NPOESS System Architecture

NASA Astrophysics Data System (ADS)

Hinnant, F.

2009-12-01

The National Oceanic and Atmospheric Administration (NOAA), Department of Defense (DoD), and National Aeronautics and Space Administration (NASA) are jointly acquiring the next-generation weather and environmental satellite system; the National Polar-orbiting Operational Environmental Satellite System (NPOESS). NPOESS replaces the current Polar-orbiting Operational Environmental Satellites (POES) managed by NOAA and the Defense Meteorological Satellite Program (DMSP) managed by the DoD and will provide continuity for the NASA Earth Observation System with the launch of the NPOESS Preparatory Project. This poster will provide a top level status update of the program, as well as an overview of the NPOESS system architecture, which includes four segments. The space segment includes satellites in two orbits that carry a suite of sensors that collect meteorological, oceanographic, climatological, and solar-geophysical observations of the earth, atmosphere, and space. The NPOESS system design allows centralized mission management and delivers high quality environmental products to military, civil and scientific users through a Command, Control, and Communication Segment (C3S). The data processing for NPOESS is accomplished through an Interface Data Processing Segment (IDPS)/Field Terminal Segment (FTS) that processes NPOESS satellite data to provide environmental data products to NOAA and DoD processing centers operated by the United States government as well as remote terminal users. The Launch Support Segment completes the four segments that make up the NPOESS system that will enhance the connectivity between research and operations and provide critical operational and scientific environmental measurements to military, civil, and scientific users until 2026.

National Polar-orbiting Operational Environmental Satellite System (NPOESS) Design and Architecture

NASA Astrophysics Data System (ADS)

Hinnant, F.

2008-12-01

The National Oceanic and Atmospheric Administration (NOAA), Department of Defense (DoD), and National Aeronautics and Space Administration (NASA) are jointly acquiring the next-generation weather and environmental satellite system - the National Polar-orbiting Operational Environmental Satellite System (NPOESS). NPOESS will replace the current Polar-orbiting Operational Environmental Satellites (POES) managed by NOAA and the Defense Meteorological Satellite Program (DMSP) managed by the DoD and will provide continuity for the NASA Earth Observing System (EOS) with the launch of the NPOESS Preparatory Project (NPP). This poster will provide an overview of the NPOESS architecture, which includes four segments. The space segment includes satellites in two orbits that carry a suite of sensors to collect meteorological, oceanographic, climatological, and solar-geophysical observations of the Earth, atmosphere, and near-Earth space environment. The NPOESS design allows centralized mission management and delivers high quality environmental products to military, civil and scientific users through a Command, Control, and Communication Segment (C3S). The data processing for NPOESS is accomplished through an Interface Data Processing Segment (IDPS)/Field Terminal Segment (FTS) that processes NPOESS satellite data to provide environmental data products to NOAA and DoD processing centers operated by the United States government as well as to remote terminal users. The Launch Support Segment completes the four segments that make up NPOESS that will enhance the connectivity between research and operations and provide critical operational and scientific environmental measurements to military, civil, and scientific users until 2026.

Nitrogen Isotopic Composition of Organic Matter in a Pristine Collection IDP

NASA Technical Reports Server (NTRS)

Messenger, S.; Nakamura-Messenger, K.; Keller, L. P.; Clemett, S. J.; Nguyen, A. N.; Walker, Robert M.

2012-01-01

Anhydrous chondritic porous interplanetary dust particles (CP IDPs) are probable cometary materials that show primitive characteristics, such as unequilibrated mineralogy, fragile structure, and abundant presolar grains and organic matter [1-3]. CP IDPs are richer in aliphatic species and N-bearing aromatic hydrocarbons than meteoritic organics and commonly exhibit highly anomalous H and N isotopic compositions [4,5]. Cometary organic matter is of interest in part because it has escaped the hydrothermal processing experienced by meteorites. However, IDPs are collected using silicon oil that must be removed with strong organic solvents such as hexane. This procedure is likely to have removed some fraction of soluble organic phases in IDPs. We recently reported the first stratospheric collection of IDPs without the use of silicone oil [6]. Here we present initial studies of the carbonaceous material in an IDP from this collection.

Assemblage of Presolar Materials and Early Solar System Condensates in Chondritic Porous Interplanetary Dust Particles

NASA Technical Reports Server (NTRS)

Nguyen, A. N.; Nakamura-Messenger, K.; Messenger, S.; Keller, L. P.; Kloeck, W.

2015-01-01

Anhydrous chondritic porous inter-planetary dust particles (CP IDPs) contain an assortment of highly primitive solar system components, molecular cloud matter, and presolar grains. These IDPs have largely escaped parent body processing that has affected meteorites, advocating cometary origins. Though the stardust abundance in CP IDPs is generally greater than in primitive meteorites, it can vary widely among individual CP IDPs. The average abundance of silicate stardust among isotopically primitive IDPs is approx. 375 ppm while some have extreme abundances up to approx. 1.5%. H and N isotopic anomalies are common in CP IDPs and the carrier of these anomalies has been traced to organic matter that has experienced chemical reactions in cold molecular clouds or the outer protosolar disk. Significant variations in these anomalies may reflect different degrees of nebular processing. Refractory inclusions are commonly observed in carbonaceous chondrites. These inclusions are among the first solar system condensates and display 16O-rich isotopic compositions. Refractory grains have also been observed in the comet 81P/Wild-2 samples re-turned from the Stardust Mission and in CP IDPs, but they occur with much less frequency. Here we conduct coordinated mineralogical and isotopic analyses of CP IDPs that were characterized for their bulk chemistry by to study the distribution of primitive components and the degree of nebular alteration incurred.

Skin tumor area extraction using an improved dynamic programming approach.

PubMed

Abbas, Qaisar; Celebi, M E; Fondón García, Irene

2012-05-01

Border (B) description of melanoma and other pigmented skin lesions is one of the most important tasks for the clinical diagnosis of dermoscopy images using the ABCD rule. For an accurate description of the border, there must be an effective skin tumor area extraction (STAE) method. However, this task is complicated due to uneven illumination, artifacts present in the lesions and smooth areas or fuzzy borders of the desired regions. In this paper, a novel STAE algorithm based on improved dynamic programming (IDP) is presented. The STAE technique consists of the following four steps: color space transform, pre-processing, rough tumor area detection and refinement of the segmented area. The procedure is performed in the CIE L(*) a(*) b(*) color space, which is approximately uniform and is therefore related to dermatologist's perception. After pre-processing the skin lesions to reduce artifacts, the DP algorithm is improved by introducing a local cost function, which is based on color and texture weights. The STAE method is tested on a total of 100 dermoscopic images. In order to compare the performance of STAE with other state-of-the-art algorithms, various statistical measures based on dermatologist-drawn borders are utilized as a ground truth. The proposed method outperforms the others with a sensitivity of 96.64%, a specificity of 98.14% and an error probability of 5.23%. The results demonstrate that this STAE method by IDP is an effective solution when compared with other state-of-the-art segmentation techniques. The proposed method can accurately extract tumor borders in dermoscopy images. © 2011 John Wiley & Sons A/S.

High-Nickel Iron-Sulfides in Anhydrous, Gems-Rich CP IDPs

NASA Technical Reports Server (NTRS)

FLynn, G. J.; Keller, L. P.; Wirick, S.; Hu, W.; Li, L.; Yan, H.; Huang, X.; Nazaretski, E.; Lauer, K.; Chu, Y. S.

2016-01-01

Chondritic porous interplanetary dust particles (CP IDPs) that were not severly heated during atmospheric deceleration are the best preserved samples of the solids that condensed from the Solar protoplanetary disk, as well as pre-Solar grains thatr survived incorporation into the disk, currently available for laboratory analysis [1]. These CP IDPs never experienced the aqueous and/or thermal processing, gravitational compaction, and shock effects that overprinted the record of Solar nebula processes in meteorites.

An Overview of the JPSS Ground Project Algorithm Integration Process

NASA Astrophysics Data System (ADS)

Vicente, G. A.; Williams, R.; Dorman, T. J.; Williamson, R. C.; Shaw, F. J.; Thomas, W. M.; Hung, L.; Griffin, A.; Meade, P.; Steadley, R. S.; Cember, R. P.

2015-12-01

The smooth transition, implementation and operationalization of scientific software's from the National Oceanic and Atmospheric Administration (NOAA) development teams to the Join Polar Satellite System (JPSS) Ground Segment requires a variety of experiences and expertise. This task has been accomplished by a dedicated group of scientist and engineers working in close collaboration with the NOAA Satellite and Information Services (NESDIS) Center for Satellite Applications and Research (STAR) science teams for the JPSS/Suomi-NPOES Preparatory Project (S-NPP) Advanced Technology Microwave Sounder (ATMS), Cross-track Infrared Sounder (CrIS), Visible Infrared Imaging Radiometer Suite (VIIRS) and Ozone Mapping and Profiler Suite (OMPS) instruments. The presentation purpose is to describe the JPSS project process for algorithm implementation from the very early delivering stages by the science teams to the full operationalization into the Interface Processing Segment (IDPS), the processing system that provides Environmental Data Records (EDR's) to NOAA. Special focus is given to the NASA Data Products Engineering and Services (DPES) Algorithm Integration Team (AIT) functional and regression test activities. In the functional testing phase, the AIT uses one or a few specific chunks of data (granules) selected by the NOAA STAR Calibration and Validation (cal/val) Teams to demonstrate that a small change in the code performs properly and does not disrupt the rest of the algorithm chain. In the regression testing phase, the modified code is placed into to the Government Resources for Algorithm Verification, Integration, Test and Evaluation (GRAVITE) Algorithm Development Area (ADA), a simulated and smaller version of the operational IDPS. Baseline files are swapped out, not edited and the whole code package runs in one full orbit of Science Data Records (SDR's) using Calibration Look Up Tables (Cal LUT's) for the time of the orbit. The purpose of the regression test is to identify unintended outcomes. Overall the presentation provides a general and easy to follow overview of the JPSS Algorithm Change Process (ACP) and is intended to facility the audience understanding of a very extensive and complex process.

The Abundance and Distribution of Presolar Materials in Cluster IDPS

NASA Technical Reports Server (NTRS)

Messenger, Scott; Keller, Lindsay; Nakamura-Messenger, Keiko; Ito, Motoo

2007-01-01

Presolar grains and remnants of interstellar organic compounds occur in a wide range of primitive solar system materials, including meteorites, interplanetary dust particles (IDPs), and comet Wild-2 samples. Among the most abundant presolar phases are silicate stardust grains and molecular cloud material. However, these materials have also been susceptible to destruction and alteration during parent body and nebular processing. In addition to their importance as direct samples of remote and ancient astrophysical environments, presolar materials thus provide a measure of how well different primitive bodies have preserved the original solar system starting materials. The matrix normalized abundances of presolar silicate grains in meteorites range from 20 ppm in Semarkona and Bishunpur to 170 ppm for Acfer 094. The lower abundances of presolar silicates in Bishunpur and Semarkona has been ascribed to the destruction of presolar silicates during aqueous processes. Presolar silicates appear to be significantly more abundant in anhydrous IDPs, possibly because these materials did not experience parent body hydrothermal alteration. Among IDPs the estimated abundances of presolar silicates vary by more than an order of magnitude, from 480 to 5500 ppm. The wide disparity in the abundances of presolar silicates of IDPs may be a consequence of the relatively small total area analyzed in those studies and the fine grain sizes of the IDPs. Alternatively, there may be a wide range in presolar silicate abundances between different IDPs. This view is supported by the observation that 15N-rich IDPs have higher presolar silicate abundances than those with isotopically normal N.

A Fragment-Based Method of Creating Small-Molecule Libraries to Target the Aggregation of Intrinsically Disordered Proteins.

PubMed

Joshi, Priyanka; Chia, Sean; Habchi, Johnny; Knowles, Tuomas P J; Dobson, Christopher M; Vendruscolo, Michele

2016-03-14

The aggregation process of intrinsically disordered proteins (IDPs) has been associated with a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Currently, however, no drug in clinical use targets IDP aggregation. To facilitate drug discovery programs in this important and challenging area, we describe a fragment-based approach of generating small-molecule libraries that target specific IDPs. The method is based on the use of molecular fragments extracted from compounds reported in the literature to inhibit of the aggregation of IDPs. These fragments are used to screen existing large generic libraries of small molecules to form smaller libraries specific for given IDPs. We illustrate this approach by describing three distinct small-molecule libraries to target, Aβ, tau, and α-synuclein, which are three IDPs implicated in Alzheimer's and Parkinson's diseases. The strategy described here offers novel opportunities for the identification of effective molecular scaffolds for drug discovery for neurodegenerative disorders and to provide insights into the mechanism of small-molecule binding to IDPs.

JPSS Cryosphere Algorithms: Integration and Testing in Algorithm Development Library (ADL)

NASA Astrophysics Data System (ADS)

Tsidulko, M.; Mahoney, R. L.; Meade, P.; Baldwin, D.; Tschudi, M. A.; Das, B.; Mikles, V. J.; Chen, W.; Tang, Y.; Sprietzer, K.; Zhao, Y.; Wolf, W.; Key, J.

2014-12-01

JPSS is a next generation satellite system that is planned to be launched in 2017. The satellites will carry a suite of sensors that are already on board the Suomi National Polar-orbiting Partnership (S-NPP) satellite. The NOAA/NESDIS/STAR Algorithm Integration Team (AIT) works within the Algorithm Development Library (ADL) framework which mimics the operational JPSS Interface Data Processing Segment (IDPS). The AIT contributes in development, integration and testing of scientific algorithms employed in the IDPS. This presentation discusses cryosphere related activities performed in ADL. The addition of a new ancillary data set - NOAA Global Multisensor Automated Snow/Ice data (GMASI) - with ADL code modifications is described. Preliminary GMASI impact on the gridded Snow/Ice product is estimated. Several modifications to the Ice Age algorithm that demonstrates mis-classification of ice type for certain areas/time periods are tested in the ADL. Sensitivity runs for day time, night time and terminator zone are performed and presented. Comparisons between the original and modified versions of the Ice Age algorithm are also presented.

Principal components - Petrology and chemistry of polyphase units in chondritic porous interplanetary dust particles

NASA Astrophysics Data System (ADS)

Rietmeijer, Frans J. M.

1997-03-01

Chondritic porous (CP) interplanetary dust particles (IDPs) can be described as 'cosmic sediments'. It should be possible to recognize in these IDPs the 4500 Myrs old solar nebula dusts. The studies of unaltered chondritic IDPs show that their matrices are a mixture of three different principal components (PCs) that also describe variable C/Si ratios of chondritic IDPs. Among others, PCs include polyphase units (PUs) that are amorphous to holocrystalline, both ultrafine- and coarse-grained, ferromagnesiosilica(te) materials with minor Al and Ca. The properties of PCs and their alteration products define the physical and chemical processes that produced and altered these components. PCs are also cornerstones of IDP classification. For example, the bulk composition of ultrafine-grained PCs can be reconstructed using the 'butterfly method' and also allows an evaluation of the metamorphic signatures, (e.g., dynamic pyrometamorphism), in chondritic IDPs.

Challenges to polycentric governance of an international development project tackling land degradation in Swaziland.

PubMed

Orchard, Steven E; Stringer, Lindsay C

2016-11-01

To effectively address the drivers and impacts of land degradation requires polycentric governance systems that facilitate international development projects (IDPs). This paper analyses an IDP aiming to reduce land degradation in Swaziland. A longitudinal-style qualitative approach draws on repeat household surveys, semi-structured interviews and focus groups. We aim to identify the changes that have taken place since the departure of the IDP funders, and the subsequent dynamics between stakeholders. We: (1) chart the evolution of the institutional structures and processes of the IDP; and (2) assess community perceptions of IDP outcomes. Lack of meaningful participation at various stages of the PMC caused the project to lose momentum following the departure of the funders. We discuss these findings in relation to a polycentric approach, and identify how multi-stakeholder IDP can be facilitated as part of wider polycentric governance approaches to inform policies to combat land degradation within Swaziland and more widely.

Incorporating prototyping and iteration into intervention development: a case study of a dining hall-based intervention.

PubMed

McClain, Arianna D; Hekler, Eric B; Gardner, Christopher D

2013-01-01

Previous research from the fields of computer science and engineering highlight the importance of an iterative design process (IDP) to create more creative and effective solutions. This study describes IDP as a new method for developing health behavior interventions and evaluates the effectiveness of a dining hall-based intervention developed using IDP on college students' eating behavior and values. participants were 458 students (52.6% female, age = 19.6 ± 1.5 years [M ± SD]). The intervention was developed via an IDP parallel process. A cluster-randomized controlled study compared differences in eating behavior among students in 4 university dining halls (2 intervention, 2 control). The final intervention was a multicomponent, point-of-selection marketing campaign. Students in the intervention dining halls consumed significantly less junk food and high-fat meat and increased their perceived importance of eating a healthful diet relative to the control group. IDP may be valuable for the development of behavior change interventions.

Algorithm integration using ADL (Algorithm Development Library) for improving CrIMSS EDR science product quality

NASA Astrophysics Data System (ADS)

Das, B.; Wilson, M.; Divakarla, M. G.; Chen, W.; Barnet, C.; Wolf, W.

2013-05-01

Algorithm Development Library (ADL) is a framework that mimics the operational system IDPS (Interface Data Processing Segment) that is currently being used to process data from instruments aboard Suomi National Polar-orbiting Partnership (S-NPP) satellite. The satellite was launched successfully in October 2011. The Cross-track Infrared and Microwave Sounder Suite (CrIMSS) consists of the Advanced Technology Microwave Sounder (ATMS) and Cross-track Infrared Sounder (CrIS) instruments that are on-board of S-NPP. These instruments will also be on-board of JPSS (Joint Polar Satellite System) that will be launched in early 2017. The primary products of the CrIMSS Environmental Data Record (EDR) include global atmospheric vertical temperature, moisture, and pressure profiles (AVTP, AVMP and AVPP) and Ozone IP (Intermediate Product from CrIS radiances). Several algorithm updates have recently been proposed by CrIMSS scientists that include fixes to the handling of forward modeling errors, a more conservative identification of clear scenes, indexing corrections for daytime products, and relaxed constraints between surface temperature and air temperature for daytime land scenes. We have integrated these improvements into the ADL framework. This work compares the results from ADL emulation of future IDPS system incorporating all the suggested algorithm updates with the current official processing results by qualitative and quantitative evaluations. The results prove these algorithm updates improve science product quality.

Discovery of Brownleeite: a New Manganese Silicide Mineral in an Interplanetary Dust Particle

NASA Technical Reports Server (NTRS)

Keller, Lindsay P.; Nakamura-Messenger, Keiko; Clemett, Simon J.; Messenger, Scott; Jones, John H.; Palma, Russell L.; Pepin, Robert O.; Klock, Wolfgang; Zolensky, Michael E.; Tatsuoka, Hirokazu

2011-01-01

The Earth accretes approximately 40,000 tons of cosmic dust annually, originating mainly from the disintegration of comets and collisions among asteroids. This cosmic dust, also known as interplanetary dust particles (IDPs), is a subject of intense interest since it is made of the original building blocks of our Solar System. Although the specific parent bodies of IDPs are unknown, the anhydrous chondritic-porous IDPs (CP-IDPs) subset has been potentially linked to a cometary source. The CP-IDPs are extremely primitive materials based on their unequilibrated mineralogy, C-rich chemistry, and anomalous isotopic signatures. In particular, some CP-IDPs escaped the thermal, aqueous and impact shock processing that has modified or destroyed the original mineralogy of meteorites. Thus, the CP-IDPs represent some of the most primitive solar system materials available for laboratory study. Most CP-IDPs are comprised of minerals that are common on Earth. However, in the course of an examination of one of the CP-IDPs, we encountered three sub-micrometer sized grains of manganese silicide (MnSi), a phase that has heretofore not been found in nature. In the seminar, we would like to focus on IDP studies and this manganese silicide phase that has been approved as the first new mineral identified from a comet by the International Mineralogical Association (IMA) in 2008. The mineral is named in honour of Donald E. Brownlee, an American astronomer and a founder of the field of cosmic dust research who is the principal investigator of the NASA Stardust Mission that collected dust samples from Comet 81P/Wild-2 and returned them to Earth. Much of our current view and understanding of the early solar system would not exist without the pioneering work of professor Don Brownlee in the study of IDPs.

In vitro-analysis of kinematics and intradiscal pressures in cervical arthroplasty versus fusion--A biomechanical study in a sheep model with two semi-constrained prosthesis.

PubMed

Daentzer, Dorothea; Welke, Bastian; Hurschler, Christof; Husmann, Nathalie; Jansen, Christina; Flamme, Christian Heinrich; Richter, Berna Ida

2015-03-24

As an alternative technique to arthrodesis of the cervical spine, total disc replacement (TDR) has increasingly been used with the aim of restoration of the physiological function of the treated and adjacent motions segments. The purpose of this experimental study was to analyze the kinematics of the target level as well as of the adjacent segments, and to measure the pressures in the proximal and distal disc after arthrodesis as well as after arthroplasty with two different semi-constrained types of prosthesis. Twelve cadaveric ovine cervical spines underwent polysegmental (C2-5) multidirectional flexibility testing with a sensor-guided industrial serial robot. Additionally, pressures were recorded in the proximal and distal disc. The following three conditions were tested: (1) intact specimen, (2) single-level arthrodesis C3/4, (3) single-level TDR C3/4 using the Discover® in the first six specimens and the activ® C in the other six cadavers. Statistical analysis was performed for the total range of motion (ROM), the intervertebral ROM (iROM) and the intradiscal pressures (IDP) to compare both the three different conditions as well as the two disc prosthesis among each other. The relative iROM in the target level was always lowered after fusion in the three directions of motion. In almost all cases, the relative iROM of the adjacent segments was almost always higher compared to the physiologic condition. After arthroplasty, we found increased relative iROM in the treated level in comparison to intact state in almost all cases, with relative iROM in the adjacent segments observed to be lower in almost all situations. The IDP in both adjacent discs always increased in flexion and extension after arthrodesis. In all but five cases, the IDP in each of the adjacent level was decreased below the values of the intact specimens after TDR. Overall, in none of the analyzed parameters were statistically significantly differences between both types of prostheses investigated. The results of this biomechanical study indicate that single-level implantation of semi-constrained TDR lead to a certain hypermobility in the treated segments with lowering the ROM in the adjacent levels in almost all situations.

Analytical electron microscopy of fine-grained phases in primitive interplanetary dust particles and carbonaceous chondrites

NASA Technical Reports Server (NTRS)

Mackinnon, Ian D. R.; Rietmeijer, Frans J. M.; Mckay, David S.

1987-01-01

In order to describe the total mineralogical diversity within primitive extraterrestrial materials, individual interplanetary dust particles (IDPs) collected from the stratosphere as part of the JSC Cosmic Dust Curatorial Program were analyzed using a variety of AEM techniques. Identification of over 250 individual grains within one chondritic porous (CP) IDP shows that most phases could be formed by low temperature processes and that heating of the IDP during atmospheric entry is minimal and less than 600 C. In a review of the mineralogy of IDPs, it was suggested that the occurrence of other silicates such as enstatite whiskers is consistent with the formation in an early turbulent period of the solar nebula. Experimental confirmation of fundamental chemical and physical processes in a stellar environment, such as vapor phase condensation, nucleation, and growth by annealing, is an important aspect of astrophysical models for the evolution of the Solar System. A detailed comparison of chondritic IDP and carbonaceous chondrite mineralogies shows significant differences between the types of silicate minerals as well as the predominant oxides.

Thin-sectioning and analysis of fine-grained meteoritic materials

NASA Technical Reports Server (NTRS)

Brooks, Donald A. (Editor); Bradley, John P.

1992-01-01

The overall theme of the work was the identification of the sources and formation/aggregation mechanisms of the various classes of interplanetary dust particles (IDP's) and to clarify the relationship between IDP's and conventional meteorites. IDP's are believed to be derived from a much broader range of parent bodies than conventional meteorites. Some of these parent bodies (e.g., comets) have escaped that post accretional processing that has affected the parent bodies of meteorites. Therefore, IDP's are likely to preserve a record of early solar system and possibly presolar grain forming reactions. Using analytical electron microscopy (AEM) and more recently micro-infrared (IR) microspectroscopy to examine ultramicrotomed thin sections, we have addressed the questions of IDP formation mechanisms, sources, and their relationship to conventional meteorites. The following sections describe specific findings resulting from these studies.

Biomechanical effects of hybrid stabilization on the risk of proximal adjacent-segment degeneration following lumbar spinal fusion using an interspinous device or a pedicle screw-based dynamic fixator.

PubMed

Lee, Chang-Hyun; Kim, Young Eun; Lee, Hak Joong; Kim, Dong Gyu; Kim, Chi Heon

2017-12-01

OBJECTIVE Pedicle screw-rod-based hybrid stabilization (PH) and interspinous device-based hybrid stabilization (IH) have been proposed to prevent adjacent-segment degeneration (ASD) and their effectiveness has been reported. However, a comparative study based on sound biomechanical proof has not yet been reported. The aim of this study was to compare the biomechanical effects of IH and PH on the transition and adjacent segments. METHODS A validated finite element model of the normal lumbosacral spine was used. Based on the normal model, a rigid fusion model was immobilized at the L4-5 level by a rigid fixator. The DIAM or NFlex model was added on the L3-4 segment of the fusion model to construct the IH and PH models, respectively. The developed models simulated 4 different loading directions using the hybrid loading protocol. RESULTS Compared with the intact case, fusion on L4-5 produced 18.8%, 9.3%, 11.7%, and 13.7% increments in motion at L3-4 under flexion, extension, lateral bending, and axial rotation, respectively. Additional instrumentation at L3-4 (transition segment) in hybrid models reduced motion changes at this level. The IH model showed 8.4%, -33.9%, 6.9%, and 2.0% change in motion at the segment, whereas the PH model showed -30.4%, -26.7%, -23.0%, and 12.9%. At L2-3 (adjacent segment), the PH model showed 14.3%, 3.4%, 15.0%, and 0.8% of motion increment compared with the motion in the IH model. Both hybrid models showed decreased intradiscal pressure (IDP) at the transition segment compared with the fusion model, but the pressure at L2-3 (adjacent segment) increased in all loading directions except under extension. CONCLUSIONS Both IH and PH models limited excessive motion and IDP at the transition segment compared with the fusion model. At the segment adjacent to the transition level, PH induced higher stress than IH model. Such differences may eventually influence the likelihood of ASD.

Identification of pixels with stray light and cloud shadow contaminations in the satellite ocean color data processing.

PubMed

Jiang, Lide; Wang, Menghua

2013-09-20

A new flag/masking scheme has been developed for identifying stray light and cloud shadow pixels that significantly impact the quality of satellite-derived ocean color products. Various case studies have been carried out to evaluate the performance of the new cloud contamination flag/masking scheme on ocean color products derived from the Visible Infrared Imaging Radiometer Suite (VIIRS) onboard the Suomi National Polar-orbiting Partnership (SNPP). These include direct visual assessments, detailed quantitative case studies, objective statistic analyses, and global image examinations and comparisons. The National Oceanic and Atmospheric Administration (NOAA) Multisensor Level-1 to Level-2 (NOAA-MSL12) ocean color data processing system has been used in the study. The new stray light and cloud shadow identification method has been shown to outperform the current stray light flag in both valid data coverage and data quality of satellite-derived ocean color products. In addition, some cloud-related flags from the official VIIRS-SNPP data processing software, i.e., the Interface Data Processing System (IDPS), have been assessed. Although the data quality with the IDPS flags is comparable to that of the new flag implemented in the NOAA-MSL12 ocean color data processing system, the valid data coverage from the IDPS is significantly less than that from the NOAA-MSL12 using the new stray light and cloud shadow flag method. Thus, the IDPS flag/masking algorithms need to be refined and modified to reduce the pixel loss, e.g., the proposed new cloud contamination flag/masking can be implemented in IDPS VIIRS ocean color data processing.

Continued Investigations of the Accretion History of Extraterrestrial Matter over Geologic Time

NASA Technical Reports Server (NTRS)

Farley, Kenneth

2001-01-01

This grant supported our ongoing project to characterize the accretion rate of interplanetary dust particles (IDPs) to Earth over geologic time using He-3 as a tracer. IDPs are derived from collisions in the asteroid belt and from disaggregation of active comets. Owing to their small size (few to few hundred micrometers diameter) these particles spiral into the sun under Poynting-Robertson drag typically in less than a few tens of kyrs. Thus IDPs must be continually resupplied to the zodiacal cloud, and because the processes of IDP production are likely to be sporadic, time variation in the IDP accretion rate to Earth is likely to be time-varying. For example, major asteroidal collisions and comet showers should greatly enhance the IDP accretion rate. Our ultimate objective (still ongoing) is to document this time variance so as to better understand the history of the solar system, the source of IDPs accreting to Earth, and the details of the mechanism by which particles are captured by Earth. To document variations in IDP accretion rate through time we use He-3 as a tracer. This isotope is in extremely low abundance in terrestrial matter, but IDPs have very high concentrations of He-3 from implantation of solar wind ions. By measuring He-3 in seafloor sediments, we can estimate the IDP accretion rate for at least the last few hundred Myrs. Under an earlier NASA grant we identified the existence of a large increase in He-3 flux in the Late Eocene (35 Myr ago), coincident with the two largest impact craters of the Cenozoic Era. The simplest interpretation of this observation is the occurrence of a shower of long period comets at that time, simultaneously increasing the impact cratering probability and accretion rate of IDPs to Earth (Farley et al., 1998). Comet showers produced by stellar perturbation of the Oort cloud should be fairly common in the geologic record, so this is not an unreasonable interpretation of our observations.

Carbon petrology in cometary dust

NASA Technical Reports Server (NTRS)

Rietmeijer, Frans J. M.

1992-01-01

Chondritic porous (CP) interplanetary dust particles (IDP's) are collected in the Earth's stratosphere. There exists an extensive database on major and minor element chemistry, stable isotopes, noble gas abundances and mineralogy of many CP IDP's, as well as infrared and Raman spectroscopic properties. For details on the mineralogy, chemistry and physical properties of IDP's, I refer to the reviews by Mackinnon and Rietmeijer (1987), Bradley et al. (1988) and Sandford (1987). Texture, mineralogy (Mackinnon and Rietmeijer, 1987) and chemistry (Schramm et al., 1989; Flynn and Sutton, 1991) support the notion that CP IDP's are a unique group of ultrafine-grained extraterrestiral materials that are distinct from any known meteorite class. Their fluffy, or porous, morphology suggests that CP IDP's probably endured minimal alteration by protoplanetary processes since their formation. It is generally accepted that CP IDP's are solid debris from short-period comets. The evidence is mostly circumstantial but this notion gained significant support based on the comet Halley dust data (Brownlee, 1990). In this paper, I will accept that CP IDP's are indeed cometary dust. The C/Si ratio in CP IDP's is 3.3 times higher than in CI carbonaceous chondrites (Schramm et al. 1989). The intraparticle carbon distribution is heteorogeneous (Rietmeijer and McKay, 1986). Carbon occurs both in oxidized and reduced forms. Analytical electron microscope (AEM) and Raman spectroscopic analyses have shown the presence of several carbon forms in CP IDP's but the data are scattered in the literature. Carbons in cometary CP IDP's are among the most pristine Solar System carbons available for laboratory study. Similar to a recently developed petrological model for the diversity of layer silicates in CP IDP's (Zolensky, 1991) that is useful to constrain in situ aqueous alteration in comets (Rietmeijer and Mackinnon, 1987a), I here present the first effort to develop a petrological concept of carbons in CP IDP's. This concept is useful to constrain comet evolution. I also present the philosophical constraint facing Earth Scientists in studies of protoplanets that require a new approach to cometary dust studies.

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

McAfee, J.G.; Krauss, D.J.; Subramanian, G.

The 3-hour biodistribution of /sup 99m/Tc complexes of five diphosphonates (HMDP, NMMDP, DMAD, DPD, and APD), imidodiphosphonate (IDP), and pyrophosphate (PYP) was compared in rats with segmental renal infarction induced by a 1-hour occlusion of a renal artery branch. /sup 95m/Tc labeled MDP was a reference substance in all animals. Three agents (APD, HMDP and IDP) had a higher infarct/normal kidney concentration ratio than MDP, the latter two by virtue of a lower content in normal kidney. HMDP, DPD, and IDP had very high liver concentrations. DPD showed relatively high concentrations in soft tissues and blood. The blood and kidneymore » levels of PYP were higher than those of MDP but the infarct/normal kidney ratios were similar. None of the agents had a higher uptake in bone than MDP: four had a significantly lower uptake. The increased concentration of /sup 99m/Tc MDP in the infarcts was readily seen in camera images one day after renal artery occlusion, but not at three or seven days. Increased diphosphonate uptake was accompanied by an influx of calcium in both cortex and medulla. The accumulation of diphosphonate in areas of infarction was not modified by infusions of verapamil or Captopril.« less

Improving the automated detection of refugee/IDP dwellings using the multispectral bands of the WorldView-2 satellite

NASA Astrophysics Data System (ADS)

Kemper, Thomas; Gueguen, Lionel; Soille, Pierre

2012-06-01

The enumeration of the population remains a critical task in the management of refugee/IDP camps. Analysis of very high spatial resolution satellite data proofed to be an efficient and secure approach for the estimation of dwellings and the monitoring of the camp over time. In this paper we propose a new methodology for the automated extraction of features based on differential morphological decomposition segmentation for feature extraction and interactive training sample selection from the max-tree and min-tree structures. This feature extraction methodology is tested on a WorldView-2 scene of an IDP camp in Darfur Sudan. Special emphasis is given to the additional available bands of the WorldView-2 sensor. The results obtained show that the interactive image information tool is performing very well by tuning the feature extraction to the local conditions. The analysis of different spectral subsets shows that it is possible to obtain good results already with an RGB combination, but by increasing the number of spectral bands the detection of dwellings becomes more accurate. Best results were obtained using all eight bands of WorldView-2 satellite.

Interstellar and Solar System Organic Matter Preserved in Interplanetary Dust

NASA Technical Reports Server (NTRS)

Messenger, Scott; Nakamura-Messenger, Keiko

2015-01-01

Interplanetary dust particles (IDPs) collected in the Earth's stratosphere derive from collisions among asteroids and by the disruption and outgassing of short-period comets. Chondritic porous (CP) IDPs are among the most primitive Solar System materials. CP-IDPs have been linked to cometary parent bodies by their mineralogy, textures, C-content, and dynamical histories. CP-IDPs are fragile, fine-grained (less than um) assemblages of anhydrous amorphous and crystalline silicates, oxides and sulfides bound together by abundant carbonaceous material. Ancient silicate, oxide, and SiC stardust grains exhibiting highly anomalous isotopic compositions are abundant in CP-IDPs, constituting 0.01 - 1 % of the mass of the particles. The organic matter in CP-IDPs is isotopically anomalous, with enrichments in D/H reaching 50x the terrestrial SMOW value and 15N/14N ratios up to 3x terrestrial standard compositions. These anomalies are indicative of low T (10-100 K) mass fractionation in cold molecular cloud or the outermost reaches of the protosolar disk. The organic matter shows distinct morphologies, including sub-um globules, bubbly textures, featureless, and with mineral inclusions. Infrared spectroscopy and mass spectrometry studies of organic matter in IDPs reveals diverse species including aliphatic and aromatic compounds. The organic matter with the highest isotopic anomalies appears to be richer in aliphatic compounds. These materials also bear similarities and differences with primitive, isotopically anomalous organic matter in carbonaceous chondrite meteorites. The diversity of the organic chemistry, morphology, and isotopic properties in IDPs and meteorites reflects variable preservation of interstellar/primordial components and Solar System processing. One unifying feature is the presence of sub-um isotopically anomalous organic globules among all primitive materials, including IDPs, meteorites, and comet Wild-2 samples returned by the Stardust mission.

Oxygen isotopic composition of chondritic interplanetary dust particles: A genetic link between carbonaceous chondrites and comets

NASA Astrophysics Data System (ADS)

Aléon, J.; Engrand, C.; Leshin, L. A.; McKeegan, K. D.

2009-08-01

Oxygen isotopes were measured in four chondritic hydrated interplanetary dust particles (IDPs) and five chondritic anhydrous IDPs including two GEMS-rich particles (Glass embedded with metal and sulfides) by a combination of high precision and high lateral resolution ion microprobe techniques. All IDPs have isotopic compositions tightly clustered around that of solar system planetary materials. Hydrated IDPs have mass-fractionated oxygen isotopic compositions similar to those of CI and CM carbonaceous chondrites, consistent with hydration of initially anhydrous protosolar dust. Anhydrous IDPs have small 16O excesses and depletions similar to those of carbonaceous chondrites, the largest 16O variations being hosted by the two GEMS-rich IDPs. Coarse-grained forsteritic olivine and enstatite in anhydrous IDPs are isotopically similar to their counterparts in comet Wild 2 and in chondrules suggesting a high temperature inner solar system origin. The small variations in the 16O content of GEMS-rich IDPs suggest that most GEMS either do not preserve a record of interstellar processes or the initial interstellar dust is not 16O-rich as expected by self-shielding models, although a larger dataset is required to verify these conclusions. Together with other chemical and mineralogical indicators, O isotopes show that the parent-bodies of carbonaceous chondrites, of chondritic IDPs, of most Antarctic micrometeorites, and comet Wild 2 belong to a single family of objects of carbonaceous chondrite chemical affinity as distinct from ordinary, enstatite, K- and R-chondrites. Comparison with astronomical observations thus suggests a chemical continuum of objects including main belt and outer solar system asteroids such as C-type, P-type and D-type asteroids, Trojans and Centaurs as well as short-period comets and other Kuiper Belt Objects.

Validation of S-NPP VIIRS Day-Night Band and M Bands Performance Using Ground Reference Targets of Libya 4 and Dome C

NASA Technical Reports Server (NTRS)

Chen, Xuexia; Wu, Aisheng; Xiong, Xiaoxiong; Lei, Ning; Wang, Zhipeng; Chiang, Kwofu

2015-01-01

This paper provides methodologies developed and implemented by the NASA VIIRS Calibration Support Team (VCST) to validate the S-NPP VIIRS Day-Night band (DNB) and M bands calibration performance. The Sensor Data Records produced by the Interface Data Processing Segment (IDPS) and NASA Land Product Evaluation and Algorithm Testing Element (PEATE) are acquired nearly nadir overpass for Libya 4 desert and Dome C snow surfaces. In the past 3.5 years, the modulated relative spectral responses (RSR) change with time and lead to 3.8% increase on the DNB sensed solar irradiance and 0.1% or less increases on the M4-M7 bands. After excluding data before April 5th, 2013, IDPS DNB radiance and reflectance data are consistent with Land PEATE data with 0.6% or less difference for Libya 4 site and 2% or less difference for Dome C site. These difference are caused by inconsistent LUTs and algorithms used in calibration. In Libya 4 site, the SCIAMACHY spectral and modulated RSR derived top of atmosphere (TOA) reflectance are compared with Land PEATE TOA reflectance and they indicate a decrease of 1.2% and 1.3%, respectively. The radiance of Land PEATE DNB are compared with the simulated radiance from aggregated M bands (M4, M5, and M7). These data trends match well with 2% or less difference for Libya 4 site and 4% or less difference for Dome C. This study demonstrate the consistent quality of DNB and M bands calibration for Land PEATE products during operational period and for IDPS products after April 5th, 2013.

Sequence Determinants of Compaction in Intrinsically Disordered Proteins

PubMed Central

Marsh, Joseph A.; Forman-Kay, Julie D.

2010-01-01

Abstract Intrinsically disordered proteins (IDPs), which lack folded structure and are disordered under nondenaturing conditions, have been shown to perform important functions in a large number of cellular processes. These proteins have interesting structural properties that deviate from the random-coil-like behavior exhibited by chemically denatured proteins. In particular, IDPs are often observed to exhibit significant compaction. In this study, we have analyzed the hydrodynamic radii of a number of IDPs to investigate the sequence determinants of this compaction. Net charge and proline content are observed to be strongly correlated with increased hydrodynamic radii, suggesting that these are the dominant contributors to compaction. Hydrophobicity and secondary structure, on the other hand, appear to have negligible effects on compaction, which implies that the determinants of structure in folded and intrinsically disordered proteins are profoundly different. Finally, we observe that polyhistidine tags seem to increase IDP compaction, which suggests that these tags have significant perturbing effects and thus should be removed before any structural characterizations of IDPs. Using the relationships observed in this analysis, we have developed a sequence-based predictor of hydrodynamic radius for IDPs that shows substantial improvement over a simple model based upon chain length alone. PMID:20483348

Element Mapping in Anhydrous IDPs: Identification of the Host Phases of Major/Minor Elements as a Test of Nebula Condensation Models

NASA Technical Reports Server (NTRS)

Flynn, G. J.; Keller, L. P.; Wirick, S.; Jacobsen, C.

2004-01-01

Many anhydrous interplanetary dust particles (IDPs) are the most pristine samples of primitive solar system dust currently available for laboratory analysis. Their primitive nature is demonstrated by: 1) the high content of moderately volatile elements, indicating they have not been heated significantly since formation, 2) the absence of hydrated material, indicating they never experienced aqueous processing, 3) the presence of unequilibrated mineral assemblages, 4) the presence of large isotopic anomalies (e.g., D and 15N enrichment), in these IDPs.

The JPSS Ground Project Algorithm Verification, Test and Evaluation System

NASA Astrophysics Data System (ADS)

Vicente, G. A.; Jain, P.; Chander, G.; Nguyen, V. T.; Dixon, V.

2016-12-01

The Government Resource for Algorithm Verification, Independent Test, and Evaluation (GRAVITE) is an operational system that provides services to the Suomi National Polar-orbiting Partnership (S-NPP) Mission. It is also a unique environment for Calibration/Validation (Cal/Val) and Data Quality Assessment (DQA) of the Join Polar Satellite System (JPSS) mission data products. GRAVITE provides a fast and direct access to the data and products created by the Interface Data Processing Segment (IDPS), the NASA/NOAA operational system that converts Raw Data Records (RDR's) generated by sensors on the S-NPP into calibrated geo-located Sensor Data Records (SDR's) and generates Mission Unique Products (MUPS). It also facilitates algorithm investigation, integration, checkouts and tuning, instrument and product calibration and data quality support, monitoring and data/products distribution. GRAVITE is the portal for the latest S-NPP and JPSS baselined Processing Coefficient Tables (PCT's) and Look-Up-Tables (LUT's) and hosts a number DQA offline tools that takes advantage of the proximity to the near-real time data flows. It also contains a set of automated and ad-hoc Cal/Val tools used for algorithm analysis and updates, including an instance of the IDPS called GRAVITE Algorithm Development Area (G-ADA), that has the latest installation of the IDPS algorithms running in an identical software and hardware platforms. Two other important GRAVITE component are the Investigator-led Processing System (IPS) and the Investigator Computing Facility (ICF). The IPS is a dedicated environment where authorized users run automated scripts called Product Generation Executables (PGE's) to support Cal/Val and data quality assurance offline. This data-rich and data-driven service holds its own distribution system and allows operators to retrieve science data products. The ICF is a workspace where users can share computing applications and resources and have full access to libraries and science and sensor quality analysis tools. In this presentation we will describe the GRAVITE systems and subsystems, architecture, technical specifications, capabilities and resources, distributed data and products and the latest advances to support the JPSS science algorithm implementation, validation and testing.

A proposition for the classification of carbonaceous chondritic micrometeorites

NASA Technical Reports Server (NTRS)

Rietmeijer, Frans J. M.

1994-01-01

Classification of interplanetary dust particles (IDP's) should be unambiguous and, if possible, provide an opportunity to interrelate these ultrafine IDP's with the matrices of undifferentiated meteorites. I prefer a scheme of chemical groupings and petrologic classes that is based on primary IDP properties that can be determined without prejudice by individual investigators. For IDP's of 2-50 microns these properties are bulk elemental chemistry, morphology, shape, and optical properties. The two major chemical groups are readily determined by energy dispersive spectroscopic analysis using the scanning or analytical electron microscope. Refinement of chondritic IDP classification is possible using the dominant mineral species, e.g. olivine, pyroxene, and layer silicates, and is readily inferred from FTIR, and automated chemical analysis. Petrographic analysis of phyllosilicate-rich IDP's will identify smectite-rich and serpentine-rich particles. Chondritic IDP's are also classified according to morphology, viz., CP and CF IDP's are aggregate particles that differ significantly in porosity, while the dense CS IDP's have a smooth surface. The CP IDP's are characterized by an anhydrous silicate mineralogy, but small amounts of layer silicates may be present. Distinction between the CP and CF IDP's is somewhat ambiguous, but the unique CP IDP's are fluffy, or porous, ultrafine-grained aggregates. The CP IDP's, which may contain silicate whiskers, are the most carbon-rich extraterrestrial material presently known. The CF IDP's are much less porous that CP IDP's. Using particle type definitions, CP IDP's in the NASA JSC Cosmic Dust Catalogs are approx. 15 percent of all IDP's that include nonchondritic spheres. Most aggregate particles are of the CF type.

Large Stratospheric IDPs: Chemical Compostion and Comparison with Smaller Stratospheric IDPs

NASA Astrophysics Data System (ADS)

Flynn, G. J.; Bajt, S.; Sutton, S. R.; Klock, W.

1995-09-01

Six large stratospheric IDPs, each greater than 35 microns, previously analyzed using the X-Ray Microprobe at the National Synchrotron Light Source showed an average volatile content consistent with CI or CM meteorites [1]. Seven additional large IDPs, ranging from 37x33 to 50x44 microns in size and having chondritic major element abundances, have been analyzed using the same instrument. Each of these 7 IDPs is depleted in Ca compared to CI (Avg. Ca = 0.48xCI), a feature also observed in the first set of 6, suggesting most or all of these IDPs are hydrated. The average trace element content of these 7 large IDPs is similar to the previous set of 6 (see Figure 1), though Mn and Cu are about 70% higher in this set. The average composition of these large IDPs is distinctly different from that of smaller IDPs (generally 10 to 20 microns), which show enrichments of the volatiles Cu, Zn, Ga, Ge, and Se by factors of 1.5 to 3 over CI [2]. This suggests large IDPs which are strong enough to resist fragmentation on collection are chemically different from typical smaller IDPs. This may reflect a difference in the source(s) being sampled by the two types of IDPs. A subgroup of the smaller IDPs (9 of 51 particles) have a composition similar to CI meteorites and these large IDPs [2]. Bromine is enriched in most of these large IDPs. Two Br-rich IDPs (Br >300 ppm) and one Br-poor IDP (Br ~5 ppm) were each analyzed twice. The two Br-rich IDPs showed about a factor of two Br loss between the first and second analyses, presumably due to sample heating during the first analysis. This suggests some of the Br is very weakly bound in these Br-rich IDPs, a possible signature of Br surface contamination. However, the Br contents measured in the second analyses were still ~50xCI. No loss of Cu, Zn, Ga, Ge or Se was detected in these IDPs, suggesting these elements are in more retentive sites. The Br-poor IDP (Br ~1.5xCI) showed no Br loss in the second analysis. Only one of these IDPs, L2008G10, showed a large Zn depletion (Zn/Fe <0.01xCI). This was accompanied by low contents of Ga, Ge and Br (see Figure 1). This pattern of Zn, Ge, Br and Ga depletions was previously seen in smaller IDPs which were severely heated, presumably on atmospheric entry [2]. Sulfur and K are also low in L2008G10, suggesting these elements are also lost during heating, but the Se content is 0.8xCI. A second particle, L2009C8, has a Zn/Fe=0.26xCI, possibly indicating less severe heating. The low fraction of severely heated IDPs, only one in this set of 7 and none in the set of 6 [1] suggests a very low atmospheric entry velocity for these large IDPs [3]. References: [1] Flynn G. J. et al. (1995) LPS XXVI, 407-408. [2] Flynn G. J. et al. (1993) LPS XXIV, 495-496. [3] Flynn G. J., this volume. Figure 1: Average Fe and CI normalized element abundances in 7 large IDPs, 6 different large IDPs [1], 51 smaller IDPs [2], and the single low-Zn IDP, L2008G10, included in the set of 7 large IDPs.

UV production of methane from surface and sedimenting IDPs on Mars in light of REMS data and with insights for TGO

NASA Astrophysics Data System (ADS)

Moores, John E.; Smith, Christina L.; Schuerger, Andrew C.

2017-11-01

This paper refines model predictions for the production of methane from UV-irradiated interplanetary dust particles (IDPs) now that the Rover Environmental Monitoring Station (REMS) instrument onboard the Mars Science Laboratory (MSL) Rover has made the first measurements of the UV environment on the surface of Mars, at Gale Crater. Once these measurements are included in a UV radiative transfer model, we find that modelled UV sol-integrated energies across the planet are lower than pre-measurement estimates by 35% on average, considering all latitudes and seasons. This reduction, in turn, reduces the predicted production of methane from individual accreting IDPs, extending their lifetimes and increasing the surface concentration of organics that must accumulate in order to emit sufficient methane to balance the accretion of organic compounds to Mars. Emission from reasonable accumulations of IDPs could range up to ∼7.9 × 10-4 ppbv sol-1. Richer deposits of organic carbon at the surface may emit methane at no more than 3.9 ppbv sol-1. An examination of IDP-derived methane production during atmospheric settling indicates that no more than 0.32% of organic carbon from meteor streams may be deposited in the atmosphere. Thus, such a process cannot explain either the spikes observed in methane nor the low equilibrium values observed by MSL. Instead, this discrepancy may be explained if < 80 tons per year of organic carbon survives to the surface, the atmospheric lifetime of methane is < 110 years or the efficiency of the UV-CH4 process is <7%. Under the assumption of reduced carbon input cycling in the Martian system from these processes, both soil concentrations of organic carbon and atmospheric measurements of methane observed by MSL are consistent with the UV-CH4 process. This refinement of methane production from IDPs and its geographical and vertical distribution will be an important input for models attempting to understand the results to be derived from the Trace Gas Orbiter (TGO) mission that will map methane concentrations in the martian atmosphere in 2018 at 0.01 ppbv.

Incorporating Prototyping and Iteration into Intervention Development: A Case Study of a Dining Hall-Based Intervention

ERIC Educational Resources Information Center

McClain, Arianna D.; Hekler, Eric B.; Gardner, Christopher D.

2013-01-01

Background: Previous research from the fields of computer science and engineering highlight the importance of an iterative design process (IDP) to create more creative and effective solutions. Objective: This study describes IDP as a new method for developing health behavior interventions and evaluates the effectiveness of a dining hall--based…

The Butterflies of Principal Components: A Case of Ultrafine-Grained Polyphase Units

NASA Astrophysics Data System (ADS)

Rietmeijer, F. J. M.

1996-03-01

Dusts in the accretion regions of chondritic interplanetary dust particles [IDPs] consisted of three principal components: carbonaceous units [CUs], carbon-bearing chondritic units [GUs] and carbon-free silicate units [PUs]. Among others, differences among chondritic IDP morphologies and variable bulk C/Si ratios reflect variable mixtures of principal components. The spherical shapes of the initially amorphous principal components remain visible in many chondritic porous IDPs but fusion was documented for CUs, GUs and PUs. The PUs occur as coarse- and ultrafine-grained units that include so called GEMS. Spherical principal components preserved in an IDP as recognisable textural units have unique proporties with important implications for their petrological evolution from pre-accretion processing to protoplanet alteration and dynamic pyrometamorphism. Throughout their lifetime the units behaved as closed-systems without chemical exchange with other units. This behaviour is reflected in their mineralogies while the bulk compositions of principal components define the environments wherein they were formed.

Automated thin-film analyses of hydrated interplanetary dust particles in the analytical electron microscope

NASA Technical Reports Server (NTRS)

Germani, M. S.; Bradley, J. P.; Brownlee, D. E.

1990-01-01

A 200 keV electron microscope was used to obtain elemental analyses from over 4000 points on thin sections of eight 'layer silicate' class interplanetary dust particles (IDPs). Major and minor element abundances from a volume approaching that of a cylinder 50 nm in diameter were observed. Mineral phases and their relative abundances in the thin sections were identified and petrographic characteristics were determined. Three of the particles contained smectite (1.0-1.2 nm basal spacing) and two contained serpentine (0.7 nm basal spacing). The point count analyses and Mg-Si-Fe ternary diagrams show that one of the serpentine-containing IDPs is similar to CI and CM chondritic meteorites. The IDPs exhibit evidence of aqueous processing, but they have typically experienced only short range, submicrometer scale alteration. The IDPs may provide a broad sampling of the asteroid belt.

Development of Innovative Design Processor

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

Park, Y.S.; Park, C.O.

2004-07-01

The nuclear design analysis requires time-consuming and erroneous model-input preparation, code run, output analysis and quality assurance process. To reduce human effort and improve design quality and productivity, Innovative Design Processor (IDP) is being developed. Two basic principles of IDP are the document-oriented design and the web-based design. The document-oriented design is that, if the designer writes a design document called active document and feeds it to a special program, the final document with complete analysis, table and plots is made automatically. The active documents can be written with ordinary HTML editors or created automatically on the web, which ismore » another framework of IDP. Using the proper mix-up of server side and client side programming under the LAMP (Linux/Apache/MySQL/PHP) environment, the design process on the web is modeled as a design wizard style so that even a novice designer makes the design document easily. This automation using the IDP is now being implemented for all the reload design of Korea Standard Nuclear Power Plant (KSNP) type PWRs. The introduction of this process will allow large reduction in all reload design efforts of KSNP and provide a platform for design and R and D tasks of KNFC. (authors)« less

Mineralogical Study of Hydrated IDPs: X-Ray Diffraction and Transmission Electron Microscopy

NASA Technical Reports Server (NTRS)

Nakamura, K.; Keller, L. P.; Nakamura, T.; Noguchi, T.; Zolensky, M. E.

2004-01-01

Chondritic hydrated interplanetary dust particles (IDPs) comprise up to 50% of all IDPs collected in the stratosphere [1]. Hydrated IDPs are generally believed to be derived from asteroidal sources that have undergone aqueous alteration. However, the high C contents of hydrated IDPs (by 2 to 6X CI levels [2,3]) indicate that they are probably not derived from the same parent bodies sampled by the known chondritic meteorites. Some hydrated IDPs exhibit large deuterium enrichments [4] similar to those observed in anhydrous IDPs. Both anhydrous and hydrated IDPs contain a variety of anhydrous minerals such as silicates, sulfides, oxides, and carbonates. Controversies on hydrated IDPs still exist regarding their formation, history, and relationship to other primitive solar system materials, because of the lack of a systematic series of analysis on individual hydrated IDPs. In this study, we combine our observations of the bulk mineralogy, mineral/ organic chemistry in order to derive a more complete picture of hydrated IDPs.

Heterogeneous access and processing of EO-Data on a Cloud based Infrastructure delivering operational Products

NASA Astrophysics Data System (ADS)

Niggemann, F.; Appel, F.; Bach, H.; de la Mar, J.; Schirpke, B.; Dutting, K.; Rucker, G.; Leimbach, D.

2015-04-01

To address the challenges of effective data handling faced by Small and Medium Sized Enterprises (SMEs) a cloud-based infrastructure for accessing and processing of Earth Observation(EO)-data has been developed within the project APPS4GMES(www.apps4gmes.de). To gain homogenous multi mission data access an Input Data Portal (IDP) been implemented on this infrastructure. The IDP consists of an Open Geospatial Consortium (OGC) conformant catalogue, a consolidation module for format conversion and an OGC-conformant ordering framework. Metadata of various EO-sources and with different standards is harvested and transferred to an OGC conformant Earth Observation Product standard and inserted into the catalogue by a Metadata Harvester. The IDP can be accessed for search and ordering of the harvested datasets by the services implemented on the cloud infrastructure. Different land-surface services have been realised by the project partners, using the implemented IDP and cloud infrastructure. Results of these are customer ready products, as well as pre-products (e.g. atmospheric corrected EO data), serving as a basis for other services. Within the IDP an automated access to ESA's Sentinel-1 Scientific Data Hub has been implemented. Searching and downloading of the SAR data can be performed in an automated way. With the implementation of the Sentinel-1 Toolbox and own software, for processing of the datasets for further use, for example for Vista's snow monitoring, delivering input for the flood forecast services, can also be performed in an automated way. For performance tests of the cloud environment a sophisticated model based atmospheric correction and pre-classification service has been implemented. Tests conducted an automated synchronised processing of one entire Landsat 8 (LS-8) coverage for Germany and performance comparisons to standard desktop systems. Results of these tests, showing a performance improvement by the factor of six, proved the high flexibility and computing power of the cloud environment. To make full use of the cloud capabilities a possibility for automated upscaling of the hardware resources has been implemented. Together with the IDP infrastructure fast and automated processing of various satellite sources to deliver market ready products can be realised, thus increasing customer needs and numbers can be satisfied without loss of accuracy and quality.

Modeling phase separation in mixtures of intrinsically-disordered proteins

NASA Astrophysics Data System (ADS)

Gu, Chad; Zilman, Anton

Phase separation in a pure or mixed solution of intrinsically-disordered proteins (IDPs) and its role in various biological processes has generated interest from the theoretical biophysics community. Phase separation of IDPs has been implicated in the formation of membrane-less organelles such as nucleoli, as well as in a mechanism of selectivity in transport through the nuclear pore complex. Based on a lattice model of polymers, we study the phase diagram of IDPs in a mixture and describe the selective exclusion of soluble proteins from the dense-phase IDP aggregates. The model captures the essential behaviour of phase separation by a minimal set of coarse-grained parameters, corresponding to the average monomer-monomer and monomer-protein attraction strength, as well as the protein-to-monomer size ratio. Contrary to the intuition that strong monomer-monomer interaction increases exclusion of soluble proteins from the dense IDP aggregates, our model predicts that the concentration of soluble proteins in the aggregate phase as a function of monomer-monomer attraction is non-monotonic. We corroborate the predictions of the lattice model using Langevin dynamics simulations of grafted polymers in planar and cylindrical geometries, mimicking various in-vivo and in-vitro conditions.

Carbon Raman Spectroscopy of 36 Inter-Planetary Dust Particles

NASA Technical Reports Server (NTRS)

Busemann, H.; Nittler, L. R.; Davidson, J.; Franchi, I. A.; Messenger, S.; Nakamura-Messenger, K.; Palma, R. L.; Pepin, R. O.

2009-01-01

Carbon Raman spectroscopy is a useful tool to determine the degree of order of organic material (OM) in extra-terrestrial matter. As shown for meteoritic OM [e.g., 2], peak parameters of D and G bands are a measure of thermal alteration, causing graphitization (order), and amorphization, e.g. during protoplanetary irradiation, causing disorder. Th e most pristine interplanetary dust particles (IDPs) may come from comets. However, their exact provenance is unknown. IDP collection during Earth?s passage through comet Grigg-Skjellerup?s dust stream ("GSC" collectors) may increase the probability of collecting fresh IDPs from a known, cometary source. We used Raman spectroscopy to compare 21 GSC-IDPs with 15 IDPs collected at different periods, and found that the variation among GSC-IDPs is larger than among non-GSC IDPs, with the most primitive IDPs being mostly GSC-IDPs.

Proteus: a random forest classifier to predict disorder-to-order transitioning binding regions in intrinsically disordered proteins

NASA Astrophysics Data System (ADS)

Basu, Sankar; Söderquist, Fredrik; Wallner, Björn

2017-05-01

The focus of the computational structural biology community has taken a dramatic shift over the past one-and-a-half decades from the classical protein structure prediction problem to the possible understanding of intrinsically disordered proteins (IDP) or proteins containing regions of disorder (IDPR). The current interest lies in the unraveling of a disorder-to-order transitioning code embedded in the amino acid sequences of IDPs/IDPRs. Disordered proteins are characterized by an enormous amount of structural plasticity which makes them promiscuous in binding to different partners, multi-functional in cellular activity and atypical in folding energy landscapes resembling partially folded molten globules. Also, their involvement in several deadly human diseases (e.g. cancer, cardiovascular and neurodegenerative diseases) makes them attractive drug targets, and important for a biochemical understanding of the disease(s). The study of the structural ensemble of IDPs is rather difficult, in particular for transient interactions. When bound to a structured partner, an IDPR adapts an ordered conformation in the complex. The residues that undergo this disorder-to-order transition are called protean residues, generally found in short contiguous stretches and the first step in understanding the modus operandi of an IDP/IDPR would be to predict these residues. There are a few available methods which predict these protean segments from their amino acid sequences; however, their performance reported in the literature leaves clear room for improvement. With this background, the current study presents `Proteus', a random forest classifier that predicts the likelihood of a residue undergoing a disorder-to-order transition upon binding to a potential partner protein. The prediction is based on features that can be calculated using the amino acid sequence alone. Proteus compares favorably with existing methods predicting twice as many true positives as the second best method (55 vs. 27%) with a much higher precision on an independent data set. The current study also sheds some light on a possible `disorder-to-order' transitioning consensus, untangled, yet embedded in the amino acid sequence of IDPs. Some guidelines have also been suggested for proceeding with a real-life structural modeling involving an IDPR using Proteus.

Infrared spectroscopy of interplanetary dust in the laboratory

NASA Technical Reports Server (NTRS)

Fraundorf, P.; Patel, R. I.; Freeman, J. J.

1981-01-01

A mount containing three crushed chondritic interplanetary dust particles (IDPs) collected in the earth's stratosphere and subjected to infrared spectroscopic measurements shows features near 1000 and 500/cm, suggesting crystalline pyroxene rather than crystalline olivine, amorphous olivine, or meteoritic clay minerals. Chondritic IDP structural diversity and atmospheric heating effects must be considered when comparing this spectrum with interplanetary and cometary dust astrophysical spectra. TEM and infrared observations of one member of the rare subset of IDPs resembling hydrated carbonaceous chondrite matrix material shows a close infrared spectrum resemblance between 4000 and 400/cm to the C2 meteorite Murchison. TEM observations suggest that this class of particles may be used as an atmospheric entry heating-process thermometer.

NPOESS C3S Expandability: SafetyNetTM and McMurdo Improvements

NASA Astrophysics Data System (ADS)

Jamilkowski, M. L.; Paciaroni, J.; Pela, F.

2010-12-01

The National Oceanic & Atmospheric Administration (NOAA), Department of Defense (DoD), and National Aeronautics & Space Administration (NASA) are jointly acquiring the next-generation weather & environmental satellite system; the National Polar-orbiting Operational Environmental Satellite System (NPOESS). NPOESS replaces the current NOAA Polar-orbiting Operational Environmental Satellites (POES) and Dod's Defense Meteorological Satellite Program (DMSP). The NPOESS satellites carry a suite of sensors that collect meteorological, oceanographic, climatological, and solar-geophysical observations of the earth, atmosphere, and space. The command & telemetry portion of NPOESS is the Command, Control and Communications Segment (C3S), developed by Raytheon Intelligence & Information Systems. C3S is responsible for managing the overall NPOESS mission from control and status of the space and ground assets to ensuring delivery of timely, high quality data from the Space Segment (SS) to the Interface Data Processing Segment (IDPS) for processing. In addition, the C3S provides the globally distributed ground assets necessary to collect and transport mission, telemetry, and command data between the satellites and the processing locations. The C3S provides all functions required for day-to-day commanding & state-of-health monitoring of the NPP & NPOESS satellites, and delivery of Stored Mission Data (SMD) to each US Weather Central Interface Data Processor (IDP) for data products development and transfer to System subscribers. The C3S also monitors and reports system-wide health and status & data communications with external systems and between NPOESS segments. Two crucial elements of NPOESS C3S expandability are SafetyNetTM and communications improvements to McMurdo Station, Antarctica. SafetyNetTM is a key feature of NPOESS and a vital element of the C3S and Northrop Grumman Aerospace Systems patented data collection architecture. The centerpiece of SafetyNetTM is the system of fifteen globally-distributed ground receptors developed by Raytheon Company. These antennae will collect up to five times as much environmental data approximately four times faster than current polar-orbiting weather satellites. Once collected, these data will be forwarded near-instantaneously to US weather centrals via the global fiber optic network for processing in environmental prediction models. In January 2008, Raytheon Company achieved a significant milestone for the NPOESS program by successfully completing the first phase of a major communications upgrade for Antarctica. The upgrade of the off-continent satellite communications link at McMurdo Station more than tripled the bandwidth available for scientific research, weather prediction, and health & safety of those stationed at McMurdo. The project is part of the company’s C3S under development for NPOESS. This upgrade paves the way for a second major communications upgrade planned for 2012 in preparation for the use of McMurdo Station as one of the 15 NPOESS ground stations worldwide that will be receiving environmental data collected by the NPOESS satellites. SafetyNet is a trademark of Northrop Grumman Aerospace Systems.

Fibrillation mechanism of a model intrinsically disordered protein revealed by 2D correlation deep UV resonance Raman spectroscopy.

PubMed

Sikirzhytski, Vitali; Topilina, Natalya I; Takor, Gaius A; Higashiya, Seiichiro; Welch, John T; Uversky, Vladimir N; Lednev, Igor K

2012-05-14

Understanding of numerous biological functions of intrinsically disordered proteins (IDPs) is of significant interest to modern life science research. A large variety of serious debilitating diseases are associated with the malfunction of IDPs including neurodegenerative disorders and systemic amyloidosis. Here we report on the molecular mechanism of amyloid fibrillation of a model IDP (YE8) using 2D correlation deep UV resonance Raman spectroscopy. YE8 is a genetically engineered polypeptide, which is completely unordered at neutral pH yet exhibits all properties of a fibrillogenic protein at low pH. The very first step of the fibrillation process involves structural rearrangements of YE8 at the global structure level without the detectable appearance of secondary structural elements. The formation of β-sheet species follows the global structural changes and proceeds via the simultaneous formation of turns and β-strands. The kinetic mechanism revealed is an important new contribution to understanding of the general fibrillation mechanism proposed for IDP.

Coordinates Analyses of Hydrated Interplanetary Dust Particles: Samples of Primitive Solar System Bodies

NASA Technical Reports Server (NTRS)

Keller, L. P.; Snead, C.; McKeegan, K. D.

2016-01-01

Interplanetary dust particles (IDPs) collected in the stratosphere fall into two major groups: an anhydrous group termed the "chondritic-porous (CP) IDPs and a hydrated group, the "chondritic-smooth (CS) IDPs, although rare IDPs with mineralogies intermediate between these two groups are known [1]. The CP-IDPs are widely believed to be derived from cometary sources [e.g. 2]. The hydrated CS-IDPs show mineralogical similarities to heavily aqueously altered carbonaceous chondrites (e.g. CI chondrites), but only a few have been directly linked to carbonaceous meteorite parent bodies [e.g. 3, 4]. Most CS-IDPs show distinct chemical [5] and oxygen isotopic composition differences [6-8] from primitive carbonaceous chondrites. Here, we report on our coordinated analyses of a suite of carbon-rich CS-IDPs focusing on their bulk compositions, mineralogy, mineral chemistry, and isotopic compositions.

Sequence fingerprints distinguish erroneous from correct predictions of intrinsically disordered protein regions.

PubMed

Saravanan, Konda Mani; Dunker, A Keith; Krishnaswamy, Sankaran

2017-12-27

More than 60 prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the World Wide Web. Nearly, all of these predictors give balanced accuracies in the ~65%-~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions. In the present work, we make use of sequences of 100% predicted IDP regions, false positive disorder predictions, and experimentally determined IDP regions to distinguish the characteristics of native versus predicted IDP regions. A higher occurrence of asparagine is observed in sequences of native IDP regions but not in sequences of false positive predictions of IDP regions. The occurrences of certain combinations of amino acids at the pentapeptide level provide a distinguishing feature in the IDPs with respect to globular proteins. The distinguishing features presented in this paper provide insights into the sequence fingerprints of amino acid residues in experimentally determined as compared to predicted IDP regions. These observations and additional work along these lines should enable the development of improvements in the accuracy of disorder prediction algorithm.

Relations between aliphatics and silicate components in 12 stratospheric particles deduced from vibrational spectroscopy

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

Merouane, S.; Djouadi, Z.; Le Sergeant d'Hendecourt, L., E-mail: sihane.merouane@ias.u-psud.fr

2014-01-10

Interplanetary dust particles (IDPs) are among the most pristine extraterrestrial samples available in the laboratory for analyses with moderate to high spatial- and spectral-resolution spectroscopic techniques. Their composition can provide precious information on the early stages of the solar nebula as well as on the processes on the surfaces of different small bodies in the solar system from which IDPs originate. In this work, we have analyzed six anhydrous IDPs and six stratospheric particles possibly of cosmic origin through infrared (IR) and Raman micro-spectroscopy to study and investigate their silicate and organic components. We find that the length/ramification of themore » aliphatic organics given by the CH{sub 2}/CH{sub 3} ratios in the IDPs is closely linked to the silicate family (pyroxene or olivine) present in the samples. Both IR and Raman data suggest that this relation is not correlated with either aqueous (as evidenced by the absence of aqueous related minerals) or thermal processes (as deduced from Raman measurements). Therefore, this observation might be related to the initial path of formation of the organics on the silicate surfaces, thus tracing a possible catalytic role that silicates would play in the formation and/or ramification of organic matter in the primitive nebula.« less

Nitrogen Isotopic Anomalies in a Hydrous Interplanetary Dust Particle

NASA Technical Reports Server (NTRS)

Smith, J. B.; Dai, Z. R.; Weber, P. K.; Graham, G. A.; Hutcheon, I. D.; Bajt, S.; Ishii, H.; Bradley, J. P.

2005-01-01

Interplanetary dust particles (IDPs) collected in the stratosphere are the fine-grained end member (5 - 50 microns in size) of the meteoritic material available for investigation in the laboratory. IDPs are derived from either cometary or asteroidal sources. Some IDPs contain cosmically primitive materials with isotopic signatures reflecting presolar origins. Recent detailed studies using the NanoSIMS have shown there is a wide variation of isotopic signatures within individual IDPs; grains with a presolar signature have been observed surrounded by material with a solar isotopic composition. The majority of IDPs studied have been anhydrous. We report here results from integrated NanoSIMS/FIB/TEM/Synchrotron IR studies of a hydrous IDP, focused on understanding the correlations between the isotopic, mineralogical and chemical compositions of IDPs.

Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations.

PubMed

Ithuralde, Raúl Esteban; Roitberg, Adrián Enrique; Turjanski, Adrián Gustavo

2016-07-20

Intrinsically disordered proteins (IDPs) are a set of proteins that lack a definite secondary structure in solution. IDPs can acquire tertiary structure when bound to their partners; therefore, the recognition process must also involve protein folding. The nature of the transition state (TS), structured or unstructured, determines the binding mechanism. The characterization of the TS has become a major challenge for experimental techniques and molecular simulations approaches since diffusion, recognition, and binding is coupled to folding. In this work we present atomistic molecular dynamics (MD) simulations that sample the free energy surface of the coupled folding and binding of the transcription factor c-myb to the cotranscription factor CREB binding protein (CBP). This process has been recently studied and became a model to study IDPs. Despite the plethora of available information, we still do not know how c-myb binds to CBP. We performed a set of atomistic biased MD simulations running a total of 15.6 μs. Our results show that c-myb folds very fast upon binding to CBP with no unique pathway for binding. The process can proceed through both structured or unstructured TS's with similar probabilities. This finding reconciles previous seemingly different experimental results. We also performed Go-type coarse-grained MD of several structured and unstructured models that indicate that coupled folding and binding follows a native contact mechanism. To the best of our knowledge, this is the first atomistic MD simulation that samples the free energy surface of the coupled folding and binding processes of IDPs.

ff14IDPs Force Field Improving the Conformation Sampling of Intrinsically Disordered Proteins

PubMed Central

Song, Dong; Wang, Wei; Ye, Wei; Ji, Dingjue; Luo, Ray; Chen, Hai-Feng

2017-01-01

Intrinsically disordered proteins (IDPs) are proteins which lack of specific tertiary structure and unable to fold spontaneously without the partner binding. These IDPs are found to associate with various diseases, such as diabetes, cancer, and neurodegenerative diseases. However, current widely used force fields, such as ff99SB, ff14SB, OPLS/AA, and Charmm27 are insufficient in sampling the conformational characters of IDPs. In this study, the CMAP method was used to correct the φ/ψ distributions of disorder-promoting amino acids. The simulation results show that the force filed parameters (ff14IDPs) can improve the φ/ψ distributions of the disorder-promoting amino acids, with RMSD less than 0.10% relative to the benchmark data of IDPs. Further test suggests that the calculated secondary chemical shifts under ff14IDPs force field are in quantitative agreement with the data of NMR experiment for five tested systems. In addition, the simulation results show that ff14IDPs can still be used to model structural proteins, such as tested lysozyme and ubiquitin, with better performance in coil regions than the original general Amber force field ff14SB. These findings confirm that the newly developed Amber ff14IDPs force field is a robust model for improving the conformation sampling of IDPs. PMID:27484738

Interplanetary Dust Particles

NASA Astrophysics Data System (ADS)

Bradley, J. P.

2003-12-01

One of the fundamental goals of the study of meteorites is to understand how the solar system and planetary systems around other stars formed. It is known that the solar system formed from pre-existing (presolar) interstellar dust grains and gas. The grains originally formed in the circumstellar outflows of other stars. They were modified to various degrees, ranging from negligible modification to complete destruction and reformation during their ˜108 yr lifetimes in the interstellar medium (ISM) (Seab, 1987; Mathis, 1993). Finally, they were incorporated into the solar system. Submicrometer-sized silicates and carbonaceous material are believed to be the most common grains in the ISM ( Mathis, 1993; Sandford, 1996), but it is not known how much of this presolar particulate matter was incorporated into the solar system, to what extent it has survived, and how it might be distinguished from solar system grains. In order to better understand the process of solar system formation, it is important to identify and analyze these solid grains. Since all of the alteration processes that modified solids in the solar nebula presumably had strong radial gradients, the logical place to find presolar grains is in small primitive bodies like comets and asteroids that have undergone little, if any, parent-body alteration.Trace quantities of refractory presolar grains (e.g., SiC and Al2O3) survive in the matrices of the most primitive carbon-rich chondritic meteorites (Anders and Zinner, 1993; Bernatowicz and Zinner, 1996; Bernatowicz and Walker, 1997; Hoppe and Zinner, 2000; see Chapter 1.02). Chondritic meteorites are believed to be from the asteroid belt, a narrow region between 2.5 and 3.5 astronomical units (AU) that marks the transition from the terrestrial planets to the giant gas-rich planets. The spectral properties of the asteroids suggest a gradation in properties with some inner and main belt C and S asteroids (the source region of most meteorites and polar micrometeorites) containing layer silicates indicative of parent-body aqueous alteration and the more distant anhydrous P and D asteroids exhibiting no evidence of (aqueous) alteration (Gradie and Tedesco, 1982). This gradation in spectral properties presumably extends several hundred AU out to the Kuiper belt, the source region of most short-period comets, where the distinction between comets and outer asteroids may simply be one of the orbital parameters ( Luu, 1993; Brownlee, 1994; Jessberger et al., 2001). The mineralogy and petrography of meteorites provides direct confirmation of aqueous alteration, melting, fractionation, and thermal metamorphism among the inner asteroids ( Zolensky and McSween, 1988; Farinella et al., 1993; Brearley and Jones, 1998). Because the most common grains in the ISM (silicates and carbonaceous matter) are not as refractory as those found in meteorites, it is unlikely that they have survived in significant quantities in meteorites. Despite a prolonged search, not a single presolar silicate grain has yet been identified in any meteorite.Interplanetary dust particles (IDPs) are the smallest and most fine-grained meteoritic objects available for laboratory investigation (Figure 1). In contrast to meteorites, IDPs are derived from a broad range of dust-producing bodies extending from the inner main belt of the asteroids to the Kuiper belt (Flynn, 1996, 1990; Dermott et al., 1994; Liou et al., 1996). After release from their asteroidal or cometary parent bodies the orbits of IDPs evolve by Poynting-Robertson (PR) drag (the combined influence of light pressure and radiation drag) ( Dermott et al., 2001). Irrespective of the location of their parent bodies nearly all IDPs under the influence of PR drag can eventually reach Earth-crossing orbits. IDPs are collected in the stratosphere at 20-25 km altitude using NASA ER2 aircraft ( Sandford, 1987; Warren and Zolensky, 1994). Laboratory measurements of implanted rare gases, solar flare tracks ( Figure 2), and isotope abundances have confirmed that the collected particles are indeed extraterrestrial and that, prior to atmospheric entry, they spent 104-105 yr as small particles orbiting the Sun (Rajan et al., 1977; Hudson et al., 1981; Bradley et al., 1984a; McKeegan et al., 1985; Messenger, 2000). (21K)Figure 1. (a)-(c) Secondary electron images. (a) Anhydrous CP IDP. (b) Hydrated CS IDP (RB12A44). (c) Single-mineral forsterite grain with adhering chondritic material. (d) Optical micrograph (transmitted light) of giant cluster IDP (U220GCA) in silicone oil on ER2 collection flag. (14K)Figure 2. Darkfield transmission electron micrographs. (a) Solar-wind sputtered rim on exterior surface plus implanted solar flare tracks in chondritic IDP U220A19 (from Bradley and Brownlee, 1986). (b) Solar flare tracks in a forsterite crystal in chondritic IDP U220B11 (from Bradley et al., 1984a). The track densities in both IDPs are ˜1010-1011 cm2 corresponding to an orbital exposure age of ˜104yr. During atmospheric entry most IDPs are frictionally heated to within 100 °C of their peak heating temperature for ˜1 s and, to a first-order approximation, the smallest particles are the least strongly heated. Although some IDPs may experience thermal pulses in excess of 1,000 °C for up to 10 s (depending on particle size, mass, entry angle, and speed) (Love and Brownlee, 1991, 1996), the presence of solar flare tracks in an IDP establishes that it was not heated above ˜650 °C ( Bradley et al., 1984a). Since IDPs decelerate from cosmic velocities at altitudes >90 km, where the maximum aerodynamic ram pressure is a factor of ˜103 less than that exerted on conventional meteorites, extremely fragile meteoritic materials that cannot survive as large objects can survive as small IDPs (Figure 1(a)) ( Brownlee, 1994). Such fragile materials are suspected to be among the most primitive objects and potentially the most informative regarding early solar system and presolar processes. (Conventional meteorites penetrate deep into the atmosphere such that only relatively well-indurated rocks can survive.) Collected IDPs are briefly exposed to the terrestrial environment but since their residence time in the stratosphere is short (˜2 weeks), they are not subjected to longer-term weathering that affects the surfaces of most meteorites (Flynn, 1994a).This chapter examines the compositions, mineralogy, sources, and geochemical significance of IDPs. Additional reading can be found in reviews by Fraundorf (1981), Brownlee (1985), Sandford (1987), Bradley et al. (1988), Jessberger et al. (2001), Rietmeijer (1998), and the book edited by Zolensky et al. (1994). Despite their micrometer-scale dimensions and nanogram masses it is now possible, primarily as a result of advances in small particle handling techniques and analytical instrumentation, to examine IDPs at close to atomic-scale resolution. The most widely used instruments for IDP studies are presently the analytical electron microscope, synchrotron facilities, and the ion microprobe. These laboratory analytical techniques are providing fundamental insights about IDP origins, mechanisms of formation, and grain processing phenomena that were important in the early solar system and presolar environments. At the same time, laboratory data from IDPs are being compared with astronomical data from dust in comets, circumstellar disks, and the ISM. The direct comparison of grains in the laboratory with grains in astronomical environments defines the new discipline of "astromineralogy" ( Jaeger et al., 1998; Bradley et al., 1999a, b; Molster et al., 2001; Keller et al., 2001; Flynn et al., 2002). ,

Carbon abundances, major element chemistry, and mineralogy of hydrated interplanetary dust particles

NASA Technical Reports Server (NTRS)

Keller, L. P.; Thomas, K. L.; Mckay, D. S.

1993-01-01

Hydrated interplanetary dust particles (IDP's) comprise a major fraction of the interplanetary dust particles collected in the stratosphere. While much is known about the mineralogy and chemistry of hydrated IDP's, little is known about the C abundance in this class of IDP's, the nature of the C-bearing phases, and how the C abundance is related to other physical properties of hydrated IDP's. Bulk compositional data (including C and O) for 11 hydrated IDP's that were subsequently examined by the transition electron microscopy (TEM) to determine their mineralogy and mineral chemistry are reported. Our analysis indicates that these hydrated IDP's are strongly enriched in C relative to the most C-rich meteorites. The average abundance of C in these hydrated IDP's is 4X CI chondrite values. The bulk compositions (including C and O) of 11 hydrated IDP's were determined by thin-window, energy-dispersive x ray (EDX) spectroscopy of the uncoated IDP's on Be substrates in the scanning electron microscopy (SEM). As a check on our C measurements, one of the IDP's (L2006H5) was embedded in glassy S, and microtome thin sections were prepared and placed onto Be substrates. Thin-film EDX analyses of multiple thin sections of L2006H5 show good agreement with the bulk value determined in the SEM. Following EDX analysis, the mineralogy and mineral chemistry of each IDP was determined by analyzing ultramicrotome thin sections in a TEM equipped with an EDX spectrometer.

Presolar Materials in a Giant Cluster IDP of Probable Cometary Origin

NASA Technical Reports Server (NTRS)

Messenger, S.; Brownlee, D. E.; Joswiak, D. J.; Nguyen, A. N.

2015-01-01

Chondritic porous interplanetary dust particles (CP-IDPs) have been linked to comets by their fragile structure, primitive mineralogy, dynamics, and abundant interstellar materials. But differences have emerged between 'cometary' CP-IDPs and comet 81P/Wild 2 Stardust Mission samples. Particles resembling Ca-Al-rich inclusions (CAIs), chondrules, and amoeboid olivine aggregates (AOAs) in Wild 2 samples are rare in CP-IDPs. Unlike IDPs, presolar materials are scarce in Wild 2 samples. These differences may be due to selection effects, such as destruction of fine grained (presolar) components during the 6 km/s aerogel impact collection of Wild 2 samples. Large refractory grains observed in Wild 2 samples are also unlikely to be found in most (less than 30 micrometers) IDPs. Presolar materials provide a measure of primitive-ness of meteorites and IDPs. Organic matter in IDPs and chondrites shows H and N isotopic anomalies attributed to low-T interstellar or protosolar disk chemistry, where the largest anomalies occur in the most primitive samples. Presolar silicates are abundant in meteorites with low levels of aqueous alteration (Acfer 094 approximately 200 ppm) and scarce in altered chondrites (e.g. Semarkona approximately 20 ppm). Presolar silicates in minimally altered CP-IDPs range from approximately 400 ppm to 15,000 ppm, possibly reflecting variable levels of destruction in the solar nebula or statistical variations due to small sample sizes. Here we present preliminary isotopic and mineralogical studies of a very large CP-IDP. The goals of this study are to more accurately determine the abundances of presolar components of CP-IDP material for comparison with comet Wild 2 samples and meteorites. The large mass of this IDP presents a unique opportunity to accurately determine the abundance of pre-solar grains in a likely cometary sample.

Image processing and products for the Magellan mission to Venus

NASA Technical Reports Server (NTRS)

Clark, Jerry; Alexander, Doug; Andres, Paul; Lewicki, Scott; Mcauley, Myche

1992-01-01

The Magellan mission to Venus is providing planetary scientists with massive amounts of new data about the surface geology of Venus. Digital image processing is an integral part of the ground data system that provides data products to the investigators. The mosaicking of synthetic aperture radar (SAR) image data from the spacecraft is being performed at JPL's Multimission Image Processing Laboratory (MIPL). MIPL hosts and supports the Image Data Processing Subsystem (IDPS), which was developed in a VAXcluster environment of hardware and software that includes optical disk jukeboxes and the TAE-VICAR (Transportable Applications Executive-Video Image Communication and Retrieval) system. The IDPS is being used by processing analysts of the Image Data Processing Team to produce the Magellan image data products. Various aspects of the image processing procedure are discussed.

A Small Molecule Causes a Population Shift in the Conformational Landscape of an Intrinsically Disordered Protein.

PubMed

Ban, David; Iconaru, Luigi I; Ramanathan, Arvind; Zuo, Jian; Kriwacki, Richard W

2017-10-04

Intrinsically disordered proteins (IDPs) have roles in myriad biological processes and numerous human diseases. However, kinetic and amplitude information regarding their ground-state conformational fluctuations has remained elusive. We demonstrate using nuclear magnetic resonance (NMR)-based relaxation dispersion that the D2 domain of p27 Kip1 , a prototypical IDP, samples multiple discrete, rapidly exchanging conformational states. By combining NMR with mutagenesis and small-angle X-ray scattering (SAXS), we show that these states involve aromatic residue clustering through long-range hydrophobic interactions. Theoretical studies have proposed that small molecules bind promiscuously to IDPs, causing expansion of their conformational landscapes. However, on the basis of previous NMR-based screening results, we show here that compound binding only shifts the populations of states that existed within the ground state of apo p27-D2 without changing the barriers between states. Our results provide atomic resolution insight into how a small molecule binds an IDP and emphasize the need to examine motions on the low microsecond time scale when probing these types of interactions.

The Nature and Origin of Interplanetary Dust: High Temperature Components

NASA Technical Reports Server (NTRS)

Keller, L. P.; Messenger, S.

2004-01-01

The specific parent bodies of individual interplanetary dust particles (IDPs) are un-known, but the anhydrous chondritic-porous (CP) sub-set has been linked directly to cometary sources [1]. The CP IDPs escaped the thermal processing and water-rock interactions that have severely modified or destroyed the original mineralogy of primitive meteorites. Their origin in the outer regions of the solar system suggests they should retain primitive chemical and physical characteristics from the earliest stages of solar system formation (including abundant presolar materials). Indeed, CP IDPs are the most primitive extraterrestrial materials available for laboratory studies based on their unequilibrated mineralogy [2], high concentrations of carbon, nitrogen and volatile trace elements relative to CI chondrites [3, 4, 5], presolar hydrogen and nitrogen isotopic signatures [6, 7] and abundant presolar silicates [8].

The effects of interplanetary dust impacts on the accumulation of volatiles in the lunar permanently shadowed regions

NASA Astrophysics Data System (ADS)

Horanyi, Mihaly; Szalay, Jamey

2017-10-01

The lunar regolith has been formed, and remains continually reworked, by the intermitten impacts of comets, asteroids, meteoroids, and the continual bombardment by interplanetary dust particles (IDP). Thick atmospheres protect Venus, Earth, and Mars, ablating the incoming IDPs into “shooting stars” that rarely reach the surface. However, the surfaces of airless bodies near 1 AU are directly exposed to the high-speed (>> 1 km/s) IDP impacts. The Moon is expected to be bombarded by 5x103 kg/day of IDPs arriving with a characteristic speed of ~ 20 km/s. The IDP sources impacting the Moon at high latitudes remain largely uncharacterized due to the lack of optical and radar observations in the polar regions on Earth. These high latitude sources have very large impact speeds in the range of 30 < v < 50 km/ hence they are expected to have a significant effect on the lunar surface, including the removal and burial of volatile deposits in the lunar polar regions.Water is thought to be continually delivered to the Moon through geological timescales by water-bearing comets and asteroids, and produced continuously in situ by the impacts of solar wind protons of oxygen rich minerals exposed on the surface. IDPs are an unlikely source of water due to their long UV exposure in the inner solar system, but their high-speed impacts can mobilize secondary ejecta dust particles, atoms and molecules, some with high-enough speed to escape the Moon. Other surface processes that can lead to mobilization, transport and loss of water molecules and other volatiles include solar heating, photochemical processes, and solar wind sputtering. Since none of these are at work in permanently shadowed regions (PSR), dust impacts remain the dominant process to dictate the evolution of volatiles in PSRs. The competing effects of dust impacts are: a) ejecta production leading to loss out of a PSR; b) gardening and overturning the regolith; and c) the possible accumulation of impact ejecta, leading to the burial of the volatiles. This talk will summarize the expected effects of dust impacts on volatile accumulation in the lunar PSRs based on theoretical models, recent laboratory results, and observations by the LADEE spacecraft.

Pre-accretional sorting of grains in the outer solar nebula

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

Wozniakiewicz, P. J.; Bradley, J. P.; Ishii, H. A.

2013-12-20

Despite their micrometer-scale dimensions and nanogram masses, chondritic porous interplanetary dust particles (CP IDPs) are an important class of extraterrestrial material since their properties are consistent with a cometary origin and they show no evidence of significant post-accretional parent body alteration. Consequently, they can provide information about grain accretion in the comet-forming region of the outer solar nebula. We have previously reported our comparative study of the sizes and size distributions of crystalline silicate and sulfide grains in CP IDPs, in which we found these components exhibit a size-density relationship consistent with having been sorted together prior to accretion. Heremore » we extend our data set and include GEMS (glass with embedded metal and sulfide), the most abundant amorphous silicate phase observed in CP IDPs. We find that while the silicate and sulfide sorting trend previously observed is maintained, the GEMS size data do not exhibit any clear relationship to these crystalline components. Therefore, GEMS do not appear to have been sorted with the silicate and sulfide crystals. The disparate sorting trends observed in GEMS and the crystalline grains in CP IDPs present an interesting challenge for modeling early transport and accretion processes. They may indicate that several sorting mechanisms operated on these CP IDP components, or alternatively, they may simply be a reflection of different source environments.« less

Processing techniques for software based SAR processors

NASA Technical Reports Server (NTRS)

Leung, K.; Wu, C.

1983-01-01

Software SAR processing techniques defined to treat Shuttle Imaging Radar-B (SIR-B) data are reviewed. The algorithms are devised for the data processing procedure selection, SAR correlation function implementation, multiple array processors utilization, cornerturning, variable reference length azimuth processing, and range migration handling. The Interim Digital Processor (IDP) originally implemented for handling Seasat SAR data has been adapted for the SIR-B, and offers a resolution of 100 km using a processing procedure based on the Fast Fourier Transformation fast correlation approach. Peculiarities of the Seasat SAR data processing requirements are reviewed, along with modifications introduced for the SIR-B. An Advanced Digital SAR Processor (ADSP) is under development for use with the SIR-B in the 1986 time frame as an upgrade for the IDP, which will be in service in 1984-5.

Porosity of an Anhydrous Chondritic Interplanetary Dust Particle

NASA Astrophysics Data System (ADS)

Strait, M. M.; Thomas, K. L.; McKay, D. S.

1995-09-01

Determination of the density and porosity of Interplanetary Dust Particles (IDPs) is important in the dynamics of collisional and orbital evolution of small-sized particles. These measurements are also useful to suggest possible sources for IDPs based on comparisons with known extraterrestrial materials (e.g., chondrites). Previous work on IDPs shows a wide range of densities from very low (0.08 g/cm3 [1]) through low (0.3 g/cm3 [2]) to high (6.2 g/cm3 [3]), with an average density at 2.0 g/cm3 for 150 particles [2]. In another study, IDPs fall into two distinct density groups with mean values of 0.6 g/cm3 and 1.9g/cm3 [3]. In general, chondritic IDPs with lower density values most likely have appreciable porosity, suggesting they are primitive, uncompacted particles. It is believed that porosities greater than 70% are rare [2]. Sample In this study, porosity measurements were determined for one IDP, Clu17. This chondritic particle is a fragment of a large-sized IDP (L2008#5) known as a cluster particle. The cluster is composed of 53 fragments >5 micrometers in diameter; a detailed description of the cluster is given in [4]. IDP Clu17 has ~12 wt.% C and contains chondritic abundances (within 2xCI) for major elements. This fragment is dominated by fine-grained aggregates, also known as GEMS (glass with embedded metal and sulfide [5]), and contains some olivine, pyroxene, Fe-Ni sulfides, and carbonaceous material. Methods IDP Clu17 was analyzed for light elements quantitatively analysis using scanning electron microscopy and thin-window energy dispersive spectrometry [details of technique in 4]. Following the initial bulk chemical analysis, the particle was embedded in epoxy, thin sectioned using an ultramicrotome, and examined with a JEOL 2000 FX transmission electron microscope. Many of the sections were not complete; individual grains in some sections are lost during microtoming. Photos from nine of the best sections were digitized by scanning at 1200 dpi. The images were cropped and reduced in size to fit the memory capabilities of the computer analysis program. The digitized images were measured using NIH Image on a Macintosh computer. Results Using a combination of tools, including density slicing, area selection and a graphics tablet, to measure porosity, the sections give values from 9 to 15% porosity. There are a variety of errors that can enter into the measurement process: (1) defining exterior surface boundaries, which can vary between sections, (2) presence of holes in the sections where grains fell out during microtoming, and (3) differentiation between the mounting medium (epoxy) and extraterrestrial components (carbonaceous material can look similar to epoxy). As noted in earlier work [6], image processing is somewhat subjective and requires careful judgment in setting the conditions for electron microscopy and digital scanning. Conclusions Typical published anhydrous IDP porosities are in the 40% range [2], a value significantly higher than the 9-15% porosity range for IDP Clu17. The porosity values for cluster particles may be more difficult to determine because both the inter- and intra-fragment porosities must be considered. The inter-fragment porosity of ~10% for Clu17 is probably much lower than the intra-fragment porosity for cluster L2008#5 because this IDP remained intact on the collection surface while the cluster particle was fragmented into hundreds of smaller units, likely reflecting an high initial cluster porosity and low coherence. We conclude that image analysis combined with microtome sectioning offers a useful new tool for porosity measurements of IDPs and other kinds of extraterrestrial materials. Acknowledgments: This work was supported by NASA/JOVE Grant #NAG8-999. References: [1] Rietmeijer F. (1993) EPSL, 117, 609. [2] Love S. et al. (1994) Icarus, 111, 227. [3] Flynn G. and Sutton S. (1991) Proc. LPS, Vol. 21, 541. [4] Thomas K. et al. (1995) GCA, in press. [5] Bradley J. (1994) Science, 265, 925. [6] Strait M. et. al. (1994) Meteoritics, 29, 537.

The Joint Polar Satellite System (JPSS) Program's Algorithm Change Process (ACP): Past, Present and Future

NASA Technical Reports Server (NTRS)

Griffin, Ashley

2017-01-01

The Joint Polar Satellite System (JPSS) Program Office is the supporting organization for the Suomi National Polar Orbiting Partnership (S-NPP) and JPSS-1 satellites. S-NPP carries the following sensors: VIIRS, CrIS, ATMS, OMPS, and CERES with instruments that ultimately produce over 25 data products that cover the Earths weather, oceans, and atmosphere. A team of scientists and engineers from all over the United States document, monitor and fix errors in operational software code or documentation with the algorithm change process (ACP) to ensure the success of the S-NPP and JPSS 1 missions by maintaining quality and accuracy of the data products the scientific community relies on. This poster will outline the programs algorithm change process (ACP), identify the various users and scientific applications of our operational data products and highlight changes that have been made to the ACP to accommodate operating system upgrades to the JPSS programs Interface Data Processing Segment (IDPS), so that the program is ready for the transition to the 2017 JPSS-1 satellite mission and beyond.

NPOESS C3S Expandability: SafetyNet(TM) and McMurdo Improvements

NASA Astrophysics Data System (ADS)

Paciaroni, J.; Jamilkowski, M. L.

2009-12-01

The National Oceanic & Atmospheric Administration (NOAA), Department of Defense (DoD), and National Aeronautics and Space Administration (NASA) are jointly acquiring the next-generation weather and environmental satellite system; the National Polar-orbiting Operational Environmental Satellite System (NPOESS). NPOESS replaces the current Polar-orbiting Operational Environmental Satellites (POES) managed by NOAA and the Defense Meteorological Satellite Program (DMSP) managed by the DoD. The NPOESS satellites carry a suite of sensors that collect meteorological, oceanographic, climatological, and solar-geophysical observations of the earth, atmosphere, and space. The command and telemetry portion of NPOESS is the Command, Control and Communications Segment (C3S), developed by Raytheon Intelligence & Information Systems. C3S is responsible for managing the overall NPOESS mission from control and status of the space and ground assets to ensuring delivery of timely, high quality data from the Space Segment (SS) to the Interface Data Processing Segment (IDPS) for processing. In addition, the C3S provides the globally distributed ground assets necessary to collect and transport mission, telemetry, and command data between the satellites and the processing locations. The C3S provides all functions required for day-to-day commanding and state-of-health monitoring of the NPP and NPOESS satellites, and delivery of Stored Mission Data (SMD) to each U.S. Weather Central Interface Data Processor (IDP) for data products development and transfer to System subscribers. The C3S also monitors and reports system-wide health and status and data communications with external systems and between the NPOESS segments. Two crucial elements of NPOESS C3S expandability are SafetyNet(TM) and communications improvements to McMurdo Station, Antarctica. ‘SafetyNet(TM)’ is a key feature of the National Polar-orbiting Operational Environmental Satellite System (NPOESS), vital element of the C3S and Northrop Grumman Space Technology patented data collection architecture. The centerpiece of SafetyNet(TM) is the system of fifteen globally-distributed ground receptors developed by Raytheon Company. These receptors or antennae will collect up to five times as much environmental data approximately four times faster than current polar-orbiting weather satellites. Once collected, these data will be forwarded near-instantaneously to U.S. weather centrals via global fiber optic network for processing and production of data records for use in environmental prediction models. In January 2008, Raytheon Company achieved a significant milestone for the NPOESS program by successfully completing the first phase of a major communications upgrade for Antarctica. The upgrade of the off-continent satellite communications link at McMurdo Station more than tripled the bandwidth available for scientific research, weather prediction, and health and safety of those stationed at McMurdo. The project is part of the company’s C3S under development for NPOESS. This upgrade paves the way for a second major communications upgrade planned for 2012 in preparation for the use of McMurdo Station as one of the 15 NPOESS ground stations worldwide that will be receiving environmental data collected by the NPOESS satellites.

Pre-Launch Evaluation of the NPP VIIRS Land and Cryosphere EDRs to Meet NASA's Science Requirements

NASA Technical Reports Server (NTRS)

Roman, Miguel O.; Justice, Chris; Csiszar, Ivan; Key, Jeffrey R.; Devadiga, Sadashiva; Davidson, carol; Wolfe, Robert; Privette, Jeff

2011-01-01

This paper summarizes the NASA Visible Infrared Imaging Radiometer Suite (VIIRS) Land Science team's findings to date with respect to the utility of the VIIRS Land and Cryosphere EDRs to meet NASA's science requirements. Based on previous assessments and results from a recent 51-day global test performed by the Land Product Evaluation and Analysis Tool Element (Land PEATE), the NASA VIIRS Land Science team has determined that, if all the Land and Cryosphere EDRs are to serve the needs of the science community, a number of changes to several products and the Interface Data Processing Segment (IDPS) algorithm processing chain will be needed. In addition, other products will also need to be added to the VIIRS Land product suite to provide continuity for all of the MODIS land data record. As the NASA research program explores new global change research areas, the VIIRS instrument should also provide the polar-orbiting imager data from which new algorithms could be developed, produced, and validated.

Putting PhDs to Work: Career Planning for Today's Scientist

ERIC Educational Resources Information Center

Hobin, Jennifer A.; Clifford, Philip S.; Dunn, Ben M.; Rich, Susan; Justement, Louis B.

2014-01-01

Individual development plans (IDPs) have been promoted nationally as a tool to help research trainees explore career opportunities and set career goals. Despite the interest in IDPs from a policy perspective, there is little information about how they have been used. The authors examined IDP awareness and use, the benefits of creating an IDP, and…

The Management Strategy of Benign Solitary Intraductal Papilloma on Breast Core Biopsy.

PubMed

Ko, Dayoung; Kang, Eunyoung; Park, So Yeon; Kim, Sun Mi; Jang, Mijung; Yun, Bo La; Chae, Sumin; Jang, Yerang; Kim, Hye Jin; Kim, Sung-Won; Kim, Eun-Kyu

2017-08-01

Intraductal papilloma (IDP) is well-known as one of the common benign breast lesions requiring excision. However, treatment of IDP without atypia is controversial. The aim of our study was to determine the proper management of solitary IDP by core needle biopsy (CNB). We retrospectively reviewed patients with solitary IDP confirmed by CNB from March 2003 to March 2015. We collected data about final pathology after excision, as well as clinical, histologic, and radiologic findings at initial diagnosis. The final pathology was categorized as benign or malignant. We evaluated the rate of upgrade to malignancy and factors associated with malignancy. We identified 405 patients who presented benign solitary IDP by CNB. The mean age was 46.1 years (range, 15-86 years). In total, 135 patients underwent surgical excision, and 211 underwent vacuum-assisted excision. Of 346 patients, malignant lesions were found in 8 patients (2.3%): 7 underwent surgical excision, and 1 underwent vacuum-assisted excision. Only the size of IDP was significantly associated with cancer upgrade (P = .003). Our study shows that overall malignancy upgrade rate of benign solitary IDP after excision is very low (2.3%). Even when the size of IDP was less than 1 cm, the upgrade rate to cancer was only 0.9%. Therefore, for patients with small solitary IDP, we recommend close follow-up with ultrasound instead of excision. Copyright © 2017 Elsevier Inc. All rights reserved.

Does Comet WILD-2 contain Gems?

NASA Technical Reports Server (NTRS)

Chi, M.; Ishii, H.; Dai, Z. R.; Toppani, A.; Joswiak, D. J.; Leroux, H.; Zolensky, M.; Keller, L. P.; Browning, N. D.

2007-01-01

It is expected that Comet Wild-2 dust should resemble anhydrous carbon-rich, chondritic porous (CP) interplanetary dust particles (IDPs) collected in the stratosphere because some CP IDPs are suspected to be from comets. The rarity of carbonaceous grains and presolar silicates, as well as the presence of high-temperature inner solar nebula minerals in the Wild-2 sample (e.g. osbornite and melilite), appear incompatible with most CP IDPs. However, it is premature to draw firm conclusions about the mineralogy of comet Wild-2 because only approx. 1% of the sample has been examined. The most abundant silicates in CP IDPs are GEMS (glass with embedded metal and sulfides). Nonsolar O isotopic compositions confirm that at least some GEMS in IDPs are presolar amorphous silicates. The presence or absence of GEMS in the Wild-2 sample is important because it addresses, (a) the relationship between CP IDPs and comets, and (b) the hypothesis that other GEMS in IDPs formed in the solar nebula. Here we show that most of the GEMSlike materials so far identified in Stardust aerogel were likely impact generated during collection. At the nanometer scale, they are compositionally and crystallographically distinct from GEMS in IDPs.

Water and organics in interplanetary dust particles

NASA Astrophysics Data System (ADS)

Bradley, John

Interplanetary dust particles (IDPs) and larger micrometeorites (MMs) impinge on the upper atmosphere where they decelerate at 90 km altitude and settle to the Earths surface. Comets and asteroids are the major sources and the flux, 30,000-40,000 tons/yr, is comparable to the mass of larger meteorites impacting the Earths surface. The sedimentary record suggests that the flux was much higher on the early Earth. The chondritic porous (CP) subset of IDPs together with their larger counterparts, ultracarbonaceous micrometeorites (UCMMs), appear to be unique among known meteoritic materials in that they are composed almost exclusively of anhydrous minerals, some of them contain >> 50% organic carbon by volume as well as the highest abundances of presolar silicate grains including GEMS. D/H and 15N abundances implicate the Oort Cloud or presolar molecular cloud as likely sources of the organic carbon. Prior to atmospheric entry, IDPs and MMs spend 104-105 year lifetimes in solar orbit where their surfaces develop amorphous space weathered rims from exposure to the solar wind (SW). Similar rims are observed on lunar soil grains and on asteroid Itokawa regolith grains. Using valence electron energy-loss spectroscopy (VEELS) we have detected radiolytic water in the rims on IDPs formed by the interaction of solar wind protons with oxygen in silicate minerals. Therefore, IDPs and MMs continuously deliver both water and organics to the earth and other terrestrial planets. The interaction of protons with oxygen-rich minerals to form water is a universal process.

N-15-Rich Organic Globules in a Cluster IDP and the Bells CM2 Chondrite

NASA Technical Reports Server (NTRS)

Messenger, S.; Nakamura-Messenger, K.; Keller, Lindsay P.

2008-01-01

Organic matter in primitive meteorites and chondritic porous interplanetary dust particles (CP IDPs) is commonly enriched in D/H and 15N/14N relative to terrestrial values [1-3]. These anomalies are ascribed to the partial preservation of presolar cold molecular cloud material [1]. Some meteorites and IDPs contain m-size inclusions with extreme H and N isotopic anomalies [2-4], possibly due to preserved pristine primordial organic grains. We recently showed that the in the Tagish Lake meteorite, the principle carriers of these anomalies are sub- m, hollow organic globules [5]. The globules likely formed by photochemical processing of organic ices in a cold molecular cloud or the outermost regions of the protosolar disk [5]. We proposed that similar materials should be common among primitive meteorites, IDPs, and comets. Similar objects have been observed in organic extracts of carbonaceous chondrites [6-8], however their N and H isotopic compositions are generally unknown. Bulk H and N isotopic compositions may indicate which meteorites best preserve interstellar organic compounds. Thus, we selected the Bells CM2 carbonaceous chondrites for study based on its large bulk 15N (+335 %) and D (+990 %) [9].

A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP.

PubMed

Rozentur-Shkop, Eva; Goobes, Gil; Chill, Jordan H

2016-12-01

Intrinsically disordered proteins (IDPs) are multi-conformational polypeptides that lack a single stable three-dimensional structure. It has become increasingly clear that the versatile IDPs play key roles in a multitude of biological processes, and, given their flexible nature, NMR is a leading method to investigate IDP behavior on the molecular level. Here we present an IDP-tailored J-modulated experiment designed to monitor changes in the conformational ensemble characteristic of IDPs by accurately measuring backbone one- and two-bond J( 15 N, 13 Cα) couplings. This concept was realized using a unidirectional (H)NCO 13 C-detected experiment suitable for poor spectral dispersion and optimized for maximum coverage of amino acid types. To demonstrate the utility of this approach we applied it to the disordered actin-binding N-terminal domain of WASp interacting protein (WIP), a ubiquitous key modulator of cytoskeletal changes in a range of biological systems. One- and two-bond J( 15 N, 13 Cα) couplings were acquired for WIP residues 2-65 at various temperatures, and in denaturing and crowding environments. Under native conditions fitted J-couplings identified in the WIP conformational ensemble a propensity for extended conformation at residues 16-23 and 45-60, and a helical tendency at residues 28-42. These findings are consistent with a previous study of the based upon chemical shift and RDC data and confirm that the WIP 2-65 conformational ensemble is biased towards the structure assumed by this fragment in its actin-bound form. The effects of environmental changes upon this ensemble were readily apparent in the J-coupling data, which reflected a significant decrease in structural propensity at higher temperatures, in the presence of 8 M urea, and under the influence of a bacterial cell lysate. The latter suggests that crowding can cause protein unfolding through protein-protein interactions that stabilize the unfolded state. We conclude that J-couplings are a useful measureable in characterizing structural ensembles in IDPs, and that the proposed experiment provides a practical method for accurately performing such measurements, once again emphasizing the power of NMR in studying IDP behavior.

Unfoldomics of human diseases: linking protein intrinsic disorder with diseases

PubMed Central

Uversky, Vladimir N; Oldfield, Christopher J; Midic, Uros; Xie, Hongbo; Xue, Bin; Vucetic, Slobodan; Iakoucheva, Lilia M; Obradovic, Zoran; Dunker, A Keith

2009-01-01

Background Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack stable tertiary and/or secondary structure yet fulfills key biological functions. The recent recognition of IDPs and IDRs is leading to an entire field aimed at their systematic structural characterization and at determination of their mechanisms of action. Bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. These activities complement the functions of structured proteins. IDPs and IDRs were shown to participate in both one-to-many and many-to-one signaling. Alternative splicing and posttranslational modifications are frequently used to tune the IDP functionality. Several individual IDPs were shown to be associated with human diseases, such as cancer, cardiovascular disease, amyloidoses, diabetes, neurodegenerative diseases, and others. This raises questions regarding the involvement of IDPs and IDRs in various diseases. Results IDPs and IDRs were shown to be highly abundant in proteins associated with various human maladies. As the number of IDPs related to various diseases was found to be very large, the concepts of the disease-related unfoldome and unfoldomics were introduced. Novel bioinformatics tools were proposed to populate and characterize the disease-associated unfoldome. Structural characterization of the members of the disease-related unfoldome requires specialized experimental approaches. IDPs possess a number of unique structural and functional features that determine their broad involvement into the pathogenesis of various diseases. Conclusion Proteins associated with various human diseases are enriched in intrinsic disorder. These disease-associated IDPs and IDRs are real, abundant, diversified, vital, and dynamic. These proteins and regions comprise the disease-related unfoldome, which covers a significant part of the human proteome. Profound association between intrinsic disorder and various human diseases is determined by a set of unique structural and functional characteristics of IDPs and IDRs. Unfoldomics of human diseases utilizes unrivaled bioinformatics and experimental techniques, paves the road for better understanding of human diseases, their pathogenesis and molecular mechanisms, and helps develop new strategies for the analysis of disease-related proteins. PMID:19594884

Charge pattern matching as a ‘fuzzy’ mode of molecular recognition for the functional phase separations of intrinsically disordered proteins

NASA Astrophysics Data System (ADS)

Lin, Yi-Hsuan; Brady, Jacob P.; Forman-Kay, Julie D.; Chan, Hue Sun

2017-11-01

Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is currently known about the molecular recognition mechanisms for distributing different IDP sequences into various cellular membraneless compartments. Pertinent physics was addressed recently by applying random-phase-approximation (RPA) polymer theory to electrostatics, which is a major energetic component governing IDP phase properties. RPA accounts for charge patterns and thus has advantages over Flory-Huggins (FH) and Overbeek-Voorn mean-field theories. To make progress toward deciphering the phase behaviors of multiple IDP sequences, the RPA formulation for one IDP species plus solvent is hereby extended to treat polyampholyte solutions containing two IDP species plus solvent. The new formulation generally allows for binary coexistence of two phases, each containing a different set of volume fractions ({φ }1,{φ }2) for the two different IDP sequences. The asymmetry between the two predicted coexisting phases with regard to their {φ }1/{φ }2 ratios for the two sequences increases with increasing mismatch between their charge patterns. This finding points to a multivalent, stochastic, ‘fuzzy’ mode of molecular recognition that helps populate various IDP sequences differentially into separate phase compartments. An intuitive illustration of this trend is provided by FH models, whereby a hypothetical case of ternary coexistence is also explored. Augmentations of the present RPA theory with a relative permittivity {ɛ }{{r}}(φ ) that depends on IDP volume fraction φ ={φ }1+{φ }2 lead to higher propensities to phase separate, in line with the case with one IDP species we studied previously. Notably, the cooperative, phase-separation-enhancing effects predicted by the prescriptions for {ɛ }{{r}}(φ ) we deem physically plausible are much more prominent than that entailed by common effective medium approximations based on Maxwell Garnett and Bruggeman mixing formulas. Ramifications of our findings on further theoretical development for IDP phase separation are discussed.

Medical effects of iodine disinfection products in spacecraft water

NASA Technical Reports Server (NTRS)

Sauer, Richard L.; Janik, Daniel S.; Thorstenson, Yvonne R.

1987-01-01

Various iodination products (IDPs), including iodinated and iodine-induced new compounds, will be present in the iodine-disinfected water that is expected to be used by crews on the NASA Space Station and on long duration missions. The metabolic intermediaries created by such a process may be more important to crew health than the parent IDPs, and reclamation and recycling may be expected to produce additional products. These medical effects may be expressed in crews as hypersensitivity, allergic, acute toxic, and chronic toxic reactions, as well as modifications of immune system response.

Infrared Spectroscopy of Anhydrous Interplanetary Dust Particles

NASA Technical Reports Server (NTRS)

Keller, L. P.; Flynn, G. J.

2003-01-01

Infrared (IR) spectroscopy is the primary means of mineralogical analysis of materials outside our solar system. The identity and properties of circumstellar grains are inferred from spectral comparisons between astronomical observations and laboratory data from natural and synthetic materials. These comparisons have been facilitated by the Infrared Space Observatory (ISO), which obtained IR spectra from numerous astrophysical objects over a wide spectral range (out to 50/cm) where crystalline silicates and other phases have distinct features. The anhydrous interplanetary dust particles (IDPs) are particularly important comparison materials because some IDPs contain carbonaceous material with non-solar D/H and N-15/N-14 ratios and amorphous and crystalline silicates with non-solar 0- isotopic ratios, demonstrating that these IDPs contain preserved interstellar material. Here, we report on micro- Fourier transform (FT) IR spectrometry of IDPs, focusing on the inorganic components of primitive IDPs (FTIR spectra from the organic/carbonacecous materials in IDPs are described elsewhere).

The Interaction with Disabled Persons scale: revisiting its internal consistency and factor structure, and examining item-level properties.

PubMed

Iacono, Teresa; Tracy, Jane; Keating, Jenny; Brown, Ted

2009-01-01

The Interaction with Disabled Persons scale (IDP) has been used in research into baseline attitudes and to evaluate whether a shift in attitudes towards people with developmental disabilities has occurred following some form of intervention. This research has been conducted on the assumption that the IDP measures attitudes as a multidimensional construct and has good internal consistency. Such assumptions about the IDP appear flawed, particularly in light of failures to replicate its underlying factor structure. The aim of this study was to evaluate the construct validity and dimensionality of the IDP. This study used a prospective survey approach. Participants were recruited from first and second year undergraduate university students enrolled in health sciences, occupational therapy, physiotherapy, community and emergency health, nursing, and combined degrees of nursing and midwifery, and health sciences and social work at a large Australian university (n=373). Students completed the IDP, a 20-item self-report scale of attitudes towards people with disabilities. The IDP data were analysed using a combination of factor analysis (Classical Test Theory approach) and Rasch analysis (Item Response Theory approach). The results indicated that the original IDP 6-factor solution was not supported. Instead, one factor consisting of five IDP items (9, 11, 12, 17, and 18) labelled Discomfort met the four criteria for empirical validation of test quality: interval level scaling (scalability), unidimensionality, lacked of DIF across the two participant groups and data collection occasions, and hierarchical ordering. Researchers should consider using the Discomfort subscale of the IDP in future attitude research since it exhibits sound measurement properties.

Impact of interventions on malaria in internally displaced persons along the China-Myanmar border: 2011-2014.

PubMed

Zhou, Guofa; Lo, Eugenia; Zhong, Daibin; Wang, Xiaoming; Wang, Ying; Malla, Sameer; Lee, Ming-Chieh; Yang, Zhaoqing; Cui, Liwang; Yan, Guiyun

2016-09-15

Internally displaced persons (IDP) represent vulnerable populations whose public health conditions merit special attention. In the China-Myanmar border area, human movement and resettlements of IDP can influence malaria transmission. Comparison of disease incidence and vector densities between IDP camps and surrounding local villages allows for better understanding of current epidemiology and to evaluate the effectiveness of interventions in the region. Malaria and vector surveillance was conducted in three IDP camps and three local villages neighbouring the camps along the China-Myanmar border in Myanmar. Clinical malaria cases were collected from seven hospitals/clinics from April 2011 to December 2014. Malaria vector population dynamics were monitored using CDC light traps. The use of malaria preventive measures and information on aid agencies and their activities was obtained through questionnaire surveys. Malaria was confirmed in 1832 patients. Of these cases, 85.4 % were Plasmodium vivax and 11.4 % were Plasmodium falciparum malaria. Annual malaria incidence rates were 38.8 and 127.0 cases/1000 person year in IDP camps and local villages, respectively. Older children of 5-14 years had the highest incidence rate in the camps regardless of gender, while male adults had significantly higher incidence rates than females in local villages and females child-bearing age had significantly lower risk to malaria in IDP camps compare to local villages. Seasonal malaria outbreaks were observed both in the IDP camps and in the local villages from May to August 2013. The proportion of P. vivax remained unchanged in local villages but increased by approximately tenfold in IDP camps from 2011 to 2014. Anopheles vector density was tenfold higher in local villages compared to IDP camps (2.0:0.2 females/trap/night). Over 99 % of households in both communities owned bed nets. While long-lasting insecticidal nets accounted for 61 % of nets used in IDPs, nearly all residents of local villages owned regular nets without insecticide-impregnation. There were more active aid agencies in the camps than in local villages. Malaria in IDP camps was significantly lower than the surrounding villages through effective control management. The observation of P. vivax outbreaks in the study area highlights the need for increased control efforts. Expansion of malaria intervention strategies in IDP camps to local surrounding villages is critical to malaria control in the border area.

Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing

PubMed Central

Weirather, Jason L.; Afshar, Pegah Tootoonchi; Clark, Tyson A.; Tseng, Elizabeth; Powers, Linda S.; Underwood, Jason G.; Zabner, Joseph; Korlach, Jonas; Wong, Wing Hung; Au, Kin Fai

2015-01-01

We developed an innovative hybrid sequencing approach, IDP-fusion, to detect fusion genes, determine fusion sites and identify and quantify fusion isoforms. IDP-fusion is the first method to study gene fusion events by integrating Third Generation Sequencing long reads and Second Generation Sequencing short reads. We applied IDP-fusion to PacBio data and Illumina data from the MCF-7 breast cancer cells. Compared with the existing tools, IDP-fusion detects fusion genes at higher precision and a very low false positive rate. The results show that IDP-fusion will be useful for unraveling the complexity of multiple fusion splices and fusion isoforms within tumorigenesis-relevant fusion genes. PMID:26040699

Comparison of the oxidation state of Fe in comet 81P/Wild 2 and chondritic-porous interplanetary dust particles

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

Ogliore, Ryan C.; Butterworth, Anna L.; Fakra, Sirine C.

2010-07-16

The fragile structure of chondritic-porous interplanetary dust particles (CP-IDPs) and their minimal parent-body alteration have led researchers to believe these particles originate in comets rather than asteroids where aqueous and thermal alterations have occurred. The solar elemental abundances and atmospheric entry speed of CP-IDPs also suggest a cometary origin. With the return of the Stardust samples from Jupiter-family comet 81P/Wild 2, this hypothesis can be tested. We have measured the Fe oxidation state of 15 CP-IDPs and 194 Stardust fragments using a synchrotron-based x-ray microprobe. We analyzed {approx}300 ng of Wild 2 material - three orders of magnitude more materialmore » than other analyses comparing Wild 2 and CP-IDPs. The Fe oxidation state of these two samples of material are > 2{sigma} different: the CP-IDPs are more oxidized than the Wild 2 grains. We conclude that comet Wild 2 contains material that formed at a lower oxygen fugacity than the parent-body, or parent bodies, of CP-IDPs. If all Jupiter-family comets are similar, they do not appear to be consistent with the origin of CP-IDPs. However, comets that formed from a different mix of nebular material and are more oxidized than Wild 2 could be the source of CP-IDPs.« less

Genome-wide analysis of protein disorder in Arabidopsis thaliana: implications for plant environmental adaptation.

PubMed

Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto; Pazos, Florencio

2013-01-01

Intrinsically disordered proteins/regions (IDPs/IDRs) are currently recognized as a widespread phenomenon having key cellular functions. Still, many aspects of the function of these proteins need to be unveiled. IDPs conformational flexibility allows them to recognize and interact with multiple partners, and confers them larger interaction surfaces that may increase interaction speed. For this reason, molecular interactions mediated by IDPs/IDRs are particularly abundant in certain types of protein interactions, such as those of signaling and cell cycle control. We present the first large-scale study of IDPs in Arabidopsis thaliana, the most widely used model organism in plant biology, in order to get insight into the biological roles of these proteins in plants. The work includes a comparative analysis with the human proteome to highlight the differential use of disorder in both species. Results show that while human proteins are in general more disordered, certain functional classes, mainly related to environmental response, are significantly more enriched in disorder in Arabidopsis. We propose that because plants cannot escape from environmental conditions as animals do, they use disorder as a simple and fast mechanism, independent of transcriptional control, for introducing versatility in the interaction networks underlying these biological processes so that they can quickly adapt and respond to challenging environmental conditions.

Chemical Heterogeneity of a Large Cluster IDP: Clues to its Formation History Using X-ray Fluorescence Mapping and XANES Spectroscopy

NASA Technical Reports Server (NTRS)

Wirick, S.; Flynn, G. J.; Sutton, S.; Zolensky, M. E.

2013-01-01

Chondritic porous IDPs may be among the most primitive objects found in our solar system [1]. They consist of many micron to submicron minerals, glasses and carbonaceous matter [2,3,4,5,6,7] with > 10(exp 4) grains in a 10 micron cluster [8]. Speculation on the environment where these fine grained, porous IDPs formed varies with possible sources being presolar dusty plasma clouds, protostellar condensation, solar asteroids or comets [4,6,9]. Also, fine grained dust forms in our solar system today [10,11]. Isotopic anomalies in some particles in IDPs suggest an interstellar source[4,7,12]. IDPs contain relic particles left from the dusty plasma that existed before the protostellar disk formed and other grains in the IDPs formed later after the cold dense nebula cloud collapsed to form our protostar and other grains formed more recently. Fe and CR XANES spectroscopy is used here to investigate the oxygen environment in a large (>50 10 micron or larger sub-units) IDP. Conclusions: Analyzing large (>50 10 micron or larger sub-units) CP IDPs gives one a view on the environments where these fine dust grains formed which is different from that found by only analyzing the small, 10 micron IDPs. As with cluster IDP L2008#5 [3], L2009R2 cluster #13 appears to be an aggregate of grains that sample a diversity of solar and perhaps presolar environments. Sub-micron, grain by grain measurement of trace element contents and elemental oxidation states determined by XANES spectroscopy offers the possibility of understanding the environments in which these grains formed when compared to standard spectra. By comparing thermodynamic modeling of condensates with analytical data an understanding of transport mechanisms operating in the early solar system may be attained.

Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.

PubMed

Higo, Junichi; Umezawa, Koji

2014-01-01

We introduce computational studies on intrinsically disordered proteins (IDPs). Especially, we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner systems: NRSF-mSin3 and pKID-KIX. McMD is one of enhanced conformational sampling methods useful for conformational sampling of biomolecular systems. IDP adopts a specific tertiary structure upon binding to its partner molecule, although it is unstructured in the unbound state (i.e. the free state). This IDP-specific property is called "coupled folding and binding". The McMD simulation treats the biomolecules with an all-atom model immersed in an explicit solvent. In the initial configuration of simulation, IDP and its partner molecules are set to be distant from each other, and the IDP conformation is disordered. The computationally obtained free-energy landscape for coupled folding and binding has shown that native- and non-native-complex clusters distribute complicatedly in the conformational space. The all-atom simulation suggests that both of induced-folding and population-selection are coupled complicatedly in the coupled folding and binding. Further analyses have exemplified that the conformational fluctuations (dynamical flexibility) in the bound and unbound states are essentially important to characterize IDP functioning.

What does the fine-scale petrography of IDPs reveal about grain formation and evolution in the early solar system?

NASA Technical Reports Server (NTRS)

Bradley, John

1994-01-01

The 'pyroxene' interplanetary dust particles (IDP's) may be the best samples for investigation of primordial grain-forming reactions because they appear to have experienced negligible post-accretional alteration. They are likely to continue to yield information about gas-to-solid condensation and other grain-forming reactions that may have occurred either in the solar nebular or presolar interstellar environments. An immediate challenge lies in understanding the nanometer-scale petrography of the ultrafine-grained aggregates in 'pyroxene' IDP's. Whether these aggregates contain components from diverse grain-forming environments may ultimately be answered by systematic petrographic studies using electron microscopes capable of high spatial resolution microanalysis. It may be more difficult to decipher evidence of grain formation and evolution in 'olivine' and 'layer silicate' IDP's because they appear to have experienced post-accretional alteration. Most of the studied 'olivine' IDPs have been subjected to heating and equilibration, perhaps during atmospheric entry, while the 'layer silicate' IDP's have experienced aqueous alteration.

Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity

NASA Astrophysics Data System (ADS)

Simon, Joseph R.; Carroll, Nick J.; Rubinstein, Michael; Chilkoti, Ashutosh; López, Gabriel P.

2017-06-01

Dynamic protein-rich intracellular structures that contain phase-separated intrinsically disordered proteins (IDPs) composed of sequences of low complexity (SLC) have been shown to serve a variety of important cellular functions, which include signalling, compartmentalization and stabilization. However, our understanding of these structures and our ability to synthesize models of them have been limited. We present design rules for IDPs possessing SLCs that phase separate into diverse assemblies within droplet microenvironments. Using theoretical analyses, we interpret the phase behaviour of archetypal IDP sequences and demonstrate the rational design of a vast library of multicomponent protein-rich structures that ranges from uniform nano-, meso- and microscale puncta (distinct protein droplets) to multilayered orthogonally phase-separated granular structures. The ability to predict and program IDP-rich assemblies in this fashion offers new insights into (1) genetic-to-molecular-to-macroscale relationships that encode hierarchical IDP assemblies, (2) design rules of such assemblies in cell biology and (3) molecular-level engineering of self-assembled recombinant IDP-rich materials.

Breast intraductal papillomas without atypia in radiologic-pathologic concordant core-needle biopsies: Rate of upgrade to carcinoma at excision.

PubMed

Pareja, Fresia; Corben, Adriana D; Brennan, Sandra B; Murray, Melissa P; Bowser, Zenica L; Jakate, Kiran; Sebastiano, Christopher; Morrow, Monica; Morris, Elizabeth A; Brogi, Edi

2016-09-15

The surgical management of mammary intraductal papilloma without atypia (IDP) identified at core-needle biopsy (CNB) is controversial. This study assessed the rate of upgrade to carcinoma at surgical excision (EXC). This study identified women with a CNB diagnosis of intraductal papilloma without atypia or carcinoma at a cancer center between 2003 and 2013. Radiologic-pathologic concordance was assessed for all cases, and discordant cases were excluded. The radiologic and clinicopathologic features of patients with a CNB diagnosis of IDP were correlated with an upgrade to carcinoma at EXC. The study population consists of 189 women with 196 IDPs; 166 women (171 IDPs) underwent EXC. The upgrade rate was 2.3% (4 of 171). The upgraded lesions were 2 invasive lobular carcinomas and 2 cases of ductal carcinoma in situ (DCIS). One case of DCIS involved the residual IDP, whereas the other 3 carcinomas were ≥ 8 mm away. Twenty-four women (25 IDPs) did not undergo EXC and had stable imaging on follow-up (median, 23.5 months). The upgrade rate at EXC for IDPs diagnosed at CNB with radiologic-pathologic concordance was 2.3%. These findings suggest that observation is appropriate for patients with radiologic-pathologic concordant CNB yielding IDP, regardless of its size. Cancer 2016. © 2016 American Cancer Society. Cancer 2016;122:2819-2827. © 2016 American Cancer Society. © 2016 American Cancer Society.

Electrostatically Accelerated Coupled Binding and Folding of Intrinsically Disordered Proteins

PubMed Central

Ganguly, Debabani; Otieno, Steve; Waddell, Brett; Iconaru, Luigi; Kriwacki, Richard W.; Chen, Jianhan

2012-01-01

Intrinsically disordered proteins (IDPs) are now recognized to be prevalent in biology, and many potential functional benefits have been discussed. However, the frequent requirement of peptide folding in specific interactions of IDPs could impose a kinetic bottleneck, which could be overcome only by efficient folding upon encounter. Intriguingly, existing kinetic data suggest that specific binding of IDPs is generally no slower than that of globular proteins. Here, we exploited the cell cycle regulator p27Kip1 (p27) as a model system to understand how IDPs might achieve efficient folding upon encounter for facile recognition. Combining experiments and coarse-grained modeling, we demonstrate that long-range electrostatic interactions between enriched charges on p27 and near its binding site on cyclin A not only enhance the encounter rate (i.e., electrostatic steering), but also promote folding-competent topologies in the encounter complexes, allowing rapid subsequent formation of short-range native interactions en route to the specific complex. In contrast, nonspecific hydrophobic interactions, while hardly affecting the encounter rate, can significantly reduce the efficiency of folding upon encounter and lead to slower binding kinetics. Further analysis of charge distributions in a set of known IDP complexes reveals that, although IDP binding sites tend to be more hydrophobic compared to the rest of the target surface, their vicinities are frequently enriched with charges to complement those on IDPs. This observation suggests that electrostatically accelerated encounter and induced folding might represent a prevalent mechanism for promoting facile IDP recognition. PMID:22721951

The Abundance and Distribution of Presolar Materials in Cluster IDPS

NASA Technical Reports Server (NTRS)

Messenger, Scott; Keller, Lindsay; Nakamura-Messenger, Keiko; Ito, Motoo

2007-01-01

Presolar grains and remnants of interstellar organic compounds occur in a wide range of primitive solar system materials, including meteorites, interplanetary dust particles (IDPs), and comet Wild-2 samples. Among the most abundant presolar phases are silicate stardust grains and molecular cloud material. However, these materials have also been susceptible to destruction and alteration during parent body and nebular processing. In addition to their importance as direct samples of remote and ancient astrophysical environments, presolar materials thus provide a measure of how well different primitive bodies have preserved the original solar system starting materials.

Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.

PubMed

Weirather, Jason L; Afshar, Pegah Tootoonchi; Clark, Tyson A; Tseng, Elizabeth; Powers, Linda S; Underwood, Jason G; Zabner, Joseph; Korlach, Jonas; Wong, Wing Hung; Au, Kin Fai

2015-10-15

We developed an innovative hybrid sequencing approach, IDP-fusion, to detect fusion genes, determine fusion sites and identify and quantify fusion isoforms. IDP-fusion is the first method to study gene fusion events by integrating Third Generation Sequencing long reads and Second Generation Sequencing short reads. We applied IDP-fusion to PacBio data and Illumina data from the MCF-7 breast cancer cells. Compared with the existing tools, IDP-fusion detects fusion genes at higher precision and a very low false positive rate. The results show that IDP-fusion will be useful for unraveling the complexity of multiple fusion splices and fusion isoforms within tumorigenesis-relevant fusion genes. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy.

PubMed

Delaforge, Elise; Kragelj, Jaka; Tengo, Laura; Palencia, Andrés; Milles, Sigrid; Bouvignies, Guillaume; Salvi, Nicola; Blackledge, Martin; Jensen, Malene Ringkjøbing

2018-01-24

Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions, or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state. Knowledge of the dynamics of IDP complexes is of fundamental importance to understand how IDPs engage in highly specific interactions without concomitantly high binding affinity. Here, we combine rotating-frame R 1ρ , Carr-Purcell-Meiboom Gill relaxation dispersion as well as chemical exchange saturation transfer to decipher the dynamic interaction profile of an IDP in complex with its partner. We apply the approach to the dynamic signaling complex formed between the mitogen-activated protein kinase (MAPK) p38α and the intrinsically disordered regulatory domain of the MAPK kinase MKK4. Our study demonstrates that MKK4 employs a subtle combination of interaction modes in order to bind to p38α, leading to a complex displaying significantly different dynamics across the bound regions.

Structural biology of intrinsically disordered proteins: Revisiting unsolved mysteries.

PubMed

Sigalov, Alexander B

2016-06-01

The emergence of intrinsically disordered proteins (IDPs) has challenged the classical protein structure-function paradigm by introducing a new paradigm of "coupled binding and folding". This paradigm suggests that IDPs fold upon binding to their partners. Further studies, however, revealed a novel and previously unrecognized phenomenon of "uncoupled binding and folding" suggesting that IDPs do not necessarily fold upon interaction with their lipid and protein partners. The complex and often unusual biophysics of IDPs makes structural characterization of these proteins and their complexes not only challenging but often resulting in opposite conclusions. For this reason, some crucial questions in this field remain unsolved for well over a decade. Considering an important role of IDPs in cellular regulation, signaling and control in health and disease, more efforts are needed to solve these mysteries. Here, I focus on two long-standing contradictions in the literature concerning dimerization and membrane-binding activities of IDPs. Molecular explanation of these discrepancies is provided. I also demonstrate how resolution of these critical issues in the field of IDPs results in our expanded understanding of cell function and has multiple applications in biology and medicine. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Identification of a Compound Spinel and Silicate Presolar Grain in a Chondritic Interplanetary Dust Particle

NASA Technical Reports Server (NTRS)

Nguyen, A. N.; Nakamura-Messenger, K.; Messenger, S.; Keller, L. P.; Kloeck, W.

2014-01-01

Anhydrous chondritic porous interplanetary dust particles (CP IDPs) have undergone minimal parent body alteration and contain an assemblage of highly primitive materials, including molecular cloud material, presolar grains, and material that formed in the early solar nebula [1-3]. The exact parent bodies of individual IDPs are not known, but IDPs that have extremely high abundances of presolar silicates (up to 1.5%) most likely have cometary origins [1, 4]. The presolar grain abundance among these minimally altered CP IDPs varies widely. "Isotopically primitive" IDPs distinguished by anomalous bulk N isotopic compositions, numerous 15N-rich hotspots, and some C isotopic anomalies have higher average abundances of presolar grains (375 ppm) than IDPs with isotopically normal bulk N (<10 ppm) [5]. Some D and N isotopic anomalies have been linked to carbonaceous matter, though this material is only rarely isotopically anomalous in C [1, 5, 6]. Previous studies of the bulk chemistry and, in some samples, the mineralogy of select anhydrous CP IDPs indicate a link between high C abundance and pyroxene-dominated mineralogy [7]. In this study, we conduct coordinated mineralogical and isotopic analyses of samples that were analyzed by [7] to characterize isotopically anomalous materials and to establish possible correlations with C abundance.

Mortality and health among internally displaced persons in western Kenya following post-election violence, 2008: novel use of demographic surveillance.

PubMed

Feikin, Daniel R; Adazu, Kubaje; Obor, David; Ogwang, Sheila; Vulule, John; Hamel, Mary J; Laserson, Kayla

2010-08-01

To evaluate mortality and morbidity among internally displaced persons (IDPs) who relocated in a demographic surveillance system (DSS) area in western Kenya following post-election violence. In 2007, 204 000 individuals lived in the DSS area, where field workers visit households every 4 months to record migrations, births and deaths. We collected data on admissions among children < 5 years of age in the district hospital and developed special questionnaires to record information on IDPs. Mortality, migration and hospitalization rates among IDPs and regular DSS residents were compared, and verbal autopsies were performed for deaths. Between December 2007 and May 2008, 16 428 IDPs migrated into the DSS, and over half of them stayed 6 months or longer. In 2008, IDPs aged 15-49 years died at higher rates than regular residents of the DSS (relative risk, RR: 1.34; 95% confidence interval, CI: 1.004-1.80). A greater percentage of deaths from human immunodeficiency virus (HIV) infection occurred among IDPs aged > or = 5 years (53%) than among regular DSS residents (25-29%) (P < 0.001). Internally displaced children < 5 years of age did not die at higher rates than resident children but were hospitalized at higher rates (RR: 2.95; 95% CI: 2.44-3.58). HIV-infected internally displaced adults in conflict-ridden parts of Africa are at increased risk of HIV-related death. Relief efforts should extend to IDPs who have relocated outside IDP camps, particularly if afflicted with HIV infection or other chronic conditions.

Utilization of protein intrinsic disorder knowledge in structural proteomics

PubMed Central

Oldfield, Christopher J.; Xue, Bin; Van, Ya-Yue; Ulrich, Eldon L.; Markley, John L.; Dunker, A. Keith; Uversky, Vladimir N.

2014-01-01

Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed. PMID:23232152

A road damage and life-cycle greenhouse gas comparison of trucking and pipeline water delivery systems for hydraulically fractured oil and gas field development in Colorado

PubMed Central

Duthu, Ray C.

2017-01-01

The process of hydraulic fracturing for recovery of oil and natural gas uses large amounts of fresh water and produces a comparable amount of wastewater, much of which is typically transported by truck. Truck transport of water is an expensive and energy-intensive process with significant external costs including roads damages, and pollution. The integrated development plan (IDP) is the industry nomenclature for an integrated oil and gas infrastructure system incorporating pipeline-based transport of water and wastewater, centralized water treatment, and high rates of wastewater recycling. These IDP have been proposed as an alternative to truck transport systems so as to mitigate many of the economic and environmental problems associated with natural gas production, but the economic and environmental performance of these systems have not been analyzed to date. This study presents a quantification of lifecycle greenhouse gas (GHG) emissions and road damages of a generic oil and gas field, and of an oil and gas development sited in the Denver-Julesburg basin in the northern Colorado region of the US. Results demonstrate that a reduction in economic and environmental externalities can be derived from the development of these IDP-based pipeline water transportation systems. IDPs have marginal utility in reducing GHG emissions and road damage when they are used to replace in-field water transport, but can reduce GHG emissions and road damage by factors of as much as 6 and 7 respectively, when used to replace fresh water transport and waste-disposal routes for exemplar Northern Colorado oil and gas fields. PMID:28686682

A road damage and life-cycle greenhouse gas comparison of trucking and pipeline water delivery systems for hydraulically fractured oil and gas field development in Colorado.

PubMed

Duthu, Ray C; Bradley, Thomas H

2017-01-01

The process of hydraulic fracturing for recovery of oil and natural gas uses large amounts of fresh water and produces a comparable amount of wastewater, much of which is typically transported by truck. Truck transport of water is an expensive and energy-intensive process with significant external costs including roads damages, and pollution. The integrated development plan (IDP) is the industry nomenclature for an integrated oil and gas infrastructure system incorporating pipeline-based transport of water and wastewater, centralized water treatment, and high rates of wastewater recycling. These IDP have been proposed as an alternative to truck transport systems so as to mitigate many of the economic and environmental problems associated with natural gas production, but the economic and environmental performance of these systems have not been analyzed to date. This study presents a quantification of lifecycle greenhouse gas (GHG) emissions and road damages of a generic oil and gas field, and of an oil and gas development sited in the Denver-Julesburg basin in the northern Colorado region of the US. Results demonstrate that a reduction in economic and environmental externalities can be derived from the development of these IDP-based pipeline water transportation systems. IDPs have marginal utility in reducing GHG emissions and road damage when they are used to replace in-field water transport, but can reduce GHG emissions and road damage by factors of as much as 6 and 7 respectively, when used to replace fresh water transport and waste-disposal routes for exemplar Northern Colorado oil and gas fields.

An Interesting Case of Oral Inverted Ductal Papilloma.

PubMed

Berridge, Natasha; Kumar, Mahesh

2016-12-01

Ductal papillomas are rare benign papillary tumours of the minor salivary glands. Previously they have been classified into three subtypes: inverted ductal papilloma (IDP), sialadenoma papilliferum and intraductal papilloma. The oral inverted ductal papilloma is the least common of these lesions, with 48 cases reported to date in a search of the English-language literature. We describe an interesting case of oral IDP and highlight the pertinent clinical and histopathological features. Importantly, unlike the histologically similar inverted papilloma (IP) of the nose and paranasal sinuses, oral IDP is a completely benign lesion and is not associated with malignant change. Clinical relevance: This case report aims to raise awareness of the lesion, oral inverted ductal papilloma (IDP). We outline the clinical features and unique histopathology of oral IDP so that clinicians may correctly diagnose such a lesion and implement appropriate treatment.

Suomi NPP VIIRS active fire product status

NASA Astrophysics Data System (ADS)

Ellicott, E. A.; Csiszar, I. A.; Schroeder, W.; Giglio, L.; Wind, B.; Justice, C. O.

2012-12-01

We provide an overview of the evaluation and development of the Active Fires product derived from the Visible Infrared Imager Radiometer Suite (VIIRS) sensor on the Suomi National Polar-orbiting Partnership (SNPP) satellite during the first year of on-orbit data. Results from the initial evaluation of the standard SNPP Active Fires product, generated by the SNPP Interface Data Processing System (IDPS), supported the stabilization of the VIIRS Sensor Data Record (SDR) product. This activity focused in particular on the processing of the dual-gain 4 micron VIIRS M13 radiometric measurements into 750m aggregated data, which are fundamental for active fire detection. Following the VIIRS SDR product's Beta maturity status in April 2012, correlative analysis between VIIRS and near-simultaneous fire detections from the Moderate Resolution Imaging Spectroradiometer (MODIS) on the NASA Earth Observing System Aqua satellite confirmed the expected relative detection rates driven primarily by sensor differences. The VIIRS Active Fires Product Development and Validation Team also developed a science code that is based on the latest MODIS Collection 6 algorithm and provides a full spatially explicit fire mask to replace the sparse array output of fire locations from a MODIS Collection 4 equivalent algorithm in the current IDPS product. The Algorithm Development Library (ADL) was used to support the planning for the transition of the science code into IDPS operations in the future. Product evaluation and user outreach was facilitated by a product website that provided end user access to fire data in user-friendly format over North America as well as examples of VIIRS-MODIS comparisons. The VIIRS fire team also developed an experimental product based on 375m VIIRS Imagery band measurements and provided high quality imagery of major fire events in US. By August 2012 the IDPS product achieved Beta maturity, with some known and documented shortfalls related to the processing of incorrect SDR input data and to apparent algorithm deficiencies in select observing and environmental conditions.

Unusual biophysics of intrinsically disordered proteins.

PubMed

Uversky, Vladimir N

2013-05-01

Research of a past decade and a half leaves no doubt that complete understanding of protein functionality requires close consideration of the fact that many functional proteins do not have well-folded structures. These intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered protein regions (IDPRs) are highly abundant in nature and play a number of crucial roles in a living cell. Their functions, which are typically associated with a wide range of intermolecular interactions where IDPs possess remarkable binding promiscuity, complement functional repertoire of ordered proteins. All this requires a close attention to the peculiarities of biophysics of these proteins. In this review, some key biophysical features of IDPs are covered. In addition to the peculiar sequence characteristics of IDPs these biophysical features include sequential, structural, and spatiotemporal heterogeneity of IDPs; their rough and relatively flat energy landscapes; their ability to undergo both induced folding and induced unfolding; the ability to interact specifically with structurally unrelated partners; the ability to gain different structures at binding to different partners; and the ability to keep essential amount of disorder even in the bound form. IDPs are also characterized by the "turned-out" response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins. It is proposed that the heterogeneous spatiotemporal structure of IDPs/IDPRs can be described as a set of foldons, inducible foldons, semi-foldons, non-foldons, and unfoldons. They may lose their function when folded, and activation of some IDPs is associated with the awaking of the dormant disorder. It is possible that IDPs represent the "edge of chaos" systems which operate in a region between order and complete randomness or chaos, where the complexity is maximal. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly. Copyright © 2012 Elsevier B.V. All rights reserved.

Hygienic practices and diarrheal illness among persons living in at-risk settings in Kabul, Afghanistan: a cross-sectional study.

PubMed

Mubarak, Mohammad Yousuf; Wagner, Abram L; Asami, Mari; Carlson, Bradley F; Boulton, Matthew L

2016-08-31

Sustained civil and military conflict, resulting in large numbers of internally displaced persons (IDP), in combination with rapid urbanization has strained public health and sanitation within cities in Afghanistan. In order to examine the association between preventive sanitary behaviors and diarrhea within two high risk settings located within Kabul, Afghanistan, this study aimed to evaluate the prevalence of hygienic practices and diarrheal illness in an IDP camp and an urban slum. In this cross sectional study, a convenience sample of residents of an IDP camp and an urban slum in Kabul, Afghanistan, was used. Participants were asked to describe their hygienic practices and interviewers independently documented household sanitation. The knowledge and attitudes about and practice of hygienic activities to prevent diarrhea were compared between the two settings. Two hundred participants, 100 from each setting, were enrolled. Knowledge, attitudes, and practices regarding hygienic activities to prevent diarrhea were greater among the slum dwellers than the IDP. Fewer than half of participants washed their hands with soap before eating or after eating: 31 % of slum dwellers washed before eating compared to 11 % of IDPs (P = 0.0050), and 25 % of slum dwellers washed after defecating compared to 4 % of IDPs (P = 0.0020). The IDPs were more likely to share a latrine (P = 0.0144) and less likely to disinfect their latrine than slum dwellers. Diarrhea in the household within the past 3 months was more common in the IDP camp (54 %) than the slum (20 %) (P = 0.0020). Even though certain sanitary and hygienic practices were more common among slum dwellers than IDPs, the lack of hygienic activities in both setting indicates that interventions to change behavior, like increasing the availability of soap and encouraging hand washing, are needed. Any initiative will have to be developed in the context of pervasive illiteracy among persons in both of these settings.

The mental health, quality of life and life satisfaction of internally displaced persons living in Nakuru County, Kenya.

PubMed

Getanda, Elijah Mironga; Papadopoulos, Chris; Evans, Hala

2015-08-06

Internally displaced persons (IDPs) are among the most vulnerable people in the world today. Previous research highlights that conflict-induced forced displacement can cause problems with mental health and wellbeing. This study aimed to contribute to this body of knowledge by investigating the mental health, quality of life, and life satisfaction among IDPs living in Nakuru, Kenya. A questionnaire that included the General Health Questionnaire-12, Satisfaction with Life Scale, and a modified version of the WHO Quality of Life-BREF tool was used for data collection. The questionnaire also included an open-ended question inviting qualitative responses about their experience as an IDP. The questionnaire was distributed through a three-stage sampling approach across four refugee camps from four regions of the Nakuru County in Kenya. One hundred IDPs participated in this study. All participants scored substantially higher than the applied GHQ-12 threshold for caseness (mean GHQ-12 score = 28.7, SD = 3.6). Quality of life and life satisfaction scores were also very poor (M = 10.24, SD = 1.9; M = 6.82, SD = 1.5 respectively). The qualitative results reflected these findings with statements reflecting suicidal thoughts, unhappiness with the government, lack of support, and fear for themselves and their children. Significantly higher GHQ-12 scores were found among older IDPs (rho = .202, sig = .046), widowers compared to married IDPs (mean difference = -2.41, SE = .885, sig = .027), while lower scores were found among IDPs who reported having friends as a source of support (U = 834, sig = .045), while quality of life scores were higher among IDPs who reported receiving governmental support (U = 248, sig = .018). The findings revealed poor levels of mental health, quality of life and life satisfaction. Older, widowed IDPs and those who did not perceive support from friends or the government were found to be at the highest risk of poor health and wellbeing.

Sub-Micrometer Scale Minor Element Mapping in Interplanetary Dust Particles: A Test for Stratospheric Contamination

NASA Technical Reports Server (NTRS)

Flynn, G. J.; Keller, L. P.; Sutton, S. R.

2004-01-01

Combined X-ray microprobe (XRM), energy dispersive x-ray fluorescence using a Transmission Electron Microscope (TEM), and electron microprobe measurements have determined that the average bulk chemical composition of the interplanetary dust particles (IDPs) collected from the Earth s stratosphere is enriched relative to the CI meteorite composition by a factor of 2 to 4 for carbon and for the moderately volatile elements Na, K, P, Mn, Cu, Zn, Ga, Ge, and Se, and enriched to approximately 30 times CI for Br. However, Jessberger et al., who have reported similar bulk enrichments using Proton Induced X-ray Emission (PIXE), attribute the enrichments to contamination by meteor-derived atmospheric aerosols during the several weeks these IDPs reside in the Earth s atmosphere prior to collection. Using scanning Auger spectroscopy, a very sensitive surface analysis technique, Mackinnon and Mogk have observed S contamination on the surface of IDPs, presumably due to the accretion of sulfate aerosols during stratospheric residence. But the S-rich layer they detected was so thin (approximately 100 angstroms thick) that the total amount of S on the surface was too small to significantly perturb the bulk S-content of a chondritic IDP. Stephan et al. provide support for the contamination hypothesis by reporting the enrichment of Br on the edges of the IDPs using Time-of-Flight Secondary-Ion Mass-Spectrometry (TOFSIMS), but TOF-SIMS is notorious for producing false edge-effects, particularly on irregularly-shaped samples like IDPs. Sutton et al. mapped the spatial distribution of Fe, Ni, Zn, Br, and Sr, at the approximately 2 m scale, in four IDPs using element-specific x-ray fluorescence (XRF) computed microtomography. They found the moderately volatile elements Zn and Br, although spatially inhomogeneous, were not concentrated on the surface of any of the IDPs they examined, suggesting that the Zn and the Br enrichments in the IDPs are not due to contamination during stratospheric residence.

Disorder-function relationships for the cell cycle regulatory proteins p21 and p27.

PubMed

Mitrea, Diana M; Yoon, Mi-Kyung; Ou, Li; Kriwacki, Richard W

2012-04-01

The classic structure-function paradigm has been challenged by a recently identified class of proteins: intrinsically disordered proteins (IDPs). Despite their lack of stable secondary or tertiary structure, IDPs are prevalent in all forms of life and perform myriad cellular functions, including signaling and regulation. Importantly, disruption of IDP homeostasis is associated with numerous human diseases, including cancer and neurodegeneration. Despite wide recognition of IDPs, the molecular mechanisms underlying their functions are not fully understood. Here we review the structural features and disorder-function relationships for p21 and p27, two cyclin-dependent kinase (Cdk) regulators involved in controlling cell division and fate. Studies of p21 bound to Cdk2/cyclin A revealed that a helix stretching mechanism mediates binding promiscuity. Further, investigations of Tyr88-phosphorylated p27 identified a signaling conduit that controls cell division and is disrupted in certain cancers. These mechanisms rely upon a balance between nascent structure in the free state, induced folding upon binding, and persistent flexibility within functional complexes. Although these disorder-function relationships are likely to be recapitulated in other IDPs, it is also likely that the vocabulary of their mechanisms is much more extensive than is currently understood. Further study of the physical properties of IDPs and elucidation of their links with function are needed to fully understand the mechanistic language of IDPs.

Ethical challenges in mental health research among internally displaced people: ethical theory and research implementation

PubMed Central

2013-01-01

Millions of people undergo displacement in the world. Internally displaced people (IDP) are especially vulnerable as they are not protected by special legislation in contrast to other migrants. Research conducted among IDPs must be correspondingly sensitive in dealing with ethical issues that may arise. Muslim IDPs in Puttalam district in the North-Western province of Sri Lanka were initially displaced from Northern Sri Lanka due to the conflict in 1991. In the backdrop of a study exploring the prevalence of common mental disorders among the IDPs, researchers encountered various ethical challenges. These included inter-related issues of autonomy, non-maleficence, beneficence, confidentiality and informed consent, and how these were tailored in a culture-specific way to a population that has increased vulnerability. This paper analyses how these ethical issues were perceived, detected and managed by the researchers, and the role of ethics review committees in mental health research concerning IDPs. The relevance of guidelines and methodologies in the context of an atypical study population and the benefit versus risk potential of research for IDPs are also discussed. The limitations that were encountered while dealing with ethical challenges during the study are discussed. The concept of post-research ethical conduct audit is suggested to be considered as a potential step to minimize the exploitation of vulnerable populations such as IDPs in mental health research. PMID:23497333

Intrinsically Disordered Protein Specific Force Field CHARMM36IDPSFF.

PubMed

Liu, Hao; Song, Dong; Lu, Hui; Luo, Ray; Chen, Hai-Feng

2018-05-28

Intrinsically disordered proteins (IDPs) are closely related to various human diseases. Because IDPs lack certain tertiary structure, it is difficult to use X-ray and NMR methods to measure their structures. Therefore, molecular dynamics simulation is a useful tool to study the conformer distribution of IDPs. However, most generic protein force fields were found to be insufficient in simulations of IDPs. Here we report our development for the CHARMM community. Our residue-specific IDP force field (CHARMM36IDPSFF) was developed based on the base generic force field with CMAP corrections of for all 20 naturally occurring amino acids. Multiple tests show that the simulated chemical shifts with the newly developed force field are in quantitative agreement with NMR experiment and are more accurate than the base generic force field. Comparison of J-couplings with previous work shows that CHARMM36IDPSFF and its corresponding base generic force field have their own advantages. In addition, CHARMM36IDPSFF simulations also agree with experiment for SAXS profiles and radii of gyration of IDPs. Detailed analysis shows that CHARMM36IDPSFF can sample more diverse and disordered conformers. These findings confirm that the newly developed force field can improve the balance of accuracy and efficiency for the conformer sampling of IDPs. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Ethical challenges in mental health research among internally displaced people: ethical theory and research implementation.

PubMed

Siriwardhana, Chesmal; Adikari, Anushka; Jayaweera, Kaushalya; Sumathipala, Athula

2013-03-12

Millions of people undergo displacement in the world. Internally displaced people (IDP) are especially vulnerable as they are not protected by special legislation in contrast to other migrants. Research conducted among IDPs must be correspondingly sensitive in dealing with ethical issues that may arise. Muslim IDPs in Puttalam district in the North-Western province of Sri Lanka were initially displaced from Northern Sri Lanka due to the conflict in 1991. In the backdrop of a study exploring the prevalence of common mental disorders among the IDPs, researchers encountered various ethical challenges. These included inter-related issues of autonomy, non-maleficence, beneficence, confidentiality and informed consent, and how these were tailored in a culture-specific way to a population that has increased vulnerability. This paper analyses how these ethical issues were perceived, detected and managed by the researchers, and the role of ethics review committees in mental health research concerning IDPs. The relevance of guidelines and methodologies in the context of an atypical study population and the benefit versus risk potential of research for IDPs are also discussed. The limitations that were encountered while dealing with ethical challenges during the study are discussed. The concept of post-research ethical conduct audit is suggested to be considered as a potential step to minimize the exploitation of vulnerable populations such as IDPs in mental health research.

Spatially Resolved Analysis of Amines Using a Fluorescence Molecular Probe: Molecular Analysis of IDPs

NASA Technical Reports Server (NTRS)

Clemett, S. J.; Messenger, S.; Thomas-Keprta, K. L.; Wentworth, S. J.; Robinson, G. A.; McKay, D. S.

2002-01-01

Some Interplanetary Dust Particles (IDPs) have large isotope anomalies in H and N. To address the nature of the carrier phase, we are developing a procedure to spatially resolve the distribution of organic species on IDP thin sections utilizing fluorescent molecular probes. Additional information is contained in the original extended abstract.

Refugee Education: The State of Nigeria's Preparedness

ERIC Educational Resources Information Center

Obashoro-John, Oluwayemisi A.; Oni, Gbolabo J.

2017-01-01

The spate of insurgences and conflicts in the country and around the sub-region has led to the increased presence of refugees and Internally Displaced People (IDPs) in Nigeria. This has resultant challenges on the basic needs of refugees and IDPs at different levels. One of the highest priorities of refugees and IDPs communities is education.…

Mortality and health among internally displaced persons in western Kenya following post-election violence, 2008: novel use of demographic surveillance

PubMed Central

Adazu, Kubaje; Obor, David; Ogwang, Sheila; Vulule, John; Hamel, Mary J; Laserson, Kayla

2010-01-01

Abstract Objective To evaluate mortality and morbidity among internally displaced persons (IDPs) who relocated in a demographic surveillance system (DSS) area in western Kenya following post-election violence. Methods In 2007, 204 000 individuals lived in the DSS area, where field workers visit households every 4 months to record migrations, births and deaths. We collected data on admissions among children < 5 years of age in the district hospital and developed special questionnaires to record information on IDPs. Mortality, migration and hospitalization rates among IDPs and regular DSS residents were compared, and verbal autopsies were performed for deaths. Findings Between December 2007 and May 2008, 16 428 IDPs migrated into the DSS, and over half of them stayed 6 months or longer. In 2008, IDPs aged 15–49 years died at higher rates than regular residents of the DSS (relative risk, RR: 1.34; 95% confidence interval, CI: 1.004–1.80). A greater percentage of deaths from human immunodeficiency virus (HIV) infection occurred among IDPs aged ≥ 5 years (53%) than among regular DSS residents (25–29%) (P < 0.001). Internally displaced children < 5 years of age did not die at higher rates than resident children but were hospitalized at higher rates (RR: 2.95; 95% CI: 2.44–3.58). Conclusion HIV-infected internally displaced adults in conflict-ridden parts of Africa are at increased risk of HIV-related death. Relief efforts should extend to IDPs who have relocated outside IDP camps, particularly if afflicted with HIV infection or other chronic conditions. PMID:20680125

Internal displacement and health among the Palestinian minority in Israel.

PubMed

Daoud, Nihaya; Shankardass, Ketan; O'Campo, Patricia; Anderson, Kim; Agbaria, Ayman K

2012-04-01

Long term health impacts of internal displacement (ID) resulting from political violence are not well documented or understood. One such case is the ID of 300,000-420,000 Palestinian citizens of Israel and their descendants during the Nakba of 1948 (Palestinian Catastrophe). We aim to document the long term health impacts of this ID. We draw on data collected in 2005 from a nationwide random sample of 902 individuals aged 30-70. Research participants were interviewed in person after being selected through a multistage sampling procedure. About 24% of participants reported that either they or their families had been internally displaced. Palestinian internally displaced persons (IDPs), that is, those who were forcibly displaced and dispossessed from their homes and lands during the Nakba and its aftermath, as well as their families and descendants, and who reside within the current borders of Israel, had an odds ratio of 1.45 (95% CI = 1.02-2.07) for poor self-rated health (SRH) compared to non-IDPs after controlling for demographic, socioeconomic and psychosocial factors. No difference was found between IDPs and non-IDPs in limiting longstanding illness following control for confounders. Low socioeconomic position and chronic stress were significantly related to ID and to SRH. Our findings suggest adverse long term health impacts of the Nakba on the IDPs when compared to non-IDPs. We propose that these disparities might stem from IDPs' unhealed post-traumatic scars from the Nakba, or from becoming a marginalized minority within their own society due to their displacement and loss of collective identity. Given these long term health consequences, we conclude that displacement should be addressed with health and social policies for IDPs. Copyright © 2012 Elsevier Ltd. All rights reserved.

Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins

PubMed Central

Ganguly, Debabani; Zhang, Weihong; Chen, Jianhan

2013-01-01

Achieving facile specific recognition is essential for intrinsically disordered proteins (IDPs) that are involved in cellular signaling and regulation. Consideration of the physical time scales of protein folding and diffusion-limited protein-protein encounter has suggested that the frequent requirement of protein folding for specific IDP recognition could lead to kinetic bottlenecks. How IDPs overcome such potential kinetic bottlenecks to viably function in signaling and regulation in general is poorly understood. Our recent computational and experimental study of cell-cycle regulator p27 (Ganguly et al., J. Mol. Biol. (2012)) demonstrated that long-range electrostatic forces exerted on enriched charges of IDPs could accelerate protein-protein encounter via “electrostatic steering” and at the same time promote “folding-competent” encounter topologies to enhance the efficiency of IDP folding upon encounter. Here, we further investigated the coupled binding and folding mechanisms and the roles of electrostatic forces in the formation of three IDP complexes with more complex folded topologies. The surface electrostatic potentials of these complexes lack prominent features like those observed for the p27/Cdk2/cyclin A complex to directly suggest the ability of electrostatic forces to facilitate folding upon encounter. Nonetheless, similar electrostatically accelerated encounter and folding mechanisms were consistently predicted for all three complexes using topology-based coarse-grained simulations. Together with our previous analysis of charge distributions in known IDP complexes, our results support a prevalent role of electrostatic interactions in promoting efficient coupled binding and folding for facile specific recognition. These results also suggest that there is likely a co-evolution of IDP folded topology, charge characteristics, and coupled binding and folding mechanisms, driven at least partially by the need to achieve fast association kinetics for cellular signaling and regulation. PMID:24278008

Generating intrinsically disordered protein conformational ensembles from a Markov chain

NASA Astrophysics Data System (ADS)

Cukier, Robert I.

2018-03-01

Intrinsically disordered proteins (IDPs) sample a diverse conformational space. They are important to signaling and regulatory pathways in cells. An entropy penalty must be payed when an IDP becomes ordered upon interaction with another protein or a ligand. Thus, the degree of conformational disorder of an IDP is of interest. We create a dichotomic Markov model that can explore entropic features of an IDP. The Markov condition introduces local (neighbor residues in a protein sequence) rotamer dependences that arise from van der Waals and other chemical constraints. A protein sequence of length N is characterized by its (information) entropy and mutual information, MIMC, the latter providing a measure of the dependence among the random variables describing the rotamer probabilities of the residues that comprise the sequence. For a Markov chain, the MIMC is proportional to the pair mutual information MI which depends on the singlet and pair probabilities of neighbor residue rotamer sampling. All 2N sequence states are generated, along with their probabilities, and contrasted with the probabilities under the assumption of independent residues. An efficient method to generate realizations of the chain is also provided. The chain entropy, MIMC, and state probabilities provide the ingredients to distinguish different scenarios using the terminologies: MoRF (molecular recognition feature), not-MoRF, and not-IDP. A MoRF corresponds to large entropy and large MIMC (strong dependence among the residues' rotamer sampling), a not-MoRF corresponds to large entropy but small MIMC, and not-IDP corresponds to low entropy irrespective of the MIMC. We show that MorFs are most appropriate as descriptors of IDPs. They provide a reasonable number of high-population states that reflect the dependences between neighbor residues, thus classifying them as IDPs, yet without very large entropy that might lead to a too high entropy penalty.

Computer Simulations of Intrinsically Disordered Proteins

NASA Astrophysics Data System (ADS)

Chong, Song-Ho; Chatterjee, Prathit; Ham, Sihyun

2017-05-01

The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields. Thus, achieving an accurate structural characterization of IDPs via simulations is a challenge. It is also daunting to perform a configuration-space integration over heterogeneous structural ensembles sampled by IDPs to extract, in particular, protein configurational entropy. In this review, we summarize recent efforts devoted to the development of force fields and the critical evaluations of their performance when applied to IDPs. We also survey recent advances in computational methods for protein configurational entropy that aim to provide a thermodynamic link between structural disorder and protein activity.

The sexual and reproductive rights of internally displaced women: the embodiment of Colombia's crisis.

PubMed

Alzate, Mónica M

2008-03-01

As of 30 June 2006, more than 3.5 million Colombians are internally displaced persons (IDPs), the second largest IDP population in the world after that of Sudan. While most IDP studies treat the plight of internally displaced women (IDW) as an isolated phenomenon, this paper demonstrates that their situation reflects Colombia's chronic cultural, political and socio-economic crisis. This paper uses a sexual and reproductive rights framework to establish a connection between IDW and Colombia's culture of violence, discrimination and inequality. The effects of this culture of violence, discrimination and inequality are highlighted during a discussion of the rights to health, reproduction, privacy, physical integrity, education, and freedom from violence and sexual exploitation. This paper argues that a holistic understanding of Colombia's humanitarian emergency is essential to improving the lives of IDPs. It ends with some concrete, short-term recommendations to meet some of the needs of IDPs and other vulnerable populations.

Collection and curation of IDPs in the stratosphere and below. Part 2: The Greenland and Antarctic ice sheets

NASA Technical Reports Server (NTRS)

Maurette, Michel; Hammer, C.; Harvey, R.; Immel, G.; Kurat, G.; Taylor, S.

1994-01-01

In a companion paper, Zolensky discusses interplanetary dust particles (IDP's) collected in the stratosphere. Here, we describe the recovery of much larger unmelted to partially melted IDP's from the Greenland and Antarctica ice sheet, and discuss problems arising in their collection and curation, as well as future prospects for tackling these problems.

Meteoric Material: An Important Component of Planetary Atmospheres

NASA Technical Reports Server (NTRS)

Grebowsky, Joseph M.; Moses, Julianne I.; Pesnell, W. Dean; Vondrak, Richard R. (Technical Monitor)

2001-01-01

Interplanetary dust particles (IDPs) interact with all planetary atmospheres and leave their imprint as perturbations of the background atmospheric chemistry and structure. They lead to layers of metal ions that can become the dominant positively charged species in lower ionospheric regions. Theoretical models and radio occultation measurements provide compelling evidence that such layers exist in all planetary atmospheres. In addition IDP ablation products can affect neutral atmospheric chemistry, particularly at the outer planets where the IDPs supply oxygen compounds like water and carbon dioxide to the upper atmospheres. Aerosol or smoke particles from incomplete ablation or recondensation of ablated IDP vapors may also have a significant impact on atmospheric properties.

Evidence-based diuretics: focus on chlorthalidone and indapamide.

PubMed

DiNicolantonio, James J; Bhutani, Jaikrit; Lavie, Carl J; O'Keefe, James H

2015-03-01

Thiazide and thiazide-like diuretics are cornerstone treatments for hypertension. However, unlike chlorthalidone (CTD) and indapamide (IDP), hydrochlorothiazide (HCTZ) lacks evidence for reducing morbidity and mortality as monotherapy compared with placebo or control. Despite this fact, HCTZ is prescribed much more frequently than CTD or IDP. We believe that all hypertension guidelines should follow the National Institute for Health and Excellence (NICE) and make IDP and CTD first choice 'thiazide-like diuretics.' This article will focus on the available evidence pertaining to HCTZ versus CTD and IDP. We will review the pharmacological differences between these three diuretics, as well as the clinical trial data and important side effects.

Combined infrared and analytical electron microscope studies of interplanetary dust particles

NASA Technical Reports Server (NTRS)

Bradley, J. P.; Humecki, H. J.; Germani, M. S.

1992-01-01

Ultramicrotomed thin sections (less than 100 nm thick) of eight chondritic interplanetary dust particles (IDPs) were studied by analytical electron microscopy and IR microspectroscopy with the objective of identifying IDPs or their specific components with IR spectral transmission characteristics at 10 microns similar to those of comets. Two IDPs are identified whose silicate emission characteristics between 8 and 12 microns are similar to those of comets Halley and Bradfield. Implanted solar flare tracks and sputtered rims resulting from solar wind damage suggest that the minerology and petrography of these IDPs have not been significantly perturbed since ejection from their parent bodies.

Intradiscal Pressure Changes during Manual Cervical Distraction: A Cadaveric Study

PubMed Central

Gudavalli, M. R.; Potluri, T.; Carandang, G.; Havey, R. M.; Voronov, L. I.; Cox, J. M.; Rowell, R. M.; Kruse, R. A.; Joachim, G. C.; Patwardhan, A. G.; Henderson, C. N. R.; Goertz, C.

2013-01-01

The objective of this study was to measure intradiscal pressure (IDP) changes in the lower cervical spine during a manual cervical distraction (MCD) procedure. Incisions were made anteriorly, and pressure transducers were inserted into each nucleus at lower cervical discs. Four skilled doctors of chiropractic (DCs) performed MCD procedure on nine specimens in prone position with contacts at C5 or at C6 vertebrae with the headpiece in different positions. IDP changes, traction forces, and manually applied posterior-to-anterior forces were analyzed using descriptive statistics. IDP decreases were observed during MCD procedure at all lower cervical levels C4-C5, C5-C6, and C6-C7. The mean IDP decreases were as high as 168.7 KPa. Mean traction forces were as high as 119.2 N. Posterior-to-anterior forces applied during manual traction were as high as 82.6 N. Intraclinician reliability for IDP decrease was high for all four DCs. While two DCs had high intraclinician reliability for applied traction force, the other two DCs demonstrated only moderate reliability. IDP decreases were greatest during moving flexion and traction. They were progressevely less pronouced with neutral traction, fixed flexion and traction, and generalized traction. PMID:24023587

An automated procedure for detection of IDP's dwellings using VHR satellite imagery

NASA Astrophysics Data System (ADS)

Jenerowicz, Malgorzata; Kemper, Thomas; Soille, Pierre

2011-11-01

This paper presents the results for the estimation of dwellings structures in Al Salam IDP Camp, Southern Darfur, based on Very High Resolution multispectral satellite images obtained by implementation of Mathematical Morphology analysis. A series of image processing procedures, feature extraction methods and textural analysis have been applied in order to provide reliable information about dwellings structures. One of the issues in this context is related to similarity of the spectral response of thatched dwellings' roofs and the surroundings in the IDP camps, where the exploitation of multispectral information is crucial. This study shows the advantage of automatic extraction approach and highlights the importance of detailed spatial and spectral information analysis based on multi-temporal dataset. The additional data fusion of high-resolution panchromatic band with lower resolution multispectral bands of WorldView-2 satellite has positive influence on results and thereby can be useful for humanitarian aid agency, providing support of decisions and estimations of population especially in situations when frequent revisits by space imaging system are the only possibility of continued monitoring.

An introduction to the interim digital SAR processor and the characteristics of the associated Seasat SAR imagery

NASA Technical Reports Server (NTRS)

Wu, C.; Barkan, B.; Huneycutt, B.; Leang, C.; Pang, S.

1981-01-01

Basic engineering data regarding the Interim Digital SAR Processor (IDP) and the digitally correlated Seasat synthetic aperature radar (SAR) imagery are presented. The correlation function and IDP hardware/software configuration are described, and a preliminary performance assessment presented. The geometric and radiometric characteristics, with special emphasis on those peculiar to the IDP produced imagery, are described.

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: On the Accuracy of the TIP4P-D Water Model and the Representativeness of Protein Disorder Models.

PubMed

Henriques, João; Skepö, Marie

2016-07-12

Here, we first present a follow-up to a previous work by our group on the problematic of molecular dynamics simulations of intrinsically disordered proteins (IDPs) [ Henriques et al. J. Chem. Theory Comput. 2015 , 11 , 3420 - 3431 ], using the recently developed TIP4P-D water model. When used in conjunction with the standard AMBER ff99SB-ILDN force field and applied to the simulation of Histatin 5, our IDP model, we obtain results which are in excellent agreement with the best performing IDP-suitable force field from the earlier study and with experiment. We then assess the representativeness of the IDP models used in these and similar studies, finding that most are too short in comparison to the average IDP and contain a bias toward hydrophilic amino acid residues. Moreover, several key order- and disorder-promoting residues are also found to be misrepresented. It seems appropriate for future studies to address these issues.

Forced migration and mental health: prolonged internal displacement, return migration and resilience.

PubMed

Siriwardhana, Chesmal; Stewart, Robert

2013-03-01

Forced internal displacement has been rising steadily, mainly due to conflict. Many internally displaced people (IDP) experience prolonged displacement. Global research evidence suggests that many of these IDP are at high risk for developing mental disorders, adding weight to the global burden of disease. However, individual and community resilience may act as protective factors. Return migration may be an option for some IDP populations, especially when conflicts end, although return migration may itself be associated with worse mental health. Limited evidence is available on effects of resettlement or return migration following prolonged forced internal displacement on mental health. Also, the role of resilience factors remains to be clarified following situations of prolonged displacement. The public health impact of internal displacement is not clearly understood. Epidemiological and interventional research in IDP mental health needs to look beyond medicalised models and encompass broader social and cultural aspects. The resilience factor should be integrated and explored more in mental health research among IDP and a clearly focused multidisciplinary approach is advocated.

Wrecked regulation of intrinsically disordered proteins in diseases: pathogenicity of deregulated regulators

PubMed Central

Uversky, Vladimir N.

2014-01-01

Biologically active proteins without stable tertiary structure are common in all known proteomes. Functions of these intrinsically disordered proteins (IDPs) are typically related to regulation, signaling, and control. Cellular levels of these important regulators are tightly regulated by a variety mechanisms ranging from firmly controlled expression to precisely targeted degradation. Functions of IDPs are controlled by binding to specific partners, alternative splicing, and posttranslational modifications among other means. In the norm, right amounts of precisely activated IDPs have to be present in right time at right places. Wrecked regulation brings havoc to the ordered world of disordered proteins, leading to protein misfolding, misidentification, and missignaling that give rise to numerous human diseases, such as cancer, cardiovascular disease, neurodegenerative diseases, and diabetes. Among factors inducing pathogenic transformations of IDPs are various cellular mechanisms, such as chromosomal translocations, damaged splicing, altered expression, frustrated posttranslational modifications, aberrant proteolytic degradation, and defective trafficking. This review presents some of the aspects of deregulated regulation of IDPs leading to human diseases. PMID:25988147

What if chondritic porous interplanetary dust particles are not the real McCoy

NASA Astrophysics Data System (ADS)

Rietmeijer, Frans J. M.

To select a target comet for a Comet Nucleus Sample Return Mission (CNSRM) it is necessary to have an experimental data base to evaluate the extent of diversity and similarity of comets. For example, the physical properties (e.g., low density) of chondritic porous (CP) interplanetary dust particles (IDPs) are believed to resemble these properties of cometary dust although it is yet to be demonstrated that the porous structure of CP IDPs is inherent to presolar dust particles stored in comet nuclei. Porous structures of IDPs could conceivably form during sublimation at the surface of active comet nuclei. Porous structures are also obtained during annealing of amorphous Mg-SiO smokes which initially forms porous aggregates of olivine + platey tridymite and which, upon continued annealing, react to fluffy enstatite aggregates. It is therefore uncertain that CP IDPs are entirely composed of unmetamorphosed presolar dust. Conceivably, new minerals and textures may form in situ in nuclei of active comets as a function of their individual thermal history. Unmetamorphosed comet dust is probably structurally amorphous. Thermal annealing of this dust can produce ultra fine-grained minerals and this ultrafine grain size of CP IDPs should be considered in assessments of aqueous alterations that could affect presolar dust in comet nuclei between 200 and 400 K. Devitrification and hydration may occur in situ in ice-dust mixtures and the mantle of active comet nuclei. Devitrification, or uncontrolled crystallization, of amorphous precursor dust can produce a range of chemical compositions of ultrafine-grained minerals and (non-equilibrium) mineral assemblages and textures in dust contained in comet nuclei as a function of period and trajectory of orbit and number of perihelion passages (not considering internal heating). Thus, experimental data on relevant processes and reaction rates between 200 and 400 K are needed in order to evaluate comet selection, penetration depth for sampling device and curation of samples for CNSRM.

What if chondritic porous interplanetary dust particles are not the real McCoy

NASA Technical Reports Server (NTRS)

Rietmeijer, Frans J. M.

1989-01-01

To select a target comet for a Comet Nucleus Sample Return Mission (CNSRM) it is necessary to have an experimental data base to evaluate the extent of diversity and similarity of comets. For example, the physical properties (e.g., low density) of chondritic porous (CP) interplanetary dust particles (IDPs) are believed to resemble these properties of cometary dust although it is yet to be demonstrated that the porous structure of CP IDPs is inherent to presolar dust particles stored in comet nuclei. Porous structures of IDPs could conceivably form during sublimation at the surface of active comet nuclei. Porous structures are also obtained during annealing of amorphous Mg-SiO smokes which initially forms porous aggregates of olivine + platey tridymite and which, upon continued annealing, react to fluffy enstatite aggregates. It is therefore uncertain that CP IDPs are entirely composed of unmetamorphosed presolar dust. Conceivably, new minerals and textures may form in situ in nuclei of active comets as a function of their individual thermal history. Unmetamorphosed comet dust is probably structurally amorphous. Thermal annealing of this dust can produce ultra fine-grained minerals and this ultrafine grain size of CP IDPs should be considered in assessments of aqueous alterations that could affect presolar dust in comet nuclei between 200 and 400 K. Devitrification and hydration may occur in situ in ice-dust mixtures and the mantle of active comet nuclei. Devitrification, or uncontrolled crystallization, of amorphous precursor dust can produce a range of chemical compositions of ultrafine-grained minerals and (non-equilibrium) mineral assemblages and textures in dust contained in comet nuclei as a function of period and trajectory of orbit and number of perihelion passages (not considering internal heating). Thus, experimental data on relevant processes and reaction rates between 200 and 400 K are needed in order to evaluate comet selection, penetration depth for sampling device and curation of samples for CNSRM.

Submicrometer Organic Grains: Widespread Constituents of the Early Solar System

NASA Technical Reports Server (NTRS)

Messenger, Scott; Nakamuri-Messenger, Keiko; Keller, Lindsay; Matrajt, Graciela; Clemett, Simon; Ito, Motoo

2007-01-01

Primitive meteorites and interplanetary dust particles (IDPs) contain remants of interstellar organic matter, marked by anomalous H and N isotopic ratios. These isotopic anomalies are attributed to mass fractionation during chemical reactions at cryogenic temperatures (10-100K) in a cold molecular cloud. Significant variations in the chemistry and isotopic compositions of organic compounds within and between these samples suggest varying histories of alteration and dilution of the presolar components. Recent studies have reported large H and N isotopic anomalies preserved in sub-m organic inclusions in both meteorites and IDPs. In the Tagish Lake meteorite, the largest H and N isotopic anomalies are associated with sub-m, hollow organic globules. The common physical, chemical, and isotopic characteristics of these globules suggest that they formed before being incorporated into their parent meteorite. These organic globules probably originated as organic ice coatings that formed on preexisting ice or mineral grains in a cold molecular cloud. Radiation driven photochemistry may have processed them into refractory organic grains. This model implies that submicrometer organic grains were widely distributed throughout the solar nebula during the epoch of planet formation. Submicrometer organic particles were detected by the Giotto and Vega encounters with comet Halley, termed CHON particles based on their major element chemistry. The first direct samples of cometary dust (comet Wild-2) were returned by the Stardust spacecraft in January 2006. These samples exhibit widely varying, fine grained mineralogy similar to anhydrous IDPs, including submicrometer carbonaceous grains. The submicrometer organic grains from comet Wild-2 exhibit H and N isotopic anomalies of similar magnitude to those commonly observed in primitive meteorites and IDPs. Isotopically anomalous, submicrometer organic grains have now been observed in meteorites, IDPs, the Oort-cloud comet Halley, and the Kuiper-belt comet Wild-2, suggesting that such grains were prevalent throughout the protoplanetary disk.

Water and organics in interplanetary dust particles

NASA Astrophysics Data System (ADS)

Bradley, John P.

2015-08-01

Interplanetary dust particles (IDPs) and larger micrometeorites (MMs) impinge on the upper atmosphere where they decelerate at ~90 km altitude and settle to the Earth’s surface. Comets and asteroids are the major sources and the flux, 30,000-40,000 tons/yr, is comparable to the mass of larger meteorites impacting the Earth’s surface. The sedimentary record suggests that the flux was much higher on the early Earth. The chondritic porous (CP) subset of IDPs together with their larger counterparts, ultracarbonaceous micrometeorites (UCMMs), appear to be unique among known meteoritic materials in that they are composed almost exclusively of anhydrous minerals, some of them contain >> 50% organic carbon by volume as well as the highest abundances of presolar silicate grains including GEMS. D/H and 15N abundances implicate the Oort Cloud or presolar molecular cloud as likely sources of the organic carbon. Prior to atmospheric entry, IDPs and MMs spend ~104-105 year lifetimes in solar orbit where their surfaces develop amorphous space weathered rims from exposure to the solar wind (SW). Similar rims are observed on lunar soil grains and on asteroid Itokawa regolith grains. Using valence electron energy-loss spectroscopy (VEELS) we have detected radiolytic water in the rims on IDPs formed by the interaction of solar wind protons with oxygen in silicate minerals. Therefore, IDPs and MMs continuously deliver both water and organics to the earth and other terrestrial planets. The interaction of protons with oxygen-rich minerals to form water is a universal process.Affiliations:a University of Hawaii at Manoa, Hawaii Institute of Geophysics and Planetology, 1680 East-West Road, Honolulu, HI 96822, USA.b National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.c Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.d Department of Materials Science & Engineering, University of California, Berkeley, CA 94720, USA.e Advanced Light Source Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Intrinsically Disordered Proteins and the Origins of Multicellular Organisms

NASA Astrophysics Data System (ADS)

Dunker, A. Keith

In simple multicellular organisms all of the cells are in direct contact with the surrounding milieu, whereas in complex multicellular organisms some cells are completely surrounded by other cells. Current phylogenetic trees indicate that complex multicellular organisms evolved independently from unicellular ancestors about 10 times, and only among the eukaryotes, including once for animals, twice each for green, red, and brown algae, and thrice for fungi. Given these multiple independent evolutionary lineages, we asked two questions: 1. Which molecular functions underpinned the evolution of multicellular organisms?; and, 2. Which of these molecular functions depend on intrinsically disordered proteins (IDPs)? Compared to unicellularity, multicellularity requires the advent of molecules for cellular adhesion, for cell-cell communication and for developmental programs. In addition, the developmental programs need to be regulated over space and time. Finally, each multicellular organism has cell-specific biochemistry and physiology. Thus, the evolution of complex multicellular organisms from unicellular ancestors required five new classes of functions. To answer the second question we used Key-words in Swiss Protein ranked for associations with predictions of protein structure or disorder. With a Z-score of 18.8 compared to random-function proteins, à differentiation was the biological process most strongly associated with IDPs. As expected from this result, large numbers of individual proteins associated with differentiation exhibit substantial regions of predicted disorder. For the animals for which there is the most readily available data all five of the underpinning molecular functions for multicellularity were found to depend critically on IDP-based mechanisms and other evidence supports these ideas. While the data are more sparse, IDPs seem to similarly underlie the five new classes of functions for plants and fungi as well, suggesting that IDPs were indeed crucial for the evolution of complex multicellular organisms. These new findings necessitate a rethinking of the gene regulatory network models currently used to explain cellular differentiation and the evolution of complex multicellular organisms.

Consequences of inducing intrinsic disorder in a high-affinity protein-protein interaction.

PubMed

Papadakos, Grigorios; Sharma, Amit; Lancaster, Lorna E; Bowen, Rebecca; Kaminska, Renata; Leech, Andrew P; Walker, Daniel; Redfield, Christina; Kleanthous, Colin

2015-04-29

The kinetic and thermodynamic consequences of intrinsic disorder in protein-protein recognition are controversial. We address this by inducing one partner of the high-affinity colicin E3 rRNase domain-Im3 complex (K(d) ≈ 10(-12) M) to become an intrinsically disordered protein (IDP). Through a variety of biophysical measurements, we show that a single alanine mutation at Tyr507 within the hydrophobic core of the isolated colicin E3 rRNase domain causes the enzyme to become an IDP (E3 rRNase(IDP)). E3 rRNase(IDP) binds stoichiometrically to Im3 and forms a structure that is essentially identical to the wild-type complex. However, binding of E3 rRNase(IDP) to Im3 is 4 orders of magnitude weaker than that of the folded rRNase, with thermodynamic parameters reflecting the disorder-to-order transition on forming the complex. Critically, pre-steady-state kinetic analysis of the E3 rRNase(IDP)-Im3 complex demonstrates that the decrease in affinity is mostly accounted for by a drop in the electrostatically steered association rate. Our study shows that, notwithstanding the advantages intrinsic disorder brings to biological systems, this can come at severe kinetic and thermodynamic cost.

Benign Intraductal Papilloma without Atypia on Core Needle Biopsy Has a Low Rate of Upgrading to Malignancy after Excision.

PubMed

Han, Song-Hee; Kim, Milim; Chung, Yul Ri; Yun, Bo La; Jang, Mijung; Kim, Sun Mi; Kang, Eunyoung; Kim, Eun-Kyu; Park, So Yeon

2018-03-01

The management of benign intraductal papilloma (IDP) without atypia diagnosed on core needle biopsy (CNB) remains controversial. This study was performed to evaluate the rate of upgrading to malignancy or high-risk lesions after excision and to identify factors associated with upgrading using a large series of benign IDP cases without atypia. We included patients who were diagnosed as having benign IDP without atypia on CNB and underwent surgical or vacuum-assisted excision between 2010 and 2015. We analyzed the clinical, radiologic, and histopathologic features of IDPs that were upgraded to malignancy or high-risk lesions after excision. A total of 511 benign IDPs without atypia diagnosed via CNB were identified, of which 398 cases were treated with excision. After reviewing these cases, four cases of high-risk lesions in adjacent tissue on CNB, two cases which were revealed as papilloma with atypia, and nine cases of malignancy in the same breast were excluded. In the remaining 383 cases, the rate of upgrading to malignancy and high-risk lesions after excision was 0.8% and 4.4%, respectively. The presence of concurrent contralateral breast cancer, the presence of symptoms, and multifocality were factors significantly associated with upgrading to malignancy on subsequent excision. Surgical excision rather than vacuum-assisted excision was significantly associated with upgrading to high-risk lesions or malignancy. The rate of upgrading to malignancy for benign IDP without atypia was very low, suggesting that close clinical and radiologic observation may be sufficient for patients with benign IDP without atypia on CNB under proper settings.

GeoInt: the first macroseismic intensity database for the Republic of Georgia

NASA Astrophysics Data System (ADS)

Varazanashvili, O.; Tsereteli, N.; Bonali, F. L.; Arabidze, V.; Russo, E.; Pasquaré Mariotto, F.; Gogoladze, Z.; Tibaldi, A.; Kvavadze, N.; Oppizzi, P.

2018-05-01

Our work is intended to present the new macroseismic intensity database for the Republic of Georgia—hereby named GeoInt—which includes earthquakes from the historical (from 1250 B.C. onwards) to the instrumental era. Such database is composed of 111 selected earthquakes and related 3944 intensity data points (IDPs) for 1509 different localities, reported in the Medvedev-Sponheuer-Karnik scale (MSK). Regarding the earthquakes, the M S is in the 3.3-7 range and the depth is in the 2-36 km range. The entire set of IDPs is characterized by intensities ranging from 2-3 to 9-10 and covers an area spanning from 39.508° N to 45.043° N in a N-S direction and from 37.324° E to 48.500° E in an E-W direction, with some of the IDPs located outside the Georgian border, in the (i) Republic of Armenia, (ii) Russian Federation, (iii) Republic of Turkey, and (iv) Republic of Azerbaijan. We have revised each single IDP and have reevaluated and homogenized intensity values to the MSK scale. In particular, regarding the whole set of 3944 IDPs, 348 belong to the Historical era (pre-1900) and 3596 belong to the instrumental era (post-1900). With particular regard to the 3596 IDPs, 105 are brand new (3%), whereas the intensity values for 804 IDPs have been reevaluated (22%); for 2687 IDPs (75%), intensities have been confirmed from previous interpretations. We introduce this database as a key input for further improvements in seismic hazard modeling and seismic risk calculation for this region, based on macroseismic intensity; we report all the 111 earthquakes with available macroseismic information. The GeoInt database is also accessible online at http://www.enguriproject.unimib.it and will be kept updated in the future.

GeoInt: the first macroseismic intensity database for the Republic of Georgia

NASA Astrophysics Data System (ADS)

Varazanashvili, O.; Tsereteli, N.; Bonali, F. L.; Arabidze, V.; Russo, E.; Pasquaré Mariotto, F.; Gogoladze, Z.; Tibaldi, A.; Kvavadze, N.; Oppizzi, P.

2018-01-01

Our work is intended to present the new macroseismic intensity database for the Republic of Georgia—hereby named GeoInt—which includes earthquakes from the historical (from 1250 B.C. onwards) to the instrumental era. Such database is composed of 111 selected earthquakes and related 3944 intensity data points (IDPs) for 1509 different localities, reported in the Medvedev-Sponheuer-Karnik scale (MSK). Regarding the earthquakes, the M S is in the 3.3-7 range and the depth is in the 2-36 km range. The entire set of IDPs is characterized by intensities ranging from 2-3 to 9-10 and covers an area spanning from 39.508° N to 45.043° N in a N-S direction and from 37.324° E to 48.500° E in an E-W direction, with some of the IDPs located outside the Georgian border, in the (i) Republic of Armenia, (ii) Russian Federation, (iii) Republic of Turkey, and (iv) Republic of Azerbaijan. We have revised each single IDP and have reevaluated and homogenized intensity values to the MSK scale. In particular, regarding the whole set of 3944 IDPs, 348 belong to the Historical era (pre-1900) and 3596 belong to the instrumental era (post-1900). With particular regard to the 3596 IDPs, 105 are brand new (3%), whereas the intensity values for 804 IDPs have been reevaluated (22%); for 2687 IDPs (75%), intensities have been confirmed from previous interpretations. We introduce this database as a key input for further improvements in seismic hazard modeling and seismic risk calculation for this region, based on macroseismic intensity; we report all the 111 earthquakes with available macroseismic information. The GeoInt database is also accessible online at http://www.enguriproject.unimib.it and will be kept updated in the future.

Interplanetary dust particles collected in the stratosphere: observations of atmospheric heating and constraints on their interrelationships and sources.

PubMed

Sandford, S A; Bradley, J P

1989-01-01

The majority of the interplanetary dust particles (IDPs) collected in the stratosphere belong to one of three major classes, the first two dominated by the anhydrous minerals olivine and pyroxene, and the third by hydrous layer-lattice silicates. Infrared spectroscopy and transmission electron microscopy studies show that the different IDP classes represent different types of dust that exist as individual particles in interplanetary space. The majority of the collected IDPs smaller than 30 micrometers in diameter in the layer-lattice silicate and pyroxene classes appear not to have been heated to temperatures above 600 degrees C during atmospheric entry. The relatively low maximum temperatures experienced by these IDPs during atmospheric entry imply that they arrive at the top of the atmosphere with low geocentric encounter velocities. This limits the possible encounter trajectories for these particles to relatively circular, prograde orbits. As a result, it is unlikely that these IDPs are from Earth-crossing comets or asteroids. Asteroids, and comets having low inclinations and perihelia outside 1.2 AU, appear to be the best candidates for the parent bodies of the pyroxene and layer-lattice silicate particles. Chemical and mineralogical information suggests that the pyroxene-rich IDPs are from comets and the layer-lattice silicate-rich IDPs are from asteroids. The collected IDPs dominated by olivine appear to include a larger fraction of particles heating above 600 degrees C, suggesting that these particles were captured from more eccentric orbits. This, and the observation of the infrared spectral features of olivine in several comets suggest these particles have a cometary origin. Since much of the collected dust has apparently been captured from nearly circular, prograde orbits and since there are no appropriate parent bodies presently in such orbits, these results provide an experimental confirmation that the Poynting-Robertson effect exists as a nongravitational force important in the orbital evolution of dust in the Solar System.

Tin in a chondritic interplanetary dust particle

NASA Technical Reports Server (NTRS)

Rietmeijer, Frans J. M.

1989-01-01

Submicron platey Sn-rich grains are present in chondritic porous interplanetary dust particle (IDP) W7029 A and it is the second occurrence of a tin mineral in a stratospheric micrometeorite. Selected Area Electron Diffraction data for the Sn-rich grains match with Sn2O3 and Sn3O4. The oxide(s) may have formed in the solar nebula when tin metal catalytically supported reduction of CO or during flash heating on atmospheric entry of the IDP. The presence of tin is consistent with enrichments for other volatile trace elements in chondritic IDPs and may signal an emerging trend toward nonchondritic volatile element abundances in chondritic IDPs. The observation confirms small-scale mineralogical heterogeneity in fine-grained chondritic porous interplanetary dust.

Diversity and adaptation of shelters in transitional settlements for IDPs in Afghanistan.

PubMed

Ashmore, Joseph; Babister, Elizabeth; Corsellis, Tom; Fowler, Jon; Kelman, Ilan; McRobie, Allan; Manfield, Peter; Spence, Robin; Vitale, Antonella; Battilana, Rachel; Crawford, Kate

2003-12-01

The diversity of shelters used in transitional settlements for internally displaced persons (IDPs) in Herat, Afghanistan is described. The information is based on a field survey undertaken in March 2002 and highlights the adaptation techniques, which IDPs undertake to improve any provided shelter. Potential areas for improvement are indicated; for example, the possibility for using insulated, demountable liners to prevent cold-related deaths without sacrificing shelter flexibility along with the likely need for better agency coordination of the shelter responses they provide. The wider context in which the technical recommendations would be implemented must also be considered. Such issues include agency resources, political impediments to providing the desired option, and the preference of many IDPs that the best shelter would be their home.

Benign Intraductal Papilloma without Atypia on Core Needle Biopsy Has a Low Rate of Upgrading to Malignancy after Excision

PubMed Central

Han, Song-Hee; Kim, Milim; Chung, Yul Ri; Yun, Bo La; Jang, Mijung; Kim, Sun Mi; Kang, Eunyoung; Kim, Eun-Kyu

2018-01-01

Purpose The management of benign intraductal papilloma (IDP) without atypia diagnosed on core needle biopsy (CNB) remains controversial. This study was performed to evaluate the rate of upgrading to malignancy or high-risk lesions after excision and to identify factors associated with upgrading using a large series of benign IDP cases without atypia. Methods We included patients who were diagnosed as having benign IDP without atypia on CNB and underwent surgical or vacuum-assisted excision between 2010 and 2015. We analyzed the clinical, radiologic, and histopathologic features of IDPs that were upgraded to malignancy or high-risk lesions after excision. Results A total of 511 benign IDPs without atypia diagnosed via CNB were identified, of which 398 cases were treated with excision. After reviewing these cases, four cases of high-risk lesions in adjacent tissue on CNB, two cases which were revealed as papilloma with atypia, and nine cases of malignancy in the same breast were excluded. In the remaining 383 cases, the rate of upgrading to malignancy and high-risk lesions after excision was 0.8% and 4.4%, respectively. The presence of concurrent contralateral breast cancer, the presence of symptoms, and multifocality were factors significantly associated with upgrading to malignancy on subsequent excision. Surgical excision rather than vacuum-assisted excision was significantly associated with upgrading to high-risk lesions or malignancy. Conclusion The rate of upgrading to malignancy for benign IDP without atypia was very low, suggesting that close clinical and radiologic observation may be sufficient for patients with benign IDP without atypia on CNB under proper settings. PMID:29628987

Volatiles in interplanetary dust particles: A comparison with CI and CM chondrites

NASA Technical Reports Server (NTRS)

Bustin, Roberta

1992-01-01

In an effort to classify and determine the origin of interplanetary dust particles (IDPs), 14 of these particles were studied using a laser microprobe/mass spectrometer. The mass spectra for these particles varied dramatically. Some particles released hydroxide or water which probably originated in hydroxide-bearing minerals or hydrates. Others produced spectra which included a number of hydrocarbons and resembled meteorite spectra. However, none of the individual IDPs gave spectra which could be matched identically with a particular meteorite type such as a CI or CM carbonaceous chondrite. We believe this was due to the fact that 10-20 micron size IDPs are too small to be representative of the parent body. To verify that the diversity was due primarily to the small particle sizes, small grains of approximately the same size range as the IDPs were obtained from two primitive meteorites, Murchison and Orgueil, and these small meteorite particles were treated exactly like the IDPs. Considerable diversity was observed among individual grains, but a composite spectrum of all the grains from one meteorite closely resembled the spectrum obtained from a much larger sample of that meteorite. A composite spectrum of the 14 IDPs also resembled the spectra of the CM and CI meteorites, pointing to a possible link between IDPs and carbonaceous chondrites. This also illustrates that despite the inherent diversity in particles as small as 10-20 micron, conclusions can be drawn about the possible origin and overall composition of such particles by looking not only at results from individual particles but also by including many particles in a study and basing conclusions on some kind of composite data.

Predicting positive mental health in internally displaced persons in Indonesia: the roles of economic improvement and exposure to violent conflict.

PubMed

Saragih Turnip, Sherly; Sörbom, Dag; Hauff, Edvard

2016-01-01

Positive mental health, rather than just the absence of mental illness, is rarely investigated among the internally displaced persons (IDPs) affected by violent conflict in low-income countries. The purpose of this study was to investigate a model that could explain the interrelationship between factors contributing to positive mental health in displaced populations. In a longitudinal study we examine poverty, exposure to traumatic events and the change of material well-being after one year. We collected data in two consecutive years (2005 and 2006) from a community-based sample of IDPs in Ambon, Indonesia, through face-to-face structured interviews with consenting adults. Participants of this study were IDPs lived in Ambon during the violent conflict period. We interviewed 471 IDPs in the first year and reinterviewed 399 (85%) of the same subjects in the second year. The IDPs possessed good sense of coherence and subjective well-being. Our final model, which was generated by the use of structural equation modeling, fits the data well (χ(2) = 52.51, df = 45, p = .21, CFI = .99, RMSEA = .019). Exposure to violent conflict had a negative impact on IDPs' mental health initially and better economic conditions improved it (r = -.30 and .29 respectively). Mental health status one year previously was a strong predictor of future mental health, followed by individual economic growth in the past year (r = .43 and .29 respectively). On a group level the IDPs were resilient and adaptive to survive in adverse living conditions after devastating violent conflict, and the economic improvement contributed to it.

Principal Components Constrain Dynamic Pyrometamorphism in a Partially Melted Interplanetary Dust Particle

NASA Astrophysics Data System (ADS)

Rietmeijer, F. J. M.

1996-03-01

All interplanetary dust particles [IDPs] that decelerate in the Earth's atmosphere experience flash heating whereby their orbital velocity (km s^-1) is reduced to cm s^-1. Iron-oxide rims that may either be continuous on the particle surface, or discontinuous along its perimeter, occur on many IDPs. It is the most conspicuous mineralogical indicator of dynamic pyrometamorphism and its formation is interpreted as 'intense' IDP heating. It appears that the formation of these magnetite and maghemite rims is intimately linked to the presence of Fe,Ni-sulfides in the pre-entry particle. In this regard chondritic porous (CP) IDP L2011K7 may be an unusual particle. This porous aggregate consists of S-free polyphase units (PUs), nonstoichiometric diopside and Mg-rich wollastonite single-crystals and small, accessory Fe,Ni-sulfide grains. Only a few Fe-oxide nanograins are present along its perimeter. The nonstoichiometry of its Ca,Mg-clinopyroxenes indicates incongruent melting or vaporization that was experimentally determined at 1300 degrees-1400 degrees C. The CP IDP L2011K7 is probably of cometary origin since active comet nuclei are the most likely sources for uncompacted aggregate IDPs whereby their low density (< 1 g cm^-3) enhances atmospheric entry survival of large particles. In addition, the fluffy texture which inhibits chemical exchange among its components further enhances their survival unless compaction occurs during deceleration in the Earth's atmosphere.

Maternal and Child Health of Internally Displaced Persons in Ukraine: A Qualitative Study

PubMed Central

Nidzvetska, Svitlana; Rodriguez-Llanes, Jose M.; Aujoulat, Isabelle; Gil Cuesta, Julita; Tappis, Hannah; van Loenhout, Joris A. F.; Guha-Sapir, Debarati

2017-01-01

Due to the conflict that started in spring 2014 in Eastern Ukraine, a total of 1.75 million internally displaced persons (IDPs) fled the area and have been registered in government-controlled areas of the country. This paper explores perceived health, barriers to access to healthcare, caring practices, food security, and overall financial situation of mothers and young children displaced by the conflict in Ukraine. This is a qualitative study, which collected data through semi-structured in-depth interviews with nine IDP mothers via Skype and Viber with a convenience sample of participants selected through snowball technique. Contrary to the expectations, the perceived physical health of mothers and their children was found not to be affected by conflict and displacement, while psychological distress was often reported. A weak healthcare system, Ukraine’s proneness to informal payments, and heavy bureaucracy to register as an IDP were reported in our study. A precarious social safety net to IDP mothers in Ukraine, poor dietary diversity, and a generalized rupture of vaccine stocks, with halted or delayed vaccinations in children were identified. Increasing social allowances and their timely delivery to IDP mothers might be the most efficient policy measure to improve health and nutrition security. Reestablishment and sustainability of vaccine stocks in Ukraine is urgent to avoid the risks of a public health crisis. Offering psychological support for IDP mothers is recommended. PMID:28075363

Maternal and Child Health of Internally Displaced Persons in Ukraine: A Qualitative Study.

PubMed

Nidzvetska, Svitlana; Rodriguez-Llanes, Jose M; Aujoulat, Isabelle; Gil Cuesta, Julita; Tappis, Hannah; van Loenhout, Joris A F; Guha-Sapir, Debarati

2017-01-09

Due to the conflict that started in spring 2014 in Eastern Ukraine, a total of 1.75 million internally displaced persons (IDPs) fled the area and have been registered in government-controlled areas of the country. This paper explores perceived health, barriers to access to healthcare, caring practices, food security, and overall financial situation of mothers and young children displaced by the conflict in Ukraine. This is a qualitative study, which collected data through semi-structured in-depth interviews with nine IDP mothers via Skype and Viber with a convenience sample of participants selected through snowball technique. Contrary to the expectations, the perceived physical health of mothers and their children was found not to be affected by conflict and displacement, while psychological distress was often reported. A weak healthcare system, Ukraine's proneness to informal payments, and heavy bureaucracy to register as an IDP were reported in our study. A precarious social safety net to IDP mothers in Ukraine, poor dietary diversity, and a generalized rupture of vaccine stocks, with halted or delayed vaccinations in children were identified. Increasing social allowances and their timely delivery to IDP mothers might be the most efficient policy measure to improve health and nutrition security. Reestablishment and sustainability of vaccine stocks in Ukraine is urgent to avoid the risks of a public health crisis. Offering psychological support for IDP mothers is recommended.

Carbon analyses of IDP's sectioned in sulfur and supported on beryllium films

NASA Technical Reports Server (NTRS)

Bradley, J. P.; Keller, L.; Thomas, K. L.; Vanderwood, T. B.; Brownlee, D. E.

1993-01-01

Carbon is the only major element in interplanetary dust whose abundance, distribution and chemical state are not well understood. Information about carbon could clarify the relationship between the various classes of IDP's, conventional meteorites, and sources (e.g., comets vs. asteroids). To date, the most reliable estimates of C abundance in Interplanetary Dust Particles (IDP's) have been obtained by analyzing particles on thick-flat Be substrates using thin-window energy-dispersive spectroscopy in the SEM. These estimates of C abundance are valid only if C is homogeneously distributed, because detected C x-rays originate from the outer 0.1 micrometers of the particle. An alternative and potentially more accurate method of measuring C abundances is to analyze multiple thin sections (each less than 0.1 less than 0.1 micrometers thick) of IDP's. These efforts however, have been stymied because of a lack of a suitable non-carbonaceous embedding medium and the availability of C-free conductive substrates. We have embedded and thin-sectioned IDP's in glassy sulfur, and transferred the thin sections to Be support films approximately 25 nm thick. The sections were then analyzed in a 200 KeV analytical TEM. S sublimes rapidly under vacuum in the TEM, leaving non-embedded sections supported on Be. Apart from quantitative C (and O) analyses, S sectioning dramatically expands the range of analytical measurements that can be performed on a single IDP.

Molecular inference of sources and spreading patterns of Plasmodium falciparum malaria parasites in internally displaced persons settlements in Myanmar-China border area.

PubMed

Lo, Eugenia; Zhou, Guofa; Oo, Winny; Lee, Ming-Chieh; Baum, Elisabeth; Felgner, Philip L; Yang, Zhaoqing; Cui, Liwang; Yan, Guiyun

2015-07-01

In Myanmar, civil unrest and establishment of internally displaced persons (IDP) settlement along the Myanmar-China border have impacted malaria transmission. The growing IDP populations raise deep concerns about health impact on local communities. Microsatellite markers were used to examine the source and spreading patterns of Plasmodium falciparum between IDP settlement and surrounding villages in Myanmar along the China border. Genotypic structure of P. falciparum was compared over the past three years from the same area and the demographic history was inferred to determine the source of recent infections. In addition, we examined if border migration is a factor of P. falciparum infections in China by determining gene flow patterns across borders. Compared to local community, the IDP samples showed a reduced and consistently lower genetic diversity over the past three years. A strong signature of genetic bottleneck was detected in the IDP samples. P. falciparum infections from the border regions in China were genetically similar to Myanmar and parasite gene flow was not constrained by geographical distance. Reduced genetic diversity of P. falciparum suggested intense malaria control within the IDP settlement. Human movement was a key factor to the spread of malaria both locally in Myanmar and across the international border. Copyright © 2015 Elsevier B.V. All rights reserved.

Outward foreign direct investments and home country's economic growth

NASA Astrophysics Data System (ADS)

Ciesielska, Dorota; Kołtuniak, Marcin

2017-09-01

The study examines the time stability of the causality direction and cross-correlations between the home country's economic growth and pace of growth of its outward foreign direct investment (OFDI) stocks within the complex system of the Polish national economy. The research has been performed in order to verify, using both the time and frequency domains time series analyses, if economic agents' long term decisions on outward foreign direct investments, leading to cross-border value chains and production fragmentation processes, are of adaptive or predictive character. Consequently, the aim was to check if the home country's economic growth leads the internationalization processes of domestic enterprises, which stays in line with Dunning's Investment Development Path (IDP) paradigm, or if these complex processes, thanks to entrepreneurs' ability to formulate relevant rational expectations, precede the home country's economic growth, which would be supported with the introduction of the policy on reinforcing the internationalization processes of domestic enterprises. The presence of the unidirectional economic growth-led internationalization, consistent with the IDP concept's base assumptions, has been ascertained by the results of the short term Granger causality tests. Nevertheless, the results of the wavelet analyses, supported with the results of the econometric block exogeneity long term causality Wald tests, have revealed that in the long term the OFDI stocks' growth permanently precedes the home country's economic growth, which stays in the unequivocal contrast with the IDP paradigm's premises, as well as with the indicated above short term Granger causality tests' outcomes and indicates that economic agents' choices are not strictly of adaptive but also of predictive character, which influences the current state of knowledge on economic complex systems' characteristics. Such a result is of a great importance in the light of the existence of the significant and still unexploited internationalization potential of Polish enterprises.

Inclusion of climate change strategies in municipal Integrated Development Plans: A case from seven municipalities in Limpopo Province, South Africa

PubMed Central

2016-01-01

The Intergovernmental Panel on Climate Change (IPCC) has made it clear that anthropogenic greenhouse gasses are the main cause of observed global warming that leads to climate change. Climate change is now a global reality. In the South African political set-up, local municipalities are the structures that are in direct contact with communities and they draw up Integrated Development Plans (IDPs), which are reviewed and upgraded annually. The article seeks to investigate the extent to which climate change adaptation and mitigation strategies are embedded IDPs in seven vulnerable municipalities in the Limpopo Province. The article conducted an in-depth content analysis of the IDPs of the seven municipalities and the results have revealed that these municipalities have not included adaptation and mitigation strategies adequately in their IDPs despite being the most vulnerable municipalities in the province. The article concludes that these municipalities have not as yet institutionalised climate change in their daily operations, planning and decision making. To this end, the paper recommends that local municipalities should include climate change adaptation and mitigation strategies in their IDPs.

Phosphorylation of the IDP KID Modulates Affinity for KIX by Increasing the Lifetime of the Complex.

PubMed

Dahal, Liza; Shammas, Sarah L; Clarke, Jane

2017-12-19

Intrinsically disordered proteins (IDPs) are known to undergo a range of posttranslational modifications, but by what mechanism do such modifications affect the binding of an IDP to its partner protein? We investigate this question using one such IDP, the kinase inducible domain (KID) of the transcription factor CREB, which interacts with the KIX domain of CREB-binding protein upon phosphorylation. As with many other IDPs, KID undergoes coupled folding and binding to form α-helical structure upon interacting with KIX. This single site phosphorylation plays an important role in the control of transcriptional activation in vivo. Here we show that, contrary to expectation, phosphorylation has no effect on association rates-unphosphorylated KID binds just as rapidly as pKID, the phosphorylated form-but rather, acts by increasing the lifetime of the complex. We propose that by controlling the lifetime of the bound complex of pKID:KIX via altering the dissociation rate, phosphorylation can facilitate effective control of transcription regulation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

New Manganese Silicide Mineral Phase in an Interplanetary Dust Particle

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Keller, L. P.; Clemett, S. J.; Jones, J. H.; Palma, R. L.; Pepin, R. O.; Kloeck, W.; Zolensky, M. E.; Messenger, S.

2008-01-01

Comet 26P/Grigg-Skjellerup was identified as a source of an Earth-crossing dust stream with low Earth-encounter velocities, with peak anticipated fluxes during April in 2003 and 2004 [1]. In response to this prediction, NASA performed dedicated stratospheric dust collections using high altitude aircraft to target potential interplanetary dust particles (IDPs) from this comet stream in April 2003. Several IDPs from this collection have shown unusually low noble gas abundances [2] consistent with the predicted short space exposure ages of Grigg-Skjellerup dust particles [1]. High abundances of large D enrichments [3] and presolar grains [4] in IDPs from this collection are also consistent with an origin from the comet Grigg-Skjellerup. Here we report a new mineral from one of the cluster IDPs of the "Grigg-Skjellerup" collection, L2055. Our report focuses on an unusual manganese-iron-chromium silicide phase that, to our knowledge, has not been observed previously in nature. This unique phase may also shed light on the genesis of the enigmatic low-Fe,Mn-enriched (LIME) olivine that has been previously reported in IDPs and meteorites [5].

Delivery of Exogenous Complex Organic Compounds by Solar System Small Bodies and Space Dusts and Its Relevance to Origins of Life

NASA Astrophysics Data System (ADS)

Kobayashi, Kensei; Fushimi, Hidehiko; Motoyama, Takuya; Kaneko, Takeo; Obayashi, Yumiko; Yoshida, Satoshi; Mita, Hajime; Yabuta, Hikaru; Okudaira, Kyoko; Hashimoto, Hirofumi; Yokobori, Shin-Ichi; Yamagishi, Akihiko

A wide variety of organic compounds including amino acid precursors have been detected in such extraterrestrial bodies as carbonaceous chondrites and comets. It was suggested that these organics were formed in quite cold environments. We irradiated frozen mixtures of possible constituents of ice mantles of interstellar dust particles including water, methanol and ammonia with high-energy heavy ions from HIMAC, National Institute of Radiological Science, Japan. Amino acid precursors with complex structures were detected whose molecular weights are up to a few thousands. Such complex amino acid precursors are much stronger than free amino acids against radiation. Such organics could have been incorporated in solar system small bodies after the formation of the solar system and delivered to the primitive Earth. Possible carriers of such organics are meteorites, comets and interplanetary dust particles (IDPs) that were formed from comets and meteorites. It is suggested that IDPs brought much more organics than meteorites and comets. However, nature of organics in IDPs is little known, since they have been collected only in terrestrial biosphere. We are planning a space experiments named Tanpopo, where IDPs would be collected in aerogel equipped on the Exposure Facility of the International Space Station. In addition, amino acids and their relating compounds would be exposed to space environments to see their possible alteration processes in the interplanetary space. We will report some preliminary results for the preparation of the mission including the capture of amino acid-containing particles at high velocity with ultra-low density aerogel.

Native Hydrophobic Binding Interactions at the Transition State for Association between the TAZ1 Domain of CBP and the Disordered TAD-STAT2 Are Not a Requirement.

PubMed

Lindström, Ida; Dogan, Jakob

2017-08-15

A significant fraction of the eukaryotic proteome consists of proteins that are either partially or completely disordered under native-like conditions. Intrinsically disordered proteins (IDPs) are common in protein-protein interactions and are involved in numerous cellular processes. Although many proteins have been identified as disordered, much less is known about the binding mechanisms of the coupled binding and folding reactions involving IDPs. Here we have analyzed the rate-limiting transition state for binding between the TAZ1 domain of CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2) by site-directed mutagenesis and kinetic experiments (Φ-value analysis) and found that the native protein-protein binding interface is not formed at the transition state for binding. Instead, native hydrophobic binding interactions form late, after the rate-limiting barrier has been crossed. The association rate constant in the absence of electrostatic enhancement was determined to be rather high. This is consistent with the Φ-value analysis, which showed that there are few or no obligatory native contacts. Also, linear free energy relationships clearly demonstrate that native interactions are cooperatively formed, a scenario that has usually been observed for proteins that fold according to the so-called nucleation-condensation mechanism. Thus, native hydrophobic binding interactions at the rate-limiting transition state for association between TAD-STAT2 and TAZ1 are not a requirement, which is generally in agreement with previous findings on other IDP systems and might be a common mechanism for IDPs.

The spectral properties of interplanetary dust particles

NASA Technical Reports Server (NTRS)

Sandford, Scott A.

1988-01-01

The observed spectral and mineralogical properties of interplanetary dust particles (IDP) allows the conclusion that: (1) the majority of IDP infrared spectra are dominated by olivine, pyroxene, or layer lattice silicate minerals, (2) to the first order the emission spectra of comets Halley and Kohoutek can be matched by mixtures of these IDP infrared types, implying that comets contain mixtures of these different crystalline silicates and may vary from comet to comet and perhaps even within a single comet, (3) do not expect to observe a single 20 micron feature in cometary spectra, (4) carbonaceous materials dominate the visible spectra properties of the IDPs even though the mass in these particles consists primarily of silicates, and (5) the particle characteristics summarized need to be properly accounted for in future cometary emission models.

Nebular and Interstellar Materials in a Giant Cluster IDP of Probable Cometary Origin

NASA Technical Reports Server (NTRS)

Messenger, S.; Brownlee, D. E.; Joswiak, D. J.; Nguyen, A. N.

2015-01-01

Comets contain a complex mixture of materials with presolar and Solar System origins. Chondritic porous interplanetary dust particles (CP-IDPs) are associated with comets by their fragile nature, unequilibrated anhydrous mineralogy and high abundances of circumstellar grains and isotopically anomalous organic materials. Comet 81P/Wild 2 samples returned by the Stardust spacecraft contain presolar materials as well as refractory 16O-rich Ca-Al-rich inclusion- (CAI), chondrule-, and AOA-like materials. We are conducting coordinated chemical, mineralogical, and isotopic studies of a giant cluster CP-IDP (U2-20-GCA) to determine the proportions of inner Solar System and interstellar materials. We previously found that this IDP contains abundant presolar silicates (approx. 1,800 ppm) and 15N-rich hotspots [6].

Analysis of organic grain coatings in primitive interplanetary dust particles: Implications for the origin of Solar System organic matter

NASA Astrophysics Data System (ADS)

Flynn, George

Analysis of organic grain coatings in primitive interplanetary dust particles: Implications for the origin of Solar System organic matter Chondritic, porous interplanetary dust particles (CP IDPs), the most primitive samples of extraterrestrial material available for laboratory analysis [1], are unequilibrated aggregates of mostly submicron, anhydrous grains of a diverse mineralogy. They contain organic matter not produced by parent body aqueous processing [2], some carrying H and N isotopic anomalies consistent with molecular cloud or outer Solar System material [3]. Scanning Transmission X-Ray Microscope (STXM) imaging at the C K-edge shows the individual grains in 10 micron aggregate CP IDPs are coated by a layer of carbonaceous material 100 nm thick. This structure implies a three-step formation sequence. First, individual grains condensed from the cooling nebular gas. Then complex, refractory organic molecules covered the surfaces of the grains either by deposition, formation in-situ, or a combination of both processes. Finally, the grains collided and stuck together forming the first dust-size material in the Solar System. Ultramicrotome sections, 70 to 100 nm thick were cut from several CP IDPs, embedded in elemental S to avoid exposure to C-based embedding media. X-ray Absorption Near Edge Structure (XANES) spectra were derived from image stacks obtained using a STXM. "Cluster analysis" was used to compare the C-XANES spectra from each of the pixels in an image stack and identify pixels exhibiting similar spectra. When applied to a CP IDP, cluster analysis identifies most carbonaceous grain coatings in a particle as having similar C-XANES spectra. Two processes are commonly suggested in the literature for production of organic grain coatings. The similarity in thickness and C-XANES spectra of the coatings on different minerals in the same IDP indicates the first, mineral specific catalysis, was not the process that produced these organic rims. Our results are consistent with this primitive organic matter being produced by the alternative process of condensation of C-bearing ices onto the grain surfaces and production of refractory organic matter by UV or other ionizing radiation bombardment of the ices [4]. The processes by which primitive grains aggregate to form the first dust of our Solar System are not well understood. Collision experiments indicate that bare rocky grains bounce apart at collision speeds ¡30 to 50 m/s and shatter at larger speeds [5]. However, experiments indicate grains coated with organic matter stick quite easily, even at speeds up to 5 m/s -an order of magnitude higher than the speed at which silicate grains accrete [6]. Thus the organic grain coatings we identified likely played a critical role in dust aggregation in the early Solar System. References: [1] Ishii, H. et al. Science 2009. [2] Flynn, G. J. et al. (2003) Geochim. Cosmochim. Acta, 67, 4791-4806. [3] Keller L. P. et al. GCA (2004) Geochim. Cosmochim. Acta, 68, 2577-2589. [4] Bernstein, M. P. et al. (1995) Astrophys. J., 454, 327-344. [5] Hartmann, W. K. (1978) Icarus, 33, 50-61. [6] Kudo, T. et al. (2002) Meteoritics Planet. Sci., 37, 1975-1983.

Results of the Excreta Bioassay Quality Control Program for April 1, 2009 through March 31, 2010

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

Antonio, Cheryl L.

2012-07-19

A total of 58 urine samples and 10 fecal samples were submitted during the report period (April 1, 2009 through March 31, 2010) to General Engineering Laboratories, South Carolina by the Hanford Internal Dosimetry Program (IDP) to check the accuracy, precision, and detection levels of their analyses. Urine analyses for Sr, 238Pu, 239Pu, 241Am, 243Am 235U, 238U, elemental uranium and fecal analyses for 241Am, 238Pu and 239Pu were tested this year as well as four tissue samples for 238Pu, 239Pu, 241Am and 241Pu. The number of QC urine samples submitted during the report period represented 1.3% of the total samplesmore » submitted. In addition to the samples provided by IDP, GEL was also required to conduct their own QC program, and submit the results of analyses to IDP. About 33% of the analyses processed by GEL during the third year of this contract were quality control samples. GEL tested the performance of 21 radioisotopes, all of which met or exceeded the specifications in the Statement of Work within statistical uncertainty (Table 4).« less

Results of The Excreta Bioassay Quality Control Program For April 1, 2010 Through March 31, 2011

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

Antonio, Cheryl L.

2012-07-19

A total of 76 urine samples and 10 spiked fecal samples were submitted during the report period (April 1, 2010 through March 31, 2011) to GEL Laboratories, LLC in South Carolina by the Hanford Internal Dosimetry Program (IDP) to check the accuracy, precision, and detection levels of their analyses. Urine analyses for 14C, Sr, for 238Pu, 239Pu, 241Am, 243Am, 235U, 238U, 238U-mass and fecal analyses for 241Am, 238Pu and 239Pu were tested this year. The number of QC urine samples submitted during the report period represented 1.1% of the total samples submitted. In addition to the samples provided by IDP,more » GEL was also required to conduct their own QC program, and submit the results of analyses to IDP. About 31% of the analyses processed by GEL during the first year of contract 112512 were quality control samples. GEL tested the performance of 23 radioisotopes, all of which met or exceeded the specifications in the Statement of Work within statistical uncertainty except the slightly elevated relative bias for 243,244Cm (Table 4).« less

TERENA eScience PKI

NASA Astrophysics Data System (ADS)

Sova, Milan

Several National Research and Education Networks associated in TERENA have joined their efforts to build a shared PKI able to serve potentially millions of users from their constituency. The TCS eScience Personal CA takes advantage of national identity federations to facilitate user identity vetting and enrollment procedures. The system uses identity management systems (IdMS) at participating institutions to perform the functions of registration authorities. The certificate enrollment application acts as a SAML Service Provider relying on information provided by IdMS performing as SAML Identity Providers (IdP). When applying for a personal certificate, users authenticate at their home IdP using credentials they normally use to access local services. The IdP controls the certificate issuance process by releasing SAML attributes specifying the user's eligibility for the service and the information to be included in the certificate such as the user's name and email address. The TCS eScience Personal CA is part of the TERENA Certificate Service that uses a commercial PKI provider. Outsourcing the actual CA machinery to a specialized company results in professional-level services such as CRL and OCSP management. The paper describes the legal, organizational and technical aspects of the TCS eScience PKI.

On the Origin of GEMS

NASA Technical Reports Server (NTRS)

Keller, L. P.; Messenger, S.

2004-01-01

GEMS (glass with embedded metal and sulfides) are a major component of anhydrous interplanetary dust particles (IDPs) their physical and chemical characteristics show marked similarities to contemporary interstellar dust. Recent oxygen isotopic measurements confirm that at least a small fraction (less than 5%) of GEMS are demonstrably presolar, while the remainder have ratios that are indistinguishable from solar values. GEMS with solar oxygen isotopic compositions either (1) had their isotopic compositions homogenized through processing in the interstellar medium (ISM), or (2) formed in the early solar system. Isotopic homogenization necessarily implies chemical homogenization, so (interstellar) GEMS compositions should reflect the average composition of dust in the local ISM. We performed a systematic examination of the bulk chemistry of GEMS in primitive IDPs in order to test this hypothesis.

Summer 2006 war on Lebanon: a lesson in community resilience.

PubMed

Nuwayhid, Iman; Zurayk, Huda; Yamout, Rouham; Cortas, Chadi S

2011-01-01

The internally displaced persons (IDPs) during the July 2006 war in Lebanon exhibited a high level of community resilience, affirmed by relief agencies and public health professionals. Data from personal observations, interviews, meetings and published material were used to examine factors contributing to this resilience. Findings suggested that community resilience is a process rather than an outcome. The sense of a collective identity, prior experience with wars and social support networks have contributed to building up IDP's resilience over time, while community cohesiveness, adequate public health interventions, social solidarity and a connected political leadership helped to sustain it during and shortly after the war. This paper examines implications for public health professionals and argues for a paradigm shift in disaster relief practice.

Acid dissolution experiments - Carbonates and the 6.8-micrometer bands in interplanetary dust particles

NASA Technical Reports Server (NTRS)

Sandford, S. A.

1986-01-01

A chemical dissolution experiment on an interplanetary dust particle (IDP) showed that carbonates, not acid-insoluble organic compounds, were responsible for virtually all the absorption at 6.8 micrometers seen in the infrared spectra of this particle. The IDP examined had an infrared spectrum characteristic of layer-lattice silicates and belongs to a class of IDP's whose spectra resemble those of protostellar objects like W33 A, which also exhibit a band at 6.8 micrometers.

Discovery of nuclear tracks in interplanetary dust

NASA Technical Reports Server (NTRS)

Bradley, J. P.; Brownlee, D. E.; Fraundorf, P.

1984-01-01

Nuclear tracks have been identified in interplanetary dust particles (IDP's) collected from the stratosphere. The presence of tracks unambiguously confirms the extraterrestrial nature of IDP's, and the high track densities (10 to the 10th to 10 to the 11th per square centimeter) suggest an exposure age of approximately 10,000 years within the inner solar system. Tracks also provide an upper temperature limit for the heating of IDP's during atmospheric entry, thereby making it possible to distinguish between pristine and thermally modified micrometeorites.

Nitrogen in Interplanetary Dust Particles

NASA Astrophysics Data System (ADS)

Keller, L. P.; Thomas, K. L.; Bradley, J. P.; McKay, D. S.

1995-09-01

Little is known about the abundance, distribution and chemical state of nitrogen in IDPs with the exceptions of the isotopic enrichment in 15N displayed by many particles [1-3], and the inferred association of nitrogen with polyaromatic hydrocarbons in some IDPs [4]. Like carbon, nitrogen is strongly fractionated among meteoritic materials and it is well known that the most primitive carbon-rich meteorites also tend to have high nitrogen abundances [5]. Nitrogen-bearing compounds are also a significant component of the carbonaceous material (CHON particles) sampled during the comet Halley encounter [e.g. 6]. We describe here the first reported detection and location of nitrogen concentrations in several IDPs using electron energy-loss spectroscopy. Three chondritic, anhydrous IDPs (L2011R11, L2008F13, and a fragment from L2006, cluster 14) were embedded in sulfur [7] and tranmission electron microscope (TEM) specimens were prepared by ultramicrotomy. The IDP thin sections were placed on copper TEM grids with SiO thin film substrates and analyzed using a JEOL 2010 TEM equipped with a thin-window energy-dispersive X-ray detector and a Gatan 666 parallel EELS spectrometer. We also analyzed W7027H14, a carbon-rich, chondritic-porous IDP that was embedded in epoxy. The EELS data from carbon-rich amorphous regions of the analyzed IDPs typically show a small, but distinct nitrogen edge at ~400 eV (Figure 1). The nitrogen is not homogeneously distributed in the carbonaceous material in the four IDPs analyzed to date, but occurs in "hot spots". However, these "hot spots" do not appear to be associated with a distinct N-bearing mineral (e.g. nitrides); the nitrogen is indigenous to the carbonaceous material in these IDPs. Although the quantitative N analyses using EELS are still in progress, the preliminary data from one IDP (L2011R11) indicates an upper N/C atom ratio of ~0.1, which is comparable to the chondritic value (N/C ~0.08, [8]). It should be noted however, that the SEM/EDX analysis of L2011R11 shows that it has a bulk C abundance of ~9 wt.% (nearly 3X the CI abundance), which indicates that, for this particle, the absolute N abundance is also enriched above CI levels. EELS is well-suited for this analysis because of its sensitivity for light element detection and quantification, and also for the additional data on bonding environment that can be deduced from the near-edge structure. References: [1] Stadermann F. J. et al. (1989) Meteoritics, 24, 327. [2] Stadermann F. J. et al. (1990) LPS XXI, 1190. [3] Messenger S. et al., this volume. [4] Clemett S. J. et al. (1993) Science, 262, 721. [5] Kerridge J. F. (1985) GCA, 49, 1707. [6] Fomenkova M. N. et al. (1994) GCA, 58, 4503. [7] Bradley J. P. et al. (1993) LPS XXIV, 173. [8] Anders E. and Grevesse N. (1989) GCA, 53, 197. FIGURE 1. Electron energy-loss data from carbonaceous material in L2011R11 (a pyroxene-rich, anhydrous IDP) showing detectable nitrogen associated with carbon. The lower spectrum is a 2nd difference spectrum of the raw data.

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

Riback, Joshua A.; Bowman, Micayla A.; Zmyslowski, Adam M.

A substantial fraction of the proteome is intrinsically disordered, and even well-folded proteins adopt non-native geometries during synthesis, folding, transport, and turnover. Characterization of intrinsically disordered proteins (IDPs) is challenging, in part because of a lack of accurate physical models and the difficulty of interpreting experimental results. We have developed a general method to extract the dimensions and solvent quality (self-interactions) of IDPs from a single small-angle x-ray scattering measurement. We applied this procedure to a variety of IDPs and found that even IDPs with low net charge and high hydrophobicity remain highly expanded in water, contrary to the generalmore » expectation that protein-like sequences collapse in water. Our results suggest that the unfolded state of most foldable sequences is expanded; we conjecture that this property was selected by evolution to minimize misfolding and aggregation.« less

MFIB: a repository of protein complexes with mutual folding induced by binding.

PubMed

Fichó, Erzsébet; Reményi, István; Simon, István; Mészáros, Bálint

2017-11-15

It is commonplace that intrinsically disordered proteins (IDPs) are involved in crucial interactions in the living cell. However, the study of protein complexes formed exclusively by IDPs is hindered by the lack of data and such analyses remain sporadic. Systematic studies benefited other types of protein-protein interactions paving a way from basic science to therapeutics; yet these efforts require reliable datasets that are currently lacking for synergistically folding complexes of IDPs. Here we present the Mutual Folding Induced by Binding (MFIB) database, the first systematic collection of complexes formed exclusively by IDPs. MFIB contains an order of magnitude more data than any dataset used in corresponding studies and offers a wide coverage of known IDP complexes in terms of flexibility, oligomeric composition and protein function from all domains of life. The included complexes are grouped using a hierarchical classification and are complemented with structural and functional annotations. MFIB is backed by a firm development team and infrastructure, and together with possible future community collaboration it will provide the cornerstone for structural and functional studies of IDP complexes. MFIB is freely accessible at http://mfib.enzim.ttk.mta.hu/. The MFIB application is hosted by Apache web server and was implemented in PHP. To enrich querying features and to enhance backend performance a MySQL database was also created. simon.istvan@ttk.mta.hu, meszaros.balint@ttk.mta.hu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Discrete Molecular Dynamics Can Predict Helical Prestructured Motifs in Disordered Proteins

PubMed Central

Han, Kyou-Hoon; Dokholyan, Nikolay V.; Tompa, Péter; Kalmár, Lajos; Hegedűs, Tamás

2014-01-01

Intrinsically disordered proteins (IDPs) lack a stable tertiary structure, but their short binding regions termed Pre-Structured Motifs (PreSMo) can form transient secondary structure elements in solution. Although disordered proteins are crucial in many biological processes and designing strategies to modulate their function is highly important, both experimental and computational tools to describe their conformational ensembles and the initial steps of folding are sparse. Here we report that discrete molecular dynamics (DMD) simulations combined with replica exchange (RX) method efficiently samples the conformational space and detects regions populating α-helical conformational states in disordered protein regions. While the available computational methods predict secondary structural propensities in IDPs based on the observation of protein-protein interactions, our ab initio method rests on physical principles of protein folding and dynamics. We show that RX-DMD predicts α-PreSMos with high confidence confirmed by comparison to experimental NMR data. Moreover, the method also can dissect α-PreSMos in close vicinity to each other and indicate helix stability. Importantly, simulations with disordered regions forming helices in X-ray structures of complexes indicate that a preformed helix is frequently the binding element itself, while in other cases it may have a role in initiating the binding process. Our results indicate that RX-DMD provides a breakthrough in the structural and dynamical characterization of disordered proteins by generating the structural ensembles of IDPs even when experimental data are not available. PMID:24763499

Conformational transition of κ-casein in micellar environment: Insight from the tryptophan fluorescence

NASA Astrophysics Data System (ADS)

Mishra, Smruti; Meher, Geetanjali; Chakraborty, Hirak

2017-11-01

Intrinsically disordered proteins (IDPs) are under intense analysis due to their structural flexibility and importance in biological functions. Minuscule modulation in the microenvironment induces significant conformational changes in IDPs, and these non-native conformations of the IDPs often induce aggregation and cause cell death. Changes in the membrane composition often change the microenvironment, which promote conformational change and aggregation of IDPs. κ-Casein, an important milk protein, belongs to the class of IDPs containing net negative charges. In this present work, we have studied the interaction of κ-casein with cetyltrimethyl ammonium bromide (CTAB), a positively charged surfactant, utilizing various steady state fluorescence, time-resolved fluorescence and circular dichroism spectroscopy. Our results clearly indicate that κ-casein undergoes at least two conformational transitions in presence of various concentrations of CTAB. The intrinsically disordered κ-casein assumes a partially folded conformation at lower concentration of CTAB, which adopts an unstructured conformation at higher concentration of CTAB. The partially folded conformation of κ-casein at a lower CTAB concentration might be induced by the favorable electrostatic interaction between the positively charged surfactant headgroup and net negative charges of the protein, whereas surfactant nature of CTAB is being pronounced at higher concentration of CTAB.

Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations.

PubMed

Bernetti, Mattia; Masetti, Matteo; Pietrucci, Fabio; Blackledge, Martin; Jensen, Malene Ringkjobing; Recanatini, Maurizio; Mollica, Luca; Cavalli, Andrea

2017-10-19

Intrinsically disordered proteins (IDPs) are emerging as an important class of the proteome. Being able to interact with different molecular targets, they participate in many physiological and pathological activities. However, due to their intrinsically heterogeneous nature, determining the equilibrium properties of IDPs is still a challenge for biophysics. Herein, we applied state-of-the-art enhanced sampling methods to Sev N TAIL , a test case of IDPs, and constructed a bin-based kinetic model to unveil the underlying kinetics. To validate our simulation strategy, we compared the predicted NMR properties against available experimental data. Our simulations reveal a rough free-energy surface comprising multiple local minima, which are separated by low energy barriers. Moreover, we identified interconversion rates between the main kinetic states, which lie in the sub-μs time scales, as suggested in previous works for Sev N TAIL . Therefore, the emerging picture is in agreement with the atomic-level properties possessed by the free IDP in solution. By providing both a thermodynamic and kinetic characterization of this IDP test case, our study demonstrates how computational methods can be effective tools for studying this challenging class of proteins.

The Syrian public health and humanitarian crisis: A 'displacement' in global governance?

PubMed

Akbarzada, Sumaira; Mackey, Tim K

2018-07-01

Ongoing failure by the international community to resolve the Syrian conflict has led to destruction of critical infrastructure. This includes the collapse of the Syrian health system, leaving millions of internally displaced persons (IDPs) in urgent need of healthcare services. As the conflict intensifies, IDP populations are suffering from infectious and non-communicable disease risks, poor maternal and child health outcomes, trauma, and mental health issues, while healthcare workers continually exit the country. Healthcare workers who remain face significant challenges, including systematic attacks on healthcare facilities and conditions that severely inhibit healthcare delivery and assistance. Within this conflict-driven public health crisis, the most susceptible population is arguably the IDP. Though the fundamental 'right to health' is a recognised international legal principle, its application is inadequate due to limited recognition by the UN Security Council and stymied global governance by the broader international community. These factors have also negatively impacted other vulnerable groups other than IDPs, such as refugees and ethnic minorities, who may or may not be displaced. Hence, this article reviews the current Syrian conflict, assesses challenges with local and global governance for IDPs, and explores potential governance solutions needed to address this health and humanitarian crisis.

Proteins without unique 3D structures: biotechnological applications of intrinsically unstable/disordered proteins.

PubMed

Uversky, Vladimir N

2015-03-01

Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins or regions that do not have unique 3D structures under functional conditions. Therefore, from the viewpoint of their lack of stable 3D structure, IDPs/IDPRs are inherently unstable. As much as structure and function of normal ordered globular proteins are determined by their amino acid sequences, the lack of unique 3D structure in IDPs/IDPRs and their disorder-based functionality are also encoded in the amino acid sequences. Because of their specific sequence features and distinctive conformational behavior, these intrinsically unstable proteins or regions have several applications in biotechnology. This review introduces some of the most characteristic features of IDPs/IDPRs (such as peculiarities of amino acid sequences of these proteins and regions, their major structural features, and peculiar responses to changes in their environment) and describes how these features can be used in the biotechnology, for example for the proteome-wide analysis of the abundance of extended IDPs, for recombinant protein isolation and purification, as polypeptide nanoparticles for drug delivery, as solubilization tools, and as thermally sensitive carriers of active peptides and proteins. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamical Coupling of Intrinsically Disordered Proteins and Their Hydration Water: Comparison with Folded Soluble and Membrane Proteins

PubMed Central

Gallat, F.-X.; Laganowsky, A.; Wood, K.; Gabel, F.; van Eijck, L.; Wuttke, J.; Moulin, M.; Härtlein, M.; Eisenberg, D.; Colletier, J.-P.; Zaccai, G.; Weik, M.

2012-01-01

Hydration water is vital for various macromolecular biological activities, such as specific ligand recognition, enzyme activity, response to receptor binding, and energy transduction. Without hydration water, proteins would not fold correctly and would lack the conformational flexibility that animates their three-dimensional structures. Motions in globular, soluble proteins are thought to be governed to a certain extent by hydration-water dynamics, yet it is not known whether this relationship holds true for other protein classes in general and whether, in turn, the structural nature of a protein also influences water motions. Here, we provide insight into the coupling between hydration-water dynamics and atomic motions in intrinsically disordered proteins (IDP), a largely unexplored class of proteins that, in contrast to folded proteins, lack a well-defined three-dimensional structure. We investigated the human IDP tau, which is involved in the pathogenic processes accompanying Alzheimer disease. Combining neutron scattering and protein perdeuteration, we found similar atomic mean-square displacements over a large temperature range for the tau protein and its hydration water, indicating intimate coupling between them. This is in contrast to the behavior of folded proteins of similar molecular weight, such as the globular, soluble maltose-binding protein and the membrane protein bacteriorhodopsin, which display moderate to weak coupling, respectively. The extracted mean square displacements also reveal a greater motional flexibility of IDP compared with globular, folded proteins and more restricted water motions on the IDP surface. The results provide evidence that protein and hydration-water motions mutually affect and shape each other, and that there is a gradient of coupling across different protein classes that may play a functional role in macromolecular activity in a cellular context. PMID:22828339

Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein

PubMed Central

Wang, Yong; Chu, Xiakun; Longhi, Sonia; Roche, Philippe; Han, Wei; Wang, Erkang; Wang, Jin

2013-01-01

Numerous relatively short regions within intrinsically disordered proteins (IDPs) serve as molecular recognition elements (MoREs). They fold into ordered structures upon binding to their partner molecules. Currently, there is still a lack of in-depth understanding of how coupled binding and folding occurs in MoREs. Here, we quantified the unbound ensembles of the α-MoRE within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein. We developed a multiscaled approach by combining a physics-based and an atomic hybrid model to decipher the mechanism by which the α-MoRE interacts with the X domain of the measles virus phosphoprotein. Our multiscaled approach led to remarkable qualitative and quantitative agreements between the theoretical predictions and experimental results (e.g., chemical shifts). We found that the free α-MoRE rapidly interconverts between multiple discrete partially helical conformations and the unfolded state, in accordance with the experimental observations. We quantified the underlying global folding–binding landscape. This leads to a synergistic mechanism in which the recognition event proceeds via (minor) conformational selection, followed by (major) induced folding. We also provided evidence that the α-MoRE is a compact molten globule-like IDP and behaves as a downhill folder in the induced folding process. We further provided a theoretical explanation for the inherent connections between “downhill folding,” “molten globule,” and “intrinsic disorder” in IDP-related systems. Particularly, we proposed that binding and unbinding of IDPs proceed in a stepwise way through a “kinetic divide-and-conquer” strategy that confers them high specificity without high affinity. PMID:24043820

Insights into the Molecular Mechanisms of Alzheimer's and Parkinson's Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology.

PubMed

Coskuner-Weber, Orkid; Uversky, Vladimir N

2018-01-24

Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer's and Parkinson's disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer's and Parkinson's diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects. Classical molecular dynamics simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β and α-synuclein in relation to the pathologies of Alzheimer's and Parkinson's diseases. Furthermore, there are several natural genetic variations that play a role in the pathogenesis of familial cases of Alzheimer's and Parkinson's diseases, which are related to specific genetic defects inherited in dominant or recessive patterns. The present review summarizes the current understanding of monomeric and oligomeric forms of amyloid-β and α-synuclein, as well as the impacts of artificial and pathological missense mutations on the structural ensembles of these IDPs using molecular dynamics simulations. We also emphasize the recent investigations on residual secondary structure formation in dynamic conformational ensembles of amyloid-β and α-synuclein, such as β-structure linked to the oligomerization and fibrillation mechanisms related to the pathologies of Alzheimer's and Parkinson's diseases. This information represents an important foundation for the successful and efficient drug design studies.

The Effects of Differentiated Instruction on the Literacy Process of Learners with Interrupted Schooling

ERIC Educational Resources Information Center

Niño Santisteban, Liliana

2014-01-01

This research study analyzes the literacy and foreign langauge processes of learners in the "Procesos Básicos" Program. The participants were 15 Spanish-speaking children and young adolescents, whose highest level of education was first grade. Eight of the 15 children were Internally Displaced Persons (IDPs), and the others were affected…

Sequence charge decoration dictates coil-globule transition in intrinsically disordered proteins.

PubMed

Firman, Taylor; Ghosh, Kingshuk

2018-03-28

We present an analytical theory to compute conformations of heteropolymers-applicable to describe disordered proteins-as a function of temperature and charge sequence. The theory describes coil-globule transition for a given protein sequence when temperature is varied and has been benchmarked against the all-atom Monte Carlo simulation (using CAMPARI) of intrinsically disordered proteins (IDPs). In addition, the model quantitatively shows how subtle alterations of charge placement in the primary sequence-while maintaining the same charge composition-can lead to significant changes in conformation, even as drastic as a coil (swelled above a purely random coil) to globule (collapsed below a random coil) and vice versa. The theory provides insights on how to control (enhance or suppress) these changes by tuning the temperature (or solution condition) and charge decoration. As an application, we predict the distribution of conformations (at room temperature) of all naturally occurring IDPs in the DisProt database and notice significant size variation even among IDPs with a similar composition of positive and negative charges. Based on this, we provide a new diagram-of-states delineating the sequence-conformation relation for proteins in the DisProt database. Next, we study the effect of post-translational modification, e.g., phosphorylation, on IDP conformations. Modifications as little as two-site phosphorylation can significantly alter the size of an IDP with everything else being constant (temperature, salt concentration, etc.). However, not all possible modification sites have the same effect on protein conformations; there are certain "hot spots" that can cause maximal change in conformation. The location of these "hot spots" in the parent sequence can readily be identified by using a sequence charge decoration metric originally introduced by Sawle and Ghosh. The ability of our model to predict conformations (both expanded and collapsed states) of IDPs at a high-throughput level can provide valuable insights into the different mechanisms by which phosphorylation/charge mutation controls IDP function.

An exploration of social determinants of health amongst internally displaced persons in northern Uganda

PubMed Central

2009-01-01

Social determinants of health describe the conditions in which people are born, grow, live, work and age and their influence on health. These circumstances are shaped by the distribution of money, power and resources at global, national and local levels, which are themselves influenced by policy choices. Armed conflict and forced displacement are important influences on the social determinants of health. There is limited evidence on the social determinants of health of internally displaced persons (IDPs) who have been forced from their homes due to armed conflict but remain within the borders of their country. The aim of this study was to explore the social determinants of overall physical and mental health of IDPs, including the response strategies used by IDPs to support their health needs. Northern Uganda was chosen as a case-study, and 21 face-to-face semi-structured interviews with IDPs were conducted in fifteen IDP camps between November and December 2006. The findings indicated a number of key social determinants. Experiencing traumatic events could cause "over thinking" which in turn could lead to "madness" and physical ailments. Respondents also attributed "over thinking" to the spirit (cen) of a killed person returning to disturb its killer. Other social determinants included overcrowding which affected physical health and contributed to an emotional sense of loss of freedom; and poverty and loss of land which affected physical health from lack of food and income, and mental health because of worry and uncertainty. Respondents also commented on how the conflict and displacement and led to changes in social and cultural norms such as increased "adultery", "defilement", and "thieving". Response strategies included a combination of biopsychosocial health services, traditional practices, religion, family and friends, and isolating. This study supports work exploring the political, environmental, economic, and socio-cultural determinants of health of IDPs. Addressing these determinants is essential to fundamentally improving the overall physical and mental health of IDPs. PMID:20003516

Results of Automated Retinal Image Analysis for Detection of Diabetic Retinopathy from the Nakuru Study, Kenya.

PubMed

Hansen, Morten B; Abràmoff, Michael D; Folk, James C; Mathenge, Wanjiku; Bastawrous, Andrew; Peto, Tunde

2015-01-01

Digital retinal imaging is an established method of screening for diabetic retinopathy (DR). It has been established that currently about 1% of the world's blind or visually impaired is due to DR. However, the increasing prevalence of diabetes mellitus and DR is creating an increased workload on those with expertise in grading retinal images. Safe and reliable automated analysis of retinal images may support screening services worldwide. This study aimed to compare the Iowa Detection Program (IDP) ability to detect diabetic eye diseases (DED) to human grading carried out at Moorfields Reading Centre on the population of Nakuru Study from Kenya. Retinal images were taken from participants of the Nakuru Eye Disease Study in Kenya in 2007/08 (n = 4,381 participants [NW6 Topcon Digital Retinal Camera]). First, human grading was performed for the presence or absence of DR, and for those with DR this was sub-divided in to referable or non-referable DR. The automated IDP software was deployed to identify those with DR and also to categorize the severity of DR. The primary outcomes were sensitivity, specificity, and positive and negative predictive value of IDP versus the human grader as reference standard. Altogether 3,460 participants were included. 113 had DED, giving a prevalence of 3.3% (95% CI, 2.7-3.9%). Sensitivity of the IDP to detect DED as by the human grading was 91.0% (95% CI, 88.0-93.4%). The IDP ability to detect DED gave an AUC of 0.878 (95% CI 0.850-0.905). It showed a negative predictive value of 98%. The IDP missed no vision threatening retinopathy in any patients and none of the false negative cases met criteria for treatment. In this epidemiological sample, the IDP's grading was comparable to that of human graders'. It therefore might be feasible to consider inclusion into usual epidemiological grading.

Sequence charge decoration dictates coil-globule transition in intrinsically disordered proteins

NASA Astrophysics Data System (ADS)

Firman, Taylor; Ghosh, Kingshuk

2018-03-01

We present an analytical theory to compute conformations of heteropolymers—applicable to describe disordered proteins—as a function of temperature and charge sequence. The theory describes coil-globule transition for a given protein sequence when temperature is varied and has been benchmarked against the all-atom Monte Carlo simulation (using CAMPARI) of intrinsically disordered proteins (IDPs). In addition, the model quantitatively shows how subtle alterations of charge placement in the primary sequence—while maintaining the same charge composition—can lead to significant changes in conformation, even as drastic as a coil (swelled above a purely random coil) to globule (collapsed below a random coil) and vice versa. The theory provides insights on how to control (enhance or suppress) these changes by tuning the temperature (or solution condition) and charge decoration. As an application, we predict the distribution of conformations (at room temperature) of all naturally occurring IDPs in the DisProt database and notice significant size variation even among IDPs with a similar composition of positive and negative charges. Based on this, we provide a new diagram-of-states delineating the sequence-conformation relation for proteins in the DisProt database. Next, we study the effect of post-translational modification, e.g., phosphorylation, on IDP conformations. Modifications as little as two-site phosphorylation can significantly alter the size of an IDP with everything else being constant (temperature, salt concentration, etc.). However, not all possible modification sites have the same effect on protein conformations; there are certain "hot spots" that can cause maximal change in conformation. The location of these "hot spots" in the parent sequence can readily be identified by using a sequence charge decoration metric originally introduced by Sawle and Ghosh. The ability of our model to predict conformations (both expanded and collapsed states) of IDPs at a high-throughput level can provide valuable insights into the different mechanisms by which phosphorylation/charge mutation controls IDP function.

Biomechanical analysis of disc pressure and facet contact force after simulated two-level cervical surgeries (fusion and arthroplasty) and hybrid surgery.

PubMed

Park, Jon; Shin, Jun Jae; Lim, Jesse

2014-12-01

The objective of this study was designed to compare 2-level cervical disc surgery (2-level anterior cervical discectomy and fusion [ACDF] or disc arthroplasty) and hybrid surgery (ACDF/arthroplasty) in terms of postoperative adjacent-level intradiscal pressure (IDP) and facet contact force (FCF). Twenty-four cadaveric cervical spines (C3-T2) were tested in various modes, including extension, flexion, and bilateral axial rotation, to compare adjacent-level IDP and FCF after specified treatments as follows: 1) C5-C6 arthroplasty using ProDisc-C (Synthes Spine, West Chester, Pennsylvania, USA) and C6-C7 ACDF, 2) C5-C6 ACDF and C6-C7 arthroplasty using ProDisc-C, 3) 2-level C5-C6/C6-C7 disc arthroplasties, and 4) 2-level C5-C6/C6-C7 ACDF. IDPs were recorded at anterior, central, and posterior disc portions. After 2-level cervical arthrodesis (ACDF), IDP increased significantly at the anterior annulus of distal adjacent-level disc during flexion and axial rotation and at the center of proximal adjacent-level disc during flexion. In contrast, after cervical specified treatments, including disc arthroplasty (2-level disc arthroplasties and hybrid surgery), IDP decreased significantly at the anterior annulus of distal adjacent-level disc during flexion and extension and was unchanged at the center of proximal adjacent-level disc during flexion. Two-level cervical arthrodesis also tended to adversely impact facet loads, increasing distal rather than proximal adjacent-level FCF. Both hybrid surgery and 2-level arthroplasties seem to offer significant advantages over 2-level arthrodesis by reducing IDP at adjacent levels and approximating FCF of an intact spine. These findings suggest that cervical arthroplasties and hybrid surgery are an alternative to reduce IDP and facet loads at adjacent levels. Copyright © 2014 Elsevier Inc. All rights reserved.

Cometary dust in Antarctic ice and snow: Past and present chondritic porous micrometeorites preserved on the Earth's surface

NASA Astrophysics Data System (ADS)

Noguchi, Takaaki; Ohashi, Noriaki; Tsujimoto, Shinichi; Mitsunari, Takuya; Bradley, John P.; Nakamura, Tomoki; Toh, Shoichi; Stephan, Thomas; Iwata, Naoyoshi; Imae, Naoya

2015-01-01

Chondritic porous interplanetary dust particles (CP IDPs) collected in the stratosphere are regarded as possibly being cometary dust, and are therefore the most primitive solar system material that is currently available for analysis in laboratories. In this paper we report the discovery of more than 40 chondritic porous micrometeorites (CP MMs) in the surface snow and blue ice of Antarctica, which are indistinguishable from CP IDPs. The CP MMs are botryoidal aggregates, composed mainly of sub-micrometer-sized constituents. They contain two components that characterize them as CP IDPs: enstatite whiskers and GEMS (glass with embedded metal and sulfides). Enstatite whiskers appear as <2-μm-long acicular objects that are attached on, or protrude from the surface, and when included in the interior of the CP MMs are composed of a unit-cell scale mixture of clino- and ortho-enstatite, and elongated along the [100] direction. GEMS appear as 100-500 nm spheroidal objects containing <50 nm Fe-Ni metal and Fe sulfide. The CP MMs also contain low-iron-manganese-enriched (LIME) and low-iron-chromium-enriched (LICE) ferromagnesian silicates, kosmochlor (NaCrSi2O6)-rich high-Ca pyroxene, roedderite (K, Na)2Mg5Si12O30, and carbonaceous nanoglobules. These components have previously been discovered in primitive solar system materials such as the CP IDPs, matrices of primitive chondrites, phyllosilicate-rich MMs, ultracarbonaceous MMs, and cometary particles recovered from the 81P/Wild 2 comet. The most outstanding feature of these CP MMs is the presence of kosmochlor-rich high-Ca pyroxene and roedderite, which suggest that they have building blocks in common with CP IDPs and cometary dust particles and therefore suggest a possible cometary origin of both CP MMs and CP IDPs. It is therefore considered that CP MMs are CP IDPs that have fallen to Earth and have survived the terrestrial environment.

The alphabet of intrinsic disorder

PubMed Central

Theillet, Francois-Xavier; Kalmar, Lajos; Tompa, Peter; Han, Kyou-Hoon; Selenko, Philipp; Dunker, A. Keith; Daughdrill, Gary W.; Uversky, Vladimir N

2013-01-01

A significant fraction of every proteome is occupied by biologically active proteins that do not form unique three-dimensional structures. These intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) have essential biological functions and are characterized by extensive structural plasticity. Such structural and functional behavior is encoded in the amino acid sequences of IDPs/IDPRs, which are enriched in disorder-promoting residues and depleted in order-promoting residues. In fact, amino acid residues can be arranged according to their disorder-promoting tendency to form an alphabet of intrinsic disorder that defines the structural complexity and diversity of IDPs/IDPRs. This review is the first in a series of publications dedicated to the roles that different amino acid residues play in defining the phenomenon of protein intrinsic disorder. We start with proline because data suggests that of the 20 common amino acid residues, this one is the most disorder-promoting. PMID:28516008

Biophysical characterization of α-synuclein and its controversial structure

PubMed Central

Alderson, T Reid; Markley, John L

2013-01-01

α-synuclein, a presynaptic protein of poorly defined function, constitutes the main component of Parkinson disease-associated Lewy bodies. Extensive biophysical investigations have provided evidence that isolated α-synuclein is an intrinsically disordered protein (IDP) in vitro. Subsequently serving as a model IDP in numerous studies, α-synuclein has aided in the development of many technologies used to characterize IDPs and arguably represents the most thoroughly analyzed IDP to date. Recent reports, however, have challenged the disordered nature of α-synuclein inside cells and have instead proposed a physiologically relevant helical tetramer. Despite α-synuclein’s rich biophysical history, a single coherent picture has not yet emerged concerning its in vivo structure, dynamics, and physiological role(s). We present herein a review of the biophysical discoveries, developments, and models pertinent to the characterization of α-synuclein’s structure and analysis of the native tetramer controversy. PMID:24634806

Diagnostic value of the near-nerve needle sensory nerve conduction in sensory inflammatory demyelinating polyneuropathy.

PubMed

Odabasi, Zeki; Oh, Shin J

2018-03-01

In this study we report the diagnostic value of the near-nerve needle sensory nerve conduction study (NNN-SNCS) in sensory inflammatory demyelinating polyneuropathy (IDP) in which the routine nerve conduction study was normal or non-diagnostic. The NNN-SNCS was performed to identify demyelination in the plantar nerves in 14 patients and in the median or ulnar nerve in 2 patients with sensory IDP. In 16 patients with sensory IDP, routine NCSs were either normal or non-diagnostic for demyelination. Demyelination was identified by NNN-SNCS by dispersion and/or slow nerve conduction velocity (NCV) below the demyelination marker. Immunotherapy was initiated in 11 patients, 10 of whom improved or remained stable. NNN-SNCS played an essential role in identifying demyelinaton in 16 patients with sensory IDP, leading to proper treatment. Muscle Nerve 57: 414-418, 2018. © 2017 Wiley Periodicals, Inc.

Photographic photometry with Iris diaphragm photometers

NASA Technical Reports Server (NTRS)

Schaefer, B. E.

1981-01-01

A general method is presented for solving problems encountered in the analysis of Iris diaphragm photometer (IDP) data. The method is used to derive the general shape of the calibration curve, allowing both a more accurate fit to the IDP data for comparison stars and extrapolation to magnitude ranges for which no comparison stars are measured. The profile of starlight incident and the characteristic curve of the plate are both assumed and then used to derive the profile of the star image. An IDP reading is then determined for each star image. A procedure for correcting the effects of a nonconstant background fog level on the plate is also demonstrated. Additional applications of the method are made in the appendix to determine the relation between the radius of a photographic star image and the star's magnitude, and to predict the IDP reading of the 'point of optimum density'.

Analysis of the Organic Matter in Interplanetary Dust Particles: Clues to the Organic Matter in Comets, Asteroids, and Interstellar Grains

NASA Technical Reports Server (NTRS)

Flynn, G. J.; Keller, L. P.

2003-01-01

Reflection spectroscopy suggests the C- , P-, and D-types of asteroids contain abundant carbon, but these Vis-nearIR spectra are featureless, providing no information on the type(s) of carbonaceous matter. Infrared spectroscopy demonstrates that organic carbon is a significant component in comets and as grains or grain coatings in the interstellar medium. Most of the interplanetary dust particles (IDPs) recovered from the Earth s stratosphere are believed to be fragments from asteroids or comets, thus characterization of the carbon in IDPs provides the opportunity to determine the type(s) and abundance of organic matter in asteroids and comets. Some IDPs exhibit isotopic excesses of D and N-15, indicating the presence of interstellar material. The characterization of the carbon in these IDPs, and particularly any carbon spatially associated with the isotopic anomalies, provides the opportunity to characterize interstellar organic matter.

Meta-structure correlation in protein space unveils different selection rules for folded and intrinsically disordered proteins.

PubMed

Naranjo, Yandi; Pons, Miquel; Konrat, Robert

2012-01-01

The number of existing protein sequences spans a very small fraction of sequence space. Natural proteins have overcome a strong negative selective pressure to avoid the formation of insoluble aggregates. Stably folded globular proteins and intrinsically disordered proteins (IDPs) use alternative solutions to the aggregation problem. While in globular proteins folding minimizes the access to aggregation prone regions, IDPs on average display large exposed contact areas. Here, we introduce the concept of average meta-structure correlation maps to analyze sequence space. Using this novel conceptual view we show that representative ensembles of folded and ID proteins show distinct characteristics and respond differently to sequence randomization. By studying the way evolutionary constraints act on IDPs to disable a negative function (aggregation) we might gain insight into the mechanisms by which function-enabling information is encoded in IDPs.

Possible prevalence and transmission of acute respiratory tract infections caused by Streptococcus pneumoniae and Haemophilus influenzae among the internally displaced persons in tsunami disaster evacuation camps of Sri Lanka.

PubMed

Watanabe, Hiroshi; Batuwanthudawe, Ranjith; Thevanesam, Vasanthi; Kaji, Chiharu; Qin, Liang; Nishikiori, Nobuyuki; Saito, Wakana; Saito, Mariko; Watanabe, Kiwao; Oishi, Kazunori; Abeysinghe, Nihal; Kunii, Osamu

2007-01-01

The objective of this prospective study was to investigate the status of acute respiratory tract infections caused by Haemophilus influenzae and Streptococcus pneumoniae in tsunami disaster evacuation camps. Nasopharyngeal swabs (NP) of 324 internally displaced persons (IDP) in 3 different tsunami disaster evacuation camps of Sri Lanka were collected between March 18th and 20th, 2005, and analyzed for MIC, beta-lactamase production, serotypes, PCR and pulsed-field gel electrophoresis (PFGE). Many IDP had respiratory symptoms and the prevalence of cough and/or sputum was 84%, 70.5% and 64.7% in the three camps. Twenty-one H. influenzae from 20 IDP and 25 S. pneumoniae from 22 IDP were isolated from the NP. All H. influenzae isolates were nontypeable, and 5 were beta-lactamase producing. Seventeen pneumococci were susceptible, 5 showed intermediate resistance and 3 were fully resistant to penicillin G. Molecular analysis showed the 21 H. influenzae strains had 13 PFGE patterns and 25 pneumococci had 16 PFGE patterns. All 4 different PFGE patterns of H. influenzae strains were detected in a few IDP in camps 1 and 3, and 5 different PFGE patterns of serotype 3, 22A, 9A, 10A and 11A pneumococci were detected in a few IDP in camps 1 and 3. Our data indicate acute respiratory tract infections caused by various types of H. influenzae and S. pneumoniae appear to have been prevalent, some of which were potentially transmitted from person to person in tsunami disaster evacuation camps.

Cell cycle regulation by the intrinsically disordered proteins p21 and p27.

PubMed

Yoon, Mi-Kyung; Mitrea, Diana M; Ou, Li; Kriwacki, Richard W

2012-10-01

Today, it is widely accepted that proteins that lack highly defined globular three-dimensional structures, termed IDPs (intrinsically disordered proteins), play key roles in myriad biological processes. Our understanding of how intrinsic disorder mediates biological function is, however, incomplete. In the present paper, we review disorder-mediated cell cycle regulation by two intrinsically disordered proteins, p21 and p27. A structural adaptation mechanism involving a stretchable dynamic linker helix allows p21 to promiscuously recognize the various Cdk (cyclin-dependent kinase)-cyclin complexes that regulate cell division. Disorder within p27 mediates transmission of an N-terminal tyrosine phosphorylation signal to a C-terminal threonine phosphorylation, constituting a signalling conduit. These mechanisms are mediated by folding upon binding p21/p27's regulatory targets. However, residual disorder within the bound state contributes critically to these functional mechanisms. Our studies provide insights into how intrinsic protein disorder mediates regulatory processes and opportunities for designing drugs that target cancer-associated IDPs.

Dynamics of partially folded and unfolded proteins investigated with quasielastic neutron spectroscopy

NASA Astrophysics Data System (ADS)

Stadler, Andreas M.

2018-05-01

Molecular dynamics in proteins animate and play a vital role for biologically relevant processes of these biomacromolecules. Quasielastic incoherent neutron scattering (QENS) is a well-suited experimental method to study protein dynamics from the picosecond to several nanoseconds and in the Ångström length-scale. In QENS experiments of protein solutions hydrogens act as reporters for the motions of methyl groups or amino acids to which they are bound. Neutron Spin-Echo spectroscopy (NSE) offers the highest energy resolution in the field of neutron spectroscopy and allows the study of slow collective motions in proteins up to several hundred nanoseconds and in the nanometer length-scale. In the following manuscript I will review recent studies that stress the relevance of molecular dynamics for protein folding and for conformational transitions of intrinsically disordered proteins (IDPs). During the folding collapse the protein is exploring its accessible conformational space via molecular motions. A large flexibility of partially folded and unfolded proteins, therefore, is mandatory for rapid protein folding. IDPs are a special case as they are largely unstructured under physiological conditions. A large flexibility is a characteristic property of IDPs as it allows, for example, the interaction with various binding partners or the rapid response to different conditions.

Insomnia in a displaced population is related to war-associated remembered stress.

PubMed

Basishvili, Tamar; Eliozishvili, Marine; Maisuradze, Lia; Lortkipanidze, Nani; Nachkebia, Nargiz; Oniani, Tengiz; Gvilia, Irma; Darchia, Nato

2012-08-01

Although traumatic events are presumed to cause sleep disturbances, particularly insomnia, sleep in populations subjected to forced displacement has received little attention. The present study examined the prevalence of insomnia and associated factors in internally displaced persons (IDPs) from Abkhazia 15 years after displacement to Tbilisi. Detailed subjective information about sleep-wake habits, sleep-related and stress-related parameters were obtained from 87 IDPs categorized into good sleepers and insomniacs. The Insomnia Severity Index, Perceived Stress Scale and Beck Depression Inventory were administered. The incidence of insomnia was 41.4%. The majority of insomniacs strongly believed that war-related stress accounted for the onset of their insomnia. Stepwise regression (95% confidence interval) revealed four variables significantly associated with insomnia status: self-estimated influence of war related stress (odds ratio (OR) = 2.51), frequency of nightmares (OR = 1.6), Perceived Stress Scale score (OR = 1.14) and Beck Depression Inventory score (OR = 1.12). Insomnia in IDPs was strongly related to war-associated remembered stress. ‛Over thinking' about major stress exposure enhanced IDPs' vulnerability to insomnia. These findings have implications for the management of insomnia and associated impairment of daytime functioning in IDPs. Copyright © 2011 John Wiley & Sons, Ltd.

DIBS: a repository of disordered binding sites mediating interactions with ordered proteins.

PubMed

Schad, Eva; Fichó, Erzsébet; Pancsa, Rita; Simon, István; Dosztányi, Zsuzsanna; Mészáros, Bálint

2018-02-01

Intrinsically Disordered Proteins (IDPs) mediate crucial protein-protein interactions, most notably in signaling and regulation. As their importance is increasingly recognized, the detailed analyses of specific IDP interactions opened up new opportunities for therapeutic targeting. Yet, large scale information about IDP-mediated interactions in structural and functional details are lacking, hindering the understanding of the mechanisms underlying this distinct binding mode. Here, we present DIBS, the first comprehensive, curated collection of complexes between IDPs and ordered proteins. DIBS not only describes by far the highest number of cases, it also provides the dissociation constants of their interactions, as well as the description of potential post-translational modifications modulating the binding strength and linear motifs involved in the binding. Together with the wide range of structural and functional annotations, DIBS will provide the cornerstone for structural and functional studies of IDP complexes. DIBS is freely accessible at http://dibs.enzim.ttk.mta.hu/. The DIBS application is hosted by Apache web server and was implemented in PHP. To enrich querying features and to enhance backend performance a MySQL database was also created. dosztanyi@caesar.elte.hu or bmeszaros@caesar.elte.hu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

The measurement of trace elements in interplanetary dust and cometary particles by ultra-high sensitivity INAA

NASA Technical Reports Server (NTRS)

Zolensky, M. E.; Lindstrom, David J.; Lindstrom, Richard M.; Lindstrom, M. M.

1989-01-01

Today the major elemental composition of interplanetary dust particles (IDPs) is routinely determined in many laboratories. These and mineralogical studies have revealed the presence of at least two major types of IDPs, chondritic and refractory. Preliminary results of a successful attempt to determine abundances of a large suite of trace elements from both chondritic and refractory IDPs are reported. The analytical procedure can be used in the grain-by-grain analysis of returned cometary samples. Chondritic and refractory IDPs are characterized by standard scanning electron microscopy and energy dispersive x ray spectroscopy (SEM-EDX) techniques. With this system, detection limits for many elements are well below picogram levels, and some approach femtogram levels. This technique is non-destructive, although some sample handling is required, so particles can be analyzed by other techniques after instrument neutron activation analysis (INAA) is completed. Data is presently being reduced from the analyses of 7 IDPs. These are U2015E10, U2015F1, W7029-A2, W7029-A3, W7013A8, LACl (all chondritic) and 705 (refractory). So far, 17 different major and trace elements were detected and measured in these particles, including rare earths and some very volatile elements (Br and Zn).

Dust in the Solar System - Properties and Origins

NASA Technical Reports Server (NTRS)

Messenger, Scott; Keller, Lindsay; Nakamura-Messenger, Keiko

2013-01-01

Interplanetary dust pervades the inner Solar System, giving rise to a prominent glow above the horizon at sunrise and sunset known as the zodiacal light. This dust derives from the disintegration of comets as they approach the Sun and from collisions among main-belt asteroids. The Earth accretes roughly 4x10(exp 6) kg/year of 1 - 1,000 micron dust particles as they spiral into the Sun under the influence of Poynting-Robertson drag and solar wind drag. Samples of these grains have been collected from deep sea sediments, Antarctic ice and by high-altitude aircraft and balloon flights. Interplanetary dust particles (IDPs) collected in the stratosphere have been classified by their IR spectra into olivine, pyroxene, and hydrated silicate-dominated classes. Most IDPs have bulk major and minor element abundances that are similar to carbonaceous chondrite meteorites. Hydrated silicate-rich IDPs are thought to derive from asteroids based on their mineralogy and low atmospheric entry velocities estimated from peak temperatures reached during atmospheric entry. Anhydrous IDPs are typically aggregates of 0.1 - approx. 1 micron Mg-rich olivine and pyroxene, amorphous silicates (GEMS), Fe, Nisulfides and rare spinel and oxides bound together by carbonaceous material. These IDPs are often argued to derive from comets based on compositional similarities and high atmospheric entry velocities that imply high eccentricity orbits. Infrared spectra obtained from anhydrous IDPs closely match remote IR spectra obtained from comets. The most primitive (anhydrous) IDPs appear to have escaped the parent-body thermal and aqueous alteration that has affected meteorites. These samples thus consist entirely of grains that formed in the ancient solar nebula and pre-solar interstellar and circumstellar environments. Isotopic studies of IDPs have identified silicate stardust grains that formed in the outflows of red giant and asymptotic giant branch stars and supernovae]. These stardust grains include both amorphous and crystalline silicates. The organic matter in these samples also exhibits highly anomalous H, C, and N isotopic compositions that are consistent with formation in low temperature environments at the outermost regions of the solar nebula or presolar cold molecular cloud. The scientific frontiers for these samples include working toward a better understanding of the origins of the solar system amorphous and crystalline grains in IDPs and the very challenging task of determining the chemical composition of sub-micron organic grains. Laboratory studies of ancient and present-day dust in the Solar System thus reveal in exquisite detail the chemistry, mineralogy and isotopic properties of materials that derive from a range of astrophysical environments. These studies are an important complement to astronomical observations that help to place the laboratory observations into broader context.

Latency features of SafetyNet ground systems architecture for the National Polar-orbiting Operational Environmental Satellite System (NPOESS)

NASA Astrophysics Data System (ADS)

Duda, James L.; Mulligan, Joseph; Valenti, James; Wenkel, Michael

2005-01-01

A key feature of the National Polar-orbiting Operational Environmental Satellite System (NPOESS) is the Northrop Grumman Space Technology patent-pending innovative data routing and retrieval architecture called SafetyNetTM. The SafetyNetTM ground system architecture for the National Polar-orbiting Operational Environmental Satellite System (NPOESS), combined with the Interface Data Processing Segment (IDPS), will together provide low data latency and high data availability to its customers. The NPOESS will cut the time between observation and delivery by a factor of four when compared with today's space-based weather systems, the Defense Meteorological Satellite Program (DMSP) and NOAA's Polar-orbiting Operational Environmental Satellites (POES). SafetyNetTM will be a key element of the NPOESS architecture, delivering near real-time data over commercial telecommunications networks. Scattered around the globe, the 15 unmanned ground receptors are linked by fiber-optic systems to four central data processing centers in the U. S. known as Weather Centrals. The National Environmental Satellite, Data and Information Service; Air Force Weather Agency; Fleet Numerical Meteorology and Oceanography Center, and the Naval Oceanographic Office operate the Centrals. In addition, this ground system architecture will have unused capacity attendant with an infrastructure that can accommodate additional users.

Mental health problems among internally displaced persons in Darfur.

PubMed

Hamid, Abdalla A R M; Musa, Saif A

2010-08-01

War victims are regarded as one of the highest risk groups for mental disturbances. This study investigated the effects of the Darfur conflict on mental health of 430 internally displaced persons (IDPs) from three camps located around Fasher and Nyala towns. A stratified random sampling technique was used to select participants. Male participants represented 50.6% of the sample while female participants represented 49.4%. The Posttraumatic Stress Disorder Checklist and the General Health Questionnaire (GHQ-28) were used in addition to a questionnaire measuring demographic variables and living conditions. It was hypothesized that high prevalence of posttraumatic stress disorder (PTSD) symptoms and of nonpsychotic psychiatric symptoms will be evident. Results showed a high dissatisfaction rate (72%) with living conditions among IDPs. There was also high prevalence of PTSD (54%) and general distress (70%) among IDPs. Female participants showed more somatic symptoms than their male counterparts. Married participants were more distressed, anxious, and showed more social dysfunction, while single ones reported more avoidance symptoms. Significant differences related to date of displacement were found in PTSD and hyperarousal. The group of IDPs displaced in 2003 scored higher on these scales than those displaced in 2004 and 2005. There was also significant difference related to date of displacement in distress, somatic symptoms, depression, anxiety, and social dysfunction. IDPs displaced in 2003 scored higher on these scales. Results are discussed in light of the study hypotheses and previous findings. It is concluded that three factors might affect the dissatisfaction of IDPs with living conditions inside camps. These are: lack of employment, unsuitability of food items, and lack of security around camps. It was recommended that psychological support services should be among the prime relief services provided by aid agencies.

Vaccination coverage survey versus administrative data in the assessment of mass yellow fever immunization in internally displaced persons--Liberia, 2004.

PubMed

Huhn, Gregory D; Brown, Jennifer; Perea, William; Berthe, Adama; Otero, Hansel; LiBeau, Genevieve; Maksha, Nuhu; Sankoh, Mohammed; Montgomery, Susan; Marfin, Anthony; Admassu, Mekonnen

2006-02-06

Yellow fever (YF) is a mosquito-borne vaccine-preventable disease with high mortality. In West Africa, low population immunity increases the risk of epidemic transmission. A cluster survey was conducted to determine the effectiveness of a mass immunization campaign using 17D YF vaccine in internally displaced person (IDP) camps following a reported outbreak of YF in Liberia in February 2004. Administrative data of vaccination coverage were reviewed. A cluster sample size was determined among 17,384 shelters using an 80% vaccination coverage threshold. A questionnaire eliciting demographic information, household size, and vaccination status was distributed to randomly selected IDPs. Data were analyzed to compare vaccination coverage rates of administrative versus survey data. Among 87,000 persons estimated living in IDP camps, administrative data recorded 49,395 (57%) YF vaccinated persons. A total of 237 IDPs were surveyed. Of survey respondents, 215 (91.9%, 95% CI 88.4-95.4) reported being vaccinated during the campaign and 196 (83.5%, 95% CI 78.6-88.5) possessed a valid campaign vaccination card. The median number of IDPs living in a shelter was 4 (range, 1-8) and 69,536 persons overall were estimated to be living in IDP camps. Coverage rates from a rapid survey exceeded 90% by self-report and 80% by evidence of a vaccination card, indicating that the YF immunization campaign was effective. Survey results suggested that administrative data overestimated the camp population by at least 20%. An emergency, mop-up vaccination campaign was avoided. Coverage surveys can be vital in the evaluation of emergency vaccination campaigns by influencing both imminent and future immunization strategies.

Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB

NASA Astrophysics Data System (ADS)

Liu, Hao; Guo, Xiang; Han, Jingcheng; Luo, Ray; Chen, Hai-Feng

2018-06-01

Transcription factor cyclic Adenosine monophosphate response-element binding protein plays a critical role in the cyclic AMP response pathway via its intrinsically disordered kinase inducible transactivation domain (KID). KID is one of the most studied intrinsically disordered proteins (IDPs), although most previous studies focus on characterizing its disordered state structures. An interesting question that remains to be answered is how the order-disorder transition occurs at experimental conditions. Thanks to the newly developed IDP-specific force field ff14IDPSFF, the quality of conformer sampling for IDPs has been dramatically improved. In this study, molecular dynamics (MD) simulations were used to study the order-to-disorder transition kinetics of KID based on the good agreement with the experiment on its disordered-state properties. Specifically, we tested four force fields, ff99SBildn, ff99IDPs, ff14IDPSFF, and ff14IDPs in the simulations of KID and found that ff14IDPSFF can generate more diversified disordered conformers and also reproduce more accurate experimental secondary chemical shifts. Kinetics analysis of MD simulations demonstrates that the order-disorder transition of KID obeys the first-order kinetics, and the transition nucleus is I127/L128/L141. The possible transition pathways from the nucleus to the last folded residues were identified as I127-R125-L138-L141-S143-A145 and L128-R125-L138-L141-S143-A145 based on a residue-level dynamical network analysis. These computational studies not only provide testable prediction/hypothesis on the order-disorder transition of KID but also confirm that the ff14IDPSFF force field can be used to explore the correlation between the structure and function of IDPs.

Soft interactions and volume exclusion by polymeric crowders can stabilize or destabilize transient structure in disordered proteins depending on polymer concentration.

PubMed

Rusinga, Farai I; Weis, David D

2017-08-01

The effects of macromolecular crowding on the transient structure of intrinsically disordered proteins is not well-understood. Crowding by biological molecules inside cells could modulate transient structure and alter IDP function. Volume exclusion theory and observations of structured proteins suggest that IDP transient structure would be stabilized by macromolecular crowding. Amide hydrogen exchange (HX) of IDPs in highly concentrated polymer solutions would provide valuable insights into IDP transient structure under crowded conditions. Here, we have used mass spectrometry to measure HX by a transiently helical random coil domain of the activator of thyroid and retinoid receptor (ACTR) in solutions containing 300 g L -1 and 400 g L -1 of Ficoll, a synthetic polysaccharide, using a recently-developed strong cation exchange-based cleanup method [Rusinga, et al., Anal Chem 2017;89:1275-1282]. Transiently helical regions of ACTR exchanged faster in 300 g L -1 Ficoll than in dilute buffer. In contrast, one transient helix exchanged more slowly in 400 g L -1 Ficoll. Nonspecific interactions destabilize ACTR helicity in 300 g L -1 Ficoll because ACTR engages with the Ficoll polymer mesh. In contrast, 400 g L -1 Ficoll is a semi-dilute solution where ACTR cannot engage the Ficoll mesh. At this higher concentration, volume exclusion stabilizes ACTR helicity because ACTR is compacted in interstitial spaces between Ficoll molecules. Our results suggest that the interplay between nonspecific interactions and volume exclusion in different cellular compartments could modulate IDP function by altering the stability of IDP transient structures. Proteins 2017; 85:1468-1479. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Atomic force microscopy based nanoassay: a new method to study α-Synuclein-dopamine bioaffinity interactions

NASA Astrophysics Data System (ADS)

Corvaglia, Stefania; Sanavio, Barbara; Sorce, Barbara; Bosco, Alessandro; Sabella, Stefania; Pompa, Pierpaolo; Scoles, Giacinto; Casalis, Loredana

2015-03-01

Intrinsically Disordered Proteins (IDPs) are characterized by the lack of well-defined 3-D structure and show high conformational plasticity. For this reason, they are a strong challenge for the traditional characterization of structure, supramolecular assembly and biorecognition phenomena. We show here how the fine tuning of protein orientation on a surface turns useful in the reliable testing of biorecognition interactions of IDPs, in particular α-Synuclein. We exploited atomic force microscopy (AFM) for the selective, nanoscale confinement of α-Synuclein on gold to study the early stages of α-Synuclein aggregation and the effect of small molecules, like dopamine, on the aggregation process. Capitalizing on the high sensitivity of AFM topographic height measurements we determined, for the first time in the literature, the dissociation constant of dopamine- α-Synuclein adducts.

Atomic force microscopy based nanoassay: a new method to study α-Synuclein-dopamine bioaffinity interactions

NASA Astrophysics Data System (ADS)

Corvaglia, Stefania; Sanavio, Barbara; Hong Enriquez, Rolando P.; Sorce, Barbara; Bosco, Alessandro; Scaini, Denis; Sabella, Stefania; Pompa, Pier Paolo; Scoles, Giacinto; Casalis, Loredana

2014-06-01

Intrinsically Disordered Proteins (IDPs) are characterized by the lack of well-defined 3-D structure and show high conformational plasticity. For this reason, they are a strong challenge for the traditional characterization of structure, supramolecular assembly and biorecognition phenomena. We show here how the fine tuning of protein orientation on a surface turns useful in the reliable testing of biorecognition interactions of IDPs, in particular α-Synuclein. We exploited atomic force microscopy (AFM) for the selective, nanoscale confinement of α-Synuclein on gold to study the early stages of α-Synuclein aggregation and the effect of small molecules, like dopamine, on the aggregation process. Capitalizing on the high sensitivity of AFM topographic height measurements we determined, for the first time in the literature, the dissociation constant of dopamine-α-Synuclein adducts.

Understanding disordered and unfolded proteins using single-molecule FRET and polymer theory.

PubMed

Hofmann, Hagen

2016-11-17

Understanding protein folding and the functional properties of intrinsically disordered proteins (IDPs) requires detailed knowledge of the forces that act in polypeptide chains. These forces determine the dimensions and dynamics of unfolded and disordered proteins and have been suggested to impact processes such as the coupled binding and folding of IDPs, or the rate of protein folding reactions. Much of the progress in understanding the physical and chemical properties of unfolded and intrinsically disordered polypeptide chains has been made possible by the recent developments in single-molecule fluorescence techniques. However, the interpretation of the experimental results requires concepts from polymer physics in order to be understood. Here, I review some of the theories used to describe the dimensions of unfolded polypeptide chains under varying solvent conditions together with their more recent application to experimental data.

Ultrafine-grained mineralogy and matrix chemistry of olivine-rich chondritic interplanetary dust particles

NASA Technical Reports Server (NTRS)

Rietmeijer, F. J. M.

1989-01-01

Olivine-rich chondritic interplanetary dust particles (IDPs) are an important subset of fluffy chondritic IDPs collected in the earth's stratosphere. Particles in this subset are characterized by a matrix of nonporous, ultrafine-grained granular units. Euhedral single crystals, crystals fragments, and platey single crystals occur dispersed in the matrix. Analytical electron microscopy of granular units reveals predominant magnesium-rich olivines and FeNi-sulfides embedded in amorphous carbonaceous matrix material. The variable ratio of ultrafine-grained minerals vs. carbonaceous matrix material in granular units support variable C/Si ratios, and some fraction of sulfur is associated with carbonaceous matrix material. The high Mg/(Mg+Fe) ratios in granular units is similar to this distribution in P/Comet Halley dust. The chondritic composition of fine-grained, polycrystalline IDPs gradually breaks down into nonchondritic, and ultimately, single mineral compositions as a function of decreased particle mass. The relationship between particle mass and composition in the matrix of olivine-rich chondritic IDPs is comparable with the relationship inferred for P/Comet Halley dust.

Consensus on updating immunizations in patients with primary immunodeficiencies

PubMed

2018-04-01

Las inmunodeficiencias primarias (IDP) constituyen un grupo de enfermedades hereditarias que afectan el número y/o la función de los distintos componentes del sistema inmune. Su prevalencia es de 1:1000-2000 nacimientos. Comprenden defectos de la inmunidad adaptativa, defectos de la inmunidad innata, inmunodeficiencias con fenotipos característicos, trastornos de la regulación inmune, síndromes autoinflamatorios, defectos de los fagocitos y del sistema del complemento y defectos considerados fenocopias de IDP. La vacunación con vacunas inactivadas es segura y puede ser efectiva en muchas inmunodeficiencias; las vacunas vivas atenuadas pueden no ser protectoras en ciertas IDP o presentarse como enfermedad vacunal asociada a la inmunización, lo que conlleva una alta morbimortalidad. Con el objetivo de actualizar las recomendaciones de vacunas en pacientes con IDP, el Comité Nacional de Infectología y el Grupo de Trabajo de Inmunología trabajaron sobre las vacunas que podían indicarse a estos pacientes, convivientes y el equipo de salud.

Looking at the Disordered Proteins through the Computational Microscope.

PubMed

Das, Payel; Matysiak, Silvina; Mittal, Jeetain

2018-05-23

Intrinsically disordered proteins (IDPs) have attracted wide interest over the past decade due to their surprising prevalence in the proteome and versatile roles in cell physiology and pathology. A large selection of IDPs has been identified as potential targets for therapeutic intervention. Characterizing the structure-function relationship of disordered proteins is therefore an essential but daunting task, as these proteins can adapt transient structure, necessitating a new paradigm for connecting structural disorder to function. Molecular simulation has emerged as a natural complement to experiments for atomic-level characterizations and mechanistic investigations of this intriguing class of proteins. The diverse range of length and time scales involved in IDP function requires performing simulations at multiple levels of resolution. In this Outlook, we focus on summarizing available simulation methods, along with a few interesting example applications. We also provide an outlook on how these simulation methods can be further improved in order to provide a more accurate description of IDP structure, binding, and assembly.

Intrinsic disorder mediates the diverse regulatory functions of the Cdk inhibitor p21

PubMed Central

Wang, Yuefeng; Fisher, John C.; Mathew, Rose; Ou, Li; Otieno, Steve; Sublett, Jack; Xiao, Limin; Chen, Jianhan; Roussel, Martine F.; Kriwacki, Richard W.

2011-01-01

Traditionally, well-defined three-dimensional structure was thought to be essential for protein function. However, myriad biological functions are performed by highly dynamic, intrinsically disordered proteins (IDPs). IDPs often fold upon binding their biological targets and frequently exhibit “binding diversity” by targeting multiple ligands. We sought to understand the physical basis of IDP binding diversity and herein report that the cyclin-dependent kinase (Cdk) inhibitor, p21Cip1, adaptively binds to and inhibits the various Cdk/cyclin complexes that regulate eukaryotic cell division. Based on results from NMR spectroscopy, and biochemical and cellular assays, we show that structural adaptability of a helical sub-domain within p21 termed LH enables two other sub-domains termed D1 and D2 to specifically bind conserved surface features of the cyclin and Cdk subunits, respectively, within otherwise structurally distinct Cdk/cyclin complexes. Adaptive folding upon binding is likely to mediate the diverse biological functions of the thousands of IDPs present in eukaryotes. PMID:21358637

Skin diseases among internally displaced Tawerghans living in camps in Benghazi, Libya.

PubMed

Elfaituri, Safa S

2016-09-01

Benghazi has received many internally displaced persons (IDPs) from other Libyan cities as a result of the armed conflict in Libya. These groups have significant health problems associated with their displacement, including skin diseases. This study aimed to determine the spectrum and frequency of skin diseases among people living in IDP camps in Benghazi. A total of 480 IDP camp residents with complaints of skin diseases were studied over a period of 6 months. All subjects were ethnic Tawerghans; about three-quarters were female and half were adults. The disease types found to occur at the highest frequencies were skin infections (40.0%), followed by xerosis (31.3%), eczema (18.3%), acne (17.0%), hair-related diseases (6.7%), and psychosomatic diseases (3.0%). People who are resident in IDP camps have skin problems similar to those of other populations in similar circumstances. They have increased vulnerability to infections, environment-associated disorders such as xerosis cutis and eczema, and diseases of psychosomatic origin. © 2015 The International Society of Dermatology.

Multi-level partnerships to promote health services among internally displaced in eastern Burma.

PubMed

Mahn, M; Maung, C; Oo, E K Shwe; Smith, L; Lee, C I; Whichard, E; Neumann, C; Richards, A K; Mullany, L C; Kuiper, H; Lee, T J

2008-01-01

Ethnic populations in eastern Burma are the target of military policies that result in forced labour, destruction of food supplies, and massive forced displacement. Despite international assistance to Burmese refugees along the Thai-Burma border, traditional humanitarian models have failed to reach these internally displaced persons (IDPs) within Burma. Nevertheless, through the cultivation of a model (cross border local-global partnerships) 300,000 IDPs in eastern Burma now receive critical health services where, otherwise, there would be none. We describe key elements of the partnership model's genesis in eastern Burma. The role of the local partner, Backpack Health Worker Team (BPHWT), is highlighted for its indigenous access to the IDP populations and its maintenance of programmatic autonomy. These local elements are potentiated by international support for technical assistance, training, resources, and advocacy. International policy and investment should prioritize support of locally-driven health initiatives that utilize local-global partnerships to reach not only IDPs but also other war-torn or traditionally inaccessible populations worldwide.

Mineralogy of interplanetary dust particles from the 'olivine' infrared class

NASA Technical Reports Server (NTRS)

Christoffersen, R.; Buseck, P. R.

1986-01-01

Analytical electron microscopy observations establish that olivine is abundant and the predominant silicate phase in three interplanetary dust particles (IDPs) from the 'olivine' infrared spectra category. Two of the particles have microstructures resembling those of most nonhydrous chondritic IDPs, consisting of micron to submicron grains together with a matrix composed of amorphous carbonaceous material and sub-500 A grains. In addition to olivine these particles respectively contain enstatite and magnetite, and pentlandite plus Ca-rich clinopyroxene. The third IDP consists mostly of olivine and pyrrhotite with little or no matrix material. Olivine grains in this particle contain prominent solar-flare ion tracks with densities corresponding to a space-exposure age between 1000 to 100,000 years. Although the three particles have olivine-rich mineralogies in common, other aspects of their mineralogies and microstructures suggest that they experienced different formation histories. The differences between the particles indicate that the olivine infrared spectral category is a diverse collection of IDPs that probably incorporates several genetic groups.

The thermal history of interplanetary dust particles collected in the Earth's stratosphere

NASA Technical Reports Server (NTRS)

Nier, A. O.; Schlutter, D. J.

1993-01-01

Fragments of 24 individual interplanetary dust particles (IDPs) collected in the Earth's stratosphere were obtained from NASA's Johnson Space Center collection and subjected to pulse-heating sequences to extract He and Ne and to learn about the thermal history of the particles. A motivation for the investigation was to see if the procedure would help distinguish between IDPs of asteroidal and cometary origin. The use of a sequence of short-duration heat pulses to perform the extractions is an improvement over the employment of a step-heating sequence, as was used in a previous investigation. The particles studied were fragments of larger parent IDPs, other fragments of which, in coordinated experiments, are undergoing studies of elemental and mineralogical composition in other laboratories. While the present investigation will provide useful temperature history data for the particles, the relatively large size of the parent IDPs (approximately 40 micrometers in diameter) resulted in high entry deceleration temperatures. This limited the usefulness of the study for distinguishing between particles of asteroidal and cometary origin.

Looking at the Disordered Proteins through the Computational Microscope

PubMed Central

2018-01-01

Intrinsically disordered proteins (IDPs) have attracted wide interest over the past decade due to their surprising prevalence in the proteome and versatile roles in cell physiology and pathology. A large selection of IDPs has been identified as potential targets for therapeutic intervention. Characterizing the structure–function relationship of disordered proteins is therefore an essential but daunting task, as these proteins can adapt transient structure, necessitating a new paradigm for connecting structural disorder to function. Molecular simulation has emerged as a natural complement to experiments for atomic-level characterizations and mechanistic investigations of this intriguing class of proteins. The diverse range of length and time scales involved in IDP function requires performing simulations at multiple levels of resolution. In this Outlook, we focus on summarizing available simulation methods, along with a few interesting example applications. We also provide an outlook on how these simulation methods can be further improved in order to provide a more accurate description of IDP structure, binding, and assembly.

Training and deployment of lay refugee/internally displaced persons to provide basic health services in camps: a systematic review.

PubMed

Ehiri, John E; Gunn, Jayleen K L; Center, Katherine E; Li, Ying; Rouhani, Mae; Ezeanolue, Echezona E

2014-01-01

Training of lay refugees/internally displaced persons (IDPs) and deploying them to provide basic health services to other women, children, and families in camps is perceived to be associated with public health benefits. However, there is limited evidence to support this hypothesis. To assess the effects of interventions to train and deploy lay refugees and/or IDPs for the provision of basic health service to other women, children, and families in camps. PubMed, Science and Social Science Citation Indices, PsycINFO, EMBASE, POPLINE, CINAHL, and reference lists of relevant articles were searched (from inception to June 30, 2014) with the aim of identifying studies that reported the effects of interventions that trained and deployed lay refugees and/or IDPs for the provision of basic health service to other women, children, and families in camps. Two investigators independently reviewed all titles and abstracts to identify potentially relevant articles. Discrepancies were resolved by repeated review, discussion, and consensus. Study quality assessment was undertaken using standard protocols. Ten studies (five cross-sectional, four pre-post, and one post-test only) conducted in Africa (Guinea and Tanzania), Central America (Belize), and Asia (Myanmar) were included. The studies demonstrated some positive impact on population health associated with training and deployment of trained lay refugees/IDPs as health workers in camps. Reported effects included increased service coverage, increased knowledge about disease symptoms and prevention, increased adoption of improved treatment seeking and protective behaviors, increased uptake of services, and improved access to reproductive health information. One study, which assessed the effect of peer refugee health education on sexual and reproductive health, did not demonstrate a marked reduction in unintended pregnancies among refugee/IDP women. Although available evidence suggests a positive impact of training and deployment of lay refugees/IDPs as health workers in camps, existing body of evidence is weak, and calls for a re-examination of current practices. Interventions that promote training and deployment of lay refugees/IDPs as health workers in camps should include strong evaluation components in order to facilitate assessment of effects on population health.

Training and deployment of lay refugee/internally displaced persons to provide basic health services in camps: a systematic review

PubMed Central

Ehiri, John E.; Gunn, Jayleen K.L.; Center, Katherine E.; Li, Ying; Rouhani, Mae; Ezeanolue, Echezona E.

2014-01-01

Background Training of lay refugees/internally displaced persons (IDPs) and deploying them to provide basic health services to other women, children, and families in camps is perceived to be associated with public health benefits. However, there is limited evidence to support this hypothesis. Objectives To assess the effects of interventions to train and deploy lay refugees and/or IDPs for the provision of basic health service to other women, children, and families in camps. Methods PubMed, Science and Social Science Citation Indices, PsycINFO, EMBASE, POPLINE, CINAHL, and reference lists of relevant articles were searched (from inception to June 30, 2014) with the aim of identifying studies that reported the effects of interventions that trained and deployed lay refugees and/or IDPs for the provision of basic health service to other women, children, and families in camps. Two investigators independently reviewed all titles and abstracts to identify potentially relevant articles. Discrepancies were resolved by repeated review, discussion, and consensus. Study quality assessment was undertaken using standard protocols. Results Ten studies (five cross-sectional, four pre-post, and one post-test only) conducted in Africa (Guinea and Tanzania), Central America (Belize), and Asia (Myanmar) were included. The studies demonstrated some positive impact on population health associated with training and deployment of trained lay refugees/IDPs as health workers in camps. Reported effects included increased service coverage, increased knowledge about disease symptoms and prevention, increased adoption of improved treatment seeking and protective behaviors, increased uptake of services, and improved access to reproductive health information. One study, which assessed the effect of peer refugee health education on sexual and reproductive health, did not demonstrate a marked reduction in unintended pregnancies among refugee/IDP women. Conclusion Although available evidence suggests a positive impact of training and deployment of lay refugees/IDPs as health workers in camps, existing body of evidence is weak, and calls for a re-examination of current practices. Interventions that promote training and deployment of lay refugees/IDPs as health workers in camps should include strong evaluation components in order to facilitate assessment of effects on population health. PMID:25280734

Delivery of organics to Mars through asteroid and comet impacts

NASA Astrophysics Data System (ADS)

Frantseva, K.; Mueller, M.; van der Tak, F. F. S.; ten Kate, I. L.; Greenstreet, S.

2017-09-01

Preliminary results show that the asteroid-borne organic flux on Mars is comparable to the IPD rate; asteroids certainly cannot be neglected. Comets, on the other hand, contribute only 0.01% of the IDP-borne rate and can be neglected in the process of organic delivery to Mars.

Entropic Elasticity in the Giant Muscle Protein Titin

NASA Astrophysics Data System (ADS)

Morgan, Ian; Saleh, Omar

Intrinsically disordered proteins (IDPs) are a large and functionally important class of proteins that lack a fixed three-dimensional structure. Instead, they adopt a conformational ensemble of states which facilitates their biological function as molecular linkers, springs, and switches. Due to their conformational flexibility, it can be difficult to study IDPs using typical experimental methods. To overcome this challenge, we use a high-resolution single-molecule magnetic stretching technique to quantify IDP flexibility. We apply this technique to the giant muscle protein titin, measuring its elastic response at low forces. We present results demonstrating that titin's native elastic response derives from the combined entropic elasticity of its ordered and disordered domains.

Improving the Quality of Life of Persons with Intellectual Disabilities Through ICTs.

PubMed

Ferreras, Alberto; Poveda, Rakel; Quílez, Manuel; Poll, Nuria

2017-01-01

Removing barriers to accessing Information and Communication Technologies (ICTs) by Persons with Intellectual Disabilities (IDPs) is crucial. Being excluded from ICTs implies being shut down from the information society, but also from accessing essential public services, as well as from the opportunity of living an independent life. The IdICT project has the general objective of increasing the competences of IDPs, their families and the professionals that work with them to exploit ICTs with a Quality of Life approach. To do that, a training platform and a training program has been developed and tested by IDPs, relatives and professionals in six European Countries.

Trace Element Abundance Measurements on Cosmic Dust Particles

NASA Technical Reports Server (NTRS)

Flynn, George

1996-01-01

The X-Ray Microprobe on beamline X-26A at the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory was used to determine the abundances of elements from Cr through Sr in individual interplanetary dust particles (IDPs) collected from the Earth's stratosphere and the Scanning Transmission X-ray Microscope (STXM) on beamline X-1A at the NSLS was used to determine the carbon abundances and spatial distributions in IDPs. In addition, modeling was performed in an attempt to associate particular types of IDPs with specific types of parent bodies, and thus to infer the chemistry, mineralogy, and structural properties of those parent bodies.

Depletions of sulfur and/or zinc in IDPs: Are they reliable indicators of atmospheric entry heating?

NASA Technical Reports Server (NTRS)

Flynn, G. J.; Sutton, S. R.; Bajt, S.; Kloeck, W.; Thomas, K. L.; Keller, L. P.

1993-01-01

The degree of heating of interplanetary dust particles (IDP's) on Earth atmospheric entry is important in distinguishing cometary particles from main-belt asteroidal particles. Depletions in the volatile elements S and Zn were proposed as chemical indicators of significant entry heating. The S and Zn contents of cosmic dust particles were correlated with physical indicators of atmospheric entry heating, such as the production of magnetite and the loss of solar wind implanted He. The results indicate that the Zn content of IDP's is a useful indicator of entry heating, but the S content seems to be less useful.

A late Miocene dust shower from the break-up of an asteroid in the main belt.

PubMed

Farley, Kenneth A; Vokrouhlický, David; Bottke, William F; Nesvorný, David

2006-01-19

Throughout the history of the Solar System, Earth has been bombarded by interplanetary dust particles (IDPs), which are asteroid and comet fragments of diameter approximately 1-1,000 microm. The IDP flux is believed to be in quasi-steady state: particles created by episodic main belt collisions or cometary fragmentation replace those removed by comminution, dynamical ejection, and planetary or solar impact. Because IDPs are rich in 3He, seafloor sediment 3He concentrations provide a unique means of probing the major events that have affected the IDP flux and its source bodies over geological timescales. Here we report that collisional disruption of the >150-km-diameter asteroid that created the Veritas family 8.3 +/- 0.5 Myr ago also produced a transient increase in the flux of interplanetary dust-derived 3He. The increase began at 8.2 +/- 0.1 Myr ago, reached a maximum of approximately 4 times pre-event levels, and dissipated over approximately 1.5 Myr. The terrestrial IDP accretion rate was overwhelmingly dominated by Veritas family fragments during the late Miocene. No other event of this magnitude over the past approximately 10(8) yr has been deduced from main belt asteroid orbits. One remarkably similar event is present in the 3He record 35 Myr ago, but its origin by comet shower or asteroid collision remains uncertain.

Si Isotopes of Brownleeite

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Messenger, Scott R.; Ito, M.; Keller, L. P.; Clemett, S. J.; Jones, J. H.; Tatsuoka, H.; Zolensky, M. E.; Tatsuoka, H.

2010-01-01

Brownleeite is a manganese silicide, ideally stoichiometric MnSi, not previously observed in nature until its discovery within an interplanetary dust particle (IDP) that likely originated from a comet [1]. Three discrete brownleeite grains in the IDP L2055 I3 (4 microns in size, hereafter IDP I3) were identified with maximum dimensions of 100, 250 and 600 nm and fully analyzed using scanning-transmission electron microscopy (STEM) [1]. One of the grains (100 nm in size) was poikilitically enclosed by low-Fe, Mn-enriched (LIME) olivine. LIME olivine is epitaxial to the brownleeite with the brownleeite (200) parallel to the olivine c* [1]. LIME olivine is an enigmatic phase first reported from chondritic porous IDPs and some unequilibrated ordinary chondrites [ 2], that is commonly observed in chondritic-porous IDPs. Recently, LIME olivine has been also found in comet Wild-2 (Stardust) samples [3], indicating that LIME olivine is a common mineral component of comets. LIME olivine has been proposed to form as a high temperature condensate in the protosolar nebula [2]. Brownleeite grains also likely formed as high-temperature condensates either in the early Solar System or in the outflow of an evolved star or supernova explosion [1]. The isotopic composition of the brownleeite grains may strongly constrain their ultimate source. To test this hypothesis, we performed isotopic analyses of the brownleeite and the associated LIME olivine, using the NASA/JSC NanoSIMS 50L ion microprobe.

Validation Test Report for the Automated Optical Processing System (AOPS) Version 4.12

DTIC Science & Technology

2015-09-03

the Geostationary Ocean Color Imager (GOCI) sensor, aboard the Communication Ocean and Meteorological Satellite (COMS) satellite. Additionally, this...this capability works in conjunction with AOPS • Improvements to the AOPS mosaicking capability • Prepare the NRT Geostationary Ocean Color Imager...Warfare (EXW) Geostationary Ocean Color Imager (GOCI) Gulf of Mexico (GOM) Hierarchical Data Format (HDF) Integrated Data Processing System (IDPS

Spatially Resolved Acid Dissolution of IDPs: The State of Carbon and the Abundance of Diamonds in the Dust

NASA Technical Reports Server (NTRS)

Brownlee, D. E.; Joswiak, D. J.; Bradley, J. P.; Gezo, J. C.; Hill, H. G. M.

2000-01-01

Ultramicrotome sections of IDPs have been successfully etched with HF to isolate and reveal the microdistribution of carbonaceous material. The sections are evaluated for nanodiamonds, 3.4 micron feature, GEMS and the origin of low albedo in small interplanetary particles.

Individual Development Plans as Governance Tools--Changed Governance of Teachers' Work

ERIC Educational Resources Information Center

Parding, Karolina; Liljegren, Andreas

2017-01-01

Auditing, accountability, and transparency are concepts that greatly impact the working conditions of today's public sector professionals, including teachers. Documentation requirements have been on the increase for some time, which can be seen in the education sector's Individual Development Plans (IDPs), for example. These IDPs are pedagogical…

The CCC Institutional Development Program: Organizational Change from the Chief Executive's Perspective.

ERIC Educational Resources Information Center

Ellison, Nolen M.; Eadie, Douglas C.

Cuyahoga Community College's three-phase Institutional Development Program (IDP) was established in January, 1975, to provide systematic and uniform college-wide planning and management procedures. This report first discusses the social forces which led the college to undertake the IDP; identifies the long-range planning, governance, and…

NASA Science Data Processing for SNPP

NASA Astrophysics Data System (ADS)

Hall, A.; Behnke, J.; Lowe, D. R.; Ho, E. L.

2014-12-01

NASA's ESDIS Project has been operating the Suomi National Polar-Orbiting Partnership (SNPP) Science Data Segment (SDS) since the launch in October 2011. The science data processing system includes a Science Data Depository and Distribution Element (SD3E) and five Product Evaluation and Analysis Tool Elements (PEATEs): Land, Ocean, Atmosphere, Ozone, and Sounder. The SDS has been responsible for assessing Environmental Data Records (EDRs) for climate quality, providing and demonstrating algorithm improvements/enhancements and supporting the calibration/validation activities as well as instrument calibration and sensor table uploads for mission planning. The SNPP also flies two NASA instruments: OMPS Limb and CERES. The SNPP SDS has been responsible for producing, archiving and distributing the standard products for those instruments in close association with their NASA science teams. The PEATEs leveraged existing science data processing techniques developed under the EOSDIS Program. This enabled he PEATEs to do an excellent job in supporting Science Team analysis for SNPP. The SDS acquires data from three sources: NESDIS IDPS (Raw Data Records (RDRs)), GRAVITE (Retained Intermediate Products (RIPs)), and the NOAA/CLASS (higher level products). The SD3E component aggregates the RDRs, and distributes them to each of the PEATEs for further analysis and processing. It provides a ~32 day rolling storage of data, available for pickup by the PEATEs. The current system used by NASA will be presented along with plans for streamlining the system in support of continuing the NASA's EOS measurements.

Insight into Primordial Solar System Oxygen Reservoirs from Returned Cometary Samples

NASA Technical Reports Server (NTRS)

Brownlee, D. E.; Messenger, S.

2004-01-01

The recent successful rendezvous of the Stardust spacecraft with comet Wild-2 will be followed by its return of cometary dust to Earth in January 2006. Results from two separate dust impact detectors suggest that the spacecraft collected approximately the nominal fluence of at least 1,000 particles larger than 15 micrometers in size. While constituting only about one microgram total, these samples will be sufficient to answer many outstanding questions about the nature of cometary materials. More than two decades of laboratory studies of stratospherically collected interplanetary dust particles (IDPs) of similar size have established the necessary microparticle handling and analytical techniques necessary to study them. It is likely that some IDPs are in fact derived from comets, although complex orbital histories of individual particles have made these assignments difficult to prove. Analysis of bona fide cometary samples will be essential for answering some fundamental outstanding questions in cosmochemistry, such as (1) the proportion of interstellar and processed materials that comprise comets and (2) whether the Solar System had a O-16-rich reservoir. Abundant silicate stardust grains have recently been discovered in anhydrous IDPs, in far greater abundances (200 5,500 ppm) than those in meteorites (25 ppm). Insight into the more subtle O isotopic variations among chondrites and refractory phases will require significantly higher precision isotopic measurements on micrometer-sized samples than are currently available.

Bridge over troubled proline: assignment of intrinsically disordered proteins using (HCA)CON(CAN)H and (HCA)N(CA)CO(N)H experiments concomitantly with HNCO and i(HCA)CO(CA)NH.

PubMed

Hellman, Maarit; Piirainen, Henni; Jaakola, Veli-Pekka; Permi, Perttu

2014-01-01

NMR spectroscopy is by far the most versatile and information rich technique to study intrinsically disordered proteins (IDPs). While NMR is able to offer residue level information on structure and dynamics, assignment of chemical shift resonances in IDPs is not a straightforward process. Consequently, numerous pulse sequences and assignment protocols have been developed during past several years, targeted especially for the assignment of IDPs, including experiments that employ H(N), H(α) or (13)C detection combined with two to six indirectly detected dimensions. Here we propose two new HN-detection based pulse sequences, (HCA)CON(CAN)H and (HCA)N(CA)CO(N)H, that provide correlations with (1)H(N)(i - 1), (13)C'(i - 1) and (15)N(i), and (1)H(N)(i + 1), (13)C'(i) and (15)N(i) frequencies, respectively. Most importantly, they offer sequential links across the proline bridges and enable filling the single proline gaps during the assignment. We show that the novel experiments can efficiently complement the information available from existing HNCO and intraresidual i(HCA)CO(CA)NH pulse sequences and their concomitant usage enabled >95 % assignment of backbone resonances in cytoplasmic tail of adenosine receptor A2A in comparison to 73 % complete assignment using the HNCO/i(HCA)CO(CA)NH data alone.

Automated thin-film analyses of anhydrous interplanetary dust particles in the analytical electron microscope

NASA Technical Reports Server (NTRS)

Bradley, J. P.; Germani, M. S.; Brownlee, D. E.

1989-01-01

An AEM apparatus equipped with digital beam control has obtained quantitative point-count analyses of thin sections taken from eight anhydrous chondritic interplanetary dust particles (IDPs); between 200 and 500 X-ray analyses were collected from each thin section and analyzed for Mg, Al, Si, S, Ca, Cr, Mn, Fe, and Ni. Two types of anhydrous chondritic aggregates were observed in the eight IDPs: one highly porous, the other less so. The eight anhydrous IDPs are characterizable as mixtures of fine- and coarse-grained aggregates, large mineral grains, glass, and carbonaceous materials. Their elemental concentrations follow those of solar abundances, suggesting that they are unperturbed by aqueous alteration.

Focused Ion Beam Recovery and Analysis of Interplanetary Dust Particles (IDPs) and Stardust Analogues

NASA Technical Reports Server (NTRS)

Graham, G. A.; Bradley, J. P.; Bernas, M.; Stroud, R. M.; Dai, Z. R.; Floss, C.; Stadermann, F. J.; Snead, C. J.; Westphal, A. J.

2004-01-01

Meteoritics research is a major beneficiary of recent developments in analytical instrumentation [1,2]. Integrated studies in which multiple analytical techniques are applied to the same specimen are providing new insight about the nature of IDPs [1]. Such studies are dependent on the ability to prepare specimens that can be analyzed in multiple instruments. Focused ion beam (FIB) microscopy has revolutionized specimen preparation in materials science [3]. Although FIB has successfully been used for a few IDP and meteorite studies [1,4-6], it has yet to be widely utilized in meteoritics. We are using FIB for integrated TEM/NanoSIMS/synchrotron infrared (IR) studies [1].

Abundant Solar Nebula Solids in Comets

NASA Technical Reports Server (NTRS)

Messenger, S.; Keller, L. P.; Nakamura-Messenger, K.; Nguyen, A. N.; Clemett, S.

2016-01-01

Comets have been proposed to consist of unprocessed interstellar materials together with a variable amount of thermally annealed interstellar grains. Recent studies of cometary solids in the laboratory have shown that comets instead consist of a wide range of materials from across the protoplanetary disk, in addition to a minor complement of interstellar materials. These advances were made possible by the return of direct samples of comet 81P/Wild 2 coma dust by the NASA Stardust mission and recent advances in microscale analytical techniques. Isotopic studies of 'cometary' chondritic porous interplanetary dust particles (CP-IDPs) and comet 81P/Wild 2 Stardust samples show that preserved interstellar materials are more abundant in comets than in any class of meteorite. Identified interstellar materials include sub-micron-sized presolar silicates, oxides, and SiC dust grains and some fraction of the organic material that binds the samples together. Presolar grain abundances reach 1 weight percentage in the most stardust-rich CP-IDPs, 50 times greater than in meteorites. Yet, order of magnitude variations in presolar grain abundances among CP-IDPs suggest cometary solids experienced significant variations in the degree of processing in the solar nebula. Comets contain a surprisingly high abundance of nebular solids formed or altered at high temperatures. Comet 81P/Wild 2 samples include 10-40 micron-sized, refractory Ca- Al-rich inclusion (CAI)-, chondrule-, and ameboid olivine aggregate (AOA)-like materials. The O isotopic compositions of these refractory materials are remarkably similar to their meteoritic counterparts, ranging from 5 percent enrichments in (sup 16) O to near-terrestrial values. Comet 81P/Wild 2 and CP-IDPs also contain abundant Mg-Fe crystalline and amorphous silicates whose O isotopic compositions are also consistent with Solar System origins. Unlike meteorites, that are dominated by locally-produced materials, comets appear to be composed of materials that were formed across a wide swath of the early protoplanetary disk.

Calibration of Crustal Historical Earthquakes from Intra-Carpathian Region of Romania

NASA Astrophysics Data System (ADS)

Oros, Eugen; Popa, Mihaela; Rogozea, Maria

2017-12-01

The main task of the presented study is to elaborate a set of relations of mutual conversion macroseismic intensity - magnitude, necessary for the calibration of the historical crustal earthquakes produced in the Intra - Carpathian region of Romania, as a prerequisite for homogenization of the parametric catalogue of Romanian earthquakes. To achieve the goal, we selected a set of earthquakes for which we have quality macroseismic data and the Mw moment magnitude obtained instrumentally. These seismic events were used to determine the relations between the Mw and the peak/epicentral intensity, the isoseist surface area for I=3, I=4 and I=5: Mw = f (Imax / Io), Mw = f (Imax / Io, h), Mw = f (A3, A4; A5). We investigated several variants of such relationships and combinations, taking into account that the macroseismic data necessary for the re-evaluation of historical earthquakes in the investigated region are available in several forms. Thus, a number of investigations provided various information resulted after revising initial historical data: 1) Intensity data point (IDP) assimilated or not with the epicentre intensity after analysis of the correlation level with recent seismicity data and / or active tectonics / seismotectonics, 2) Sets of intensities obtained in several localities (IDPs) with variable values having maxims that can be considered equal to epicentral intensity (Io), 3) Sets of intensities obtained in several localities (IDPs) but without obvious maximum values, assimilable with the epicentral intensity, 4) maps with isoseismals, 5) Information on the areas in which the investigated earthquake was felt or the area of perceptiveness (e.g. I = 3 EMS during the day and I = 4 EMS at night) or the surfaces corresponding to a certain degree of well-defined intensity. The obtained relationships were validated using a set of earthquakes with instrumental source parameters (localization, depth, Mw). These relationships lead to redundant results meaningful in the process of estimating the quality and credibility of the primary data used (e.g. IDPs, isoseismals) and in the correct determination of Mw.

Origins of GEMS Grains

NASA Technical Reports Server (NTRS)

Messenger, S.; Walker, R. M.

2012-01-01

Interplanetary dust particles (IDPs) collected in the Earth s stratosphere contain high abundances of submicrometer amorphous silicates known as GEMS grains. From their birth as condensates in the outflows of oxygen-rich evolved stars, processing in interstellar space, and incorporation into disks around new stars, amorphous silicates predominate in most astrophysical environments. Amorphous silicates were a major building block of our Solar System and are prominent in infrared spectra of comets. Anhydrous interplanetary dust particles (IDPs) thought to derive from comets contain abundant amorphous silicates known as GEMS (glass with embedded metal and sulfides) grains. GEMS grains have been proposed to be isotopically and chemically homogenized interstellar amorphous silicate dust. We evaluated this hypothesis through coordinated chemical and isotopic analyses of GEMS grains in a suite of IDPs to constrain their origins. GEMS grains show order of magnitude variations in Mg, Fe, Ca, and S abundances. GEMS grains do not match the average element abundances inferred for ISM dust containing on average, too little Mg, Fe, and Ca, and too much S. GEMS grains have complementary compositions to the crystalline components in IDPs suggesting that they formed from the same reservoir. We did not observe any unequivocal microstructural or chemical evidence that GEMS grains experienced prolonged exposure to radiation. We identified four GEMS grains having O isotopic compositions that point to origins in red giant branch or asymptotic giant branch stars and supernovae. Based on their O isotopic compositions, we estimate that 1-6% of GEMS grains are surviving circumstellar grains. The remaining 94-99% of GEMS grains have O isotopic compositions that are indistinguishable from terrestrial materials and carbonaceous chondrites. These isotopically solar GEMS grains either formed in the Solar System or were completely homogenized in the interstellar medium (ISM). However, the chemical compositions of GEMS grains are extremely heterogeneous and seem to rule out this possibility. Based on their solar isotopic compositions and their non-solar elemental compositions we propose that most GEMS grains formed in the nebula as late-stage non-equilibrium condensates.

Insights into the Molecular Mechanisms of Alzheimer’s and Parkinson’s Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology

PubMed Central

Coskuner-Weber, Orkid

2018-01-01

Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer’s and Parkinson’s disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer’s and Parkinson’s diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects. Classical molecular dynamics simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β and α-synuclein in relation to the pathologies of Alzheimer’s and Parkinson’s diseases. Furthermore, there are several natural genetic variations that play a role in the pathogenesis of familial cases of Alzheimer’s and Parkinson’s diseases, which are related to specific genetic defects inherited in dominant or recessive patterns. The present review summarizes the current understanding of monomeric and oligomeric forms of amyloid-β and α-synuclein, as well as the impacts of artificial and pathological missense mutations on the structural ensembles of these IDPs using molecular dynamics simulations. We also emphasize the recent investigations on residual secondary structure formation in dynamic conformational ensembles of amyloid-β and α-synuclein, such as β-structure linked to the oligomerization and fibrillation mechanisms related to the pathologies of Alzheimer’s and Parkinson’s diseases. This information represents an important foundation for the successful and efficient drug design studies. PMID:29364151

Norwegian Field Research Projects in Industrial Democracy.

ERIC Educational Resources Information Center

Qvale, Thoralf Ulrik

The Industrial Democracy Programme (IDP) of Norway seeks to create conditions for a self-supporting change process in industry, rather than implementing a ready-made model, believing that it is more valuable for employees to learn to change their organization than for the specific solution to be found. The central problems, therefore, have been to…

Small Particles Intact Capture Experiment (SPICE)

NASA Technical Reports Server (NTRS)

Nishioka, Ken-Ji; Carle, G. C.; Bunch, T. E.; Mendez, David J.; Ryder, J. T.

1994-01-01

The Small Particles Intact Capture Experiment (SPICE) will develop technologies and engineering techniques necessary to capture nearly intact, uncontaminated cosmic and interplanetary dust particles (IDP's). Successful capture of such particles will benefit the exobiology and planetary science communities by providing particulate samples that may have survived unaltered since the formation of the solar system. Characterization of these particles may contribute fundamental data to our knowledge of how these particles could have formed into our planet Earth and, perhaps, contributed to the beginnings of life. The term 'uncontaminated' means that captured cosmic and IDP particles are free of organic contamination from the capture process and the term 'nearly intact capture' means that their chemical and elemental components are not materially altered during capture. The key to capturing cosmic and IDP particles that are organic-contamination free and nearly intact is the capture medium. Initial screening of capture media included organic foams, multiple thin foil layers, and aerogel (a silica gel); but, with the exception of aerogel, the requirements of no contamination or nearly intact capture were not met. To ensure no contamination of particles in the capture process, high-purity aerogel was chosen. High-purity aerogel results in high clarity (visual clearness), a useful quality in detection and recovery of embedded captured particles from the aerogel. P. Tsou at the Jet Propulsion Laboratory (JPL) originally described the use of aerogel for this purpose and reported laboratory test results. He has flown aerogel as a 'GAS-can Lid' payload on STS-47 and is evaluating the results. The Timeband Capture Cell Experiment (TICCE), a Eureca 1 experiment, is also flying aerogel and is scheduled for recovery in late April.

Genome-Wide Prediction of Intrinsic Disorder; Sequence Alignment of Intrinsically Disordered Proteins

ERIC Educational Resources Information Center

Midic, Uros

2012-01-01

Intrinsic disorder (ID) is defined as a lack of stable tertiary and/or secondary structure under physiological conditions in vitro. Intrinsically disordered proteins (IDPs) are highly abundant in nature. IDPs possess a number of crucial biological functions, being involved in regulation, recognition, signaling and control, e.g. their functional…

Academics as Part-Time Marketers in University Offshore Programs: An Exploratory Study

ERIC Educational Resources Information Center

Poole, David; Ewan, Craig

2010-01-01

Australian universities maintain almost 900 offshore programs delivered to more than 100 000 students, primarily in the nations of Singapore, Malaysia, China, and Hong Kong (Universities Australia, 2009; IDP, 2009a). Although offshore students comprise an estimated 30 per cent of international student enrolments at Australian universities (IDP,…

Abstracts for the 54th Annual Meeting of the Meteoritical Society

NASA Technical Reports Server (NTRS)

1991-01-01

Abstracts of the papers presented at 54th Annual Meeting of the Meteoritic Society are compiled. The following subject areas are covered: Antarctic meteorites; nebula and parent body processing; primary and secondary SNC parent planet processes; enstatite chondrites and aubrites; achondrite stew; refractory inclusions; meteorite exposure ages and sizes; interstellar/meteorite connections; lunar origins, processes and meteorites; craters, cratering and tektites; cretaceous-tertiary impact(s); IDPs (LDEF, stratosphere, Greenland and Antarctica); chondrules; and chondrites.

Binding Mechanisms of Intrinsically Disordered Proteins: Theory, Simulation, and Experiment

PubMed Central

Mollica, Luca; Bessa, Luiza M.; Hanoulle, Xavier; Jensen, Malene Ringkjøbing; Blackledge, Martin; Schneider, Robert

2016-01-01

In recent years, protein science has been revolutionized by the discovery of intrinsically disordered proteins (IDPs). In contrast to the classical paradigm that a given protein sequence corresponds to a defined structure and an associated function, we now know that proteins can be functional in the absence of a stable three-dimensional structure. In many cases, disordered proteins or protein regions become structured, at least locally, upon interacting with their physiological partners. Many, sometimes conflicting, hypotheses have been put forward regarding the interaction mechanisms of IDPs and the potential advantages of disorder for protein-protein interactions. Whether disorder may increase, as proposed, e.g., in the “fly-casting” hypothesis, or decrease binding rates, increase or decrease binding specificity, or what role pre-formed structure might play in interactions involving IDPs (conformational selection vs. induced fit), are subjects of intense debate. Experimentally, these questions remain difficult to address. Here, we review experimental studies of binding mechanisms of IDPs using NMR spectroscopy and transient kinetic techniques, as well as the underlying theoretical concepts and numerical methods that can be applied to describe these interactions at the atomic level. The available literature suggests that the kinetic and thermodynamic parameters characterizing interactions involving IDPs can vary widely and that there may be no single common mechanism that can explain the different binding modes observed experimentally. Rather, disordered proteins appear to make combined use of features such as pre-formed structure and flexibility, depending on the individual system and the functional context. PMID:27668217

A decade and a half of protein intrinsic disorder: Biology still waits for physics

PubMed Central

Uversky, Vladimir N

2013-01-01

The abundant existence of proteins and regions that possess specific functions without being uniquely folded into unique 3D structures has become accepted by a significant number of protein scientists. Sequences of these intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are characterized by a number of specific features, such as low overall hydrophobicity and high net charge which makes these proteins predictable. IDPs/IDPRs possess large hydrodynamic volumes, low contents of ordered secondary structure, and are characterized by high structural heterogeneity. They are very flexible, but some may undergo disorder to order transitions in the presence of natural ligands. The degree of these structural rearrangements varies over a very wide range. IDPs/IDPRs are tightly controlled under the normal conditions and have numerous specific functions that complement functions of ordered proteins and domains. When lacking proper control, they have multiple roles in pathogenesis of various human diseases. Gaining structural and functional information about these proteins is a challenge, since they do not typically “freeze” while their “pictures are taken.” However, despite or perhaps because of the experimental challenges, these fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting targets for modern protein research. This review briefly summarizes some of the recent advances in this exciting field and considers some of the basic lessons learned from the analysis of physics, chemistry, and biology of IDPs. PMID:23553817

Outreach to internally displaced persons in Bogotá, Colombia: challenges and potential solutions

PubMed Central

Shultz, James M; García, Natalia Muñoz; Ceballos, Ángela Milena Gómez; Florez, Luis Jorge Hernandez; Araya, Ricardo; Verdeli, Helen; Espinel, Zelde; Bolivar, Sandra Patricia Cipagauta; Neria, Yuval

2014-01-01

Programs that provide services for internally displaced persons (IDPs) in Colombia, South America face challenges when attempting to engage and enroll the target population of forced migrants they intend to serve. Innovative multi-strategy outreach approaches must be used in order to effectively seek, recruit, provide services, monitor, and retain IDPs. PMID:28229001

Long-term effects of traumatic experience: Comparison study in the adolescent IDPs in Serbia.

PubMed

Matsunaga, Chieko; Ristic, Dragana; Niregi, Mitsuki

2006-12-01

The purpose of this study is to examine the long term psychological effects of war stress regarded as traumatic experience. The subjects are Serbian internally displaced people (IDP) of adolescent population from Kosovo. It is a very big concern whether the adolescents would overcome the social and psychological difficulties caused by the war stress in order to reconstruct the better society. The result came out that the long-term effects still exist in PTSD, depression and hopelessness, which affects self-esteem and the attitude in purpose in life that are important factors for personality development. This paper also examines the difference between IDPs with war stress and the adolescent sufferers of the big earthquake in Japan.

The Suomi National Polar-Orbiting Partnership (SNPP): Continuing NASA Research and Applications

NASA Technical Reports Server (NTRS)

Butler, James; Gleason, James; Jedlovec, Gary; Coronado, Patrick

2015-01-01

The Suomi National Polar-orbiting Partnership (SNPP) satellite was successfully launched into a polar orbit on October 28, 2011 carrying 5 remote sensing instruments designed to provide data to improve weather forecasts and to increase understanding of long-term climate change. SNPP provides operational continuity of satellite-based observations for NOAA's Polar-orbiting Operational Environmental Satellites (POES) and continues the long-term record of climate quality observations established by NASA's Earth Observing System (EOS) satellites. In the 2003 to 2011 pre-launch timeframe, NASA's SNPP Science Team assessed the adequacy of the operational Raw Data Records (RDRs), Sensor Data Records (SDRs), and Environmental Data Records (EDRs) from the SNPP instruments for use in NASA Earth Science research, examined the operational algorithms used to produce those data records, and proposed a path forward for the production of climate quality products from SNPP. In order to perform these tasks, a distributed data system, the NASA Science Data Segment (SDS), ingested RDRs, SDRs, and EDRs from the NOAA Archive and Distribution and Interface Data Processing Segments, ADS and IDPS, respectively. The SDS also obtained operational algorithms for evaluation purposes from the NOAA Government Resource for Algorithm Verification, Independent Testing and Evaluation (GRAVITE). Within the NASA SDS, five Product Evaluation and Test Elements (PEATEs) received, ingested, and stored data and performed NASA's data processing, evaluation, and analysis activities. The distributed nature of this data distribution system was established by physically housing each PEATE within one of five Climate Analysis Research Systems (CARS) located at either at a NASA or a university institution. The CARS were organized around 5 key EDRs directly in support of the following NASA Earth Science focus areas: atmospheric sounding, ocean, land, ozone, and atmospheric composition products. The PEATES provided the system level interface with members of the NASA SNPP Science Team and other science investigators within each CARS. A sixth Earth Radiation Budget CARS was established at NASA Langley Research Center (NASA LaRC) to support instrument performance, data evaluation, and analysis for the SNPP Clouds and the Earth's Radiant Budget Energy System (CERES) instrument. Following the 2011 launch of SNPP, spacecraft commissioning, and instrument activation, the NASA SNPP Science Team evaluated the operational RDRs, SDRs, and EDRs produced by the NOAA ADS and IDPS. A key part in that evaluation was the NASA Science Team's independent processing of operational RDRs and SDRs to EDRs using the latest NASA science algorithms. The NASA science evaluation was completed in the December 2012 to April 2014 timeframe with the release of a series of NASA Science Team Discipline Reports. In summary, these reports indicated that the RDRs produced by the SNPP instruments were of sufficiently high quality to be used to create data products suitable for NASA Earth System science and applications. However, the quality of the SDRs and EDRs were found to vary greatly when considering suitability for NASA science. The need for improvements in operational algorithms, adoption of different algorithmic approaches, greater monitoring of on-orbit instrument calibration, greater attention to data product validation, and data reprocessing were prominent findings in the reports. In response to these findings, NASA, in late 2013, directed the NASA SNPP Science Team to use SNPP instrument data to develop data products of sufficiently high quality to enable the continuation of EOS time series data records and to develop innovative, practical applications of SNPP data. This direction necessitated a transition of the SDS data system from its pre-launch assessment mode to one of full data processing and production. To do this, the PEATES, which served as NASA's data product testing environment during the prelaunch and early on-orbit periods, were transitioned to Science Investigator-led Processing Systems (SIPS). The distributed data architecture was maintained in this new system by locating the SIPS at the same institutions at which the CARS and PEATES were located. The SIPS acquire raw SNPP instrument Level 0 (i.e. RDR) data over the full SNPP mission from the NOAA ADS and IDPS through the NASA SDS Data Distribution and Depository Element (SD3E). The SIPS process those data into NASA Level 1, Level 2, and global, gridded Level 3 standard products using peer-reviewed algorithms provided by members of the NASA Science Team. The SIPS work with the NASA SNPP Science Team in obtaining enhanced, refined, or alternate real-time algorithms to support the capabilities of the Direct Readout Laboratory (DRL). All data products, algorithm source codes, coefficients, and auxiliary data used in product generation are archived in an assigned NASA Distributed Active Archive Center (DAAC).

Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins.

PubMed

Mercadante, Davide; Wagner, Johannes A; Aramburu, Iker V; Lemke, Edward A; Gräter, Frauke

2017-09-12

Molecular dynamics (MD) simulations have valuably complemented experiments describing the dynamics of intrinsically disordered proteins (IDPs), particularly since the proposal of models to solve the artificial collapse of IDPs in silico. Such models suggest redefining nonbonded interactions, by either increasing water dispersion forces or adopting the Kirkwood-Buff force field. These approaches yield extended conformers that better comply with experiments, but it is unclear if they all sample the same intrachain dynamics of IDPs. We have tested this by employing MD simulations and single-molecule Förster resonance energy transfer spectroscopy to sample the dimensions of systems with different sequence compositions, namely strong and weak polyelectrolytes. For strong polyelectrolytes in which charge effects dominate, all the proposed solutions equally reproduce the expected ensemble's dimensions. For weak polyelectrolytes, at lower cutoffs, force fields abnormally alter intrachain dynamics, overestimating excluded volume over chain flexibility or reporting no difference between the dynamics of different chains. The TIP4PD water model alone can reproduce experimentally observed changes in extensions (dimensions), but not quantitatively and with only weak statistical significance. Force field limitations are reversed with increased interaction cutoffs, showing that chain dynamics are critically defined by the presence of long-range interactions. Force field analysis aside, our study provides the first insights into how long-range interactions critically define IDP dimensions and raises the question of which length range is crucial to correctly sample the overall dimensions and internal dynamics of the large group of weakly charged yet highly polar IDPs.

Atomistic details of the disordered states of KID and pKID. Implications in coupled binding and folding.

PubMed

Ganguly, Debabani; Chen, Jianhan

2009-04-15

Intrinsically disordered proteins (IDPs) are a newly recognized class of functional proteins for which a lack of stable tertiary fold is required for function. Because of the heterogeneous and dynamical nature, molecular modeling is necessary to provide the missing details of disordered states of IDP that are crucial for understanding their functions. In particular, generalized Born (GB) implicit solvent, combined with replica exchange (REX), might offer an optimal balance between accuracy and efficiency for modeling IDPs. We carried out extensive REX simulations in an optimized GB force field to characterize the disordered states of a regulatory IDP, KID domain of transcription factor CREB, and its phosphorylated form, pKID. The results revealed that both KID and pKID, though highly disordered on the tertiary level, are compact and mainly occupy a small number of helical substates. Interestingly, although phosphorylation of KID Ser133 leads only to marginal changes in average helicities on the ensemble level, underlying conformational substates differ significantly. In particular, pSer133 appears to restrict the accessible conformational space of the loop region and thus reduces the entropic cost of KID folding upon binding to the KIX domain of CREB-binding protein. Such an expanded role of phosphorylation in the KID:KIX recognition was not previously recognized because of a lack of substantial conformational changes on the ensemble level and inaccessibility of the structural details from experiments. The results also suggest that an implicit solvent-based modeling framework, despite various existing limitations, might be feasible for accurate atomistic simulation of small IDPs in general.

Novel Experimental Simulations of the Atmospheric Injection of Meteoric Metals

NASA Astrophysics Data System (ADS)

Gómez Martín, J. C.; Bones, D. L.; Carrillo-Sánchez, J. D.; James, A. D.; Trigo-Rodríguez, J. M.; Fegley, B., Jr.; Plane, J. M. C.

2017-02-01

A newly developed laboratory, Meteoric Ablation Simulator (MASI), is used to test model predictions of the atmospheric ablation of interplanetary dust particles (IDPs) with experimental Na, Fe, and Ca vaporization profiles. MASI is the first laboratory setup capable of performing time-resolved atmospheric ablation simulations, by means of precision resistive heating and atomic laser-induced fluorescence detection. Experiments using meteoritic IDP analogues show that at least three mineral phases (Na-rich plagioclase, metal sulfide, and Mg-rich silicate) are required to explain the observed appearance temperatures of the vaporized elements. Low melting temperatures of Na-rich plagioclase and metal sulfide, compared to silicate grains, preclude equilibration of all the elemental constituents in a single melt. The phase-change process of distinct mineral components determines the way in which Na and Fe evaporate. Ca evaporation is dependent on particle size and on the initial composition of the molten silicate. Measured vaporized fractions of Na, Fe, and Ca as a function of particle size and speed confirm differential ablation (I.e., the most volatile elements such as Na ablate first, followed by the main constituents Fe, Mg, and Si, and finally the most refractory elements such as Ca). The Chemical Ablation Model (CABMOD) provides a reasonable approximation to this effect based on chemical fractionation of a molten silicate in thermodynamic equilibrium, even though the compositional and geometric description of IDPs is simplistic. Improvements in the model are required in order to better reproduce the specific shape of the elemental ablation profiles.

The "Interaction with Disabled Persons" Scale: Revisiting Its Internal Consistency and Factor Structure, and Examining Item-Level Properties

ERIC Educational Resources Information Center

Iacono, Teresa; Tracy, Jane; Keating, Jenny; Brown, Ted

2009-01-01

The "Interaction with Disabled Persons" scale (IDP) has been used in research into baseline attitudes and to evaluate whether a shift in attitudes towards people with developmental disabilities has occurred following some form of intervention. This research has been conducted on the assumption that the IDP measures attitudes as a…

Invention Development Program Helps Nurture NCI at Frederick Technologies | Poster

Cancer.gov

The Invention Development Fund (IDF) was piloted by the Technology Transfer Center (TTC) in 2014 to facilitate the commercial development of NCI technologies. The IDF received a second round of funding from the NCI Office of the Director and the Office of Budget and Management to establish the Invention Development Program (IDP) for fiscal year 2016. The IDP is using these

The alphabet of intrinsic disorder

PubMed Central

Uversky, Vladimir N

2013-01-01

The ability of a protein to fold into unique functional state or to stay intrinsically disordered is encoded in its amino acid sequence. Both ordered and intrinsically disordered proteins (IDPs) are natural polypeptides that use the same arsenal of 20 proteinogenic amino acid residues as their major building blocks. The exceptional structural plasticity of IDPs, their capability to exist as heterogeneous structural ensembles and their wide array of important disorder-based biological functions that complements functional repertoire of ordered proteins are all rooted within the peculiar differential usage of these building blocks by ordered proteins and IDPs. In fact, some residues (so-called disorder-promoting residues) are noticeably more common in IDPs than in sequences of ordered proteins, which, in their turn, are enriched in several order-promoting residues. Furthermore, residues can be arranged according to their “disorder promoting potencies,” which are evaluated based on the relative abundances of various amino acids in ordered and disordered proteins. This review continues a series of publications on the roles of different amino acids in defining the phenomenon of protein intrinsic disorder and concerns glutamic acid, which is the second most disorder-promoting residue. PMID:28516010

Are Charge-State Distributions a Reliable Tool Describing Molecular Ensembles of Intrinsically Disordered Proteins by Native MS?

NASA Astrophysics Data System (ADS)

Natalello, Antonino; Santambrogio, Carlo; Grandori, Rita

2017-01-01

Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution. However, structural rearrangements during electrospray-ionization (ESI) or after the transfer to the gas phase could affect data obtained by native ESI-MS. In particular, charge-state distributions (CSDs) are affected by protein conformation inside ESI droplets, while ion mobility (IM) reflects protein conformation in the gas phase. This review focuses on the available evidence relating IDP solution ensembles with CSDs, trying to summarize cases of apparent consistency or discrepancy. The protein-specificity of ionization patterns and their responses to ligands and buffer conditions suggests that CSDs are imprinted to protein structural features also in the case of IDPs. Nevertheless, it seems that these proteins are more easily affected by electrospray conditions, leading in some cases to rearrangements of the conformational ensembles.

Post-entry and volcanic contaminant abundances of zinc, copper, selenium, germanium and gallium in stratospheric micrometeorites

NASA Technical Reports Server (NTRS)

Rietmeijer, Frans J. M.

1995-01-01

Some fraction of Zn, Cu, Se, Ga and Ge in chondritic interplanetary dust particles (IDPs) collected in the lower stratosphere between 1981 May and 1984 June has a volcanic origin. I present a method to evaluate the extent of this unavoidable type of stratospheric contamination for individual particles. The mass-normalized abundances for Cu and Ge as a function of mass-normalized stratospheric residence time show their time-integrated stratospheric aerosol abundances. The Zn, Se and Ga abundances show a subdivision into two groups that span approximately two-year periods following the eruptions of the Mount St. Helens (1980 May) and El Chichon (1982 April) volcanoes. Elemental abundances in particles collected at the end of each two-year period indicate low, but not necessarily ambient, volcanic stratospheric abundances. Using this time-integrated baseline, I calculate the straospheric contaminant fractions in nine IDPs and show that Zn, SE and Ga abundances in chondritic IDPs derive in part from stratospheric aerosol contaminants. Post-entry elemental abundances (i.e., the amount that survived atmospheric entry heating of the IDP) show enrichments relative to the CI abundances but in a smaller number of particles than previously suggested.

Thermodynamic contribution of backbone conformational entropy in the binding between SH3 domain and proline-rich motif.

PubMed

Zeng, Danyun; Shen, Qingliang; Cho, Jae-Hyun

2017-02-26

Biological functions of intrinsically disordered proteins (IDPs), and proteins containing intrinsically disordered regions (IDRs) are often mediated by short linear motifs, like proline-rich motifs (PRMs). Upon binding to their target proteins, IDPs undergo a disorder-to-order transition which is accompanied by a large conformational entropy penalty. Hence, the molecular mechanisms underlying control of conformational entropy are critical for understanding the binding affinity and selectivity of IDPs-mediated protein-protein interactions (PPIs). Here, we investigated the backbone conformational entropy change accompanied by binding of the N-terminal SH3 domain (nSH3) of CrkII and PRM derived from guanine nucleotide exchange factor 1 (C3G). In particular, we focused on the estimation of conformational entropy change of disordered PRM upon binding to the nSH3 domain. Quantitative characterization of conformational dynamics of disordered peptides like PRMs is limited. Hence, we combined various methods, including NMR model-free analysis, δ2D, DynaMine, and structure-based calculation of entropy loss. This study demonstrates that the contribution of backbone conformational entropy change is significant in the PPIs mediated by IDPs/IDRs. Copyright © 2017 Elsevier Inc. All rights reserved.

IDPT: Insights into potential intrinsically disordered proteins through transcriptomic analysis of genes for prostate carcinoma epigenetic data.

PubMed

Mallik, Saurav; Sen, Sagnik; Maulik, Ujjwal

2016-07-15

Involvement of intrinsically disordered proteins (IDPs) with various dreadful diseases like cancer is an interesting research topic. In order to gain novel insights into the regulation of IDPs, in this article, we perform a transcriptomic analysis of mRNAs (genes) for transcripts encoding IDPs on a human multi-omics prostate carcinoma dataset having both gene expression and methylation data. In this regard, firstly the genes that consist of both the expression and methylation data, and that are corresponding to the cancer-related prostate-tissue-specific disordered proteins of MobiDb database, are selected. We apply standard t-test for determining differentially expressed genes as well as differentially methylated genes. A network having these genes and their targeter miRNAs from Diana Tarbase v7.0 database and corresponding Transcription Factors from TRANSFAC and ITFP databases, is then built. Thereafter, we perform literature search, and KEGG pathway and Gene Ontology analyses using DAVID database. Finally, we report several significant potential gene-markers (with the corresponding IDPs) that have inverse relationship between differential expression and methylation patterns, and that are hub genes of the TF-miRNA-gene network. Copyright © 2016 Elsevier B.V. All rights reserved.

Are Charge-State Distributions a Reliable Tool Describing Molecular Ensembles of Intrinsically Disordered Proteins by Native MS?

PubMed

Natalello, Antonino; Santambrogio, Carlo; Grandori, Rita

2017-01-01

Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution. However, structural rearrangements during electrospray-ionization (ESI) or after the transfer to the gas phase could affect data obtained by native ESI-MS. In particular, charge-state distributions (CSDs) are affected by protein conformation inside ESI droplets, while ion mobility (IM) reflects protein conformation in the gas phase. This review focuses on the available evidence relating IDP solution ensembles with CSDs, trying to summarize cases of apparent consistency or discrepancy. The protein-specificity of ionization patterns and their responses to ligands and buffer conditions suggests that CSDs are imprinted to protein structural features also in the case of IDPs. Nevertheless, it seems that these proteins are more easily affected by electrospray conditions, leading in some cases to rearrangements of the conformational ensembles. Graphical Abstract ᅟ.

Isotopic and Trace Element Compositions of Antarctic Micrometeorites and Comparison with IDPs

NASA Astrophysics Data System (ADS)

Stadermann, F. J.; Olinger, C. T.

1992-07-01

Antarctic micrometeorites (AMMs) show resemblances and differences to both stratospheric interplanetary dust particles (IDPs) and chondritic meteorites, but the exact nature of this relationship has yet to be established. We measured Ne, H, C, and N isotopic compositions, as well as trace element abundances in several AMMs in order to compare the results to similar measurements of IDPs (Stadermann, 1991). AMMs for this study were collected near Cap-Prudhomme (Maurette et al., 1989), and optically selected (Olinger et al., 1990). Noble gases of 23 selected AMMs were extracted through laser vaporization. Nine of these particles contained implanted solar Ne and one showed a clear signature from spallogenic Ne, confirming their extraterrestrial origin. We selected fragments from 6 of these particles, plus 2 containing apparent Ne excess and one with a roughly chondritic bulk chemistry but immeasurably low Ne, for further analyses. Secondary ion mass spectrometry (SIMS) was used to measure the H, C, and N isotopic compositions. These measurements turned out to be difficult, since the concentrations of H and C in the analyzed samples were significantly lower than in IDPs. The low concentration of C also affected the N isotopic measurements because N could only be measured as CN-. We were able to measure H in 9, as well as C and N in 3 AMMs. All measurements yielded isotopically normal results. Previous determinations of the O isotopic compositions of the same samples (Virag, pers. comm.) also gave no indication of isotopic anomalies. These results are significantly different from measurements of IDPs, where isotopic anomalies in H and N were found in roughly 1/2 and 1/3 of the particles, respectively. SIMS was also used to measure the rare earth and trace element abundances in up to 4 different fragments of 6 AMMs. Although most particles had roughly chondritic abundances, anomalous concentrations were found for Ca, Li, Co, Ni, and Ba. Significant Ca depletions up to 0.03 x C1 were observed in 5 out of 6 particles. This effect is well known from IDPs but nonetheless little understood. Enrichments up to 10 x C1 in Li and up to 100 x C1 in Ba were detected in 4 particles each. The Ba enrichment in AMMs has been observed before and can most likely be attributed to terrestrial contamination (Maurette et al., 1992). The origin of the unusual Li enrichment is unknown. Ni was depleted in all analyzed particles and was strongly correlated with Co, whose depletions relative to C1 were always smaller than for Ni. In the particle with the largest Ni-Co depletion, a melted sphere, this effect was accompanied by an Fe depletion. The Fe/Si, Co/Si and Ni/Si ratios relative to C1 were (0.4, 0.06, 0.02). Similar correlated depletions of Fe, Co, and Ni were also found in 2 out of 13 IDPs with otherwise chondritic abundances (Stadermann, 1991). The ratios of their Fe, Co, Ni depletions were (0.2, 0.07, 0.01) and (0.3, 0.03, 0.01), respectively. Interestingly, these 2 IDPs also contained H with isotopically normal composition and C concentrations that were too low for C and N isotopic measurements. One of these particles was a melted spherule. All these similarities suggest that some AMMs and some IDPs may have close relationships, although AMMs and IDPs in general do not represent the same class of extraterrestrial material. Maurette M. et al. (1989) Lunar Planet. Sci. 20, 644-645. Maurette M. et al. (1992) Lunar Planet. Sci. 23, 859-860. Olinger C.T. et al. (1990) Earth Planet. Sci. Lett. 100, 77-93. Stadermann F.J. (1991) Lunar Planet. Sci. 22, 1311-1312.

Pristine Stratospheric Collections of Cosmic Dust

NASA Technical Reports Server (NTRS)

Messenger, S.; Keller, L. P.; Nakamura-Messenger, K.; Clemett, S. J.

2012-01-01

Since 1981, NASA has routinely collected interplanetary dust particles (IDPs) in the stratosphere by inertial impact onto silicone oil-coated flat plate collectors deployed on the wings of high-altitude aircraft [1]. The highly viscous oil traps and localizes the particles, which can fragment during collection. Particles are removed from the collectors with a micromanipulator and washed of the oil using organic solvents, typically hexane or xylene. While silicone oil is an efficient collection medium, its use is problematic. All IDPs are initially coated with this material (polydimethylsiloxane, n(CH3)2SiO) and traces of oil may remain after cleaning. The solvent rinse itself is also a concern as it likely removes indigenous organics from the particles. To avoid these issues, we used a polyurethane foam substrate for the oil-free stratospheric collection of IDPs.

Fuel Efficient Stoves for Darfur Camps of Internally DisplacedPersons - Report of Field Trip to North and South Darfur, Nov. 16 -Dec.17, 2005

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

Galitsky, Christina; Gadgil, Ashok; Jacobs, Mark

Approximately 2.2 million internally displaced persons (''IDPs'') in Darfur are living in dense camps scattered in arid areas with low fuelwood productivity. Unsustainable harvesting of fuelwood by the IDPs has created ever increasing zones of denudation, that now (in November 2005) have reached several kilometers from the camp boundaries. Leaving the safety of the camps to fetch fuelwood from farther and farther away imposes great risk and hardship on the IDP women. Three different metal fuel efficient stove (''FES'') designs were tested in Darfur IDP camps for their suitability to substantially reduce the fuelwood needs of IDPs. The mud-and-dung ''ITDG''more » stoves being promoted under the current FES program were also examined and tested. A modified design of the ITDG mud-and-dung stove, ''Avi'', was developed, built and tested. Systematic informal surveys of IDP households were undertaken in North and South Darfur to understand the household parameters related to family size, food, fuel, cooking habits, cooking pots, expenditure on fuel, and preferences related to alternative ways to spend time/money if fuel could be saved. Surveys found that a significant fraction of families are missing meals for lack of fuel (50% in South Darfur, and 90% in the North Darfur camps visited by the mission). About 60% of women in South Darfur, and about 90% of women in North Darfur camps purchase fuelwood. Selling some of the food rations to purchase fuel to cook meals was significant (40%) in South Darfur and has become common (80%) in North Darfur. The LBNL mission found that two of the metal stoves and the mud-and-dung Avi can significantly reduce fuelwood consumption using the same fuel, pot, cooking methods, and food ingredients used by Darfur IDPs. The most suitable design for Darfur conditions would be a modified ''Tara'' stove. With training of the cooks in tending the fire, this stove can save 50% fuel for the IDPs. The stove costs less than $10 (US) to produce in Darfur, and saves fuelwood worth $160 annually at local market prices. For programmatic and administrative reasons, the LBNL mission do not recommend a mud-and-dung stove, for which control of quality and dimensional accuracy is expensive and cumbersome to administer, particularly in a rapid large rollout effort. A light metal stove, on the other hand, can be rapidly produced in large numbers locally in Darfur, with good quality control exercised on the material and dimensions of the stoves right at the workshop where it is produced. LBNL mission also recommends immediate trials of 50 Tara stoves in a pilot technical rollout, 500 Tara stoves in a pilot social rollout, in parallel with a technical effort to modify the Tara design to make it better suited for Darfur camp conditions. The mission also recommends a program for manufacturing, disseminating the metal stoves, and educating the IDPs in fuel-efficient cooking practices. Monitoring of the stove quality, dissemination effort and training should be an integral part of the program, with systematic summaries planned with 10,000, 50,000 and 100,000 stoves have been disseminated. In the above pilot rollouts as well as in the final implementation, it is important to continue to pay attention to training of the cooks in tending the cooking fire in the stoves, and offer continued social reinforcement to this training (e.g., through periodic competitions to cook normal meals with the least fuelwood use.)« less

Backbone conformational preferences of an intrinsically disordered protein in solution.

PubMed

Espinoza-Fonseca, L Michel; Ilizaliturri-Flores, Ian; Correa-Basurto, José

2012-06-01

We have performed a 4-μs molecular dynamics simulation to investigate the native conformational preferences of the intrinsically disordered kinase-inducible domain (KID) of the transcription factor CREB in solution. There is solid experimental evidence showing that KID does not possess a bound-like structure in solution; however, it has been proposed that coil-to-helix transitions upon binding to its binding partner (CBP) are template-driven. While these studies indicate that IDPs possess a bias towards the bound structure, they do not provide direct evidence on the time-dependent conformational preferences of IDPs in atomic detail. Our simulation captured intrinsic conformational characteristics of KID that are in good agreement with experimental data such as a very small percentage of helical structure in its segment α(B) and structural disorder in solution. We used dihedral principal component analysis dPCA to map the conformations of KID in the microsecond timescale. By using principal components as reaction coordinates, we further constructed dPCA-based free energy landscapes of KID. Analysis of the free energy landscapes showed that KID is best characterized as a conformational ensemble of rapidly interconverting conformations. Interestingly, we found that despite the conformational heterogeneity of the backbone and the absence of substantial secondary structure, KID does not randomly sample the conformational space in solution: analysis of the (Φ, Ψ) dihedral angles showed that several individual residues of KID possess a strong bias toward the helical region of the Ramachandran plot. We suggest that the intrinsic conformational preferences of KID provide a bias toward the folded state without having to populate bound-like conformations before binding. Furthermore, we argue that these conformational preferences do not represent actual structural constraints which drive binding through a single pathway, which allows for specific interactions with multiple binding partners. Based on this evidence, we propose that the backbone conformational preferences of KID provide a thermodynamic advantage for folding and binding without negatively affecting the kinetics of binding. We further discuss the relation of our results to previous studies to rationalize the functional implications of the conformational preferences of IDPs, such as the optimization of structural disorder in protein-protein interactions. This study illustrates the importance in obtaining atomistic information of intrinsically disordered proteins in real time to reveal functional features arising from their complex conformational space.

Local constructions of gender-based violence amongst IDPs in northern Uganda: analysis of archival data collected using a gender- and age-segmented participatory ranking methodology.

PubMed

Ager, Alastair; Bancroft, Carolyn; Berger, Elizabeth; Stark, Lindsay

2018-01-01

Gender-based violence (GBV) is a significant problem in conflict-affected settings. Understanding local constructions of such violence is crucial to developing preventive and responsive interventions to address this issue. This study reports on a secondary analysis of archived data collected as part of formative qualitative work - using a group participatory ranking methodology (PRM) - informing research on the prevalence of GBV amongst IDPs in northern Uganda in 2006. Sixty-four PRM group discussions were held with women, with men, with girls (aged 14 to 18 years), and with boys (aged 14 to 18 years) selected on a randomized basis across four internally displaced persons (IDP) camps in Lira District. Discussions elicited problems facing women in the camps, and - through structured participatory methods - consensus ranking of their importance and narrative accounts explaining these judgments. Amongst forms of GBV faced by women, rape was ranked as the greatest concern amongst participants (with a mean problem rank of 3.4), followed by marital rape (mean problem rank of 4.5) and intimate partner violence (mean problem rank of 4.9). Girls ranked all forms of GBV as higher priority concerns than other participants. Discussions indicated that these forms of GBV were generally considered normalized within the camp. Gender roles and power, economic deprivation, and physical and social characteristics of the camp setting emerged as key explanatory factors in accounts of GBV prevalence, although these played out in different ways with respect to differing forms of violence. All groups acknowledged GBV to represent a significant threat - among other major concerns such as transportation, water, shelter, food and security - for women residing in the camps. Given evidence of the significantly higher risk in the camp of intimate partner violence and marital rape, the relative prominence of the issue of rape in all rankings suggests normalization of violence within the home. Programs targeting reduction in GBV need to address community-identified root causes such as economic deprivation and social norms related to gender roles. More generally, PRM appears to offer an efficient means of identifying local constructions of prevailing challenges in a manner that can inform programming.

Cometary dust: the diversity of primitive refractory grains

PubMed Central

Ishii, H. A.

2017-01-01

Comet dust is primitive and shows significant diversity. Our knowledge of the properties of primitive cometary particles has expanded significantly through microscale investigations of cosmic dust samples (anhydrous interplanetary dust particles (IDPs), chondritic porous (CP) IDPs and UltraCarbonaceous Antarctic micrometeorites, Stardust and Rosetta), as well as through remote sensing (Spitzer IR spectroscopy). Comet dust are aggregate particles of materials unequilibrated at submicrometre scales. We discuss the properties and processes experienced by primitive matter in comets. Primitive particles exhibit a diverse range of: structure and typology; distribution of constituents; concentration and form of carbonaceous and refractory organic matter; Mg- and Fe-contents of the silicate minerals; sulfides; existence/abundance of type II chondrule fragments; high-temperature calcium–aluminium inclusions and ameboid-olivine aggregates; and rarely occurring Mg-carbonates and magnetite, whose explanation requires aqueous alteration on parent bodies. The properties of refractory materials imply there were disc processes that resulted in different comets having particular selections of primitive materials. The diversity of primitive particles has implications for the diversity of materials in the protoplanetary disc present at the time and in the region where the comets formed. This article is part of the themed issue ‘Cometary science after Rosetta’. PMID:28554979

Precision Oxygen Isotope Measurements of Two C-Rich Hydrated Interplanetary Dust Particles

NASA Technical Reports Server (NTRS)

Snead, C. J.; Keller, L. P.; McKeegan, K. D.; Messenger, S.

2016-01-01

Introduction: Chondritic-smooth IDPs (Interplanetary Dust Particles) are low porosity objects whose mineralogy is dominated by aqueous alteration products such as Mg-rich phyllosilicates (smectite and serpentine group) and Mg-Fe carbonate minerals. Their hydrated mineralogy combined with low atmospheric entry velocities have been used to infer an origin largely from asteroidal sources. Spectroscopic studies show that the types and abundance of organic matter in CS IDPs is similar to that in CP IDPs. Although CS IDPs show broad similarities to primitive carbonaceous chondrites, only a few particles have been directly linked to specific meteorite groups such as CM and CI chondrites based on the presence of diagnostic minerals. Many CS IDPs however, have carbon contents that greatly exceed that of known meteorite groups suggesting that they either may derive from comets or represent samples of more primitive parent bodies than do meteorites. It is now recognized that many large, dark primitive asteroids in the outer main belt, as well as some trans-Neptunian objects, show spectroscopic evidence for aqueous alteration products on their surfaces. Some CS IDPs exhibit large bulk D enrichments similar to those observed in the cometary CP IDPs. While hydrated minerals in comets have not been unambiguously identified to date, the presence of the smectite group mineral nontronite has been inferred from infrared spectra obtained from the ejecta from comet 9P/Tempel 1 during the Deep Impact mission. Recent observations of low temperature sulfide minerals in Stardust mission samples suggest that limited aqueous activity occurred on comet Wild-2. All of these observations, taken together, suggest that the high-carbon hydrated IDPs are abundant and important samples of primitive solar system objects not represented in meteorite collections. Oxygen isotopic compositions of chondrites reflect mixing between a 16O-rich reservoir and a 17O,18O-rich reservoir produced via mass-independent fractionation. The composition of the 16O-rich reservoir is well constrained but material representing the 17O,18O-rich end-member is rare. Self-shielding models predict that cometary water, presumed to represent this reservoir, should be enriched in 17O and 18O by greater than 200 per mille. The high-carbon hydrated IDPs may be among the best materials available to search for preserved "cometary" H2O signatures. In order to better understand the origin and evolution of these particles, we have obtained 10 hydrated interplanetary dust particles for coordinated mineralogical, isotopic and organic analyses. We have previously reported the results of mineralogical and O isotopic measurements of two hydrated IDPs; here we present results of O isotopic measurements of three additional IDPs. Samples and Methods: Three interplanetary dust particles (L2079C35, L2083D46 and L2083E46) were embedded in S and partially ultramicrotomed into approximately 70 nanometer sections for analysis via transmission electron microscopy (TEM). The remainders of the unsliced particles were removed from S and pressed into high purity Au foil that was cleaned with HF acid and annealed at 800 degrees Centigrade. The pressed IDPs were analyzed via electron microprobe analysis (EPMA) for quantitative bulk chemical analysis. After EPMA analysis, the IDPs were subjected to precision O isotope analysis with the UCLA Cameca IMS-1270 ion probe. A 20 kiloelectronvolt, 0.5 nanoangstrom Cs+ primary beam of approximately 15 micrometers diameter was used for each measurement. Small particles of San Carlos olivine and Burma spinel were pressed into the Au foil for use as standards to correct for instrumental mass fractionation. The detection system was configured for multicollection, with 16O measured on a Faraday cup, and 17O and 18O measured on electron multipliers (EMs). Individual analyses consisted of 15 cycles of 10 seconds per cycle. Additionally, two microtome thin sections were measured for H isotopic compositions with the JSC NanoSIMS 50L ion probe. An 8 picoangstrom, 16 kiloelectronvolt Cs plus primary beam was used. Measurements consisted of H, C, 12C, 16O, and 18O collected with EMs in multicollection. Terrestrial biotite and kerogen were used for isotopic standards. A significant challenge in O isotope measurement of hydrated minerals is the interference from 16OH at mass 17O. We ensured that the 17O and 16OH peaks were fully resolved by using a mass resolution of greater than 7000 and by careful analyses of San Carlos olivine, Burma spinel and chlorite hydrated mineral standards. The hydride was further suppressed with a cold finger attached to an LN2 dewar to trap volatiles in the sample chamber. All sputtered ions were counted (i.e. presputtering was not used); after applying background, yield and deadtime corrections, we performed a change-point analysis on our data via R in order to determine when the sample reached sputtering equilibrium; data points collected prior to the change point were excluded. Change-point analysis was also used to determine whether the IDP had completely sputtered. Results: Mineralogy. IDPs C35 and E46 exhibited hydrated mineralogies, Fe-Ni sulfide grains, nanoglobules and occasional enstatite grains distributed throughout a fine-grained Mg-Fe saponite matrix. C35 also contained breunnerite (Mg,Fe)CO3; solar flare tracks were observed in enstatite, indicating minimal atmospheric entry heating. The mineralogy of D46 is dominated by a large FeS grain with a minor component of adhering silicate material. D46 was strongly heated during atmorpheric entry as evidenced by a well-developed magnetite rim. EPMA analyses show that both C35 and E46 have high carbon contents of 20 weight percentage (approximately 6X CI). D46 contains approximately 6 wt.weight percentage C. A significant amount of the carbon is present as carbon nanoglobules. Results: Hydrogen isotopes: Although the bulk delta D values of both sections of L2079C35 were within error of SMOW (minus 33 plus or minus 19 per mille, 1 plus or minus 14 per mille 1 sigma), several delta D-rich hotspots were also identified, reaching 2000 per mille. As shown in Fig. 1, these hotspots are clearly associated with discrete carbonaceous inclusions that are akin to nanoglobules found in many meteorites and other IDPs. Oxygen Isotopes. Results of the oxygen isotope measurements are shown in Figure 1. The oxygen isotope composition for L2079C35 was delta 18O equals plus11.6 plus or minus 1.9per mille, delta 17O equals plus 7.9 plus or minus 1.9per mille (2 standard errors). The oxygen isotope composition for L2083D46 was delta 18O equals minus 8.1 plus or minus 1.9 per mille, delta 17O equals minus 6.4 plus or minus 3.1 per mille (2 standard errors). The oxygen isotope composition for L2083E46 was delta 18O equals plus 12.0 plus or minus 1.9 per mille, delta 17O equals plus 9.2 plus or minus 2.0 per mille (2 standard errors). Discussion: Despite mineralogical similarities to highly aqueously altered carbonaceous chondrites, the hydrated IDPs we analyzed have oxygen isotopic compositions that are distinct from matrix materials in the CI, CM, and CR chondrites. The IDPs plot along the Young-Russell line, with delta 17O values for C35 and E46 suggestive of interaction with a 16O-poor reservoir. However, we have thus far not observed evidence of extreme 16O-poor reservoirs expected from self-shielding models and observed in Acfer 094 simplectite. The high carbon contents of the IDPs also set them apart from known meteoritic samples. The lack of atmospheric entry heating effects are consistent with low encounter velocities and suggest either an asteroidal source, or a low inclination, low eccentricity cometary origin. Conclusions: The unusual oxygen isotopic compositions, high carbon contents, and the abundance of Drich nanoglobules, together, suggest that the high-carbon, hydrated IDPs are derived from a primitive source that is not yet represent ed in meteorite collections.

The 8-13 micron spectra of comets and the composition of silicate grains

NASA Technical Reports Server (NTRS)

Hanner, Martha S.; Lynch, David K.; Russell, Ray W.

1994-01-01

We have analyzed the existing spectra of seven comets which show an emission feature at 7.8-13 micrometers. Most have been converted to a common calibration, taking into account the SiO feature in late-type standard stars. The spectra are compared with spectra of the Trapezium, interplanetary dust particles (IDPs), laboratory mineral samples, and small particle emission models. The emission spectra show a variety of shapes; there is no unique 'cometary silicate'. A peak at 11.20-11.25 micrometers, indicative of small crystalline olivine particles, is seen in only three comets of this sample, P/Halley, Bradfield 1987 XXIX, and Levy 1990 XX. The widths of the emission features range from 2.6 to 4.1 micrometers (FWHM). To explain the differing widths and the broad 9.8 micrometers maximum, glassy silicate particles, including both pyroxene and olivine compositions, are the most plausible candidates. Calculations of emission models confirm that small grains of glassy silicate well mixed with carbonaceous material are plausible cometary constituents. No single class of chondritic aggregate IDPs exhibits spectra closely matching the comet spectra. A mixture of IDP spectra, particularly the glass-rich aggregates, approximately matches the spectra of comets P/Halley, Levy, and Bradfield 1987 XXIX. Yet, if comets are simply a mix of IDP types, it is puzzling that the classes of IDPs are so distinct. None of the comet spectra match the spectrum of the Trapezium. Thus, the mineralogy of the cometary silicates is not the same as that of the interstellar medium. The presence of a component of crystalline silicates in comets may be evidence of mixing between high- and low-temperature regions in the solar nebula.

The Impact of O-Glycan Chemistry on the Stability of Intrinsically Disordered Proteins

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

Beckham, Gregg T; Prates, Erica T; Crowley, Michael F

2018-03-02

Protein glycosylation is a diverse post-translational modification that serves myriad biological functions. O-linked glycans in particular vary widely in extent and chemistry in eukaryotes, with secreted proteins from fungi and yeast commonly exhibiting O-mannosylation in intrinsically disordered regions of proteins, likely for proteolysis protection, among other functions. However, it is not well understood why mannose is often the preferred glycan, and more generally, if the neighboring protein sequence and glycan have coevolved to protect against proteolysis in glycosylated intrinsically disordered proteins (IDPs). Here, we synthesized variants of a model IDP, specifically a natively O-mannosylated linker from a fungal enzyme, withmore » a-O-linked mannose, glucose, and galactose moieties, along with a non-glycosylated linker. Upon exposure to thermolysin, O-mannosylation, by far, provides the highest extent of proteolysis protection. To explain this observation, extensive molecular dynamics simulations were conducted, revealing that the axial configuration of the C2-hydroxyl group (2-OH) of a-mannose adjacent to the glycan-peptide bond strongly influences the conformational features of the linker. Specifically, a-mannose restricts the torsions of the IDP main chain more than other glycans whose equatorial 2-OH groups exhibit interactions that favor perpendicular glycan-protein backbone orientation. We suggest that IDP stiffening due to O-mannosylation impairs protease action, with contributions from protein-glycan interactions, protein flexibility, and protein stability. Our results further imply that resistance to proteolysis is an important driving force for evolutionary selection of a-mannose in eukaryotic IDPs, and more broadly, that glycan motifs for proteolysis protection likely coevolve with the protein sequence to which they attach.« less

Validity and reliability of Arabic version of the ID Pain screening questionnaire in the assessment of neuropathic pain.

PubMed

Abu-Shaheen, Amani; Yousef, Shehu; Riaz, Muhammad; Nofal, Abdullah; Khan, Sarfaraz; Heena, Humariya

2018-01-01

Diagnosis of neuropathic pain (NP) can be challenging. The ID Pain (ID-P) questionnaire, a screening tool for NP, has been used widely both in the original version and translated forms. The aim of this study was to develop an Arabic version of ID-P and assess its validity and reliability in detecting neuropathic pain. The original ID-P was translated in Arabic language and administered to the study population. Reliability of the Arabic version was evaluated by percentage observed agreement, and Cohen's kappa; and validity by sensitivity, specificity, correctly classified, and receiver operating characteristic (ROC) curve. Physician diagnosis was considered as the gold standard for comparing the diagnostic accuracy. The study included 375 adult patients (153 [40.8%] with NP; 222 [59.2%] with nociceptive pain). Overall observed percentage agreement and Cohen's kappa were >90% and >0.80, respectively. Median (range) score of ID-P scale was 3 (2-4) and 1 (0-2) in the NP group and NocP group, respectively (p<0.001). Area under the ROC curve was 0.808 (95% CI, 0.764-0.851). For the cut-off value of ≥2, sensitivity was 84.3%, specificity was 66.7%, and correct classification was 73.9%. Thus, the Arabic version of ID-P showed moderate reliability and validity as a pain assessment tool. This article presents the psychometric properties of the Arabic version of ID Pain questionnaire. This Arabic version may serve as a simple yet important screening tool, and help in appropriate management of neuropathic pain, specifically in primary care centers in the Kingdom of Saudi Arabia.

Intrinsically Disordered Proteins as Important Players during Desiccation Stress of Soybean Radicles.

PubMed

Liu, Yun; Wu, Jiahui; Sun, Nan; Tu, Chengjian; Shi, Xiaoying; Cheng, Hua; Liu, Simu; Li, Shuiming; Wang, Yong; Zheng, Yizhi; Uversky, Vladimir N

2017-07-07

Intrinsically disordered proteins (IDPs) play a variety of important physiological roles in all living organisms. However, there is no comprehensive analysis of the abundance of IDPs associated with environmental stress in plants. Here, we show that a set of heat-stable proteins (i.e., proteins that do not denature after boiling at 100 °C for 10 min) was present in R 0mm and R 15mm radicles (i.e., before radicle emergence and 15 mm long radicles) of soybean (Glycine max) seeds. This set of 795 iTRAQ-quantified heat-stable proteins contained a high proportion of wholly or highly disordered proteins (15%), which was significantly higher than that estimated for the whole soybean proteome containing 55,787 proteins (9%). The heat-stable proteome of soybean radicles that contain many IDPs could protect lactate dehydrogenase (LDH) during freeze-thaw cycles. Comparison of the 795 heat-stable proteins in the R 0mm and R 15mm soybean radicles revealed that many of these proteins changed abundance during seedling growth with 170 and 89 proteins being more abundant in R 0mm and R 15mm , respectively. KEGG analysis identified 18 proteins from the cysteine and methionine metabolism pathways and nine proteins from the phenylpropanoid biosynthesis pathway. As an important type of IDP related to stress, 30 late embryogenesis abundant proteins were also found. Ten selected proteins with high levels of predicted intrinsic disorder were able to efficiently protect LDH from the freeze-thaw-induced inactivation, but the protective ability was not correlated with the disorder content of these proteins. These observations suggest that protection of the enzymes and other proteins in a stressed cell can be one of the biological functions of plant IDPs.

Should we excise? Are there any clinical or histologic features that predict upgrade in papillomas, incidental or non-incidental?

PubMed

Zaleski, Michael; Chen, Yun An; Chetlen, Alison L; Mack, Julie; Xu, Liyan; Dodge, Daleela G; Karamchandani, Dipti M

2018-05-11

The clinical decision to excise intraductal papilloma (IDP) without atypia diagnosed on biopsy remains controversial. We sought to establish clinical and histologic predictors (if any) which may predict upgrade in IDP. 296 biopsies (in 278 women) with histologic diagnosis of IDP without atypia were retrospectively identified and placed into Incidental (no corresponding imaging correlate), or Non-incidental (positive imaging correlate) groups. 253/296 (85.5%) cases were non-incidental, and 43/296 (14.5%) were incidental. 73.1% (185/253) non-incidental and 48.8% (21/43) incidental cases underwent excision. 12.4% (23/185) non-incidental cases underwent an upgrade to cancer or high-risk lesion; namely 8-Ductal carcinoma in situ (DCIS), 8-atypical ductal hyperplasia (ADH), 6-lobular neoplasia, and 1-flat epithelial atypia. There was no histopathologic feature on the biopsy in the non-incidental group which predicted upgrade; however a past history of atypia was significantly associated with upgrade. 2 of the 21 incidental cases upgraded (1 to ADH and 1 to lobular neoplasia); the former had a past history of ADH. Both incidental upgrades were >1 mm in size, and were not completely excised on the biopsy. None of the incidental cases which appeared completely excised on biopsy upgraded, irrespective of the size on biopsy. These findings suggest that all non-incidental IDPs should be considered candidates for surgical excision, given the 12.4% upgrade rate and no definitive histologic predictors of upgrade. Patients with incidental IDPs (if <1 mm, completely excised on biopsy and with no history of high risk breast lesion) can be spared excision. Copyright © 2018 Elsevier Inc. All rights reserved.

Topology-based modeling of intrinsically disordered proteins: balancing intrinsic folding and intermolecular interactions.

PubMed

Ganguly, Debabani; Chen, Jianhan

2011-04-01

Coupled binding and folding is frequently involved in specific recognition of so-called intrinsically disordered proteins (IDPs), a newly recognized class of proteins that rely on a lack of stable tertiary fold for function. Here, we exploit topology-based Gō-like modeling as an effective tool for the mechanism of IDP recognition within the theoretical framework of minimally frustrated energy landscape. Importantly, substantial differences exist between IDPs and globular proteins in both amino acid sequence and binding interface characteristics. We demonstrate that established Gō-like models designed for folded proteins tend to over-estimate the level of residual structures in unbound IDPs, whereas under-estimating the strength of intermolecular interactions. Such systematic biases have important consequences in the predicted mechanism of interaction. A strategy is proposed to recalibrate topology-derived models to balance intrinsic folding propensities and intermolecular interactions, based on experimental knowledge of the overall residual structure level and binding affinity. Applied to pKID/KIX, the calibrated Gō-like model predicts a dominant multistep sequential pathway for binding-induced folding of pKID that is initiated by KIX binding via the C-terminus in disordered conformations, followed by binding and folding of the rest of C-terminal helix and finally the N-terminal helix. This novel mechanism is consistent with key observations derived from a recent NMR titration and relaxation dispersion study and provides a molecular-level interpretation of kinetic rates derived from dispersion curve analysis. These case studies provide important insight into the applicability and potential pitfalls of topology-based modeling for studying IDP folding and interaction in general. Copyright © 2011 Wiley-Liss, Inc.

Establishment of an immortalized mouse dermal papilla cell strain with optimized culture strategy.

PubMed

Guo, Haiying; Xing, Yizhan; Zhang, Yiming; He, Long; Deng, Fang; Ma, Xiaogen; Li, Yuhong

2018-01-01

Dermal papilla (DP) plays important roles in hair follicle regeneration. Long-term culture of mouse DP cells can provide enough cells for research and application of DP cells. We optimized the culture strategy for DP cells from three dimensions: stepwise dissection, collagen I coating, and optimized culture medium. Based on the optimized culture strategy, we immortalized primary DP cells with SV40 large T antigen, and established several immortalized DP cell strains. By comparing molecular expression and morphologic characteristics with primary DP cells, we found one cell strain named iDP6 was similar with primary DP cells. Further identifications illustrate that iDP6 expresses FGF7 and α-SMA, and has activity of alkaline phosphatase. During the process of characterization of immortalized DP cell strains, we also found that cells in DP were heterogeneous. We successfully optimized culture strategy for DP cells, and established an immortalized DP cell strain suitable for research and application of DP cells.

Establishment of an immortalized mouse dermal papilla cell strain with optimized culture strategy

PubMed Central

Zhang, Yiming; He, Long; Deng, Fang; Ma, Xiaogen

2018-01-01

Dermal papilla (DP) plays important roles in hair follicle regeneration. Long-term culture of mouse DP cells can provide enough cells for research and application of DP cells. We optimized the culture strategy for DP cells from three dimensions: stepwise dissection, collagen I coating, and optimized culture medium. Based on the optimized culture strategy, we immortalized primary DP cells with SV40 large T antigen, and established several immortalized DP cell strains. By comparing molecular expression and morphologic characteristics with primary DP cells, we found one cell strain named iDP6 was similar with primary DP cells. Further identifications illustrate that iDP6 expresses FGF7 and α-SMA, and has activity of alkaline phosphatase. During the process of characterization of immortalized DP cell strains, we also found that cells in DP were heterogeneous. We successfully optimized culture strategy for DP cells, and established an immortalized DP cell strain suitable for research and application of DP cells. PMID:29383288

Dynamic protein interaction networks and new structural paradigms in signaling

PubMed Central

Csizmok, Veronika; Follis, Ariele Viacava; Kriwacki, Richard W.; Forman-Kay, Julie D.

2017-01-01

Understanding signaling and other complex biological processes requires elucidating the critical roles of intrinsically disordered proteins and regions (IDPs/IDRs), which represent ~30% of the proteome and enable unique regulatory mechanisms. In this review we describe the structural heterogeneity of disordered proteins that underpins these mechanisms and the latest progress in obtaining structural descriptions of ensembles of disordered proteins that are needed for linking structure and dynamics to function. We describe the diverse interactions of IDPs that can have unusual characteristics such as “ultrasensitivity” and “regulated folding and unfolding”. We also summarize the mounting data showing that large-scale assembly and protein phase separation occurs within a variety of signaling complexes and cellular structures. In addition, we discuss efforts to therapeutically target disordered proteins with small molecules. Overall, we interpret the remodeling of disordered state ensembles due to binding and post-translational modifications within an expanded framework for allostery that provides significant insights into how disordered proteins transmit biological information. PMID:26922996

CONFLICT IN EASTERN UKRAINE: STRATEGY FOR TUBERCULOSIS.

PubMed

Kuchuloria, T; Akhvlediani, T; Akhvlediani, N

2016-09-01

This root cause analysis concerns the conflict in the Eastern Ukraine and its impact on healthcare delivery in the context of treating internally displaced persons (IDPs). Inadequate treatment of tuberculosis (TB) was selected as a major topic for intervention planning in conflict areas in Ukraine. With respect to treating TB among IDPs, rapid diagnosis and adequate nutrition and shelter are important components of care and disease control. The DOT, supported by trained primary healthcare providers equipped with rapid MDR TB diagnostic capacities, need to provide appropriate shelter and nutrition to IDPs. In addition to active disease management, this paper discusses the important role of ongoing project monitoring and communicating evaluation findings with all the major stakeholders shaping the national TB strategy in Ukraine. A comprehensive strategy is essential for successful transitioning and re-structuring of TB healthcare delivery both during after conflict resolution.

Defining the safe current limit for opening ID photon shutter

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

Seletskiy, S.

The NSLS-II storage ring is protected from possible damage from insertion devices (IDs) synchrotron radiation by a dedicated active interlock system (AIS). It monitors electron beam position and angle and triggers beam drop if beam orbit exceeds the boundaries of pre-calculated active interlock envelope (AIE). The beamlines (BL) and beamline frontends (FE) are designed under assumption that the electron beam is interlocked within the AIE. For historic reasons the AIS engages the ID active interlock (AI-ID) at any non-zero beam current whenever the ID photon shutter (IDPS) is getting opened. Such arrangement creates major inconveniences for BLs commissioning. Apparently theremore » is some IDPS safe current limit (SCL) under which the IDPS can be opened without interlocking the e-beam. The goal of this paper is to find such limit.« less

Radar-acoustic interaction for IFF applications

NASA Astrophysics Data System (ADS)

Saffold, James A.; Williamson, Frank R.; Ahuja, Krishan; Stein, Lawrence R.; Muller, Marjorie

1998-08-01

This paper describes the results of an internal development program (IDP) No. 97-1 conducted from August 1-October 1 1996 at the Georgia Tech Research Institute. The IDP program was implemented to establish theoretical relationships and verify the interaction between X-band radar waves and ultrasonic acoustics. Low cost, off-the-shelf components were used for the verification in order to illustrate the cost savings potential of developing and utilizing these systems. The measured data was used to calibrate the developed models of the phenomenology and to support extrapolation for radar systems which can exploit these interactions. One such exploitation is for soldier identification IFF and radar taggant concepts. The described IDP program provided the phenomenological data which is being used to extrapolate concept system performances based on technological limitations and battlefield conditions for low cost IFF and taggant configurations.

Trace element content of chondritic cosmic dust: Volatile enrichments, thermal alterations, and the possibility of contamination

NASA Technical Reports Server (NTRS)

Flynn, G. J.; Sutton, S. R.; Bajt, S.

1993-01-01

Trace element abundances in 51 chondritic Interplanetary Dust Particles (IDP's) were measured by Synchrotron X-Ray Fluorescence (SXRF). The data allow us to determine an average composition of chondritic IDP's and to examine the questions of volatile loss during the heating pulse experienced on atmospheric entry and possible element addition due to contamination during atmospheric entry, stratospheric residence, and curation.

Social phobia among long-term internally displaced persons: An epidemiological study of adults in two internally displaced person settlements in Sudan.

PubMed

Salah, Tarig Taha Mohamed; Ayazi, Touraj; Lien, Lars; Eide, Arne; Hauff, Edvard

2015-09-01

Despite the high worldwide prevalence and association with other mental disorders and disability, only few studies are available on social phobia in low-income countries. This study aims to assess the prevalence, socio-demographic correlates and comorbidity of social phobia and its association with disability among long-term internally displaced persons (IDPs) in one urban and one rural area in Central Sudan. This cross-sectional study was implemented in two IDP areas in Central Sudan. Data were collected during face-to-face interviews using structured questionnaires to assess socio-demographic factors and the Mini International Neuropsychiatric Interview (MINI) to determine psychiatric diagnoses. A total of 1,876 adults were enrolled from both study areas. The overall lifetime prevalence of social phobia was 14.2%, with higher rates among IDPs in the rural area and among those who were less educated. Social phobia was associated with other mental disorders in both study areas. Disability and prolonged displacement increased the risk of having social phobia in the rural area. Further work needs to be done to improve our understanding and to establish proper interventions in dealing with social phobia, other common mental disorders and disability among long-term IDPs in these impoverished areas. © The Author(s) 2014.

The transition state structure for binding between TAZ1 of CBP and the disordered Hif-1α CAD.

PubMed

Lindström, Ida; Andersson, Eva; Dogan, Jakob

2018-05-18

Intrinsically disordered proteins (IDPs) are common in eukaryotes. However, relatively few experimental studies have addressed the nature of the rate-limiting transition state for the coupled binding and folding reactions involving IDPs. By using site-directed mutagenesis in combination with kinetics measurements we have here characterized the transition state for binding between the globular TAZ1 domain of CREB binding protein and the intrinsically disordered C-terminal activation domain of Hif-1α (Hif-1α CAD). A total of 17 Hif-1α CAD point-mutations were generated and a Φ-value binding analysis was carried out. We found that native hydrophobic binding interactions are not formed at the transition state. We also investigated the effect the biologically important Hif-1α CAD Asn-803 hydroxylation has on the binding kinetics, and found that the whole destabilization effect due the hydroxylation is within the dissociation rate constant. Thus, the rate-limiting transition state is "disordered-like", with native hydrophobic binding contacts being formed cooperatively after the rate-limiting barrier, which is clearly shown by linear free energy relationships. The same behavior was observed in a previously characterized TAZ1/IDP interaction, which may suggest common features for the rate-limiting transition state for TAZ1/IDP interactions.

Accelerating the Conformational Sampling of Intrinsically Disordered Proteins.

PubMed

Do, Trang Nhu; Choy, Wing-Yiu; Karttunen, Mikko

2014-11-11

Intrinsically disordered proteins (IDPs) are a class of proteins lacking a well-defined secondary structure. Instead, they are able to attain multiple conformations, bind to multiple targets, and respond to changes in their surroundings. Functionally, IDPs have been associated with molecular recognition, cell regulation, and signal transduction. The dynamic conformational ensemble of IDPs is highly environmental and binding partner dependent, rendering the characterization of IDPs extremely challenging. Here, we compare the sampling efficiencies of conventional molecular dynamics (MD), well-tempered metadynamics (WT-META), and bias-exchange metadynamics (BE-META). The total simulation time was over 10 μs, and a 20-mer peptide derived from the Neh2 domain of the Nuclear factor erythroid 2-related factor 2 (Nrf2) protein was simulated. BE-META, with a neutral replica and seven biased replicas employing a set of seven relevant collective variables (CVs), provided the most reliable and efficient sampling. Finally, we propose a free-energy reconstruction method based on the probability distribution of the secondary structure contents. This postprocessing analysis confirms the presence of not only the β-hairpin conformation of the free Neh2 peptide but also its rare bound-state-like conformation, both of that have been experimentally observed. In addition, our simulations also predict other possible conformations to be verified with future experiments.

Chain Collapse of an Amyloidogenic Intrinsically Disordered Protein

PubMed Central

Jain, Neha; Bhattacharya, Mily; Mukhopadhyay, Samrat

2011-01-01

Natively unfolded or intrinsically disordered proteins (IDPs) are under intense scrutiny due to their involvement in both normal biological functions and abnormal protein misfolding disorders. Polypeptide chain collapse of amyloidogenic IDPs is believed to play a key role in protein misfolding, oligomerization, and aggregation leading to amyloid fibril formation, which is implicated in a number of human diseases. In this work, we used bovine κ-casein, which serves as an archetypal model protein for amyloidogenic IDPs. Using a variety of biophysical tools involving both prediction and spectroscopic techniques, we first established that monomeric κ-casein adopts a collapsed premolten-globule-like conformational ensemble under physiological conditions. Our time-resolved fluorescence and light-scattering data indicate a change in the mean hydrodynamic radius from ∼4.6 nm to ∼1.9 nm upon chain collapse. We then took the advantage of two cysteines separated by 77 amino-acid residues and covalently labeled them using thiol-reactive pyrene maleimide. This dual-labeled protein demonstrated a strong excimer formation upon renaturation from urea- and acid-denatured states under both equilibrium and kinetic conditions, providing compelling evidence of polypeptide chain collapse under physiological conditions. The implication of the IDP chain collapse in protein aggregation and amyloid formation is also discussed. PMID:21961598

Comparing the VIRTIS Spectrum of 67P/Churyumov-Gerasimenko to Wild 2 and in Primitive Interplanetary Dust Particles

NASA Astrophysics Data System (ADS)

Flynn, George

2016-04-01

The Visible and Infrared Thermal Imaging Spectrometer (VIRTIS) instrument, a point spectrometer with high spectral resolution covering the range from 2 to 5 microns, on the ESA Rosetta spacecraft obtained spectra of the surface of Comet 67P/Churyumov-Gerasimenko. The spectral region covered by VIRTIS has been well studied in meteorites, interplanetary dust particles (IDPs) collected by NASA from the Earth's stratosphere, and the samples of Comet 81P/Wild 2 that were delivered to Earth by the NASA Stardust spacecraft. Infrared spectra of the nucleus of Comet 67P/Churyumov-Gerasimenko acquired by VIRTIS show a broad absorption band observed at ~3.3 μm, a region of the spectrum where C-H, O-H, and N-H stretching features occur (Capaccioni et al., 2015). This broad feature is similar to the O-H feature exhibited by hydrous minerals, but shifted to a significantly longer wavelength. Capaccioni et al. (2015) compared the VIRTIS spectra to laboratory spectra of carbonaceous chondrite meteorites of the CI, CM, and CR types and concluded that none of the typical features of these meteorite spectra are compatible with the spectra of the surface of 67P/Churyumov-Gerasimenko. Comparison of VIRTIS spectra of 67P/ Churyumov-Gerasimenko to the laboratory spectra of well-characterized extraterrestrial materials including the Wild 2 dust and the IDPs, a significant fraction of which are believed to be cometary, could aid in the interpretation of the 67P/Churyumov-Gerasimenko spectra. None of the Wild 2 particles examined by infrared spectroscopy exhibit an O-H feature, but this may be due to the high temperature reached during their capture in the aerogel collection medium. The O-H feature is also absent in all anhydrous IDPs. The hydrous IDPs exhibit varying strengths of both aliphatic C-H absorption features and the O-H absorption feature, but, as with the meteorites, the O-H feature occurs at a significantly shorter wavelength than the broad feature detected in 67P/Churyumov-Gerasimenko. Only one of the more than 50 IDPs analyzed by infrared spectroscopy has an infrared spectrum similar to that of 67P/Churyumov-Gerasimenko. This large, hydrous IDP, L2021 C10, has a broad absorption feature centered at the same position as the feature observed in 67P/Churyumov-Gerasimenko. In the case of L2021 C10 this feature is attributed to an O-H absorption feature in the position normally seen in hydrous minerals as well as a broad aromatic C-H feature, rarely detected in IDPs, and the aliphatic C-H feature seen in all IDPs examined thus far (Flynn et al., 2004). In the case of the VIRTIS spectrum of 67P/Churyumov-Gerasimenko the apparent shift of the broad O-H feature may actually result from the superposition of O-H and aromatic C-H features, both at their normal wavelengths. References: Capaccioni, F. et al. (2015) Science, 347 no. 6220, DOI: 10.1126/science.aaa0628. Flynn, G. J. et al. (2004) Advances in Space Research, 33, 57-66.

Novel Experimental Simulations of the Atmospheric Injection of Meteoric Metals

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

Gómez Martín, J. C.; Bones, D. L.; Carrillo-Sánchez, J. D.

2017-02-20

A newly developed laboratory, Meteoric Ablation Simulator (MASI), is used to test model predictions of the atmospheric ablation of interplanetary dust particles (IDPs) with experimental Na, Fe, and Ca vaporization profiles. MASI is the first laboratory setup capable of performing time-resolved atmospheric ablation simulations, by means of precision resistive heating and atomic laser-induced fluorescence detection. Experiments using meteoritic IDP analogues show that at least three mineral phases (Na-rich plagioclase, metal sulfide, and Mg-rich silicate) are required to explain the observed appearance temperatures of the vaporized elements. Low melting temperatures of Na-rich plagioclase and metal sulfide, compared to silicate grains, precludemore » equilibration of all the elemental constituents in a single melt. The phase-change process of distinct mineral components determines the way in which Na and Fe evaporate. Ca evaporation is dependent on particle size and on the initial composition of the molten silicate. Measured vaporized fractions of Na, Fe, and Ca as a function of particle size and speed confirm differential ablation (i.e., the most volatile elements such as Na ablate first, followed by the main constituents Fe, Mg, and Si, and finally the most refractory elements such as Ca). The Chemical Ablation Model (CABMOD) provides a reasonable approximation to this effect based on chemical fractionation of a molten silicate in thermodynamic equilibrium, even though the compositional and geometric description of IDPs is simplistic. Improvements in the model are required in order to better reproduce the specific shape of the elemental ablation profiles.« less

Invention Development Program Helps Nurture NCI at Frederick Technologies | Poster

Cancer.gov

The Invention Development Fund (IDF) was piloted by the Technology Transfer Center (TTC) in 2014 to facilitate the commercial development of NCI technologies. The IDF received a second round of funding from the NCI Office of the Director and the Office of Budget and Management to establish the Invention Development Program (IDP) for fiscal year 2016. The IDP is using these funds to help advance a second set of inventions.

Synchrotron FTIR Examination of Interplanetary Dust Particles: An Effort to Determine the Compounds and Minerals in Interstellar and Circumstellar Dust

NASA Technical Reports Server (NTRS)

Flynn, G. J.; Keller, L. P.

2002-01-01

Some interplanetary dust particles (IDPs), collected by NASA from the Earth's stratosphere, are the most primitive extraterrestrial material available for laboratory analysis. Many exhibit isotopic anomalies in H, N, and O, suggesting they contain preserved interstellar matter. We report the preliminary results of a comparison of the infrared absorption spectra of subunits of the IDPs with astronomical spectra of interstellar grains.

Unusual olivine and pyroxene composition in interplanetary dust and unequilibrated ordinary chondrites

NASA Technical Reports Server (NTRS)

Klock, W.; Mckay, D. S.; Thomas, K. L.; Palme, H.

1989-01-01

The presence, in both a number of interplanetary dust particles (IDPs) and in meteorite matrices, of olivine and orthopyroxene grains, low in FeO but containing up to 5 wt pct MnO, is reported. The majority of olivines and pyroxenes in meteorites contain less than 0.5 wt pct MnO. The presence of these low-iron, manganese-enriched (LIME) olivines and pyroxenes in IDPs and meteorites may indicate a link between the origin and history of IDPs and the matrix material of primitive meteorites. The origin of the LIME silicates could be explained by condensation from a gas of solar composition. Forsterite is the first major silicate phase to condense from a solar nebula gas, and Mn, which is not stable as a metal under solar nebula conditions, would condense at about 1100 K as Mn2SiO4 in solid solution with forsterite.

Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings.

PubMed

Sanchez-Martinez, M; Crehuet, R

2014-12-21

We present a method based on the maximum entropy principle that can re-weight an ensemble of protein structures based on data from residual dipolar couplings (RDCs). The RDCs of intrinsically disordered proteins (IDPs) provide information on the secondary structure elements present in an ensemble; however even two sets of RDCs are not enough to fully determine the distribution of conformations, and the force field used to generate the structures has a pervasive influence on the refined ensemble. Two physics-based coarse-grained force fields, Profasi and Campari, are able to predict the secondary structure elements present in an IDP, but even after including the RDC data, the re-weighted ensembles differ between both force fields. Thus the spread of IDP ensembles highlights the need for better force fields. We distribute our algorithm in an open-source Python code.

Financing of internal displacement: excerpts from the Sri Lankan experience.

PubMed

Amirthalingam, Kopalapillai; Lakshman, Rajith W D

2010-04-01

This paper investigates how internally displaced persons (IDPs) in Batticaloa, Sri Lanka, financed their first year of displacement. We conducted extensive fieldwork in August 2007 in numerous welfare centres in Batticaloa that have received persons displaced from the Mutur divisional secretariat (DS) in the Trincomalee district. The sample was selected from the village of Sampur in Mutur DS. The displaced from Sampur are of Tamil origin and our findings reveal certain coping strategies that may be particular to this community, including the selling or mortgaging of gold jewellery to address the effects of displacement. We found that the IDPs in this region rely heavily on jewellery and other forms of savings to ensure their survival. There is also strong evidence to support the critically important coping role played by livelihoods. These coping strategies have enabled the IDP households in the present sample to live marginally above the poverty line.

Dancing Protein Clouds: The Strange Biology and Chaotic Physics of Intrinsically Disordered Proteins*

PubMed Central

2016-01-01

Biologically active but floppy proteins represent a new reality of modern protein science. These intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered and intrinsically disordered protein regions (IDPRs) constitute a noticeable part of any given proteome. Functionally, they complement ordered proteins, and their conformational flexibility and structural plasticity allow them to perform impossible tricks and be engaged in biological activities that are inaccessible to well folded proteins with their unique structures. The major goals of this minireview are to show that, despite their simplified amino acid sequences, IDPs/IDPRs are complex entities often resembling chaotic systems, are structurally and functionally heterogeneous, and can be considered an important part of the structure-function continuum. Furthermore, IDPs/IDPRs are everywhere, and are ubiquitously engaged in various interactions characterized by a wide spectrum of binding scenarios and an even wider spectrum of structural and functional outputs. PMID:26851286

Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings.

PubMed

Jensen, Malene Ringkjøbing; Markwick, Phineus R L; Meier, Sebastian; Griesinger, Christian; Zweckstetter, Markus; Grzesiek, Stephan; Bernadó, Pau; Blackledge, Martin

2009-09-09

Intrinsically disordered proteins (IDPs) inhabit a conformational landscape that is too complex to be described by classical structural biology, posing an entirely new set of questions concerning the molecular understanding of functional biology. The characterization of the conformational properties of IDPs, and the elucidation of the role they play in molecular function, is therefore one of the major challenges remaining for modern structural biology. NMR is the technique of choice for studying this class of proteins, providing information about structure, flexibility, and interactions at atomic resolution even in completely disordered states. In particular, residual dipolar couplings (RDCs) have been shown to be uniquely sensitive and powerful tools for characterizing local and long-range structural behavior in disordered proteins. In this review we describe recent applications of RDCs to quantitatively describe the level of local structure and transient long-range order in IDPs involved in viral replication, neurodegenerative disease, and cancer.

From Sequence and Forces to Structure, Function and Evolution of Intrinsically Disordered Proteins

PubMed Central

Forman-Kay, Julie D.; Mittag, Tanja

2015-01-01

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales and compactness is shaping a unified understanding of structure-dynamics-disorder/function relationships. On the 20th anniversary of this journal, Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional and evolutionary properties. PMID:24010708

From sequence and forces to structure, function, and evolution of intrinsically disordered proteins.

PubMed

Forman-Kay, Julie D; Mittag, Tanja

2013-09-03

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics, and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales, and compactness are shaping a unified understanding of structure-dynamics-disorder/function relationships. In the 20(th) anniversary of Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional, and evolutionary properties. Copyright © 2013 Elsevier Ltd. All rights reserved.

Clay minerals in primitive meteorites and interplanetary dust 1

NASA Technical Reports Server (NTRS)

Zolensky, M. E.; Keller, L. P.

1991-01-01

Many meteorites and interplanetary dust particles (IDPs) with primitive compositions contain significant amounts of phyllosilicate minerals, which are generally interpreted as evidence of protoplanetary aqueous alteration at an early period of the solar system. These meteorites are chondrites (near solar composition) of the carbonaceous and ordinary varieties. The former are subdivided (according to bulk composition and petrology) into CI, CM, CV, CO, CR, and ungrouped classes. IDPs are extraterrestrial particulates, collected in stratosphere, which have chemical compositions indicative of a primitive origin; they are typically distinct from the primitive meteorites. Characterization of phyllosilicates in these materials is a high priority because of the important physico-chemical information they hold. The most common phyllosilicates present in chondritic extraterrestrial materials are serpentine-group minerals, smectites, and micas. We discuss these phyllosilicates and describe the interpretation of their occurrence in meteorites and IDPs and what this indicates about history of their parent bodies, which are probably the hydrous asteroids.

GEMS and New Pre-Accretionally Irradiated RELICT Grains in Interplanetary Dust - The Plot Thickens

NASA Astrophysics Data System (ADS)

Bradley, J.

1995-09-01

The hypothesis that GEMS (glass with embedded metal and sulfides) in interplanetary dust particles (IDPs) might be the long-sought interstellar silicate grains is undergoing close scrutiny [1-3]. GEMS are proposed to be interstellar because: (a) they are abundant in cometary IDPs; (b) they were irradiated prior to incorporation into IDPs; (c) both their size distribution and Oamorphous silicate" microstructures are consistent with those of interstellar silicates; (d) they contain nanometer-sized (superparamagnetic) alpha-iron inclusions, which provides a simple explanation for the observed interstellar grain alignment and polarization [4,5]. Challenges to the GEMS hypothesis include the following: (a) GEMS may have formed and been irradiated in the solar nebula rather than a presolar interstellar environment; (b) non-solar isotope abundances have yet to be measured in GEMS; (c) the irradiation regime required to produce the observed effects in GEMS might be incompatible with the interstellar medium; (b) relationships between GEMS and carbon (e.g. core/mantle) need clarification; (c) major element abundances in GEMS should be consistent with observed interstellar gas phase depletions [2,3]. GEMS may indeed have formed in the solar nebula, in which case they would be the oldest known solar nebula solids [2]. An interstellar origin for GEMS does not require detection of non-solar isotope abundances [6]. Irradiation experiments are in progress to simulate the properties of GEMS. The petrographic relationship between GEMS and carbon in IDPs is being investigated (by examining IDPs embedded and thin-sectioned in carbon-free media). Major element abundances in GEMS are being evaluated in terms on interstellar gas phase abundances. For example, sulfur is not highly depleted in the interstellar gas, implying that it must be significantly depleted in interstellar grains [3]. GEMS are significantly depleted in sulfur relative to solar abundances. Analytical electron microscopic studies of the local petrographic environment of GEMS in IDPs are continuing. There is evidence of a population of relict grains associated with GEMS. Some of these relict grains have distinctive compositions and they appear to have functioned as (pre-existing) depositional substrates while GEMS were being formed. Thus, it may be possible to begin to assign a chronology to the seemingly complex admixture of grains that make up the ultrafine-grained matrices of anhydrous chondritic IDPs. References: [1] Bradley J. P. (1994) Science, 265, 925-929. [2] Flynn G. J. (1994) Nature, 371, 287-288. [3] Martin P. G. (1995) Astrophys. J., 445, L63-L66. [4] Mathis J. S. (1986) Astrophys. J., 308, 281-287. [5] Mathis J. S. (1993) Rept. Prog. Phys., 56, 605-652. [6] Walker R. M. (1994) in Analysis of Interplanetary Dust (M. E. Zolensky et al., eds.), pp. 203-209, AIP Conf. Proc. 310.

Frequent Spread of Plasmodium vivax Malaria Maintains High Genetic Diversity at the Myanmar-China Border, Without Distance and Landscape Barriers.

PubMed

Lo, Eugenia; Lam, Nancy; Hemming-Schroeder, Elizabeth; Nguyen, Jennifer; Zhou, Guofa; Lee, Ming-Chieh; Yang, Zhaoqing; Cui, Liwang; Yan, Guiyun

2017-12-05

In Myanmar, civil unrest and the establishment of internally displaced person (IDP) settlements along the Myanmar-China border have impacted malaria transmission. Microsatellite markers were used to examine source-sink dynamics for Plasmodium vivax between IDP settlements and surrounding villages in the border region. Genotypic structure and diversity were compared across the 3 years following the establishment of IDP settlements, to infer demographic history. We investigated whether human migration and landscape heterogeneity contributed to P. vivax transmission. P. vivax from IDP settlements and local communities consistently exhibited high genetic diversity within populations but low polyclonality within individuals. No apparent genetic structure was observed among populations and years. P. vivax genotypes in China were similar to those in Myanmar, and parasite introduction was unidirectional. Landscape factors, including distance, elevation, and land cover, do not appear to impede parasite gene flow. The admixture of P. vivax genotypes suggested that parasite gene flow via human movement contributes to the spread of malaria both locally in Myanmar and across the international border. Our genetic findings highlight the presence of large P. vivax gene reservoirs that can sustain transmission. Thus, it is important to reinforce and improve existing control efforts along border areas. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Fluid-induced organic synthesis in the solar nebula recorded in extraterrestrial dust from meteorites.

PubMed

Vollmer, Christian; Kepaptsoglou, Demie; Leitner, Jan; Busemann, Henner; Spring, Nicole H; Ramasse, Quentin M; Hoppe, Peter; Nittler, Larry R

2014-10-28

Isotopically anomalous carbonaceous grains in extraterrestrial samples represent the most pristine organics that were delivered to the early Earth. Here we report on gentle aberration-corrected scanning transmission electron microscopy investigations of eight (15)N-rich or D-rich organic grains within two carbonaceous Renazzo-type (CR) chondrites and two interplanetary dust particles (IDPs) originating from comets. Organic matter in the IDP samples is less aromatic than that in the CR chondrites, and its functional group chemistry is mainly characterized by C-O bonding and aliphatic C. Organic grains in CR chondrites are associated with carbonates and elemental Ca, which originate either from aqueous fluids or possibly an indigenous organic source. One distinct grain from the CR chondrite NWA 852 exhibits a rim structure only visible in chemical maps. The outer part is nanoglobular in shape, highly aromatic, and enriched in anomalous nitrogen. Functional group chemistry of the inner part is similar to spectra from IDP organic grains and less aromatic with nitrogen below the detection limit. The boundary between these two areas is very sharp. The direct association of both IDP-like organic matter with dominant C-O bonding environments and nanoglobular organics with dominant aromatic and C-N functionality within one unique grain provides for the first time to our knowledge strong evidence for organic synthesis in the early solar system activated by an anomalous nitrogen-containing parent body fluid.

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

Matrajt, G.; Flynn, G.; Brownlee, D.

We analyzed two ultracarbonaceous interplanetary dust particles (IDPs) and two cometary Wild 2 particles with infrared spectroscopy. We characterized the carrier of the 3.4 {mu}m band in these samples and compared its profile and the CH{sub 2}/CH{sub 3} ratios to the 3.4 {mu}m band in the diffuse interstellar medium (DISM), in the insoluble organic matter from three primitive meteorites, in asteroid 24 Themis, and in the coma of comet 103P/Hartley 2. We found that the 3.4 {mu}m band in both Wild 2 and IDPs is similar, but different from all of the other astrophysical environments that we compared it to.more » The 3.4 {mu}m band in the IDPs and Wild 2 particles is dominated by CH{sub 2} groups, the peaks are narrower and stronger than in the meteorites, asteroid Themis, and the DISM. Also, the presence of the carbonyl group C=O at {approx}1700 cm{sup -1} (5.8 {mu}m) in most of the spectra of our samples indicates that these aliphatic chains have O bonded to them, which is quite different from astronomical spectra of the DISM. Based on all of these observations, we conclude that the origin of the carrier of the 3.4 {mu}m band in the IDPs and Wild 2 samples is not interstellar; instead, we suggest that the origin lies in the outermost parts of the solar nebula.« less

Prolonged displacement may compromise resilience in Eritrean mothers.

PubMed

Almedom, Astier; Tesfamichael, Berhe; Mohammed, Zein; Mascie-Taylor, Nick; Muller, Jocelyn; Alemu, Zemui

2005-12-01

to assess the impact of prolonged displacement on the resilience of Eritrean mothers. an adapted SOC scale (short form) was administered. Complementary qualitative data were gathered from study participants' spontaneous reactions to and commentaries on the SOC scale. Displaced women's SOC scores were significantly less than those of the non-displaced: Mean = 54.84; SD = 6.48 in internally displaced person (IDP) camps, compared to non-displaced urban and rural/pastoralist: Mean = 48. 94, SD = 11.99; t = 3.831, p < .001. Post hoc tests revealed that the main difference is between IDP camp dwellers and urban (non-displaced). Rural but traditionally mobile (pastoralist or transhumant) communities scored more or less the same as the urban non-displaced--i.e., significantly higher than those in IDP camps (p < 0.05). Analysis of variance confirmed that gender is critical: displacement has significantly negative effects on women compared to men: RR = .262, p < .001. SOC scores of urban and pastoralist/transhumant groups were similar, while women in IDP camps were lower scoring--RR = .268, p < .001. The implications of these findings for health policy are critical. It is incumbent on the international health institutions including the World Health Organization and regional as well as local players to address the plight of internally displaced women, their families and communities in Eritrea and other places of dire conditions such as, for example Darfur in the Sudan.

Automated analysis of retinal images for detection of referable diabetic retinopathy.

PubMed

Abràmoff, Michael D; Folk, James C; Han, Dennis P; Walker, Jonathan D; Williams, David F; Russell, Stephen R; Massin, Pascale; Cochener, Beatrice; Gain, Philippe; Tang, Li; Lamard, Mathieu; Moga, Daniela C; Quellec, Gwénolé; Niemeijer, Meindert

2013-03-01

The diagnostic accuracy of computer detection programs has been reported to be comparable to that of specialists and expert readers, but no computer detection programs have been validated in an independent cohort using an internationally recognized diabetic retinopathy (DR) standard. To determine the sensitivity and specificity of the Iowa Detection Program (IDP) to detect referable diabetic retinopathy (RDR). In primary care DR clinics in France, from January 1, 2005, through December 31, 2010, patients were photographed consecutively, and retinal color images were graded for retinopathy severity according to the International Clinical Diabetic Retinopathy scale and macular edema by 3 masked independent retinal specialists and regraded with adjudication until consensus. The IDP analyzed the same images at a predetermined and fixed set point. We defined RDR as more than mild nonproliferative retinopathy and/or macular edema. A total of 874 people with diabetes at risk for DR. Sensitivity and specificity of the IDP to detect RDR, area under the receiver operating characteristic curve, sensitivity and specificity of the retinal specialists' readings, and mean interobserver difference (κ). The RDR prevalence was 21.7% (95% CI, 19.0%-24.5%). The IDP sensitivity was 96.8% (95% CI, 94.4%-99.3%) and specificity was 59.4% (95% CI, 55.7%-63.0%), corresponding to 6 of 874 false-negative results (none met treatment criteria). The area under the receiver operating characteristic curve was 0.937 (95% CI, 0.916-0.959). Before adjudication and consensus, the sensitivity/specificity of the retinal specialists were 0.80/0.98, 0.71/1.00, and 0.91/0.95, and the mean intergrader κ was 0.822. The IDP has high sensitivity and specificity to detect RDR. Computer analysis of retinal photographs for DR and automated detection of RDR can be implemented safely into the DR screening pipeline, potentially improving access to screening and health care productivity and reducing visual loss through early treatment.

Contribution of industrial density and socioeconomic status to the spatial distribution of thyroid cancer risk in Hangzhou, China.

PubMed

Fei, Xufeng; Lou, Zhaohan; Christakos, George; Liu, Qingmin; Ren, Yanjun; Wu, Jiaping

2018-02-01

The thyroid cancer (TC) incidence in China has increased dramatically during the last three decades. Typical in this respect is the case of Hangzhou city (China), where 7147 new TC cases were diagnosed during the period 2008-2012. Hence, the assessment of the TC incidence risk increase due to environmental exposure is an important public health matter. Correlation analysis, Analysis of Variance (ANOVA) and Poisson regression were first used to evaluate the statistical association between TC and key risk factors (industrial density and socioeconomic status). Then, the Bayesian maximum entropy (BME) theory and the integrative disease predictability (IDP) criterion were combined to quantitatively assess both the overall and the spatially distributed strength of the "exposure-disease" association. Overall, higher socioeconomic status was positively correlated with higher TC risk (Pearson correlation coefficient=0.687, P<0.01). Compared to people of low socioeconomic status, people of median and high socioeconomic status showed higher TC risk: the Relative Risk (RR) and associated 95% confidence interval (CI) were found to be, respectively, RR=2.29 with 95% CI=1.99 to 2.63, and RR=3.67 with 95% CI=3.22 to 4.19. The "industrial density-TC incidence" correlation, however, was non-significant. Spatially, the "socioeconomic status-TC" association measured by the corresponding IDP coefficient was significant throughout the study area: the mean IDP value was -0.12 and the spatial IDP values were consistently negative at the township level. It was found that stronger associations were distributed among residents mainly on a stripe of land from northeast to southwest (consisting mainly of sub-district areas). The "industrial density-TC" association measured by its IDP coefficient was spatially non-consistent. Socioeconomic status is an important indicator of TC risk factor in Hangzhou (China) whose effect varies across space. Hence, socioeconomic status shows the highest TC risk effect in sub-district areas. Copyright © 2017. Published by Elsevier B.V.

Hanford Internal Dosimetry Program Manual, PNL-MA-552

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

Carbaugh, Eugene H.; Bihl, Donald E.; Maclellan, Jay A.

2003-10-10

This manual is a guide to the services provided by the Hanford Internal Dosimetry Program (IDP). It describes the roles of and relationships between the IDP and site contractors, and provides recommendations and guidance for consideration in implementing bioassay monitoring and internal dosimetry elements of radiation protection programs. Guidance includes identifying conditions under which workers should be placed on bioassay programs, types, descritptions, and capabilities of measurements, suggested routine bioassay programs, limitations on services, and practices for recording and reporting results.

Hanford Internal Dosimetry Program Manual, PNL-MA-552

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

Carbaugh, Eugene H.; Bihl, Donald E.; Maclellan, Jay A.

2009-09-24

This manual is a guide to the services provided by the Hanford Internal Dosimetry Program (IDP), which is operated by the Pacific Northwest National Laboratory.( ) for the U.S. Department of Energy Richland Operations Office, Office of River Protection and their Hanford Site contractors. The manual describes the roles of and relationships between the IDP and the radiation protection programs of the Hanford Site contractors. Recommendations and guidance are also provided for consideration in implementing bioassay monitoring and internal dosimetry elements of radiation protection programs.

GEMS Revealed: Spectrum Imaging of Aggregate Grains in Interplanetary Dust

NASA Technical Reports Server (NTRS)

Keller, L. P.; Messenger, S.; Christoffersen, R.

2005-01-01

Anhydrous interplanetary dust particles (IDPs) of cometary origin contain abundant materials that formed in the early solar nebula. These materials were transported outward and subsequently mixed with molecular cloud materials and presolar grains in the region where comets accreted [1]. GEMS (glass with embedded metal and sulfides) grains are a major component of these primitive anhydrous IDPs, along with crystalline Mg-rich silicates, Fe-Ni sulfides, carbonaceous material, and other trace phases. Some GEMS grains (5%) are demonstrably presolar based on their oxygen isotopic compositions [2]. However, most GEMS grains are isotopically solar and have bulk chemical compositions that are incompatible with inferred compositions of interstellar dust, suggesting a solar system origin [3]. An alternative hypothesis is that GEMS grains represent highly irradiated interstellar grains whose oxygen isotopic compositions were homogenized through processing in the interstellar medium (ISM) [4]. We have obtained the first quantitative X-ray maps (spectrum images) showing the distribution of major and minor elements in individual GEMS grains. Nanometer-scale chemical maps provide critical data required to evaluate the differing models regarding the origin of GEMS grains.

Multiple generations of grain aggregation in different environments preceded solar system body formation.

PubMed

Ishii, Hope A; Bradley, John P; Bechtel, Hans A; Brownlee, Donald E; Bustillo, Karen C; Ciston, James; Cuzzi, Jeffrey N; Floss, Christine; Joswiak, David J

2018-06-26

The solar system formed from interstellar dust and gas in a molecular cloud. Astronomical observations show that typical interstellar dust consists of amorphous ( a -) silicate and organic carbon. Bona fide physical samples for laboratory studies would yield unprecedented insight about solar system formation, but they were largely destroyed. The most likely repositories of surviving presolar dust are the least altered extraterrestrial materials, interplanetary dust particles (IDPs) with probable cometary origins. Cometary IDPs contain abundant submicron a- silicate grains called GEMS (glass with embedded metal and sulfides), believed to be carbon-free. Some have detectable isotopically anomalous a- silicate components from other stars, proving they are preserved dust inherited from the interstellar medium. However, it is debated whether the majority of GEMS predate the solar system or formed in the solar nebula by condensation of high-temperature (>1,300 K) gas. Here, we map IDP compositions with single nanometer-scale resolution and find that GEMS contain organic carbon. Mapping reveals two generations of grain aggregation, the key process in growth from dust grains to planetesimals, mediated by carbon. GEMS grains, some with a- silicate subgrains mantled by organic carbon, comprise the earliest generation of aggregates. These aggregates (and other grains) are encapsulated in lower-density organic carbon matrix, indicating a second generation of aggregation. Since this organic carbon thermally decomposes above ∼450 K, GEMS cannot have accreted in the hot solar nebula, and formed, instead, in the cold presolar molecular cloud and/or outer protoplanetary disk. We suggest that GEMS are consistent with surviving interstellar dust, condensed in situ, and cycled through multiple molecular clouds. Copyright © 2018 the Author(s). Published by PNAS.

Interfacial Properties of NTAIL, an Intrinsically Disordered Protein.

PubMed

Bénarouche, Anaïs; Habchi, Johnny; Cagna, Alain; Maniti, Ofelia; Girard-Egrot, Agnès; Cavalier, Jean-François; Longhi, Sonia; Carrière, Frédéric

2017-12-19

Intrinsically disordered proteins (IDPs) lack stable secondary and tertiary structure under physiological conditions in the absence of their biological partners and thus exist as dynamic ensembles of interconverting conformers, often highly soluble in water. However, in some cases, IDPs such as the ones involved in neurodegenerative diseases can form protein aggregates and their aggregation process may be triggered by the interaction with membranes. Although the interfacial behavior of globular proteins has been extensively studied, experimental data on IDPs at the air/water (A/W) and water/lipid interfaces are scarce. We studied here the intrinsically disordered C-terminal domain of the Hendra virus nucleoprotein (N TAIL ) and compared its interfacial properties to those of lysozyme that is taken as a model globular protein of similar molecular mass. Adsorption of N TAIL at the A/W interface was studied in the absence and presence of phospholipids using Langmuir films, polarization modulated-infrared reflection-absorption spectroscopy, and an automated drop tensiometer for interfacial tension and elastic modulus determination with oscillating bubbles. N TAIL showed a significant surface activity, with a higher adsorption capacity at the A/W interface and penetration into egg phosphatidylcholine monolayer compared to lysozyme. Whereas lysozyme remains folded upon compression of the protein layer at the A/W interface and shows a quasi-pure elastic behavior, N TAIL shows a much higher molecular area and forms a highly viscoelastic film with a high dilational modulus. To our knowledge, a new disorder-to-order transition is thus observed for the N TAIL protein that folds into an antiparallel β-sheet at the A/W interface and presents strong intermolecular interactions. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Dancing Protein Clouds: The Strange Biology and Chaotic Physics of Intrinsically Disordered Proteins.

PubMed

Uversky, Vladimir N

2016-03-25

Biologically active but floppy proteins represent a new reality of modern protein science. These intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered and intrinsically disordered protein regions (IDPRs) constitute a noticeable part of any given proteome. Functionally, they complement ordered proteins, and their conformational flexibility and structural plasticity allow them to perform impossible tricks and be engaged in biological activities that are inaccessible to well folded proteins with their unique structures. The major goals of this minireview are to show that, despite their simplified amino acid sequences, IDPs/IDPRs are complex entities often resembling chaotic systems, are structurally and functionally heterogeneous, and can be considered an important part of the structure-function continuum. Furthermore, IDPs/IDPRs are everywhere, and are ubiquitously engaged in various interactions characterized by a wide spectrum of binding scenarios and an even wider spectrum of structural and functional outputs. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Identification of a Drug Targeting an Intrinsically Disordered Protein Involved in Pancreatic Adenocarcinoma

NASA Astrophysics Data System (ADS)

Neira, José L.; Bintz, Jennifer; Arruebo, María; Rizzuti, Bruno; Bonacci, Thomas; Vega, Sonia; Lanas, Angel; Velázquez-Campoy, Adrián; Iovanna, Juan L.; Abián, Olga

2017-01-01

Intrinsically disordered proteins (IDPs) are prevalent in eukaryotes, performing signaling and regulatory functions. Often associated with human diseases, they constitute drug-development targets. NUPR1 is a multifunctional IDP, over-expressed and involved in pancreatic ductal adenocarcinoma (PDAC) development. By screening 1120 FDA-approved compounds, fifteen candidates were selected, and their interactions with NUPR1 were characterized by experimental and simulation techniques. The protein remained disordered upon binding to all fifteen candidates. These compounds were tested in PDAC-derived cell-based assays, and all induced cell-growth arrest and senescence, reduced cell migration, and decreased chemoresistance, mimicking NUPR1-deficiency. The most effective compound completely arrested tumor development in vivo on xenografted PDAC-derived cells in mice. Besides reporting the discovery of a compound targeting an intact IDP and specifically active against PDAC, our study proves the possibility to target the ‘fuzzy’ interface of a protein that remains disordered upon binding to its natural biological partners or to selected drugs.

Identification of a Drug Targeting an Intrinsically Disordered Protein Involved in Pancreatic Adenocarcinoma

PubMed Central

Neira, José L.; Bintz, Jennifer; Arruebo, María; Rizzuti, Bruno; Bonacci, Thomas; Vega, Sonia; Lanas, Angel; Velázquez-Campoy, Adrián; Iovanna, Juan L.; Abián, Olga

2017-01-01

Intrinsically disordered proteins (IDPs) are prevalent in eukaryotes, performing signaling and regulatory functions. Often associated with human diseases, they constitute drug-development targets. NUPR1 is a multifunctional IDP, over-expressed and involved in pancreatic ductal adenocarcinoma (PDAC) development. By screening 1120 FDA-approved compounds, fifteen candidates were selected, and their interactions with NUPR1 were characterized by experimental and simulation techniques. The protein remained disordered upon binding to all fifteen candidates. These compounds were tested in PDAC-derived cell-based assays, and all induced cell-growth arrest and senescence, reduced cell migration, and decreased chemoresistance, mimicking NUPR1-deficiency. The most effective compound completely arrested tumor development in vivo on xenografted PDAC-derived cells in mice. Besides reporting the discovery of a compound targeting an intact IDP and specifically active against PDAC, our study proves the possibility to target the ‘fuzzy’ interface of a protein that remains disordered upon binding to its natural biological partners or to selected drugs. PMID:28054562

Comprehensive development and testing of the ASIST-GBV, a screening tool for responding to gender-based violence among women in humanitarian settings.

PubMed

Wirtz, A L; Glass, N; Pham, K; Perrin, N; Rubenstein, L S; Singh, S; Vu, A

2016-01-01

Conflict affected refugees and internally displaced persons (IDPs) are at increased vulnerability to gender-based violence (GBV). Health, psychosocial, and protection services have been implemented in humanitarian settings, but GBV remains under-reported and available services under-utilized. To improve access to existing GBV services and facilitate reporting, the ASIST-GBV screening tool was developed and tested for use in humanitarian settings. This process was completed in four phases: 1) systematic literature review, 2) qualitative research that included individual interviews and focus groups with GBV survivors and service providers, respectively, 3) pilot testing of the developed screening tool, and 4) 3-month implementation testing of the screening tool. Research was conducted among female refugees, aged ≥15 years in Ethiopia, and female IDPs, aged ≥18 years in Colombia. The systematic review and meta-analysis identified a range of GBV experiences and estimated a 21.4 % prevalence of sexual violence (95 % CI:14.9-28.7) among conflict-affected populations. No existing screening tools for GBV in humanitarian settings were identified. Qualitative research with GBV survivors in Ethiopia and Colombia found multiple forms of GBV experienced by refugees and IDPs that occurred during conflict, in transit, and in displaced settings. Identified forms of violence were combined into seven key items on the screening tool: threats of violence, physical violence, forced sex, sexual exploitation, forced pregnancy, forced abortion, and early or forced marriage. Cognitive testing further refined the tool. Pilot testing in both sites demonstrated preliminary feasibility where 64.8 % of participants in Ethiopia and 44.9 % of participants in Colombia were identified with recent (last 12 months) cases of GBV. Implementation testing of the screening tool, conducted as a routine service in camp/district hospitals, allowed for identification of GBV cases and referrals to services. In this phase, 50.6 % of participants in Ethiopia and 63.4 % in Colombia screened positive for recent experiences of GBV. Psychometric testing demonstrated appropriate internal consistency of the tool (Cronbach's α = 0.77) and item response theory demonstrated appropriate discrimination and difficulty of the tool. The ASIST-GBV screening tool has demonstrated utility and validity for use in confidential identification and referral of refugees and IDPs who experience GBV.

Fluid-induced organic synthesis in the solar nebula recorded in extraterrestrial dust from meteorites

PubMed Central

Vollmer, Christian; Kepaptsoglou, Demie; Leitner, Jan; Busemann, Henner; Spring, Nicole H.; Ramasse, Quentin M.; Hoppe, Peter; Nittler, Larry R.

2014-01-01

Isotopically anomalous carbonaceous grains in extraterrestrial samples represent the most pristine organics that were delivered to the early Earth. Here we report on gentle aberration-corrected scanning transmission electron microscopy investigations of eight 15N-rich or D-rich organic grains within two carbonaceous Renazzo-type (CR) chondrites and two interplanetary dust particles (IDPs) originating from comets. Organic matter in the IDP samples is less aromatic than that in the CR chondrites, and its functional group chemistry is mainly characterized by C–O bonding and aliphatic C. Organic grains in CR chondrites are associated with carbonates and elemental Ca, which originate either from aqueous fluids or possibly an indigenous organic source. One distinct grain from the CR chondrite NWA 852 exhibits a rim structure only visible in chemical maps. The outer part is nanoglobular in shape, highly aromatic, and enriched in anomalous nitrogen. Functional group chemistry of the inner part is similar to spectra from IDP organic grains and less aromatic with nitrogen below the detection limit. The boundary between these two areas is very sharp. The direct association of both IDP-like organic matter with dominant C–O bonding environments and nanoglobular organics with dominant aromatic and C–N functionality within one unique grain provides for the first time to our knowledge strong evidence for organic synthesis in the early solar system activated by an anomalous nitrogen-containing parent body fluid. PMID:25288736

Fullerenes and interplanetary dust at the Permian-Triassic boundary.

PubMed

Poreda, Robert J; Becker, Luann

2003-01-01

We recently presented new evidence that an impact occurred approximately 250 million years ago at the Permian-Triassic boundary (PTB), triggering the most severe mass extinction in the history of life on Earth. We used a new extraterrestrial tracer, fullerene, a third carbon carrier of noble gases besides diamond and graphite. By exploiting the unique properties of this molecule to trap noble gases inside of its caged structure (helium, neon, argon), the origin of the fullerenes can be determined. Here, we present new evidence for fullerenes with extraterrestrial noble gases in the PTB at Graphite Peak, Antarctica, similar to PTB fullerenes from Meishan, China and Sasayama, Japan. In addition, we isolated a (3)He-rich magnetic carrier phase in three fractions from the Graphite Peak section. The noble gases in this magnetic fraction were similar to zero-age deep-sea interplanetary dust particles (IDPs) and some magnetic grains isolated from the Cretaceous-Tertiary boundary. The helium and neon isotopic compositions for both the bulk Graphite Peak sediments and an isolated magnetic fraction from the bulk material are consistent with solar-type gases measured in zero-age deep-sea sediments and point to a common source, namely, the flux of IDPs to the Earth's surface. In this instance, the IDP noble gas signature for the bulk sediment can be uniquely decoupled from fullerene, demonstrating that two separate tracers are present (direct flux of IDPs for (3)He vs. giant impact for fullerene).

Evidence for Changes in 81PIWild 2 Organic Matter Since Collection and Comparison of 82PIWild 2 and IDP Organic Matter to Access the Thermal Effects of Aerogel Capture

NASA Technical Reports Server (NTRS)

Wirick, S.; Flynn, G. J.; Keller, L.; Messenger, Nakamura; Sandford, S. A.; Zolensky, M. E.; Peltzer, C.; Jacobsen, C.

2009-01-01

NASA s Stardust spacecraft collected cometary material during its passage through the dust coma of comet 81P/Wild 2 on January 2nd, 2004 and delivered this material to Earth on January 15th 2006. The first fragment we analyzed during the preliminary examination was partially vaporized by the X-ray beam. The carbonaceous material that survived was re-analysis approx.2 months later and the carbon spectrum for this material had significantly changed from what we first observed.. We have observed similar changes to the carbonaceous matter in some interplanetary dust particles ( IDPs). Some of the 81P/Wild 2 organic matter volatilized upon impact with the aerogel as observed using IR spectroscopy where IR spectra were collected several mms away from sample tracks [1]. The time-temperature profile experienced by any particular 81P/Wild 2 grain during aerogel capture is not known, although Brownlee, et al. suggest that fine-grained materials, <1 micron in size, fragmented and then partially vaporized during collection, while particles much larger then 1 micron in size were captured intact [2]. Nearly all organic matter is subject to thermal alteration. To assess the heating and alteration experienced by the 81P/Wild 2 organic matter during capture we are comparing 81P/Wild2 organic matter with IDP organic matter where we have evidence of heating in the IDP [3,4].

Accretion of Interplanetary Dust Particles by the Earth

NASA Astrophysics Data System (ADS)

Kortenkamp, Stephen J.; Dermott, Stanley F.

1998-10-01

Analyses of hypervelocity micrometeoroid impact craters preserved in lunar material and on the panels of the Long Duration Exposure Facility (LDEF) indicate that each year Earth accretes about 3 × 107kg of interplanetary dust particles (IDPs) from the zodiacal cloud (E. Grünet al.1985,Astron. Astrophys.286, 915-924; S. G. Love and D. E. Brownlee, 1993,Science262, 550-553). The size distributions of these lunar and LDEF craters indicate that the mass distribution of IDPs encountering Earth peaks at about 200 μm diameter. This particle-size cutoff may be indicative of collisionally evolved asteroidal dust, where the collisional lifetime of dust particles larger than ∼100 μm is shorter than the time required for their orbits to decay under Poynting-Robertson light drag from the asteroid belt to Earth (B. Å. S. Gustafson, 1994,Annu. Rev. Earth Planet. Sci.22, 553-595). Additionally, analyses of IDPs collected from the stratosphere by high-flying aircraft reveal a diversity in chemical composition which is even narrower than that of the meteorites (G. J. Flynn, 1995,Nature376, 114). Together these findings suggest that IDPs present in the atmosphere and our collections may originate from very limited sources in the asteroid belt. The most abundant sources of dust to be unambiguously linked to the zodiacal cloud are the three asteroid families Eos, Themis, and Koronis-the progenitors of the ten-degree and low-latitude dust bands discovered by the Infrared Astronomical Satellite in 1984. We use direct numerical integration of the full equations of motion to model the orbital evolution of dust particles from these three families as well as from other nonfamily asteroids and from the population of known short period comets. Our simulations include gravitational perturbations from the planets, radiation pressure, and solar wind drag. We find that a large, and perhaps the dominant, fraction of the IDPs accreted by Earth comes from the asteroid families Eos, Themis, and Koronis and that probably fewer than 25% of accreted IDPs come from comets. We also find a seasonal variation in the distribution of ascending nodes of the Themis and Koronis dust particle orbits near Earth. Earth-orbiting instruments utilizing aero-gels could exploit these seasonal variations to collect and return intact samples of these two asteroid families. Finally, we demonstrate how the long-term accretion rate of asteroidal dust from all sources should be anti-correlated with Earth's changing orbital eccentricity.

NMR contributions to structural dynamics studies of intrinsically disordered proteins☆

PubMed Central

Konrat, Robert

2014-01-01

Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions. PMID:24656082

Spin-State-Dependent Ion-Molecule Chemistry as the Origin of N-15 and D Isotopic Anomalies in Primitive Matter.

NASA Technical Reports Server (NTRS)

Wirstrom, E. S.; Charnley, S. B.; Cordiner, M. A.; Milam, S. N.

2012-01-01

Many meteoritic and interplanetary dust particle (IDP) samples contain bulk enhancements and hotspots rich in N-15. Similarly low C(14)N/C(15)N ratios have been observed in numerous comets, An almost constant enrichment factor in comets from disti'nct formation zones in the nebular disk (i.e. both Jupiter Family and Oort Cloud comets), strongly suggests that this fractionation is primordial and was set in the protsolar cloud core. Deuterium enrichment is observed in both meteorites and IDPs

Cometary and interstellar dust grains - Analysis by ion microprobe mass spectrometry and other techniques

NASA Technical Reports Server (NTRS)

Zinner, Ernst

1991-01-01

A survey of microanalytical measurements on interplanetary dust particles (IDPs) and interstellar dust grains from primitive meteorites is presented. Ion-microprobe mass spectrometry with its capability to determine isotopic compositions of many elements on a micron spatial scale has played a special role. Examples are measurements of H, N, and O isotopes and refractory trace elements in IDPs; C, N, Mg, and Si isotopes in interstellar SiC grains; and C and N isotopes and H, N, Al, and Si concentrations in interstellar graphite grains.

Stardust (Comet 81P/Wild-2) Samples and Early Solar Sys-tem Processes

NASA Astrophysics Data System (ADS)

Ebel, Denton S.; Weisberg, M. K.; Connolly, H. C.; Zolensky, M.; Mineralogy/Petrology Preliminary Examination Subteam, Stardust

2006-12-01

Dust particles from comet 81P/Wild-2 were captured in silica aerogel (also as impact debris on Al-foil strips) at 6.1 km/s relative velocity by the Stardust spacecraft on 2-Jan-2004, and returned to Earth 15-Jan-2006 [1]. A pre-liminary examination team (PET) of 150 are preparing reports on a subset of samples [2, 3, e.g., 4]. PET investigations in a short time on a limited number of <10 micron grains show that olivine, pyroxene, FeNi-metal and sulfide are common. Olivine and low-Ca pyroxene are unequilibrated in Mg/(Fe+Mg). Some for-sterite is low-iron, Mn-enriched as also found in some in-terplanetary dust particles (IDPs), and in matrix and amoe-boid olivine aggregates in CR carbonaceous chondrites (CC)[5]. Diopside and melilite are found, similar to those in spinel-pyroxene aggregates in CM chondrites and in re-fractory IDPs[6,7]. FeNi-metal and Fe-Ni, Fe-Ni-Cu and Fe-Zn sulfides are observed, and the highly reduced phase osbornite (TiN). Hydrous silicates and carbonates are not observed. A primary result is the preponderance of high temperature and reduced crystalline phases. These may form from amorphous precursors heated near the sun[8], or by viscosity-related processes farther out in the disk[9]. Silicate, metal and sulfide compositions are consistent with chondrites, particularly the CR clan. A better comparison may perhaps be made to anhydrous IDPs, which probably sample outer regions of the Solar System. The isotopic homogeneity of the grains will have important implications for mixing in the early disk. References: [1] Brownlee et al. (2004) Science 304, 1764.[2] ftp://ftp.lpi.usra.edu/pub/outgoing/lpsc2006/full101.pdf [3] Zolensky et al. (2006) LPSC XXXVII #1203. [4] Zolensky et al. (2006, in prep.) Science. [5] Weisberg et al. (2004) MaPS 39, 1741. [6] McKeegan (1987) Science 237, 1468. [7] Zolensky (1987) Science 237, 1466. [8] Scott and Krot (2005) Chondrules and the Protoplanetary Disk, 15-54. [9] Joung et al. (2004) ApJ 606, 532.

An improved automated procedure for informal and temporary dwellings detection and enumeration, using mathematical morphology operators on VHR satellite data

NASA Astrophysics Data System (ADS)

Jenerowicz, Małgorzata; Kemper, Thomas

2016-10-01

Every year thousands of people are displaced by conflicts or natural disasters and often gather in large camps. Knowing how many people have been gathered is crucial for an efficient relief operation. However, it is often difficult to collect exact information on the total number of the population. This paper presents the improved morphological methodology for the estimation of dwellings structures located in several Internally Displaced Persons (IDPs) Camps, based on Very High Resolution (VHR) multispectral satellite imagery with pixel sizes of 1 meter or less including GeoEye-1, WorldView-2, QuickBird-2, Ikonos-2, Pléiades-A and Pléiades-B. The main topic of this paper is the approach enhancement with selection of feature extraction algorithm, the improvement and automation of pre-processing and results verification. For the informal and temporary dwellings extraction purpose the high quality of data has to be ensured. The pre-processing has been extended by including the input data hierarchy level assignment and data fusion method selection and evaluation. The feature extraction algorithm follows the procedure presented in Jenerowicz, M., Kemper, T., 2011. Optical data are analysed in a cyclic approach comprising image segmentation, geometrical, textural and spectral class modeling aiming at camp area identification. The successive steps of morphological processing have been combined in a one stand-alone application for automatic dwellings detection and enumeration. Actively implemented, these approaches can provide a reliable and consistent results, independent of the imaging satellite type and different study sites location, providing decision support in emergency response for the humanitarian community like United Nations, European Union and Non-Governmental relief organizations.

[Effect of lumbar hybrid instrumentation and rigid fusion on the treated and the adjacent segments. A biomechanical study].

PubMed

Wiedenhöfer, B; Akbar, M; Fürstenberg, C H; Carstens, C; Hemmer, S; Schilling, C

2011-02-01

Degeneration of the upper adjacent segment after operative treatment of degenerative spinal diseases of the lumbar spine (degenerative disc disease DDD) is an unsolved problem. There is also no consensus on whether a rigid or dynamic treatment of DDD should be carried out to protect the segments. This study was carried out to evaluate the effect of bisegmental rigid 360° fusion and bisegmental hybrid fusion on the treated segment as well as on the upper adjacent segment under the aspect of segment protection. A total of six human spinal column preparations (L2-5) were tested under native conditions (NAT), with bisegmental rigid fusion (RIG 360°) and with hybrid fusion (Hybrid) in all three movement directions under physical load and with an preload. The range of motion (ROM) and neutral zone (NZ) were evaluated. The intradiscal pressure (IDP) was measured in the upper adjacent segment (OAS). The RIG 360° led to a significant reduction in movement in all directions compared to NAT but Hybrid only in lateral bending (LB). In the OAS the NZ was showed a much greater increase than the ROM. The RIG 360° showed an increase of the NZ in flexion-extension of 86.8% and in LB of 49.6% as well as a significant increase in axial rotation of 52.5%. The increase in the Hybrid was not significant compared to NAT in all directions. Pressure measurements in OAS showed no significant differences for RIG 360° and for Hybrid compared to NAT for both load scenarios. The range of motion of the treated segments for Hybrid were close to NAT in comparison to RIG 360° indicating a segment-protective effect. The hypothesis that rigid fusion has a significant effect on intersegmental mobility and the increase in intradiscal pressure in the upper adjacent segment could not be confirmed. The data indicate that the primary effect of fusion on the adjacent segment is very low but the fusion-linked increased frequency of extreme loads of the OAS falling within the significance level leads to degeneration. Even if the NZ values for Hybrid and RIG 360° do not significantly differ from NAT, the NZ alterations between the instrumentations tend to be strongly shifted in favor of Hybrid. The data confirm that the clear and sometimes significant alterations of the NZ can be an essential factor for development of adjacent segment degeneration. A dynamic conclusion of instrumentation in the sense of a topping-off would appear to be useful if pathoanatomical indications for an intervertebral disc prosthesis are present.

Wide-line NMR and DSC studies on intrinsically disordered p53 transactivation domain and its helically pre-structured segment

PubMed Central

Tompa, Peter; Han, Kyou-Hoon; Bokor, Mónika; Kamasa, Pawel; Tantos, Ágnes; Fritz, Beáta; Kim, Do-Hyoung; Lee, Chewook; Verebélyi, Tamás; Tompa, Kálmán

2016-01-01

Wide-line 1H NMR intensity and differential scanning calorimetry measurements were carried out on the intrinsically disordered 73-residue full transactivation domain (TAD) of the p53 tumor suppressor protein and two peptides: one a wild type p53 TAD peptide with a helix pre-structuring property, and a mutant peptide with a disabled helix-forming propensity. Measurements were carried out in order to characterize their water and ion binding characteristics. By quantifying the number of hydrate water molecules, we provide a microscopic description for the interactions of water with a wild-type p53 TAD and two p53 TAD peptides. The results provide direct evidence that intrinsically disordered proteins (IDPs) and a less structured peptide not only have a higher hydration capacity than globular proteins, but are also able to bind a larger amount of charged solute ions. [BMB Reports 2016; 49(9): 497-501] PMID:27418282

Impact of Ionic Liquids on the Structure and Dynamics of Collagen.

PubMed

Tarannum, Aafiya; Adams, Alina; Blümich, Bernhard; Fathima, Nishter Nishad

2018-01-25

The changes in the structure and dynamics of collagen treated with two different classes of ionic liquids, bis-choline sulfate (CS) and 1-butyl-3-methyl imidazolium dimethyl phosphate (IDP), have been studied at the molecular and fibrillar levels. At the molecular level, circular dichroic studies revealed an increase in molar ellipticity values for CS when compared with native collagen, indicating cross-linking, albeit pronounced conformational changes for IDP were witnessed indicating denaturation. The impedance was analyzed to correlate the conformational changes with the hydration dynamics of protein. Changes in the dielectric properties of collagen observed upon treatment with CS and IDP reported molecular reorientation in the surrounding water milieu, suggesting compactness or destabilization of the collagen. This was further confirmed by proton transverse NMR relaxation time measurements, which demonstrated that the water mobility changes in the presence of the ILs. At the fibrillar level, differential scanning calorimetry thermograms for rat tail tendon collagen fibers treated with CS show a 5 °C increase in denaturation temperature, suggesting imparted stability. On the contrary, a significant temperature decrease was noticed for IDP, indicating the destabilization of collagen fibers. The obtained results clearly indicate that the changes in the secondary structure of protein are due to the changes in the hydration dynamics of collagen upon interaction with ILs. Thus, this study on the interaction of collagen with ionic liquids unfolds the propensity of ILs to stabilize or destabilize collagen depending on the changes invoked at the molecular level in terms of structure and dynamics of protein, which also got manifested at the fibrillar level.

Equation Chapter 1 Section 1Sequence-To-Conformation Relationships of Disordered Regions Tethered to Folded Domains of Proteins.

PubMed

Mittal, Anuradha; Holehouse, Alex S; Cohan, Megan C; Pappu, Rohit V

2018-05-12

Intrinsically disordered proteins and regions (IDPs / IDRs) are characterized by well-defined sequence-to-conformation relationships (SCRs). These relationships refer to the sequence-specific preferences for average sizes, shapes, residue-specific secondary structure propensities, and amplitudes of multiscale conformational fluctuations. SCRs are discerned from the sequence-specific conformational ensembles of IDPs. A vast majority of IDPs are actually tethered to folded domains (FDs). This raises the question of whether or not SCRs inferred for IDPs are applicable to IDRs tethered to folded domains. Here, we use atomistic simulations based on a well-established forcefield paradigm and an enhanced sampling method to obtain comparative assessments of SCRs for thirteen archetypal IDRs modeled as autonomous units, as C-terminal tails connected to folded domains, and as linkers between pairs of folded domains. Our studies uncover a set of general observations regarding context-independent versus context-dependent SCRs of IDRs. SCRs are minimally perturbed upon tethering to folded domains if the IDRs are deficient in charged residues and for polyampholytic IDRs where the oppositely charged residues within the sequence of the IDR are separated into distinct blocks. In contrast, the interplay between IDRs and tethered folded domains has a significant modulatory effect on SCRs if the IDRs have intermediate fractions of charged residues or if they have sequence-intrinsic conformational preferences for canonical random coils. Our findings suggest that IDRs with context-independent SCRs might be independent evolutionary modules whereas IDRs with context-dependent intrinsic SCRs might co-evolve with the FDs to which they are tethered. Copyright © 2018. Published by Elsevier Ltd.

Use of 'sense of coherence (SOC)' scale to measure resilience in Eritrea: interrogating both the data and the scale.

PubMed

Almedom, Astier M; Tesfamichael, Berhe; Saeed Mohammed, Zein; Mascie-Taylor, C G N; Alemu, Zemui

2007-01-01

An adapted 'sense of coherence' scale short form (SOC-13) was administered in nine languages of Eritrea with a total of 265 participants (162 women and 103 men) in order to assess 'resilience' in quantitative terms. Statistical analysis yielded significant differences in SOC scores between the displaced and non-displaced: mean=54.84 (SD=6.48) in internally displaced person (IDP) camps, compared with mean=48.94 (SD=11.99) in urban and rural settlements (t=3.831, p<0.001). Post-hoc tests revealed that the main difference is between IDP camp dwellers and urban (non-displaced) residents. Those in rural but traditionally mobile (pastoralist or transhumant) communities scored more or less the same as the urban non-displaced - i.e. significantly higher than those in IDP camps (p<0.05). Analysis of variance showed that displacement has a significantly negative effect on women compared with men (RR=0.262, p<0.001). Repeating the analysis for the three groups confirmed that urban and pastoralist/transhumant groups are similar, while women in IDP camps are lower scoring (RR=0.268, p<0.001), Hamboka women being worst affected due to their experience of serial displacement. These findings are interpreted and discussed in the light of qualitative information gleaned from the study participants' interrogation of the content of the SOC scale; and in the wider context of historical, socio-political and cultural characteristics of Eritrea. The study's implications for humanitarian and public health policy are considered.

Cloning of a cDNA encoding bovine mitochondrial NADP(+)-specific isocitrate dehydrogenase and structural comparison with its isoenzymes from different species.

PubMed Central

Huh, T L; Ryu, J H; Huh, J W; Sung, H C; Oh, I U; Song, B J; Veech, R L

1993-01-01

Mitochondrial NADP(+)-specific isocitrate dehydrogenase (IDP) was co-purified with the pyruvate dehydrogenase complex from bovine kidney mitochondria. The determination of its N-terminal 16-amino-acid sequence revealed that it is highly similar to the IDP from yeast. A cDNA clone (1.8 kb long) encoding this protein was isolated from a bovine kidney lambda gt11 cDNA library using a synthetic oligodeoxynucleotide. The deduced protein sequence of this cDNA clone rendered a precursor protein of 452 amino-acid residues (50,830 Da) and a mature protein of 413 amino-acid residues (46,519 Da). It is 100% identical to the internal tryptic peptide sequences of the autologous form from pig heart and 62% similar to that from yeast. However, it shares little similarity with the mitochondrial NAD(+)-specific isoenzyme from yeast. Structural analyses of the deduced proteins of IDP isoenzymes from different species indicated that similarity exists in certain regions, which may represent the common domains for the active sites or coenzyme-binding sites. In Northern-blot analysis, one species of mRNA (about 2.2 kb for both bovine and human) was hybridized with a 32P-labelled cDNA probe. Southern-blot analysis of genomic DNAs verified simple patterns of hybridization with this cDNA. These results strongly indicate that the mitochondrial IDP may be derived from a single gene family which does not appear to be closely related to that of the NAD(+)-specific isoenzyme. Images Figure 1 Figure 3 Figure 4 Figure 5 PMID:8318002

Spontaneous Fluctuations can Guide Drug Design Strategies for Structurally Disordered Proteins.

PubMed

Maity, Barun Kumar; Vishvakarma, Vicky; Surendran, Dayana; Rawat, Anoop; Das, Anirban; Pramanik, Shreya; Arfin, Najmul; Maiti, Sudipta

2018-06-21

Structure-based 'rational' drug-design strategies fail for diseases associated with intrinsically disordered proteins (IDPs). However, structural disorder allows large amplitude spontaneous intramolecular dynamics in a protein. We demonstrate a method that exploits this dynamics to provide quantitative information about the degree of interaction of an IDP with other molecules. A candidate ligand molecule may not bind strongly, but even momentary interactions can be expected to perturb the fluctuations. We measure the amplitude and frequency of the equilibrium fluctuations of fluorescently labeled small oligomers of hIAPP (an IDP associated with Type II diabetes) in a physiological solution, using nanosecond fluorescence cross-correlation spectroscopy. We show that the inter-terminal distance fluctuates at a characteristic timescale of 134 ± 10 ns, and 6.4 ± 0.2 % of the population is in the 'closed' (quenched) state at equilibrium. These fluctuations are affected in a dose-dependent manner by a series of small molecules known to reduce the toxicity of various amyloid peptides. The degree of interaction shows the following order: resveratrol < epicatechin ~ quercetin < congo red < epigallocatechin-3-gallate. Such ordering can provide a direction for exploring the chemical space for finding stronger-binding ligands. We test the biological relevance of these measurements by measuring the effect of these molecules on the affinity of hIAPP for lipid vesicles and cell membranes. We find that the ability of a molecule to modulate intramolecular fluctuations correlates well with its ability to lower membrane affinity. We conclude that structural disorder may provide new avenues for rational drug design for IDPs.

Thermodynamic characterization of the multivalent interactions underlying rapid and selective translocation through the nuclear pore complex

PubMed Central

Hayama, Ryo; Sparks, Samuel; Hecht, Lee M.; Dutta, Kaushik; Karp, Jerome M.; Cabana, Christina M.; Rout, Michael P.; Cowburn, David

2018-01-01

Intrinsically disordered proteins (IDPs) play important roles in many biological systems. Given the vast conformational space that IDPs can explore, the thermodynamics of the interactions with their partners is closely linked to their biological functions. Intrinsically disordered regions of Phe–Gly nucleoporins (FG Nups) that contain multiple phenylalanine–glycine repeats are of particular interest, as their interactions with transport factors (TFs) underlie the paradoxically rapid yet also highly selective transport of macromolecules mediated by the nuclear pore complex. Here, we used NMR and isothermal titration calorimetry to thermodynamically characterize these multivalent interactions. These analyses revealed that a combination of low per-FG motif affinity and the enthalpy–entropy balance prevents high-avidity interaction between FG Nups and TFs, whereas the large number of FG motifs promotes frequent FG–TF contacts, resulting in enhanced selectivity. Our thermodynamic model underlines the importance of functional disorder of FG Nups. It helps explain the rapid and selective translocation of TFs through the nuclear pore complex and further expands our understanding of the mechanisms of “fuzzy” interactions involving IDPs. PMID:29374059

Measurement of polycyclic aromatic hydrocarbon (PAHs) in interplanetary dust particles

NASA Technical Reports Server (NTRS)

Clemett, S. J.; Maechling, C. R.; Zare, R. N.; Swan, P. D.; Walker, R. M.

1993-01-01

We report here the first definitive measurements of specific organic molecules (polycyclic aromatic hydrocarbons (PAH's)) in interplanetary dust particles (IDP's). An improved version of the microbeam-two-step laser mass spectrometer was used for the analysis. Two IDP's gave similar mass spectra showing an abundance of PAH's. Control samples, including particles of probable terrestrial origin from the same stratospheric collector, gave either null results or quite different spectra. We conclude that the PAH's are probably indigenous to the IDP's and are not terrestrial contaminants. The instrument used to study the particles is a two-step laser mass spectrometer. Constituent neutral molecules of the sample are first desorbed with a pulsed infrared laser beam focussed to 40 micrometers. In the second step, PAH's in the desorbed plume are preferentially ionized by a pulsed UV laser beam. Resulting ions produced by resonant absorption are extracted into a reflectron time-of-flight mass spectrometer. This instrument has high spatial resolution, high ion transmission, unlimited mass range, and multichannel detection of all ion masses from a single laser shot.

Binding of Disordered Peptides to Kelch: Insights from Enhanced Sampling Simulations.

PubMed

Do, Trang Nhu; Choy, Wing-Yiu; Karttunen, Mikko

2016-01-12

Keap1 protein plays an essential role in regulating cellular oxidative stress response and is a crucial binding hub for multiple proteins, several of which are intrinsically disordered proteins (IDP). Among Kelch's IDP binding partners, NRF2 and PTMA are the two most interesting cases. They share a highly similar binding motif; however, NRF2 binds to Kelch with a binding affinity of approximately 100-fold higher than that of PTMA. In this study, we perform an exhaustive sampling composed of 6 μs well-tempered metadynamics and 2 μs unbiased molecular dynamics (MD) simulations aiming at characterizing the binding mechanisms and structural properties of these two peptides. Our results agree with previous experimental observations that PTMA is remarkably more disordered than NRF2 in both the free and bound states. This explains PTMA's lower binding affinity. Our extensive sampling also provides valuable insights into the vast conformational ensembles of both NRF2 and PTMA, supports the hypothesis of coupled folding-binding, and confirms the essential role of linear motifs in IDP binding.

JPSS Common Ground System Multimission Support

NASA Astrophysics Data System (ADS)

Jamilkowski, M. L.; Miller, S. W.; Grant, K. D.

2013-12-01

NOAA & NASA jointly acquire the next-generation civilian operational weather satellite: Joint Polar Satellite System (JPSS). JPSS contributes the afternoon orbit & restructured NPOESS ground system (GS) to replace the current Polar-orbiting Operational Environmental Satellite (POES) system run by NOAA. JPSS sensors will collect meteorological, oceanographic, climatological & solar-geophysical observations of the earth, atmosphere & space. The JPSS GS is the Common Ground System (CGS), consisting of Command, Control, & Communications (C3S) and Interface Data Processing (IDPS) segments, both developed by Raytheon Intelligence, Information & Services (IIS). CGS now flies the Suomi National Polar-orbiting Partnership (S-NPP) satellite, transfers its mission data between ground facilities and processes its data into Environmental Data Records for NOAA & Defense (DoD) weather centers. CGS will expand to support JPSS-1 in 2017. The JPSS CGS currently does data processing (DP) for S-NPP, creating multiple TBs/day across over two dozen environmental data products (EDPs). The workload doubles after JPSS-1 launch. But CGS goes well beyond S-NPP & JPSS mission management & DP by providing data routing support to operational centers & missions worldwide. The CGS supports several other missions: It also provides raw data acquisition, routing & some DP for GCOM-W1. The CGS does data routing for numerous other missions & systems, including USN's Coriolis/Windsat, NASA's SCaN network (including EOS), NSF's McMurdo Station communications, Defense Meteorological Satellite Program (DMSP), and NOAA's POES & EUMETSAT's MetOp satellites. Each of these satellite systems orbits the Earth 14 times/day, downlinking data once or twice/orbit at up to 100s of MBs/second, to support the creation of 10s of TBs of data/day across 100s of EDPs. Raytheon and the US government invested much in Raytheon's mission-management, command & control and data-processing products & capabilities. CGS's flexible, multimission capabilities offer major chances for cost reduction & improved information integration across missions. Raytheon has a unique ability to provide complex, highly-secure, multi-mission GSs. As disaggregation, hosted CGS multimission payloads, and other space-architecture trades are implemented and new sensors come on line that collect orders of magnitude more data, the importance of a flexible, expandable and virtualized modern GS architecture increases. The CGS offers that solution support. JPSS CGS supports 5 global ground stations that can receive S-NPP & JPSS-1 mission data. These, linked with high-bandwidth commercial fiber, quickly transport data to the IDPS for EDP creation & delivery. CGS will process & deliver JPSS-1 data to US operational users in < 80 minutes from time of collection. And CGS leverages this fiber network to provide added data routing for a wide array of global missions. The JPSS CGS is a mature, tested solution for support to operational weather forecasting for civil, military and international partners and climate research. It features a flexible design handling order-of-magnitude increases in data over legacy satellite GSs and meets demanding science accuracy needs. The Raytheon-built JPSS CGS gives the full GS capability, from design & development through operations & sustainment. This lays the foundation for CGS future evolution to support additional missions like Polar Free Flyers.

Factors associated with the health status of internally displaced persons in northern Uganda

PubMed Central

Roberts, B; Ocaka, K Felix; Browne, J; Oyok, T; Sondorp, E

2009-01-01

Background: Globally, there are over 24 million internally displaced persons (IDPs) who have fled their homes due to violence and insecurity but who remain within their own country. There have been up to 2 million IDPs in northern Uganda alone. The objective of this study was to investigate factors associated with mental and physical health status of IDPs in northern Uganda. Methods: A cross-sectional survey was conducted in November 2006 in IDP camps in the Gulu and Amuru districts of northern Uganda. The study outcome of physical and mental health was measured using the SF-8 instrument, which produces physical (PCS) and mental (MCS) component summary measures. Independent demographic, socio-economic, and trauma exposure (using the Harvard Trauma Questionnaire) variables were also measured. Multivariate regression linear regression analysis was conducted to investigate associations of the independent variables on the PCS and MCS outcomes. Results: 1206 interviews were completed. The respective mean PCS and MCS scores were 42.2 (95% CI 41.32 to 43.10) and 39.3 (95% CI 38.42 to 40.13), well below the instrument norm of 50, indicating poor health. Variables with negative associations with physical or mental health included gender, age, marital status, income, distance of camp from home areas, food security, soap availability, and sense of safety in the camp. A number of individual trauma variables and the frequency of trauma exposure also had negative associations with physical and mental health. Conclusions: This study provides evidence on the impact on health of deprivation of basic goods and services, traumatic events, and fear and uncertainty amongst displaced and crisis affected populations. PMID:19028730

Nutrition among men and household food security in an internally displaced persons camp in Kenya.

PubMed

Singh, Kamal P; Bhoopathy, Sankara Varun; Worth, Heather; Seale, Holly; Richmond, Robyn L

2016-03-01

To determine the nutritional status of men and the food security status of their households in an internally displaced persons (IDP) camp in Kenya. A descriptive, cross-sectional study using a questionnaire and biometric measurements was completed in June 2013. IDP camp, Rongai, Kenya. A total of 267 men aged ≥18 years residing within the camp were recruited via respondent-driven sampling. Statistical associations between categorical variables were analysed using Pearson's χ 2 tests, while independent t tests were used for continuous variables. Among the men surveyed, we found a mean BMI of 20·3 (sd 2·5) kg/m2, with 23·9% of participants in the underweight category (BMI<18·5 kg/m2). The mean Individual Dietary Diversity Score was 6 out of a maximum score of 9. The mean Household Food Insecurity Access Scale score was 11·6 (sd 6·8), with 180 participants (71·7%) residing in households categorised as severely food insecure. Low monthly household income (<2000 Kenyan Shillings, or $US 25) was associated with a higher food insecurity score (P<0·001), greater likelihood of residing in a severely food-insecure household (P<0·001), low dietary diversity score (P<0·05) and being underweight (P<0·01). While the nutritional status of men in the IDP camp is comparable to non-displaced men in Kenya, household food insecurity is relatively high. Efforts to improve food security for the future are essential to minimise the impact of severe food insecurity on mental health, disease profiles and family well-being reported in other IDP settings.

The impact of internal displacement on child mortality in post-earthquake Haiti: a difference-in-differences analysis.

PubMed

Chen, Bradley; Halliday, Timothy J; Fan, Victoria Y

2016-07-19

The Haiti earthquake in 2010 resulted in 1.5 million internally displaced people (IDP), yet little is known about the impact of displacement on health. In this study, we estimate the impact of displacement on infant and child mortality and key health-behavior mechanisms. We employ a difference-in-differences (DID) design with coarsened exact matching (CEM) to ensure comparability among groups with different displacement status using the 2012 Haiti Demographic and Health Survey (DHS). The participants are 21,417 births reported by a nationally representative sample of 14,287 women aged 15-49. The main independent variables are household displacement status which includes households living in camps, IDP households (not in camps), and households not displaced. The main outcomes are infant and child mortality; health status (height-for-age, anemia); uptake of public health interventions (bed net use, spraying against mosquitoes, and vaccinations); and other conditions (hunger; cholera). Births from the camp households have higher infant mortality (OR = 2.34, 95 % CI 1.15 to 4.75) and child mortality (OR = 2.34, 95 % CI 1.10 to 5.00) than those in non-camp IDP households following the earthquake. These odds are higher despite better access to food, water, bed net use, mosquito spraying, and vaccines among camp households. IDP populations are heterogeneous and households that are displaced outside of camps may be self-selected or self-insured. Meanwhile, even households not displaced by a disaster may face challenges in access to basic necessities and health services. Efforts are needed to identify vulnerable populations to provide targeted assistance in post-disaster relief.

Bisphosphonate Inhibitors Reveal a Large Elasticity of Plastidic Isoprenoid Synthesis Pathway in Isoprene-Emitting Hybrid Aspen1

PubMed Central

2015-01-01

Recently, a feedback inhibition of the chloroplastic 1-deoxy-d-xylulose 5-phosphate (DXP)/2-C-methyl-d-erythritol 4-phosphate (MEP) pathway of isoprenoid synthesis by end products dimethylallyl diphosphate (DMADP) and isopentenyl diphosphate (IDP) was postulated, but the extent to which DMADP and IDP can build up is not known. We used bisphosphonate inhibitors, alendronate and zoledronate, that inhibit the consumption of DMADP and IDP by prenyltransferases to gain insight into the extent of end product accumulation and possible feedback inhibition in isoprene-emitting hybrid aspen (Populus tremula × Populus tremuloides). A kinetic method based on dark release of isoprene emission at the expense of substrate pools accumulated in light was used to estimate the in vivo pool sizes of DMADP and upstream metabolites. Feeding with fosmidomycin, an inhibitor of DXP reductoisomerase, alone or in combination with bisphosphonates was used to inhibit carbon input into DXP/MEP pathway or both input and output. We observed a major increase in pathway intermediates, 3- to 4-fold, upstream of DMADP in bisphosphonate-inhibited leaves, but the DMADP pool was enhanced much less, 1.3- to 1.5-fold. In combined fosmidomycin/bisphosphonate treatment, pathway intermediates accumulated, reflecting cytosolic flux of intermediates that can be important under strong metabolic pull in physiological conditions. The data suggested that metabolites accumulated upstream of DMADP consist of phosphorylated intermediates and IDP. Slow conversion of the huge pools of intermediates to DMADP was limited by reductive energy supply. These data indicate that the DXP/MEP pathway is extremely elastic, and the presence of a significant pool of phosphorylated intermediates provides an important valve for fine tuning the pathway flux. PMID:25926480

Factors associated with post-traumatic stress disorder and depression amongst internally displaced persons in northern Uganda

PubMed Central

Roberts, Bayard; Ocaka, Kaducu Felix; Browne, John; Oyok, Thomas; Sondorp, Egbert

2008-01-01

Background The 20 year war in northern Uganda between the Lord's Resistance Army and the Ugandan government has resulted in the displacement of up to 2 million people within Uganda. The purpose of the study was to measure rates of post-traumatic stress disorder (PTSD) and depression amongst these internally displaced persons (IDPs), and investigate associated demographic and trauma exposure risk factors. Methods A cross-sectional multi-staged, random cluster survey with 1210 adult IDPs was conducted in November 2006 in Gulu and Amuru districts of northern Uganda. Levels of exposure to traumatic events and PTSD were measured using the Harvard Trauma Questionnaire (original version), and levels of depression were measured using the Hopkins Symptom Checklist-25. Multivariate logistic regression was used to analyse the association of demographic and trauma exposure variables on the outcomes of PTSD and depression. Results Over half (54%) of the respondents met symptom criteria for PTSD, and over two thirds (67%) of respondents met symptom criteria for depression. Over half (58%) of respondents had experienced 8 or more of the 16 trauma events covered in the questionnaire. Factors strongly linked with PTSD and depression included gender, marital status, distance of displacement, experiencing ill health without medical care, experiencing rape or sexual abuse, experiencing lack of food or water, and experiencing higher rates of trauma exposure. Conclusion This study provides evidence of exposure to traumatic events and deprivation of essential goods and services suffered by IDPs, and the resultant effect this has upon their mental health. Protection and social and psychological assistance are urgently required to help IDPs in northern Uganda re-build their lives. PMID:18489768

Mineralogy of Interplanetary Dust Particles from the Comet Giacobini-Zinner Dust Stream Collections

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Messenger, S.; Westphal, A. J.; Palma, R. L.

2015-01-01

The Draconoid meteor shower, originating from comet 21P/Giacobini-Zinner, is a low-velocity Earth-crossing dust stream that had a peak anticipated flux on Oct. 8, 2012. In response to this prediction, NASA performed dedicated stratospheric dust collections to target interplanetary dust particles (IDPs) from this comet stream on Oct 15-17, 2012 [3]. Twelve dust particles from this targeted collection were allocated to our coordinated analysis team for studies of noble gas (Univ. Minnesota, Minnesota State Univ.), SXRF and Fe-XANES (SSL Berkeley) and mineralogy/isotopes (JSC). Here we report a mineralogical study of 3 IDPs from the Draconoid collection..

Multimode Jahn-Teller effect in bulk systems: A case of the N V 0 center in diamond

DOE PAGES

Zhang, Jianhua; Wang, Cai -Zhuang; Zhu, Zizhong; ...

2018-04-15

Here, the multimode Jahn-Teller (JT) effect in a bulk system of a neutral nitrogen-vacancy (NV 0) center in diamond is investigated via first-principles density-functional-theory calculations and the intrinsic distortion path (IDP) method. The adiabatic potential energy surface of the electronic ground state of the NV 0 center is calculated based on the local spin-density approximation. Our calculations confirm the presence of the dynamic Jahn-Teller effect in the ground 2E state of the NV 0 center. Within the harmonic approximation, the IDP method provides the reactive path of JT distortion from unstable high-symmetry geometry to stable low-symmetry energy minimum geometry, andmore » it describes the active normal modes participating in the distortion. We find that there is more than one vibrational mode contributing to the distortion, and their contributions change along the IDP. Several vibrational modes with large contributions to JT distortion, especially those modes close to 44 meV, are clearly observed as the phonon sideband in photoluminescence spectra in a series of experiments, indicating that the dynamic Jahn-Teller effect plays an important role in the optical transition of the NV 0 center.« less

Multimode Jahn-Teller effect in bulk systems: A case of the N V0 center in diamond

NASA Astrophysics Data System (ADS)

Zhang, Jianhua; Wang, Cai-Zhuang; Zhu, Zizhong; Liu, Qing Huo; Ho, Kai-Ming

2018-04-01

The multimode Jahn-Teller (JT) effect in a bulk system of a neutral nitrogen-vacancy (N V0 ) center in diamond is investigated via first-principles density-functional-theory calculations and the intrinsic distortion path (IDP) method. The adiabatic potential energy surface of the electronic ground state of the N V0 center is calculated based on the local spin-density approximation. Our calculations confirm the presence of the dynamic Jahn-Teller effect in the ground 2E state of the N V0 center. Within the harmonic approximation, the IDP method provides the reactive path of JT distortion from unstable high-symmetry geometry to stable low-symmetry energy minimum geometry, and it describes the active normal modes participating in the distortion. We find that there is more than one vibrational mode contributing to the distortion, and their contributions change along the IDP. Several vibrational modes with large contributions to JT distortion, especially those modes close to 44 meV, are clearly observed as the phonon sideband in photoluminescence spectra in a series of experiments, indicating that the dynamic Jahn-Teller effect plays an important role in the optical transition of the N V0 center.

Optimization algorithms for large-scale multireservoir hydropower systems

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

Hiew, K.L.

Five optimization algorithms were vigorously evaluated based on applications on a hypothetical five-reservoir hydropower system. These algorithms are incremental dynamic programming (IDP), successive linear programing (SLP), feasible direction method (FDM), optimal control theory (OCT) and objective-space dynamic programming (OSDP). The performance of these algorithms were comparatively evaluated using unbiased, objective criteria which include accuracy of results, rate of convergence, smoothness of resulting storage and release trajectories, computer time and memory requirements, robustness and other pertinent secondary considerations. Results have shown that all the algorithms, with the exception of OSDP converge to optimum objective values within 1.0% difference from one another.more » The highest objective value is obtained by IDP, followed closely by OCT. Computer time required by these algorithms, however, differ by more than two orders of magnitude, ranging from 10 seconds in the case of OCT to a maximum of about 2000 seconds for IDP. With a well-designed penalty scheme to deal with state-space constraints, OCT proves to be the most-efficient algorithm based on its overall performance. SLP, FDM, and OCT were applied to the case study of Mahaweli project, a ten-powerplant system in Sri Lanka.« less

Multimode Jahn-Teller effect in bulk systems: A case of the N V 0 center in diamond

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

Zhang, Jianhua; Wang, Cai -Zhuang; Zhu, Zizhong

Here, the multimode Jahn-Teller (JT) effect in a bulk system of a neutral nitrogen-vacancy (NV 0) center in diamond is investigated via first-principles density-functional-theory calculations and the intrinsic distortion path (IDP) method. The adiabatic potential energy surface of the electronic ground state of the NV 0 center is calculated based on the local spin-density approximation. Our calculations confirm the presence of the dynamic Jahn-Teller effect in the ground 2E state of the NV 0 center. Within the harmonic approximation, the IDP method provides the reactive path of JT distortion from unstable high-symmetry geometry to stable low-symmetry energy minimum geometry, andmore » it describes the active normal modes participating in the distortion. We find that there is more than one vibrational mode contributing to the distortion, and their contributions change along the IDP. Several vibrational modes with large contributions to JT distortion, especially those modes close to 44 meV, are clearly observed as the phonon sideband in photoluminescence spectra in a series of experiments, indicating that the dynamic Jahn-Teller effect plays an important role in the optical transition of the NV 0 center.« less

Structural disorder in plant proteins: where plasticity meets sessility.

PubMed

Covarrubias, Alejandra A; Cuevas-Velazquez, Cesar L; Romero-Pérez, Paulette S; Rendón-Luna, David F; Chater, Caspar C C

2017-09-01

Plants are sessile organisms. This intriguing nature provokes the question of how they survive despite the continual perturbations caused by their constantly changing environment. The large amount of knowledge accumulated to date demonstrates the fascinating dynamic and plastic mechanisms, which underpin the diverse strategies selected in plants in response to the fluctuating environment. This phenotypic plasticity requires an efficient integration of external cues to their growth and developmental programs that can only be achieved through the dynamic and interactive coordination of various signaling networks. Given the versatility of intrinsic structural disorder within proteins, this feature appears as one of the leading characters of such complex functional circuits, critical for plant adaptation and survival in their wild habitats. In this review, we present information of those intrinsically disordered proteins (IDPs) from plants for which their high level of predicted structural disorder has been correlated with a particular function, or where there is experimental evidence linking this structural feature with its protein function. Using examples of plant IDPs involved in the control of cell cycle, metabolism, hormonal signaling and regulation of gene expression, development and responses to stress, we demonstrate the critical importance of IDPs throughout the life of the plant.

Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities

PubMed Central

Tomasso, Maria E.; Tarver, Micheal J.; Devarajan, Deepa; Whitten, Steven T.

2016-01-01

The properties of disordered proteins are thought to depend on intrinsic conformational propensities for polyproline II (PP II) structure. While intrinsic PP II propensities have been measured for the common biological amino acids in short peptides, the ability of these experimentally determined propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs) has not been established. Presented here are results from molecular simulations of disordered proteins showing that the hydrodynamic radius (R h) can be predicted from experimental PP II propensities with good agreement, even when charge-based considerations are omitted. The simulations demonstrate that R h and chain propensity for PP II structure are linked via a simple power-law scaling relationship, which was tested using the experimental R h of 22 IDPs covering a wide range of peptide lengths, net charge, and sequence composition. Charge effects on R h were found to be generally weak when compared to PP II effects on R h. Results from this study indicate that the hydrodynamic dimensions of IDPs are evidence of considerable sequence-dependent backbone propensities for PP II structure that qualitatively, if not quantitatively, match conformational propensities measured in peptides. PMID:26727467

Applying Thiessen Polygon Catchment Areas and Gridded Population Weights to Estimate Conflict-Driven Population Changes in South Sudan

NASA Astrophysics Data System (ADS)

Jordan, L.

2017-10-01

Recent violence in South Sudan produced significant levels of conflict-driven migration undermining the accuracy and utility of both national and local level population forecasts commonly used in demographic estimates, public health metrics and food security proxies. This article explores the use of Thiessen Polygons and population grids (Gridded Population of the World, WorldPop and LandScan) as weights for estimating the catchment areas for settlement locations that serve large populations of internally displaced persons (IDP), in order to estimate the county-level in- and out-migration attributable to conflict-driven displacement between 2014-2015. Acknowledging IDP totals improves internal population estimates presented by global population databases. Unlike other forecasts, which produce spatially uniform increases in population, accounting for displaced population reveals that 15 percent of counties (n = 12) increased in population over 20 percent, and 30 percent of counties (n = 24) experienced zero or declining population growth, due to internal displacement and refugee out-migration. Adopting Thiessen Polygon catchment zones for internal migration estimation can be applied to other areas with United Nations IDP settlement data, such as Yemen, Somalia, and Nigeria.

Intrinsically Disordered Energy Landscapes

PubMed Central

Chebaro, Yassmine; Ballard, Andrew J.; Chakraborty, Debayan; Wales, David J.

2015-01-01

Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such ‘intrinsically disordered’ landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an -helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium. PMID:25999294

Using Quality Attributes to Bridge Systems Engineering Gaps : A Juno Ground Data Systems Case Study

NASA Technical Reports Server (NTRS)

Dubon, Lydia P.; Jackson, Maddalena M.; Thornton, Marla S.

2012-01-01

The Juno Mission to Jupiter is the second mission selected by the NASA New Frontiers Program. Juno launched August 2011 and will reach Jupiter July 2016. Juno's payload system is composed of nine instruments plus a gravity science experiment. One of the primary functions of the Juno Ground Data System (GDS) is the assembly and distribution of the CFDP (CCSDS File Delivery Protocol) product telemetry, also referred to as raw science data, for eight out of the nine instruments. The GDS accomplishes this with the Instrument Data Pipeline (IDP). During payload integration, the first attempt to exercise the IDP in a flight like manner revealed that although the functional requirements were well understood, the system was unable to meet latency requirements with the as-is heritage design. A systems engineering gap emerged between Juno instrument data delivery requirements and the assumptions behind the heritage flight-ground interactions. This paper describes the use of quality attributes to measure and overcome this gap by introducing a new systems engineering activity, and a new monitoring service architecture that successfully delivered the performance metrics needed to validate Juno IDP.

Hydrocarbons on Saturns Satellites: Relationship to Interstellar Dust and the Solar Nebula

NASA Technical Reports Server (NTRS)

Cruikshank, D. P.

2012-01-01

To understand the origin and evolution of our Solar System, and the basic components that led to life on Earth, we study interstellar and planetary spectroscopic signatures. The possible relationship of organic material detected in carbonaceous meteorites, interplanetary dust particles (IDPs), comets and the interstellar medium have been the source of speculation over the years as the composition and processes that governed the early solar nebula have been explored to understand the extent to which primitive material survived or became processed. The Cassini VIMS has provided new data relevant to this problem. Three of Saturn's satellites, Phoebe, Iapetus, and Hyperion, are found to have aromatic and aliphatic hydrocarbons on their surfaces. The aromatic hydrocarbon signature (C-H stretching mode at 3.28 micrometers) is proportionally significantly stronger (relative to the aliphatic bands) than that seen in other Solar System bodies (e.g., comets) and materials (Stardust samples, IDPs, meteorites) and the distinctive sub-features of the 3.4 micrometer aliphatic band (CH2 and CH3 groups) are reminiscent of those widely detected throughout the diffuse ISM. Phoebe may be a captured object that originated in the region beyond the present orbit of Neptune, where the solar nebula contained a large fraction of original interstellar ice and dust that was less processed than material closer to the Sun. Debris from Phoebe now resident on Iapetus and Hyperion, as well as o Phoebe itself, thus presents a unique blend of hydrocarbons, amenable to comparisons with interstellar hydrocarbons and other Solar System materials. The dust ring surrounding Saturn, in which Phoebe is embedded, probably originated from a collision with Phoebe. Dust ring particles are the likely source of the organic-bearing materials, and perhaps the recently identified small particles of Fe detected on Saturn's satellites. Lab measurements of the absolute band strengths of representative aliphatic and aromatic molecules, together with measurements from the VIMS data, allow us to calculate the number of C atoms to find the relative abundances of C atoms in the two kinds of organic molecules. The strength of the prominent aromatic C-H stretch band relative to the aliphatic band complex in Phoebe and Iapetus indicates that the relative abundance of aromatic to aliphatic carbon is very large (greater than 200). In contract, the aromatic band is nearly imperceptible in spectra of interplanetary dust particles (IDP), returned samples from comet 91P/Wild 2, insoluable carbonaceous material in most meteorites, and the diffuse interstellar dust (DISM) (although aromatics are known in all these materials-here we consider only the spectroscopic signature)

Weather Satellite Enterprise Information Chain

NASA Astrophysics Data System (ADS)

Jamilkowski, M. L.; Grant, K. D.; Miller, S. W.; Cochran, S.

2015-12-01

NOAA & NASA are acquiring the next-generation civilian operational weather satellite: Joint Polar Satellite System (JPSS). Contributing the afternoon orbit & ground system (GS) to replace current NOAA POES Satellites, its sensors will collect meteorological, oceanographic & climatological data. The JPSS Common Ground System (CGS), consisting of C3 and IDP segments, is developed by Raytheon. It now flies the Suomi National Polar-orbiting Partnership (S-NPP) satellite, transferring data between ground facilities, processing them into environmental products for NOAA weather centers, and expanding to support JPSS-1 in 2017. As a multi-mission system, CGS provides combinations of C3, data processing, and product delivery for numerous NASA, NOAA, DoD and international missions.The CGS provides a wide range of support to a number of missions: Command and control and mission management for the S-NPP mission today, expanding this support to the JPSS-1 satellite mission in 2017 Data acquisition for S-NPP, the JAXA's Global Change Observation Mission - Water (GCOM-W1), POES, and the Defense Meteorological Satellite Program (DMSP) and Coriolis/WindSat for the DoD Data routing over a global fiber network for S-NPP, JPSS-1, GCOM-W1, POES, DMSP, Coriolis/WindSat, NASA EOS missions, MetOp for EUMETSAT and the National Science Foundation Environmental data processing and distribution for S-NPP, GCOM-W1 and JPSS-1 The CGS plays a key role in facilitating the movement and value-added enhancement of data all the way from satellite-based sensor data to delivery to the consumers who generate forecasts and produce watches and warnings. This presentation will discuss the information flow from sensors, through data routing and processing, and finally to product delivery. It will highlight how advances in architecture developed through lessons learned from S-NPP and implemented for JPSS-1 will increase data availability and reduce latency for end user applications.

Interstellar and Solar Nebula Materials in Cometary Dust

NASA Technical Reports Server (NTRS)

Messenger, Scott; Nakamura-Messenger, Keiko; Keller, Lindsay; Nguyen, Ann; Clemett, Simon

2017-01-01

Laboratory studies of cometary dust collected in the stratosphere and returned from comet 81P/Wild 2 by the Stardust spacecraft have revealed ancient interstellar grains and molecular cloud organic matter that record a range of astrophysical processes and the first steps of planetary formation. Presolar materials are rarer meteorites owing to high temperature processing in the solar nebula and hydrothermal alteration on their asteroidal parent bodies. The greater preservation of presolar materials in comets is attributed to their low accretion temperatures and limited planetary processing. Yet, comets also contain a large complement of high temperature materials from the inner Solar System. Owing to the limited and biased sampling of comets to date, the proportions of interstellar and Solar System materials within them remains highly uncertain. Interstellar materials are identified by coordinated isotopic, mineralogical, and chemical measurements at the scale of individual grains. Chondritic porous interplanetary dust particles (CP IDPs) that likely derive from comets are made up of 0.1 - 10 micron-sized silicates, Fe-Ni-sulfides, oxides, and other phases bound by organic material. As much as 1% of the silicates are interstellar grains that have exotic isotopic compositions imparted by nucleosynthetic processes in their parent stars. Crystalline silicates in CP IDPs dominantly have normal isotopic compositions and probably formed in the Solar System. 81P samples include isotopically normal refractory minerals that resemble Ca-Al rich inclusions and chondrules common in meteorites. The origins of sub-micron amorphous silicates in IDPs are not certain, but at least a few % of them are interstellar grains. The remainder have isotopic compositions consistent with Solar System origins and elemental compositions that are inconsistent with interstellar grain properties, thus favoring formation in the solar nebula [4]. The organic component in comets and primitive meteorites has large enrichments in D/H and N-15/N-14 relative to terrestrial materials. These isotopic signatures are probably due to low temperature chemical processes in cold molecular clouds or the outermost reaches of the protoplanetary disk. The greatest isotopic anomalies are found in sub-micron organic nanoglobules that show chemical signatures of interstellar chemistry. The observation that cometary dust is mostly composed of isotopically normal minerals within isotopically anomalous organic matter is difficult to reconcile with the formation models of each component. The mineral component likely formed in high temperature processes in the inner Solar System, while the organic fraction shows isotopic and chemical signatures of formation near 10 K. Studying more primitive remnants of the Solar System starting materials would help in resolving this paradox. Comets formed across a vast expanse of the outer disk under differing thermal and collisional regimes, and some are likely to be better preserved than others. Finding truly pristine aggregates of presolar materials may require return of a pristine sample of comet nucleus material.

Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1

PubMed Central

Chu, Wen-Ting; Clarke, Jane; Shammas, Sarah L.; Wang, Jin

2017-01-01

PUMA, which belongs to the BH3-only protein family, is an intrinsically disordered protein (IDP). It binds to its cellular partner Mcl-1 through its BH3 motif, which folds upon binding into an α helix. We have applied a structure-based coarse-grained model, with an explicit Debye—Hückel charge model, to probe the importance of electrostatic interactions both in the early and the later stages of this model coupled folding and binding process. This model was carefully calibrated with the experimental data on helical content and affinity, and shown to be consistent with previously published experimental data on binding rate changes with respect to ionic strength. We find that intramolecular electrostatic interactions influence the unbound states of PUMA only marginally. Our results further suggest that intermolecular electrostatic interactions, and in particular non-native electrostatic interactions, are involved in formation of the initial encounter complex. We are able to reveal the binding mechanism in more detail than is possible using experimental data alone however, and in particular we uncover the role of non-native electrostatic interactions. We highlight the potential importance of such electrostatic interactions for describing the binding reactions of IDPs. Such approaches could be used to provide predictions for the results of mutational studies. PMID:28369057

Porosity and Permeability of Chondritic Materials

NASA Technical Reports Server (NTRS)

Zolensky, Michael E.; Corrigan, Catherine M.; Dahl, Jason; Long, Michael

1996-01-01

We have investigated the porosity of a large number of chondritic interplanetary dust particles and meteorites by three techniques: standard liquid/gas flow techniques, a new, non-invasive ultrasonic technique, and image processing of backscattered images . The latter technique is obviously best suited to sub-kg sized samples. We have also measured the gas and liquid permeabilities of some chondrites by two techniques: standard liquid/gas flow techniques, and a new, non-destructive pressure release technique. We find that chondritic IDP's have a somewhat bimodal porosity distribution. Peaks are present at 0 and 4% porosity; a tail then extends to 53%. These values suggest IDP bulk densities of 1.1 to 3.3 g/cc. Type 1-3 chondrite matrix porosities range up to 30%, with a peak at 2%. The bulk porosities for type 1-3 chondrites have the same approximate range as exhibited by matrix, indicating that other components of the bulk meteorites (including chondrules and aggregates) have the same average porosity as matrix. These results reveal that the porosity of primitive materials at scales ranging from nanogram to kilogram are similar, implying similar accretion dynamics operated through 12 orders of size magnitude. Permeabilities of the investigated chondrites vary by several orders of magnitude, and there appears to be no simple dependence of permeability with degree of aqueous alteration, or chondrite type.

Chemical perturbation of an intrinsically disordered region of TFIID distinguishes two modes of transcription initiation

PubMed Central

Zhang, Zhengjian; Boskovic, Zarko; Hussain, Mahmud M; Hu, Wenxin; Inouye, Carla; Kim, Han-Je; Abole, A Katherine; Doud, Mary K; Lewis, Timothy A; Koehler, Angela N; Schreiber, Stuart L; Tjian, Robert

2015-01-01

Intrinsically disordered proteins/regions (IDPs/IDRs) are proteins or peptide segments that fail to form stable 3-dimensional structures in the absence of partner proteins. They are abundant in eukaryotic proteomes and are often associated with human diseases, but their biological functions have been elusive to study. In this study, we report the identification of a tin(IV) oxochloride-derived cluster that binds an evolutionarily conserved IDR within the metazoan TFIID transcription complex. Binding arrests an isomerization of promoter-bound TFIID that is required for the engagement of Pol II during the first (de novo) round of transcription initiation. However, the specific chemical probe does not affect reinitiation, which requires the re-entry of Pol II, thus, mechanistically distinguishing these two modes of transcription initiation. This work also suggests a new avenue for targeting the elusive IDRs by harnessing certain features of metal-based complexes for mechanistic studies, and for the development of novel pharmaceutical interventions. DOI: http://dx.doi.org/10.7554/eLife.07777.001 PMID:26314865

Goulds Belt, Interstellar Clouds, and the Eocene Oligocene Helium-3 Enhancement

NASA Technical Reports Server (NTRS)

Rubincam, David Parry

2015-01-01

Drag from hydrogen in the interstellar cloud which formed Gould's Belt may have sent interplanetary dust particle (IDPs) and small meteoroids with embedded helium to the Earth, perhaps explaining part the helium-3 flux increase seen in the sedimentary record near the Eocene-Oligocene transition. Assuming the Solar System passed through part of the cloud, IDPs in the inner Solar System may have been dragged to Earth, while dust and small meteoroids in the asteroid belt up to centimeter size may have been dragged to the resonances, where their orbital eccentricities were pumped up into Earth-crossing orbits; however, this hypotheses does not explain the Popigai and Chesapeake Bay impacts.

Fossil diatoms imply common cometary origin of space-dust and the Polonnaruwa meteorite

NASA Astrophysics Data System (ADS)

Miyake, N.; Wallis, M. K.; Wickramasinghe, N. C.

2013-09-01

IDPs collected in 2001 at 40km altitude by cryosamplers studied via scanning electron microscopy and EDX were found to contain siliceous fibres and whiskers, some isolated but often embedded in a mineral matrix. The newly-arrived Polonnaruwa meteorite gives strong evidence for the hypothesis that they are fragments of diatoms agglomerating on solar system icy bodies. Diatom frustules and even whole diatom skeletons are identifiable within the meteorite. Specimens of a siliceous exoskeleton with multiple spines/whiskers have also been found, thought to be freshwater diatoms. As diatoms are dependent on a source of nitrogenous organics, the siliceous whiskers within IDPs would be an indicator of a photosynthesizing ecosystem, probably on a comet.

Coordinated Stem and NanoSIMS Analysis of Enstatite Whiskers in Interplanetary Dust Particles

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Messenger, Scott; Keller, L. P.

2009-01-01

Enstatite whiskers (less than 10 micrometer length, less than 200 nanometer width) occur in chondritic-porous interplanetary dust particles (CP IDPs), an Antarctic micrometeorite and a comet 81P/Wild-2 sample. The whiskers are typically elongated along the [100] axis and contain axial screw dislocations, while those in terrestrial rocks and meteorites are elongated along [001]. The unique crystal morphologies and microstructures are consistent with the enstatite whiskers condensing above approximately 1300 K in a low-pressure nebular or circumstellar gas. To constrain the site of enstatite whisker formation, we carried out coordinated mineralogical, chemical and oxygen isotope measurements on enstatite whiskers in a CP IDP.

Spatiotemporal Co-existence of Female Thyroid and Breast Cancers in Hangzhou, China

NASA Astrophysics Data System (ADS)

Fei, Xufeng; Christakos, George; Lou, Zhaohan; Ren, Yanjun; Liu, Qingmin; Wu, Jiaping

2016-06-01

Thyroid and breast cancers (TC, BC) are common female malignant tumors worldwide. Studies suggest that TC patients have a higher BC risk, and vice versa. However, it has not been investigated quantitatively if there is an association between the space-time TC and BC incidence distributions at the population level. This work aims to answer this question. 5358 TC and 8784 BC (female) cases were diagnosed in Hangzhou (China, 2008-2012). Pearson and Spearman rank correlation coefficients of the TC and BC incidences were high, and their patterns were geographically similar. The spatiotemporal co-existence of TC and BC distributions was investigated using the integrative disease predictability (IDP) criterion: if TC-BC association is part of the disease mapping knowledge bases, it should yield improved space-time incidence predictions. Improved TC (BC) incidence predictions were generated when integrating both TC and BC data than when using only TC (BC) data. IDP consistently demonstrated the spatiotemporal co-existence of TC and BC distributions throughout Hangzhou (2008-2012), which means that when the population experiences high incidences of one kind of cancer attention should be paid to the other kind of cancer too. The strength of TC-BC association was measured by the IDP coefficients and incidence prediction accuracy.

Comparison of Carbon XANES Spectra from an Iron Sulfide from Comet Wild 2 with an Iron Sulfide Interplanetary Dust Particle

NASA Technical Reports Server (NTRS)

Wirick, S.; Flynn, G. J.; Keller, L. P.; Sanford, S. A.; Zolensky, M. E.; Messenger, Nakamura K.; Jacobsen, C.

2008-01-01

Among one of the first particles removed from the aerogel collector from the Stardust sample return mission was an approx. 5 micron sized iron sulfide. The majority of the spectra from 5 different sections of this particle suggests the presence of aliphatic compounds. Due to the heat of capture in the aerogel we initially assumed these aliphatic compounds were not cometary but after comparing these results to a heated iron sulfide interplanetary dust particle (IDP) we believe our initial interpretation of these spectra was not correct. It has been suggested that ice coating on iron sulfides leads to aqueous alteration in IDP clusters which can then lead to the formation of complex organic compounds from unprocessed organics in the IDPs similar to unprocessed organics found in comets [1]. Iron sulfides have been demonstrated to not only transform halogenated aliphatic hydrocarbons but also enhance the bonding of rubber to steel [2,3]. Bromfield and Coville (1997) demonstrated using Xray photoelectron spectroscopy that "the surface enhancement of segregated sulfur to the surface of sulfided precipitated iron catalysts facilitates the formation of a low-dimensional structure of extraordinary properties" [4]. It may be that the iron sulfide acts in some way to protect aliphatic compounds from alteration due to heat.

Advantages of synchrotron radiation circular dichroism spectroscopy to study intrinsically disordered proteins.

PubMed

Kumagai, Patricia S; DeMarco, Ricardo; Lopes, Jose L S

2017-10-01

The unordered secondary structural content of an intrinsically disordered protein (IDP) is susceptible to conformational changes induced by many different external factors, such as the presence of organic solvents, removal of water, changes in temperature, binding to partner molecules, and interaction with lipids and/or other ligands. In order to characterize the high-flexibility nature of an IDP, circular dichroism (CD) spectroscopy is a particularly useful method due to its capability of monitoring both subtle and remarkable changes in different environments, relative ease in obtaining measurements, the small amount of sample required, and the capability for sample recovery (sample not damaged) and others. Using synchrotron radiation as the light source for CD spectroscopy represents the state-of-the-art version of this technique with feasibility of accessing the lower wavelength UV region, and therefore presenting a series of advantages over conventional circular dichroism (cCD) to monitor a protein conformational behavior, check protein stability, detect ligand binding, and many others. In this paper, we have performed a comparative study using cCD and SRCD methods for investigating the secondary structure and the conformational behavior of natively unfolded proteins: MEG-14 and soybean trypsin inhibitor. We show that the SRCD technique greatly improves the analysis and accuracy of the studies on the conformations of IDPs.

Spatiotemporal Co-existence of Female Thyroid and Breast Cancers in Hangzhou, China

PubMed Central

Fei, Xufeng; Christakos, George; Lou, Zhaohan; Ren, Yanjun; Liu, Qingmin; Wu, Jiaping

2016-01-01

Thyroid and breast cancers (TC, BC) are common female malignant tumors worldwide. Studies suggest that TC patients have a higher BC risk, and vice versa. However, it has not been investigated quantitatively if there is an association between the space-time TC and BC incidence distributions at the population level. This work aims to answer this question. 5358 TC and 8784 BC (female) cases were diagnosed in Hangzhou (China, 2008–2012). Pearson and Spearman rank correlation coefficients of the TC and BC incidences were high, and their patterns were geographically similar. The spatiotemporal co-existence of TC and BC distributions was investigated using the integrative disease predictability (IDP) criterion: if TC-BC association is part of the disease mapping knowledge bases, it should yield improved space-time incidence predictions. Improved TC (BC) incidence predictions were generated when integrating both TC and BC data than when using only TC (BC) data. IDP consistently demonstrated the spatiotemporal co-existence of TC and BC distributions throughout Hangzhou (2008–2012), which means that when the population experiences high incidences of one kind of cancer attention should be paid to the other kind of cancer too. The strength of TC-BC association was measured by the IDP coefficients and incidence prediction accuracy. PMID:27341638

pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins.

PubMed

Varadi, Mihaly; Kosol, Simone; Lebrun, Pierre; Valentini, Erica; Blackledge, Martin; Dunker, A Keith; Felli, Isabella C; Forman-Kay, Julie D; Kriwacki, Richard W; Pierattelli, Roberta; Sussman, Joel; Svergun, Dmitri I; Uversky, Vladimir N; Vendruscolo, Michele; Wishart, David; Wright, Peter E; Tompa, Peter

2014-01-01

The goal of pE-DB (http://pedb.vib.be) is to serve as an openly accessible database for the deposition of structural ensembles of intrinsically disordered proteins (IDPs) and of denatured proteins based on nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and other data measured in solution. Owing to the inherent flexibility of IDPs, solution techniques are particularly appropriate for characterizing their biophysical properties, and structural ensembles in agreement with these data provide a convenient tool for describing the underlying conformational sampling. Database entries consist of (i) primary experimental data with descriptions of the acquisition methods and algorithms used for the ensemble calculations, and (ii) the structural ensembles consistent with these data, provided as a set of models in a Protein Data Bank format. PE-DB is open for submissions from the community, and is intended as a forum for disseminating the structural ensembles and the methodologies used to generate them. While the need to represent the IDP structures is clear, methods for determining and evaluating the structural ensembles are still evolving. The availability of the pE-DB database is expected to promote the development of new modeling methods and leads to a better understanding of how function arises from disordered states.

Chemically anomalous, pre-accretionally irradiated grains in interplanetary dust -- interstellar grains?. [Abstract only

NASA Technical Reports Server (NTRS)

Bradley, J. P.

1994-01-01

Ultrafine-grained matrix is a unique and fundamental building block of chondritic porous (CP) interplanetary dust particles. Most IDPs so far determined to be of cometary origin belong to the CP class. The matrix in CP IDPs is not homogeneous but rather a loose mixture of discrete single crystals (e.g., olivine, pyroxene, Fe sulfides) and polyphase grains. The petrographic diversity observed among the polyphase grains suggest that they were formed under variable physiochemical conditions. One particular class of polyphase grains are a dominant component in cometary IDPs. Although their occurrence is well documented, the terminology used to describe them is confused. They have been called many names. Here they are simply called GEMS (Glass with Embedded Metal and Sulfides). The bulk compositions of GEMS are within a factor of 3 chondritic (solar) for all major elements except C. Quantitative thin-film X-ray (EDS) analyses have shown that GEMS are systematically depleted in Mg and Si, enriched in S, Fe, and Ni, and stoichiometrically enriched in O. Electron energy-loss spectroscopy (EELS) suggests that the excess O is present as hydroxyl (-OH) groups. These same chemical 'anomalies' were observed in solar-wind-irradiated amorphous rims on the surfaces of IDPs, suggesting that the compositions of GEMS reflect prior exposure to ionizing radiation. In order to test this hypothesis, a sample of Allende (CV3) matrix was exposed to proton flux. Radiation-damaged amorphous rims on olivine and pyroxene crystals in the Allende sample were found to be depleted in Mg and Ca, enriched in S, Fe, and Ni, and stoichiometrically enriched in O. Thus, the compositions of GEMS are indeed consistent with exposure to ionizing radiation. This study suggests that chemical as well as isotopic anomalies may be used to identify presolar interstellar grains in primitive meteoritic materials.

Binding Rate Constants Reveal Distinct Features of Disordered Protein Domains.

PubMed

Dogan, Jakob; Jonasson, Josefin; Andersson, Eva; Jemth, Per

2015-08-04

Intrinsically disordered proteins (IDPs) are abundant in the proteome and involved in key cellular functions. However, experimental data about the binding kinetics of IDPs as a function of different environmental conditions are scarce. We have performed an extensive characterization of the ionic strength dependence of the interaction between the molten globular nuclear co-activator binding domain (NCBD) of CREB binding protein and five different protein ligands, including the intrinsically disordered activation domain of p160 transcriptional co-activators (SRC1, TIF2, ACTR), the p53 transactivation domain, and the folded pointed domain (PNT) of transcription factor ETS-2. Direct comparisons of the binding rate constants under identical conditions show that the association rate constant, kon, for interactions between NCBD and disordered protein domains is high at low salt concentrations (90-350 × 10(6) M(-1) s(-1) at 4 °C) but is reduced significantly (10-30-fold) with an increasing ionic strength and reaches a plateau around physiological ionic strength. In contrast, the kon for the interaction between NCBD and the folded PNT domain is only 7 × 10(6) M(-1) s(-1) (4 °C and low salt) and displays weak ionic strength dependence, which could reflect a distinctly different association that relies less on electrostatic interactions. Furthermore, the basal rate constant (in the absence of electrostatic interactions) is high for the NCBD interactions, exceeding those typically observed for folded proteins. One likely interpretation is that disordered proteins have a large number of possible collisions leading to a productive on-pathway encounter complex, while folded proteins are more restricted in terms of orientation. Our results highlight the importance of electrostatic interactions in binding involving IDPs and emphasize the significance of including ionic strength as a factor in studies that compare the binding properties of IDPs to those of ordered proteins.

Dome C ultracarbonaceous Antarctic micrometeorites. Infrared and Raman fingerprints

NASA Astrophysics Data System (ADS)

Dartois, E.; Engrand, C.; Duprat, J.; Godard, M.; Charon, E.; Delauche, L.; Sandt, C.; Borondics, F.

2018-01-01

Context. UltraCarbonaceous Antarctic MicroMeteorites (UCAMMs) represent a small fraction of interplanetary dust particles reaching the Earth's surface and contain large amounts of an organic component not found elsewhere. They are most probably sampling a contribution from the outer regions of the solar system to the local interplanetary dust particle (IDP) flux. Aims: We characterize UCAMMs composition focusing on the organic matter, and compare the results to the insoluble organic matter (IOM) from primitive meteorites, IDPs, and the Earth. Methods: We acquired synchrotron infrared microspectroscopy (μFTIR) and μRaman spectra of eight UCAMMs from the Concordia/CSNSM collection, as well as N/C atomic ratios determined with an electron microprobe. Results: The spectra are dominated by an organic component with a low aliphatic CH versus aromatic C=C ratio, and a higher nitrogen fraction and lower oxygen fraction compared to carbonaceous chondrites and IDPs. The UCAMMs carbonyl absorption band is in agreement with a ketone or aldehyde functional group. Some of the IR and Raman spectra show a C≡N band corresponding to a nitrile. The absorption band profile from 1400 to 1100 cm-1 is compatible with the presence of C-N bondings in the carbonaceous network, and is spectrally different from that reported in meteorite IOM. We confirm that the silicate-to-carbon content in UCAMMs is well below that reported in IDPs and meteorites. Together with the high nitrogen abundance relative to carbon building the organic matter matrix, the most likely scenario for the formation of UCAMMs occurs via physicochemical mechanisms taking place in a cold nitrogen rich environment, like the surface of icy parent bodies in the outer solar system. The composition of UCAMMs provides an additional hint of the presence of a heliocentric positive gradient in the C/Si and N/C abundance ratios in the solar system protoplanetary disc evolution. Part of the equipment used in this work has been financed by the French INSU-CNRS program "Physique et Chimie du Milieu Interstellaire" (PCMI).

Malnutrition and mortality patterns among internally displaced and non-displaced population living in a camp, a village or a town in Eastern Chad.

PubMed

Guerrier, Gilles; Zounoun, Malaïka; Delarosa, Olimpia; Defourny, Isabelle; Lacharite, Michelo; Brown, Vincent; Pedalino, Biagio

2009-11-26

Certain population groups have been rendered vulnerable in Chad because of displacement of more than 200,000 people over the last three years as a result of mass violence against civilians in the east of the country. The objective of the study was to assess mortality and nutritional patterns among displaced and non-displaced population living in camps, villages and a town in the Ouddaï and Salamat regions of Chad. Between May and October 2007, two stage, 30-cluster household surveys were conducted among 43,900 internally displaced persons (IDPs) living in camps in Ouaddai region (n = 898 households), among 19,400 non-displaced persons (NDPs) living in 42 villages in Ouaddai region (n = 900 households) and among 17,000 NDPs living in a small town in Salamat region (n = 901 households). Data collection included anthropometric measurements, measles vaccination rates and retrospective mortality. Crude mortality rate (CMR), mortality rate among children younger than 5 years (U5MR), causes of death and the prevalence of wasting (weight-for-height z score <-2) among children aged 6 to 59 months were the main outcome measures. The CMR among the 4902 IDPs in Gozbeida camps, 4477 NDPs living in a village and 4073 NDPs living in a town surveyed was 1.8 (95% CI, 1.2-2.8), 0.3 (95% CI, 0.2-0.4), 0.3 (95% CI, 0.2-0.5) per 10,000 per day, respectively. The U5MR in a camp (n = 904), a village (n = 956) and a town (n = 901) was 4.1 (95% CI, 2.1-7.7), 0.5 (95% CI, 0.3-0.9) and 0.7 (95% CI, 0.4-1.4) per 10,000 per day, respectively. Diarrhoea was reported to be the main cause of death. Acute malnutrition rates (according to the WHO definition) among 904 IDP children, 956 NDPs children living in a village, 901 NDP children living in a town aged 6 to 59 months were 20.6% (95% CI, 17.9%-23.3%), 16.4% (95% CI, 14.0%-18.8%) and 10.1% (95% CI, 8.1%-12.2%) respectively. The study found a high mortality rate among IDPs and an elevated prevalence of wasting not only in IDP camps but also in villages located in the same region. The town-dweller population remains at risk of malnutrition. Appropriate contingency plans need to be made to ensure acceptable living standards for these populations.

Nuclear Weapon Effect Research at PSR (Pacific-Sierra Research Corporation) - 1983. Acute Radiation Effects on Individual Crewmember Performance

DTIC Science & Technology

1984-08-31

information and data from other IDP investigations. Along with the IDP Core Group, DNA staff members David L. Auton and Robert W . Young of Science and...questijonna ire for tli.i s p ilIot riiii wals a moSt ident ica I to tihe f inal version * w ith a few di fterences in I nu ige an normal tIinme va ti...46J a C) C 7 r- A *.- . -4 0 - W - 24AJC a) -~ý 4 -4 m’.*4 W ~C V- CL CC Cý C) Z, Q) > :J U.- .0 M 0 -0t4. )v. , (1) wl a)r 0 )-4 1 QC ) f O * - 1J) a

Everyone Wins: A Mars-Impact Origin for Carbonaceous Phobos and Deimos

NASA Technical Reports Server (NTRS)

Fries, M.; Welzenbach, L.; Steele, A.

2016-01-01

Discussions of Phobos' and Deimos' origin(s) tend to feature an orthogonally opposed pair of observations: dynamical studies which favor coalescence of the moons from an orbital debris ring arising from a large impact on Mars; and reflectance spectroscopy of the moons that indicate a carbonaceous composition that is not consistent with Martian surface materials. One way to reconcile this discrepancy is to consider the option of a Mars-impact origin for Phobos and Deimos, followed by surficial decoration of carbon-rich materials by interplanetary dust particles (IDP). The moons experience a high IDP flux because of their location in Mars' gravity well. Calculations show that accreted carbon is sufficient to produce a surface with reflectance spectra resembling carbonaceous chondrites.

Multielement analysis of interplanetary dust particles using TOF-SIMS

NASA Technical Reports Server (NTRS)

Stephan, T.; Kloeck, W.; Jessberger, E. K.; Rulle, H.; Zehnpfenning, J.

1993-01-01

Sections of three stratospheric particles (U2015G1, W7029*A27, and L2005P9) were analyzed with TOF-SIMS (Time Of Flight-Secondary Ion Mass Spectrometry) continuing our efforts to investigate the element distribution in interplanetary dust particles (IDP's) with high lateral resolution (approximately 0.2 micron), to examine possible atmospheric contamination effects, and to further explore the abilities of this technique for element analysis of small samples. The samples, previously investigated with SXRF (synchrotron X-ray fluorescence analysis), are highly enriched in Br (Br/Fe: 59 x CI, 9.2 x CI, and 116 x CI, respectively). U2015G1 is the IDP with the by far highest Zn/Fe-ratio (81 x CI) ever reported in chondritic particles.

Organics Captured from Comet Wild 2 by the Stardust Spacecraft

NASA Technical Reports Server (NTRS)

Sandford, Scott A.; Aleon, Jerome; Araki, Tohru; Bajt, Sasa; Baratta, Giuseppe A.; Borg, Janet; Brucato, John R.; Burchell, Mark J.; Busemann, Henner; Butterworth, Anna;

The prevalence of HBV infection in the cohort of IDPs of war against terrorism in Malakand Division of Northern Pakistan

PubMed Central

2011-01-01

Background Hepatitis B is an important public health problem in the Pakistani population and is the major cause of chronic hepatitis, cirrhosis, fibrosis and hepatocellular carcinoma. High prevalence of HBV infections has been observed especially in areas of low economic status. In spite of effective immunization programs, no significant change has been observed in the epidemiology of HBV in the rural areas of Pakistan (~67.5% of the total population) mainly due to lack of interest from government authorities and poor hygienic measures. The current study was aimed at estimating the prevalence and risk factors associated with HBV infection within internally displaced persons (IDPs) due to war against terrorism in the Malakand Division of Northern Pakistan. Methods Blood samples from 950 IDPs suspected with HBV infection (including both males and females) were collected and processed with commercial ELISA kits for HBsAg, Anti HBs, HBeAg, Anti HBe antibodies. The samples positive by ELISA were confirmed for HBV DNA by real-time PCR analysis. Results The overall prevalence of HBV observed was 21.05% of which 78.5% were males and 21.5% were females. Most confirmed HBV patients belong to the Malakand and Dir (lower) district. High-risk of infection was found in the older subjects 29.13% (46-60 years), while a lower incidence (11.97%) was observed in children aged <15 years. Lack of awareness, socioecomic conditions, sexual activities and sharing of razor blades, syringes and tattooing needles were the most common risk factors of HBV infection observed during the cohort of patients. Conclusion The present study, revealed for the first time a high degree of prevalence of HBV infection in rural areas of Northern Pakistan. The noticed prevalence is gender- and age-dependent that might be due to their high exposures to the common risk factors. To avoid the transmission of HBV infection proper awareness about the possible risk factors and extension of immunization to the rural areas are recommended. PMID:21689435

Coordinated Analyses of Mineral-organic Matter Associations in Interplanetary Dust Particles

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Herzog, G. F.; Smith, T.; Keller, L. P.; Flynn, G. J.; Khodja, H.; Taylor, S.; Wirick, S.; Messenger, S.

2012-01-01

Little is known about the timing and processes involved in the incorporation of organic matter with inorganic materials in early Solar System bodies. Recently, X-ray absorption near-edge spectroscopy (XANES) studies showed carbon-rich rims surrounding individual mineral grains in anhydrous IDPs [1,2]. These carbonaceous rims are believed to have formed prior to parent body formation and likely served to bond mineral grains during accretion into larger aggregates. We are exploring the nature of these carbonaceous rims through coordinated analyses of their chemistry, mineralogy, spectroscopy and isotopic characteristics. Here we report our preliminary mineralogical observations.

Ensemble characterization of an intrinsically disordered FG-Nup peptide and its F>A mutant in DMSO-d6.

PubMed

Reid, Korey M; Sunanda, Punnepalli; Raghothama, S; Krishnan, V V

2017-11-01

Intrinsically disordered proteins (IDP) lack a well-defined 3D-structure under physiological conditions, yet, the inherent disorder represented by an ensemble of conformation plays a critical role in many cellular and regulatory processes. Nucleoporins, or Nups, are the proteins found in the nuclear pore complex (NPC). The central pore of the NPC is occupied by Nups, which have phenylalanine-glycine domain repeats and are intrinsically disordered, and therefore are termed FG-Nups. These FG-domain repeats exhibit differing cohesiveness character and differ from least (FG) to most (GLFG) cohesive. The designed FG-Nup is a 25 AA model peptide containing a noncohesive FG-motif flanked by two cohesive GLFG-motifs (WT peptide). Complete NMR-based ensemble characterization of this peptide along with a control peptide with an F>A substitution (MU peptide) are discussed. Ensemble characterization of the NMR-determined models suggests that both the peptides do not have consistent secondary structures and continue to be disordered. Nonetheless, the role of cohesive elements mediated by the GLFG motifs is evident in the WT ensemble of structures that are more compact than the MU peptide. The approach presented here allows an alternate way to investigate the specific roles of distinct amino acid motifs that translate into the long-range organization of the ensemble of structures and in general on the nature of IDPs. © 2017 Wiley Periodicals, Inc.

Detecting Interplanetary Dust Particles with Radars to Study the Dynamics at the Edge of the Space

NASA Technical Reports Server (NTRS)

Janches, Diego

2015-01-01

The Earth's mesosphere is the region of the atmosphere between approximately 60-120 km altitude, where the transition from hydrodynamic flow to molecular diffusion occurs. It is highly dynamic region where turbulence by wave braking is produced and energy is deposited from sources from both, below and above this altitude range. Because aircraft and nearly all balloons reach altitudes below approximately 50 km and orbital spacecrafts are well above approximately 400 km, the mesosphere has only been accessed through the use of sounding rockets or remote sensing techniques, and as a result, it is the most poorly understood part of the atmosphere. In addition, millions of Interplanetary Dust Particles (IDPs) enter the atmosphere. Within the mesosphere most of these IDPs melt or vaporize as a result of collisions with the air particles producing meteors that can be detected with radars. This provides a mean to study the dynamics of this region. In this lecture the basic principles of the utilization of meteor radars to study the dynamics of the mesosphere will be presented. A system overview of these systems will be provided as well as discuss the advantages/disadvantages of these systems, provide details of the data processing methodology and give a brief overview of the current status of the field as well as the vision for the next decade.

Effects of correcting in situ ruminal microbial colonization of feed particles on the relationship between ruminally undegraded and intestinally digested crude protein in concentrate feeds.

PubMed

González, Javier; Mouhbi, Rabiaa; Guevara-González, Jesús Alberto; Arroyo, José María

2018-02-01

In situ estimates of ruminally undegraded protein (RUP) and intestinally digested protein (IDP) of ten concentrates, uncorrected or corrected for the ruminal microbial colonization, were used to examine the effects of this correction on the relationship between IDP and RUP values. Both variables were established for three rumen and duodenum cannulated wethers using 15 N labeling-techniques and considering measured rates of ruminal particle comminution (k c ) and outflow (k p ). A covariance analysis showed that the close relationship found between both variables (IDP = -0.0132 ± 0.00679 + 0.776 ± 0.0002 RUP; n = 60; P < 0.001; r = 0.960) is not affected by correcting for microbial colonization (P = 0.682). The IDP content in concentrates and industrial by-products can be predicted from RUP values, thus avoiding the laborious and complex procedure of determining intestinal digestibility; however, a larger sample of feeds is necessary to achieve more accurate predictions. The lack of influence of the correction for microbial contamination on the prediction observed in the present study increases the data available for this prediction. However, only the use of corrected values may provide an accurate evaluation. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Site-Specific Modulation of Charge Controls the Structure and Stimulus Responsiveness of Intrinsically Disordered Peptide Brushes.

PubMed

Bhagawati, Maniraj; Rubashkin, Matt G; Lee, Jessica P; Ananthanarayanan, Badriprasad; Weaver, Valerie M; Kumar, Sanjay

2016-06-14

Intrinsically disordered proteins (IDPs) are an important and emerging class of materials for tailoring biointerfaces. While the importance of chain charge and resultant electrostatic interactions in controlling conformational properties of IDPs is beginning to be explored through in silico approaches, there is a dearth of experimental studies motivated toward a systematic study of these effects. In an effort to explore this relationship, we measured the conformations of two peptides derived from the intrinsically disordered neurofilament (NF) side arm domain: one depicting the wild-type sequence with four lysine-serine-proline repeats (KSP peptide) and another in which the serine residues were replaced with aspartates (KDP peptide), a strategy sometimes used to mimic phosphorylation. Using a variety of biophysical measurements including a novel application of scanning angle interference microscopy, we demonstrate that the KDP peptide assumes comparatively more expanded conformations in solution and forms significantly thicker brushes when immobilized on planar surfaces at high densities. In both settings, the peptides respond to changes in ambient ionic strength, with each peptide showing distinct stimulus-responsive characteristics. While the KDP peptide undergoes compaction with increasing ionic strength as would be expected for a polyampholyte, the KSP peptide shows biphasic behavior, with an initial compaction followed by an expanded state at a higher ionic strength. Together these results support the notion that modulation of charge on IDPs can regulate conformational and interfacial properties.

Comparison of Nickel XANES Spectra and Elemental Maps from a Ureilite, a LL3.8 Ordinary Chondrite, Two Carbonaceous Chondrites and Two Large Cluster IDPs

NASA Technical Reports Server (NTRS)

Wirick, S.; Flynn, G. J.; Sutton, S.; Zolensky, M. E.

2014-01-01

Nickel in the extraterrestrial world is commonly found in both Fe-Ni sulfide and Fe-Ni met-al forms [1] and in the pure metal state in the interior of iron meteorites where it is not easily oxidized. Ni is also found in olivine, pyroxene and glasses and in some melts the partitioning of Ni between the olivines and glass is controlled by the amount of S in the melt [2]. Its most common valence state is Ni(2+) but Ni also occurs as Ni(0), Ni(+), and Ni(3+) and rarely as Ni(2-), Ni(1-) and Ni(4+) [3]. It's valence state in olivines is Ni(2+) in octa-hedral coordination on the M1 site and rarely on the M2 site.[4]. The chemical sensitivity of X-ray absorp-tion near-edge structure (XANES) spectroscopy is well established and can be used to determine not only va-lence states but also coordination sites [5]. We report here Ni XANES spectroscopy and elemental maps collected from 2 carbonaceous chondrites, 2 large clus-ter IDPs, 1 ureilite and 1 LL3 orginary chondrite.Using XANES it may be possible to find a common trait in the large cluster IDPs that will also be found in mete-orite samples.

Comparing Wild 2 Particles to Chondrites and IDPS

NASA Technical Reports Server (NTRS)

Zolensky, Michael; Nakamura-Messenger, Keiko; Rietmeijer, Frans; Leroux, Hugues; Mikouchi, Takashi; Ohsumi, Kazumasa; Simon, Steven; Grossman, Lawrence; Stephan, Thomas; Weisberg, Michael;

IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing

PubMed Central

Deonovic, Benjamin; Wang, Yunhao; Weirather, Jason; Wang, Xiu-Jie; Au, Kin Fai

2017-01-01

Abstract Allele-specific expression (ASE) is a fundamental problem in studying gene regulation and diploid transcriptome profiles, with two key challenges: (i) haplotyping and (ii) estimation of ASE at the gene isoform level. Existing ASE analysis methods are limited by a dependence on haplotyping from laborious experiments or extra genome/family trio data. In addition, there is a lack of methods for gene isoform level ASE analysis. We developed a tool, IDP-ASE, for full ASE analysis. By innovative integration of Third Generation Sequencing (TGS) long reads with Second Generation Sequencing (SGS) short reads, the accuracy of haplotyping and ASE quantification at the gene and gene isoform level was greatly improved as demonstrated by the gold standard data GM12878 data and semi-simulation data. In addition to methodology development, applications of IDP-ASE to human embryonic stem cells and breast cancer cells indicate that the imbalance of ASE and non-uniformity of gene isoform ASE is widespread, including tumorigenesis relevant genes and pluripotency markers. These results show that gene isoform expression and allele-specific expression cooperate to provide high diversity and complexity of gene regulation and expression, highlighting the importance of studying ASE at the gene isoform level. Our study provides a robust bioinformatics solution to understand ASE using RNA sequencing data only. PMID:27899656

The Mineralogy of Circumstellar Silicates Preserved in Cometary Dust

NASA Technical Reports Server (NTRS)

Keller, L. P.; Messenger, S.

2010-01-01

Interplanetary dust particles (IDPs) contain a record of the building blocks of the solar system including presolar grains, molecular cloud material, and materials formed in the early solar nebula. Cometary IDPs have remained relatively unaltered since their accretion because of the lack of parent body thermal and aqueous alteration. We are using coordinated transmission electron microscope (TEM) and ion microprobe studies to establish the origins of the various components within cometary IDPs. Of particular interest is the nature and abundance of presolar silicates in these particles because astronomical observations suggest that crystalline and amorphous silicates are the dominant grain types produced in young main sequence stars and evolved O-rich stars. Five circumstellar grains have been identified including three amorphous silicate grains and two polycrystalline aggregates. All of these grains are between 0.2 and 0.5 micrometers in size. The isotopic compositions of all five presolar silicate grains fall within the range of presolar oxides and silicates, having large (17)O-enrichments and normal (18)O/(16)O ratios (Group 1 grains from AGB and RG stars). The amorphous silicates are chemically heterogeneous and contain nanophase FeNi metal and FeS grains in a Mg-silicate matrix. Two of the amorphous silicate grains are aggregates with subgrains showing variable Mg/Si ratios in chemical maps. The polycrystalline grains show annealed textures (equilibrium grains boundaries, uniform Mg/Fe ratios), and consist of 50-100 nm enstatite and pyrrhotite grains with lesser forsterite. One of the polycrystalline aggregates contains a subgrain of diopside. The polycrystalline aggregates form by subsolidus annealing of amorphous precursors. The bulk compositions of the five grains span a wide range in Mg/Si ratios from 0.4 to 1.2 (avg. 0.86). The average Fe/Si (0.40) and S/Si (0.21) ratios show a much narrower range of values and are approximately 50% of their solar abundances. The latter observation may indicate a decoupling of the silicate and sulfide components in grains that condense in stellar outflows. The amorphous silicate grains described here were not extensively affected by irradiation, sputtering, or thermal processing and may represent relatively pristine circumstellar grains. They are strong candidates for the "dirty silicates" in astronomical observations of circumstellar dust shells. The polycrystalline grains were originally amorphous silicate grains that were likely annealed in the early solar nebula but the processing was not sufficient to erase their anomalous oxygen isotopic compositions.

3D Observation of GEMS by Electron Tomography

NASA Technical Reports Server (NTRS)

Matsuno, Junya; Miyake, Akira; Tsuchiyama, Akira; Nakamura-Messenger, Keiko; Messenger, Scott

2014-01-01

Amorphous silicates in chondritic porous interplanetary dust particles (CP-IDPs) coming from comets are dominated by glass with embedded metal and sulfides (GEMS). GEMS grains are submicron-sized rounded objects (typically 100-500) nm in diameter) with anaometer-sized (10-50 nm) Fe-Ni metal and sulfide grains embedded in an amorphous silicate matrix. Several formation processes for GEMS grains have been proposed so far, but these models are still being debated [2-5]. Bradley et al. proposed that GEMS grains are interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk and that they are amorphiation products of crystalline silicates in the interstellar medium by sputter-deposition of cosmic ray irradiation, similar to space weathering [2,4]. This consideration is based on the observation of nano-sized crystals (approximately 10 nm) called relict grains in GEMS grains and their shapes are pseudomorphs to the host GEMS grains. On the other hand, Keller and Messenger proposed that most GEMS formed in the protoplanetary disk as condensates from high temperature gas [3,5]. This model is based on the fact that most GEMS grains have solar isotopic compositions and have extremely heterogeneous and non-solar elemental compositions. Keller and Messenger (2011) also reported that amorphous silicates in GEMS grains are surrounded by sulfide grains, which formed as sulfidization of metallic iron grains located on the GEMS surface. The previous studies were performed with 2D observation by using transmission electron microscopy (TEM) or scanning TEM (STEM). In order to understand the structure of GEMS grains described above more clearly, we observed 3D structure of GEMS grains by electron tomography using a TEM/STEM (JEM-2100F, JEOL) at Kyoto University. Electron tomography gives not only 3D structures but also gives higher spatial resolution (approximately a few nm) than that in conventional 2D image, which is restricted by sample thickness ) approx. or greater than 50 nm). Three cluster IDPs (L2036AA5 cluster4, L2009L8 cluster 13 and W726A2) were used for the observations. ID W726A2 was collected without silicon oil, which is ordinary used to collect IDPs, so this sample has no possibility of contaminations caused by silicon oil or solvent to rinse it [6]. The samples were embedded in epoxy risin and sliced into ultrathin sections (50-300 nm) using an ultramicotome. The sections were observed by BF-TEM and HAADF-STEM (high angle annular dark field-scanning TEM) modes. Images were obtained by rotating the sample tilt angle over a range of +/- 65 deg in 1 deg steps. The obtained images were reconstructed to slice images. Mineral phases in the slice images were estimated by comparing with a 2D elemental map obtained by an EDS (energy dispersive X-ray spectroscopy) system equipped in the TEM/STEM. Careful examination of the slice images confirmed that iron grains are embedded in the amorphous silicate matrix of the GEMS grains, but sulfide grains were mainly present on the surface of the amorphous silicate. These results are consistent with the model that GEMS grains formed as condensates [3,5], although more data are needed to conclude the origin of GEMS grains. The present study is the first successful example adapting the electron tomography to the IDPs. This type of analysis will be important for planetary material sciences in the future.

Densities of 5-15 micron interplanetary dust particles

NASA Technical Reports Server (NTRS)

Love, S. G.; Joswiak, D. J.; Brownlee, D. E.

1993-01-01

We have measured the densities of about 100 5-15 micron stratospheric IDPs. Great care was taken to minimize selection bias in the sample population. Masses were determined using an absolute x-ray analysis technique with a transmission electron microscope, and volumes were found using scanning electron microscope imagery. Unmelted chondritic particles have densities between 0.5 and 6.0 g/cc. Roughly half of the particles have densities below 2 g/cc, indicating appreciable porosity, but porosities greater than about 70 percent are rare. IDPs with densities above 3.5 g/cc usually contain large sulfide grains. We find no evidence of bimodality in the unmelted particle density distribution. Chondritic spherules (melted particles) have densities near 3.5 g/cc, consistent with previous results for deep sea spherules.

Malnutrition and Mortality Patterns among Internally Displaced and Non-Displaced Population Living in a Camp, a Village or a Town in Eastern Chad

PubMed Central

Guerrier, Gilles; Zounoun, Malaïka; Delarosa, Olimpia; Defourny, Isabelle; Lacharite, Michelo; Brown, Vincent; Pedalino, Biagio

2009-01-01

Background Certain population groups have been rendered vulnerable in Chad because of displacement of more than 200,000 people over the last three years as a result of mass violence against civilians in the east of the country. The objective of the study was to assess mortality and nutritional patterns among displaced and non-displaced population living in camps, villages and a town in the Ouddaï and Salamat regions of Chad. Methodology Between May and October 2007, two stage, 30-cluster household surveys were conducted among 43,900 internally displaced persons (IDPs) living in camps in Ouaddai region (n = 898 households), among 19,400 non-displaced persons (NDPs) living in 42 villages in Ouaddai region (n = 900 households) and among 17,000 NDPs living in a small town in Salamat region (n = 901 households). Data collection included anthropometric measurements, measles vaccination rates and retrospective mortality. Crude mortality rate (CMR), mortality rate among children younger than 5 years (U5MR), causes of death and the prevalence of wasting (weight-for-height z score <−2) among children aged 6 to 59 months were the main outcome measures. Conclusions The CMR among the 4902 IDPs in Gozbeida camps, 4477 NDPs living in a village and 4073 NDPs living in a town surveyed was 1.8 (95% CI, 1.2–2.8), 0.3 (95% CI, 0.2–0.4), 0.3 (95% CI, 0.2–0.5) per 10,000 per day, respectively. The U5MR in a camp (n = 904), a village (n = 956) and a town (n = 901) was 4.1 (95% CI, 2.1–7.7), 0.5 (95% CI, 0.3–0.9) and 0.7 (95% CI, 0.4–1.4) per 10,000 per day, respectively. Diarrhoea was reported to be the main cause of death. Acute malnutrition rates (according to the WHO definition) among 904 IDP children, 956 NDPs children living in a village, 901 NDP children living in a town aged 6 to 59 months were 20.6% (95% CI, 17.9%–23.3%), 16.4% (95% CI, 14.0%–18.8%) and 10.1% (95% CI, 8.1%–12.2%) respectively. The study found a high mortality rate among IDPs and an elevated prevalence of wasting not only in IDP camps but also in villages located in the same region. The town-dweller population remains at risk of malnutrition. Appropriate contingency plans need to be made to ensure acceptable living standards for these populations. PMID:19956627

Cometary Evolution: Clues on Physical Properties from Chondritic Interplanetary Dust Particles

NASA Technical Reports Server (NTRS)

Reitmeijer, Frans J. M.; Mackinnon, Ian D. R.

1997-01-01

The degree of diversity or similarity detected in comets depends primarily on the lifetimes of the individual cometary nuclei at the time of analysis. It is inherent in our understanding of cometary orbital dynamics and the seminal model of comet origins that cometary evolution is the natural order of events in our Solar System. Thus, predictions of cometary behaviour in terms of bulk physical, mineralogical or chemical parameters should contain an appreciation of temporal variation(s). Previously, Rietmeijer and Mackinnon [1987] developed mineralogical bases for the chemical evolution of cometary nuclei primarily with regard to the predominantly silicate fraction of comet nuclei. We suggested that alteration of solids in cometary nuclei should be expected and that indications of likely reactants and products can be derived from judicious comparison with terrestrial diagenetic environments which include hydrocryogenic and low-temperature aqueous alterations. In a further development of this concept, Rietmeijer [1988] provides indirect evidence for the formation of sulfides and oxides in comet nuclei. Furthermore, Rietmeijer [1988] noted that timescales for hydrocryogenic and low-temperature reactions involving liquid water are probably adequate for relatively mature comets, e.g. P/comet Halley. In this paper, we will address the evolution of comet nuclei physical parameters such as solid particle grain size, porosity and density. In natural environments, chemical evolution (e.g. mineral reactions) is often accompanied by changes in physical properties. These concurrent changes are well-documented in the terrestrial geological literature, especially in studies of sediment diagenesis and we suggest that similar basic principles apply within the upper few meters of active comet nuclei. The database for prediction of comet nuclei physical parameters is, in principle, the same as used for the proposition of chemical evolution. We use detailed mineralogical studies of chondritic interplanetary dust particles (IDPS) as a guide to the likely constitution of mature comets traversing the inner Solar System. While there is, as yet, no direct proof that a specific sub-group or type of chondritic IDP is derived from a specific comet, it is clear that these particles are extraterrestrial in origin and that a certain portion of the interplanetary flux received by the Earth is cometary in origin. Two chondritic porous (CP) IDPS, sample numbers W701OA2 and W7029CI, from the Johnson Space Center Cosmic Dust Collection have been selected for this study of putative cometary physical parameters. This particular type of particle is considered a likely candidate for a cometary origin on the basis of mineralogy, bulk composition and morphology. While many IDPs have been subjected to intensive study over the past decade, we can develop a physical parameter model on only these two CP IDPs because few others have been studied in sufficient detail.

Gender-based violence in conflict and displacement: qualitative findings from displaced women in Colombia.

PubMed

Wirtz, Andrea L; Pham, Kiemanh; Glass, Nancy; Loochkartt, Saskia; Kidane, Teemar; Cuspoca, Decssy; Rubenstein, Leonard S; Singh, Sonal; Vu, Alexander

2014-01-01

Gender-based violence (GBV) is prevalent among, though not specific to, conflict affected populations and related to multifarious levels of vulnerability of conflict and displacement. Colombia has been marked with decades of conflict, with an estimated 5.2 million internally displaced persons (IDPs) and ongoing violence. We conducted qualitative research to understand the contexts of conflict, displacement and dynamics with GBV. This as part of a multi-phase, mixed method study, in collaboration with UNHCR, to develop a screening tool to confidentially identify cases of GBV for referral among IDP women who were survivors of GBV. Qualitative research was used to identify the range of GBV, perpetrators, contexts in conflict and displacement, barriers to reporting and service uptake, as well as to understand experiences of service providers. Thirty-five female IDPs, aged 18 years and older, who self-identified as survivors of GBV were enrolled for in-depth interviews in San Jose de Guaviare and Quibdo, Colombia in June 2012. Thirty-one service providers participated in six focus group discussions and four interviews across these sites. Survivors described a range of GBV across conflict and displacement settings. Armed actors in conflict settings perpetrated threats of violence and harm to family members, child recruitment, and, to a lesser degree, rape and forced abortion. Opportunistic violence, including abduction, rape, and few accounts of trafficking were more commonly reported to occur in the displacement setting, often perpetrated by unknown individuals. Intrafamilial violence, intimate partner violence, including physical and sexual violence and reproductive control were salient across settings and may be exacerbated by conflict and displacement. Barriers to reporting and services seeking were reported by survivors and providers alike. Findings highlight the need for early identification of GBV cases, with emphasis on confidential approaches and active engagement of survivors in available, quality services. Such efforts may facilitate achievement of the goals of new Colombian laws, which seek to prevent and respond to GBV, including in conflict settings. Ongoing conflict and generalized GBV in displacement, as well as among the wider population, suggests a need to create sustainable solutions that are accessible to both IDPs and general populations.

Proton-decoupled CPMG: a better experiment for measuring (15)N R2 relaxation in disordered proteins.

PubMed

Yuwen, Tairan; Skrynnikov, Nikolai R

2014-04-01

(15)N R2 relaxation is one of the most informative experiments for characterization of intrinsically disordered proteins (IDPs). Small changes in nitrogen R2 rates are often used to determine how IDPs respond to various biologically relevant perturbations such as point mutations, posttranslational modifications and weak ligand interactions. However collecting high-quality (15)N relaxation data can be difficult. Of necessity, the samples of IDPs are often prepared with low protein concentration and the measurement time can be limited because of rapid sample degradation. Furthermore, due to hardware limitations standard experiments such as (15)N spin-lock and CPMG can sample the relaxation decay only to ca. 150ms. This is much shorter than (15)N T2 times in disordered proteins at or near physiological temperature. As a result, the sampling of relaxation decay profiles in these experiments is suboptimal, which further lowers the precision of the measurements. Here we report a new implementation of the proton-decoupled (PD) CPMG experiment which allows one to sample (15)N R2 relaxation decay up to ca. 0.5-1s. The new experiment has been validated through comparison with the well-established spin-lock measurement. Using dilute samples of denatured ubiquitin, we have demonstrated that PD-CPMG produces up to 3-fold improvement in the precision of the data. It is expected that for intrinsically disordered proteins the gains may be even more substantial. We have also shown that this sequence has a number of favorable properties: (i) the spectra are recorded with narrow linewidth in nitrogen dimension; (ii) (15)N offset correction is small and easy to calculate; (iii) the experiment is immune to various spurious effects arising from solvent exchange; (iv) the results are stable with respect to pulse miscalibration and rf field inhomogeneity; (v) with minimal change, the pulse sequence can also be used to measure R2 relaxation of (15)N(ε) spins in arginine side chains. We anticipate that the new experiment will be a valuable addition to the NMR toolbox for studies of IDPs. Copyright © 2013 Elsevier Inc. All rights reserved.

Gender-based violence in conflict and displacement: qualitative findings from displaced women in Colombia

PubMed Central

2014-01-01

Introduction Gender-based violence (GBV) is prevalent among, though not specific to, conflict affected populations and related to multifarious levels of vulnerability of conflict and displacement. Colombia has been marked with decades of conflict, with an estimated 5.2 million internally displaced persons (IDPs) and ongoing violence. We conducted qualitative research to understand the contexts of conflict, displacement and dynamics with GBV. This as part of a multi-phase, mixed method study, in collaboration with UNHCR, to develop a screening tool to confidentially identify cases of GBV for referral among IDP women who were survivors of GBV. Methods Qualitative research was used to identify the range of GBV, perpetrators, contexts in conflict and displacement, barriers to reporting and service uptake, as well as to understand experiences of service providers. Thirty-five female IDPs, aged 18 years and older, who self-identified as survivors of GBV were enrolled for in-depth interviews in San Jose de Guaviare and Quibdo, Colombia in June 2012. Thirty-one service providers participated in six focus group discussions and four interviews across these sites. Results Survivors described a range of GBV across conflict and displacement settings. Armed actors in conflict settings perpetrated threats of violence and harm to family members, child recruitment, and, to a lesser degree, rape and forced abortion. Opportunistic violence, including abduction, rape, and few accounts of trafficking were more commonly reported to occur in the displacement setting, often perpetrated by unknown individuals. Intrafamilial violence, intimate partner violence, including physical and sexual violence and reproductive control were salient across settings and may be exacerbated by conflict and displacement. Barriers to reporting and services seeking were reported by survivors and providers alike. Conclusions Findings highlight the need for early identification of GBV cases, with emphasis on confidential approaches and active engagement of survivors in available, quality services. Such efforts may facilitate achievement of the goals of new Colombian laws, which seek to prevent and respond to GBV, including in conflict settings. Ongoing conflict and generalized GBV in displacement, as well as among the wider population, suggests a need to create sustainable solutions that are accessible to both IDPs and general populations. PMID:25076981

Needs of Internally Displaced Women and Children in Baghdad, Karbala, and Kirkuk, Iraq

PubMed Central

Lafta, Riyadh; Aflouk, Nesreen A; Dhiaa, Saba; Lyles, Emily; Burnham, Gilbert

2016-01-01

Background: The continuing conflict in Iraq has now created an estimated four million internally displaced persons (IDPs). The bulk of recently displaced persons are in Central Iraq, often in insecure and difficult situations. Objective: To determine the health status and health needs of women and children, age 15 and under, among a sample of this IDP population in Kirkuk, Baghdad, and Karbala governorates. Methods: Data were collected from the senior female in 1216 families which contained 3665 children living in 45 makeshift settlements. Findings: The majority of IDPs were living in tents or religious centers. Repeated displacements were common. Kidnappings were reported by 5.2% of families, and 7.9% of families reported a death of a family member during or after displacement. Intentional violence accounted for 72.3% of deaths. Only a third of children in school at the time of displacement continued in school. On average, households had received assistance on 3.2 occasions since displacement, food being the most common form. Access to health services was difficult. Some form of transport was often required. Few women knew where to secure antenatal services and many did not know where childhood immunization services were available. During or after displacement 307 women had delivered or were currently pregnant. Complications of pregnancies were common, with a quarter reporting anemia, and 22.1% experiencing hemorrhage. Both communicable and non-communicable diseases (NCDs) were common in the women and children in the survey. Scabies, diarrhea and lice were common among children. Among women, hypertension accounted for 36.6% of NCDs and type 2 diabetes for 15.9%. Domestic violence directed against women was reported in 17.4% of families and against children in 26.6% Interpretation: Women and children in IDP settlements of Central Iraq experience many vulnerabilities involving their health, education and their environment, in addition to living in physical danger. While some external assistance was received, much more is needed to meet the needs of a displaced population which is unlikely to return home soon. PMID:28966867

Coordinated STEM/FIB/NanoSIMS Analyses of Presolar Silicates in Comet Dust and Primitive Meteorites

NASA Technical Reports Server (NTRS)

Keller, Lindsay; Nguyen, A.; Rahman, Z.; Messenger, S.

2012-01-01

Silicate grains were among the most abundant mineralogical building blocks of our Solar System. These grains were the detritus from earlier generations of stars that have been recycled in the early solar nebula. Rare sub-micrometer survivors of this processing have been identified in meteorites, micrometeorites and interplanetary dust particles (IDPs). These silicate grains are recognized as presolar in origin because of their extremely anomalous isotopic compositions that reflect nucleosynthetic processes in their stellar sources (evolved stars, novae and supernovae). We perform coordinated chemical, mineralogical and isotopic studies of these grains to determine their origins and histories. We examine the complex mineralogy and petrography of presolar silicates using imaging, diffraction and chemical data obtained from thin sections with the JSC JEOL 2500 field-emission STEM equipped with a Noran thin window energy dispersive x-ray (EDX) spectrometer and a Gatan Tridiem GIF. Quantitative element x-ray maps (spectrum images) are acquired by rastering a 4 nm incident probe whose dwell time is minimized to avoid beam damage and element diffusion during mapping. Successive image layers are acquired and combined in order to achieve approx 1% counting statistics for major elements. The IDP samples are prepared by ultramicrotomy of particles embedded in epoxy or elemental sulfur. After EDX mapping, the sections are subjected to C, N, and O isotopic imaging with the JSC NanoSIMS 50L ion microprobe. We prepare sections of some meteorite grains using the JSC FEI Quanta 3D focused ion beam (FIB) instrument. The specimen surface is protected from the FIB milling process by layers of electron beam-deposited C and Pt followed by an ion-deposited Pt layer. We also use the FIB to preferentially remove surrounding grains to reduce the background in subsequent NanoSIMS measurements. For mineralogical studies, we again employ the FIB instrument to deposit a protective cap over the grain of interest and then extract the grain and thin it to electron transparency for TEM analysis.

Collected Extraterrestrial Materials: Constraints on Meteor and Fireball Compositions

NASA Astrophysics Data System (ADS)

Rietmeijer, Frans J. M.; Nuth, Joseph A., III

The bulk density and bulk porosity of IDPs and various meteorite classes show that protoplanet accretion and evolution were arrested at different stages as a function of parent body modification. The collected IDPs, micrometeorites and meteorites are aggregates of different structural entities that were inherited from the earliest times of solar system evolution. These structural entities and the extent of parent body lithification will determine the material strength of the meteoroids entering the Earth's atmosphere. There is a need for measurements of the material strength of collected extraterrestrial materials because they will in part determine the nature of the chemical interactions of descending meteors and fireballs in the atmosphere. High-precision determinations of meteor and fireball compositions are required to search for anhydrous, carbon-rich proto-CI material that has survived in the boulders of comet nuclei.

Dynamics, Conformational Entropy, and Frustration in Protein-Protein Interactions Involving an Intrinsically Disordered Protein Domain.

PubMed

Lindström, Ida; Dogan, Jakob

2018-05-18

Intrinsically disordered proteins (IDPs) are abundant in the eukaryotic proteome. However, little is known about the role of subnanosecond dynamics and the conformational entropy that it represents in protein-protein interactions involving IDPs. Using nuclear magnetic resonance side chain and backbone relaxation, stopped-flow kinetics, isothermal titration calorimetry, and computational studies, we have characterized the interaction between the globular TAZ1 domain of the CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2). We show that the TAZ1/TAD-STAT2 complex retains considerable subnanosecond motions, with TAD-STAT2 undergoing only a partial disorder-to-order transition. We report here the first experimental determination of the conformational entropy change for both binding partners in an IDP binding interaction and find that the total change even exceeds in magnitude the binding enthalpy and is comparable to the contribution from the hydrophobic effect, demonstrating its importance in the binding energetics. Furthermore, we show that the conformational entropy change for TAZ1 is also instrumental in maintaining a biologically meaningful binding affinity. Strikingly, a spatial clustering of very high amplitude motions and a cluster of more rigid sites in the complex exist, which through computational studies we found to overlap with regions that experience energetic frustration and are less frustrated, respectively. Thus, the residual dynamics in the bound state could be necessary for faster dissociation, which is important for proteins that interact with multiple binding partners.

How Robust Is the Mechanism of Folding-Upon-Binding for an Intrinsically Disordered Protein?

PubMed

Bonetti, Daniela; Troilo, Francesca; Brunori, Maurizio; Longhi, Sonia; Gianni, Stefano

2018-04-24

The mechanism of interaction of an intrinsically disordered protein (IDP) with its physiological partner is characterized by a disorder-to-order transition in which a recognition and a binding step take place. Even if the mechanism is quite complex, IDPs tend to bind their partner in a cooperative manner such that it is generally possible to detect experimentally only the disordered unbound state and the structured complex. The interaction between the disordered C-terminal domain of the measles virus nucleoprotein (N TAIL ) and the X domain (XD) of the viral phosphoprotein allows us to detect and quantify the two distinct steps of the overall reaction. Here, we analyze the robustness of the folding of N TAIL upon binding to XD by measuring the effect on both the folding and binding steps of N TAIL when the structure of XD is modified. Because it has been shown that wild-type XD is structurally heterogeneous, populating an on-pathway intermediate under native conditions, we investigated the binding to 11 different site-directed variants of N TAIL of one particular variant of XD (I504A XD) that populates only the native state. Data reveal that the recognition and the folding steps are both affected by the structure of XD, indicating a highly malleable pathway. The experimental results are briefly discussed in the light of previous experiments on other IDPs. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

High Precision Oxygen Three Isotope Analysis of Wild-2 Particles and Anhydrous Chondritic Interplanetary Dust Particles

NASA Technical Reports Server (NTRS)

Nakashima, D.; Ushikubo, T.; Zolensky, Michael E.; Weisberg, M. K.; Joswiak, D. J.; Brownlee, D. E.; Matrajt, G.; Kita, N. T.

2011-01-01

One of the most important discoveries from comet Wild-2 samples was observation of crystalline silicate particles that resemble chondrules and CAIs in carbonaceous chondrites. Previous oxygen isotope analyses of crystalline silicate terminal particles showed heterogeneous oxygen isotope ratios with delta(sup 18)O to approx. delta(sup 17)O down to -50% in the CAI-like particle Inti, a relict olivine grain in Gozen-sama, and an olivine particle. However, many Wild-2 particles as well as ferromagnesian silicates in anhydrous interplanetary dust particles (IDPs) showed Delta(sup 17)O values that cluster around -2%. In carbonaceous chondrites, chondrules seem to show two major isotope reservoirs with Delta(sup 17)O values at -5% and -2%. It was suggested that the Delta(sup 17)O = -2% is the common oxygen isotope reservoir for carbonaceous chondrite chondrules and cometary dust, from the outer asteroid belt to the Kuiper belt region. However, a larger dataset with high precision isotope analyses (+/-1-2%) is still needed to resolve the similarities or distinctions among Wild-2 particles, IDPs and chondrules in meteorites. We have made signifi-cant efforts to establish routine analyses of small particles (< or =10micronsm) at 1-2% precision using IMS-1280 at WiscSIMS laboratory. Here we report new results of high precision oxygen isotope analyses of Wild-2 particles and anhydrous chondritic IDPs, and discuss the relationship between the cometary dust and carbonaceous chondrite chondrules.

Student performance in a flipped classroom dental anatomy course.

PubMed

Chutinan, S; Riedy, C A; Park, S E

2017-11-09

The purpose of this study was to assess dental student learning in a dental anatomy module between traditional lecture and flipped classroom cohorts. Two cohorts of predoctoral dental students (N = 70 within each cohort) participated in a dental anatomy module within an Introduction to the Dental Patient (IDP) course ([traditional/lecture cohort: academic year (AY) 2012, 2013] and [flipped classroom cohort: AY 2014, 2015]). For the dental anatomy module, both cohorts were evaluated on pre-clinical tooth waxing exercises immediately after each of five lectures and tooth identification after all lectures were given. Additionally, the cohorts' performance on the overall IDP course examination was compared. The flipped classroom cohort had statistically significant higher waxing scores (dental anatomy module) than students in the traditional classroom. There was no statistically significant difference for tooth identification scores and the overall IDP course examination between the traditional vs flipped approach cohorts. This is due to the latter two assessments conducted at the end of the course gave all students enough time to review the lecture content prior to the assessment resulting in similar scores for both cohorts. The flipped classroom cohort promoted students' individual learning and resulted in improved students' performance on immediate evaluation but not on the end of the course evaluation. Redesign of courses to include a new pedagogical approach should be carefully implemented and evaluated for student's educational success. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Papillary lesions of the breast: To excise or observe?

PubMed

Khan, Sidrah; Diaz, Adrian; Archer, Kellie J; Lehman, Rebecca R; Mullins, Tiffany; Cardenosa, Gilda; Bear, Harry D

2018-05-01

Papillary lesions of the breast range from benign to atypical to malignant. Although papillomas without frank cancer are benign, their management remains controversial. When a core needle biopsy of a lesion yields a diagnosis of intraductal papilloma with atypia, excision is generally recommended to rule out a concurrent malignant neoplasm. For intraductal papillomas without atypia, however, recommendations for excision versus observation are variable. The aims of this study are to evaluate the rate of concurrent malignancies for intraductal papilloma diagnosed on core needle biopsy and to assess the long-term risk of developing cancer after the diagnosis of a papillary lesion. This single institution retrospective study analyzed 259 patients that were diagnosed with intraductal papilloma (IDP) by core needle biopsy from 1995 to 2010. Patients were grouped by initial diagnosis into three groups (papilloma without atypia, papilloma with atypia, and papilloma with atypical duct hyperplasia or atypical lobular hyperplasia (ADH/ALH) and followed up for long-term outcomes. After a core needle biopsy showing IDP with atypia or IDP + ADH/ALH, surgical excision yielded a diagnosis of concomitant invasive or ductal in situ cancer in greater that 30% of cases. For intraductal papilloma without atypia, the likelihood of cancer was much lower. Moreover, even with excision, the finding of intraductal papilloma with atypia carries a significant risk of developing cancer long-term, and such patients should be followed carefully and perhaps should be considered for chemoprevention. © 2017 Wiley Periodicals, Inc.

Physics of interplanetary dust capture via impact into organic polymer foams

NASA Technical Reports Server (NTRS)

Anderson, William W.; Ahrens, Thomas J.

1994-01-01

The physics of hypervelocity impacts into foams is of interest because of the possible application to interplanetary dust particle (IDP) capture by spacecraft. We present a model for the phenomena occurring in such impacts into low-density organic polymer foams. Particles smaller than foam cells behave as if the foam is a series of solid slabs and are fragmented and, at higher velocities, thermally altered. Particles much larger than the foam cells behave as if the foam were a continuum, allowing the use of a continuum mechanics model to describe the effects of drag and ablation. Fragmentation is expected to be a major process, especially for aggregates of small grains. Calculations based on these arguments accurately predict experimental data and, for hypothetical IDPs, indicate that recovery of organic materials will be low for encounter velocities greater than 5 km/s. For an organic particle 100 micrometers in diameter, approx. 35% of the original mass would be collected in an impact at 5 km/s, dropping to approx. 10% at 10 km/s and approx. 0% at 15 km/s. For the same velocities the recovery ratios for troilite (FeS) are approx. 95%, 65%, and 50%, and for olivine (Mg2SiO4) they are approx. 98%, 80%, and 65%, demonstrating that inorganic materials are much more easily collected. The density of the collector material has only a second-order effect, changing the recovered mass by less than 10% of the original mass.

An Algorithm For Climate-Quality Atmospheric Profiling Continuity From EOS Aqua To Suomi-NPP

NASA Astrophysics Data System (ADS)

Moncet, J. L.

2015-12-01

We will present results from an algorithm that is being developed to produce climate-quality atmospheric profiling earth system data records (ESDRs) for application to hyperspectral sounding instrument data from Suomi-NPP, EOS Aqua, and other spacecraft. The current focus is on data from the S-NPP Cross-track Infrared Sounder (CrIS) and Advanced Technology Microwave Sounder (ATMS) instruments as well as the Atmospheric InfraRed Sounder (AIRS) on EOS Aqua. The algorithm development at Atmospheric and Environmental Research (AER) has common heritage with the optimal estimation (OE) algorithm operationally processing S-NPP data in the Interface Data Processing Segment (IDPS), but the ESDR algorithm has a flexible, modular software structure to support experimentation and collaboration and has several features adapted to the climate orientation of ESDRs. Data record continuity benefits from the fact that the same algorithm can be applied to different sensors, simply by providing suitable configuration and data files. The radiative transfer component uses an enhanced version of optimal spectral sampling (OSS) with updated spectroscopy, treatment of emission that is not in local thermodynamic equilibrium (non-LTE), efficiency gains with "global" optimal sampling over all channels, and support for channel selection. The algorithm is designed for adaptive treatment of clouds, with capability to apply "cloud clearing" or simultaneous cloud parameter retrieval, depending on conditions. We will present retrieval results demonstrating the impact of a new capability to perform the retrievals on sigma or hybrid vertical grid (as opposed to a fixed pressure grid), which particularly affects profile accuracy over land with variable terrain height and with sharp vertical structure near the surface. In addition, we will show impacts of alternative treatments of regularization of the inversion. While OE algorithms typically implement regularization by using background estimates from climatological or numerical forecast data, those sources are problematic for climate applications due to the imprint of biases from past climate analyses or from model error.

MyelStones: the executive roles of myelin basic protein in myelin assembly and destabilization in multiple sclerosis.

PubMed

Vassall, Kenrick A; Bamm, Vladimir V; Harauz, George

2015-11-15

The classic isoforms of myelin basic protein (MBP, 14-21.5 kDa) are essential to formation of the multilamellar myelin sheath of the mammalian central nervous system (CNS). The predominant 18.5-kDa isoform links together the cytosolic surfaces of oligodendrocytes, but additionally participates in cytoskeletal turnover and membrane extension, Fyn-mediated signalling pathways, sequestration of phosphoinositides and maintenance of calcium homoeostasis. All MBP isoforms are intrinsically disordered proteins (IDPs) that interact via molecular recognition fragments (MoRFs), which thereby undergo local disorder-to-order transitions. Their conformations and associations are modulated by environment and by a dynamic barcode of post-translational modifications, particularly phosphorylation by mitogen-activated and other protein kinases and deimination [a hallmark of demyelination in multiple sclerosis (MS)]. The MBPs are thus to myelin what basic histones are to chromatin. Originally thought to be merely structural proteins forming an inert spool, histones are now known to be dynamic entities involved in epigenetic regulation and diseases such as cancer. Analogously, the MBPs are not mere adhesives of compact myelin, but active participants in oligodendrocyte proliferation and in membrane process extension and stabilization during myelinogenesis. A central segment of these proteins is pivotal in membrane-anchoring and SH3 domain (Src homology 3) interaction. We discuss in the present review advances in our understanding of conformational conversions of this classic basic protein upon membrane association, including new thermodynamic analyses of transitions into different structural ensembles and how a shift in the pattern of its post-translational modifications is associated with the pathogenesis and potentially onset of demyelination in MS. © 2015 Authors; published by Portland Press Limited.

Abiogenic synthesis of nucleotides on the surface of small space bodies with high energy particles

NASA Astrophysics Data System (ADS)

Simakov, M. B.; Kuzicheva, E. A.; Antropov, A. E.; Dodonova, N. Ya

Abiotic formation of such complex biochemical compounds as nucleotides and oligopeptides on the surface of interstellar and interplanetary dust particles (IDP) by cosmic radiation was examined. In order to study the formation of organic compounds on IDPs, solid films prepared from nucleososide and inorganic phosphate were irradiated with high energy protons. Irradiated products were analyzed with HPLC. The natural nucleotides were detected. The main products were 5' AMP (3.2%) and 2'3' cAMP (2.7%). The results were compared with others experiments on the action of ultraviolet radiation with different wavelengths, γ-radiation and heat on solid mixtures of biologically significant compounds. The experiment on abiogenic synthesis of nucleotides on board of space satellite "BION-11" was compared also. The present results suggest that a considerable amount of complex biochemical compounds formed in extraterrestrial environments could have been supplied to the primitive earth before the origin of life.

Carriers of the astronomical 2175 ? extinction feature

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

Bradley, J; Dai, Z; Ernie, R

2004-07-20

The 2175 {angstrom} extinction feature is by far the strongest spectral signature of interstellar dust observed by astronomers. Forty years after its discovery the origin of the feature and the nature of the carrier remain controversial. The feature is enigmatic because although its central wavelength is almost invariant its bandwidth varies strongly from one sightline to another, suggesting multiple carriers or a single carrier with variable properties. Using a monochromated transmission electron microscope and valence electron energy-loss spectroscopy we have detected a 5.7 eV (2175 {angstrom}) feature in submicrometer-sized interstellar grains within interplanetary dust particles (IDPs) collected in the stratosphere.more » The carriers are organic carbon and amorphous silicates that are abundant and closely associated with one another both in IDPs and in the interstellar medium. Multiple carriers rather than a single carrier may explain the invariant central wavelength and variable bandwidth of the astronomical 2175 {angstrom} feature.« less

Final Assessment: U.S. Virgin Islands Industrial Development Park and Adjacent Facilities Energy-Efficiency and Micro-Grid Infrastructure

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

Petersen, Joseph M.; Boyd, Paul A.; Dahowski, Robert T.

The purpose of this assessment was to undertake an assessment and analysis of cost-effective options for energy-efficiency improvements and the deployment of a micro-grid to increase the energy resilience at the U.S. Virgin Islands Industrial Development Park (IDP) and adjacent facilities in St. Croix, Virgin Islands. The Economic Development Authority sought assistance from the U.S. Department of Energy to undertake this assessment undertaken by Pacific Northwest National Laboratory. The assessment included 18 buildings plus the perimeter security lighting at the Virgin Islands Bureau of Correctional Facility, four buildings plus exterior lighting at the IDP, and five buildings (one of whichmore » is to be constructed) at the Virgin Islands Police Department for a total of 27 buildings with a total of nearly 323,000 square feet.« less

Pristine extraterrestrial material with unprecedented nitrogen isotopic variation.

PubMed

Briani, Giacomo; Gounelle, Matthieu; Marrocchi, Yves; Mostefaoui, Smail; Leroux, Hugues; Quirico, Eric; Meibom, Anders

2009-06-30

Pristine meteoritic materials carry light element isotopic fractionations that constrain physiochemical conditions during solar system formation. Here we report the discovery of a unique xenolith in the metal-rich chondrite Isheyevo. Its fine-grained, highly pristine mineralogy has similarity with interplanetary dust particles (IDPs), but the volume of the xenolith is more than 30,000 times that of a typical IDP. Furthermore, an extreme continuum of N isotopic variation is present in this xenolith: from very light N isotopic composition (delta(15)N(AIR) = -310 +/- 20 per thousand), similar to that inferred for the solar nebula, to the heaviest ratios measured in any solar system material (delta(15)N(AIR) = 4,900 +/- 300 per thousand). At the same time, its hydrogen and carbon isotopic compositions exhibit very little variation. This object poses serious challenges for existing models for the origin of light element isotopic anomalies.

Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements

PubMed Central

Fuertes, Gustavo; Banterle, Niccolò; Ruff, Kiersten M.; Chowdhury, Aritra; Mercadante, Davide; Koehler, Christine; Kachala, Michael; Estrada Girona, Gemma; Milles, Sigrid; Mishra, Ankur; Onck, Patrick R.; Gräter, Frauke; Esteban-Martín, Santiago; Pappu, Rohit V.; Svergun, Dmitri I.; Lemke, Edward A.

2017-01-01

Unfolded states of proteins and native states of intrinsically disordered proteins (IDPs) populate heterogeneous conformational ensembles in solution. The average sizes of these heterogeneous systems, quantified by the radius of gyration (RG), can be measured by small-angle X-ray scattering (SAXS). Another parameter, the mean dye-to-dye distance (RE) for proteins with fluorescently labeled termini, can be estimated using single-molecule Förster resonance energy transfer (smFRET). A number of studies have reported inconsistencies in inferences drawn from the two sets of measurements for the dimensions of unfolded proteins and IDPs in the absence of chemical denaturants. These differences are typically attributed to the influence of fluorescent labels used in smFRET and to the impact of high concentrations and averaging features of SAXS. By measuring the dimensions of a collection of labeled and unlabeled polypeptides using smFRET and SAXS, we directly assessed the contributions of dyes to the experimental values RG and RE. For chemically denatured proteins we obtain mutual consistency in our inferences based on RG and RE, whereas for IDPs under native conditions, we find substantial deviations. Using computations, we show that discrepant inferences are neither due to methodological shortcomings of specific measurements nor due to artifacts of dyes. Instead, our analysis suggests that chemical heterogeneity in heteropolymeric systems leads to a decoupling between RE and RG that is amplified in the absence of denaturants. Therefore, joint assessments of RG and RE combined with measurements of polymer shapes should provide a consistent and complete picture of the underlying ensembles. PMID:28716919

In situ 3-D mapping of pore structures and hollow grains of interplanetary dust particles with phase contrast X-ray nanotomography

NASA Astrophysics Data System (ADS)

Hu, Z. W.; Winarski, R. P.

2016-09-01

Unlocking the 3-D structure and properties of intact chondritic porous interplanetary dust particles (IDPs) in nanoscale detail is challenging, which is also complicated by atmospheric entry heating, but is important for advancing our understanding of the formation and origins of IDPs and planetary bodies as well as dust and ice agglomeration in the outer protoplanetary disk. Here, we show that indigenous pores, pristine grains, and thermal alteration products throughout intact particles can be noninvasively visualized and distinguished morphologically and microstructurally in 3-D detail down to ~10 nm by exploiting phase contrast X-ray nanotomography. We have uncovered the surprisingly intricate, submicron, and nanoscale pore structures of a ~10-μm-long porous IDP, consisting of two types of voids that are interconnected in 3-D space. One is morphologically primitive and mostly submicron-sized intergranular voids that are ubiquitous; the other is morphologically advanced and well-defined intragranular nanoholes that run through the approximate centers of ~0.3 μm or lower submicron hollow grains. The distinct hollow grains exhibit complex 3-D morphologies but in 2-D projections resemble typical organic hollow globules observed by transmission electron microscopy. The particle, with its outer region characterized by rough vesicular structures due to thermal alteration, has turned out to be an inherently fragile and intricately submicron- and nanoporous aggregate of the sub-μm grains or grain clumps that are delicately bound together frequently with little grain-to-grain contact in 3-D space.

Understanding the Structural Ensembles of a Highly Extended Disordered Protein†

PubMed Central

Daughdrill, Gary W.; Kashtanov, Stepan; Stancik, Amber; Hill, Shannon E.; Helms, Gregory; Muschol, Martin

2013-01-01

Developing a comprehensive description of the equilibrium structural ensembles for intrinsically disordered proteins (IDPs) is essential to understanding their function. The p53 transactivation domain (p53TAD) is an IDP that interacts with multiple protein partners and contains numerous phosphorylation sites. Multiple techniques were used to investigate the equilibrium structural ensemble of p53TAD in its native and chemically unfolded states. The results from these experiments show that the native state of p53TAD has dimensions similar to a classical random coil while the chemically unfolded state is more extended. To investigate the molecular properties responsible for this behavior, a novel algorithm that generates diverse and unbiased structural ensembles of IDPs was developed. This algorithm was used to generate a large pool of plausible p53TAD structures that were reweighted to identify a subset of structures with the best fit to small angle X-ray scattering data. High weight structures in the native state ensemble show features that are localized to protein binding sites and regions with high proline content. The features localized to the protein binding sites are mostly eliminated in the chemically unfolded ensemble; while, the regions with high proline content remain relatively unaffected. Data from NMR experiments support these results, showing that residues from the protein binding sites experience larger environmental changes upon unfolding by urea than regions with high proline content. This behavior is consistent with the urea-induced exposure of nonpolar and aromatic side-chains in the protein binding sites that are partially excluded from solvent in the native state ensemble. PMID:21979461

What Factors Contribute to Intimate Partner Violence Against Women in Urban, Conflict-Affected Settings? Qualitative Findings from Abidjan, Côte d'Ivoire.

PubMed

Cardoso, L F; Gupta, J; Shuman, S; Cole, H; Kpebo, D; Falb, K L

2016-04-01

Rapid urbanization is a key driver of the unique set of health risks facing urban populations. One of the most critical health hazards facing urban women is intimate partner violence (IPV). In post-conflict urban areas, women may face an even greater risk of IPV. Yet, few studies have examined the IPV experiences of urban-dwelling, conflict-affected women, including those who have been internally displaced. This study qualitatively examined the social and structural characteristics of the urban environment that contributed to the IPV experiences of women residing in post-conflict Abidjan, Côte d'Ivoire. Ten focus groups were conducted with men and women, both internally displaced (IDPs) and non-displaced. Lack of support networks, changing gender roles, and tensions between traditional gender norms and those of the "modern" city were reported as key contributors to IPV. Urban poverty and with it unemployment, food insecurity, and housing instability also played a role. Finally, IDPs faced heightened vulnerability to IPV as a result of displacement and discrimination. The relationship between economic strains and IPV are similar to other conflict-affected settings, but Abidjan's urban environment presented other unique characteristics contributing to IPV. Understanding these factors is crucial to designing appropriate services for women and for implementing IPV reduction interventions in urban areas. Strengthening formal and informal mechanisms for help-seeking, utilizing multi-modal interventions that address economic stress and challenge inequitable gender norms, as well as tailoring programs specifically for IDPs, are some considerations for IPV program planning focused on conflict-affected women in urban areas.

Trapped Xenon in Interplanetary Dust Particles and Antarctic Micrometeorites

NASA Astrophysics Data System (ADS)

Spring, N. H.; Busemann, H.; Crowther, S. A.; Gilmour, J. D.

2014-09-01

We analysed the Xe inventory of several IDPs and AMMs and infer that cometary solids may contain the same mix of organic matter and trapped Xe carriers as found in carbonaceous chondrite matrices, although in higher relative abundances.

Further analysis of LDEF FRECOPA micrometeroid remnants

NASA Technical Reports Server (NTRS)

Borg, J.; Bunch, T. E.; Radicatidibrozolo, Filippo

1992-01-01

Experiments dedicated to the detection of interplanetary dust particles (IDP's) were exposed within the FRECOPA payload, installed on the face of the LDEF directly opposed to the velocity vector (west facing direction, location B3). We were mainly interested in the analysis of hypervelocity impact features of sizes less than or = 10 microns, found in thick Al targets devoted to the research of impact features. In the 15 craters found in the scanned area (approximately 4 sq. cm), the chemical analysis suggests an extraterrestrial origin for the impacting particles. The main elements we identified are usually refered to as chondrite elements: Na, Mg, Si, S, Ca, and Fe are found in various proportions, intrinsic Al being masked by the Al target; we notice a strong depletion in Ni, never observed in our samples. Furthermore, C and O are present in 90 percent of the cases; the C/O peak height ratio varies from 0.1 to 3. Impactor simulations by light gas gun hypervelocity impact experiments have shown that meaningful biogenic element and compound information maybe obtained from IDP residues below impacts of critical velocities, that are less than or = 4 km/sec for particles larger than 100 microns in diameter. Our results obtained for the smaller size fraction IDP's suggest that at such sizes, the critical velocity could be higher by a factor of 2 or 3, as chemical analysis of the remnants were possible in all the identified impact craters, performed on targets possibly hit at velocities greater than or = 7.5 km/s, which is the spacecraft velocity. These samples are now subjected to an imagery and analytical protocol that includes FESEM (field emission scanning electron microscopy) and LIMS (laser ionization mass spectrometry). The LIMS analyses were performed using the LIMA-ZA instrument. Results are presented, clearly indicating that such small events show crater features analogous to what is observed at larger sizes; our first analytical results, obtained for 2 events (P6 and P10) suggest that N is present in the IDP's remnants in which C and O were identified by EDX analysis. In one case (P6), enrichment in K and P is observed. Surface contamination by NaCl is evident on the FRECOPA surfaces.

Presolar Organic Globules in Astromaterials

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Messenger, S.; Keller, L. P.; Clemett, S. J.

2012-01-01

Presolar grains were identified in meteorite residues 20 years ago based on their exotic isotopic compositions [1]. Their study has provide new insights into stellar evolution and the first view of the original building blocks of the solar system. Organic matter in meteorites and IDPs is highly enriched in D/H and N-15/N-14 at micron scales, possibly due to presolar organic grains [2-4]. These anomalies are ascribed to the partial preservation of presolar cold molecular cloud material. Identifying the carriers of these anomalies and elucidating their physical and chemical properties may give new views of interstellar chemistry and better understanding of the original components of the protosolar disk. However, identifying the carriers has been hampered by their small size and the inability to chemically isolate them. Thanks to major advances in nano-scale analytical techniques and advanced sample preparation, we were able to show that in the Tagish Lake meteorite, the principle carriers of these isotopic anomalies are sub-microns, hollow organic globules [5]. The organic globules likely formed by photochemical processing of organic ices in a cold molecular cloud or the outermost regions of the protosolar disk [5]. Organic globules with similar physical, chemical, and isotopic properties are also recently found from Bells CM2 carbonaceous chondrite, in IDPs [6] and in the comet Wild-2 samples returned by Stardust [7]. These results support the view that microscopic organic grains were widespread constituents of the protoplanetary disk. Their exotic isotopic compositions trace their origins to the outermost portions of the protosolar disk or a presolar cold molecular cloud.

Ion Microprobe Measurements of Comet Dust and Implications for Models of Oxygen Isotope Heterogeneity in the Solar System

NASA Technical Reports Server (NTRS)

Snead, C. J.; McKeegan, K. D.; Keller, L. P.; Messenger, S.

2017-01-01

The oxygen isotopic compositions of anhydrous minerals in carbonaceous chondrites reflect mixing between a O-16-rich and O-17, O18-rich reservoir. The UV photodissociation of CO (i.e. selfshielding) has been proposed as a mass-independent mechanism for producing these isotopically distinct reservoirs. Self-shielding models predict the composition for the CO gas reservoir to be O-16-rich, and that the accreting primordial dust was in isotopic equilibrium with the gaseous reservoir [1, 2]. Self-shielding also predicts that cometary water, presumed to represent the O-17, O-18-rich reservoir, should be enriched in O-17 and O-18, with compositions of 200 -1000per mille, and that the interaction with this O-17, O-18-rich H2O reservoir altered the compositions of the primordial dust toward planetary values. The bulk composition of the solar nebula, which may be an approximation to the 16O-rich gaseous reservoir, has been constrained by the Genesis results [3]. However, material representing the O-17, O-18-rich end-member is rare [4], and dust representing the original accreting primordial dust has been challenging to conclusively identify in current collections. Anhydrous dust from comets, which accreted in the distal cold regions of the nebula at temperatures below approximately 30K, may provide the best opportunity to measure the oxygen isotope composition of primordial dust. Chondritic porous interplanetary dust particles (CP-IDPs) have been suggested as having cometary origins [5]; however, until direct comparisons with dust from a known comet parent body were made, link between CP-IDPs and comets remained circumstantial. Oxygen isotope analyses of particles from comet 81P/Wild 2 collected by NASA's Stardust mission have revealed surprising similarities to minerals in carbonaceous chondrites which have been interpreted as evidence for large scale radial migration of dust components from the inner solar nebula to the accretion regions of Jupiter- family comets [6]. These studies have been largely focused on the coarse-grained terminal particles extracted from aerogel collectors; hypervelocity capture into aerogel resulted in fine-grained material that was melted and intimately mixed with the SiO2 capture medium. Hypervelocity impacts into Al foils surrounding the aerogel tiles produced impact craters that captured material from the impactor without significant oxygen contamination, allowing for analysis of both the coarse and fine-grained components of the Wild 2 dust. To date, no particles with definitive hydrated mineralogy have been observed in Stardust samples, though this may be a result of alteration due to hypervelocity capture. High-carbon hydrated CS-IDPs have been suggested as resulting from the aqueous alteration of CP-IDPs [7], and may retain evidence for interaction with O-17, O-18-enriched "cometary" water predicted by CO self-shielding. Here we present results of oxygen isotope measurements of twelve Stardust foil craters and four C-rich hydrated IDPs [8, 9], and discuss implications for models of oxygen isotope heterogeneity in the early solar system.

Image Segmentation Using Minimum Spanning Tree

NASA Astrophysics Data System (ADS)

Dewi, M. P.; Armiati, A.; Alvini, S.

2018-04-01

This research aim to segmented the digital image. The process of segmentation is to separate the object from the background. So the main object can be processed for the other purposes. Along with the development of technology in digital image processing application, the segmentation process becomes increasingly necessary. The segmented image which is the result of the segmentation process should accurate due to the next process need the interpretation of the information on the image. This article discussed the application of minimum spanning tree on graph in segmentation process of digital image. This method is able to separate an object from the background and the image will change to be the binary images. In this case, the object that being the focus is set in white, while the background is black or otherwise.

Assessment of the Interstellar Processes Leading to Deuterium Enrichment in Meteoritic Organics

NASA Technical Reports Server (NTRS)

Sandford, Scott A.; Bernstein, Max P.; Dworkin, Jason P.; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

The presence of isotopic anomalies is the most unequivocal demonstration that meteoritic material contains circumstellar or interstellar components. In the case of organic compounds in meteorites and interplanetary dust particles (IDPs), the most useful isotopic tracer has been deuterium (D). We discuss four processes that are expected to lead to D enrichment in interstellar materials and describe how their unique characteristics can be used to assess their relative importance for the organics in meteorites. These enrichment processes are low temperature gas phase ion-molecule reactions, low temperature gas-grain reactions, gas phase unimolecular photodissociation, and ultraviolet photolysis in D-enriched ice mantles. Each of these processes is expected to be associated with distinct regiochemical signatures (D placement on the product molecules, correlation with specific chemical functionalities, etc.), especially in the molecular population of polycyclic aromatic hydrocarbons (PAHs). We describe these differences and discuss how they may be used to delineate the various interstellar processes that may have contributed to meteoritic D enrichments. We also briefly discuss how these processes may affect the isotopic distributions in C, 0, and N in the same compounds.

Complete Tem-Tomography: 3D Structure of Gems Cluster

NASA Technical Reports Server (NTRS)

Matsuno, J.; Miyake, A.; Tsuchiyama, A.; Messenger, S.; Nakamura-Messenger, K.

2015-01-01

GEMS (glass with embedded metal and sulfide) grains in interplanetary dust particles (IDPs) are considered to be one of the ubiquitous and fundamental building blocks of solids in the Solar System. They have been considered to be interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk but the elemental and isotopic composition measurements suggest that most of them have been formed in the protoplanetary disk as condensates from high temperature gas. This formation model is also supported by the formation of GEMS-like grains with respect to the size, mineral assemblage, texture and infrared spectrum by condensation experiments from mean GEMS composition materials. Previous GEMS studies were performed only with 2D observation by transmission electron microscopy (TEM) or scanning TEM (STEM). However, the 3D shape and structure of GEMS grains and the spatial distribution of Fe/FeS's has critical information about their formation and origin. Recently, the 3D structure of GEMS grains in ultrathin sections of cluster IDPs was revealed by electron tomography using a TEM/STEM (JEM-2100F, JEOL). However, CT images of thin sections mounted on Cu grids acquired by conventional TEM-tomography are limited to low tilt angles (e. g., less than absolute value of 75 deg. In fact, previous 3D TEM observations of GEMS were affected by some artifacts related to the limited tilt range in the TEM used. Complete tomographic images should be acquired by rotating the sample tilt angle over a range of more than absolute value of 80 deg otherwise the CT images lose their correct structures. In order to constrain the origin and formation process of GEMS grains more clearly, we performed complete electron tomography for GEMS grains. Here we report the sample preparation method we have developed for this study, and the preliminary results.

Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.

PubMed

Fuertes, Gustavo; Banterle, Niccolò; Ruff, Kiersten M; Chowdhury, Aritra; Mercadante, Davide; Koehler, Christine; Kachala, Michael; Estrada Girona, Gemma; Milles, Sigrid; Mishra, Ankur; Onck, Patrick R; Gräter, Frauke; Esteban-Martín, Santiago; Pappu, Rohit V; Svergun, Dmitri I; Lemke, Edward A

2017-08-01

Unfolded states of proteins and native states of intrinsically disordered proteins (IDPs) populate heterogeneous conformational ensembles in solution. The average sizes of these heterogeneous systems, quantified by the radius of gyration ( R G ), can be measured by small-angle X-ray scattering (SAXS). Another parameter, the mean dye-to-dye distance ( R E ) for proteins with fluorescently labeled termini, can be estimated using single-molecule Förster resonance energy transfer (smFRET). A number of studies have reported inconsistencies in inferences drawn from the two sets of measurements for the dimensions of unfolded proteins and IDPs in the absence of chemical denaturants. These differences are typically attributed to the influence of fluorescent labels used in smFRET and to the impact of high concentrations and averaging features of SAXS. By measuring the dimensions of a collection of labeled and unlabeled polypeptides using smFRET and SAXS, we directly assessed the contributions of dyes to the experimental values R G and R E For chemically denatured proteins we obtain mutual consistency in our inferences based on R G and R E , whereas for IDPs under native conditions, we find substantial deviations. Using computations, we show that discrepant inferences are neither due to methodological shortcomings of specific measurements nor due to artifacts of dyes. Instead, our analysis suggests that chemical heterogeneity in heteropolymeric systems leads to a decoupling between R E and R G that is amplified in the absence of denaturants. Therefore, joint assessments of R G and R E combined with measurements of polymer shapes should provide a consistent and complete picture of the underlying ensembles.

Partner-Mediated Polymorphism of an Intrinsically Disordered Protein.

PubMed

Bignon, Christophe; Troilo, Francesca; Gianni, Stefano; Longhi, Sonia

2017-11-29

Intrinsically disordered proteins (IDPs) recognize their partners through molecular recognition elements (MoREs). The MoRE of the C-terminal intrinsically disordered domain of the measles virus nucleoprotein (N TAIL ) is partly pre-configured as an α-helix in the free form and undergoes α-helical folding upon binding to the X domain (XD) of the viral phosphoprotein. Beyond XD, N TAIL also binds the major inducible heat shock protein 70 (hsp70). So far, no structural information is available for the N TAIL /hsp70 complex. Using mutational studies combined with a protein complementation assay based on green fluorescent protein reconstitution, we have investigated both N TAIL /XD and N TAIL /hsp70 interactions. Although the same N TAIL region binds the two partners, the binding mechanisms are different. Hsp70 binding is much more tolerant of MoRE substitutions than XD, and the majority of substitutions lead to an increased N TAIL /hsp70 interaction strength. Furthermore, while an increased and a decreased α-helicity of the MoRE lead to enhanced and reduced interaction strength with XD, respectively, the impact on hsp70 binding is negligible, suggesting that the MoRE does not adopt an α-helical conformation once bound to hsp70. Here, by showing that the α-helical conformation sampled by the free form of the MoRE does not systematically commit it to adopt an α-helical conformation in the bound form, we provide an example of partner-mediated polymorphism of an IDP and of the relative insensitiveness of the bound structure to the pre-recognition state. The present results therefore contribute to shed light on the molecular mechanisms by which IDPs recognize different partners. Copyright © 2017 Elsevier Ltd. All rights reserved.

Improved Automated Detection of Diabetic Retinopathy on a Publicly Available Dataset Through Integration of Deep Learning.

PubMed

Abràmoff, Michael David; Lou, Yiyue; Erginay, Ali; Clarida, Warren; Amelon, Ryan; Folk, James C; Niemeijer, Meindert

2016-10-01

To compare performance of a deep-learning enhanced algorithm for automated detection of diabetic retinopathy (DR), to the previously published performance of that algorithm, the Iowa Detection Program (IDP)-without deep learning components-on the same publicly available set of fundus images and previously reported consensus reference standard set, by three US Board certified retinal specialists. We used the previously reported consensus reference standard of referable DR (rDR), defined as International Clinical Classification of Diabetic Retinopathy moderate, severe nonproliferative (NPDR), proliferative DR, and/or macular edema (ME). Neither Messidor-2 images, nor the three retinal specialists setting the Messidor-2 reference standard were used for training IDx-DR version X2.1. Sensitivity, specificity, negative predictive value, area under the curve (AUC), and their confidence intervals (CIs) were calculated. Sensitivity was 96.8% (95% CI: 93.3%-98.8%), specificity was 87.0% (95% CI: 84.2%-89.4%), with 6/874 false negatives, resulting in a negative predictive value of 99.0% (95% CI: 97.8%-99.6%). No cases of severe NPDR, PDR, or ME were missed. The AUC was 0.980 (95% CI: 0.968-0.992). Sensitivity was not statistically different from published IDP sensitivity, which had a CI of 94.4% to 99.3%, but specificity was significantly better than the published IDP specificity CI of 55.7% to 63.0%. A deep-learning enhanced algorithm for the automated detection of DR, achieves significantly better performance than a previously reported, otherwise essentially identical, algorithm that does not employ deep learning. Deep learning enhanced algorithms have the potential to improve the efficiency of DR screening, and thereby to prevent visual loss and blindness from this devastating disease.

Outcomes of Extremely Preterm Infants Born to Insulin-Dependent Diabetic Mothers

PubMed Central

Boghossian, Nansi S.; Hansen, Nellie I.; Brumbaugh, Jane E.; Stoll, Barbara J.; Laptook, Abbot R.; Shankaran, Seetha; Wyckoff, Myra H.; Colaizy, Tarah T.; Das, Abhik; Higgins, Rosemary D.

2016-01-01

BACKGROUND AND OBJECTIVE: Little is known about in-hospital morbidities and neurodevelopmental outcomes among extremely preterm infants born to women with insulin-dependent diabetes mellitus (IDDM). We examined risks of mortality, in-hospital morbidities, and neurodevelopmental outcomes at 18 to 22 months’ corrected age between extremely preterm infants of women with insulin use before pregnancy (IBP), with insulin use started during pregnancy (IDP), and without IDDM. METHODS: Infants 22 to 28 weeks’ gestation born or cared for at a Eunice Kennedy Shriver National Institute of Child Health and Human Development Neonatal Research Network center (2006–2011) were studied. Regression models compared the association between maternal IDDM and timing of insulin use and the outcomes of the 3 groups. RESULTS: Of 10 781 infants, 536 (5%) were born to women with IDDM; 58% had IBP, and 36% had IDP. Infants of mothers with IBP had higher risks of necrotizing enterocolitis (adjusted relative risk [RR] = 1.55 [95% confidence interval (CI) 1.17–2.05]) and late-onset sepsis (adjusted RR = 1.26 [95% CI 1.07–1.48]) than infants of mothers without IDDM. There was some indication of higher in-hospital mortality risk among infants of mothers with IBP compared with those with IDP (adjusted RR = 1.33 [95% CI 1.00–1.79]). Among survivors evaluated at 18 to 22 months’ corrected age, average head circumference z score was lower for infants of mothers with IBP compared with those without IDDM, but there were no differences in risk of neurodevelopmental impairment. CONCLUSIONS: In this cohort of extremely preterm infants, infants of mothers with IBP had higher risks of necrotizing enterocolitis, sepsis, and small head circumference. PMID:27244849

Analysis of the relationships between evolvability, thermodynamics, and the functions of intrinsically disordered proteins/regions.

PubMed

Huang, He; Sarai, Akinori

2012-12-01

The evolvability of proteins is not only restricted by functional and structural importance, but also by other factors such as gene duplication, protein stability, and an organism's robustness. Recently, intrinsically disordered proteins (IDPs)/regions (IDRs) have been suggested to play a role in facilitating protein evolution. However, the mechanisms by which this occurs remain largely unknown. To address this, we have systematically analyzed the relationship between the evolvability, stability, and function of IDPs/IDRs. Evolutionary analysis shows that more recently emerged IDRs have higher evolutionary rates with more functional constraints relaxed (or experiencing more positive selection), and that this may have caused accelerated evolution in the flanking regions and in the whole protein. A systematic analysis of observed stability changes due to single amino acid mutations in IDRs and ordered regions shows that while most mutations induce a destabilizing effect in proteins, mutations in IDRs cause smaller stability changes than in ordered regions. The weaker impact of mutations in IDRs on protein stability may have advantages for protein evolvability in the gain of new functions. Interestingly, however, an analysis of functional motifs in the PROSITE and ELM databases showed that motifs in IDRs are more conserved, characterized by smaller entropy and lower evolutionary rate, than in ordered regions. This apparently opposing evolutionary effect may be partly due to the flexible nature of motifs in IDRs, which require some key amino acid residues to engage in tighter interactions with other molecules. Our study suggests that the unique conformational and thermodynamic characteristics of IDPs/IDRs play an important role in the evolvability of proteins to gain new functions. Copyright © 2012 Elsevier Ltd. All rights reserved.

The neglected functions of intrinsically disordered proteins and the origin of life.

PubMed

Jaeken, Laurent

2017-07-01

The example of gelatine shows that extended proteins behave quite differently than globular ones: with water they form a gel. Historically the colloid view of protoplasm was discredited in favour of membrane-(pump)-theory (MPT), but unjustified. In his association-induction hypothesis Ling demonstrates that MPT is full of contradictions and that the colloid view has to be re-considered. In that case IDP's play a crucial role in this. What Ling calls the 'living state' consists of the unitary protoplasmic structure from which it was experimentally demonstrated that it can survive and keep Na + and K + concentrations without a delineating membrane. It consists of unfolded polypeptide chains whereby the repetitive backbone peptide groups orient and polarise many layers of water, in which Na + and other solutes have reduced solubility and whereby the polypeptide β- and ϒ-carboxyl-groups adsorb K + . This 'associated' state is the resting state: a coherent high-energy low-entropy meta-stable state. It can be kept by adsorbed ATP (NTP) eventually for years without consumption of ATP as demonstrated by Clegg on Artemia embryo's. Stimuli can transform this state into a lower-energy higher-entropy action state with dissociation of ADP and P i and newly synthesised ATP can reinstall it. Rest-to-action and action-to-rest were shown to be real phase-shifts. Ling's theory is a complete quantitative theory with corroborated equations for solute distribution, transport, cell potentials and osmotic behaviour and describing the cell's energy cycle. IDP's are involved in all this. The new view on IDP's leads to new insights on the origin of life. Copyright © 2017 Elsevier Ltd. All rights reserved.

DIFFERENT ORIGINS OR DIFFERENT EVOLUTIONS? DECODING THE SPECTRAL DIVERSITY AMONG C-TYPE ASTEROIDS

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

Vernazza, P.; Marsset, M.; Groussin, O.

Anhydrous pyroxene-rich interplanetary dust particles (IDPs) have been proposed as surface analogs for about two-thirds of all C-complex asteroids. However, this suggestion appears to be inconsistent with the presence of hydrated silicates on the surfaces of some of these asteroids, including Ceres. Here, we report the presence of enstatite (pyroxene) on the surface of two C-type asteroids (Ceres and Eugenia) based on their spectral properties in the mid-infrared range. The presence of this component is particularly unexpected in the case of Ceres, because most thermal evolution models predict a surface consisting of hydrated compounds only. The most plausible scenario is that Ceres’more » surface has been partially contaminated by exogenous enstatite-rich material, possibly coming from the Beagle asteroid family. This scenario questions a similar origin for Ceres and the remaining C-types, and it possibly supports recent results obtained by the Dawn mission (NASA) that Ceres may have formed in the very outer solar system. Concerning the smaller D  ∼ 200 km C-types such as Eugenia, both their derived surface composition (enstatite and amorphous silicates) and low density (<1.5 g cm{sup −3}) suggest that these bodies accreted from the same building blocks, namely chondritic porous, pyroxene-rich IDPs and volatiles (mostly water ice), and that a significant volume fraction of these bodies has remained unaffected by hydrothermal activity likely implying a late accretion. In addition, their current heliocentric distance may best explain the presence or absence of water ice at their surfaces. Finally, we raise the possibility that CI chondrites, Tagish-Lake-like material, or hydrated IDPs may be representative samples of the cores of these bodies.« less

Biophysical characterization of the structural change of Nopp140, an intrinsically disordered protein, in the interaction with CK2α

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

Na, Jung-Hyun; Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792; Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760

2016-08-19

Nucleolar phosphoprotein 140 (Nopp140) is a nucleolar protein, more than 80% of which is disordered. Previous studies have shown that the C-terminal region of Nopp140 (residues 568–596) interacts with protein kinase CK2α, and inhibits the catalytic activity of CK2. Although the region of Nopp140 responsible for the interaction with CK2α was identified, the structural features and the effect of this interaction on the structure of Nopp140 have not been defined due to the difficulty of structural characterization of disordered protein. In this study, the disordered feature of Nopp140 and the effect of CK2α on the structure of Nopp140 were examinedmore » using single-molecule fluorescence resonance energy transfer (smFRET) and electron paramagnetic resonance (EPR). The interaction with CK2α was increased conformational rigidity of the CK2α-interacting region of Nopp140 (Nopp140C), suggesting that the disordered and flexible conformation of Nopp140C became more rigid conformation as it binds to CK2α. In addition, site specific spin labeling and EPR analysis confirmed that the residues 574–589 of Nopp140 are critical for binding to CK2α. Similar technical approaches can be applied to analyze the conformational changes in other IDPs during their interactions with binding partners. - Highlights: • Nopp140 is intrinsically disordered protein (IDP). • Conformation of Nopp140 became more rigid conformation due to interaction with CK2α. • smFRET and EPR could be applied to analyze the structural changes of IDPs.« less

Different Origins or Different Evolutions? Decoding the Spectral Diversity Among C-type Asteroids

NASA Astrophysics Data System (ADS)

Vernazza, P.; Castillo-Rogez, J.; Beck, P.; Emery, J.; Brunetto, R.; Delbo, M.; Marsset, M.; Marchis, F.; Groussin, O.; Zanda, B.; Lamy, P.; Jorda, L.; Mousis, O.; Delsanti, A.; Djouadi, Z.; Dionnet, Z.; Borondics, F.; Carry, B.

2017-02-01

Anhydrous pyroxene-rich interplanetary dust particles (IDPs) have been proposed as surface analogs for about two-thirds of all C-complex asteroids. However, this suggestion appears to be inconsistent with the presence of hydrated silicates on the surfaces of some of these asteroids, including Ceres. Here, we report the presence of enstatite (pyroxene) on the surface of two C-type asteroids (Ceres and Eugenia) based on their spectral properties in the mid-infrared range. The presence of this component is particularly unexpected in the case of Ceres, because most thermal evolution models predict a surface consisting of hydrated compounds only. The most plausible scenario is that Ceres’ surface has been partially contaminated by exogenous enstatite-rich material, possibly coming from the Beagle asteroid family. This scenario questions a similar origin for Ceres and the remaining C-types, and it possibly supports recent results obtained by the Dawn mission (NASA) that Ceres may have formed in the very outer solar system. Concerning the smaller D ˜ 200 km C-types such as Eugenia, both their derived surface composition (enstatite and amorphous silicates) and low density (<1.5 g cm-3) suggest that these bodies accreted from the same building blocks, namely chondritic porous, pyroxene-rich IDPs and volatiles (mostly water ice), and that a significant volume fraction of these bodies has remained unaffected by hydrothermal activity likely implying a late accretion. In addition, their current heliocentric distance may best explain the presence or absence of water ice at their surfaces. Finally, we raise the possibility that CI chondrites, Tagish-Lake-like material, or hydrated IDPs may be representative samples of the cores of these bodies.

Anatomy of a cluster IDP. Part 2: Noble gas abundances, trace element geochemistry, isotopic abundances, and trace organic chemistry of several fragments from L2008#5

NASA Technical Reports Server (NTRS)

Thomas, K. L.; Clemett, S. J.; Flynn, G. J.; Keller, L. P.; Mckay, David S.; Messenger, S.; Nier, A. O.; Schlutter, D. J.; Sutton, S. R.; Walker, R. M.

1994-01-01

The topics discussed include the following: noble gas content and release temperatures; trace element abundances; heating summary of cluster fragments; isotopic measurements; and trace organic chemistry.

IDP camp evolvement analysis in Darfur using VHSR optical satellite image time series and scientific visualization on virtual globes

NASA Astrophysics Data System (ADS)

Tiede, Dirk; Lang, Stefan

2010-11-01

In this paper we focus on the application of transferable, object-based image analysis algorithms for dwelling extraction in a camp for internally displaced people (IDP) in Darfur, Sudan along with innovative means for scientific visualisation of the results. Three very high spatial resolution satellite images (QuickBird: 2002, 2004, 2008) were used for: (1) extracting different types of dwellings and (2) calculating and visualizing added-value products such as dwelling density and camp structure. The results were visualized on virtual globes (Google Earth and ArcGIS Explorer) revealing the analysis results (analytical 3D views,) transformed into the third dimension (z-value). Data formats depend on virtual globe software including KML/KMZ (keyhole mark-up language) and ESRI 3D shapefiles streamed as ArcGIS Server-based globe service. In addition, means for improving overall performance of automated dwelling structures using grid computing techniques are discussed using examples from a similar study.

Setting up an early warning system for epidemic-prone diseases in Darfur: a participative approach.

PubMed

Pinto, Augusto; Saeed, Mubarak; El Sakka, Hammam; Rashford, Adrienne; Colombo, Alessandro; Valenciano, Marta; Sabatinelli, Guido

2005-12-01

In April-May 2004, the World Health Organization (WHO) implemented, with local authorities, United Nations (UN) agencies and non-governmental organisations (NGOs), an early warning system (EWS) in Darfur, West Sudan, for internally displaced persons (IDPs). The number of consultations and deaths per week for 12 health events is recorded for two age groups (less than five years and five years and above). Thresholds are used to detect potential outbreaks. Ten weeks after the introduction of the system, NGOs were covering 54 camps, and 924,281 people (IDPs and the host population). Of these 54 camps, 41 (76%) were reporting regularly under the EWS. Between 22 May and 30 July, 179,795 consultations were reported: 18.7% for acute respiratory infections; 15% for malaria; 8.4% for bloody diarrhoea; and 1% for severe acute malnutrition. The EWS is useful for detecting outbreaks and monitoring the number of consultations required to trigger actions, but not for estimating mortality.

The molecular mechanism of nuclear transport revealed by atomic-scale measurements

PubMed Central

Hough, Loren E; Dutta, Kaushik; Sparks, Samuel; Temel, Deniz B; Kamal, Alia; Tetenbaum-Novatt, Jaclyn; Rout, Michael P; Cowburn, David

2015-01-01

Nuclear pore complexes (NPCs) form a selective filter that allows the rapid passage of transport factors (TFs) and their cargoes across the nuclear envelope, while blocking the passage of other macromolecules. Intrinsically disordered proteins (IDPs) containing phenylalanyl-glycyl (FG)-rich repeats line the pore and interact with TFs. However, the reason that transport can be both fast and specific remains undetermined, through lack of atomic-scale information on the behavior of FGs and their interaction with TFs. We used nuclear magnetic resonance spectroscopy to address these issues. We show that FG repeats are highly dynamic IDPs, stabilized by the cellular environment. Fast transport of TFs is supported because the rapid motion of FG motifs allows them to exchange on and off TFs extremely quickly through transient interactions. Because TFs uniquely carry multiple pockets for FG repeats, only they can form the many frequent interactions needed for specific passage between FG repeats to cross the NPC. DOI: http://dx.doi.org/10.7554/eLife.10027.001 PMID:26371551

Folding propensity of intrinsically disordered proteins by osmotic stress

DOE PAGES

Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.; ...

2016-10-11

Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR). Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scatteringmore » (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.« less

Dust Infall Onto Phobos and Deimos Can Explain Their Carbonaceous Reflectance Signature, Perhaps Overlying a Mars-Impact-Origin Core: A Hypothesis

NASA Technical Reports Server (NTRS)

Fries, M.; Cintala, M.; Steele, A.; Welzenbach, L. C.

2017-01-01

Discussions of Phobos' and Deimos' (henceforth P&D) origin(s) include an unresolved conflict: dynamical studies which favor coalescence of the moons from a large impact on Mars [1,2], versus reflectance spectroscopy of the moons showing a carbonaceous composition that is not consistent with martian surface materials [3-5]. One way to reconcile this discrepancy is to consider the combined options of a Mars impact origin for Phobos and Deimos, followed by deposition of carbon-rich materials by interplanetary dust particle (IDP) infall. This is significant because, unlike asteroidal bodies, P&D experience a high IDP flux due to their location in Mars' gravity well. We present some relatively simple, initial calculations which indicate that accreted carbon may be sufficient to produce a surface with sufficient added carbon to account for P&D's reflectance spectra. If this is true, then a major objection to an impact origin for P&D is resolved.

Gender, health, and human rights in sites of political exclusion.

PubMed

Laurie, M; Petchesky, R P

2008-01-01

In this paper, we investigate the intersections of gender, health and human rights in sites of political exclusion. We apply the political theory of Giorgio Agamben on 'states of exception', seeking to better understand how the recent 'war on terror', that seemingly knows no limits of time or space, is driving health outcomes in refugee and Internally Displaced Persons (IDP) camps. Reproductive health, militarization, and gender-based violence in camps are explored in depth. The evidence presented reveals a number of contradictions of refugee and IDP camps, further highlighting the need for a more rights based humanitarianism. We conclude that foregrounding states of exception, as a way of understanding current gender dynamics in the social determinants of health, is both epidemiologically necessary and conceptually useful. We find that, in these sites of exclusion, the indispensability of a human rights approach to gender and health equity issues is revealed most directly. Furthermore, we are able to make new connections between the 'crisis of humanitarianism', gender, and health.

Folding propensity of intrinsically disordered proteins by osmotic stress

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

Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.

Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR). Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scatteringmore » (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.« less

Internal displacement in Burma.

PubMed

Lanjouw, S; Mortimer, G; Bamforth, V

2000-09-01

The internal displacement of populations in Burma is not a new phenomenon. Displacement is caused by numerous factors. Not all of it is due to outright violence, but much is a consequence of misguided social and economic development initiatives. Efforts to consolidate the state by assimilating populations in government-controlled areas by military authorities on the one hand, while brokering cease-fires with non-state actors on the other, has uprooted civilian populations throughout the country. Very few areas in which internally displaced persons (IDPs) are found are not facing social turmoil within a climate of impunity. Humanitarian access to IDP populations remains extremely problematic. While relatively little information has been collected, assistance has been focused on targeting accessible groups. International concern within Burma has couched the problems of displacement within general development modalities, while international attention along its borders has sought to contain displacement. With the exception of several recent initiatives, few approaches have gone beyond assistance and engaged in the prevention or protection of the displaced.

DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex.

PubMed

Ketterer, Philip; Ananth, Adithya N; Laman Trip, Diederik S; Mishra, Ankur; Bertosin, Eva; Ganji, Mahipal; van der Torre, Jaco; Onck, Patrick; Dietz, Hendrik; Dekker, Cees

2018-03-02

The nuclear pore complex (NPC) is the gatekeeper for nuclear transport in eukaryotic cells. A key component of the NPC is the central shaft lined with intrinsically disordered proteins (IDPs) known as FG-Nups, which control the selective molecular traffic. Here, we present an approach to realize artificial NPC mimics that allows controlling the type and copy number of FG-Nups. We constructed 34 nm-wide 3D DNA origami rings and attached different numbers of NSP1, a model yeast FG-Nup, or NSP1-S, a hydrophilic mutant. Using (cryo) electron microscopy, we find that NSP1 forms denser cohesive networks inside the ring compared to NSP1-S. Consistent with this, the measured ionic conductance is lower for NSP1 than for NSP1-S. Molecular dynamics simulations reveal spatially varying protein densities and conductances in good agreement with the experiments. Our technique provides an experimental platform for deciphering the collective behavior of IDPs with full control of their type and position.

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

PubMed

Zerze, Gül H; Miller, Cayla M; Granata, Daniele; Mittal, Jeetain

2015-06-09

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data.

Carbonate in Comets: A Comparison of Comets 1P/Halley, 9P/Temple 1, and 81P/Wild 2

NASA Technical Reports Server (NTRS)

Flynn, G. J.; Leroux, H.; Tomeoka, K.; Tomioka, N.; Ohnishi, I.; Mikouchi, T.; Wirick, S.; Keller, L. P.; Jacobsen, C.; Sanford, S. A.

2008-01-01

Comets are generally believed to have formed in a cold region, trapping in the cometary ices the original low-temperature condensate grains of our Solar System. These grains would have been preserved in cold-storage, at a temperature below the freezing point of CO2, for the last 4.5+ billion years. Carbonates are common in hydrous meteorites and hydrous interplanetary dust particles (IDPs), where they are believed to have formed by parent-body aqueous processing. Since simple models of cometary evolution involve no aqueous processing, carbonates were generally presumed not to occur in comets. However, Toppani et al. [1] have performed experiments that indicate carbonate can be formed by non-equilibrium condensation in circumstellar environments where water is present as a vapor, not as a liquid. This suggests carbonate might have condensed in cold regions of the Solar Nebula, and might be present in comets.

The REFANI-S study protocol: a non-randomised cluster controlled trial to assess the role of an unconditional cash transfer, a non-food item kit, and free piped water in reducing the risk of acute malnutrition among children aged 6-59 months living in camps for internally displaced persons in the Afgooye corridor, Somalia.

PubMed

Jelle, Mohamed; Grijalva-Eternod, Carlos S; Haghparast-Bidgoli, Hassan; King, Sarah; Cox, Cassy L; Skordis-Worrall, Jolene; Morrison, Joanna; Colbourn, Timothy; Fottrell, Edward; Seal, Andrew J

2017-07-06

The prevalence of acute malnutrition is often high in emergency-affected populations and is associated with elevated mortality risk and long-term health consequences. Increasingly, cash transfer programmes (CTP) are used instead of direct food aid as a nutritional intervention, but there is sparse evidence on their nutritional impact. We aim to understand whether CTP reduces acute malnutrition and its known risk factors. A non-randomised, cluster-controlled trial will assess the impact of an unconditional cash transfer of US$84 per month for 5 months, a single non-food items kit, and free piped water on the risk of acute malnutrition in children, aged 6-59 months. The study will take place in camps for internally displaced persons (IDP) in peri-urban Mogadishu, Somalia. A cluster will consist of one IDP camp and 10 camps will be allocated to receive the intervention based on vulnerability targeting criteria. The control camps will then be selected from the same geographical area. Needs assessment data indicates small differences in vulnerability between camps. In each trial arm, 120 households will be randomly sampled and two detailed household surveys will be implemented at baseline and 3 months after the initiation of the cash transfer. The survey questionnaire will cover risk factors for malnutrition including household expenditure, assets, food security, diet diversity, coping strategies, morbidity, WASH, and access to health care. A community surveillance system will collect monthly mid-upper arm circumference measurements from all children aged 6-59 months in the study clusters to assess the incidence of acute malnutrition over the duration of the intervention. Process evaluation data will be compiled from routine quantitative programme data and primary qualitative data collected using key informant interviews and focus group discussions. The UK Department for International Development will provide funding for this study. The European Civil Protection and Humanitarian Aid Operations will fund the intervention. Concern Worldwide will implement the intervention as part of their humanitarian programming. This non-randomised cluster controlled trial will provide needed evidence on the role of unconditional CTP in reducing the risk of acute malnutrition among IDP in this context. ISRCTN29521514 . Registered 19 January 2016.

Possible Gems and Ultra-Fine Grained Polyphase Units in Comet Wild 2.

NASA Technical Reports Server (NTRS)

Gainsforth, Z.; Butterworth, A. L.; Jilly-Rehak, C. E.; Westphal, A. J.; Brownlee, D. E.; Joswiak, D.; Ogliore, R. C.; Zolensky, M. E.; Bechtel, H. A.; Ebel, D. S.;

The PMDP Roadmap

NASA Technical Reports Server (NTRS)

2004-01-01

NASA's complex and highly technical missions rely on effective project teams and managers. Since 1993, through its Project Management Development Process (PMDP), the Academy of Program and Project Leadership (APPL) has offered direction to the Agency's project practitioners as they advance in their careers. PMDP helps identify and sequence professional experiences, courses, and other project-based learning experiences that support individual career goals and center activities by outlining competencies at four levels of development. The result is that PMDP provides NASA project practitioners with a road map to the knowledge and competencies appropriate for their job and the jobs to which they aspire. Plus, new this year, APPL has rolled out its electronic Project Management Development Process (ePMDP) tool, a learning management system that includes a dynamic presentation of the PMDP levels, competency areas, competency organizational structures, Individual Development Plans (IDP), and online PMDP enrollment. APPL's website, www.appl.nasa.gov, provides access to ePMDP as well as other online resources for NASA practitioners enrolled in the Project Management Development Process.

OTOTOXICITY OF 3,3'-IMINODIPROPIONITRILE: FUNCTIONAL AND MORPHOLOGICAL EVIDENCE OF COCHLEAR DAMAGE

EPA Science Inventory

Previous reports suggested that IDPN may be ototoxic (Wolff et al. 1977; Crofton and Knight, 1991). The purpose of this research was to investigate the ototoxicity of IDPN using behavioral, physiological and morphological approaches. Three groups of adult rats were exposed to IDP...

Assisting Groundwater Exploration for Refugee/IDP Camps by Remote Sensing and GIS

NASA Astrophysics Data System (ADS)

Wendt, Lorenz; Robl, Jörg; Hilberg, Sylke; Braun, Andreas; Rogenhofer, Edith; Dirnberger, Daniel; Strasser, Thomas; Füreder, Petra; Lang, Stefan

2015-04-01

Refugee camps and camps of internally displaced people (IDP) often form spontaneously or have to be established rapidly in remote, rural areas, where little is known about the hydrogeological situation. This requires a rapid assessment of the availability of groundwater to enable humanitarian organisations like Médecins Sans Frontières (MSF) to supply the camp population with sufficient potable water. Within the project EO4HumEn, hydrogeological reconnaissance maps are produced for MSF by integrating remote sensing data like SRTM, Landsat, ASTER, optical very-high resolution (VHR) imagery, and SAR data. Depending on the specific situation of the camps, these maps contain topography, permanent and temporary water bodies, hard rock outcrops and their geological variability, locations of existing boreholes and wells (if available), potential contamination sources, roads and obstacles (e.g. swampland). In areas characterized by unconsolidated sediments, specific landforms like alluvial fans, meanders, levees, deltas or beach ridges are identified. Here, the reconnaissance map can be sufficient to plan drill sites for groundwater abstraction. In hard rock areas, the lithology is determined, if the vegetation cover allows it. Fractures, faults and karst features are mapped to resolve the structural setting. Anomalous vegetation patterns are interpreted in terms of near-surface groundwater. The maps provide an overview of the camp surroundings, and allow the field hydrogeologists to focus their investigations on the most promising locations. The maps are complemented by a literature review on geological maps, articles and reports available for the area of interest. Assisting groundwater exploration by remote sensing data analysis is not a new development, but it has not been widely adopted by the humanitarian community as interfaces between humanitarian organisations and GI-scientists were missing. EO4HumEn fills this gap by a strong interdisciplinary cooperation between MSF, GI-scientists and geologists. This allows exploiting the potential of remote sensing and in particular of the freely available datasets (SRTM, Landsat, Sentinel 1+2) for the water supply of refugee/IDP camps, and to receive feedback on the validity of the delivered map products. EO4HumEn is funded by the Austrian Research Promotion Agency (EO-based services to support humanitarian operations: monitoring population and natural resources in refugee/IDP camps; FFG, ASAP 9, Nr 840081). Besides hydrogeological assessments, further products and services developed in EO4HumEn comprise the estimation and monitoring of camp population numbers by semi-automatically extracting dwellings from VHR imagery using object-based image analysis (OBIA), and the monitoring of changes of the environment in the vicinity of camps.

Enhancing the Capacity of Policy-Makers to Develop Evidence-Informed Policy Brief on Infectious Diseases of Poverty in Nigeria

PubMed Central

Uneke, Chigozie Jesse; Ezeoha, Abel Ebeh; Uro-Chukwu, Henry; Ezeonu, Chinonyelum Thecla; Ogbu, Ogbonnaya; Onwe, Friday; Edoga, Chima

2015-01-01

Background: The lack of effective use of research evidence in policy-making is a major challenge in most low- and middle-income countries (LMICs). There is need to package research data into effective policy tools that will help policy-makers to make evidence-informed policy regarding infectious diseases of poverty (IDP). The objective of this study was to assess the usefulness of training workshops and mentoring to enhance the capacity of Nigerian health policy-makers to develop evidence-informed policy brief on the control of IDP. Methods: A modified "before and after" intervention study design was used in which outcomes were measured on the target participants both before the intervention is implemented and after. A 4-point Likert scale according to the degree of adequacy; 1 = "grossly inadequate," 4 = "very adequate" was employed. The main parameter measured was participants’ perceptions of their own knowledge/understanding. This study was conducted at subnational level and the participants were the career health policy-makers drawn from Ebonyi State in the South-Eastern Nigeria. A one-day evidence-to-policy workshop was organized to enhance the participants’ capacity to develop evidence-informed policy brief on IDP in Ebonyi State. Topics covered included collaborative initiative; preparation and use of policy briefs; policy dialogue; ethics in health policy-making; and health policy and politics. Results: The preworkshop mean of knowledge and capacity ranged from 2.49-3.03, while the postworkshop mean ranged from 3.42–3.78 on 4-point scale. The percentage increase in mean of knowledge and capacity at the end of the workshop ranged from 20.10%–45%. Participants were divided into 3 IDP mentorship groups (malaria, schistosomiasis, lymphatic filariasis [LF]) and were mentored to identify potential policy options/recommendations for control of the diseases for the policy briefs. These policy options were subjected to research evidence synthesis by each group to identify the options that have the support of research evidence (mostly systematic reviews) from PubMed, Cochrane database and Google Scholar. After the evidence synthesis, five policy options were selected out of 13 for malaria, 3 out of 10 for schistosomiasis and 5 out of 11 for LF. Conclusion: The outcome suggests that an evidence-to-policy capacity enhancement workshop combined with a mentorship programme can improve policy-makers’ capacity for evidence-informed policy-making (EIP). PMID:26340489

The impact of post-election violence on HIV and other clinical services and on mental health-Kenya, 2008.

PubMed

Bamrah, Sapna; Mbithi, Agneta; Mermin, Jonathan H; Boo, Thomas; Bunnell, Rebecca E; Sharif, Sk; Cookson, Susan Temporado

2013-02-01

In December 2007, civil disruption and violence erupted in Kenya following national elections, displacing 350,000 people and affecting supply chains and services. The Kenyan government and partners were interested in assessing the extent of disruption in essential health services, especially HIV treatment. A two-stage cluster sampling for patients taking antiretroviral therapy (ART) was implemented ten weeks after elections, March 10-21, 2008, at twelve health facilities providing ART randomly selected in each of the three provinces most affected by post-election disruption-Rift Valley, Nyanza, and Central Provinces. Convenience samples of patients with tuberculosis, hypertension, or diabetes were also interviewed from the same facilities. Finally, a convenience sampling of internally displaced persons (IDPs) in the three provinces was conducted. Three hundred thirty-six IDPs in nine camps and 1,294 patients in 35 health facilities were interviewed. Overall, nine percent of patients reported having not returned to their routine health care facility; 9%-25% (overall 16%) reported a temporary inability for themselves or their children to access care at some point during January-February 2008. Less than 15% of patients on long-term therapies for HIV, tuberculosis, diabetes, or hypertension had treatment interruptions compared with 2007. The proportion of tuberculosis patients receiving a ≥45-day supply of medication increased from five percent in November 2007 to 69% in December 2007. HIV testing decreased in January 2008 compared with November 2007 among women in labor wards and among persons tested through voluntary counseling and testing services in Nyanza and Rift Valley Provinces. Patients and their family members witnessed violence, especially in Nyanza and Rift Valley Provinces (54%-59%), but few patients (2.5%-14%, 10% overall) personally experienced violence. More IDPs reported witnessing (80%) or personally experiencing (38%) violence than did patients. About half of patients and three-quarters of IDPs interviewed had anxiety or depression symptoms during the four weeks before the assessment. There was no association among patients between the presence of HIV, tuberculosis, diabetes, and hypertension and the prevalence of anxiety or depression symptoms. More than 85% of patients in highly affected provinces avoided treatment interruptions; this may be in part related to practitioners anticipating potential disruption and providing patients with medications for an extended period. During periods of similar crisis, anticipating potential limitations on medication access and increased mental health needs could potentially prevent negative health impacts.

Enhancing the Capacity of Policy-Makers to Develop Evidence-Informed Policy Brief on Infectious Diseases of Poverty in Nigeria.

PubMed

Uneke, Chigozie Jesse; Ezeoha, Abel Ebeh; Uro-Chukwu, Henry; Ezeonu, Chinonyelum Thecla; Ogbu, Ogbonnaya; Onwe, Friday; Edoga, Chima

2015-05-20

The lack of effective use of research evidence in policy-making is a major challenge in most low- and middle-income countries (LMICs). There is need to package research data into effective policy tools that will help policy-makers to make evidence-informed policy regarding infectious diseases of poverty (IDP). The objective of this study was to assess the usefulness of training workshops and mentoring to enhance the capacity of Nigerian health policy-makers to develop evidence-informed policy brief on the control of IDP. A modified "before and after" intervention study design was used in which outcomes were measured on the target participants both before the intervention is implemented and after. A 4-point Likert scale according to the degree of adequacy; 1 = "grossly inadequate," 4 = "very adequate" was employed. The main parameter measured was participants' perceptions of their own knowledge/understanding. This study was conducted at subnational level and the participants were the career health policy-makers drawn from Ebonyi State in the South-Eastern Nigeria. A one-day evidence-to-policy workshop was organized to enhance the participants' capacity to develop evidence-informed policy brief on IDP in Ebonyi State. Topics covered included collaborative initiative; preparation and use of policy briefs; policy dialogue; ethics in health policy-making; and health policy and politics. The preworkshop mean of knowledge and capacity ranged from 2.49-3.03, while the postworkshop mean ranged from 3.42-3.78 on 4-point scale. The percentage increase in mean of knowledge and capacity at the end of the workshop ranged from 20.10%-45%. Participants were divided into 3 IDP mentorship groups (malaria, schistosomiasis, lymphatic filariasis [LF]) and were mentored to identify potential policy options/recommendations for control of the diseases for the policy briefs. These policy options were subjected to research evidence synthesis by each group to identify the options that have the support of research evidence (mostly systematic reviews) from PubMed, Cochrane database and Google Scholar. After the evidence synthesis, five policy options were selected out of 13 for malaria, 3 out of 10 for schistosomiasis and 5 out of 11 for LF. The outcome suggests that an evidence-to-policy capacity enhancement workshop combined with a mentorship programme can improve policy-makers' capacity for evidence-informed policy-making (EIP). © 2015 by Kerman University of Medical Sciences.

Psychometric properties and reliability of the Assessment Screen to Identify Survivors Toolkit for Gender Based Violence (ASIST-GBV): results from humanitarian settings in Ethiopia and Colombia.

PubMed

Vu, Alexander; Wirtz, Andrea; Pham, Kiemanh; Singh, Sonal; Rubenstein, Leonard; Glass, Nancy; Perrin, Nancy

2016-01-01

Refugees and internally displaced persons who are affected by armed-conflict are at increased vulnerability to some forms of sexual violence or other types of gender-based violence. A validated, brief and easy-to-administer screening tool will help service providers identify GBV survivors and refer them to appropriate GBV services. To date, no such GBV screening tool exists. We developed the 7-item ASIST-GBV screening tool from qualitative research that included individual interviews and focus groups with GBV refugee and IDP survivors. This study presents the psychometric properties of the ASIST-GBV with female refugees living in Ethiopia and IDPs in Colombia. Several strategies were used to validate ASIST-GBV, including a 3 month implementation to validate the brief screening tool with women/girls seeking health services, aged ≥15 years in Ethiopia (N = 487) and female IDPs aged ≥ 18 years in Colombia (N = 511). High proportions of women screened positive for past-year GBV according to the ASIST-GBV: 50.6 % in Ethiopia and 63.4 % in Colombia. The factor analysis identified a single dimension, meaning that all items loaded on the single factor. Cronbach's α = 0.77. A 2-parameter logistic IRT model was used for estimating the precision and discriminating power of each item. Item difficulty varied across the continuum of GBV experiences in the following order (lowest to highest): threats of violence (0.690), physical violence (1.28), forced sex (2.49), coercive sex for survival (2.25), forced marriage (3.51), and forced pregnancy (6.33). Discrimination results showed that forced pregnancy was the item with the strongest ability to discriminate between different levels of GBV. Physical violence and forced sex also have higher levels of discrimination with threats of violence discriminating among women at the low end of the GBV continuum and coercive sex for survival among women at the mid-range of the continuum. The findings demonstrate that the ASIST-GBV has strong psychometric properties and good reliability. The tool can be used to screen and identify female GBV survivors confidentially and efficiently among IDPs in Colombia and refugees in Ethiopia. Early identification of GBV survivors can enable safety planning, early referral for treatment, and psychosocial support to prevent long-term harmful consequence of GBV.

Operationalizing a Research Sensor: MODIS to VIIRS

NASA Astrophysics Data System (ADS)

Grant, K. D.; Miller, S. W.; Puschell, J.

2012-12-01

The National Oceanic and Atmospheric Administration (NOAA) and NASA are jointly acquiring the next-generation civilian environmental satellite system: the Joint Polar Satellite System (JPSS). JPSS will replace the afternoon orbit component and ground processing system of the current Polar-orbiting Operational Environmental Satellites (POES) managed by NOAA. The JPSS satellite will carry a suite of sensors designed to collect meteorological, oceanographic, climatological, and solar-geophysical observations of the earth, atmosphere, and space. The primary sensor for the JPSS mission is the Visible/Infrared Imager Radiometer Suite (VIIRS) developed by Raytheon Space and Airborne Systems (SAS). The ground processing system for the JPSS mission is known as the Common Ground System (JPSS CGS), and consists of a Command, Control, and Communications Segment (C3S) and the Interface Data Processing Segment (IDPS) which are both developed by Raytheon Intelligence and Information Systems (IIS). The Moderate Resolution Imaging Spectroradiometer (MODIS) was developed by Raytheon SAS for the NASA Earth Observing System (EOS) as a research instrument to capture data in 36 spectral bands, ranging in wavelength from 0.4 μm to 14.4 μm and at varying spatial resolutions (2 bands at 250 m, 5 bands at 500 m and 29 bands at 1 km). MODIS data provides unprecedented insight into large-scale Earth system science questions related to cloud and aerosol characteristics, surface emissivity and processes occurring in the oceans, on land, and in the lower atmosphere. MODIS has flown on the EOS Terra satellite since 1999 and on the EOS Aqua satellite since 2002 and provided excellent data for scientific research and operational use for more than a decade. The value of MODIS-derived products for operational environmental monitoring motivated led to the development of an operational counterpart to MODIS for the next-generation polar-orbiting environmental satellites, the Visible/Infrared Imager Radiometer Suite (VIIRS). VIIRS combines the demonstrated high value spectral coverage and radiometric accuracy of MODIS with the legacy spectral bands and radiometric accuracy of the Advanced Very High Resolution Radiometer (AVHRR) and the high spatial resolution (0.75 km) of the Operational Linescan System (OLS). Except for MODIS bands designed for deriving vertical temperature and humidity structure in the atmosphere, VIIRS uses identical or very similar bands from MODIS that have the most interest and usefulness to operational customers in NOAA, the USAF and the USN. The development of VIIRS and JPSS reaps the benefit of investments in MODIS and the NASA EOS and the early development of operational algorithms by NOAA and DoD using MODIS data. This presentation will cover the different aspects of transitioning a research system into an operational system. These aspects include: (1) sensor (hardware & software) operationalization, (2) system performance operational factors, (3) science changes to algorithms reflecting the operational performance factors, and (4) the operationalization and incorporation of the science into a fully 24 x 7 production system, tasked with meeting stringent operational needs. Benefits of early operationalization are discussed along with suggested areas for improvement in this process that could benefit future work such as operationalizing Earth Science Decadal Survey missions.

78 FR 36223 - Extension and Redesignation of Syria for Temporary Protected Status

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-17

... toll-free number). Note: The phone number provided here is solely for questions regarding this TPS... Authorization Document FSA--Free Syrian Army Government--U.S. Government IDP--Internally Displaced Persons IJ.... In addition to the Free Syrian Army (FSA) and Syrian National Army, reports published in 2012...

Monkey primary somatosensory cortical activity during the early reaction time period differs with cues that guide movements

PubMed Central

Liu, Yu; Denton, John M.; Nelson, Randall J.

2009-01-01

Vibration-related neurons in monkey primary somatosensory cortex (SI) discharge rhythmically when vibratory stimuli are presented. It remains unclear how functional information carried by vibratory inputs is coded in rhythmic neuronal activity. In the present study, we compared neuronal activity during wrist movements in response to two sets of cues. In the first, movements were guided by vibratory cue only (VIB trials). In the second, movements were guided by simultaneous presentation of both vibratory and visual cues (COM trials). SI neurons were recorded extracellularly during both wrist extensions and flexions. Neuronal activity during the instructed delay period (IDP) and the early reaction time period (RTP) were analyzed. A total of 96 cases from 48 neurons (each neuron contributed two cases, one each for extension and flexion) showed significant vibration entrainment during the early RTPs, as determined by circular statistics (Rayleigh test). Of these, 50 cases had cutaneous (CUTA) and 46 had deep (DEEP) receptive fields. The CUTA neurons showed lower firing rates during the IDPs and greater firing rate changes during the early RTPs when compared with the DEEP neurons. The CUTA neurons also demonstrated decreases in activity entrainment during VIB trials when compared with COM trials. For the DEEP neurons, the difference of entrainment between VIB and COM trials was not statistically significant. The results suggest that somatic vibratory input is coded by both the firing rate and the activity entrainment of the CUTA neurons in SI. The results also suggest that when vibratory inputs are required for successful task completion, the activity of the CUTA neurons increases but the entrainment degrades. The DEEP neurons may be tuned before movement initiation for processing information encoded by proprioceptive afferents. PMID:18288475

Promoting Evidence to Policy Link on the Control of Infectious Diseases of Poverty in Nigeria: Outcome of A Multi-Stakeholders Policy Dialogue

PubMed Central

Uneke, Chigozie Jesse; Ebeh Ezeoha, Abel; Uro-Chukwu, Henry; Ezeonu, Chinonyelum Thecla; Ogbu, Ogbonnaya; Onwe, Friday; Edoga, Chima

2015-01-01

Background: In Nigeria, malaria, schistosomiasis and lymphatic filariasis are among infectious diseases of poverty (IDP) with severe health burden and require effective policy strategies for their control. In this study, we investigated the value of policy brief and policy dialogue as excellent policymaking mechanisms that enable policymakers to adapt effective evidence informed policy for IDP control. Methods: A policy brief was developed on the control of malaria, schistosomiasis and lymphatic filariasis and subjected to deliberations in a one-day multi-stakeholder policy dialogue held in Ebonyi State Nigeria. A modified cross sectional intervention study design was used in this investigation. Structured pre-tested questionnaires were used to evaluate the policy brief document and policy dialogue process at the end of the policy dialogue. Results: Forty-seven policymakers participated in the dialogue. An analysis of the response on the policy brief regarding context, different features of the problem; policy options and key implementation considerations indicated the mean ratings (MNRs) mostly ranged from 6.40-6.85 on 7 point scale. The over-all assessment of the policy brief had MNR at 6.54. The analysis of the response on the policy dialogue regarding the level of priority of policy issue, opportunity to discuss different features of the problem and options for addressing the problem, and the MNRs mostly ranged from 6.50-6.82. The overall assessment of the policy dialogue had MNR at 6.72. Conclusion: Policy dialogues can allow research evidence to be considered together with views, experiences and tacit knowledge of policymakers and can enhance evidence-to-policy link. PMID:26290826

Cancer/Testis Antigens: “Smart” Biomarkers for Diagnosis and Prognosis of Prostate and Other Cancers

PubMed Central

Kulkarni, Prakash; Uversky, Vladimir N.

2017-01-01

A clinical dilemma in the management of prostate cancer (PCa) is to distinguish men with aggressive disease who need definitive treatment from men who may not require immediate intervention. Accurate prediction of disease behavior is critical because radical treatment is associated with high morbidity. Here, we highlight the cancer/testis antigens (CTAs) as potential PCa biomarkers. The CTAs are a group of proteins that are typically restricted to the testis in the normal adult but are aberrantly expressed in several types of cancers. Interestingly, >90% of CTAs are predicted to belong to the realm of intrinsically disordered proteins (IDPs), which do not have unique structures and exist as highly dynamic conformational ensembles, but are known to play important roles in several biological processes. Using prostate-associated gene 4 (PAGE4) as an example of a disordered CTA, we highlight how IDP conformational dynamics may regulate phenotypic heterogeneity in PCa cells, and how it may be exploited both as a potential biomarker as well as a promising therapeutic target in PCa. We also discuss how in addition to intrinsic disorder and post-translational modifications, structural and functional variability induced in the CTAs by alternate splicing represents an important feature that might have different roles in different cancers. Although it is clear that significant additional work needs to be done in the outlined direction, this novel concept emphasizing (multi)functionality as an important trait in selecting a biomarker underscoring the theranostic potential of CTAs that is latent in their structure (or, more appropriately, the lack thereof), and casts them as next generation or “smart” biomarker candidates. PMID:28362316

Slow-down or speed-up of inter- and intra-cluster diffusion of controversial knowledge in stubborn communities based on a small world network

NASA Astrophysics Data System (ADS)

Ausloos, Marcel

2015-06-01

Diffusion of knowledge is expected to be huge when agents are open minded. The report concerns a more difficult diffusion case when communities are made of stubborn agents. Communities having markedly different opinions are for example the Neocreationist and Intelligent Design Proponents (IDP), on one hand, and the Darwinian Evolution Defenders (DED), on the other hand. The case of knowledge diffusion within such communities is studied here on a network based on an adjacency matrix built from time ordered selected quotations of agents, whence for inter- and intra-communities. The network is intrinsically directed and not necessarily reciprocal. Thus, the adjacency matrices have complex eigenvalues; the eigenvectors present complex components. A quantification of the slow-down or speed-up effects of information diffusion in such temporal networks, with non-Markovian contact sequences, can be made by comparing the real time dependent (directed) network to its counterpart, the time aggregated (undirected) network, - which has real eigenvalues. In order to do so, small world networks which both contain an odd number of nodes are studied and compared to similar networks with an even number of nodes. It is found that (i) the diffusion of knowledge is more difficult on the largest networks; (ii) the network size influences the slowing-down or speeding-up diffusion process. Interestingly, it is observed that (iii) the diffusion of knowledge is slower in IDP and faster in DED communities. It is suggested that the finding can be "rationalized", if some "scientific quality" and "publication habit" is attributed to the agents, as common sense would guess. This finding offers some opening discussion toward tying scientific knowledge to belief.

Monkey primary somatosensory cortical activity during the early reaction time period differs with cues that guide movements.

PubMed

Liu, Yu; Denton, John M; Nelson, Randall J

2008-05-01

Vibration-related neurons in monkey primary somatosensory cortex (SI) discharge rhythmically when vibratory stimuli are presented. It remains unclear how functional information carried by vibratory inputs is coded in rhythmic neuronal activity. In the present study, we compared neuronal activity during wrist movements in response to two sets of cues. In the first, movements were guided by vibratory cue only (VIB trials). In the second, movements were guided by simultaneous presentation of both vibratory and visual cues (COM trials). SI neurons were recorded extracellularly during both wrist extensions and flexions. Neuronal activity during the instructed delay period (IDP) and the early reaction time period (RTP) were analyzed. A total of 96 cases from 48 neurons (each neuron contributed two cases, one each for extension and flexion) showed significant vibration entrainment during the early RTPs, as determined by circular statistics (Rayleigh test). Of these, 50 cases had cutaneous (CUTA) and 46 had deep (DEEP) receptive fields. The CUTA neurons showed lower firing rates during the IDPs and greater firing rate changes during the early RTPs when compared with the DEEP neurons. The CUTA neurons also demonstrated decreases in activity entrainment during VIB trials when compared with COM trials. For the DEEP neurons, the difference of entrainment between VIB and COM trials was not statistically significant. The results suggest that somatic vibratory input is coded by both the firing rate and the activity entrainment of the CUTA neurons in SI. The results also suggest that when vibratory inputs are required for successful task completion, the activity of the CUTA neurons increases but the entrainment degrades. The DEEP neurons may be tuned before movement initiation for processing information encoded by proprioceptive afferents.

MoRFPred-plus: Computational Identification of MoRFs in Protein Sequences using Physicochemical Properties and HMM profiles.

PubMed

Sharma, Ronesh; Bayarjargal, Maitsetseg; Tsunoda, Tatsuhiko; Patil, Ashwini; Sharma, Alok

2018-01-21

Intrinsically Disordered Proteins (IDPs) lack stable tertiary structure and they actively participate in performing various biological functions. These IDPs expose short binding regions called Molecular Recognition Features (MoRFs) that permit interaction with structured protein regions. Upon interaction they undergo a disorder-to-order transition as a result of which their functionality arises. Predicting these MoRFs in disordered protein sequences is a challenging task. In this study, we present MoRFpred-plus, an improved predictor over our previous proposed predictor to identify MoRFs in disordered protein sequences. Two separate independent propensity scores are computed via incorporating physicochemical properties and HMM profiles, these scores are combined to predict final MoRF propensity score for a given residue. The first score reflects the characteristics of a query residue to be part of MoRF region based on the composition and similarity of assumed MoRF and flank regions. The second score reflects the characteristics of a query residue to be part of MoRF region based on the properties of flanks associated around the given residue in the query protein sequence. The propensity scores are processed and common averaging is applied to generate the final prediction score of MoRFpred-plus. Performance of the proposed predictor is compared with available MoRF predictors, MoRFchibi, MoRFpred, and ANCHOR. Using previously collected training and test sets used to evaluate the mentioned predictors, the proposed predictor outperforms these predictors and generates lower false positive rate. In addition, MoRFpred-plus is a downloadable predictor, which makes it useful as it can be used as input to other computational tools. https://github.com/roneshsharma/MoRFpred-plus/wiki/MoRFpred-plus:-Download. Copyright © 2017 Elsevier Ltd. All rights reserved.

How to Design Buildings, Housing Estates and Towns So That Their Impact On the Environment Will Be Acceptable?

NASA Astrophysics Data System (ADS)

Majerska-Pałubicka, Beata

2017-10-01

Currently, there is a tendency in architecture to search for solutions implementing the assumptions of the sustainable development paradigm. A number of them are components of architecture, which in the future will certainly affect urban planning and architecture to a much greater extent. On the one hand, an issue of great significance is the need to integrate sustainable system elements with the spatial structure of environmentally friendly architectural facilities and complexes and to determine their influence on design solutions as well as the implementation, operation and recycling, while on the other hand, it is very important to solve the problem of how to design buildings, housing estates and towns so that their impact on the environment will be acceptable, i.e. will not exceed the possibilities of natural environment regeneration and, how to cooperate in interdisciplinary design teams to reach an agreement and acceptance so as to achieve harmony between the built and natural environment, which is a basis of sustainable development. In this broad interdisciplinary context an increasing importance is being attached to design strategies, systems of evaluating designs and buildings as well as tools to support integrated activities in the field of architectural design. The above topics are the subject of research presented in this paper. The basic research aim of the paper is: to look for a current method of solving design tasks within the framework of Integrated Design Process (IDP) using modern design tools and technical possibilities, in the context of sustainable development imperative, including, the optimisation of IDP design strategies regarding the assumptions of conscious creation of sustainable built environment, adjusted to Polish conditions. As a case study used examples of Scandinavian housing settlements, sustainable in a broad context.

The remote sensing image segmentation mean shift algorithm parallel processing based on MapReduce

NASA Astrophysics Data System (ADS)

Chen, Xi; Zhou, Liqing

2015-12-01

With the development of satellite remote sensing technology and the remote sensing image data, traditional remote sensing image segmentation technology cannot meet the massive remote sensing image processing and storage requirements. This article put cloud computing and parallel computing technology in remote sensing image segmentation process, and build a cheap and efficient computer cluster system that uses parallel processing to achieve MeanShift algorithm of remote sensing image segmentation based on the MapReduce model, not only to ensure the quality of remote sensing image segmentation, improved split speed, and better meet the real-time requirements. The remote sensing image segmentation MeanShift algorithm parallel processing algorithm based on MapReduce shows certain significance and a realization of value.

Method of Adjusting Acoustic Impedances for Impedance-Tunable Acoustic Segments

NASA Technical Reports Server (NTRS)

Jones, Kennie H (Inventor); Nark, Douglas M. (Inventor); Jones, Michael G. (Inventor); Parrott, Tony L. (Inventor); Lodding, Kenneth N. (Inventor)

2012-01-01

A method is provided for making localized decisions and taking localized actions to achieve a global solution. In an embodiment of the present invention, acoustic impedances for impedance-tunable acoustic segments are adjusted. A first acoustic segment through an N-th acoustic segment are defined. To start the process, the first acoustic segment is designated as a leader and a noise-reducing impedance is determined therefor. This is accomplished using (i) one or more metrics associated with the acoustic wave at the leader, and (ii) the metric(s) associated with the acoustic wave at the N-th acoustic segment. The leader, the N-th acoustic segment, and each of the acoustic segments exclusive of the leader and the N-th acoustic segment, are tuned to the noise-reducing impedance. The current leader is then excluded from subsequent processing steps. The designation of leader is then given one of the remaining acoustic segments, and the process is repeated for each of the acoustic segments through an (N-1)-th one of the acoustic segments.

Origin of cometary and chondritic refractory organics: Ion irradiation experiments

NASA Astrophysics Data System (ADS)

Quirico, E.; Faure, M.; Faure, A.; Baklouti, D.; Boduch, P.; Rothard, H.; Ballanzat, E.; Dartois, E.; Brunetto, R.; Bonal, L.; Beck, P.; Schmitt, B.; Duprat, J.; Engrand, C.

2017-09-01

The formation process of Refractory Organic matter present in chondrites and Interplanetary Dust Particles (IDPs) of cometary and asteroidal origin is a debated issue. Earlier studies have advocated a formation step in a hot environment, however the potential role of ion irradiation has been so far poorly constrained. We present here experimental simulations that address this issue, comprising thermal degradation and ion irradiation experiments conducted at GANIL (Caen France) and CSNSM (Orsay France). We show that unlike thermal reactions, ion irradiation might lead to ROM-like material under very stringent conditions on both the nuclear dose and the nature of precursor. These very narrow conditions suggest that forming ROM without any action of thermal reactions is extremely difficult in astrophysical environments, either ISM or the proto-solar disk.

On College Formation of Future Lawyers' Professional Readiness to Work in Social Welfare Institutions

ERIC Educational Resources Information Center

Nikitina, Natalya Ivanovna; Grebennikova, Veronica Mikhailovna; Nikishina, Irina Nikolaevna; Galkina, Tatyana Engersovna; Tolstikova, Svetlana Nikolaevna

2016-01-01

In Russia today, more than ever, various social welfare institutions (Centers for social services, Social assistance centers for families and children, Rehabilitation centers for disabled children and their families, Centers for work with refugees and IDPs, Centers of medico-social rehabilitation of military men, etc.) require legal profile…

An Autonomic Framework for Integrating Security and Quality of Service Support in Databases

ERIC Educational Resources Information Center

Alomari, Firas

2013-01-01

The back-end databases of multi-tiered applications are a major data security concern for enterprises. The abundance of these systems and the emergence of new and different threats require multiple and overlapping security mechanisms. Therefore, providing multiple and diverse database intrusion detection and prevention systems (IDPS) is a critical…

U.S. EPA, Pesticide Product Label, , 06/30/1976

EPA Pesticide Factsheets

2011-04-14

... l' -/VI' i'- I~Q !h(. ~"'cliL;t ~ (If do iln~,rt',J ",i',:'- If _d', r"'-l ,l't" ! 'l{- 1fl1() ;f,~ i)t lppwtt: lf1 t'lhltll)f I, ,'- A Hest '1I'dP) . It !, v' ·1''''' l!er)! ... I . " " A-Hest T ablf' ' " ...

Serpentine by Hydrogenation of Fe-rich Ferromagnesiosilica PCs in Aggregate IDPs

NASA Technical Reports Server (NTRS)

Rietmeijer, F. J. M.; Nuth, J. A., III

2001-01-01

Condensed hydrogen-bearing magnesiosilica smokes support that hydrogenation at H2/H2O ratios may lead to the formation of rare Fe-rich serpentine plus metallic iron in ferromagnesiosilica PCs with appropriate (Mg,Fe)/Si ratios that were acquired during their formation. Additional information is contained in the original extended abstract.

Enzymatic cycling method using creatine kinase to measure creatine by real-time detection.

PubMed

Ueda, Shigeru; Sakasegawa, Shin-Ichi

2016-08-01

We have developed a novel enzymatic cycling method that uses creatine kinase (CK) to measure creatine. The method takes advantage of the reversibility of the CK reaction in which the forward (creatine phosphate forming) and reverse reactions are catalyzed in the presence of an excess amount of ATP and IDP, respectively. Real-time detection was accomplished using ADP-dependent glucokinase (ADP-GK) together with glucose-6-phosphate dehydrogenase. ADP, one of the cycling reaction products, was distinguished from IDP by using the nucleotide selectivity of the ADP-GK. The increasing level of ADP was measured from the level of reduced NADP at 340 nm. The method is appropriate for an assay that requires high sensitivity because the rate of increase in absorbance at 340 nm is proportional to the amount of CK present in the reaction mix. We reasoned that the method with CK in combination with creatinine amidohydrolase could be used to assay creatinine, an important marker of kidney function. Our results confirmed the quantitative capability of the assay. Copyright © 2016 Elsevier Inc. All rights reserved.

Site-Specific Three-Color Labeling of α-Synuclein via Conjugation to Uniquely Reactive Cysteines during Assembly by Native Chemical Ligation.

PubMed

Lee, Taehyung C; Moran, Crystal R; Cistrone, Philip A; Dawson, Philip E; Deniz, Ashok A

2018-04-12

Single-molecule fluorescence is widely used to study conformational complexity in proteins, and has proven especially valuable with intrinsically disordered proteins (IDPs). Protein studies using dual-color single-molecule Förster resonance energy transfer (smFRET) are now quite common, but many could benefit from simultaneous measurement of multiple distances through multi-color labeling. Such studies, however, have suffered from limitations in site-specific incorporation of more than two dyes per polypeptide. Here we present a fully site-specific three-color labeling scheme for α-synuclein, an IDP with important putative functions and links to Parkinson disease. The convergent synthesis combines native chemical ligation with regiospecific cysteine protection of expressed protein fragments to permit highly controlled labeling via standard cysteine-maleimide chemistry, enabling more global smFRET studies. Furthermore, this modular approach is generally compatible with recombinant proteins and expandable to accommodate even more complex experiments, such as by labeling with additional colors. Copyright © 2018 Elsevier Ltd. All rights reserved.

Origins and Dynamics of Interplanetary Dust Particles

NASA Technical Reports Server (NTRS)

Dermott, Stanley F.

2005-01-01

This is a final report for research supported by the National Aeronautics and Space Administration issued through the Office of Space Science Planetary Geology and Geophysics Program, covering all relevant activities during its 3-year period of funding from 02/01/2002 through to 01/31/2005. The ongoing aim of the research supported through this grant, and now through a successor award, is to investigate the origin of interplanetary dust particles (IDPs) and their dynamical and collisional evolution, in order to: (1) understand the provenance of zodiacal cloud particles and their transport from their source regions to the inner solar system; (2) produce detailed models of the zodiacal cloud and its constituent components; (3) determine the origin of the dust particles accreted by the Earth; (4) ascertain the level of temporal variations in the dust environment of the inner solar system and the accretion rate of IDPs by the Earth, and evaluate potential effects on global climate; and to (5) exploit this research as a basis for interpreting the structure observed in exozodiacal clouds that may result from the collisional evolution of planetesimals and the presence of unseen planets.

Concentrated Solutions of Single-Chain Nanoparticles: A Simple Model for Intrinsically Disordered Proteins under Crowding Conditions.

PubMed

Moreno, Angel J; Lo Verso, Federica; Arbe, Arantxa; Pomposo, José A; Colmenero, Juan

2016-03-03

By means of large-scale computer simulations and small-angle neutron scattering (SANS), we investigate solutions of single-chain nanoparticles (SCNPs), covering the whole concentration range from infinite dilution to melt density. The analysis of the conformational properties of the SCNPs reveals that these synthetic nano-objects share basic ingredients with intrinsically disordered proteins (IDPs), as topological polydispersity, generally sparse conformations, and locally compact domains. We investigate the role of the architecture of the SCNPs in their collapse behavior under macromolecular crowding. Unlike in the case of linear macromolecules, which experience the usual transition from self-avoiding to Gaussian random-walk conformations, crowding leads to collapsed conformations of SCNPs resembling those of crumpled globules. This behavior is already found at volume fractions (about 30%) that are characteristic of crowding in cellular environments. The simulation results are confirmed by the SANS experiments. Our results for SCNPs--a model system free of specific interactions--propose a general scenario for the effect of steric crowding on IDPs: collapse from sparse conformations at high dilution to crumpled globular conformations in cell environments.

Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles

NASA Astrophysics Data System (ADS)

Wei, Ming-Tzo; Elbaum-Garfinkle, Shana; Holehouse, Alex S.; Chen, Carlos Chih-Hsiung; Feric, Marina; Arnold, Craig B.; Priestley, Rodney D.; Pappu, Rohit V.; Brangwynne, Clifford P.

2017-11-01

Many intracellular membraneless organelles form via phase separation of intrinsically disordered proteins (IDPs) or regions (IDRs). These include the Caenorhabditis elegans protein LAF-1, which forms P granule-like droplets in vitro. However, the role of protein disorder in phase separation and the macromolecular organization within droplets remain elusive. Here, we utilize a novel technique, ultrafast-scanning fluorescence correlation spectroscopy, to measure the molecular interactions and full coexistence curves (binodals), which quantify the protein concentration within LAF-1 droplets. The binodals of LAF-1 and its IDR display a number of unusual features, including 'high concentration' binodal arms that correspond to remarkably dilute droplets. We find that LAF-1 and other in vitro and intracellular droplets are characterized by an effective mesh size of ∼3-8 nm, which determines the size scale at which droplet properties impact molecular diffusion and permeability. These findings reveal how specific IDPs can phase separate to form permeable, low-density (semi-dilute) liquids, whose structural features are likely to strongly impact biological function.

Adherence to antiretroviral therapy and treatment outcomes among conflict-affected and forcibly displaced populations: a systematic review

PubMed Central

2012-01-01

Background Optimal adherence to highly active antiretroviral therapy (HAART) is required to promote viral suppression and to prevent disease progression and mortality. Forcibly displaced and conflict-affected populations may face challenges succeeding on HAART. We performed a systematic review of the literature on adherence to HAART and treatment outcomes in these groups, including refugees and internally-displaced persons (IDPs), assessed the quality of the evidence and suggest a future research program. Methods Medline, Embase, and Global Health databases for 1995–2011 were searched using the Ovid platform. A backward citation review of subsequent work that had cited the Ovid results was performed using the Web of Science database. ReliefWeb and Médecins Sans Frontières (MSF) websites were searched for additional grey literature. Results and conclusion We screened 297 records and identified 17 reports covering 15 quantitative and two qualitative studies from 13 countries. Three-quarters (11/15) of the quantitative studies were retrospective studies based on chart review; five studies included <100 clients. Adherence or treatment outcomes were reported in resettled refugees, conflict-affected persons, internally-displaced persons (IDPs), and combinations of refugees, IDPs and other foreign-born persons. The reviewed reports showed promise for conflict-affected and forcibly-displaced populations; the range of optimal adherence prevalence reported was 87–99.5%. Treatment outcomes, measured using virological, immunological and mortality estimates, were good in relation to non-affected groups. Given the diversity of settings where forcibly-displaced and conflict-affected persons access ART, further studies on adherence and treatment outcomes are needed to support scale-up and provide evidence-based justifications for inclusion of these vulnerable groups in national treatment plans. Future studies and program evaluations should focus on systematic monitoring of adherence and treatment interruptions by using facility-based pharmacy records, understanding threats to optimal adherence and timely linkage to care throughout the displacement cycle, and testing interventions designed to support adherence and treatment outcomes in these settings. PMID:23110782

Application of an alkylammonium method for characterization of phyllosilicates in CI chondrites

NASA Technical Reports Server (NTRS)

Golden, D. C.; Ming, D. W.; Zolensky, M. E.; Yang, S. V.

1994-01-01

Many meteorites and interplanetary dust particles (IDP's) with primitive compositions contain significant amounts of phyllosilicates, which are generally interpreted as evidence of protoplanetary aqueous alteration at an early period in the solar system. These meteorites are chondrites of the carbonaceous and ordinary varieties. Characterization of phyllosilicates in these materials is important because of the important physico-chemical information they hold, e.g., from well characterized phyllosilicates, thermodynamic stability relations and hence the conditions of formation of phyllosilicates in the parent body of the meteorite can be predicted. Although we are at a rudimentary level of understanding of the minerals resulting from the aqueous alteration in the early solar nebula, we know that the most common phyllosilicates present in chondritic extraterrestrial materials are serpentines, smectites, chlorites, and micas. The characterization of fine grained minerals in meteorites and IDP's rely heavily on electron beam instruments, especially transmission electron microscopy (TEM). Typically, phyllosilicates are identified by a combination of high resolution imaging of basal spacings, electron diffraction analysis, and chemical analysis. Smectites can be difficult to differentiate from micas because the smectites loose their interlayer water and the interlayers collapse to the same basal spacing as mica in the high vacuum of the TEM. In high-resolution TEM (HRTEM) images, smectite basal spacings vary from 1 nm up to 1.5 nm, while micas show 1 or 2 nm basal spacings. Not only is it difficult to differentiate smectites from micas, but there is no way of identifying different classes of smectites in meteorites and IDP's. To differentiate smectites from micas and also to recognize the charge differences among smectites, an alkylammonium method can be employed because the basal spacings of alkylammonium saturated smectites expand as a function of alkylamine chain length and the layer-charge density of the 2:1 expanding phyllosilicate, and the final product is significantly more stable under electron beam examination. Such a method was tested on standard clays and several meteorite samples using four alkylammonium salts.

The chromatin nuclear protein NUPR1L is intrinsically disordered and binds to the same proteins as its paralogue.

PubMed

Neira, José L; López, María Belén; Sevilla, Paz; Rizzuti, Bruno; Cámara-Artigas, Ana; Vidal, Miguel; Iovanna, Juan L

2018-06-20

NUPR1 is a protumoral multifunctional intrinsically disordered protein (IDP), which is activated during the acute phases of pancreatitis. It interacts with other IDPs such as prothymosin α, as well as with folded proteins such as the C-terminal region of RING1-B (C-RING1B) of the Polycomb complex; in all those interactions, residues around Ala33 and Thr68 (the "hot-spot" region) of NUPR1 intervene. Its paralogue, NUPR1L, is also expressed in response to DNA-damage, it is p53-regulated, and its expression down-regulates that of the NUPR1 gene. In this work, we characterized the conformational preferences of isolated NUPR1L and its possible interactions with the same molecular partners of NUPR1. Our results show that NUPR1L was an oligomeric IDP from pH 2.0 to 12.0, as judged by steady-state fluorescence, circular dichroism (CD), dynamic light scattering (DLS), 1D 1 H-NMR, and as indicated by structural modelling. However, in contrast to NUPR1, there was evidence of local helical- or turn-like structures; these structures were not rigid, as judged by the lack of sigmoidal behaviour in the chemical and thermal denaturation curves obtained by CD and fluorescence. Interestingly enough, NUPR1L interacted with prothymosin α and C-RING1B, and with a similar affinity to that of NUPR1 (in the low micromolar range). Moreover, NUPR1L hetero-associated with NUPR1 with an affinity of 0.4 μM, and interacted with the "hot-spot" region of NUPR1. Thus, we suggest that the regulation of NUPR1 gene by NUPR1L does not only happen at the DNA level, but it could also involve direct interactions with NUPR1 natural partners. ©2018 The Author(s).

Delivery of HIV care during the 2007 post-election crisis in Kenya: a case study analyzing the response of the Academic Model Providing Access to Healthcare (AMPATH) program

PubMed Central

2013-01-01

Background Widespread violence followed the 2007 presidential elections in Kenya resulting in the deaths of a reported 1,133 people and the displacement of approximately 660,000 others. At the time of the crisis the United States Agency for International Development-Academic Model Providing Access to Healthcare (USAID-AMPATH) Partnership was operating 17 primary HIV clinics in western Kenya and treating 59,437 HIV positive patients (23,437 on antiretroviral therapy (ART)). Methods This case study examines AMPATH’s provision of care and maintenance of patients on ART throughout the period of disruption. This was accomplished by implementing immediate interventions including rapid information dissemination through the media, emergency hotlines and community liaisons; organization of a Crisis Response leadership team; the prompt assembly of multidisciplinary teams to address patient care, including psychological support staff (in clinics and in camps for internally displaced persons (IDP)); and the use of the AMPATH Medical Records System to identify patients on ART who had missed clinic appointments. Results These interventions resulted in the opening of all AMPATH clinics within five days of their scheduled post-holiday opening dates, 23,949 patient visits in January 2008 (23,259 previously scheduled), uninterrupted availability of antiretrovirals at all clinics, treatment of 1,420 HIV patients in IDP camps, distribution of basic provisions, mobilization of outreach services to locate missing AMPATH patients and delivery of psychosocial support to 300 staff members and 632 patients in IDP camps. Conclusion Key lessons learned in maintaining the delivery of HIV care in a crisis situation include the importance of advance planning to develop programs that can function during a crisis, an emphasis on a rapid programmatic response, the ability of clinics to function autonomously, patient knowledge of their disease, the use of community and patient networks, addressing staff needs and developing effective patient tracking systems. PMID:24289095

Do Chinese Readers Follow the National Standard Rules for Word Segmentation during Reading?

PubMed Central

Liu, Ping-Ping; Li, Wei-Jun; Lin, Nan; Li, Xing-Shan

2013-01-01

We conducted a preliminary study to examine whether Chinese readers’ spontaneous word segmentation processing is consistent with the national standard rules of word segmentation based on the Contemporary Chinese language word segmentation specification for information processing (CCLWSSIP). Participants were asked to segment Chinese sentences into individual words according to their prior knowledge of words. The results showed that Chinese readers did not follow the segmentation rules of the CCLWSSIP, and their word segmentation processing was influenced by the syntactic categories of consecutive words. In many cases, the participants did not consider the auxiliary words, adverbs, adjectives, nouns, verbs, numerals and quantifiers as single word units. Generally, Chinese readers tended to combine function words with content words to form single word units, indicating they were inclined to chunk single words into large information units during word segmentation. Additionally, the “overextension of monosyllable words” hypothesis was tested and it might need to be corrected to some degree, implying that word length have an implicit influence on Chinese readers’ segmentation processing. Implications of these results for models of word recognition and eye movement control are discussed. PMID:23408981

Molecular Age-Related Changes in the Anterior Segment of the Eye.

PubMed

Hernandez-Zimbron, Luis Fernando; Gulias-Cañizo, Rosario; Golzarri, María F; Martínez-Báez, Blanca Elizabeth; Quiroz-Mercado, Hugo; Gonzalez-Salinas, Roberto

2017-01-01

To examine the current knowledge about the age-related processes in the anterior segment of the eye at a biological, clinical, and molecular level. We reviewed the available published literature that addresses the aging process of the anterior segment of the eye and its associated molecular and physiological events. We performed a search on PubMed, CINAHL, and Embase using the MeSH terms "eye," "anterior segment," and "age." We generated searches to account for synonyms of these keywords and MESH headings as follows: (1) "Eye" AND "ageing process" OR "anterior segment ageing" and (2) "Anterior segment" AND "ageing process" OR "anterior segment" AND "molecular changes" AND "age." Results . Among the principal causes of age-dependent alterations in the anterior segment of the eye, we found the mutation of the TGF- β gene and loss of autophagy in addition to oxidative stress, which contributes to the pathogenesis of degenerative diseases. In this review, we summarize the current knowledge regarding some of the molecular mechanisms related to aging in the anterior segment of the eye. We also introduce and propose potential roles of autophagy, an important mechanism responsible for maintaining homeostasis and proteostasis under stress conditions in the anterior segment during aging.

Cometary Evolution: Clues on Physical Properties from Chondritic Interplanetary Dust Particles

NASA Technical Reports Server (NTRS)

Rietmeijer, Frans J. M.; Mackinnon, Ian D. R.

1989-01-01

The degree of diversity or similarity detected in comets depends primarily on the lifetimes of the individual cometary nuclei at the time of analysis. It is inherent in our understanding of cometary orbital dynamics and the seminal model of comet origins by Oort that cometary evolution is the natural order of events in our Solar System. Thus, predictions of cometary behaviour in terms of bulk physical, mineralogical or chemical parameters should contain an appreciation of temporal variation(s). Previously, Rietmeijer and Mackinnon developed mineralogical bases for the chemical evolution of cometary nuclei primarily with regard to the predominantly silicate fraction of comet nuclei. We suggested that alteration of solids in cometary nuclei should be expected and that indications of likely reactants and products can be derived from judicious comparison with terrestrial diagenetic environments which include hydrocryogenic and low-temperature aqueous alterations. In a further development of this concept, Rietmeijer provides indirect evidence for the formation of sulfides and oxides in comet nuclei. Furthermore, Rietmeijer noted that timescales for hydrocryogenic and low-temperature reactions involving liquid water are probably adequate for relatively mature comets, e.g. P/comet Halley. In this paper, we will address the evolution of comet nuclei physical parameters such as solid particle grain size, porosity and density. In natural environments, chemical evolution (e.g. mineral reactions) is often accompanied by changes in physical properties. These concurrent changes are well-documented in the terrestrial geological literature, especially in studies of sediment diagenesis and we suggest that similar basic principles apply within the upper few meters of active comet nuclei. The database for prediction of comet nuclei physical parameters is, in principle, the same as used for the proposition of chemical evolution. We use detailed mineralogical studies of chondritic interplanetary dust particles (IDPS) as a guide to the likely constitution of mature comets traversing the inner Solar System. While there is, as yet, no direct proof that a specific sub-group or type of chondritic IDP is derived from a specific comet, it is clear that these particles are extraterrestrial in origin and that a certain portion of the interplanetary flux received by the Earth is cometary in origin. Two chondritic porous (CP) MPs, sample numbers W7010A2 and W7029Cl, from the Johnson Space Center Cosmic Dust Collection have been selected for this study of putative cometary physical parameters. This particular type of particle is considered a likely candidate for a cometary origin on the basis of mineralogy, bulk composition and morphology. While many IDPs have been subjected to intensive study over the past decade, we can develop a physical parameter model on only these two CP IDPs because few others have been studied in sufficient detail.

Computer-aided liver volumetry: performance of a fully-automated, prototype post-processing solution for whole-organ and lobar segmentation based on MDCT imaging.

PubMed

Fananapazir, Ghaneh; Bashir, Mustafa R; Marin, Daniele; Boll, Daniel T

2015-06-01

To evaluate the performance of a prototype, fully-automated post-processing solution for whole-liver and lobar segmentation based on MDCT datasets. A polymer liver phantom was used to assess accuracy of post-processing applications comparing phantom volumes determined via Archimedes' principle with MDCT segmented datasets. For the IRB-approved, HIPAA-compliant study, 25 patients were enrolled. Volumetry performance compared the manual approach with the automated prototype, assessing intraobserver variability, and interclass correlation for whole-organ and lobar segmentation using ANOVA comparison. Fidelity of segmentation was evaluated qualitatively. Phantom volume was 1581.0 ± 44.7 mL, manually segmented datasets estimated 1628.0 ± 47.8 mL, representing a mean overestimation of 3.0%, automatically segmented datasets estimated 1601.9 ± 0 mL, representing a mean overestimation of 1.3%. Whole-liver and segmental volumetry demonstrated no significant intraobserver variability for neither manual nor automated measurements. For whole-liver volumetry, automated measurement repetitions resulted in identical values; reproducible whole-organ volumetry was also achieved with manual segmentation, p(ANOVA) 0.98. For lobar volumetry, automated segmentation improved reproducibility over manual approach, without significant measurement differences for either methodology, p(ANOVA) 0.95-0.99. Whole-organ and lobar segmentation results from manual and automated segmentation showed no significant differences, p(ANOVA) 0.96-1.00. Assessment of segmentation fidelity found that segments I-IV/VI showed greater segmentation inaccuracies compared to the remaining right hepatic lobe segments. Automated whole-liver segmentation showed non-inferiority of fully-automated whole-liver segmentation compared to manual approaches with improved reproducibility and post-processing duration; automated dual-seed lobar segmentation showed slight tendencies for underestimating the right hepatic lobe volume and greater variability in edge detection for the left hepatic lobe compared to manual segmentation.

Segmentation of 3D ultrasound computer tomography reflection images using edge detection and surface fitting

NASA Astrophysics Data System (ADS)

Hopp, T.; Zapf, M.; Ruiter, N. V.

2014-03-01

An essential processing step for comparison of Ultrasound Computer Tomography images to other modalities, as well as for the use in further image processing, is to segment the breast from the background. In this work we present a (semi-) automated 3D segmentation method which is based on the detection of the breast boundary in coronal slice images and a subsequent surface fitting. The method was evaluated using a software phantom and in-vivo data. The fully automatically processed phantom results showed that a segmentation of approx. 10% of the slices of a dataset is sufficient to recover the overall breast shape. Application to 16 in-vivo datasets was performed successfully using semi-automated processing, i.e. using a graphical user interface for manual corrections of the automated breast boundary detection. The processing time for the segmentation of an in-vivo dataset could be significantly reduced by a factor of four compared to a fully manual segmentation. Comparison to manually segmented images identified a smoother surface for the semi-automated segmentation with an average of 11% of differing voxels and an average surface deviation of 2mm. Limitations of the edge detection may be overcome by future updates of the KIT USCT system, allowing a fully-automated usage of our segmentation approach.

On diamond, graphitic and amorphous carbons in primitive extraterrestrial solar system materials

NASA Technical Reports Server (NTRS)

Rietmeijer, Frans J. M.

1990-01-01

Carbon is among the most abundant elements in the universe and carbon chemistry in meteorites and comets is an important key to understanding many Solar System and interstellar processes. Yet, the mineralogical properties and interrelations between various structural forms of elemental carbon remain ambiguous. Crystalline elemental carbons include rhombohedral graphite, hexagonal graphite, cubic diamond, hexagonal diamond (i.e., lonsdaleite or carbon-2H) and chaoite. Elemental carbon also occurs as amorphous carbon and poorly graphitized (or turbostratic) carbon but of all the forms of elemental carbon only graphite is stable under physical conditions that prevail in small Solar System bodies and in the interstellar medium. The recent discovery of cubic diamond in carbonaceous chondrites and hexagonal diamond in chondritic interplanetary dust particles (IDPs) have created a renewed interest in the crystalline elemental carbons that were not formed by shock processes on a parent body. Another technique, Raman spectroscopy, confirms a widespread occurrence of disordered graphite in the Allende carbonaceous chondrite and in chondritic IDPs. Elemental carbons have also been identified by their characteristic K-edge features in electron energy loss spectra (EELS). However, the spectroscopic data do not necessarily coincide with those obtained by selected area electron diffraction (SAED). In order to interpret these data in terms of rational crystalline structures, it may be useful to consider the principles underlying electron diffraction and spectroscopic analyses. Electron diffraction depends on electron scattering, on the type of atom and the distance between atoms in a crystal lattice. Spectroscopic data are a function of the type of atom and the energy of bonds between atoms. Also, SAED is a bulk sampling technique when compared to techniques such as Raman spectroscopy or EELS. Thus, it appears that combined analyses provide contradictory results and that amorphous, or short-range ordered, carbon identified by conventional TEM imaging and SAED may show evidence for sp(3) bonds in EELS spectra. It is suggested that complex, nanometer-scale, mineralogical interrelations are common to all elemental carbons irrespective of their origin. The subsequent thermal history, or energy balance, will determine the ultimate microstructure.

Observations of Carbon Isotopic Fractionation in Interstellar Formaldehyde

NASA Technical Reports Server (NTRS)

Wirstrom, E. S.; Charnley, S. B.; Geppert, W. D.; Persson, C. M.

2012-01-01

Primitive Solar System materials (e.g. chondrites. IDPs, the Stardust sample) show large variations in isotopic composition of the major volatiles (H, C, N, and O ) even within samples, witnessing to various degrees of processing in the protosolar nebula. For ex ample. the very pronounced D enhancements observed in IDPs [I] . are only generated in the cold. dense component of the interstellar medium (ISM), or protoplanetary disks, through ion-molecule reactions in the presence of interstellar dust. If this isotopic anomaly has an interstellar origin, this leaves open the possibility for preservation of other isotopic signatures throughout the form ation of the Solar System. The most common form of carbon in the ISM is CO molecules, and there are two potential sources of C-13 fractionation in this reservoir: low temperature chemistry and selective photodissociation. While gas-phase chemistry in cold interstellar clouds preferentially incorporates C-13 into CO [2], the effect of self-shielding in the presence of UV radiation instead leads to a relative enhancement of the more abundant isotopologue, 12CO. Solar System organic material exhibit rather small fluctuations in delta C-13 as compared to delta N-15 and delta D [3][1], the reason for which is still unclear. However, the fact that both C-13 depleted and enhanced material exists could indicate an interstellar origin where the two fractionation processes have both played a part. Formaldehyde (H2CO) is observed in the gas-phase in a wide range of interstellar environments, as well as in cometary comae. It is proposed as an important reactant in the formation of more complex organic molecules in the heated environments around young stars, and formaldehyde polymers have been suggested as the common origin of chondritic insoluable organic matter (IOM) and cometary refractory organic solids [4]. The relatively high gas-phase abundance of H2CO observed in molecular clouds (10(exp- 9) - 10(exp- 8) relative to H2) makes it feasible to observe its less common isotopologues. As a step in our investigation of C-13 fractionation patterns in the ISM, we here present comparisons between observations of the C-13 fraction in formaldehyde, and chemical fractionation models.

Three-dimensional rendering of segmented object using matlab - biomed 2010.

PubMed

Anderson, Jeffrey R; Barrett, Steven F

2010-01-01

The three-dimensional rendering of microscopic objects is a difficult and challenging task that often requires specialized image processing techniques. Previous work has been described of a semi-automatic segmentation process of fluorescently stained neurons collected as a sequence of slice images with a confocal laser scanning microscope. Once properly segmented, each individual object can be rendered and studied as a three-dimensional virtual object. This paper describes the work associated with the design and development of Matlab files to create three-dimensional images from the segmented object data previously mentioned. Part of the motivation for this work is to integrate both the segmentation and rendering processes into one software application, providing a seamless transition from the segmentation tasks to the rendering and visualization tasks. Previously these tasks were accomplished on two different computer systems, windows and Linux. This transition basically limits the usefulness of the segmentation and rendering applications to those who have both computer systems readily available. The focus of this work is to create custom Matlab image processing algorithms for object rendering and visualization, and merge these capabilities to the Matlab files that were developed especially for the image segmentation task. The completed Matlab application will contain both the segmentation and rendering processes in a single graphical user interface, or GUI. This process for rendering three-dimensional images in Matlab requires that a sequence of two-dimensional binary images, representing a cross-sectional slice of the object, be reassembled in a 3D space, and covered with a surface. Additional segmented objects can be rendered in the same 3D space. The surface properties of each object can be varied by the user to aid in the study and analysis of the objects. This inter-active process becomes a powerful visual tool to study and understand microscopic objects.

12om Limited Objective Experiment #2: Final Results Summary and Recommendations

DTIC Science & Technology

2014-03-31

Acronym Definition ARP CD CF CFD CG CIM COA CONOPS CSE Dev DFATD DP DRDC FGS Gov HREC IDP KR LOE LOC MA MARS NASA TLX NGO OP OPP Ops ROC SA...weight Ratings (OPP Support) Ratings (IP) Ratings (CU) Ratings (CS) Ratings (Usability) Ratings (Training T/E) Ratings (Use T/E) NASA TLX Mental demand

The Howard University Program in Atmospheric Sciences (HUPAS): A Program Exemplifying Diversity and Opportunity

ERIC Educational Resources Information Center

Morris, Vernon R.; Joseph, Everette; Smith, Sonya; Yu, Tsann-wang

2012-01-01

This paper discusses experiences and lessons learned from developing an interdisciplinary graduate program (IDP) during the last 10 y: The Howard University Graduate Program in Atmospheric Sciences (HUPAS). HUPAS is the first advanced degree program in the atmospheric sciences, or related fields such as meteorology and earth system sciences,…

A fast and efficient segmentation scheme for cell microscopic image.

PubMed

Lebrun, G; Charrier, C; Lezoray, O; Meurie, C; Cardot, H

2007-04-27

Microscopic cellular image segmentation schemes must be efficient for reliable analysis and fast to process huge quantity of images. Recent studies have focused on improving segmentation quality. Several segmentation schemes have good quality but processing time is too expensive to deal with a great number of images per day. For segmentation schemes based on pixel classification, the classifier design is crucial since it is the one which requires most of the processing time necessary to segment an image. The main contribution of this work is focused on how to reduce the complexity of decision functions produced by support vector machines (SVM) while preserving recognition rate. Vector quantization is used in order to reduce the inherent redundancy present in huge pixel databases (i.e. images with expert pixel segmentation). Hybrid color space design is also used in order to improve data set size reduction rate and recognition rate. A new decision function quality criterion is defined to select good trade-off between recognition rate and processing time of pixel decision function. The first results of this study show that fast and efficient pixel classification with SVM is possible. Moreover posterior class pixel probability estimation is easy to compute with Platt method. Then a new segmentation scheme using probabilistic pixel classification has been developed. This one has several free parameters and an automatic selection must dealt with, but criteria for evaluate segmentation quality are not well adapted for cell segmentation, especially when comparison with expert pixel segmentation must be achieved. Another important contribution in this paper is the definition of a new quality criterion for evaluation of cell segmentation. The results presented here show that the selection of free parameters of the segmentation scheme by optimisation of the new quality cell segmentation criterion produces efficient cell segmentation.

Semi-automated Neuron Boundary Detection and Nonbranching Process Segmentation in Electron Microscopy Images

PubMed Central

Jurrus, Elizabeth; Watanabe, Shigeki; Giuly, Richard J.; Paiva, Antonio R. C.; Ellisman, Mark H.; Jorgensen, Erik M.; Tasdizen, Tolga

2013-01-01

Neuroscientists are developing new imaging techniques and generating large volumes of data in an effort to understand the complex structure of the nervous system. The complexity and size of this data makes human interpretation a labor-intensive task. To aid in the analysis, new segmentation techniques for identifying neurons in these feature rich datasets are required. This paper presents a method for neuron boundary detection and nonbranching process segmentation in electron microscopy images and visualizing them in three dimensions. It combines both automated segmentation techniques with a graphical user interface for correction of mistakes in the automated process. The automated process first uses machine learning and image processing techniques to identify neuron membranes that deliniate the cells in each two-dimensional section. To segment nonbranching processes, the cell regions in each two-dimensional section are connected in 3D using correlation of regions between sections. The combination of this method with a graphical user interface specially designed for this purpose, enables users to quickly segment cellular processes in large volumes. PMID:22644867

Integrated circuit layer image segmentation

NASA Astrophysics Data System (ADS)

Masalskis, Giedrius; Petrauskas, Romas

2010-09-01

In this paper we present IC layer image segmentation techniques which are specifically created for precise metal layer feature extraction. During our research we used many samples of real-life de-processed IC metal layer images which were obtained using optical light microscope. We have created sequence of various image processing filters which provides segmentation results of good enough precision for our application. Filter sequences were fine tuned to provide best possible results depending on properties of IC manufacturing process and imaging technology. Proposed IC image segmentation filter sequences were experimentally tested and compared with conventional direct segmentation algorithms.

Structural analysis of vibroacoustical processes

NASA Technical Reports Server (NTRS)

Gromov, A. P.; Myasnikov, L. L.; Myasnikova, Y. N.; Finagin, B. A.

1973-01-01

The method of automatic identification of acoustical signals, by means of the segmentation was used to investigate noises and vibrations in machines and mechanisms, for cybernetic diagnostics. The structural analysis consists of presentation of a noise or vibroacoustical signal as a sequence of segments, determined by the time quantization, in which each segment is characterized by specific spectral characteristics. The structural spectrum is plotted as a histogram of the segments, also as a relation of the probability density of appearance of a segment to the segment type. It is assumed that the conditions of ergodic processes are maintained.

Single-Molecule FISH Reveals Non-selective Packaging of Rift Valley Fever Virus Genome Segments

PubMed Central

Wichgers Schreur, Paul J.; Kortekaas, Jeroen

2016-01-01

The bunyavirus genome comprises a small (S), medium (M), and large (L) RNA segment of negative polarity. Although genome segmentation confers evolutionary advantages by enabling genome reassortment events with related viruses, genome segmentation also complicates genome replication and packaging. Accumulating evidence suggests that genomes of viruses with eight or more genome segments are incorporated into virions by highly selective processes. Remarkably, little is known about the genome packaging process of the tri-segmented bunyaviruses. Here, we evaluated, by single-molecule RNA fluorescence in situ hybridization (FISH), the intracellular spatio-temporal distribution and replication kinetics of the Rift Valley fever virus (RVFV) genome and determined the segment composition of mature virions. The results reveal that the RVFV genome segments start to replicate near the site of infection before spreading and replicating throughout the cytoplasm followed by translocation to the virion assembly site at the Golgi network. Despite the average intracellular S, M and L genome segments approached a 1:1:1 ratio, major differences in genome segment ratios were observed among cells. We also observed a significant amount of cells lacking evidence of M-segment replication. Analysis of two-segmented replicons and four-segmented viruses subsequently confirmed the previous notion that Golgi recruitment is mediated by the Gn glycoprotein. The absence of colocalization of the different segments in the cytoplasm and the successful rescue of a tri-segmented variant with a codon shuffled M-segment suggested that inter-segment interactions are unlikely to drive the copackaging of the different segments into a single virion. The latter was confirmed by direct visualization of RNPs inside mature virions which showed that the majority of virions lack one or more genome segments. Altogether, this study suggests that RVFV genome packaging is a non-selective process. PMID:27548280

Optimal segmentation and packaging process

DOEpatents

Kostelnik, Kevin M.; Meservey, Richard H.; Landon, Mark D.

1999-01-01

A process for improving packaging efficiency uses three dimensional, computer simulated models with various optimization algorithms to determine the optimal segmentation process and packaging configurations based on constraints including container limitations. The present invention is applied to a process for decontaminating, decommissioning (D&D), and remediating a nuclear facility involving the segmentation and packaging of contaminated items in waste containers in order to minimize the number of cuts, maximize packaging density, and reduce worker radiation exposure. A three-dimensional, computer simulated, facility model of the contaminated items are created. The contaminated items are differentiated. The optimal location, orientation and sequence of the segmentation and packaging of the contaminated items is determined using the simulated model, the algorithms, and various constraints including container limitations. The cut locations and orientations are transposed to the simulated model. The contaminated items are actually segmented and packaged. The segmentation and packaging may be simulated beforehand. In addition, the contaminated items may be cataloged and recorded.

Semi-Automated Neuron Boundary Detection and Nonbranching Process Segmentation in Electron Microscopy Images

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

Jurrus, Elizabeth R.; Watanabe, Shigeki; Giuly, Richard J.

2013-01-01

Neuroscientists are developing new imaging techniques and generating large volumes of data in an effort to understand the complex structure of the nervous system. The complexity and size of this data makes human interpretation a labor-intensive task. To aid in the analysis, new segmentation techniques for identifying neurons in these feature rich datasets are required. This paper presents a method for neuron boundary detection and nonbranching process segmentation in electron microscopy images and visualizing them in three dimensions. It combines both automated segmentation techniques with a graphical user interface for correction of mistakes in the automated process. The automated processmore » first uses machine learning and image processing techniques to identify neuron membranes that deliniate the cells in each two-dimensional section. To segment nonbranching processes, the cell regions in each two-dimensional section are connected in 3D using correlation of regions between sections. The combination of this method with a graphical user interface specially designed for this purpose, enables users to quickly segment cellular processes in large volumes.« less

Colour application on mammography image segmentation

NASA Astrophysics Data System (ADS)

Embong, R.; Aziz, N. M. Nik Ab.; Karim, A. H. Abd; Ibrahim, M. R.

2017-09-01

The segmentation process is one of the most important steps in image processing and computer vision since it is vital in the initial stage of image analysis. Segmentation of medical images involves complex structures and it requires precise segmentation result which is necessary for clinical diagnosis such as the detection of tumour, oedema, and necrotic tissues. Since mammography images are grayscale, researchers are looking at the effect of colour in the segmentation process of medical images. Colour is known to play a significant role in the perception of object boundaries in non-medical colour images. Processing colour images require handling more data, hence providing a richer description of objects in the scene. Colour images contain ten percent (10%) additional edge information as compared to their grayscale counterparts. Nevertheless, edge detection in colour image is more challenging than grayscale image as colour space is considered as a vector space. In this study, we implemented red, green, yellow, and blue colour maps to grayscale mammography images with the purpose of testing the effect of colours on the segmentation of abnormality regions in the mammography images. We applied the segmentation process using the Fuzzy C-means algorithm and evaluated the percentage of average relative error of area for each colour type. The results showed that all segmentation with the colour map can be done successfully even for blurred and noisy images. Also the size of the area of the abnormality region is reduced when compare to the segmentation area without the colour map. The green colour map segmentation produced the smallest percentage of average relative error (10.009%) while yellow colour map segmentation gave the largest percentage of relative error (11.367%).

Family Formation, Labor Market Experience, and the Wages of Married Women.

ERIC Educational Resources Information Center

Cogan, John F.; Berger, Franklin

The impact of the timing, spacing, and number of children on a married woman's wage growth over her life cycle was examined. The data used for the analysis were information pertaining to the labor market experience of women and the birth dates of their children, taken from the 1976 survey of the Michigan Panel Study of Income Dynamics (IDP). There…

Computational Amide I Spectroscopy for Refinement of Disordered Peptide Ensembles: Maximum Entropy and Related Approaches

NASA Astrophysics Data System (ADS)

Reppert, Michael; Tokmakoff, Andrei

The structural characterization of intrinsically disordered peptides (IDPs) presents a challenging biophysical problem. Extreme heterogeneity and rapid conformational interconversion make traditional methods difficult to interpret. Due to its ultrafast (ps) shutter speed, Amide I vibrational spectroscopy has received considerable interest as a novel technique to probe IDP structure and dynamics. Historically, Amide I spectroscopy has been limited to delivering global secondary structural information. More recently, however, the method has been adapted to study structure at the local level through incorporation of isotope labels into the protein backbone at specific amide bonds. Thanks to the acute sensitivity of Amide I frequencies to local electrostatic interactions-particularly hydrogen bonds-spectroscopic data on isotope labeled residues directly reports on local peptide conformation. Quantitative information can be extracted using electrostatic frequency maps which translate molecular dynamics trajectories into Amide I spectra for comparison with experiment. Here we present our recent efforts in the development of a rigorous approach to incorporating Amide I spectroscopic restraints into refined molecular dynamics structural ensembles using maximum entropy and related approaches. By combining force field predictions with experimental spectroscopic data, we construct refined structural ensembles for a family of short, strongly disordered, elastin-like peptides in aqueous solution.

Tick receptor for outer surface protein A from Ixodes ricinus — the first intrinsically disordered protein involved in vector-microbe recognition

NASA Astrophysics Data System (ADS)

Urbanowicz, Anna; Lewandowski, Dominik; Szpotkowski, Kamil; Figlerowicz, Marek

2016-04-01

The tick receptor for outer surface protein A (TROSPA) is the only identified factor involved in tick gut colonization by various Borrelia species. TROSPA is localized in the gut epithelium and can recognize and bind the outer surface bacterial protein OspA via an unknown mechanism. Based on earlier reports and our latest observations, we considered that TROSPA would be the first identified intrinsically disordered protein (IDP) involved in the interaction between a vector and a pathogenic microbe. To verify this hypothesis, we performed structural studies of a TROSPA mutant from Ixodes ricinus using both computational and experimental approaches. Irrespective of the method used, we observed that the secondary structure content of the TROSPA polypeptide chain is low. In addition, the collected SAXS data indicated that this protein is highly extended and exists in solution as a set of numerous conformers. These features are all commonly considered hallmarks of IDPs. Taking advantage of our SAXS data, we created structural models of TROSPA and proposed a putative mechanism for the TROSPA-OspA interaction. The disordered nature of TROSPA may explain the ability of a wide spectrum of Borrelia species to colonize the tick gut.

Structure-properties relationships of novel poly(carbonate-co-amide) segmented copolymers with polyamide-6 as hard segments and polycarbonate as soft segments

NASA Astrophysics Data System (ADS)

Yang, Yunyun; Kong, Weibo; Yuan, Ye; Zhou, Changlin; Cai, Xufu

2018-04-01

Novel poly(carbonate-co-amide) (PCA) block copolymers are prepared with polycarbonate diol (PCD) as soft segments, polyamide-6 (PA6) as hard segments and 4,4'-diphenylmethane diisocyanate (MDI) as coupling agent through reactive processing. The reactive processing strategy is eco-friendly and resolve the incompatibility between polyamide segments and PCD segments in preparation processing. The chemical structure, crystalline properties, thermal properties, mechanical properties and water resistance were extensively studied by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), Differential scanning calorimetry (DSC), Thermal gravity analysis (TGA), Dynamic mechanical analysis (DMA), tensile testing, water contact angle and water absorption, respectively. The as-prepared PCAs exhibit obvious microphase separation between the crystalline hard PA6 phase and amorphous PCD soft segments. Meanwhile, PCAs showed outstanding mechanical with the maximum tensile strength of 46.3 MPa and elongation at break of 909%. The contact angle and water absorption results indicate that PCAs demonstrate outstanding water resistance even though possess the hydrophilic surfaces. The TGA measurements prove that the thermal stability of PCA can satisfy the requirement of multiple-processing without decomposition.

GeoSegmenter: A statistically learned Chinese word segmenter for the geoscience domain

NASA Astrophysics Data System (ADS)

Huang, Lan; Du, Youfu; Chen, Gongyang

2015-03-01

Unlike English, the Chinese language has no space between words. Segmenting texts into words, known as the Chinese word segmentation (CWS) problem, thus becomes a fundamental issue for processing Chinese documents and the first step in many text mining applications, including information retrieval, machine translation and knowledge acquisition. However, for the geoscience subject domain, the CWS problem remains unsolved. Although a generic segmenter can be applied to process geoscience documents, they lack the domain specific knowledge and consequently their segmentation accuracy drops dramatically. This motivated us to develop a segmenter specifically for the geoscience subject domain: the GeoSegmenter. We first proposed a generic two-step framework for domain specific CWS. Following this framework, we built GeoSegmenter using conditional random fields, a principled statistical framework for sequence learning. Specifically, GeoSegmenter first identifies general terms by using a generic baseline segmenter. Then it recognises geoscience terms by learning and applying a model that can transform the initial segmentation into the goal segmentation. Empirical experimental results on geoscience documents and benchmark datasets showed that GeoSegmenter could effectively recognise both geoscience terms and general terms.

Nonparametric Bayesian Segmentation of a Multivariate Inhomogeneous Space-Time Poisson Process.

PubMed

Ding, Mingtao; He, Lihan; Dunson, David; Carin, Lawrence

2012-12-01

A nonparametric Bayesian model is proposed for segmenting time-evolving multivariate spatial point process data. An inhomogeneous Poisson process is assumed, with a logistic stick-breaking process (LSBP) used to encourage piecewise-constant spatial Poisson intensities. The LSBP explicitly favors spatially contiguous segments, and infers the number of segments based on the observed data. The temporal dynamics of the segmentation and of the Poisson intensities are modeled with exponential correlation in time, implemented in the form of a first-order autoregressive model for uniformly sampled discrete data, and via a Gaussian process with an exponential kernel for general temporal sampling. We consider and compare two different inference techniques: a Markov chain Monte Carlo sampler, which has relatively high computational complexity; and an approximate and efficient variational Bayesian analysis. The model is demonstrated with a simulated example and a real example of space-time crime events in Cincinnati, Ohio, USA.