew M.; Potter, Barry V. L.; Taylor, Colin W.

2013-01-01

Inositol 1,4,5-trisphosphate receptors (IP3R) are intracellular Ca2+ channels. Most animal cells express mixtures of the three IP3R subtypes encoded by vertebrate genomes. Adenophostin A (AdA) is the most potent naturally occurring agonist of IP3R and it shares with IP3 the essential features of all IP3R agonists, namely structures equivalent to the 4,5-bisphosphate and 6-hydroxyl of IP3. The two essential phosphate groups contribute to closure of the clam-like IP3-binding core (IBC), and thereby IP3R activation, by binding to each of its sides (the α- and β-domains). Regulation of the three subtypes of IP3R by AdA and its analogues has not been examined in cells expressing defined homogenous populations of IP3R. We measured Ca2+ release evoked by synthetic adenophostin A (AdA) and its analogues in permeabilized DT40 cells devoid of native IP3R and stably expressing single subtypes of mammalian IP3R. The determinants of high-affinity binding of AdA and its analogues were indistinguishable for each IP3R subtype. The results are consistent with a cation-π interaction between the adenine of AdA and a conserved arginine within the IBC α-domain contributing to closure of the IBC. The two complementary contacts between AdA and the α-domain (cation-π interaction and 3″-phosphate) allow activation of IP3R by an analogue of AdA (3″-dephospho-AdA) that lacks a phosphate group equivalent to the essential 5-phosphate of IP3. These data provide the first structure-activity analyses of key AdA analogues using homogenous populations of all mammalian IP3R subtypes. They demonstrate that differences in the Ca2+ signals evoked by AdA analogues are unlikely to be due to selective regulation of IP3R subtypes. PMID:23469136

GnT1IP-L specifically inhibits MGAT1 in the Golgi via its luminal domain.

PubMed

Huang, Hung-Hsiang; Hassinen, Antti; Sundaram, Subha; Spiess, Andrej-Nikolai; Kellokumpu, Sakari; Stanley, Pamela

2015-09-15

Mouse GnT1IP-L, and membrane-bound GnT1IP-S (MGAT4D) expressed in cultured cells inhibit MGAT1, the N-acetylglucosaminyltransferase that initiates the synthesis of hybrid and complex N-glycans. However, it is not known where in the secretory pathway GnT1IP-L inhibits MGAT1, nor whether GnT1IP-L inhibits other N-glycan branching N-acetylglucosaminyltransferases of the medial Golgi. We show here that the luminal domain of GnT1IP-L contains its inhibitory activity. Retention of GnT1IP-L in the endoplasmic reticulum (ER) via the N-terminal region of human invariant chain p33, with or without C-terminal KDEL, markedly reduced inhibitory activity. Dynamic fluorescent resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC) assays revealed homomeric interactions for GnT1IP-L in the ER, and heteromeric interactions with MGAT1 in the Golgi. GnT1IP-L did not generate a FRET signal with MGAT2, MGAT3, MGAT4B or MGAT5 medial Golgi GlcNAc-tranferases. GnT1IP/Mgat4d transcripts are expressed predominantly in spermatocytes and spermatids in mouse, and are reduced in men with impaired spermatogenesis.

MOBE-ChIP: Probing Cell Type-Specific Binding Through Large-Scale Chromatin Immunoprecipitation.

PubMed

Wang, Shenqi; Lau, On Sun

2018-01-01

In multicellular organisms, the initiation and maintenance of specific cell types often require the activity of cell type-specific transcriptional regulators. Understanding their roles in gene regulation is crucial but probing their DNA targets in vivo, especially in a genome-wide manner, remains a technical challenge with their limited expression. To improve the sensitivity of chromatin immunoprecipitation (ChIP) for detecting the cell type-specific signals, we have developed the Maximized Objects for Better Enrichment (MOBE)-ChIP, where ChIP is performed at a substantially larger experimental scale and under low background conditions. Here, we describe the procedure in the study of transcription factors in the model plant Arabidopsis. However, with some modifications, the technique should also be implemented in other systems. Besides cell type-specific studies, MOBE-ChIP can also be used as a general strategy to improve ChIP signals.

Dynamic autonomous routing technology for IP-based satellite ad hoc networks

NASA Astrophysics Data System (ADS)

Wang, Xiaofei; Deng, Jing; Kostas, Theresa; Rajappan, Gowri

2014-06-01

IP-based routing for military LEO/MEO satellite ad hoc networks is very challenging due to network and traffic heterogeneity, network topology and traffic dynamics. In this paper, we describe a traffic priority-aware routing scheme for such networks, namely Dynamic Autonomous Routing Technology (DART) for satellite ad hoc networks. DART has a cross-layer design, and conducts routing and resource reservation concurrently for optimal performance in the fluid but predictable satellite ad hoc networks. DART ensures end-to-end data delivery with QoS assurances by only choosing routing paths that have sufficient resources, supporting different packet priority levels. In order to do so, DART incorporates several resource management and innovative routing mechanisms, which dynamically adapt to best fit the prevailing conditions. In particular, DART integrates a resource reservation mechanism to reserve network bandwidth resources; a proactive routing mechanism to set up non-overlapping spanning trees to segregate high priority traffic flows from lower priority flows so that the high priority flows do not face contention from low priority flows; a reactive routing mechanism to arbitrate resources between various traffic priorities when needed; a predictive routing mechanism to set up routes for scheduled missions and for anticipated topology changes for QoS assurance. We present simulation results showing the performance of DART. We have conducted these simulations using the Iridium constellation and trajectories as well as realistic military communications scenarios. The simulation results demonstrate DART's ability to discriminate between high-priority and low-priority traffic flows and ensure disparate QoS requirements of these traffic flows.

Inhibition by salmeterol and cilomilast of fluticasone-enhanced IP-10 release in airway epithelial cells.

PubMed

Reddy, P J; Aksoy, Mark O; Yang, Yi; Li, Xiu Xia; Ji, Rong; Kelsen, Steven G

2008-02-01

The CXC chemokines, IP-10/CXCL10 and IL-8/CXCL8, play a role in obstructive lung disease by attracting Th1/Tc1 lymphocytes and neutrophils, respectively. Inhaled corticosteroids (ICS) and long acting beta 2-agonists (LABA) are widely used. However, their effect(s) on the release of IP-10 and IL-8 by airway epithelial cells are poorly understood. This study examined the effects of fluticasone, salmeterol, and agents which raise intracellular cAMP (cilomilast and db-cAMP) on the expression of IP-10 and IL-8 protein and mRNA. Studies were performed in cultured human airway epithelial cells during cytokine-stimulated IP-10 and IL-8 release. Cytokine treatment (TNF-alpha, IL-1beta and IFN-gamma) increased IP-10 and IL-8 protein and mRNA levels. Fluticasone (0.1 nM to 1 microM) increased IP-10 but reduced IL-8 protein release without changing IP-10 mRNA levels assessed by real time RT-PCR. The combination of salmeterol (1 micro M) and cilomilast (1-10 mu M) reduced IP-10 but had no effect on IL-8 protein. Salmeterol alone (1 micro M) and db-cAMP alone (1 mM) antagonised the effects of fluticasone on IP-10 but not IL-8 protein. In human airway epithelial cells, inhibition by salmeterol of fluticasone-enhanced IP-10 release may be an important therapeutic effect of the LABA/ICS combination not present when the two drugs are used separately.

Nebula--a web-server for advanced ChIP-seq data analysis.

PubMed

Boeva, Valentina; Lermine, Alban; Barette, Camille; Guillouf, Christel; Barillot, Emmanuel

2012-10-01

ChIP-seq consists of chromatin immunoprecipitation and deep sequencing of the extracted DNA fragments. It is the technique of choice for accurate characterization of the binding sites of transcription factors and other DNA-associated proteins. We present a web service, Nebula, which allows inexperienced users to perform a complete bioinformatics analysis of ChIP-seq data. Nebula was designed for both bioinformaticians and biologists. It is based on the Galaxy open source framework. Galaxy already includes a large number of functionalities for mapping reads and peak calling. We added the following to Galaxy: (i) peak calling with FindPeaks and a module for immunoprecipitation quality control, (ii) de novo motif discovery with ChIPMunk, (iii) calculation of the density and the cumulative distribution of peak locations relative to gene transcription start sites, (iv) annotation of peaks with genomic features and (v) annotation of genes with peak information. Nebula generates the graphs and the enrichment statistics at each step of the process. During Steps 3-5, Nebula optionally repeats the analysis on a control dataset and compares these results with those from the main dataset. Nebula can also incorporate gene expression (or gene modulation) data during these steps. In summary, Nebula is an innovative web service that provides an advanced ChIP-seq analysis pipeline providing ready-to-publish results. Nebula is available at http://nebula.curie.fr/ Supplementary data are available at Bioinformatics online.

The auxiliary subunit KChIP2 is an essential regulator of homeostatic excitability.

PubMed

Wang, Hong-Gang; He, Xiao Ping; Li, Qiang; Madison, Roger D; Moore, Scott D; McNamara, James O; Pitt, Geoffrey S

2013-05-10

The necessity for, or redundancy of, distinctive KChIP proteins is not known. Deletion of KChIP2 leads to increased susceptibility to epilepsy and to a reduction in IA and increased excitability in pyramidal hippocampal neurons. KChIP2 is essential for homeostasis in hippocampal neurons. Mutations in K(A) channel auxiliary subunits may be loci for epilepsy. The somatodendritic IA (A-type) K(+) current underlies neuronal excitability, and loss of IA has been associated with the development of epilepsy. Whether any one of the four auxiliary potassium channel interacting proteins (KChIPs), KChIP1-KChIP4, in specific neuronal populations is critical for IA is not known. Here we show that KChIP2, which is abundantly expressed in hippocampal pyramidal cells, is essential for IA regulation in hippocampal neurons and that deletion of Kchip2 affects susceptibility to limbic seizures. The specific effects of Kchip2 deletion on IA recorded from isolated hippocampal pyramidal neurons were a reduction in amplitude and shift in the V½ for steady-state inactivation to hyperpolarized potentials when compared with WT neurons. Consistent with the relative loss of IA, hippocampal neurons from Kchip2(-/-) mice showed increased excitability. WT cultured neurons fired only occasional single action potentials, but the average spontaneous firing rate (spikes/s) was almost 10-fold greater in Kchip2(-/-) neurons. In slice preparations, spontaneous firing was detected in CA1 pyramidal neurons from Kchip2(-/-) mice but not from WT. Additionally, when seizures were induced by kindling, the number of stimulations required to evoke an initial class 4 or 5 seizure was decreased, and the average duration of electrographic seizures was longer in Kchip2(-/-) mice compared with WT controls. Together, these data demonstrate that the KChIP2 is essential for physiologic IA modulation and homeostatic stability and that there is a lack of functional redundancy among the different KChIPs in hippocampal

Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.

PubMed

Chabbert, Christophe D; Adjalley, Sophie H; Steinmetz, Lars M; Pelechano, Vicent

2018-01-01

Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) or microarray hybridization (ChIP-on-chip) are standard methods for the study of transcription factor binding sites and histone chemical modifications. However, these approaches only allow profiling of a single factor or protein modification at a time.In this chapter, we present Bar-ChIP, a higher throughput version of ChIP-Seq that relies on the direct ligation of molecular barcodes to chromatin fragments. Bar-ChIP enables the concurrent profiling of multiple DNA-protein interactions and is therefore amenable to experimental scale-up, without the need for any robotic instrumentation.

cChIP-seq: a robust small-scale method for investigation of histone modifications.

PubMed

Valensisi, Cristina; Liao, Jo Ling; Andrus, Colin; Battle, Stephanie L; Hawkins, R David

2015-12-21

ChIP-seq is highly utilized for mapping histone modifications that are informative about gene regulation and genome annotations. For example, applying ChIP-seq to histone modifications such as H3K4me1 has facilitated generating epigenomic maps of putative enhancers. This powerful technology, however, is limited in its application by the large number of cells required. ChIP-seq involves extensive manipulation of sample material and multiple reactions with limited quality control at each step, therefore, scaling down the number of cells required has proven challenging. Recently, several methods have been proposed to overcome this limit but most of these methods require extensive optimization to tailor the protocol to the specific antibody used or number of cells being profiled. Here we describe a robust, yet facile method, which we named carrier ChIP-seq (cChIP-seq), for use on limited cell amounts. cChIP-seq employs a DNA-free histone carrier in order to maintain the working ChIP reaction scale, removing the need to tailor reactions to specific amounts of cells or histone modifications to be assayed. We have applied our method to three different histone modifications, H3K4me3, H3K4me1 and H3K27me3 in the K562 cell line, and H3K4me1 in H1 hESCs. We successfully obtained epigenomic maps for these histone modifications starting with as few as 10,000 cells. We compared cChIP-seq data to data generated as part of the ENCODE project. ENCODE data are the reference standard in the field and have been generated starting from tens of million of cells. Our results show that cChIP-seq successfully recapitulates bulk data. Furthermore, we showed that the differences observed between small-scale ChIP-seq data and ENCODE data are largely to be due to lab-to-lab variability rather than operating on a reduced scale. Data generated using cChIP-seq are equivalent to reference epigenomic maps from three orders of magnitude more cells. Our method offers a robust and straightforward

An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example.

PubMed

Cheng, Chia-Yang; Chu, Chia-Han; Hsu, Hung-Wei; Hsu, Fang-Rong; Tang, Chung Yi; Wang, Wen-Ching; Kung, Hsing-Jien; Chang, Pei-Ching

2014-01-01

Post-translational modification (PTM) of transcriptional factors and chromatin remodelling proteins is recognized as a major mechanism by which transcriptional regulation occurs. Chromatin immunoprecipitation (ChIP) in combination with high-throughput sequencing (ChIP-seq) is being applied as a gold standard when studying the genome-wide binding sites of transcription factor (TFs). This has greatly improved our understanding of protein-DNA interactions on a genomic-wide scale. However, current ChIP-seq peak calling tools are not sufficiently sensitive and are unable to simultaneously identify post-translational modified TFs based on ChIP-seq analysis; this is largely due to the wide-spread presence of multiple modified TFs. Using SUMO-1 modification as an example; we describe here an improved approach that allows the simultaneous identification of the particular genomic binding regions of all TFs with SUMO-1 modification. Traditional peak calling methods are inadequate when identifying multiple TF binding sites that involve long genomic regions and therefore we designed a ChIP-seq processing pipeline for the detection of peaks via a combinatorial fusion method. Then, we annotate the peaks with known transcription factor binding sites (TFBS) using the Transfac Matrix Database (v7.0), which predicts potential SUMOylated TFs. Next, the peak calling result was further analyzed based on the promoter proximity, TFBS annotation, a literature review, and was validated by ChIP-real-time quantitative PCR (qPCR) and ChIP-reChIP real-time qPCR. The results show clearly that SUMOylated TFs are able to be pinpointed using our pipeline. A methodology is presented that analyzes SUMO-1 ChIP-seq patterns and predicts related TFs. Our analysis uses three peak calling tools. The fusion of these different tools increases the precision of the peak calling results. TFBS annotation method is able to predict potential SUMOylated TFs. Here, we offer a new approach that enhances ChIP

78 FR 36725 - Numbering Policies for Modern Communications; IP-Enabled Services; Telephone Number Requirements...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-19

... sections 251 and 252 of the Act. 4. In order to provide interconnected VoIP service, a provider must offer... interconnected VoIP customer using his PSTN service. Interconnected VoIP providers often cannot obtain telephone... offerings. This will in turn spur consumer demand for these services, thereby increasing demand for...

The UCSD Time-dependent Tomography and IPS use for Exploring Space Weather Events

NASA Astrophysics Data System (ADS)

Yu, H. S.; Jackson, B. V.; Buffington, A.; Hick, P. P.; Tokumaru, M.; Odstrcil, D.; Kim, J.; Yun, J.

2016-12-01

The University of California, San Diego (UCSD) time-dependent, iterative, kinematic reconstruction technique has been used and expanded upon for over two decades. It provides some of the most-accurate predictions and three-dimensional (3D) analyses of heliospheric solar-wind parameters now available using interplanetary scintillation (IPS) data. The parameters provided include reconstructions of velocity, density, and three-component magnetic fields. Precise time-dependent results are now obtained at any solar distance in the inner heliosphere using ISEE (formerly STELab), Japan, IPS data sets, and can be used to drive 3D-MHD models including ENLIL. Using IPS data, these reconstructions provide a real-time prediction of the global solar wind parameters across the whole heliosphere with a time cadence of about one day (see http://ips.ucsd.edu). Here we compare the results (such as density, velocity, and magnetic fields) from the IPS tomography with different in-situ measurements and discuss several specific space weather events that demonstrate the issues resulting from these analyses.

IP-10 protects while MIP-2 promotes experimental anesthetic hapten - induced hepatitis

PubMed Central

Njoku, Dolores B.; Li, Zhaoxia; Mellerson, Jenelle L; Sharma, Rajni; Talor, Monica V.; Barat, Nicole; Rose, Noel R.

2009-01-01

MIP-2 and IFN-γ inducible protein-10 (IP-10) and their respective receptors, CXCR2 and CXCR3, modulate tissue inflammation by recruiting neutrophils or T cells from the spleen or bone marrow. Yet, how these chemokines modulate diseases such as immune-mediated drug-induced liver injury (DILI) is essentially unknown. To investigate how chemokines modulate experimental DILI in our model we used susceptible BALB/c (WT) and IL-4−/− (KO) mice that develop significantly reduced hepatitis and splenic T cell priming to anesthetic haptens and self proteins following TFA-S100 immunizations. We detected CXCR2+ splenic granulocytes in all mice two weeks following immunizations; by 3 weeks, MIP-2 levels (p<0.001) and GR1+ cells were elevated in WT livers, suggesting MIP-2-recruited granulocytes. Elevated splenic CXCR3+ CD4+T cells were identified after 2 weeks in KO mice indicating elevated IP-10 levels which were confirmed during T cell priming. This result suggested that IP-10 reduced T cell priming to critical DILI antigens. Increased T cell proliferation following co-culture of TFA-S100-primed WT splenocytes with anti-IP-10 (p<0.05) confirmed that IP-10 reduced T cell priming to CYP2E1 and TFA. We propose that MIP-2 promotes and IP-10 protects against the development of hepatitis and T cell priming in this murine model. PMID:19131211

TRAF3IP2 Mediates Aldosterone/Salt-Induced Cardiac Hypertrophy and Fibrosis

PubMed Central

Sakamuri, Siva S.V.P; Valente, Anthony J.; Siddesha, Jalahalli M.; Delafontaine, Patrice; Siebenlist, Ulrich; Gardner, Jason D.; Chandrasekar, Bysani

2016-01-01

Aberrant activation of the renin-angiotensin-aldosterone system (RAAS) contributes to adverse cardiac remodeling and eventual failure. Here we investigated whether TRAF3-interacting Protein 2 (TRAF3IP2), a redox-sensitive cytoplasmic adaptor molecule and an upstream regulator of nuclear factor-κB (NF-κB) and activator protein-1 (AP-1), mediates aldosterone-induced cardiac hypertrophy and fibrosis. Wild type (WT) and TRAF3IP2-null mice were infused with aldosterone (0.2mg/kg/day) for 4 weeks along with 1%NaCl in drinking water. Aldosterone/salt, but not salt alone, upregulated TRAF3IP2 expression in WT mouse hearts. Aldosterone elevated blood pressure to a similar extent in both WT and TRAF3IP2-null groups. Importantly, TRAF3IP2 gene deletion attenuated aldosterone/salt-induced (i) p65 and c-Jun activation, (ii) extracellular matrix (collagen Iα1 and collagen 3α1), matrix metalloproteinase (MMP2), lysyl oxidase (LOX), inflammatory cytokine (IL-6 and IL-18), chemokine (CXCL1 and CXCL2), and adhesion molecule (ICAM1) gene expression in hearts, (iii) IL-6, IL-18, and MMP2 protein levels, (iv) systemic IL-6 and IL-18 levels, and (iv) cardiac hypertrophy and fibrosis. These results indicate that TRAF3IP2 is a critical signaling intermediate in aldosterone/salt-induced myocardial hypertrophy and fibrosis, and thus a potential therapeutic target in hypertensive heart disease. PMID:27040306

How To: Be VoIP-Savvy

ERIC Educational Resources Information Center

Branzburg, Jeffrey

2005-01-01

Cablevision, Comcast, Verizon, and many other high-speed broadband Internet providers are now also offering telephone services through "Voice over Internet Protocol" (VoIP). This technology sends ordinary telephone calls over the Internet rather than over telephone lines. While impractical without the use of a broadband Internet connection, with…

ß-Phellandrene: Kairomone for Pine Engraver, Ips pini (Say) (Coleoptera: Scolytidae)

Treesearch

Daniel R. Miller; John H. Borden

1990-01-01

The responses of Ips pini (Scolytidae) to multiple-funnel traps baited with the pheromone, ipsdienol, and various monoterpenes were determined in stands of lodgepole pine in southern and central British Columbia. Ips pini was attracted to both ipsdienol and ß-phellandrene, demonstrating that ß-phellandrene is a kairomone for this...

[DAB2IP expression in bladder transitional cell carcinoma and its correlation with clinical outcome].

PubMed

Zhu, Jian-Ning; Wu, Kai-Jie; Guan, Zhen-Feng; Liu, Li-Xia; Ning, Zhong-Yun; Zhou, Jian-Cheng; Wang, Xin-Yang; Fan, Jin-Hai

2014-07-01

To investigate the expression of DAB2IP in bladder transitional cell carcinoma (BTCC) and its correlation with clinical characteristics and prognosis of BTCC patients. Immunohistochemical staining was applied to detect DAB2IP protein level in 79 cases of TCCB tissues and 11 cases of normal bladder tissues, and the relationships of the staining results with pathological grade, stage, lymph node metastasis, gender, age and the 3-year survival rate of the patients were analyzed. The expression of DAB2IP in BTCC tissues was significantly lower than that in normal bladder epithelium, and the expression score and rate of DAB2IP in the high-grade, invasive and metastatic BTCC were significantly lower than those in low-grade, superficial and non-metastatic BTCC (P < 0.05). The 3-year survival rate of the patients with high DAB2IP expression was significantly higher than that of the patients with low DAB2IP expression. DAB2IP may be one of the important inhibitory factors during the occurrence and progression of BTCC.

Regulation of myeloid leukemia factor-1 interacting protein (MLF1IP) expression in glioblastoma.

PubMed

Hanissian, Silva H; Teng, Bin; Akbar, Umar; Janjetovic, Zorica; Zhou, Qihong; Duntsch, Christopher; Robertson, Jon H

2005-06-14

The myelodysplasia/myeloid leukemia factor 1-interacting protein MLF1IP is a novel gene which encodes for a putative transcriptional repressor. It is localized to human chromosome 4q35.1 and is expressed in both the nuclei and cytoplasm of cells. Northern and Western blot analyses have revealed MLF1IP to be present at very low amounts in normal brain tissues, whereas a number of human and rat glioblastoma (GBM) cell lines demonstrated a high level expression of the MLF1IP protein. Immunohistochemical analysis of rat F98 and C6 GBM tumor models showed that MLF1IP was highly expressed in the tumor core where it was co-localized with MLF1 and nestin. Moreover, MLF1IP expression was elevated in the contralateral brain where no tumor cells were detected. These observations, together with previous data demonstrating a role for MLF1IP in erythroleukemias, suggest a possible function for this protein in glioma pathogenesis and potentially in other types of malignancies.

Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus.

PubMed

Hansen, Peter; Hecht, Jochen; Ibn-Salem, Jonas; Menkuec, Benjamin S; Roskosch, Sebastian; Truss, Matthias; Robinson, Peter N

2016-11-04

ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data. Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal of PCR duplicates and for quality control. Furthermore, we developed bespoke methods to estimate the width of the protected region resulting from protein-DNA binding and to infer binding positions from ChIP-nexus data. Finally, we applied our peak calling method as well as the two other methods MACE and MACS2 to the available ChIP-nexus data. The Q-nexus software is efficient and easy to use. Novel statistics about duplication rates in consideration of random barcodes are calculated. Our method for the estimation of the width of the protected region yields unbiased signatures that are highly reproducible for biological replicates and at the same time very specific for the respective factors analyzed. As judged by the irreproducible discovery rate (IDR), our peak calling algorithm shows a substantially better reproducibility. An implementation of Q-nexus is available at http://charite.github.io/Q/ .

Business innovation symposium ‘At what price? IP-related thoughts on new business models for space information’

NASA Astrophysics Data System (ADS)

Smith, Lesley Jane

2011-09-01

Spatial data and imagery generators are set to become tomorrow's key players in the information society. This is why satellite owners and operators are examining new revenue-producing models for developing space-related products and services. The use and availability of broadband internet width and satellite data-based services will continue to increase in the future. With the capacity to deliver real time precision downstream data, space agencies and the satellite industry can respond to the demand for high resolution digital space information which, with the appropriate technology, can be integrated into a variety of web-based applications. At a time when the traditional roles of space agencies are becoming more hybrid, largely as a result of the greater drive towards commercial markets, new value-added markets for space-related information products are continuing to attract attention. This paper discusses whether traditional data policies on space data access and IP licensing schemes stand to remain the feasible prototype for distributing and marketing space data, and how this growth market might benefit from looking at an 'up and running' global IP management system already operating to manage end user digital demand. PrefaceThe terminology describing the various types of spatial data and space-based information is not uniformly used within the various principles, laws and policies that govern space data. For convenience only this paper refers to primary or raw data gathered by the space-based industry as spatial or raw data, and the data as processed and sold on or distributed by ground-based companies as space information products and services. In practise, spatial data range from generic to specific data sets, digital topography, through to pictures and imagery services at various resolutions, with 3-D perspectives underway. The paper addresses general IP considerations relating to spatial data, with some reference to remote sensing itself. Exact IP details

Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis.

PubMed

Cormier, Nathan; Kolisnik, Tyler; Bieda, Mark

2016-07-05

There has been an enormous expansion of use of chromatin immunoprecipitation followed by sequencing (ChIP-seq) technologies. Analysis of large-scale ChIP-seq datasets involves a complex series of steps and production of several specialized graphical outputs. A number of systems have emphasized custom development of ChIP-seq pipelines. These systems are primarily based on custom programming of a single, complex pipeline or supply libraries of modules and do not produce the full range of outputs commonly produced for ChIP-seq datasets. It is desirable to have more comprehensive pipelines, in particular ones addressing common metadata tasks, such as pathway analysis, and pipelines producing standard complex graphical outputs. It is advantageous if these are highly modular systems, available as both turnkey pipelines and individual modules, that are easily comprehensible, modifiable and extensible to allow rapid alteration in response to new analysis developments in this growing area. Furthermore, it is advantageous if these pipelines allow data provenance tracking. We present a set of 20 ChIP-seq analysis software modules implemented in the Kepler workflow system; most (18/20) were also implemented as standalone, fully functional R scripts. The set consists of four full turnkey pipelines and 16 component modules. The turnkey pipelines in Kepler allow data provenance tracking. Implementation emphasized use of common R packages and widely-used external tools (e.g., MACS for peak finding), along with custom programming. This software presents comprehensive solutions and easily repurposed code blocks for ChIP-seq analysis and pipeline creation. Tasks include mapping raw reads, peakfinding via MACS, summary statistics, peak location statistics, summary plots centered on the transcription start site (TSS), gene ontology, pathway analysis, and de novo motif finding, among others. These pipelines range from those performing a single task to those performing full analyses of

KChIP2 genotype dependence of transient outward current (Ito) properties in cardiomyocytes isolated from male and female mice

PubMed Central

Waldschmidt, Lara; Junkereit, Vera; Bähring, Robert

2017-01-01

The transient outward current (Ito) in cardiomyocytes is largely mediated by Kv4 channels associated with Kv Channel Interacting Protein 2 (KChIP2). A knockout model has documented the critical role of KChIP2 in Ito expression. The present study was conducted to characterize in both sexes the dependence of Ito properties, including current magnitude, inactivation kinetics, recovery from inactivation and voltage dependence of inactivation, on the number of functional KChIP2 alleles. For this purpose we performed whole-cell patch-clamp experiments on isolated left ventricular cardiomyocytes from male and female mice which had different KChIP2 genotypes; i.e., wild-type (KChIP2+/+), heterozygous knockout (KChIP2+/-) or complete knockout of KChIP2 (KChIP2-/-). We found in both sexes a KChIP2 gene dosage effect (i.e., a proportionality between number of alleles and phenotype) on Ito magnitude, however, concerning other Ito properties, KChIP2+/- resembled KChIP2+/+. Only in the total absence of KChIP2 (KChIP2-/-) we observed a slowing of Ito kinetics, a slowing of recovery from inactivation and a negative shift of a portion of the voltage dependence of inactivation. In a minor fraction of KChIP2-/- myocytes Ito was completely lost. The distinct KChIP2 genotype dependences of Ito magnitude and inactivation kinetics, respectively, seen in cardiomyocytes were reproduced with two-electrode voltage-clamp experiments on Xenopus oocytes expressing Kv4.2 and different amounts of KChIP2. Our results corroborate the critical role of KChIP2 in controlling Ito properties. They demonstrate that the Kv4.2/KChIP2 interaction in cardiomyocytes is highly dynamic, with a clear KChIP2 gene dosage effect on Kv4 channel surface expression but not on inactivation gating. PMID:28141821

KChIP2 genotype dependence of transient outward current (Ito) properties in cardiomyocytes isolated from male and female mice.

PubMed

Waldschmidt, Lara; Junkereit, Vera; Bähring, Robert

2017-01-01

The transient outward current (Ito) in cardiomyocytes is largely mediated by Kv4 channels associated with Kv Channel Interacting Protein 2 (KChIP2). A knockout model has documented the critical role of KChIP2 in Ito expression. The present study was conducted to characterize in both sexes the dependence of Ito properties, including current magnitude, inactivation kinetics, recovery from inactivation and voltage dependence of inactivation, on the number of functional KChIP2 alleles. For this purpose we performed whole-cell patch-clamp experiments on isolated left ventricular cardiomyocytes from male and female mice which had different KChIP2 genotypes; i.e., wild-type (KChIP2+/+), heterozygous knockout (KChIP2+/-) or complete knockout of KChIP2 (KChIP2-/-). We found in both sexes a KChIP2 gene dosage effect (i.e., a proportionality between number of alleles and phenotype) on Ito magnitude, however, concerning other Ito properties, KChIP2+/- resembled KChIP2+/+. Only in the total absence of KChIP2 (KChIP2-/-) we observed a slowing of Ito kinetics, a slowing of recovery from inactivation and a negative shift of a portion of the voltage dependence of inactivation. In a minor fraction of KChIP2-/- myocytes Ito was completely lost. The distinct KChIP2 genotype dependences of Ito magnitude and inactivation kinetics, respectively, seen in cardiomyocytes were reproduced with two-electrode voltage-clamp experiments on Xenopus oocytes expressing Kv4.2 and different amounts of KChIP2. Our results corroborate the critical role of KChIP2 in controlling Ito properties. They demonstrate that the Kv4.2/KChIP2 interaction in cardiomyocytes is highly dynamic, with a clear KChIP2 gene dosage effect on Kv4 channel surface expression but not on inactivation gating.

Analysis of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Tiling Microarray (ChIP-on-chip).

PubMed

Gao, Hui; Zhao, Chunyan

2018-01-01

Chromatin immunoprecipitation (ChIP) has become the most effective and widely used tool to study the interactions between specific proteins or modified forms of proteins and a genomic DNA region. Combined with genome-wide profiling technologies, such as microarray hybridization (ChIP-on-chip) or massively parallel sequencing (ChIP-seq), ChIP could provide a genome-wide mapping of in vivo protein-DNA interactions in various organisms. Here, we describe a protocol of ChIP-on-chip that uses tiling microarray to obtain a genome-wide profiling of ChIPed DNA.

Influence of Security Mechanisms on the Quality of Service of VoIP

NASA Astrophysics Data System (ADS)

Backs, Peter; Pohlmann, Norbert

While Voice over IP (VoIP) is advancing rapidly in the telecommunications market, the interest to protect the data transmitted by this new service is also rising. However, in contrast to other internet services such as email or HTTP, VoIP is real-time media, and therefore must meet a special requirement referred to as Quality-of-Service to provide a comfortable flow of speech. Speech quality is worsened when transmitted over the network due to delays in transmission or loss of packets. Often, voice quality is at a level that even prevents comprehensive dialog. Therefore, an administrator who is to setup a VoIP infrastructure might consider avoiding additional decreases in voice quality resulting from security mechanisms, and might leave internet telephony unprotected as a result. The inspiration for this paper is to illustrate that security mechanisms have negligible impact on speech quality and should in fact be encouraged.

CANOPEN Controller IP Core

NASA Astrophysics Data System (ADS)

Caramia, Maurizio; Montagna, Mario; Furano, Gianluca; Winton, Alistair

2010-08-01

This paper will describe the activities performed by Thales Alenia Space Italia supported by the European Space Agency in the definition of a CAN bus interface to be used on Exomars. The final goal of this activity is the development of an IP core, to be used in a slave node, able to manage both the CAN bus Data Link and Application Layer totally in hardware. The activity has been focused on the needs of the EXOMARS mission where devices with different computational performances are all managed by the onboard computer through the CAN bus.

TRAF3IP2 mediates aldosterone/salt-induced cardiac hypertrophy and fibrosis.

PubMed

Sakamuri, Siva S V P; Valente, Anthony J; Siddesha, Jalahalli M; Delafontaine, Patrice; Siebenlist, Ulrich; Gardner, Jason D; Bysani, Chandrasekar

2016-07-05

Aberrant activation of the renin-angiotensin-aldosterone system (RAAS) contributes to adverse cardiac remodeling and eventual failure. Here we investigated whether TRAF3 Interacting Protein 2 (TRAF3IP2), a redox-sensitive cytoplasmic adaptor molecule and an upstream regulator of nuclear factor-κB (NF-κB) and activator protein-1 (AP-1), mediates aldosterone-induced cardiac hypertrophy and fibrosis. Wild type (WT) and TRAF3IP2-null mice were infused with aldosterone (0.2 mg/kg/day) for 4 weeks along with 1%NaCl in drinking water. Aldosterone/salt, but not salt alone, upregulated TRAF3IP2 expression in WT mouse hearts. Further, aldosterone elevated blood pressure to a similar extent in both WT and TRAF3IP2-null groups. However, TRAF3IP2 gene deletion attenuated aldosterone/salt-induced (i) p65 and c-Jun activation, (ii) extracellular matrix (collagen Iα1 and collagen IIIα1), matrix metalloproteinase (MMP2), lysyl oxidase (LOX), inflammatory cytokine (IL-6 and IL-18), chemokine (CXCL1 and CXCL2), and adhesion molecule (ICAM1) mRNA expression in hearts, (iii) IL-6, IL-18, and MMP2 protein levels, (iv) systemic IL-6 and IL-18 levels, and (iv) cardiac hypertrophy and fibrosis. These results indicate that TRAF3IP2 is a critical signaling intermediate in aldosterone/salt-induced myocardial hypertrophy and fibrosis, and thus a potential therapeutic target in hypertensive heart disease. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Semiochemical -Based Communication in interspecific interactions between IPS PINI and Pityogenes Knecteli (Swaine) (Coleoptera: Scolytidae) in Lodgepole Pine

Treesearch

Therese M. Poland; John H. Borden

1994-01-01

The pine engraver, Ips pini Say, and Pityogenes knechteli Swaine often co-exist in lodgepole pine, Pinus contorta var. latifolia Engelmann. We tested the hypotheses that P. knechteli produces an attractive pheromone and that the attraction of P. knechteli...

The directed differentiation of human iPS cells into kidney podocytes.

PubMed

Song, Bi; Smink, Alexandra M; Jones, Christina V; Callaghan, Judy M; Firth, Stephen D; Bernard, Claude A; Laslett, Andrew L; Kerr, Peter G; Ricardo, Sharon D

2012-01-01

The loss of glomerular podocytes is a key event in the progression of chronic kidney disease resulting in proteinuria and declining function. Podocytes are slow cycling cells that are considered terminally differentiated. Here we provide the first report of the directed differentiation of induced pluripotent stem (iPS) cells to generate kidney cells with podocyte features. The iPS-derived podocytes share a morphological phenotype analogous with cultured human podocytes. Following 10 days of directed differentiation, iPS podocytes had an up-regulated expression of mRNA and protein localization for podocyte markers including synaptopodin, nephrin and Wilm's tumour protein (WT1), combined with a down-regulation of the stem cell marker OCT3/4. In contrast to human podocytes that become quiescent in culture, iPS-derived cells maintain a proliferative capacity suggestive of a more immature phenotype. The transduction of iPS podocytes with fluorescent labeled-talin that were immunostained with podocin showed a cytoplasmic contractile response to angiotensin II (AII). A permeability assay provided functional evidence of albumin uptake in the cytoplasm of iPS podocytes comparable to human podocytes. Moreover, labeled iPS-derived podocytes were found to integrate into reaggregated metanephric kidney explants where they incorporated into developing glomeruli and co-expressed WT1. This study establishes the differentiation of iPS cells to kidney podocytes that will be useful for screening new treatments, understanding podocyte pathogenesis, and offering possibilities for regenerative medicine.

Resveratrol-induced autophagy is dependent on IP3Rs and on cytosolic Ca2.

PubMed

Luyten, Tomas; Welkenhuyzen, Kirsten; Roest, Gemma; Kania, Elzbieta; Wang, Liwei; Bittremieux, Mart; Yule, David I; Parys, Jan B; Bultynck, Geert

2017-06-01

Previous work revealed that intracellular Ca 2+ signals and the inositol 1,4,5-trisphosphate (IP 3 ) receptors (IP 3 R) are essential to increase autophagic flux in response to mTOR inhibition, induced by either nutrient starvation or rapamycin treatment. Here, we investigated whether autophagy induced by resveratrol, a polyphenolic phytochemical reported to trigger autophagy in a non-canonical way, also requires IP 3 Rs and Ca 2+ signaling. Resveratrol augmented autophagic flux in a time-dependent manner in HeLa cells. Importantly, autophagy induced by resveratrol (80μM, 2h) was completely abolished in the presence of 10μM BAPTA-AM, an intracellular Ca 2+ -chelating agent. To elucidate the IP 3 R's role in this process, we employed the recently established HEK 3KO cells lacking all three IP 3 R isoforms. In contrast to the HEK293 wt cells and to HEK 3KO cells re-expressing IP 3 R1, autophagic responses in HEK 3KO cells exposed to resveratrol were severely impaired. These altered autophagic responses could not be attributed to alterations in the mTOR/p70S6K pathway, since resveratrol-induced inhibition of S6 phosphorylation was not abrogated by chelating cytosolic Ca 2+ or by knocking out IP 3 Rs. Finally, we investigated whether resveratrol by itself induced Ca 2+ release. In permeabilized HeLa cells, resveratrol neither affected the sarco- and endoplasmic reticulum Ca 2+ ATPase (SERCA) activity nor the IP 3 -induced Ca 2+ release nor the basal Ca 2+ leak from the ER. Also, prolonged (4 h) treatment with 100μM resveratrol did not affect subsequent IP 3 -induced Ca 2+ release. However, in intact HeLa cells, although resveratrol did not elicit cytosolic Ca 2+ signals by itself, it acutely decreased the ER Ca 2+ -store content irrespective of the presence or absence of IP 3 Rs, leading to a dampened agonist-induced Ca 2+ signaling. In conclusion, these results reveal that IP 3 Rs and cytosolic Ca 2+ signaling are fundamentally important for driving autophagic flux

Improved i.p. drug delivery with bioadhesive nanoparticles

PubMed Central

Deng, Yang; Yang, Fan; Cocco, Emiliano; Song, Eric; Zhang, Junwei; Cui, Jiajia; Mohideen, Muneeb; Bellone, Stefania; Santin, Alessandro D.; Saltzman, W. Mark

2016-01-01

The i.p. administration of chemotherapy in ovarian and uterine serous carcinoma patients by biodegradable nanoparticles may represent a highly effective way to suppress peritoneal carcinomatosis. However, the efficacy of nanoparticles loaded with chemotherapeutic agents is currently hampered by their fast clearance by lymphatic drainage. Here, we show that a unique formulation of bioadhesive nanoparticles (BNPs) can interact with mesothelial cells in the abdominal cavity and significantly extend the retention of the nanoparticles in the peritoneal space. BNPs loaded with a potent chemotherapeutic agent [epothilone B (EB)] showed significantly lower systemic toxicity and higher therapeutic efficacy against i.p. chemotherapy-resistant uterine serous carcinoma-derived xenografts compared with free EB and non-BNPs loaded with EB. PMID:27663731

Interferon gamma-inducible protein-10 (IP-10) and eotaxin as biomarkers in age-related macular degeneration.

PubMed

Mo, Fong Ming; Proia, Alan D; Johnson, Walter H; Cyr, Desiree; Lashkari, Kameran

2010-08-01

To analyze serum cytokine levels in subjects with different stages of AMD and to study the expression of salient cytokines in postmortem eyes with AMD. A suspension array system was used to analyze sera (n = 18 to 20/group) from control subjects and those with early AMD (AREDS stage 1), intermediate dry AMD (AREDS stage 3), advanced AMD with geographic atrophy (GA), or neovascular AMD (CNV). Postmortem eyes with AMD or control eyes were examined immunohistochemically for expression of IP-10 and eotaxin (n = 4 to 8/group). Serum eotaxin and IP-10 levels were significantly elevated in all stages of AMD, except for eotaxin levels in neovascular AMD (P < 0.07). The peak of serum IP-10 concentration was at intermediate dry AMD. In donor eyes, IP-10 and eotaxin expressions were increased in the RPE of eyes with early AMD, GA, and CNV. Eotaxin accumulated within the layer of basal linear/laminar deposits in all stages of AMD, while IP-10 was mainly in eyes with GA and CNV. IP-10 was abundant in the connective tissue matrix associated with CNV, and eotaxin was usually present but more focally and with less intense staining. Both IP-10 and eotaxin were expressed by neovascular endothelial cells. Both IP-10 and eotaxin were expressed in the neurosensory retina, but there was no detectable difference in staining between eyes with or without AMD. IP-10 and eotaxin may be early biomarkers in AMD. The authors hypothesize that the relative balance between levels of IP-10 and eotaxin is critical in regulating the neovascular response.

The Spacelab IPS Star Simulator

NASA Astrophysics Data System (ADS)

Wessling, Francis C., III

The cost of doing business in space is very high. If errors occur while in orbit the costs grow and desired scientific data may be corrupted or even lost. The Spacelab Instrument Pointing System (IPS) Star Simulator is a unique test bed that allows star trackers to interface with simulated stars in a laboratory before going into orbit. This hardware-in-the loop testing of equipment on earth increases the probability of success while in space. The IPS Star Simulator provides three fields of view 2.55 x 2.55 degrees each for input into star trackers. The fields of view are produced on three separate monitors. Each monitor has 4096 x 4096 addressable points and can display 50 stars (pixels) maximum at a given time. The pixel refresh rate is 1000 Hz. The spectral output is approximately 550 nm. The available relative visual magnitude range is 2 to 8 visual magnitudes. The star size is less than 100 arc seconds. The minimum star movement is less than 5 arc seconds and the relative position accuracy is approximately 40 arc seconds. The purpose of this paper is to describe the LPS Star Simulator design and to provide an operational scenario so others may gain from the approach and possible use of the system.

Dental anomalies in 14 patients with IP: clinical and radiological analysis and review.

PubMed

Santa-Maria, Fernanda D; Mariath, Luiza Monteavaro; Poziomczyk, Cláudia S; Maahs, Marcia A P; Rosa, Rafael F M; Zen, Paulo R G; Schüller-Faccini, Lavínia; Kiszewski, Ana Elisa

2017-06-01

Current knowledge on dental anomalies in patients with incontinentia pigmenti (IP) has been obtained by examining case reports; however, an overall characterization of such alterations remains lacking. The objective of this study was to determine the frequency, type and location of dental alterations in IP using a case series. Fourteen patients (9 children and 5 adults) with a clinical diagnosis of IP who presented dental anomalies were included in this study. All patients were administered a clinical questionnaire, dental examination and radiological investigation. In the present case series, agenesis of primary dentition was present in 60 % of patients and agenesis of permanent tooth was present in 92.8 % of patients. Most cases were missing at least 6 teeth. Second molar agenesis was present in 13 patients (92.8 %). Anomalies in dental crowns occurred in 71.4 % of cases, and the central incisor was most frequently affected. Two adult patients still had primary teeth. Malocclusion was found in 10 patients (71.4 %). High-arched palate was observed in 7 (50 %) patients. Patients with IP present alterations in both primary and permanent dentition. Because the agenesis of permanent teeth is more common, primary teeth are not always replaced. In addition, the durability of primary dentition appears to be greater in IP. This study shows that patients with IP experience significant loss of teeth, especially in permanent dentition, and have an increased risk of high-arched palate compared to the general population. Prophylactic care of primary teeth in IP is relevant for improving functional and aesthetic outcomes until dental prostheses are implanted.

[Clinical application of IPS-empress 2 pressable all-ceramic crowns].

PubMed

Wang, Ai-jun; He, Xiao-ming; Liu, Li-xia; Zhang, Chao-biao; Zhang, Min; Shen, Bei-yong

2007-02-01

To evaluate the clinical prosthetic effect of IPS-Empress 2 pressahie ceramic crowns. 198 teeth of 70 patients were restored with IPS-Empress 2 pressahie ceramic crowns. The patients were asked to return in one week and every half year. The clinical prosthetic effect was evaluated. Through follow-up of 3-38 months, the veneer porcelain crowns of 3 teeth were broken. 2 crowns fall off due to teeth fracture, gingivitis occurred in 2 teeth, pulpitis or periapical periodontitis occurred in 3 teeth. The shades of 3 crowns were darkening. The prosthetic effect of 185 teeth was satisfied. The rate of satisfaction was 93.4%. IPS-Empress 2 pressable all-ceramic crown has the advantages of aesthetic effect, good hiocompatihility and simple fabrication. But its strength is not enough for posterior teeth and it can not cover the deep color of non-vital teeth and metal materials.

DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP.

PubMed

Mitra, Sneha; Biswas, Anushua; Narlikar, Leelavati

2018-04-01

Genome-wide in vivo protein-DNA interactions are routinely mapped using high-throughput chromatin immunoprecipitation (ChIP). ChIP-reported regions are typically investigated for enriched sequence-motifs, which are likely to model the DNA-binding specificity of the profiled protein and/or of co-occurring proteins. However, simple enrichment analyses can miss insights into the binding-activity of the protein. Note that ChIP reports regions making direct contact with the protein as well as those binding through intermediaries. For example, consider a ChIP experiment targeting protein X, which binds DNA at its cognate sites, but simultaneously interacts with four other proteins. Each of these proteins also binds to its own specific cognate sites along distant parts of the genome, a scenario consistent with the current view of transcriptional hubs and chromatin loops. Since ChIP will pull down all X-associated regions, the final reported data will be a union of five distinct sets of regions, each containing binding sites of one of the five proteins, respectively. Characterizing all five different motifs and the corresponding sets is important to interpret the ChIP experiment and ultimately, the role of X in regulation. We present diversity which attempts exactly this: it partitions the data so that each partition can be characterized with its own de novo motif. Diversity uses a Bayesian approach to identify the optimal number of motifs and the associated partitions, which together explain the entire dataset. This is in contrast to standard motif finders, which report motifs individually enriched in the data, but do not necessarily explain all reported regions. We show that the different motifs and associated regions identified by diversity give insights into the various complexes that may be forming along the chromatin, something that has so far not been attempted from ChIP data. Webserver at http://diversity.ncl.res.in/; standalone (Mac OS X/Linux) from https

DNA damage response curtails detrimental replication stress and chromosomal instability induced by the dietary carcinogen PhIP

PubMed Central

Mimmler, Maximilian; Peter, Simon; Kraus, Alexander; Stroh, Svenja; Nikolova, Teodora; Seiwert, Nina; Hasselwander, Solveig; Neitzel, Carina; Haub, Jessica; Monien, Bernhard H.; Nicken, Petra; Steinberg, Pablo; Shay, Jerry W.; Kaina, Bernd; Fahrer, Jörg

2016-01-01

PhIP is an abundant heterocyclic aromatic amine (HCA) and important dietary carcinogen. Following metabolic activation, PhIP causes bulky DNA lesions at the C8-position of guanine. Although C8-PhIP-dG adducts are mutagenic, their interference with the DNA replication machinery and the elicited DNA damage response (DDR) have not yet been studied. Here, we analyzed PhIP-triggered replicative stress and elucidated the role of the apical DDR kinases ATR, ATM and DNA-PKcs in the cellular defense response. First, we demonstrate that PhIP induced C8-PhIP-dG adducts and DNA strand breaks. This stimulated ATR-CHK1 signaling, phosphorylation of histone 2AX and the formation of RPA foci. In proliferating cells, PhIP treatment increased the frequency of stalled replication forks and reduced fork speed. Inhibition of ATR in the presence of PhIP-induced DNA damage strongly promoted the formation of DNA double-strand breaks, activation of the ATM-CHK2 pathway and hyperphosphorylation of RPA. The abrogation of ATR signaling potentiated the cell death response and enhanced chromosomal aberrations after PhIP treatment, while ATM and DNA-PK inhibition had only marginal effects. These results strongly support the notion that ATR plays a key role in the defense against cancer formation induced by PhIP and related HCAs. PMID:27599846

Interoperation of an UHF RFID Reader and a TCP/IP Device via Wired and Wireless Links

PubMed Central

Lee, Sang Hoon; Jin, Ik Soo

2011-01-01

A main application in radio frequency identification (RFID) sensor networks is the function that processes real-time tag information after gathering the required data from multiple RFID tags. The component technologies that contain an RFID reader, called the interrogator, which has a tag chip, processors, coupling antenna, and a power management system have advanced significantly over the last decade. This paper presents a system implementation for interoperation between an UHF RFID reader and a TCP/IP device that is used as a gateway. The proposed system consists of an UHF RFID tag, an UHF RFID reader, an RF end-device, an RF coordinator, and a TCP/IP I/F. The UHF RFID reader, operating at 915 MHz, is compatible with EPC Class-0/Gen1, Class-1/Gen1 and 2, and ISO18000-6B. In particular, the UHF RFID reader can be combined with the RF end-device/coordinator for a ZigBee (IEEE 802.15.4) interface, which is a low-power wireless standard. The TCP/IP device communicates with the RFID reader via wired links. On the other hand, it is connected to the ZigBee end-device via wireless links. The web based test results show that the developed system can remotely recognize information of multiple tags through the interoperation between the RFID reader and the TCP/IP device. PMID:22346665

Interoperation of an UHF RFID reader and a TCP/IP device via wired and wireless links.

PubMed

Lee, Sang Hoon; Jin, Ik Soo

2011-01-01

A main application in radio frequency identification (RFID) sensor networks is the function that processes real-time tag information after gathering the required data from multiple RFID tags. The component technologies that contain an RFID reader, called the interrogator, which has a tag chip, processors, coupling antenna, and a power management system have advanced significantly over the last decade. This paper presents a system implementation for interoperation between an UHF RFID reader and a TCP/IP device that is used as a gateway. The proposed system consists of an UHF RFID tag, an UHF RFID reader, an RF end-device, an RF coordinator, and a TCP/IP I/F. The UHF RFID reader, operating at 915 MHz, is compatible with EPC Class-0/Gen1, Class-1/Gen1 and 2, and ISO18000-6B. In particular, the UHF RFID reader can be combined with the RF end-device/coordinator for a ZigBee (IEEE 802.15.4) interface, which is a low-power wireless standard. The TCP/IP device communicates with the RFID reader via wired links. On the other hand, it is connected to the ZigBee end-device via wireless links. The web based test results show that the developed system can remotely recognize information of multiple tags through the interoperation between the RFID reader and the TCP/IP device.

The Worldwide Interplanetary Scintillation (IPS) Stations (WIPSS) Network in support of Space-Weather Science and Forecasting

NASA Astrophysics Data System (ADS)

Bisi, M. M.; Gonzalez-Esparza, A.; Jackson, B. V.; Aguilar-Rodriguez, E.; Tokumaru, M.; Chashei, I. V.; Tyul'bashev, S. A.; Manoharan, P. K.; Fallows, R. A.; Chang, O.; Mejia-Ambriz, J. C.; Yu, H. S.; Fujiki, K.; Shishov, V.

2016-12-01

The phenomenon of space weather - analogous to terrestrial weather which describes the changing low-altitude atmospheric conditions on Earth - is essentially a description of the changes in the plasma environment at and near the Earth. Some key parameters for space-weather purposes driving space weather at the Earth include velocity, density, magnetic field, high-energy particles, and radiation coming into and within the near-Earth space environment. Interplanetary scintillation (IPS) can be used to provide a global measure of velocity and density as well as indications of changes in the plasma and magnetic-field rotations along each observational line of sight. If the observations are formally inverted into a three-dimensional (3-D) tomographic reconstruction (such as using the University of California, San Diego - UCSD - kinematic model and reconstruction technique), then source-surface magnetic fields can also be propagated out to the Earth (and beyond) as well as in-situ data also being incorporated into the reconstruction. Currently, this has been done using IPS data only from the Institute for Space-Earth Environmental (ISEE) and has been scientifically since the 1990s, and in a forecast mode since around 2000. There is now a defined IPS Common Data Format (IPSCDFv1.0) which is being implemented by the majority of the IPS community (this also feeds into the tomography). The Worldwide IPS Stations (WIPSS) Network aims to bring together, using IPSCDFv1.0, the worldwide real-time capable IPS observatories with well-developed and tested analyses techniques being unified across all single-site systems (such as MEXART, Pushchino, and Ooty) and cross-calibrated to the multi-site ISEE system (as well as learning from the scientific-based systems such as EISCAT, LOFAR, and the MWA), into the UCSD 3-D tomography to improve the accuracy, spatial and temporal data coverage, and both the spatial and temporal resolution for improved space-weather science and forecast

The Worldwide Interplanetary Scintillation (IPS) Stations (WIPSS) Network in support of Space-Weather Science and Forecasting

NASA Astrophysics Data System (ADS)

Bisi, Mario Mark; Americo Gonzalez-Esparza, J.; Jackson, Bernard; Aguilar-Rodriguez, Ernesto; Tokumaru, Munetoshi; Chashei, Igor; Tyul'bashev, Sergey; Manoharan, Periasamy; Fallows, Richard; Chang, Oyuki; Yu, Hsiu-Shan; Fujiki, Ken'ichi; Shishov, Vladimir; Barnes, David

2017-04-01

The phenomenon of space weather - analogous to terrestrial weather which describes the changing low-altitude atmospheric conditions on Earth - is essentially a description of the changes in the plasma environment at and near the Earth. Some key parameters for space-weather purposes driving space weather at the Earth include velocity, density, magnetic field, high-energy particles, and radiation coming into and within the near-Earth space environment. Interplanetary scintillation (IPS) can be used to provide a global measure of velocity and density as well as indications of changes in the plasma and magnetic-field rotations along each observational line of sight. If the observations are formally inverted into a three-dimensional (3-D) tomographic reconstruction (such as using the University of California, San Diego - UCSD - kinematic model and reconstruction technique), then source-surface magnetic fields can also be propagated out to the Earth (and beyond) as well as in-situ data also being incorporated into the reconstruction. Currently, this has been done using IPS data only from the Institute for Space-Earth Environmental (ISEE) and has been scientifically since the 1990s, and in a forecast mode since around 2000. There is now a defined (and updated) IPS Common Data Format (IPSCDFv1.1) which is being implemented by the majority of the IPS community (this also feeds into the UCSD tomography). The Worldwide IPS Stations (WIPSS) Network aims to bring together, using IPSCDFv1.1, the worldwide real-time capable IPS observatories with well-developed and tested analyses techniques being unified across all single-site systems (such as MEXART, Pushchino, and Ooty) and cross-calibrated to the multi-site ISEE system (as well as learning from the scientific-based systems such as EISCAT, LOFAR, and the MWA), into the UCSD 3-D tomography to improve the accuracy, spatial and temporal data coverage, and both the spatial and temporal resolution for improved space-weather science

Normalization, bias correction, and peak calling for ChIP-seq

PubMed Central

Diaz, Aaron; Park, Kiyoub; Lim, Daniel A.; Song, Jun S.

2012-01-01

Next-generation sequencing is rapidly transforming our ability to profile the transcriptional, genetic, and epigenetic states of a cell. In particular, sequencing DNA from the immunoprecipitation of protein-DNA complexes (ChIP-seq) and methylated DNA (MeDIP-seq) can reveal the locations of protein binding sites and epigenetic modifications. These approaches contain numerous biases which may significantly influence the interpretation of the resulting data. Rigorous computational methods for detecting and removing such biases are still lacking. Also, multi-sample normalization still remains an important open problem. This theoretical paper systematically characterizes the biases and properties of ChIP-seq data by comparing 62 separate publicly available datasets, using rigorous statistical models and signal processing techniques. Statistical methods for separating ChIP-seq signal from background noise, as well as correcting enrichment test statistics for sequence-dependent and sonication biases, are presented. Our method effectively separates reads into signal and background components prior to normalization, improving the signal-to-noise ratio. Moreover, most peak callers currently use a generic null model which suffers from low specificity at the sensitivity level requisite for detecting subtle, but true, ChIP enrichment. The proposed method of determining a cell type-specific null model, which accounts for cell type-specific biases, is shown to be capable of achieving a lower false discovery rate at a given significance threshold than current methods. PMID:22499706

IP-10 and MIG are compartmentalized at the site of disease during pleural and meningeal tuberculosis and are decreased after antituberculosis treatment.

PubMed

Yang, Qianting; Cai, Yi; Zhao, Wei; Wu, Fan; Zhang, Mingxia; Luo, Kai; Zhang, Yan; Liu, Haiying; Zhou, Boping; Kornfeld, Hardy; Chen, Xinchun

2014-12-01

The diagnosis of active tuberculosis (TB) disease remains a challenge, especially in high-burden settings. Cytokines and chemokines are important in the pathogenesis of TB. Here we investigate the usefulness of circulating and compartmentalized cytokines/chemokines for diagnosis of TB. The levels of multiple cytokines/chemokines in plasma, pleural fluid (PF), and cerebrospinal fluid (CSF) were determined by Luminex liquid array-based multiplexed immunoassays. Three of 26 cytokines/chemokines in plasma were significantly different between TB and latent tuberculosis infection (LTBI). Among them, IP-10 and MIG had the highest diagnostic values, with an area under the receiver operating characteristic curve (ROC AUC) of 0.92 for IP-10 and 0.86 for MIG for distinguishing TB from LTBI. However, IP-10 and MIG levels in plasma were not different between TB and non-TB lung disease. In contrast, compartmentalized IP-10 and MIG in the PF and CSF showed promising diagnostic values in discriminating TB and non-TB pleural effusion (AUC = 0.87 for IP-10 and 0.93 for MIG), as well as TB meningitis and non-TB meningitis (AUC = 0.9 for IP-10 and 0.95 for MIG). A longitudinal study showed that the plasma levels of IP-10, MIG, granulocyte colony-stimulating factor (G-CSF), and gamma interferon (IFN-γ) decreased, while the levels of MCP-1/CCL2 and eotaxin-1/CCL11 increased, after successful treatment of TB. Our findings provide a practical methodology for discriminating active TB from LTBI by sequential IFN-γ release assays (IGRAs) and plasma IP-10 testing, while increased IP-10 and MIG at the site of infection (PF or CSF) can be used as a marker for distinguishing pleural effusion and meningitis caused by TB from those of non-TB origins. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Forwarding techniques for IP fragmented packets in a real 6LoWPAN network.

PubMed

Ludovici, Alessandro; Calveras, Anna; Casademont, Jordi

2011-01-01

Wireless Sensor Networks (WSNs) are attracting more and more interest since they offer a low-cost solution to the problem of providing a means to deploy large sensor networks in a number of application domains. We believe that a crucial aspect to facilitate WSN diffusion is to make them interoperable with external IP networks. This can be achieved by using the 6LoWPAN protocol stack. 6LoWPAN enables the transmission of IPv6 packets over WSNs based on the IEEE 802.15.4 standard. IPv6 packet size is considerably larger than that of IEEE 802.15.4 data frame. To overcome this problem, 6LoWPAN introduces an adaptation layer between the network and data link layers, allowing IPv6 packets to be adapted to the lower layer constraints. This adaptation layer provides fragmentation and header compression of IP packets. Furthermore, it also can be involved in routing decisions. Depending on which layer is responsible for routing decisions, 6LoWPAN divides routing in two categories: mesh under if the layer concerned is the adaptation layer and route over if it is the network layer. In this paper we analyze different routing solutions (route over, mesh under and enhanced route over) focusing on how they forward fragments. We evaluate their performance in terms of latency and energy consumption when transmitting IP fragmented packets. All the tests have been performed in a real 6LoWPAN implementation. After consideration of the main problems in forwarding of mesh frames in WSN, we propose and analyze a new alternative scheme based on mesh under, which we call controlled mesh under.

Forwarding Techniques for IP Fragmented Packets in a Real 6LoWPAN Network

PubMed Central

Ludovici, Alessandro; Calveras, Anna; Casademont, Jordi

2011-01-01

Wireless Sensor Networks (WSNs) are attracting more and more interest since they offer a low-cost solution to the problem of providing a means to deploy large sensor networks in a number of application domains. We believe that a crucial aspect to facilitate WSN diffusion is to make them interoperable with external IP networks. This can be achieved by using the 6LoWPAN protocol stack. 6LoWPAN enables the transmission of IPv6 packets over WSNs based on the IEEE 802.15.4 standard. IPv6 packet size is considerably larger than that of IEEE 802.15.4 data frame. To overcome this problem, 6LoWPAN introduces an adaptation layer between the network and data link layers, allowing IPv6 packets to be adapted to the lower layer constraints. This adaptation layer provides fragmentation and header compression of IP packets. Furthermore, it also can be involved in routing decisions. Depending on which layer is responsible for routing decisions, 6LoWPAN divides routing in two categories: mesh under if the layer concerned is the adaptation layer and route over if it is the network layer. In this paper we analyze different routing solutions (route over, mesh under and enhanced route over) focusing on how they forward fragments. We evaluate their performance in terms of latency and energy consumption when transmitting IP fragmented packets. All the tests have been performed in a real 6LoWPAN implementation. After consideration of the main problems in forwarding of mesh frames in WSN, we propose and analyze a new alternative scheme based on mesh under, which we call controlled mesh under. PMID:22346615

A Spiking Strategy for ChIP-chip Data Normalization in S. cerevisiae.

PubMed

Jeronimo, Célia; Robert, François

2017-01-01

Chromatin immunoprecipitation coupled to DNA microarrays (ChIP-chip) is widely used in the chromatin field, notably to map the position of histone variants or histone modifications along the genome. Often, the position and the occupancy of these epigenetic marks are to be compared between different experiments. It is now increasingly recognized that such cross-sample comparison is better done using externally added exogenous controls for normalization but no such method has been described for ChIP-chip. Here we describe a spiking normalization strategy that makes use of phiX174 phage DNA as a spiked control for normalization of ChIP-chip signals across different experiments.

Evaluating the Effectiveness of IP Hopping via an Address Routing Gateway

DTIC Science & Technology

2013-03-01

37 DARPA Defense Advanced Research Projects Agency . . . . . . . . . . . . . . . . . . . . . . . . . . 20 DHCP Dynamic Host...Protocol ( DHCP ) to force the changes. Through the use of a slightly intelligent DHCP server that leases IPs for a only a short time frame (on the order of...tens of minutes) and only offers IPs that have not been used recently, most networks already using DHCP can quickly change to a randomized scheme. This

78 FR 49717 - Speech-to-Speech and Internet Protocol (IP) Speech-to-Speech Telecommunications Relay Services...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-15

...] Speech-to-Speech and Internet Protocol (IP) Speech-to-Speech Telecommunications Relay Services... Internet Protocol (IP) Speech-to-Speech Telecommunications Relay Services; Telecommunications Relay... (IP Relay) and video relay service (VRS), the Commission should bundle national STS outreach efforts...

Innovative polymeric system (IPS) for solvent-free lipophilic drug transdermal delivery via dissolving microneedles.

PubMed

Dangol, Manita; Yang, Huisuk; Li, Cheng Guo; Lahiji, Shayan Fakhraei; Kim, Suyong; Ma, Yonghao; Jung, Hyungil

2016-02-10

Lipophilic drugs are potential drug candidates during drug development. However, due to the need for hazardous organic solvents for their solubilization, these drugs often fail to reach the pharmaceutical market, and in doing so highlight the importance of solvent free systems. Although transdermal drug delivery systems (TDDSs) are considered prospective safe drug delivery routes, a system involving lipophilic drugs in solvent free or powder form has not yet been described. Here, we report, for the first time, a novel approach for the delivery of every kind of lipophilic drug in powder form based on an innovative polymeric system (IPS). The phase transition of powder form of lipophilic drugs due to interior chemical bonds between drugs and biodegradable polymers and formation of nano-sized colloidal structures allowed the fabrication of dissolving microneedles (DMNs) to generate a powerful TDDS. We showed that IPS based DMN with powder capsaicin enhances the therapeutic effect for treatment of the rheumatic arthritis in a DBA/1 mouse model compared to a solvent-based system, indicating the promising potential of this new solvent-free platform for lipophilic drug delivery. Copyright © 2016 Elsevier B.V. All rights reserved.

Blind source computer device identification from recorded VoIP calls for forensic investigation.

PubMed

Jahanirad, Mehdi; Anuar, Nor Badrul; Wahab, Ainuddin Wahid Abdul

2017-03-01

The VoIP services provide fertile ground for criminal activity, thus identifying the transmitting computer devices from recorded VoIP call may help the forensic investigator to reveal useful information. It also proves the authenticity of the call recording submitted to the court as evidence. This paper extended the previous study on the use of recorded VoIP call for blind source computer device identification. Although initial results were promising but theoretical reasoning for this is yet to be found. The study suggested computing entropy of mel-frequency cepstrum coefficients (entropy-MFCC) from near-silent segments as an intrinsic feature set that captures the device response function due to the tolerances in the electronic components of individual computer devices. By applying the supervised learning techniques of naïve Bayesian, linear logistic regression, neural networks and support vector machines to the entropy-MFCC features, state-of-the-art identification accuracy of near 99.9% has been achieved on different sets of computer devices for both call recording and microphone recording scenarios. Furthermore, unsupervised learning techniques, including simple k-means, expectation-maximization and density-based spatial clustering of applications with noise (DBSCAN) provided promising results for call recording dataset by assigning the majority of instances to their correct clusters. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

The Spacelab Instrument Pointing System (IPS) and its first flight

NASA Astrophysics Data System (ADS)

Heusmann, H.; Wolf, P.

1985-11-01

The development of the Instrument Pointing System (IPS) as part of Spacelab's experimental apparatus for open Pallet direct space exposure, and its test flight aboard the Shuttle Orbiter are discussed. The IPS is a three-axis-controlled platform with stellar, sun and earth pointing modes, and a better than 1 arcsec pointing ability. The development of an 'inside-out gimbal' configuration with the platform acting like a joint between the unstable Shuttle and the inertially stabilized payload facilitated close to hemispherical pointing and the adaptability for payloads of almost any size. Gimbal axes torquers counteract Orbiter acceleration due to crew movement and thruster firings, and facilitate target acquisition and precision pointing, by command from a crew-engaged computer preprogrammed for all possible control steps. Carrying an experimental solar-physics payload, the IPS correctly performed all intended functions and withstood launch and orbital loads. Several anomalies were detected and successfully corrected in-flight.

Preparation of Low-Input and Ligation-Free ChIP-seq Libraries Using Template-Switching Technology.

PubMed

Bolduc, Nathalie; Lehman, Alisa P; Farmer, Andrew

2016-10-10

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) has become the gold standard for mapping of transcription factors and histone modifications throughout the genome. However, for ChIP experiments involving few cells or targeting low-abundance transcription factors, the small amount of DNA recovered makes ligation of adapters very challenging. In this unit, we describe a ChIP-seq workflow that can be applied to small cell numbers, including a robust single-tube and ligation-free method for preparation of sequencing libraries from sub-nanogram amounts of ChIP DNA. An example ChIP protocol is first presented, resulting in selective enrichment of DNA-binding proteins and cross-linked DNA fragments immobilized on beads via an antibody bridge. This is followed by a protocol for fast and easy cross-linking reversal and DNA recovery. Finally, we describe a fast, ligation-free library preparation protocol, featuring DNA SMART technology, resulting in samples ready for Illumina sequencing. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

[Microstructure and mechanical property of a new IPS-Empress 2 dental glass-ceramic].

PubMed

Luo, Xiao-ping; Watts, D C; Wilson, N H F; Silsons, N; Cheng, Ya-qin

2005-03-01

To investigate the microstructure and mechanical properties of a new IPS-Empress 2 dental glass-ceramic. AFM, SEM and XRD were used to analyze the microstructure and crystal phase of IPS-Empress 2 glass-ceramic. The flexural strength and fracture toughness were tested using 3-point bending method and indentation method respectively. IPS-Empress 2 glass-ceramic mainly consisted of lithium disilicate crystal, lithium phosphate and glass matrix, which formed a continuous interlocking structure. The crystal phases were not changed before and after hot-pressed treatment. AFM showed nucleating agent particles of different sizes distributed on the highly polished ceramic surface. The strength and fracture toughness were 300 MPa and 3.1 MPam(1/2). The high strength and fracture toughness of IPS-Empress 2 glass ceramic are attributed to the fine lithium disilicate crystalline, interlocking microstructure and crack deflection.

Internet over the VDL-2 Subnetwork: the VDL-2/IP Aviation Datalink System

NASA Technical Reports Server (NTRS)

Grappel, R. D.

2000-01-01

This report describes the design to operate the standard Internet communications protocols (IP) over the VHF aviation Data Link Mode 2 (VDL-2) subnetwork. The VDL-2/IP system specified in this report can operate transparently with the current aviation users of VDL-2 (Airline Communications and Reporting System, ACARS and Aeronautical Telecommunications Network, ATN) and proposed users (Flight Information Service via Broadcast, FIS-B). The VDL-2/IP system provides a straightforward mechanisms to utilize inexpensive, commercial off-the-shelf (COTS) communications packages developed for the Internet as part of the aviation datalink system.

Life History and Biology of Ips latidens (LeConte) (Coleoptera: Scolytidae)\\t

Treesearch

D.R. Miller; J.H. Borden

1985-01-01

The life history and biology of Ips latidens (LeConte) were investigated using bark-sandwich and whole-log rearing methods. In contrast with other Ips spp., some females initiated galleries under conditions of female-biased sex ratios, and sometimes 2 or more males were present in a gallery. In general, however, I....

Massive stars dying alone: the extremely remote environment of SN 2009ip

NASA Astrophysics Data System (ADS)

Smith, Nathan; Andrews, Jennifer E.; Mauerhan, Jon C.

2016-12-01

We present late-time Hubble Space Telescope (HST) images of the site of supernova (SN) 2009ip taken almost 3 yr after its bright 2012 luminosity peak. SN 2009ip is now slightly fainter in broad filters than the progenitor candidate detected by HST in 1999. The current source continues to be dominated by ongoing late-time circumstellar material interaction that produces strong Hα emission and a weak pseudo-continuum, as found previously for 1-2 yr after explosion. The intent of these observations was to search for evidence of recent star formation in the local (˜1 kpc; 10 arcsec) environment around SN 2009ip, in the remote outskirts of its host spiral galaxy NGC 7259. We can rule out the presence of any massive star-forming complexes like 30 Dor or the Carina nebula at the SN site or within a few kpc. If the progenitor of SN 2009ip was really a 50-80 M⊙ star as archival HST images suggested, then it is strange that there is no sign of this type of massive star formation anywhere in the vicinity. A possible explanation is that the progenitor was the product of a merger or binary mass transfer, rejuvenated after a lifetime that was much longer than 4-5 Myr, allowing its natal H II region to have faded. A smaller region like the Orion nebula would be an unresolved but easily detected point source. This is ruled out within ˜1.5 kpc around SN 2009ip, but a small H II region could be hiding in the glare of SN 2009ip itself. Later images after a few more years have passed are needed to confirm that the progenitor candidate is truly gone and to test for the possibility of a small H II region or cluster at the SN position.

An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition

PubMed Central

Yuan, Chih-Chi; Craske, Madeleine Lisa; Labhart, Paul; Guler, Gulfem D.; Arnott, David; Maile, Tobias M.; Busby, Jennifer; Henry, Chisato; Kelly, Theresa K.; Tindell, Charles A.; Jhunjhunwala, Suchit; Zhao, Feng; Hatton, Charlie; Bryant, Barbara M.

2016-01-01

Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) has been instrumental in inferring the roles of histone post-translational modifications in the regulation of transcription, chromatin compaction and other cellular processes that require modulation of chromatin structure. However, analysis of ChIP-seq data is challenging when the manipulation of a chromatin-modifying enzyme significantly affects global levels of histone post-translational modifications. For example, small molecule inhibition of the methyltransferase EZH2 reduces global levels of histone H3 lysine 27 trimethylation (H3K27me3). However, standard ChIP-seq normalization and analysis methods fail to detect a decrease upon EZH2 inhibitor treatment. We overcome this challenge by employing an alternative normalization approach that is based on the addition of Drosophila melanogaster chromatin and a D. melanogaster-specific antibody into standard ChIP reactions. Specifically, the use of an antibody that exclusively recognizes the D. melanogaster histone variant H2Av enables precipitation of D. melanogaster chromatin as a minor fraction of the total ChIP DNA. The D. melanogaster ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO and EZH2 inhibitor-treated samples. Employing this strategy, a substantial reduction in H3K27me3 signal is now observed in ChIP-seq data from EZH2 inhibitor treated samples. PMID:27875550

An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition.

PubMed

Egan, Brian; Yuan, Chih-Chi; Craske, Madeleine Lisa; Labhart, Paul; Guler, Gulfem D; Arnott, David; Maile, Tobias M; Busby, Jennifer; Henry, Chisato; Kelly, Theresa K; Tindell, Charles A; Jhunjhunwala, Suchit; Zhao, Feng; Hatton, Charlie; Bryant, Barbara M; Classon, Marie; Trojer, Patrick

2016-01-01

Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) has been instrumental in inferring the roles of histone post-translational modifications in the regulation of transcription, chromatin compaction and other cellular processes that require modulation of chromatin structure. However, analysis of ChIP-seq data is challenging when the manipulation of a chromatin-modifying enzyme significantly affects global levels of histone post-translational modifications. For example, small molecule inhibition of the methyltransferase EZH2 reduces global levels of histone H3 lysine 27 trimethylation (H3K27me3). However, standard ChIP-seq normalization and analysis methods fail to detect a decrease upon EZH2 inhibitor treatment. We overcome this challenge by employing an alternative normalization approach that is based on the addition of Drosophila melanogaster chromatin and a D. melanogaster-specific antibody into standard ChIP reactions. Specifically, the use of an antibody that exclusively recognizes the D. melanogaster histone variant H2Av enables precipitation of D. melanogaster chromatin as a minor fraction of the total ChIP DNA. The D. melanogaster ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO and EZH2 inhibitor-treated samples. Employing this strategy, a substantial reduction in H3K27me3 signal is now observed in ChIP-seq data from EZH2 inhibitor treated samples.

Classifier fusion for VoIP attacks classification

NASA Astrophysics Data System (ADS)

Safarik, Jakub; Rezac, Filip

2017-05-01

SIP is one of the most successful protocols in the field of IP telephony communication. It establishes and manages VoIP calls. As the number of SIP implementation rises, we can expect a higher number of attacks on the communication system in the near future. This work aims at malicious SIP traffic classification. A number of various machine learning algorithms have been developed for attack classification. The paper presents a comparison of current research and the use of classifier fusion method leading to a potential decrease in classification error rate. Use of classifier combination makes a more robust solution without difficulties that may affect single algorithms. Different voting schemes, combination rules, and classifiers are discussed to improve the overall performance. All classifiers have been trained on real malicious traffic. The concept of traffic monitoring depends on the network of honeypot nodes. These honeypots run in several networks spread in different locations. Separation of honeypots allows us to gain an independent and trustworthy attack information.

Ataxia-telangiectasia mutated (ATM) deficiency decreases reprogramming efficiency and leads to genomic instability in iPS cells

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

Kinoshita, Taisuke; Nagamatsu, Go, E-mail: gonag@sc.itc.keio.ac.jp; Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012

2011-04-08

Highlights: {yields} iPS cells were induced with a fluorescence monitoring system. {yields} ATM-deficient tail-tip fibroblasts exhibited quite a low reprogramming efficiency. {yields} iPS cells obtained from ATM-deficient cells had pluripotent cell characteristics. {yields} ATM-deficient iPS cells had abnormal chromosomes, which were accumulated in culture. -- Abstract: During cell division, one of the major features of somatic cell reprogramming by defined factors, cells are potentially exposed to DNA damage. Inactivation of the tumor suppressor gene p53 raised reprogramming efficiency but resulted in an increased number of abnormal chromosomes in established iPS cells. Ataxia-telangiectasia mutated (ATM), which is critical in the cellularmore » response to DNA double-strand breaks, may also play an important role during reprogramming. To clarify the function of ATM in somatic cell reprogramming, we investigated reprogramming in ATM-deficient (ATM-KO) tail-tip fibroblasts (TTFs). Although reprogramming efficiency was greatly reduced in ATM-KO TTFs, ATM-KO iPS cells were successfully generated and showed the same proliferation activity as WT iPS cells. ATM-KO iPS cells had a gene expression profile similar to ES cells and WT iPS cells, and had the capacity to differentiate into all three germ layers. On the other hand, ATM-KO iPS cells accumulated abnormal genome structures upon continuous passages. Even with the abnormal karyotype, ATM-KO iPS cells retained pluripotent cell characteristics for at least 20 passages. These data indicate that ATM does participate in the reprogramming process, although its role is not essential.« less

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

Periodontal response to all-ceramic crowns (IPS Empress) in general practice.

PubMed

Al-Wahadni, A M; Mansour, Y; Khader, Y

2006-02-01

The purpose of this study was to investigate the periodontal response to the presence of all-ceramic crowns (IPS Empress) in general practice patients. The convenience sample included 82 IPS Empress crowns placed in 64 patients. These crowns had been in place for an average of 16.27 (SD 9.26) months and ranged from 6.2 to 48.87 months at the time of clinical examination. Periodontal health status (as determined by dental plaque, gingival health status, periodontal pockets) was assessed around all crowned teeth and around matched contralateral teeth by one calibrated examiner. Periodontal indices utilized included the Plaque Index (PI), Gingival Index (GI) and pocket depth (PD) with calibrated probes graduated in millimetres. Plaque, gingival and PD values for crowned teeth were compared with those for control teeth using Wilcoxon signed-rank test for each clinical parameters. Chi-square was used to test the significance of the difference in their distribution between crowns and control teeth. Statistically, PI (0.35), GI (0.41) and mean PD scores (1.42) of IPS Empress crowned teeth compared less favourably with scores of the control teeth (0.27, 0.23 and 0.86 respectively). Teeth with IPS Empress crowns had poorer periodontal health and more clinically evident plaque than uncrowned teeth.

MLF1IP promotes normal erythroid proliferation and is involved in the pathogenesis of polycythemia vera.

PubMed

Feng, Gege; Zhang, Tianjiao; Liu, Jinqin; Ma, Xiaotang; Li, Bing; Yang, Lin; Zhang, Yue; Xu, Zefeng; Qin, Tiejun; Zhou, Jiaxi; Huang, Gang; Shi, Lihong; Xiao, Zhijian

2017-03-01

Myelodysplasia/myeloid leukemia factor 1-interacting protein (MLF1IP) appears to be an erythroid lineage-specific gene in mice; however, its role in normal erythropoiesis and erythropoietic disorders have not yet been elucidated. Here, we found that MLF1IP is abundantly expressed in human erythroid progenitor cells and that MLF1IP-deficiency reduces cell proliferation resulting from cell cycle arrest. Moreover, MLF1IP expression is exclusively elevated in CFU-E cells from polycythemia vera (PV) patients, and MLF1IP transgenic mice develop a PV-like disorder. Further analyses revealed that the erythroid progenitors and early-stage erythroblasts from these transgenic mice expand by up-regulating cyclin D2 and down-regulating p27 and p21. Thus, our data demonstrate that MLF1IP promotes erythroid proliferation and is involved in the pathogenesis of PV, suggesting that it might be a novel molecular target for erythropoietic disorders. © 2017 Federation of European Biochemical Societies.

Inflammation and Atrophy Precede Prostate Neoplasia in PhIP Induced Rat Model

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

Borowsky, A D; Dingley, K; Ubick, E

2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine (PhIP) has been implicated as a major mutagenic heterocyclic amine in the human diet and is carcinogenic in the rat prostate. In order to validate PhIP induced rat prostate neoplasia as a model of human prostate cancer progression, we sought to study the earliest histologic and morphologic changes in the prostate and to follow the progressive changes over time. We fed 67 male Fischer F344 5 week old rats with PhIP (400 PPM) or control diets for 20 weeks, and then sacrificed animals for histomorphologic examination at age 25 weeks, 45 weeks, and 65 weeks. Animals treated with PhIPmore » showed significantly more inflammation (P=.002 (25wk), >.001(45wk), .016(65wk)) and atrophy (P=.003(25wk), >.001(45wk), .006 (65wk)) in their prostate glands relative to controls. Prostatic intraepithelial neoplasia (PIN) occurred only in PhIP treated rats. PIN lesions arose in areas of glandular atrophy, most often in the ventral prostate. Atypical cells in areas of atrophy show loss of glutathione S-transferase pi immunostaining preceding development of PIN. None of the animals in this study developed invasive carcinomas differing from previous reports. Overall, these findings suggest that the pathogenesis of prostatic neoplasia in the PhIP treated rat prostate proceeds from inflammation to post-inflammatory proliferative atrophy to PIN.« less

Unusual Father-to-Daughter Transmission of Incontinentia Pigmenti Due to Mosaicism in IP Males.

PubMed

Fusco, Francesca; Conte, Matilde Immacolata; Diociaiuti, Andrea; Bigoni, Stefania; Branda, Maria Francesca; Ferlini, Alessandra; El Hachem, Maya; Ursini, Matilde Valeria

2017-09-01

Incontinentia pigmenti (IP; Online Mendelian Inheritance in Man catalog #308300) is an X-linked dominant ectodermal disorder caused by mutations of the inhibitor of κ polypeptide gene enchancer in B cells, kinase γ ( IKBKG )/ nuclear factor κB, essential modulator ( NEMO ) gene. Hemizygous IKBKG/NEMO loss-of-function (LoF) mutations are lethal in males, thus patients are female, and the disease is always transmitted from an IP-affected mother to her daughter. We present 2 families with father-to-daughter transmission of IP and provide for the first time molecular evidence that the combination of somatic and germ-line mosaicism for IKBKG/NEMO loss of function mutations in IP males resulted in the transmission of the disease to a female child. We searched for the IKBKG/NEMO mutant allele in blood, urine, skin, and sperm DNA and found that the 2 fathers were somatic and germ-line mosaics for the p.Gln132×mutation or the exon 4-10 deletion of IKBKG/NEMO , respectively. The highest level of IKBKG/NEMO mutant cells was detected in the sperm, which might explain the recurrence of the disease. We therefore recommend careful clinical evaluation in IP male cases and the genetic investigation in sperm DNA to ensure correct genetic counseling and prevent the risk of paternal transmission of IP. Copyright © 2017 by the American Academy of Pediatrics.

The PLC/IP3R/PKC Pathway is Required for Ethanol-enhanced GABA Release

PubMed Central

Kelm, M. Katherine; Weinberg, Richard J.; Criswell, Hugh E.; Breese, George R.

2010-01-01

Summary Research on the actions of ethanol at the GABAergic synapse has traditionally focused on postsynaptic mechanisms, but recent data demonstrate that ethanol also increases both evoked and spontaneous GABA release in many brain regions. Using whole-cell voltage-clamp recordings, we previously showed that ethanol increases spontaneous GABA release at the rat interneuron-Purkinje cell synapse. This presynaptic ethanol effect is dependent on calcium release from internal stores, possibly through activation of inositol 1,4,5-trisphosphate receptors (IP3Rs). After confirming that ethanol targets vesicular GABA release, in the present study we used electron microscopic immunohistochemistry to demonstrate that IP3Rs are located in presynaptic terminals of cerebellar interneurons. Activation of IP3Rs requires binding of IP3, generated through activation of phospholipase C (PLC). We find that the PLC antagonist edelfosine prevents ethanol from increasing spontaneous GABA release. Diacylglycerol generated by PLC and calcium released by activation of the IP3R activate protein kinase C (PKC). Ethanol-enhanced GABA release was blocked by two PKC antagonists, chelerythrine and calphostin C. When a membrane impermeable PKC antagonist, PKC (19-36), was delivered intracellularly to the postsynaptic neuron, ethanol continued to increase spontaneous GABA release. Overall, these results suggest that activation of the PLC/IP3R/PKC pathway is necessary for ethanol to increase spontaneous GABA release from presynaptic terminals onto Purkinje cells. PMID:20206640

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

PubMed

Chung, Dongjun; Kuan, Pei Fen; Li, Bo; Sanalkumar, Rajendran; Liang, Kun; Bresnick, Emery H; Dewey, Colin; Keleş, Sündüz

2011-07-01

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.

Teaching Network Security with IP Darkspace Data

ERIC Educational Resources Information Center

Zseby, Tanja; Iglesias Vázquez, Félix; King, Alistair; Claffy, K. C.

2016-01-01

This paper presents a network security laboratory project for teaching network traffic anomaly detection methods to electrical engineering students. The project design follows a research-oriented teaching principle, enabling students to make their own discoveries in real network traffic, using data captured from a large IP darkspace monitor…

High throughput mutagenesis for identification of residues regulating human prostacyclin (hIP) receptor expression and function.

PubMed

Bill, Anke; Rosethorne, Elizabeth M; Kent, Toby C; Fawcett, Lindsay; Burchell, Lynn; van Diepen, Michiel T; Marelli, Anthony; Batalov, Sergey; Miraglia, Loren; Orth, Anthony P; Renaud, Nicole A; Charlton, Steven J; Gosling, Martin; Gaither, L Alex; Groot-Kormelink, Paul J

2014-01-01

The human prostacyclin receptor (hIP receptor) is a seven-transmembrane G protein-coupled receptor (GPCR) that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR) mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structure-function relationship of GPCRs.

High Throughput Mutagenesis for Identification of Residues Regulating Human Prostacyclin (hIP) Receptor Expression and Function

PubMed Central

Kent, Toby C.; Fawcett, Lindsay; Burchell, Lynn; van Diepen, Michiel T.; Marelli, Anthony; Batalov, Sergey; Miraglia, Loren; Orth, Anthony P.; Renaud, Nicole A.; Charlton, Steven J.; Gosling, Martin; Gaither, L. Alex; Groot-Kormelink, Paul J.

2014-01-01

The human prostacyclin receptor (hIP receptor) is a seven-transmembrane G protein-coupled receptor (GPCR) that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR) mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structure-function relationship of GPCRs. PMID:24886841

Chromatin immunoprecipitation assays: application of ChIP-on-chip for defining dynamic transcriptional mechanisms in bone cells.

PubMed

van der Deen, Margaretha; Hassan, Mohammad Q; Pratap, Jitesh; Teplyuk, Nadiya M; Young, Daniel W; Javed, Amjad; Zaidi, Sayyed K; Lian, Jane B; Montecino, Martin; Stein, Janet L; Stein, Gary S; van Wijnen, Andre J

2008-01-01

Normal cell growth and differentiation of bone cells requires the sequential expression of cell type specific genes to permit lineage specification and development of cellular phenotypes. Transcriptional activation and repression of distinct sets of genes support the anabolic functions of osteoblasts and the catabolic properties of osteoclasts. Furthermore, metastasis of tumors to the bone environment is controlled by transcriptional mechanisms. Insights into the transcriptional regulation of genes in bone cells may provide a conceptual basis for improved therapeutic approaches to treat bone fractures, genetic osteopathologies, and/or cancer metastases to bone. Chromatin immunoprecipitation (ChIP) is a powerful technique to establish in vivo binding of transcription factors to the promoters of genes that are either activated or repressed in bone cells. Combining ChIP with genomic microarray analysis, colloquially referred to as "ChIP-on-chip," has become a valuable method for analysis of endogenous protein/DNA interactions. This technique permits assessment of chromosomal binding sites for transcription factors or the location of histone modifications at a genomic scale. This chapter discusses protocols for performing chromatin immunoprecipitation experiments, with a focus on ChIP-on-chip analysis. The information presented is based on the authors' experience with defining interactions of Runt-related (RUNX) transcription factors with bone-related genes within the context of the native nucleosomal organization of intact osteoblastic cells.

Multi-layer service function chaining scheduling based on auxiliary graph in IP over optical network

NASA Astrophysics Data System (ADS)

Li, Yixuan; Li, Hui; Liu, Yuze; Ji, Yuefeng

2017-10-01

Software Defined Optical Network (SDON) can be considered as extension of Software Defined Network (SDN) in optical networks. SDON offers a unified control plane and makes optical network an intelligent transport network with dynamic flexibility and service adaptability. For this reason, a comprehensive optical transmission service, able to achieve service differentiation all the way down to the optical transport layer, can be provided to service function chaining (SFC). IP over optical network, as a promising networking architecture to interconnect data centers, is the most widely used scenarios of SFC. In this paper, we offer a flexible and dynamic resource allocation method for diverse SFC service requests in the IP over optical network. To do so, we firstly propose the concept of optical service function (OSF) and a multi-layer SFC model. OSF represents the comprehensive optical transmission service (e.g., multicast, low latency, quality of service, etc.), which can be achieved in multi-layer SFC model. OSF can also be considered as a special SF. Secondly, we design a resource allocation algorithm, which we call OSF-oriented optical service scheduling algorithm. It is able to address multi-layer SFC optical service scheduling and provide comprehensive optical transmission service, while meeting multiple optical transmission requirements (e.g., bandwidth, latency, availability). Moreover, the algorithm exploits the concept of Auxiliary Graph. Finally, we compare our algorithm with the Baseline algorithm in simulation. And simulation results show that our algorithm achieves superior performance than Baseline algorithm in low traffic load condition.

KChIPs and Kv4 alpha subunits as integral components of A-type potassium channels in mammalian brain.

PubMed

Rhodes, Kenneth J; Carroll, Karen I; Sung, M Amy; Doliveira, Lisa C; Monaghan, Michael M; Burke, Sharon L; Strassle, Brian W; Buchwalder, Lynn; Menegola, Milena; Cao, Jie; An, W Frank; Trimmer, James S

2004-09-08

Voltage-gated potassium (Kv) channels from the Kv4, or Shal-related, gene family underlie a major component of the A-type potassium current in mammalian central neurons. We recently identified a family of calcium-binding proteins, termed KChIPs (Kv channel interacting proteins), that bind to the cytoplasmic N termini of Kv4 family alpha subunits and modulate their surface density, inactivation kinetics, and rate of recovery from inactivation (An et al., 2000). Here, we used single and double-label immunohistochemistry, together with circumscribed lesions and coimmunoprecipitation analyses, to examine the regional and subcellular distribution of KChIPs1-4 and Kv4 family alpha subunits in adult rat brain. Immunohistochemical staining using KChIP-specific monoclonal antibodies revealed that the KChIP polypeptides are concentrated in neuronal somata and dendrites where their cellular and subcellular distribution overlaps, in an isoform-specific manner, with that of Kv4.2 and Kv4.3. For example, immunoreactivity for KChIP1 and Kv4.3 is concentrated in the somata and dendrites of hippocampal, striatal, and neocortical interneurons. Immunoreactivity for KChIP2, KChIP4, and Kv4.2 is concentrated in the apical and basal dendrites of hippocampal and neocortical pyramidal cells. Double-label immunofluorescence labeling revealed that throughout the forebrain, KChIP2 and KChIP4 are frequently colocalized with Kv4.2, whereas in cortical, hippocampal, and striatal interneurons, KChIP1 is frequently colocalized with Kv4.3. Coimmunoprecipitation analyses confirmed that all KChIPs coassociate with Kv4 alpha subunits in brain membranes, indicating that KChIPs 1-4 are integral components of native A-type Kv channel complexes and are likely to play a major role as modulators of somatodendritic excitability.

Validation of DAB2IP methylation and its relative significance in predicting outcome in renal cell carcinoma

PubMed Central

Zhao, Liang-Yun; Kapur, Payal; Wu, Kai-Jie; Wang, Bin; Yu, Yan-Hong; Liao, Bing; He, Da-Lin; Chen, Wei; Margulis, Vitaly; Hsieh, Jer-Tsong; Luo, Jun-Hang

2016-01-01

We have recently reported tumor suppressive role of DAB2IP in RCC development. In this study, We identified one CpG methylation biomarker (DAB2IP CpG1) located UTSS of DAB2IP that was associated with poor overall survival in a cohort of 318 ccRCC patients from the Cancer Genome Atlas (TCGA). We further validated the prognostic accuracy of DAB2IP CpG methylation by pyrosequencing quantitative methylation assay in 224 ccRCC patients from multiple Chinese centers (MCHC set), and 239 patients from University of Texas Southwestern Medical Center at Dallas (UTSW set) by using FFPE samples. DAB2IP CpG1 can predict the overall survival of patients in TCGA, MCHC, and UTSW sets independent of patient age, Fuhrman grade and TNM stage (all p<0.05). DAB2IP CpG1 successfully categorized patients into high-risk and low-risk groups with significant differences of clinical outcome in respective clinical subsets, regardless of age, sex, grade, stage, or race (HR: 1.63-7.83; all p<0.05). The detection of DAB2IP CpG1 methylation was minimally affected by ITH in ccRCC. DAB2IP mRNA expression was regulated by DNA methylation in vitro. DAB2IP CpG1 methylation is a practical and repeatable biomarker for ccRCC, which can provide prognostic value that complements the current staging system. PMID:27129174

Investigation of tissue-specific expression and functions of MLF1-IP during development and in the immune system.

PubMed

Wang, Xuehai; Marcinkiewicz, Martin; Gatain, Yaned; Bouchard, Maxime; Mao, Jianning; Tremblay, Michel; Uetani, Noriko; Hanissian, Silva; Qi, Shijie; Wu, Jiangping; Luo, Hongyu

2013-01-01

Myeloid leukemia factor 1-interacting protein (MLF1-IP) has been found to exert functions in mitosis, although studies have been conducted only in cell lines up to now. To understand its roles during ontogeny and immunity, we analyzed its mRNA expression pattern by in situ hybridization and generated MLF1-IP gene knockout (KO) mice. MLF1-IP was expressed at elevated levels in most rudimentary tissues during the mid-gestation stage, between embryonic day 9.5 (e9.5) and e15.5. It declined afterwards in these tissues, but was very high in the testes and ovaries in adulthood. At post-natal day 10 (p10), the retina and cerebellum still expressed moderate MLF1-IP levels, although these tissues do not contain fast-proliferating cells at this stage. MLF1-IP expression in lymphoid organs, such as the thymus, lymph nodes, spleen and bone marrow, was high between e15.5 and p10, and decreased in adulthood. MLF1-IP KO embryos failed to develop beyond e6.5. On the other hand, MLF1-IP(+/-) mice were alive and fertile, with no obvious anomalies. Lymphoid organ size, weight, cellularity and cell sub-populations in MLF1-IP(+/-) mice were in the normal range. The functions of MLF1-IP(+/-) T cells and naïve CD4 cells, in terms of TCR-stimulated proliferation and Th1, Th17 and Treg cell differentiation in vitro, were comparable to those of wild type T cells. Our study demonstrates that MLF1-IP performs unique functions during mouse embryonic development, particularly around e6.5, when there was degeneration of epiblasts. However, the cells could proliferate dozens of rounds without MLF1-IP. MLF1-IP expression at about 50% of its normal level is sufficient to sustain mice life and the development of their immune system without apparent abnormalities. Our results also raise an intriguing question that MLF1-IP might have additional functions unrelated to cell proliferation.

Investigation of Tissue-Specific Expression and Functions of MLF1-IP during Development and in the Immune System

PubMed Central

Wang, Xuehai; Marcinkiewicz, Martin; Gatain, Yaned; Bouchard, Maxime; Mao, Jianning; Tremblay, Michel; Uetani, Noriko; Hanissian, Silva; Qi, Shijie; Wu, Jiangping; Luo, Hongyu

2013-01-01

Myeloid leukemia factor 1-interacting protein (MLF1-IP) has been found to exert functions in mitosis, although studies have been conducted only in cell lines up to now. To understand its roles during ontogeny and immunity, we analyzed its mRNA expression pattern by in situ hybridization and generated MLF1-IP gene knockout (KO) mice. MLF1-IP was expressed at elevated levels in most rudimentary tissues during the mid-gestation stage, between embryonic day 9.5 (e9.5) and e15.5. It declined afterwards in these tissues, but was very high in the testes and ovaries in adulthood. At post-natal day 10 (p10), the retina and cerebellum still expressed moderate MLF1-IP levels, although these tissues do not contain fast-proliferating cells at this stage. MLF1-IP expression in lymphoid organs, such as the thymus, lymph nodes, spleen and bone marrow, was high between e15.5 and p10, and decreased in adulthood. MLF1-IP KO embryos failed to develop beyond e6.5. On the other hand, MLF1-IP+/− mice were alive and fertile, with no obvious anomalies. Lymphoid organ size, weight, cellularity and cell sub-populations in MLF1-IP+/− mice were in the normal range. The functions of MLF1-IP+/− T cells and naïve CD4 cells, in terms of TCR-stimulated proliferation and Th1, Th17 and Treg cell differentiation in vitro, were comparable to those of wild type T cells. Our study demonstrates that MLF1-IP performs unique functions during mouse embryonic development, particularly around e6.5, when there was degeneration of epiblasts. However, the cells could proliferate dozens of rounds without MLF1-IP. MLF1-IP expression at about 50% of its normal level is sufficient to sustain mice life and the development of their immune system without apparent abnormalities. Our results also raise an intriguing question that MLF1-IP might have additional functions unrelated to cell proliferation. PMID:23724000

Inorganic SnIP-Type Double Helices in Main-Group Chemistry.

PubMed

Baumgartner, Maximilian; Weihrich, Richard; Nilges, Tom

2017-05-05

Inspired by the synthesis of the first atomic-scale double-helix semiconductor SnIP, this study deals with the question of whether more atomistic, inorganic double-helix compounds are accessible. With the aid of quantum chemical calculations, we have identified 31 candidates by a homoatomic substitution in MXPn, varying the Group 14 M-element from Si to Pb, the Group 17 X-element from F to I and replacing the pnictide (Pn) phosphorus by arsenic. The double-helical structure of SnIP has been used as the starting model for all candidates and the electronic structure and vibrational spectra were determined within the framework of density functional theory (DFT). Varying the outer MX or the inner Pn helix led to the conclusion that iodide- and bromide-containing MXPn compounds show similar structures to SnIP. Here, the calculations indicate interesting effects for electronic band-gap tuning. For the highly polarized fluorides, a segregation of the helices to more complex MX substructures is predicted. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fast rerouting schemes for protected mobile IP over MPLS networks

NASA Astrophysics Data System (ADS)

Wen, Chih-Chao; Chang, Sheng-Yi; Chen, Huan; Chen, Kim-Joan

2005-10-01

Fast rerouting is a critical traffic engineering operation in the MPLS networks. To implement the Mobile IP service over the MPLS network, one can collaborate with the fast rerouting operation to enhance the availability and survivability. MPLS can protect critical LSP tunnel between Home Agent (HA) and Foreign Agent (FA) using the fast rerouting scheme. In this paper, we propose a simple but efficient algorithm to address the triangle routing problem for the Mobile IP over the MPLS networks. We consider this routing issue as a link weighting and capacity assignment (LW-CA) problem. The derived solution is used to plan the fast restoration mechanism to protect the link or node failure. In this paper, we first model the LW-CA problem as a mixed integer optimization problem. Our goal is to minimize the call blocking probability on the most congested working truck for the mobile IP connections. Many existing network topologies are used to evaluate the performance of our scheme. Results show that our proposed scheme can obtain the best performance in terms of the smallest blocking probability compared to other schemes.

Plasma interferon-gamma-inducible protein-10 (IP-10) levels during acute hepatitis C virus infection

PubMed Central

Grebely, Jason; Feld, Jordan J.; Applegate, Tanya; Matthews, Gail V.; Hellard, Margaret; Sherker, Alana; Petoumenos, Kathy; Zang, Geng; Shaw, Ineke; Yeung, Barbara; George, Jacob; Teutsch, Suzy; Kaldor, John M.; Cherepanov, Vera; Bruneau, Julie; Shoukry, Naglaa H.; Lloyd, Andrew R.; Dore, Gregory J.

2013-01-01

Systemic levels of interferon-gamma-inducible protein-10 (IP-10) are predictive of treatment-induced clearance in chronic HCV. In the present study, factors associated with plasma IP-10 levels at the time of acute HCV detection and the association between IP-10 levels and spontaneous clearance were assessed in three cohorts of acute HCV infection. Among 300 individuals, 245 (181 male, 47 HIV+) were HCV RNA+ at acute HCV detection. In adjusted analysis, factors independently associated with IP-10 levels ≥150 pg/mL (median level) included HCV RNA levels >6 log IU/mL, HIV co-infection and non-Aboriginal ethnicity. Among 245 HCV RNA+ at acute HCV detection, 214 were untreated (n=137) or had persistent infection (infection duration ≥26 weeks) at treatment initiation (n=77). Spontaneous clearance occurred in 14% (29 of 214). Individuals without spontaneous clearance had significantly higher mean plasma IP-10 levels at the time of acute HCV detection than those with clearance (248±32 vs. 142±22 pg/mL, P=0.008). The proportion of individuals with spontaneous clearance was 0% (0 of 22, P=0.048) and 16% (27 of 165) and in those in those with and without plasma IP-10 levels ≥380 pg/mL. In adjusted analyses, favourable IL28B genotype was associated with spontaneous clearance, while higher HCV RNA level was independently associated with lower odds of spontaneous clearance. Conclusion High IP-10 levels at acute HCV detection were associated with failure to spontaneously clear HCV. Patients with acute HCV and high baseline IP-10 levels, particularly >380 pg/mL, should be considered for early therapeutic intervention, and those with low levels should defer therapy for potential spontaneous clearance. PMID:23325615

Aeronautical Related Applications Using ATN and TCP/IP Research Report

NASA Technical Reports Server (NTRS)

Dhas, C.; Mulkerin, T.; Wargo, C.; Nielsen, R.; Gaughan, T.; Griner, James H., Jr. (Technical Monitor)

2000-01-01

The course for the future aeronautical communications architecture has been defined for more than 10 years and is known as the Aeronautical Telecommunication Network (ATN). However, the operational implementations of making use of the ATN remain 3-5 years away, and these implementations are still only in the early phases of long-range projects. Thus, it is an objective of this effort to consider what the potential outcome within the air transport industry may be, given the rapid growth in commercial-off-the-shelf (COTS) products, networks, and services that are based upon the Internet TCP/IP protocol suite.

Differential principal component analysis of ChIP-seq.

PubMed

Ji, Hongkai; Li, Xia; Wang, Qian-fei; Ning, Yang

2013-04-23

We propose differential principal component analysis (dPCA) for analyzing multiple ChIP-sequencing datasets to identify differential protein-DNA interactions between two biological conditions. dPCA integrates unsupervised pattern discovery, dimension reduction, and statistical inference into a single framework. It uses a small number of principal components to summarize concisely the major multiprotein synergistic differential patterns between the two conditions. For each pattern, it detects and prioritizes differential genomic loci by comparing the between-condition differences with the within-condition variation among replicate samples. dPCA provides a unique tool for efficiently analyzing large amounts of ChIP-sequencing data to study dynamic changes of gene regulation across different biological conditions. We demonstrate this approach through analyses of differential chromatin patterns at transcription factor binding sites and promoters as well as allele-specific protein-DNA interactions.

ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data.

PubMed

Ravanmehr, Vida; Kim, Minji; Wang, Zhiying; Milenkovic, Olgica

2018-03-15

Chromatin immunoprecipitation sequencing (ChIP-seq) experiments are inexpensive and time-efficient, and result in massive datasets that introduce significant storage and maintenance challenges. To address the resulting Big Data problems, we propose a lossless and lossy compression framework specifically designed for ChIP-seq Wig data, termed ChIPWig. ChIPWig enables random access, summary statistics lookups and it is based on the asymptotic theory of optimal point density design for nonuniform quantizers. We tested the ChIPWig compressor on 10 ChIP-seq datasets generated by the ENCODE consortium. On average, lossless ChIPWig reduced the file sizes to merely 6% of the original, and offered 6-fold compression rate improvement compared to bigWig. The lossy feature further reduced file sizes 2-fold compared to the lossless mode, with little or no effects on peak calling and motif discovery using specialized NarrowPeaks methods. The compression and decompression speed rates are of the order of 0.2 sec/MB using general purpose computers. The source code and binaries are freely available for download at https://github.com/vidarmehr/ChIPWig-v2, implemented in C ++. milenkov@illinois.edu. Supplementary data are available at Bioinformatics online.

The CANopen Controller IP Core: Implementation, Synthesis and Test Results

NASA Astrophysics Data System (ADS)

Caramia, Maurizio; Bolognino, Luca; Montagna, Mario; Tosi, Pietro; Errico, Walter; Bigongiari, Franco; Furano, Gianluca

2011-08-01

This paper will describe the implementation and test results of the CANopen Controller IP Core (CCIPC) implemented by Thales Alenia Space and SITAEL Aerospace with the support of ESA in the frame of the EXOMARS Project. The CCIPC is a configurable VHDL implementation of the CANOPEN protocol [1]; it is foreseen to be used as CAN bus slave controller within the EXOMARS Entry Descending and Landing Demonstrato Module (EDM) and Rover Module. The CCIPC features, configuration capability, synthesis and test results will be described and the evidence of the state of maturity of this innovative IP core will be demonstrated.

Buffer kinetics shape the spatiotemporal patterns of IP3-evoked Ca2+ signals

PubMed Central

Dargan, Sheila L; Parker, Ian

2003-01-01

Ca2+ liberation through inositol 1,4,5-trisphosphate receptors (IP3Rs) plays a universal role in cell regulation, and specificity of cell signalling is achieved through the spatiotemporal patterning of Ca2+ signals. IP3Rs display Ca2+-induced Ca2+ release (CICR), but are grouped in clusters so that regenerative Ca2+ signals may remain localized to individual clusters, or propagate globally between clusters by successive cycles of Ca2+ diffusion and CICR. We used confocal microscopy and photoreleased IP3 in Xenopus oocytes to study how these properties are modulated by mobile cytosolic Ca2+ buffers. EGTA (a buffer with slow ‘on-rate’) speeded Ca2+ signals and ‘balkanized’ Ca2+ waves by dissociating them into local signals. In contrast, BAPTA (a fast buffer with similar affinity) slowed Ca2+ responses and promoted ‘globalization’ of spatially uniform Ca2+ signals. These actions are likely to arise through differential effects on Ca2+ feedback within and between IP3R clusters, because Ca2+ signals evoked by influx through voltage-gated channels were little affected. We propose that cell-specific expression of Ca2+-binding proteins with distinct kinetics may shape the time course and spatial distribution of IP3-evoked Ca2+ signals for specific physiological roles. PMID:14555715

Optical switching using IP protocol

NASA Astrophysics Data System (ADS)

Utreras, Andres J.; Gusqui, Luis; Reyes, Andres; Mena, Ricardo I.; Licenko, Gennady L.; Amirgaliyev, Yedilkhan; Komada, Paweł; Luganskaya, Saule; Kashaganova, Gulzhan

2017-08-01

To understand and evaluate the Optical Layer, and how it will affect the IP protocols over WDM (Switching), the present analyse is proposed. Optical communications have attractive proprieties, but also have some disadvantages, so the challenge is to combine the best of both branches. In this paper, general concepts for different options of switching are reviewed as: optical burst switching (OBS) and automatically switching optical network (ASON). Specific details such as their architectures are also discussed. In addition, the relevant characteristics of each variation for switching are reviewed.

The conserved Wdr8-hMsd1/SSX2IP complex localises to the centrosome and ensures proper spindle length and orientation

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

Hori, Akiko; Morand, Agathe; Ikebe, Chiho

2015-12-04

The centrosome plays a pivotal role in a wide range of cellular processes and its dysfunction is causally linked to many human diseases including cancer and developmental and neurological disorders. This organelle contains more than one hundred components, and yet many of them remain uncharacterised. Here we identified a novel centrosome protein Wdr8, based upon the structural conservation of the fission yeast counterpart. We showed that Wdr8 constitutively localises to the centrosome and super resolution microscopy uncovered that this protein is enriched at the proximal end of the mother centriole. Furthermore, we identified hMsd1/SSX2IP, a conserved spindle anchoring protein, asmore » one of Wdr8 interactors by mass spectrometry. Wdr8 formed a complex and partially colocalised with hMsd1/SSX2IP. Intriguingly, knockdown of Wdr8 or hMsd1/SSX2IP displayed very similar mitotic defects, in which spindle microtubules became shortened and misoriented. Indeed, Wdr8 depletion resulted in the reduced recruitment of hMsd1/SSX2IP to the mitotic centrosome, though the converse is not true. Together, we propose that the conserved Wdr8-hMsd1/SSX2IP complex plays a critical role in controlling proper spindle length and orientation. - Highlights: • Human Wdr8 is a centrosomal protein enriched in the proximal end of the centriole. • Wdr8 and hMsd1/SSX2IP form a complex conserved in fungi. • Depletion of Wdr8 results in shorter, tilted spindle microtubules. • Depletion phenotypes of Wdr8 are very similar to those of hMsd1/SSX2IP knockdown.« less

Msd1/SSX2IP-dependent microtubule anchorage ensures spindle orientation and primary cilia formation

PubMed Central

Hori, Akiko; Ikebe, Chiho; Tada, Masazumi; Toda, Takashi

2014-01-01

Anchoring microtubules to the centrosome is critical for cell geometry and polarity, yet the molecular mechanism remains unknown. Here we show that the conserved human Msd1/SSX2IP is required for microtubule anchoring. hMsd1/SSX2IP is delivered to the centrosome in a centriolar satellite-dependent manner and binds the microtubule-nucleator γ-tubulin complex. hMsd1/SSX2IP depletion leads to disorganised interphase microtubules and misoriented mitotic spindles with reduced length and intensity. Furthermore, hMsd1/SSX2IP is essential for ciliogenesis, and during zebrafish embryogenesis, knockdown of its orthologue results in ciliary defects and disturbs left-right asymmetry. We propose that the Msd1 family comprises conserved microtubule-anchoring proteins. PMID:24397932

Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data.

PubMed

Teng, Mingxiang; Irizarry, Rafael A

2017-11-01

The main application of ChIP-seq technology is the detection of genomic regions that bind to a protein of interest. A large part of functional genomics' public catalogs is based on ChIP-seq data. These catalogs rely on peak calling algorithms that infer protein-binding sites by detecting genomic regions associated with more mapped reads (coverage) than expected by chance, as a result of the experimental protocol's lack of perfect specificity. We find that GC-content bias accounts for substantial variability in the observed coverage for ChIP-seq experiments and that this variability leads to false-positive peak calls. More concerning is that the GC effect varies across experiments, with the effect strong enough to result in a substantial number of peaks called differently when different laboratories perform experiments on the same cell line. However, accounting for GC content bias in ChIP-seq is challenging because the binding sites of interest tend to be more common in high GC-content regions, which confounds real biological signals with unwanted variability. To account for this challenge, we introduce a statistical approach that accounts for GC effects on both nonspecific noise and signal induced by the binding site. The method can be used to account for this bias in binding quantification as well to improve existing peak calling algorithms. We use this approach to show a reduction in false-positive peaks as well as improved consistency across laboratories. © 2017 Teng and Irizarry; Published by Cold Spring Harbor Laboratory Press.

Determination of the Parameter Sets for the Best Performance of IPS-driven ENLIL Model

NASA Astrophysics Data System (ADS)

Yun, Jongyeon; Choi, Kyu-Cheol; Yi, Jonghyuk; Kim, Jaehun; Odstrcil, Dusan

2016-12-01

Interplanetary scintillation-driven (IPS-driven) ENLIL model was jointly developed by University of California, San Diego (UCSD) and National Aeronaucics and Space Administration/Goddard Space Flight Center (NASA/GSFC). The model has been in operation by Korean Space Weather Cetner (KSWC) since 2014. IPS-driven ENLIL model has a variety of ambient solar wind parameters and the results of the model depend on the combination of these parameters. We have conducted researches to determine the best combination of parameters to improve the performance of the IPS-driven ENLIL model. The model results with input of 1,440 combinations of parameters are compared with the Advanced Composition Explorer (ACE) observation data. In this way, the top 10 parameter sets showing best performance were determined. Finally, the characteristics of the parameter sets were analyzed and application of the results to IPS-driven ENLIL model was discussed.

The conserved Wdr8-hMsd1/SSX2IP complex localises to the centrosome and ensures proper spindle length and orientation

PubMed Central

Hori, Akiko; Morand, Agathe; Ikebe, Chiho; Frith, David; Snijders, Ambrosius P.; Toda, Takashi

2015-01-01

The centrosome plays a pivotal role in a wide range of cellular processes and its dysfunction is causally linked to many human diseases including cancer and developmental and neurological disorders. This organelle contains more than one hundred components, and yet many of them remain uncharacterised. Here we identified a novel centrosome protein Wdr8, based upon the structural conservation of the fission yeast counterpart. We showed that Wdr8 constitutively localises to the centrosome and super resolution microscopy uncovered that this protein is enriched at the proximal end of the mother centriole. Furthermore, we identified hMsd1/SSX2IP, a conserved spindle anchoring protein, as one of Wdr8 interactors by mass spectrometry. Wdr8 formed a complex and partially colocalised with hMsd1/SSX2IP. Intriguingly, knockdown of Wdr8 or hMsd1/SSX2IP displayed very similar mitotic defects, in which spindle microtubules became shortened and misoriented. Indeed, Wdr8 depletion resulted in the reduced recruitment of hMsd1/SSX2IP to the mitotic centrosome, though the converse is not true. Together, we propose that the conserved Wdr8-hMsd1/SSX2IP complex plays a critical role in controlling proper spindle length and orientation. PMID:26545777

Protein kinase C (PKC) phosphorylates human platelet inositol trisphosphate 5/sup +/-/-phosphomonoesterase (IP/sub 3/ 5'-p'tase) increasing phosphatase activity

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

Connolly, T.M.; Majerus, P.W.

1986-05-01

Phosphoinositide breakdown in response to thrombin stimulation of human platelets generates messenger molecules that activate PKC (diglyceride) and mobilize Ca/sup + +/ (inositol tris-phosphates). The water soluble products of phospholipase C-mediated metabolism of phosphatidylinositol 4,5-diphosphate are inositol 1,4,5 P/sub 3/ (IP/sub 3/) and inositol 1:2-cyclic 4,5 P/sub 3/ (cIP/sub 3/). A specific phosphatase, IP/sub 3/ 5'-p'tase, cleaves the 5 phosphate from IP/sub 3/ or cIP/sub 3/ to form IP/sub 2/ or cIP/sub 2/ and P/sub i/, none of which mobilizes Ca/sup + +/. Thus, the IP/sub 3/ 5'-p'tase may regulate cellular responses to IP/sub 3/ or cIP/sub 3/. The authorsmore » find that IP/sub 3/ 5'-p'tase isolated from human platelets is phosphorylated by rat brain PKC, resulting in a 4-fold increase in IP/sub 3/ 5'-p'tase activity. The authors phosphorylated IP/sub 3/ 5'-p'tase using ..gamma.. /sup 32/P-ATP and found that the labeled enzyme comigrated on SDS-PAGE with the previously described 40K protein phosphorylated in response to thrombin stimulation of platelets. The similarity of the PKC-phosphorylated IP/sub 3/ 5'-p'tase observed in vitro and the thrombin-stimulated phosphorylated 40K protein known to be phosphorylated by PKC in vivo, suggests that these proteins may be the same. These results suggest that platelet Ca/sup + +/ mobilization maybe regulated by PKC phosphorylation of the IP/sub 3/ 5'-p'tase and can explain the observation that phorbol ester treatment of intact human platelets results in decreased production of IP/sub 3/ and decreased Ca/sup + +/ mobilization upon subsequent thrombin addition.« less

CTSA‐IP: A Solution to Identifying and Aggregating Intellectual Property across the NIH Clinical Translational Science Award (CTSA) Consortium of Biomedical Research Institutes

PubMed Central

Hazard, Mike; Steele, Scott; Wang, Dongwen; Pearson, Thomas; Scheideler, Mark; Dewhurst, Steve

2011-01-01

Abstract  One of the objectives of the Consortium of Institutions with Clinical and Translational Science Awards (CTSAs) is to enhance technology transfer among the CTSAs and with public and private sector partners. Clinical and Translational Sciences Award Intellectual Property (CTSA‐IP; http://www.CTSAIP.org) is a web‐based, open access IP search tool that aggregates and promotes technologies from member institutions of the National Institutes of Health’s (NIH) CTSAs consortium. Its ultimate aim is to stimulate collaborative research activity by encouraging the formation of public‐private partnerships with CTSA institutions and the NIH. First launched in 2009, CTSA‐IP has grown rapidly and met its first objectives of developing wide member institution participation and site usage. This communication will discuss the strategy employed in the initiative of aggregating IP across institutional boundaries, the promise that lies therein, as well as the challenges encountered and lessons learned in promoting CTSA‐wide engagement. Clin Trans Sci 2011; Volume 4: 328–331 PMID:22029803

IP-10 measured by Dry Plasma Spots as biomarker for therapy responses in Mycobacterium Tuberculosis infection.

PubMed

Tonby, Kristian; Ruhwald, Morten; Kvale, Dag; Dyrhol-Riise, Anne Ma

2015-03-18

Tuberculosis (TB) has huge impact on human morbidity and mortality and biomarkers to support rapid TB diagnosis and ensure treatment initiation and cure are needed, especially in regions with high prevalence of multi-drug resistant TB. Soluble interferon gamma inducible protein 10 (IP-10) analyzed from dry plasma spots (DPS) has potential as an immunodiagnostic marker in TB infection. We analyzed IP-10 levels in plasma directly and extracted from DPS in parallel by ELISA from 34 clinically well characterized patients with TB disease before and throughout 24 weeks of effective anti-TB chemotherapy. We detected a significant decline of IP-10 levels in both plasma and DPS already after two weeks of therapy with good correlation between the tests. This was observed both in pulmonary and extrapulmonary TB. In conclusion, plasma IP-10 may serve as an early biomarker for anti-TB chemotherapy responses and the IP-10 DPS method has potential to be developed into a point-of care test for use in resource-limited settings. Further studies must be performed to validate the use of IP-10 DPS in TB high endemic countries.

KChIP1 modulation of Kv4.3-mediated A-type K(+) currents and repetitive firing in hippocampal interneurons.

PubMed

Bourdeau, M L; Laplante, I; Laurent, C E; Lacaille, J-C

2011-03-10

Neuronal A-type K(+) channels regulate action potential waveform, back-propagation and firing frequency. In hippocampal CA1 interneurons located at the stratum lacunosum-moleculare/radiatum junction (LM/RAD), Kv4.3 mediates A-type K(+) currents and a Kv4 β-subunit of the Kv channel interacting protein (KChIP) family, KChIP1, appears specifically expressed in these cells. However, the functional role of this accessory subunit in A-type K(+) currents and interneuron excitability remains largely unknown. Thus, first we studied KChIP1 and Kv4.3 channel interactions in human embryonic kidney 293 (HEK293) cells and determined that KChIP1 coexpression modulated the biophysical properties of Kv4.3 A-type currents (faster recovery from inactivation, leftward shift of activation curve, faster rise time and slower decay) and this modulation was selectively prevented by KChIP1 short interfering RNA (siRNA) knockdown. Next, we evaluated the effects of KChIP1 down-regulation by siRNA on A-type K(+) currents in LM/RAD interneurons in slice cultures. Recovery from inactivation of A-type K(+) currents was slower after KChIP1 down-regulation but other properties were unchanged. In addition, down-regulation of KChIP1 levels did not affect action potential waveform and firing, but increased firing frequency during suprathreshold depolarizations, indicating that KChIP1 regulates interneuron excitability. The effects of KChIP1 down-regulation were cell-specific since CA1 pyramidal cells that do not express KChIP1 were unaffected. Overall, our findings suggest that KChIP1 interacts with Kv4.3 in LM/RAD interneurons, enabling faster recovery from inactivation of A-type currents and thus promoting stronger inhibitory control of firing during sustained activity. Copyright © 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

76 FR 59916 - Interconnected VoIP Service; Wireless E911 Location Accuracy Requirements; E911 Requirements for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-28

... FEDERAL COMMUNICATIONS COMMISSION 47 CFR Part 20 [PS Docket No. 07-114, GN Docket No. 11-117, WC...; E911 Requirements for IP-Enabled Service Providers AGENCY: Federal Communications Commission. ACTION...-based standard over time. We also require all Commercial Mobile Radio Service (CMRS) providers...

High intercontinental migration rates and population admixture in the sapstain fungus Ophiostoma ips

Treesearch

Xudong Zhou; Treena I. Burgess; Wilhelm De Beer; Francois Lieutier; Annie Yart; Angus Carnegie; Julio Mena Portales; Brenda D. Wingfield; Michael J. Wingfield

2007-01-01

Ophiostoma ips is a common fungal associate of various conifer-infesting bark beetles in their native ranges and has been introduced into non-native pine plantations in the Southern Hemisphere. In this study, we used 10 microsatellite markers to investigate the population biology of O. ips in native (Cuba, France, Morocco and USA) and non-native (Australia, Chile and...

High intercontinental migration rates and population admixture in the sapstain fungus Ophiostoma ips

Treesearch

Xudong Zhou; Treena I. Burgess; Z. Wilhelm De Beer; Francois Lieutier; Annie Yart; Kier Klepzig; Angus Carnegie; Julio Mena Portales; Brenda D. Wingfield; Michael J. Wingfield

2006-01-01

Ophiostoma ips is a common fungal associate of various conifer-infesting bark beetles in their native ranges and has been introduced into non-native pine plantations in the Southern Hemisphere. In this study, we used 10 microsatellite markers to investigate the population biology of O. ips in native (Cuba, France, Morocco and USA) and non-native (...

Digital controller design: Continuous and discrete describing function analysis of the IPS system

NASA Technical Reports Server (NTRS)

1977-01-01

The dynamic equations and the mathematical model of the continuous-data IPS control system are developed. The IPS model considered included one flexible body mode and was hardmounted to the Orbiter/Pallet. The model contains equations describing a torque feed-forward loop (using accelerometers as inputs) which will aid in reducing the pointing errors caused by Orbiter disturbances.

Rapid Recycling of Ca2+ between IP3-Sensitive Stores and Lysosomes

PubMed Central

López Sanjurjo, Cristina I.; Tovey, Stephen C.; Taylor, Colin W.

2014-01-01

Inositol 1,4,5-trisphosphate (IP3) evokes release of Ca2+ from the endoplasmic reticulum (ER), but the resulting Ca2+ signals are shaped by interactions with additional intracellular organelles. Bafilomycin A1, which prevents lysosomal Ca2+ uptake by inhibiting H+ pumping into lysosomes, increased the amplitude of the initial Ca2+ signals evoked by carbachol in human embryonic kidney (HEK) cells. Carbachol alone and carbachol in combination with parathyroid hormone (PTH) evoke Ca2+ release from distinct IP3-sensitive Ca2+ stores in HEK cells stably expressing human type 1 PTH receptors. Bafilomycin A1 similarly exaggerated the Ca2+ signals evoked by carbachol or carbachol with PTH, indicating that Ca2+ released from distinct IP3-sensitive Ca2+ stores is sequestered by lysosomes. The Ca2+ signals resulting from store-operated Ca2+ entry, whether evoked by thapsigargin or carbachol, were unaffected by bafilomycin A1. Using Gd3+ (1 mM) to inhibit both Ca2+ entry and Ca2+ extrusion, HEK cells were repetitively stimulated with carbachol to assess the effectiveness of Ca2+ recycling to the ER after IP3-evoked Ca2+ release. Blocking lysosomal Ca2+ uptake with bafilomycin A1 increased the amplitude of each carbachol-evoked Ca2+ signal without affecting the rate of Ca2+ recycling to the ER. This suggests that Ca2+ accumulated by lysosomes is rapidly returned to the ER. We conclude that lysosomes rapidly, reversibly and selectively accumulate the Ca2+ released by IP3 receptors residing within distinct Ca2+ stores, but not the Ca2+ entering cells via receptor-regulated, store-operated Ca2+ entry pathways. PMID:25337829

Rapid recycling of Ca2+ between IP3-sensitive stores and lysosomes.

PubMed

López Sanjurjo, Cristina I; Tovey, Stephen C; Taylor, Colin W

2014-01-01

Inositol 1,4,5-trisphosphate (IP3) evokes release of Ca2+ from the endoplasmic reticulum (ER), but the resulting Ca2+ signals are shaped by interactions with additional intracellular organelles. Bafilomycin A1, which prevents lysosomal Ca2+ uptake by inhibiting H+ pumping into lysosomes, increased the amplitude of the initial Ca2+ signals evoked by carbachol in human embryonic kidney (HEK) cells. Carbachol alone and carbachol in combination with parathyroid hormone (PTH) evoke Ca2+ release from distinct IP3-sensitive Ca2+ stores in HEK cells stably expressing human type 1 PTH receptors. Bafilomycin A1 similarly exaggerated the Ca2+ signals evoked by carbachol or carbachol with PTH, indicating that Ca2+ released from distinct IP3-sensitive Ca2+ stores is sequestered by lysosomes. The Ca2+ signals resulting from store-operated Ca2+ entry, whether evoked by thapsigargin or carbachol, were unaffected by bafilomycin A1. Using Gd3+ (1 mM) to inhibit both Ca2+ entry and Ca2+ extrusion, HEK cells were repetitively stimulated with carbachol to assess the effectiveness of Ca2+ recycling to the ER after IP3-evoked Ca2+ release. Blocking lysosomal Ca2+ uptake with bafilomycin A1 increased the amplitude of each carbachol-evoked Ca2+ signal without affecting the rate of Ca2+ recycling to the ER. This suggests that Ca2+ accumulated by lysosomes is rapidly returned to the ER. We conclude that lysosomes rapidly, reversibly and selectively accumulate the Ca2+ released by IP3 receptors residing within distinct Ca2+ stores, but not the Ca2+ entering cells via receptor-regulated, store-operated Ca2+ entry pathways.

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.

PubMed

Chen, Li; Wang, Chi; Qin, Zhaohui S; Wu, Hao

2015-06-15

ChIP-seq is a powerful technology to measure the protein binding or histone modification strength in the whole genome scale. Although there are a number of methods available for single ChIP-seq data analysis (e.g. 'peak detection'), rigorous statistical method for quantitative comparison of multiple ChIP-seq datasets with the considerations of data from control experiment, signal to noise ratios, biological variations and multiple-factor experimental designs is under-developed. In this work, we develop a statistical method to perform quantitative comparison of multiple ChIP-seq datasets and detect genomic regions showing differential protein binding or histone modification. We first detect peaks from all datasets and then union them to form a single set of candidate regions. The read counts from IP experiment at the candidate regions are assumed to follow Poisson distribution. The underlying Poisson rates are modeled as an experiment-specific function of artifacts and biological signals. We then obtain the estimated biological signals and compare them through the hypothesis testing procedure in a linear model framework. Simulations and real data analyses demonstrate that the proposed method provides more accurate and robust results compared with existing ones. An R software package ChIPComp is freely available at http://web1.sph.emory.edu/users/hwu30/software/ChIPComp.html. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets.

PubMed

Zuo, Chandler; Chen, Kailei; Keleş, Sündüz

2017-06-01

Current analytic approaches for querying large collections of chromatin immunoprecipitation followed by sequencing (ChIP-seq) data from multiple cell types rely on individual analysis of each data set (i.e., peak calling) independently. This approach discards the fact that functional elements are frequently shared among related cell types and leads to overestimation of the extent of divergence between different ChIP-seq samples. Methods geared toward multisample investigations have limited applicability in settings that aim to integrate 100s to 1000s of ChIP-seq data sets for query loci (e.g., thousands of genomic loci with a specific binding site). Recently, Zuo et al. developed a hierarchical framework for state-space matrix inference and clustering, named MBASIC, to enable joint analysis of user-specified loci across multiple ChIP-seq data sets. Although this versatile framework estimates both the underlying state-space (e.g., bound vs. unbound) and also groups loci with similar patterns together, its Expectation-Maximization-based estimation structure hinders its applicability with large number of loci and samples. We address this limitation by developing MAP-based asymptotic derivations from Bayes (MAD-Bayes) framework for MBASIC. This results in a K-means-like optimization algorithm that converges rapidly and hence enables exploring multiple initialization schemes and flexibility in tuning. Comparison with MBASIC indicates that this speed comes at a relatively insignificant loss in estimation accuracy. Although MAD-Bayes MBASIC is specifically designed for the analysis of user-specified loci, it is able to capture overall patterns of histone marks from multiple ChIP-seq data sets similar to those identified by genome-wide segmentation methods such as ChromHMM and Spectacle.

Host-tree monoterpenes and biosynthesis of aggregation pheromones in the bark beetle ips paraconfusus

USDA-ARS?s Scientific Manuscript database

In the 1970-80s, vapors of the common conifer tree monoterpenes, myrcene and a-pinene, were shown to serve as precursors of ipsenol, ipsdienol and cis-verbenol, aggregation pheromone components of Ips paraconfusus. A paradigm developed that Ips bark beetles utilize pre-formed monoterpene precursors ...

Current advances in the generation of human iPS cells: implications in cell-based regenerative medicine.

PubMed

Revilla, Ana; González, Clara; Iriondo, Amaia; Fernández, Bárbara; Prieto, Cristina; Marín, Carlos; Liste, Isabel

2016-11-01

Over the last few years, the generation of induced pluripotent stem cells (iPSCs) from human somatic cells has proved to be one of the most potentially useful discoveries in regenerative medicine. iPSCs are becoming an invaluable tool to study the pathology of different diseases and for drug screening. However, several limitations still affect the possibility of applying iPS cell-based technology in therapeutic prospects. Most strategies for iPSCs generation are based on gene delivery via retroviral or lentiviral vectors, which integrate into the host's cell genome, causing a remarkable risk of insertional mutagenesis and oncogenic transformation. To avoid such risks, significant advances have been made with non-integrative reprogramming strategies. On the other hand, although many different kinds of somatic cells have been employed to generate iPSCs, there is still no consensus about the ideal type of cell to be reprogrammed. In this review we present the recent advances in the generation of human iPSCs, discussing their advantages and limitations in terms of safety and efficiency. We also present a selection of somatic cell sources, considering their capability to be reprogrammed and tissue accessibility. From a translational medicine perspective, these two topics will provide evidence to elucidate the most suitable combination of reprogramming strategy and cell source to be applied in each human iPSC-based therapy. The wide variety of diseases this technology could treat opens a hopeful future for regenerative medicine. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Saturation analysis of ChIP-seq data for reproducible identification of binding peaks

PubMed Central

Hansen, Peter; Hecht, Jochen; Ibrahim, Daniel M.; Krannich, Alexander; Truss, Matthias; Robinson, Peter N.

2015-01-01

Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) is a powerful technology to identify the genome-wide locations of transcription factors and other DNA binding proteins. Computational ChIP-seq peak calling infers the location of protein–DNA interactions based on various measures of enrichment of sequence reads. In this work, we introduce an algorithm, Q, that uses an assessment of the quadratic enrichment of reads to center candidate peaks followed by statistical analysis of saturation of candidate peaks by 5′ ends of reads. We show that our method not only is substantially faster than several competing methods but also demonstrates statistically significant advantages with respect to reproducibility of results and in its ability to identify peaks with reproducible binding site motifs. We show that Q has superior performance in the delineation of double RNAPII and H3K4me3 peaks surrounding transcription start sites related to a better ability to resolve individual peaks. The method is implemented in C+l+ and is freely available under an open source license. PMID:26163319

Enhancing the Classification Accuracy of IP Geolocation

DTIC Science & Technology

2013-10-01

accurately identify the geographic location of Internet devices has signficant implications for online- advertisers, application developers , network...Real Media, Comedy Central, Netflix and Spotify) and target advertising (e.g., Google). More re- cently, IP geolocation techniques have been deployed...distance to delay function and how they triangulate the position of the target. Statistical Geolocation [14] develops a joint probability density

Comparison of Integer Programming (IP) Solvers for Automated Test Assembly (ATA). Research Report. ETS RR-15-05

ERIC Educational Resources Information Center

Donoghue, John R.

2015-01-01

At the heart of van der Linden's approach to automated test assembly (ATA) is a linear programming/integer programming (LP/IP) problem. A variety of IP solvers are available, ranging in cost from free to hundreds of thousands of dollars. In this paper, I compare several approaches to solving the underlying IP problem. These approaches range from…

Ripk3 regulates cardiac microvascular reperfusion injury: The role of IP3R-dependent calcium overload, XO-mediated oxidative stress and F-action/filopodia-based cellular migration.

PubMed

Zhou, Hao; Wang, Jin; Zhu, Pingjun; Hu, Shunying; Ren, Jun

2018-05-01

Ripk3-mediated cellular apoptosis is a major contributor to the pathogenesis of myocardial ischemia reperfusion (IR) injury. However, the mechanisms by which Ripk3 influences microvascular homeostasis and endothelial apoptosis are not completely understood. In this study, loss of Ripk3 inhibited endothelial apoptosis, alleviated luminal swelling, maintained microvasculature patency, reduced the expression of adhesion molecules and limited the myocardial inflammatory response. In vitro, Ripk3 deficiency protected endothelial cells from apoptosis and migratory arrest induced by HR injury. Mechanistically, Ripk3 had the ability to migrate onto the endoplasmic reticulum (ER), leading to ER damage, as evidenced by increased IP3R and XO expression. The higher IP3R content was associated with cellular calcium overload, and increased XO expression was involved in cellular oxidative injury. Furthermore, IP3R-mediated calcium overload and XO-dependent oxidative damage were able to initiate cellular apoptosis. More importantly, IP3R and XO also caused F-actin degradation into G-actin via post-transcriptional modification of cofilin, impairing the formation of the filopodia and limiting the migratory response of endothelial cells. Altogether, our data confirmed that Ripk3 was involved in microvascular IR injury via regulation of IP3R-mediated calcium overload, XO-dependent oxidative damage and filopodia-related cellular migration, ultimately leading to endothelial apoptosis and migratory inhibition. These findings provide a potential target for treating cardiac microcirculatory IR injury. Copyright © 2018 Elsevier Inc. All rights reserved.

Preservation of cardiac function by prolonged action potentials in mice deficient of KChIP2.

PubMed

Grubb, Søren; Aistrup, Gary L; Koivumäki, Jussi T; Speerschneider, Tobias; Gottlieb, Lisa A; Mutsaers, Nancy A M; Olesen, Søren-Peter; Calloe, Kirstine; Thomsen, Morten B

2015-08-01

Inherited ion channelopathies and electrical remodeling in heart disease alter the cardiac action potential with important consequences for excitation-contraction coupling. Potassium channel-interacting protein 2 (KChIP2) is reduced in heart failure and interacts under physiological conditions with both Kv4 to conduct the fast-recovering transient outward K(+) current (Ito,f) and with CaV1.2 to mediate the inward L-type Ca(2+) current (ICa,L). Anesthetized KChIP2(-/-) mice have normal cardiac contraction despite the lower ICa,L, and we hypothesized that the delayed repolarization could contribute to the preservation of contractile function. Detailed analysis of current kinetics shows that only ICa,L density is reduced, and immunoblots demonstrate unaltered CaV1.2 and CaVβ₂ protein levels. Computer modeling suggests that delayed repolarization would prolong the period of Ca(2+) entry into the cell, thereby augmenting Ca(2+)-induced Ca(2+) release. Ca(2+) transients in disaggregated KChIP2(-/-) cardiomyocytes are indeed comparable to wild-type transients, corroborating the preserved contractile function and suggesting that the compensatory mechanism lies in the Ca(2+)-induced Ca(2+) release event. We next functionally probed dyad structure, ryanodine receptor Ca(2+) sensitivity, and sarcoplasmic reticulum Ca(2+) load and found that increased temporal synchronicity of the Ca(2+) release in KChIP2(-/-) cardiomyocytes may reflect improved dyad structure aiding the compensatory mechanisms in preserving cardiac contractile force. Thus the bimodal effect of KChIP2 on Ito,f and ICa,L constitutes an important regulatory effect of KChIP2 on cardiac contractility, and we conclude that delayed repolarization and improved dyad structure function together to preserve cardiac contraction in KChIP2(-/-) mice. Copyright © 2015 the American Physiological Society.

Changes in IP3 Receptor Expression and Function in Aortic Smooth Muscle of Atherosclerotic Mice

PubMed Central

Ewart, Marie-Ann; Ugusman, Azizah; Vishwanath, Anisha; Almabrouk, Tarek A.M.; Alganga, Husam; Katwan, Omar J.; Hubanova, Pavlina; Currie, Susan; Kennedy, Simon

2017-01-01

Peroxynitrite is an endothelium-independent vasodilator that induces relaxation via membrane hyperpolarization. The activation of IP3 receptors triggers the opening of potassium channels and hyperpolarization. Previously we found that relaxation to peroxynitrite was maintained during the development of atherosclerosis due to changes in the expression of calcium-regulatory proteins. In this study we investigated: (1) the mechanism of peroxynitrite-induced relaxation in the mouse aorta, (2) the effect of atherosclerosis on relaxation to peroxynitrite and other vasodilators, and (3) the effect of atherosclerosis on the expression and function of the IP3 receptor. Aortic function was studied using wire myography, and atherosclerosis was induced by fat-feeding ApoE−/− mice. The expression of IP3 receptors was studied using Western blotting and immunohistochemistry. Relaxation to peroxynitrite was attenuated by the IP3 antagonists 2-APB and xestospongin C and also the Kv channel blocker 4-aminopyridine (4-AP). Atherosclerosis attenuated vasodilation to cromakalim and the AMPK activator A769662 but not peroxynitrite. Relaxation was attenuated to a greater extent by 2-APB in atherosclerotic aortae despite the reduced expression of IP3 receptors. 4-AP was less effective in ApoE−/− mice fat-fed for 4 months. Peroxynitrite relaxation involves an IP3-induced calcium release and KV channel activation. This mechanism becomes less important as atherosclerosis develops, and relaxation to peroxynitrite may be maintained by increased calcium extrusion. PMID:28365690

IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria.

PubMed

Baumgart, Meike; Luder, Kerstin; Grover, Shipra; Gätgens, Cornelia; Besra, Gurdyal S; Frunzke, Julia

2013-12-30

The development of new drugs against tuberculosis and diphtheria is focused on disrupting the biogenesis of the cell wall, the unique architecture of which confers resistance against current therapies. The enzymatic pathways involved in the synthesis of the cell wall by these pathogens are well understood, but the underlying regulatory mechanisms are largely unknown. Here, we characterize IpsA, a LacI-type transcriptional regulator conserved among Mycobacteria and Corynebacteria that plays a role in the regulation of cell wall biogenesis. IpsA triggers myo-inositol formation by activating ino1, which encodes inositol phosphate synthase. An ipsA deletion mutant of Corynebacterium glutamicum cultured on glucose displayed significantly impaired growth and presented an elongated cell morphology. Further studies revealed the absence of inositol-derived lipids in the cell wall and a complete loss of mycothiol biosynthesis. The phenotype of the C. glutamicum ipsA deletion mutant was complemented to different extend by homologs from Corynebacterium diphtheriae (dip1969) and Mycobacterium tuberculosis (rv3575), indicating the conserved function of IpsA in the pathogenic species. Additional targets of IpsA with putative functions in cell wall biogenesis were identified and IpsA was shown to bind to a conserved palindromic motif within the corresponding promoter regions. Myo-inositol was identified as an effector of IpsA, causing the dissociation of the IpsA-DNA complex in vitro. This characterization of IpsA function and of its regulon sheds light on the complex transcriptional control of cell wall biogenesis in the mycolata taxon and generates novel targets for drug development.

Transportation of phytopathogenic fungi by the bark beetle Ips sexdentatus boerner and associated mites

Treesearch

J. Levieux; F. Lieutier; John C. Moser; Thelma J. Perry

1989-01-01

The bark beetle Ips sexdentatrds carries several types of conidiospores and ascopores in the pronotal punctures located around the setae on the sides of the pronotum. For swarming beetles, some of the spores seem to be germinating. Nine species of mites were phoretic on swarming Ips sexdentutus in France. Hypophoretic...

Validation of the Children's Interview for Psychiatric Syndromes (ChIPS) with Psychiatrically Hospitalized Adolescents

ERIC Educational Resources Information Center

Swenson, Lance P.; Esposito-Smythers, Christianne; Hunt, Jeffrey I.; Hollander, Beth L. G.; Dyl, Jennifer; Rizzo, Christie J.; Steinley, Douglas L.; Spirito, Anthony

2007-01-01

A study was conducted to examine the concurrent validity of the Children's Interview for Psychiatric Syndromes (ChIPS) for adolescent inpatients aged 12 to 18. The results reveal moderate agreement between ChIPS diagnoses and Schedule for Affective Disorder sand Schizophrenia for School-Age Children-Present and Lifetime version diagnoses.

Impact of dextran sulphate sodium-induced colitis on the intestinal transport of the colon carcinogen PhIP.

PubMed

Nicken, Petra; von Keutz, Anne; Willenberg, Ina; Ostermann, Annika I; Schebb, Nils Helge; Giovannini, Samoa; Kershaw, Olivia; Breves, Gerhard; Steinberg, Pablo

2016-05-01

Colorectal cancer is one of the most frequent cancers in Western countries. Chronic intestinal diseases such as Crohn's disease and ulcerative colitis, in which the intestinal barrier is massively disturbed, significantly raise the risk of developing a colorectal tumour. 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a genotoxic heterocyclic aromatic amine that is formed after strongly heating fish and meat. In this study, the hypothesis that PhIP uptake in the gut is increased during chronic colitis was tested. Chronic colitis was induced by oral administration of dextran sulphate sodium (DSS) to Fischer 344 rats. The transport of PhIP in eight different rat intestinal segments was examined in Ussing chambers. The tissues were incubated with 10 µM PhIP for 90 min, and the concentration of PhIP was determined in the mucosal and serosal compartments of the Ussing chambers as well as in the clamped tissues by LC-MS. Although chronic colitis was clearly induced in the rats, no differences in the intestinal transport of PhIP were observed between control and DSS-treated animals. The hypothesis that in the course of chronic colitis more PhIP is taken up by the intestinal epithelium, thereby increasing the risk of developing colorectal cancer, could not be confirmed in the present report.

78 FR 78319 - Media Bureau Seeks Comment on Application of the IP Closed Captioning Rules to Video Clips

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-26

... Seeks Comment on Application of the IP Closed Captioning Rules to Video Clips AGENCY: Federal... captioning of video clips delivered by Internet protocol (``IP''), including the extent to which industry has voluntarily captioned IP- delivered video clips. The Commission directed the Media Bureau to issue this...

BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates.

PubMed

Goren, Emily; Liu, Peng; Wang, Chao; Wang, Chong

2018-04-19

ChIP-seq experiments that are aimed at detecting DNA-protein interactions require biological replication to draw inferential conclusions, however there is no current consensus on how to analyze ChIP-seq data with biological replicates. Very few methodologies exist for the joint analysis of replicated ChIP-seq data, with approaches ranging from combining the results of analyzing replicates individually to joint modeling of all replicates. Combining the results of individual replicates analyzed separately can lead to reduced peak classification performance compared to joint modeling. Currently available methods for joint analysis may fail to control the false discovery rate at the nominal level. We propose BinQuasi, a peak caller for replicated ChIP-seq data, that jointly models biological replicates using a generalized linear model framework and employs a one-sided quasi-likelihood ratio test to detect peaks. When applied to simulated data and real datasets, BinQuasi performs favorably compared to existing methods, including better control of false discovery rate than existing joint modeling approaches. BinQuasi offers a flexible approach to joint modeling of replicated ChIP-seq data which is preferable to combining the results of replicates analyzed individually. Source code is freely available for download at https://cran.r-project.org/package=BinQuasi, implemented in R. pliu@iastate.edu or egoren@iastate.edu. Supplementary material is available at Bioinformatics online.

Research on an IP disaster recovery storage system

NASA Astrophysics Data System (ADS)

Zeng, Dong; Wang, Yusheng; Zhu, Jianfeng

2008-12-01

According to both the Fibre Channel (FC) Storage Area Network (SAN) switch and Fabric Application Interface Standard (FAIS) mechanism, an iSCSI storage controller is put forward and based upon it, an internet Small Computer System Interface (iSCSI) SAN construction strategy for disaster recovery (DR) is proposed and some multiple sites replication models and a closed queue performance analysis method are also discussed in this paper. The iSCSI storage controller lies in the fabric level of the networked storage infrastructure, and it can be used to connect to both the hybrid storage applications and storage subsystems, besides, it can provide virtualized storage environment and support logical volume access control, and by cooperating with the remote peerparts, a disaster recovery storage system can be built on the basis of the data replication, block-level snapshot and Internet Protocol (IP) take-over functions.

Dispersal of the spruce beetle, Dendroctonus rufipennis, and the engraver beetle, Ips perturbatus, in Alaska.

Treesearch

Richard A. Werner; Edward H. Holsten

1997-01-01

Mark-release-recapture experiments were performed with spruce beetles (Dendroctonus rufipennis (Kirby)) and Ips engraver beetles (Ips perturbatus (Eichhoff)) to determine distance and direction of dispersal. The recapture rate of beetles marked with fluorescent powder was extremely low. Most I. perturbatus...

77 FR 48549 - Eastman Kodak Company, IPS-Dayton Location, Dayton, OH; Notice of Affirmative Determination...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-14

... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-81,387] Eastman Kodak Company, IPS--Dayton Location, Dayton, OH; Notice of Affirmative Determination Regarding Application for...) applicable to workers and former workers of Eastman Kodak Company, IPS- Dayton Location, Dayton, Ohio...

A comparative study of ChIP-seq sequencing library preparation methods.

PubMed

Sundaram, Arvind Y M; Hughes, Timothy; Biondi, Shea; Bolduc, Nathalie; Bowman, Sarah K; Camilli, Andrew; Chew, Yap C; Couture, Catherine; Farmer, Andrew; Jerome, John P; Lazinski, David W; McUsic, Andrew; Peng, Xu; Shazand, Kamran; Xu, Feng; Lyle, Robert; Gilfillan, Gregor D

2016-10-21

ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo "library preparation" to enable subsequent high-throughput sequencing. To facilitate the analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low-input DNA amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures. Notably, recently developed single-cell ChIP procedures employing microfluidics must also employ library preparation reagents to allow downstream sequencing. In this study, seven methods designed for low-input DNA/ChIP-seq sample preparation (Accel-NGS® 2S, Bowman-method, HTML-PCR, SeqPlex™, DNA SMART™, TELP and ThruPLEX®) were performed on five replicates of 1 ng and 0.1 ng input H3K4me3 ChIP material, and compared to a "gold standard" reference PCR-free dataset. The performance of each method was examined for the prevalence of unmappable reads, amplification-derived duplicate reads, reproducibility, and for the sensitivity and specificity of peak calling. We identified consistent high performance in a subset of the tested reagents, which should aid researchers in choosing the most appropriate reagents for their studies. Furthermore, we expect this work to drive future advances by identifying and encouraging use of the most promising methods and reagents. The results may also aid judgements on how comparable are existing datasets that have been prepared with different sample library preparation reagents.

THE 2012 RISE OF THE REMARKABLE TYPE IIn SN 2009ip

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

Prieto, Jose L.; Brimacombe, J.; Drake, A. J.

2013-02-01

Recent observations by Mauerhan et al. have shown the unprecedented transition of the previously identified luminous blue variable (LBV) and supernova (SN) impostor SN 2009ip to a real Type IIn SN explosion. We present {approx}100 optical R- and I-band photometric measurements of SN 2009ip obtained between UT 2012 September 23.6 and October 9.6, using 0.3-0.4 m aperture telescopes from the Coral Towers Observatory in Cairns, Australia. The light curves show well-defined phases, including very rapid brightening early on (0.5 mag in 6 hr observed during the night of September 24), a transition to a much slower rise between September 25more » and September 28, and a plateau/peak around October 7. These changes are coincident with the reported spectroscopic changes that most likely mark the start of a strong interaction between the fast SN ejecta and a dense circumstellar medium formed during the LBV eruptions observed in recent years. In the 16-day observing period, SN 2009ip brightened by 3.7 mag from I = 17.4 mag on September 23.6 (M{sub I} {approx_equal} -14.2) to I = 13.7 mag (M{sub I} {approx_equal} -17.9) on October 9.6, radiating {approx}3 Multiplication-Sign 10{sup 49} erg in the optical wavelength range. As of 2012 October 9.6, SN 2009ip is more luminous than most Type IIP SN and comparable to other Type IIn SN.« less

Role of Caspase-3 Cleaved IP3R1 on Ca2+ Homeostasis and Developmental Competence of Mouse Oocytes and Eggs

PubMed Central

Zhang, Nan; Fissore, Rafael. A.

2014-01-01

Apoptosis in most cell types is accompanied by altered Ca2+ homeostasis. During apoptosis, caspase-3 mediated cleavage of the type 1 inositol 1,4,5-trisphosphate receptor (IP3R1) generates a 95-kDa C-terminal fragment (C-IP3R1), which represents the channel domain of the receptor. Aged mouse eggs display abnormal Ca2+ homeostasis and express C-IP3R1, although whether or not C-IP3R1 expression contributes to Ca2+ misregulation or a decrease in developmental competency is unknown. We sought to answer these questions by injecting in mouse oocytes and eggs cRNAs encoding CIP3R1. We found that: 1) expression of C-IP3R1 in eggs lowered the Ca2+ content of the endoplasmic reticulum (ER), although, as C-IP3R1 is quickly degraded at this stage, its expression did not impair pre-implantation embryo development; 2) expression of CIP3R1 in eggs enhanced fragmentation associated with aging; 3) endogenous IP3R1 is required for aging associated apoptosis, as its down-regulation prevented fragmentation, and expression of C-IP3R1 in eggs with downregulated IP3R1 partly restored fragmentation; 4) C-IP3R1 expression in GV oocytes resulted in persistent levels of protein, which abolished the increase in the ER releasable Ca2+ pool that occurs during maturation, undermined the Ca2+ oscillatory ability of matured eggs and their activation potential. Collectively, this study supports a role for IP3R1 and C-IP3R1 in regulating Ca2+ homeostasis and the ER Ca2+ content during oocyte maturation. Nevertheless, the role of C-IP3R1 on Ca2+ homeostasis in aged eggs seems minor, as in MII eggs the majority of endogenous IP3R1 remains intact and C-IP3R1 undergoes rapid turnover. PMID:24692207

Phoretic mites associated with spruce bark beetle Ips typographus L. (Curculionidae: Scolytinae) from Bulgaria

Treesearch

Danail Takov; Daniela Pilarska; John Moser

2010-01-01

A total of 818 specimens of Ips typographus L. were investigated for the presence of phoretic mites. They were collected from 4 localities in Vitosha Mountain, near Sofia. Five phoretic mites were found: Dendrolaelaps quadrisetus, Trichouropoda polytricha, Histiostoma piceae, Uroobovella ipidis and Proctolaelaps jiseri. 11.1 % from all investigated specimens of Ips...

78 FR 53684 - Misuse of Internet Protocol (IP) Captioned Telephone Service; Telecommunications Relay Services...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-30

... eligibility in order to get a free IP CTS device should be made under penalty of perjury; whether to prohibit the free or significantly subsidized distribution of end user equipment by IP CTS providers; whether... and restrictions on rewards and free equipment. 4. Legal Authority. Section 225(b) of the Act directs...

Mobile Vehicle Teleoperated Over Wireless IP

DTIC Science & Technology

2007-06-13

VideoLAN software suite. The VLC media player portion of this suite handles net- work streaming of video, as well as the receipt and display of the video...is found in appendix C.7. Video Display The video feed is displayed for the operator using VLC opened independently from the control sending program...This gives the operator the most choice in how to configure the display. To connect VLC to the feed all you need is the IP address from the Java

Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for Transcription Factors and Chromatin Factors in Arabidopsis thaliana Roots: From Material Collection to Data Analysis.

PubMed

Cortijo, Sandra; Charoensawan, Varodom; Roudier, François; Wigge, Philip A

2018-01-01

Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) is a powerful technique to investigate in vivo transcription factor (TF) binding to DNA, as well as chromatin marks. Here we provide a detailed protocol for all the key steps to perform ChIP-seq in Arabidopsis thaliana roots, also working on other A. thaliana tissues and in most non-ligneous plants. We detail all steps from material collection, fixation, chromatin preparation, immunoprecipitation, library preparation, and finally computational analysis based on a combination of publicly available tools.

Research study on IPS digital controller design

NASA Technical Reports Server (NTRS)

Kuo, B. C.; Folkerts, C.

1976-01-01

The performance is investigated of the simplified continuous-data model of the Instrument Pointing System (IPS). Although the ultimate objective is to study the digital model of the system, knowledge on the performance of the continuous-data model is important in the sense that the characteristics of the digital system should approach those of the continuous-data system as the sampling period approaches zero.

Network Quality of Service Monitoring for IP Telephony.

ERIC Educational Resources Information Center

Ghita, B. V.; Furnell, S. M.; Lines, B. M.; Le-Foll, D.; Ifeachor, E. C.

2001-01-01

Discusses the development of real-time applications on the Internet for telecommunications and presents a non-intrusive way of determining network performance parameters for voice packet flows within a voice over IP (Internet Protocol), or Internet telephony call. Considers measurement of quality of service and describes results of a preliminary…

IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria

PubMed Central

2013-01-01

Background The development of new drugs against tuberculosis and diphtheria is focused on disrupting the biogenesis of the cell wall, the unique architecture of which confers resistance against current therapies. The enzymatic pathways involved in the synthesis of the cell wall by these pathogens are well understood, but the underlying regulatory mechanisms are largely unknown. Results Here, we characterize IpsA, a LacI-type transcriptional regulator conserved among Mycobacteria and Corynebacteria that plays a role in the regulation of cell wall biogenesis. IpsA triggers myo-inositol formation by activating ino1, which encodes inositol phosphate synthase. An ipsA deletion mutant of Corynebacterium glutamicum cultured on glucose displayed significantly impaired growth and presented an elongated cell morphology. Further studies revealed the absence of inositol-derived lipids in the cell wall and a complete loss of mycothiol biosynthesis. The phenotype of the C. glutamicum ipsA deletion mutant was complemented to different extend by homologs from Corynebacterium diphtheriae (dip1969) and Mycobacterium tuberculosis (rv3575), indicating the conserved function of IpsA in the pathogenic species. Additional targets of IpsA with putative functions in cell wall biogenesis were identified and IpsA was shown to bind to a conserved palindromic motif within the corresponding promoter regions. Myo-inositol was identified as an effector of IpsA, causing the dissociation of the IpsA-DNA complex in vitro. Conclusions This characterization of IpsA function and of its regulon sheds light on the complex transcriptional control of cell wall biogenesis in the mycolata taxon and generates novel targets for drug development. PMID:24377418

Somatodendritic surface expression of epitope-tagged and KChIP binding-deficient Kv4.2 channels in hippocampal neurons.

PubMed

Prechtel, Helena; Hartmann, Sven; Minge, Daniel; Bähring, Robert

2018-01-01

Kv4.2 channels mediate a subthreshold-activating somatodendritic A-type current (ISA) in hippocampal neurons. We examined the role of accessory Kv channel interacting protein (KChIP) binding in somatodendritic surface expression and activity-dependent decrease in the availability of Kv4.2 channels. For this purpose we transfected cultured hippocampal neurons with cDNA coding for Kv4.2 wild-type (wt) or KChIP binding-deficient Kv4.2 mutants. All channels were equipped with an externally accessible hemagglutinin (HA)-tag and an EGFP-tag, which was attached to the C-terminal end. Combined analyses of EGFP self-fluorescence, surface HA immunostaining and patch-clamp recordings demonstrated similar dendritic trafficking and functional surface expression for Kv4.2[wt]HA,EGFP and the KChIP binding-deficient Kv4.2[A14K]HA,EGFP. Coexpression of exogenous KChIP2 augmented the surface expression of Kv4.2[wt]HA,EGFP but not Kv4.2[A14K]HA,EGFP. Notably, activity-dependent decrease in availability was more pronounced in Kv4.2[wt]HA,EGFP + KChIP2 coexpressing than in Kv4.2[A14K]HA,EGFP + KChIP2 coexpressing neurons. Our results do not support the notion that accessory KChIP binding is a prerequisite for dendritic trafficking and functional surface expression of Kv4.2 channels, however, accessory KChIP binding may play a potential role in Kv4.2 modulation during intrinsic plasticity processes.

Mutation and repair induced by the carcinogen 2-(hydroxyamino)-1-methyl-6-phenylimidazo[4,5-b]pyridine (N-OH-PhIP) in the dihydrofolate reductase gene of Chinese hamster ovary cells and conformational modeling of the dG-C8-PhIP adduct in DNA.

PubMed

Carothers, A M; Yuan, W; Hingerty, B E; Broyde, S; Grunberger, D; Snyderwine, E G

1994-01-01

Three experiments using 20 microM 2-(hydroxyamino)-1-methyl-6-phenylimidazo[4,5-b]pyridine (N-OH-PhIP) were performed to induce mutations in the dihydrofolate reductase (DHFR) gene of a hemizygous Chinese hamster ovary (CHO) cell line (UA21). Metabolized forms of this chemical primarily bind at the C-8 position of guanine in DNA. In total, 21 independent induced mutants were isolated and 20 were characterized. DNA sequencing showed that the preferred mutation type found in 75% of the induced DHFR- clones was G.C-->T.A single and tandem double transversions. In addition to base substitutions, one mutant carried a-1 frameshift and another one had lost the entire locus by deletion. The induced changes affected purine targets on the nontranscribed strand of the gene in nearly all of the mutants sequenced (18/19). At the time that the first two experiments were performed, the initial adduct levels were quantitated in treated cells at the mutagenic dose by 32P-postlabeling. While the induced frequency of mutation was relatively low (approximately 5 x 10(-6), the adduct levels after a 1-h exposure of UA21 cells to 20 microM N-OH-PhIP were relatively high (13 adducts x 10(-6) nucleotides). This latter method was then employed to learn if the induced mutation frequency correlated with rapid overall genome repair of PhIP-DNA adducts. Total adduct levels, determined using DNA samples from treated cells collected after intervals of time, were reduced by about 50% after 6 h, and about 70% after 24 h. Since overall genome repair in CHO cells is relatively slow compared with preferential gene repair, the removal of dG-C8-PhIP adducts was apparently efficient. In order to better understand the mutational and repair results, we performed computational modeling to determine the lowest energy structure for the major dG-C8-PhIP adduct in a repetitively mutated duplex sequence opposite dA. Results of this analysis indicate that the PhIP-modified base resembles previous structural

IP-FCM measures physiologic protein-protein interactions modulated by signal transduction and small-molecule drug inhibition.

PubMed

Smith, Stephen E P; Bida, Anya T; Davis, Tessa R; Sicotte, Hugues; Patterson, Steven E; Gil, Diana; Schrum, Adam G

2012-01-01

Protein-protein interactions (PPI) mediate the formation of intermolecular networks that control biological signaling. For this reason, PPIs are of outstanding interest in pharmacology, as they display high specificity and may represent a vast pool of potentially druggable targets. However, the study of physiologic PPIs can be limited by conventional assays that often have large sample requirements and relatively low sensitivity. Here, we build on a novel method, immunoprecipitation detected by flow cytometry (IP-FCM), to assess PPI modulation during either signal transduction or pharmacologic inhibition by two different classes of small-molecule compounds. First, we showed that IP-FCM can detect statistically significant differences in samples possessing a defined PPI change as low as 10%. This sensitivity allowed IP-FCM to detect a PPI that increases transiently during T cell signaling, the antigen-inducible interaction between ZAP70 and the T cell antigen receptor (TCR)/CD3 complex. In contrast, IP-FCM detected no ZAP70 recruitment when T cells were stimulated with antigen in the presence of the src-family kinase inhibitor, PP2. Further, we tested whether IP-FCM possessed sufficient sensitivity to detect the effect of a second, rare class of compounds called SMIPPI (small-molecule inhibitor of PPI). We found that the first-generation non-optimized SMIPPI, Ro-26-4550, inhibited the IL-2:CD25 interaction detected by IP-FCM. This inhibition was detectable using either a recombinant CD25-Fc chimera or physiologic full-length CD25 captured from T cell lysates. Thus, we demonstrate that IP-FCM is a sensitive tool for measuring physiologic PPIs that are modulated by signal transduction and pharmacologic inhibition.

Long-term Culture of Human iPS Cell-derived Telencephalic Neuron Aggregates on Collagen Gel.

PubMed

Oyama, Hiroshi; Takahashi, Koji; Tanaka, Yoshikazu; Takemoto, Hiroshi; Haga, Hisashi

2018-01-01

It takes several months to form the 3-dimensional morphology of the human embryonic brain. Therefore, establishing a long-term culture method for neuronal tissues derived from human induced pluripotent stem (iPS) cells is very important for studying human brain development. However, it is difficult to keep primary neurons alive for more than 3 weeks in culture. Moreover, long-term adherent culture to maintain the morphology of telencephalic neuron aggregates induced from human iPS cells is also difficult. Although collagen gel has been widely used to support long-term culture of cells, it is not clear whether human iPS cell-derived neuron aggregates can be cultured for long periods on this substrate. In the present study, we differentiated human iPS cells to telencephalic neuron aggregates and examined long-term culture of these aggregates on collagen gel. The results indicated that these aggregates could be cultured for over 3 months by adhering tightly onto collagen gel. Furthermore, telencephalic neuronal precursors within these aggregates matured over time and formed layered structures. Thus, long-term culture of telencephalic neuron aggregates derived from human iPS cells on collagen gel would be useful for studying human cerebral cortex development.Key words: Induced pluripotent stem cell, forebrain neuron, collagen gel, long-term culture.

An Elevation in Physical Coupling of Type 1 IP3 Receptors to TRPC3 Channels Constricts Mesenteric Arteries in Genetic Hypertension

PubMed Central

Adebiyi, Adebowale; Thomas-Gatewood, Candice M.; Leo, M. Dennis; Kidd, Michael W.; Neeb, Zachary P.; Jaggar, Jonathan H.

2013-01-01

Hypertension is associated with an elevation in agonist-induced vasoconstriction, but mechanisms involved require further investigation. Many vasoconstrictors bind to phospholipase C-coupled receptors, leading to an elevation in inositol 1,4,5-trisphosphate (IP3) that activates sarcoplasmic reticulum (SR) IP3 receptors (IP3Rs). In cerebral artery myocytes, IP3Rs release SR Ca2+ and can physically couple to canonical transient receptor potential 3 (TRPC3) channels in a caveolin-1-containing macromolecular complex, leading to cation current (ICat) activation that stimulates vasoconstriction. Here, we investigated mechanisms by which IP3Rs control vascular contractility in systemic arteries and IP3R involvement in elevated agonist-induced vasoconstriction during hypertension. Total and plasma membrane-localized TRPC3 protein was ~2.7- and 2-fold higher in mesenteric arteries of hypertensive spontaneously hypertensive rats (SHR) than in Wistar-Kyoto (WKY) rat controls, respectively. In contrast, IP3R1, TRPC1, TRPC6, and caveolin-1 expression was similar. TRPC3 expression was also similar in arteries of pre-hypertensive SHR and WKY rats. Control, IP3- and endothelin-1 (ET-1)-induced FRET between IP3R1 and TRPC3 was higher in hypertensive SHR than WKY myocytes. IP3-induced ICat was ~3-fold larger in SHR myocytes. Pyr3, a selective TRPC3 channel blocker, and CIRBP-TAT, an IP3R-TRP physical coupling inhibitor, reduced IP3-induced ICat and ET-1-induced vasoconstriction more in SHR than WKY myocytes and arteries. Thapsigargin, a SR Ca2+-ATPase blocker, did not alter ET-1-stimulated vasoconstriction in SHR or WKY arteries. These data indicate that ET-1 stimulates physical coupling of IP3R1 to TRPC3 channels in mesenteric artery myocytes, leading to vasoconstriction. Furthermore, an elevation in IP3R1 to TRPC3 channel molecular coupling augments ET-1-induced vasoconstriction during hypertension. PMID:23045459

Synthesis of dimeric analogs of adenophostin A that potently evoke Ca2+ release through IP3 receptors.

PubMed

Vibhute, Amol M; Pushpanandan, Poornenth; Varghese, Maria; Koniecnzy, Vera; Taylor, Colin W; Sureshan, Kana M

2016-11-03

Inositol 1,4,5-trisphosphate receptors (IP 3 Rs) are tetrameric intracellular channels through which many extracellular stimuli initiate the Ca 2+ signals that regulate diverse cellular responses. There is considerable interest in developing novel ligands of IP 3 R. Adenophostin A (AdA) is a potent agonist of IP 3 R and since some dimeric analogs of IP 3 R ligands are more potent than the corresponding monomer; we considered whether dimeric AdA analogs might provide agonists with increased potency. We previously synthesized traizolophostin, in which a simple triazole replaced the adenine of AdA, and showed it to be equipotent to AdA. Here, we used click chemistry to synthesize four homodimeric analogs of triazolophostin, connected by oligoethylene glycol chains of different lengths. We evaluated the potency of these analogs to release Ca 2+ through type 1 IP 3 R and established that the newly synthesized dimers are equipotent to AdA and triazolophostin.

IPS analysis on relationship among velocity, density and temperature of the solar wind

NASA Astrophysics Data System (ADS)

Hayashi, K.; Tokumaru, M.; Fujiki, K.

2015-12-01

The IPS(Interplanetary Scintillation)-MHD(magnetohydrodynamics) tomography is a method we have developed to determine three-dimensional MHD solution of the solar wind that best matches the line-of-sight IPS solar-wind speed data (Hayashi et al., 2003). The tomographic approach is an iteration method in which IPS observations are simulated in MHD steady-state solution, then differences between the simulated observation and the actual IPS observation is reduced by modifying solar-wind boundary map at 50 solar radii. This forward model needs to assume solar wind density and temperature as function of speed. We use empirical functions, N(V) and T(V), derived from Helios in-situ measurement data within 0.5 AU in 1970s. For recent years, especially after 2006, these functions yield higher densities and lower temperatures than in-situ measurements indicate. To characterize the differences between the simulated and actual solar wind plasma, we tune parameters in the functions so that agreements with in-situ data (near the Earth and at Ulysses) will be optimized. This optimization approach can help better simulations of the solar corona and heliosphere, and will help our understandings on roles of magnetic field in solar wind heating and acceleration.

MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.

PubMed

Ozaki, Haruka; Iwasaki, Wataru

2016-08-01

As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory networks and evaluating mutations in cis-regulatory elements. Although chromatin immunoprecipitation sequencing (ChIP-seq) now provides abundant data on the genomic sequences to which a given TF binds, existing motif discovery methods are unable to directly answer whether a given TF can bind to a specific DNA-binding motif. Here, we report a method for clarifying the DNA-binding motif ambiguity, MOCCS. Given ChIP-Seq data of any TF, MOCCS comprehensively analyzes and describes every k-mer to which that TF binds. Analysis of simulated datasets revealed that MOCCS is applicable to various ChIP-Seq datasets, requiring only a few minutes per dataset. Application to the ENCODE ChIP-Seq datasets proved that MOCCS directly evaluates whether a given TF binds to each DNA-binding motif, even if known position weight matrix models do not provide sufficient information on DNA-binding motif ambiguity. Furthermore, users are not required to provide numerous parameters or background genomic sequence models that are typically unavailable. MOCCS is implemented in Perl and R and is freely available via https://github.com/yuifu/moccs. By complementing existing motif-discovery software, MOCCS will contribute to the basic understanding of how the genome controls diverse cellular processes via DNA-protein interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

The mites associated with Ips typographus in Sweden

Treesearch

John C. Moser; Hubertus H. Eidmann; Jan R. Regnander

1989-01-01

Twenty-four species of mites were found associated with Ips typographus (Linnaeus) collected from pherommone traps in Sweden, bringing to 38 the total recorded for this scolytid. Because three of the species are parasites, it may be possible to use them in biological control of I. typographus. Couplets from an earlier key to these...

miRNA-556-3p promotes human bladder cancer proliferation, migration and invasion by negatively regulating DAB2IP expression.

PubMed

Feng, Chen; Sun, Ping; Hu, Jing; Feng, Hua; Li, Mingqiu; Liu, Guibo; Pan, Yanming; Feng, Ying; Xu, Yongliang; Feng, Kejian; Feng, Yukuan

2017-06-01

MicroRNAs (miRNAs) play critical roles in tumorigenesis and metastasis by negatively regulating gene expression through complementary binding to the 3'-untranslated region of target mRNAs. The role of miRNAs in expression of the tumor suppressor DAB2IP in bladder cancer (BC) remains unknown. The aim of the present study was to identify miRNAs targeting DAB2IP and determine their expression and function in BC. We predicted candidate miRNAs targeting DAB2IP using TargetScan software. Dual-luciferase reporter assays confirmed that miRNA-556-3p directly regulated DAB2IP expression. Quantitative RT-PCR and RNase protection assays showed that endogenous miRNA-556-3p expression was significantly upregulated in clinical samples of BC patients and BC cell lines and western blot analysis indicated that DAB2IP expression in BC tissues and BC cell lines was concurrently downregulated. Gain or loss of function studies showed that upregulation of miRNA-556-3p promoted proliferation, invasion, migration and colony formation of BC cells, whereas downregulation resulted in opposite effects. Importantly, restoration of DAB2IP expression rescued the effects induced by miRNA-556-3p. Overexpression of miRNA-556-3p in BC cells not only decreased DAB2IP expression, but also markedly increased Ras GTPase activity and ERK1/2 phosphorylation level. These findings suggest that DAB2IP is a direct target of miRNA-556-3p, and endogenous miRNA-556-3p expression shows inverse correlation with simultaneous DAB2IP expression in BC tissues and cells. miRNA-556-3p functions as a tumor promoter in tumorigenesis and metastasis of BC by targeting DAB2IP. Moreover, miRNA-556-3p-mediated DAB2IP suppression plays an oncogenic role by partial activation of the Ras-ERK pathway.

The MEXART ips observations in route to the next solar maximum

NASA Astrophysics Data System (ADS)

Carrillo-Vargas, Armando; Gonzalez-Esparza, Americo; Andrade, Ernesto; Perez-Enriquez, Roman; Aguilar-Rodriguez, Ernesto; Casillas-Perez, Gilberto; Jeyakumar, Solai; Kurtz, Stanley; Sierra, Pablo; Vazquez, Samuel

We report the status of the Mexican Array Radio Telescope (MEXART) in preparation for the next solar maximum. During this epoch, the MEXART will be one of the four dedicated radio telescopes (with the ORT in India; STEL in Japan; and MWA in Australia) to track large-scale structures in the solar wind using the interplanetary scintillation (IPS) technique. This network of IPS observatories would produce, for the first time four g maps of the sky showing the size and shape of disturbances between the Sun and the Earth. We describe the operation and current observations of the first IPS radio sources at 140 MHz detected by the MEXART. These observations use a plane dipole array of 1024 elements (16 lines with 64 dipoles each one), feeding a Butler matrix of 16x16 ports. This system generates a 16 lobes at fixed declinations covering 120 degrees (from 40 degrees South to 80 degrees North). The beam fan uses the Earth's rotation to cover the whole sky. The observations that will be made with the network of observatories of interplanetary flashing will complement the observations of other observatories, instruments in situ, space probes, satellite, among others.

Multiprotein assembly of Kv4.2, KChIP3 and DPP10 produces ternary channel complexes with ISA-like properties.

PubMed

Jerng, Henry H; Kunjilwar, Kumud; Pfaffinger, Paul J

2005-11-01

Kv4 pore-forming subunits are the principal constituents of the voltage-gated K+ channel underlying somatodendritic subthreshold A-type currents (I(SA)) in neurones. Two structurally distinct types of Kv4 channel modulators, Kv channel-interacting proteins (KChIPs) and dipeptidyl-peptidase-like proteins (DPLs: DPP6 or DPPX, DPP10 or DPPY), enhance surface expression and modify functional properties. Since KChIP and DPL distributions overlap in the brain, we investigated the potential coassembly of Kv4.2, KChIP3 and DPL proteins, and the contribution of DPLs to ternary complex properties. Immunoprecipitation results show that KChIP3 and DPP10 associate simultaneously with Kv4.2 proteins in rat brain as well as heterologously expressing Xenopus oocytes, indicating Kv4.2 + KChIP3 + DPP10 multiprotein complexes. Consistent with ternary complex formation, coexpression of Kv4.2, KChIP3 and DPP10 in oocytes and CHO cells results in current waveforms distinct from the arithmetic sum of Kv4.2 + KChIP3 and Kv4.2 + DPP10 currents. Furthermore, the Kv4.2 + KChIP3 + DPP10 channels recover from inactivation very rapidly (tau(rec) approximately 18-26 ms), closely matching that of native I(SA) and significantly faster than the recovery of Kv4.2 + KChIP3 or Kv4.2 + DPP10 channels. For comparison, identical triple coexpression experiments were performed using DPP6 variants. While most results are similar, the Kv4.2 + KChIP3 + DPP6 channels exhibit inactivation that slows with increasing membrane potential, resulting in inactivation slower than that of Kv4.2 + KChIP3 + DPP10 channels at positive voltages. In conclusion, the native neuronal subthreshold A-type channel is probably a macromolecular complex formed from Kv4 and a combination of both KChIP and DPL proteins, with the precise composition of channel alpha and auxiliary subunits underlying tissue and regional variability in I(SA) properties.

Enhanced service zone architecture for multiservices over IP

NASA Astrophysics Data System (ADS)

Michaely, Boaz; Mohan, Seshadri

2001-07-01

Recently, the field of IP Telephony has been experienced considerable evolution through the specification of new protocols and introduction of products implementing these protocols. We visualize IP Telephony evolving to soon offer multiservices encompassing not only voice, but also data, video and multimedia. While the progress has focused on refining protocols and architectures, very little attention has been given to business models for offering these services. This paper introduces the concept of a Service Zone, which from a service provider/network operator perspective fits within the operator's administrative domain, but is viewed as an independent zone with its own management and services, requiring minimal integration with the core network services. Besides its own management, the Enhanced Services Zone may also provide provisioning and maintenance features needed to provide the customer services and availability that subscribers expect from a telephony service providers. The platform must provide reliable service over time, be scalable to meet increased capacity demands, and be upgradeable to incorporate advanced services and features as they become available. Signaling flows are illustrated using SIP and H.323.

Bilateral lesions of nucleus subpretectalis/interstitio-pretecto-subpretectalis (SP/IPS) selectively impair figure-ground discrimination in pigeons.

PubMed

Scully, Erin N; Acerbo, Martin J; Lazareva, Olga F

2014-01-01

Earlier, we reported that nucleus rotundus (Rt) together with its inhibitory complex, nucleus subpretectalis/interstitio-pretecto-subpretectalis (SP/IPS), had significantly higher activity in pigeons performing figure-ground discrimination than in the control group that did not perform any visual discriminations. In contrast, color discrimination produced significantly higher activity than control in the Rt but not in the SP/IPS. Finally, shape discrimination produced significantly lower activity than control in both the Rt and the SP/IPS. In this study, we trained pigeons to simultaneously perform three visual discriminations (figure-ground, color, and shape) using the same stimulus displays. When birds learned to perform all three tasks concurrently at high levels of accuracy, we conducted bilateral chemical lesions of the SP/IPS. After a period of recovery, the birds were retrained on the same tasks to evaluate the effect of lesions on maintenance of these discriminations. We found that the lesions of the SP/IPS had no effect on color or shape discrimination and that they significantly impaired figure-ground discrimination. Together with our earlier data, these results suggest that the nucleus Rt and the SP/IPS are the key structures involved in figure-ground discrimination. These results also imply that thalamic processing is critical for figure-ground segregation in avian brain.

Glial cells isolated from dorsal root ganglia express prostaglandin E(2) (EP(4)) and prostacyclin (IP) receptors.

PubMed

Ng, Kai Yu; Wong, Yung Hou; Wise, Helen

2011-07-01

Isolated cells from adult rat dorsal root ganglia (DRG) are frequently used as a model system to study responses of primary sensory neurons to nociceptor sensitizing agents such as prostaglandin E(2) and prostacyclin, which are presumed to act only on the neurons in typical mixed cell cultures. In the present study, we evaluated the expression of prostaglandin E(2) (EP(4)) and prostacyclin (IP) receptors in cultures of mixed DRG cells and in purified DRG glia. We show here that EP(4) and IP receptor agonists stimulated adenylyl cyclase activity in both mixed DRG cells and in purified DRG glia, and that these responses were specifically inhibited by EP(4) and IP receptor antagonists, respectively. The presence of EP(4) and IP receptors in DRG glia was further confirmed by the expression of EP(4) and IP receptor immunoreactivity and mRNA. With the increasing awareness of neuron-glial interactions within intact DRG and the use of isolated DRG cells in the study of mechanisms underlying nociception, it will be essential to consider the role played by EP(4) and IP receptor-expressing glial cells when evaluating prostanoid-induced sensitization of DRG neurons. Copyright © 2011 Elsevier B.V. All rights reserved.

Unanticipated region- and cell-specific downregulation of individual KChIP auxiliary subunit isotypes in Kv4.2 knock-out mouse brain.

PubMed

Menegola, Milena; Trimmer, James S

2006-11-22

Kv4 family voltage-gated potassium channel alpha subunits and Kv channel-interacting protein (KChIP) and dipeptidyl aminopeptidase-like protein subunits comprise somatodendritic A-type channels in mammalian neurons. Recently, a mouse was generated with a targeted deletion of Kv4.2, a Kv4 alpha subunit expressed in many but not all mammalian brain neurons. Kv4.2-/- mice are grossly indistinguishable from wild-type (WT) littermates. Here we used immunohistochemistry to analyze expression of component Kv4 and KChIP subunits of A-type channels in WT and Kv4.2-/- brains. We found that the expression level, and cellular and subcellular distribution of the other prominent brain Kv4 family member Kv4.3, was indistinguishable between WT and Kv4.2-/- samples. However, we found unanticipated regional and cell-specific decreases in expression of KChIPs. The degree of altered expression of individual KChIP isoforms in different regions and neurons precisely follows the level of Kv4.2 normally found at those sites and presumably their extent of association of these KChIPs with Kv4.2. The dramatic effects of Kv4.2 deletion on KChIP expression suggest that, in addition to previously characterized effects of KChIPs on the functional properties, trafficking, and turnover rate of Kv4 channels, Kv4:KChIP association may confer reciprocal Kv4.2-dependent effects on KChIPs. The impact of Kv4.2 deletion on KChIP expression also supports the major role of KChIPs as auxiliary subunits of Kv4 channels.

Dose validation of PhIP hair level as a biomarker of heterocyclic aromatic amines exposure: a feeding study

PubMed Central

Le Marchand, Loïc; Yonemori, Kim; White, Kami K.; Franke, Adrian A.; Wilkens, Lynne R.; Turesky, Robert J.

2016-01-01

Hair measurement of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a promising biomarker of exposure to this carcinogen formed in cooked meats. However, the dose relationship between normal range intake and hair levels and the modulating effects of CYP1A2 metabolism and hair melanin need to be evaluated. We conducted a randomized, cross-over feeding study among 41 non-smokers using ground beef cooked to two different levels of doneness, 5 days a week for 1 month. PhIP was measured by liquid chromatography/mass spectrometry in food (mean low dose = 0.72 µg/serving; mean high dose = 2.99 µg/serving), and change in PhIP hair level was evaluated. CYP1A2 activity was assessed in urine with the caffeine challenge test and head hair melanin was estimated by UV spectrophotometry. We observed a strong dose-dependent increase in hair PhIP levels. This increase was highly correlated with dose received (ρ = 0.68, P < 0.0001). CYP1A2 activity and normalizing for hair melanin did not modify the response to the intervention. Consumption of PhIP at doses similar to those in the American diet results in a marked dose-dependent accumulation of PhIP in hair. Hair PhIP levels may be used as a biomarker of dietary exposure in studies investigating disease risk. PMID:27207666

Benefit-Cost Analysis of Integrated Paratransit Systems : Volume 4. Issues in Community Acceptance and IP Implementation.

DOT National Transportation Integrated Search

1979-09-01

The report describes various factors which influence community acceptance of integrated paratransit (IP) systems. In order to fully explore past events in those communities which have already accepted IP, a case study approach has been used. Seven we...

From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data

PubMed Central

Lun, Aaron T. L.; Smyth, Gordon K.

2016-01-01

Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify the genomic binding sites for protein of interest. Most conventional approaches to ChIP-seq data analysis involve the detection of the absolute presence (or absence) of a binding site. However, an alternative strategy is to identify changes in the binding intensity between two biological conditions, i.e., differential binding (DB). This may yield more relevant results than conventional analyses, as changes in binding can be associated with the biological difference being investigated. The aim of this article is to facilitate the implementation of DB analyses, by comprehensively describing a computational workflow for the detection of DB regions from ChIP-seq data. The workflow is based primarily on R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, from alignment of read sequences to interpretation and visualization of putative DB regions. In particular, detection of DB regions will be conducted using the counts for sliding windows from the csaw package, with statistical modelling performed using methods in the edgeR package. Analyses will be demonstrated on real histone mark and transcription factor data sets. This will provide readers with practical usage examples that can be applied in their own studies. PMID:26834993

Space exploration by dendritic cells requires maintenance of myosin II activity by IP3 receptor 1

PubMed Central

Solanes, Paola; Heuzé, Mélina L; Maurin, Mathieu; Bretou, Marine; Lautenschlaeger, Franziska; Maiuri, Paolo; Terriac, Emmanuel; Thoulouze, Maria-Isabel; Launay, Pierre; Piel, Matthieu; Vargas, Pablo; Lennon-Duménil, Ana-Maria

2015-01-01

Dendritic cells (DCs) patrol the interstitial space of peripheral tissues. The mechanisms that regulate their migration in such constrained environment remain unknown. We here investigated the role of calcium in immature DCs migrating in confinement. We found that they displayed calcium oscillations that were independent of extracellular calcium and more frequently observed in DCs undergoing strong speed fluctuations. In these cells, calcium spikes were associated with fast motility phases. IP3 receptors (IP3Rs) channels, which allow calcium release from the endoplasmic reticulum, were identified as required for immature DCs to migrate at fast speed. The IP3R1 isoform was further shown to specifically regulate the locomotion persistence of immature DCs, that is, their capacity to maintain directional migration. This function of IP3R1 results from its ability to control the phosphorylation levels of myosin II regulatory light chain (MLC) and the back/front polarization of the motor protein. We propose that by upholding myosin II activity, constitutive calcium release from the ER through IP3R1 maintains DC polarity during migration in confinement, facilitating the exploration of their environment. PMID:25637353

Fracture strength of three all-ceramic systems: Top-Ceram compared with IPS-Empress and In-Ceram.

PubMed

Quran, Firas Al; Haj-Ali, Reem

2012-03-01

The purpose of this study was to investigate the fracture loads and mode of failure of all-ceramic crowns fabricated using Top-Ceram and compare it with all-ceramic crowns fabricated from well-established systems: IPS-Empress II, In-Ceram. Thirty all-ceramic crowns were fabricated; 10 IPS-Empress II, 10 In-Ceram alumina and 10 Top-Ceram. Instron testing machine was used to measure the loads required to introduce fracture of each crown. Mean fracture load for In-Ceram alumina [941.8 (± 221.66) N] was significantly (p > 0.05) higher than those of Top-Ceram and IPS-Empress II. There was no statistically significant difference between Top-Ceram and IPS-Empress II mean fracture loads; 696.20 (+222.20) and 534 (+110.84) N respectively. Core fracture pattern was highest seen in Top- Ceram specimens.

Rationale, Scenarios, and Profiles for the Application of the Internet Protocol Suite (IPS) in Space Operations

NASA Technical Reports Server (NTRS)

Benbenek, Daniel B.; Walsh, William

2010-01-01

This greenbook captures some of the current, planned and possible future uses of the Internet Protocol (IP) as part of Space Operations. It attempts to describe how the Internet Protocol is used in specific scenarios. Of primary focus is low-earth-orbit space operations, which is referred to here as the design reference mission (DRM). This is because most of the program experience drawn upon derives from this type of mission. Application profiles are provided. This includes parameter settings programs have proposed for sending IP datagrams over CCSDS links, the minimal subsets and features of the IP protocol suite and applications expected for interoperability between projects, and the configuration, operations and maintenance of these IP functions. Of special interest is capturing the lessons learned from the Constellation Program in this area, since that program included a fairly ambitious use of the Internet Protocol.

Exploring perceptions of occupational competence among participants in Individual Placement and Support (IPS).

PubMed

Nygren, Ulla; Sandlund, Mikael; Bernspång, Birgitta; Fisher, Anne G

2013-11-01

The purpose of this study was to explore perceptions of occupational competence and occupational value among a group of clients engaged in Individual Placement and Support (IPS). The Occupational Self-Assessment (OSA), based on the Model of Human Occupation, was used with 65 men and women with mental illness, and 45 of these completed the study. Rasch analyses showed that the participants perceived "Managing my finances", "Managing my basic needs", and "Doing activities I like" as the most valued occupations. Most competence was perceived in "Taking care of myself". Among the occupations where the participants perceived least competence, "Getting done what I need to do" and "Accomplishing what I set out to do" were the occupations that most stand out. Significant differences were also found between perceived competence and value in most of the occupations. Beyond those occupations valued as most important among the participants, it is essential also to pay attention to those in which they perceived least competence, as they are important for being able to achieve a desired occupation. Support related to perceptions of occupational competence can contribute to enabling clients in IPS to master a desired working life.

Stably Fluorescent Cell Line of Human Ovarian Epithelial Cancer Cells SK-OV-3ip-red.

PubMed

Konovalova, E V; Shulga, A A; Chumakov, S P; Khodarovich, Yu M; Woo, Eui-Jeon; Deev, S M

2017-11-01

Stable red fluorescing line of human ovarian epithelial cancer cells SK-OV-3ip-red was generated expressing gene coding for protein TurboFP635 (Katushka) fluorescing in the far-red spectrum region with excitation and emission peaks at 588 and 635 nm, respectively. Fluorescence of SK-OV-3ip-red line remained high during long-term cell culturing and after cryogenic freezing. The obtained cell line SK-OV-3ip-red can serve a basis for a model of a scattered tumor with numerous/extended metastases and used both for testing anticancer drugs inhibiting metastasis growth and for non-invasive monitoring of the growth dynamics with high precision.

Blockade of IP[subscript 3]-Mediated SK Channel Signaling in the Rat Medial Prefrontal Cortex Improves Spatial Working Memory

ERIC Educational Resources Information Center

Brennan, Avis R.; Dolinsky, Beth; Vu, Mai-Anh T.; Stanley, Marion; Yeckel, Mark F.; Arnsten, Amy F. T.

2008-01-01

Planning and directing thought and behavior require the working memory (WM) functions of prefrontal cortex. WM is compromised by stress, which activates phosphatidylinositol (PI)-mediated IP[subscript 3]-PKC intracellular signaling. PKC overactivation impairs WM operations and in vitro studies indicate that IP[subscript 3] receptor (IP[subscript…

Synomones of two sympatric species deter attack by the pine engraver, Ips pini (Coleoptera: Scolytidae)

Treesearch

John H. Borde; D.R. Delvin; Dan R. Miller

1991-01-01

The capture of pine engravers, Ips pini (Say), in ipdienol-baited, multiple-funnel traps in British Columbia was significantly reduced when devices releasing ipsenol or verbenone were placed in the traps. These results suggest that ipsenol and verbenone are synomones release by Ips latidens (LeC.) and the mountain pine beetle,

MultiNet TCP/P/IP for VAX/VMS update

NASA Technical Reports Server (NTRS)

Vance, L. Stuart

1991-01-01

Outlines of device support; DECnet interoperability; installation; MultiNet services; domain name server; Telnet; FTP; SMTP; DECwindows over TCP/IP; BSD r services; remote printing; RPC services and NFS server; NFS client; netcontrol; diagnostics; programming support; and MultiNet features are presented in viewgraph format.

ATF7IP-Mediated Stabilization of the Histone Methyltransferase SETDB1 Is Essential for Heterochromatin Formation by the HUSH Complex.

PubMed

Timms, Richard T; Tchasovnikarova, Iva A; Antrobus, Robin; Dougan, Gordon; Lehner, Paul J

2016-10-11

The histone methyltransferase SETDB1 plays a central role in repressive chromatin processes, but the functional requirement for its binding partner ATF7IP has remained enigmatic. Here, we show that ATF7IP is essential for SETDB1 stability: nuclear SETDB1 protein is degraded by the proteasome upon ablation of ATF7IP. As a result, ATF7IP is critical for repression that requires H3K9 trimethylation by SETDB1, including transgene silencing by the HUSH complex. Furthermore, we show that loss of ATF7IP phenocopies loss of SETDB1 in genome-wide assays. ATF7IP and SETDB1 knockout cells exhibit near-identical defects in the global deposition of H3K9me3, which results in similar dysregulation of the transcriptome. Overall, these data identify a critical functional role for ATF7IP in heterochromatin formation by regulating SETDB1 abundance in the nucleus. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

A System Implementation for Cooperation between UHF RFID Reader and TCP/IP Device

NASA Astrophysics Data System (ADS)

Lee, Sang Hoon; Jin, Ik Soo

This paper presents a system implementation for cooperation between UHF RFID reader and TCP/IP device that can be used as a home gateway. The system consists of an UHF RFID tag, an UHF RFID reader, a RF end-device, a RF coordinator and a TCP/IP I/F. The UHF RFID reader is compatible with EPC Class-0/Gen1, Class-1/Gen1, 2 and ISO18000-6B, operating at the 915MHz. In particular, UHF RFID reader can be combined with a RF end device/coordinator for ZigBee(IEEE 802.15.4) interface which is low power wireless standard. The TCP/IP device is communicated with RFID reader via wired type. On the other hand, it is connected with ZigBee end-device via wireless type. The experimental results show that the developed system can provide the right networking.

Pancreatic β-Cell-Derived IP-10/CXCL10 Isletokine Mediates Early Loss of Graft Function in Islet Cell Transplantation.

PubMed

Yoshimatsu, Gumpei; Kunnathodi, Faisal; Saravanan, Prathab Balaji; Shahbazov, Rauf; Chang, Charles; Darden, Carly M; Zurawski, Sandra; Boyuk, Gulbahar; Kanak, Mazhar A; Levy, Marlon F; Naziruddin, Bashoo; Lawrence, Michael C

2017-11-01

Pancreatic islets produce and secrete cytokines and chemokines in response to inflammatory and metabolic stress. The physiological role of these "isletokines" in health and disease is largely unknown. We observed that islets release multiple inflammatory mediators in patients undergoing islet transplants within hours of infusion. The proinflammatory cytokine interferon-γ-induced protein 10 (IP-10/CXCL10) was among the highest released, and high levels correlated with poor islet transplant outcomes. Transgenic mouse studies confirmed that donor islet-specific expression of IP-10 contributed to islet inflammation and loss of β-cell function in islet grafts. The effects of islet-derived IP-10 could be blocked by treatment of donor islets and recipient mice with anti-IP-10 neutralizing monoclonal antibody. In vitro studies showed induction of the IP-10 gene was mediated by calcineurin-dependent NFAT signaling in pancreatic β-cells in response to oxidative or inflammatory stress. Sustained association of NFAT and p300 histone acetyltransferase with the IP-10 gene required p38 and c-Jun N-terminal kinase mitogen-activated protein kinase (MAPK) activity, which differentially regulated IP-10 expression and subsequent protein release. Overall, these findings elucidate an NFAT-MAPK signaling paradigm for induction of isletokine expression in β-cells and reveal IP-10 as a primary therapeutic target to prevent β-cell-induced inflammatory loss of graft function after islet cell transplantation. © 2017 by the American Diabetes Association.

Linear Collider Test Facility: Twiss Parameter Analysis at the IP/Post-IP Location of the ATF2 Beam Line

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

Bolzon, Benoit; /Annecy, LAPP; Jeremie, Andrea

2012-07-02

At the first stage of the ATF2 beam tuning, vertical beam size is usually bigger than 3 {micro}m at the IP. Beam waist measurements using wire scanners and a laser wire are usually performed to check the initial matching of the beam through to the IP. These measurements are described in this paper for the optics currently used ({beta}{sub x} = 4cm and {beta}{sub y} = 1mm). Software implemented in the control room to automate these measurements with integrated analysis is also described. Measurements showed that {beta} functions and emittances were within errors of measurements when no rematching and couplingmore » corrections were done. However, it was observed that the waist in the horizontal (X) and vertical (Y) plane was abnormally shifted and simulations were performed to try to understand these shifts. They also showed that multiknobs are needed in the current optics to correct simultaneously {alpha}{sub x}, {alpha}{sub y} and the horizontal dispersion (D{sub x}). Such multiknobs were found and their linearity and orthogonality were successfully checked using MAD optics code. The software for these multiknobs was implemented in the control room and waist scan measurements using the {alpha}{sub y} knob were successfully performed.« less

TCP/IP Interface for the Satellite Orbit Analysis Program (SOAP)

NASA Technical Reports Server (NTRS)

Carnright, Robert; Stodden, David; Coggi, John

2009-01-01

The Transmission Control Protocol/ Internet protocol (TCP/IP) interface for the Satellite Orbit Analysis Program (SOAP) provides the means for the software to establish real-time interfaces with other software. Such interfaces can operate between two programs, either on the same computer or on different computers joined by a network. The SOAP TCP/IP module employs a client/server interface where SOAP is the server and other applications can be clients. Real-time interfaces between software offer a number of advantages over embedding all of the common functionality within a single program. One advantage is that they allow each program to divide the computation labor between processors or computers running the separate applications. Secondly, each program can be allowed to provide its own expertise domain with other programs able to use this expertise.

Design and implementation of a VoIP broadcasting service over embedded systems in a heterogeneous network environment.

PubMed

Leu, Jenq-Shiou; Lin, Wei-Hsiang; Hsieh, Wen-Bin; Lo, Chien-Chih

2014-01-01

As the digitization is integrated into daily life, media including video and audio are heavily transferred over the Internet nowadays. Voice-over-Internet Protocol (VoIP), the most popular and mature technology, becomes the focus attracting many researches and investments. However, most of the existing studies focused on a one-to-one communication model in a homogeneous network, instead of one-to-many broadcasting model among diverse embedded devices in a heterogeneous network. In this paper, we present the implementation of a VoIP broadcasting service on the open source-Linphone-in a heterogeneous network environment, including WiFi, 3G, and LAN networks. The proposed system featuring VoIP broadcasting over heterogeneous networks can be integrated with heterogeneous agile devices, such as embedded devices or mobile phones. VoIP broadcasting over heterogeneous networks can be integrated into modern smartphones or other embedded devices; thus when users run in a traditional AM/FM signal unreachable area, they still can receive the broadcast voice through the IP network. Also, comprehensive evaluations are conducted to verify the effectiveness of the proposed implementation.

Design and Implementation of a VoIP Broadcasting Service over Embedded Systems in a Heterogeneous Network Environment

PubMed Central

Lin, Wei-Hsiang; Hsieh, Wen-Bin; Lo, Chien-Chih

2014-01-01

As the digitization is integrated into daily life, media including video and audio are heavily transferred over the Internet nowadays. Voice-over-Internet Protocol (VoIP), the most popular and mature technology, becomes the focus attracting many researches and investments. However, most of the existing studies focused on a one-to-one communication model in a homogeneous network, instead of one-to-many broadcasting model among diverse embedded devices in a heterogeneous network. In this paper, we present the implementation of a VoIP broadcasting service on the open source—Linphone—in a heterogeneous network environment, including WiFi, 3G, and LAN networks. The proposed system featuring VoIP broadcasting over heterogeneous networks can be integrated with heterogeneous agile devices, such as embedded devices or mobile phones. VoIP broadcasting over heterogeneous networks can be integrated into modern smartphones or other embedded devices; thus when users run in a traditional AM/FM signal unreachable area, they still can receive the broadcast voice through the IP network. Also, comprehensive evaluations are conducted to verify the effectiveness of the proposed implementation. PMID:25300280

Arpeggio: harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures

PubMed Central

Stanton, Kelly Patrick; Parisi, Fabio; Strino, Francesco; Rabin, Neta; Asp, Patrik; Kluger, Yuval

2013-01-01

Researchers generating new genome-wide data in an exploratory sequencing study can gain biological insights by comparing their data with well-annotated data sets possessing similar genomic patterns. Data compression techniques are needed for efficient comparisons of a new genomic experiment with large repositories of publicly available profiles. Furthermore, data representations that allow comparisons of genomic signals from different platforms and across species enhance our ability to leverage these large repositories. Here, we present a signal processing approach that characterizes protein–chromatin interaction patterns at length scales of several kilobases. This allows us to efficiently compare numerous chromatin-immunoprecipitation sequencing (ChIP-seq) data sets consisting of many types of DNA-binding proteins collected from a variety of cells, conditions and organisms. Importantly, these interaction patterns broadly reflect the biological properties of the binding events. To generate these profiles, termed Arpeggio profiles, we applied harmonic deconvolution techniques to the autocorrelation profiles of the ChIP-seq signals. We used 806 publicly available ChIP-seq experiments and showed that Arpeggio profiles with similar spectral densities shared biological properties. Arpeggio profiles of ChIP-seq data sets revealed characteristics that are not easily detected by standard peak finders. They also allowed us to relate sequencing data sets from different genomes, experimental platforms and protocols. Arpeggio is freely available at http://sourceforge.net/p/arpeggio/wiki/Home/. PMID:23873955

Arpeggio: harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures.

PubMed

Stanton, Kelly Patrick; Parisi, Fabio; Strino, Francesco; Rabin, Neta; Asp, Patrik; Kluger, Yuval

2013-09-01

Researchers generating new genome-wide data in an exploratory sequencing study can gain biological insights by comparing their data with well-annotated data sets possessing similar genomic patterns. Data compression techniques are needed for efficient comparisons of a new genomic experiment with large repositories of publicly available profiles. Furthermore, data representations that allow comparisons of genomic signals from different platforms and across species enhance our ability to leverage these large repositories. Here, we present a signal processing approach that characterizes protein-chromatin interaction patterns at length scales of several kilobases. This allows us to efficiently compare numerous chromatin-immunoprecipitation sequencing (ChIP-seq) data sets consisting of many types of DNA-binding proteins collected from a variety of cells, conditions and organisms. Importantly, these interaction patterns broadly reflect the biological properties of the binding events. To generate these profiles, termed Arpeggio profiles, we applied harmonic deconvolution techniques to the autocorrelation profiles of the ChIP-seq signals. We used 806 publicly available ChIP-seq experiments and showed that Arpeggio profiles with similar spectral densities shared biological properties. Arpeggio profiles of ChIP-seq data sets revealed characteristics that are not easily detected by standard peak finders. They also allowed us to relate sequencing data sets from different genomes, experimental platforms and protocols. Arpeggio is freely available at http://sourceforge.net/p/arpeggio/wiki/Home/.

Control of IP3-mediated Ca2+ puffs in Xenopus laevis oocytes by the Ca2+-binding protein parvalbumin

PubMed Central

John, Linu M; Mosquera-Caro, Monica; Camacho, Patricia; Lechleiter, James D

2001-01-01

Elementary events of Ca2+ release (Ca2+ puffs) can be elicited from discrete clusters of inositol 1,4,5 trisphosphate receptors (IP3Rs) at low concentrations of IP3. Ca2+ puffs have rarely been observed unless elicited by either hormone treatment or introduction of IP3 into the cell. However, cells appear to have sufficient concentrations of IP3 (0.1-3.0 μM) to induce Ca2+ release under resting conditions. Here, we investigated Ca2+ puff activity in non-stimulated Xenopus oocytes using confocal microscopy. The fluorescent Ca2+ dye indicators Calcium Green 1 and Oregon Green 488 BAPTA-2 were injected into oocytes to monitor basal Ca2+ activity. In this preparation, injection or overexpression of parvalbumin, an EF-hand Ca2+-binding protein (CaBP), induced Ca2+ puffs in resting Xenopus oocytes. This activity was inhibited by heparin, an IP3R channel blocker, and by mutation of the Ca2+-binding sites in parvalbumin. Ca2+ puff activity was also evoked by injection of low concentrations of the Ca2+ chelator EGTA, but not by calbindin D28k, another member of the EF-hand CaBP superfamily. BAPTA and the Ca2+ indicator dye Oregon Green 488 BAPTA-1 evoked Ca2+ puff activity, while the dextran conjugate of Oregon Green 488 BAPTA-1 did not. These data indicate that a Ca2+ buffer must be mobile in order to increase Ca2+ puff activity. Together, the data indicate that some IP3Rs spontaneously release Ca2+ under resting concentrations of IP3. These elementary Ca2+ events appear to be below the level of detection of current imaging techniques. We suggest that parvalbumin evokes Ca2+ puffs by coordinating the activity of elementary IP3R channel openings. We conclude that Ca2+ release can be evoked not only by hormone-induced increases in IP3, but also by expression of mobile cytosolic CaBPs under resting concentrations of IP3. PMID:11507154

Arl6IP1 has the ability to shape the mammalian ER membrane in a reticulon-like fashion.

PubMed

Yamamoto, Yasunori; Yoshida, Asuka; Miyazaki, Naoyuki; Iwasaki, Kenji; Sakisaka, Toshiaki

2014-02-15

The ER (endoplasmic reticulum) consists of the nuclear envelope and a peripheral network of membrane sheets and tubules. Two classes of the evolutionarily conserved ER membrane proteins, reticulons and REEPs (receptor expression-enhancing proteins)/DP1 (deleted in polyposis locus 1)/Yop1 (YIP 1 partner), shape high-curvature ER tubules. In mammals, four members of the reticulon family and six members of the REEP family have been identified so far. In the present paper we report that Arl6IP1(ADP-ribosylation factor-like 6 interacting protein 1), an anti-apoptotic protein specific to multicellular organisms, is a potential player in shaping the ER tubules in mammalian cells. Arl6IP1, which does not share an overall primary sequence homology with reticulons, harbours reticulon-like short hairpin transmembrane domains and binds to atlastin, a GTPase that mediates the formation of the tubular ER network. Overexpression of Arl6IP1 induced extensive tubular structures of the ER and excluded a luminal protein. Furthermore, overexpression of Arl6IP1 stabilized the ER tubules, allowing the cells to maintain the ER tubules even in the absence of microtubules. Arl6IP1 constricted liposomes into tubules. The short hairpin structures of the transmembrane domains were required for the membrane-shaping activity of Arl6IP1. The results of the present study indicate that Arl6IP1 has the ability to shape high-curvature ER tubules in a reticulon-like fashion.

EPOS-IP WP10: services and data provision for the GNSS community

NASA Astrophysics Data System (ADS)

Fernandes, Rui

2016-04-01

The EPOS-IP WP10 - "GNSS Data & Products" is the Working Package of the EPOS-IP project in charge of implementing the necessary services in order that the geo-sciences community can access the existing Pan-European Geodetic Infrastructures. The WP10 is formed by representatives of the participating institutions (10) but it is also open to the entire geodetic community. In fact, WP10 also includes members from other institutions/countries that formally are not participating in the EPOS-IP. During the EPOS-IP project, the geodetic component of EPOS (WP10) is dealing essentially with Research Infrastructures focused on continuous operating GNSS (cGNSS). The option of concentrating the efforts on the presently most generalized geodetic tool supporting research on Solid Earth was decided in order to optimize the existing resources. Furthermore, although the focus is on Solid Earth applications, other research and technical applications (e.g., reference frames, meteorology, space weather) can also benefit from the efforts of WP10 towards the optimization of the geodetic resources in Europe. We will present and discuss the plans for the implementation of the thematic and core services (TCS) for GNSS data within EPOS and the related business plan. We will focus on strategies towards the implementation of the best solutions that will permit to the end-users, and in particular geo-scientists, to access the geodetic data, derived solutions, and associated metadata using transparent and uniform processes. The collaboration with EUREF is also an essential component of the implementation plan.

Interferon-gamma inducible protein 10 (IP10) induced cisplatin resistance of HCC after liver transplantation through ER stress signaling pathway

PubMed Central

Geng, Wei; Lo, Chung-Mau; Ng, Kevin T.P.; Ling, Chang-Chun; Qi, Xiang; Li, Chang-Xian; Zhai, Yuan; Liu, Xiao-Bing; Ma, Yuen-Yuen; Man, Kwan

2015-01-01

Tumor recurrence remains an obstacle after liver surgery, especially in living donor liver transplantation (LDLT) for patients with hepatocellular carcinoma (HCC). The acute-phase liver graft injury might potentially induce poor response to chemotherapy in recurrent HCC after liver transplantation. We here intended to explore the mechanism and to identify a therapeutic target to overcome such chemoresistance. The associations among graft injury, overexpression of IP10 and multidrug resistant genes were investigated in a rat liver transplantation model, and further validated in clinical cohort. The role of IP10 on HCC cell proliferation and tumor growth under chemotherapy was studied both in vitro and in vivo. The underlying mechanism was revealed by detecting the activation of endoplasmic reticulum (ER) stress signaling pathways. Moreover, the effect of IP10 neutralizing antibody sensitizing cisplatin treatment was further explored. In rat liver transplantation model, significant up-regulation of IP10 associated with multidrug resistant genes was found in small-for-size liver graft. Clinically, high expression of circulating IP10 was significant correlated with tumor recurrence in HCC patients underwent LDLT. Overexpression of IP10 promoted HCC cell proliferation and tumor growth under cisplatin treatment by activation of ATF6/Grp78 signaling. IP10 neutralizing antibody sensitized cisplatin treatment in nude mice. The overexpression of IP10, which induced by liver graft injury, may lead to cisplatin resistance via ATF6/Grp78 ER stress signaling pathway. IP10 neutralizing antibody could be a potential adjuvant therapy to sensitize cisplatin treatment. PMID:26336986

The Bcl-2 homolog Nrz inhibits binding of IP3 to its receptor to control calcium signaling during zebrafish epiboly.

PubMed

Bonneau, Benjamin; Nougarède, Adrien; Prudent, Julien; Popgeorgiev, Nikolay; Peyriéras, Nadine; Rimokh, Ruth; Gillet, Germain

2014-02-11

Members of the Bcl-2 protein family regulate mitochondrial membrane permeability and also localize to the endoplasmic reticulum where they control Ca(2+) homeostasis by interacting with inositol 1,4,5-trisphosphate (IP3) receptors (IP3Rs). In zebrafish, Bcl-2-like 10 (Nrz) is required for Ca(2+) signaling during epiboly and gastrulation. We characterized the mechanism by which Nrz controls IP3-mediated Ca(2+) release during this process. We showed that Nrz was phosphorylated during early epiboly, and that in embryos in which Nrz was knocked down, reconstitution with Nrz bearing mutations designed to prevent its phosphorylation disrupted cyclic Ca(2+) transients and the assembly of the actin-myosin ring and led to epiboly arrest. In cultured cells, wild-type Nrz, but not Nrz with phosphomimetic mutations, interacted with the IP3 binding domain of IP3R1, inhibited binding of IP3 to IP3R1, and prevented histamine-induced increases in cytosolic Ca(2+). Collectively, these data suggest that Nrz phosphorylation is necessary for the generation of IP3-mediated Ca(2+) transients and the formation of circumferential actin-myosin cables required for epiboly. Thus, in addition to their role in apoptosis, by tightly regulating Ca(2+) signaling, Bcl-2 family members participate in the cellular events associated with early vertebrate development, including cytoskeletal dynamics and cell movement.

Phase I study of intravenous (IV) docetaxel and intraperitoneal (IP) oxaliplatin in recurrent ovarian and fallopian tube cancer.

PubMed

Taylor, Sarah E; Li, Ruosha; Petschauer, Jennifer S; Donovan, Heidi; O'Neal, Sara; Keeler, Amanda W; Zamboni, William C; Edwards, Robert P; Zorn, Kristin K

2015-09-01

The primary objective was to define the maximum tolerated dose (MTD) and dose-limiting toxicity (DLT) of IV docetaxel and IP oxaliplatin in women with recurrent ovarian (OV), fallopian tube (FT) or peritoneal (PP) cancer. Secondary objectives included response rate, time to progression, pharmacokinetics (PK) and quality of life (QoL). Patients received docetaxel 75mg/m(2) IV day (d) 1 and oxaliplatin escalating from 50mg/m(2) IP d2 every 3weeks using a 3+3 design. Treatment continued until disease progression, remission, or intolerable toxicity. Plasma and IP samples were taken to determine drug concentrations. MD Anderson Symptom Inventory and symptom interference scale were completed weekly. Thirteen patients were included. Median number of cycles was 6 (range 1-10). Ten patients had measureable disease. Best response was partial response (PR-2), stable disease (SD-7), and progressive disease (PD-1). Twenty-one Grades 3-4 toxicities were noted, commonly hematologic. Two patients had DLTs: prolonged neutropenia (1) and abdominal pain (1). MTD was d1 docetaxel 75mg/m(2) IV and d2 oxaliplatin 50mg/m(2) IP. Symptom burden peaked week one and returned to baseline by week two of each cycle on dose level 1. Dose level 2 had persistently high symptom burden and interference. At IP oxaliplatin doses of 50mg/m(2), total unbound drug exposure (AUC) averaged 8 times larger and Cmax reached concentrations 50-fold greater in IP fluid compared to plasma. Docetaxel 75mg/m(2) IV d1 and oxaliplatin 50mg/m(2) IP d2 is the MTD. Most patients had PR or SD. Patient-reported outcomes demonstrate temporary but tolerable decrements in QoL. IP oxaliplatin provides PK advantages over IV administration. Copyright © 2015 Elsevier Inc. All rights reserved.

A comprehensive comparison of tools for differential ChIP-seq analysis

PubMed Central

Steinhauser, Sebastian; Kurzawa, Nils; Eils, Roland

2016-01-01

ChIP-seq has become a widely adopted genomic assay in recent years to determine binding sites for transcription factors or enrichments for specific histone modifications. Beside detection of enriched or bound regions, an important question is to determine differences between conditions. While this is a common analysis for gene expression, for which a large number of computational approaches have been validated, the same question for ChIP-seq is particularly challenging owing to the complexity of ChIP-seq data in terms of noisiness and variability. Many different tools have been developed and published in recent years. However, a comprehensive comparison and review of these tools is still missing. Here, we have reviewed 14 tools, which have been developed to determine differential enrichment between two conditions. They differ in their algorithmic setups, and also in the range of applicability. Hence, we have benchmarked these tools on real data sets for transcription factors and histone modifications, as well as on simulated data sets to quantitatively evaluate their performance. Overall, there is a great variety in the type of signal detected by these tools with a surprisingly low level of agreement. Depending on the type of analysis performed, the choice of method will crucially impact the outcome. PMID:26764273

Two-year clinical evaluation of IPS Empress II ceramic onlays/inlays.

PubMed

Tagtekin, D A; Ozyöney, G; Yanikoglu, F

2009-01-01

The stronger the ceramic material, the longer the restoration stays in the mouth. The current study evaluated the two-year clinical performance of a strong ceramic system, IPS Empress II, with increased strength on onlay/inlay restorations of molars. Teeth from 35 patients, including three premolars and 32 molars, were prepared for 28 onlay and seven inlay restorations with IPS Empress II ceramics. The restorations were cemented with a highly viscous, dual-curing luting composite cement (Bifix) and evaluated by two examiners using USPHS criteria at baseline (one week following insertion), six months, one year and two years. The baseline scores and recalls were assessed by Wilcoxon signed rank test. Statistically significant marginal discoloration at the Bravo level was found at the 12- and 24-month recalls (p=0.046). One debonding was statistically insignificant. No changes were observed with respect to anamnesis, such as any symptom from the TMJ or masticatory muscles. No restorations were replaced due to hypersensitivity or were missing at the two-year evaluation. Any wear on the restoration, antagonist tooth or any changes of proximal contacts were not observed. IPS Empress II Ceramics were found to be appropriate as onlay/inlay restorations for clinical use under the conditions of the current study.

Clinical performance of IPS-Empress 2 ceramic crowns inserted by general dental practitioners.

PubMed

Mansour, Yasar F; Al-Omiri, Mahmoud K; Khader, Yousef Saleh; Al-Wahadni, Ahed

2008-05-01

The aim of this study was to evaluate the clinical performance of IPS-Empress 2(R) all-ceramic crowns placed by general dental practitioners. Eighty-two IPS-Empress 2 crowns placed in 64 patients (27 females and 37 males) were evaluated. These crowns had been in place for 15.2 to 57.2 months (mean 25.3 months, SD=9.3). Survival analysis was conducted using the Kaplan-Meier method. Of the 82 crowns 93.9% were rated satisfactory. In terms of the integrity of the restorations, fracture was observed in three crowns and two showed a crack upon transillumination. Five crowns were rated unsatisfactory for color match; one for marginal adaptation; and none for discoloration, secondary caries, or sensitivity. IPS-Empress 2(R) is a suitable material to fabricate all-ceramic crowns; when these all-ceramic crowns were inserted by general dental practitioners, they functioned satisfactorily with low failure rates during an observation period ranging between 15.2 to 57.2 months.

An interactive environment for agile analysis and visualization of ChIP-sequencing data.

PubMed

Lerdrup, Mads; Johansen, Jens Vilstrup; Agrawal-Singh, Shuchi; Hansen, Klaus

2016-04-01

To empower experimentalists with a means for fast and comprehensive chromatin immunoprecipitation sequencing (ChIP-seq) data analyses, we introduce an integrated computational environment, EaSeq. The software combines the exploratory power of genome browsers with an extensive set of interactive and user-friendly tools for genome-wide abstraction and visualization. It enables experimentalists to easily extract information and generate hypotheses from their own data and public genome-wide datasets. For demonstration purposes, we performed meta-analyses of public Polycomb ChIP-seq data and established a new screening approach to analyze more than 900 datasets from mouse embryonic stem cells for factors potentially associated with Polycomb recruitment. EaSeq, which is freely available and works on a standard personal computer, can substantially increase the throughput of many analysis workflows, facilitate transparency and reproducibility by automatically documenting and organizing analyses, and enable a broader group of scientists to gain insights from ChIP-seq data.

Draft Genome Sequence of Sphingobium chinhatense Strain IP26T, Isolated from a Hexachlorocyclohexane Dumpsite

PubMed Central

Niharika, Neha; Sangwan, Naseer; Ahmad, Salar; Singh, Priya; Khurana, J. P.

2013-01-01

Sphingobium chinhatense strain IP26T is a conducive hexachlorocyclohexane (HCH) degrader isolated from a heavily contaminated (450 mg HCH/g soil) HCH dumpsite. IP26T degrades α-, β-, γ-, and δ-HCH, which are highly persistent in the environment. Here we report the draft genome sequence (~5.8 Mbp) of this strain. PMID:23990581

TRAF3IP2 mediates atherosclerotic plaque development and vulnerability in ApoE−/− mice

PubMed Central

Prasad, Sakamuri Siva Sankara Vara; Higashi, Yusuke; Sukhanov, Sergiy; Siddesha, Jalahalli M; Delafontaine, Patrice; Siebenlist, Ulrich; Chandrasekar, Bysani

2016-01-01

Background and aims Atherosclerosis is a major cause of heart attack and stroke. Inflammation plays a critical role in the development of atherosclerosis. Since the cytoplasmic adaptor molecule TRAF3IP2 (TRAF3-Interacting Protein 2) plays a causal role in various autoimmune and inflammatory diseases, we hypothesized that TRAF3IP2 mediates atherosclerotic plaque development. Methods TRAF3IP2/ApoE double knockout (DKO) mice were generated by crossing TRAF3IP2−/− and ApoE−/− mice. ApoE−/− mice served as controls. Both DKO and control mice were fed a high-fat diet for 12 weeks. Plasma lipids were measured by ELISA, atherosclerosis by en face analysis of aorta and plaque cross-section measurements at the aortic valve region, plaque necrotic core area, collagen and smooth muscle cell content by histomorphometry, and aortic gene expression by RT-qPCR. Results The plasma lipoprotein profile was not altered by TRAF3IP2 gene deletion in ApoE−/− mice. While total aortic plaque area was decreased in DKO female, but not male mice, the plaque necrotic area was significantly decreased in DKO mice of both genders. Plaque collagen and smooth muscle cell contents were increased significantly in both female and male DKO mice compared to respective controls. Aortic expression of proinflammatory cytokine (Tumor necrosis factor α, TNFα), chemokine (Chemokine (C-X-C motif) Ligand 1, CXCL1) and adhesion molecule (Vascular cell adhesion molecule 1, VCAM1; and Intercellular adhesion molecule 1, ICAM1) gene expression were decreased in both male and female DKO mice. In addition, the male DKO mice showed a markedly reduced expression of extracellular matrix (ECM)-related genes, including TIMP1 (Tissue inhibitor of metalloproteinase 1), RECK (Reversion-Inducing- Cysteine-Rich Protein with Kazal Motifs) and ADAM17 (A Disintegrin And Metalloproteinase 17). Conclusions TRAF3IP2 plays a causal role in atherosclerotic plaque development and vulnerability, possibly by inducing the

An in vitro model demonstrates the potential of neoplastic human germ cells to influence the tumour microenvironment.

PubMed

Klein, B; Schuppe, H-C; Bergmann, M; Hedger, M P; Loveland, B E; Loveland, K L

2017-07-01

Testicular germ cell tumours (TGCT) typically contain high numbers of infiltrating immune cells, yet the functional nature and consequences of interactions between GCNIS (germ cell neoplasia in situ) or seminoma cells and immune cells remain unknown. A co-culture model using the seminoma-derived TCam-2 cell line and peripheral blood mononuclear cells (PBMC, n = 7 healthy donors) was established to investigate how tumour and immune cells each contribute to the cytokine microenvironment associated with TGCT. Three different co-culture approaches were employed: direct contact during culture to simulate in situ cellular interactions occurring within seminomas (n = 9); indirect contact using well inserts to mimic GCNIS, in which a basement membrane separates the neoplastic germ cells and immune cells (n = 3); and PBMC stimulation prior to direct contact during culture to overcome the potential lack of immune cell activation (n = 3). Transcript levels for key cytokines in PBMC and TCam-2 cell fractions were determined using RT-qPCR. TCam-2 cell fractions showed an immediate increase (within 24 h) in several cytokine mRNAs after direct contact with PBMC, whereas immune cell fractions did not. The high levels of interleukin-6 (IL6) mRNA and protein associated with TCam-2 cells implicate this cytokine as important to seminoma physiology. Use of PBMCs from different donors revealed a robust, repeatable pattern of changes in TCam-2 and PBMC cytokine mRNAs, independent of potential inter-donor variation in immune cell responsiveness. This in vitro model recapitulated previous data from clinical TGCT biopsies, revealing similar cytokine expression profiles and indicating its suitability for exploring the in vivo circumstances of TGCT. Despite the limitations of using a cell line to mimic in vivo events, these results indicate how neoplastic germ cells can directly shape the surrounding tumour microenvironment, including by influencing local immune responses. IL6

Interferon-γ–Inducible Protein 10 (IP-10) as a Screening Tool to Optimize Human Immunodeficiency Virus RNA Monitoring in Resource-Limited Settings

PubMed Central

Pastor, Lucía; Casellas, Aina; Carrillo, Jorge; Maculuve, Sonia; Jairoce, Chenjerai; Paredes, Roger; Blanco, Julià; Naniche, Denise

2017-01-01

Abstract Background Achieving effective antiretroviral treatment (ART) monitoring is a key determinant to ensure viral suppression and reach the UNAIDS 90-90-90 targets. The gold standard for detecting virological failure is plasma human immunodeficiency virus (HIV) RNA (viral load [VL]) testing; however, its availability is very limited in low-income countries due to cost and operational constraints. Methods HIV-1–infected adults on first-line ART attending routine visits at the Manhiça District Hospital, Mozambique, were previously evaluated for virologic failure. Plasma levels of interferon-γ–inducible protein 10 (IP-10) were quantified by enzyme-linked immunosorbent assay. Logistic regression was used to build an IP-10–based model able to identify individuals with VL >150 copies/mL. From the 316 individuals analyzed, 253 (80%) were used for model training and 63 (20%) for validation. Receiver operating characteristic curves were employed to evaluate model prediction. Results From the individuals included in the training set, 34% had detectable VL. Mean age was 41 years, 70% were females, and median time on ART was 3.4 years. IP-10 levels were significantly higher in subjects with detectable VL (108.2 pg/mL) as compared to those with undetectable VL (38.0 pg/mL) (P < .0001, U test). IP-10 univariate model demonstrated high classification performance (area under the curve = 0.85 [95% confidence interval {CI}, .80–.90]). Using a cutoff value of IP-10 ≥44.2 pg/mL, the model identified detectable VL with 91.9% sensitivity (95% CI, 83.9%–96.7%) and 59.9% specificity (95% CI, 52.0%–67.4%), values confirmed in the validation set. Conclusions IP-10 is an accurate biomarker to screen individuals on ART for detectable viremia. Further studies should evaluate the benefits of IP-10 as a triage approach to monitor ART in resource-limited settings. PMID:29020145

ELRIS2D: A MATLAB Package for the 2D Inversion of DC Resistivity/IP Data

NASA Astrophysics Data System (ADS)

Akca, Irfan

2016-04-01

ELRIS2D is an open source code written in MATLAB for the two-dimensional inversion of direct current resistivity (DCR) and time domain induced polarization (IP) data. The user interface of the program is designed for functionality and ease of use. All available settings of the program can be reached from the main window. The subsurface is discre-tized using a hybrid mesh generated by the combination of structured and unstructured meshes, which reduces the computational cost of the whole inversion procedure. The inversion routine is based on the smoothness constrained least squares method. In order to verify the program, responses of two test models and field data sets were inverted. The models inverted from the synthetic data sets are consistent with the original test models in both DC resistivity and IP cases. A field data set acquired in an archaeological site is also used for the verification of outcomes of the program in comparison with the excavation results.

75 FR 29914 - Telecommunications Relay Services, Speech-to-Speech Services, E911 Requirements for IP-Enabled...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-28

... FEDERAL COMMUNICATIONS COMMISSION 47 CFR Part 64 [CG Docket No. 03-123; WC Docket No. 05-196; FCC 08-275] Telecommunications Relay Services, Speech-to-Speech Services, E911 Requirements for IP... Requirements for IP-Enabled Service Providers, Report Order and Order on Reconsideration (Second Report and...

77 FR 43538 - Misuse of Internet Protocol (IP) Relay Service; Telecommunications Relay Services and Speech-to...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-25

... the Internet, this service has become subject to abuse. Among other things, persons have been using IP...] Misuse of Internet Protocol (IP) Relay Service; Telecommunications Relay Services and Speech-to-Speech.... ACTION: Final rule. SUMMARY: In this document, the Commission adopts a measure that prohibits Internet...

In-situ calibration: migrating control system IP module calibration from the bench to the storage ring

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

Weber, Jonah M.; Chin, Michael

2002-04-30

The Control System for the Advanced Light Source (ALS) at Lawrence Berkeley National Lab (LBNL) uses in-house designed IndustryPack(registered trademark) (IP) modules contained in compact PCI (cPCI) crates with 16-bit analog I/O to control instrumentation. To make the IP modules interchangeable, each module is calibrated for gain and offset compensation. We initially developed a method of verifying and calibrating the IP modules in a lab bench test environment using a PC with LabVIEW. The subsequent discovery that the ADCs have significant drift characteristics over periods of days of installed operation prompted development of an ''in-situ'' calibration process--one in which themore » IP modules can be calibrated without removing them from the cPCI crates in the storage ring. This paper discusses the original LabVIEW PC calibration and the migration to the proposed in-situ EPICS control system calibration.« less

First results of coupled IPS/NIMROD/GENRAY simulations

NASA Astrophysics Data System (ADS)

Jenkins, Thomas; Kruger, S. E.; Held, E. D.; Harvey, R. W.; Elwasif, W. R.; Schnack, D. D.

2010-11-01

The Integrated Plasma Simulator (IPS) framework, developed by the SWIM Project Team, facilitates self-consistent simulations of complicated plasma behavior via the coupling of various codes modeling different spatial/temporal scales in the plasma. Here, we apply this capability to investigate the stabilization of tearing modes by ECCD. Under IPS control, the NIMROD code (MHD) evolves fluid equations to model bulk plasma behavior, while the GENRAY code (RF) calculates the self-consistent propagation and deposition of RF power in the resulting plasma profiles. GENRAY data is then used to construct moments of the quasilinear diffusion tensor (induced by the RF) which influence the dynamics of momentum/energy evolution in NIMROD's equations. We present initial results from these coupled simulations and demonstrate that they correctly capture the physics of magnetic island stabilization [Jenkins et al, PoP 17, 012502 (2010)] in the low-beta limit. We also discuss the process of code verification in these simulations, demonstrating good agreement between NIMROD and GENRAY predictions for the flux-surface-averaged, RF-induced currents. An overview of ongoing model development (synthetic diagnostics/plasma control systems; neoclassical effects; etc.) is also presented. Funded by US DoE.

[Survival rate of IPS-Empress 2 all-ceramic crowns and bridges: three year's results].

PubMed

Zimmer, Doris; Gerds, Thomas; Strub, Jörg R

2004-01-01