Computational analyses of spectral trees from electrospray multi-stage mass spectrometry to aid metabolite identification.

PubMed

Cao, Mingshu; Fraser, Karl; Rasmussen, Susanne

2013-10-31

Mass spectrometry coupled with chromatography has become the major technical platform in metabolomics. Aided by peak detection algorithms, the detected signals are characterized by mass-over-charge ratio (m/z) and retention time. Chemical identities often remain elusive for the majority of the signals. Multi-stage mass spectrometry based on electrospray ionization (ESI) allows collision-induced dissociation (CID) fragmentation of selected precursor ions. These fragment ions can assist in structural inference for metabolites of low molecular weight. Computational investigations of fragmentation spectra have increasingly received attention in metabolomics and various public databases house such data. We have developed an R package "iontree" that can capture, store and analyze MS2 and MS3 mass spectral data from high throughput metabolomics experiments. The package includes functions for ion tree construction, an algorithm (distMS2) for MS2 spectral comparison, and tools for building platform-independent ion tree (MS2/MS3) libraries. We have demonstrated the utilization of the package for the systematic analysis and annotation of fragmentation spectra collected in various metabolomics platforms, including direct infusion mass spectrometry, and liquid chromatography coupled with either low resolution or high resolution mass spectrometry. Assisted by the developed computational tools, we have demonstrated that spectral trees can provide informative evidence complementary to retention time and accurate mass to aid with annotating unknown peaks. These experimental spectral trees once subjected to a quality control process, can be used for querying public MS2 databases or de novo interpretation. The putatively annotated spectral trees can be readily incorporated into reference libraries for routine identification of metabolites.

MetaNetter 2: A Cytoscape plugin for ab initio network analysis and metabolite feature classification.

PubMed

Burgess, K E V; Borutzki, Y; Rankin, N; Daly, R; Jourdan, F

2017-12-15

Metabolomics frequently relies on the use of high resolution mass spectrometry data. Classification and filtering of this data remain a challenging task due to the plethora of complex mass spectral artefacts, chemical noise, adducts and fragmentation that occur during ionisation and analysis. Additionally, the relationships between detected compounds can provide a wealth of information about the nature of the samples and the biochemistry that gave rise to them. We present a biochemical networking tool: MetaNetter 2 that is based on the original MetaNetter, a Cytoscape plugin that creates ab initio networks. The new version supports two major improvements: the generation of adduct networks and the creation of tables that map adduct or transformation patterns across multiple samples, providing a readout of compound relationships. We have applied this tool to the analysis of adduct patterns in the same sample separated under two different chromatographies, allowing inferences to be made about the effect of different buffer conditions on adduct detection, and the application of the chemical transformation analysis to both a single fragmentation analysis and an all-ions fragmentation dataset. Finally, we present an analysis of a dataset derived from anaerobic and aerobic growth of the organism Staphylococcus aureus demonstrating the utility of the tool for biological analysis. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Discrimination Between Peptide O-Sulfo- and O-Phosphotyrosine Residues by Negative Ion Mode Electrospray Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Edelson-Averbukh, Marina; Shevchenko, Andrej; Pipkorn, Rüdiger; Lehmann, Wolf D.

2011-12-01

Unambiguous differentiation between isobaric sulfated and phosphorylated tyrosine residues (sTyr and pTyr) of proteins by mass spectrometry is challenging, even using high resolution mass spectrometers. Here we show that upon negative ion mode collision-induced dissociation (CID), pTyr- and sTyr-containing peptides exhibit entirely different modification-specific fragmentation patterns leading to a rapid discrimination between the isobaric covalent modifications using the tandem mass spectral data. This study reveals that the ratio between the relative abundances of [M-H-80]- and [M-H-98]- fragment ions in ion-trap CID and higher energy collision dissociation (HCD) spectra of singly deprotonated +80 Da Tyr-peptides can be used as a reliable indication of the Tyr modification group nature. For multiply deprotonated +80 Da Tyr-peptides, CID spectra of sTyr- and pTyr-containing sequences can be readily distinguished based on the presence/absence of the [M-nH-79](n-1)- and [M-nH-79-NL]( n-1)- ( n = 2, 3) fragment ions (NL = neutral loss).

Prospects for quantifying structure, floristic composition and species richness of tropical forests

USGS Publications Warehouse

Gillespie, T.W.; Brock, J.; Wright, C.W.

2004-01-01

Airborne spectral and light detection and ranging (lidar) sensors have been used to quantify biophysical characteristics of tropical forests. Lidar sensors have provided high-resolution data on forest height, canopy topography, volume, and gap size; and provided estimates on number of strata in a forest, successional status of forests, and above-ground biomass. Spectral sensors have provided data on vegetation types, foliar biochemistry content of forest canopies, tree and canopy phenology, and spectral signatures for selected tree species. A number of advances are theoretically possible with individual and combined spectral and lidar sensors for the study of forest structure, floristic composition and species richness. Delineating individual canopies of over-storey trees with small footprint lidar and discrimination of tree architectural types with waveform distributions is possible and would provide scientists with a new method to study tropical forest structure. Combined spectral and lidar data can be used to identify selected tree species and identify the successional status of tropical forest fragments in order to rank forest patches by levels of species richness. It should be possible in the near future to quantify selected patterns of tropical forests at a higher resolution than can currently be undertaken in the field or from space. ?? 2004 Taylor and Francis Ltd.

Methodological aspects of an adaptive multidirectional pattern search to optimize speech perception using three hearing-aid algorithms

NASA Astrophysics Data System (ADS)

Franck, Bas A. M.; Dreschler, Wouter A.; Lyzenga, Johannes

2004-12-01

In this study we investigated the reliability and convergence characteristics of an adaptive multidirectional pattern search procedure, relative to a nonadaptive multidirectional pattern search procedure. The procedure was designed to optimize three speech-processing strategies. These comprise noise reduction, spectral enhancement, and spectral lift. The search is based on a paired-comparison paradigm, in which subjects evaluated the listening comfort of speech-in-noise fragments. The procedural and nonprocedural factors that influence the reliability and convergence of the procedure are studied using various test conditions. The test conditions combine different tests, initial settings, background noise types, and step size configurations. Seven normal hearing subjects participated in this study. The results indicate that the reliability of the optimization strategy may benefit from the use of an adaptive step size. Decreasing the step size increases accuracy, while increasing the step size can be beneficial to create clear perceptual differences in the comparisons. The reliability also depends on starting point, stop criterion, step size constraints, background noise, algorithms used, as well as the presence of drifting cues and suboptimal settings. There appears to be a trade-off between reliability and convergence, i.e., when the step size is enlarged the reliability improves, but the convergence deteriorates. .

Long-wave, infrared laser-induced breakdown (LIBS) spectroscopy emissions from energetic materials.

PubMed

Yang, Clayton S-C; Brown, Ei E; Hommerich, Uwe; Jin, Feng; Trivedi, Sudhir B; Samuels, Alan C; Snyder, A Peter

2012-12-01

Laser-induced breakdown spectroscopy (LIBS) has shown great promise for applications in chemical, biological, and explosives sensing and has significant potential for real-time standoff detection and analysis. In this study, LIBS emissions were obtained in the mid-infrared (MIR) and long-wave infrared (LWIR) spectral regions for potential applications in explosive material sensing. The IR spectroscopy region revealed vibrational and rotational signatures of functional groups in molecules and fragments thereof. The silicon-based detector for conventional ultraviolet-visible LIBS operations was replaced with a mercury-cadmium-telluride detector for MIR-LWIR spectral detection. The IR spectral signature region between 4 and 12 μm was mined for the appearance of MIR and LWIR-LIBS emissions directly indicative of oxygenated breakdown products as well as dissociated, and/or recombined sample molecular fragments. Distinct LWIR-LIBS emission signatures from dissociated-recombination sample molecular fragments between 4 and 12 μm are observed for the first time.

The impact of habitat fragmentation on tsetse abundance on the plateau of eastern Zambia.

PubMed

Ducheyne, E; Mweempwa, C; De Pus, C; Vernieuwe, H; De Deken, R; Hendrickx, G; Van den Bossche, P

2009-09-01

Tsetse-transmitted human or livestock trypanosomiasis is one of the major constraints to rural development in sub-Saharan Africa. The epidemiology of the disease is determined largely by tsetse fly density. A major factor, contributing to tsetse population density is the availability of suitable habitat. In large parts of Africa, encroachment of people and their livestock resulted in a destruction and fragmentation of such suitable habitat. To determine the effect of habitat change on tsetse density a study was initiated in a tsetse-infested zone of eastern Zambia. The study area represents a gradient of habitat change, starting from a zone with high levels of habitat destruction and ending in an area where livestock and people are almost absent. To determine the distribution and density of the fly, tsetse surveys were conducted throughout the study area in the dry and in the rainy season. Landsat ETM+ imagery covering the study area were classified into four land cover classes (munga, miombo, agriculture and settlements) and two auxiliary spectral classes (clouds and shadow) using a Gaussian Maximum Likelihood Classifier. The classes were regrouped into natural vegetation and agricultural zone. The binary images were overlaid with hexagons to obtain the spatial spectrum of spatial pattern. Hexagonal coverage was selected because of its compact and regular form. To identify scale-specific spatial patterns and associated entomological phenomena, the size of the hexagonal coverage was varied (250 and 500 m). Per coverage, total class area, mean patch size, number of patches and patch size standard deviation were used as fragmentation indices. Based on the fragmentation index values, the study zone was classified using a Partitioning Around Mediods (PAM) method. The number of classes was determined using the Wilks' lambda coefficient. To determine the impact of habitat fragmentation on tsetse abundance, the correlation between the fragmentation indices and the index of apparent density of the flies was determined and habitat changes most affecting tsetse abundance was identified. From this it followed that there is a clear relationship between habitat fragmentation and the abundance of tsetse flies. Heavily fragmented areas have lower numbers of tsetse flies, but when the fragmentation of natural vegetation decreases, the number of tsetse flies increases following a sigmoidal-like curve.

Could the differences in the biochemistry of prostate carcinoma compared to benign prostate tissue biopsy fragments be evaluated through Raman spectroscopy?

NASA Astrophysics Data System (ADS)

Silveira, Landulfo; Leite, Kátia Ramos M.; Srougi, Miguel; Silveira, Fabrício L.; Pacheco, Marcos Tadeu T.; Zângaro, Renato A.; Pasqualucci, Carlos A.

2013-03-01

It has been proposed a spectral model to evaluate the biochemical differences between prostate carcinoma and benign fragments using dispersive Raman spectroscopy. We have examined 51 prostate fragments from surgically removed PrCa; each fragment was snap-frozen and stored (-80°C) prior spectral analysis. Raman spectrum was measured using a Raman spectrometer (830 nm excitation) coupled to a fiber-optic probe. Integration time and laser power were set to 50 s and 300 mW, respectively. It has been collected triplicate spectra from each fragment (total 153 spectra). Some samples exhibited a strong fluorescence, which was removed by a 7th order polynomial fitting. It has been developed a spectral model based on the least-squares fitting of the spectra of pure biochemicals (actin, collagen, elastin, carotene, glycogen, phosphatidylcholine, hemoglobin, and water) with the spectra of tissues, where the fitting parameters are the relative contribution of the compounds to the tissue spectrum. The spectra (600-1800 cm-1 range) are dominated by bands of proteins; it has been found a small difference in the mean spectra of PrCa compared to the benign tissue, mainly in the 1000-1400 cm-1 region, indicating similar biochemical constitution. The spectral fitting model revealed that elastin and phosphatidylcholine were increased in PrCa, whereas blood and water were reduced in malignant lesions (p < 0.05). A discrimination of PrCa from benign tissue using Mahalanobis distance applied to the contribution of elastin, hemoglobin and phosphatidylcholine resulted in sensitivity of 72% and specificity of 70%.

Characterizing GEO Titan IIIC Transtage Fragmentations Using Ground-Based and Telescopic Measurements

NASA Technical Reports Server (NTRS)

Cowardin, H.

2017-01-01

In a continued effort to better characterize the Geosynchronous Orbit (GEO) environment, NASA's Orbital Debris Program Office (ODPO) utilizes various ground-based optical assets to acquire photometric and spectral data of known debris associated with fragmentations in or near GEO. The Titan IIIC Transtage upper stage is known to have fragmented four times. Two of the four fragmentations were in GEO while a third Transtage fragmented in GEO transfer orbit. The forth fragmentation occurred in Low Earth Orbit. In order to better assess and characterize these fragmentations, the NASA ODPO acquired a Titan Transtage test and display article previously in the custody of the 309th Aerospace Maintenance and Regeneration Group (AMARG) in Tucson, Arizona. After initial inspections at AMARG demonstrated that the test article was of sufficient fidelity to be of interest, the test article was brought to JSC to continue material analysis and historical documentation of the Titan Transtage. The Transtage has been subject to two separate spectral measurement campaigns to characterize the reflectance spectroscopy of historical aerospace materials. These data have been incorporated into the NASA Spectral Database, the goal being to enable comparison with telescopic data and potential material identification. A LIDAR scan has been completed and a scale model has been created for use in the Optical Measurement Center for photometric analysis of an intact Transtage, including a BRDF. An historical overview of the Titan IIIC Transtage, the current analysis that has been done to date, and the future work to be completed in support of characterizing the GEO and near GEO orbital debris environment will be discussed in the subsequent presentation.

[Evolution pattern of impervious surface in the Yuqiao Reservoir Watershed, Tianjin, China during the process of urbanization.

PubMed

Xie, Hui Jun; Li, Chong Wei; Zhang, Ya Juan; Song, Ai Yun

2016-04-22

Imperviousness in watershed is a key index to measure urbanization status which exerts an important impact on both eco-hydrological process and spatio-temporal pattern. Taking Yuqiao Reservoir Watershed as a case study area, based on the ENVI 5.1 software, the basic impervious surface information was extracted from remote sensing images taken in 1984, 1994, 2004 and 2013. The linear spectral mixture analysis (LSMA) model was applied to extract the impervious surface area (ISA) in nine coverage classes of watershed in order to analyze its spatio-temporal varying trend in terms of the landscape pattern metrics. Results showed that the RMSE and IS pixel accuracy of all samples were 0.005 and 85.4% respectively, which indicated that the method of extracting impervious surface on a basin scale was feasible. The average of ISA showed a linear growth, from 0.16 to 0.23, the impervious surface area increased by 4.9% in the whole watershed, and the total impervious surface area increased by 1 time. In the sub-basin road network, the impervious surface area increased gradually with the density of the road network, and its expansion pattern was of infilling growth. The patch shape of the middle coverage degree was irregular, and its fragmentation degree was the highest. The fragmentation degree and diversity of the landscape in the whole river basin increased year by year due to increasing human disturbance.

Metabolomic spectral libraries for data-independent SWATH liquid chromatography mass spectrometry acquisition.

PubMed

Bruderer, Tobias; Varesio, Emmanuel; Hidasi, Anita O; Duchoslav, Eva; Burton, Lyle; Bonner, Ron; Hopfgartner, Gérard

2018-03-01

High-quality mass spectral libraries have become crucial in mass spectrometry-based metabolomics. Here, we investigate a workflow to generate accurate mass discrete and composite spectral libraries for metabolite identification and for SWATH mass spectrometry data processing. Discrete collision energy (5-100 eV) accurate mass spectra were collected for 532 metabolites from the human metabolome database (HMDB) by flow injection analysis and compiled into composite spectra over a large collision energy range (e.g., 10-70 eV). Full scan response factors were also calculated. Software tools based on accurate mass and predictive fragmentation were specially developed and found to be essential for construction and quality control of the spectral library. First, elemental compositions constrained by the elemental composition of the precursor ion were calculated for all fragments. Secondly, all possible fragments were generated from the compound structure and were filtered based on their elemental compositions. From the discrete spectra, it was possible to analyze the specific fragment form at each collision energy and it was found that a relatively large collision energy range (10-70 eV) gives informative MS/MS spectra for library searches. From the composite spectra, it was possible to characterize specific neutral losses as radical losses using in silico fragmentation. Radical losses (generating radical cations) were found to be more prominent than expected. From 532 metabolites, 489 provided a signal in positive mode [M+H] + and 483 in negative mode [M-H] - . MS/MS spectra were obtained for 399 compounds in positive mode and for 462 in negative mode; 329 metabolites generated suitable spectra in both modes. Using the spectral library, LC retention time, response factors to analyze data-independent LC-SWATH-MS data allowed the identification of 39 (positive mode) and 72 (negative mode) metabolites in a plasma pool sample (total 92 metabolites) where 81 previously were reported in HMDB to be found in plasma. Graphical abstract Library generation workflow for LC-SWATH MS, using collision energy spread, accurate mass, and fragment annotation.

Normalized spectral damage of a linear system over different spectral loading patterns

NASA Astrophysics Data System (ADS)

Kim, Chan-Jung

2017-08-01

Spectral fatigue damage is affected by different loading patterns; the damage may be accumulated in a different manner because the spectral pattern has an influence on stresses or strains. The normalization of spectral damage with respect to spectral loading acceleration is a novel solution to compare the accumulated fatigue damage over different spectral loading patterns. To evaluate the sensitivity of fatigue damage over different spectral loading cases, a simple notched specimen is used to conduct a uniaxial vibration test for two representative spectral patterns-random and harmonic-between 30 and 3000 Hz. The fatigue damage to the simple specimen is analyzed for different spectral loading cases using the normalized spectral damage from the measured response data for both acceleration and strain. The influence of spectral loading patterns is discussed based on these analyses.

Characterizing GEO Titan IIIC Transtage Fragmentations using Ground-Based and Telescopic Measurements

NASA Technical Reports Server (NTRS)

Cowardin, Heather; Anz-Meador, Phillip; Reyes, Jacqueline A.

2017-01-01

In a continued effort to better characterize the geosynchronous orbit (GEO) environment, NASA's Orbital Debris Program Office (ODPO) utilizes various ground-based optical assets to acquire photometric and spectral data of known debris associated with fragmentations in or near GEO. The Titan IIIC Transtage upper stage is known to have fragmented four times. Two of the four fragmentations were in GEO while the Transtage fragmented a third time in GEO transfer orbit. The forth fragmentation occurred in low Earth orbit. To better assess and characterize these fragmentations, the NASA ODPO acquired a Titan Transtage test and display article previously in the custody of the 309th Aerospace Maintenance and Regeneration Group (AMARG) in Tucson, Arizona. After initial inspections at AMARG demonstrated that it was of sufficient fidelity to be of interest, the test article was brought to NASA Johnson Space Center (JSC) to continue material analysis and historical documentation. The Transtage has undergone two separate spectral measurement campaigns to characterize the reflectance spectroscopy of historical aerospace materials. These data have been incorporated into the NASA Spectral Database, with the goal of using telescopic data comparisons for potential material identification. A Light Detection and Ranging (LIDAR) system scan also has been completed and a scale model has been created for use in the Optical Measurement Center (OMC) for photometric analysis of an intact Transtage, including bidirectional reflectance distribution function (BRDF) measurements. An historical overview of the Titan IIIC Transtage, the current analysis that has been done to date, and the future work to be completed in support of characterizing the GEO and near GEO orbital debris environment will be discussed in the subsequent presentation.

Characterizing GEO Titan IIIC Transtage Fragmentations Using Ground-based and Telescopic Measurements

NASA Astrophysics Data System (ADS)

Cowardin, H.; Anz-Meador, P.; Reyes, J. A.

In a continued effort to better characterize the geosynchronous orbit (GEO) environment, NASA’s Orbital Debris Program Office (ODPO) utilizes various ground-based optical assets to acquire photometric and spectral data of known debris associated with fragmentations in or near GEO. The Titan IIIC Transtage upper stage is known to have fragmented four times. Two of the four fragmentations were in GEO while the Transtage fragmented a third time in GEO transfer orbit. The forth fragmentation occurred in low Earth orbit. To better assess and characterize these fragmentations, the NASA ODPO acquired a Titan Transtage test and display article previously in the custody of the 309th Aerospace Maintenance and Regeneration Group (AMARG) in Tucson, Arizona. After initial inspections at AMARG demonstrated that it was of sufficient fidelity to be of interest, the test article was brought to NASA Johnson Space Center (JSC) to continue material analysis and historical documentation. The Transtage has undergone two separate spectral measurement campaigns to characterize the reflectance spectroscopy of historical aerospace materials. These data have been incorporated into the NASA Spectral Database, with the goal of using telescopic data comparisons for potential material identification. A Light Detection and Ranging (LIDAR) system scan also has been completed and a scale model has been created for use in the Optical Measurement Center (OMC) for photometric analysis of an intact Transtage, including bidirectional reflectance distribution function (BRDF) measurements. An historical overview of the Titan IIIC Transtage, the current analysis that has been done to date, and the future work to be completed in support of characterizing the GEO and near GEO orbital debris environment will be discussed in the subsequent presentation.

Structural characterization of constituents with molecular diversity in fractions from Lysidice brevicalyx by liquid chromatography/diode-array detection/electrospray ionization tandem mass spectrometry and liquid chromatography/nuclear magnetic resonance.

PubMed

Qu, Jing; Hu, You-cai; Li, Jian-bei; Wang, Ying-hong; Zhang, Jin-lan; Abliz, Zeper; Yu, Shi-shan; Liu, Yun-bao

2008-01-01

A combination of electrospray ionization tandem mass spectrometry with high-performance liquid chromatography (HPLC/ESI-MSn), and hyphenation of liquid chromatography to nuclear magnetic resonance spectroscopy (HPLC/NMR), have been extensively utilized for on-line analysis of natural products, analyzing metabolite and drug impurity. In our last paper, we reported an on-line analytical method for structural identification of trace alkaloids in the same class. However, the structural types of the constituents in plants were various, such as flavanoids, terpenoids and steroids. It is important to establish an effective analytical method for on-line structural identification of constituents with molecular diversity in extracts of plants. So, in the present study, the fragmentation patterns of some isolated stilbenes, phloroglucinols and flavanoids from Lysidice rhodostegia were investigated by ESI-MSn. Their fragmentation rules and UV characteristics are summarized, and the relationship between the spectral characteristics, rules and the structures is described. According to the fragmentation rules, NMR and UV spectral characteristics, 24 constituents of different types in the fractions from L. brevicalyx of the same genus were structurally characterized on the basis of HPLC/HRMS, HPLC-UV/ESI-MSn, HPLC/1H NMR and HPLC/1H-1H COSY rapidly. Of these, six (10, 13, 14, 16, 17 and 23) are new compounds and all of them are reported from L. brevicalyx for the first time. The aim is to develop an effective analytical method for on-line structural identification of natural products with molecular diversity in plants, and to guide the rapid and direct isolation of novel compounds by chemical screening.

Control of photosynthetic membrane assembly in Rhodobacter sphaeroides mediated by puhA and flanking sequences.

PubMed Central

Sockett, R E; Donohue, T J; Varga, A R; Kaplan, S

1989-01-01

A reaction center H- strain (RCH-) of Rhodobacter sphaeroides, PUHA1, was made by in vitro deletion of an XhoI restriction endonuclease fragment from the puhA gene coupled with insertion of a kanamycin resistance gene cartridge. The resulting construct was delivered to R. sphaeroides wild-type 2.4.1, with the defective puhA gene replacing the wild-type copy by recombination, followed by selection for kanamycin resistance. When grown under conditions known to induce intracytoplasmic membrane development, PUHA1 synthesized a pigmented intracytoplasmic membrane. Spectral analysis of this membrane showed that it was deficient in B875 spectral complexes as well as functional reaction centers and that the level of B800-850 spectral complexes was greater than in the wild type. The RCH- strain was photosythetically incompetent, but photosynthetic growth was restored by complementation with a 1.45-kilobase (kb) BamHI restriction endonuclease fragment containing the puhA gene carried in trans on plasmid pRK404. B875 spectral complexes were not restored by complementation with the 1.45-kb BamHI restriction endonuclease fragment containing the puhA gene but were restored along with photosynthetic competence by complementation with DNA from a cosmid carrying the puhA gene, as well as a flanking DNA sequence. Interestingly, B875 spectral complexes, but not photosynthetic competence, were restored to PUHA1 by introduction in trans of a 13-kb BamHI restriction endonuclease fragment carrying genes encoding the puf operon region of the DNA. The effect of the puhA deletion was further investigated by an examination of the levels of specific mRNA species derived from the puf and puc operons, as well as by determinations of the relative abundances of polypeptides associated with various spectral complexes by immunological methods. The roles of puhA and other genetic components in photosynthetic gene expression and membrane assembly are discussed. Images PMID:2644200

Mating patterns and pollinator mobility are critical traits in forest fragmentation genetics

PubMed Central

Breed, M F; Ottewell, K M; Gardner, M G; Marklund, M H K; Dormontt, E E; Lowe, A J

2015-01-01

Most woody plants are animal-pollinated, but the global problem of habitat fragmentation is changing the pollination dynamics. Consequently, the genetic diversity and fitness of the progeny of animal-pollinated woody plants sired in fragmented landscapes tend to decline due to shifts in plant-mating patterns (for example, reduced outcrossing rate, pollen diversity). However, the magnitude of this mating-pattern shift should theoretically be a function of pollinator mobility. We first test this hypothesis by exploring the mating patterns of three ecologically divergent eucalypts sampled across a habitat fragmentation gradient in southern Australia. We demonstrate increased selfing and decreased pollen diversity with increased fragmentation for two small-insect-pollinated eucalypts, but no such relationship for the mobile-bird-pollinated eucalypt. In a meta-analysis, we then show that fragmentation generally does increase selfing rates and decrease pollen diversity, and that more mobile pollinators tended to dampen these mating-pattern shifts. Together, our findings support the premise that variation in pollinator form contributes to the diversity of mating-pattern responses to habitat fragmentation. PMID:24002239

Broad screening of illicit ingredients in cosmetics using ultra-high-performance liquid chromatography-hybrid quadrupole-Orbitrap mass spectrometry with customized accurate-mass database and mass spectral library.

PubMed

Meng, Xianshuang; Bai, Hua; Guo, Teng; Niu, Zengyuan; Ma, Qiang

2017-12-15

Comprehensive identification and quantitation of 100 multi-class regulated ingredients in cosmetics was achieved using ultra-high-performance liquid chromatography (UHPLC) coupled with hybrid quadrupole-Orbitrap high-resolution mass spectrometry (Q-Orbitrap HRMS). A simple, efficient, and inexpensive sample pretreatment protocol was developed using ultrasound-assisted extraction (UAE), followed by dispersive solid-phase extraction (dSPE). The cosmetic samples were analyzed by UHPLC-Q-Orbitrap HRMS under synchronous full-scan MS and data-dependent MS/MS (full-scan MS 1 /dd-MS 2 ) acquisition mode. The mass resolution was set to 70,000 FWHM (full width at half maximum) for full-scan MS 1 and 17,500 FWHM for dd-MS 2 stage with the experimentally measured mass deviations of less than 2ppm (parts per million) for quasi-molecular ions and 5ppm for characteristic fragment ions for each individual analyte. An accurate-mass database and a mass spectral library were built in house for searching the 100 target compounds. Broad screening was conducted by comparing the experimentally measured exact mass of precursor and fragment ions, retention time, isotopic pattern, and ionic ratio with the accurate-mass database and by matching the acquired MS/MS spectra against the mass spectral library. The developed methodology was evaluated and validated in terms of limits of detection (LODs), limits of quantitation (LOQs), linearity, stability, accuracy, and matrix effect. The UHPLC-Q-Orbitrap HRMS approach was applied for the analysis of 100 target illicit ingredients in 123 genuine cosmetic samples, and exhibited great potential for high-throughput, sensitive, and reliable screening of multi-class illicit compounds in cosmetics. Copyright © 2017 Elsevier B.V. All rights reserved.

Incorporation of satellite remote sensing pan-sharpened imagery into digital soil prediction and mapping models to characterize soil property variability in small agricultural fields

NASA Astrophysics Data System (ADS)

Xu, Yiming; Smith, Scot E.; Grunwald, Sabine; Abd-Elrahman, Amr; Wani, Suhas P.

2017-01-01

Soil prediction models based on spectral indices from some multispectral images are too coarse to characterize spatial pattern of soil properties in small and heterogeneous agricultural lands. Image pan-sharpening has seldom been utilized in Digital Soil Mapping research before. This research aimed to analyze the effects of pan-sharpened (PAN) remote sensing spectral indices on soil prediction models in smallholder farm settings. This research fused the panchromatic band and multispectral (MS) bands of WorldView-2, GeoEye-1, and Landsat 8 images in a village in Southern India by Brovey, Gram-Schmidt and Intensity-Hue-Saturation methods. Random Forest was utilized to develop soil total nitrogen (TN) and soil exchangeable potassium (Kex) prediction models by incorporating multiple spectral indices from the PAN and MS images. Overall, our results showed that PAN remote sensing spectral indices have similar spectral characteristics with soil TN and Kex as MS remote sensing spectral indices. There is no soil prediction model incorporating the specific type of pan-sharpened spectral indices always had the strongest prediction capability of soil TN and Kex. The incorporation of pan-sharpened remote sensing spectral data not only increased the spatial resolution of the soil prediction maps, but also enhanced the prediction accuracy of soil prediction models. Small farms with limited footprint, fragmented ownership and diverse crop cycle should benefit greatly from the pan-sharpened high spatial resolution imagery for soil property mapping. Our results show that multiple high and medium resolution images can be used to map soil properties suggesting the possibility of an improvement in the maps' update frequency. Additionally, the results should benefit the large agricultural community through the reduction of routine soil sampling cost and improved prediction accuracy.

Model Calculations with Excited Nuclear Fragmentations and Implications of Current GCR Spectra

NASA Astrophysics Data System (ADS)

Saganti, Premkumar

As a result of the fragmentation process in nuclei, energy from the excited states may also contribute to the radiation damage on the cell structure. Radiation induced damage to the human body from the excited states of oxygen and several other nuclei and its fragments are of a concern in the context of the measured abundance of the current galactic cosmic rays (GCR) environment. Nuclear Shell model based calculations of the Selective-Core (Saganti-Cucinotta) approach are being expanded for O-16 nuclei fragments into N-15 with a proton knockout and O-15 with a neutron knockout are very promising. In our on going expansions of these nuclear fragmentation model calculations and assessments, we present some of the prominent nuclei interactions from a total of 190 isotopes that were identified for the current model expansion based on the Quantum Multiple Scattering Fragmentation Model (QMSFRG) of Cucinotta. Radiation transport model calculations with the implementation of these energy level spectral characteristics are expected to enhance the understanding of radiation damage at the cellular level. Implications of these excited energy spectral calculations in the assessment of radiation damage to the human body may provide enhanced understanding of the space radiation risk assessment.

Hot-stage microscopy for determination of API fragmentation: comparison with other methods.

PubMed

Šimek, Michal; Grünwaldová, Veronika; Kratochvíl, Bohumil

2016-08-01

Although the fragmentation of the active pharmaceutical ingredient (API) is a phenomenon that is mentioned in many literature sources, no well-suited analytical tools for its investigation are currently known. We used the hot-stage microscopy method, already presented in our previous work, and studied the real fragmentation of the tadalafil particles in model tablets which were prepared under different compaction pressures. The morphology, spectral imaging and evaluation of plastic and elastic energies were also analyzed to support the hot-stage method. The prepared blend of tadalafil and excipients was compacted under a several forces from 5 to 35 kN to reveal the trend of fragmentation. The exact fragmentation of tadalafil with increased compaction pressure was revealed by the hot-stage microscopic method and it was in good agreement with plastic and elastic energies. Conversely, spectral imaging, which is being used for this analysis, was considered to be inaccurate methodology as mainly agglomerates, not individual particles, were measured. The availability of the hot-stage microscopic method equips pharmaceutical scientists with an in vitro assessment technique that will more reliably determine the fragmentation of the API in finished tablets and the behavior of the particles when compacted.

Pattern Recognition-Assisted Infrared Library Searching of the Paint Data Query Database to Enhance Lead Information from Automotive Paint Trace Evidence.

PubMed

Lavine, Barry K; White, Collin G; Allen, Matthew D; Weakley, Andrew

2017-03-01

Multilayered automotive paint fragments, which are one of the most complex materials encountered in the forensic science laboratory, provide crucial links in criminal investigations and prosecutions. To determine the origin of these paint fragments, forensic automotive paint examiners have turned to the paint data query (PDQ) database, which allows the forensic examiner to compare the layer sequence and color, texture, and composition of the sample to paint systems of the original equipment manufacturer (OEM). However, modern automotive paints have a thin color coat and this layer on a microscopic fragment is often too thin to obtain accurate chemical and topcoat color information. A search engine has been developed for the infrared (IR) spectral libraries of the PDQ database in an effort to improve discrimination capability and permit quantification of discrimination power for OEM automotive paint comparisons. The similarity of IR spectra of the corresponding layers of various records for original finishes in the PDQ database often results in poor discrimination using commercial library search algorithms. A pattern recognition approach employing pre-filters and a cross-correlation library search algorithm that performs both a forward and backward search has been used to significantly improve the discrimination of IR spectra in the PDQ database and thus improve the accuracy of the search. This improvement permits inter-comparison of OEM automotive paint layer systems using the IR spectra alone. Such information can serve to quantify the discrimination power of the original automotive paint encountered in casework and further efforts to succinctly communicate trace evidence to the courts.

Myo-inositol esters of indole-3-acetic acid are endogenous components of Zea mays L. shoot tissue

NASA Technical Reports Server (NTRS)

Chisnell, J. R.

1984-01-01

Indole-3-acetyl-myo-inositol esters have been demonstrated to be endogenous components of etiolated Zea mays shoots tissue. This was accomplished by comparison of the putative compounds with authentic, synthetic esters. The properties compared were liquid and gas-liquid chromatographic retention times and the 70-ev mass spectral fragmentation pattern of the pentaacetyl derivative. The amount of indole-3-acetyl-myo-inositol esters in the shoots was determined to be 74 nanomoles per kilogram fresh weight as measured by isotope dilution, accounting for 19% of the ester indole-3-acetic acid of the shoot. This work is the first characterization of an ester conjugate of indole-3-acetate acid from vegetative shoot tissue using multiple chromatographic properties and mass spectral identification. The kernel and the seedling shoot both contain indole-3-acetyl-myo-inositol esters, and these esters comprise approximately the same percentage of the total ester content of the kernel and of the shoot.

Short-Term EEG Spectral Pattern as a Single Event in EEG Phenomenology

PubMed Central

Fingelkurts, Al. A; Fingelkurts, An. A

2010-01-01

Spectral decomposition, to this day, still remains the main analytical paradigm for the analysis of EEG oscillations. However, conventional spectral analysis assesses the mean characteristics of the EEG power spectra averaged out over extended periods of time and/or broad frequency bands, thus resulting in a “static” picture which cannot reflect adequately the underlying neurodynamic. A relatively new promising area in the study of EEG is based on reducing the signal to elementary short-term spectra of various types in accordance with the number of types of EEG stationary segments instead of using averaged power spectrum for the whole EEG. It is suggested that the various perceptual and cognitive operations associated with a mental or behavioural condition constitute a single distinguishable neurophysiological state with a distinct and reliable spectral pattern. In this case, one type of short-term spectral pattern may be considered as a single event in EEG phenomenology. To support this assumption the following issues are considered in detail: (a) the relations between local EEG short-term spectral pattern of particular type and the actual state of the neurons in underlying network and a volume conduction; (b) relationship between morphology of EEG short-term spectral pattern and the state of the underlying neurodynamical system i.e. neuronal assembly; (c) relation of different spectral pattern components to a distinct physiological mechanism; (d) relation of different spectral pattern components to different functional significance; (e) developmental changes of spectral pattern components; (f) heredity of the variance in the individual spectral pattern and its components; (g) intra-individual stability of the sets of EEG short-term spectral patterns and their percent ratio; (h) discrete dynamics of EEG short-term spectral patterns. Functional relevance (consistency) of EEG short-term spectral patterns in accordance with the changes of brain functional state, cognitive task and with different neuropsychopathologies is demonstrated. PMID:21379390

Curatr: a web application for creating, curating and sharing a mass spectral library.

PubMed

Palmer, Andrew; Phapale, Prasad; Fay, Dominik; Alexandrov, Theodore

2018-04-15

We have developed a web application curatr for the rapid generation of high quality mass spectral fragmentation libraries from liquid-chromatography mass spectrometry datasets. Curatr handles datasets from single or multiplexed standards and extracts chromatographic profiles and potential fragmentation spectra for multiple adducts. An intuitive interface helps users to select high quality spectra that are stored along with searchable molecular information, the providence of each standard and experimental metadata. Curatr supports exports to several standard formats for use with third party software or submission to repositories. We demonstrate the use of curatr to generate the EMBL Metabolomics Core Facility spectral library http://curatr.mcf.embl.de. Source code and example data are at http://github.com/alexandrovteam/curatr/. palmer@embl.de. Supplementary data are available at Bioinformatics online.

Variable Gene Dispersal Conditions and Spatial Deforestation Patterns Can Interact to Affect Tropical Tree Conservation Outcomes

PubMed Central

Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H.

2015-01-01

Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with ‘Near’ distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal regimens will be a likely outcome of fragmentation. Conservation implications include possible manual interventions (manual manipulations of offspring dispersers and/or pollinators) in forest fragments to increase population recovery and genetic diversity retention. PMID:26000951

Variable gene dispersal conditions and spatial deforestation patterns can interact to affect tropical tree conservation outcomes.

PubMed

Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H

2015-01-01

Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with 'Near' distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal regimens will be a likely outcome of fragmentation. Conservation implications include possible manual interventions (manual manipulations of offspring dispersers and/or pollinators) in forest fragments to increase population recovery and genetic diversity retention.

Mass spectral analysis of long chain alkyl aromatic compounds synthesized from alpha-olefin alkylation

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

Cheng, M.T.; Hudson, J.D.

1994-12-31

Long chain alkyl aromatic compounds are important petrochemicals with many applications. They are generally synthesized by alkylating the corresponding aromatic nucleus. In this report, the authors will describe the mass spectral fragmentation of alkylphenols and alkylsalicylates.

Characterizing GEO Titan Transtage Fragmentations using Ground-based Measurements

NASA Technical Reports Server (NTRS)

Cowardin, H.; Anz-Meador, P.

2016-01-01

In a continued effort to better characterize the Geosynchronous Orbit (GEO) environment, NASA's Orbital Debris Program Office (ODPO) utilizes various ground-based optical assets to acquire photometric and spectral data of known debris associated with fragmentations in or near GEO. The Titan IIIC Transtage upper stage is known to have fragmented four times. Two of the four fragmentations were in GEO while a third Transtage fragmented in GEO transfer orbit. The forth fragmentation occurred in Low Earth Orbit. In order to better assess what may be causing these fragmentations, the NASA ODPO recently acquired a Titan Transtage test and display article that was previously in the custody of the 309th Aerospace Maintenance and Regeneration Group (AMARG) in Tucson, Arizona. After initial inspections at AMARG demonstrated that the test article was of sufficient fidelity to be of interest, the test article was brought to JSC to continue material analysis and historical documentation of the Titan Transtage. The Transtage will be a subject of forensic analysis using spectral measurements to compare with telescopic data; as well, a scale model will be created to use in the Optical Measurement Center for photometric analysis of an intact Transtage, including a BRDF. The following presentation will provide a review of the Titan Transtage, the current analysis that has been done to date, and the future work to be completed in support of characterizing the GEO and near GEO orbital debris environment.

Forest fragmentation in Massachusetts, USA: a town-level assessment using Morphological Spatial Pattern Analysis and affinity propagation

Treesearch

J. Rogan; T.M. Wright; J. Cardille; H. Pearsall; Y. Ogneva-Himmelberger; Rachel Riemann; Kurt Riitters; K. Partington

2016-01-01

Forest fragmentation has been studied extensively with respect to biodiversity loss, disruption of ecosystem services, and edge effects although the relationship between forest fragmentation and human activities is still not well understood. We classified the pattern of forests in Massachusetts using fragmentation indicators to address...

Enabling Efficient and Confident Annotation of LC−MS Metabolomics Data through MS1 Spectrum and Time Prediction

DOE PAGES

Broeckling, Corey D.; Ganna, Andrea; Layer, Mark; ...

2016-09-08

Liquid chromatography coupled to electrospray ionization-mass spectrometry (LC–ESI-MS) is a versatile and robust platform for metabolomic analysis. However, while ESI is a soft ionization technique, in-source phenomena including multimerization, nonproton cation adduction, and in-source fragmentation complicate interpretation of MS data. Here, we report chromatographic and mass spectrometric behavior of 904 authentic standards collected under conditions identical to a typical nontargeted profiling experiment. The data illustrate that the often high level of complexity in MS spectra is likely to result in misinterpretation during the annotation phase of the experiment and a large overestimation of the number of compounds detected. However, ourmore » analysis of this MS spectral library data indicates that in-source phenomena are not random but depend at least in part on chemical structure. These nonrandom patterns enabled predictions to be made as to which in-source signals are likely to be observed for a given compound. Using the authentic standard spectra as a training set, we modeled the in-source phenomena for all compounds in the Human Metabolome Database to generate a theoretical in-source spectrum and retention time library. A novel spectral similarity matching platform was developed to facilitate efficient spectral searching for nontargeted profiling applications. Taken together, this collection of experimental spectral data, predictive modeling, and informatic tools enables more efficient, reliable, and transparent metabolite annotation.« less

Enabling Efficient and Confident Annotation of LC-MS Metabolomics Data through MS1 Spectrum and Time Prediction

DOE PAGES

Broeckling, Corey D.; Ganna, Andrea; Layer, Mark; ...

2016-08-25

Liquid chromatography coupled to electrospray ionization-mass spectrometry (LC–ESI-MS) is a versatile and robust platform for metabolomic analysis. However, while ESI is a soft ionization technique, in-source phenomena including multimerization, nonproton cation adduction, and in-source fragmentation complicate interpretation of MS data. Here, we report chromatographic and mass spectrometric behavior of 904 authentic standards collected under conditions identical to a typical nontargeted profiling experiment. The data illustrate that the often high level of complexity in MS spectra is likely to result in misinterpretation during the annotation phase of the experiment and a large overestimation of the number of compounds detected. However, ourmore » analysis of this MS spectral library data indicates that in-source phenomena are not random but depend at least in part on chemical structure. These nonrandom patterns enabled predictions to be made as to which in-source signals are likely to be observed for a given compound. Using the authentic standard spectra as a training set, we modeled the in-source phenomena for all compounds in the Human Metabolome Database to generate a theoretical in-source spectrum and retention time library. A novel spectral similarity matching platform was developed to facilitate efficient spectral searching for nontargeted profiling applications. Taken together, this collection of experimental spectral data, predictive modeling, and informatic tools enables more efficient, reliable, and transparent metabolite annotation.« less

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

Loehle, Stefan; Zander, Fabian; Hermann, Tobias

Three different types of rocks were tested in a high enthalpy air plasma flow. Two terrestrial rocks, basalt and argillite, and an ordinary chondrite, with a 10 mm diameter cylindrical shape were tested in order to observe decomposition, potential fragmentation, and spectral signature. The goal was to simulate meteoroid ablation to interpret meteor observation and compare these observations with ground based measurements. The test flow with a local mass-specific enthalpy of 70 MJ kg{sup −1} results in a surface heat flux at the meteorite fragment surface of approximately 16 MW m{sup −2}. The stagnation pressure is 24 hPa, which correspondsmore » to a flight condition in the upper atmosphere around 80 km assuming an entry velocity of 10 km s{sup −1}. Five different diagnostic methods were applied simultaneously to characterize the meteorite fragmentation and destruction in the ground test: short exposure photography, regular video, high-speed imaging with 10 kHz frame rate, thermography, and Echelle emission spectroscopy. This is the first time that comprehensive testing of various meteorite fragments under the same flow condition was conducted. The data sets indeed show typical meteorite ablation behavior. The cylindrically shaped fragments melt and evaporate within about 4 s. The spectral data allow the identification of the material from the spectra which is of particular importance for future spectroscopic meteor observations. For the tested ordinary chondrite sample a comparison to an observed meteor spectra shows good agreement. The present data show that this testing methodology reproduces the ablation phenomena of meteoritic material alongside the corresponding spectral signatures.« less

Experimental Simulation of Meteorite Ablation during Earth Entry using a Plasma Wind Tunnel

NASA Astrophysics Data System (ADS)

Loehle, Stefan; Zander, Fabian; Hermann, Tobias; Eberhart, Martin; Meindl, Arne; Oefele, Rainer; Vaubaillon, Jeremie; Colas, Francois; Vernazza, Pierre; Drouard, Alexis; Gattacceca, Jerome

2017-03-01

Three different types of rocks were tested in a high enthalpy air plasma flow. Two terrestrial rocks, basalt and argillite, and an ordinary chondrite, with a 10 mm diameter cylindrical shape were tested in order to observe decomposition, potential fragmentation, and spectral signature. The goal was to simulate meteoroid ablation to interpret meteor observation and compare these observations with ground based measurements. The test flow with a local mass-specific enthalpy of 70 MJ kg-1 results in a surface heat flux at the meteorite fragment surface of approximately 16 MW m-2. The stagnation pressure is 24 hPa, which corresponds to a flight condition in the upper atmosphere around 80 km assuming an entry velocity of 10 km s-1. Five different diagnostic methods were applied simultaneously to characterize the meteorite fragmentation and destruction in the ground test: short exposure photography, regular video, high-speed imaging with 10 kHz frame rate, thermography, and Echelle emission spectroscopy. This is the first time that comprehensive testing of various meteorite fragments under the same flow condition was conducted. The data sets indeed show typical meteorite ablation behavior. The cylindrically shaped fragments melt and evaporate within about 4 s. The spectral data allow the identification of the material from the spectra which is of particular importance for future spectroscopic meteor observations. For the tested ordinary chondrite sample a comparison to an observed meteor spectra shows good agreement. The present data show that this testing methodology reproduces the ablation phenomena of meteoritic material alongside the corresponding spectral signatures.

Characterization of the diversity of mycosporine-like amino acids in lichens from high altitude region of Himalaya.

PubMed

Shukla, Vertika; Kumari, Rupender; Patel, Davendra K; Upreti, Dalip K

2016-01-01

Lichens are tolerant to a number of environmental variables including high-intensity solar radiations, which is mainly due to the presence of chemical substances in the thallus. Especially, cyanobacterial lichens synthesize a unique class of chemical substances known as mycosporine-like amino acids (MAAs) the primary characteristic of which is strong ultraviolet (UV) absorption between 300 and 360 nm. In view of its UV-protecting potential, the applicability of mass spectral fragmentation using electrospray ionization tandem mass spectrometric analysis for the characterization of MAAs in lichen samples was explored. MAA compounds were characterized in four cyanobacteria-containing lichen species belonging to genus Peltigera, Stereocaulon and Lobaria. Among them, Peltigera and Lobaria are true cyanobacteria containing lichens (cyanolichens) while Stereocaulon is a tripartite lichen, as it contains both green algae (in the thallus) and cyanobacteria (in the cephalodia), collected from higher altitudes of Himalaya (Tungnath-Chopta in Garhwal Himalaya, 3432 m) from an exposed locality experiencing high light intensity. Mass spectral data of distinctive fragmentation pattern revealed that all the four species have good diversity of MAA compounds, especially Lobaria retigera was found to be enriched with highest diversity of oxo and imino MAAs. Overall, different numbers of oxo and imino MAA compounds were detected in the remaining lichen species. Good diversity of imino MAAs has ecological significance which is required to be investigated further. Moreover, the impressive diversity characterized in each lichen species suggests that lichens should be thoroughly studied for their MAAs contents.

Map misclassifications can cause large errors in landscape pattern indices: examples from habitat fragmentation.

Treesearch

William T. Langford; Sarah E. Gergel; Thomas G. Dietterich; Warren Cohen

2006-01-01

Although habitat fragmentation is one of the greatest threats to biodiversity worldwide, virtually no attention has been paid to the quantification of error in fragmentation statistics. Landscape pattern indices (LPIs), such as mean patch size and number of patches, are routinely used to quantify fragmentation and are often calculated using remote sensing imagery that...

Differentiating Positional Isomers of Nucleoside Modifications by Higher-Energy Collisional Dissociation Mass Spectrometry (HCD MS)

NASA Astrophysics Data System (ADS)

Jora, Manasses; Burns, Andrew P.; Ross, Robert L.; Lobue, Peter A.; Zhao, Ruoxia; Palumbo, Cody M.; Beal, Peter A.; Addepalli, Balasubrahmanyam; Limbach, Patrick A.

2018-06-01

The analytical identification of positional isomers (e.g., 3-, N 4-, 5-methylcytidine) within the > 160 different post-transcriptional modifications found in RNA can be challenging. Conventional liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) approaches rely on chromatographic separation for accurate identification because the collision-induced dissociation (CID) mass spectra of these isomers nearly exclusively yield identical nucleobase ions (BH2 +) from the same molecular ion (MH+). Here, we have explored higher-energy collisional dissociation (HCD) as an alternative fragmentation technique to generate more informative product ions that can be used to differentiate positional isomers. LC-MS/MS of modified nucleosides characterized using HCD led to the creation of structure- and HCD energy-specific fragmentation patterns that generated unique fingerprints, which can be used to identify individual positional isomers even when they cannot be separated chromatographically. While particularly useful for identifying positional isomers, the fingerprinting capabilities enabled by HCD also offer the potential to generate HPLC-independent spectral libraries for the rapid analysis of modified ribonucleosides. [Figure not available: see fulltext.

Dynamics of Hierarchical Urban Green Space Patches and Implications for Management Policy.

PubMed

Yu, Zhoulu; Wang, Yaohui; Deng, Jinsong; Shen, Zhangquan; Wang, Ke; Zhu, Jinxia; Gan, Muye

2017-06-06

Accurately quantifying the variation of urban green space is the prerequisite for fully understanding its ecosystem services. However, knowledge about the spatiotemporal dynamics of urban green space is still insufficient due to multiple challenges that remain in mapping green spaces within heterogeneous urban environments. This paper uses the city of Hangzhou to demonstrate an analysis methodology that integrates sub-pixel mapping technology and landscape analysis to fully investigate the spatiotemporal pattern and variation of hierarchical urban green space patches. Firstly, multiple endmember spectral mixture analysis was applied to time series Landsat data to derive green space coverage at the sub-pixel level. Landscape metric analysis was then employed to characterize the variation pattern of urban green space patches. Results indicate that Hangzhou has experienced a significant loss of urban greenness, producing a more fragmented and isolated vegetation landscape. Additionally, a remarkable amelioration of urban greenness occurred in the city core from 2002 to 2013, characterized by the significant increase of small-sized green space patches. The green space network has been formed as a consequence of new urban greening strategies in Hangzhou. These strategies have greatly fragmented the built-up areas and enriched the diversity of the urban landscape. Gradient analysis further revealed a distinct pattern of urban green space landscape variation in the process of urbanization. By integrating both sub-pixel mapping technology and landscape analysis, our approach revealed the subtle variation of urban green space patches which are otherwise easy to overlook. Findings from this study will help us to refine our understanding of the evolution of heterogeneous urban environments.

Dynamics of Hierarchical Urban Green Space Patches and Implications for Management Policy

PubMed Central

Yu, Zhoulu; Wang, Yaohui; Deng, Jinsong; Shen, Zhangquan; Wang, Ke; Zhu, Jinxia; Gan, Muye

2017-01-01

Accurately quantifying the variation of urban green space is the prerequisite for fully understanding its ecosystem services. However, knowledge about the spatiotemporal dynamics of urban green space is still insufficient due to multiple challenges that remain in mapping green spaces within heterogeneous urban environments. This paper uses the city of Hangzhou to demonstrate an analysis methodology that integrates sub-pixel mapping technology and landscape analysis to fully investigate the spatiotemporal pattern and variation of hierarchical urban green space patches. Firstly, multiple endmember spectral mixture analysis was applied to time series Landsat data to derive green space coverage at the sub-pixel level. Landscape metric analysis was then employed to characterize the variation pattern of urban green space patches. Results indicate that Hangzhou has experienced a significant loss of urban greenness, producing a more fragmented and isolated vegetation landscape. Additionally, a remarkable amelioration of urban greenness occurred in the city core from 2002 to 2013, characterized by the significant increase of small-sized green space patches. The green space network has been formed as a consequence of new urban greening strategies in Hangzhou. These strategies have greatly fragmented the built-up areas and enriched the diversity of the urban landscape. Gradient analysis further revealed a distinct pattern of urban green space landscape variation in the process of urbanization. By integrating both sub-pixel mapping technology and landscape analysis, our approach revealed the subtle variation of urban green space patches which are otherwise easy to overlook. Findings from this study will help us to refine our understanding of the evolution of heterogeneous urban environments. PMID:28587309

Detection of pit fragments in fresh cherries using near infrared spectroscopy

USDA-ARS?s Scientific Manuscript database

NIR spectroscopy in the wavelength region from 900nm to 2600nm was evaluated as the basis for a rapid, non-destructive method for the detection of pits and pit fragments in fresh cherries. Partial Least Squares discriminant analysis (PLS-DA) following various spectral pretreatments was applied to sp...

Identification of substances migrating from plastic baby bottles using a combination of low-resolution and high-resolution mass spectrometric analysers coupled to gas and liquid chromatography.

PubMed

Onghena, Matthias; Van Hoeck, Els; Van Loco, Joris; Ibáñez, María; Cherta, Laura; Portolés, Tania; Pitarch, Elena; Hernandéz, Félix; Lemière, Filip; Covaci, Adrian

2015-11-01

This work presents a strategy for elucidation of unknown migrants from plastic food contact materials (baby bottles) using a combination of analytical techniques in an untargeted approach. First, gas chromatography (GC) coupled to mass spectrometry (MS) in electron ionisation mode was used to identify migrants through spectral library matching. When no acceptable match was obtained, a second analysis by GC-(electron ionisation) high resolution mass spectrometry time of flight (TOF) was applied to obtain accurate mass fragmentation spectra and isotopic patterns. Databases were then searched to find a possible elemental composition for the unknown compounds. Finally, a GC hybrid quadrupole-TOF-MS with an atmospheric pressure chemical ionisation source was used to obtain the molecular ion or the protonated molecule. Accurate mass data also provided additional information on the fragmentation behaviour as two acquisition functions with different collision energies were available (MS(E) approach). In the low-energy function, limited fragmentation took place, whereas for the high-energy function, fragmentation was enhanced. For less volatile unknowns, ultra-high pressure liquid chromatography-quadrupole-TOF-MS was additionally applied. Using a home-made database containing common migrating compounds and plastic additives, tentative identification was made for several positive findings based on accurate mass of the (de)protonated molecule, product ion fragments and characteristic isotopic ions. Six illustrative examples are shown to demonstrate the modus operandi and the difficulties encountered during identification. The combination of these techniques was proven to be a powerful tool for the elucidation of unknown migrating compounds from plastic baby bottles. Copyright © 2015 John Wiley & Sons, Ltd.

Absorption and dissociative photoionization cross sections of NH3 from 80 to 1120 A

NASA Technical Reports Server (NTRS)

Samson, James A. R.; Haddad, G. N.; Kilcoyne, L. D.

1987-01-01

The total absorption, photoionization, and dissociative photoionization cross sections of ammonia have been measured from 80 to 1120 A. All possible fragment ions have been observed including doubly ionized ammonia. The absolute ionization efficiencies have also been measured in this spectral range. The appearance potentials of the fragment ions have been measured and are compared with the calculated appearance potentials derived from published heats of formation and ionization potentials of the fragments.

Mass spectral analysis of C3 and C4 aliphatic amino acid derivatives.

NASA Technical Reports Server (NTRS)

Lawless, J. G.; Chadha, M. S.

1971-01-01

Diagnostic criteria are obtained for the distinction of alpha, beta, gamma, and N-methyl isomers of the C3 and C4 aliphatic amino acids, using mass spectral analysis of the derivatives of these acids. The use of deuterium labeling has helped in the understanding of certain fragmentation pathways.

Discrimination of static and dynamic spectral patterns by children and young adults in relationship to speech perception in noise.

PubMed

Rayes, Hanin; Sheft, Stanley; Shafiro, Valeriy

2014-01-01

Past work has shown relationship between the ability to discriminate spectral patterns and measures of speech intelligibility. The purpose of this study was to investigate the ability of both children and young adults to discriminate static and dynamic spectral patterns, comparing performance between the two groups and evaluating within-group results in terms of relationship to speech-in-noise perception. Data were collected from normal-hearing children (age range: 5.4 - 12.8 yrs) and young adults (mean age: 22.8 yrs) on two spectral discrimination tasks and speech-in-noise perception. The first discrimination task, involving static spectral profiles, measured the ability to detect a change in the phase of a low-density sinusoidal spectral ripple of wideband noise. Using dynamic spectral patterns, the second task determined the signal-to-noise ratio needed to discriminate the temporal pattern of frequency fluctuation imposed by stochastic low-rate frequency modulation (FM). Children performed significantly poorer than young adults on both discrimination tasks. For children, a significant correlation between speech-in-noise perception and spectral-pattern discrimination was obtained only with the dynamic patterns of the FM condition, with partial correlation suggesting that factors related to the children's age mediated the relationship.

Activity budget and ranging patterns of Colobus vellerosus in forest fragments in central Ghana.

PubMed

Wong, Sarah N P; Sicotte, Pascale

2007-01-01

The forest fragments surrounding the 192-ha Boabeng-Fiema Monkey Sanctuary (BFMS) in central Ghana contain small populations of Colobus vellerosus. Data were collected on activity budget, ranging patterns and habitat use of 3 groups living in these small fragments in August-November 2003, and compared to 3 BFMS groups. Fragment groups spent less time moving and more time resting than BFMS groups. Home ranges of fragment groups tended to be smaller than those of BFMS groups. Fragment and BFMS groups used similarly sized trees. Comparisons of activity budget and ranging between fragments and the BFMS suggest that fragment habitat quality was sufficient to sustain current numbers. These behavioral trends are consistent with a concurrent study that we conducted investigating ecological quality in the same fragments. Copyright 2007 S. Karger AG, Basel.

Microsynthesis and electron ionization mass spectral studies of O(S)-alkyl N,N-dimethyl alkylphosphono(thiolo)thionoamidates for Chemical Weapons Convention verification.

PubMed

Saeidian, Hamdollah; Babri, Mehran; Abdoli, Morteza; Sarabadani, Mansour; Ashrafi, Davood; Naseri, Mohammad Taghi

2012-12-15

The availability of mass spectra and interpretation skills are essential for unambiguous identification of the Chemical Weapons Convention (CWC)-related chemicals. The O(S)-alkyl N,N-dimethyl alkylphosphono(thiolo)thionoamidates are included in the list of scheduled CWC-related compounds, but there are very few spectra from these compounds in the literature. This paper examines these spectra and their mass spectral fragmentation routes. The title chemicals were prepared through microsynthetic protocols and were analyzed using electron ionization mass spectrometry with gas chromatography as a MS-inlet system. Structures of fragments were confirmed using analysis of fragment ions of deuterated analogs, tandem mass spectrometry and density functional theory (DFT) calculations. Mass spectrometric studies revealed some interesting fragmentation pathways during the ionization process, such as alkene and amine elimination and McLafferty-type rearrangements. The most important fragmentation route of the chemicals is the thiono-thiolo rearrangement. DFT calculations are used to support MS results and to reveal relative preference formation of fragment ions. The retention indices (RIs) of all the studied compounds are also reported. Mass spectra of the synthesized compounds were investigated with the aim to enrich the Organization for the Prohibition of Chemical Weapons (OPCW) Central Analytical Database (OCAD) which may be used for detection and identification of CWC-related chemicals during on-site inspection and/or off-site analysis such as OPCW proficiency tests. Copyright © 2012 John Wiley & Sons, Ltd.

Hungaria Asteroid Region Telescopic Spectral Survey (HARTSS) II: Spectral Homogeneity Among Hungaria Family Asteroids

NASA Astrophysics Data System (ADS)

Lucas, Michael P.; Emery, Joshua; Pinilla-Alonso, Noemi; Lindsay, Sean S.; MacLennan, Eric M.; Cartwright, Richard; Reddy, Vishnu; Sanchez, Juan A.; Thomas, Cristina A.; Lorenzi, Vania

2017-10-01

Spectral observations of asteroid family members provide valuable information regarding parent body interiors, the source regions of near-Earth asteroids, and the link between meteorites and their parent bodies. Hungaria family asteroids constitute the closest samples to the Earth from a collisional family (~1.94 AU), permitting observations of smaller fragments than accessible for Main Belt families. We have carried out a ground-based observational campaign - Hungaria Asteroid Region Telescopic Spectral Survey (HARTSS) - to record reflectance spectra of these preserved samples from the inner-most primordial asteroid belt. During HARTSS phase one (Lucas et al. [2017]. Icarus 291, 268-287) we found that ~80% of the background population is comprised of stony S-complex asteroids that exhibit considerable spectral and mineralogical diversity. In HARTSS phase two, we turn our attention to family members and hypothesize that the Hungaria collisional family is homogeneous. We test this hypothesis through taxonomic classification, albedo estimates, and spectral properties.During phase two of HARTSS we acquired near-infrared (NIR) spectra of 50 new Hungarias (19 family; 31 background) with SpeX/IRTF and NICS/TNG. We analyzed X-type family spectra for NIR color indices (0.85-J J-K), and a subtle ~0.9 µm absorption feature that may be attributed to Fe-poor orthopyroxene. Surviving fragments of an asteroid collisional family typically exhibit similar taxonomies, albedos, and spectral properties. Spectral analysis of X-type Hungaria family members and independently calculated WISE albedo determinations for 428 Hungaria asteroids is consistent with this scenario. Furthermore, ~1/4 of the background population exhibit similar spectral properties and albedos to family X-types.Spectral observations of 92 Hungaria region asteroids acquired during both phases of HARTSS uncover a compositionally heterogeneous background and spectral homogeneity down to ~2 km for collisional family members. Taxonomy, albedos, and spectral properties reveal that the Hungaria family progenitor was an igneous body that formed under reduced conditions, and was compositionally consistent with the enstatite achondrite (i.e., aubrite) meteorite group.

Thermal signature characteristics of vehicle/terrain interaction disturbances: implications for battlefield vehicle classification.

PubMed

Eastes, John W; Mason, George L; Kusinger, Alan E

2004-05-01

Thermal emissivity spectra (8-14 microm) of track impressions/background were determined in conjunction with operation of six military vehicle types, T-72 and M1 Tanks, an M2 Bradley Fighting Vehicle, a 5-ton truck, a D7 tractor, and a High Mobility Multipurpose Wheeled Vehicle (HMMWV), over diverse soil surfaces to determine if vehicle type could be related to track thermal signatures. Results suggest soil compaction and fragmentation/pulverization are primary parameters affecting track signatures and that soil and vehicle/terrain-contact type determine which parameter dominates. Steel-tracked vehicles exert relatively low ground-contact pressure but tend to fragment/pulverize soil more so than do rubber-tired vehicles, which tend mainly to compact. In quartz-rich, lean clay soil tracked vehicles produced impressions with spectral contrast of the quartz reststrahlen features decreased from that of the background. At the same time, 5-ton truck tracks exhibited increased contrast on the same surface, suggesting that steel tracks fragmented soil while rubber tires mainly produced compaction. The structure of materials such as sand and moist clay-rich river sediment makes them less subject to further fragmentation/pulverization; thus, compaction was the main factor affecting signatures in these media, and both tracked and wheeled vehicles created impressions with increased spectral contrast on these surfaces. These results suggest that remotely sensed thermal signatures could differentiate tracked and wheeled vehicles on terrain in many areas of the world of strategic interest. Significant applications include distinguishing visually/spectrally identical lightweight decoys from actual threat vehicles.

Strong and nonlinear effects of fragmentation on ecosystem service provision at multiple scales

NASA Astrophysics Data System (ADS)

Mitchell, Matthew G. E.; Bennett, Elena M.; Gonzalez, Andrew

2015-09-01

Human actions, such as converting natural land cover to agricultural or urban land, result in the loss and fragmentation of natural habitat, with important consequences for the provision of ecosystem services. Such habitat loss is especially important for services that are supplied by fragments of natural land cover and that depend on flows of organisms, matter, or people across the landscape to produce benefits, such as pollination, pest regulation, recreation and cultural services. However, our quantitative knowledge about precisely how different patterns of landscape fragmentation might affect the provision of these types of services is limited. We used a simple, spatially explicit model to evaluate the potential impact of natural land cover loss and fragmentation on the provision of hypothetical ecosystem services. Based on current literature, we assumed that fragments of natural land cover provide ecosystem services to the area surrounding them in a distance-dependent manner such that ecosystem service flow depended on proximity to fragments. We modeled seven different patterns of natural land cover loss across landscapes that varied in the overall level of landscape fragmentation. Our model predicts that natural land cover loss will have strong and unimodal effects on ecosystem service provision, with clear thresholds indicating rapid loss of service provision beyond critical levels of natural land cover loss. It also predicts the presence of a tradeoff between maximizing ecosystem service provision and conserving natural land cover, and a mismatch between ecosystem service provision at landscape versus finer spatial scales. Importantly, the pattern of landscape fragmentation mitigated or intensified these tradeoffs and mismatches. Our model suggests that managing patterns of natural land cover loss and fragmentation could help influence the provision of multiple ecosystem services and manage tradeoffs and synergies between services across different human-dominated landscapes.

Synthesis and testing of ZnO nanoparticles for photo-initiation: experimental observation of two different non-migration initiators for bulk polymerization

NASA Astrophysics Data System (ADS)

Schmitt, M.

2015-05-01

The migration and transport of polymerization initiators are problematic for commercially used polymerization procedures. For example, UV printing of packaging generates products with potentially harmful components that come in contact with food. Enlarging the size of the initiator is the only way to prevent contamination, e.g., by gas phase transport. In this manuscript, the synthesis and advanced and full analyses of novel nanoparticle-based types of non-migration, fragmenting and non-fragmenting photo-initiators will be presented in detail. This study introduces non-fragmenting/``Norrish type II'' and fragmenting/``Norrish type I'' ZnO nanoparticle-based initiators and compares them with two commercial products, a ``Norrish type I'' initiator and a ``Norrish type II'' initiator. Therefore, inter alia, the recently developed analysis involves examining the solidification by UV-vis and the double bond content by Raman. Irradiation is performed using absolute and spectrally calibrated xenon flash lights. A novel procedure for absolute and spectral calibration of such light sources is also presented. The non-optimized ``Norrish type II'' particle-based initiator is already many times faster than benzophenone, which is a molecular initiator of the same non-fragmenting type. This experimentally observed difference in reactive particle-based systems without co-initiators is unexpected. Co-initiators are normally an additional molecular species, which leads to migration problems. The discovery of significant initiation potential resulting in a very well-dispersed organic-inorganic hybrid material suggests a new field of research opportunities at the interface of physical chemistry, polymer chemistry and engineering science, with enormous value for human health.The migration and transport of polymerization initiators are problematic for commercially used polymerization procedures. For example, UV printing of packaging generates products with potentially harmful components that come in contact with food. Enlarging the size of the initiator is the only way to prevent contamination, e.g., by gas phase transport. In this manuscript, the synthesis and advanced and full analyses of novel nanoparticle-based types of non-migration, fragmenting and non-fragmenting photo-initiators will be presented in detail. This study introduces non-fragmenting/``Norrish type II'' and fragmenting/``Norrish type I'' ZnO nanoparticle-based initiators and compares them with two commercial products, a ``Norrish type I'' initiator and a ``Norrish type II'' initiator. Therefore, inter alia, the recently developed analysis involves examining the solidification by UV-vis and the double bond content by Raman. Irradiation is performed using absolute and spectrally calibrated xenon flash lights. A novel procedure for absolute and spectral calibration of such light sources is also presented. The non-optimized ``Norrish type II'' particle-based initiator is already many times faster than benzophenone, which is a molecular initiator of the same non-fragmenting type. This experimentally observed difference in reactive particle-based systems without co-initiators is unexpected. Co-initiators are normally an additional molecular species, which leads to migration problems. The discovery of significant initiation potential resulting in a very well-dispersed organic-inorganic hybrid material suggests a new field of research opportunities at the interface of physical chemistry, polymer chemistry and engineering science, with enormous value for human health. Electronic supplementary information (ESI) available: Multiple additional figures and images concerning the synthesis, characterization, data evaluation, TEMs and ESR spectra are available free of charge. See DOI: 10.1039/c5nr00850f

Libraries of Peptide Fragmentation Mass Spectra Database

National Institute of Standards and Technology Data Gateway

SRD 1C NIST Libraries of Peptide Fragmentation Mass Spectra Database (Web, free access)   The purpose of the library is to provide peptide reference data for laboratories employing mass spectrometry-based proteomics methods for protein analysis. Mass spectral libraries identify these compounds in a more sensitive and robust manner than alternative methods. These databases are freely available for testing and development of new applications.

Effects of fragmentation on the spatial ecology of the California Kingsnake (Lampropeltis californiae)

USGS Publications Warehouse

Anguiano, Michael P.; Diffendorfer, James E.

2015-01-01

We investigated the spatial ecology of the California Kingsnake (Lampropeltis californiae) in unfragmented and fragmented habitat with varying patch sizes and degrees of exposure to urban edges. We radiotracked 34 Kingsnakes for up to 3 yr across four site types: interior areas of unfragmented ecological reserves, the urbanized edge of these reserves, large habitat fragments, and small habitat fragments. There was no relationship between California Kingsnake movements and the degree of exposure to urban edges and fragmentation. Home range size and movement patterns of Kingsnakes on edges and fragments resembled those in unfragmented sites. Average home-range size on each site type was smaller than the smallest fragment in which snakes were tracked. The persistence of California Kingsnakes in fragmented landscapes may be related directly to their small spatial movement patterns, home-range overlap, and ability to use urban edge habitat.

Ar-40/Ar-39 ages and cosmic ray exposure ages of Apollo 14 samples.

NASA Technical Reports Server (NTRS)

Turner, G.; Huneke, J. C.; Podosek, F. A.; Wasserburg, G. J.

1971-01-01

We have used the Ar-40/Ar-39 dating technique on eight samples of Apollo 14 rocks (14053, 14310), breccia fragments (14321), and soil fragments (14001, 14167). The large basalt fragments give reasonable Ar-40/Ar-39 release patterns and yield well defined crystallization ages of 3.89-3.95 aeons. Correlation of the Ar-40/Ar-39 release patterns with Ar-39/Ar-37 patterns showed that the low temperature fractions with high radiogenic argon loss came from K-rich phases. A highly shocked sample and fragments included in the breccia yield complex release patterns with a low temperature peak. The total argon age of these fragments is 3.95 aeons. Cosmic ray exposure ages on these samples are obtained from the ratio of spallogenic Ar-38 to reactor induced Ar-37 and show a distinct grouping of low exposure ages of 26 m.y. correlated with Cone crater. Other samples have exposure ages of more than 260 m.y. and identify material with a more complex integrated cosmic age exposure history.

Characterization of Cryptosporidium parvum by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Magnuson, Matthew L.; Owens, James H.; Kelty, Catherine A.

2000-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) was used to investigate whole and freeze-thawed Cryptosporidium parvum oocysts. Whole oocysts revealed some mass spectral features. Reproducible patterns of spectral markers and increased sensitivity were obtained after the oocysts were lysed with a freeze-thaw procedure. Spectral-marker patterns for C. parvum were distinguishable from those obtained for Cryptosporidium muris. One spectral marker appears specific for the genus, while others appear specific at the species level. Three different C. parvum lots were investigated, and similar spectral markers were observed in each. Disinfection of the oocysts reduced and/or eliminated the patterns of spectral markers. PMID:11055915

Comprehensive Study On The Metastable Negative Ion Fragmentation Of Individual Dna Components And Larger Oligonucleotides

NASA Astrophysics Data System (ADS)

Ingolfsson, O.; Flosadottir, H. D.; Omarsson, B.; Ilko, B.

2010-07-01

Here we present a systematic study on the unimolecular decay pathways of the deprotonated building blocks of DNA and RNA to address the following questions: 1. Are the negative ion fragmentation patterns observed in the metastable decay of individual DNA components still evident when these are combined to larger oligonucleotides? 2. What is the significance of the charge location in determining the fragmentation pathways in the metastable decay process? 3. Are those metastable decay channels relevant in dissociative electron attachment to DNA components? To address these questions we have studied the fragmentation patterns of the deprotonated ribose and ribose 5'-monophosphate, the fragmentation patterns of the individual bases, all nucleosides and all 2'-deoxynucleosides as well as the individual nucleotides and several combinations of hexameric oligonucleotides. Furthermore, to understand the significance of the charge location in determining the fragmentation path in the metastable decay process of these deprotonated ions we have also studied modified uridine and guanosine. These have been modified to block different deprotonation sites and thus to control the initial step in the in the fragmentation process i.e. the site of deprotonation. In addition to our experimental approach we have also simulated the metastable fragmentation of the deprotonated uridine and 2'-deoxyguanosine to clarify the mechanisms and fragmentation patterns observed. Where data is available, the results are compared to dissociative electron attachment to DNA components and discussed in context to the underlying mechanism. Experiments on modified nucleosides where selected deprotonation sites have been blocked are used to verify the predicted reaction paths and imulations on uridine and 2'-deoxyguanosine are compared to the experimental results and used to shed light on the mechanisms involved.

Anthropogenic ecosystem fragmentation drives shared and unique patterns of sexual signal divergence among three species of Bahamian mosquitofish.

PubMed

Giery, Sean T; Layman, Craig A; Langerhans, R Brian

2015-08-01

When confronted with similar environmental challenges, different organisms can exhibit dissimilar phenotypic responses. Therefore, understanding patterns of phenotypic divergence for closely related species requires considering distinct evolutionary histories. Here, we investigated how a common form of human-induced environmental alteration, habitat fragmentation, may drive phenotypic divergence among three closely related species of Bahamian mosquitofish (Gambusia spp.). Focusing on one phenotypic trait (male coloration), having a priori predictions of divergence, we tested whether populations persisting in fragmented habitats differed from those inhabiting unfragmented habitats and examined the consistency of the pattern across species. Species exhibited both shared and unique patterns of phenotypic divergence between the two types of habitats, with shared patterns representing the stronger effect. For all species, populations in fragmented habitats had fewer dorsal-fin spots. In contrast, the magnitude and trajectory of divergence in dorsal-fin color, a sexually selected trait, differed among species. We identified fragmentation-mediated increased turbidity as a possible driver of these trait shifts. These results suggest that even closely related species can exhibit diverse phenotypic responses when encountering similar human-mediated selection regimes. This element of unpredictability complicates forecasting the phenotypic responses of wild organisms faced with anthropogenic change - an important component of biological conservation and ecosystem management.

Anthropogenic ecosystem fragmentation drives shared and unique patterns of sexual signal divergence among three species of Bahamian mosquitofish

PubMed Central

Giery, Sean T; Layman, Craig A; Langerhans, R Brian

2015-01-01

When confronted with similar environmental challenges, different organisms can exhibit dissimilar phenotypic responses. Therefore, understanding patterns of phenotypic divergence for closely related species requires considering distinct evolutionary histories. Here, we investigated how a common form of human-induced environmental alteration, habitat fragmentation, may drive phenotypic divergence among three closely related species of Bahamian mosquitofish (Gambusia spp.). Focusing on one phenotypic trait (male coloration), having a priori predictions of divergence, we tested whether populations persisting in fragmented habitats differed from those inhabiting unfragmented habitats and examined the consistency of the pattern across species. Species exhibited both shared and unique patterns of phenotypic divergence between the two types of habitats, with shared patterns representing the stronger effect. For all species, populations in fragmented habitats had fewer dorsal-fin spots. In contrast, the magnitude and trajectory of divergence in dorsal-fin color, a sexually selected trait, differed among species. We identified fragmentation-mediated increased turbidity as a possible driver of these trait shifts. These results suggest that even closely related species can exhibit diverse phenotypic responses when encountering similar human-mediated selection regimes. This element of unpredictability complicates forecasting the phenotypic responses of wild organisms faced with anthropogenic change – an important component of biological conservation and ecosystem management. PMID:26240605

The investigation of substituent effects on the fragmentation pathways of pentacoordinated phenoxyspirophosphoranes by ESI-MSn.

PubMed

Cui, Xiaoyan; Sun, Can; Zhao, Pei; Wang, Yanyan; Guo, Yanchun; Zhao, Yufen; Cao, Shuxia

2018-04-01

The fragmentation pathways of pentacoordinated phenoxyspirophosphoranes were investigated in the positive mode by electrospray ionization multistage mass spectrometry. The results demonstrate that the sodium adducts of the title compounds undergo two competitive fragmentation pathways, and the fragmentation patterns are heavily dependent on the various substituent patterns at the phenolic group. An electron-withdrawing substituent at the ortho-position always results in the removal of a corresponding phenol analogue, while cleavage by spiroring opening becomes the predominant fragmentation pathway if an electron-donating substituent is at the phenolic group. The substituent effects on the competitive fragmentation pathways were further elucidated by theoretical calculations, single crystal structure analysis, and high-resolution mass spectrometry. The results contribute to the understanding of the gas-phase fragmentation reactions and the structure identification of spirophosphorane analogues by electrospray ionization multistage mass spectrometry. Copyright © 2018 John Wiley & Sons, Ltd.

Cultural and environmental influences on temporal-spectral development patterns of corn and soybeans

NASA Technical Reports Server (NTRS)

Crist, E. P.

1982-01-01

A technique for evaluating crop temporal-spectral development patterns is described and applied to the analysis of cropping practices and environmental conditions as they affect reflectance characteristics of corn and soybean canopies. Typical variations in field conditions are shown to exert significant influences on the spectral development patterns, and thereby to affect the separability of the two crops.

Structural, electronic and spectral properties of carborane-containing boron dipyrromethenes (BODIPYs): A first-principles study

NASA Astrophysics Data System (ADS)

Li, Xiaojun

2017-10-01

In this work, we reported the geometrical structures, electronic and spectral properties of the carborane-containing BODIPYs complexes using the density functional theory calculations. In two structures, the calculated main bond lengths and bond angels of structural framework are consistent with X-ray experiment, and the two BODIPYs complexes are thermodynamically and kinetically stable. The strongest DOS band is mainly dominated by the Bsbnd B and Bsbnd H σ-bonds of carborane fragment, whereas the π-type MOs on the pyrromethene fragment contribute to the high-energy DOS bands. Analysis of the AdNDP chemical bonding indicates that the carborane cage can be stabilized by eleven delocalized 3csbnd 2e and two delocalized 4csbnd 2e σ-bonds, while the pyrromethene fragment corresponds to five delocalized 3csbnd 2e π-bonds. In addition, the main characteristic peaks of the two simulated IR spectra for the BODIPYs complexes are properly assigned. Hopefully, all these results will be helpful for understanding the electronic structures, and further stimulate the study on the biological and medical applications.

Lactobacillus delbrueckii subsp. sunkii subsp. nov., isolated from sunki, a traditional Japanese pickle.

PubMed

Kudo, Yuko; Oki, Kaihei; Watanabe, Koichi

2012-11-01

Although four strains of bacteria isolated from sunki, a traditional Japanese, non-salted pickle, were initially identified as Lactobacillus delbrueckii, the molecular and phenotypic characteristics of the strains did not match those of any of the four recognized subspecies of L. delbrueckii. Together, the results of phenotypic characterization, DNA-DNA hybridizations (in which the relatedness values between the novel strains and type strains of the recognized subspecies of L. delbrueckii were all >88.7%) and 16S rRNA gene sequence, amplified fragment length polymorphism (AFLP) and whole-cell MALDI-TOF/MS spectral pattern analyses indicated that the four novel strains represented a single, novel subspecies, for which the name Lactobacillus delbrueckii subsp. sunkii subsp. nov. is proposed. The type strain is YIT 11221(T) (=JCM 17838(T) =DSM 24966(T)).

Fingerprints of Both Watson-Crick and Hoogsteen Isomers of the Isolated (Cytosine-Guanine)H+ Pair.

PubMed

Cruz-Ortiz, Andrés F; Rossa, Maximiliano; Berthias, Francis; Berdakin, Matías; Maitre, Philippe; Pino, Gustavo A

2017-11-16

 Gas phase protonated guanine-cytosine (CGH + ) pair was generated using an electrospray ionization source from solutions at two different pH (5.8 and 3.2). Consistent evidence from MS/MS fragmentation patterns and differential ion mobility spectra (DIMS) point toward the presence of two isomers of the CGH + pair, whose relative populations depend strongly on the pH of the solution. Gas phase infrared multiphoton dissociation (IRMPD) spectroscopy in the 900-1900 cm -1 spectral range further confirms that the Watson-Crick isomer is preferentially produced (91%) at pH = 5.8, while the Hoogsteen isomer predominates (66%) at pH = 3.2). These fingerprint signatures are expected to be useful for the development of new analytical methodologies and to trigger isomer selective photochemical studies of protonated DNA base pairs.

Mechanics of fragmentation of crocodile skin and other thin films.

PubMed

Qin, Zhao; Pugno, Nicola M; Buehler, Markus J

2014-05-27

Fragmentation of thin layers of materials is mediated by a network of cracks on its surface. It is commonly seen in dehydrated paintings or asphalt pavements and even in graphene or other two-dimensional materials, but is also observed in the characteristic polygonal pattern on a crocodile's head. Here, we build a simple mechanical model of a thin film and investigate the generation and development of fragmentation patterns as the material is exposed to various modes of deformation. We find that the characteristic size of fragmentation, defined by the mean diameter of polygons, is strictly governed by mechanical properties of the film material. Our result demonstrates that skin fragmentation on the head of crocodiles is dominated by that it features a small ratio between the fracture energy and Young's modulus, and the patterns agree well with experimental observations. Understanding this mechanics-driven process could be applied to improve the lifetime and reliability of thin film coatings by mimicking crocodile skin.

Mechanics of fragmentation of crocodile skin and other thin films

PubMed Central

Qin, Zhao; Pugno, Nicola M.; Buehler, Markus J.

2014-01-01

Fragmentation of thin layers of materials is mediated by a network of cracks on its surface. It is commonly seen in dehydrated paintings or asphalt pavements and even in graphene or other two-dimensional materials, but is also observed in the characteristic polygonal pattern on a crocodile's head. Here, we build a simple mechanical model of a thin film and investigate the generation and development of fragmentation patterns as the material is exposed to various modes of deformation. We find that the characteristic size of fragmentation, defined by the mean diameter of polygons, is strictly governed by mechanical properties of the film material. Our result demonstrates that skin fragmentation on the head of crocodiles is dominated by that it features a small ratio between the fracture energy and Young's modulus, and the patterns agree well with experimental observations. Understanding this mechanics-driven process could be applied to improve the lifetime and reliability of thin film coatings by mimicking crocodile skin. PMID:24862190

Mechanics of fragmentation of crocodile skin and other thin films

NASA Astrophysics Data System (ADS)

Qin, Zhao; Pugno, Nicola M.; Buehler, Markus J.

2014-05-01

Fragmentation of thin layers of materials is mediated by a network of cracks on its surface. It is commonly seen in dehydrated paintings or asphalt pavements and even in graphene or other two-dimensional materials, but is also observed in the characteristic polygonal pattern on a crocodile's head. Here, we build a simple mechanical model of a thin film and investigate the generation and development of fragmentation patterns as the material is exposed to various modes of deformation. We find that the characteristic size of fragmentation, defined by the mean diameter of polygons, is strictly governed by mechanical properties of the film material. Our result demonstrates that skin fragmentation on the head of crocodiles is dominated by that it features a small ratio between the fracture energy and Young's modulus, and the patterns agree well with experimental observations. Understanding this mechanics-driven process could be applied to improve the lifetime and reliability of thin film coatings by mimicking crocodile skin.

Comparing forest fragmentation and its drivers in China and the USA with Globcover v2.2

USGS Publications Warehouse

Chen, Mingshi; Mao, Lijun; Zhou, Chunguo; Vogelmann, James E.; Zhu, Zhiliang

2010-01-01

Forest loss and fragmentation are of major concern to the international community, in large part because they impact so many important environmental processes. The main objective of this study was to assess the differences in forest fragmentation patterns and drivers between China and the conterminous United States (USA). Using the latest 300-m resolution global land cover product, Globcover v2.2, a comparative analysis of forest fragmentation patterns and drivers was made. The fragmentation patterns were characterized by using a forest fragmentation model built on the sliding window analysis technique in association with landscape indices. Results showed that China’s forests were substantially more fragmented than those of the USA. This was evidenced by a large difference in the amount of interior forest area share, with China having 48% interior forest versus the 66% for the USA. China’s forest fragmentation was primarily attributed to anthropogenic disturbances, driven particularly by agricultural expansion from an increasing and large population, as well as poor forest management practices. In contrast, USA forests were principally fragmented by natural land cover types. However, USA urban sprawl contributed more to forest fragmentation than in China. This is closely tied to the USA’s economy, lifestyle and institutional processes. Fragmentation maps were generated from this study, which provide valuable insights and implications regarding habitat planning for rare and endangered species. Such maps enable development of strategic plans for sustainable forest management by identifying areas with high amounts of human-induced fragmentation, which improve risk assessments and enable better targeting for protection and remediation efforts. Because forest fragmentation is a long-term, complex process that is highly related to political, institutional, economic and philosophical arenas, both nations need to take effective and comprehensive measures to mitigate the negative effects of forest loss and fragmentation on the existing forest ecosystems.

Comparing forest fragmentation and its drivers in China and the USA with Globcover v2.2.

PubMed

Li, Mingshi; Mao, Lijun; Zhou, Chunguo; Vogelmann, James E; Zhu, Zhiliang

2010-12-01

Forest loss and fragmentation are of major concern to the international community, in large part because they impact so many important environmental processes. The main objective of this study was to assess the differences in forest fragmentation patterns and drivers between China and the conterminous United States (USA). Using the latest 300-m resolution global land cover product, Globcover v2.2, a comparative analysis of forest fragmentation patterns and drivers was made. The fragmentation patterns were characterized by using a forest fragmentation model built on the sliding window analysis technique in association with landscape indices. Results showed that China's forests were substantially more fragmented than those of the USA. This was evidenced by a large difference in the amount of interior forest area share, with China having 48% interior forest versus the 66% for the USA. China's forest fragmentation was primarily attributed to anthropogenic disturbances, driven particularly by agricultural expansion from an increasing and large population, as well as poor forest management practices. In contrast, USA forests were principally fragmented by natural land cover types. However, USA urban sprawl contributed more to forest fragmentation than in China. This is closely tied to the USA's economy, lifestyle and institutional processes. Fragmentation maps were generated from this study, which provide valuable insights and implications regarding habitat planning for rare and endangered species. Such maps enable development of strategic plans for sustainable forest management by identifying areas with high amounts of human-induced fragmentation, which improve risk assessments and enable better targeting for protection and remediation efforts. Because forest fragmentation is a long-term, complex process that is highly related to political, institutional, economic and philosophical arenas, both nations need to take effective and comprehensive measures to mitigate the negative effects of forest loss and fragmentation on the existing forest ecosystems. Copyright © 2010 Elsevier Ltd. All rights reserved.

Linkage and Anomeric Differentiation in Trisaccharides by Sequential Fragmentation and Variable-Wavelength Infrared Photodissociation

NASA Astrophysics Data System (ADS)

Tan, Yanglan; Polfer, Nicolas C.

2015-02-01

Carbohydrates and their derivatives play important roles in biological systems, but their isomeric heterogeneity also presents a considerable challenge for analytical techniques. Here, a stepwise approach using infrared multiple-photon dissociation (IRMPD) via a tunable CO2 laser (9.2-10.7 μm) was employed to characterize isomeric variants of glucose-based trisaccharides. After the deprotonated trisaccharides were trapped and fragmented to disaccharide C2 fragments in a Fourier transform ion cyclotron resonance (FTICR) cell, a further variable-wavelength infrared irradiation of the C2 ion produced wavelength-dependent dissociation patterns that are represented as heat maps. The photodissociation patterns of these C2 fragments are shown to be strikingly similar to the photodissociation patterns of disaccharides with identical glycosidic bonds. Conversely, the photodissociation patterns of different glycosidic linkages exhibit considerable differences. On the basis of these results, the linkage position and anomericity of glycosidic bonds of disaccharide units in trisaccharides can be systematically differentiated and identified, providing a promising approach to characterize the structures of isomeric oligosaccharides.

Multiscale assessment of landscape structure in heterogeneous forested area

NASA Astrophysics Data System (ADS)

Simoniello, T.; Pignatti, S.; Carone, M. T.; Fusilli, L.; Lanfredi, M.; Coppola, R.; Santini, F.

2010-05-01

The characterization of landscape structure in space or time is fundamental to infer ecological processes (Ingegnoli, 2002). Landscape pattern arrangements strongly influence forest ecological functioning and biodiversity, as an example landscape fragmentation can induce habitat degradation reducing forest species populations or limiting their recolonization. Such arrangements are spatially correlated and scale-dependent, therefore they have distinctive operational-scales at which they can be best characterized (Wu, 2004). In addition, the detail of the land cover classification can have substantial influences on resulting pattern quantification (Greenberg et al.2001). In order to evaluate the influence of the observational scales and labelling details, we investigated a forested area (Pollino National Park; southern Italy) by analyzing the patch arrangement derived from three remote sensing sensors having different spectral and spatial resolutions. In particular, we elaborated data from the hyperspectral MIVIS (102 bands; ~7m) and Hyperion (220 bands; 30m), and the multispectral Landsat-TM (7 bands; 30m). Moreover, to assess the landscape evolution we investigated the hierarchical structure of the study area (landscape, class, patch) by elaborating two Landsat-TM acquired in 1987 and 1998. Preprocessed data were classified by adopting a supervised procedure based on the Minimum Distance classifier. The obtained labelling correspond to Corine level 5 for the high resolution MIVIS data, to Corine level 4 for Hyperion and to an intermediate level 4-3 for TM data. The analysis was performed by taking into account patch density, diversity and evenness at landscape level; mean patch size and interdispersion at class level; patch structure and perimeter regularity at patch level. The three sensors described a landscape with a quite high level of richness and distribution. The high spectral and spatial resolution of MIVIS data provided the highest diversity level (SHDI = 2.05), even if the results obtained for TM were not so different (1.93), Hyperion showed the lowest value (1.79). The obtained evenness index was similar for all the landscapes (~ 0.72). At class level, the interdispersion increases as the spatial and spectral resolution power decrease. Due to the low labelling detail, TM classes represent an aggregation of MIVIS and Hyperion classes; therefore they result larger and more diffused over the territory favouring higher interspersion values in the computation. The investigation of the patch structure highlighted the highest MIVIS capability in describing the patch articulation; Hyperion and TM showed quite similar situation. The historical analysis based on TM imagery showed a fragmentation process for some forested patches (mainly beeches): an increase of structure complexity (higher FRACT) is coupled with a higher patch number and an extension reduction. On the whole, the obtained results showed that the multispectral Landsat-TM images represent a good data source for supporting studies on landscape structure of forested areas and that for analyzing the articulation of particular species the high spectral resolution needs to be coupled with a high spatial resolution, i.e. Hyperion sampling is not adequate for such a purpose.

Fragmentation modes and the evolution of life cycles.

PubMed

Pichugin, Yuriy; Peña, Jorge; Rainey, Paul B; Traulsen, Arne

2017-11-01

Reproduction is a defining feature of living systems. To reproduce, aggregates of biological units (e.g., multicellular organisms or colonial bacteria) must fragment into smaller parts. Fragmentation modes in nature range from binary fission in bacteria to collective-level fragmentation and the production of unicellular propagules in multicellular organisms. Despite this apparent ubiquity, the adaptive significance of fragmentation modes has received little attention. Here, we develop a model in which groups arise from the division of single cells that do not separate but stay together until the moment of group fragmentation. We allow for all possible fragmentation patterns and calculate the population growth rate of each associated life cycle. Fragmentation modes that maximise growth rate comprise a restrictive set of patterns that include production of unicellular propagules and division into two similar size groups. Life cycles marked by single-cell bottlenecks maximise population growth rate under a wide range of conditions. This surprising result offers a new evolutionary explanation for the widespread occurrence of this mode of reproduction. All in all, our model provides a framework for exploring the adaptive significance of fragmentation modes and their associated life cycles.

Fragmentation modes and the evolution of life cycles

PubMed Central

Rainey, Paul B.

2017-01-01

Reproduction is a defining feature of living systems. To reproduce, aggregates of biological units (e.g., multicellular organisms or colonial bacteria) must fragment into smaller parts. Fragmentation modes in nature range from binary fission in bacteria to collective-level fragmentation and the production of unicellular propagules in multicellular organisms. Despite this apparent ubiquity, the adaptive significance of fragmentation modes has received little attention. Here, we develop a model in which groups arise from the division of single cells that do not separate but stay together until the moment of group fragmentation. We allow for all possible fragmentation patterns and calculate the population growth rate of each associated life cycle. Fragmentation modes that maximise growth rate comprise a restrictive set of patterns that include production of unicellular propagules and division into two similar size groups. Life cycles marked by single-cell bottlenecks maximise population growth rate under a wide range of conditions. This surprising result offers a new evolutionary explanation for the widespread occurrence of this mode of reproduction. All in all, our model provides a framework for exploring the adaptive significance of fragmentation modes and their associated life cycles. PMID:29166656

Assessment of forest fragmentation in southern New England using remote sensing and geographic information systems technology

USGS Publications Warehouse

Vogelmann, James E.

1995-01-01

Spatial patterns and rates of forest fragmentation were assessed using digital remote sensing data for a region in southern New England that included 157 townships in southern New Hampshire and northeastern Massachusetts. The study area has undergone marked population increases over the last several decades. Following classification of 1973 and 1988 Landsat Multispectral Scanner data into forest and nonforest classes, data were incorporated into a geographic information system. The natural logarithms of forest area to perimeter ratios, referred to as the forest continuity index, were used to assess patterns and trends of forest fragmentation across the region Forest continuity index values were extracted from each township for both data sets and compared with population data. Forest continuity index values were found to decrease with increasing population density until about 200 persons per square kilometer, after which the relationship stabilized. With slight population increases at low densities forest continuity index values declined sharply, implying abrupt increases in forest fragmentation. Results from the study indicated good negative correlations (r2 values of 0.81 and 0.77) between the Multispectral Scanner-derived forest continuity index and natural logs of township population density. Socioeconomic indicators such as affluence and commuting patterns did not appear to correlate well with forest fragmentation estimates. Decreases in forest continuity index values occurred throughout much of the study region between 1973 and 1988, suggesting that forest fragmentation is occurring over large regions within the eastern United States. It is technologically feasible to assess patterns and rates of forest fragmentation across much larger areas than analyzed in this study; such analyses would provide useful overviews enabling objective assessment of the magnitude of forest fragmentation.

Computerized recognition of persons by EEG spectral patterns.

PubMed

Stassen, H H

1980-07-01

Modified techniques of communication theory in connection with multivariate statistical procedures were applied to a sample of 82 patients for the purpose of defining EEG spectral patterns and for solving the relevant classification problems. Ten measurements per patient were made and it could be shown that a subject can be characterized and be recognized by his EEG spectral pattern with high reliability and a confidence probability of almost 90%. This result is valid not only for normal adults but also for schizophrenic patients, implying a close relationship between the EEG spectral pattern and the individual person. At the moment the nature of this relationship is not clear; in particular the supposed relationship to psychopathology could not be proved.

[Progress in the spectral library based protein identification strategy].

PubMed

Yu, Derui; Ma, Jie; Xie, Zengyan; Bai, Mingze; Zhu, Yunping; Shu, Kunxian

2018-04-25

Exponential growth of the mass spectrometry (MS) data is exhibited when the mass spectrometry-based proteomics has been developing rapidly. It is a great challenge to develop some quick, accurate and repeatable methods to identify peptides and proteins. Nowadays, the spectral library searching has become a mature strategy for tandem mass spectra based proteins identification in proteomics, which searches the experiment spectra against a collection of confidently identified MS/MS spectra that have been observed previously, and fully utilizes the abundance in the spectrum, peaks from non-canonical fragment ions, and other features. This review provides an overview of the implement of spectral library search strategy, and two key steps, spectral library construction and spectral library searching comprehensively, and discusses the progress and challenge of the library search strategy.

Selected issues connected with determination of requirements of spectral properties of camouflage patterns

NASA Astrophysics Data System (ADS)

Racek, František; Jobánek, Adam; Baláž, Teodor; Krejčí, Jaroslav

2017-10-01

Traditionally spectral reflectance of the material is measured and compared with permitted spectral reflectance boundaries. The boundaries are limited by upper and lower curve of spectral reflectance. The boundaries for unique color has to fulfil the operational requirements as a versatility of utilization through the all year seasons, day and weather condition on one hand and chromatic and spectral matching with background as well as the manufacturability on the other hand. The interval between the boundaries suffers with ambivalent feature. Camouflage pattern producer would be happy to see it much wider, but blending effect into its particular background could be better with narrower tolerance limits. From the point of view of long time user of camouflage pattern battledress, there seems to be another ambivalent feature. Width of the tolerance zone reflecting natural dispersion of spectral reflectance values allows the significant distortions of shape of the spectral curve inside the given boundaries.

Development of a digital-micromirror-device-based multishot snapshot spectral imaging system.

PubMed

Wu, Yuehao; Mirza, Iftekhar O; Arce, Gonzalo R; Prather, Dennis W

2011-07-15

We report on the development of a digital-micromirror-device (DMD)-based multishot snapshot spectral imaging (DMD-SSI) system as an alternative to current piezostage-based multishot coded aperture snapshot spectral imager (CASSI) systems. In this system, a DMD is used to implement compressive sensing (CS) measurement patterns for reconstructing the spatial/spectral information of an imaging scene. Based on the CS measurement results, we demonstrated the concurrent reconstruction of 24 spectral images. The DMD-SSI system is versatile in nature as it can be used to implement independent CS measurement patterns in addition to spatially shifted patterns that piezostage-based systems can offer. © 2011 Optical Society of America

Influence of volcanic activity on the population genetic structure of Hawaiian Tetragnatha spiders: Fragmentation, rapid population growth and the potential for accelerated evolution

USGS Publications Warehouse

Vandergast, A.G.; Gillespie, R.G.; Roderick, G.K.

2004-01-01

Volcanic activity on the island of Hawaii results in a cyclical pattern of habitat destruction and fragmentation by lava, followed by habitat regeneration on newly formed substrates. While this pattern has been hypothesized to promote the diversification of Hawaiian lineages, there have been few attempts to link geological processes to measurable changes in population structure. We investigated the genetic structure of three species of Hawaiian spiders in forests fragmented by a 150-year-old lava flow on Mauna Loa Volcano, island of Hawaii: Tetragnatha quasimodo (forest and lava flow generalist), T. anuenue and T. brevignatha (forest specialists). To estimate fragmentation effects on population subdivision in each species, we examined variation in mitochondrial and nuclear genomes (DNA sequences and allozymes, respectively). Population subdivision was higher for forest specialists than for the generalist in fragments separated by lava. Patterns of mtDNA sequence evolution also revealed that forest specialists have undergone rapid expansion, while the generalist has experienced more gradual population growth. Results confirm that patterns of neutral genetic variation reflect patterns of volcanic activity in some Tetragnatha species. Our study further suggests that population subdivision and expansion can occur across small spatial and temporal scales, which may facilitate the rapid spread of new character states, leading to speciation as hypothesized by H. L. Carson 30 years ago.

Chromatographic and mass spectral methods of identification for the side-chain and ring regioisomers of methylenedioxymethamphetamine.

PubMed

Aalberg, L; DeRuiter, J; Noggle, F T; Sippola, E; Clark, C R

2000-08-01

The popular drug of abuse 3,4-methylenedioxymethamphetamine (MDMA) is one of a total of 10 regioisomeric 2,3- and 3,4-methylenedioxyphenethylamines of MW 193 that yields regioisomeric fragment ions with equivalent mass (m/z 58 and 135/136) in the electron-impact (EI) mass spectrum. Thus, these 10 methylenedioxyphenethylamines are uniquely isomeric; they have the same molecular weight and equivalent major fragments in their mass spectra. The specific identification of one of these compounds (i.e., Ecstasy or 3,4-MDMA) in a forensic drug sample depends upon the analyst's ability to eliminate the other regioisomers as possible interfering or coeluting substances. This study reports the synthesis, chemical properties, spectral characterization, and chromatographic analysis of these 10 unique regioisomers. The ten 2,3- and 3,4-regioisomers of MDMA are synthesized from commercially available precursor chemicals. In the EI mass spectra, the side-chain regioisomers show some variation in the relative intensity of the major ions, with the exception of only one or two minor ions that might be considered side-chain specific fragments. The position of substitution for the methylenedioxy ring is not easily determined by mass spectral techniques, and the ultimate identification of any one of these amines with the elimination of the other nine must depend heavily upon chromatographic methods. The chromatographic separation of these 10 uniquely regioisomeric amines are studied using reversed-phase liquid chromatographic methods with gradient elution and gas chromatographic techniques with temperature program optimization.

Slow wave sleep in the chronically fatigued: Power spectra distribution patterns in chronic fatigue syndrome and primary insomnia.

PubMed

Neu, Daniel; Mairesse, Olivier; Verbanck, Paul; Le Bon, Olivier

2015-10-01

To investigate slow wave sleep (SWS) spectral power proportions in distinct clinical conditions sharing non-restorative sleep and fatigue complaints without excessive daytime sleepiness (EDS), namely the chronic fatigue syndrome (CFS) and primary insomnia (PI). Impaired sleep homeostasis has been suspected in both CFS and PI. We compared perceived sleep quality, fatigue and sleepiness symptom-intensities, polysomnography (PSG) and SWS spectral power distributions of drug-free CFS and PI patients without comorbid sleep or mental disorders, with a good sleeper control group. Higher fatigue without EDS and impaired perceived sleep quality were confirmed in both patient groups. PSG mainly differed in sleep fragmentation and SWS durations. Spectral analysis revealed a similar decrease in central ultra slow power (0.3-0.79Hz) proportion during SWS for both CFS and PI and an increase in frontal power proportions of faster frequencies during SWS in PI only. The latter was correlated to affective symptoms whereas lower central ultra slow power proportions were related to fatigue severity and sleep quality impairment. In combination with normal (PI) or even increased SWS durations (CFS), we found consistent evidence for lower proportions of slow oscillations during SWS in PI and CFS. Observing normal or increased SWS durations but lower proportions of ultra slow power, our findings suggest a possible quantitative compensation of altered homeostatic regulation. Copyright © 2015 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Typing of Human Mycobacterium avium Isolates in Italy by IS1245-Based Restriction Fragment Length Polymorphism Analysis

PubMed Central

Lari, Nicoletta; Cavallini, Michela; Rindi, Laura; Iona, Elisabetta; Fattorini, Lanfranco; Garzelli, Carlo

1998-01-01

All but 2 of 63 Mycobacterium avium isolates from distinct geographic areas of Italy exhibited markedly polymorphic, multibanded IS1245 restriction fragment length polymorphism (RFLP) patterns; 2 isolates showed the low-number banding pattern typical of bird isolates. By computer analysis, 41 distinct IS1245 patterns and 10 clusters of essentially identical strains were detected; 40% of the 63 isolates showed genetic relatedness, suggesting the existence of a predominant AIDS-associated IS1245 RFLP pattern. PMID:9817900

DNA fingerprinting and analysis of population structure in the chestnut blight fungus, Cryphonectria parasitica.

PubMed

Milgroom, M G; Lipari, S E; Powell, W A

1992-06-01

We analyzed DNA fingerprints in the chestnut blight fungus, Cryphonectria parasitica, for stability, inheritance, linkage and variability in a natural population. DNA fingerprints resulting from hybridization with a dispersed moderately repetitive DNA sequence of C. parasitica in plasmid pMS5.1 hybridized to 6-17 restriction fragments per individual isolate. In a laboratory cross and from progeny from a single perithecium collected from a field population, the presence/absence of 11 fragments in the laboratory cross and 12 fragments in the field progeny set segregated in 1:1 ratios. Two fragments in each progeny set cosegregated; no other linkage was detected among the segregating fragments. Mutations, identified by missing bands, were detected for only one fragment in which 4 of 43 progeny lacked a band present in both parents; no novel fragments were detected in any progeny. All other fragments appeared to be stably inherited. Hybridization patterns did not change during vegetative growth or sporulation. However, fingerprint patterns of single conidial isolates of strains EP155 and EP67 were found to be heterogenous due to mutations that occurred during culturing in the laboratory since these strains were first isolated in 1976-1977. In a population sample of 39 C. parasitica isolates, we found 33 different fingerprint patterns with pMS5.1. Most isolates differed from all other isolates by the presence or absence of several fragments. Six fingerprint patterns each occurred twice. Isolates with identical fingerprints occurred in cankers on the same chestnut stems three times; isolates within the other three pairs were isolated from cankers more than 5 m apart. The null hypothesis of random mating in this population could not be rejected if the six putative clones were removed from the analysis. Thus, a rough estimate of the clonal fraction of this population is 6 in 39 isolates (15.4%).

Analysis of In-Flight Collision Process During V-Type Firing Pattern in Surface Blasting Using Simple Physics

NASA Astrophysics Data System (ADS)

Chouhan, Lalit Singh; Raina, Avtar K.

2015-10-01

Blasting is a unit operation in Mine-Mill Fragmentation System (MMFS) and plays a vital role in mining cost. One of the goals of MMFS is to achieve optimum fragment size at minimal cost. Blast fragmentation optimization is known to result in better explosive energy utilization. Fragmentation depends on the rock, explosive and blast design variables. If burden, spacing and type of explosive used in a mine are kept constant, the firing sequence of blast-holes plays a vital role in rock fragmentation. To obtain smaller fragmentation size, mining professionals and relevant publications recommend V- or extended V-pattern of firing sequence. In doing so, it is assumed that the in-flight air collision breaks larger rock fragments into smaller ones, thus aiding further fragmentation. There is very little support to the phenomenon of breakage during in-flight collision of fragments during blasting in published literature. In order to assess the breakage of in-flight fragments due to collision, a mathematical simulation was carried over using basic principles of physics. The calculations revealed that the collision breakage is dependent on velocity of fragments, mass of fragments, the strength of the rock and the area of fragments over which collision takes place. For higher strength rocks, the in-flight collision breakage is very difficult to achieve. This leads to the conclusion that the concept demands an in-depth investigation and validation.

Synthesis and testing of ZnO nanoparticles for photo-initiation: experimental observation of two different non-migration initiators for bulk polymerization.

PubMed

Schmitt, M

2015-06-07

The migration and transport of polymerization initiators are problematic for commercially used polymerization procedures. For example, UV printing of packaging generates products with potentially harmful components that come in contact with food. Enlarging the size of the initiator is the only way to prevent contamination, e.g., by gas phase transport. In this manuscript, the synthesis and advanced and full analyses of novel nanoparticle-based types of non-migration, fragmenting and non-fragmenting photo-initiators will be presented in detail. This study introduces non-fragmenting/"Norrish type II" and fragmenting/"Norrish type I" ZnO nanoparticle-based initiators and compares them with two commercial products, a "Norrish type I" initiator and a "Norrish type II" initiator. Therefore, inter alia, the recently developed analysis involves examining the solidification by UV-vis and the double bond content by Raman. Irradiation is performed using absolute and spectrally calibrated xenon flash lights. A novel procedure for absolute and spectral calibration of such light sources is also presented. The non-optimized "Norrish type II" particle-based initiator is already many times faster than benzophenone, which is a molecular initiator of the same non-fragmenting type. This experimentally observed difference in reactive particle-based systems without co-initiators is unexpected. Co-initiators are normally an additional molecular species, which leads to migration problems. The discovery of significant initiation potential resulting in a very well-dispersed organic-inorganic hybrid material suggests a new field of research opportunities at the interface of physical chemistry, polymer chemistry and engineering science, with enormous value for human health.

Design of a variable-line-spacing grating pattern for spectrometers based on a grating Fresnel device.

PubMed

Li, Xinghui; Zhang, Jinchao; Zhou, Qian; Ni, Kai; Pang, Jinchao; Tian, Rui

2016-04-01

In this Letter, we propose a variable-line-spacing (VLS) grating pattern for a hybrid diffractive device termed a grating Fresnel (G-Fresnel) lens, which is used in spectrometers to improve spectral resolution over a wide spectral range. The VLS grating pattern disperses light of specific wavelengths with a different angle and position such that the aberration caused by the Fresnel surface can be compensated for. In this manner, high resolution can be achieved over a relatively wide spectral range. The VLS grating pattern is designed based on the least wave-change principle and simulated by ZEMAX. Results reveal that the VLS G-Fresnel device allows a subnanometer resolution over a spectral range of 200 nm.

Coulomb Fission in Multiply-Charged Ammonia Clusters: Accurate Measurements of the Rayleigh Instability Limit from Fragmentation Patterns.

PubMed

Harris, Christopher; Stace, Anthony J

2018-03-15

A series of experiments have been undertaken on the fragmentation of multiply charged ammonia clusters, (NH 3 ) n z+ , where z ≤ 8 and n ≤ 850, to establish Rayleigh instability limits, whereby clusters at certain critical sizes become unstable due to Coulomb repulsion between the resident charges. Experimental results on size-selected clusters are found to be in excellent agreement with theoretical predictions of Rayleigh instability limits at all values of the charge. Electrostatic theory has been used to help identify fragmentation patterns on the assumption that the clusters separate into two dielectric spheres, and the predicted Coulomb repulsion energies used to establish pathways and the sizes of cluster fragments. The results show that fragmentation is very asymmetric in terms of both the numbers of molecules involved and the amount of charge each fragment accommodates. For clusters carrying a charge ≤+4, the results show that fragmentation proceeds via the loss of small, singly charged clusters. When clusters carry a charge of +5 or more, the experimental observations suggest a marked switch in behavior. Although the laboratory measurements equate to fragmentation via the loss of a large dication cluster, electrostatic theory supports an interpretation that involves the sequential loss of two smaller, singly charged clusters possibly accompanied by the extensive evaporation of neutral molecules. It is suggested that this change in fragmentation pattern is driven by the channelling of Coulomb repulsion energy into intermolecular modes within these larger clusters. Overall, the results appear to support the ion evaporation model that is frequently used to interpret electrospray experiments.

Classification of time-of-flight secondary ion mass spectrometry spectra from complex Cu-Fe sulphides by principal component analysis and artificial neural networks.

PubMed

Kalegowda, Yogesh; Harmer, Sarah L

2013-01-08

Artificial neural network (ANN) and a hybrid principal component analysis-artificial neural network (PCA-ANN) classifiers have been successfully implemented for classification of static time-of-flight secondary ion mass spectrometry (ToF-SIMS) mass spectra collected from complex Cu-Fe sulphides (chalcopyrite, bornite, chalcocite and pyrite) at different flotation conditions. ANNs are very good pattern classifiers because of: their ability to learn and generalise patterns that are not linearly separable; their fault and noise tolerance capability; and high parallelism. In the first approach, fragments from the whole ToF-SIMS spectrum were used as input to the ANN, the model yielded high overall correct classification rates of 100% for feed samples, 88% for conditioned feed samples and 91% for Eh modified samples. In the second approach, the hybrid pattern classifier PCA-ANN was integrated. PCA is a very effective multivariate data analysis tool applied to enhance species features and reduce data dimensionality. Principal component (PC) scores which accounted for 95% of the raw spectral data variance, were used as input to the ANN, the model yielded high overall correct classification rates of 88% for conditioned feed samples and 95% for Eh modified samples. Copyright © 2012 Elsevier B.V. All rights reserved.

Structure of indazole N1-oxide derivatives studied by X-ray, theoretical methods, 1H, 13C, 15N NMR and EI/MS

NASA Astrophysics Data System (ADS)

Gerpe, Alejandra; Piro, Oscar E.; Cerecetto, Hugo; González, Mercedes

2007-12-01

A series of indazole N1-oxide derivatives has been spectroscopically studied in solution using 1H, 13C, and 15N NMR based on pulsed field gradient selected PFG 1H sbnd X (X = 13C and 15N) gHMQC and gHMBC experiments. Some indazoles were prepared using a new methodology to compare its spectral and structural data with the indazole N1-oxide parent compounds. The 13C resonances of the indazole N1-oxide carbon 3 and 7a demonstrate the N-oxide push-electron capability. The 15N resonances of the indazole N-oxide, nitrogen 1, are near to 30 ppm more shielded than the corresponding values in the indazole heterocycle (deoxygenated form). Moreover, the structures of one indazole and one indazole N-oxide were unambiguously confirmed by X-ray crystallography. The solid state structures were contrasted with the theoretical ones obtained in vacuo at different calculus level. The aromaticity of the derivatives was studied analyzing the H sbnd H coupling constants of indazole's aromatic hydrogens and measuring C sbnd C distances in the solid state. The fragmentation that takes place in EI/MS was gathered for all the indazole N-oxide derivatives and the general fragmentation pattern analyzed.

Evaluating differences in forest fragmentation and restoration between western natural forests and southeastern plantation forests in the United States.

PubMed

Ren, Xinyu; Lv, Yingying; Li, Mingshi

2017-03-01

Changes in forest ecosystem structure and functions are considered some of the research issues in landscape ecology. In this study, advancing Forman's theory, we considered five spatially explicit processes associated with fragmentation, including perforation, dissection, subdivision, shrinkage, and attrition, and two processes associated with restoration, i.e., increment and expansion processes. Following this theory, a forest fragmentation and restoration process model that can detect the spatially explicit processes and ecological consequences of forest landscape change was developed and tested in the current analysis. Using the National Land Cover Databases (2001, 2006 and 2011), the forest fragmentation and restoration process model was applied to US western natural forests and southeastern plantation forests to quantify and classify forest patch losses into one of the four fragmentation processes (the dissection process was merged into the subdivision process) and to classify the newly gained forest patches based on the two restoration processes. At the same time, the spatio-temporal differences in fragmentation and restoration patterns and trends between natural forests and plantations were further compared. Then, through overlaying the forest fragmentation/restoration processes maps with targeting year land cover data and land ownership vectors, the results from forest fragmentation and the contributors to forest restoration in federal and nonfederal lands were identified. Results showed that, in natural forests, the forest change patches concentrated around the urban/forest, cultivated/forest, and shrubland/forest interfaces, while the patterns of plantation change patches were scattered sparsely and irregularly. The shrinkage process was the most common type in forest fragmentation, and the average size was the smallest. Expansion, the most common restoration process, was observed in both natural forests and plantations and often occurred around the previous expansion or covered the previous subdivision or shrinkage processes. The overall temporal fragmentation pattern of natural forests had a "perforation-subdivision/shrinkage-attrition" pathway, which corresponded to Forman's landscape fragmentation rule, while the plantation forests did not follow the rule strictly. The main land cover types resulted from forest fragmentation in natural forests and plantation forests were shrubland and herbaceous, mainly through subdivision and shrinkages process. The processes and effects of restoration of plantation forests were more diverse and efficient, compared to the natural forest, which were simpler with a lower regrowth rate. The fragmentation mostly occurred in nonfederal lands. In natural forests, forest fragmentation pattern differed in different land tenures, yet plantations remained the same in federal and nonfederal lands. Copyright © 2016 Elsevier Ltd. All rights reserved.

Behavioral response of the coachwhip (Masticophis flagellum) to habitat fragment size and isolation in an urban landscape

USGS Publications Warehouse

Mitrovich, Milan J.; Diffendorfer, Jay E.; Fisher, Robert N.

2009-01-01

Habitat fragmentation is a significant threat to biodiversity worldwide. Habitat loss and the isolation of habitat fragments disrupt biological communities, accelerate the extinction of populations, and often lead to the alteration of behavioral patterns typical of individuals in large, contiguous natural areas. We used radio-telemetry to study the space-use behavior of the Coachwhip, a larger-bodied, wide-ranging snake species threatened by habitat fragmentation, in fragmented and contiguous areas of coastal southern California. We tracked 24 individuals at three sites over two years. Movement patterns of Coachwhips changed in habitat fragments. As area available to the snakes was reduced, individuals faced increased crowding, had smaller home-range sizes, tolerated greater home-range overlap, and showed more concentrated movement activity and convoluted movement pathways. The behavioral response shown by Coachwhips suggests, on a regional level, area-effects alone cannot explain observed extinctions on habitat fragments but, instead, suggests changes in habitat configuration are more likely to explain the decline of this species. Ultimately, if "edge-exposure" is a common cause of decline, then isolated fragments, appropriately buffered to reduce emigration and edge effects, may support viable populations of fragmentation-sensitive species.

Identification of cardiac glycosides in fractions from Periploca forrestii by high-performance liquid chromatography/diode-array detection/electrospray ionization multi-stage tandem mass spectrometry and liquid chromatography/nuclear magnetic resonance.

PubMed

Li, Yong; Wu, Xianfu; Li, Jianbei; Wang, Yinghong; Yu, Shishan; Lv, Haining; Qu, Jing; Abliz, Zeper; Liu, Jing; Liu, Yuanyan; Du, Dan

2010-02-01

Cardiac glycosides are a class of naturally occurring compounds that are characterized by some interesting biological activities and are widely distributed in the plant kingdom and can also be found in some animals. There is an interest in the chemical characterization of these molecules due to their toxicity and their use in medicines. In the study reported here, a combination of electrospray ionization tandem mass spectrometry with high-performance liquid chromatography equipped with diode-array detector (HPLC-DAD/ESI-MS(n)), and hyphenation to both liquid chromatography and nuclear magnetic resonance spectroscopy (HPLC/NMR) were utilized for the on-line analyses of cardiac glycosides from Periploca forrestii. The fragmentation patterns and (1)H NMR spectra of nine isolated cardiac glycosides were investigated; their fragmentation rules and (1)H NMR spectral characteristics were summarized and applied to the structural identification of similar constituents in fractions from P. forrestii. As a result, a total of nine trace cardiac glycosides were tentatively determined by analyses of accurate molecular masses, representative fragment ions and characteristic (1)H NMR signals provided by HPLC/high-resolution mass spectrometry (HRMS), HPLC-DAD/ESI-MS(n) and HPLC/(1)H NMR experiments, respectively. Of these, eight (2-9) are new compounds and one (1) is reported from P. forrestii for the first time. Results of the present study can benefit the rapid identification and targeted isolation of new cardiac glycosides from crude plant extracts. 2009 Elsevier B.V. All rights reserved.

Spectral and thermal study of the ternary complexes of nickel with sulfasalazine and some amino acids

NASA Astrophysics Data System (ADS)

Soliman, Ahmed A.

2006-12-01

The ternary complexes of Ni(II) with sulfasalazine (H 3SS) as a primary ligand and alanine (ala), aspartic acid (asp), histidene (hist), methionine (meth) and serine (ser) amino acids as secondary ligands have been synthesized. Characterization of the complexes was based on elemental analyses, IR, UV-vis, mass spectra, magnetic moment and thermal analysis (TG). The isolated complexes were found to have the general formula [M(HSS)(AA)]4H 2O (AA = ala, asp, hist, meth, or ser amino acid) where nickel is tetra-coordinated. The thermal stability of the complexes was studied and the weight losses for the decomposition of the complexes were calculated and correlated with the mass fragmentation pattern. In most cases, the amino acid moiety is removed along with the Schiff base moiety leaving NiO as a metallic residue. The metallic residue was confirmed by powder XRD measurements.

Azide derivatized anticancer agents of Vitamin K 3: X-ray structural, DSC, resonance spectral and API studies

NASA Astrophysics Data System (ADS)

Badave, Kirti; Patil, Yogesh; Gonnade, Rajesh; Srinivas, Darbha; Dasgupta, Rajan; Khan, Ayesha; Rane, Sandhya

2011-12-01

Compound 1 [1-imino (acetyl hydrazino)-Vitamin K 3], displays valence tautomerically related electronic isomers as Form I and Form II. Form I exhibits 2D packing fragment with 1D ribbon chains of N-H⋯O hydrogen bonds and shows EPR silent features. While Form II is EPR active and exhibits biradical nature with double quantum transitions at g = 2.0040. 1H NMR of compound 2, [1-imino (hydrazino carboxylate)-Vitamin K 3] and Form II exhibit π delocalization via resonance assisted H-bonding [RAHB] effect compared to Form I. Molecular interactions in Form I and II are visualized by DSC. The electronic structures of compounds 1 and 2 have been correlated to their API values by measuring anticancer activities, mitochondrial potentials and DNA shearing patterns. Form II and compound 2 indicate mitochondria mediated apoptosis (˜75% cell death) while Form I causes 35% cell death.

Efficient source for the production of ultradense deuterium D(-1) for laser-induced fusion (ICF).

PubMed

Andersson, Patrik U; Lönn, Benny; Holmlid, Leif

2011-01-01

A novel source which simplifies the study of ultradense deuterium D(-1) is now described. This means one step further toward deuterium fusion energy production. The source uses internal gas feed and D(-1) can now be studied without time-of-flight spectral overlap from the related dense phase D(1). The main aim here is to understand the material production parameters, and thus a relatively weak laser with focused intensity ≤10(12) W cm(-2) is employed for analyzing the D(-1) material. The properties of the D(-1) material at the source are studied as a function of laser focus position outside the emitter, deuterium gas feed, laser pulse repetition frequency and laser power, and temperature of the source. These parameters influence the D(-1) cluster size, the ionization mode, and the laser fragmentation patterns.

Signal Partitioning Algorithm for Highly Efficient Gaussian Mixture Modeling in Mass Spectrometry

PubMed Central

Polanski, Andrzej; Marczyk, Michal; Pietrowska, Monika; Widlak, Piotr; Polanska, Joanna

2015-01-01

Mixture - modeling of mass spectra is an approach with many potential applications including peak detection and quantification, smoothing, de-noising, feature extraction and spectral signal compression. However, existing algorithms do not allow for automated analyses of whole spectra. Therefore, despite highlighting potential advantages of mixture modeling of mass spectra of peptide/protein mixtures and some preliminary results presented in several papers, the mixture modeling approach was so far not developed to the stage enabling systematic comparisons with existing software packages for proteomic mass spectra analyses. In this paper we present an efficient algorithm for Gaussian mixture modeling of proteomic mass spectra of different types (e.g., MALDI-ToF profiling, MALDI-IMS). The main idea is automated partitioning of protein mass spectral signal into fragments. The obtained fragments are separately decomposed into Gaussian mixture models. The parameters of the mixture models of fragments are then aggregated to form the mixture model of the whole spectrum. We compare the elaborated algorithm to existing algorithms for peak detection and we demonstrate improvements of peak detection efficiency obtained by using Gaussian mixture modeling. We also show applications of the elaborated algorithm to real proteomic datasets of low and high resolution. PMID:26230717

Tandem mass spectrometry spectral libraries and library searching.

PubMed

Deutsch, Eric W

2011-01-01

Spectral library searching in the field of proteomics has been gaining visibility and use in the last few years, primarily due to the expansion of public proteomics data repositories and the large spectral libraries that can be generated from them. Spectral library searching has several advantages over conventional sequence searching: it is generally much faster, and has higher specificity and sensitivity. The speed increase is primarily, due to having a smaller, fully indexable search space of real spectra that are known to be observable. The increase in specificity and sensitivity is primarily due to the ability of a search engine to utilize the known intensities of the fragment ions, rather than just comparing with theoretical spectra as is done with sequence searching. The main disadvantage of spectral library searching is that one can only identify peptide ions that have been seen before and are stored in the spectral library. In this chapter, an overview of spectral library searching and the libraries currently available are presented.

Associations between forest fragmentation patterns and geneticstructure in Pfrimer’s Parakeet (Pyrrhura pfrimeri), an endangered endemic to central Brazil’s dry forests

USGS Publications Warehouse

Haig, Susan M.; Miller, Leonard F.; Bianchi, Carlos; Mullins, Thomas D.

2012-01-01

When habitat becomes fragmented, populations of species may become increasingly isolated. In the absence of habitat corridors, genetic structure may develop and populations risk reductions in genetic diversity from increased genetic drift and inbreeding. Deforestation of the Cerrado biome of Brazil, particularly of the dry forests within the Parana˜ River Basin, has incrementally occurred since the 1970s and increased forest fragmentation within the region. We performed landscape genetic analyses of Pfrimer’s parakeet (Pyrrhura pfrimeri), a globally endangered endemic to the region, to determine if forest fragmentation patterns were associated with genetic structuring in this species. We used previously generated satellite imagery that identified the locations of Parana˜ River Basin forest fragments in 1977, 1993/94, and 2008. Behavioral data quantifying the affinity of Pfrimer’s parakeet for forest habitat was used to parameterize empirically derived landscape conductance surfaces. Though genetic structure was observed among Pfrimer’s parakeet populations, no association between genetic and geographic distance was detected. Likewise, least cost path lengths, circuit theorybased resistance distances, and a new measure of least cost path length complexity could not be conclusively associated with genetic structure patterns. Instead, a new quantity that encapsulated connection redundancy from the 1977 forest fragmentation data provided the clearest associations with pairwise genetic differentiation patterns (Jost’s D: r = 0.72, P = 0.006; FST: r = 0.741, P = 0.001). Our analyses suggest a 35-year or more lag between deforestation and its effect on genetic structure. Because 66 % of the Parana˜ River Basin has been deforested since 1977, we expect that genetic structure will increase substantially among Pfrimer’s Parakeet populations in the future, especially if fragmentation continues at its current pace.

Global-scale patterns of forest fragmentation

Treesearch

Kurt H. Riitters; James D. Wickham; R. O' Neill; B. Jones; E. Smith

2000-01-01

We report an analysis of forest fragmentation based on 1-km resolution land-cover maps for the globe. Measurements in analysis windows from 81 km 2 (9 x 9 pixels, "small" scale) to 59,049 km 2 (243 x 243 pixels, "large" scale) were used to characterize the fragmentation around each forested pixel. We identified six categories of fragmentation (...

Chips off of Asteroid 4 Vesta: Evidence for the Parent Body of Basaltic Achondrite Meteorites.

PubMed

Binzel, R P; Xu, S

1993-04-09

For more than two decades, asteroid 4 Vesta has been debated as the source for the eucrite, diogenite, and howardite classes of basaltic achondrite meteorites. Its basaltic achondrite spectral properties are unlike those of other large main-belt asteroids. Telescopic measurements have revealed 20 small (diameters

Identifying scales of pattern in ecological data: a comparison of lacunarity, spectral and wavelet analyses

Treesearch

Sari C. Saunders; Jiquan Chen; Thomas D. Drummer; Eric J. Gustafson; Kimberley D. Brosofske

2005-01-01

Identifying scales of pattern in ecological systems and coupling patterns to processes that create them are ongoing challenges. We examined the utility of three techniques (lacunarity, spectral, and wavelet analysis) for detecting scales of pattern of ecological data. We compared the information obtained using these methods for four datasets, including: surface...

Time-aware service-classified spectrum defragmentation algorithm for flex-grid optical networks

NASA Astrophysics Data System (ADS)

Qiu, Yang; Xu, Jing

2018-01-01

By employing sophisticated routing and spectrum assignment (RSA) algorithms together with a finer spectrum granularity (namely frequency slot) in resource allocation procedures, flex-grid optical networks can accommodate diverse kinds of services with high spectrum-allocation flexibility and resource-utilization efficiency. However, the continuity and the contiguity constraints in spectrum allocation procedures may always induce some isolated, small-sized, and unoccupied spectral blocks (known as spectrum fragments) in flex-grid optical networks. Although these spectrum fragments are left unoccupied, they can hardly be utilized by the subsequent service requests directly because of their spectral characteristics and the constraints in spectrum allocation. In this way, the existence of spectrum fragments may exhaust the available spectrum resources for a coming service request and thus worsens the networking performance. Therefore, many reactive defragmentation algorithms have been proposed to handle the fragmented spectrum resources via re-optimizing the routing paths and the spectrum resources for the existing services. But the routing-path and the spectrum-resource re-optimization in reactive defragmentation algorithms may possibly disrupt the traffic of the existing services and require extra components. By comparison, some proactive defragmentation algorithms (e.g. fragmentation-aware algorithms) were proposed to suppress spectrum fragments from their generation instead of handling the fragmented spectrum resources. Although these proactive defragmentation algorithms induced no traffic disruption and required no extra components, they always left the generated spectrum fragments unhandled, which greatly affected their efficiency in spectrum defragmentation. In this paper, by comprehensively considering the characteristics of both the reactive and the proactive defragmentation algorithms, we proposed a time-aware service-classified (TASC) spectrum defragmentation algorithm, which simultaneously employed proactive and reactive mechanisms in suppressing spectrum fragments with the awareness of services' types and their duration times. By dividing the spectrum resources into several flexible groups according to services' types and limiting both the spectrum allocation and the spectrum re-tuning for a certain service inside one specific spectrum group according to its type, the proposed TASC defragmentation algorithm cannot only suppress spectrum fragments from generation inside each spectrum group, but also handle the fragments generated between two adjacent groups. In this way, the proposed TASC algorithm gains higher efficiency in suppressing spectrum fragments than both the reactive and the proactive defragmentation algorithms. Additionally, as the generation of spectrum fragments is retrained between spectrum groups and the defragmentation procedure is limited inside each spectrum group, the induced traffic disruption for the existing services can be possibly reduced. Besides, the proposed TASC defragmentation algorithm always re-tunes the spectrum resources of the service with the maximum duration time first in spectrum defragmentation procedure, which can further reduce spectrum fragments because of the fact that the services with longer duration times always have higher possibility in inducing spectrum fragments than the services with shorter duration times. The simulation results show that the proposed TASC defragmentation algorithm can significantly reduce the number of the generated spectrum fragments while improving the service blocking performance.

Mass spectrometry analysis of terpene lactones in Ginkgo biloba.

PubMed

Ding, Shujing; Dudley, Ed; Song, Qingbao; Plummer, Sue; Tang, Jiandong; Newton, Russell P; Brenton, A Gareth

2008-01-01

Terpene lactones are a family of compounds with unique chemical structures, first recognised in an extract of Ginkgo biloba. The discovery of terpene lactone derivatives has recently been reported in more and more plant extracts and even food products. In this study, mass spectrometric characteristics of the standard terpene lactones in Ginkgo biloba were comprehensively studied using both an ion trap and a quadrupole time-of-flight (QTOF) mass spectrometer. The mass spectral fragmentation data from both techniques was compared to obtain the mass spectrometric fragmentation pathways of the terpene lactones with high confidence. The data obtained will facilitate the analysis and identification of terpene lactones in future plant research via the fragmentation knowledge reported here.

Characterizing fragmentation of the collective forests in southern China from multitemporal Landsat imagery: A case study from Kecheng district of Zhejiang province

USGS Publications Warehouse

Li, M.; Zhu, Z.; Vogelmann, James E.; Xu, D.; Wen, W.; Liu, A.

2011-01-01

Tropical and subtropical forests provide important ecosystem goods and services including carbon sequestration and biodiversity conservation. These forests are facing increasing socioeconomic pressures and are rapidly being degraded and fragmented. This analysis focuses on the rate of change and patterns of fragmentation in a collective forest area in Zhejiang province, China, during the time period 1988–2005. The research consisted of two parts. The first was the development of general land cover maps and the identification of land cover changes by interpreting Landsat Thematic Mapper (TM) and Enhanced Thematic Mapper Plus (ETM+) time series imagery. The second part involved the computation and analysis of forest fragmentation metrics. For this portion of the study, fragmentation statistics were analyzed, and images were developed to depict forest fragmentation patterns and trends. Results revealed that there was a net loss of 7.8% in forest coverage, dropping from 66.8% in 1988 to 59.0% in 2005, primarily caused by agricultural expansion and poor forest management practices. An acceleration of forest fragmentation was also witnessed during the time intervals, which was evidenced by a decreasing trend in interior forest (57.2% in 1988, 55.0% in 1996 and 54.8% in 2005 respectively) coupled with the scales of the selected geospatial metrics. Continued forest loss and fragmentation are closely correlated with the existing political, educational, institutional and economic processes of contemporary China. To unlock the developmental potentials of the collective forests and to effectively mitigate the rate of forest loss and fragmentation, reforms of forest tenure and ecological immigration practices are recognized as a prospective alternative. The produced fragmentation maps further illustrates the importance of assessing landscape change history, especially the spatiotemporal patterns of forest fragments, when developing landscape level plans for biodiversity conservation, land use management and ecologically sustainable forestry.

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. A comparison of fragmentation patterns of linear dextran obtained by in-source decay, post-source decay and collision-induced dissociation and the stability of linear and cyclic glucans studied by in-source decay.

PubMed

Bashir, Sajid; Giannakopulos, Anastassios E; Derrick, Peter J; Critchley, Peter; Bottrill, Andrew; Padley, Henry J

2004-01-01

In the first part of this study fragmentation patterns from a range of dextran oligomers (containing 4-20 anhydroglucose units) were compared in three different methods of analysis coupled with matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry. Collision-induced-dissociation (CID), prompt in-source decay (ISD) and post-source decay (PSD) all caused cleavage of the glycosidic bonds. Both CID and to a lesser extent ISD caused further cleavage of pyranose rings of the individual sugar residues. There was very little cleavage of pyranose rings detected in the PSD spectrum. Derivatisation of the reducing end-groups of the oligodextrans with 1-phenyl-3-methyl-5-pyrazolone (PMP) restricted cleavage in the MALDI mass spectrometer to the non-reducing end, and further it enabled the saccharides to be separated by HPLC so that a single chain length could be examined as a standard. Maltoheptaose was also used as a standard. In the second part of the study prompt ISD-MALDI mass spectrometry was used to compare the fragmentation of three oligoglucans, dextran, maltodextrin and gamma cyclodextrin, that have different linkages and different secondary structure. The results showed that the degree of fragmentation correlated with the degree of freedom in the saccharide chains in solution determined by NMR. Dextran the most random conformation was fragmented most whereas there was little evidence of any fragments, not even glycosidic bond breakage from cyclodextrin, even when the laser power was increased considerably. The fragmentation pattern of maltodextrin was intermediate. The patterns of fragmentation produced by MALDI mass spectrometry, particularly where standards are available to calibrate the spectrum and the energy of the laser is controlled, can be used to predict the type of linkage present.

Evaluation of the performance of a tandem mass spectral library with mass spectral data extracted from literature.

PubMed

Würtinger, Philipp; Oberacher, Herbert

2012-01-01

MSforID represents a database of tandem mass spectral data obtained from (quasi-)molecular ions produced by atmospheric pressure ionization methods. At the current stage of development the library contains 12 122 spectra of 1208 small (bio-)organic molecules. The present work was aimed to evaluate the performance of the MSforID library in terms of accuracy and transferability with a collection of fragment ion mass spectra from various compounds acquired on multiple instruments. A literature survey was conducted to collect the set of sample spectra. A total number of 554 spectra covering 291 compounds were extracted from 109 publications. The majority of spectra originated from publications on applications of LC/MS/MS in drug monitoring, pharmacokinetics, environmental analysis, forensic analysis as well as food analysis. Almost all types of tandem mass spectrometric instruments distributed by the five most important instrument vendors were included in the study. The overall sensitivity of library search was found to be 96.4%, which clearly proves that the MSforID library can successfully handle data from a huge variety of mass spectrometric instruments to allow accurate compound identification. Only for spectra containing three or more fragment ions, however, the rate of classified matches (= matches with a relative average match probability (ramp) score > 40.0) was 95%. Ambiguous or unclassified results were mainly obtained for searches with single precursor-to-fragment ion transitions due to the insufficient specificity of such a low amount of structural information to unequivocally define a single compound. Copyright © 2011 John Wiley & Sons, Ltd.

Defining and Detecting Complex Peak Relationships in Mass Spectral Data: The Mz.unity Algorithm.

PubMed

Mahieu, Nathaniel G; Spalding, Jonathan L; Gelman, Susan J; Patti, Gary J

2016-09-20

Analysis of a single analyte by mass spectrometry can result in the detection of more than 100 degenerate peaks. These degenerate peaks complicate spectral interpretation and are challenging to annotate. In mass spectrometry-based metabolomics, this degeneracy leads to inflated false discovery rates, data sets containing an order of magnitude more features than analytes, and an inefficient use of resources during data analysis. Although software has been introduced to annotate spectral degeneracy, current approaches are unable to represent several important classes of peak relationships. These include heterodimers and higher complex adducts, distal fragments, relationships between peaks in different polarities, and complex adducts between features and background peaks. Here we outline sources of peak degeneracy in mass spectra that are not annotated by current approaches and introduce a software package called mz.unity to detect these relationships in accurate mass data. Using mz.unity, we find that data sets contain many more complex relationships than we anticipated. Examples include the adduct of glutamate and nicotinamide adenine dinucleotide (NAD), fragments of NAD detected in the same or opposite polarities, and the adduct of glutamate and a background peak. Further, the complex relationships we identify show that several assumptions commonly made when interpreting mass spectral degeneracy do not hold in general. These contributions provide new tools and insight to aid in the annotation of complex spectral relationships and provide a foundation for improved data set identification. Mz.unity is an R package and is freely available at https://github.com/nathaniel-mahieu/mz.unity as well as our laboratory Web site http://pattilab.wustl.edu/software/ .

An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile.

PubMed

Prakash, Celine; Haeseler, Arndt Von

2017-03-01

RNA sequencing (RNA-seq) has emerged as the method of choice for measuring the expression of RNAs in a given cell population. In most RNA-seq technologies, sequencing the full length of RNA molecules requires fragmentation into smaller pieces. Unfortunately, the issue of nonuniform sequencing coverage across a genomic feature has been a concern in RNA-seq and is attributed to biases for certain fragments in RNA-seq library preparation and sequencing. To investigate the expected coverage obtained from fragmentation, we develop a simple fragmentation model that is independent of bias from the experimental method and is not specific to the transcript sequence. Essentially, we enumerate all configurations for maximal placement of a given fragment length, F, on transcript length, T, to represent every possible fragmentation pattern, from which we compute the expected coverage profile across a transcript. We extend this model to incorporate general empirical attributes such as read length, fragment length distribution, and number of molecules of the transcript. We further introduce the fragment starting-point, fragment coverage, and read coverage profiles. We find that the expected profiles are not uniform and that factors such as fragment length to transcript length ratio, read length to fragment length ratio, fragment length distribution, and number of molecules influence the variability of coverage across a transcript. Finally, we explore a potential application of the model where, with simulations, we show that it is possible to correctly estimate the transcript copy number for any transcript in the RNA-seq experiment.

An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile

PubMed Central

Haeseler, Arndt Von

2017-01-01

Abstract RNA sequencing (RNA-seq) has emerged as the method of choice for measuring the expression of RNAs in a given cell population. In most RNA-seq technologies, sequencing the full length of RNA molecules requires fragmentation into smaller pieces. Unfortunately, the issue of nonuniform sequencing coverage across a genomic feature has been a concern in RNA-seq and is attributed to biases for certain fragments in RNA-seq library preparation and sequencing. To investigate the expected coverage obtained from fragmentation, we develop a simple fragmentation model that is independent of bias from the experimental method and is not specific to the transcript sequence. Essentially, we enumerate all configurations for maximal placement of a given fragment length, F, on transcript length, T, to represent every possible fragmentation pattern, from which we compute the expected coverage profile across a transcript. We extend this model to incorporate general empirical attributes such as read length, fragment length distribution, and number of molecules of the transcript. We further introduce the fragment starting-point, fragment coverage, and read coverage profiles. We find that the expected profiles are not uniform and that factors such as fragment length to transcript length ratio, read length to fragment length ratio, fragment length distribution, and number of molecules influence the variability of coverage across a transcript. Finally, we explore a potential application of the model where, with simulations, we show that it is possible to correctly estimate the transcript copy number for any transcript in the RNA-seq experiment. PMID:27661099

The evolution of urban sprawl: evidence of spatial heterogeneity and increasing land fragmentation.

PubMed

Irwin, Elena G; Bockstael, Nancy E

2007-12-26

We investigate the dynamics and spatial distribution of land use fragmentation in a rapidly urbanizing region of the United States to test key propositions regarding the evolution of sprawl. Using selected pattern metrics and data from 1973 and 2000 for the state of Maryland, we find significant increases in developed and undeveloped land fragmentation but substantial spatial heterogeneity as well. Estimated fragmentation gradients that describe mean fragmentation as a function of distance from urban centers confirm the hypotheses that fragmentation rises and falls with distance and that the point of maximum fragmentation shifted outward over time. However, rather than outward increases in sprawl balanced by development infill, we find substantial and significant increases in mean fragmentation values along the entire urban-rural gradient. These findings are in contrast to the results of Burchfield et al. [Burchfield M, Overman HG, Puga D, Turner MA (2006) Q J Econ 121:587-633], who conclude that the extent of sprawl remained roughly unchanged in the Unites States between 1976 and 1992. As demonstrated here, both the data and pattern measure used in their study are systematically biased against recording low-density residential development, the very land use that we find is most strongly associated with fragmentation. Other results demonstrate the association between exurban growth and increasing fragmentation and the systematic variation of fragmentation with nonurban factors. In particular, proximity to the Chesapeake Bay is negatively associated with fragmentation, suggesting that an attraction effect associated with this natural amenity has concentrated development.

The Multiple Impacts of Tropical Forest Fragmentation on Arthropod Biodiversity and on their Patterns of Interactions with Host Plants.

PubMed

Benítez-Malvido, Julieta; Dáttilo, Wesley; Martínez-Falcón, Ana Paola; Durán-Barrón, César; Valenzuela, Jorge; López, Sara; Lombera, Rafael

2016-01-01

Tropical rain forest fragmentation affects biotic interactions in distinct ways. Little is known, however, about how fragmentation affects animal trophic guilds and their patterns of interactions with host plants. In this study, we analyzed changes in biotic interactions in forest fragments by using a multitrophic approach. For this, we classified arthropods associated with Heliconia aurantiaca herbs into broad trophic guilds (omnivores, herbivores and predators) and assessed the topological structure of intrapopulation plant-arthropod networks in fragments and continuous forests. Habitat type influenced arthropod species abundance, diversity and composition with greater abundance in fragments but greater diversity in continuous forest. According to trophic guilds, coleopteran herbivores were more abundant in continuous forest and overall omnivores in fragments. Continuous forest showed a greater diversity of interactions than fragments. Only in fragments, however, did the arthropod community associated with H aurantiaca show a nested structure, suggesting novel and/or opportunistic host-arthropod associations. Plants, omnivores and predators contributed more to nestedness than herbivores. Therefore, Heliconia-arthropod network properties do not appear to be maintained in fragments mainly caused by the decrease of herbivores. Our study contributes to the understanding of the impact of fragmentation on the structure and dynamics of multitrophic arthropod communities associated with a particular plant species of the highly biodiverse tropical forests. Nevertheless, further replication of study sites is needed to strengthen the conclusion that forest fragmentation negatively affects arthropod assemblages.

The Multiple Impacts of Tropical Forest Fragmentation on Arthropod Biodiversity and on their Patterns of Interactions with Host Plants

PubMed Central

Benítez-Malvido, Julieta; Dáttilo, Wesley; Martínez-Falcón, Ana Paola; Durán-Barrón, César; Valenzuela, Jorge; López, Sara; Lombera, Rafael

2016-01-01

Tropical rain forest fragmentation affects biotic interactions in distinct ways. Little is known, however, about how fragmentation affects animal trophic guilds and their patterns of interactions with host plants. In this study, we analyzed changes in biotic interactions in forest fragments by using a multitrophic approach. For this, we classified arthropods associated with Heliconia aurantiaca herbs into broad trophic guilds (omnivores, herbivores and predators) and assessed the topological structure of intrapopulation plant-arthropod networks in fragments and continuous forests. Habitat type influenced arthropod species abundance, diversity and composition with greater abundance in fragments but greater diversity in continuous forest. According to trophic guilds, coleopteran herbivores were more abundant in continuous forest and overall omnivores in fragments. Continuous forest showed a greater diversity of interactions than fragments. Only in fragments, however, did the arthropod community associated with H aurantiaca show a nested structure, suggesting novel and/or opportunistic host-arthropod associations. Plants, omnivores and predators contributed more to nestedness than herbivores. Therefore, Heliconia-arthropod network properties do not appear to be maintained in fragments mainly caused by the decrease of herbivores. Our study contributes to the understanding of the impact of fragmentation on the structure and dynamics of multitrophic arthropod communities associated with a particular plant species of the highly biodiverse tropical forests. Nevertheless, further replication of study sites is needed to strengthen the conclusion that forest fragmentation negatively affects arthropod assemblages. PMID:26731271

Spectro-temporal modulation masking patterns reveal frequency selectivity.

PubMed

Oetjen, Arne; Verhey, Jesko L

2015-02-01

The present study investigated the possibility that the human auditory system demonstrates frequency selectivity to spectro-temporal amplitude modulations. Threshold modulation depth for detecting sinusoidal spectro-temporal modulations was measured using a generalized masked threshold pattern paradigm with narrowband masker modulations. Four target spectro-temporal modulations were examined, differing in their temporal and spectral modulation frequencies: a temporal modulation of -8, 8, or 16 Hz combined with a spectral modulation of 1 cycle/octave and a temporal modulation of 4 Hz combined with a spectral modulation of 0.5 cycles/octave. The temporal center frequencies of the masker modulation ranged from 0.25 to 4 times the target temporal modulation. The spectral masker-modulation center-frequencies were 0, 0.5, 1, 1.5, and 2 times the target spectral modulation. For all target modulations, the pattern of average thresholds for the eight normal-hearing listeners was consistent with the hypothesis of a spectro-temporal modulation filter. Such a pattern of modulation-frequency sensitivity was predicted on the basis of psychoacoustical data for purely temporal amplitude modulations and purely spectral amplitude modulations. An analysis of separability indicates that, for the present data set, selectivity in the spectro-temporal modulation domain can be described by a combination of a purely spectral and a purely temporal modulation filter function.

Solid-state NMR spectroscopy of 18.5 kDa myelin basic protein reconstituted with lipid vesicles: spectroscopic characterisation and spectral assignments of solvent-exposed protein fragments.

PubMed

Zhong, Ligang; Bamm, Vladimir V; Ahmed, Mumdooh A M; Harauz, George; Ladizhansky, Vladimir

2007-12-01

Myelin basic protein (MBP, 18.5 kDa isoform) is a peripheral membrane protein that is essential for maintaining the structural integrity of the multilamellar myelin sheath of the central nervous system. Reconstitution of the most abundant 18.5 kDa MBP isoform with lipid vesicles yields an aggregated assembly mimicking the protein's natural environment, but which is not amenable to standard solution NMR spectroscopy. On the other hand, the mobility of MBP in such a system is variable, depends on the local strength of the protein-lipid interaction, and in general is of such a time scale that the dipolar interactions are averaged out. Here, we used a combination of solution and solid-state NMR (ssNMR) approaches: J-coupling-driven polarization transfers were combined with magic angle spinning and high-power decoupling to yield high-resolution spectra of the mobile fragments of 18.5 kDa murine MBP in membrane-associated form. To partially circumvent the problem of short transverse relaxation, we implemented three-dimensional constant-time correlation experiments (NCOCX, NCACX, CONCACX, and CAN(CO)CX) that were able to provide interresidue and intraresidue backbone correlations. These experiments resulted in partial spectral assignments for mobile fragments of the protein. Additional nuclear Overhauser effect spectroscopy (NOESY)-based experiments revealed that the mobile fragments were exposed to solvent and were likely located outside the lipid bilayer, or in its hydrophilic portion. Chemical shift index analysis showed that the fragments were largely disordered under these conditions. These combined approaches are applicable to ssNMR investigations of other peripheral membrane proteins reconstituted with lipids.

Chronic escitalopram treatment attenuated the accelerated rapid eye movement sleep transitions after selective rapid eye movement sleep deprivation: a model-based analysis using Markov chains.

PubMed

Kostyalik, Diána; Vas, Szilvia; Kátai, Zita; Kitka, Tamás; Gyertyán, István; Bagdy, Gyorgy; Tóthfalusi, László

2014-11-19

Shortened rapid eye movement (REM) sleep latency and increased REM sleep amount are presumed biological markers of depression. These sleep alterations are also observable in several animal models of depression as well as during the rebound sleep after selective REM sleep deprivation (RD). Furthermore, REM sleep fragmentation is typically associated with stress procedures and anxiety. The selective serotonin reuptake inhibitor (SSRI) antidepressants reduce REM sleep time and increase REM latency after acute dosing in normal condition and even during REM rebound following RD. However, their therapeutic outcome evolves only after weeks of treatment, and the effects of chronic treatment in REM-deprived animals have not been studied yet. Chronic escitalopram- (10 mg/kg/day, osmotic minipump for 24 days) or vehicle-treated rats were subjected to a 3-day-long RD on day 21 using the flower pot procedure or kept in home cage. On day 24, fronto-parietal electroencephalogram, electromyogram and motility were recorded in the first 2 h of the passive phase. The observed sleep patterns were characterized applying standard sleep metrics, by modelling the transitions between sleep phases using Markov chains and by spectral analysis. Based on Markov chain analysis, chronic escitalopram treatment attenuated the REM sleep fragmentation [accelerated transition rates between REM and non-REM (NREM) stages, decreased REM sleep residence time between two transitions] during the rebound sleep. Additionally, the antidepressant avoided the frequent awakenings during the first 30 min of recovery period. The spectral analysis showed that the SSRI prevented the RD-caused elevation in theta (5-9 Hz) power during slow-wave sleep. Conversely, based on the aggregate sleep metrics, escitalopram had only moderate effects and it did not significantly attenuate the REM rebound after RD. In conclusion, chronic SSRI treatment is capable of reducing several effects on sleep which might be the consequence of the sub-chronic stress caused by the flower pot method. These data might support the antidepressant activity of SSRIs, and may allude that investigating the rebound period following the flower pot protocol could be useful to detect antidepressant drug response. Markov analysis is a suitable method to study the sleep pattern.

Behavioral and physiological responses to fruit availability of spider monkeys ranging in a small forest fragment

PubMed Central

Rimbach, Rebecca; Link, Andrés; Montes-Rojas, Andrés; Di Fiore, Anthony; Heistermann, Michael; Heymann, Eckhard W

2014-01-01

Numerous animal species currently experience habitat loss and fragmentation. This might result in behavioral and dietary adjustments, especially because fruit availability is frequently reduced in fragments. Food scarcity can result in elevated physiological stress levels, and chronic stress often has detrimental effects on individuals. Some animal species exhibit a high degree of fission–fusion dynamics, and theory predicts that these species reduce intragroup feeding competition by modifying their subgroup size according to resource availability. Until now, however, there have been few studies on how species with such fission–fission dynamics adjust their grouping patterns and social behavior in small fragments or on how food availability influences their stress levels. We collected data on fruit availability, feeding behavior, stress hormone levels (measured through fecal glucocorticoid metabolites (FGCM)), subgroup size, and aggression for two groups of brown spider monkeys (Ateles hybridus) in a small forest fragment in Colombia and examined whether fruit availability influences these variables. Contrary to our predictions, spider monkeys ranged in smaller subgroups, had higher FGCM levels and higher aggression rates when fruit availability was high compared to when it was low. The atypical grouping pattern of the study groups seems to be less effective at mitigating contest competition over food resources than more typical fission–fusion patterns. Overall, our findings illustrate that the relationship between resource availability, grouping patterns, aggression rates, and stress levels can be more complex than assumed thus far. Additional studies are needed to investigate the long-term consequences on the health and persistence of spider monkeys in fragmented habitats. PMID:24820229

Compressive spectral testbed imaging system based on thin-film color-patterned filter arrays.

PubMed

Rueda, Hoover; Arguello, Henry; Arce, Gonzalo R

2016-11-20

Compressive spectral imaging systems can reliably capture multispectral data using far fewer measurements than traditional scanning techniques. In this paper, a thin-film patterned filter array-based compressive spectral imager is demonstrated, including its optical design and implementation. The use of a patterned filter array entails a single-step three-dimensional spatial-spectral coding on the input data cube, which provides higher flexibility on the selection of voxels being multiplexed on the sensor. The patterned filter array is designed and fabricated with micrometer pitch size thin films, referred to as pixelated filters, with three different wavelengths. The performance of the system is evaluated in terms of references measured by a commercially available spectrometer and the visual quality of the reconstructed images. Different distributions of the pixelated filters, including random and optimized structures, are explored.

Self-organized mechano-chemical dynamics in amoeboid locomotion of Physarum fragments

NASA Astrophysics Data System (ADS)

Zhang, Shun; Guy, Robert D.; Lasheras, Juan C.; del Álamo, Juan C.

2017-05-01

The aim of this work is to quantify the spatio-temporal dynamics of flow-driven amoeboid locomotion in small (∼100 μm) fragments of the true slime mold Physarum polycephalum. In this model organism, cellular contraction drives intracellular flows, and these flows transport the chemical signals that regulate contraction in the first place. As a consequence of these non-linear interactions, a diversity of migratory behaviors can be observed in migrating Physarum fragments. To study these dynamics, we measure the spatio-temporal distributions of the velocities of the endoplasm and ectoplasm of each migrating fragment, the traction stresses it generates on the substratum, and the concentration of free intracellular calcium. Using these unprecedented experimental data, we classify migrating Physarum fragments according to their dynamics, finding that they often exhibit spontaneously coordinated waves of flow, contractility and chemical signaling. We show that Physarum fragments exhibiting symmetric spatio-temporal patterns of endoplasmic flow migrate significantly slower than fragments with asymmetric patterns. In addition, our joint measurements of ectoplasm velocity and traction stress at the substratum suggest that forward motion of the ectoplasm is enabled by a succession of stick-slip transitions, which we conjecture are also organized in the form of waves. Combining our experiments with a simplified convection-diffusion model, we show that the convective transport of calcium ions may be key for establishing and maintaining the spatio-temporal patterns of calcium concentration that regulate the generation of contractile forces.

Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

PubMed

van Agthoven, Maria A; Barrow, Mark P; Chiron, Lionel; Coutouly, Marie-Aude; Kilgour, David; Wootton, Christopher A; Wei, Juan; Soulby, Andrew; Delsuc, Marc-André; Rolando, Christian; O'Connor, Peter B

2015-12-01

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules. Graphical Abstract ᅟ.

Discovery of C5-C17 poly- and perfluoroalkyl substances in water by in-line SPE-HPLC-Orbitrap with in-source fragmentation flagging.

PubMed

Liu, Yanna; Pereira, Alberto Dos Santos; Martin, Jonathan W

2015-04-21

The presence of unknown organofluorine compounds in environmental samples has prompted the development of nontargeted analytical methods capable of detecting new perfluoroalkyl and polyfluoroalkyl substances (PFASs). By combining high volume injection with high performance liquid chromatography (HPLC) and ultrahigh resolution Orbitrap mass spectrometry, a sensitive (0.003-0.2 ng F/mL for model mass-labeled PFASs) untargeted workflow was developed for discovery and characterization of novel PFASs in water. In the first step, up to 5 mL of water is injected to in-line solid phase extraction, chromatographed by HPLC, and detected by electrospray ionization with mass spectral acquisition in parallel modes cycling back and forth: (i) full scan with ultrahigh resolving power (RP = 120,000, mass accuracy ≤3 ppm), and (ii) in-source fragmentation flagging scans designed to yield marker fragment ions including [C2F5](-) (m/z 118.992), [C3F7](-) (m/z 168.988), [SO4H](-) (m/z 96.959), and [Cl](-) (m/z 34.9). For flagged PFASs, plausible empirical formulas were generated from accurate masses, isotopic patterns, and fragment ions. In the second step, another injection is made to collect high resolution MS/MS spectra of suspect PFAS ions, allowing further confirmation of empirical formulas while also enabling preliminary structural characterization. The method was validated by applying it to an industrial wastewater, and 36 new PFASs were discovered. Of these, 26 were confidently assigned to 3 new PFAS classes that have not previously been reported in the environment: polyfluorinated sulfates (CnFn+3Hn-2SO4(-); n = 5, 7, 9, 11, 13, and 15), chlorine substituted perfluorocarboxylates (ClCnF2nCO2(-); n = 4-11), and hydro substituted perfluorocarboxylates (HCnF2nCO2(-); n = 5-16). Application of the technique to environmental water samples is now warranted.

Interactions between colloidal silver and photosynthetic pigments located in cyanobacteria fragments and in solution.

PubMed

Siejak, Przemysław; Frackowiak, Danuta

2007-09-25

Changes in the yield of the fluorescence emitted by pigments of photosynthetic organisms could be used for the establishment of the presence of some toxic substances. The presence of colloidal metals can be indicated by enhancement of pigments' emission as a result of plasmons generation. The spectra of the pigments of cyanobacterium Synechocystis located in the bacterium fragments and in solutions with and without colloidal silver additions have been measured. The quantum yield of the pigments' fluorescence in solution has been observed to increase at some wavelength of excitation, while the fluorescence of the pigments in the bacteria fragments has been only quenched as a consequence of interactions with colloidal silver particles. Close contact between pigment molecules located in bacteria fragments and silver particles is probably not possible. We plan in future to investigate the influence of other, more typical metal pollutants of water, using similar spectral methods and several other photosynthetic bacteria pigments, in solution, in cell fragments and in the whole bacteria organisms.

GUIDOS: tools for the assessment of pattern, connectivity, and fragmentation

NASA Astrophysics Data System (ADS)

Vogt, Peter

2013-04-01

Pattern, connectivity, and fragmentation can be considered as pillars for a quantitative analysis of digital landscape images. The free software toolbox GUIDOS (http://forest.jrc.ec.europa.eu/download/software/guidos) includes a variety of dedicated methodologies for the quantitative assessment of these features. Amongst others, Morphological Spatial Pattern Analysis (MSPA) is used for an intuitive description of image pattern structures and the automatic detection of connectivity pathways. GUIDOS includes tools for the detection and quantitative assessment of key nodes and links as well as to define connectedness in raster images and to setup appropriate input files for an enhanced network analysis using Conefor Sensinode. Finally, fragmentation is usually defined from a species point of view but a generic and quantifiable indicator is needed to measure fragmentation and its changes. Some preliminary results for different conceptual approaches will be shown for a sample dataset. Complemented by pre- and post-processing routines and a complete GIS environment the portable GUIDOS Toolbox may facilitate a holistic assessment in risk assessment studies, landscape planning, and conservation/restoration policies. Alternatively, individual analysis components may contribute to or enhance studies conducted with other software packages in landscape ecology.

Determination of awareness in patients with severe brain injury using EEG power spectral analysis

PubMed Central

Goldfine, Andrew M.; Victor, Jonathan D.; Conte, Mary M.; Bardin, Jonathan C.; Schiff, Nicholas D.

2011-01-01

Objective To determine whether EEG spectral analysis could be used to demonstrate awareness in patients with severe brain injury. Methods We recorded EEG from healthy controls and three patients with severe brain injury, ranging from minimally conscious state (MCS) to locked-in-state (LIS), while they were asked to imagine motor and spatial navigation tasks. We assessed EEG spectral differences from 4 to 24 Hz with univariate comparisons (individual frequencies) and multivariate comparisons (patterns across the frequency range). Results In controls, EEG spectral power differed at multiple frequency bands and channels during performance of both tasks compared to a resting baseline. As patterns of signal change were inconsistent between controls, we defined a positive response in patient subjects as consistent spectral changes across task performances. One patient in MCS and one in LIS showed evidence of motor imagery task performance, though with patterns of spectral change different from the controls. Conclusion EEG power spectral analysis demonstrates evidence for performance of mental imagery tasks in healthy controls and patients with severe brain injury. Significance EEG power spectral analysis can be used as a flexible bedside tool to demonstrate awareness in brain-injured patients who are otherwise unable to communicate. PMID:21514214

Dependence of astigmatism, far-field pattern, and spectral envelope width on active layer thickness of gain guided lasers with narrow stripe geometry

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

Mamine, T.

1984-06-15

The effects of active layer thickness on the astigmatism, the angle of far-field pattern width parallel to the junction, and the spectral envelope width of a gain guided laser with a narrow stripe geometry have been investigated analytically and experimentally. It is concluded that a large level of astigmatism, a narrow far-field pattern width, and a rapid convergence of the spectral envelope width are inherent to the gain guided lasers with thin active layers.

Care fragmentation, quality, and costs among chronically ill patients.

PubMed

Frandsen, Brigham R; Joynt, Karen E; Rebitzer, James B; Jha, Ashish K

2015-05-01

To assess the relationship between care fragmentation and both quality and costs of care for commercially insured, chronically ill patients. We used claims data from 2004 to 2008 for 506,376 chronically ill, privately insured enrollees of a large commercial insurance company to construct measures of fragmentation. We included patients in the sample if they had chronic conditions in any of the following categories: cardiovascular disease, diabetes, asthma, arthritis, or migraine. We assigned each patient a fragmentation index based on the patterns of care of their primary care provider (PCP), with care patterns spread across a higher number of providers considered to be more fragmented. We used regression analysis to examine the relationship between fragmentation and both quality and cost outcomes. Patients of PCPs in the highest quartile of fragmentation had a higher chance of having a departure from clinical best practice (32.8%, vs 25.9% among patients of PCPs in the lowest quartile of fragmentation; P < .001). Similarly, patients of PCPs with high fragmentation had higher rates of preventable hospitalizations (9.1% in highest quartile vs 7.1% in lowest quartile; P < .001). High fragmentation was associated with $4542 higher healthcare spending ($10,396 in the highest quartile vs $5854 in the lowest quartile; P < .001). We found similar or larger effects on quality and costs among patients when we examined the most frequently occurring disease groups individually. Chronically ill patients whose primary care providers offer highly fragmented care more often experience lapses in care quality and incur greater healthcare costs.

Analysis of human blood plasma cell-free DNA fragment size distribution using EvaGreen chemistry based droplet digital PCR assays.

PubMed

Fernando, M Rohan; Jiang, Chao; Krzyzanowski, Gary D; Ryan, Wayne L

2018-04-12

Plasma cell-free DNA (cfDNA) fragment size distribution provides important information required for diagnostic assay development. We have developed and optimized droplet digital PCR (ddPCR) assays that quantify short and long DNA fragments. These assays were used to analyze plasma cfDNA fragment size distribution in human blood. Assays were designed to amplify 76,135, 490 and 905 base pair fragments of human β-actin gene. These assays were used for fragment size analysis of plasma cell-free, exosome and apoptotic body DNA obtained from normal and pregnant donors. The relative percentages for 76, 135, 490 and 905 bp fragments from non-pregnant plasma and exosome DNA were 100%, 39%, 18%, 5.6% and 100%, 40%, 18%,3.3%, respectively. The relative percentages for pregnant plasma and exosome DNA were 100%, 34%, 14%, 23%, and 100%, 30%, 12%, 18%, respectively. The relative percentages for non-pregnant plasma pellet (obtained after 2nd centrifugation step) were 100%, 100%, 87% and 83%, respectively. Non-pregnant Plasma cell-free and exosome DNA share a unique fragment distribution pattern which is different from pregnant donor plasma and exosome DNA fragment distribution indicating the effect of physiological status on cfDNA fragment size distribution. Fragment distribution pattern for plasma pellet that includes apoptotic bodies and nuclear DNA was greatly different from plasma cell-free and exosome DNA. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation

NASA Astrophysics Data System (ADS)

Ren, Jianhua; Tian, Yuan; Hossain, Ekram; Connolly, Michael D.

2016-04-01

Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry.

Spatial-temporal-spectral EEG patterns of BOLD functional network connectivity dynamics

NASA Astrophysics Data System (ADS)

Lamoš, Martin; Mareček, Radek; Slavíček, Tomáš; Mikl, Michal; Rektor, Ivan; Jan, Jiří

2018-06-01

Objective. Growing interest in the examination of large-scale brain network functional connectivity dynamics is accompanied by an effort to find the electrophysiological correlates. The commonly used constraints applied to spatial and spectral domains during electroencephalogram (EEG) data analysis may leave part of the neural activity unrecognized. We propose an approach that blindly reveals multimodal EEG spectral patterns that are related to the dynamics of the BOLD functional network connectivity. Approach. The blind decomposition of EEG spectrogram by parallel factor analysis has been shown to be a useful technique for uncovering patterns of neural activity. The simultaneously acquired BOLD fMRI data were decomposed by independent component analysis. Dynamic functional connectivity was computed on the component’s time series using a sliding window correlation, and between-network connectivity states were then defined based on the values of the correlation coefficients. ANOVA tests were performed to assess the relationships between the dynamics of between-network connectivity states and the fluctuations of EEG spectral patterns. Main results. We found three patterns related to the dynamics of between-network connectivity states. The first pattern has dominant peaks in the alpha, beta, and gamma bands and is related to the dynamics between the auditory, sensorimotor, and attentional networks. The second pattern, with dominant peaks in the theta and low alpha bands, is related to the visual and default mode network. The third pattern, also with peaks in the theta and low alpha bands, is related to the auditory and frontal network. Significance. Our previous findings revealed a relationship between EEG spectral pattern fluctuations and the hemodynamics of large-scale brain networks. In this study, we suggest that the relationship also exists at the level of functional connectivity dynamics among large-scale brain networks when no standard spatial and spectral constraints are applied on the EEG data.

The effect of change in spectral slope and formant frequencies on the perception of loudness.

PubMed

Duvvuru, Sirisha; Erickson, Molly

2013-11-01

This study attempts to understand how changes in spectral slope and formant frequency influence changes in perceived loudness. It was hypothesized that voices synthesized with steeper spectral slopes will be perceived as less loud than voices synthesized with less steep spectral slopes, in spite of the fact that they are of equal root mean square (RMS) amplitude. It was also hypothesized that stimuli with higher formant patterns will be perceived as louder than those with lower formant patterns, in spite of the fact that they are of equal RMS amplitude. Repeated measures factorial design. For the pitches A3, C4, B4, and F5, three different source signals were synthesized with varying slopes of -9, -12, and -15 dB/octave using a frequency vibrato rate of 5.6 Hz and a frequency vibrato extent of 50 cents. Each of the three source signals were filtered using two formant patterns, a lower formant pattern typical of a mezzo-soprano (pattern A) and a higher formant pattern typical of a soprano (pattern B) for the vowel /a/. For each pitch, the six stimuli were combined into all possible pairs and normalized to equal RMS amplitude. Listeners were presented with 120 paired stimuli (60 pairs repeated twice). The listener's task was to indicate whether the first or second stimulus in the pair was louder. Generally, as the spectral slope decreased, perceived loudness increased, with the magnitude of the perceived difference in loudness being related to the degree of difference in spectral slope. Likewise, at all pitches except A3, perceived loudness increased as formant frequency increased. RMS amplitude is an important predictor of loudness perception, but many other factors also affect the perception of this important vocal parameter. Spectral composition is one such factor and must be considered when using loudness perception in the process of clinical diagnostics. Copyright © 2013 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

LC/QTOF-MS fragmentation of N-nitrosodimethylamine precursors in drinking water supplies is predictable and aids their identification.

PubMed

Hanigan, David; Ferrer, Imma; Thurman, E Michael; Herckes, Pierre; Westerhoff, Paul

2017-02-05

N-Nitrosodimethylamine (NDMA) is carcinogenic in rodents and occurs in chloraminated drinking water and wastewater effluents. NDMA forms via reactions between chloramines and mostly unidentified, N-containing organic matter. We developed a mass spectrometry technique to identify NDMA precursors by analyzing 25 model compounds with LC/QTOF-MS. We searched isolates of 11 drinking water sources and 1 wastewater using a custom MATLAB ® program and extracted ion chromatograms for two fragmentation patterns that were specific to the model compounds. Once a diagnostic fragment was discovered, we conducted MS/MS during a subsequent injection to confirm the precursor ion. Using non-target searches and two diagnostic fragmentation patterns, we discovered 158 potential NDMA precursors. Of these, 16 were identified using accurate mass combined with fragment and retention time matches of analytical standards when available. Five of these sixteen NDMA precursors were previously unidentified in the literature, three of which were metabolites of pharmaceuticals. Except methadone, the newly identified precursors all had NDMA molar yields of less than 5%, indicating that NDMA formation could be additive from multiple compounds, each with low yield. We demonstrate that the method is applicable to other disinfection by-product precursors by predicting and verifying the fragmentation patterns for one nitrosodiethylamine precursor. Copyright © 2016. Published by Elsevier B.V.

Tropical forest fragmentation affects floral visitors but not the structure of individual-based palm-pollinator networks.

PubMed

Dáttilo, Wesley; Aguirre, Armando; Quesada, Mauricio; Dirzo, Rodolfo

2015-01-01

Despite increasing knowledge about the effects of habitat loss on pollinators in natural landscapes, information is very limited regarding the underlying mechanisms of forest fragmentation affecting plant-pollinator interactions in such landscapes. Here, we used a network approach to describe the effects of forest fragmentation on the patterns of interactions involving the understory dominant palm Astrocaryum mexicanum (Arecaceae) and its floral visitors (including both effective and non-effective pollinators) at the individual level in a Mexican tropical rainforest landscape. Specifically, we asked: (i) Does fragment size affect the structure of individual-based plant-pollinator networks? (ii) Does the core of highly interacting visitor species change along the fragmentation size gradient? (iii) Does forest fragment size influence the abundance of effective pollinators of A. mexicanum? We found that fragment size did not affect the topological structure of the individual-based palm-pollinator network. Furthermore, while the composition of peripheral non-effective pollinators changed depending on fragment size, effective core generalist species of pollinators remained stable. We also observed that both abundance and variance of effective pollinators of male and female flowers of A. mexicanum increased with forest fragment size. These findings indicate that the presence of effective pollinators in the core of all forest fragments could keep the network structure stable along the gradient of forest fragmentation. In addition, pollination of A. mexicanum could be more effective in larger fragments, since the greater abundance of pollinators in these fragments may increase the amount of pollen and diversity of pollen donors between flowers of individual plants. Given the prevalence of fragmentation in tropical ecosystems, our results indicate that the current patterns of land use will have consequences on the underlying mechanisms of pollination in remnant forests.

Thermal History and Fragmentation of Ureilitic Asteroids: Insights from the Almahata Sitta Fall

NASA Technical Reports Server (NTRS)

Herrin, J. S.; Ito, M.; Zolensky, M. E.; Mittlefehldt, D. M.; Jenniskens, P. M.; Shaddad, M. H.

2010-01-01

Prior to recovery the Almahata Sitta fall was observed as the asteroid 2008 TC3 on an Earth-bound trajectory, providing a unique link between spectral data and ureilite composition. The event has also provided insight into the nature of ureilitic objects in space. In particular, the large size (4 m3) and low density (2.2 g/cm3) of the object combined with near-complete disintegration upon entry suggest a porous and loosely-consolidated body [1]. Accordingly, recovered fragments are small in size (1.5-283g) and represent several different ureilite lithologies. Some recovered fragments appear brecciated while others do not. We use chemical and mineralogic data to dissect the thermal history of this new ureilite, then use this information to compare the inferred size of fragments within the asteroid to those initially dislodged from a common ureilite parent body (UPB).

Fragmentation and flow of grazed coastal Bermudagrass through the digestive tract of cattle.

PubMed

Pond, K R; Ellis, W C; Lascano, C E; Akin, D E

1987-08-01

Samples of forage fragments were obtained from the upper (RUS) and lower (RLS) strata of the reticulorumen and feces (F) of four Brahman X Jersey steers grazing Coastal bermudagrass (CB) of two maturities with dry matter digestibilities (DMD) of 54.8 and 64.3%. Forage fragments were separated by particle size and evaluated histochemically for tissue type and fragmentation pattern. Fragmentation pattern was similar to that previously observed due to ingestive mastication. There was longitudinal separation of vascular bundles (VB) and severing at VB ends. Microscopically, similar size fragments from RUS were indistinguishable from those of RLS. The major difference between RUS and RLS was the distribution of different size particles. Larger particles were associated with the RUS in cattle consuming immature and mature CB. More large particles were associated with mature compared with the immature CB in the RUS and RLS. The distribution of different size particles in the F was similar for both maturities, suggesting that similar particle size reduction was required regardless of maturity. Smaller particles in the rumen and F appeared to contain more lignin (determined histochemically) and were composed of indigestible fragments of cuticle and lignified vascular tissue. Cattle grazing mature CB had higher ruminal fills (2.40 vs 2.02 kg dry matter/100 kg body weight), reduced rates of passage and lower voluntary intake (2.50 vs 3.14 kg DM/100 kg body weight). Lower intake of mature CB may have resulted from a reduced rate of particle size reduction. Similarities in fragmentation patterns due to ingestive and ruminative mastication were interpreted to indicate that mastication was responsible for most of the particle size reduction of CB and that mastication facilitated digestion of potentially digestible tissues.

The evolution of urban sprawl: Evidence of spatial heterogeneity and increasing land fragmentation

PubMed Central

Irwin, Elena G.; Bockstael, Nancy E.

2007-01-01

We investigate the dynamics and spatial distribution of land use fragmentation in a rapidly urbanizing region of the United States to test key propositions regarding the evolution of sprawl. Using selected pattern metrics and data from 1973 and 2000 for the state of Maryland, we find significant increases in developed and undeveloped land fragmentation but substantial spatial heterogeneity as well. Estimated fragmentation gradients that describe mean fragmentation as a function of distance from urban centers confirm the hypotheses that fragmentation rises and falls with distance and that the point of maximum fragmentation shifted outward over time. However, rather than outward increases in sprawl balanced by development infill, we find substantial and significant increases in mean fragmentation values along the entire urban–rural gradient. These findings are in contrast to the results of Burchfield et al. [Burchfield M, Overman HG, Puga D, Turner MA (2006) Q J Econ 121:587–633], who conclude that the extent of sprawl remained roughly unchanged in the Unites States between 1976 and 1992. As demonstrated here, both the data and pattern measure used in their study are systematically biased against recording low-density residential development, the very land use that we find is most strongly associated with fragmentation. Other results demonstrate the association between exurban growth and increasing fragmentation and the systematic variation of fragmentation with nonurban factors. In particular, proximity to the Chesapeake Bay is negatively associated with fragmentation, suggesting that an attraction effect associated with this natural amenity has concentrated development. PMID:18093930

Spectral pattern recognition of controlled substances in street samples using artificial neural network system

NASA Astrophysics Data System (ADS)

Poryvkina, Larisa; Aleksejev, Valeri; Babichenko, Sergey M.; Ivkina, Tatjana

2011-04-01

The NarTest fluorescent technique is aimed at the detection of analyte of interest in street samples by recognition of its specific spectral patterns in 3-dimentional Spectral Fluorescent Signatures (SFS) measured with NTX2000 analyzer without chromatographic or other separation of controlled substances from a mixture with cutting agents. The illicit drugs have their own characteristic SFS features which can be used for detection and identification of narcotics, however typical street sample consists of a mixture with cutting agents: adulterants and diluents. Many of them interfere the spectral shape of SFS. The expert system based on Artificial Neural Networks (ANNs) has been developed and applied for such pattern recognition in SFS of street samples of illicit drugs.

Non-REM sleep EEG power distribution in fatigue and sleepiness.

PubMed

Neu, Daniel; Mairesse, Olivier; Verbanck, Paul; Linkowski, Paul; Le Bon, Olivier

2014-04-01

The aim of this study is to contribute to the sleep-related differentiation between daytime fatigue and sleepiness. 135 subjects presenting with sleep apnea-hypopnea syndrome (SAHS, n=58) or chronic fatigue syndrome (CFS, n=52) with respective sleepiness or fatigue complaints and a control group (n=25) underwent polysomnography and psychometric assessments for fatigue, sleepiness, affective symptoms and perceived sleep quality. Sleep EEG spectral analysis for ultra slow, delta, theta, alpha, sigma and beta power bands was performed on frontal, central and occipital derivations. Patient groups presented with impaired subjective sleep quality and higher affective symptom intensity. CFS patients presented with highest fatigue and SAHS patients with highest sleepiness levels. All groups showed similar total sleep time. Subject groups mainly differed in sleep efficiency, wake after sleep onset, duration of light sleep (N1, N2) and slow wave sleep, as well as in sleep fragmentation and respiratory disturbance. Relative non-REM sleep power spectra distributions suggest a pattern of power exchange in higher frequency bands at the expense of central ultra slow power in CFS patients during all non-REM stages. In SAHS patients, however, we found an opposite pattern at occipital sites during N1 and N2. Slow wave activity presents as a crossroad of fatigue and sleepiness with, however, different spectral power band distributions during non-REM sleep. The homeostatic function of sleep might be compromised in CFS patients and could explain why, in contrast to sleepiness, fatigue does not resolve with sleep in these patients. The present findings thus contribute to the differentiation of both phenomena. Copyright © 2014 Elsevier Inc. All rights reserved.

Efficiency of the spectral-spatial classification of hyperspectral imaging data

NASA Astrophysics Data System (ADS)

Borzov, S. M.; Potaturkin, O. I.

2017-01-01

The efficiency of methods of the spectral-spatial classification of similarly looking types of vegetation on the basis of hyperspectral data of remote sensing of the Earth, which take into account local neighborhoods of analyzed image pixels, is experimentally studied. Algorithms that involve spatial pre-processing of the raw data and post-processing of pixel-based spectral classification maps are considered. Results obtained both for a large-size hyperspectral image and for its test fragment with different methods of training set construction are reported. The classification accuracy in all cases is estimated through comparisons of ground-truth data and classification maps formed by using the compared methods. The reasons for the differences in these estimates are discussed.

Detection of undistorted continuous wave (CW) electron paramagnetic resonance (EPR) spectra with non-adiabatic rapid sweep (NARS) of the magnetic field

PubMed Central

Kittell, Aaron W.; Camenisch, Theodore G.; Ratke, Joseph J.; Sidabras, Jason W.; Hyde, James S.

2011-01-01

A continuous wave (CW) electron paramagnetic resonance (EPR) spectrum is typically displayed as the first harmonic response to the application of 100 kHz magnetic field modulation, which is used to enhance sensitivity by reducing the level of 1/f noise. However, magnetic field modulation of any amplitude causes spectral broadening and sacrifices EPR spectral intensity by at least a factor of two. In the work presented here, a CW rapid-scan spectroscopic technique that avoids these compromises and also provides a means of avoiding 1/f noise is developed. This technique, termed non-adiabatic rapid sweep (NARS) EPR, consists of repetitively sweeping the polarizing magnetic field in a linear manner over a spectral fragment with a small coil at a repetition rate that is sufficiently high that receiver noise, microwave phase noise, and environmental microphonics, each of which has 1/f characteristics, are overcome. Nevertheless, the rate of sweep is sufficiently slow that adiabatic responses are avoided and the spin system is always close to thermal equilibrium. The repetitively acquired spectra from the spectral fragment are averaged. Under these conditions, undistorted pure absorption spectra are obtained without broadening or loss of signal intensity. A digital filter such as a moving average is applied to remove high frequency noise, which is approximately equivalent in bandwidth to use of an integrating time constant in conventional field modulation with lock-in detection. Nitroxide spectra at L- and X-band are presented. PMID:21741868

Global patterns of fragmentation and connectivity of mammalian carnivore habitat.

PubMed

Crooks, Kevin R; Burdett, Christopher L; Theobald, David M; Rondinini, Carlo; Boitani, Luigi

2011-09-27

Although mammalian carnivores are vulnerable to habitat fragmentation and require landscape connectivity, their global patterns of fragmentation and connectivity have not been examined. We use recently developed high-resolution habitat suitability models to conduct comparative analyses and to identify global hotspots of fragmentation and connectivity for the world's terrestrial carnivores. Species with less fragmentation (i.e. more interior high-quality habitat) had larger geographical ranges, a greater proportion of habitat within their range, greater habitat connectivity and a lower risk of extinction. Species with higher connectivity (i.e. less habitat isolation) also had a greater proportion of high-quality habitat, but had smaller, not larger, ranges, probably reflecting shorter distances between habitat patches for species with restricted distributions; such species were also more threatened, as would be expected given the negative relationship between range size and extinction risk. Fragmentation and connectivity did not differ among Carnivora families, and body mass was associated with connectivity but not fragmentation. On average, only 54.3 per cent of a species' geographical range comprised high-quality habitat, and more troubling, only 5.2 per cent of the range comprised such habitat within protected areas. Identification of global hotspots of fragmentation and connectivity will help guide strategic priorities for carnivore conservation.

Geometry analysis for landscape fragmentation in coastal areas of China

NASA Astrophysics Data System (ADS)

Zhang, Tianhai; Yu, Ning; Mu, Hongdu; Tuo, Tao

2017-08-01

In recent years, the continuous expansion of urban-transport networks in China has aggravated the fragmentation of regional landscapes and led to the degradation of multiple ecological functions. In this study, Geographic Information System (GIS) techniques, patch size of fragmentation geometry were used to identify and monitor spatial distribution patterns of landscape fragmentation due to urban-transport networks in Fujian Province. This network has caused serious damage to regional ecological functions, and risks to the persistence of animal populations and biodiversity. This analysis revealed that the smallest patch class (0-15 km2) occurred with a much greater frequency than all other larger patch sizes. In the coastal cities of Xiamen, Zhangzhou and Quanzhou, the percentage of the number of patches less than 300 km2 was higher than in the western cities of Nanping, Sanming and Longyan, and the percentage of the area of patches less than 300 km2 was also higher. Based on a holistic identification of the structure of the network and its landscape division, we found that: Fujian Province has a spatial pattern of landscape fragmentation, with less fragmentation in western and northern regions, and most fragmentation in southern and eastern regions. Coastal regions and areas close to the main transport routes were more seriously fragmented and contained most of the small patches.

Global patterns of fragmentation and connectivity of mammalian carnivore habitat

PubMed Central

Crooks, Kevin R.; Burdett, Christopher L.; Theobald, David M.; Rondinini, Carlo; Boitani, Luigi

2011-01-01

Although mammalian carnivores are vulnerable to habitat fragmentation and require landscape connectivity, their global patterns of fragmentation and connectivity have not been examined. We use recently developed high-resolution habitat suitability models to conduct comparative analyses and to identify global hotspots of fragmentation and connectivity for the world's terrestrial carnivores. Species with less fragmentation (i.e. more interior high-quality habitat) had larger geographical ranges, a greater proportion of habitat within their range, greater habitat connectivity and a lower risk of extinction. Species with higher connectivity (i.e. less habitat isolation) also had a greater proportion of high-quality habitat, but had smaller, not larger, ranges, probably reflecting shorter distances between habitat patches for species with restricted distributions; such species were also more threatened, as would be expected given the negative relationship between range size and extinction risk. Fragmentation and connectivity did not differ among Carnivora families, and body mass was associated with connectivity but not fragmentation. On average, only 54.3 per cent of a species' geographical range comprised high-quality habitat, and more troubling, only 5.2 per cent of the range comprised such habitat within protected areas. Identification of global hotspots of fragmentation and connectivity will help guide strategic priorities for carnivore conservation. PMID:21844043

Peptide Fragmentation Induced by Radicals at Atmospheric Pressure

PubMed Central

Vilkov, Andrey N.; Laiko, Victor V.; Doroshenko, Vladimir M.

2009-01-01

A novel ion dissociation technique, which is capable of providing an efficient fragmentation of peptides at essentially atmospheric pressure conditions, is developed. The fragmentation patterns observed often contain c-type fragments that are specific to ECD/ETD, along with the y-/b- fragments that are specific to CAD. In the presented experimental setup, ion fragmentation takes place within a flow reactor located in the atmospheric pressure region between the ion source and the mass spectrometer. According to a proposed mechanism, the fragmentation results from the interaction of ESI-generated analyte ions with the gas-phase radical species produced by a corona discharge source. PMID:19034885

Consequences of Landscape Fragmentation on Lyme Disease Risk: A Cellular Automata Approach

PubMed Central

Li, Sen; Hartemink, Nienke; Speybroeck, Niko; Vanwambeke, Sophie O.

2012-01-01

The abundance of infected Ixodid ticks is an important component of human risk of Lyme disease, and various empirical studies have shown that this is associated, at least in part, to landscape fragmentation. In this study, we aimed at exploring how varying woodland fragmentation patterns affect the risk of Lyme disease, through infected tick abundance. A cellular automata model was developed, incorporating a heterogeneous landscape with three interactive components: an age-structured tick population, a classical disease transmission function, and hosts. A set of simplifying assumptions were adopted with respect to the study objective and field data limitations. In the model, the landscape influences both tick survival and host movement. The validation of the model was performed with an empirical study. Scenarios of various landscape configurations (focusing on woodland fragmentation) were simulated and compared. Lyme disease risk indices (density and infection prevalence of nymphs) differed considerably between scenarios: (i) the risk could be higher in highly fragmented woodlands, which is supported by a number of recently published empirical studies, and (ii) grassland could reduce the risk in adjacent woodland, which suggests landscape fragmentation studies of zoonotic diseases should not focus on the patch-level woodland patterns only, but also on landscape-level adjacent land cover patterns. Further analysis of the simulation results indicated strong correlations between Lyme disease risk indices and the density, shape and aggregation level of woodland patches. These findings highlight the strong effect of the spatial patterns of local host population and movement on the spatial dynamics of Lyme disease risks, which can be shaped by woodland fragmentation. In conclusion, using a cellular automata approach is beneficial for modelling complex zoonotic transmission systems as it can be combined with either real world landscapes for exploring direct spatial effects or artificial representations for outlining possible empirical investigations. PMID:22761842

Age-related differences in human skin proteoglycans.

PubMed

Carrino, David A; Calabro, Anthony; Darr, Aniq B; Dours-Zimmermann, Maria T; Sandy, John D; Zimmermann, Dieter R; Sorrell, J Michael; Hascall, Vincent C; Caplan, Arnold I

2011-02-01

Previous work has shown that versican, decorin and a catabolic fragment of decorin, termed decorunt, are the most abundant proteoglycans in human skin. Further analysis of versican indicates that four major core protein species are present in human skin at all ages examined from fetal to adult. Two of these are identified as the V0 and V1 isoforms, with the latter predominating. The other two species are catabolic fragments of V0 and V1, which have the amino acid sequence DPEAAE as their carboxyl terminus. Although the core proteins of human skin versican show no major age-related differences, the glycosaminoglycans (GAGs) of adult skin versican are smaller in size and show differences in their sulfation pattern relative to those in fetal skin versican. In contrast to human skin versican, human skin decorin shows minimal age-related differences in its sulfation pattern, although, like versican, the GAGs of adult skin decorin are smaller than those of fetal skin decorin. Analysis of the catabolic fragments of decorin from adult skin reveals the presence of other fragments in addition to decorunt, although the core proteins of these additional decorin catabolic fragments have not been identified. Thus, versican and decorin of human skin show age-related differences, versican primarily in the size and the sulfation pattern of its GAGs and decorin in the size of its GAGs. The catabolic fragments of versican are detected at all ages examined, but appear to be in lower abundance in adult skin compared with fetal skin. In contrast, the catabolic fragments of decorin are present in adult skin, but are virtually absent from fetal skin. Taken together, these data suggest that there are age-related differences in the catabolism of proteoglycans in human skin. These age-related differences in proteoglycan patterns and catabolism may play a role in the age-related changes in the physical properties and injury response of human skin.

A k-mer-based barcode DNA classification methodology based on spectral representation and a neural gas network.

PubMed

Fiannaca, Antonino; La Rosa, Massimo; Rizzo, Riccardo; Urso, Alfonso

2015-07-01

In this paper, an alignment-free method for DNA barcode classification that is based on both a spectral representation and a neural gas network for unsupervised clustering is proposed. In the proposed methodology, distinctive words are identified from a spectral representation of DNA sequences. A taxonomic classification of the DNA sequence is then performed using the sequence signature, i.e., the smallest set of k-mers that can assign a DNA sequence to its proper taxonomic category. Experiments were then performed to compare our method with other supervised machine learning classification algorithms, such as support vector machine, random forest, ripper, naïve Bayes, ridor, and classification tree, which also consider short DNA sequence fragments of 200 and 300 base pairs (bp). The experimental tests were conducted over 10 real barcode datasets belonging to different animal species, which were provided by the on-line resource "Barcode of Life Database". The experimental results showed that our k-mer-based approach is directly comparable, in terms of accuracy, recall and precision metrics, with the other classifiers when considering full-length sequences. In addition, we demonstrate the robustness of our method when a classification is performed task with a set of short DNA sequences that were randomly extracted from the original data. For example, the proposed method can reach the accuracy of 64.8% at the species level with 200-bp fragments. Under the same conditions, the best other classifier (random forest) reaches the accuracy of 20.9%. Our results indicate that we obtained a clear improvement over the other classifiers for the study of short DNA barcode sequence fragments. Copyright © 2015 Elsevier B.V. All rights reserved.

Small-scale swirl events in the quiet Sun chromosphere

NASA Astrophysics Data System (ADS)

Wedemeyer-Böhm, S.; Rouppe van der Voort, L.

2009-11-01

Context: Recent progress in instrumentation enables solar observations with high resolution simultaneously in the spatial, temporal, and spectral domains. Aims: We use such high-resolution observations to study small-scale structures and dynamics in the chromosphere of the quiet Sun. Methods: We analyse time series of spectral scans through the Ca ii 854.2 nm spectral line obtained with the CRISP instrument at the Swedish 1-m Solar Telescope. The targets are quiet Sun regions inside coronal holes close to disc-centre. Results: The line core maps exhibit relatively few fibrils compared to what is normally observed in quiet Sun regions outside coronal holes. The time series show a chaotic and dynamic scene that includes spatially confined “swirl” events. These events feature dark and bright rotating patches, which can consist of arcs, spiral arms, rings or ring fragments. The width of the fragments typically appears to be of the order of only 0.2 arcsec, which is close to the effective spatial resolution. They exhibit Doppler shifts of -2 to -4 km s-1 but sometimes up to -7 km s-1, indicating fast upflows. The diameter of a swirl is usually of the order of 2´´. At the location of these swirls, the line wing and wide-band maps show close groups of photospheric bright points that move with respect to each other. Conclusions: A likely explanation is that the relative motion of the bright points twists the associated magnetic field in the chromosphere above. Plasma or propagating waves may then spiral upwards guided by the magnetic flux structure, thereby producing the observed intensity signature of Doppler-shifted ring fragments. The movie is only available in electronic form at http://www.aanda.org Marie Curie Intra-European Fellow of the European Commission.

Urbanization-induced habitat fragmentation erodes multiple components of temporal diversity in a Southern California native bee assemblage

PubMed Central

Ascher, John S.; Holway, David A.

2017-01-01

Despite a large number of ecological studies that document diversity loss resulting from anthropogenic disturbance, surprisingly few consider how disturbance affects temporal patterns of diversity that result from seasonal turnover of species. Temporal dynamics can play an important role in the structure and function of biological assemblages. Here, we investigate the temporal diversity patterns of bee faunas in Southern California coastal sage scrub ecosystems that have been extensively fragmented by urbanization. Using a two-year dataset of 235 bee species (n = 12,036 specimens), we compared 1-ha plots in scrub fragments and scrub reserves with respect to three components of temporal diversity: overall plot-level diversity pooled over time (temporal gamma diversity), diversity at discrete points in time (temporal alpha diversity), and seasonal turnover in assemblage composition (temporal beta diversity). Compared to reserves, fragments harbored bee assemblages with lower species richness and assemblage evenness both when summed across temporal samples (i.e., lower temporal gamma diversity) and at single points in time (i.e., lower temporal alpha diversity). Bee assemblages in fragments also exhibited reduced seasonal turnover (i.e., lower temporal beta diversity). While fragments and reserves did not differ in overall bee abundance, bee abundance in fragments peaked later in the season compared to that in reserves. Our results argue for an increased awareness of temporal diversity patterns, as information about the distinct components of temporal diversity is essential both for characterizing the assemblage dynamics of seasonal organisms and for identifying potential impacts of anthropogenic disturbance on ecosystem function through its effects on assemblage dynamics. PMID:28854229

Habitat fragmentation and the Burrowing Owls (Speotyto cunicularia) in Saskatchewan

Treesearch

Robert G. Warnock; Paul C. James

1997-01-01

The relationship between landscape (125,664 ha circular plots) fragmentation patterns and the spatial distribution of Burrowing Owls (Speotyto cunicularia) was investigated in the heavily fragmented grasslands of Saskatchewan. Data were collected from 152 Burrowing Owl sites and 250 random sites located on 1990 LANDSAT-TM satellite images and 1:250,...

Qualitative analysis of seized synthetic cannabinoids and synthetic cathinones by gas chromatography triple quadrupole tandem mass spectrometry.

PubMed

Gwak, Seongshin; Arroyo-Mora, Luis E; Almirall, José R

2015-02-01

Designer drugs are analogues or derivatives of illicit drugs with a modification of their chemical structure in order to circumvent current legislation for controlled substances. Designer drugs of abuse have increased dramatically in popularity all over the world for the past couple of years. Currently, the qualitative seized-drug analysis is mainly performed by gas chromatography-electron ionization-mass spectrometry (GC-EI-MS) in which most of these emerging designer drug derivatives are extensively fragmented not presenting a molecular ion in their mass spectra. The absence of molecular ion and/or similar fragmentation pattern among these derivatives may cause the equivocal identification of unknown seized-substances. In this study, the qualitative identification of 34 designer drugs, mainly synthetic cannabinoids and synthetic cathinones, were performed by gas chromatography-triple quadrupole-tandem mass spectrometry with two different ionization techniques, including electron ionization (EI) and chemical ionization (CI) only focusing on qualitative seized-drug analysis, not from the toxicological point of view. The implementation of CI source facilitates the determination of molecular mass and the identification of seized designer drugs. Developed multiple reaction monitoring (MRM) mode may increase sensitivity and selectivity in the analysis of seized designer drugs. In addition, CI mass spectra and MRM mass spectra of these designer drug derivatives can be used as a potential supplemental database along with EI mass spectral database. Copyright © 2014 John Wiley & Sons, Ltd.

Heart Rate Fragmentation: A Symbolic Dynamical Approach.

PubMed

Costa, Madalena D; Davis, Roger B; Goldberger, Ary L

2017-01-01

Background: We recently introduced the concept of heart rate fragmentation along with a set of metrics for its quantification. The term was coined to refer to an increase in the percentage of changes in heart rate acceleration sign, a dynamical marker of a type of anomalous variability. The effort was motivated by the observation that fragmentation, which is consistent with the breakdown of the neuroautonomic-electrophysiologic control system of the sino-atrial node, could confound traditional short-term analysis of heart rate variability. Objective: The objectives of this study were to: (1) introduce a symbolic dynamical approach to the problem of quantifying heart rate fragmentation; (2) evaluate how the distribution of the different dynamical patterns ("words") varied with the participants' age in a group of healthy subjects and patients with coronary artery disease (CAD); and (3) quantify the differences in the fragmentation patterns between the two sample populations. Methods: The symbolic dynamical method employed here was based on a ternary map of the increment NN interval time series and on the analysis of the relative frequency of symbolic sequences (words) with a pre-defined set of features. We analyzed annotated, open-access Holter databases of healthy subjects and patients with CAD, provided by the University of Rochester Telemetric and Holter ECG Warehouse (THEW). Results: The degree of fragmentation was significantly higher in older individuals than in their younger counterparts. However, the fragmentation patterns were different in the two sample populations. In healthy subjects, older age was significantly associated with a higher percentage of transitions from acceleration/deceleration to zero acceleration and vice versa (termed "soft" inflection points). In patients with CAD, older age was also significantly associated with higher percentages of frank reversals in heart rate acceleration (transitions from acceleration to deceleration and vice versa , termed "hard" inflection points). Compared to healthy subjects, patients with CAD had significantly higher percentages of soft and hard inflection points, an increased percentage of words with a high degree of fragmentation and a decreased percentage of words with a lower degree of fragmentation. Conclusion: The symbolic dynamical method employed here was useful to probe the newly recognized property of heart rate fragmentation. The findings from these cross-sectional studies confirm that CAD and older age are associated with higher levels of heart rate fragmentation. Furthermore, fragmentation with healthy aging appears to be phenotypically different from fragmentation in the context of CAD.

Peripheral absolute threshold spectral sensitivity in retinitis pigmentosa.

PubMed Central

Massof, R W; Johnson, M A; Finkelstein, D

1981-01-01

Dark-adapted spectral sensitivities were measured in the peripheral retinas of 38 patients diagnosed as having typical retinitis pigmentosa (RP) and in 3 normal volunteers. The patients included those having autosomal dominant and autosomal recessive inheritance patterns. Results were analysed by comparisons with the CIE standard scotopic spectral visibility function and with Judd's modification of the photopic spectral visibility function, with consideration of contributions from changes in spectral transmission of preretinal media. The data show 3 general patterns. One group of patients had absolute threshold spectral sensitivities that were fit by Judd's photopic visibility curve. Absolute threshold spectral sensitivities for a second group of patients were fit by a normal scotopic spectral visibility curve. The third group of patients had absolute threshold spectral sensitivities that were fit by a combination of scotopic and photopic spectral visibility curves. The autosomal dominant and autosomal recessive modes of inheritance were represented in each group of patients. These data indicate that RP patients have normal rod and/or cone spectral sensitivities, and support the subclassification of patients described previously by Massof and Finkelstein. PMID:7459312

[Research of Identify Spatial Object Using Spectrum Analysis Technique].

PubMed

Song, Wei; Feng, Shi-qi; Shi, Jing; Xu, Rong; Wang, Gong-chang; Li, Bin-yu; Liu, Yu; Li, Shuang; Cao Rui; Cai, Hong-xing; Zhang, Xi-he; Tan, Yong

2015-06-01

The high precision scattering spectrum of spatial fragment with the minimum brightness of 4.2 and the resolution of 0.5 nm has been observed using spectrum detection technology on the ground. The obvious differences for different types of objects are obtained by the normalizing and discrete rate analysis of the spectral data. Each of normalized multi-frame scattering spectral line shape for rocket debris is identical. However, that is different for lapsed satellites. The discrete rate of the single frame spectrum of normalized space debris for rocket debris ranges from 0.978% to 3.067%, and the difference of oscillation and average value is small. The discrete rate for lapsed satellites ranges from 3.118 4% to 19.472 7%, and the difference of oscillation and average value relatively large. The reason is that the composition of rocket debris is single, while that of the lapsed satellites is complex. Therefore, the spectrum detection technology on the ground can be used to the classification of the spatial fragment.

Measuring forest landscape patterns in the Cascade Range of Oregon, USA

NASA Technical Reports Server (NTRS)

Ripple, William J.; Bradshaw, G. A.; Spies, Thomas A.

1995-01-01

This paper describes the use of a set of spatial statistics to quantify the landscape pattern caused by the patchwork of clearcuts made over a 15-year period in the western Cascades of Oregon. Fifteen areas were selected at random to represent a diversity of landscape fragmentation patterns. Managed forest stands (patches) were digitized and analyzed to produce both tabular and mapped information describing patch size, shape, abundance and spacing, and matrix characteristics of a given area. In addition, a GIS fragmentation index was developed which was found to be sensitive to patch abundance and to the spatial distribution of patches. Use of the GIS-derived index provides an automated method of determining the level of forest fragmentation and can be used to facilitate spatial analysis of the landscape for later coordination with field and remotely sensed data. A comparison of the spatial statistics calculated for the two years indicates an increase in forest fragmentation as characterized by an increase in mean patch abundance and a decrease in interpatch distance, amount of interior natural forest habitat, and the GIS fragmentation index. Such statistics capable of quantifying patch shape and spatial distribution may prove important in the evaluation of the changing character of interior and edge habitats for wildlife.

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens.

PubMed

Weiß, Clemens L; Schuenemann, Verena J; Devos, Jane; Shirsekar, Gautam; Reiter, Ella; Gould, Billie A; Stinchcombe, John R; Krause, Johannes; Burbano, Hernán A

2016-06-01

Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 × 10(-4) per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

Isoschizomers and amplified fragment length polymorphism for the detection of specific cytosine methylation changes.

PubMed

Ruiz-García, Leonor; Cabezas, Jose Antonio; de María, Nuria; Cervera, María-Teresa

2010-01-01

Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is a modification of the Amplified Fragment Length Polymorphism (AFLP) technique that has been used to study methylation of anonymous CCGG sequences in different fungi, plant and animal species. The main variation of this technique is based on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent cutter restriction enzyme. For each sample, AFLP analysis is performed using both EcoRI/HpaII and EcoRI/MspI digested samples. Comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) "Methylation-insensitive polymorphisms" that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples; and (2) "Methylation-sensitive polymorphisms" that are associated with amplified fragments differing in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses modifications that can be applied to adjust the technology to different species of interest.

Consequences of extensive habitat fragmentation in landscape-level patterns of genetic diversity and structure in the Mediterranean esparto grasshopper

PubMed Central

Ortego, Joaquín; Aguirre, María P; Noguerales, Víctor; Cordero, Pedro J

2015-01-01

Anthropogenic habitat fragmentation has altered the distribution and population sizes in many organisms worldwide. For this reason, understanding the demographic and genetic consequences of this process is necessary to predict the fate of populations and establish management practices aimed to ensure their viability. In this study, we analyse whether the spatial configuration of remnant semi-natural habitat patches within a chronically fragmented landscape has shaped the patterns of genetic diversity and structure in the habitat-specialist esparto grasshopper (Ramburiella hispanica). In particular, we predict that agricultural lands constitute barriers to gene flow and hypothesize that fragmentation has restricted interpopulation dispersal and reduced local levels of genetic diversity. Our results confirmed the expectation that isolation and habitat fragmentation have reduced the genetic diversity of local populations. Landscape genetic analyses based on circuit theory showed that agricultural land offers ∽1000 times more resistance to gene flow than semi-natural habitats, indicating that patterns of dispersal are constrained by the spatial configuration of remnant patches of suitable habitat. Overall, this study shows that semi-natural habitat patches act as corridors for interpopulation gene flow and should be preserved due to the disproportionately large ecological function that they provide considering their insignificant area within these human-modified landscapes. PMID:26136826

Global patterns of tropical forest fragmentation

NASA Astrophysics Data System (ADS)

Taubert, Franziska; Fischer, Rico; Groeneveld, Jürgen; Lehmann, Sebastian; Müller, Michael S.; Rödig, Edna; Wiegand, Thorsten; Huth, Andreas

2018-02-01

Remote sensing enables the quantification of tropical deforestation with high spatial resolution. This in-depth mapping has led to substantial advances in the analysis of continent-wide fragmentation of tropical forests. Here we identified approximately 130 million forest fragments in three continents that show surprisingly similar power-law size and perimeter distributions as well as fractal dimensions. Power-law distributions have been observed in many natural phenomena such as wildfires, landslides and earthquakes. The principles of percolation theory provide one explanation for the observed patterns, and suggest that forest fragmentation is close to the critical point of percolation; simulation modelling also supports this hypothesis. The observed patterns emerge not only from random deforestation, which can be described by percolation theory, but also from a wide range of deforestation and forest-recovery regimes. Our models predict that additional forest loss will result in a large increase in the total number of forest fragments—at maximum by a factor of 33 over 50 years—as well as a decrease in their size, and that these consequences could be partly mitigated by reforestation and forest protection.

Loggers and Forest Fragmentation: Behavioral Models of Road Building in the Amazon Basin

NASA Technical Reports Server (NTRS)

Arima, Eugenio Y.; Walker, Robert T.; Perz, Stephen G.; Caldas, Marcellus

2005-01-01

Although a large literature now exists on the drivers of tropical deforestation, less is known about its spatial manifestation. This is a critical shortcoming in our knowledge base since the spatial pattern of land-cover change and forest fragmentation, in particular, strongly affect biodiversity. The purpose of this article is to consider emergent patterns of road networks, the initial proximate cause of fragmentation in tropical forest frontiers. Specifically, we address the road-building processes of loggers who are very active in the Amazon landscape. To this end, we develop an explanation of road expansions, using a positive approach combining a theoretical model of economic behavior with geographic information systems (GIs) software in order to mimic the spatial decisions of road builders. We simulate two types of road extensions commonly found in the Amazon basin in a region: showing the fishbone pattern of fragmentation. Although our simulation results are only partially successful, they call attention to the role of multiple agents in the landscape, the importance of legal and institutional constraints on economic behavior, and the power of GIs as a research tool.

Analysis of DNA Cytosine Methylation Patterns Using Methylation-Sensitive Amplification Polymorphism (MSAP).

PubMed

Guevara, María Ángeles; de María, Nuria; Sáez-Laguna, Enrique; Vélez, María Dolores; Cervera, María Teresa; Cabezas, José Antonio

2017-01-01

Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is the methylation-sensitive amplified polymorphism technique (MSAP) which is a modification of amplified fragment length polymorphism (AFLP). It has been used to study methylation of anonymous CCGG sequences in different fungi, plants, and animal species. The main variation of this technique resides on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent-cutter restriction enzyme. For each sample, MSAP analysis is performed using both EcoRI/HpaII- and EcoRI/MspI-digested samples. A comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) methylation-insensitive polymorphisms that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples and (2) methylation-sensitive polymorphisms which are associated with the amplified fragments that differ in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses the modifications that can be applied to adjust the technology to different species of interest.

Discerning fragmentation dynamics of tropical forest and wetland during reforestation, urban sprawl, and policy shifts.

PubMed

Gao, Qiong; Yu, Mei

2014-01-01

Despite the overall trend of worldwide deforestation over recent decades, reforestation has also been found and is expected in developing countries undergoing fast urbanization and agriculture abandonment. The consequences of reforestation on landscape patterns are seldom addressed in the literature, despite their importance in evaluating biodiversity and ecosystem functions. By analyzing long-term land cover changes in Puerto Rico, a rapidly reforested (6 to 42% during 1940-2000) and urbanized tropical island, we detected significantly different patterns of fragmentation and underlying mechanisms among forests, urban areas, and wetlands. Forest fragmentation is often associated with deforestation. However, we also found significant fragmentation during reforestation. Urban sprawl and suburb development have a dominant impact on forest fragmentation. Reforestation mostly occurs along forest edges, while significant deforestation occurs in forest interiors. The deforestation process has a much stronger impact on forest fragmentation than the reforestation process due to their different spatial configurations. In contrast, despite the strong interference of coastal urbanization, wetland aggregation has occurred due to the effective implementation of laws/regulations for wetland protection. The peak forest fragmentation shifted toward rural areas, indicating progressively more fragmentation in forest interiors. This shift is synchronous with the accelerated urban sprawl as indicated by the accelerated shift of the peak fragmentation index of urban cover toward rural areas, i.e., 1.37% yr-1 in 1977-1991 versus 2.17% yr-1 in 1991-2000. Based on the expected global urbanization and the regional forest transition from deforested to reforested, the fragmented forests and aggregated wetlands in this study highlight possible forest fragmentation processes during reforestation in an assessment of biodiversity and functions and suggest effective laws/regulations in land planning to reduce future fragmentation.

Discerning Fragmentation Dynamics of Tropical Forest and Wetland during Reforestation, Urban Sprawl, and Policy Shifts

PubMed Central

Gao, Qiong; Yu, Mei

2014-01-01

Despite the overall trend of worldwide deforestation over recent decades, reforestation has also been found and is expected in developing countries undergoing fast urbanization and agriculture abandonment. The consequences of reforestation on landscape patterns are seldom addressed in the literature, despite their importance in evaluating biodiversity and ecosystem functions. By analyzing long-term land cover changes in Puerto Rico, a rapidly reforested (6 to 42% during 1940–2000) and urbanized tropical island, we detected significantly different patterns of fragmentation and underlying mechanisms among forests, urban areas, and wetlands. Forest fragmentation is often associated with deforestation. However, we also found significant fragmentation during reforestation. Urban sprawl and suburb development have a dominant impact on forest fragmentation. Reforestation mostly occurs along forest edges, while significant deforestation occurs in forest interiors. The deforestation process has a much stronger impact on forest fragmentation than the reforestation process due to their different spatial configurations. In contrast, despite the strong interference of coastal urbanization, wetland aggregation has occurred due to the effective implementation of laws/regulations for wetland protection. The peak forest fragmentation shifted toward rural areas, indicating progressively more fragmentation in forest interiors. This shift is synchronous with the accelerated urban sprawl as indicated by the accelerated shift of the peak fragmentation index of urban cover toward rural areas, i.e., 1.37% yr−1 in 1977–1991 versus 2.17% yr−1 in 1991–2000. Based on the expected global urbanization and the regional forest transition from deforested to reforested, the fragmented forests and aggregated wetlands in this study highlight possible forest fragmentation processes during reforestation in an assessment of biodiversity and functions and suggest effective laws/regulations in land planning to reduce future fragmentation. PMID:25409016

Application of microtomography and image analysis to the quantification of fragmentation in ceramics after impact loading

NASA Astrophysics Data System (ADS)

Forquin, Pascal; Ando, Edward

2017-01-01

Silicon carbide ceramics are widely used in personal body armour and protective solutions. However, during impact, an intense fragmentation develops in the ceramic tile due to high-strain-rate tensile loadings. In this work, microtomography equipment was used to analyse the fragmentation patterns of two silicon carbide grades subjected to edge-on impact (EOI) tests. The EOI experiments were conducted in two configurations. The so-called open configuration relies on the use of an ultra-high-speed camera to visualize the fragmentation process with an interframe time set to 1 µs. The so-called sarcophagus configuration consists in confining the target in a metallic casing to avoid any dispersion of fragments. The target is infiltrated after impact so the final damage pattern is entirely scanned using X-ray tomography and a microfocus source. Thereafter, a three-dimensional (3D) segmentation algorithm was tested and applied in order to separate fragments in 3D allowing a particle size distribution to be obtained. Significant differences between the two specimens of different SiC grades were noted. To explain such experimental results, numerical simulations were conducted considering the Denoual-Forquin-Hild anisotropic damage model. According to the calculations, the difference of crack pattern in EOI tests is related to the population of defects within the two ceramics. This article is part of the themed issue 'Experimental testing and modelling of brittle materials at high strain rates'.

MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics.

PubMed

The, Matthew; Käll, Lukas

2016-03-04

Shotgun proteomics experiments generate large amounts of fragment spectra as primary data, normally with high redundancy between and within experiments. Here, we have devised a clustering technique to identify fragment spectra stemming from the same species of peptide. This is a powerful alternative method to traditional search engines for analyzing spectra, specifically useful for larger scale mass spectrometry studies. As an aid in this process, we propose a distance calculation relying on the rarity of experimental fragment peaks, following the intuition that peaks shared by only a few spectra offer more evidence than peaks shared by a large number of spectra. We used this distance calculation and a complete-linkage scheme to cluster data from a recent large-scale mass spectrometry-based study. The clusterings produced by our method have up to 40% more identified peptides for their consensus spectra compared to those produced by the previous state-of-the-art method. We see that our method would advance the construction of spectral libraries as well as serve as a tool for mining large sets of fragment spectra. The source code and Ubuntu binary packages are available at https://github.com/statisticalbiotechnology/maracluster (under an Apache 2.0 license).

Combinatorial Labeling Method for Improving Peptide Fragmentation in Mass Spectrometry

NASA Astrophysics Data System (ADS)

Kuchibhotla, Bhanuramanand; Kola, Sankara Rao; Medicherla, Jagannadham V.; Cherukuvada, Swamy V.; Dhople, Vishnu M.; Nalam, Madhusudhana Rao

2017-06-01

Annotation of peptide sequence from tandem mass spectra constitutes the central step of mass spectrometry-based proteomics. Peptide mass spectra are obtained upon gas-phase fragmentation. Identification of the protein from a set of experimental peptide spectral matches is usually referred as protein inference. Occurrence and intensity of these fragment ions in the MS/MS spectra are dependent on many factors such as amino acid composition, peptide basicity, activation mode, protease, etc. Particularly, chemical derivatizations of peptides were known to alter their fragmentation. In this study, the influence of acetylation, guanidinylation, and their combination on peptide fragmentation was assessed initially on a lipase (LipA) from Bacillus subtilis followed by a bovine six protein mix digest. The dual modification resulted in improved fragment ion occurrence and intensity changes, and this resulted in the equivalent representation of b- and y-type fragment ions in an ion trap MS/MS spectrum. The improved representation has allowed us to accurately annotate the peptide sequences de novo. Dual labeling has significantly reduced the false positive protein identifications in standard bovine six peptide digest. Our study suggests that the combinatorial labeling of peptides is a useful method to validate protein identifications for high confidence protein inference. [Figure not available: see fulltext.

Geographic variation in cowbird distribution, abundance, and parasitism

USGS Publications Warehouse

Morrison, M.L.; Hahn, D.C.; George, T. Luke; Dobkin, David S.

2002-01-01

We evaluated geographical patterns in the abundance and distribution of Brown-headed Cowbirds (Molothrus ater), and in the frequency of cowbird parasitism, across North America in relation to habitat fragmentation. We found no distinctive parasitism patterns at the national or even regional scales, but the species is most abundant in the Great Plains, the heart of their original range, and least common in the southeastern U.S. This situation is dynamic, because both the Brown-headed and two other cowbird species are actively expanding their ranges in the southern U.S. We focused almost entirely in this paper on the Brown-headed Cowbird, because it is the only endemic North American cowbird, its distribution is much wider, and it has been much more intensively studied. We determined that landscape is the most meaningful unit of scale for comparing cowbird parasitism patterns as, for example, in comparisons of northeastern and central hardwood forests within agricultural matrices, and suburbanized areas versus western coniferous forests. We concluded that cowbird parasitism patterns were broadly similar within all landscapes. Even comparisons between prominently dissimilar landscapes, such as hardwoods in agriculture and suburbia versus coniferous forest, display a striking similarity in the responses of cowbirds. Our review clearly indicated that proximity of feeding areas is the key factor influencing presence and parasitism patterns within the landscape. We considered intensity of landscape fragmentation from forest-dominated landscapes altered in a forest management context to fragmentation characterized by mixed suburbanization or agricultural development. Our review consistently identified an inverse relationship between extent of forest cover across the landscape and cowbird presence. Invariably, the variation seen in parasitism frequencies within a region was at least partially explained as a response to changes in forest cover. The most salient geographic aspect of cowbirds' response to landscape fragmentation is the time since fragmentation occurred. Eastern landscapes generally experienced 200 years ago the development and fragmentation that western landscapes experienced less than 75 years ago. Consequently, there is a broad east-west contrast in which more numerous human settlements and smaller unbroken forest stands are found in the East, a difference that permits cowbirds to be more pervasive and ubiquitous. The locality of suitable feeding areas is a hallmark trait of the cowbirds' strategy in exploiting specific forest fragments. Host abundance influences parasitism patterns only secondarily at the landscape scale. These two limiting factors come into play differently in different landscapes. For example, cowbird abundance in unbroken forested landscapes are limited primarily by the availability of foraging areas rather than by host density, whereas cowbirds are limited primarily by host availability in landscapes that are extensively fragmented with feeding areas.

Structure identification by Mass Spectrometry Non-Targeted Analysis using the US EPA’s CompTox Chemistry Dashboard

EPA Science Inventory

Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, r...

Sharpness of interference pattern of the 3-pole wiggler

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

Dejus, Roger J., E-mail: dejus@aps.anl.gov; Kim, Kwang-Je

2016-07-27

Due to the small emittance, radiation from neighboring poles of a strong wiggler in future multi-bend achromat-based storage rings can exhibit sharp interference patterns. The spectral-angular distributions of the 3-pole wiggler for the proposed Advanced Photon Source (APS) upgrade were computed and prominent interference patterns were found. In this paper we provide an understanding of such interference patterns. The equations governing the interference pattern are described and computed spectral-angular distributions of a modeled 3-pole wiggler magnetic field using these equations are presented.

Sharpness of Interference Pattern of the 3-Pole Wiggler

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

Dejus, Roger J.; Kim, Kwang-Je

2016-07-02

Due to the small emittance, radiation from neighboring poles of a strong wiggler in future multi-bend achromat-based storage rings can exhibit sharp interference patterns. The spectral-angular distributions of the 3-pole wiggler for the proposed Advanced Photon Source (APS) upgrade were computed and prominent interference patterns were found. In this paper we provide an understanding of such interference patterns. The equations governing the interference pattern are described and computed spectral-angular distributions of a modeled 3-pole wiggler magnetic field using these equations are presented.

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

Shumway, R.H.; McQuarrie, A.D.

Robust statistical approaches to the problem of discriminating between regional earthquakes and explosions are developed. We compare linear discriminant analysis using descriptive features like amplitude and spectral ratios with signal discrimination techniques using the original signal waveforms and spectral approximations to the log likelihood function. Robust information theoretic techniques are proposed and all methods are applied to 8 earthquakes and 8 mining explosions in Scandinavia and to an event from Novaya Zemlya of unknown origin. It is noted that signal discrimination approaches based on discrimination information and Renyi entropy perform better in the test sample than conventional methods based onmore » spectral ratios involving the P and S phases. Two techniques for identifying the ripple-firing pattern for typical mining explosions are proposed and shown to work well on simulated data and on several Scandinavian earthquakes and explosions. We use both cepstral analysis in the frequency domain and a time domain method based on the autocorrelation and partial autocorrelation functions. The proposed approach strips off underlying smooth spectral and seasonal spectral components corresponding to the echo pattern induced by two simple ripple-fired models. For two mining explosions, a pattern is identified whereas for two earthquakes, no pattern is evident.« less

Design Fragments

DTIC Science & Technology

2007-04-19

define the patterns and are better at analyzing behavior. SPQR (System for Pattern Query and Recognition) [18, 58] can recognize pattern vari- ants...Stotts. SPQR : Flexible automated design pattern extraction from source code. ase, 00:215, 2003. ISSN 1527-1366. doi: http://doi.ieeecomputersociety. org

Proteomic Analysis of Tendon Extracellular Matrix Reveals Disease Stage-specific Fragmentation and Differential Cleavage of COMP (Cartilage Oligomeric Matrix Protein)*

PubMed Central

Dakin, Stephanie Georgina; Smith, Roger Kenneth Whealands; Heinegård, Dick; Önnerfjord, Patrik; Khabut, Areej; Dudhia, Jayesh

2014-01-01

During inflammatory processes the extracellular matrix (ECM) is extensively remodeled, and many of the constituent components are released as proteolytically cleaved fragments. These degradative processes are better documented for inflammatory joint diseases than tendinopathy even though the pathogenesis has many similarities. The aims of this study were to investigate the proteomic composition of injured tendons during early and late disease stages to identify disease-specific cleavage patterns of the ECM protein cartilage oligomeric matrix protein (COMP). In addition to characterizing fragments released in naturally occurring disease, we hypothesized that stimulation of tendon explants with proinflammatory mediators in vitro would induce fragments of COMP analogous to natural disease. Therefore, normal tendon explants were stimulated with IL-1β and prostaglandin E2, and their effects on the release of COMP and its cleavage patterns were characterized. Analyses of injured tendons identified an altered proteomic composition of the ECM at all stages post injury, showing protein fragments that were specific to disease stage. IL-1β enhanced the proteolytic cleavage and release of COMP from tendon explants, whereas PGE2 had no catabolic effect. Of the cleavage fragments identified in early stage tendon disease, two fragments were generated by an IL-1-mediated mechanism. These fragments provide a platform for the development of neo-epitope assays specific to injury stage for tendon disease. PMID:24398684

Quantitative analysis of forest fragmentation in the atlantic forest reveals more threatened bird species than the current red list.

PubMed

Schnell, Jessica K; Harris, Grant M; Pimm, Stuart L; Russell, Gareth J

2013-01-01

Habitat loss and attendant fragmentation threaten the existence of many species. Conserving these species requires a straightforward and objective method that quantifies how these factors affect their survival. Therefore, we compared a variety of metrics that assess habitat fragmentation in bird ranges, using the geographical ranges of 127 forest endemic passerine birds inhabiting the Atlantic Forest of Brazil. A common, non-biological metric - cumulative area of size-ranked fragments within a species range - was misleading, as the least threatened species had the most habitat fragmentation. Instead, we recommend a modified version of metapopulation capacity. The metric links detailed spatial information on fragment sizes and spatial configuration to the birds' abilities to occupy and disperse across large areas (100,000+ km(2)). In the Atlantic Forest, metapopulation capacities were largely bimodal, in that most species' ranges had either low capacity (high risk of extinction) or high capacity (very small risk of extinction). This pattern persisted within taxonomically and ecologically homogenous groups, indicating that it is driven by fragmentation patterns and not differences in species ecology. Worryingly, we found IUCN considers some 28 of 58 species in the low metapopulation capacity cluster to not be threatened. We propose that assessing the effect of fragmentation will separate species more clearly into distinct risk categories than does a simple assessment of remaining habitat.

Anthropogenic fragmentation may not alter pre-existing patterns of genetic diversity and differentiation in perennial shrubs.

PubMed

Llorens, Tanya M; Ayre, David J; Whelan, Robert J

2018-04-01

Many plant species have pollination and seed dispersal systems and evolutionary histories that have produced strong genetic structuring. These genetic patterns may be consistent with expectations following recent anthropogenic fragmentation, making it difficult to detect fragmentation effects if no prefragmentation genetic data are available. We used microsatellite markers to investigate whether severe habitat fragmentation may have affected the structure and diversity of populations of the endangered Australian bird-pollinated shrub Grevillea caleyi R.Br., by comparing current patterns of genetic structure and diversity with those of the closely related G. longifolia R.Br. that has a similar life history but has not experienced anthropogenic fragmentation. Grevillea caleyi and G. longifolia showed similar and substantial population subdivision at all spatial levels (global F' ST  = 0.615 and 0.454; S p  = 0.039 and 0.066), marked isolation by distance and large heterozygous deficiencies. These characteristics suggest long-term effects of inbreeding in self-compatible species that have poor seed dispersal, limited connectivity via pollen flow and undergo population bottlenecks because of periodic fires. Highly structured allele size distributions, most notably in G. caleyi, imply historical processes of drift and mutation were important in isolated subpopulations. Genetic diversity did not vary with population size but was lower in more isolated populations for both species. Through this comparison, we reject the hypothesis that anthropogenic fragmentation has impacted substantially on the genetic composition or structure of G. caleyi populations. Our results suggest that highly self-compatible species with limited dispersal may be relatively resilient to the genetic changes predicted to follow habitat fragmentation. © 2018 John Wiley & Sons Ltd.

Recent (2000-2015) developments in the analysis of minor unknown natural products based on characteristic fragment information using LC-MS.

PubMed

Cai, Tian; Guo, Ze-Qin; Xu, Xiao-Ying; Wu, Zhi-Jun

2018-03-01

Liquid chromatography-Mass Spectrometry (LC-MS) has been widely used in natural product analysis. Global detection and identification of nontargeted components are desirable in natural product research, for example, in quality control of Chinese herbal medicine. Nontargeted components analysis continues to expand to exciting life science application domains such as metabonomics. With this background, the present review summarizes recent developments in the analysis of minor unknown natural products using LC-MS and mainly focuses on the determination of the molecular formulae, selection of precursor ions, and characteristic fragmentation patterns of the known compounds. This review consists of three parts. Firstly, the methods used to determine unique molecular formula of unknown compounds such as accurate mass measurements, MS n spectra, or relative isotopic abundance information, are introduced. Secondly, the methods improving signal-to-noise ratio of MS/MS spectra by manual-MS/MS or workflow targeting-only signals were elucidated; pure precursor ions can be selected by changing the precursor ion isolated window. Lastly, characteristic fragmentation patterns such as Retro-Diels-Alder (RDA), McLafferty rearrangements, "internal residue loss," and so on, occurring in the molecular ions of natural products are summarized. Classical application of characteristic fragmentation patterns in identifying unknown compounds in extracts and relevant fragmentation mechanisms are presented (RDA reactions occurring readily in the molecular ions of flavanones or isoflavanones, McLafferty-type fragmentation reactions of some natural products such as epipolythiodioxopiperazines; fragmentation by "internal residue loss" possibly involving ion-neutral complex intermediates). © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:202-216, 2018. © 2016 Wiley Periodicals, Inc.

Enterobacterial repetitive intergenic consensus sequences and the PCR to generate fingerprints of genomic DNAs from Vibrio cholerae O1, O139, and non-O1 strains.

PubMed

Rivera, I G; Chowdhury, M A; Huq, A; Jacobs, D; Martins, M T; Colwell, R R

1995-08-01

Enterobacterial repetitive intergenic consensus (ERIC) sequence polymorphism was studied in Vibrio Cholerae strains isolated before and after the cholera epidemic in Brazil (in 1991), along with epidemic strains from Peru, Mexico, and India, by PCR. A total of 17 fingerprint patterns (FPs) were detected in the V. cholerae strains examined; 96.7% of the toxigenic V. cholerae O1 strains and 100% of the O139 serogroup strains were found to belong to the same FP group comprising four fragments (FP1). The nontoxigenic V. cholerae O1 also yielded four fragments but constituted a different FP group (FP2). A total of 15 different patterns were observed among the V. cholerae non-O1 strains. Two patterns were observed most frequently for V. cholerae non-01 strains, 25% of which have FP3, with five fragments, and 16.7% of which have FP4, with two fragments. Three fragments, 1.75, 0.79, and 0.5 kb, were found to be common to both toxigenic and nontoxigenic V. cholerae O1 strains as well as to group FP3, containing V. cholerae non-O1 strains. Two fragments of group FP3, 1.3 and 1.0 kb, were present in FP1 and FP2 respectively. The 0.5-kb fragment was common to all strains and serogroups of V. cholerae analyzed. It is concluded from the results of this study, based on DNA FPs of environmental isolates, that it is possible to detect an emerging virulent strain in a cholera-endemic region. ERIC-PCR constitutes a powerful tool for determination of the virulence potential of V. cholerae O1 strains isolated in surveillance programs and for molecular epidemiological investigations.

Implications of discontinuous elevation gradients on fragmentation and restoration in patterned wetlands

USGS Publications Warehouse

Zweig, Christa L.; Reichert, Brian E.; Kitchens, Wiley M.

2011-01-01

Large wetlands around the world face the possibility of degradation, not only from complete conversion, but also from subtle changes in their structure and function. While fragmentation and isolation of wetlands within heterogeneous landscapes has received much attention, the disruption of spatial patterns/processes within large wetland systems and the resulting fragmentation of community components are less well documented. A greater understanding of pattern/process relationships and landscape gradients, and what occurs when they are altered, could help avoid undesirable consequences of restoration actions. The objective of this study is to determine the amount of fragmentation of sawgrass ridges due to artificial impoundment of water and how that may be differentially affected by spatial position relative to north and south levees. We also introduce groundbreaking evidence of landscape-level discontinuous elevation gradients within WCA3AS by comparing generalized linear and generalized additive models. These relatively abrupt breaks in elevation may have non-linear effects on hydrology and vegetation communities and would be crucial in restoration considerations. Modeling suggests there are abrupt breaks in elevation as a function of northing (Y-coordinate). Fragmentation indices indicate that fragmentation is a function of elevation and easting (X-coordinate), and that fragmentation has increased from 1988-2002. When landscapes change and the changes are compounded by non-linear landscape variables that are described herein, the maintenance processes change with them, creating a degraded feedback loop that alters the system's response to structuring variables and diminishes our ability to predict the effects of restoration projects or climate change. Only when these landscape variables and linkages are clearly defined can we predict the response to potential perturbations and apply the knowledge to other landscape-level wetland systems in need of future restoration.

ION COMPOSITION ELUCIDATION (ICE): A HIGH ...

EPA Pesticide Factsheets

Identifying compounds found in the environment without knowledge of their origin is a very difficult analytical problem. Comparison of the low resolution mass spectrum of a compound with those in the NIST or Wiley mass spectral libraries can provide a tentative identification when the mass spectrum is free of interferences, at least several prominent ions are observed in the mass spectrum, the mass spectrum is in the library, and only one plausible match is found. Because these libraries contain only 226,334 distinct compounds (1) compared to the 16 million compounds that have been synthesized or isolated from natural sources (2), most compounds are not found in the libraries. In addition, most compounds are ionic, too polar, too thermolabile, or too high in mass to traverse a GC column or to volatilize from a probe. For these compounds, liquid sample introduction with electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) provides few fragment ions for pattern matching, and adduct ions complicate the mass spectra. Commercial ESI and APCI mass spectral libraries are not available. Consequently, low resolution mass spectrometry cannot identify most compounds-. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support

Ecological impacts of tropical forest fragmentation: how consistent are patterns in species richness and nestedness?

PubMed

Hill, Jane K; Gray, Michael A; Khen, Chey Vun; Benedick, Suzan; Tawatao, Noel; Hamer, Keith C

2011-11-27

Large areas of tropical forest now exist as remnants scattered across agricultural landscapes, and so understanding the impacts of forest fragmentation is important for biodiversity conservation. We examined species richness and nestedness among tropical forest remnants in birds (meta-analysis of published studies) and insects (field data for fruit-feeding Lepidoptera (butterflies and moths) and ants). Species-area relationships were evident in all four taxa, and avian and insect assemblages in remnants typically were nested subsets of those in larger areas. Avian carnivores and nectarivores and predatory ants were more nested than other guilds, implying that the sequential loss of species was more predictable in these groups, and that fragmentation alters the trophic organization of communities. For butterflies, the ordering of fragments to achieve maximum nestedness was by fragment area, suggesting that differences among fragments were driven mainly by extinction. In contrast for moths, maximum nestedness was achieved by ordering species by wing length; species with longer wings (implying better dispersal) were more likely to occur at all sites, including low diversity sites, suggesting that differences among fragments were driven more strongly by colonization. Although all four taxa exhibited high levels of nestedness, patterns of species turnover were also idiosyncratic, and thus even species-poor sites contributed to landscape-scale biodiversity, particularly for insects.

Ecological impacts of tropical forest fragmentation: how consistent are patterns in species richness and nestedness?

PubMed Central

Hill, Jane K.; Gray, Michael A.; Khen, Chey Vun; Benedick, Suzan; Tawatao, Noel; Hamer, Keith C.

2011-01-01

Large areas of tropical forest now exist as remnants scattered across agricultural landscapes, and so understanding the impacts of forest fragmentation is important for biodiversity conservation. We examined species richness and nestedness among tropical forest remnants in birds (meta-analysis of published studies) and insects (field data for fruit-feeding Lepidoptera (butterflies and moths) and ants). Species–area relationships were evident in all four taxa, and avian and insect assemblages in remnants typically were nested subsets of those in larger areas. Avian carnivores and nectarivores and predatory ants were more nested than other guilds, implying that the sequential loss of species was more predictable in these groups, and that fragmentation alters the trophic organization of communities. For butterflies, the ordering of fragments to achieve maximum nestedness was by fragment area, suggesting that differences among fragments were driven mainly by extinction. In contrast for moths, maximum nestedness was achieved by ordering species by wing length; species with longer wings (implying better dispersal) were more likely to occur at all sites, including low diversity sites, suggesting that differences among fragments were driven more strongly by colonization. Although all four taxa exhibited high levels of nestedness, patterns of species turnover were also idiosyncratic, and thus even species-poor sites contributed to landscape-scale biodiversity, particularly for insects. PMID:22006967

Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: Phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus)

USGS Publications Warehouse

Vandergast, A.G.; Bohonak, A.J.; Weissman, D.B.; Fisher, R.N.

2007-01-01

Habitat loss and fragmentation due to urbanization are the most pervasive threats to biodiversity in southern California. Loss of habitat and fragmentation can lower migration rates and genetic connectivity among remaining populations of native species, reducing genetic variability and increasing extinction risk. However, it may be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric fragmentation due to previous natural geological and climatic changes. To address these challenges, we examined the phylogenetic and population genetic structure of a flightless insect endemic to cismontane southern California, Stenopelmatus 'mahogani' (Orthoptera: Stenopelmatidae). Analyses of mitochondrial DNA sequence data suggest that diversification across southern California began during the Pleistocene, with most haplotypes currently restricted to a single population. Patterns of genetic divergence correlate with contemporary urbanization, even after correcting for (geographical information system) GIS-based reconstructions of fragmentation during the Pleistocene. Theoretical simulations confirm that contemporary patterns of genetic structure could be produced by recent urban fragmentation using biologically reasonable assumptions about model parameters. Diversity within populations was positively correlated with current fragment size, but not prehistoric fragment size, suggesting that the effects of increased drift following anthropogenic fragmentation are already being seen. Loss of genetic connectivity and diversity can hinder a population's ability to adapt to ecological perturbations commonly associated with urbanization, such as habitat degradation, climatic changes and introduced species. Consequently, our results underscore the importance of preserving and restoring landscape connectivity for long-term persistence of low vagility native species. Journal compilation ?? 2006 Blackwell Publishing Ltd.

Hierarchical Fragmentation in the Perseus Molecular Cloud: From the Cloud Scale to Protostellar Objects

NASA Astrophysics Data System (ADS)

Pokhrel, Riwaj; Myers, Philip C.; Dunham, Michael M.; Stephens, Ian W.; Sadavoy, Sarah I.; Zhang, Qizhou; Bourke, Tyler L.; Tobin, John J.; Lee, Katherine I.; Gutermuth, Robert A.; Offner, Stella S. R.

2018-01-01

We present a study of hierarchical structure in the Perseus molecular cloud, from the scale of the entire cloud (≳ 10 pc) to smaller clumps (∼1 pc), cores (∼0.05–0.1 pc), envelopes (∼300–3000 au), and protostellar objects (∼15 au). We use new observations from the Submillimeter Array (SMA) large project “Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES)” to probe the envelopes, and recent single-dish and interferometric observations from the literature for the remaining scales. This is the first study to analyze hierarchical structure over five scales in the same cloud complex. We compare the number of fragments with the number of Jeans masses in each scale to calculate the Jeans efficiency, or the ratio of observed to expected number of fragments. The velocity dispersion is assumed to arise either from purely thermal motions or from combined thermal and non-thermal motions inferred from observed spectral line widths. For each scale, thermal Jeans fragmentation predicts more fragments than observed, corresponding to inefficient thermal Jeans fragmentation. For the smallest scale, thermal plus non-thermal Jeans fragmentation also predicts too many protostellar objects. However, at each of the larger scales thermal plus non-thermal Jeans fragmentation predicts fewer than one fragment, corresponding to no fragmentation into envelopes, cores, and clumps. Over all scales, the results are inconsistent with complete Jeans fragmentation based on either thermal or thermal plus non-thermal motions. They are more nearly consistent with inefficient thermal Jeans fragmentation, where the thermal Jeans efficiency increases from the largest to the smallest scale.

Characterizing the forest fragmentation of Canada's national parks.

PubMed

Soverel, Nicholas O; Coops, Nicholas C; White, Joanne C; Wulder, Michael A

2010-05-01

Characterizing the amount and configuration of forests can provide insights into habitat quality, biodiversity, and land use. The establishment of protected areas can be a mechanism for maintaining large, contiguous areas of forests, and the loss and fragmentation of forest habitat is a potential threat to Canada's national park system. Using the Earth Observation for Sustainable Development of Forests (EOSD) land cover product (EOSD LC 2000), we characterize the circa 2000 forest patterns in 26 of Canada's national parks and compare these to forest patterns in the ecological units surrounding these parks, referred to as the greater park ecosystem (GPE). Five landscape pattern metrics were analyzed: number of forest patches, mean forest patch size (hectare), standard deviation of forest patch size (hectare), mean forest patch perimeter-to-area ratio (meters per hectare), and edge density of forest patches (meters per hectare). An assumption is often made that forests within park boundaries are less fragmented than the surrounding GPE, as indicated by fewer forest patches, a larger mean forest patch size, less variability in forest patch size, a lower perimeter-to-area ratio, and lower forest edge density. Of the 26 national parks we analyzed, 58% had significantly fewer patches, 46% had a significantly larger mean forest patch size (23% were not significantly different), and 46% had a significantly smaller standard deviation of forest patch size (31% were not significantly different), relative to their GPEs. For forest patch perimeter-to-area ratio and forest edge density, equal proportions of parks had values that were significantly larger or smaller than their respective GPEs and no clear trend emerged. In summary, all the national parks we analyzed, with the exception of the Georgian Bay Islands, were found to be significantly different from their corresponding GPE for at least one of the five metrics assessed, and 50% of the 26 parks were significantly different from their respective GPEs for all of the metrics assessed. The EOSD LC 2000 provides a heretofore unavailable dataset for characterizing broad trends in forest fragmentation in Canada's national parks and in their surrounding GPEs. The interpretation of forest fragmentation metrics must be guided by the underlying land cover context, as many forested ecosystems in Canada are naturally fragmented due to wetlands and topography. Furthermore, interpretation must also consider the management context, as some parks are designed to preserve fragmented habitats. An analysis of forest pattern such as that described herein provides a baseline, from which changes in fragmentation patterns over time could be monitored, enabled by earth observation data.

Filetype Identification Using Long, Summarized N-Grams

DTIC Science & Technology

2011-03-01

compressed or encrypted data . If the algorithm used to compress or encrypt the data can be determined, then it is frequently possible to uncom- press...fragments. His implementation utilized the bzip2 library to compress the file fragments. The bzip2 library is based off the Lempel - Ziv -Markov chain... algorithm that uses a dictionary compression scheme to remove repeating data patterns within a set of data . The removed patterns are listed within the

Closed-cage tungsten oxide clusters in the gas phase.

PubMed

Singh, D M David Jeba; Pradeep, T; Thirumoorthy, Krishnan; Balasubramanian, Krishnan

2010-05-06

During the course of a study on the clustering of W-Se and W-S mixtures in the gas phase using laser desorption ionization (LDI) mass spectrometry, we observed several anionic W-O clusters. Three distinct species, W(6)O(19)(-), W(13)O(29)(-), and W(14)O(32)(-), stand out as intense peaks in the regular mass spectral pattern of tungsten oxide clusters suggesting unusual stabilities for them. Moreover, these clusters do not fragment in the postsource decay analysis. While trying to understand the precursor material, which produced these clusters, we found the presence of nanoscale forms of tungsten oxide. The structure and thermodynamic parameters of tungsten clusters have been explored using relativistic quantum chemical methods. Our computed results of atomization energy are consistent with the observed LDI mass spectra. The computational results suggest that the clusters observed have closed-cage structure. These distinct W(13) and W(14) clusters were observed for the first time in the gas phase.

Identification of the chemical components of Saussurea involucrata by high-resolution mass spectrometry and the mass spectral trees similarity filter technique.

PubMed

Jia, Zhixin; Wu, Caisheng; Jin, Hongtao; Zhang, Jinlan

2014-11-15

Saussurea involucrata is a rare traditional Chinese medicine (TCM) that displays anti-fatigue, anti-inflammatory and anti-tumor effects. In this paper, the different chemical components of Saussurea involucrata were characterized and identified over a wide dynamic range by high-performance liquid chromatography coupled with high-resolution hybrid mass spectrometry (HPLC/HRMS/MS(n)) and the mass spectral trees similarity filter (MTSF) technique. The aerial parts of Saussurea involucrata were extracted with 75% ethanol. The partial extract was separated on a chromatography column to concentrate the low-concentration compounds. Mass data were acquired using full-scan mass analysis (resolving power 50,000) with data-dependent incorporation of dynamic exclusion analysis. The identified compounds were used as templates to construct a database of mass spectral trees. Data for the unknown compounds were matched with those templates and matching candidate structures were obtained. The detected compounds were characterized based on matching to candidate structures by the MTSF technique and were further identified by their accurate mass weight, multiple-stage analysis and fragmentation patterns and through comparison with literature data. A total of 38 compounds were identified including 19 flavones, 11 phenylpropanoids and 8 sphingolipids. Among them, 7 flavonoids, 8 phenylpropanoids and 8 sphingolipids were identified for the first time in Saussurea involucrata. HPLC/HRMS/MS(n) combined with MTSF was successfully used to discover and identify the chemical compounds in Saussurea involucrata. The results indicated that this combined technique was extremely useful for the rapid detection and identification of the chemical components in TCMs. Copyright © 2014 John Wiley & Sons, Ltd.

Demosaicking for full motion video 9-band SWIR sensor

NASA Astrophysics Data System (ADS)

Kanaev, Andrey V.; Rawhouser, Marjorie; Kutteruf, Mary R.; Yetzbacher, Michael K.; DePrenger, Michael J.; Novak, Kyle M.; Miller, Corey A.; Miller, Christopher W.

2014-05-01

Short wave infrared (SWIR) spectral imaging systems are vital for Intelligence, Surveillance, and Reconnaissance (ISR) applications because of their abilities to autonomously detect targets and classify materials. Typically the spectral imagers are incapable of providing Full Motion Video (FMV) because of their reliance on line scanning. We enable FMV capability for a SWIR multi-spectral camera by creating a repeating pattern of 3x3 spectral filters on a staring focal plane array (FPA). In this paper we present the imagery from an FMV SWIR camera with nine discrete bands and discuss image processing algorithms necessary for its operation. The main task of image processing in this case is demosaicking of the spectral bands i.e. reconstructing full spectral images with original FPA resolution from spatially subsampled and incomplete spectral data acquired with the choice of filter array pattern. To the best of author's knowledge, the demosaicking algorithms for nine or more equally sampled bands have not been reported before. Moreover all existing algorithms developed for demosaicking visible color filter arrays with less than nine colors assume either certain relationship between the visible colors, which are not valid for SWIR imaging, or presence of one color band with higher sampling rate compared to the rest of the bands, which does not conform to our spectral filter pattern. We will discuss and present results for two novel approaches to demosaicking: interpolation using multi-band edge information and application of multi-frame super-resolution to a single frame resolution enhancement of multi-spectral spatially multiplexed images.

Lensless Photoluminescence Hyperspectral Camera Employing Random Speckle Patterns.

PubMed

Žídek, Karel; Denk, Ondřej; Hlubuček, Jiří

2017-11-10

We propose and demonstrate a spectrally-resolved photoluminescence imaging setup based on the so-called single pixel camera - a technique of compressive sensing, which enables imaging by using a single-pixel photodetector. The method relies on encoding an image by a series of random patterns. In our approach, the image encoding was maintained via laser speckle patterns generated by an excitation laser beam scattered on a diffusor. By using a spectrometer as the single-pixel detector we attained a realization of a spectrally-resolved photoluminescence camera with unmatched simplicity. We present reconstructed hyperspectral images of several model scenes. We also discuss parameters affecting the imaging quality, such as the correlation degree of speckle patterns, pattern fineness, and number of datapoints. Finally, we compare the presented technique to hyperspectral imaging using sample scanning. The presented method enables photoluminescence imaging for a broad range of coherent excitation sources and detection spectral areas.

Building patterns and landscape fragmentation in northern Wisconsin, USA

Treesearch

Charlotte E. Gonzalez-Abraham; Volker C. Radeloff; Roger B. Hammer; Todd J. Hawbaker; Susan I. Stewart; Murray K. Clayton

2007-01-01

Housing growth is prevalent in rural areas in the United States and landscape fragmentation is one of its many effects. Since the 1930s, rural sprawl has been increasing in areas rich in recreational amenities. The question is how housing growth has affected landscape fragmentation. We thus tested three hypotheses relating land cover and land ownership to density and...

Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications.

PubMed

Cheng, Chia-Ying; Tsai, Chia-Feng; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian

2013-05-03

As spectral library searching has received increasing attention for peptide identification, constructing good decoy spectra from the target spectra is the key to correctly estimating the false discovery rate in searching against the concatenated target-decoy spectral library. Several methods have been proposed to construct decoy spectral libraries. Most of them construct decoy peptide sequences and then generate theoretical spectra accordingly. In this paper, we propose a method, called precursor-swap, which directly constructs decoy spectral libraries directly at the "spectrum level" without generating decoy peptide sequences by swapping the precursors of two spectra selected according to a very simple rule. Our spectrum-based method does not require additional efforts to deal with ion types (e.g., a, b or c ions), fragment mechanism (e.g., CID, or ETD), or unannotated peaks, but preserves many spectral properties. The precursor-swap method is evaluated on different spectral libraries and the results of obtained decoy ratios show that it is comparable to other methods. Notably, it is efficient in time and memory usage for constructing decoy libraries. A software tool called Precursor-Swap-Decoy-Generation (PSDG) is publicly available for download at http://ms.iis.sinica.edu.tw/PSDG/.

20180318 - Structure identification by Mass Spectrometry Non-Targeted Analysis using the US EPA’s CompTox Chemistry Dashboard (ACS Spring)

EPA Science Inventory

Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, r...

Ultra-High Spectral Resolution Observations of Fragmentation in Dark Cloud Cores

NASA Technical Reports Server (NTRS)

Velusamy, T.; Langer, W.; Kuiper, T; Levin, S.; Olsen, E.

1993-01-01

This paper presents new evidence of the fragmentary structure of dense cores in dark clouds using the high resolution spectra of the carbon chain molecule CCS transition (J subscript N = 2 subscript 1 - 1 subscript o) at 22.344033 GHz with 0.008 km s superscript -1 resolution.

Multiplex analysis of DNA

DOEpatents

Church, George M.; Kieffer-Higgins, Stephen

1992-01-01

This invention features vectors and a method for sequencing DNA. The method includes the steps of: a) ligating the DNA into a vector comprising a tag sequence, the tag sequence includes at least 15 bases, wherein the tag sequence will not hybridize to the DNA under stringent hybridization conditions and is unique in the vector, to form a hybrid vector, b) treating the hybrid vector in a plurality of vessels to produce fragments comprising the tag sequence, wherein the fragments differ in length and terminate at a fixed known base or bases, wherein the fixed known base or bases differs in each vessel, c) separating the fragments from each vessel according to their size, d) hybridizing the fragments with an oligonucleotide able to hybridize specifically with the tag sequence, and e) detecting the pattern of hybridization of the tag sequence, wherein the pattern reflects the nucleotide sequence of the DNA.

Multitemporal spatial pattern analysis of Tulum's tropical coastal landscape

NASA Astrophysics Data System (ADS)

Ramírez-Forero, Sandra Carolina; López-Caloca, Alejandra; Silván-Cárdenas, José Luis

2011-11-01

The tropical coastal landscape of Tulum in Quintana Roo, Mexico has a high ecological, economical, social and cultural value, it provides environmental and tourism services at global, national, regional and local levels. The landscape of the area is heterogeneous and presents random fragmentation patterns. In recent years, tourist services of the region has been increased promoting an accelerate expansion of hotels, transportation and recreation infrastructure altering the complex landscape. It is important to understand the environmental dynamics through temporal changes on the spatial patterns and to propose a better management of this ecological area to the authorities. This paper addresses a multi-temporal analysis of land cover changes from 1993 to 2000 in Tulum using Thematic Mapper data acquired by Landsat-5. Two independent methodologies were applied for the analysis of changes in the landscape and for the definition of fragmentation patterns. First, an Iteratively Multivariate Alteration Detection (IR-MAD) algorithm was used to detect and localize land cover change/no-change areas. Second, the post-classification change detection evaluated using the Support Vector Machine (SVM) algorithm. Landscape metrics were calculated from the results of IR-MAD and SVM. The analysis of the metrics indicated, among other things, a higher fragmentation pattern along roadways.

BBN: Description of the PLUM System as Used for MUC-4

DTIC Science & Technology

1992-01-01

in the MUC-4 corpus’ . Here are the 8 parse fragments generated by FPP for the first sentence of TST2- MUC4 -0048 : ("SALVADORAN PRESIDENT-ELECT ALFREDO...extensive patterns for fragment combination . Figure 2 shows a graphical version of the semantics generated for the first fragment of S1 in TST2- MUC4 ...trigger. Following is the discourse event structure for the first event in TST2- MUC4 -0048 : Event MURDER Trigger fragments: "SALVADORAN PRESIDENT

Identification of triacylglycerol using automated annotation of high resolution multistage mass spectral trees.

PubMed

Wang, Xiupin; Peng, Qingzhi; Li, Peiwu; Zhang, Qi; Ding, Xiaoxia; Zhang, Wen; Zhang, Liangxiao

2016-10-12

High complexity of identification for non-target triacylglycerols (TAGs) is a major challenge in lipidomics analysis. To identify non-target TAGs, a powerful tool named accurate MS(n) spectrometry generating so-called ion trees is used. In this paper, we presented a technique for efficient structural elucidation of TAGs on MS(n) spectral trees produced by LTQ Orbitrap MS(n), which was implemented as an open source software package, or TIT. The TIT software was used to support automatic annotation of non-target TAGs on MS(n) ion trees from a self-built fragment ion database. This database includes 19108 simulate TAG molecules from a random combination of fatty acids and corresponding 500582 self-built multistage fragment ions (MS ≤ 3). Our software can identify TAGs using a "stage-by-stage elimination" strategy. By utilizing the MS(1) accurate mass and referenced RKMD, the TIT software can discriminate unique elemental composition candidates. The regiospecific isomers of fatty acyl chains will be distinguished using MS(2) and MS(3) fragment spectra. We applied the algorithm to the selection of 45 TAG standards and demonstrated that the molecular ions could be 100% correctly assigned. Therefore, the TIT software could be applied to TAG identification in complex biological samples such as mouse plasma extracts. Copyright © 2016 Elsevier B.V. All rights reserved.

Cultural and environmental effects on the spectral development patterns of corn and soybeans: Field data analysis

NASA Technical Reports Server (NTRS)

Crist, E. P. (Principal Investigator)

1982-01-01

An overall approach to crop spectral understanding is presented which serves to maintain a strong link between actual plant responses and characteristics and spectral observations from ground based and spaceborne sensors. A specific technique for evaluating field reflectance data, as a part of the overall approach, is also described. Results of the application of this technique to corn and soybeans reflectance data collected by and at Purdue/LARS indicate that a number of common cultural and environmental factors can significantly affect the temporal spectral development patterns of these crops in tasseled cap greenness (a transformed variable of LANDSAT MSS signals).

Use of Amplified Fragment Length Polymorphisms for Typing Corynebacterium diphtheriae

PubMed Central

De Zoysa, Aruni; Efstratiou, Androulla

2000-01-01

Amplified fragment length polymorphism (AFLP) was investigated for the differentiation of Corynebacterium diphtheriae isolates. Analysis using Taxotron revealed 10 distinct AFLP profiles among 57 isolates. Strains with ribotype patterns D1, D4, and D12 could not be distinguished; however, the technique discriminated isolates of ribotype patterns D3, D6, and D7 further. AFLP was rapid, fairly inexpensive, and reproducible and could be used as an alternative to ribotyping. PMID:11015416

WHAT IS CONTROLLING THE FRAGMENTATION IN THE INFRARED DARK CLOUD G14.225–0.506?: DIFFERENT LEVELS OF FRAGMENTATION IN TWIN HUBS

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

Busquet, Gemma; Girart, Josep Miquel; Estalella, Robert

We present observations of the 1.3 mm continuum emission toward hub-N and hub-S of the infrared dark cloud G14.225–0.506 carried out with the Submillimeter Array, together with observations of the dust emission at 870 and 350 μm obtained with APEX and CSO telescopes. The large-scale dust emission of both hubs consists of a single peaked clump elongated in the direction of the associated filament. At small scales, the SMA images reveal that both hubs fragment into several dust condensations. The fragmentation level was assessed under the same conditions and we found that hub-N presents 4 fragments while hub-S is moremore » fragmented, with 13 fragments identified. We studied the density structure by means of a simultaneous fit of the radial intensity profile at 870 and 350 μm and the spectral energy distribution adopting a Plummer-like function to describe the density structure. The parameters inferred from the model are remarkably similar in both hubs, suggesting that density structure could not be responsible for determining the fragmentation level. We estimated several physical parameters, such as the level of turbulence and the magnetic field strength, and we found no significant differences between these hubs. The Jeans analysis indicates that the observed fragmentation is more consistent with thermal Jeans fragmentation compared with a scenario in which turbulent support is included. The lower fragmentation level observed in hub-N could be explained in terms of stronger UV radiation effects from a nearby H ii region, evolutionary effects, and/or stronger magnetic fields at small scales, a scenario that should be further investigated.« less

Voronoi cell patterns: Theoretical model and applications

NASA Astrophysics Data System (ADS)

González, Diego Luis; Einstein, T. L.

2011-11-01

We use a simple fragmentation model to describe the statistical behavior of the Voronoi cell patterns generated by a homogeneous and isotropic set of points in 1D and in 2D. In particular, we are interested in the distribution of sizes of these Voronoi cells. Our model is completely defined by two probability distributions in 1D and again in 2D, the probability to add a new point inside an existing cell and the probability that this new point is at a particular position relative to the preexisting point inside this cell. In 1D the first distribution depends on a single parameter while the second distribution is defined through a fragmentation kernel; in 2D both distributions depend on a single parameter. The fragmentation kernel and the control parameters are closely related to the physical properties of the specific system under study. We use our model to describe the Voronoi cell patterns of several systems. Specifically, we study the island nucleation with irreversible attachment, the 1D car-parking problem, the formation of second-level administrative divisions, and the pattern formed by the Paris Métro stations.

reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

PubMed Central

Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

2016-01-01

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contributes to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), that enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the following iterations. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. PMID:26419769

Sustained Sleep Fragmentation Induces Sleep Homeostasis in Mice

PubMed Central

Baud, Maxime O.; Magistretti, Pierre J.; Petit, Jean-Marie

2015-01-01

Study Objectives: Sleep fragmentation (SF) is an integral feature of sleep apnea and other prevalent sleep disorders. Although the effect of repetitive arousals on cognitive performance is well documented, the effects of long-term SF on electroencephalography (EEG) and molecular markers of sleep homeostasis remain poorly investigated. To address this question, we developed a mouse model of chronic SF and characterized its effect on EEG spectral frequencies and the expression of genes previously linked to sleep homeostasis including clock genes, heat shock proteins, and plasticity-related genes. Design: N/A. Setting: Animal sleep research laboratory. Participants : Sixty-six C57BL6/J adult mice. Interventions: Instrumental sleep disruption at a rate of 60/h during 14 days Measurements and Results: Locomotor activity and EEG were recorded during 14 days of SF followed by recovery for 2 days. Despite a dramatic number of arousals and decreased sleep bout duration, SF minimally reduced total quantity of sleep and did not significantly alter its circadian distribution. Spectral analysis during SF revealed a homeostatic drive for slow wave activity (SWA; 1–4 Hz) and other frequencies as well (4–40 Hz). Recordings during recovery revealed slow wave sleep consolidation and a transient rebound in SWA, and paradoxical sleep duration. The expression of selected genes was not induced following chronic SF. Conclusions: Chronic sleep fragmentation (SF) increased sleep pressure confirming that altered quality with preserved quantity triggers core sleep homeostasis mechanisms. However, it did not induce the expression of genes induced by sleep loss, suggesting that these molecular pathways are not sustainably activated in chronic diseases involving SF. Citation: Baud MO, Magistretti PJ, Petit JM. Sustained sleep fragmentation induces sleep homeostasis in mice. SLEEP 2015;38(4):567–579. PMID:25325477

reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

PubMed

Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W; Moritz, Robert L

2015-11-01

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. Graphical Abstract ᅟ.

reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

NASA Astrophysics Data System (ADS)

Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

2015-11-01

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website.

Theoretical Determination of Energy Transfer Processes and Influence of Symmetry in Lanthanide(III) Complexes: Methodological Considerations.

PubMed

Beltrán-Leiva, María J; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro

2018-05-07

This work presents a theoretical protocol to analyze the symmetry effect on the allowed character of the transitions and to estimate the probability of energy transfer in lanthanide(III) complexes. For this purpose, a complete study was performed based on the multireference CASSCF/PT2 technique along with TDDFT, to build the energy level diagrams and determine the spectral overlap integrals, respectively. This approach was applied on a series of LnIII complexes, viz. [LnCl 3 (DMF) 2 (Dpq)]/[Ln(NO 3 ) 3 (DMF) 2 (Dpq)], where Ln = Sm III , Tb III , Er III /Eu III , Nd III and dpq = dipyridoquinoxaline, synthesized and characterized by Patra et al. ( Dalton Trans. 2015 , 44 ( 46 ), 19844 - 19855 ; CrystEngComm 2016 , 18 ( 23 ), 4313 - 4322 ; Inorg. Chim. Acta 2016 , 451 , 73 - 81 ). A fragmentation scheme was applied where both the ligand and the lanthanide fragments were treated separately but at the same level of theory. The symmetry analysis only partially reproduced the expected results, and a more detailed analysis of the crystal field became necessary. On the other hand, the most probable energy transfer pathways that take place in the complexes were elucidated from the energy gaps between the ligand-localized triplet state and the emitting levels of the lanthanide fragments. These gaps, which are related to the energy transfer rate, properly reproduced the trend reported experimentally for the best and worst yields. Finally, the spectral overlap integral was calculated from the emission spectra of the dpq ligand and the absorption spectra of the lanthanide fragment. The obtained values are in good agreement with the quantum yields calculated for the systems. The most remarkable aspect of this protocol was its ability to explain the emission and nonemission of the studied compounds.

Deforestation and Forest Fragmentation in South Ecuador since the 1970s - Losing a Hotspot of Biodiversity.

PubMed

Tapia-Armijos, María Fernanda; Homeier, Jürgen; Espinosa, Carlos Iván; Leuschner, Christoph; de la Cruz, Marcelino

2015-01-01

Deforestation and fragmentation are major components of global change; both are contributing to the rapid loss of tropical forest area with important implications for ecosystem functioning and biodiversity conservation. The forests of South Ecuador are a biological 'hotspot' due to their high diversity and endemism levels. We examined the deforestation and fragmentation patterns in this area of high conservation value using aerial photographs and Aster satellite scenes. The registered annual deforestation rates of 0.75% (1976-1989) and 2.86% (1989-2008) for two consecutive survey periods, the decreasing mean patch size and the increasing isolation of the forest fragments show that the area is under severe threat. Approximately 46% of South Ecuador's original forest cover had been converted by 2008 into pastures and other anthropogenic land cover types. We found that deforestation is more intense at lower elevations (premontane evergreen forest and shrubland) and that the deforestation front currently moves in upslope direction. Improved awareness of the spatial extent, dynamics and patterns of deforestation and forest fragmentation is urgently needed in biologically diverse areas like South Ecuador.

The influence of arbuscular mycorrhizae on root precision nutrient foraging of two pioneer plant species during early reclamation

NASA Astrophysics Data System (ADS)

Boldt-Burisch, Katja; Naeth, M. Anne

2017-04-01

On many post mining sites in the Lusatian Mining District (East Germany) soil heterogeneity consists of sandy soil with embedded clay-silt fragments. Those clays silt fragments might act as nutrient hotspots. Arbuscular mycorrhizal fungi in an infertile ecosystem could enhance a plant's ability to selectively forage for those nutrients and thus to improve plants nutrient supply. In our study we investigated whether silt-clay fragments within a sandy soil matrix induced preferential root growth of Lotus corniculatus and Calamagrostis epigeios, whether arbuscular mycorrhizae influenced root foraging patterns, and to what extent selective rooting in clay silt fragments influenced plant growth were addressed in this research. Soil types were sterile and non-sterile sandy soil and clay-silt fragments. Treatments were with and without arbuscular mycorrhizae, with and without soil solution, and soil solution and mycorrhizal inoculum combined. Root biomass, root density and intraradical fungal alkaline phosphatase activity and frequency were determined in fragments relative to sandy soil. Furthermore, temporal relationship of number of roots in fragments and plant height was assessed. Lotus corniculatus showed strong selective rooting into fragments especially with those plants treated with commercial cultivated arbuscular mycorrhizae; Calamagrostis epigeios did not. Without arbuscular mycorrhizae, L. corniculatus growth was significantly reduced and selective rooting did not occur. Selective rooting induced significant growth spurts of L. corniculatus. Roots in fragments had higher fungal alkaline phosphatase activity suggesting that mycorrhizal efficiency and related plants phosphorus supply is enhanced in roots in fragments. The application of cultivated arbuscular mycorrhizal fungi significantly and quickly influenced root foraging patterns, especially those of L. corniculatus, suggesting mycorrhizae may also enhance the ability of other plants to selectively forage for nutrients and could therefore play an important role in early plant establishment on infertile reclamation sites.

Spectral Irradiance Calibration in the Infrared. 4; 1.2-35um Spectra of Six Standard Stars

NASA Technical Reports Server (NTRS)

Cohen, Martin; Witteborn, Fred C.; Walker, Russell G.; Bregman, Jesse D.; Wooden, Diane H.

1995-01-01

We present five new absolutely calibrated continuous stellar spectra from 1.2 to 35 microns, constructed as far as possible from actual observed spectral fragments taken from the ground, the Kuiper Airborne Observatory (KAO), and the IRAS Low Resolution Spectrometer (LRS). These stars, Beta Peg, Delta Boo, Beta And, Beta Gem, and Delta Hya, augment our already created complete absolutely calibrated spectrum for a Tau. All these spectra have a common calibration pedigree. The wavelength coverage is ideal for calibration of many existing and proposed ground-based, airborne, and satellite sensors.

Spectral Irradiance Calibration in the Infrared. Part 4; 1.2 - 35 microns Spectra of Six Standard Stars

NASA Technical Reports Server (NTRS)

Cohen, Martin; Witteborn, Fred C.; Walker, Russell G.; Bregman, Jesse D.; Wooden, Diane H.

1995-01-01

We present five new absolutely calibrated continuous stellar spectra from 1.2 to 35 microns, constructed as far as possible from actual observed spectral fragments taken from the ground, the Kuiper Airborne Observatory (KAO), and the IRAS Low Resolution Spectrometer (LRS). These stars- beta Peg, alpha Boo, beta And, beta Gem, and alpha Hya-augment our already created complete absolutely calibrated spectrum for alpha Tau. All these spectra have a common calibration pedigree. The wavelength coverage is ideal for calibration of many existing and proposed ground-based, airborne, and satellite sensors.

Tempest: GPU-CPU computing for high-throughput database spectral matching.

PubMed

Milloy, Jeffrey A; Faherty, Brendan K; Gerber, Scott A

2012-07-06

Modern mass spectrometers are now capable of producing hundreds of thousands of tandem (MS/MS) spectra per experiment, making the translation of these fragmentation spectra into peptide matches a common bottleneck in proteomics research. When coupled with experimental designs that enrich for post-translational modifications such as phosphorylation and/or include isotopically labeled amino acids for quantification, additional burdens are placed on this computational infrastructure by shotgun sequencing. To address this issue, we have developed a new database searching program that utilizes the massively parallel compute capabilities of a graphical processing unit (GPU) to produce peptide spectral matches in a very high throughput fashion. Our program, named Tempest, combines efficient database digestion and MS/MS spectral indexing on a CPU with fast similarity scoring on a GPU. In our implementation, the entire similarity score, including the generation of full theoretical peptide candidate fragmentation spectra and its comparison to experimental spectra, is conducted on the GPU. Although Tempest uses the classical SEQUEST XCorr score as a primary metric for evaluating similarity for spectra collected at unit resolution, we have developed a new "Accelerated Score" for MS/MS spectra collected at high resolution that is based on a computationally inexpensive dot product but exhibits scoring accuracy similar to that of the classical XCorr. In our experience, Tempest provides compute-cluster level performance in an affordable desktop computer.

Fragmentation characteristics of hydroxycinnamic acids in ESI-MSn by density functional theory.

PubMed

Yin, Zhi-Hui; Sun, Chang-Hai; Fang, Hong-Zhuang

2017-07-01

This work aims to analyze the electrospray ionization multistage mass spectrometry (ESI-MS n ) fragmentation characteristics of hydroxycinnamic acids (HCAs) in negative ion mode. The geometric parameters, energies, natural bond orbitals and frontier orbitals of fragments were calculated by density functional theory (DFT) to investigate mass spectral fragmentation mechanisms. The results showed that proton transfer always occurred during fragmentation of HCAs; their quasi-molecular ions ([M - H] - ) existed in more than one form and were mainly with the lowest energy. The fragmentation characteristics included the followings: (1) according to the different substitution position of phenolic hydroxyl group, the ring contraction reaction by CO elimination from benzene was in an increasingly difficult order: m-phenolic hydroxyl > p-phenolic hydroxyl > o-phenolic hydroxyl; and (2) ortho effect always occurred in o-dihydroxycinnamic acids (o-diHCAs), i.e. one phenolic hydroxyl group offered H + , which combined with the other one to lose H 2 O. In addition, there was a nucleophilic reaction during ring contraction in diHCAs that oxygen atom attacked the carbon atom binding with the other phenolic hydroxyl to lose CO 2 . The fragmentation characteristics and mechanism of HCAs could be used for analysis and identification of such compounds quickly and effectively, and as reference for structural analogues by ESI-MS. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics.

PubMed

García-Garcerà, Marc; Gigli, Elena; Sanchez-Quinto, Federico; Ramirez, Oscar; Calafell, Francesc; Civit, Sergi; Lalueza-Fox, Carles

2011-01-01

Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. METHODOLOGY/PRINCIPALS FINDINGS: To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants. We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5' and 3' ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.

THE ADVANTAGES OF FEMTOSECOND LASER-ASSISTED CATARACT SURGERY

PubMed Central

Gavris, M Monica; Belicioiu, Roxana; Olteanu, Ioana; Horge, Ioan

2015-01-01

Purpose: To present the advantages of performing femtosecond laser-assisted (Alcon-LenSx Inc.) cataract surgery. Methods: Cataract surgery was performed with the LenSx femtosecond laser (Alcon-LenSx Inc.) in 50 eyes of 50 patients. The laser was programmed to perform a 4,9-4,5 mm capsulorhexis, a 2,3 mm main corneal incision, two 1,3 mm side-port incisions and either a hybrid-pattern or a cylinder-pattern fragmentation of the nucleus. The evaluated parameters were the capsulotomy, the corneal wounds and the nucleus fragmentation. Phacoemulsification of the nucleus and aspiration of the cortex were performed with the Alcon Centurion Vision System and monofocal, toric and multifocal IOLs were successfully implanted. Results: A continuous, central, curvilinear capsulorhexis was performed in 48 cases, 96% (free-floating capsulotomy). In 2 cases, micro-adhesions were reported and detached with the Utrata forceps. Femtolaser capsulotomy resulted in a complete overlap of the anterior capsule over the IOL optics in all cases. Horizontal decentration was found in 2 cases, 4% and vertical decentration in 1 case, 2%. The main corneal incision was self-sealing in 49 cases, 98%. Sutures were used in 1 case, 2%. The hybrid pattern of nucleus fragmentation was used in 42 cases, 84% and the cylindrical pattern in 8 cases, 16%. The fragmentation was incomplete in one case of white cataract and in one case of traumatic cataract. Conclusions: The main advantages of femtolaser cataract surgery are standardized corneal incisions, perfectly centered, round capsulorhexis, and lens nucleus fragmentation even in eyes with hard cataracts. The laser precision is due to the real time OCT software programs, which cover the whole anterior segment, up to the posterior lens capsule. PMID:27373114

Ericson fluctuations in an open deterministic quantum system: theory meets experiment.

PubMed

Madroñero, Javier; Buchleitner, Andreas

2005-12-31

We provide numerically exact photoexcitation cross sections of rubidium Rydberg states in crossed, static electric, and magnetic fields, in quantitative agreement with recent experimental results. Their spectral backbone underpins a clear transition towards the Ericson regime, associated with a universal, fluctuating behavior of the cross section of strongly coupled, fragmenting quantum systems.

Structure identification for Non-Targeted Analytical Chemistry using the US EPA’s CompTox Chemistry Dashboard (ACS 2017 Fall meeting 3 of 3)

EPA Science Inventory

Identification of unknowns in non-targeted analyses (NTA) requires the integration of complementary data types to generate a confident consensus structure. Researchers use a variety of data and tools (e.g., chemical reference databases, spectral matching, fragment prediction too...

Respiratory and spontaneous arousals in patients with Sleep Apnea Hypopnea Syndrome.

PubMed

Mesquita, J; Porée, F; Carrault, G; Fiz, J A; Abad, J; Jané, R

2012-01-01

Sleep in patients with Sleep Apnea-Hypopnea Syndrome (SAHS) is frequently interrupted with arousals. Increased amounts of arousals result in shortening total sleep time and repeated sleep-arousal change can result in sleep fragmentation. According to the American Sleep Disorders Association (ASDA) an arousal is a marker of sleep disruption representing a detrimental and harmful feature for sleep. The nature of arousals and its role on the regulation of the sleep process raises controversy and has sparked the debate in the last years. In this work, we analyzed and compared the EEG spectral content of respiratory and spontaneous arousals on a database of 45 SAHS subjects. A total of 3980 arousals (1996 respiratory and 1984 spontaneous) were analyzed. The results showed no differences between the spectral content of the two kinds of arousals. Our findings raise doubt as to whether these two kinds of arousals are truly triggered by different organic mechanisms. Furthermore, they may also challenge the current beliefs regarding the underestimation of the importance of spontaneous arousals and their contribution to sleep fragmentation in patients suffering from SAHS.

Calculations on the orientation of the CH fragment in Co 3(CO) 9(μ 3-CH): Implications for metal surfaces

NASA Astrophysics Data System (ADS)

DeKock, Roger L.; Fehlner, Thomas P.

1982-07-01

A series of molecular orbital calculations using the Fenske-Hall method have been carried out on Co 3(CO) 9(μ 3-CH), in which the orientation of the CH fragment is varied with respect to the triangular plane of the three Co atoms. The calculations show that the energy differences between the orbitals that are predominantly CH in character are affected very little by the orientation of the CH fragment. These calculated differences are Δ(2 σ-1 σ)≅7 eV and Δ(1 π-1 σ)≅ 10.5 eV. The calculated splitting of the degenerate 1π orbitals for geometries with tilted CH fragments never amounted to more than 0.46 eV. Mixing of CH orbitals into the predominantly Co 3d manifold was extensive in all of the calculations. These calculations provide no support for the interpretation of energy loss and photoemission electron spectroscopy experiments in terms of CH fragments that are tilted with respect to the metal surface, but such an interpretation cannot be eliminated due to the diffuse nature of the spectral bands in the photoemission experiments.

Pixelated camouflage patterns from the perspective of hyperspectral imaging

NASA Astrophysics Data System (ADS)

Racek, František; Jobánek, Adam; Baláž, Teodor; Krejčí, Jaroslav

2016-10-01

Pixelated camouflage patterns fulfill the role of both principles the matching and the disrupting that are exploited for blending the target into the background. It means that pixelated pattern should respect natural background in spectral and spatial characteristics embodied in micro and macro patterns. The HS imaging plays the similar, however the reverse role in the field of reconnaissance systems. The HS camera fundamentally records and extracts both the spectral and spatial information belonging to the recorded scenery. Therefore, the article deals with problems of hyperspectral (HS) imaging and subsequent processing of HS images of pixelated camouflage patterns which are among others characterized by their specific spatial frequency heterogeneity.

Association of spectral development patterns with development stages of corn

NASA Technical Reports Server (NTRS)

Crist, E. P. (Principal Investigator)

1982-01-01

Association is made between the development stages of corn as defined by Hanway and the temporal-spectral development pattern of corn in a transformed data space derived from Landsat-MSS band reflectance values, using field-collected reflectance and associated data. Results indicate that the spectral vegetation index used (a reflectance equivalent of Tasseled Cap Greenness) reaches a maximum well before the stage at which corn is expected to achieve its peak leaf area index. Possible physiological and canopy geometry related causes for this and other results are presented.

Landscape Fragmentation as a Risk Factor for Buruli Ulcer Disease in Ghana

PubMed Central

Wu, Jianyong; Smithwick, Erica A. H.

2016-01-01

Land cover and its change have been linked to Buruli ulcer (BU), a rapidly emerging tropical disease. However, it is unknown whether landscape structure affects the disease prevalence. To examine the association between landscape pattern and BU presence, we obtained land cover information for 20 villages in southwestern Ghana from high resolution satellite images, and analyzed the landscape pattern surrounding each village. Eight landscape metrics indicated that landscape patterns between BU case and reference villages were different (P < 0.05) at the broad spatial extent examined (4 km). The logistic regression models showed that landscape fragmentation and diversity indices were positively associated with BU presence in a village. Specifically, for each increase in patch density and edge density by 100 units, the likelihood of BU presence in a village increased 2.51 (95% confidence interval [CI] = 1.36–4.61) and 4.18 (95% CI = 1.63–10.76) times, respectively. The results suggest that increased landscape fragmentation may pose a risk to the emergence of BU. PMID:27185767

Biogenic volatile organic compound analyses by PTR-TOF-MS: Calibration, humidity effect and reduced electric field dependency.

PubMed

Pang, Xiaobing

2015-06-01

Green leaf volatiles (GLVs) emitted by plants after stress or damage induction are a major part of biogenic volatile organic compounds (BVOCs). Proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) is a high-resolution and sensitive technique for in situ GLV analyses, while its performance is dramatically influenced by humidity, electric field, etc. In this study the influence of gas humidity and the effect of reduced field (E/N) were examined in addition to measuring calibration curves for the GLVs. Calibration curves measured for seven of the GLVs in dry air were linear, with sensitivities ranging from 5 to 10 ncps/ppbv (normalized counts per second/parts per billion by volume). The sensitivities for most GLV analyses were found to increase by between 20% and 35% when the humidity of the sample gas was raised from 0% to 70% relative humidity (RH) at 21°C, with the exception of (E)-2-hexenol. Product ion branching ratios were also affected by humidity, with the relative abundance of the protonated molecular ions and higher mass fragment ions increasing with humidity. The effect of reduced field (E/N) on the fragmentation of GLVs was examined in the drift tube of the PTR-TOF-MS. The structurally similar GLVs are acutely susceptible to fragmentation following ionization and the fragmentation patterns are highly dependent on E/N. Overall the measured fragmentation patterns contain sufficient information to permit at least partial separation and identification of the isomeric GLVs by looking at differences in their fragmentation patterns at high and low E/N. Copyright © 2015. Published by Elsevier B.V.

Abundance and fragmentation patterns of the ecosystem engineer Lithophyllum byssoides (Lamarck) Foslie along the Iberian Peninsula Atlantic coast. Conservation and management implications

NASA Astrophysics Data System (ADS)

Veiga, Puri; Rubal, Marcos; Cacabelos, Eva; Moreira, Juan; Sousa-Pinto, Isabel

2013-10-01

The crustose calcareous red macroalgae Lithophyllum byssoides (Lamarck) Foslie is a common ecosystem engineer along the Atlantic and Mediterranean coast of the Iberian Peninsula. This species is threatened by several anthropogenic impacts acting at different spatial scales, such as pollution or global warming. The aim of this study is to identify scales of spatial variation in the abundance and fragmentation patterns of L. byssoides along the Atlantic coast of the Iberian Peninsula. For this aim we used a hierarchical sampling design considering four spatial scales (from metres to 100s of kilometres). Results of the present study indicated no significant variability among regions investigated whereas significant variability was found at the scales of shore and site in spatial patterns of abundance and fragmentation of L. byssoides. Variance components were higher at the spatial scale of shore for abundance and fragmentation of L. byssoides with the only exception of percentage cover and thus, processes acting at the scale of 10s of kilometres seem to be more relevant in shaping the spatial variability both in abundance and fragmentation of L. byssoides. These results provided quantitative estimates of abundance and fragmentation of L. byssoides at the Atlantic coast of the Iberian Peninsula establishing the observational basis for future assessment, monitoring and experimental investigations to identify the processes and anthropogenic impacts affecting L. byssoides populations. Finally we have also identified percentage cover and patch density as the best variables for long-term monitoring programs aimed to detect future anthropogenic impacts on L. byssoides. Therefore, our results have important implications for conservation and management of this valuable ecosystem engineer along the Atlantic coast of the Iberian Peninsula.

Habitat Fragmentation and Species Extirpation in Freshwater Ecosystems; Causes of Range Decline of the Indus River Dolphin (Platanista gangetica minor)

PubMed Central

Braulik, Gill T.; Arshad, Masood; Noureen, Uzma; Northridge, Simon P.

2014-01-01

Habitat fragmentation of freshwater ecosystems is increasing rapidly, however the understanding of extinction debt and species decline in riverine habitat fragments lags behind that in other ecosystems. The mighty rivers that drain the Himalaya - the Ganges, Brahmaputra, Indus, Mekong and Yangtze - are amongst the world’s most biodiverse freshwater ecosystems. Many hundreds of dams have been constructed, are under construction, or are planned on these rivers and large hydrological changes and losses of biodiversity have occurred and are expected to continue. This study examines the causes of range decline of the Indus dolphin, which inhabits one of the world’s most modified rivers, to demonstrate how we may expect other vertebrate populations to respond as planned dams and water developments come into operation. The historical range of the Indus dolphin has been fragmented into 17 river sections by diversion dams; dolphin sighting and interview surveys show that river dolphins have been extirpated from ten river sections, they persist in 6, and are of unknown status in one section. Seven potential factors influencing the temporal and spatial pattern of decline were considered in three regression model sets. Low dry-season river discharge, due to water abstraction at irrigation barrages, was the principal factor that explained the dolphin’s range decline, influencing 1) the spatial pattern of persistence, 2) the temporal pattern of subpopulation extirpation, and 3) the speed of extirpation after habitat fragmentation. Dolphins were more likely to persist in the core of the former range because water diversions are concentrated near the range periphery. Habitat fragmentation and degradation of the habitat were inextricably intertwined and in combination caused the catastrophic decline of the Indus dolphin. PMID:25029270

Habitat fragmentation and species extirpation in freshwater ecosystems; causes of range decline of the Indus river dolphin (Platanista gangetica minor).

PubMed

Braulik, Gill T; Arshad, Masood; Noureen, Uzma; Northridge, Simon P

2014-01-01

Habitat fragmentation of freshwater ecosystems is increasing rapidly, however the understanding of extinction debt and species decline in riverine habitat fragments lags behind that in other ecosystems. The mighty rivers that drain the Himalaya - the Ganges, Brahmaputra, Indus, Mekong and Yangtze - are amongst the world's most biodiverse freshwater ecosystems. Many hundreds of dams have been constructed, are under construction, or are planned on these rivers and large hydrological changes and losses of biodiversity have occurred and are expected to continue. This study examines the causes of range decline of the Indus dolphin, which inhabits one of the world's most modified rivers, to demonstrate how we may expect other vertebrate populations to respond as planned dams and water developments come into operation. The historical range of the Indus dolphin has been fragmented into 17 river sections by diversion dams; dolphin sighting and interview surveys show that river dolphins have been extirpated from ten river sections, they persist in 6, and are of unknown status in one section. Seven potential factors influencing the temporal and spatial pattern of decline were considered in three regression model sets. Low dry-season river discharge, due to water abstraction at irrigation barrages, was the principal factor that explained the dolphin's range decline, influencing 1) the spatial pattern of persistence, 2) the temporal pattern of subpopulation extirpation, and 3) the speed of extirpation after habitat fragmentation. Dolphins were more likely to persist in the core of the former range because water diversions are concentrated near the range periphery. Habitat fragmentation and degradation of the habitat were inextricably intertwined and in combination caused the catastrophic decline of the Indus dolphin.

Evidence for Sequence Scrambling and Divergent H/D Exchange Reactions of Doubly-Charged Isobaric b-Type Fragment Ions

NASA Astrophysics Data System (ADS)

Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H.; Somogyi, Arpad; Solouki, Touradj

2014-02-01

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10 2+ that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10 2+ and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10 2+, suggesting that b10 2+ may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10 2+; over 30 % of the observed SORI-CID fragment ions from substance P b10 2+ had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10 2+, whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10 2+.

Evidence for sequence scrambling and divergent H/D exchange reactions of doubly-charged isobaric b-type fragment ions.

PubMed

Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H; Somogyi, Arpad; Solouki, Touradj

2014-02-01

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10(2+) that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10(2+) and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10(2+), suggesting that b10(2+) may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10(2+); over 30% of the observed SORI-CID fragment ions from substance P b10(2+) had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10(2+), whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10(2+).

sc-PDB-Frag: a database of protein-ligand interaction patterns for Bioisosteric replacements.

PubMed

Desaphy, Jérémy; Rognan, Didier

2014-07-28

Bioisosteric replacement plays an important role in medicinal chemistry by keeping the biological activity of a molecule while changing either its core scaffold or substituents, thereby facilitating lead optimization and patenting. Bioisosteres are classically chosen in order to keep the main pharmacophoric moieties of the substructure to replace. However, notably when changing a scaffold, no attention is usually paid as whether all atoms of the reference scaffold are equally important for binding to the desired target. We herewith propose a novel database for bioisosteric replacement (scPDBFrag), capitalizing on our recently published structure-based approach to scaffold hopping, focusing on interaction pattern graphs. Protein-bound ligands are first fragmented and the interaction of the corresponding fragments with their protein environment computed-on-the-fly. Using an in-house developed graph alignment tool, interaction patterns graphs can be compared, aligned, and sorted by decreasing similarity to any reference. In the herein presented sc-PDB-Frag database ( http://bioinfo-pharma.u-strasbg.fr/scPDBFrag ), fragments, interaction patterns, alignments, and pairwise similarity scores have been extracted from the sc-PDB database of 8077 druggable protein-ligand complexes and further stored in a relational database. We herewith present the database, its Web implementation, and procedures for identifying true bioisosteric replacements based on conserved interaction patterns.

Tools for neuroanatomy and neurogenetics in Drosophila

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

Pfeiffer, Barret D.; Jenett, Arnim; Hammonds, Ann S.

2008-08-11

We demonstrate the feasibility of generating thousands of transgenic Drosophila melanogaster lines in which the expression of an exogenous gene is reproducibly directed to distinct small subsets of cells in the adult brain. We expect the expression patterns produced by the collection of 5,000 lines that we are currently generating to encompass all neurons in the brain in a variety of intersecting patterns. Overlapping 3-kb DNA fragments from the flanking noncoding and intronic regions of genes thought to have patterned expression in the adult brain were inserted into a defined genomic location by site-specific recombination. These fragments were then assayedmore » for their ability to function as transcriptional enhancers in conjunction with a synthetic core promoter designed to work with a wide variety of enhancer types. An analysis of 44 fragments from four genes found that >80% drive expression patterns in the brain; the observed patterns were, on average, comprised of <100 cells. Our results suggest that the D. melanogaster genome contains >50,000 enhancers and that multiple enhancers drive distinct subsets of expression of a gene in each tissue and developmental stage. We expect that these lines will be valuable tools for neuroanatomy as well as for the elucidation of neuronal circuits and information flow in the fly brain.« less

Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching.

PubMed

Pai, Pei-Jing; Hu, Yingwei; Lam, Henry

2016-08-31

Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a new computational tool which combines the spectral library building/searching tool, SpectraST (Lam et al. Nat. Methods2008, 5, 873-875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. Anal. Chem.2010, 82, 10194-10202) for intact glycopeptide analysis has been developed. Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer-predicted spectra is built using SpectraST. Glycan identification from CID spectra is achieved by spectral library searching against this library, in which both m/z and intensity information of the possible fragmentation ions are taken into consideration for improved accuracy. We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC-MS/MS. In addition, we further applied our method to reveal, for the first time, the site-specific N-glycosylation profile of recombinant human acetylcholinesterase expressed in HEK293 cells. For maximum usability, SpectraST is developed as part of the Trans-Proteomic Pipeline (TPP), a freely available and open-source software suite for MS data analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment

PubMed Central

Dasari, Surendra; Chambers, Matthew C.; Martinez, Misti A.; Carpenter, Kristin L.; Ham, Amy-Joan L.; Vega-Montoto, Lorenzo J.; Tabb, David L.

2012-01-01

Spectral libraries have emerged as a viable alternative to protein sequence databases for peptide identification. These libraries contain previously detected peptide sequences and their corresponding tandem mass spectra (MS/MS). Search engines can then identify peptides by comparing experimental MS/MS scans to those in the library. Many of these algorithms employ the dot product score for measuring the quality of a spectrum-spectrum match (SSM). This scoring system does not offer a clear statistical interpretation and ignores fragment ion m/z discrepancies in the scoring. We developed a new spectral library search engine, Pepitome, which employs statistical systems for scoring SSMs. Pepitome outperformed the leading library search tool, SpectraST, when analyzing data sets acquired on three different mass spectrometry platforms. We characterized the reliability of spectral library searches by confirming shotgun proteomics identifications through RNA-Seq data. Applying spectral library and database searches on the same sample revealed their complementary nature. Pepitome identifications enabled the automation of quality analysis and quality control (QA/QC) for shotgun proteomics data acquisition pipelines. PMID:22217208

Power spectral analysis of R-R interval variability before and during the sinusoidal heart rate pattern in fetal lambs.

PubMed

Suzuki, T; Okamura, K; Kimura, Y; Watanabe, T; Yaegashi, N; Murotsuki, J; Uehara, S; Yajima, A

2000-05-01

The appearance of the sinusoidal heart rate pattern found on fetal cardiotocograms has not been fully explained, either physiologically or clinically. In this study we performed power spectral analysis on the sinusoidal heart rate pattern obtained by administration of arginine vasopressin and atropine sulfate to investigate its frequency components in fetal lambs with long-term instrument implantation. Eleven tests were performed in 4 fetal lambs at 120 to 130 days' gestation. An artificial sinusoidal heart rate pattern was obtained by administration of atropine sulfate and arginine vasopressin in 9 tests. An autoregression model was used to compare the spectral patterns before and during the sinusoidal heart rate pattern. Marked decreases in low-frequency (0.025-0.125 cycles/beat) and high-frequency (0.2-0.5 cycles/beat) areas were observed in the presence of the sinusoidal heart rate pattern. However, there were no significant changes in the very-low-frequency area (0.01-0.025 cycles/beat), which corresponds to the frequency of the sinusoidal heart rate pattern. The sinusoidal heart rate pattern may represent a very low-frequency component inherent in fetal heart rate variability that appears when low- and high-frequency components are reduced as a result of strongly suppressed autonomic nervous activity.

Spectral pattern of urinary water as a biomarker of estrus in the giant panda

NASA Astrophysics Data System (ADS)

Kinoshita, Kodzue; Miyazaki, Mari; Morita, Hiroyuki; Vassileva, Maria; Tang, Chunxiang; Li, Desheng; Ishikawa, Osamu; Kusunoki, Hiroshi; Tsenkova, Roumiana

2012-11-01

Near infrared spectroscopy (NIRS) has been successfully used for non-invasive diagnosis of diseases and abnormalities where water spectral patterns are found to play an important role. The present study investigates water absorbance patterns indicative of estrus in the female giant panda. NIR spectra of urine samples were acquired from the same animal on a daily basis over three consecutive putative estrus periods. Characteristic water absorbance patterns based on 12 specific water absorbance bands were discovered, which displayed high urine spectral variation, suggesting that hydrogen-bonded water structures increase with estrus. Regression analysis of urine spectra and spectra of estrone-3-glucuronide standard concentrations at these water bands showed high correlation with estrogen levels. Cluster analysis of urine spectra grouped together estrus samples from different years. These results open a new avenue for using water structure as a molecular mirror for fast estrus detection.

Spectral pattern of urinary water as a biomarker of estrus in the giant panda.

PubMed

Kinoshita, Kodzue; Miyazaki, Mari; Morita, Hiroyuki; Vassileva, Maria; Tang, Chunxiang; Li, Desheng; Ishikawa, Osamu; Kusunoki, Hiroshi; Tsenkova, Roumiana

2012-01-01

Near infrared spectroscopy (NIRS) has been successfully used for non-invasive diagnosis of diseases and abnormalities where water spectral patterns are found to play an important role. The present study investigates water absorbance patterns indicative of estrus in the female giant panda. NIR spectra of urine samples were acquired from the same animal on a daily basis over three consecutive putative estrus periods. Characteristic water absorbance patterns based on 12 specific water absorbance bands were discovered, which displayed high urine spectral variation, suggesting that hydrogen-bonded water structures increase with estrus. Regression analysis of urine spectra and spectra of estrone-3-glucuronide standard concentrations at these water bands showed high correlation with estrogen levels. Cluster analysis of urine spectra grouped together estrus samples from different years. These results open a new avenue for using water structure as a molecular mirror for fast estrus detection.

Spectral pattern of urinary water as a biomarker of estrus in the giant panda

PubMed Central

Kinoshita, Kodzue; Miyazaki, Mari; Morita, Hiroyuki; Vassileva, Maria; Tang, Chunxiang; Li, Desheng; Ishikawa, Osamu; Kusunoki, Hiroshi; Tsenkova, Roumiana

2012-01-01

Near infrared spectroscopy (NIRS) has been successfully used for non-invasive diagnosis of diseases and abnormalities where water spectral patterns are found to play an important role. The present study investigates water absorbance patterns indicative of estrus in the female giant panda. NIR spectra of urine samples were acquired from the same animal on a daily basis over three consecutive putative estrus periods. Characteristic water absorbance patterns based on 12 specific water absorbance bands were discovered, which displayed high urine spectral variation, suggesting that hydrogen-bonded water structures increase with estrus. Regression analysis of urine spectra and spectra of estrone-3-glucuronide standard concentrations at these water bands showed high correlation with estrogen levels. Cluster analysis of urine spectra grouped together estrus samples from different years. These results open a new avenue for using water structure as a molecular mirror for fast estrus detection. PMID:23181188

Spectral singularities and Bragg scattering in complex crystals

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

Longhi, S.

2010-02-15

Spectral singularities that spoil the completeness of Bloch-Floquet states may occur in non-Hermitian Hamiltonians with complex periodic potentials. Here an equivalence is established between spectral singularities in complex crystals and secularities that arise in Bragg diffraction patterns. Signatures of spectral singularities in a scattering process with wave packets are elucidated for a PT-symmetric complex crystal.

Study of Structure and Small-Scale Fragmentation in TMC-1

NASA Technical Reports Server (NTRS)

Langer, W. D.; Velusamy, T.; Kuiper, T. B.; Levin, S.; Olsen, E.; Migenes, V.

1995-01-01

Large-scale C(sup 18)O maps show that the Taurus molecular cloud 1 (TMC-1) has numerous cores located along a ridge which extends about 12 minutes by at least 35 minutes. The cores traced by C(sup 18)O are about a few arcminutes (0.1-0.2 pc) in extent, typically contain about 0.5-3 solar mass, and are probably gravitationally bound. We present a detailed study of the small-scale fragmentary structure of one of these cores, called core D, within TMC-1 using very high spectral and spatial resolution maps of CCS and CS. The CCS lines are excellent tracers for investigating the density, temperature, and velocity structure in dense cores. The high spectral resolution, 0.008 km /s, data consist mainly of single-dish, Nyquist-sampled maps of CCS at 22 GHz with 45 sec spatial resolution taken with NASA's 70 m DSN antenna at Goldstone. The high spatial resolution spectral line maps were made with the Very Large Array (9 sec resolution) at 22 GHz and with the OVRO millimeter array in CCS and CS at 93 GHz and 98 GHz, respectively, with 6 sec resolution. These maps are supplemented with single-dish observations of CCS and CC(sup 34)S spectra at 33 GHz using a NASA 34 m DSN antenna, CCS 93 GHz, C(sup 34)S (2-1), and C(sup 18)O (1-0) single-dish observations made with the AT&T Bell Laboratories 7 m antenna. Our high spectral and spatial CCS and CS maps show that core D is highly fragmented. The single-dish CCS observations map out several clumps which range in size from approx. 45 sec to 90 sec (0.03-0.06 pc). These clumps have very narrow intrinsic line widths, 0.11-0.25 km/s, slightly larger than the thermal line width for CCS at 10 K, and masses about 0.03-0.2 solar mass. Interferometer observations of some of these clumps show that they have considerable additional internal structure, consisting of several condensations ranging in size from approx. 10 sec- 30 sec (0.007-0.021 pc), also with narrow line widths. The mass of these smallest fragments is of order 0.01 solar mass. These small-scale structures traced by CCS appear to be gravitationally unbound by a large factor. Most of these objects have masses that fall below those of the putative proto-brown dwarfs (approx. less than 0.1 solar mass). The presence of many small gravitationally unbound clumps suggests that fragmentation mechanisms other than a purely Jeans gravitational instability may be important for the dynamics of these cold dense cores.

Novel approach of fragment-based lead discovery applied to renin inhibitors.

PubMed

Tawada, Michiko; Suzuki, Shinkichi; Imaeda, Yasuhiro; Oki, Hideyuki; Snell, Gyorgy; Behnke, Craig A; Kondo, Mitsuyo; Tarui, Naoki; Tanaka, Toshimasa; Kuroita, Takanobu; Tomimoto, Masaki

2016-11-15

A novel approach was conducted for fragment-based lead discovery and applied to renin inhibitors. The biochemical screening of a fragment library against renin provided the hit fragment which showed a characteristic interaction pattern with the target protein. The hit fragment bound only to the S1, S3, and S3 SP (S3 subpocket) sites without any interactions with the catalytic aspartate residues (Asp32 and Asp215 (pepsin numbering)). Prior to making chemical modifications to the hit fragment, we first identified its essential binding sites by utilizing the hit fragment's substructures. Second, we created a new and smaller scaffold, which better occupied the identified essential S3 and S3 SP sites, by utilizing library synthesis with high-throughput chemistry. We then revisited the S1 site and efficiently explored a good building block attaching to the scaffold with library synthesis. In the library syntheses, the binding modes of each pivotal compound were determined and confirmed by X-ray crystallography and the library was strategically designed by structure-based computational approach not only to obtain a more active compound but also to obtain informative Structure Activity Relationship (SAR). As a result, we obtained a lead compound offering synthetic accessibility as well as the improved in vitro ADMET profiles. The fragments and compounds possessing a characteristic interaction pattern provided new structural insights into renin's active site and the potential to create a new generation of renin inhibitors. In addition, we demonstrated our FBDD strategy integrating highly sensitive biochemical assay, X-ray crystallography, and high-throughput synthesis and in silico library design aimed at fragment morphing at the initial stage was effective to elucidate a pocket profile and a promising lead compound. Copyright © 2016 Elsevier Ltd. All rights reserved.

Haloacetic acid-degrading bacterial communities in drinking water systems as determined by cultivation and by terminal restriction fragment length polymorphism of PCR-amplified haloacid dehalogenase gene fragments.

PubMed

Grigorescu, A S; Hozalski, R M; Lapara, T M

2012-04-01

To characterize the HAA-degrading bacteria in drinking water systems. Haloacetic acid (HAA)-degrading bacteria were analysed in drinking water systems by cultivation and by a novel application of terminal restriction fragment length polymorphism (tRFLP). Substantial similarities were observed among the tRFLP patterns of dehI and dehII gene fragments in drinking water samples obtained from three different cities (Minneapolis, MN; St Paul, MN; Bucharest, Romania) and from one biologically active granular activated carbon filter (Hershey, PA). The dominant fragment in the tRFLP profiles of dehI genes from the drinking water samples matched the pattern from an Afipia sp. that was previously isolated from drinking water. In contrast, the dominant fragment in the tRFLP profiles of dehII genes did not match any previously characterized dehII gene fragment. PCR cloning was used to characterize this gene fragment, which had <65% nucleotide sequence identity with any previously characterized dehII gene. Afipia spp. are an appropriate model organism for studying the biodegradation of HAAs in drinking water distribution systems as encoded by dehI genes; the organism that harbours the most prominent dehII gene in drinking water has yet to be cultivated and identified. The development of a novel application of tRFLP targeting dehI and dehII genes could be broadly useful in understanding HAA-degrading bacteria in numerous environments. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

The 'fragmented' scintigraphic lung pattern in pulmonary lymphangitic carcinomatosis secondary to breast cancer.

PubMed

Vattimo, A V; Burroni, L; Bertelli, P; Vella, A; Volterrani, D

1998-01-01

Pulmonary lymphangitic carcinomatosis (PLC) is an unusual presentation of diffuse infiltrative lung disease. In this report we present two cases secondary to breast cancer; the diagnosis was made by means of transbronchial lung biopsy or postmortem examination. The goal of this study was to analyze the scintigraphic pattern of pulmonary perfusion performed with technetium-99m macroaggregated albumin (99mTc-MAA) in the hope of achieving improved recognition of PLC and its subsequent diagnosis. Upon admission, both patients underwent routine clinical exams followed by chest X-rays. The second patient also underwent CT examination, and both were ultimately examined using pulmonary perfusion scintigraphy with 99mTc-MAA. In the various exams performed, the most reliable and easily identified diagnostic finding turned out to be a characteristic 'fragmented' lung pattern revealed with the perfusion lung scan. Unfortunately, in both cases the patients' conditions rapidly worsened and death occurred shortly following scintigraphy. We were able to conclude that the recognition of the mentioned fragmented scintigraphic lung pattern may be useful in suspected PLC, whereas the nonspecific clinical presentation of this pathology makes diagnosis extremely difficult, with the most significant results being achieved through a comparison of scintigraphic and high resolution CT data.

Deforestation and Forest Fragmentation in South Ecuador since the 1970s – Losing a Hotspot of Biodiversity

PubMed Central

Tapia-Armijos, María Fernanda; Homeier, Jürgen; Espinosa, Carlos Iván; Leuschner, Christoph; de la Cruz, Marcelino

2015-01-01

Deforestation and fragmentation are major components of global change; both are contributing to the rapid loss of tropical forest area with important implications for ecosystem functioning and biodiversity conservation. The forests of South Ecuador are a biological ‘hotspot’ due to their high diversity and endemism levels. We examined the deforestation and fragmentation patterns in this area of high conservation value using aerial photographs and Aster satellite scenes. The registered annual deforestation rates of 0.75% (1976–1989) and 2.86% (1989–2008) for two consecutive survey periods, the decreasing mean patch size and the increasing isolation of the forest fragments show that the area is under severe threat. Approximately 46% of South Ecuador’s original forest cover had been converted by 2008 into pastures and other anthropogenic land cover types. We found that deforestation is more intense at lower elevations (premontane evergreen forest and shrubland) and that the deforestation front currently moves in upslope direction. Improved awareness of the spatial extent, dynamics and patterns of deforestation and forest fragmentation is urgently needed in biologically diverse areas like South Ecuador. PMID:26332681

Deforestation trends of tropical dry forests in central Brazil

USGS Publications Warehouse

Bianchi, Carlos A.; Haig, Susan M.

2013-01-01

Tropical dry forests are the most threatened forest type in the world yet a paucity of research about them stymies development of appropriate conservation actions. The Paranã River Basin has the most significant dry forest formations in the Cerrado biome of central Brazil and is threatened by intense land conversion to pastures and agriculture. We examined changes in Paranã River Basin deforestation rates and fragmentation across three time intervals that covered 31 yr using Landsat imagery. Our results indicated a 66.3 percent decrease in forest extent between 1977 and 2008, with an annual rate of forest cover change of 3.5 percent. Landscape metrics further indicated severe forest loss and fragmentation, resulting in an increase in the number of fragments and reduction in patch sizes. Forest fragments in flatlands have virtually disappeared and the only significant forest remnants are mostly found over limestone outcrops in the eastern part of the basin. If current patterns persist, we project that these forests will likely disappear within 25 yr. These patterns may be reversed with creation of protected areas and involvement of local people to preserve small fragments that can be managed for restoration.

Relationship between Auditory and Cognitive Abilities in Older Adults

PubMed Central

Sheft, Stanley

2015-01-01

Objective The objective was to evaluate the association of peripheral and central hearing abilities with cognitive function in older adults. Methods Recruited from epidemiological studies of aging and cognition at the Rush Alzheimer’s Disease Center, participants were a community-dwelling cohort of older adults (range 63–98 years) without diagnosis of dementia. The cohort contained roughly equal numbers of Black (n=61) and White (n=63) subjects with groups similar in terms of age, gender, and years of education. Auditory abilities were measured with pure-tone audiometry, speech-in-noise perception, and discrimination thresholds for both static and dynamic spectral patterns. Cognitive performance was evaluated with a 12-test battery assessing episodic, semantic, and working memory, perceptual speed, and visuospatial abilities. Results Among the auditory measures, only the static and dynamic spectral-pattern discrimination thresholds were associated with cognitive performance in a regression model that included the demographic covariates race, age, gender, and years of education. Subsequent analysis indicated substantial shared variance among the covariates race and both measures of spectral-pattern discrimination in accounting for cognitive performance. Among cognitive measures, working memory and visuospatial abilities showed the strongest interrelationship to spectral-pattern discrimination performance. Conclusions For a cohort of older adults without diagnosis of dementia, neither hearing thresholds nor speech-in-noise ability showed significant association with a summary measure of global cognition. In contrast, the two auditory metrics of spectral-pattern discrimination ability significantly contributed to a regression model prediction of cognitive performance, demonstrating association of central auditory ability to cognitive status using auditory metrics that avoided the confounding effect of speech materials. PMID:26237423

Properties of Spectral Shapes of Whistler-Mode Emissions

NASA Astrophysics Data System (ADS)

Macusova, E.; Santolik, O.; Pickett, J. S.; Gurnett, D. A.; Cornilleau-Wehrlin, N.

2014-12-01

Whistler-mode emissions play an important role in wave-particle interactions occurring in the radiation belt region. Whistler mode chorus emissions consist of discrete wave packets which exhibit different spectral shapes. Rising tones (events with positive value of the frequency sweep rate) are frequently observed. Other categories of chorus spectral shapes, such as falling tones, hooks, broadband patterns, are also known. Whistler-mode emissions can additionally occur as hiss or combinations of hiss with discrete patterns. In this study, we have analyzed more than 11 years of high-time resolution measurements provided by the Wideband Data (WBD) instrument onboard four Cluster spacecraft to identify different spectral shapes of whistler mode emissions. We determine the distribution of individual groups of chorus spectral shapes in the Earth's magnetosphere and the effect of the different geomagnetic conditions on their occurrence. We focus on average polarization and propagation properties of the different types of spectral shapes, obtained during visually identified time intervals from multicomponent measurements of the STAFF-SA instrument recorded with a time resolution of 4 seconds.

Cloud cover analysis with Arctic Advanced Very High Resolution Radiometer data. II - Classification with spectral and textural measures

NASA Technical Reports Server (NTRS)

Key, J.

1990-01-01

The spectral and textural characteristics of polar clouds and surfaces for a 7-day summer series of AVHRR data in two Arctic locations are examined, and the results used in the development of a cloud classification procedure for polar satellite data. Since spatial coherence and texture sensitivity tests indicate that a joint spectral-textural analysis based on the same cell size is inappropriate, cloud detection with AVHRR data and surface identification with passive microwave data are first done on the pixel level as described by Key and Barry (1989). Next, cloud patterns within 250-sq-km regions are described, then the spectral and local textural characteristics of cloud patterns in the image are determined and each cloud pixel is classified by statistical methods. Results indicate that both spectral and textural features can be utilized in the classification of cloudy pixels, although spectral features are most useful for the discrimination between cloud classes.

Fragmentation of forest, grassland, and shrubland

Treesearch

Kurt H. Riitters

2013-01-01

As humans introduce competing land uses into natural landscapes, the public concerns regarding landcover patterns are expressed through headline issues such as urban sprawl, forest fragmentation, water quality, and wilderness preservation. The spatial arrangement of an environment affects all human perceptions and ecological processes within that environment, but this...

Isospin dependence of fragment spectra in heavy/super-heavy colliding nuclei at intermediate energies

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

Chugh, Rajiv, E-mail: rajivchug@gmail.com; Kumar, Rohit, E-mail: rohitksharma.pu@gmail.com; Vinayak, Karan Singh, E-mail: drksvinayak@gmail.com

2016-05-06

Using isospin-dependent quantum molecular dynamics (IQMD) approach, we performed a theoretical investigation of the evolution of various kinds of fragments in heavy and superheavy-ion reactions in the intermediate/medium energy domain. We demonstrated direct impact of symmetry energy and Coulomb interactions on the evolution of fragments. Final fragment spectra (yields) obtained from the analysis of various heavy/super-heavy ion reactions at different reaction conditions show high sensitivity towards Coulomb interactions and less significant sensitivity to symmetry energy forms. No inconsistent pattern of fragment structure is obtained in case of super-heavy ion involved reactions for all the parameterizations of density dependence of symmetrymore » energy.« less

The Fragment Network: A Chemistry Recommendation Engine Built Using a Graph Database.

PubMed

Hall, Richard J; Murray, Christopher W; Verdonk, Marcel L

2017-07-27

The hit validation stage of a fragment-based drug discovery campaign involves probing the SAR around one or more fragment hits. This often requires a search for similar compounds in a corporate collection or from commercial suppliers. The Fragment Network is a graph database that allows a user to efficiently search chemical space around a compound of interest. The result set is chemically intuitive, naturally grouped by substitution pattern and meaningfully sorted according to the number of observations of each transformation in medicinal chemistry databases. This paper describes the algorithms used to construct and search the Fragment Network and provides examples of how it may be used in a drug discovery context.

Microstructures as IR-sensors with Staphylococcus aureus bacteria

NASA Astrophysics Data System (ADS)

Baikova, T. V.; Danilov, P. A.; Gonchukov, S. A.; Yermachenko, V. M.; Ionin, A. A.; Khmelnitskii, R. A.; Kudryashov, S. I.; Nguyen, T. T. H.; Rudenko, A. A.; Saraeva, I. N.; Svistunova, T. S.; Zayarny, D. A.

2017-09-01

Using a micro-hole grating in a supported silver film as a laser-fabricated novel optical platform for surface-enhanced IR absoprtion/reflection spectroscopy, characteristic absorption bands of Staphylococcus aureus, especially - its buried carotenoid fragments - were detected in FT-IR spectra with 10-fold analytical enhancement, paving the way to spectral express-identification of the pathogenic microorganisms.

Luminescence petrography of lunar samples

NASA Technical Reports Server (NTRS)

1972-01-01

Light-colored metaclastic rock fragments, mainly anorthositic breccias, are dominant in the lithic clasts of rock 14321 and constitute about 25% of the Apollo 14 soils. Concentration of anorthositic breccias is less in the Apollo 15 soils, but is higher in the Front samples. The Rille edge soils are rich in basalt fragments. The Apollo 15 soils are also rich in green glasses. True anorthosites in the Hadley region were found only at the St. George Crater site. Varying degrees of metamorphism were found in the anorthositic fragments, and luminescence zonations give independent evidence of metamorphism. Compositional zoning verifies the interpretation of luminescence. Rock 14321 gives evidence of modest annealing, but the light metaclastic fragments were metamorphosed before incorporation into the rock. Reaction rimming on plagioclase results in mosaicism and preferentially affects grains. The spectral analysis of luminescence in plagioclase shows that a red-infrared emission band is present in a small fraction of plagioclase grains. Samples from trench bottoms and from beneath a large boulder were compared with surface samples. Large variations in soil composition indicate marked layering in the Apollo 15 soils.

Observations of Titan IIIC Transtage Fragmentation Debris

NASA Technical Reports Server (NTRS)

Cowardin, Heather; Seitzer, P.; Abercromby, K.; Barker, E.; Buckalew, B.; Cardona, T.; Krisko, P.; Lederer, S.

2013-01-01

The fragmentation of a Titan IIIC Transtage (1968-081) on 21 February 1992 is one of only two known break-ups in or near geosynchronous orbit. The original rocket body and 24 pieces of debris are currently being tracked by the U. S. Space Surveillance Network (SSN). The rocket body (SSN# 3432) and several of the original fragments (SSN# 25000, 25001, 30000, and 33511) were observed in survey mode during 2004-2010 using the 0.6-m Michigan Orbital DEbris Survey Telescope (MODEST) in Chile using a broad R filter. This paper presents a size distribution for all calibrated magnitude data acquired on MODEST. Size distribution plots are also shown using historical models for small fragmentation debris (down to 10 cm) thought to be associated with the Titan Transtage break-up. In November 2010, visible broadband photometry (Johnson/Kron-Cousins BVRI) was acquired with the 0.9-m Small and Moderate Aperture Research Telescope System (SMARTS) at the Cerro Tololo Inter-American Observatory (CTIO) in Chile on several Titan fragments (SSN 25001, 33509, and 33510) and the parent rocket body (SSN 3432). Color index data are used to determine the fragment brightness distribution and how the data compares to spacecraft materials measured in the laboratory using similar photometric measurement techniques. In order to better characterize the break-up fragments, spectral measurements were acquired on three Titan fragments (one fragment observed over two different time periods) using the 6.5-m Magellan telescopes at Las Campanas Observatory in Chile. The telescopic spectra of SSN 25000 (May 2012 and January 2013), SSN 38690, and SSN 38699 are compared with laboratory acquired spectra of materials (e.g., aluminum and various paints) to determine the surface material.

Observations of Titan IIIC Transtage Fragmentation Debris

NASA Astrophysics Data System (ADS)

Cowardin, H.; Buckalew, B.; Barker, E.; Abercromby, K.; Seitzer, P.; Cardona, T.; Krisko, P.; Lederer, S.

2013-09-01

The fragmentation of a Titan IIIC Transtage (1968-081) on 21 February 1992 is one of only two known break-ups in or near geosynchronous orbit. The original rocket body and 24 pieces of debris are currently being tracked by the U. S. Space Surveillance Network (SSN). The rocket body (SSN# 3432) and several of the original fragments (SSN# 25000, 25001, 30000, and 33511) were observed in survey mode during 2004-2010 using the 0.6 m Michigan Orbital DEbris Survey Telescope (MODEST) in Chile using a broad R filter. This paper presents a size distribution for all calibrated magnitude data acquired on MODEST. Size distribution plots are also shown using historical models for small fragmentation debris (down to 10 cm) thought to be associated with the Titan Transtage break-up. In November 2010, visible broadband photometry (Johnson/Kron-Cousins BVRI) was acquired with the 0.9 m Small and Moderate Aperture Research Telescope System (SMARTS) at the Cerro Tololo Inter-American Observatory (CTIO) in Chile on several Titan fragments (SSN 25001, 33509, and 33510) and the parent rocket body (SSN 3432). Color index data are used to determine the fragment brightness distribution and how the data compares to spacecraft materials measured in the laboratory using similar photometric measurement techniques. In order to better characterize the break-up fragments, spectral measurements were acquired on three Titan fragments (one fragment observed over two different time periods) using the 6.5-m Magellan telescopes at Las Campanas Observatory in Chile. The telescopic spectra of SSN 25000 (May 2012 and January 2013), SSN 38690, and SSN 38699 are compared with laboratory acquired spectra of materials (e.g., aluminum and various paints) to determine the surface material.

Spectral Irradiance Calibration in the Infrared. Part 4; 1.2-35 micrometer Spectra of Six Standard Stars

NASA Technical Reports Server (NTRS)

Cohen, Martin; Witteborn, Fred C.; Walker, Russell, G.; Bregman, Jesse D.; Wooden, Diane H.

1995-01-01

Five new absolutely calibrated continuous stellar spectra from 1.2 to 35 microns are presented. The spectra were constructed as far as possible from actual observed spectral fragments taken from the ground, the Kuiper Airborne Observatory (KAO), and the IRAS Low Resolution Spectrometer (LRS). These stars (beta Peg, alpha Boo, beta And, beta Gem, and alpha Hya) augment the author's already created complete absolutely calibrated spectrum for alpha Tau. All these spectra have a common calibration pedigree. The wavelength coverage is ideal for calibration of many existing and proposed ground-based, airborne, and satellite sensors.

Computed tomography of calcaneal fractures

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

Heger, L.; Wulff, K.; Seddiqi, M.S.A.

1985-07-01

Computed tomography (CT) of 25 fractured calcanei was performed to investigate the potential of CT in evaluating the pattern and biomechanics of these fractures. The characteristic findings of typical fractures are presented, including the number and type of principal fragments, size and dislocation of the sustentacular fragment, and involvement of the anterior and posterior facets of the subtalar joint. In 17 cases, the calcaneus consisted of four or more fragments. Furthermore, in 17 cases the sustentacular fragment included all or part of the posterior facet joint. In 18 of the 25 cases, the sustentacular fragment was displaced. It is concludedmore » that well performed CT is an invaluable adjunct in understanding the fracture mechanism and in detecting pain-provoking impingement between the fibular malleolus and the tuberosity fragment.« less

Rb-Sr Isotopic Systematics of Alkali-Rich Fragments in the Yamato-74442 LL-Chondritic Breccia

NASA Technical Reports Server (NTRS)

Yokoyama, T.; Misawa, K.; Okano, O.; Shih, C.-Y.; Nyquist, L. E.; Simo, J. I.; Tappa, M. J.; Yoneda, S.

2012-01-01

Alkali-rich igneous fragments were identified in the brecciated LL-chondrites, Kr henberg (LL5)], Bhola (LL3-6) and Yamato (Y)-74442 (LL4), and show characteristic fractionation patterns of alkaline elements. The K-Rb-Cs-rich fragments in Kr henberg, Bhola, and Y-74442 are very similar in mineralogy and petrography (olivine + pyroxene + glass), suggesting that they could have come from related precursor materials. We have undertaken Rb-Sr isotopic studies on alkali-rich fragments in Y-74442 to precisely determine their crystallization ages and the isotopic signatures of their precursor material(s).

Extreme ultraviolet photoionization of aldoses and ketoses

NASA Astrophysics Data System (ADS)

Shin, Joong-Won; Dong, Feng; Grisham, Michael E.; Rocca, Jorge J.; Bernstein, Elliot R.

2011-04-01

Gas phase monosaccharides (2-deoxyribose, ribose, arabinose, xylose, lyxose, glucose galactose, fructose, and tagatose), generated by laser desorption of solid sample pellets, are ionized with extreme ultraviolet photons (EUV, 46.9 nm, 26.44 eV). The resulting fragment ions are analyzed using a time of flight mass spectrometer. All aldoses yield identical fragment ions regardless of size, and ketoses, while also generating same ions as aldoses, yields additional features. Extensive fragmentation of the monosaccharides is the result the EUV photons ionizing various inner valence orbitals. The observed fragmentation patterns are not dependent upon hydrogen bonding structure or OH group orientation.

Specificity enhancement by electrospray ionization multistage mass spectrometry--a valuable tool for differentiation and identification of 'V'-type chemical warfare agents.

PubMed

Weissberg, Avi; Tzanani, Nitzan; Dagan, Shai

2013-12-01

The use of chemical warfare agents has become an issue of emerging concern. One of the challenges in analytical monitoring of the extremely toxic 'V'-type chemical weapons [O-alkyl S-(2-dialkylamino)ethyl alkylphosphonothiolates] is to distinguish and identify compounds of similar structure. MS analysis of these compounds reveals mostly fragment/product ions representing the amine-containing residue. Hence, isomers or derivatives with the same amine residue exhibit similar mass spectral patterns in both classical EI/MS and electrospray ionization-MS, leading to unavoidable ambiguity in the identification of the phosphonate moiety. A set of five 'V'-type agents, including O-ethyl S-(2-diisopropylamino)ethyl methylphosphonothiolate (VX), O-isobutyl S-(2-diethylamino)ethyl methylphosphonothiolate (RVX) and O-ethyl S-(2-diethylamino)ethyl methylphosphonothiolate (VM) were studied by liquid chromatography/electrospray ionization/MS, utilizing a QTRAP mass detector. MS/MS enhanced product ion scans and multistage MS(3) experiments were carried out. Based on the results, possible fragmentation pathways were proposed, and a method for the differentiation and identification of structural isomers and derivatives of 'V'-type chemical warfare agents was obtained. MS/MS enhanced product ion scans at various collision energies provided information-rich spectra, although many of the product ions obtained were at low abundance. Employing MS(3) experiments enhanced the selectivity for those low abundance product ions and provided spectra indicative of the different phosphonate groups. Study of the fragmentation pathways, revealing some less expected structures, was carried out and allowed the formulation of mechanistic rules and the determination of sets of ions typical of specific groups, for example, methylphosphonothiolates versus ethylphosphonothiolates. The new group-specific ions elucidated in this work are also useful for screening unknown 'V'-type agents and related compounds, utilizing precursor ion scan experiments. Copyright © 2013 John Wiley & Sons, Ltd.

Does avian species richness in natural patch mosaics follow the forest fragmentation paradigm?

USGS Publications Warehouse

Pavlacky, D.C.; Anderson, S.H.

2007-01-01

As one approaches the north-eastern limit of pinyon (Pinus spp.) juniper (Juniperus spp.) vegetation on the Colorado Plateau, USA, woodland patches become increasingly disjunct, grading into sagebrush (Artemisia spp.)-dominated landscapes. Patterns of avian species richness in naturally heterogeneous forests may or may not respond to patch discontinuity in the same manner as bird assemblages in fragmented agricultural systems. We used observational data from naturally patchy woodlands and predictions derived from studies of human-modified agricultural forests to estimate the effects of patch area, shape, isolation and distance to contiguous woodland on avian species richness. We predicted that patterns of species richness in naturally patchy juniper woodlands would differ from those observed in fragmented agricultural systems. Our objectives were to (1) estimate the effect of naturally occurring patch structure on avian species richness with respect to habitat affinity and migratory strategy and (2) assess the concordance of the effects to predictions from agricultural forest systems. We used the analogy between populations and communities to estimate species richness, where species are treated as individuals in the application of traditional capture-recapture theory. Information-theoretic model selection showed that overall species richness was explained primarily by the species area relationship. There was some support for a model with greater complexity than the equilibrium theory of island biogeography where the isolation of large patches resulted in greater species richness. Species richness of woodland-dwelling birds was best explained by the equilibrium hypothesis with partial landscape complementation by open-country species in isolated patches. Species richness within specific migratory strategies showed concomitant increases and no shifts in species composition along the patch area gradient. Our results indicate that many patterns of species richness considered to be fragmentation effects may be general consequences of patch discontinuity and are ubiquitous in naturally heterogeneous systems. There was no evidence for the effects of patch shape and distance to contiguous woodland in juniper woodland, suggesting edge effects and dependence upon regional species pools are characteristics of fragmented agricultural systems. Natural patch mosaics may provide benchmarks for evaluating fragmentation effects and managing forests by mimicking natural landscape patterns. ?? 2007 The Zoological Society of London.

Chemistry Within Molecular Clusters

DTIC Science & Technology

1992-06-01

reactions, and only occur within van der Waals clusters. 23 They include the generation of (C2H4F2),>4H+ ions from 1,1- difluoroethane clusters, 4 the...of fragment ions, and identification of the molecule must be made by the characteristic fragmentation pattern. The mass spectrum of 1,1- difluoroethane

Chemistry within Molecular Clusters

DTIC Science & Technology

1992-05-29

within van der Waals clusters. 23 They include the generation of (C2H4F 2),,>4H+ ions from 1,1- difluoroethane clusters, 24 the generation of (CH 3...fragment ions, and identification of the molecule must be made by the characteristic fragmentation pattern. The mass spectrum of 1,1- difluoroethane (DFE

Abstracts of papers presented at the 8th workshop of the Virology Section of the Deutsche Gesellschaft für Hygiene und Mikro-biologie, Würzburg, March 17-19, 1983.

PubMed

1983-09-01

17 adenovirus strains were found to be antigenically related to prototype Ad 15 by neutralization. No relationship to Ad 15, but to Ad 9 could be detected by hemagglutination-inhibition; we therefore named them Ad 15/H9 intermediate strains. After analysis of the genome by five different restriction enzymes, the fragment patterns obtained deviated widely from the prototype Ad 15, but only slightly from Ad 9. Differences could also be observed among the variants. After digestion by five restriction enzymes, altogether six genome types could be established among the 17 intermediate strains. To map the variations on the genome of the 15/H9 strains, two methods were employed: the double digestion of the DNA and DNA fragments together with the determination of the terminal fragments made it possible to construct a physical map. The second method depends on a particularity of adenoviruses: the DNA is covalently linked with a 55 kD protein at the 5' terminus. After digestion of the DNA, which does contain this protein, the terminal DNA fragments do not migrate into the agarose gel; after an additional digestion with pronase B, they do migrate into the gel. Thus the terminal fragments were determined by comparing the fragment patterns with and without previous pronase B treatment.

Land Use Change and Agricultural Land Fragmentation due to Anthropogenic Activities in an Hot Spot Area: A Case Study for Thrace Region of Turkey

NASA Astrophysics Data System (ADS)

Altürk, Bahadır; Konukcu, Fatih

2017-04-01

Agricultural lands that supply food, energy and ecosystem services for human life have been lost due to anthropogenic activities such as construction of roads, urban and industry areas. The significant reasons for the increase of artificial surfaces were poorly planned economic decisions by the government and internal migration due to this poorly planning. Unplanned urban sprawl also give rise to land fragmentation. Fragmentation of agricultural land affects both the agricultural production capacity and rural sustainable employment. In this study: i) Land use changes between 1990-2014 period were assessed using remotely sensed data and ii) Spatial and temporal agricultural land fragmentation were investigated using landscape pattern indice (effective mesh size), Morphological Spatial Pattern Analysis (MSPA) and Entropy method for 25 years period. The selected"hot spot" study area is located on east Thrace region of Turkey, being the service and industrial development zone where agricultural activities, water resources and natural habitat have been damaged due to rapid urban and industrial development for about 25 years. The results showed that agricultural lands decreased 6.44%, urban areas increased 111.68% and industry areas increased 251.19% during this 25 years period. Additionally, fragmentation analyses demonstrated that core agricultural areas sharply decreased and relative fragmentation (effective mesh size) increased from 50.68% to 56.77% during 1990 and 2014.

Observations of Titan 3C-4 Transtage Fragmentation Debris

NASA Technical Reports Server (NTRS)

Cowardin, Heather; Seitzer, P.; Abercromby, K.; Barker, E.; Cardona, T.; Krisko, P.; Lederer, S.

2013-01-01

The fragmentation of a Titan 3C-4 Transtage (1968-081) on 21 February 1992 is one of only two known break-ups in or near geosynchronous orbit. The original rocket body and 24 pieces of debris are currently being tracked by the US Space Surveillance Network (SSN). The rocket body (SSN# 3432) and several of the original fragments (SSN# 25000, 25001, 30000, and 33511) were observed in survey mode during 2004-2010 using the 0.6-m Michigan Orbital DEbris Survey Telescope (MODEST) in Chile using a broad R filter. This paper will present a size distribution for all calibrated magnitude data acquired on MODEST. Size distribution plots will also be shown using historical models for small fragmentation debris (down to 10 cm) believed to be associated with the Titan break-up. In November 2010, visible broadband photometry (Johnson/Kron-Cousins BVRI) was acquired with the 0.9-m Small and Moderate Aperture Research Telescope System (SMARTS) at the Cerro Tololo Inter-American Observatory (CTIO) in Chile on several Titan fragments (SSN# 25001, 33509, 33510) and the parent rocket body. Color index data will be used to determine the fragment brightness distribution and how the data compares to spacecraft materials measured in the laboratory using similar photometric measurement techniques. In 2012, the SSN added 16 additional fragments to the catalogue. MODEST acquired magnitude data on ten Titan fragments in late 2012 and early 2013. The magnitude distribution of all the observed fragments are analyzed as a function of time. In order to better characterize the breakup fragments spectral measurements were acquired on the original rocket body and five Titan fragments using the 6.5-m Magellan telescopes at Las Campanas Observatory in Chile. The telescopic spectra are compared with laboratory acquired spectra of materials (e.g., Aluminum and various paints) and categorized based on known absorption features for spacecraft materials.

A STUDY OF MEIOSIS IN THE PROGENY OF X-IRRADIATED LUZULA PURPUREA

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

Nordenskiold, H.

1963-01-01

In Luzula the chromosomes have diffuse or nonlocalized centromeres; thus, if the chromosomes are broken or rearranged by x-ray treatment, the changed chromosome patterns may survive through the mitotic cell divisions, on account of the centromeric action along the whole chromosomes. Hence, such plants with diffuse centromeres are able to survive and reach adult stages in spite of the fact that their chromosomes have been rearranged or broken by x-ray treatment of the seedlings. A study was made of plants selected from the progeny of material treated as seedlings with 1000 or 2500 r. Plants treated with stronger doses (5000more » to 10000 r) were almost or completely sterile. The chromosome patterns of the root tips of X/sub 2/ plants were investigated in order to find plants with desirable chrom-osome patterns for the meiotic investigation. The x-irradiated plants themselves showed intricate metaphasic configurations during meiosis. The separation of the multi-associations at first anaphase is cytologically equational, and in most cases without bridges. Migration of chromatids during second anaphase is also regular without lagging chromosomes, but chromosome sets of 4 tetrad cells usually become unbalanced, causing reduced fertility. The mitotic chromosome patterns of X/sub 2/ plants showed three categories of patterns: 2n = 6; most of these plants have all chromosomes the same size, but some of them possess one long and one short chromosome indicating a reciprocal translocation between two chromosomes; 2n = 7, with one of the original chromosomes fragmented into two pieces; and 2n = 8, with two of the original chromosomes fragmented into two pieces each. A study was made of meiosis in X/ sub 2/ plants with a cytologically observable rearrangement in the root tips, determined as a reciprocal progeny plants were obtained. Meiosis of X/sub 2/ plants heterozygous for one chromosome fragmented into two pieces, i.e., possessing 2n = 7 with five normal-sized and two small half-sized chromosomes, was also studied. The expected course of meiosis was realized, giving rise to four balanced chromosome sets of the tetrads, two of them containing three normal- sized chromosomes and the remaining two having two normal-sized and two half- sized ones. These studied plants were all fertile. Examination of somatic chromosome patterns of the progenies originating from the X/sub 2/ plants heterozygous for one fragmented chromosome revealed the three expected chromosome patterns, i.e., 2n =6, 2n =7, 2n =8. X/sub 2/ plants with 2n =8 were homozygous for the fragmented chromosome, and had a completely regular meiosis with two large and two small bivalents during first metaphase and a regular pairing and separation during the second division. Consequently they gave rise to a fertile strain with a constart chromosome pattern. The origin of the aneuploidy and endonuclear polyploidy of material with diffuse centromeres was discussed in relation to the survival of the fragmented chromosomes in L. purpurea. The survival of broken chromosomes through consecutive generations thus gives an explanation of the occurrence of aneuploid chromosome numbers in material with diffuse centromeres. However, no interpretation of the phenomenon causing the survival of the fragments was provided by this study, since sufficient knowledge about the nature of the diffuse or nonlocalized centromeres is unavailable. (BBB)« less

[A Method to Measure the Velocity of Fragments of Large Equivalence Explosion Field Based on Explosion Flame Spectral Analysis].

PubMed

Liu, Ji; Yu, Li-xia; Zhang, Bin; Zhao Dong-e; Liij, Xiao-yan; Wang, Heng-fei

2016-03-01

The deflagration fire lasting for a long time and covering a large area in the process of large equivalent explosion makes it difficult to obtain velocity parameters of fragments in the near-field. In order to solve the problem, it is proposed in this paper a photoelectric transceiver integrated method which utilize laser screen as the sensing area. The analysis of three different types of warhead explosion flame spectral distribution of radiation shows that 0.3 to 1.0 μm within the band is at relatively low intensity. On the basis of this, the optical system applies the principle of determining the fixed distance by measuring the time and the reflector technology, which consists of single longitudinal mode laser, cylindrical Fresnel lens, narrow-band filters and high-speed optical sensors, etc. The system has its advantage, such as transceiver, compact structure and combination of narrowband filter and single longitudinal mode laser, which can stop the spectrum of fire from suppressing the interference of background light effectively. Large amounts of experiments in different models and equivalent have been conducted to measure the velocity of difference kinds of warheads, obtaining higher signal-to-noise ratio of the waveform signal after a series of signal de-noising and recognition through NI company data acquisition and recording system. The experimental results show that this method can complete the accurately test velocity of fragments around center of the explosion. Specifically, the minimum size of fragments can be measured is 4 mm while the speed can be obtained is up to 1 200 m x s(-1) and the capture rate is better than 95% comparing with test results of target plate. At the same time, the system adopts Fresnel lenses-transparent to form a rectangular screen, which makes the distribution of rectangular light uniform in vertical direction, and the light intensity uniformity in horizontal direction is more than 80%. Consequently, the system can distinguish preliminarily the correspondence between the velocity and the sizes of prefabricated fragments.

Can you escape the beat? Modelling spatiotemporal biodegradation dynamics during periodic disturbances

NASA Astrophysics Data System (ADS)

König, Sara; Worrich, Anja; Wick, Lukas Y.; Miltner, Anja; Kästner, Matthias; Thullner, Martin; Centler, Florian; Banitz, Thomas; Frank, Karin

2016-04-01

Biodegradation of organic compounds in soil is an important microbial ecosystem service. Soil ecosystems are constantly exposed to disturbances of different spatial configurations and frequencies, challenging their ability to recover the biodegradation function. Thus, the response to these disturbances is crucial for the soil systems' biodegradation performance. The influence of spatial aspects of the disturbance regimes on long-term biodegradation dynamics under periodic disturbances has not been examined, yet. We applied a numerical simulation model considering bacterial growth, degradation, and dispersal to analyze the spatiotemporal biodegradation dynamics under disturbances occuring with different frequencies and with different spatial configurations. We found biodegradation performance decreasing in response to periodic disturbances but on average approaching a new quasi steady state. This mean performance of the disturbed systems increases with both, the interval length between disturbance events and the fragmentation of the spatial disturbance patterns. A detailed spatiotemporal analysis of degradation activity reveals that under highly fragmented disturbance patterns, biodegradation still takes place in the entire disturbed area. For moderately fragmented disturbance patterns, parts of the disturbed area become completely inactive. However, areas with high degradation activity emerge at the interface between disturbed and undisturbed areas, allowing the systems to maintain a relatively high degradation performance. Further decreasing the disturbance patterns' fragmentation, fewer interfaces between disturbed and undisturbed area and, thus, fewer active habitats occur, which reduces biodegradation performances. In additional simulations, we found that bacterial dispersal networks, as for example provided by fungal hyphae, usually increase the areas of high degradation activity and, thus, the biodegradation performance in presence of periodic disturbances. However, for some specific regimes with highly fragmented disturbance patterns, dispersal networks can in turn decrease the biodegradation performance. Our results show that spatial aspects of the periodic disturbance regime influence the biodegradation dynamics, indicating the relevance of spatial processes for functional stability. The level of connectivity between disturbed and undisturbed areas is crucial for the local and global dynamics of the ecosystem service biodegradation. Networks enhancing bacterial dispersal may often, but not always, increase the functional stability.

Humidity Effects on Fragmentation in Plasma-Based Ambient Ionization Sources

NASA Astrophysics Data System (ADS)

Newsome, G. Asher; Ackerman, Luke K.; Johnson, Kevin J.

2016-01-01

Post-plasma ambient desorption/ionization (ADI) sources are fundamentally dependent on surrounding water vapor to produce protonated analyte ions. There are two reports of humidity effects on ADI spectra. However, it is unclear whether humidity will affect all ADI sources and analytes, and by what mechanism humidity affects spectra. Flowing atmospheric pressure afterglow (FAPA) ionization and direct analysis in real time (DART) mass spectra of various surface-deposited and gas-phase analytes were acquired at ambient temperature and pressure across a range of observed humidity values. A controlled humidity enclosure around the ion source and mass spectrometer inlet was used to create programmed humidity and temperatures. The relative abundance and fragmentation of molecular adduct ions for several compounds consistently varied with changing ambient humidity and also were controlled with the humidity enclosure. For several compounds, increasing humidity decreased protonated molecule and other molecular adduct ion fragmentation in both FAPA and DART spectra. For others, humidity increased fragment ion ratios. The effects of humidity on molecular adduct ion fragmentation were caused by changes in the relative abundances of different reagent protonated water clusters and, thus, a change in the average difference in proton affinity between an analyte and the population of water clusters. Control of humidity in ambient post-plasma ion sources is needed to create spectral stability and reproducibility.

Humidity Effects on Fragmentation in Plasma-Based Ambient Ionization Sources.

PubMed

Newsome, G Asher; Ackerman, Luke K; Johnson, Kevin J

2016-01-01

Post-plasma ambient desorption/ionization (ADI) sources are fundamentally dependent on surrounding water vapor to produce protonated analyte ions. There are two reports of humidity effects on ADI spectra. However, it is unclear whether humidity will affect all ADI sources and analytes, and by what mechanism humidity affects spectra. Flowing atmospheric pressure afterglow (FAPA) ionization and direct analysis in real time (DART) mass spectra of various surface-deposited and gas-phase analytes were acquired at ambient temperature and pressure across a range of observed humidity values. A controlled humidity enclosure around the ion source and mass spectrometer inlet was used to create programmed humidity and temperatures. The relative abundance and fragmentation of molecular adduct ions for several compounds consistently varied with changing ambient humidity and also were controlled with the humidity enclosure. For several compounds, increasing humidity decreased protonated molecule and other molecular adduct ion fragmentation in both FAPA and DART spectra. For others, humidity increased fragment ion ratios. The effects of humidity on molecular adduct ion fragmentation were caused by changes in the relative abundances of different reagent protonated water clusters and, thus, a change in the average difference in proton affinity between an analyte and the population of water clusters. Control of humidity in ambient post-plasma ion sources is needed to create spectral stability and reproducibility.

Comparisons of molecular karyotype and RAPD patterns of anuran trypanosome isolates during long-term in vitro cultivation.

PubMed

Lun, Z R; Desser, S S

1996-01-01

The patterns of random amplified fragments and molecular karyotypes of 12 isolates of anuran trypanosomes continuously cultured in vitro were compared by random amplified polymorphic DNA (RAPD) analysis and pulsed field gradient gel electrophoresis (PFGE). The time interval between preparation of two series of samples was one year. Changes were not observed in the number and size of sharp, amplified fragments of DNA samples from both series examined with the ten primers used. Likewise, changes in the molecular karyotypes were not detected between the two samples of these isolates. These results suggest that the molecular karyotype and the RAPD patterns of the anuran trypanosomes remain stable after being cultured continuously in vitro for one year.

Voronoi Cell Patterns: theoretical model and application to submonolayer growth

NASA Astrophysics Data System (ADS)

González, Diego Luis; Einstein, T. L.

2012-02-01

We use a simple fragmentation model to describe the statistical behavior of the Voronoi cell patterns generated by a homogeneous and isotropic set of points in 1D and in 2D. In particular, we are interested in the distribution of sizes of these Voronoi cells. Our model is completely defined by two probability distributions in 1D and again in 2D, the probability to add a new point inside an existing cell and the probability that this new point is at a particular position relative to the preexisting point inside this cell. In 1D the first distribution depends on a single parameter while the second distribution is defined through a fragmentation kernel; in 2D both distributions depend on a single parameter. The fragmentation kernel and the control parameters are closely related to the physical properties of the specific system under study. We apply our model to describe the Voronoi cell patterns of island nucleation for critical island sizes i=0,1,2,3. Experimental results for the Voronoi cells of InAs/GaAs quantum dots are also described by our model.

Recent advances in secondary ion mass spectrometry of solid acid catalysts: large zeolite crystals under bombardment.

PubMed

Hofmann, Jan P; Rohnke, Marcus; Weckhuysen, Bert M

2014-03-28

This Perspective aims to inform the heterogeneous catalysis and materials science community about the recent advances in Time-of-Flight-Secondary Ion Mass Spectrometry (ToF-SIMS) to characterize catalytic solids by taking large model H-ZSM-5 zeolite crystals as a showcase system. SIMS-based techniques have been explored in the 1980-1990's to study porous catalyst materials but, due to their limited spectral and spatiotemporal resolution, there was no real major breakthrough at that time. The technical advancements in SIMS instruments, namely improved ion gun design and new mass analyser concepts, nowadays allow for a much more detailed analysis of surface species relevant to catalytic action. Imaging with high mass and lateral resolution, determination of fragment ion patterns, novel sputter ion concepts as well as new mass analysers (e.g. ToF, FTICR) are just a few novelties, which will lead to new fundamental insight from SIMS analysis of heterogeneous catalysts. The Perspective article ends with an outlook on instrumental innovations and their potential use for catalytic systems other than zeolite crystals.

The Influence of Forming Companions on the Spectral Energy Distributions of Stars with Circumstellar Discs

NASA Astrophysics Data System (ADS)

Zakhozhay, Olga V.

2017-04-01

We study a possibility to detect signatures of brown dwarf companions in a circumstellar disc based on spectral energy distributions. We present the results of spectral energy distribution simulations for a system with a 0.8 M⊙ central object and a companion with a mass of 30 M J embedded in a typical protoplanetary disc. We use a solution to the one-dimensional radiative transfer equation to calculate the protoplanetary disc flux density and assume, that the companion moves along a circular orbit and clears a gap. The width of the gap is assumed to be the diameter of the brown dwarf Hill sphere. Our modelling shows that the presence of such a gap can initiate an additional minimum in the spectral energy distribution profile of a protoplanetary disc at λ = 10-100 μm. We found that it is possible to detect signatures of the companion when it is located within 10 AU, even when it is as small as 3 M J. The spectral energy distribution of a protostellar disc with a massive fragment (of relatively cold temperature 400 K) might have a similar double peaked profile to the spectral energy distribution of a more evolved disc that contains a gap.

Tandem mass spectrometry of coprogen and deferoxamine hydroxamic siderophores.

PubMed

Simionato, Ana V C; de Souza, Gezimar D; Rodrigues-Filho, Edson; Glick, James; Vouros, Paul; Carrilho, Emanuel

2006-01-01

Mechanisms of fragmentation of hydroxamic siderophores are proposed comparing deuterated and nondeuterated samples. Standard siderophores (e.g. deferoxamine and coprogen) were directly injected into both ion trap and linear quadrupole mass spectrometers with electrospray ionization (ESI). Four and two fragmentation steps were carried out for deferoxamine and coprogen (analyzed by positive and negative ESI, respectively). Deferoxamine cleavages occurred in both peptide and hydroxamic bonds while the coprogen fragmentation pattern is more elaborate, since it contains Fe(III) in its structure.

A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates

USGS Publications Warehouse

Delaney, Kathleen Semple; Riley, Seth P.D.; Fisher, Robert N.

2010-01-01

Background: Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding. Methodology/Principal Findings: We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation. Conclusions/Significance: Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

Batman-cracks. Observations and numerical simulations

NASA Astrophysics Data System (ADS)

Selvadurai, A. P. S.; Busschen, A. Ten; Ernst, L. J.

1991-05-01

To ensure mechanical strength of fiber reinforced plastics (FRP), good adhesion between fibers and the matrix is considered to be an essential requirement. An efficient test of fiber-matrix interface characterization is the fragmentation test which provides information about the interface slip mechanism. This test consists of the longitudinal loading of a single fiber which is embedded in a matrix specimen. At critical loads the fiber experiences fragmentation. This fragmentation will terminate depending upon the shear-slip strength of the fiber-matrix adhesion, which is inversely proportional to average fragment lengths. Depending upon interface strength characteristics either bond or slip matrix fracture can occur at the onset of fiber fracture. Certain particular features of matrix fracture are observed at the locations of fiber fracture in situations where there is sufficient interface bond strength. These refer to the development of fractures with a complex surface topography. The experimental procedure involved in the fragmentation tests is discussed and the boundary element technique to examine the development of multiple matrix fractures at the fiber fracture locations is examined. The mechanics of matrix fracture is examined. When bond integrity is maintained, a fiber fracture results in a matrix fracture. The matrix fracture topography in a fragmentation test is complex; however, simplified conoidal fracture patterns can be used to investigate the crack extension phenomena. Via a mixed-mode fracture criterion, the generation of a conoidal fracture pattern in the matrix is investigated. The numerical results compare favorably with observed experimental data derived from tests conducted on fragmentation test specimens consisting of a single glass fiber which is embedded in a polyester matrix.

Spatio-temporal Genetic Structure of a Tropical Bee Species Suggests High Dispersal Over a Fragmented Landscape.

PubMed

Suni, Sevan S; Bronstein, Judith L; Brosi, Berry J

2014-03-01

Habitat destruction threatens biodiversity by reducing the amount of available resources and connectivity among geographic areas. For organisms living in fragmented habitats, population persistence may depend on dispersal, which maintains gene flow among fragments and can prevent inbreeding within them. It is centrally important to understand patterns of dispersal for bees living in fragmented areas given the importance of pollination systems and recently documented declines in bee populations. We used population and landscape genetic techniques to characterize patterns of dispersal over a large fragmented area in southern Costa Rica for the orchid bee species Euglossa championi . First, we estimated levels of genetic differentiation among forest fragments as φ pt , an analog to the traditional summary statistic F st , as well as two statistics that may more adequately represent levels of differentiation, G ' st and D est . Second, we used a Bayesian approach to determine the number and composition of genetic groups in our sample. Third we investigated how genetic differentiation changes with distance. Fourth, we determined the extent to which deforested areas restrict dispersal. Finally, we estimated the extent to which there were temporal differences in allele frequencies within the same forest fragments. Within years we found low levels of differentiation even over 80 km, and no effect of land use type on level of genetic differentiation. However, we found significant genetic differentiation between years. Taken together our results suggest that there are high levels of gene flow over this geographic area, and that individuals show low site fidelity over time.

A Rapid, Strong, and Convergent Genetic Response to Urban Habitat Fragmentation in Four Divergent and Widespread Vertebrates

PubMed Central

Delaney, Kathleen Semple; Riley, Seth P. D.; Fisher, Robert N.

2010-01-01

Background Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding. Methodology/Principal Findings We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation. Conclusions/Significance Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix. PMID:20862274

Patterns of vegetation in the Owens Valley, California

NASA Technical Reports Server (NTRS)

Ustin, S. L.; Rock, B. N.; Woodward, R. A.

1986-01-01

Spectral characteristics of semi-arid shrub communities were examined using Airborne Imaging Spectrometer (AIS) data collected in the tree mode on 23 May 1985. Mesic sites with relatively high vegetation density and distinct zonation patterns exhibited greater spectral signature variations than sites with more xeric shrub communities. Spectral signature patterns were not directly related to vegetation density or physiognomy, although spatial maps derived from an 8-channel maximum likelihood classification were supported by photo-interpreted surface features. In AIS data, the principal detected effect of shrub vegetation on the alluvial fans is to lower reflectance across the spectrum. These results are similar to those reported during a period of minimal physiological activity in autumn, indicating that shadows cast by vegetation canopies are an important element of soil-vegetation interaction under conditions of relatively low canopy cover.

The heavy particle hazard, what physical data are needed?

NASA Technical Reports Server (NTRS)

Curtis, S. B.; Wilkinson, M. C.

1972-01-01

The physical data required to evaluate the radiation hazard from heavy galactic cosmic rays to astronauts on extended missions are discussed. The spectral characteristics, nuclear interaction parameters, and track structure of particles are emphasized. The data on the lower energy portion of the differential spectrum of the iron group and nuclear fragmentation in tissue and aluminum are tested, and results are shown.

Towards a phenomenology of civil war: Hobbes meets Benjamin in Beirut.

PubMed

De Cauter, Lieven

2011-01-01

Based on interviews with Beirut intellectuals and architects, this essay endeavours to trace the contours for a phenomenology or anthropology of civil war. Thomas Hobbes serves as a guide, with his idea of civil war representing a relapse into the ‘state of nature’; as absence of sovereignty resulting in a ‘war of everybody against everybody’. The effects of ever-latent civil war in Beirut are far-reaching: the fragmentation of urban space and the disappearance of public space, the loss of memory and the fragmentation of time, even the reification of language. In the collective imagination and in the arts, Beirut appears as a ghost town, a spectral city with a spectral civility. What we discover is a city, its inhabitants, its social behaviour, but also its art and literature, in the grip of post-traumatic stress syndrome. From all this, we take home two things: first, any city can (at least in principle) relapse into a similar state of nature — Beirut can become a paradigm of latent civil war; and second, the traumatic modernity of Beirut mirrors the traumatic artistic expressions of modernism — the shock of modernity is also always a modernity of shock.

Site-targeted mutagenesis for stabilization of recombinant monoclonal antibody expressed in tobacco (Nicotiana tabacum) plants

PubMed Central

Hehle, Verena K.; Paul, Matthew J.; Roberts, Victoria A.; van Dolleweerd, Craig J.; Ma, Julian K.-C.

2016-01-01

This study examined the degradation pattern of a murine IgG1κ monoclonal antibody expressed in and extracted from transformed Nicotiana tabacum. Gel electrophoresis of leaf extracts revealed a consistent pattern of recombinant immunoglobulin bands, including intact and full-length antibody, as well as smaller antibody fragments. N-terminal sequencing revealed these smaller fragments to be proteolytic cleavage products and identified a limited number of protease-sensitive sites in the antibody light and heavy chain sequences. No strictly conserved target sequence was evident, although the peptide bonds that were susceptible to proteolysis were predominantly and consistently located within or near to the interdomain or solvent-exposed regions in the antibody structure. Amino acids surrounding identified cleavage sites were mutated in an attempt to increase resistance. Different Guy’s 13 antibody heavy and light chain mutant combinations were expressed transiently in N. tabacum and demonstrated intensity shifts in the fragmentation pattern, resulting in alterations to the full-length antibody-to-fragment ratio. The work strengthens the understanding of proteolytic cleavage of antibodies expressed in plants and presents a novel approach to stabilize full-length antibody by site-directed mutagenesis.—Hehle, V. K., Paul, M. J., Roberts, V. A., van Dolleweerd, C. J., Ma, J. K.-C. Site-targeted mutagenesis for stabilization of recombinant monoclonal antibody expressed in tobacco (Nicotiana tabacum) plants. PMID:26712217

EEG resolutions in detecting and decoding finger movements from spectral analysis

PubMed Central

Xiao, Ran; Ding, Lei

2015-01-01

Mu/beta rhythms are well-studied brain activities that originate from sensorimotor cortices. These rhythms reveal spectral changes in alpha and beta bands induced by movements of different body parts, e.g., hands and limbs, in electroencephalography (EEG) signals. However, less can be revealed in them about movements of different fine body parts that activate adjacent brain regions, such as individual fingers from one hand. Several studies have reported spatial and temporal couplings of rhythmic activities at different frequency bands, suggesting the existence of well-defined spectral structures across multiple frequency bands. In the present study, spectral principal component analysis (PCA) was applied on EEG data, obtained from a finger movement task, to identify cross-frequency spectral structures. Features from identified spectral structures were examined in their spatial patterns, cross-condition pattern changes, detection capability of finger movements from resting, and decoding performance of individual finger movements in comparison to classic mu/beta rhythms. These new features reveal some similar, but more different spatial and spectral patterns as compared with classic mu/beta rhythms. Decoding results further indicate that these new features (91%) can detect finger movements much better than classic mu/beta rhythms (75.6%). More importantly, these new features reveal discriminative information about movements of different fingers (fine body-part movements), which is not available in classic mu/beta rhythms. The capability in decoding fingers (and hand gestures in the future) from EEG will contribute significantly to the development of non-invasive BCI and neuroprosthesis with intuitive and flexible controls. PMID:26388720

Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals

PubMed Central

Crooks, Kevin R.; Burdett, Christopher L.; Theobald, David M.; King, Sarah R. B.; Rondinini, Carlo; Boitani, Luigi

2017-01-01

Although habitat fragmentation is often assumed to be a primary driver of extinction, global patterns of fragmentation and its relationship to extinction risk have not been consistently quantified for any major animal taxon. We developed high-resolution habitat fragmentation models and used phylogenetic comparative methods to quantify the effects of habitat fragmentation on the world’s terrestrial mammals, including 4,018 species across 26 taxonomic Orders. Results demonstrate that species with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, and most high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Our models provide a quantitative evaluation of extinction risk assessments for species, allow for identification of emerging threats in species not classified as threatened, and provide maps of global hotspots of fragmentation for the world’s terrestrial mammals. Quantification of habitat fragmentation will help guide threat assessment and strategic priorities for global mammal conservation. PMID:28673992

Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals.

PubMed

Crooks, Kevin R; Burdett, Christopher L; Theobald, David M; King, Sarah R B; Di Marco, Moreno; Rondinini, Carlo; Boitani, Luigi

2017-07-18

Although habitat fragmentation is often assumed to be a primary driver of extinction, global patterns of fragmentation and its relationship to extinction risk have not been consistently quantified for any major animal taxon. We developed high-resolution habitat fragmentation models and used phylogenetic comparative methods to quantify the effects of habitat fragmentation on the world's terrestrial mammals, including 4,018 species across 26 taxonomic Orders. Results demonstrate that species with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, and most high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Our models provide a quantitative evaluation of extinction risk assessments for species, allow for identification of emerging threats in species not classified as threatened, and provide maps of global hotspots of fragmentation for the world's terrestrial mammals. Quantification of habitat fragmentation will help guide threat assessment and strategic priorities for global mammal conservation.

Speaking Rate Affects the Perception of Duration as a Suprasegmental Lexical-Stress Cue

ERIC Educational Resources Information Center

Reinisch, Eva; Jesse, Alexandra; McQueen, James M.

2011-01-01

Three categorization experiments investigated whether the speaking rate of a preceding sentence influences durational cues to the perception of suprasegmental lexical-stress patterns. Dutch two-syllable word fragments had to be judged as coming from one of two longer words that matched the fragment segmentally but differed in lexical stress…

Characterizing forest fragments in boreal, temperate, and tropical ecosystems

Treesearch

Arjan J. H. Meddens; Andrew T. Hudak; Jeffrey S. Evans; William A. Gould; Grizelle Gonzalez

2008-01-01

An increased ability to analyze landscapes in a spatial manner through the use of remote sensing leads to improved capabilities for quantifying human-induced forest fragmentation. Developments of spatially explicit methods in landscape analyses are emerging. In this paper, the image delineation software program eCognition and the spatial pattern analysis program...

Fragmentation study of iridoid glycosides including epimers by liquid chromatography-diode array detection/electrospray ionization mass spectrometry and its application in metabolic fingerprint analysis of Gardenia jasminoides Ellis.

PubMed

Zhou, Tingting; Liu, Hua; Wen, Jun; Fan, Guorong; Chai, Yifeng; Wu, Yutian

2010-09-15

A high-performance liquid chromatography-diode array detection/electrospray ionization mass spectrometry (HPLC-DAD/ESI-MS) method was applied to the characterization of ten iridoid glycosides in Gardenia jasminoides Ellis, a traditional Chinese medicine. During the process of structural elucidation, two groups of isomers including two epimers were structurally characterized and differentiated according to their distinctive fragmentation patterns which were closely related to their isomeric differentiations. Subsequently, the major compounds were purified by multi-dimensional chromatography and semi-preparative HPLC and the structure identification was confirmed with NMR techniques. The major fragmentation pathways of iridoid glycosides in Gardenia jasminoides Ellis obtained through the MS data were schemed systematically, which provided the best sensitivity and specificity for characterization of the iridoid glycosides especially the isomers so far. Based on the fragmentation patterns of iridoid glycosides concluded, seven major iridoid glycosides were characterized in rat plasma after intravenous administration of Gardenia jasminoides Ellis. Copyright 2010 John Wiley & Sons, Ltd.

Distribution of IS900 restriction fragment length polymorphism types among animal Mycobacterium avium subsp. paratuberculosis isolates from Argentina and Europe.

PubMed

Moreira, A R; Paolicchi, F; Morsella, C; Zumarraga, M; Cataldi, A; Fabiana, B; Alicia, A; Piet, O; van Soolingen, D; Isabel, R M

1999-12-01

Sixty-one Mycobacterium avium subsp. paratuberculosis isolates from cattle and deer from the Buenos Aires province, an important livestock region in Argentina, were typed by restriction fragment length polymorphisms (RFLP) analysis based on IS900. Four different RFLP patterns (designated 'A', 'B', 'C' and 'E') were identified in BstEII digests of genomic DNA. The most frequently observed type, pattern 'A', was found in 46 isolates (75%). The second, pattern 'E', included 8 isolates (13%), while the third, pattern 'B', included 6 isolates (10%). Pattern 'C' was found for only one isolate. All of the deer isolates were classified as pattern 'A', while cattle isolates represented all four RFLP patterns. Twenty-one isolates representing the four different BstEII-RFLP patterns were digested with PstI. Twenty isolates showed identical PstI-RFLP pattern. BstEII-RFLP patterns from Argentine cattle and deer were compared with patterns found in cattle, goat, deer, rabbit, and human isolates from Europe. The most common pattern in Argentina, pattern 'A', was identical to a less frequently occurring pattern R9 (C17) from Europe. The other Argentine patterns 'B', 'C' and 'E', were not found in the Europe. These results indicate that the distribution of M. avium subsp. paratuberculosis genotypes in the Buenos Aires province of Argentina is different from that found in Europe.

Structural comparisons of two allelic variants of human placental alkaline phosphatase.

PubMed

Millán, J L; Stigbrand, T; Jörnvall, H

1985-01-01

A simple immunosorbent purification scheme based on monoclonal antibodies has been devised for human placental alkaline phosphatase. The two most common allelic variants, S and F, have similar amino acid compositions with identical N-terminal amino acid sequences through the first 13 residues. Both variants have identical lectin binding properties towards concanavalin A, lentil-lectin, wheat germ agglutinin, phytohemagglutinin and soybean agglutinin, and identical carbohydrate contents as revealed by methylation analysis. CNBr fragments of the variants demonstrate identical high performance liquid chromatography patterns. The carbohydrate containing fragment is different from the 32P-labeled active site fragment and the N-terminal fragment.

Movement of feeder-using songbirds: the influence of urban features.

PubMed

Cox, Daniel T C; Inger, Richard; Hancock, Steven; Anderson, Karen; Gaston, Kevin J

2016-11-23

Private gardens provide vital opportunities for people to interact with nature. The most popular form of interaction is through garden bird feeding. Understanding how landscape features and seasons determine patterns of movement of feeder-using songbirds is key to maximising the well-being benefits they provide. To determine these patterns we established three networks of automated data loggers along a gradient of greenspace fragmentation. Over a 12-month period we tracked 452 tagged blue tits Cyantistes caeruleus and great tits Parus major moving between feeder pairs 9,848 times, to address two questions: (i) Do urban features within different forms, and season, influence structural (presence-absence of connections between feeders by birds) and functional (frequency of these connections) connectivity? (ii) Are there general patterns of structural and functional connectivity across forms? Vegetation cover increased connectivity in all three networks, whereas the presence of road gaps negatively affected functional but not structural connectivity. Across networks structural connectivity was lowest in the summer when birds maintain breeding territories, however patterns of functional connectivity appeared to vary with habitat fragmentation. Using empirical data this study shows how key urban features and season influence movement of feeder-using songbirds, and we provide evidence that this is related to greenspace fragmentation.

Assessing the drivers shaping global patterns of urban vegetation landscape structure.

PubMed

Dobbs, C; Nitschke, C; Kendal, D

2017-08-15

Vegetation is one of the main resources involve in ecosystem functioning and providing ecosystem services in urban areas. Little is known on the landscape structure patterns of vegetation existing in urban areas at the global scale and the drivers of these patterns. We studied the landscape structure of one hundred cities around the globe, and their relation to demography (population), socioeconomic factors (GDP, Gini Index), climate factors (temperature and rain) and topographic characteristics (altitude, variation in altitude). The data revealed that the best descriptors of landscape structure were amount, fragmentation and spatial distribution of vegetation. Populated cities tend to have less, more fragmented, less connected vegetation with a centre of the city with low vegetation cover. Results also provided insights on the influence of socioeconomics at a global scale, as landscape structure was more fragmented in areas that are economically unequal and coming from emergent economies. This study shows the effects of the social system and climate on urban landscape patterns that gives useful insights for the distribution in the provision of ecosystem services in urban areas and therefore the maintenance of human well-being. This information can support local and global policy and planning which is committing our cities to provide accessible and inclusive green space for all urban inhabitants. Copyright © 2017 Elsevier B.V. All rights reserved.

Bird diversity along a gradient of fragmented habitats of the Cerrado.

PubMed

Jesus, Shayana DE; Pedro, Wagner A; Bispo, Arthur A

2018-01-01

Understanding the factors that affect biodiversity is of central interest to ecology, and essential to species conservation and ecosystems management. We sampled bird communities in 17 forest fragments in the Cerrado biome, the Central-West region of Brazil. We aimed to know the communities structure pattern and the influence of geographical distance and environmental variables on them, along a gradient of fragmented habitats at both local and landscape scales. Eight structural variables of the fragments served as an environmental distance measurement at the local scale while five metrics served as an environmental distance measurement at the landscape scale. Species presence-absence data were used to calculate the dissimilarity index. Beta diversity was calculated using three indices (βsim, βnes and βsor), representing the spatial species turnover, nestedness and total beta diversity, respectively. Spatial species turnover was the predominant pattern in the structure of the communities. Variations in beta diversity were explained only by the environmental variables of the landscape with spatial configuration being more important than the composition. This fact indicates that, in Cerrado of Goiás avian communities structure, deterministic ecological processes associated to differences in species responses to landscape fragmentation are more important than stochastic processes driven by species dispersal.

Dispersal of remnant endangered trees in a fragmented and disturbed forest by frugivorous birds.

PubMed

Li, Ning; Bai, Bing; Li, Xin-Hai; An, Shu-Qing; Lu, Chang-Hu

2017-07-01

Most endangered plant species in a fragmented forest behave as a unique source population, with a high dependence on frugivorous birds for recruitment and persistence. In this study, we combined field data of dispersal behavior of birds and GIS information of patch attributes to estimate how frugivorous birds could affect the effective dispersal pattern of Chinese yew (Taxus chinensis) in a fragmented and disturbed forest. Nine bird species were observed to visit T. chinensis trees, with Urocissa erythrorhyncha, Zoothera dauma and Picus canus being the most common dispersers. After foraging, six disperser species exhibited different perching patterns. Three specialist species, P. canus, Turdus hortulorum, and Z. dauma stayed in the source patch, while three generalist species, U. erythrorhyncha, Hypsipetes mcclellandii, and H. castanonotus, could perch in bamboo patches and varied in movement ability due to body size. As a consequence of perching, dispersers significantly contributed to the seed bank, but indirectly affected seedling recruitment. Moreover, the recruitment of T. chinensis was also affected by patch attributes in a fragmented forest (distances to source patch, patch type, size). Our results highlighted the ability of unique source population regeneration of T. chinensis in a fragmented forest, with high dependence on both frugivorous birds and patch attributes, which should be considered in future planning for forest management and conservation.

Effect of musical training on static and dynamic measures of spectral-pattern discrimination.

PubMed

Sheft, Stanley; Smayda, Kirsten; Shafiro, Valeriy; Maddox, W Todd; Chandrasekaran, Bharath

2013-06-01

Both behavioral and physiological studies have demonstrated enhanced processing of speech in challenging listening environments attributable to musical training. The relationship, however, of this benefit to auditory abilities as assessed by psychoacoustic measures remains unclear. Using tasks previously shown to relate to speech-in-noise perception, the present study evaluated discrimination ability for static and dynamic spectral patterns by 49 listeners grouped as either musicians or nonmusicians. The two static conditions measured the ability to detect a change in the phase of a logarithmic sinusoidal spectral ripple of wideband noise with ripple densities of 1.5 and 3.0 cycles per octave chosen to emphasize either timbre or pitch distinctions, respectively. The dynamic conditions assessed temporal-pattern discrimination of 1-kHz pure tones frequency modulated by different lowpass noise samples with thresholds estimated in terms of either stimulus duration or signal-to-noise ratio. Musicians performed significantly better than nonmusicians on all four tasks. Discriminant analysis showed that group membership was correctly predicted for 88% of the listeners with the structure coefficient of each measure greater than 0.51. Results suggest that enhanced processing of static and dynamic spectral patterns defined by low-rate modulation may contribute to the relationship between musical training and speech-in-noise perception. [Supported by NIH.].

A Fundamental Study on Spectrum Center Estimation of Solar Spectral Irradiation by the Statistical Pattern Recognition

NASA Astrophysics Data System (ADS)

Iijima, Aya; Suzuki, Kazumi; Wakao, Shinji; Kawasaki, Norihiro; Usami, Akira

With a background of environmental problems and energy issues, it is expected that PV systems will be introduced rapidly and connected with power grids on a large scale in the future. For this reason, the concern to which PV power generation will affect supply and demand adjustment in electric power in the future arises and the technique of correctly grasping the PV power generation becomes increasingly important. The PV power generation depends on solar irradiance, temperature of a module and solar spectral irradiance. Solar spectral irradiance is distribution of the strength of the light for every wavelength. As the spectrum sensitivity of solar cell depends on kind of solar cell, it becomes important for exact grasp of PV power generation. Especially the preparation of solar spectral irradiance is, however, not easy because the observational instrument of solar spectral irradiance is expensive. With this background, in this paper, we propose a new method based on statistical pattern recognition for estimating the spectrum center which is representative index of solar spectral irradiance. Some numerical examples obtained by the proposed method are also presented.

A Novel Anti-Spoofing Solution for Iris Recognition Toward Cosmetic Contact Lens Attack Using Spectral ICA Analysis.

PubMed

Hsieh, Sheng-Hsun; Li, Yung-Hui; Wang, Wei; Tien, Chung-Hao

2018-03-06

In this study, we maneuvered a dual-band spectral imaging system to capture an iridal image from a cosmetic-contact-lens-wearing subject. By using the independent component analysis to separate individual spectral primitives, we successfully distinguished the natural iris texture from the cosmetic contact lens (CCL) pattern, and restored the genuine iris patterns from the CCL-polluted image. Based on a database containing 200 test image pairs from 20 CCL-wearing subjects as the proof of concept, the recognition accuracy (False Rejection Rate: FRR) was improved from FRR = 10.52% to FRR = 0.57% with the proposed ICA anti-spoofing scheme.

Synchrotron Infrared Microspectroscopy Detecting the Evolution of Huntingtons Disease Neuropathology and Suggesting Unique Correlates of Dysfunction in White versus Gray Brain Matter

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

Bonda M.; Miller L.; Perrin V.

Huntington's disease (HD), caused by a mutation of the corresponding gene encoding the protein huntingtin (htt), is characterized by progressive deterioration of cognitive and motor functions, paralleled by extensive loss of striatal neurons. At the cellular level, pathogenesis involves an early and prolonged period of neuronal dysfunction followed by neuronal death. Understanding the molecular events driving these deleterious processes is critical to the successful development of therapies to slow down or halt the progression of the disease. Here, we examined biochemical processes in a HD ex vivo rat model, as well as in a HD model for cultured neurons usingmore » synchrotron-assisted Fourier transform infrared microspectroscopy (S-FTIRM). The model, based on lentiviral-mediated delivery of a fragment of the HD gene, expresses a mutant htt fragment in one brain hemisphere and a wild-type htt fragment in the control hemisphere. S-FTIRM allowed for high spatial resolution and distinction between spectral features occurring in gray and white matter. We measured a higher content of {beta}-sheet protein in the striatal gray matter exposed to mutant htt as early as 4 weeks following the initiation of mutant htt exposure. In contrast, white matter tracts did not exhibit any changes in protein structure but surprisingly showed reduced content of unsaturated lipids and a significant increase in spectral features associated with phosphorylation. The former is reminiscent of changes consistent with a myelination deficiency, while the latter is characteristic of early pro-apoptotic events. These findings point to the utility of the label-free FTIRM method to follow mutant htt's {beta}-sheet-rich transformation in striatal neurons ex vivo, provide further evidence for mutant htt amyloidogenesis in vivo, and demonstrate novel chemical features indicative of white matter changes in HD. Parallel studies in cultured neurons expressing the same htt fragments showed similar changes.« less

Fragmentation of Massive Dense Cores Down to <~ 1000 AU: Relation between Fragmentation and Density Structure

NASA Astrophysics Data System (ADS)

Palau, Aina; Estalella, Robert; Girart, Josep M.; Fuente, Asunción; Fontani, Francesco; Commerçon, Benoit; Busquet, Gemma; Bontemps, Sylvain; Sánchez-Monge, Álvaro; Zapata, Luis A.; Zhang, Qizhou; Hennebelle, Patrick; di Francesco, James

2014-04-01

In order to shed light on the main physical processes controlling fragmentation of massive dense cores, we present a uniform study of the density structure of 19 massive dense cores, selected to be at similar evolutionary stages, for which their relative fragmentation level was assessed in a previous work. We inferred the density structure of the 19 cores through a simultaneous fit of the radial intensity profiles at 450 and 850 μm (or 1.2 mm in two cases) and the spectral energy distribution, assuming spherical symmetry and that the density and temperature of the cores decrease with radius following power-laws. Even though the estimated fragmentation level is strictly speaking a lower limit, its relative value is significant and several trends could be explored with our data. We find a weak (inverse) trend of fragmentation level and density power-law index, with steeper density profiles tending to show lower fragmentation, and vice versa. In addition, we find a trend of fragmentation increasing with density within a given radius, which arises from a combination of flat density profile and high central density and is consistent with Jeans fragmentation. We considered the effects of rotational-to-gravitational energy ratio, non-thermal velocity dispersion, and turbulence mode on the density structure of the cores, and found that compressive turbulence seems to yield higher central densities. Finally, a possible explanation for the origin of cores with concentrated density profiles, which are the cores showing no fragmentation, could be related with a strong magnetic field, consistent with the outcome of radiation magnetohydrodynamic simulations. The James Clerk Maxwell Telescope is operated by the Joint Astronomy Centre on behalf of the Science and Technology Facilities Council of the United Kingdom, the Netherlands Organisation for Scientific Research, and the National Research Council of Canada.

Effects of habitat fragmentation on passerine birds breeding in Intermountain shrubsteppe

USGS Publications Warehouse

Knick, S.T.; Rotenberry, J.T.

2002-01-01

Habitat fragmentation and loss strongly influence the distribution and abundance of passerine birds breeding in Intermountain shrubsteppe. Wildfires, human activities, and change in vegetation communities often are synergistic in these systems and can result in radical conversion from shrubland to grasslands dominated by exotic annuals at large temporal and spatial scales from which recovery to native conditions is unlikely. As a result, populations of 5 of the 12 species in our review of Intermountain shrubsteppe birds are undergoing significant declines; 5 species are listed as at-risk or as candidates for protection in at least one state. The process by which fragmentation affects bird distributions in these habitats remains unknown because most research has emphasized the detection of population trends and patterns of habitat associations at relatively large spatial scales. Our research indicates that the distribution of shrubland-obligate species, such as Brewer's Sparrows (Spizella breweri), Sage Sparrows (Amphispiza belli), and Sage Thrashers (Oreoscoptes montanus), was highly sensitive to fragmentation of shrublands at spatial scales larger than individual home ranges. In contrast, the underlying mechanisms for both habitat change and bird population dynamics may operate independently of habitat boundaries. We propose alternative, but not necessarily exclusive, mechanisms to explain the relationship between habitat fragmentation and bird distribution and abundance. Fragmentation might influence productivity through differences in breeding density, nesting success, or predation. However, local and landscape variables were not significant determinants either of success, number fledged, or probability of predation or parasitism (although our tests had relatively low statistical power). Alternatively, relative absence of natal philopatry and redistribution by individuals among habitats following fledging or post-migration could account for the pattern of distribution and abundance. Thus, boundary dynamics may be important in determining the distribution of shrubland-obligate species but insignificant relative to the mechanisms causing the pattern of habitat and bird distribution. Because of the dichotomy in responses, Intermountain shrubsteppe systems present a unique challenge in understanding how landscape composition, configuration, and change influence bird population dynamics.

Controls on Thermal Discharge in Yellowstone NAtional Park, Wyoming

NASA Astrophysics Data System (ADS)

Mohrmann, Jacob Steven

2007-10-01

Significant fluctuations in discharge occur in hot springs in Yellowstone National Park on a seasonal to decadal scale (Ingebritsen et al., 2001) and an hourly scale (Vitale, 2002). The purpose of this study was to determine the interval of the fluctuations in discharge and to explain what causes those discharge patterns in three thermally influenced streams in Yellowstone National Park. By monitoring flow in these streams, whose primary source of input is thermal discharge, we were able to find several significant patterns of discharge fluctuations. Patterns were found by using two techniques of spectral analysis. The spectral analyses completed involved using the program "R" as well as Microsoft Excel, both of which use Fourier transforms. The Fourier transform is a linear operator that identifies frequencies in the original function. Stream flow data were collected using a FloDar open channel flow monitor. The flow meter collected data at15-minute intervals at White Creek and Rabbit Creek for a period of approximately two weeks each during the Fall. Flow data were also used from 15-minute data interval from a USGS gaging station at Tantalus Creek. Patterns of discharge fluctuation were found in each stream. By comparing spectral analysis results of flow data with spectral analysis of published tide data and barometric pressure data, connections were drawn between fluctuations in tidal and barometric-pressure patterns and flow patterns. Also, visual comparisons used to identify potential correspondence with earthquakes and precipitation events. At Tantalus Creek, patterns were affected only by barometric pressure changes. At White Creek, one pattern was attributed to barometric pressure fluctuations, and another pattern was found that could be associated with earth-tide forces. At Rabbit Creek, these patterns were absent. A pattern at 8.55 hours, which could not be attributed to barometric pressure or earth tide forces, was found at Rabbit and White Creeks. The 8.55 hour pattern in discharge found at both Rabbit and White Creeks may suggest a physical link between the sites, which are close (2.5 km). The time pattern could be a result of a shared hydrothermal aquifer, convectively heating and discharging at both streams. However, the common time pattern could also be the result of independent factors, which coincidentally caused a similar time pattern.

Coulomb fission in multiply charged molecular clusters: Experiment and theory

NASA Astrophysics Data System (ADS)

Harris, Christopher; Baptiste, Joshua; Lindgren, Eric B.; Besley, Elena; Stace, Anthony J.

2017-04-01

A series of three multiply charged molecular clusters, (C6H6)nz+ (benzene), (CH3CNnz) + (acetonitrile), and (C4H8O)nz+ (tetrahydrofuran), where the charge z is either 3 or 4, have been studied for the purpose of identifying the patterns of behaviour close to the charge instability limit. Experiments show that on a time scale of ˜10-4 s, ions close to the limit undergo Coulomb fission where the observed pathways exhibit considerable asymmetry in the sizes of the charged fragments and are all associated with kinetic (ejection) energies of between 1.4 and 2.2 eV. Accurate kinetic energies have been determined through a computer simulation of peak profiles recorded in the experiments and the results modelled using a theory formulated to describe how charged particles of dielectric materials interact with one another [E. Bichoutskaia et al., J. Chem. Phys. 133, 024105 (2010)]. The calculated electrostatic interaction energy between separating fragments gives an accurate account for the measured kinetic energies and also supports the conclusion that +4 ions fragment into +3 and +1 products as opposed to the alternative of two +2 fragments. This close match between the theory and experiment reinforces the assumption that a significant fraction of excess charge resides on the surfaces of the fragment ions. It is proposed that the high degree of asymmetry seen in the fragmentation patterns of the multiply charged clusters is due, in part, to limits imposed by the time window during which observations are made.

Amino and Acetamide Functional Group Effects on the Ionization and Fragmentation of Sugar Chains in Positive-Ion Mass Spectrometry

NASA Astrophysics Data System (ADS)

Yamagaki, Tohru; Sugahara, Kohtaro; Watanabe, Takehiro

2014-01-01

To elucidate the influence of amino (-NH2) and acetamide (-NHCOCH3, -NAc) groups in sugar chains on their ionization and fragmentation, cycloamyloses (cyclodextrins, CyDs) and lacto-oligosaccharide are analyzed by MALDI TOF/TOF and ESI Q-TOF mass spectrometry. CyD derivatives substituted by amino or acetamide groups are ideal analytes to extract the function group effects, which are amino-CyD with one hexosamine (HexNH2) and acetamide-CyD with one N-acetyl hexosamine (HexNAc). Interestingly, the relative ion intensities and isotope-like patterns in their product ion spectra depend on the functional groups and ion forms of sugar chains. Consequently, the results indicate that a proton (H+) localizes on the amino group of the amino sugar, and that the proton (H+) induces their fragmentation. Sodium cation (Na+) attachment is independent from amino group and exerts no influence on their fragmentation patterns in amino group except for mono- and disaccharide fragment ions because there is the possibility of the reducing end effect. In contrast, a sodium cation localizes much more frequently on the acetamide group in acetamide-CyDs because the chemical species with HexNAc are stable. Thus, their ions with HexNAc are abundant. These results are consistent with the fragmentation of lacto-neo- N-tetraose and maltotetraose, suggesting that a sodium cation generally localizes much more frequently on the acetamide group in sugar chains.

Differentiation of regioisomeric aromatic ketocarboxylic acids by atmospheric pressure chemical ionization CAD tandem mass spectrometry in a linear quadrupole ion trap mass spectrometer

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

Amundson, Lucas M.; Owen, Ben C.; Gallardo, Vanessa A.

2011-01-01

Positive-mode atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS n ) was tested for the differentiation of regioisomeric aromatic ketocarboxylic acids. Each analyte forms exclusively an abundant protonated molecule upon ionization via positive-mode APCI in a commercial linear quadrupole ion trap (LQIT) mass spectrometer. Energy-resolved collision-activated dissociation (CAD) experiments carried out on the protonated analytes revealed fragmentation patterns that varied based on the location of the functional groups. Unambiguous differentiation between the regioisomers was achieved in each case by observing different fragmentation patterns, different relative abundances of ion-molecule reaction products, or different relative abundances of fragment ions formed at differentmore » collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.« less

Monitoring of Water Spectral Pattern Reveals Differences in Probiotics Growth When Used for Rapid Bacteria Selection.

PubMed

Slavchev, Aleksandar; Kovacs, Zoltan; Koshiba, Haruki; Nagai, Airi; Bázár, György; Krastanov, Albert; Kubota, Yousuke; Tsenkova, Roumiana

2015-01-01

Development of efficient screening method coupled with cell functionality evaluation is highly needed in contemporary microbiology. The presented novel concept and fast non-destructive method brings in to play the water spectral pattern of the solution as a molecular fingerprint of the cell culture system. To elucidate the concept, NIR spectroscopy with Aquaphotomics were applied to monitor the growth of sixteen Lactobacillus bulgaricus one Lactobacillus pentosus and one Lactobacillus gasseri bacteria strains. Their growth rate, maximal optical density, low pH and bile tolerances were measured and further used as a reference data for analysis of the simultaneously acquired spectral data. The acquired spectral data in the region of 1100-1850nm was subjected to various multivariate data analyses - PCA, OPLS-DA, PLSR. The results showed high accuracy of bacteria strains classification according to their probiotic strength. Most informative spectral fingerprints covered the first overtone of water, emphasizing the relation of water molecular system to cell functionality.

Lithographic VCSEL array multimode and single mode sources for sensing and 3D imaging

NASA Astrophysics Data System (ADS)

Leshin, J.; Li, M.; Beadsworth, J.; Yang, X.; Zhang, Y.; Tucker, F.; Eifert, L.; Deppe, D. G.

2016-05-01

Sensing applications along with free space data links can benefit from advanced laser sources that produce novel radiation patterns and tight spectral control for optical filtering. Vertical-cavity surface-emitting lasers (VCSELs) are being developed for these applications. While oxide VCSELs are being produced by most companies, a new type of oxide-free VCSEL is demonstrating many advantages in beam pattern, spectral control, and reliability. These lithographic VCSELs offer increased power density from a given aperture size, and enable dense integration of high efficiency and single mode elements that improve beam pattern. In this paper we present results for lithographic VCSELs and describes integration into military systems for very low cost pulsed applications, as well as continuouswave applications in novel sensing applications. The VCSELs are being developed for U.S. Army for soldier weapon engagement simulation training to improve beam pattern and spectral control. Wavelengths in the 904 nm to 990 nm ranges are being developed with the spectral control designed to eliminate unwanted water absorption bands from the data links. Multiple beams and radiation patterns based on highly compact packages are being investigated for improved target sensing and transmission fidelity in free space data links. These novel features based on the new VCSEL sources are also expected to find applications in 3-D imaging, proximity sensing and motion control, as well as single mode sensors such as atomic clocks and high speed data transmission.

Land use/land cover change and their effects on landscape patterns in the Yanqi Basin, Xinjiang (China).

PubMed

Wang, Shuixian; Wang, Shengli

2013-12-01

Human modification of land use and land cover change (LUCC) drives the change of landscape patterns and limits the availability of products and services for human and livestock. LUCC can undermine environmental health. Thus, this study aimed to develop an understanding of LUCC in the Yanqi Basin, Xinjiang, China, an arid area experiencing dramatic water and land resource use. A time series of satellite images (1964, 1973, 1989, 1999, and 2009) were used to calculate the index of landscape patterns to study the processes involved in changes to land uses and landscape patterns and the influence of this changes on landscape patterns. The results show that land uses in the Yanqi Basin have changed dramatically since 1964 with grassland being mainly converted to cropland. Landscape fragmentation and diversity have decreased in the study area, although landscape fragmentation increased from 1964 to 1999 and then decreased by 2009. The index of landscape diversity decreased from 1.64 in 1964 to 0.71 in 2009. The heterogeneity and complexity of the landscape increased during this period. In contrast, the index of dominance decreased from 0.85 in 1964 to 0.83 in 2009. Land use change drives landscape patterns of the development of the watershed toward diversity and a fragmented structure. Population growth, economic development, and industrial policies were the dominant driving forces behind LUCC in the Yanqi Basin. Sustainable use of land resources is a significant factor in maintaining economic development and environmental protection in this arid inland river basin.

Mating system and early viability resistance to habitat fragmentation in a bird-pollinated eucalypt

PubMed Central

Breed, M F; Ottewell, K M; Gardner, M G; Marklund, M H K; Stead, M G; Harris, J B C; Lowe, A J

2015-01-01

Habitat fragmentation has been shown to disrupt ecosystem processes such as plant-pollinator mutualisms. Consequently, mating patterns in remnant tree populations are expected to shift towards increased inbreeding and reduced pollen diversity, with fitness consequences for future generations. However, mating patterns and phenotypic assessments of open-pollinated progeny have rarely been combined in a single study. Here, we collected seeds from 37 Eucalyptus incrassata trees from contrasting stand densities following recent clearance in a single South Australian population (intact woodland=12.6 trees ha−1; isolated pasture=1.7 trees ha−1; population area=10 km2). 649 progeny from these trees were genotyped at eight microsatellite loci. We estimated genetic diversity, spatial genetic structure, indirect contemporary pollen flow and mating patterns for adults older than the clearance events and open-pollinated progeny sired post-clearance. A proxy of early stage progeny viability was assessed in a common garden experiment. Density had no impact on mating patterns, adult and progeny genetic diversity or progeny growth, but was associated with increased mean pollen dispersal. Weak spatial genetic structure among adults suggests high historical gene flow. We observed preliminary evidence for inbreeding depression related to stress caused by fungal infection, but which was not associated with density. Higher observed heterozygosities in adults compared with progeny may relate to weak selection on progeny and lifetime-accumulated mortality of inbred adults. E. incrassata appears to be resistant to the negative mating pattern and fitness changes expected within fragmented landscapes. This pattern is likely explained by strong outcrossing and regular long-distance pollen flow. PMID:23188172

Mineralogy, Reflectance Spectra, and Physical Properties of the Chelyabinsk LL5 Chondrite - Insight Into Shock Induced Changes in Asteroid Regoliths

NASA Astrophysics Data System (ADS)

Gritsevich, Maria; Muinonen, Karri; Kohout, Tomas; Grokhovsky, Victor; Yakovlev, Grigoriy; Haloda, Jakub; Halodova, Patricie; Michallik, Radoslaw; Penttilä, Antti

On February 15, 2013, at 9:22 am, an exceptionally bright and long duration fireball was observed by many eyewitnesses in the Chelyabinsk region, Russia. Two days later the first fragments of the Chelyabinsk meteorite were reported to be found in the area, located approximately 40 km south of Chelyabinsk. We have examined a large number of the recovered Chelyabinsk meteorite fragments. Three lithologies, the light-colored, dark-colored, and impact melt, were found within the recovered meteorites. The light colored lithology is a LL5 ordinary chondrite (Fa 28, Fs 23) shocked to S4 level. The dark colored lithology is of identical LL5 composition (Fa 28, Fs 23). However, it is shocked to higher level (shock-darkened) with fine grained metal and sulfide-rich melt forming a dense network of fine veins impregnating the inter- and intra-granular pore space within crushed silicate grains. The impact melt lithology is a whole-rock melt derived from the same LL5 source material and is present within the light-colored and dark-colored lithology as inter-granular veins. The measured bulk and grain densities and the porosity closely resemble other LL chondrites. Based on the magnetic susceptibility, the Chelyabinsk meteorites are richer in metallic iron as compared to database of other LL chondrites. All three Chelyabinsk lithologies are of identical LL5 composition and origin. Both impact melting and shock darkening cause a decrease in reflectance and a suppression of the silicate absorption bands in the reflectance spectra. Such spectral changes are similar to the space weathering effects observed on asteroids. However, space weathering of chondritic materials is often accompanied with a significant spectral slope change (reddening). In our case, only negligible to minor change in the spectral slope is observed. Thus, it is possible that some dark asteroids with invisible silicate absorption bands may be composed of relatively fresh shock-darkened chondritic material. The main spectral difference of chondritic asteroid surfaces dominated by impact melt, shock darkening, or space weathering, is a significant spectral slope change in the latter case. Thus, shock does not have significant effect on meteorite properties, but causes spectral darkening and suppression of silicate absorption bands.

Fragmentation study of iridoid glucosides through positive and negative electrospray ionization, collision-induced dissociation and tandem mass spectrometry.

PubMed

Es-Safi, Nour-Eddine; Kerhoas, Lucien; Ducrot, Paul-Henri

2007-01-01

Mass spectrometric methodology based on the combined use of positive and negative electrospray ionization, collision-induced dissociation (CID) and tandem mass spectrometry (MS/MS) has been applied to the mass spectral study of a series of six naturally occurring iridoids through in-source fragmentation of the protonated [M+H]+, deprotonated [M--H]- and sodiated [M+Na]+ ions. This led to the unambiguous determination of the molecular masses of the studied compounds and allowed CID spectra of the molecular ions to be obtained. Valuable structural information regarding the nature of both the glycoside and the aglycone moiety was thus obtained. Glycosidic cleavage and ring cleavages of both aglycone and sugar moieties were the major fragmentation pathways observed during CID, where the losses of small molecules, the cinnamoyl and the cinnamate parts were also observed. The formation of the ionized aglycones, sugars and their product ions was thus obtained giving information on their basic skeleton. The protonated, i.e. [M+H]+ and deprotonated [M--H]-, ions were found to fragment mainly by glycosidic cleavages. MS/MS spectra of the [M+Na]+ ions gave complementary information for the structural characterization of the studied compounds. Unlike the dissociation of protonated molecular ions, that of sodiated molecules also provided sodiated sugar fragments where the C0+ fragment corresponding to the glucose ion was obtained as base peak for all the studied compounds. Copyright (c) 2007 John Wiley & Sons, Ltd.

Analysis of TOF-SIMS spectra from fullerene compounds

NASA Astrophysics Data System (ADS)

Kato, N.; Yamashita, Y.; Iida, S.; Sanada, N.; Kudo, M.

2008-12-01

We analyzed TOF-SIMS spectra obtained from three different size of fullerenes (C 60, C 70 and C 84) by using Ga +, Au + and Au 3+ primary ion beams and investigated the fragmentation patterns, the enhancement of secondary ion yields and the restraint of fragmentation by using cluster primary ion beams compared with monoatomic primary ion beams. In the TOS-SIMS spectra from C 70 and C 84, it was found that a fragment ion, identified as C 60+ ( m/ z = 720), showed a relatively high intensity compared with that of other fragment ions related to C 2 depletion. It was also found that the Au 3+ bombardment caused intensity enhancement of intact molecules (C 60+, C 70+ and C 84+) and restrained the fragmentation due to C 2 depletion.

Assembly and analysis of fragmentation data for liquid propellant vessels

NASA Technical Reports Server (NTRS)

Baker, W. E.; Parr, V. B.; Bessey, R. L.; Cox, P. A.

1974-01-01

Fragmentation data was assembled and analyzed for exploding liquid propellant vessels. These data were to be retrieved from reports of tests and accidents, including measurements or estimates of blast yield, etc. A significant amount of data was retrieved from a series of tests conducted for measurement of blast and fireball effects of liquid propellant explosions (Project PYRO), a few well-documented accident reports, and a series of tests to determine auto-ignition properties of mixing liquid propellants. The data were reduced and fitted to various statistical functions. Comparisons were made with methods of prediction for blast yield, initial fragment velocities, and fragment range. Reasonably good correlation was achieved. Methods presented in the report allow prediction of fragment patterns, given type and quantity of propellant, type of accident, and time of propellant mixing.

Investigation of Contingency Patterns of Teachers' Scaffolding in Teaching and Learning Mathematics

ERIC Educational Resources Information Center

Anwar; Yuwono, Ipung; Irawan, Edy Bambang; As'ari, Abdur Rahman

2017-01-01

The purpose of this study is to investigate the patterns of scaffolding contingency in teaching and learning mathematics carried out by three teachers. Contingency patterns are obtained by examining the transcription from video recording of conversation fragments between teachers and students during the provision of scaffolding. The contingency…

Some Dynamical Features of Molecular Fragmentation by Electrons and Swift Ions

NASA Astrophysics Data System (ADS)

Montenegro, E. C.; Sigaud, L.; Wolff, W.; Luna, H.; Natalia, Ferreira

To date, the large majority of studies on molecular fragmentation by swift charged particles have been carried out using simple molecules, for which reliable Potential Energy Curves are available to interpret the measured fragmentation yields. For complex molecules the scenario is quite different and such guidance is not available, obscuring even a simple organization of the data which are currently obtained for a large variety of molecules of biological or technological interest. In this work we show that a general and relatively simple methodology can be used to obtain a broader picture of the fragmentation pattern of an arbitrary molecule. The electronic ionization or excitation cross section of a given molecular orbital, which is the first part of the fragmentation process, can be well scaled by a simple and general procedure at high projectile velocities. The fragmentation fractions arising from each molecular orbital can then be achieved by matching the calculated ionization with the measured fragmentation cross sections. Examples for Oxygen, Chlorodifluoromethane and Pyrimidine molecules are presented.

Landscape-level patterns of avian diversity in the Oregon Coast Range

Treesearch

Samuel A. Cushman; Kevin McGarigal

2003-01-01

We used a comparative mensurative landscape-level experiment to quantify the relative importance of mature forest area and fragmentation and differences among watersheds in influencing avian community diversity in the Oregon Coast Range, USA. Our study design included three large hydrological basins, two levels of fragmentation, and six levels of mature forest area. We...

Effects of habitat loss and fragmentation on amphibians: A review and prospectus

Treesearch

Samuel A. Cushman

2006-01-01

Habitat loss and fragmentation are among the largest threats to amphibian populations. However, most studies have not provided clear insights into their population-level implications. There is a critical need to investigate the mechanisms that underlie patterns of distribution and abundance. In order to understand the population- and species-level implications of...

Radiative signals from impact of Shoemaker-Levy on Jupiter

NASA Technical Reports Server (NTRS)

Ahrens, Thomas J.; Orton, Glenn S.; Takata, Toshiko; Okeefe, John D.

1994-01-01

The temperature and internal energy fields calculated by Takata et al. in the plume are used to calculate the greybody thermal radiation emitted versus wavelength to predict what might be observed by several spectral sensors operating from different platforms when fragments of Comet Shoemaker-Levy 9 (SL-9) impact Jupiter in July 1994. A SPH code was used by Takata et al. to calculate the full three dimensional flow and thermodynamic fields in the comet fragment and the atmosphere of Jupiter. We determined the fragment penetration depth, energy partitioning between the atmosphere and the impactor, and energy density deposited per unit length over the trajectory. Once the impactor had disintegrated and stopped, and the strong atmospheric shock decayed, the flow is driven by buoyancy effects. We then used our SPH code to calculate the flow and thermodynamic fields: pressure, article velocity, temperature, and internal energy distributions in the plume. The calculations for 2 and 10 km cometary fragments yield maximum deposition depths of approximately 175 and 525 km, respectively (1 bar = 0 km depth). We also calculated that 0.7 and 0.6 of the initial kinetic energy of the 10 and 2 km bolides, respectively, are deposited as internal energy in Jupiter's atmosphere.

Lack of genetic structure among ecologically adapted populations of an Australian rainforest Drosophila species as indicated by microsatellite markers and mitochondrial DNA sequences.

PubMed

Schiffer, Michele; Kennington, W J; Hoffmann, A A; Blacket, M J

2007-04-01

Although fragmented rainforest environments represent hotspots for invertebrate biodiversity, few genetic studies have been conducted on rainforest invertebrates. Thus, it is not known if invertebrate species in rainforests are highly genetically fragmented, with the potential for populations to show divergent selection responses, or if there are low levels of gene flow sufficient to maintain genetic homogeneity among fragmented populations. Here we use microsatellite markers and DNA sequences from the mitochondrial ND5 locus to investigate genetic differences among Drosophila birchii populations from tropical rainforests in Queensland, Australia. As found in a previous study, mitochondrial DNA diversity was low with no evidence for population differentiation among rainforest fragments. The pattern of mitochondrial haplotype variation was consistent with D. birchii having undergone substantial past population growth. Levels of nuclear genetic variation were high in all populations while F(ST) values were very low, even for flies from geographically isolated areas of rainforest. No significant differentiation was observed between populations on either side of the Burdekin Gap (a long-term dry corridor), although there was evidence for higher gene diversity in low-latitude populations. Spatial autocorrelation coefficients were low and did not differ significantly from random, except for one locus which revealed a clinal-like pattern. Comparisons of microsatellite differentiation contrasted with previously established clinal patterns in quantitative traits in D. birchii, and indicate that the patterns in quantitative traits are likely to be due to selection. These results suggest moderate gene flow in D. birchii over large distances. Limited population structure in this species appears to be due to recent range expansions or cycles of local extinctions followed by recolonizations/expansions. Nevertheless, patterns of local adaptation have developed in D. birchii that may result in populations showing different selection responses when faced with environmental change.

Pattern recognition and image processing for environmental monitoring

NASA Astrophysics Data System (ADS)

Siddiqui, Khalid J.; Eastwood, DeLyle

1999-12-01

Pattern recognition (PR) and signal/image processing methods are among the most powerful tools currently available for noninvasively examining spectroscopic and other chemical data for environmental monitoring. Using spectral data, these systems have found a variety of applications employing analytical techniques for chemometrics such as gas chromatography, fluorescence spectroscopy, etc. An advantage of PR approaches is that they make no a prior assumption regarding the structure of the patterns. However, a majority of these systems rely on human judgment for parameter selection and classification. A PR problem is considered as a composite of four subproblems: pattern acquisition, feature extraction, feature selection, and pattern classification. One of the basic issues in PR approaches is to determine and measure the features useful for successful classification. Selection of features that contain the most discriminatory information is important because the cost of pattern classification is directly related to the number of features used in the decision rules. The state of the spectral techniques as applied to environmental monitoring is reviewed. A spectral pattern classification system combining the above components and automatic decision-theoretic approaches for classification is developed. It is shown how such a system can be used for analysis of large data sets, warehousing, and interpretation. In a preliminary test, the classifier was used to classify synchronous UV-vis fluorescence spectra of relatively similar petroleum oils with reasonable success.

Radical Anions of Oxidized vs. Reduced Oxytocin: Influence of Disulfide Bridges on CID and Vacuum UV Photo-Fragmentation

NASA Astrophysics Data System (ADS)

MacAleese, Luke; Girod, Marion; Nahon, Laurent; Giuliani, Alexandre; Antoine, Rodolphe; Dugourd, Philippe

2018-06-01

The nonapeptide oxytocin (OT) is used as a model sulfur-containing peptide to study the damage induced by vacuum UV (VUV) radiations. In particular, the effect of the presence (or absence in reduced OT) of oxytocin's internal disulfide bridge is evaluated in terms of photo-fragmentation yield and nature of the photo-fragments. Intact, as well as reduced, OT is studied as dianions and radical anions. Radical anions are prepared and photo-fragmented in two-color experiments (UV + VUV) in a linear ion trap. VUV photo-fragmentation patterns are analyzed and compared, and radical-induced mechanisms are proposed. The effect of VUV is principally to ionize but secondary fragmentation is also observed. This secondary fragmentation seems to be considerably enabled by the initial position of the radical on the molecule. In particular, the possibility to form a radical on free cysteines seems to increase the susceptibility to VUV fragmentation. Interestingly, disulfide bridges, which are fundamental for protein structure, could also be responsible for an increased resistance to ionizing radiations. [Figure not available: see fulltext.

Analysis of landscape fragmentation in the Peloncillo Mountains in relation to wildfire, prescribed burning, and cattle grazing

Treesearch

John Rogan; Kelley O' Neal; Stephen Yool

2005-01-01

This paper examined the application of state-of-the-art remote sensing image enhancement and classification techniques for mapping land cover change in the Peloncillo Mountains of Arizona and New Mexico. Spectrally enhanced images acquired August 1985, 1991, 1996, and 2000 were combined with environmental variables such as slope and aspect to map land cover...

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

Zhang, Jiang; Malmirchegini, G. Reza; Clubb, Robert T.

Native mass spectrometry (MS) has become an invaluable tool for the characterization of proteins and non-covalent protein complexes under near physiological solution conditions. Here we report the structural characterization of human hemoglobin (Hb), a 64 kDa oxygen-transporting protein complex, by high resolution native top-down mass spectrometry using electrospray ionization (ESI) and a 15-Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Native MS preserves the non-covalent interactions between the globin subunits, and electron capture dissociation (ECD) produces fragments directly from the intact Hb complex without dissociating the subunits. Using activated ion ECD, we observe the gradual unfolding process of themore » Hb complex in the gas phase. Without protein ion activation, the native Hb shows very limited ECD fragmentation from the N-termini, suggesting a tightly packed structure of the native complex and therefore low fragmentation efficiency. Precursor ion activation allows steady increase of N-terminal fragment ions, while the C-terminal fragments remain limited (38 c ions and 4 z ions on the α chain; 36 c ions and 2 z ions on the β chain). This ECD fragmentation pattern suggests that upon activation, the Hb complex starts to unfold from the N-termini of both subunits, whereas the C-terminal regions and therefore the potential regions involved in the subunit binding interactions remain intact. ECD-MS of the Hb dimer show similar fragmentation patterns as the Hb tetramer, providing further evidence for the hypothesized unfolding process of the Hb complex in the gas phase. Native top-down ECD-MS allows efficient probing of the Hb complex structure and the subunit binding interactions in the gas phase. Finally, it may provide a fast and effective means to probe the structure of novel protein complexes that are intractable to traditional structural characterization tools.« less

[Species composition and diversity of soil mesofauna in the 'Holy Hills' fragmentary tropical rain forest of Xishuangbanna, China].

PubMed

Yang, X; Sha, L

2001-04-01

The species composition and diversity of soil mesofauna were examined in fragmented dry tropical seasonal rainforest of tow 'Holy Hills' of Dai nationality, compared with the continuous moist tropical seasonal rain forest of Nature Reserve in Xishuangbanna area. 5 sample quadrats were selected along the diagonal of 20 m x 20 m sampling plot, and the samples of litterfall and 0-3 cm soil were collected from each 50 cm x 10 cm sample quadrat. Animals in soil sample were collected by using dry-funnel(Tullgren's), were identified to their groups according to the order. The H' index, D.G index and the pattern of relative abundance of species were used to compare the diversity of soil mesofauna. The results showed that the disturbance of vegetation and soil resulted by tropical rainforest fragmentation was the major factor affecting the diversity of soil mesofauna. Because the fragmented forest was intruded by some pioneer tree species and the "dry and warm" effect operated, this forest had more litterfall on the floor and more humus in the soil than the continuous moist rain forest. The soil condition with more soil organic matter, total N and P, higher pH value and lower soil bulk density became more favorable to the soil mesofauna. Therefore, the species richness, abundance and diversity of soil mesofauna in fragmented forests were higher than those in continuous forest, but the similarity of species composition in fragmented forest to the continuous forest was minimal. Soil mesofauna diversity in fragmented forests did not change with decreasing fragmented area, indicating that there was no species-area effect operation in this forest. The pattern of relative abundance of species in these forest soils was logarithmic series distribution.

The influence of spectral nudging on typhoon formation in regional climate models

NASA Astrophysics Data System (ADS)

Feser, Frauke; Barcikowska, Monika

2012-03-01

Regional climate models can successfully simulate tropical cyclones and typhoons. This has been shown and was evaluated for hindcast studies of the past few decades. But often global and regional weather phenomena are not simulated at the observed location, or occur too often or seldom even though the regional model is driven by global reanalysis data which constitute a near-realistic state of the global atmosphere. Therefore, several techniques have been developed in order to make the regional model follow the global state more closely. One is spectral nudging, which is applied for horizontal wind components with increasing strength for higher model levels in this study. The aim of this study is to show the influence that this method has on the formation of tropical cyclones (TC) in regional climate models. Two ensemble simulations (each with five simulations) were computed for Southeast Asia and the Northwestern Pacific for the typhoon season 2004, one with spectral nudging and one without. First of all, spectral nudging reduced the overall TC number by about a factor of 2. But the number of tracks which are similar to observed best track data (BTD) was greatly increased. Also, spatial track density patterns were found to be more similar when using spectral nudging. The tracks merge after a short time for the spectral nudging simulations and then follow the BTD closely; for the no nudge cases the similarity is greatly reduced. A comparison of seasonal precipitation, geopotential height, and temperature fields at several height levels with observations and reanalysis data showed overall a smaller ensemble spread, higher pattern correlations and reduced root mean square errors and biases for the spectral nudged simulations. Vertical temperature profiles for selected TCs indicate that spectral nudging is not inhibiting TC development at higher levels. Both the Madden-Julian Oscillation and monsoonal precipitation are reproduced realistically by the regional model, with results slightly closer to reanalysis data for the spectral nudged simulations. On the basis of this regional climate model hindcast study of a single typhoon season, spectral nudging seems to be favourable since it has mostly positive effects on typhoon formation, location and general circulation patterns in the generation areas of TCs.

Spectral Irradiance Calibration in the Infrared. Part 7; New Composite Spectra, Comparison with Model Atmospheres, and Far-Infrared Extrapolations

NASA Technical Reports Server (NTRS)

Cohen, Martin; Witteborn, Fred C.; Carbon, Duane F.; Davies, John K.; Wooden, Diane H.; Bregman, Jesse D.

1996-01-01

We present five new absolutely calibrated continuous stellar spectra constructed as far as possible from spectral fragments observed from the ground, the Kuiper Airborne Observatory (KAO), and the IRAS Low Resolution Spectrometer. These stars-alpha Boo, gamma Dra, alpha Cet, gamma Cru, and mu UMa-augment our six, published, absolutely calibrated spectra of K and early-M giants. All spectra have a common calibration pedigree. A revised composite for alpha Boo has been constructed from higher quality spectral fragments than our previously published one. The spectrum of gamma Dra was created in direct response to the needs of instruments aboard the Infrared Space Observatory (ISO); this star's location near the north ecliptic pole renders it highly visible throughout the mission. We compare all our low-resolution composite spectra with Kurucz model atmospheres and find good agreement in shape, with the obvious exception of the SiO fundamental, still lacking in current grids of model atmospheres. The CO fundamental seems slightly too deep in these models, but this could reflect our use of generic models with solar metal abundances rather than models specific to the metallicities of the individual stars. Angular diameters derived from these spectra and models are in excellent agreement with the best observed diameters. The ratio of our adopted Sirius and Vega models is vindicated by spectral observations. We compare IRAS fluxes predicted from our cool stellar spectra with those observed and conclude that, at 12 and 25 microns, flux densities measured by IRAS should be revised downwards by about 4.1% and 5.7%, respectively, for consistency with our absolute calibration. We have provided extrapolated continuum versions of these spectra to 300 microns, in direct support of ISO (PHT and LWS instruments). These spectra are consistent with IRAS flux densities at 60 and 100 microns.

A Novel Anti-Spoofing Solution for Iris Recognition Toward Cosmetic Contact Lens Attack Using Spectral ICA Analysis

PubMed Central

Hsieh, Sheng-Hsun; Wang, Wei; Tien, Chung-Hao

2018-01-01

In this study, we maneuvered a dual-band spectral imaging system to capture an iridal image from a cosmetic-contact-lens-wearing subject. By using the independent component analysis to separate individual spectral primitives, we successfully distinguished the natural iris texture from the cosmetic contact lens (CCL) pattern, and restored the genuine iris patterns from the CCL-polluted image. Based on a database containing 200 test image pairs from 20 CCL-wearing subjects as the proof of concept, the recognition accuracy (False Rejection Rate: FRR) was improved from FRR = 10.52% to FRR = 0.57% with the proposed ICA anti-spoofing scheme. PMID:29509692

Spatial and spectral imaging of point-spread functions using a spatial light modulator

NASA Astrophysics Data System (ADS)

Munagavalasa, Sravan; Schroeder, Bryce; Hua, Xuanwen; Jia, Shu

2017-12-01

We develop a point-spread function (PSF) engineering approach to imaging the spatial and spectral information of molecular emissions using a spatial light modulator (SLM). We show that a dispersive grating pattern imposed upon the emission reveals spectral information. We also propose a deconvolution model that allows the decoupling of the spectral and 3D spatial information in engineered PSFs. The work is readily applicable to single-molecule measurements and fluorescent microscopy.

Diurnal variations in maize and soybean vegetation indices from continuous measurements of ground-based spectral reflectance

NASA Astrophysics Data System (ADS)

Arkebauer, T. J.; Walter-Shea, E. A.

2017-12-01

Vegetation indices, based on canopy spectral reflectance, are widely used to infer physical and biological characteristics of vegetation. Understanding the changes in remotely sensed signals as vegetation responds to its changing environment is essential for full assessment of canopy structure and function. Canopy-level reflectance has been measured at Nebraska AmeriFlux sites US-Ne1, US-Ne2 and US-Ne3 for most years since flux measurements were initiated in 2001. Tower-mounted spectral sensors provided 10-minute averaged reflectance (in PAR and NIR spectral regions) every half hour through the growing season for maize and soybean. Canopy reflectance varied over diurnal and seasonal time periods which led to variations in vegetation indices. One source of variation is due to the interaction of incident solar radiant energy with canopy structure (e.g., reflectance varies with changes in solar zenith angle and direct beam fraction, vegetative fraction, and leaf angle distribution). Another source of variation results from changes in canopy function (e.g., fluctuations in gross primary production and invocation of photoprotective mechanisms with plant stress). We present here a series of diurnal "patterns" of vegetation indices (including Normalized Difference Vegetation Index and Chlorophyll Index) for maize and soybean under mostly clear sky conditions. We demonstrate that diurnal patterns change as the LAI of the canopy changes through the course of the growing season in a somewhat predictable pattern from plant emergence (low vegetative cover) through peak green LAI (full vegetation cover). However, there are changes in the diurnal pattern that we have yet to fully understand; this variation in pattern may indicate variation in canopy function. Initially, we have explored the pattern changes qualitatively and are currently developing more quantitative approaches.

Use of Raman microscopy and band-target entropy minimization analysis to identify dyes in a commercial stamp. Implications for authentication and counterfeit detection.

PubMed

Widjaja, Effendi; Garland, Marc

2008-02-01

Raman microscopy was used in mapping mode to collect more than 1000 spectra in a 100 microm x 100 microm area from a commercial stamp. Band-target entropy minimization (BTEM) was then employed to unmix the mixture spectra in order to extract the pure component spectra of the samples. Three pure component spectral patterns with good signal-to-noise ratios were recovered, and their spatial distributions were determined. The three pure component spectral patterns were then identified as copper phthalocyanine blue, calcite-like material, and yellow organic dye material by comparison to known spectral libraries. The present investigation, consisting of (1) advanced curve resolution (blind-source separation) followed by (2) spectral data base matching, readily suggests extensions to authenticity and counterfeit studies of other types of commercial objects. The presence or absence of specific observable components form the basis for assessment. The present spectral analysis (BTEM) is applicable to highly overlapping spectral information. Since a priori information such as the number of components present and spectral libraries are not needed in BTEM, and since minor signals arising from trace components can be reconstructed, this analysis offers a robust approach to a wide variety of material problems involving authenticity and counterfeit issues.

Confounder Detection in High-Dimensional Linear Models Using First Moments of Spectral Measures.

PubMed

Liu, Furui; Chan, Laiwan

2018-06-12

In this letter, we study the confounder detection problem in the linear model, where the target variable [Formula: see text] is predicted using its [Formula: see text] potential causes [Formula: see text]. Based on an assumption of a rotation-invariant generating process of the model, recent study shows that the spectral measure induced by the regression coefficient vector with respect to the covariance matrix of [Formula: see text] is close to a uniform measure in purely causal cases, but it differs from a uniform measure characteristically in the presence of a scalar confounder. Analyzing spectral measure patterns could help to detect confounding. In this letter, we propose to use the first moment of the spectral measure for confounder detection. We calculate the first moment of the regression vector-induced spectral measure and compare it with the first moment of a uniform spectral measure, both defined with respect to the covariance matrix of [Formula: see text]. The two moments coincide in nonconfounding cases and differ from each other in the presence of confounding. This statistical causal-confounding asymmetry can be used for confounder detection. Without the need to analyze the spectral measure pattern, our method avoids the difficulty of metric choice and multiple parameter optimization. Experiments on synthetic and real data show the performance of this method.

Fragmentation increases wind disturbance impacts on forest structure and carbon stocks in a western Amazonian landscape.

PubMed

Schwartz, Naomi B; Uriarte, María; DeFries, Ruth; Bedka, Kristopher M; Fernandes, Katia; Gutiérrez-Vélez, Victor; Pinedo-Vasquez, Miguel A

2017-09-01

Tropical second-growth forests could help mitigate climate change, but the degree to which their carbon potential is achieved will depend on exposure to disturbance. Wind disturbance is common in tropical forests, shaping structure, composition, and function, and influencing successional trajectories. However, little is known about the impacts of extreme winds on second-growth forests in fragmented landscapes, though these ecosystems are often located in mosaics of forest, pasture, cropland, and other land cover types. Indirect evidence suggests that fragmentation increases risk of wind damage in tropical forests, but no studies have found such impacts following severe storms. In this study, we ask whether fragmentation and forest type (old vs. second growth) were associated with variation in wind damage after a severe convective storm in a fragmented production landscape in western Amazonia. We applied linear spectral unmixing to Landsat 8 imagery from before and after the storm, and combined it with field observations of damage to map wind effects on forest structure and biomass. We also used Landsat 8 imagery to map land cover with the goals of identifying old- and second-growth forest and characterizing fragmentation. We used these data to assess variation in wind disturbance across 95,596 ha of forest, distributed over 6,110 patches. We find that fragmentation is significantly associated with wind damage, with damage severity higher at forest edges and in edgier, more isolated patches. Damage was also more severe in old-growth than in second-growth forests, but this effect was weaker than that of fragmentation. These results illustrate the importance of considering landscape context in planning tropical forest restoration and natural regeneration projects. Assessments of long-term carbon sequestration potential need to consider spatial variation in disturbance exposure. Where risk of extreme winds is high, minimizing fragmentation and isolation could increase carbon sequestration potential. © 2017 by the Ecological Society of America.

The browning value changes and spectral analysis on the Maillard reaction product from glucose and methionine model system

NASA Astrophysics Data System (ADS)

Al-Baarri, A. N.; Legowo, A. M.; Widayat

2018-01-01

D-glucose has been understood to provide the various effect on the reactivity in Maillard reaction resulting in the changes in physical performance of food product. Therefore this research was done to analyse physical appearance of Maillard reaction product made of D-glucose and methionine as a model system. The changes in browning value and spectral analysis model system were determined. The glucose-methionine model system was produced through the heating treatment at 50°C and RH 70% for 24 hours. The data were collected for every three hour using spectrophotometer. As result, browning value was elevated with the increase of heating time and remarkably high if compare to the D-glucose only. Furthermore, the spectral analysis showed that methionine turned the pattern of peak appearance. As conclusion, methionine raised the browning value and changed the pattern of spectral analysis in Maillard reaction model system.

Implementation of spectral clustering on microarray data of carcinoma using k-means algorithm

NASA Astrophysics Data System (ADS)

Frisca, Bustamam, Alhadi; Siswantining, Titin

2017-03-01

Clustering is one of data analysis methods that aims to classify data which have similar characteristics in the same group. Spectral clustering is one of the most popular modern clustering algorithms. As an effective clustering technique, spectral clustering method emerged from the concepts of spectral graph theory. Spectral clustering method needs partitioning algorithm. There are some partitioning methods including PAM, SOM, Fuzzy c-means, and k-means. Based on the research that has been done by Capital and Choudhury in 2013, when using Euclidian distance k-means algorithm provide better accuracy than PAM algorithm. So in this paper we use k-means as our partition algorithm. The major advantage of spectral clustering is in reducing data dimension, especially in this case to reduce the dimension of large microarray dataset. Microarray data is a small-sized chip made of a glass plate containing thousands and even tens of thousands kinds of genes in the DNA fragments derived from doubling cDNA. Application of microarray data is widely used to detect cancer, for the example is carcinoma, in which cancer cells express the abnormalities in his genes. The purpose of this research is to classify the data that have high similarity in the same group and the data that have low similarity in the others. In this research, Carcinoma microarray data using 7457 genes. The result of partitioning using k-means algorithm is two clusters.

Geomorphic controls of soil spatial complexity in a primeval mountain forest in the Czech Republic

NASA Astrophysics Data System (ADS)

Daněk, Pavel; Šamonil, Pavel; Phillips, Jonathan D.

2016-11-01

Soil diversity and complexity is influenced by a variety of factors, and much recent research has been focused on interpreting or modeling complexity based on soil-topography relationships, and effects of biogeomorphic processes. We aimed to (i) describe local soil diversity in one of the oldest forest reserves in Europe, (ii) employ existing graph theory concepts in pedocomplexity calculation and extend them by a novel approach based on hypothesis testing and an index measuring graph sequentiality (the extent to which soils have gradual vs. abrupt variations in underlying soil factors), and (iii) reveal the main sources of pedocomplexity, with a particular focus on geomorphic controls. A total of 954 soil profiles were described and classified to soil taxonomic units (STU) within a 46 ha area. We analyzed soil diversity using the Shannon index, and soil complexity using a novel graph theory approach. Pairwise tests of observed adjacencies, spectral radius and a newly proposed sequentiality index were used to describe and quantify the complexity of the spatial pattern of STUs. This was then decomposed into the contributions of three soil factor sequences (SFS), (i) degree of weathering and leaching processes, (ii) hydromorphology, and (iii) proportion of rock fragments. Six Reference Soil Groups and 37 second-level soil units were found. A significant portion of pedocomplexity occurred at distances shorter than the 22 m spacing of neighbouring soil profiles. The spectral radius (an index of complexity) of the pattern of soil spatial adjacency was 14.73, to which the individual SFS accounted for values of 2.0, 8.0 and 3.5, respectively. Significant sequentiality was found for degree of weathering and hydromorphology. Exceptional overall pedocomplexity was particularly caused by enormous spatial variability of soil wetness, representing a crucial soil factor sequence in the primeval forest. Moreover, the soil wetness gradient was partly spatially correlated with the gradient of soil weathering and leaching, suggesting synergistic influences of topography, climate, (hydro)geology and biomechanical and biochemical effects of individual trees. The pattern of stony soils, random in most respects, resulted probably from local geology and quaternary biogeomorphological processes. Thus, while geomorphology is the primary control over a very locally complex soil pattern, microtopography and local disturbances, mostly related to the effects of individual trees, are also critical. Considerable local pedodiversity seems to be an important component of the dynamics of old-growth mixed temperate mountain forests, with implications for decreasing pedodiversity in managed forests and deforested areas.

Investigation on the impact of irregular fringe patterns of a single-fiber Mach-Zehnder interferometer on its sensing capabilities

NASA Astrophysics Data System (ADS)

Kumar, Naveen; Kumar, Ashish

2018-07-01

A novel single-mode single-fiber (SMSF) MZI formed by cascading of two non-adiabatic fiber tapers, with stable and repeatable spectrum, has been found to be useful in sensing applications in recent times. A multimode interference based novel simulation approach is proposed to predict the sensing characteristics of SMSF-MZI and is validated with experimental observation. The proposed method includes solving of simultaneous non-homogenous equations for determining the amplitudes of the interfering modes excited in the tapered section of the interferometer. The simulated fringe pattern and the experimental spectral response converge to some important comprehension reported for the first time. A linear shift in output spectral response, of SMSF-MZI, due to change in optical path length induced by temperature/strain etc., is likely to be characterized by three modes interference occurring in the interference region of the interferometer. Whereas if the spectral shift starts saturating at moderately higher temperature/strain, then the formation of interference fringes are possibly governed by two modes interference. Further, it was also explained that a SMSF-MZI with variable fringe widths in its spectral pattern exhibits higher sensitivity than that of the SMSF-MZI having wavelength spectrum with uniform free spectral range. These findings are useful in selecting and predicting the sensitivity of a given SMSF-MZI, based on its spectrum, for sensing applications.

Random-breakage mapping method applied to human DNA sequences

NASA Technical Reports Server (NTRS)

Lobrich, M.; Rydberg, B.; Cooper, P. K.; Chatterjee, A. (Principal Investigator)

1996-01-01

The random-breakage mapping method [Game et al. (1990) Nucleic Acids Res., 18, 4453-4461] was applied to DNA sequences in human fibroblasts. The methodology involves NotI restriction endonuclease digestion of DNA from irradiated calls, followed by pulsed-field gel electrophoresis, Southern blotting and hybridization with DNA probes recognizing the single copy sequences of interest. The Southern blots show a band for the unbroken restriction fragments and a smear below this band due to radiation induced random breaks. This smear pattern contains two discontinuities in intensity at positions that correspond to the distance of the hybridization site to each end of the restriction fragment. By analyzing the positions of those discontinuities we confirmed the previously mapped position of the probe DXS1327 within a NotI fragment on the X chromosome, thus demonstrating the validity of the technique. We were also able to position the probes D21S1 and D21S15 with respect to the ends of their corresponding NotI fragments on chromosome 21. A third chromosome 21 probe, D21S11, has previously been reported to be close to D21S1, although an uncertainty about a second possible location existed. Since both probes D21S1 and D21S11 hybridized to a single NotI fragment and yielded a similar smear pattern, this uncertainty is removed by the random-breakage mapping method.

Molecular epidemiology of Escherichia coli O157:H7 strains by bacteriophage lambda restriction fragment length polymorphism analysis: application to a multistate foodborne outbreak and a day-care center cluster.

PubMed

Samadpour, M; Grimm, L M; Desai, B; Alfi, D; Ongerth, J E; Tarr, P I

1993-12-01

Genomic DNAs prepared from 168 isolates of Escherichia coli O157:H7 were analyzed for restriction fragment length polymorphisms on Southern blots probed with bacteriophage lambda DNA. The isolates analyzed included strains from a recent large multistate outbreak of E. coli O157:H7 infection associated with consumption of poorly cooked beef in restaurants, a day-care center cluster, and temporally and geographically unrelated isolates. E. coli O157:H7 isolates recovered from the incriminated meat and from 61 (96.8%) of 63 patients from Washington and Nevada possessed identical lambda restriction fragment length patterns. The lambda restriction fragment length polymorphisms observed in 11 (91.7%) of 12 day-care center patients were identical, but they differed from that of the strain associated with the multistate outbreak. E. coli O157:H7 from 42 patients temporally or geographically unrelated to either cluster of infection possessed unique and different lambda restriction fragment length patterns, except for paired isolates from three separate clusters of infection. These data demonstrate that the hybridization of DNA digests of E. coli O157:H7 with radiolabelled bacteriophage lambda DNA can be a useful, stable, and discriminatory epidemiologic tool for analyzing the linkage between strains of E. coli O157:H7.

Critical thresholds in species` responses to landscape structure

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

With, K.A.; Crist, T.O.

1995-12-01

Critical thresholds are transition ranges across which small changes in spatial pattern produce abrupt shifts in ecological responses. Habitat fragmentation provides a familiar example of a critical threshold. As the landscape becomes dissected into smaller parcels of habitat. landscape connectivity-the functional linkage among habitat patches - may suddenly become disrupted, which may have important consequences for the distribution and persistence of populations. Landscape connectivity depends not only on the abundance and spatial patterning of habitat. but also on the habitat specificity and dispersal abilities of species. Habitat specialists with limited dispersal capabilities presumably have a much lower threshold to habitatmore » fragmentation than highly vagile species, which may perceive the landscape as functionally connected across a greater range of fragmentation severity. To determine where threshold effects in species, responses to landscape structure are likely to occur, a simulation model modified from percolation theory was developed. Our simulations predicted the distributional patterns of populations in different landscape mosaics, which we tested empirically using two grasshopper species (Orthoptera: Acrididae) that occur in the shortgrass prairie of north-central Colorado. The distribution of these two species in this grassland mosaic matched the predictions from our simulations. By providing quantitative predictions of threshold effects, this modelling approach may prove useful in the formulation of conservation strategies and assessment of land-use changes on species` distributional patterns and persistence.« less

Contrasting patterns of nest survival and postfledging survival in ovenbirds and Acadian flycatchers in Missouri forest fragments

Treesearch

Julianna M. A. Jenkins; Frank R. Thompson; John Faaborg

2016-01-01

We can improve our ability to assess population viability and forecast population growth under different scenarios by understanding factors that limit population parameters in each stage of the annual cycle. Postfledging mortality rates may be as variable as nest survival across regions and fragmentation gradients, although factors that negatively impact nest survival...

Spectral signature verification using statistical analysis and text mining

NASA Astrophysics Data System (ADS)

DeCoster, Mallory E.; Firpi, Alexe H.; Jacobs, Samantha K.; Cone, Shelli R.; Tzeng, Nigel H.; Rodriguez, Benjamin M.

2016-05-01

In the spectral science community, numerous spectral signatures are stored in databases representative of many sample materials collected from a variety of spectrometers and spectroscopists. Due to the variety and variability of the spectra that comprise many spectral databases, it is necessary to establish a metric for validating the quality of spectral signatures. This has been an area of great discussion and debate in the spectral science community. This paper discusses a method that independently validates two different aspects of a spectral signature to arrive at a final qualitative assessment; the textual meta-data and numerical spectral data. Results associated with the spectral data stored in the Signature Database1 (SigDB) are proposed. The numerical data comprising a sample material's spectrum is validated based on statistical properties derived from an ideal population set. The quality of the test spectrum is ranked based on a spectral angle mapper (SAM) comparison to the mean spectrum derived from the population set. Additionally, the contextual data of a test spectrum is qualitatively analyzed using lexical analysis text mining. This technique analyzes to understand the syntax of the meta-data to provide local learning patterns and trends within the spectral data, indicative of the test spectrum's quality. Text mining applications have successfully been implemented for security2 (text encryption/decryption), biomedical3 , and marketing4 applications. The text mining lexical analysis algorithm is trained on the meta-data patterns of a subset of high and low quality spectra, in order to have a model to apply to the entire SigDB data set. The statistical and textual methods combine to assess the quality of a test spectrum existing in a database without the need of an expert user. This method has been compared to other validation methods accepted by the spectral science community, and has provided promising results when a baseline spectral signature is present for comparison. The spectral validation method proposed is described from a practical application and analytical perspective.

Mapping Candidate Ecological Restoration Areas Using Morphological Spatial Pattern Analysis (MSPA)

EPA Science Inventory

Morphological Spatial Pattern Analysis (MSPA) has been widely adopted by landscape ecologists over the past decade. A few examples of its many uses include: 1) quantifying landscape indicators and fragmentation in continental forest assessments, 2) explaining interior-exterior p...

Morphological characteristics of the posterior malleolar fragment according to ankle fracture patterns: a computed tomography-based study.

PubMed

Yi, Young; Chun, Dong-Il; Won, Sung Hun; Park, Suyeon; Lee, Sanghyeon; Cho, Jaeho

2018-02-13

The posterior malleolar fragment (PMF) of an ankle fracture can have various shapes depending on the injury mechanism. The purpose of this study was to evaluate the morphological characteristics of the PMF according to the ankle fracture pattern described in the Lauge-Hansen classification by using computed tomography (CT) images. We retrospectively analyzed CT data of 107 patients (107 ankles) who underwent surgery for trimalleolar fracture from January 2012 to December 2014. The patients were divided into two groups: 76 ankles in the supination-external rotation (SER) stage IV group and 31 ankles in the pronation-external rotation (PER) stage IV group. The PMF type of the two groups was assessed using the Haraguchi and Jan Bartonicek classification. The cross angle (α), fragment length ratio (FLR), fragment area ratio (FAR), sagittal angle (θ), and fragment height (FH) were measured to assess the morphological characteristics of the PMF. The PMF in the SER group mainly had a posterolateral shape, whereas that in the PER group mainly had a posteromedial two-part shape or a large posterolateral triangular shape (P = 0.02). The average cross angle was not significantly different between the two groups (SER group = 19.4°, PER group = 17.6°). The mean FLR and FH were significantly larger in the PER group than in the SER group (P = 0.024, P = 0.006). The mean fragment sagittal angle in the PER group was significantly smaller than that in the SER group (P = 0.017). With regard to the articular involvement, volume, and vertical nature, the SER-type fracture tends to have a smaller fragment due to the rotational force, whereas the PER-type fracture tends to have a larger fragment due to the combination of rotational and axial forces.

Landscape fragmentation affects responses of avian communities to climate change.

PubMed

Jarzyna, Marta A; Porter, William F; Maurer, Brian A; Zuckerberg, Benjamin; Finley, Andrew O

2015-08-01

Forecasting the consequences of climate change is contingent upon our understanding of the relationship between biodiversity patterns and climatic variability. While the impacts of climate change on individual species have been well-documented, there is a paucity of studies on climate-mediated changes in community dynamics. Our objectives were to investigate the relationship between temporal turnover in avian biodiversity and changes in climatic conditions and to assess the role of landscape fragmentation in affecting this relationship. We hypothesized that community turnover would be highest in regions experiencing the most pronounced changes in climate and that these patterns would be reduced in human-dominated landscapes. To test this hypothesis, we quantified temporal turnover in avian communities over a 20-year period using data from the New York State Breeding Atlases collected during 1980-1985 and 2000-2005. We applied Bayesian spatially varying intercept models to evaluate the relationship between temporal turnover and temporal trends in climatic conditions and landscape fragmentation. We found that models including interaction terms between climate change and landscape fragmentation were superior to models without the interaction terms, suggesting that the relationship between avian community turnover and changes in climatic conditions was affected by the level of landscape fragmentation. Specifically, we found weaker associations between temporal turnover and climatic change in regions with prevalent habitat fragmentation. We suggest that avian communities in fragmented landscapes are more robust to climate change than communities found in contiguous habitats because they are comprised of species with wider thermal niches and thus are less susceptible to shifts in climatic variability. We conclude that highly fragmented regions are likely to undergo less pronounced changes in composition and structure of faunal communities as a result of climate change, whereas those changes are likely to be greater in contiguous and unfragmented habitats. © 2015 John Wiley & Sons Ltd.

Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library*

PubMed Central

Yen, Chia-Yu; Houel, Stephane; Ahn, Natalie G.; Old, William M.

2011-01-01

The unambiguous assignment of tandem mass spectra (MS/MS) to peptide sequences remains a key unsolved problem in proteomics. Spectral library search strategies have emerged as a promising alternative for peptide identification, in which MS/MS spectra are directly compared against a reference library of confidently assigned spectra. Two problems relate to library size. First, reference spectral libraries are limited to rediscovery of previously identified peptides and are not applicable to new peptides, because of their incomplete coverage of the human proteome. Second, problems arise when searching a spectral library the size of the entire human proteome. We observed that traditional dot product scoring methods do not scale well with spectral library size, showing reduction in sensitivity when library size is increased. We show that this problem can be addressed by optimizing scoring metrics for spectrum-to-spectrum searches with large spectral libraries. MS/MS spectra for the 1.3 million predicted tryptic peptides in the human proteome are simulated using a kinetic fragmentation model (MassAnalyzer version2.1) to create a proteome-wide simulated spectral library. Searches of the simulated library increase MS/MS assignments by 24% compared with Mascot, when using probabilistic and rank based scoring methods. The proteome-wide coverage of the simulated library leads to 11% increase in unique peptide assignments, compared with parallel searches of a reference spectral library. Further improvement is attained when reference spectra and simulated spectra are combined into a hybrid spectral library, yielding 52% increased MS/MS assignments compared with Mascot searches. Our study demonstrates the advantages of using probabilistic and rank based scores to improve performance of spectrum-to-spectrum search strategies. PMID:21532008

Mapping the Natchez Trace Parkway

USGS Publications Warehouse

Rangoonwala, Amina; Bannister, Terri; Ramsey, Elijah W.

2011-01-01

Based on a National Park Service (NPS) landcover classification, a landcover map of the 715-km (444-mile) NPS Natchez Trace Parkway (hereafter referred to as the "Parkway") was created. The NPS landcover classification followed National Vegetation Classification (NVC) protocols. The landcover map, which extended the initial landcover classification to the entire Parkway, was based on color-infrared photography converted to 1-m raster-based digital orthophoto quarter quadrangles, according to U.S. Geological Survey mapping standards. Our goal was to include as many alliance classes as possible in the Parkway landcover map. To reach this goal while maintaining a consistent and quantifiable map product throughout the Parkway extent, a mapping strategy was implemented based on the migration of class-based spectral textural signatures and the congruent progressive refinement of those class signatures along the Parkway. Progressive refinement provided consistent mapping by evaluating the spectral textural distinctiveness of the alliance-association classes, and where necessary, introducing new map classes along the Parkway. By following this mapping strategy, the use of raster-based image processing and geographic information system analyses for the map production provided a quantitative and reproducible product. Although field-site classification data were severely limited, the combination of spectral migration of class membership along the Parkway and the progressive classification strategy produced an organization of alliances that was internally highly consistent. The organization resulted from the natural patterns or alignments of spectral variance and the determination of those spectral patterns that were compositionally similar in the dominant species as NVC alliances. Overall, the mapped landcovers represented the existent spectral textural patterns that defined and encompassed the complex variety of compositional alliances and associations of the Parkway. Based on that mapped representation, forests dominate the Parkway landscape. Grass is the second largest Parkway land cover, followed by scrub-shrub and shrubland classes and pine plantations. The map provides a good representation of the landcover patterns and their changes over the extent of the Parkway, south to north.

The relative effects of habitat loss and fragmentation on population genetic variation in the red-cockaded woodpecker (Picoides borealis).

PubMed

Bruggeman, Douglas J; Wiegand, Thorsten; Fernández, Néstor

2010-09-01

The relative influence of habitat loss, fragmentation and matrix heterogeneity on the viability of populations is a critical area of conservation research that remains unresolved. Using simulation modelling, we provide an analysis of the influence both patch size and patch isolation have on abundance, effective population size (N(e)) and F(ST). An individual-based, spatially explicit population model based on 15 years of field work on the red-cockaded woodpecker (Picoides borealis) was applied to different landscape configurations. The variation in landscape patterns was summarized using spatial statistics based on O-ring statistics. By regressing demographic and genetics attributes that emerged across the landscape treatments against proportion of total habitat and O-ring statistics, we show that O-ring statistics provide an explicit link between population processes, habitat area, and critical thresholds of fragmentation that affect those processes. Spatial distances among land cover classes that affect biological processes translated into critical scales at which the measures of landscape structure correlated best with genetic indices. Therefore our study infers pattern from process, which contrasts with past studies of landscape genetics. We found that population genetic structure was more strongly affected by fragmentation than population size, which suggests that examining only population size may limit recognition of fragmentation effects that erode genetic variation. If effective population size is used to set recovery goals for endangered species, then habitat fragmentation effects may be sufficiently strong to prevent evaluation of recovery based on the ratio of census:effective population size alone.

Genotyping of bacteria belonging to the former Erwinia genus by PCR-RFLP analysis of a recA gene fragment.

PubMed

Waleron, Małgorzata; Waleron, Krzysztof; Podhajska, Anna J; Lojkowska, Ewa

2002-02-01

Genotypic characterization, based on the analysis of restriction fragment length polymorphism of the recA gene fragment PCR product (recA PCR-RFLP), was performed on members of the former Erwinia genus. PCR primers deduced from published recA gene sequences of Erwinia carotovora allowed the amplification of an approximately 730 bp DNA fragment from each of the 19 Erwinia species tested. Amplified recA fragments were compared using RFLP analysis with four endonucleases (AluI, HinfI, TasI and Tru1I), allowing the detection of characteristic patterns of RFLP products for most of the Erwinia species. Between one and three specific RFLP groups were identified among most of the species tested (Erwinia amylovora, Erwinia ananas, Erwinia cacticida, Erwinia cypripedii, Erwinia herbicola, Erwinia mallotivora, Erwinia milletiae, Erwinia nigrifluens, Erwinia persicina, Erwinia psidii, Erwinia quercina, Erwinia rhapontici, Erwinia rubrifaciens, Erwinia salicis, Erwinia stewartii, Erwinia tracheiphila, Erwinia uredovora, Erwinia carotovora subsp. atroseptica, Erwinia carotovora subsp. betavasculorum, Erwinia carotovora subsp. odorifera and Erwinia carotovora subsp. wasabiae). However, in two cases, Erwinia chrysanthemi and Erwinia carotovora subsp. carotovora, 15 and 18 specific RFLP groups were detected, respectively. The variability of genetic patterns within these bacteria could be explained in terms of their geographic origin and/or wide host-range. The results indicated that PCR-RFLP analysis of the recA gene fragment is a useful tool for identification of species and subspecies belonging to the former Erwinia genus, as well as for differentiation of strains within E. carotovora subsp. carotovora and E. chrysanthemi.

Experimental and quantum-chemical studies on the three-particle fragmentation of neutral triatomic hydrogen

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

Galster, Ulrich; Baumgartner, Frank; Mueller, Ulrich

2005-12-15

Dissociation of well-defined H{sub 3} Rydberg states into three ground state hydrogen atoms reveals characteristic correlation patterns in the center-of-mass motion of the three fragments. We present an extensive experimental dataset of momentum correlation maps for all lower Rydberg states of H{sub 3} and D{sub 3}. In particular the states with principal quantum number n=2 feature simple correlation patterns with regular occurence of mutual affinities. Energetically higher-lying states typically show more complex patterns which are unique for each state. Quantum-chemical calculations on adiabatic potential energy surfaces of H{sub 3} Rydberg states are presented to illuminate the likely origin of thesemore » differences. We discuss the likely dissociation mechanisms and paths which are responsible for the observed continuum correlation.« less

[Landscape pattern change and its driving forces in Xixi National Wetland Park since 1993].

PubMed

Cheng, Qian; Wu, Xiuju

2006-09-01

Under the support of GIS technology and the TM images of Xixi National Wetland Park, this paper studied the past ten years' landscape pattern change and its driving forces of Xixi Wetland. The results showed that the landscape diversity index increased from 1.7854 in 1993 to 1.8438 in 2001 and 2.2096 in 2003, and the landscape fragmentation index increased from 0.0036 in 1993 to 0.0042 in 2001, and 0.0047 in 2003, suggesting that the landscape fragmentation was increased with time. Human activity was the main driving force, while the exploitation of real estate was the main internal factor of the landscape pattern change of Xixi wetland. In addition, social and economic development level had a strong effect on the overall diversity of the landscape.

Fragmented patterns of flood change across the United States

PubMed Central

Hirsch, R. M.; Viglione, A.; Blöschl, G.

2016-01-01

Abstract Trends in the peak magnitude, frequency, duration, and volume of frequent floods (floods occurring at an average of two events per year relative to a base period) across the United States show large changes; however, few trends are found to be statistically significant. The multidimensional behavior of flood change across the United States can be described by four distinct groups, with streamgages experiencing (1) minimal change, (2) increasing frequency, (3) decreasing frequency, or (4) increases in all flood properties. Yet group membership shows only weak geographic cohesion. Lack of geographic cohesion is further demonstrated by weak correlations between the temporal patterns of flood change and large‐scale climate indices. These findings reveal a complex, fragmented pattern of flood change that, therefore, clouds the ability to make meaningful generalizations about flood change across the United States. PMID:27917010

Fragmented patterns of flood change across the United States

USGS Publications Warehouse

Archfield, Stacey A.; Hirsch, Robert M.; Viglione, A.; Blöschl, G.

2016-01-01

Trends in the peak magnitude, frequency, duration, and volume of frequent floods (floods occurring at an average of two events per year relative to a base period) across the United States show large changes; however, few trends are found to be statistically significant. The multidimensional behavior of flood change across the United States can be described by four distinct groups, with streamgages experiencing (1) minimal change, (2) increasing frequency, (3) decreasing frequency, or (4) increases in all flood properties. Yet group membership shows only weak geographic cohesion. Lack of geographic cohesion is further demonstrated by weak correlations between the temporal patterns of flood change and large-scale climate indices. These findings reveal a complex, fragmented pattern of flood change that, therefore, clouds the ability to make meaningful generalizations about flood change across the United States.

The NH2-terminal and COOH-terminal fragments of dentin matrix protein 1 (DMP1) localize differently in the compartments of dentin and growth plate of bone.

PubMed

Maciejewska, Izabela; Cowan, Cameron; Svoboda, Kathy; Butler, William T; D'Souza, Rena; Qin, Chunlin

2009-02-01

Multiple studies have shown that dentin matrix protein 1 (DMP1) is essential for bone and dentin mineralization. After post-translational proteolytic cleavage, DMP1 exists within the extracellular matrix of bone and dentin as an NH2-terminal fragment, a COOH-terminal fragment, and the proteoglycan form of the NH2-terminal fragment (DMP1-PG). To begin to assess the biological function of each fragment, we evaluated the distribution of both fragments in the rat tooth and bone using antibodies specific to the NH2-terminal and COOH-terminal regions of DMP1 and confocal microscopy. In rat first molar organs, the NH2-terminal fragment localized to predentin, whereas the COOH-terminal fragment was mainly restricted to mineralized dentin. In the growth plate of bone, the NH2-terminal fragment appeared in the proliferation and hypertrophic zones, whereas the COOH-terminal fragment occupied the ossification zone. Forster resonance energy transfer analysis showed colocalization of both fragments of DMP1 in odontoblasts and predentin, as well as hypertrophic chondrocytes within the growth plates of bone. The biochemical analysis of bovine teeth showed that predentin is rich in DMP1-PG, whereas mineralized dentin primarily contains the COOH-terminal fragment. We conclude that the differential patterns of expression of NH2-terminal and COOH-terminal fragments of DMP1 reflect their potentially distinct roles in the biomineralization of dentin and bone matrices.

A novel spectral library workflow to enhance protein identifications.

PubMed

Li, Haomin; Zong, Nobel C; Liang, Xiangbo; Kim, Allen K; Choi, Jeong Ho; Deng, Ning; Zelaya, Ivette; Lam, Maggie; Duan, Huilong; Ping, Peipei

2013-04-09

The innovations in mass spectrometry-based investigations in proteome biology enable systematic characterization of molecular details in pathophysiological phenotypes. However, the process of delineating large-scale raw proteomic datasets into a biological context requires high-throughput data acquisition and processing. A spectral library search engine makes use of previously annotated experimental spectra as references for subsequent spectral analyses. This workflow delivers many advantages, including elevated analytical efficiency and specificity as well as reduced demands in computational capacity. In this study, we created a spectral matching engine to address challenges commonly associated with a library search workflow. Particularly, an improved sliding dot product algorithm, that is robust to systematic drifts of mass measurement in spectra, is introduced. Furthermore, a noise management protocol distinguishes spectra correlation attributed from noise and peptide fragments. It enables elevated separation between target spectral matches and false matches, thereby suppressing the possibility of propagating inaccurate peptide annotations from library spectra to query spectra. Moreover, preservation of original spectra also accommodates user contributions to further enhance the quality of the library. Collectively, this search engine supports reproducible data analyses using curated references, thereby broadening the accessibility of proteomics resources to biomedical investigators. This article is part of a Special Issue entitled: From protein structures to clinical applications. Copyright © 2013 Elsevier B.V. All rights reserved.

Genetic Heterogeneity in Mycobacterium tuberculosis Isolates Reflected in IS6110 Restriction Fragment Length Polymorphism Patterns as Low-Intensity Bands

PubMed Central

de Boer, Annette S.; Kremer, Kristin; Borgdorff, Martien W.; de Haas, Petra E. W.; Heersma, Herre F.; van Soolingen, Dick

2000-01-01

Mycobacterium tuberculosis isolates with identical IS6110 restriction fragment length polymorphism (RFLP) patterns are considered to originate from the same ancestral strain and thus to reflect ongoing transmission. In this study, we investigated 1,277 IS6110 RFLP patterns for the presence of multiple low-intensity bands (LIBs), which may indicate infections with multiple M. tuberculosis strains. We did not find any multiple LIBs, suggesting that multiple infections are rare in the Netherlands. However, we did observe a few LIBs in 94 patterns (7.4%) and examined the nature of this phenomenon. With single-colony cultures it was found that LIBs mostly represent mixed bacterial populations with slightly different RFLP patterns. Mixtures were expressed in RFLP patterns as LIBs when 10 to 30% of the DNA analyzed originated from a bacterial population with another RFLP pattern. Presumably, a part of the LIBs did not represent mixed bacterial populations, as in some clusters all strains exhibited LIBs in their RFLP patterns. The occurrence of LIBs was associated with increased age in patients. This may reflect either a gradual change of the bacterial population in the human body over time or IS6110-mediated genetic adaptation of M. tuberculosis to changes in the environmental conditions during the dormant state or reactivation thereafter. PMID:11101583

DIRECT IMAGING OF THE WATER SNOW LINE AT THE TIME OF PLANET FORMATION USING TWO ALMA CONTINUUM BANDS

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

Banzatti, A.; Pontoppidan, K. M.; Pinilla, P.

2015-12-10

Molecular snow lines in protoplanetary disks have been studied theoretically for decades because of their importance in shaping planetary architectures and compositions. The water snow line lies in the planet formation region at ≲10 AU, and so far its location has been estimated only indirectly from spatially unresolved spectroscopy. This work presents a proof-of-concept method to directly image the water snow line in protoplanetary disks through its physical and chemical imprint on the local dust properties. We adopt a physical disk model that includes dust coagulation, fragmentation, drift, and a change in fragmentation velocities of a factor of 10 betweenmore » dry silicates and icy grains as found by laboratory work. We find that the presence of a water snow line leads to a sharp discontinuity in the radial profile of the dust emission spectral index α{sub mm} due to replenishment of small grains through fragmentation. We use the ALMA simulator to demonstrate that this effect can be observed in protoplanetary disks using spatially resolved ALMA images in two continuum bands. We explore the model dependence on the disk viscosity and find that the spectral index reveals the water snow line for a wide range of conditions, with opposite trends when the emission is optically thin rather than thick. If the disk viscosity is low (α{sub visc} < 10{sup −3}), the snow line produces a ringlike structure with a minimum at α{sub mm} ∼ 2 in the optically thick regime, possibly similar to what has been measured with ALMA in the innermost region of the HL Tau disk.« less

Fabrication of Ocular Protective Devices against Laser Radiation and Ballistic Fragments for Evaluation in Military Scenarios

DTIC Science & Technology

1992-09-30

19 3.4.5 High Energy Laser ..... .............. .. 20 3.4.6 Solar ..................................... 21 3.4.7 Humidity...57 4.5.6 Solar ...................................... 57 4.5.7 Humidity... . .................. ...o.. ....57 4.5.8 Temperature...coated AO-ET dye 12. Effect of solar exposure on AO-ET dyeD 13. Spectral transmittance molded B-401 dye 14. Visible transmittance of typical two

Fragmentation reduces regional-scale spatial genetic structure in a wind-pollinated tree because genetic barriers are removed.

PubMed

Wang, Rong; Compton, Stephen G; Shi, Yi-Su; Chen, Xiao-Yong

2012-09-01

Gene flow strongly influences the regional genetic structuring of plant populations. Seed and pollen dispersal patterns can respond differently to the increased isolation resulting from habitat fragmentation, with unpredictable consequences for gene flow and population structuring. In a recently fragmented landscape we compared the pre- and post-fragmentation genetic structure of populations of a tree species where pollen and seed dispersal respond differentially to forest fragmentation generated by flooding. Castanopsis sclerophylla is wind-pollinated, with seeds that are dispersed by gravity and rodents. Using microsatellites, we found no significant difference in genetic diversity between pre- and post-fragmentation cohorts. Significant genetic structure was observed in pre-fragmentation cohorts, due to an unknown genetic barrier that had isolated one small population. Among post-fragmentation cohorts this genetic barrier had disappeared and genetic structure was significantly weakened. The strengths of genetic structuring were at a similar level in both cohorts, suggesting that overall gene flow of C. sclerophylla has been unchanged by fragmentation at the regional scale. Fragmentation has blocked seed dispersal among habitats, but this appears to have been compensated for by enhanced pollen dispersal, as indicated by the disappearance of a genetic barrier, probably as a result of increased wind speeds and easier pollen movement over water. Extensive pollen flow can counteract some negative effects of fragmentation and assist the long-term persistence of small remnant populations.

Propagating annotations of molecular networks using in silico fragmentation

PubMed Central

da Silva, Ricardo R.; Wang, Mingxun; Fox, Evan; Balunas, Marcy J.; Klassen, Jonathan L.; Dorrestein, Pieter C.

2018-01-01

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp. PMID:29668671

Propagating annotations of molecular networks using in silico fragmentation.

PubMed

da Silva, Ricardo R; Wang, Mingxun; Nothias, Louis-Félix; van der Hooft, Justin J J; Caraballo-Rodríguez, Andrés Mauricio; Fox, Evan; Balunas, Marcy J; Klassen, Jonathan L; Lopes, Norberto Peporine; Dorrestein, Pieter C

2018-04-01

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.

Spectral Study of Measles Epidemics: The Dependence of Spectral Gradient on the Population Size of the Community

NASA Astrophysics Data System (ADS)

Sumi, Ayako; Olsen, Lars Folke; Ohtomo, Norio; Tanaka, Yukio; Sawamura, Sadashi

2003-02-01

We have carried out spectral analysis of measles notifications in several communities in Denmark, UK and USA. The results confirm that each power spectral density (PSD) shows exponential characteristics, which are universally observed in the PSD for time series generated from nonlinear dynamical system. The exponential gradient increases with the population size. For almost all communities, many spectral lines observed in each PSD can be fully assigned to linear combinations of several fundamental periods, suggesting that the measles data are substantially noise-free. The optimum least squares fitting curve calculated using these fundamental periods essentially reproduces an underlying variation of the measles data, and an extension of the curve can be used to predict measles epidemics. For the communities with large population sizes, some PSD patterns obtained from segment time series analysis show a close resemblance to the PSD patterns at the initial stages of a period-doubling bifurcation process for the so-called susceptible/exposed/infectious/recovered (SEIR) model with seasonal forcing. The meaning of the relationship between the exponential gradient and the population size is discussed.

A landscape ecology approach to assessing development impacts in the tropics: A geothermal energy example in Hawaii

USGS Publications Warehouse

Griffith, J.A.; Trettin, C.C.; O'Neill, R. V.

2002-01-01

Geographic information systems (GIS) are increasingly being used in environmental impact assessments (EIA) because GIS is useful for analysing spatial impacts of various development scenarios. Spatially representing these impacts provides another tool for landscape ecology in environmental and geographical investigations by facilitating analysis of the effects of landscape patterns on ecological processes and examining change over time. Landscape ecological principles are applied in this study to a hypothetical geothermal development project on the Island of Hawaii. Some common landscape pattern metrics were used to analyse dispersed versus condensed development scenarios and their effect on landscape pattern. Indices of fragmentation and patch shape did not appreciably change with additional development. The amount of forest to open edge, however, greatly increased with the dispersed development scenario. In addition, landscape metrics showed that a human disturbance had a greater simplifying effect on patch shape and also increased fragmentation than a natural disturbance. The use of these landscape pattern metrics can advance the methodology of applying GIS to EIA.

Using In Silico Fragmentation to Improve Routine Residue Screening in Complex Matrices.

PubMed

Kaufmann, Anton; Butcher, Patrick; Maden, Kathryn; Walker, Stephan; Widmer, Mirjam

2017-12-01

Targeted residue screening requires the use of reference substances in order to identify potential residues. This becomes a difficult issue when using multi-residue methods capable of analyzing several hundreds of analytes. Therefore, the capability of in silico fragmentation based on a structure database ("suspect screening") instead of physical reference substances for routine targeted residue screening was investigated. The detection of fragment ions that can be predicted or explained by in silico software was utilized to reduce the number of false positives. These "proof of principle" experiments were done with a tool that is integrated into a commercial MS vendor instrument operating software (UNIFI) as well as with a platform-independent MS tool (Mass Frontier). A total of 97 analytes belonging to different chemical families were separated by reversed phase liquid chromatography and detected in a data-independent acquisition (DIA) mode using ion mobility hyphenated with quadrupole time of flight mass spectrometry. The instrument was operated in the MS E mode with alternating low and high energy traces. The fragments observed from product ion spectra were investigated using a "chopping" bond disconnection algorithm and a rule-based algorithm. The bond disconnection algorithm clearly explained more analyte product ions and a greater percentage of the spectral abundance than the rule-based software (92 out of the 97 compounds produced ≥1 explainable fragment ions). On the other hand, tests with a complex blank matrix (bovine liver extract) indicated that the chopping algorithm reports significantly more false positive fragments than the rule based software. Graphical Abstract.

Using In Silico Fragmentation to Improve Routine Residue Screening in Complex Matrices

NASA Astrophysics Data System (ADS)

Kaufmann, Anton; Butcher, Patrick; Maden, Kathryn; Walker, Stephan; Widmer, Mirjam

2017-12-01

Targeted residue screening requires the use of reference substances in order to identify potential residues. This becomes a difficult issue when using multi-residue methods capable of analyzing several hundreds of analytes. Therefore, the capability of in silico fragmentation based on a structure database ("suspect screening") instead of physical reference substances for routine targeted residue screening was investigated. The detection of fragment ions that can be predicted or explained by in silico software was utilized to reduce the number of false positives. These "proof of principle" experiments were done with a tool that is integrated into a commercial MS vendor instrument operating software (UNIFI) as well as with a platform-independent MS tool (Mass Frontier). A total of 97 analytes belonging to different chemical families were separated by reversed phase liquid chromatography and detected in a data-independent acquisition (DIA) mode using ion mobility hyphenated with quadrupole time of flight mass spectrometry. The instrument was operated in the MSE mode with alternating low and high energy traces. The fragments observed from product ion spectra were investigated using a "chopping" bond disconnection algorithm and a rule-based algorithm. The bond disconnection algorithm clearly explained more analyte product ions and a greater percentage of the spectral abundance than the rule-based software (92 out of the 97 compounds produced ≥1 explainable fragment ions). On the other hand, tests with a complex blank matrix (bovine liver extract) indicated that the chopping algorithm reports significantly more false positive fragments than the rule based software. [Figure not available: see fulltext.

Screening of Israeli Holstein-Friesian cattle for restriction fragment length polymorphisms using homologous and heterologous deoxyribonucleic acid probes.

PubMed

Hallerman, E M; Nave, A; Soller, M; Beckmann, J S

1988-12-01

Genomic DNA of Israeli Holstein-Friesian dairy cattle were screened with a battery of 17 cloned or subcloned DNA probes in an attempt to document restriction fragment length polymorphisms at a number of genetic loci. Restriction fragment length polymorphisms were observed at the chymosin, oxytocin-neurophysin I, lutropin beta, keratin III, keratin VI, keratin VII, prolactin, and dihydrofolate reductase loci. Use of certain genomic DNA fragments as probes produced hybridization patterns indicative of satellite DNA at the respective loci. Means for distinguishing hybridizations to coding sequences for unique genes from those to satellite DNA were developed. Results of this study are discussed in terms of strategy for the systematic development of large numbers of bovine genomic polymorphisms.

Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin

NASA Astrophysics Data System (ADS)

Floris, Federico; Chiron, Lionel; Lynch, Alice M.; Barrow, Mark P.; Delsuc, Marc-André; O'Connor, Peter B.

2018-06-01

Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about 23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from 23% to 42%.

Secondary forest regeneration benefits old-growth specialist bats in a fragmented tropical landscape.

PubMed

Rocha, Ricardo; Ovaskainen, Otso; López-Baucells, Adrià; Farneda, Fábio Z; Sampaio, Erica M; Bobrowiec, Paulo E D; Cabeza, Mar; Palmeirim, Jorge M; Meyer, Christoph F J

2018-02-28

Tropical forest loss and fragmentation are due to increase in coming decades. Understanding how matrix dynamics, especially secondary forest regrowth, can lessen fragmentation impacts is key to understanding species persistence in modified landscapes. Here, we use a whole-ecosystem fragmentation experiment to investigate how bat assemblages are influenced by the regeneration of the secondary forest matrix. We surveyed bats in continuous forest, forest fragments and secondary forest matrix habitats, ~15 and ~30 years after forest clearance, to investigate temporal changes in the occupancy and abundance of old-growth specialist and habitat generalist species. The regeneration of the second growth matrix had overall positive effects on the occupancy and abundance of specialists across all sampled habitats. Conversely, effects on generalist species were negligible for forest fragments and negative for secondary forest. Our results show that the conservation potential of secondary forests for reverting faunal declines in fragmented tropical landscapes increases with secondary forest age and that old-growth specialists, which are often of most conservation concern, are the greatest beneficiaries of secondary forest maturation. Our findings emphasize that the transposition of patterns of biodiversity persistence in island ecosystems to fragmented terrestrial settings can be hampered by the dynamic nature of human-dominated landscapes.

In Silico Identification Software (ISIS): A Machine Learning Approach to Tandem Mass Spectral Identification of Lipids

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

Kangas, Lars J.; Metz, Thomas O.; Isaac, Georgis

2012-05-15

Liquid chromatography-mass spectrometry-based metabolomics has gained importance in the life sciences, yet it is not supported by software tools for high throughput identification of metabolites based on their fragmentation spectra. An algorithm (ISIS: in silico identification software) and its implementation are presented and show great promise in generating in silico spectra of lipids for the purpose of structural identification. Instead of using chemical reaction rate equations or rules-based fragmentation libraries, the algorithm uses machine learning to find accurate bond cleavage rates in a mass spectrometer employing collision-induced dissocia-tion tandem mass spectrometry. A preliminary test of the algorithm with 45 lipidsmore » from a subset of lipid classes shows both high sensitivity and specificity.« less

Products and yields from O3 photodissociation at 1576 A

NASA Technical Reports Server (NTRS)

Taherian, M. R.; Slanger, T. G.

1985-01-01

An analysis has been made of the primary atomic and molecular products arising from O3 photodissociation at 1576 A. The yield of oxygen atoms is 1.90 + or - 0.30, of which 71 percent are O(3P) and 29 percent are O(1D). Since a primary yield greater than unity can only be a consequence of three-fragment dissociation, these results suggest that fragmentation into three O(3P) atoms, and production of O(1D) plus a singlet oxygen molecule, have comparable yields. Observation of prompt emission in the 7300-8100 A spectral region indicates that the singlet O2 is O2(b 1Sigma + g). Vibrational levels in the range v = 0-6 have been detected, the distribution corresponding to a vibrational temperature of 1000 K.

Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy.

PubMed

Quinn, Robert A; Nothias, Louis-Felix; Vining, Oliver; Meehan, Michael; Esquenazi, Eduardo; Dorrestein, Pieter C

2017-02-01

Molecular networking is a tandem mass spectrometry (MS/MS) data organizational approach that has been recently introduced in the drug discovery, metabolomics, and medical fields. The chemistry of molecules dictates how they will be fragmented by MS/MS in the gas phase and, therefore, two related molecules are likely to display similar fragment ion spectra. Molecular networking organizes the MS/MS data as a relational spectral network thereby mapping the chemistry that was detected in an MS/MS-based metabolomics experiment. Although the wider utility of molecular networking is just beginning to be recognized, in this review we highlight the principles behind molecular networking and its use for the discovery of therapeutic leads, monitoring drug metabolism, clinical diagnostics, and emerging applications in precision medicine. Copyright © 2016. Published by Elsevier Ltd.

Mass Spectrometric Identification of Si-O-H(g) Species from the Reaction of Silica with Water Vapor at Atmospheric Pressure

NASA Technical Reports Server (NTRS)

Opila, Elizabeth J.; Fox, Dennis S.; Jacobson, Nathan S.

1997-01-01

A high-pressure sampling mass spectrometer was used to detect the volatile species formed from SiO2 at temperatures between 1200C and 1400C in a flowing water vapor/oxygen gas mixture at 1 bar total pressure. The primary vapor species identified was Si(OH)4. The fragment ion Si(OH)3+,' was observed in quantities 3 to 5 times larger than the parent ion Si(OH)4+. The Si(OH)3+ intensity was found to have a small temperature dependence and to increase with the water vapor partial pressure as expected. In addition, SiO(OH)+ believed to be a fragment of SiO(OH)2, was observed. These mass spectral results were compared to the behavior of silicon halides.

Development and application of the maximum entropy method and other spectral estimation techniques

NASA Astrophysics Data System (ADS)

King, W. R.

1980-09-01

This summary report is a collection of four separate progress reports prepared under three contracts, which are all sponsored by the Office of Naval Research in Arlington, Virginia. This report contains the results of investigations into the application of the maximum entropy method (MEM), a high resolution, frequency and wavenumber estimation technique. The report also contains a description of two, new, stable, high resolution spectral estimation techniques that is provided in the final report section. Many examples of wavenumber spectral patterns for all investigated techniques are included throughout the report. The maximum entropy method is also known as the maximum entropy spectral analysis (MESA) technique, and both names are used in the report. Many MEM wavenumber spectral patterns are demonstrated using both simulated and measured radar signal and noise data. Methods for obtaining stable MEM wavenumber spectra are discussed, broadband signal detection using the MEM prediction error transform (PET) is discussed, and Doppler radar narrowband signal detection is demonstrated using the MEM technique. It is also shown that MEM cannot be applied to randomly sampled data. The two new, stable, high resolution, spectral estimation techniques discussed in the final report section, are named the Wiener-King and the Fourier spectral estimation techniques. The two new techniques have a similar derivation based upon the Wiener prediction filter, but the two techniques are otherwise quite different. Further development of the techniques and measurement of the technique spectral characteristics is recommended for subsequent investigation.

An explorative chemometric approach applied to hyperspectral images for the study of illuminated manuscripts

NASA Astrophysics Data System (ADS)

Catelli, Emilio; Randeberg, Lise Lyngsnes; Alsberg, Bjørn Kåre; Gebremariam, Kidane Fanta; Bracci, Silvano

2017-04-01

Hyperspectral imaging (HSI) is a fast non-invasive imaging technology recently applied in the field of art conservation. With the help of chemometrics, important information about the spectral properties and spatial distribution of pigments can be extracted from HSI data. With the intent of expanding the applications of chemometrics to the interpretation of hyperspectral images of historical documents, and, at the same time, to study the colorants and their spatial distribution on ancient illuminated manuscripts, an explorative chemometric approach is here presented. The method makes use of chemometric tools for spectral de-noising (minimum noise fraction (MNF)) and image analysis (multivariate image analysis (MIA) and iterative key set factor analysis (IKSFA)/spectral angle mapper (SAM)) which have given an efficient separation, classification and mapping of colorants from visible-near-infrared (VNIR) hyperspectral images of an ancient illuminated fragment. The identification of colorants was achieved by extracting and interpreting the VNIR spectra as well as by using a portable X-ray fluorescence (XRF) spectrometer.

Characterizing Vaccinium berry Standard Reference Materials by GC-MS using NIST spectral libraries.

PubMed

Lowenthal, Mark S; Andriamaharavo, Nirina R; Stein, Stephen E; Phinney, Karen W

2013-05-01

A gas chromatography-mass spectrometry (GC-MS)-based method was developed for qualitative characterization of metabolites found in Vaccinium fruit (berry) dietary supplement Standard Reference Materials (SRMs). Definitive identifications are provided for 98 unique metabolites determined among six Vaccinium-related SRMs. Metabolites were enriched using an organic liquid/liquid extraction, and derivatized prior to GC-MS analysis. Electron ionization (EI) fragmentation spectra were searched against EI spectra of authentic standards compiled in the National Institute of Standards and Technology's mass spectral libraries, as well as spectra selected from the literature. Metabolite identifications were further validated using a retention index match along with prior probabilities and were compared with results obtained in a previous effort using collision-induced dissociation (CID) MS/MS datasets from liquid chromatography coupled to mass spectrometry experiments. This manuscript describes a nontargeted metabolite profile of Vaccinium materials, compares results among related materials and from orthogonal experimental platforms, and discusses the feasibility and development of using mass spectral library matching for nontargeted metabolite identification.

Rural and suburban sprawl in the U.S. midwest from 1940 to 2000 in its relation to forest fragmentation

Treesearch

Volker C. Radeloff; Roger B. Hammer; Susan I. Stewart

2005-01-01

Housing growth and its environmental effects pose major conservation challenges. We sought to (]) quantify spatial and temporal patterns of housing growth across the US. Midwest from 1940-2000, (2) identify ecoregions strongly affected by housing growth, (3) assess the extent to which forests occur near housing, and (4) relate housing to forest fragmentation. We used...

Statistics of the radiated field of a space-to-earth microwave power transfer system

NASA Technical Reports Server (NTRS)

Stevens, G. H.; Leininger, G.

1976-01-01

Statistics such as average power density pattern, variance of the power density pattern and variance of the beam pointing error are related to hardware parameters such as transmitter rms phase error and rms amplitude error. Also a limitation on spectral width of the phase reference for phase control was established. A 1 km diameter transmitter appears feasible provided the total rms insertion phase errors of the phase control modules does not exceed 10 deg, amplitude errors do not exceed 10% rms, and the phase reference spectral width does not exceed approximately 3 kHz. With these conditions the expected radiation pattern is virtually the same as the error free pattern, and the rms beam pointing error would be insignificant (approximately 10 meters).

Identification of Organics in Ice Grains from Enceladus

NASA Astrophysics Data System (ADS)

Khawaja, N.; Postberg, F.; Reviol, R.; Nölle, L.; Klenner, F.; Srama, R.

2015-12-01

The Cosmic Dust Analyzer (CDA) aboard the Cassini spacecraft performs in-situ measurements of the chemical composition of icy dust grains impinging onto the target surface. The instrument recorded cationic Time-of-Flight (ToF) mass spectra of organic-bearing ice grains emitted from Enceladus at different impact velocities causing different molecular fragmentation patterns [1,2]. Here we present a detailed analysis of these spectra (Type-2) to identify the composition of organic material embedded in Enceladus ice grains. The organic compounds display a great compositional diversity, which indicates varying contributions of several organic species. The spectra analysis is supported by a large-scale laboratory ground campaign yielding a library of analogue spectra for organic material embedded in a water ice matrix. To mimic the identified pattern of cationic fragments in organic enriched spectra we use a laboratory setup: Infrared Free Liquid MALDI ToF Mass Spectrometer (IR-FL-MALDI-ToF-MS). An infrared laser is used to disperse a liquid micro-beam of a water-solution to get cationic fragments. The laser energy is adjusted to simulate different impact velocities of ice particles on CDA [3]. So far we have identified characteristic fragment patterns of at least three classes of organic molecules: (i) aromatic species, (ii) amines, and (iii) carbonyl group species. (i) ice grains containing aromatic species are identified by a series of characteristic aromatic fragment cations (ii) ice grains containing amines are identified by a pronounced ammonium cation and (iii) ice grains containing carbonyl compounds are specified by a characteristic acylium cation in conjunction with certain others mass lines. Besides aromatic, amine and carbonyl species, Type-2 spectra also show contributions from other, yet un-specified, organic species. Typically, fragment cations of aromatic compounds are stable at impact velocities up-to 15km/s whereas cations of amines and carbonyl species are stable at velocities below 8km/s. Work is in progress to quantify concentrations of the identified species and to assign yet un-specified organic mass lines in Type 2 spectra. Ref: [1]Postberg et al., Icarus-193,2008. [2]Postberg et al., Nature-459,2009. [3]Beinsen, A., University of Göttingen, Dissertation (2011).

Biophotonic patterns of optical interactions between fish eggs and embryos.

PubMed

Beloussov, L V; Burlakov, A B; Louchinskaia, N N

2003-05-01

The optical (non-substantial) interactions between various biological samples have been evident in a number of cases mainly by the effects on their functional activity and developmental patterns. However, the mechanisms of these interactions have remained obscure. Effect of optical interaction has been observed on the intensity and Fourier patterns of biophoton emission of fish embryos. We demonstrate that: (1) the short-term optical interactions are accompanied by a gradual decrease of a total emission intensity of the interacting batches; (2) this effect is spread laterally to that part of a batch which does not have any direct optical contacts with its partner; and (3) the long-term optical contacts lead to a mutual exchange of spectral characteristics of interacting batches in which the total spectral density values are reversed (often with an overshoot). The reversal rate depends upon the developmental distance between the optical partners and the initial differences of their spectral characteristics. The results are discussed in terms of a sub-radiance and Le Chatelier principle.

Effects of spectral and temporal disruption on cortical encoding of gerbil vocalizations

PubMed Central

Ter-Mikaelian, Maria; Semple, Malcolm N.

2013-01-01

Animal communication sounds contain spectrotemporal fluctuations that provide powerful cues for detection and discrimination. Human perception of speech is influenced both by spectral and temporal acoustic features but is most critically dependent on envelope information. To investigate the neural coding principles underlying the perception of communication sounds, we explored the effect of disrupting the spectral or temporal content of five different gerbil call types on neural responses in the awake gerbil's primary auditory cortex (AI). The vocalizations were impoverished spectrally by reduction to 4 or 16 channels of band-passed noise. For this acoustic manipulation, an average firing rate of the neuron did not carry sufficient information to distinguish between call types. In contrast, the discharge patterns of individual AI neurons reliably categorized vocalizations composed of only four spectral bands with the appropriate natural token. The pooled responses of small populations of AI cells classified spectrally disrupted and natural calls with an accuracy that paralleled human performance on an analogous speech task. To assess whether discharge pattern was robust to temporal perturbations of an individual call, vocalizations were disrupted by time-reversing segments of variable duration. For this acoustic manipulation, cortical neurons were relatively insensitive to short reversal lengths. Consistent with human perception of speech, these results indicate that the stable representation of communication sounds in AI is more dependent on sensitivity to slow temporal envelopes than on spectral detail. PMID:23761696

Changes of multispectral soil patterns with increasing crop canopy

NASA Technical Reports Server (NTRS)

Kristof, S. J.; Baumgardner, M. F.

1972-01-01

Multispectral data and automatic data processing were used to map surface soil patterns and to follow the changes in multispectral radiation from a field of maize (Zea mays L.) during a period from seeding to maturity. Panchromatic aerial photography was obtained in early May 1970 and multispectral scanner missions were flown on May 6, June 30, August 11 and September 5, 1970 to obtain energy measurements in 13 wavelength bands. The orange portion of the visible spectrum was used in analyzing the May and June data to cluster relative radiance of the soils into eight different radiance levels. The reflective infrared spectral band was used in analyzing the August and September data to cluster maize into different spectral categories. The computer-produced soil patterns had a striking similarity to the soil pattern of the aerial photograph. These patterns became less distinct as the maize canopy increased.

Mixed Pattern Matching-Based Traffic Abnormal Behavior Recognition

PubMed Central

Cui, Zhiming; Zhao, Pengpeng

2014-01-01

A motion trajectory is an intuitive representation form in time-space domain for a micromotion behavior of moving target. Trajectory analysis is an important approach to recognize abnormal behaviors of moving targets. Against the complexity of vehicle trajectories, this paper first proposed a trajectory pattern learning method based on dynamic time warping (DTW) and spectral clustering. It introduced the DTW distance to measure the distances between vehicle trajectories and determined the number of clusters automatically by a spectral clustering algorithm based on the distance matrix. Then, it clusters sample data points into different clusters. After the spatial patterns and direction patterns learned from the clusters, a recognition method for detecting vehicle abnormal behaviors based on mixed pattern matching was proposed. The experimental results show that the proposed technical scheme can recognize main types of traffic abnormal behaviors effectively and has good robustness. The real-world application verified its feasibility and the validity. PMID:24605045

Investigation of multimodal forward scatter phenotyping from bacterial colonies

NASA Astrophysics Data System (ADS)

Kim, Huisung

A rapid, label-free, and elastic light scattering (ELS) based bacterial colony phenotyping technology, bacterial rapid detection using optical scattering technology (BARDOT) provides a successful classification of several bacterial genus and species. For a thorough understanding of the phenomena and overcoming the limitations of the previous design, five additional modalities from a bacterial colony: 3D morphology, spatial optical density (OD) distribution, spectral forward scattering pattern, spectral OD, and surface backward reflection pattern are proposed to enhance the classification/identification ratio, and the feasibilities of each modality are verified. For the verification, three different instruments: integrated colony morphology analyzer (ICMA), multi-spectral BARDOT (MS-BARDOT) , and multi-modal BARDOT (MM-BARDOT) are proposed and developed. The ICMA can measure 3D morphology and spatial OD distribution of the colony simultaneously. A commercialized confocal displacement meter is used to measure the profiles of the bacterial colonies, together with a custom built optical density measurement unit to interrogate the biophysics behind the collective behavior of a bacterial colony. The system delivers essential information related to the quantitative growth dynamics (height, diameter, aspect ratio, optical density) of the bacterial colony, as well as, a relationship in between the morphological characteristics of the bacterial colony and its forward scattering pattern. Two different genera: Escherichia coli O157:H7 EDL933, and Staphylococcus aureus ATCC 25923 are selected for the analysis of the spatially resolved growth dynamics, while, Bacillus spp. such as B. subtilis ATCC 6633, B. cereus ATCC 14579, B. thuringiensis DUP6044, B. polymyxa B719W, and B. megaterium DSP 81319, are interrogated since some of the Bacillus spp. provides strikingly different characteristics of ELS patterns, and the origin of the speckle patterns are successfully correlated with the 2-D spatial density map from the ICMA. The MS-BARDOT can measure multispectral elastic-light-scatter patterns of the bacterial colony and its spectral OD to overcome the inherent limits of the single-wavelength BARDOT. A theoretical model for spectral forward scatter patterns from a bacterial colony based on elastic light scatter is presented. The spectral forward scatter patterns are computed by scalar diffraction theory, and compared with experimental results of three discrete wavelengths (405 nm, 635 nm, and 904 nm). Both model and experiment results show an excellent agreement; a longer wavelength induces a wider ring width, a wider ring gap, a smaller pattern size, and smaller numbers of rings. Further analysis using spatial fast Fourier transform (SFFT) shows a good agreement; the spatial frequencies are increasing towards the inward direction, and the slope is inversely proportional to the incoming wavelength. Four major pathogenic bacterial genera (Escherichia coli O157:H7 EDL933, Listeria monocytogenes F4244, Salmonella enterica serovar Enteritidis PT21, and Staphylococcus aureus ATCC 25923) and the seven major Escherichia coli serovar (O26, O45, O103, O111, O121, O145, and O157) with 3-4 strains each are measured and analyzed with the proposed instrument and algorithm. The MM-BARDOT can measure six different modalities: 1) light microscopy, 2) 3D morphology map from confocal microscopy, 3) 3D optical density map, 4) spectral forward scattering pattern, 5) spectral OD, 6) surface backward reflection pattern, and 7) fluorescence of a bacterial colony without moving the specimen. A custom-built confocal microscope with a controller which can be easily attached to an infinity-corrected commercial microscope is designed and built. Since the current BARDOT needs additional information from a bacterial colony to enhance the identification/classification ratio for a lower hierarchy of bacterial taxonomy such as serovar or strain level, the approach can offer a series of coordinates matched and correlated bio-optical characteristics of a colony and enhance the classification accuracy of the previously introduced BARDOT system. Four major pathogenic bacterial genera: Escherichia coli O157:H7 EDL933, Listeria monocytogenes F4244, Salmonella enterica serovar Enteritidis PT21, and Staphylococcus aureus ATCC 25923 are measured and analyzed with the proposed instrument and algorithm. Also, a feasibility test for a smaller colony (up to 500 mum) classification utilizing a surface backward reflection pattern from the measurement is done, and shows a potential as an additional modality for the bacterial phenotyping.

CHARACTERIZATION OF CRYPTOSPORIDIUM PARVUM BY MATRIX-ASSISTED LASER DESORPTION -- IONIZATION TIME OF FLIGHT MASS SPECTROMETRY

EPA Science Inventory

Matrix assisted laser desorption/ionization (MALDI) mass spectrometry was used to investigate whole and freeze thawed Cryptosporidium parvum oocysts. Whole oocysts revealed some mass spectral features. Reproducible patterns of spectral markers and increased sensitivity were obtai...

Factors Related to Spatial Patterns of Rural Land Fragmentation in Texas

NASA Astrophysics Data System (ADS)

Kjelland, Michael E.; Kreuter, Urs P.; Clendenin, George A.; Wilkins, R. Neal; Wu, X. Ben; Afanador, Edith Gonzalez; Grant, William E.

2007-08-01

Fragmentation of family-owned farms and ranches has been identified as the greatest single threat to wildlife habitat, water supply, and the long-term viability of agriculture in Texas. However, an integrative framework for insights into the pathways of land use change has been lacking. The specific objectives of the study are to test the hypotheses that the nonagricultural value (NAV) of rural land is a reliable indicator of trends in land fragmentation and that NAV in Texas is spatially correlated with population density, and to explore the idea that recent changes in property size patterns are better represented by a categorical model than by one that reflects incremental changes. We propose that the State-and-Transition model, developed to describe the dynamics of semi-arid ecosystems, provides an appropriate conceptual framework for characterizing categorical shifts in rural property patterns. Results suggest that changes in population density are spatially correlated with NAV and farm size, and that rural property size is spatially correlated with changes in NAV. With increasing NAV, the proportion of large properties tends to decrease while the area represented by small properties tends to increase. Although a correlation exists between NAV and population density, it is the trend in NAV that appears to be a stronger predictor of land fragmentation. The empirical relationships established herein, viewed within the conceptual framework of the State-and-Transition model, can provide a useful tool for evaluating land use policies for maintaining critical ecosystem services delivered from privately owned land in private land states, such as Texas.

Home range use and survival of southern flying squirrels in fragmented forest landscapes

USGS Publications Warehouse

Jacques, Christopher N.; Zweep, James S.; Jenkins, Sean E.; Klaver, Robert W.

2017-01-01

We studied home range use, spatial activity patterns, and annual survival of southern flying squirrels (SFS; Glaucomys volans) across fragmented landscapes of west-central Illinois. We calculated seasonal home range sizes and annual survival from 67 animals (36 males, 31 females) captured during 2014–2016. Home range and core area sizes were similar (P ≥ 0.46) among males and females across summer (April–September) and winter (October–March) seasons. Average distance between consecutive animal locations did not vary by sex, season, or year. Similarly, cumulative distance between consecutive locations did not vary by sex, season, or year and ranged from 1,189 to 1,661 m between summer and winter seasons. Mean annual composite home range and core area sizes were 10.39 and 1.25 ha, respectively; estimated home ranges (10.3 ha) of females are the largest documented for this species. We documented 8 deaths, all attributed to predation, the majority (63%) of which occurred during winter; annual survival was 71%. Our results underscore effects of habitat productivity on seasonal home range dynamics and space use patterns of SFS in fragmented landscapes. SFS may compensate for reduced availability of overstory mast-producing trees that characterize unproductive habitats and low-density populations by exhibiting similar movement patterns and use of available habitat by both sexes throughout the year. Winter communal nesting appears to be influenced by availability of cavity trees, thereby confirming the importance of standing snags in contributing essential habitat to flying squirrel populations in fragmented forests.

Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond

NASA Astrophysics Data System (ADS)

Rožman, Marko

2016-01-01

Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

GC-MS and GC-IRD studies on the ring isomers of N-methyl-2-methoxyphenyl-3-butanamines (MPBA) related to 3,4-MDMA.

PubMed

Awad, Tamer; Maher, Hadir M; DeRuiter, Jack; Clark, C Randall

2011-05-01

The mass spectra of the controlled substance 3,4-MDMA and its regioisomer 2,3-MDMA are characterized by an imine fragment base peak at m/z 58 and additional fragments at m/z 135/136 for the methylenedioxybenzyl cation and radical cation, respectively. Three positional ring methoxy isomers of N-methyl-2-(methoxyphenyl)-3-butanamine (MPBA) have an isobaric relationship to 2,3- and 3,4-MDMA. All five compounds have the same molecular weight and produce similar EI mass spectra. This lack of mass spectral specificity for the isomers in addition to the possibility of chromatographic co-elution could result in misidentification. The lack of reference materials for the potential imposter molecules constitutes a significant analytical challenge. Perfluoroacylation of the amine group reduced the nitrogen basicity and provided individual fragmentation pathways for discrimination among these compounds based on unique fragment ions and the relative abundance of common ions. Studies using gas chromatography with infrared detection provided additional structure-IR spectra relationships. The underivatized amines and the perfluoroacylated derivatives (PFPA and HFBA) were resolved by capillary gas chromatography on a 100% dimethylpolysiloxane stationary phase. The perfluoroacylated derivatives showed better resolution on a cyclodextrin modified stationary phase.

Reduced Genetic Diversity and Increased Dispersal in Guigna (Leopardus guigna) in Chilean Fragmented Landscapes.

PubMed

Napolitano, Constanza; Díaz, Diego; Sanderson, Jim; Johnson, Warren E; Ritland, Kermit; Ritland, Carol E; Poulin, Elie

2015-01-01

Landscape fragmentation is often a major cause of species extinction as it can affect a wide variety of ecological processes. The impact of fragmentation varies among species depending on many factors, including their life-history traits and dispersal abilities. Felids are one of the groups most threatened by fragmented landscapes because of their large home ranges, territorial behavior, and low population densities. Here, we model the impacts of habitat fragmentation on patterns of genetic diversity in the guigna (Leopardus guigna), a small felid that is closely associated with the heavily human-impacted temperate rainforests of southern South America. We assessed genetic variation in 1798 base pairs of mitochondrial DNA sequences, 15 microsatellite loci, and 2 sex chromosome genes and estimated genetic diversity, kinship, inbreeding, and dispersal in 38 individuals from landscapes with differing degrees of fragmentation on Chiloé Island in southern Chile. Increased fragmentation was associated with reduced genetic diversity, but not with increased kinship or inbreeding. However, in fragmented landscapes, there was a weaker negative correlation between pairwise kinship and geographic distance, suggesting increased dispersal distances. These results highlight the importance of biological corridors to maximize connectivity in fragmented landscapes and contribute to our understanding of the broader genetic consequences of habitat fragmentation, especially for forest-specialist carnivores. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A narrow band pattern-matching model of vowel perception

NASA Astrophysics Data System (ADS)

Hillenbrand, James M.; Houde, Robert A.

2003-02-01

The purpose of this paper is to propose and evaluate a new model of vowel perception which assumes that vowel identity is recognized by a template-matching process involving the comparison of narrow band input spectra with a set of smoothed spectral-shape templates that are learned through ordinary exposure to speech. In the present simulation of this process, the input spectra are computed over a sufficiently long window to resolve individual harmonics of voiced speech. Prior to template creation and pattern matching, the narrow band spectra are amplitude equalized by a spectrum-level normalization process, and the information-bearing spectral peaks are enhanced by a ``flooring'' procedure that zeroes out spectral values below a threshold function consisting of a center-weighted running average of spectral amplitudes. Templates for each vowel category are created simply by averaging the narrow band spectra of like vowels spoken by a panel of talkers. In the present implementation, separate templates are used for men, women, and children. The pattern matching is implemented with a simple city-block distance measure given by the sum of the channel-by-channel differences between the narrow band input spectrum (level-equalized and floored) and each vowel template. Spectral movement is taken into account by computing the distance measure at several points throughout the course of the vowel. The input spectrum is assigned to the vowel template that results in the smallest difference accumulated over the sequence of spectral slices. The model was evaluated using a large database consisting of 12 vowels in /hVd/ context spoken by 45 men, 48 women, and 46 children. The narrow band model classified vowels in this database with a degree of accuracy (91.4%) approaching that of human listeners.

Mitochondrial DNA pattern of the fine shrimp Metapenaeus elegans (De Man, 1907) in the lagoon of Segara Anakan, Central Java, using Hind III

NASA Astrophysics Data System (ADS)

Nugraha, Fitra Arya Dwi; Holil, Kholifah; Kurniawan, Nia

2017-05-01

Ecological damages to the Lagoon of Segara Anakan, Central Java, as well as large-scale and continuous exploitation are threatening the sustainability of fine shrimp, Metapenaeus elegans, and resources. Information in regards to genetic resources is crucial to establish long-term conservation programs and to preserve germplasm quality. This study aims to evaluate the number and size of the fragment which is digested with restriction enzyme Hind III. Seven individuals of Metapenaeus elegans from the Lagoon of Segara Anakan were examined using Hind III. Amplification of mitochondrial DNA resulted in 950 bp, and the digestion using Hind III generated four fragments consisting of 114 bp, 200 bp, 250 bp, and 386 bp, which formed a monomorphic pattern. The restriction pattern showed the probability of homozygosity of alleles that restricted using Hind III. Homozygosity indicates no variation of DNA sequence.

Mycobacterium avium restriction fragment length polymorphism-IS IS1245 and the simple double repetitive element polymerase chain reaction typing method to screen genetic diversity in Brazilian strains.

PubMed

Sequeira, Patrícia Carvalho de; Fonseca, Leila de Souza; Silva, Marlei Gomes da; Saad, Maria Helena Féres

2005-11-01

Simple double repetitive element polymerase chain reaction (MaDRE-PCR) and Pvu II-IS1245 restriction fragment length polymorphism (RFLP) typing methods were used to type 41 Mycobacterium avium isolates obtained from 14 AIDS inpatients and 10 environment and animals specimens identified among 53 mycobacteria isolated from 237 food, chicken, and pig. All environmental and animals strains showed orphan patterns by both methods. By MaDRE-PCR four patients, with multiple isolates, showed different patterns, suggesting polyclonal infection that was confirmed by RFLP in two of them. This first evaluation of MaDRE-PCR on Brazilian M. avium strains demonstrated that the method seems to be useful as simple and less expensive typing method for screening genetic diversity in M. avium strains on selected epidemiological studies, although with limitation on analysis identical patterns except for one band.

Advances in structure elucidation of small molecules using mass spectrometry

PubMed Central

Fiehn, Oliver

2010-01-01

The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. Electronic supplementary material The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users. PMID:21289855

Pattern recognition in volcano seismology - Reducing spectral dimensionality

NASA Astrophysics Data System (ADS)

Unglert, K.; Radic, V.; Jellinek, M.

2015-12-01

Variations in the spectral content of volcano seismicity can relate to changes in volcanic activity. Low-frequency seismic signals often precede or accompany volcanic eruptions. However, they are commonly manually identified in spectra or spectrograms, and their definition in spectral space differs from one volcanic setting to the next. Increasingly long time series of monitoring data at volcano observatories require automated tools to facilitate rapid processing and aid with pattern identification related to impending eruptions. Furthermore, knowledge transfer between volcanic settings is difficult if the methods to identify and analyze the characteristics of seismic signals differ. To address these challenges we evaluate whether a machine learning technique called Self-Organizing Maps (SOMs) can be used to characterize the dominant spectral components of volcano seismicity without the need for any a priori knowledge of different signal classes. This could reduce the dimensions of the spectral space typically analyzed by orders of magnitude, and enable rapid processing and visualization. Preliminary results suggest that the temporal evolution of volcano seismicity at Kilauea Volcano, Hawai`i, can be reduced to as few as 2 spectral components by using a combination of SOMs and cluster analysis. We will further refine our methodology with several datasets from Hawai`i and Alaska, among others, and compare it to other techniques.

Monitoring Urban Greenness Dynamics Using Multiple Endmember Spectral Mixture Analysis

PubMed Central

Gan, Muye; Deng, Jinsong; Zheng, Xinyu; Hong, Yang; Wang, Ke

2014-01-01

Urban greenness is increasingly recognized as an essential constituent of the urban environment and can provide a range of services and enhance residents’ quality of life. Understanding the pattern of urban greenness and exploring its spatiotemporal dynamics would contribute valuable information for urban planning. In this paper, we investigated the pattern of urban greenness in Hangzhou, China, over the past two decades using time series Landsat-5 TM data obtained in 1990, 2002, and 2010. Multiple endmember spectral mixture analysis was used to derive vegetation cover fractions at the subpixel level. An RGB-vegetation fraction model, change intensity analysis and the concentric technique were integrated to reveal the detailed, spatial characteristics and the overall pattern of change in the vegetation cover fraction. Our results demonstrated the ability of multiple endmember spectral mixture analysis to accurately model the vegetation cover fraction in pixels despite the complex spectral confusion of different land cover types. The integration of multiple techniques revealed various changing patterns in urban greenness in this region. The overall vegetation cover has exhibited a drastic decrease over the past two decades, while no significant change occurred in the scenic spots that were studied. Meanwhile, a remarkable recovery of greenness was observed in the existing urban area. The increasing coverage of small green patches has played a vital role in the recovery of urban greenness. These changing patterns were more obvious during the period from 2002 to 2010 than from 1990 to 2002, and they revealed the combined effects of rapid urbanization and greening policies. This work demonstrates the usefulness of time series of vegetation cover fractions for conducting accurate and in-depth studies of the long-term trajectories of urban greenness to obtain meaningful information for sustainable urban development. PMID:25375176

Identification of Eight Synthetic Cannabinoids, Including 5F-AKB48 in Seized Herbal Products Using DART-TOF-MS and LC-QTOF-MS as Nontargeted Screening Methods.

PubMed

Moore, Katherine N; Garvin, Demetra; Thomas, Brian F; Grabenauer, Megan

2017-09-01

Synthetic cannabinoids are sprayed onto plant material and smoked for their marijuana-like effects. Clandestine manufacturers modify synthetic cannabinoid structures by creating closely related analogs. Forensic laboratories are tasked with detection of these analog compounds, but targeted analytical methods are often thwarted by the structural modifications. Here, direct analysis in real time coupled to accurate mass time-of-flight mass spectrometry (DART-TOF-MS) in combination with liquid chromatography quadruple time-of-flight mass spectrometry (LC-QTOF-MS) are presented as a screening and nontargeted confirmation method, respectively. Methanol extracts of herbal material were run using both methods. Spectral data from four different herbal products were evaluated by comparing fragmentation pattern, accurate mass and retention time to available reference standards. JWH-018, JWH-019, AM2201, JWH-122, 5F-AKB48, AKB48-N-(4-pentenyl) analog, UR144, and XLR11 were identified in the products. Results demonstrate that DART-TOF-MS affords a useful approach for rapid screening of herbal products for the presence and identification of synthetic cannabinoids. © 2017 American Academy of Forensic Sciences.

Identification of new phytoconstituents and antimicrobial activity in stem bark of Mangifera indica (L.).

PubMed

Singh, Ruchi; Singh, S K; Maharia, R S; Garg, A N

2015-02-01

Mangifera indica, commonly called mango or amra belonging to a family of Anacardiaceae, is an important medicinal plant widely used in a variety of Ayurvedic preparations. Extract of its bark, leaves, flowers and kernels are being extensively used for curing various chronic diseases. Mango wood is used in yagya as base fire through which medicated smoke is generated. Three new compounds have been isolated from methanolic and hexane extracts of stem bark: 1,2-benzenedicarboxylic acid, mono(2-ethylhexyl)ester and 9,12-tetradecadiene-1-ol-acetate from the hexane extract and 3-chloro-N-(2-phenylethyl) propanamide from the methanolic extract. These were first separated by thin layer chromatography and later in a silica gel column and identified by characteristic infrared bands corresponding to respective functional groups. The compounds were further confirmed on the basis of GC-MS fragmentation pattern after comparing the data with NIST mass spectral database. All three compounds exhibited antimicrobial activity due to triterpenoids and flavonoids. Elemental analyses by INAA show it to be enriched in essential nutrient elements such as Ca, Fe, K, Mn and Zn which all play an important role in enzymatic processes. Copyright © 2014 Elsevier B.V. All rights reserved.

Screening of environmental contaminants in honey bee wax comb using gas chromatography-high-resolution time-of-flight mass spectrometry.

PubMed

Gómez-Ramos, M M; García-Valcárcel, A I; Tadeo, J L; Fernández-Alba, A R; Hernando, M D

2016-03-01

This study reports an analytical approach intended to be used for investigation of non-targeted environmental contaminants and to characterize the organic pollution pattern of bee wax comb samples. The method comprises a generic extraction followed by detection with gas chromatography coupled to high-resolution time-of-flight mass spectrometry (GC-TOF-MS), operated in electron impact ionization (EI) mode. The screening approach for the investigation of non-targeted contaminants consisted of initial peak detection by deconvolution and matching the first-stage mass spectra EI-MS(1) with a nominal mass spectral library. To gain further confidence in the structural characterization of the contaminants under investigation, the molecular formula of representative ions (molecular ion when present in the EI spectrum) and, for at least other two fragment ions, was provided for those with an accurate mass scoring (mass error < 5 ppm). This methodology was applied for screening environmental contaminants in 50 samples of bee wax comb. This approach has allowed the tentative identification of some GC-amenable contaminants belonging to different chemical groups, among them, phthalates and polycyclic aromatic hydrocarbons (PAHs), along with residues of veterinary treatments used in apiculture.

Correlation of MFOLD-predicted DNA secondary structures with separation patterns obtained by capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis.

PubMed

Glavac, Damjan; Potocnik, Uros; Podpecnik, Darja; Zizek, Teofil; Smerkolj, Sava; Ravnik-Glavac, Metka

2002-04-01

We have studied 57 different mutations within three beta-globin gene promoter fragments with sizes 52 bp, 77 bp, and 193 bp by fluorescent capillary electrophoresis CE-SSCP analysis. For each mutation and wild type, energetically most-favorable predicted secondary structures were calculated for sense and antisense strands using the MFOLD DNA-folding algorithm in order to investigate if any correlation exists between predicted DNA structures and actual CE migration time shifts. The overall CE-SSCP detection rate was 100% for all mutations in three studied DNA fragments. For shorter 52 bp and 77 bp DNA fragments we obtained a positive correlation between the migration time shifts and difference in free energy values of predicted secondary structures at all temperatures. For longer 193 bp beta-globin gene fragments with 46 mutations MFOLD predicted different secondary structures for 89% of mutated strands at 25 degrees C and 40 degrees C. However, the magnitude of the mobility shifts did not necessarily correlate with their secondary structures and free energy values except for the sense strand at 40 degrees C where this correlation was statistically significant (r = 0.312, p = 0.033). Results of this study provided more direct insight into the mechanism of CE-SSCP and showed that MFOLD prediction could be helpful in making decisions about the running temperatures and in prediction of CE-SSCP data patterns, especially for shorter (50-100 bp) DNA fragments. Copyright 2002 Wiley-Liss, Inc.

Identification of polycomb and trithorax group responsive elements in the regulatory region of the Drosophila homeotic gene Sex combs reduced

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

Gindhart, J.G. Jr.; Kaufman, T.C.

1995-02-01

The Drosophilia homeotic gene Sex combs reduced (Scr) is necessary for the establishment and maintenance of the morphological identity of the labial and prothoracic segments. In the early embryo, its expression pattern is established through the activity of several gap and segmentation gene products, as well as other transcription factors. Once established, the Polycomb group (Pc-G) and trithorax group (trx-G) gene products maintain the spatial pattern of Scr expression for the remainder of development. We report the identification of DNA fragments in the Scr regulatory region that may be important for its regulation by Polycomb and trithorax group gene products.more » When DNA fragments containing these regulatory sequences are subcloned into P-element vectors containing a white minigene, transformants containing these constructs exhibit mosaic patterns of pigmentation in the adult eye, indicating that white minigene expression is repressed in a clonally heritable manner. The size of pigmented and nonpigmented clones in the adult eye suggests that the event determining whether a cell in the eye anlagen will express white occurs at least as early as the first larval instar. The amount of white minigene repression is reduced in some Polycomb group mutants, whereas repression is enhanced in flies mutant for a subset of trithorax group loci. The repressor activity of one fragment, normally located in Scr Intron 2, is increased when it is able to homologously pair, a property consistent with genetic data suggesting that Scr exhibits transvection. Another Scr regulatory fragment, normally located 40 kb upstream of the Scr promoter, silences ectopic expression of an Scr-lacZ fusion gene in the embryo and does so in a Polycomb-dependent manner. We propose that the regulatory sequences located within these DNA fragments may normally mediate the regulation of Scr by proteins encoded by members of Polycomb and trithorax group loci. 98 refs., 6 figs., 4 tabs.« less

Optimizing indoor illumination quality and energy efficiency using a spectrally tunable lighting system to augment natural daylight.

PubMed

Hertog, W; Llenas, A; Carreras, J

2015-11-30

This article demonstrates the benefits of complementing a daylight-lit environment with a spectrally tunable illumination system. The spectral components of daylight present in the room are measured by a low-cost miniature spectrophotometer and processed through a number of optimization algorithms, carefully trading color fidelity for energy efficiency. Spectrally-tunable luminaires provide only those wavelengths that ensure that either the final illumination spectrum inside the room is kept constant or carefully follows the dynamic spectral pattern of natural daylight. Analyzing the measured data proves that such a hybrid illumination system brings both unprecendented illumination quality and significant energy savings.

Molecular characterization and evaluation of the emerging antibiotic-resistant Streptococcus pyogenes from eastern India.

PubMed

Ray, Dipanwita; Saha, Somnath; Sinha, Sukanta; Pal, Nishith Kumar; Bhattacharya, Basudev

2016-12-12

Group A Streptococcus strains causing wide variety of diseases, recently became noticeable in eastern India, are not amenable to standard treatment protocol thus enhancing the possibility of disease morbidity by becoming antibiotic resistance. The association of Lancefield group A Streptococcal variation with degree of vir architectural diversity was evaluated using emm typing and restriction fragment length polymorphism analyses. The antibiotic sensitivity patterns were examined by modified Kirby-Bauer method of disk diffusion. Percentage calculations, 95% confidence interval and one-way ANOVA were used to assess differences in proportions. Our observations revealed 20 different emm types and 13 different HaeIII vir typing patterns. A 1.2 kb fragment was found in all HaeIII typing pattern. Fragments of 1.2 kb and 550 bp were conserved in majority of the isolates. HinfI digestion was found proficient in differentiating the strains of same vir typing patterns. Strong predominance of speC (85%) and speF (80%) genes have been observed encoding exotoxins production. 4 isolates were found to be erythromycin resistant and were of genotype emm49. High degree of tetracycline resistance was shown by 53.57% isolates which belonged to 12 different emm genotypes. These findings suggested that in addition to emm typing, sequential application of HaeIII and HinfI restriction enzymes in vir typing analysis is an effective tool for group A streptococcal molecular characterization associated with antibiotic resistance.

Habitat and landscape characteristics underlying anuran community structure along an urban-rural gradient.

PubMed

Pillsbury, Finn C; Miller, James R

2008-07-01

Urbanization has been cited as an important factor in worldwide amphibian declines, and although recent work has illustrated the important influence of broad-scale ecological patterns and processes on amphibian populations, little is known about the factors structuring amphibian communities in urban landscapes. We therefore examined amphibian community responses to wetland habitat availability and landscape characteristics along an urban-rural gradient in central Iowa, USA, a region experiencing rapid suburban growth. We conducted call surveys at 61 wetlands to estimate anuran calling activity, and quantified wetland habitat structure and landscape context. We used canonical correspondence analysis (CCA) to examine patterns in anuran community structure and identify the most important variables associated with those patterns. Urban density at the landscape scale had a significant negative influence on overall anuran abundance and diversity. While every species exhibited a decrease in abundance with increasing urban density, this pattern was especially pronounced for species requiring post-breeding upland habitats. Anurans most affected by urbanization were those associated with short hydroperiods, early breeding activity, and substantial upland habitat use. We suggest that broad-scale landscape fragmentation is an important factor underlying anuran community structure in this region, possibly due to limitations on the accessibility of otherwise suitable habitat in fragmented urban landscapes. This study underscores the importance of a regional approach to amphibian conservation in urban and urbanizing areas; in fragmented landscapes, a network of interconnected wetland and upland habitats may be more likely to support a successful, diverse anuran community than will isolated sites.

Diagnostic fragment-ion-based and extension strategy coupled to DFIs intensity analysis for identification of chlorogenic acids isomers in Flos Lonicerae Japonicae by HPLC-ESI-MS(n).

PubMed

Zhang, Jia-Yu; Zhang, Qian; Li, Ning; Wang, Zi-Jian; Lu, Jian-Qiu; Qiao, Yan-Jiang

2013-01-30

A method of modified diagnostic fragment-ion-based extension strategy (DFIBES) coupled to DFIs (diagnostic fragmentation ions) intensity analysis was successfully established to simultaneously screen and identify the chlorogenic acids (CGAs) in Flos Lonicerae Japonicae (FLJ) by HPLC-ESI-MS(n). DFIs, such as m/z 191 [quinic acid-H](-), m/z 179 [caffeic acid-H](-) and m/z 173 [quinic acid-H-H2O](-) were determined or proposed from the fragmentation patterns analysis of corresponding reference substances for every chemical family of CGAs. A "structure extension" method was then proposed based on the well-demonstrated fragmentation patterns and was successively applied into the rapid screening of CGAs in FLJ. Considering that substitution isomerism is a common phenomenon, a full ESI-MS(n) fragmentation analysis according to the intensity of DFIs has been performed to identify the CGA isomers. Based on the DFIs and intensity analysis, 41 peaks attributed to CGAs including 4 caffeoylquinic acids (CQA), 7 CQA glycosides, 6 dicaffeoylquinic acids (DiCQA), 10 DiCQA glycosides, 1 tricaffeoylquinic acids (TriCQA), 4p-coumaroylquinic acids (pCoQA), 3 feruloylquinic acids (FQA) and 6 caffeoylferuloylquinic acids (CFQA) were identified preliminarily in a 65-min chromatographic run. It was the first time to systematically report the presence of CGAs in FLJ, especially for CQA glycosides, DiCQA glycosides, TriCQA, pCoQA and CFQA. All the results indicated that the method of developed DFIBES coupled to DFIs analysis was feasible, reliable and universal for screening and identifying the constituents with the same carbon skeletons especially the isomeric compounds from the complex extract of TCMs. Copyright © 2012 Elsevier B.V. All rights reserved.

Extrapolation of the dna fragment-size distribution after high-dose irradiation to predict effects at low doses

NASA Technical Reports Server (NTRS)

Ponomarev, A. L.; Cucinotta, F. A.; Sachs, R. K.; Brenner, D. J.; Peterson, L. E.

2001-01-01

The patterns of DSBs induced in the genome are different for sparsely and densely ionizing radiations: In the former case, the patterns are well described by a random-breakage model; in the latter, a more sophisticated tool is needed. We used a Monte Carlo algorithm with a random-walk geometry of chromatin, and a track structure defined by the radial distribution of energy deposition from an incident ion, to fit the PFGE data for fragment-size distribution after high-dose irradiation. These fits determined the unknown parameters of the model, enabling the extrapolation of data for high-dose irradiation to the low doses that are relevant for NASA space radiation research. The randomly-located-clusters formalism was used to speed the simulations. It was shown that only one adjustable parameter, Q, the track efficiency parameter, was necessary to predict DNA fragment sizes for wide ranges of doses. This parameter was determined for a variety of radiations and LETs and was used to predict the DSB patterns at the HPRT locus of the human X chromosome after low-dose irradiation. It was found that high-LET radiation would be more likely than low-LET radiation to induce additional DSBs within the HPRT gene if this gene already contained one DSB.

Landscape genetics in the subterranean rodent Ctenomys "chasiquensis" associated with highly disturbed habitats from the southeastern Pampas region, Argentina.

PubMed

Mora, Matías Sebastián; Mapelli, Fernando J; López, Aldana; Gómez Fernández, María Jimena; Mirol, Patricia M; Kittlein, Marcelo J

2017-12-01

Studies of genetic differentiation in fragmented environments help us to identify those landscape features that most affect gene flow and dispersal patterns. Particularly, the assessment of the relative significance of intrinsic biological and environmental factors affecting the genetic structure of populations becomes crucial. In this work, we assess the current dispersal patterns and population structure of Ctenomys "chasiquensis", a vulnerable and endemic subterranean rodent distributed on a small area in Central Argentina, using 9 polymorphic microsatellite loci. We use landscape genetics approaches to assess the relationship between genetic connectivity among populations and environmental attributes. Our analyses show that populations of C. "chasiquensis" are moderately to highly structured at a regional level. This pattern is most likely the outcome of substantial gene flow on the more homogeneous sand dune habitat of the Northwest of its distributional range, in conjunction with an important degree of isolation of eastern and southwestern populations, where the optimal habitat is surrounded by a highly fragmented landscape. Landscape genetics analysis suggests that habitat quality and longitude were the environmental factors most strongly associated with genetic differentiation/uniqueness of populations. In conclusion, our results indicate an important genetic structure in this species, even at a small spatial scale, suggesting that contemporary habitat fragmentation increases population differentiation.

Least loaded and route fragmentation aware RSA strategies for elastic optical networks

NASA Astrophysics Data System (ADS)

Batham, Deepak; Yadav, Dharmendra Singh; Prakash, Shashi

2017-12-01

Elastic optical networks (EONs) provide flexibility to assign wide range of spectral resources to the connection requests. In this manuscript, we address two issues related to spectrum assignment in EONs: the non uniform spectrum assignment along different links of the route and the spectrum fragmentation in the network. To address these issues, two routing and spectrum assignment (RSA) strategies have been proposed: Least Loaded RSA (LLRSA) and Route Fragmentation Aware RSA (RFARSA). The LLRSA allocates spectrum homogeneously along different links in the network, where as RFARSA accords priority to the routes which are less fragmented. To highlight the salient features of the two strategies, two new metrics, route fragmentation index (RFI) and standard deviation (SD) are introduced. RFI is defined as the ratio of non-contiguous FSs to the total available free FSs on the route, and SD relates to the measure of non-uniformity in the allocation of resources on the links in the network. A simulation program has been developed to evaluate the performance of the proposed (LLRSA and RFARSA) strategies, and the existing strategies of shortest path RSA (SPRSA) and spectrum compactness based defragmentation (SCD) strategies, on the metric of RFI, bandwidth blocking probability (BBP), network capacity utilized, and SD. The variation in the metrics on the basis of number of requests and the bandwidth (number of FSs) requested has been studied. It has been conclusively established that the proposed strategies (LLRSA and RFARSA) outperform the existing strategies in terms of all the metrics.

Ocean wavenumber estimation from wave-resolving time series imagery

USGS Publications Warehouse

Plant, N.G.; Holland, K.T.; Haller, M.C.

2008-01-01

We review several approaches that have been used to estimate ocean surface gravity wavenumbers from wave-resolving remotely sensed image sequences. Two fundamentally different approaches that utilize these data exist. A power spectral density approach identifies wavenumbers where image intensity variance is maximized. Alternatively, a cross-spectral correlation approach identifies wavenumbers where intensity coherence is maximized. We develop a solution to the latter approach based on a tomographic analysis that utilizes a nonlinear inverse method. The solution is tolerant to noise and other forms of sampling deficiency and can be applied to arbitrary sampling patterns, as well as to full-frame imagery. The solution includes error predictions that can be used for data retrieval quality control and for evaluating sample designs. A quantitative analysis of the intrinsic resolution of the method indicates that the cross-spectral correlation fitting improves resolution by a factor of about ten times as compared to the power spectral density fitting approach. The resolution analysis also provides a rule of thumb for nearshore bathymetry retrievals-short-scale cross-shore patterns may be resolved if they are about ten times longer than the average water depth over the pattern. This guidance can be applied to sample design to constrain both the sensor array (image resolution) and the analysis array (tomographic resolution). ?? 2008 IEEE.

A multimodal spectral approach to characterize rhythm in natural speech.

PubMed

Alexandrou, Anna Maria; Saarinen, Timo; Kujala, Jan; Salmelin, Riitta

2016-01-01

Human utterances demonstrate temporal patterning, also referred to as rhythm. While simple oromotor behaviors (e.g., chewing) feature a salient periodical structure, conversational speech displays a time-varying quasi-rhythmic pattern. Quantification of periodicity in speech is challenging. Unimodal spectral approaches have highlighted rhythmic aspects of speech. However, speech is a complex multimodal phenomenon that arises from the interplay of articulatory, respiratory, and vocal systems. The present study addressed the question of whether a multimodal spectral approach, in the form of coherence analysis between electromyographic (EMG) and acoustic signals, would allow one to characterize rhythm in natural speech more efficiently than a unimodal analysis. The main experimental task consisted of speech production at three speaking rates; a simple oromotor task served as control. The EMG-acoustic coherence emerged as a sensitive means of tracking speech rhythm, whereas spectral analysis of either EMG or acoustic amplitude envelope alone was less informative. Coherence metrics seem to distinguish and highlight rhythmic structure in natural speech.

High precision measurements on fission-fragment de-excitation

NASA Astrophysics Data System (ADS)

Oberstedt, Stephan; Gatera, Angélique; Geerts, Wouter; Göök, Alf; Hambsch, Franz-Josef; Vidali, Marzio; Oberstedt, Andreas

2017-11-01

In recent years nuclear fission has gained renewed interest both from the nuclear energy community and in basic science. The first, represented by the OECD Nuclear Energy Agency, expressed the need for more accurate fission cross-section and fragment yield data for safety assessments of Generation IV reactor systems. In basic science modelling made much progress in describing the de-excitation mechanism of neutron-rich isotopes, e.g. produced in nuclear fission. Benchmarking the different models require a precise experimental data on prompt fission neutron and γ-ray emission, e.g. multiplicity, average energy per particle and total dissipated energy per fission, preferably as function of fission-fragment mass and total kinetic energy. A collaboration of scientists from JRC Geel (formerly known as JRC IRMM) and other institutes took the lead in establishing a dedicated measurement programme on prompt fission neutron and γ-ray characteristics, which has triggered even more measurement activities around the world. This contribution presents new advanced instrumentation and methodology we use to generate high-precision spectral data and will give a flavour of future data needs and opportunities.

Distinct compartmentalization of dentin matrix protein 1 fragments in mineralized tissues and cells.

PubMed

Maciejewska, Izabela; Qin, Disheng; Huang, Bingzhen; Sun, Yao; Mues, Gabrielle; Svoboda, Kathy; Bonewald, Lynda; Butler, William T; Feng, Jerry Q; Qin, Chunlin

2009-01-01

Dentin matrix protein 1 (DMP1) has been shown to be critical for the formation of dentin and bone. However, the precise pathway by which DMP1 participates in dentinogenesis and osteogenesis remains to be clarified. DMP1 is present in the extracellular matrix of dentin and bone as processed NH(2)- and COOH-terminal fragments. The NH(2)-terminal fragment occurs as a proteoglycan, whereas the COOH-terminal fragment is highly phosphorylated. The differences in biochemical properties suggest that these fragments may have different tissue and cell distribution in association with distinct functions. In this study, we analyzed the distribution of the NH(2)- and COOH-terminal fragments of DMP1 in tooth, bone, osteocytes as well as MC3T3-E1 and HEK-293 cells. Immunohistochemical analyses were performed using antibodies specific to the NH(2)- or COOH-terminal region of DMP1. Clear differences in the distribution of these fragments were observed. In the teeth and bone, the NH(2)-terminal fragment was primarily located in the nonmineralized predentin and cartilage of the growth plate, while the COOH-terminal fragment accumulated in the mineralized zones. In osteocytes, the NH(2)-terminal fragment appeared more abundant along cell membrane and processes of osteocytes, while the COOH-terminal fragment was often found in the nuclei. This pattern of distribution in cellular compartments was further confirmed by analyses on MC3T3-E1 and HEK-293 cells transfected with a construct containing DMP1 cDNA. In these cell lines, the COOH-terminal fragment accumulated in cell nuclei, while the NH(2)-terminal fragment was in the cytosol. The different distribution of DMP1 fragments indicates that these DMP1 variants must perform distinct functions. Copyright 2008 S. Karger AG, Basel.

Analysis of mexicanolide- and phragmalin-type limonoids from Heynea trijuga using high-performance liquid chromatography/electrospray tandem mass spectrometry.

PubMed

Yang, Wei; Fang, Dong-Mei; He, Hong-Ping; Hao, Xiao-Jiang; Wu, Zhi-Jun; Zhang, Guo-Lin

2013-06-15

Limonoids, a class of tetranortriterpenoids, exhibit various biological effects, including acting as potent antifeedants and insect growth-regulators against various pests. The analysis of phragmalin- and mexicanolide-type limonoids by collision-induced dissociation tandem mass spectrometry (CID-MS/MS) has not been reported. A high-performance liquid chromatography/electrospray ionization (HPLC/ESI)-MS/MS method was developed to investigate the fragmentation patterns of [M+NH4 ](+) ions for nine reference phragmalin- and mexicanolide-type limonoids. The method was also used in the identification of limonoid compounds in botanic extracts of Heynea trijuga. The losses of side chains and the furan part were the major fragmentation patterns. However, there was variation in the relative abundances of product ions resulting from the same fragmentation pathways. A total of 89 phragmalin- and mexicanolide-type limonoids in botanic extracts of Heynea trijuga were detected and 50 of these compounds were identified or tentatively characterized based on elemental constituents, fragmentation pathways, and the profile of the major product ions of reference compounds. In addition, the isomers could be tentatively distinguished. An HPLC/ESI-MS/MS method was developed and could be used to simultaneously identify and screen phragmalin- and mexicanolide-type limonoids in botanic extracts of Heynea trijuga. Copyright © 2013 John Wiley & Sons, Ltd.

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

Huang, Yingying; Triscari, Joseph M.; Tseng, George C.

Data mining was performed on 28 330 unique peptide tandem mass spectra for which sequences were assigned with high confidence. By dividing the spectra into different sets based on structural features and charge states of the corresponding peptides, chemical interactions involved in promoting specific cleavage patterns in gas-phase peptides were characterized. Pairwise fragmentation maps describing cleavages at all Xxx-Zzz residue combinations for b and y ions reveal that the difference in basicity between Arg and Lys results in different dissociation patterns for singly charged Arg- and Lys-ending tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides,more » a heterogeneous population of different protonated forms or more facile interconversion of protonated forms (proton partially mobile) exists for Lys-ending peptides. Cleavage C-terminal to acidic residues dominates spectra from peptides that have a localized proton and cleavage N-terminal to Pro dominates those that have a mobile or partially mobile proton. When Pro is absent from peptides that have a mobile or partially mobile proton, cleavage at each peptide bond becomes much more prominent. Whether the above patterns can be found in b ions, y ions, or both depends on the location of the proton holder(s). Enhanced cleavages C-terminal to branched aliphatic residues (Ile, Val, Leu) are observed in both b and y ions from peptides that have a mobile proton, as well as in y ions from peptides that have a partially mobile proton; enhanced cleavages N-terminal to these residues are observed in b ions from peptides that have a partially mobile proton. Statistical tools have been designed to visualize the fragmentation maps and measure the similarity between them. The pairwise cleavage patterns observed expand our knowledge of peptide gas-phase fragmentation behaviors and should be useful in algorithm development that employs improved models to predict fragment ion intensities.« less

Sleeping Sites and Latrines of Spider Monkeys in Continuous and Fragmented Rainforests: Implications for Seed Dispersal and Forest Regeneration

PubMed Central

González-Zamora, Arturo; Arroyo-Rodríguez, Víctor; Oyama, Ken; Sork, Victoria; Chapman, Colin A.; Stoner, Kathryn E.

2012-01-01

Spider monkeys (Ateles geoffroyi) use sites composed of one or more trees for sleeping (sleeping sites and sleeping trees, respectively). Beneath these sites/trees they deposit copious amounts of dung in latrines. This behavior results in a clumped deposition pattern of seeds and nutrients that directly impacts the regeneration of tropical forests. Therefore, information on the density and spatial distribution of sleeping sites and latrines, and the characteristics (i.e., composition and structure) of sleeping trees are needed to improve our understanding of the ecological significance of spider monkeys in influencing forest composition. Moreover, since primate populations are increasingly forced to inhabit fragmented landscapes, it is important to assess if these characteristics differ between continuous and fragmented forests. We assessed this novel information from eight independent spider monkey communities in the Lacandona rainforest, Mexico: four continuous forest sites and four forest fragments. Both the density of sleeping sites and latrines did not differ between forest conditions. Latrines were uniformly distributed across sleeping sites, but the spatial distribution of sleeping sites within the areas was highly variable, being particularly clumped in forest fragments. In fact, the average inter-latrine distances were almost double in continuous forest than in fragments. Latrines were located beneath only a few tree species, and these trees were larger in diameter in continuous than fragmented forests. Because latrines may represent hotspots of seedling recruitment, our results have important ecological and conservation implications. The variation in the spatial distribution of sleeping sites across the forest indicates that spider monkeys likely create a complex seed deposition pattern in space and time. However, the use of a very few tree species for sleeping could contribute to the establishment of specific vegetation associations typical of the southeastern Mexican rainforest, such as Terminalia-Dialium, and Brosimum-Dialium. PMID:23056486

Native top-down mass spectrometry for the structural characterization of human hemoglobin

DOE PAGES

Zhang, Jiang; Malmirchegini, G. Reza; Clubb, Robert T.; ...

2015-06-09

Native mass spectrometry (MS) has become an invaluable tool for the characterization of proteins and non-covalent protein complexes under near physiological solution conditions. Here we report the structural characterization of human hemoglobin (Hb), a 64 kDa oxygen-transporting protein complex, by high resolution native top-down mass spectrometry using electrospray ionization (ESI) and a 15-Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Native MS preserves the non-covalent interactions between the globin subunits, and electron capture dissociation (ECD) produces fragments directly from the intact Hb complex without dissociating the subunits. Using activated ion ECD, we observe the gradual unfolding process of themore » Hb complex in the gas phase. Without protein ion activation, the native Hb shows very limited ECD fragmentation from the N-termini, suggesting a tightly packed structure of the native complex and therefore low fragmentation efficiency. Precursor ion activation allows steady increase of N-terminal fragment ions, while the C-terminal fragments remain limited (38 c ions and 4 z ions on the α chain; 36 c ions and 2 z ions on the β chain). This ECD fragmentation pattern suggests that upon activation, the Hb complex starts to unfold from the N-termini of both subunits, whereas the C-terminal regions and therefore the potential regions involved in the subunit binding interactions remain intact. ECD-MS of the Hb dimer show similar fragmentation patterns as the Hb tetramer, providing further evidence for the hypothesized unfolding process of the Hb complex in the gas phase. Native top-down ECD-MS allows efficient probing of the Hb complex structure and the subunit binding interactions in the gas phase. Finally, it may provide a fast and effective means to probe the structure of novel protein complexes that are intractable to traditional structural characterization tools.« less

Sleeping sites and latrines of spider monkeys in continuous and fragmented rainforests: implications for seed dispersal and forest regeneration.

PubMed

González-Zamora, Arturo; Arroyo-Rodríguez, Víctor; Oyama, Ken; Sork, Victoria; Chapman, Colin A; Stoner, Kathryn E

2012-01-01

Spider monkeys (Ateles geoffroyi) use sites composed of one or more trees for sleeping (sleeping sites and sleeping trees, respectively). Beneath these sites/trees they deposit copious amounts of dung in latrines. This behavior results in a clumped deposition pattern of seeds and nutrients that directly impacts the regeneration of tropical forests. Therefore, information on the density and spatial distribution of sleeping sites and latrines, and the characteristics (i.e., composition and structure) of sleeping trees are needed to improve our understanding of the ecological significance of spider monkeys in influencing forest composition. Moreover, since primate populations are increasingly forced to inhabit fragmented landscapes, it is important to assess if these characteristics differ between continuous and fragmented forests. We assessed this novel information from eight independent spider monkey communities in the Lacandona rainforest, Mexico: four continuous forest sites and four forest fragments. Both the density of sleeping sites and latrines did not differ between forest conditions. Latrines were uniformly distributed across sleeping sites, but the spatial distribution of sleeping sites within the areas was highly variable, being particularly clumped in forest fragments. In fact, the average inter-latrine distances were almost double in continuous forest than in fragments. Latrines were located beneath only a few tree species, and these trees were larger in diameter in continuous than fragmented forests. Because latrines may represent hotspots of seedling recruitment, our results have important ecological and conservation implications. The variation in the spatial distribution of sleeping sites across the forest indicates that spider monkeys likely create a complex seed deposition pattern in space and time. However, the use of a very few tree species for sleeping could contribute to the establishment of specific vegetation associations typical of the southeastern Mexican rainforest, such as Terminalia-Dialium, and Brosimum-Dialium.

Central cardiovascular and behavioral effects of carboxy- and amino-terminal fragments of substance P in conscious rats.

PubMed

Tschöpe, C; Jost, N; Unger, T; Culman, J

1995-08-28

The central cardiovascular and behavioral effects of carboxy- (SP 5-11, SP 6-11, SP 7-11, SP 8-11) and amino- (SP 1-7, SP 1-9) terminal substance P (SP) fragments were compared with those of SP 1-11 in conscious rats. In addition, the ability of these SP-fragments to induce desensitization of the central NK1 receptor was investigated. SP 1-11 (50 pmol) injected i.c.v. induced an increase in mean arterial blood pressure (MAP), heart rate (HR) and a typical behavioral response consisting of face washing (FW), hindquarter grooming (HQG) and wet-dog shakes (WDS). The cardiovascular and behavioral responses to equimolar doses of SP 5-11 and SP 6-11 were similar to those of SP 1-11, however, only SP 5-11 induced exactly the same behavioral pattern as SP 1-11. SP 6-11 was more potent in inducing FW and WDS than SP 1-11 or SP 5-11. The carboxy-terminal SP-fragments, SP 7-11 and SP 8-11, and the amino-terminal SP-fragments, SP 1-7, SP 1-9, did not elicit any significant cardiovascular or behavioral responses. Pretreatment with SP 1-11 reduced the cardiovascular and behavioral responses to subsequent injections of SP 1-11. Of all SP-fragments tested, only SP 5-11 was able to attenuate the cardiovascular and behavioral responses to SP 1-11. Our results demonstrate that SP 6-11 represents the shortest carboxy-terminal amino acid sequence, that after i.c.v. injection, elicits the same cardiovascular response as SP 1-11, but fails to desensitize the NK1 receptor. The carboxy-terminal fragment, SP 5-11, is the shortest amino acid sequence which produces the same pattern of central cardiovascular and behavioral responses as SP 1-11 and also retains the ability to desensitize the NK1 receptor like SP 1-11.

Color camera computed tomography imaging spectrometer for improved spatial-spectral image accuracy

NASA Technical Reports Server (NTRS)

Wilson, Daniel W. (Inventor); Bearman, Gregory H. (Inventor); Johnson, William R. (Inventor)

2011-01-01

Computed tomography imaging spectrometers ("CTIS"s) having color focal plane array detectors are provided. The color FPA detector may comprise a digital color camera including a digital image sensor, such as a Foveon X3.RTM. digital image sensor or a Bayer color filter mosaic. In another embodiment, the CTIS includes a pattern imposed either directly on the object scene being imaged or at the field stop aperture. The use of a color FPA detector and the pattern improves the accuracy of the captured spatial and spectral information.

Fluidized bed combustion of pelletized biomass and waste-derived fuels

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

Chirone, R.; Scala, F.; Solimene, R.

2008-10-15

The fluidized bed combustion of three pelletized biogenic fuels (sewage sludge, wood, and straw) has been investigated with a combination of experimental techniques. The fuels have been characterized from the standpoints of patterns and rates of fuel devolatilization and char burnout, extent of attrition and fragmentation, and their relevance to the fuel particle size distribution and the amount and size distribution of primary ash particles. Results highlight differences and similarities among the three fuels tested. The fuels were all characterized by limited primary fragmentation and relatively long devolatilization times, as compared with the time scale of particle dispersion away frommore » the fuel feeding ports in practical FBC. Both features are favorable to effective lateral distribution of volatile matter across the combustor cross section. The three fuels exhibited distinctively different char conversion patterns. The high-ash pelletized sludge burned according to the shrinking core conversion pattern with negligible occurrence of secondary fragmentation. The low-ash pelletized wood burned according to the shrinking particle conversion pattern with extensive occurrence of secondary fragmentation. The medium-ash pelletized straw yielded char particles with a hollow structure, resembling big cenospheres, characterized by a coherent inorganic outer layer strong enough to prevent particle fragmentation. Inert bed particles were permanently attached to the hollow pellets as they were incorporated into ash melts. Carbon elutriation rates were very small for all the fuels tested. For pelletized sludge and straw, this was mostly due to the shielding effect of the coherent ash skeleton. For the wood pellet, carbon attrition was extensive, but was largely counterbalanced by effective afterburning due to the large intrinsic reactivity of attrited char fines. The impact of carbon attrition on combustion efficiency was negligible for all the fuels tested. The size distribution of primary ash particles liberated upon complete carbon burnoff largely reflected the combustion pattern of each fuel. Primary ash particles of size nearly equal to that of the parent fuel were generated upon complete burnoff of the pelletized sludge. Nonetheless, secondary attrition of primary ash from pelletized sludge is large, to the point where generation of fine ash would be extensive over the typical residence time of bed ash in fluidized bed combustors. Very few and relatively fine primary ash particles were released after complete burnoff of wood pellets. Primary ash particles remaining after complete burnoff of pelletized straw had sizes and shapes that were largely controlled by the occurrence of ash agglomeration phenomena. (author)« less

Spinopelvic dissociation: multidetector computed tomographic evaluation of fracture patterns and associated injuries at a single level 1 trauma center.

PubMed

Gupta, Pushpender; Barnwell, Jonathan C; Lenchik, Leon; Wuertzer, Scott D; Miller, Anna N

2016-06-01

The objective of the present study is to evaluate multidetector computed tomographic (MDCT) fracture patterns and associated injuries in patients with spinopelvic dissociation (SPD). Our institutional trauma registry database was reviewed from Jan. 1, 2006, to Sept. 30, 2012, specifically evaluating patients with sacral fractures. MDCT scans of patients with sacral fractures were reviewed to determine the presence of SPD. SPD cases were characterized into the following fracture patterns: U-shaped, Y-shaped, T-shaped, H-shaped, and burst. The following MDCT features were recorded: level of the horizontal fracture, location of vertical fracture, kyphosis between major fracture fragments, displacement of fracture fragment, narrowing of central spinal canal, narrowing of neural foramina, and extension into sacroiliac joints. Quantitative evaluation of the sacral fractures was performed in accordance with the consensus statement by the Spine Trauma Study Group. Medical records were reviewed to determine associated pelvic and non-pelvic fractures, bladder and bowel injuries, nerve injuries, and type of surgical intervention. Twenty-one patients had SPD, of whom 13 were men and eight were women. Mean age was 41.8 years (range 18.8 to 87.7). Five fractures (24 %) were U-shaped, six (29 %) H-shaped, four (19 %) Y-shaped, and six (29 %) burst. Nine patients (43 %) had central canal narrowing, and 19 (90 %) had neural foramina narrowing. Eleven patients (52 %) had kyphotic angulation between major fracture fragments, and seven patients (33 %) had either anterior (24 %) or posterior (10 %) displacement of the proximal fracture fragment. Fourteen patients (67 %) had associated pelvic fractures, and 20 (95 %) had associated non-pelvic fractures. Two patients (10 %) had associated urethral injuries, and one (5 %) had an associated colon injury. Seven patients (33 %) had associated nerve injuries. Six patients (29 %) had surgical fixation while 15 (71 %) were managed non-operatively. On trauma MDCT examinations, patients with SPD have characteristic fracture patterns. It is important to differentiate SPD from other pelvic ring injuries due to high rate of associated injuries. Although all SPD injuries are unstable and need fixation, the decision for operative management in an individual patient depends on the systemic injury pattern, specific fracture pattern, and the ability to attain stable screw fixation.

Machine Learning Method for Pattern Recognition in Volcano Seismic Spectra

NASA Astrophysics Data System (ADS)

Radic, V.; Unglert, K.; Jellinek, M.

2016-12-01

Variations in the spectral content of volcano seismicity related to changes in volcanic activity are commonly identified manually in spectrograms. However, long time series of monitoring data at volcano observatories require tools to facilitate automated and rapid processing. Techniques such as Self-Organizing Maps (SOM), Principal Component Analysis (PCA) and clustering methods can help to quickly and automatically identify important patterns related to impending eruptions. In this study we develop and evaluate an algorithm applied on a set of synthetic volcano seismic spectra as well as observed spectra from Kılauea Volcano, Hawai`i. Our goal is to retrieve a set of known spectral patterns that are associated with dominant phases of volcanic tremor before, during, and after periods of volcanic unrest. The algorithm is based on training a SOM on the spectra and then identifying local maxima and minima on the SOM 'topography'. The topography is derived from the first two PCA modes so that the maxima represent the SOM patterns that carry most of the variance in the spectra. Patterns identified in this way reproduce the known set of spectra. Our results show that, regardless of the level of white noise in the spectra, the algorithm can accurately reproduce the characteristic spectral patterns and their occurrence in time. The ability to rapidly classify spectra of volcano seismic data without prior knowledge of the character of the seismicity at a given volcanic system holds great potential for real time or near-real time applications, and thus ultimately for eruption forecasting.

Polarization imaging of comets at geocentric distances smaller than 0.5 au: Comet 73P/Schwassmann-Wachmann 3

NASA Astrophysics Data System (ADS)

Hadamcik, E.; Levasseur-Regourd, A.-C.

2014-07-01

Remote observations of sunlight scattered by solid particles provide information on the particle properties for a large variety of comets. When comets approach the Sun, solid particles and gases are released from the surface or from the inner layers [1,2]. If the comet is close enough to the Earth, the inner coma may be studied. Different coma regions are observed corresponding to different dust properties, e.g., in jets or fresh ejected dust around the coma. Narrow-band continuum filters or broader-band filters in less contaminated spectral domains (red or near infrared) are currently used to avoid or reduce the contributions from gaseous emission. Comet 73P/Schwassmann-Wachmann 3 is a fascinating fragmenting comet. Different observations in 1995 revealed an increase of activity and at least four fragments of the nucleus. In its 2011 apparition, the fragments were well separated and appeared like small individual comets. In 2006, its apparition was very favorable and allowed high- spatial resolution imaging by different complementary techniques. We observed three fragments of comet 73P/Schwassmann-Wachmann 3 from April 27 to May 3, 2006, by imaging polarimetry with the 80-cm telescope at Observatoire de Haute-Provence. The distance to the Earth was smaller than 0.2 au. Fragment C resembles a classical active comet. Regions of high and lower polarization were observed in the inner coma, appearing to change almost periodically. The variation of polarization in the inner coma was important from one night to the next one, the whole coma polarization being about constant for nucleus distances greater than 2000 km and increasing with the phase angle. Fragment B continued its (sequential) fragmentation, with a region of secondary fragments progressively moving away from the main nucleus in the antisolar direction. The chemical composition has been reported as being similar in all the fragments [3], but differences were observed between them in polarization underlining differences in, e.g., structure or size distribution of the particles during their ejection and fragmentation. The variation of polarization in the coma and around the fragments will be presented. Finally, a comparison to other comets, including split comets observed at small geocentric distances, will be provided.

Characterization of a compact 6-band multifunctional camera based on patterned spectral filters in the focal plane

NASA Astrophysics Data System (ADS)

Torkildsen, H. E.; Hovland, H.; Opsahl, T.; Haavardsholm, T. V.; Nicolas, S.; Skauli, T.

2014-06-01

In some applications of multi- or hyperspectral imaging, it is important to have a compact sensor. The most compact spectral imaging sensors are based on spectral filtering in the focal plane. For hyperspectral imaging, it has been proposed to use a "linearly variable" bandpass filter in the focal plane, combined with scanning of the field of view. As the image of a given object in the scene moves across the field of view, it is observed through parts of the filter with varying center wavelength, and a complete spectrum can be assembled. However if the radiance received from the object varies with viewing angle, or with time, then the reconstructed spectrum will be distorted. We describe a camera design where this hyperspectral functionality is traded for multispectral imaging with better spectral integrity. Spectral distortion is minimized by using a patterned filter with 6 bands arranged close together, so that a scene object is seen by each spectral band in rapid succession and with minimal change in viewing angle. The set of 6 bands is repeated 4 times so that the spectral data can be checked for internal consistency. Still the total extent of the filter in the scan direction is small. Therefore the remainder of the image sensor can be used for conventional imaging with potential for using motion tracking and 3D reconstruction to support the spectral imaging function. We show detailed characterization of the point spread function of the camera, demonstrating the importance of such characterization as a basis for image reconstruction. A simplified image reconstruction based on feature-based image coregistration is shown to yield reasonable results. Elimination of spectral artifacts due to scene motion is demonstrated.

Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis

PubMed Central

Li, Dapeng; Baldwin, Ian T.; Gaquerel, Emmanuel

2015-01-01

Natural variation can be extremely useful in unraveling the determinants of phenotypic trait evolution but has rarely been analyzed with unbiased metabolic profiling to understand how its effects are organized at the level of biochemical pathways. Native populations of Nicotiana attenuata, a wild tobacco species, have been shown to be highly genetically diverse for traits important for their interactions with insects. To resolve the chemodiversity existing in these populations, we developed a metabolomics and computational pipeline to annotate leaf metabolic responses to Manduca sexta herbivory. We selected seeds from 43 accessions of different populations from the southwestern United States—including the well-characterized Utah 30th generation inbred accession—and grew 183 plants in the glasshouse for standardized herbivory elicitation. Metabolic profiles were generated from elicited leaves of each plant using a high-throughput ultra HPLC (UHPLC)-quadrupole TOFMS (qTOFMS) method, processed to systematically infer covariation patterns among biochemically related metabolites, as well as unknown ones, and finally assembled to map natural variation. Navigating this map revealed metabolic branch-specific variations that surprisingly only partly overlapped with jasmonate accumulation polymorphisms and deviated from canonical jasmonate signaling. Fragmentation analysis via indiscriminant tandem mass spectrometry (idMS/MS) was conducted with 10 accessions that spanned a large proportion of the variance found in the complete accession dataset, and compound spectra were computationally assembled into spectral similarity networks. The biological information captured by this networking approach facilitates the mining of the mass spectral data of unknowns with high natural variation, as demonstrated by the annotation of a strongly herbivory-inducible phenolic derivative, and can guide pathway analysis. PMID:26170304

Four new degradation products of doxorubicin: An application of forced degradation study and hyphenated chromatographic techniques.

PubMed

Kaushik, Dheeraj; Bansal, Gulshan

2015-10-01

Forced degradation study on doxorubicin (DOX) was carried out under hydrolytic condition in acidic, alkaline and neutral media at varied temperatures, as well as under peroxide, thermal and photolytic conditions in accordance with International Conference on Harmonization (ICH) guidelines Q1(R2). It was found extremely unstable to alkaline hydrolysis even at room temperature, unstable to acid hydrolysis at 80 °C, and to oxidation at room temperature. It degraded to four products (O-I-O-IV) in oxidative condition, and to single product (A-I) in acid hydrolytic condition. These products were resolved on a C 8 (150 mm×4.6 mm, 5 µm) column with isocratic elution using mobile phase consisting of HCOONH 4 (10 mM, pH 2.5), acetonitrile and methanol (65:15:20, v/v/v). Liquid chromatography-photodiode array (LC-PDA) technique was used to ascertain the purity of the products noted in LC-UV chromatogram. For their characterization, a six stage mass fragmentation (MS 6 ) pattern of DOX was outlined through mass spectral studies in positive mode of electrospray ionization (+ESI) as well as through accurate mass spectral data of DOX and the products generated through liquid chromatography-time of flight mass spectrometry (LC-MS-TOF) on degraded drug solutions. Based on it, O-I-O-IV were characterized as 3-hydroxy-9-desacetyldoxorubicin-9-hydroperoxide, 1-hydroxy-9-desacetyldoxorubicin-9-hydroperoxide, 9-desacetyldoxorubicin-9-hydroperoxide and 9-desacetyldoxorubicin, respectively, whereas A-I was characterized as deglucosaminyl doxorubicin. While A-I was found to be a pharmacopoeial impurity, all oxidative products were found to be new degradation impurities. The mechanisms and pathways of degradation of doxorubicin were outlined and discussed.

Mass Extinction and the Disappearance of Unknown Mammal Species: Scenario and Perspectives of a Biodiversity Hotspot’s Hotspot

PubMed Central

Mendes Pontes, Antonio Rossano; Beltrão, Antonio Carlos Mariz; Normande, Iran Campello; Malta, Alexandre de Jesus Rodrigues; da Silva Júnior, Antonio Paulo; Santos, André Maurício Melo

2016-01-01

We aimed to determine the conservation status of medium- and large-sized mammals and evaluate the impact of 500 years of forest fragmentation on this group of animals in the Pernambuco Endemism Center, in the biogeographical zone of the Atlantic forest north of the São Francisco River in northeastern Brazil. Line transect surveys were performed in 21 forest fragments, resulting in a checklist of the mammals of the entire Pernambuco Endemism Center area. We ran a generalized linear model (Factorial ANCOVA) to analyze to what extent the vegetation type, fragment area, isolation, sampling effort (as total kilometers walked), or higher-order interactions predicted (a) richness and (b) sighting rates. To determine if the distribution of the species within the forest fragments exhibited a nested pattern, we used the NODF metric. Subsequently, we performed a Binomial Logistic Regression to predict the probability of encountering each species according to fragment size. Out of 38 medium- and large-sized mammal species formerly occurring in the study area, only 53.8% (n = 21) were sighted. No fragment hosted the entire remaining mammal community, and only four species (19%) occurred in very small fragments (73.3% of the remaining forest fragments, with a mean size of 2.8 ha). The mammalian community was highly simplified, with all large mammals being regionally extinct. Neither the species richness nor sighting rate was controlled by the vegetation type, the area of the forest fragments, isolation or any higher-order interaction. Although a highly significant nested subset pattern was detected, it was not related to the ranking of the area of forest fragments or isolation. The probability of the occurrence of a mammal species in a given forest patch varied unpredictably, and the probability of detecting larger species was even observed to decrease with increasing patch size. In an ongoing process of mass extinction, half of the studied mammals have gone extinct. The remaining medium-sized mammal community is highly simplified and homogenized. The persistence of these species in a forest patch is determined by their ability to adapt to a novel simplified diet, the efficient use of the surrounding matrix without being engulfed by the sink effect, and escaping hunting. Our results suggest that the 21st century medium-sized mammalian fauna of this region will comprise only four species unless strict conservation measures are implemented immediately and every forest fragment is effectively protected. PMID:27191719

Mass Extinction and the Disappearance of Unknown Mammal Species: Scenario and Perspectives of a Biodiversity Hotspot's Hotspot.

PubMed

Mendes Pontes, Antonio Rossano; Beltrão, Antonio Carlos Mariz; Normande, Iran Campello; Malta, Alexandre de Jesus Rodrigues; Silva Júnior, Antonio Paulo da; Santos, André Maurício Melo

2016-01-01

We aimed to determine the conservation status of medium- and large-sized mammals and evaluate the impact of 500 years of forest fragmentation on this group of animals in the Pernambuco Endemism Center, in the biogeographical zone of the Atlantic forest north of the São Francisco River in northeastern Brazil. Line transect surveys were performed in 21 forest fragments, resulting in a checklist of the mammals of the entire Pernambuco Endemism Center area. We ran a generalized linear model (Factorial ANCOVA) to analyze to what extent the vegetation type, fragment area, isolation, sampling effort (as total kilometers walked), or higher-order interactions predicted (a) richness and (b) sighting rates. To determine if the distribution of the species within the forest fragments exhibited a nested pattern, we used the NODF metric. Subsequently, we performed a Binomial Logistic Regression to predict the probability of encountering each species according to fragment size. Out of 38 medium- and large-sized mammal species formerly occurring in the study area, only 53.8% (n = 21) were sighted. No fragment hosted the entire remaining mammal community, and only four species (19%) occurred in very small fragments (73.3% of the remaining forest fragments, with a mean size of 2.8 ha). The mammalian community was highly simplified, with all large mammals being regionally extinct. Neither the species richness nor sighting rate was controlled by the vegetation type, the area of the forest fragments, isolation or any higher-order interaction. Although a highly significant nested subset pattern was detected, it was not related to the ranking of the area of forest fragments or isolation. The probability of the occurrence of a mammal species in a given forest patch varied unpredictably, and the probability of detecting larger species was even observed to decrease with increasing patch size. In an ongoing process of mass extinction, half of the studied mammals have gone extinct. The remaining medium-sized mammal community is highly simplified and homogenized. The persistence of these species in a forest patch is determined by their ability to adapt to a novel simplified diet, the efficient use of the surrounding matrix without being engulfed by the sink effect, and escaping hunting. Our results suggest that the 21st century medium-sized mammalian fauna of this region will comprise only four species unless strict conservation measures are implemented immediately and every forest fragment is effectively protected.

LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data.

PubMed

Koelmel, Jeremy P; Kroeger, Nicholas M; Ulmer, Candice Z; Bowden, John A; Patterson, Rainey E; Cochran, Jason A; Beecher, Christopher W W; Garrett, Timothy J; Yost, Richard A

2017-07-10

Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to have great potential as candidates for elucidating biomarkers and pathway perturbations associated with disease. Methods expanding coverage of the lipidome increase the likelihood of biomarker discovery and could lead to more comprehensive understanding of disease etiology. We introduce LipidMatch, an R-based tool for lipid identification for liquid chromatography tandem mass spectrometry workflows. LipidMatch currently has over 250,000 lipid species spanning 56 lipid types contained in in silico fragmentation libraries. Unique fragmentation libraries, compared to other open source software, include oxidized lipids, bile acids, sphingosines, and previously uncharacterized adducts, including ammoniated cardiolipins. LipidMatch uses rule-based identification. For each lipid type, the user can select which fragments must be observed for identification. Rule-based identification allows for correct annotation of lipids based on the fragments observed, unlike typical identification based solely on spectral similarity scores, where over-reporting structural details that are not conferred by fragmentation data is common. Another unique feature of LipidMatch is ranking lipid identifications for a given feature by the sum of fragment intensities. For each lipid candidate, the intensities of experimental fragments with exact mass matches to expected in silico fragments are summed. The lipid identifications with the greatest summed intensity using this ranking algorithm were comparable to other lipid identification software annotations, MS-DIAL and Greazy. For example, for features with identifications from all 3 software, 92% of LipidMatch identifications by fatty acyl constituents were corroborated by at least one other software in positive mode and 98% in negative ion mode. LipidMatch allows users to annotate lipids across a wide range of high resolution tandem mass spectrometry experiments, including imaging experiments, direct infusion experiments, and experiments employing liquid chromatography. LipidMatch leverages the most extensive in silico fragmentation libraries of freely available software. When integrated into a larger lipidomics workflow, LipidMatch may increase the probability of finding lipid-based biomarkers and determining etiology of disease by covering a greater portion of the lipidome and using annotation which does not over-report biologically relevant structural details of identified lipid molecules.

Communication: Identification of daughter ions through their electronic spectroscopy at low temperature

NASA Astrophysics Data System (ADS)

Dedonder, Claude; Féraud, Géraldine; Jouvet, Christophe

2014-10-01

We present experimental results on photofragmentation of cooled fragments issued from the photofragmentation of cold parent ions. The cooling of the daughter ions at a few K allows its characterization not only through its fragmentation pattern but also through its well resolved electronic spectroscopy. The proof of principle of the method is demonstrated on the photofragment resulting from Cα-Cβ bond rupture in protonated tyrosine (TyrH+). The analysis of the daughter ion (m/z 108) photofragmentation spectrum is in agreement with the proposed mechanism implying a proton transfer to the phenyl ring as the first step of the fragmentation mechanism of TyrH+.

Intermediate mass fragment emission and iso-scaling in dissipative Ca+Sn reactions at 45 AMeV

NASA Astrophysics Data System (ADS)

Singh, H.; Quinlan, M. J.; Tõke, J.; Pawelczak, I.; Henry, E.; Schröder, W. U.; Amorini, F.; Anzalone, A.; Maiolino, C.; Auditore, L.; Loria, D.; Trifiro, A.; Trimarchi, M.; Cardella, G.; De Filippo, E.; Pagano, A.; Chatterjee, M. B.; Cavallaro, S.; Geraci, E.; Papa, M.; Pirrone, S.; Verde, G.; Grzeszczuk, A.; Guazzoni, P.; Zetta, L.; La Guidara, E.; Lanzalone, G.; Lo Nigro, S.; Politi, G.; Loria, D.; Porto, F.; Rizzo, F.; Russotto, P.; Vigilante, M.

2013-04-01

The production mechanism of intermediate-mass fragments (IMFs) with atomic numbers Z = 3 - 7 is explored in the intermediate energy regime, studying dissipative 48Ca+112Sn and 48Ca+124Sn reactions at E/A = 45MeV. Various aspects of IMF emission patterns point to an inelastic break-up type production mechanism involving excited projectile-like fragment from dissipative interactions. Isotopic yield ratios of identical IMFs from the above two dissipative reactions have been analysed using the "isoscaling" method. Observed trends are correlated with ground-state binding energy systematics and their relevance for an evaluation of the symmetry energy is discussed.

Temporal bird community dynamics are strongly affected by landscape fragmentation in a Central American tropical forest region

USGS Publications Warehouse

Blandón, A.C.; Perelman, S.B.; Ramírez, M.; López, A.; Javier, O.; Robbins, Chandler S.

2016-01-01

Habitat loss and fragmentation are considered the main causes of species extinctions, particularly in tropical ecosystems. The objective of this work was to evaluate the temporal dynamics of tropical bird communities in landscapes with different levels of fragmentation in eastern Guatemala. We evaluated five bird community dynamic parameters for forest specialists and generalists: (1) species extinction, (2) species turnover, (3) number of colonizing species, (4) relative species richness, and (5) a homogeneity index. For each of 24 landscapes, community dynamic parameters were estimated from bird point count data, for the 1998–1999 and 2008–2009 periods, accounting for species’ detection probability. Forest specialists had higher extinction rates and a smaller number of colonizing species in landscapes with higher fragmentation, thus having lower species richness in both time periods. Alternatively, forest generalists elicited a completely different pattern, showing a curvilinear association to forest fragmentation for most parameters. Thus, greater community dynamism for forest generalists was shown in landscapes with intermediate levels of fragmentation. Our study supports general theory regarding the expected negative effects of habitat loss and fragmentation on the temporal dynamics of biotic communities, particularly for forest specialists, providing strong evidence from understudied tropical bird communities.

Biophysical modeling of fragment length distributions of DNA plasmids after X and heavy-ion irradiation analyzed by atomic force microscopy.

PubMed

Elsässer, Thilo; Brons, Stephan; Psonka, Katarzyna; Scholz, Michael; Gudowska-Nowak, Ewa; Taucher-Scholz, Gisela

2008-06-01

The investigation of fragment length distributions of plasmid DNA gives insight into the influence of localized energy distribution on the induction of DNA damage, particularly the clustering of double-strand breaks. We present an approach that determines the fragment length distributions of plasmid DNA after heavy-ion irradiation by using the Local Effect Model. We find a good agreement of our simulations with experimental fragment distributions derived from atomic force microscopy (AFM) studies by including experimental constraints typical for AFM. Our calculations reveal that by comparing the fragmentation in terms of fluence, we can uniquely distinguish the effect of different radiation qualities. For very high-LET irradiation using nickel or uranium ions, no difference between their fragment distributions can be expected for the same dose level. However, for carbon ions with an intermediate LET, the fragmentation pattern differs from the distribution for very high-LET particles. The results of the model calculations can be used to determine the optimal experimental parameters for a demonstration of the influence of track structure on primary radiation damage. Additionally, we compare the results of our model for two different plasmid geometries.

An extended patch-dynamic framework for food chains in fragmented landscapes

PubMed Central

Liao, Jinbao; Chen, Jiehong; Ying, Zhixia; Hiebeler, David E.; Nijs, Ivan

2016-01-01

Habitat destruction, a key determinant of species loss, can be characterized by two components, patch loss and patch fragmentation, where the former refers to the reduction in patch availability, and the latter to the division of the remaining patches. Classical metacommunity models have recently explored how food web dynamics respond to patch loss, but the effects of patch fragmentation have largely been overlooked. Here we develop an extended patch-dynamic model that tracks the patch occupancy of the various trophic links subject to colonization-extinction-predation dynamics by incorporating species dispersal with patch connectivity. We found that, in a simple food chain, species at higher trophic level become extinct sooner with increasing patch loss and fragmentation due to the constraint in resource availability, confirming the trophic rank hypothesis. Yet, effects of fragmentation on species occupancy are largely determined by patch loss, with maximal fragmentation effects occurring at intermediate patch loss. Compared to the spatially explicit simulations that we also performed, the current model with pair approximation generates similar community patterns especially in spatially clustered landscapes. Overall, our extended framework can be applied to model more complex food webs in fragmented landscapes, broadening the scope of existing metacommunity theory. PMID:27608823

Ion-polycyclic aromatic hydrocarbon collisions: kinetic energy releases for specific fragmentation channels

NASA Astrophysics Data System (ADS)

Reitsma, G.; Zettergren, H.; Boschman, L.; Bodewits, E.; Hoekstra, R.; Schlathölter, T.

2013-12-01

We report on 30 keV He2 + collisions with naphthalene (C10H8) molecules, which leads to very extensive fragmentation. To unravel such complex fragmentation patterns, we designed and constructed an experimental setup, which allows for the determination of the full momentum vector by measuring charged collision products in coincidence in a recoil ion momentum spectrometer type of detection scheme. The determination of fragment kinetic energies is found to be considerably more accurate than for the case of mere coincidence time-of-flight spectrometers. In fission reactions involving two cationic fragments, typically kinetic energy releases of 2-3 eV are observed. The results are interpreted by means of density functional theory calculations of the reverse barriers. It is concluded that naphthalene fragmentation by collisions with keV ions clearly is much more violent than the corresponding photofragmentation with energetic photons. The ion-induced naphthalene fragmentation provides a feedstock of various small hydrocarbonic species of different charge states and kinetic energy, which could influence several molecule formation processes in the cold interstellar medium and facilitates growth of small hydrocarbon species on pre-existing polycyclic aromatic hydrocarbons.

Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin.

PubMed

Floris, Federico; Chiron, Lionel; Lynch, Alice M; Barrow, Mark P; Delsuc, Marc-André; O'Connor, Peter B

2018-06-04

Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about ~23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from ~23% to ~42%. Graphical Abstract Two-dimensional mass spectrometry, when applied to primary fragment ions from the source, allows deep-sequencing of the protein calmodulin.

Natural age dispersion arising from the analysis of broken crystals. Part I: Theoretical basis and implications for the apatite (U-Th)/He thermochronometer

NASA Astrophysics Data System (ADS)

Brown, Roderick W.; Beucher, Romain; Roper, Steven; Persano, Cristina; Stuart, Fin; Fitzgerald, Paul

2013-12-01

Over the last decade major progress has been made in developing both the theoretical and practical aspects of apatite (U-Th)/He thermochronometry and it is now standard practice, and generally seen as best practice, to analyse single grain aliquots. These individual prismatic crystals are often broken and are fragments of larger crystals that have broken during mineral separation along the weak basal cleavage in apatite. This is clearly indicated by the common occurrence of only 1 or no clear crystal terminations present on separated apatite grains, and evidence of freshly broken ends when grains are viewed using a scanning electron microscope. This matters because if the 4He distribution within the whole grain is not homogeneous, because of partial loss due to thermal diffusion for example, then the fragments will all yield ages different from each other and from the whole grain age. Here we use a numerical model with a finite cylinder geometry to approximate 4He ingrowth and thermal diffusion within hexagonal prismatic apatite crystals. This is used to quantify the amount and patterns of inherent, natural age dispersion that arises from analysing broken crystals. A series of systematic numerical experiments were conducted to explore and quantify the pattern and behaviour of this source of dispersion using a set of 5 simple thermal histories that represent a range of plausible geological scenarios. In addition some more complex numerical experiments were run to investigate the pattern and behaviour of grain dispersion seen in several real data sets. The results indicate that natural dispersion of a set of single fragment ages (defined as the range divided by the mean) arising from fragmentation alone varies from c. 7% even for rapid (c. 10 °C/Ma), monotonic cooling to over 50% for protracted, complex histories that cause significant diffusional loss of 4He. The magnitude of dispersion arising from fragmentation scales with the grain cylindrical radius, and is of a similar magnitude to dispersion expected from differences in absolute grain size alone (spherical equivalent radii of 40-150 μm). This source of dispersion is significant compared with typical analytical uncertainties on individual grain analyses (c. 6%) and standard deviations on multiple grain analyses from a single sample (c. 10-20%). Where there is a significant difference in the U and Th concentration of individual grains (eU), the effect of radiation damage accumulation on 4He diffusivity (assessed using the RDAAM model of Flowers et al. (2009)) is the primary cause of dispersion for samples that have experienced a protracted thermal history, and can cause dispersion in excess of 100% for realistic ranges of eU concentration (i.e. 5-100 ppm). Expected natural dispersion arising from the combined effects of reasonable variations in grain size (radii 40-125 μm), eU concentration (5-150 ppm) and fragmentation would typically exceed 100% for complex thermal histories. In addition to adding a significant component of natural dispersion to analyses, the effect of fragmentation also acts to decouple and corrupt expected correlations between grain ages and absolute grain size and to a lesser extent between grain age and effective uranium concentration (eU). Considering fragmentation explicitly as a source of dispersion and analysing how the different sources of natural dispersion all interact with each other provides a quantitative framework for understanding patterns of dispersion that otherwise appear chaotic. An important outcome of these numerical experiments is that they demonstrate that the pattern of age dispersion arising from fragmentation mimics the pattern of 4He distribution within the whole grains, thus providing an important source of information about the thermal history of the sample. We suggest that if the primary focus of a study is to extract the thermal history information from (U-Th)/He analyses then sampling and analytical strategies should aim to maximise the natural dispersion of grain ages, not minimise it, and should aim to analyse circa 20-30 grains from each sample. The key observations and conclusions drawn here are directly applicable to other thermochronometers, such as the apatite, rutile and titanite U-Pb systems, where the diffusion domain is approximated by the physical grain size.

The spectral changes of deforestation in the Brazilian tropical savanna.

PubMed

Trancoso, Ralph; Sano, Edson E; Meneses, Paulo R

2015-01-01

The Cerrado is a biome in Brazil that is experiencing the most rapid loss in natural vegetation. The objective of this study was to analyze the changes in the spectral response in the red, near infrared (NIR), middle infrared (MIR), and normalized difference vegetation index (NDVI) when native vegetation in the Cerrado is deforested. The test sites were regions of the Cerrado located in the states of Bahia, Minas Gerais, and Mato Grosso. For each region, a pair of Landsat Thematic Mapper (TM) scenes from 2008 (before deforestation) and 2009 (after deforestation) was compared. A set of 1,380 samples of deforested polygons and an equal number of samples of native vegetation have their spectral properties statistically analyzed. The accuracy of deforestation detections was also evaluated using high spatial resolution imagery. Results showed that the spectral data of deforested areas and their corresponding native vegetation were statistically different. The red band showed the highest difference between the reflectance data from deforested areas and native vegetation, while the NIR band showed the lowest difference. A consistent pattern of spectral change when native vegetation in the Cerrado is deforested was identified regardless of the location in the biome. The overall accuracy of deforestation detections was 97.75%. Considering both the marked pattern of spectral changes and the high deforestation detection accuracy, this study suggests that deforestation in Cerrado can be accurately monitored, but a strong seasonal and spatial variability of spectral changes might be expected.

Spatial image modulation to improve performance of computed tomography imaging spectrometer

NASA Technical Reports Server (NTRS)

Bearman, Gregory H. (Inventor); Wilson, Daniel W. (Inventor); Johnson, William R. (Inventor)

2010-01-01

Computed tomography imaging spectrometers ("CTIS"s) having patterns for imposing spatial structure are provided. The pattern may be imposed either directly on the object scene being imaged or at the field stop aperture. The use of the pattern improves the accuracy of the captured spatial and spectral information.

The Impact of Phosphorylation on Electron Capture Dissociation of Proteins: A Top-Down Perspective

NASA Astrophysics Data System (ADS)

Chen, Bifan; Guo, Xiao; Tucholski, Trisha; Lin, Ziqing; McIlwain, Sean; Ge, Ying

2017-09-01

Electron capture dissociation (ECD) is well suited for the characterization of phosphoproteins, with which labile phosphate groups are generally preserved during the fragmentation process. However, the impact of phosphorylation on ECD fragmentation of intact proteins remains unclear. Here, we have performed a systematic investigation of the phosphorylation effect on ECD of intact proteins by comparing the ECD cleavages of mono-phosphorylated α-casein, multi-phosphorylated β-casein, and immunoaffinity-purified phosphorylated cardiac troponin I with those of their unphosphorylated counterparts, respectively. In contrast to phosphopeptides, phosphorylation has significantly reduced deleterious effects on the fragmentation of intact proteins during ECD. On a global scale, the fragmentation patterns are highly comparable between unphosphorylated and phosphorylated precursors under the same ECD conditions, despite a slight decrease in the number of fragment ions observed for the phosphorylated forms. On a local scale, single phosphorylation of intact proteins imposes minimal effects on fragmentation near the phosphorylation sites, but multiple phosphorylations in close proximity result in a significant reduction of ECD bond cleavages. [Figure not available: see fulltext.

Seed-dispersal distributions by trumpeter hornbills in fragmented landscapes

PubMed Central

Lenz, Johanna; Fiedler, Wolfgang; Caprano, Tanja; Friedrichs, Wolfgang; Gaese, Bernhard H.; Wikelski, Martin; Böhning-Gaese, Katrin

2011-01-01

Frugivorous birds provide important ecosystem services by transporting seeds of fleshy fruited plants. It has been assumed that seed-dispersal kernels generated by these animals are generally leptokurtic, resulting in little dispersal among habitat fragments. However, little is known about the seed-dispersal distribution generated by large frugivorous birds in fragmented landscapes. We investigated movement and seed-dispersal patterns of trumpeter hornbills (Bycanistes bucinator) in a fragmented landscape in South Africa. Novel GPS loggers provide high-quality location data without bias against recording long-distance movements. We found a very weakly bimodal seed-dispersal distribution with potential dispersal distances up to 14.5 km. Within forest, the seed-dispersal distribution was unimodal with an expected dispersal distance of 86 m. In the fragmented agricultural landscape, the distribution was strongly bimodal with peaks at 18 and 512 m. Our results demonstrate that seed-dispersal distributions differed when birds moved in different habitat types. Seed-dispersal distances in fragmented landscapes show that transport among habitat patches is more frequent than previously assumed, allowing plants to disperse among habitat patches and to track the changing climatic conditions. PMID:21177686

rRNA gene restriction patterns as an epidemiological marker in nosocomial outbreaks of Staphylococcus aureus infections.

PubMed

Meugnier, H; Fernandez, M P; Bes, M; Brun, Y; Bornstein, N; Freney, J; Fleurette, J

1993-01-01

rRNA gene restriction patterns (ribotyping) were compared with phage typing, serotyping, enterotoxins and exfoliatin production in the analysis of 26 Staphylococcus aureus strains isolated from two different nosocomial outbreaks. Total DNA was cleaved by EcoRI restriction endonuclease. After agarose gel electrophoresis and Southern transfer, the hybridization of the membranes was done with radiolabelled 16S rRNA gene from Bacillus subtilis inserted into a plasmid vector. Six to 13 fragments were visualized. A core of common fragments was discerned for all strains tested. A full correlation between ribotyping and conventional markers was observed in only one of the outbreaks studied. In both outbreaks, ribotyping proved helpful in characterizing otherwise untypable strains.

DNA fingerprinting of isolates of Streptococcus mutans by pulsed-field gel electrophoresis.

PubMed

Mineyama, R; Yoshino, S; Maeda, N

2007-01-01

Forty isolates and five standard laboratory strains, representing serotypes c, e and f of Streptococcus mutans were analyzed by pulsed-field gel electrophoresis (PFGE) after digestion of the genomic DNA with BssH II. The digestion patterns of standard laboratory strains were characteristic of serotypes c, e and f. Serotypes c and f generated diagnostic DNA fragments of approximately 145 kbp and of approximately 130-175 kbp in length, respectively. Serotype e generated a ladder of at least 14 fragments of 15-155 kbp in length. The digestion patterns of isolates were essentially similar to those of the standard laboratory strains. The patterns of almost all isolates obtained from a single individual were identical, but patterns of a few different types were also observed among isolates obtained from two individuals. Digestion with BssH II revealed differences among isolates obtained from different individuals. We used differences in banding patterns among isolates to construct a dendrogram. The dendrogram included two major clusters, one that consisted of isolates of serotypes c and f, and an other that consisted of isolates of serotype e. Our results indicate that BssH II is a useful enzyme for distinguishing among isolates of S. mutans and that digestion patterns obtained by PFGE can be used for chromosomal DNA fingerprinting.

Methodology for diagnosing of skin cancer on images of dermatologic spots by spectral analysis.

PubMed

Guerra-Rosas, Esperanza; Álvarez-Borrego, Josué

2015-10-01

In this paper a new methodology for the diagnosing of skin cancer on images of dermatologic spots using image processing is presented. Currently skin cancer is one of the most frequent diseases in humans. This methodology is based on Fourier spectral analysis by using filters such as the classic, inverse and k-law nonlinear. The sample images were obtained by a medical specialist and a new spectral technique is developed to obtain a quantitative measurement of the complex pattern found in cancerous skin spots. Finally a spectral index is calculated to obtain a range of spectral indices defined for skin cancer. Our results show a confidence level of 95.4%.

Methodology for diagnosing of skin cancer on images of dermatologic spots by spectral analysis

PubMed Central

Guerra-Rosas, Esperanza; Álvarez-Borrego, Josué

2015-01-01

In this paper a new methodology for the diagnosing of skin cancer on images of dermatologic spots using image processing is presented. Currently skin cancer is one of the most frequent diseases in humans. This methodology is based on Fourier spectral analysis by using filters such as the classic, inverse and k-law nonlinear. The sample images were obtained by a medical specialist and a new spectral technique is developed to obtain a quantitative measurement of the complex pattern found in cancerous skin spots. Finally a spectral index is calculated to obtain a range of spectral indices defined for skin cancer. Our results show a confidence level of 95.4%. PMID:26504638

Progressively expanded neural network for automatic material identification in hyperspectral imagery

NASA Astrophysics Data System (ADS)

Paheding, Sidike

The science of hyperspectral remote sensing focuses on the exploitation of the spectral signatures of various materials to enhance capabilities including object detection, recognition, and material characterization. Hyperspectral imagery (HSI) has been extensively used for object detection and identification applications since it provides plenty of spectral information to uniquely identify materials by their reflectance spectra. HSI-based object detection algorithms can be generally classified into stochastic and deterministic approaches. Deterministic approaches are comparatively simple to apply since it is usually based on direct spectral similarity such as spectral angles or spectral correlation. In contrast, stochastic algorithms require statistical modeling and estimation for target class and non-target class. Over the decades, many single class object detection methods have been proposed in the literature, however, deterministic multiclass object detection in HSI has not been explored. In this work, we propose a deterministic multiclass object detection scheme, named class-associative spectral fringe-adjusted joint transform correlation. Human brain is capable of simultaneously processing high volumes of multi-modal data received every second of the day. In contrast, a machine sees input data simply as random binary numbers. Although machines are computationally efficient, they are inferior when comes to data abstraction and interpretation. Thus, mimicking the learning strength of human brain has been current trend in artificial intelligence. In this work, we present a biological inspired neural network, named progressively expanded neural network (PEN Net), based on nonlinear transformation of input neurons to a feature space for better pattern differentiation. In PEN Net, discrete fixed excitations are disassembled and scattered in the feature space as a nonlinear line. Each disassembled element on the line corresponds to a pattern with similar features. Unlike the conventional neural network where hidden neurons need to be iteratively adjusted to achieve better accuracy, our proposed PEN Net does not require hidden neurons tuning which achieves better computational efficiency, and it has also shown superior performance in HSI classification tasks compared to the state-of-the-arts. Spectral-spatial features based HSI classification framework has shown stronger strength compared to spectral-only based methods. In our lastly proposed technique, PEN Net is incorporated with multiscale spatial features (i.e., multiscale complete local binary pattern) to perform a spectral-spatial classification of HSI. Several experiments demonstrate excellent performance of our proposed technique compared to the more recent developed approaches.

Crystallization of DNA fragments from water-salt solutions, containing 2-methylpentane-2,3-diol.

PubMed

Osica, V D; Sukharevsky, B Y; Vasilchenko, V N; Verkin, B I; Polyvtsev, O F

1976-09-01

Fragments of calf thymus DNA have been crystallized by precipitation from water-salt solutions, containing 2-methylpentane-2,3-diol (MPD). DNA crystals usually take the form either of spherulites up to 100 mu in diameter or of needles with the length up to 50 mu. No irreversible denaturation of DNA occurs during the crystallization process. X-ray diffraction from dense slurries of DNA crystals yields crystalline powder patterns.

Rapid identification of Campylobacter, Arcobacter, and Helicobacter isolates by PCR-restriction fragment length polymorphism analysis of the 16S rRNA gene.

PubMed

Marshall, S M; Melito, P L; Woodward, D L; Johnson, W M; Rodgers, F G; Mulvey, M R

1999-12-01

A rapid two-step identification scheme based on PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 16S rRNA gene was developed in order to differentiate isolates belonging to the Campylobacter, Arcobacter, and Helicobacter genera. For 158 isolates (26 reference cultures and 132 clinical isolates), specific RFLP patterns were obtained and species were successfully identified by this assay.

Effects of food availability and climate on activity patterns of western black-crested gibbons in an isolated forest fragment in southern Yunnan, China.

PubMed

Ni, Qingyong; Xie, Meng; Grueter, Cyril C; Jiang, Xuelong; Xu, Huailiang; Yao, Yongfang; Zhang, Mingwang; Li, Yan; Yang, Jiandong

2015-10-01

The critically endangered western black-crested gibbon (Nomascus concolor) is distributed in isolated habitat fragments in northern Vietnam, northwestern Laos, and southwestern China. To assess the behavioral adaptation of this species to forest fragments and its response to seasonal variation in food availability and climate, we present activity patterns of a group inhabiting an isolated forest based on two year-long studies in southern Yunnan, China. Annually, the gibbons spent nearly half of their active time resting, followed by moving and feeding. In both study periods, the time allocated to activities varied significantly between months, and was affected by food availability and climate factors. The group delayed retirement when tree fruit was abundant, and they decreased time spent moving and playing during periods of low fruit availability. In the cold months, the gibbons decreased time spent moving, and they decreased active time and resting time when rainfall was high. The results suggest that the group may seek to maximize net energy intake like energy maximizers when high quality food is most available, and adopt an energy-conserving strategy during periods of lower food availability and temperature. The gibbons showed similar diurnal variation in activity patterns to a group inhabiting a continuous forest at Dazhaizi, Mt. Wuliang, central Yunnan. However, they had a longer active period, and devoted more time to resting but less time to feeding. The individuals also spent lower percentages of time engaged in social behavior than those at Dazhaizi. These differences may be due to their smaller home range and unusual group composition caused by habitat fragmentation.

Patterns of bird functional diversity on land-bridge island fragments.

PubMed

Ding, Zhifeng; Feeley, Kenneth J; Wang, Yanping; Pakeman, Robin J; Ding, Ping

2013-07-01

The loss of species diversity due to habitat fragmentation has been extensively studied. In contrast, the impacts of habitat fragmentation on functional diversity remains relatively poorly understood. We conducted bird functional diversity studies on a set of 41 recently isolated land-bridge islands in the Thousand Island Lake, China. We analysed differences in bird species richness and a recently developed suite of complementary functional diversity indices (FRic, volume of functional space occupied; FEve, evenness of abundance distribution in the functional trait space; FDiv, divergence in the distribution of abundance in the trait volume) across different gradients (island area and isolation). We found no correlations between FRic and FEve or FEve and FDiv, but negative correlations between FRic and FDiv. As predicted, island area accounted for most of the variation in bird species richness, whereas isolation explained most of the variation in species evenness (decreasing species evenness with increasing isolation). Functional diversity appears to be more strongly influenced by habitat filtering as opposed to limiting similarity. More specifically, across all islands, both FRic and FEve were significantly lower than expected for randomly assembled communities, but FDiv showed no clear patterns. FRic increased with island area, FEve decreased with island area and FDiv showed no clear patterns. Our finding that FEve decreases with island area at TIL may indicate low functional stability on such islands, and as such large islands and habitat patches may deserve extra attention and/or protection. These results help to demonstrate the importance of considering the effects of fragmentation on functional diversity in habitat management and reserve design plans. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Scanning force microscopy and fluorescence microscopy of microcontact printed antibodies and antibody fragments.

PubMed

LaGraff, John R; Chu-LaGraff, Quynh

2006-05-09

Unlabeled primary immunoglobulin G (IgG) antibodies and its F(ab')2 and Fc fragments were attached to oxygen-plasma-cleaned glass substrates using either microcontact printing (MCP) or physical adsorption during bath application from dilute solutions. Fluorescently labeled secondary IgGs were then bound to surface-immobilized IgG, and the relative surface coverage was determined by measuring the fluorescence intensity. Results indicated that the surface coverage of IgG increased with increasing protein solution concentration for both MCP and bath-applied IgG and that a greater concentration of IgG was transferred to a glass substrate using MCP than during physisorption during bath applications. Scanning force microscopy (SFM) showed that patterned MCP IgG monolayers were 5 nm in height, indicating that IgG molecules lie flat on the substrate. After incubation with a secondary IgG, the overall line thickness increased to around 15 nm, indicating that the secondary IgG was in a more vertical orientation with respect to the substrate. The surface roughness of these MCP patterned IgG bilayers as measured by SFM was observed to increase with increasing surface coverage. Physisorption of IgG to both unmodified patterned polydimethylsiloxane (PDMS) stamps and plasma-cleaned glass substrates was modeled by Langmuir adsorption kinetics yielding IgG binding constants of K(MCP) = 1.7(2) x 10(7) M(-1) and K(bath) = 7.8(7) x 10(5) M(-1), respectively. MCP experiments involving primary F(ab')2 and Fc fragments incubated in fluorescently labeled fragment-specific secondary IgGs were carried out to test for the function and orientation of IgG. Finally, possible origins of MCP stamping defects such as pits, pull outs, droplets, and reverse protein transfer are discussed.

Searching for a Differentiated Asteroid Family: A Spectral Survey of the Massalia, Merxia, and Agnia Families

NASA Astrophysics Data System (ADS)

Thomas, Cristina A.; Moskovitz, Nicholas; Lim, Lucy F.; Trilling, David E.

2017-10-01

Asteroid families were formed by catastrophic collisions or large cratering events that caused fragmentation of the parent body and ejection of asteroidal fragments with velocities sufficient to prevent re-accretion. Due to these formation processes, asteroid families provide us with the opportunity to probe the interiors of the former parent bodies. Differentiation of a large initially chondritic parent body is expected to result in an “onion shell" object with an iron-nickel core, a thick olivine-dominated mantle, and a thin plagioclase/pyroxene crust. However, most asteroid families tend to show similar spectra (and therefore composition) among the members. Spectroscopic studies have observed a paucity of metal-like materials and olivine-dominated assemblages within Main Belt asteroid families.The deficit of olivine-rich mantle material in the meteorite record and in asteroid observations is known as the “Missing Mantle" problem. For years the best explanation has been the “battered to bits" hypothesis: differentiated parent bodies (aside from Vesta) were disrupted very early in the Solar System and the olivine-rich material was collisionally broken down over time. Alternatively, Elkins-Tanton et al. (2013) have suggested that previous work has overestimated the amount of olivine produced by the differentiation of a chondritic parent body.We have completed a visible and near-infrared wavelength spectral survey of asteroids in the Massalia, Merxia, and Agnia S-type Main Belt asteroid families. These families were carefully chosen for the spectroscopic survey because they have compositions most closely associated with a history of thermal metamorphism and because they represent a range of collisional formation scenarios. Additionally, members of the Merxia and Agnia families were identified as products of differentiation by Sunshine et al. (2004).Our spectral analyses suggest that the observed families contain products of partial differentiation. We will present results from our spectral survey of these three families and discuss any evidence of differentiation among the family members. We will discuss our band parameter analyses and compositional results from the Modified Gaussian Model (MGM).

Applied light-side coupling with optimized spiral-patterned zinc oxide nanorod coatings for multiple optical channel alcohol vapor sensing

NASA Astrophysics Data System (ADS)

Bin Abdul Rahim, Hazli Rafis; Bin Lokman, Muhammad Quisar; Harun, Sulaiman Wadi; Hornyak, Gabor Louis; Sterckx, Karel; Mohammed, Waleed Soliman; Dutta, Joydeep

2016-07-01

The width of spiral-patterned zinc oxide (ZnO) nanorod coatings on plastic optical fiber (POF) was optimized theoretically for light-side coupling and found to be 5 mm. Structured ZnO nanorods were grown on large core POFs for the purpose of alcohol vapor sensing. The aim of the spiral patterns was to enhance signal transmission by reduction of the effective ZnO growth area, thereby minimizing light leakage due to backscattering. The sensing mechanism utilized changes in the output signal due to adsorption of methanol, ethanol, and isopropanol vapors. Three spectral bands consisting of red (620 to 750 nm), green (495 to 570 nm), and blue (450 to 495 nm) were applied in measurements. The range of relative intensity modulation (RIM) was determined to be for concentrations between 25 to 300 ppm. Methanol presented the strongest response compared to ethanol and isopropanol in all three spectral channels. With regard to alcohol detection RIM by spectral band, the green channel demonstrated the highest RIM values followed by the blue and red channels, respectively.

The effect of spatial and spectral heterogeneity of ground-based light sources on night-sky radiances

NASA Astrophysics Data System (ADS)

Kocifaj, M.; Aubé, M.; Kohút, I.

2010-12-01

Nowadays, light pollution is a permanent problem at many observatories around the world. Elimination of excessive lighting during the night is not only about reduction of the total luminous power of ground-based light sources, but also involves experimenting with the spectral features of single lamps. Astronomical photometry is typically made at specific wavelengths, and thus the analysis of the spectral effects of light pollution is highly important. Nevertheless, studies on the spectral behaviour of night light are quite rare. Instead, broad-band or integral quantities (such as sky luminance) are preferentially measured and modelled. The knowledge of night-light spectra is necessary for the proper interpretation of narrow-band photometry data. In this paper, the night-sky radiances in the nominal spectral lines of the B (445 nm) and V (551 nm) filters are determined numerically under clear-sky conditions. Simultaneously, the corresponding sky-luminance patterns are computed and compared against the spectral radiances. It is shown that spectra, patterns and distances of the most important light sources (towns) surrounding an observatory are essential for determining the light pollution levels. In addition, the optical characteristics of the local atmosphere can change the angular behaviour of the sky radiance or luminance. All these effects are evaluated for two Slovakian observatories: Stará Lesná and Vartovka.

Fragmentation of relativistic nuclei in peripheral interactions in nuclear track emulsion

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

Artemenkov, D. A., E-mail: artemenkov@lhe.jinr.ru; Bradnova, V.; Chernyavsky, M. M.

2008-09-15

The technique of nuclear track emulsions is used to explore the fragmentation of light relativistic nuclei down to the most peripheral interactions: nuclear 'white' stars. A complete pattern of the relativistic dissociation of a 8B nucleus with target fragment accompaniment is presented. Relativistic dissociation {sup 9}Be {yields} 2{alpha} is explored using significant statistics, and a relative contribution of {sup 8}Be decays from 0+ and 2+ states is established. Target fragment accompaniments are shown for relativistic fragmentation {sup 14}N {yields} 3He +H and {sup 22}Ne {yields} 5He. The leading role of the electromagnetic dissociation on heavy nuclei with respect to breakupsmore » on target protons is demonstrated in all these cases. It is possible to conclude that the peripheral dissociation of relativistic nuclei in nuclear track emulsion is a unique tool to study many-body systems composed of the lightest nuclei and nucleons in the energy scale relevant for nuclear astrophysics.« less

Fragmentation studies of fulvic acids using collision induced dissociation fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Witt, Matthias; Fuchser, Jens; Koch, Boris P

2009-04-01

The complex natural organic matter standard Suwannee river fulvic acid (SRFA) was analyzed by negative ion mode electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FTICR MS) using on-resonance collision induced dissociation (CID) of single ultrahigh resolved mass peaks in the ICR cell. Molecular formula assignment of precursor masses resulted in exactly one molecular formula for each of the peaks. Analyses of the corresponding fragment spectra and comparison to different standard substances revealed specific neutral losses and fragmentation patterns which result in structures consisting of a high degree of carboxyl- and fewer hydroxyl groups. The comparison of fragmented mass peaks within different pseudohomologous series (CH(2)-series, and CH(4) vs O exchange) suggested structurally based differences between these series. CID FTICR MS allowed isolating single mass peaks in a very complex natural organic matter spectrum. Subsequently, fragmentation gave structural insights into this material. Our results suggest that the structural diversity in complex humic substances is not as high as expected.

Halogeno-substituted 2-aminobenzoic acid derivatives for negative ion fragmentation studies of N-linked carbohydrates.

PubMed

Harvey, David J

2005-01-01

Negative ion electrospray mass spectra of high-mannose N-linked glycans derivatised with 2-aminobenzoic acids and ionised from solutions containing ammonium hydroxide gave prominent [M-H](-) ions accompanied by weaker [M-2H](2-) ions. Fragmentation of both types of ions gave prominent singly charged glycosidic cleavage ions containing the derivatised reducing terminus and ions from the non-reducing terminus that appeared to be products of cross-ring cleavages. Differentiation of these two groups of ions was conveniently achieved in a single spectrum by use of chloro- or bromo-substituted benzoic acids in order to label ions containing the derivative with an atom with a distinctive isotope pattern. Fragmentation of the doubly charged ions gave more abundant fragments, both singly and doubly charged, than did fragmentation of the singly charged ions, but information of chain branching was masked by the appearance of prominent ions produced by internal cleavages. Copyright (c) 2005 John Wiley & Sons, Ltd.

Assessing rates of forest change and fragmentation in Alabama, USA, using the vegetation change tracker model

USGS Publications Warehouse

Li, Mingshi; Huang, Chengquan; Zhu, Zhiliang; Shi, Hua; Lu, Heng; Peng, Shikui

2009-01-01

Forest change is of great concern for land use decision makers and conservation communities. Quantitative and spatial forest change information is critical for addressing many pressing issues, including global climate change, carbon budgets, and sustainability. In this study, our analysis focuses on the differences in geospatial patterns and their changes between federal forests and nonfederal forests in Alabama over the time period 1987–2005, by interpreting 163 Landsat Thematic Mapper (TM) scenes using a vegetation change tracker (VCT) model. Our analysis revealed that for the most part of 1990 s and between 2000 and 2005, Alabama lost about 2% of its forest on an annual basis due to disturbances, but much of the losses were balanced by forest regeneration from previous disturbances. The disturbance maps revealed that federal forests were reasonably well protected, with the fragmentation remaining relatively stable over time. In contrast, nonfederal forests, which are predominant in area share (about 95%), were heavily disturbed, clearly demonstrating decreasing levels of fragmentation during the time period 1987–1993 giving way to a subsequent accelerating fragmentation during the time period 1994–2005. Additionally, the identification of the statistical relationships between forest fragmentation status and forest loss rate and forest net change rate in relation to land ownership implied the distinct differences in forest cutting rate and cutting patterns between federal forests and nonfederal forests. The forest spatial change information derived from the model has provided valuable insights regarding regional forest management practices and disturbance regimes, which are closely associated with regional economics and environmental concerns.

Synergistic interactions between edge and area effects in a heavily fragmented landscape.

PubMed

Ewers, Robert M; Thorpe, Stephen; Didham, Raphael K

2007-01-01

Both area and edge effects have a strong influence on ecological processes in fragmented landscapes, but there is little understanding of how these two factors might interact to exacerbate local species declines. To test for synergistic interactions between area and edge effects, we sampled a diverse beetle community in a heavily fragmented landscape in New Zealand. More than 35,000 beetles of approximately 900 species were sampled over large gradients in habitat area (10(-2) 10(6) ha) and distance from patch edge (2(0)-2(10) m from the forest edge into both the forest and adjacent matrix). Using a new approach to partition variance following an ordination analysis, we found that a synergistic interaction between habitat area and distance to edge was a more important determinant of patterns in beetle community composition than direct edge or area effects alone. The strength of edge effects in beetle-species composition increased nonlinearly with increasing fragment area. One important consequence of the synergy is that the slopes of species area (SA) curves constructed from habitat islands depend sensitively on the distance from edge at which sampling is conducted. Surprisingly, we found negative SA curves for communities sampled at intermediate distances from habitat edges, caused by differential edge responses of matrix- vs. forest-specialist species in fragments of increasing area. Our data indicate that distance to habitat edge has a consistently greater impact on beetle community composition than habitat area and that variation in the strength of edge effects may underlie many patterns that are superficially related to habitat area.

Characterization of epoxy carotenoids by fast atom bombardment collision-induced dissociation MS/MS.

PubMed

Maoka, Takashi; Fujiwara, Yasuhiro; Hashimoto, Keiji; Akimoto, Naoshige

2004-02-01

The characterization and structure of epoxy carotenoids possessing 5,6-epoxy, 5,8-epoxy and 3,6-epoxy end groups conjugated to the polyene chain were investigated using high-energy fast atom bombardment collision-induced dissociation MS/MS methods. In addition to [M - 80](+*), a characteristic fragment ion of an epoxy carotenoid, product ions resulting from the cleavage of C-C bonds in the polyene chain from the epoxy end group, such as m/z 181 (b ion) and 121 (c ion), were detected. On the other hand, diagnostic ions of m/z 286 (e-H ion) and 312 (f-H ion) were observed, not in the 5,6-epoxy or 5,8-epoxy carotenoid but in the 3,6-epoxy carotenoid. These fragmentation patterns can be used to distinguish 3,6-epoxy carotenoids from 5,6-epoxy or 5,8-epoxy carotenoids. The structure of an epoxy carotenoid, 3,6-epoxy-5,6-dihydro-7',8'-didehydro-beta,beta-carotene-5,3'-diol (8), isolated from oyster, was characterized using FAB CID-MS/MS by comparing fragmentation patterns with those of related known compounds.

Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin

NASA Astrophysics Data System (ADS)

Lermyte, Frederik; Łącki, Mateusz Krzysztof; Valkenborg, Dirk; Gambin, Anna; Sobott, Frank

2017-01-01

Owing to its versatility, electron transfer dissociation (ETD) has become one of the most commonly utilized fragmentation techniques in both native and non-native top-down mass spectrometry. However, several competing reactions—primarily different forms of charge reduction—occur under ETD conditions, as evidenced by the distorted isotope patterns usually observed. In this work, we analyze these isotope patterns to compare the stability of nondissociative electron transfer (ETnoD) products, specifically noncovalent c/ z fragment complexes, across a range of ubiquitin conformational states. Using ion mobility, we find that more extended states are more prone to fragment release. We obtain evidence that for a given charge state, populations of ubiquitin ions formed either directly by electrospray ionization or through collapse of more extended states upon charge reduction, span a similar range of collision cross-sections. Products of gas-phase collapse are, however, less stabilized towards unfolding than the native conformation, indicating that the ions retain a memory of previous conformational states. Furthermore, this collapse of charge-reduced ions is promoted if the ions are `preheated' using collisional activation, with possible implications for the kinetics of gas-phase compaction.

Urban sprawl and fragmentation in Latin America: a dynamic quantification and characterization of spatial patterns.

PubMed

Inostroza, Luis; Baur, Rolf; Csaplovics, Elmar

2013-01-30

South America is one of the most urbanized continents in the world, where almost 84% of the total population lives in cities, more urbanized than North America (82%) and Europe (73%). Spatial dynamics, their structure, main features, land consumption rates, spatial arrangement, fragmentation degrees and comparability, remain mostly unknown for most Latin American cities. Using satellite imagery the main parameters of sprawl are quantified for 10 Latin American cities over a period of 20 years by monitoring growth patterns and identifying spatial metrics to characterize urban development and sprawling features measured with GIS tools. This quantification contributes to a better understanding of urban form in Latin America. A pervasive spatial expansion has been observed, where most of the studied cities are expanding at fast rates with falling densities trend. Although important differences in the rates of land consumption and densities exist, there is an underlying fragmentation trend towards increasing sprawl. These trends of spatial discontinuity may eventually be intensified by further economic development. Urban Sprawl/Latin America/GIS metrics/spatial development. Copyright © 2012 Elsevier Ltd. All rights reserved.

Peculiarities of RFLP of highly repetitive DNA in crow genomes

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

Chelomina, G.N.; Kryukov, A.P.; Ivanov, S.V.

1995-02-01

We present a study of the structural organization of highly repetitive DNA in genomes of hooded crow Corvus cornix L., carrion crow C. corone L., and jungle crow C. macrorhynchos Wagl. RFLP and blot-hybridization with {sup 32}P-labeled Msp I fragment from hooded crow nDNA suggest the interspecific structural conservatism of the most repetitive DNA. The family of repeats we studied had tandem organization and the same (210 bp) period of reiteration for a set of restriction enzymes. However, in parallel to the general similarity of restriction patterns, there are species-specific peculiarities. The repetitive family revealed (Alu I, BsuR I, andmore » Msp I fragments) has quantitative RFLP of nDNA and interspecific differences in the extent of the multimer {open_quotes}ladder{close_quotes} pattern of Msp I fragments. The latter is more pronounced in nDNA of carrion crow than in that of phylogenetically distant jungle crow and closely related hooded crow. This suggests a recent amplification event for highly organized homological repeats in crow genomes. 10 refs., 2 figs.« less

Wide-field depth-sectioning fluorescence microscopy using projector-generated patterned illumination

NASA Astrophysics Data System (ADS)

Delica, Serafin; Mar Blanca, Carlo

2007-10-01

We present a simple and cost-effective wide-field, depth-sectioning, fluorescence microscope utilizing a commercial multimedia projector to generate excitation patterns on the sample. Highly resolved optical sections of fluorescent pollen grains at 1.9 μm axial resolution are constructed using the structured illumination technique. This requires grid excitation patterns to be scanned across the sample, which is straightforwardly implemented by creating slideshows of gratings at different phases, projecting them onto the sample, and synchronizing camera acquisition with slide transition. In addition to rapid dynamic pattern generation, the projector provides high illumination power and spectral excitation selectivity. We exploit these properties by imaging mouse neural cells in cultures multistained with Alexa 488 and Cy3. The spectral and structural neural information is effectively resolved in three dimensions. The flexibility and commercial availability of this light source is envisioned to open multidimensional imaging to a broader user base.

A median-Gaussian filtering framework for Moiré pattern noise removal from X-ray microscopy image.

PubMed

Wei, Zhouping; Wang, Jian; Nichol, Helen; Wiebe, Sheldon; Chapman, Dean

2012-02-01

Moiré pattern noise in Scanning Transmission X-ray Microscopy (STXM) imaging introduces significant errors in qualitative and quantitative image analysis. Due to the complex origin of the noise, it is difficult to avoid Moiré pattern noise during the image data acquisition stage. In this paper, we introduce a post-processing method for filtering Moiré pattern noise from STXM images. This method includes a semi-automatic detection of the spectral peaks in the Fourier amplitude spectrum by using a local median filter, and elimination of the spectral noise peaks using a Gaussian notch filter. The proposed median-Gaussian filtering framework shows good results for STXM images with the size of power of two, if such parameters as threshold, sizes of the median and Gaussian filters, and size of the low frequency window, have been properly selected. Copyright © 2011 Elsevier Ltd. All rights reserved.

Phylogeography of the dark fruit-eating bat Artibeus obscurus in the Brazilian Amazon.

PubMed

Ferreira, Wallax Augusto Silva; Borges, Bárbara do Nascimento; Rodrigues-Antunes, Symara; de Andrade, Fernanda Atanaena Gonçalves; Aguiar, Gilberto Ferreira de Souza; de Sousa e Silva-Junior, José; Marques-Aguiar, Suely Aparecida; Harada, Maria Lúcia

2014-01-01

Artibeus obscurus (Mammalia: Chiroptera) is endemic to South America, being found in at least 18 Brazilian states. Recent studies revealed that different populations of this genus present distinct phylogeographic patterns; however, very little is known on the population genetics structure of A. obscurus in the Amazon rainforest. Here, using a fragment (1010bp) of the mitochondrial gene cytochrome b from 87 samples, we investigated patterns of genetic divergence among populations of A. obscurus from different locations in the Brazilian Amazon rainforest and compared them with other Brazilian and South American regions. Analysis of molecular variance (AMOVA), fixation index (Fst) analysis, and phylogeographic patterns showed divergence between two major monophyletic groups, each one corresponding to a geographic region associated with the Atlantic and Amazon forest biomes. The Atlantic forest clusters formed a monophyletic group with a high bootstrap support and a fragmented distribution that follows the pattern predicted by the Refuge Theory. On the other hand, a different scenario was observed for the Amazon forest, where no fragmentation was identified. The AMOVA results revealed a significant geographic heterogeneity in the distribution of genetic variation, with 70% found within populations across the studied populations (Fst values ranging from 0.05864 to 0.09673; φST = 0.55). The intrapopulational analysis revealed that one population (Bragança) showed significant evidence of population expansion, with the formation of 2 distinct phylogroups, suggesting the occurrence of a subspecies or at least a different population in this region. These results also suggest considerable heterogeneity for A. obscurus in the Amazon region.

Generating Customized Verifiers for Automatically Generated Code

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd

2008-01-01

Program verification using Hoare-style techniques requires many logical annotations. We have previously developed a generic annotation inference algorithm that weaves in all annotations required to certify safety properties for automatically generated code. It uses patterns to capture generator- and property-specific code idioms and property-specific meta-program fragments to construct the annotations. The algorithm is customized by specifying the code patterns and integrating them with the meta-program fragments for annotation construction. However, this is difficult since it involves tedious and error-prone low-level term manipulations. Here, we describe an annotation schema compiler that largely automates this customization task using generative techniques. It takes a collection of high-level declarative annotation schemas tailored towards a specific code generator and safety property, and generates all customized analysis functions and glue code required for interfacing with the generic algorithm core, thus effectively creating a customized annotation inference algorithm. The compiler raises the level of abstraction and simplifies schema development and maintenance. It also takes care of some more routine aspects of formulating patterns and schemas, in particular handling of irrelevant program fragments and irrelevant variance in the program structure, which reduces the size, complexity, and number of different patterns and annotation schemas that are required. The improvements described here make it easier and faster to customize the system to a new safety property or a new generator, and we demonstrate this by customizing it to certify frame safety of space flight navigation code that was automatically generated from Simulink models by MathWorks' Real-Time Workshop.

Polychromatic spectral pattern analysis of ultra-weak photon emissions from a human body.

PubMed

Kobayashi, Masaki; Iwasa, Torai; Tada, Mika

2016-06-01

Ultra-weak photon emission (UPE), often designated as biophoton emission, is generally observed in a wide range of living organisms, including human beings. This phenomenon is closely associated with reactive oxygen species (ROS) generated during normal metabolic processes and pathological states induced by oxidative stress. Application of UPE extracting the pathophysiological information has long been anticipated because of its potential non-invasiveness, facilitating its diagnostic use. Nevertheless, its weak intensity and UPE mechanism complexity hinder its use for practical applications. Spectroscopy is crucially important for UPE analysis. However, filter-type spectroscopy technique, used as a conventional method for UPE analysis, intrinsically limits its performance because of its monochromatic scheme. To overcome the shortcomings of conventional methods, the authors developed a polychromatic spectroscopy system for UPE spectral pattern analysis. It is based on a highly efficient lens systems and a transmission-type diffraction grating with a highly sensitive, cooled, charge-coupled-device (CCD) camera. Spectral pattern analysis of the human body was done for a fingertip using the developed system. The UPE spectrum covers the spectral range of 450-750nm, with a dominant emission region of 570-670nm. The primary peak is located in the 600-650nm region. Furthermore, application of UPE source exploration was demonstrated with the chemiluminescence spectrum of melanin and coexistence with oxidized linoleic acid. Copyright © 2016 Elsevier B.V. All rights reserved.

Spatial Pattern of Cell Damage in Tissue from Heavy Ions

NASA Technical Reports Server (NTRS)

Ponomarev, Artem L.; Huff, Janice L.; Cucinotta, Francis A.

2007-01-01

A new Monte Carlo algorithm was developed that can model passage of heavy ions in a tissue, and their action on the cellular matrix for 2- or 3-dimensional cases. The build-up of secondaries such as projectile fragments, target fragments, other light fragments, and delta-rays was simulated. Cells were modeled as a cell culture monolayer in one example, where the data were taken directly from microscopy (2-d cell matrix). A simple model of tissue was given as abstract spheres with close approximation to real cell geometries (3-d cell matrix), as well as a realistic model of tissue was proposed based on microscopy images. Image segmentation was used to identify cells in an irradiated cell culture monolayer, or slices of tissue. The cells were then inserted into the model box pixel by pixel. In the case of cell monolayers (2-d), the image size may exceed the modeled box size. Such image was is moved with respect to the box in order to sample as many cells as possible. In the case of the simple tissue (3-d), the tissue box is modeled with periodic boundary conditions, which extrapolate the technique to macroscopic volumes of tissue. For real tissue, specific spatial patterns for cell apoptosis and necrosis are expected. The cell patterns were modeled based on action cross sections for apoptosis and necrosis estimated based on BNL data, and other experimental data.

Patterns of [PSI+] aggregation allow insights into cellular organization of yeast prion aggregates

PubMed Central

Tyedmers, Jens

2012-01-01

The yeast prion phenomenon is very widespread and mounting evidence suggests that it has an impact on cellular regulatory mechanisms related to phenotypic responses to changing environments. Studying the aggregation patterns of prion amyloids during different stages of the prion life cycle is a first key step to understand major principles of how and where cells generate, organize and turn-over prion aggregates. The induction of the [PSI+] state involves the actin cytoskeleton and quality control compartments such as the Insoluble Protein Deposit (IPOD). An initially unstable transitional induction state can be visualized by overexpression of the prion determinant and displays characteristic large ring- and ribbon-shaped aggregates consisting of poorly fragmented bundles of very long prion fibrils. In the mature prion state, the aggregation pattern is characterized by highly fragmented, shorter prion fibrils that form aggregates, which can be visualized through tagging with fluorescent proteins. The number of aggregates formed varies, ranging from a single large aggregate at the IPOD to multiple smaller ones, depending on several parameters discussed. Aggregate units below the resolution of light microscopy that are detectable by fluorescence correlation spectroscopy are in equilibrium with larger aggregates in this stage and can mediate faithful inheritance of the prion state. Loss of the prion state is often characterized by reduced fragmentation of prion fibrils and fewer, larger aggregates. PMID:22449721

Evolution of the inner asteroid belt: Paradigms and paradoxes from spectral studies

NASA Technical Reports Server (NTRS)

Gaffey, Michael J.

1987-01-01

Recent years have witnessed a significant increase in the sophistication of asteroidal surface material characterizations derived from spectral data. An extensive data base of moderate to high spectral resolution, visible and near-infrared asteroid spectra is now available. Interpretive methodologies and calibrations were developed to determine phase abundance and composition in olivine-pyroxene assemblages and to estimate NiFe metal abundance from such spectra. A modified version of the asteroid classifications system more closely parallels the mineralogic variations of the major inner belt asteroid types. These improvements permit several general conclusions to be drawn concerning the nature of inner belt objects; their history, and that of the inner solar system; and the relationship between the asteroids and meteorites. Essentially all large belt asteroids have or are fragments of parent bodies which have undergone strong post-accretionary heating, varying degrees of melting and magmatic differentiation, and subsequent collisional disruption. These asteroids show a systematic, but not yet well characterized, mineralogic variation with semi-major axis. This suggests that the S-type asteroid families represent relatively recent collisions onto the cores of previously disrupted parent bodies.

Correlation Functions Aid Analyses Of Spectra

NASA Technical Reports Server (NTRS)

Beer, Reinhard; Norton, Robert H., Jr.

1989-01-01

New uses found for correlation functions in analyses of spectra. In approach combining elements of both pattern-recognition and traditional spectral-analysis techniques, spectral lines identified in data appear useless at first glance because they are dominated by noise. New approach particularly useful in measurement of concentrations of rare species of molecules in atmosphere.

Intact Spectral but Abnormal Temporal Processing of Auditory Stimuli in Autism

ERIC Educational Resources Information Center

Groen, Wouter B.; van Orsouw, Linda; ter Huurne, Niels; Swinkels, Sophie; van der Gaag, Rutger-Jan; Buitelaar, Jan K.; Zwiers, Marcel P.

2009-01-01

The perceptual pattern in autism has been related to either a specific localized processing deficit or a pathway-independent, complexity-specific anomaly. We examined auditory perception in autism using an auditory disembedding task that required spectral and temporal integration. 23 children with high-functioning-autism and 23 matched controls…

Habitat fragmentation effects depend on complex interactions between population size and dispersal ability: Modeling influences of roads, agriculture and residential development across a range of life-history characteristics [chapter 20

Treesearch

Samuel A. Cushman; Bradley W. Compton; Kevin McGarigal

2010-01-01

Habitat loss and fragmentation are widely believed to be the most important drivers of extinction (Leakey and Lewin 1995). The habitats in which organisms live are spatially structured at a number of scales, and these patterns interact with organism perception and behavior to drive population dynamics and community structure (Johnson et al. 1992). Anthropogenic habitat...

Analysis of Long Bone and Vertebral Failure Patterns.

DTIC Science & Technology

1983-03-01

apophyseal joints, lumbar spondylosis and low back pain in Jayson, M.I.V. (ed) The Lumbar Spine and Back Pain, Pitman Medical, pp. 83-114. PUBLICATIONS...NOTES Material in this report was presented at the International Society for the Study of the Lumbar Spine, Toronto, Canada, June 6-10, 1982. 19. KEY...intervertebral disc and end plate fragments were observed in the vertebral bodies (G84 L2 -3 ) of the upper lumbar levels. Also fragments of trabecular bone

Molecular Determination of Fasciola Spp. Isolates from Domestic Ruminants Fecal Samples in the Northwest of Iran

PubMed Central

IMANI BARAN, Abbas; CHERAGHI SARAY, Habib; KATIRAEE, Farzad

2017-01-01

Background: Fasciola species are the main causes for fascioliasis with great financial losses and are among the most important food/water-borne parasites worldwide. The basic proceedings such as epidemiology and effective control of fascioliasis rely mainly on precise identification of Fasciola species. The present study was conducted to determine the Fasciola species in ruminant fecal samples from East Azerbaijan Province in Iran. Methods: Overall, 2012 fecal samples were collected and processed initially for microscopic examination of Fasciola eggs in 2014–15. Then, recovered eggs were subjected to molecular identification. A fragment of 618 bp of the 28S rRNA gene pertaining to Fasciola genus was amplified under PCR. The amplified fragment was restricted by fast digest Ava II enzyme in order to a Restriction Fragment Length Polymorphism. Results: Based on microscopic examination, 72 samples were infected, from which, 10 and 62 cases pertained to cattle and sheep samples respectively. Based on RFLP, the PCR products restricted by the Ava II restriction enzyme produced 529 bp fragments only. According to the positive controls, all restriction patterns were related to Fasciola hepatica, while no restriction patterns were linked to F. gigantica. Conclusion: Based on PCR-RFLP, F. hepatica was dominant species in animals of the studied areas and no evidence of F. gigantica was observed. Therefore, further field studies to verify these results are suggested. PMID:28761485

Doppler-free spectroscopy of the atomic rubidium fine structure using ultrafast spatial coherent control method

NASA Astrophysics Data System (ADS)

Kim, Minhyuk; Kim, Kyungtae; Lee, Woojun; Kim, Hyosub; Ahn, Jaewook

2017-04-01

Spectral programming solutions for the ultrafast spatial coherent control (USCC) method to resolve the fine-structure energy levels of atomic rubidium are reported. In USCC, a pair of counter-propagating ultrashort laser pulses are programmed to make a two-photon excitation pattern specific to particular transition pathways and atom species, thus allowing the involved transitions resolvable in space simultaneously. With a proper spectral phase and amplitude modulation, USCC has been also demonstrated for the systems with many intermediate energy levels. Pushing the limit of system complexity even further, we show here an experimental demonstration of the rubidium fine-structure excitation pattern resolvable by USCC. The spectral programming solution for the given USCC is achieved by combining a double-V-shape spectral phase function and a set of phase steps, where the former distinguishes the fine structure and the latter prevents resonant transitions. The experimental results will be presented along with its application in conjunction with the Doppler-free frequency-comb spectroscopy for rubidium hyperfine structure measurements. Samsung Science and Technology Foundation [SSTFBA1301-12].

Impact of Raman scattering on pulse dynamics in a fiber laser with narrow gain bandwidth

NASA Astrophysics Data System (ADS)

Uthayakumar, T.; Alsaleh, M.; Igbonacho, J.; Tchomgo Felenou, E.; Tchofo Dinda, P.; Grelu, Ph; Porsezian, K.

2018-06-01

We examine theoretically the multi-pulse dynamics in a dispersion-managed fiber laser, in which the pulse’s spectral width is controlled by a pass-band filter. We show that in the domain of stable states with very narrow spectral width, i.e. which is one order of magnitude smaller than the bandwidth of the Raman gain of the intra-cavity fiber system, the Raman scattering (RS) significantly alters the multi-pulse dynamics. RS is found to have a greater impact in the immediate vicinity of some critical values of the pump power of the intra-cavity gain medium, where processes of pulse fragmentation occur. As a result, all the borders between the zones of stability of the multi-pulse states are altered, i.e. either shifted or suppressed.

A System for Compressive Spectral and Polarization Imaging at Short Wave Infrared (SWIR) Wavelengths

DTIC Science & Technology

2017-10-18

2016). H. Rueda, H. Arguello and G. R. Arce, “DMD-based implementation of patterned optical filter arrays for compressive spectral imaging”, Journal...3)  a  set  of   optical   filters  which   allow   to   discriminate   spectrally   the   coded   and   sheared...system   that   includes   objective   lens,   spatial   light   modulator,   dispersive   element,   optical   filters

Dynamics and pattern of a managed coniferous forest landscape in Oregon.

Treesearch

T.A. Spies; W.J. Ripple; G.A. Bradshaw

1994-01-01

We examined the process of fragmentation in a managed forest landscape by comparing rates and patterns of disturbance (primarily clear-cutting) and regrowth between 1972 and 1988 using Landsat imagery. A 2589-km2 managed forest landscape in western Oregon was classified into two forest types, closed-canopy conifer forest (CF) (typically, > 60% conifer cover) and...

The landscape context of forest and grassland in the United States

Treesearch

Kurt H. Riitters

2011-01-01

As development introduces competing land uses into forest and grassland landscapes, the public expresses concern for landscape patterns through headline issues such as urban sprawl and fragmentation. Resource managers need a deeper understanding of the causes and consequences of landscape patterns to know if, where, and how to take any needed actions. The spatial...

Landscape pattern and context of forest and grassland in Alaska, Hawaii, and Puerto Rico

Treesearch

Kurt H. Riitters

2012-01-01

As development introduces competing land uses into forest and grassland landscapes, the public concerns for landscape patterns are expressed through headline issues such as urban sprawl and forest fragmentation. The task for resource managers is to maintain an appropriate balance of biodiversity, water quality, recreation experience, and other amenities in forest and...

TagFinder for the quantitative analysis of gas chromatography--mass spectrometry (GC-MS)-based metabolite profiling experiments.

PubMed

Luedemann, Alexander; Strassburg, Katrin; Erban, Alexander; Kopka, Joachim

2008-03-01

Typical GC-MS-based metabolite profiling experiments may comprise hundreds of chromatogram files, which each contain up to 1000 mass spectral tags (MSTs). MSTs are the characteristic patterns of approximately 25-250 fragment ions and respective isotopomers, which are generated after gas chromatography (GC) by electron impact ionization (EI) of the separated chemical molecules. These fragment ions are subsequently detected by time-of-flight (TOF) mass spectrometry (MS). MSTs of profiling experiments are typically reported as a list of ions, which are characterized by mass, chromatographic retention index (RI) or retention time (RT), and arbitrary abundance. The first two parameters allow the identification, the later the quantification of the represented chemical compounds. Many software tools have been reported for the pre-processing, the so-called curve resolution and deconvolution, of GC-(EI-TOF)-MS files. Pre-processing tools generate numerical data matrices, which contain all aligned MSTs and samples of an experiment. This process, however, is error prone mainly due to (i) the imprecise RI or RT alignment of MSTs and (ii) the high complexity of biological samples. This complexity causes co-elution of compounds and as a consequence non-selective, in other words impure MSTs. The selection and validation of optimal fragment ions for the specific and selective quantification of simultaneously eluting compounds is, therefore, mandatory. Currently validation is performed in most laboratories under human supervision. So far no software tool supports the non-targeted and user-independent quality assessment of the data matrices prior to statistical analysis. TagFinder may fill this gap. TagFinder facilitates the analysis of all fragment ions, which are observed in GC-(EI-TOF)-MS profiling experiments. The non-targeted approach allows the discovery of novel and unexpected compounds. In addition, mass isotopomer resolution is maintained by TagFinder processing. This feature is essential for metabolic flux analyses and highly useful, but not required for metabolite profiling. Whenever possible, TagFinder gives precedence to chemical means of standardization, for example, the use of internal reference compounds for retention time calibration or quantitative standardization. In addition, external standardization is supported for both compound identification and calibration. The workflow of TagFinder comprises, (i) the import of fragment ion data, namely mass, time and arbitrary abundance (intensity), from a chromatography file interchange format or from peak lists provided by other chromatogram pre-processing software, (ii) the annotation of sample information and grouping of samples into classes, (iii) the RI calculation, (iv) the binning of observed fragment ions of equal mass from different chromatograms into RI windows, (v) the combination of these bins, so-called mass tags, into time groups of co-eluting fragment ions, (vi) the test of time groups for intensity correlated mass tags, (vii) the data matrix generation and (viii) the extraction of selective mass tags supported by compound identification. Thus, TagFinder supports both non-targeted fingerprinting analyses and metabolite targeted profiling. Exemplary TagFinder workspaces and test data sets are made available upon request to the contact authors. TagFinder is made freely available for academic use from http://www-en.mpimp-golm.mpg.de/03-research/researchGroups/01-dept1/Root_Metabolism/smp/TagFinder/index.html.

Analysis of the acoustic spectral signature of prosthetic heart valves in patients experiencing atrial fibrillation

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

Scott, D.D.; Jones, H.E.

1994-05-06

Prosthetic heart valves have increased the life span of many patients with life threatening heart conditions. These valves have proven extremely reliable adding years to what would have been weeks to a patient`s life. Prosthetic valves, like the heart however, can suffer from this constant work load. A small number of valves have experienced structural fractures of the outlet strut due to fatigue. To study this problem a non-intrusive method to classify valves has been developed. By extracting from an acoustic signal the opening sounds which directly contain information from the outlet strut and then developing features which are suppliedmore » to an adaptive classification scheme (neural network) the condition of the valve can be determined. The opening sound extraction process has proved to be a classification problem itself. Due to the uniqueness of each heart and the occasional irregularity of the acoustic pattern it is often questionable as to the integrity of a given signal (beat), especially one occurring during an irregular beat pattern. A common cause of these irregular patterns is a condition known as atrial fibrillation, a prevalent arrhythmia among patients with prosthetic hear valves. Atrial fibrillation is suspected when the ECG shows no obvious P-waves. The atria do not contract and relax correctly to help contribute to ventricular filling during a normal cardiac cycle. Sometimes this leads to irregular patterns in the acoustic data. This study compares normal beat patterns to irregular patterns of the same heart. By analyzing the spectral content of the beats it can be determined whether or not these irregular patterns can contribute to the classification of a heart valve or if they should be avoided. The results have shown that the opening sounds which occur during irregular beat patterns contain the same spectral information as the opening which occur during a normal beat pattern of the same heart and these beats can be used for classification.« less

Shifts in reproductive assurance strategies and inbreeding costs associated with habitat fragmentation in Central American mahogany

PubMed Central

Breed, Martin F; Gardner, Michael G; Ottewell, Kym M; Navarro, Carlos M; Lowe, Andrew J

2012-01-01

The influence of habitat fragmentation on mating patterns and progeny fitness in trees is critical for understanding the long-term impact of contemporary landscape change on the sustainability of biodiversity. We examined the relationship between mating patterns, using microsatellites, and fitness of progeny, in a common garden trial, for the insect-pollinated big-leaf mahogany, Swietenia macrophylla King, sourced from forests and isolated trees in 16 populations across Central America. As expected, isolated trees had disrupted mating patterns and reduced fitness. However, for dry provenances, fitness was negatively related to correlated paternity, while for mesic provenances, fitness was correlated positively with outcrossing rate and negatively with correlated paternity. Poorer performance of mesic provenances is likely because of reduced effective pollen donor density due to poorer environmental suitability and greater disturbance history. Our results demonstrate a differential shift in reproductive assurance and inbreeding costs in mahogany, driven by exploitation history and contemporary landscape context. PMID:22381041

Clinical proteomics: Applications for prostate cancer biomarker discovery and detection.

PubMed

Petricoin, Emanuel F; Ornstein, David K; Liotta, Lance A

2004-01-01

The science of proteomics comprises much more than simply generating lists of proteins that change in expression as a cause of or consequence of pathophysiology. The goal of proteomics should be to characterize the information flow through the intercellular protein circuitry that communicates with the extracellular microenvironment and then ultimately to the serum/plasma macroenvironment. Serum proteomic pattern diagnostics is a new type of proteomic concept in which patterns of ion signatures generated from high dimensional mass spectrometry data are used as diagnostic classifiers. This recent approach has exciting potential for clinical utility of diagnostic patterns because low molecular weight metabolites, peptides, and protein fragments may have higher accuracy than traditional biomarkers of cancer detection. Intriguingly, we now have discovered that this diagnostic information exists in a bound state, complexed with circulating highly abundant carrier proteins. These diagnostic fragments may one day be harvested by circulating nanoparticles, designed to absorb, enrich, and amplify the repertoire of diagnostic biomarkers generated-even at the critical, initial stages of carcinogenesis. Copyright 2004 Elsevier Inc.

Deactivating stimulation sites based on low-rate thresholds improves spectral ripple and speech reception thresholds in cochlear implant users.

PubMed

Zhou, Ning

2017-03-01

The study examined whether the benefit of deactivating stimulation sites estimated to have broad neural excitation was attributed to improved spectral resolution in cochlear implant users. The subjects' spatial neural excitation pattern was estimated by measuring low-rate detection thresholds across the array [see Zhou (2016). PLoS One 11, e0165476]. Spectral resolution, as assessed by spectral-ripple discrimination thresholds, significantly improved after deactivation of five high-threshold sites. The magnitude of improvement in spectral-ripple discrimination thresholds predicted the magnitude of improvement in speech reception thresholds after deactivation. Results suggested that a smaller number of relatively independent channels provide a better outcome than using all channels that might interact.

Monte Carlo simulation as a tool to predict blasting fragmentation based on the Kuz Ram model

NASA Astrophysics Data System (ADS)

Morin, Mario A.; Ficarazzo, Francesco

2006-04-01

Rock fragmentation is considered the most important aspect of production blasting because of its direct effects on the costs of drilling and blasting and on the economics of the subsequent operations of loading, hauling and crushing. Over the past three decades, significant progress has been made in the development of new technologies for blasting applications. These technologies include increasingly sophisticated computer models for blast design and blast performance prediction. Rock fragmentation depends on many variables such as rock mass properties, site geology, in situ fracturing and blasting parameters and as such has no complete theoretical solution for its prediction. However, empirical models for the estimation of size distribution of rock fragments have been developed. In this study, a blast fragmentation Monte Carlo-based simulator, based on the Kuz-Ram fragmentation model, has been developed to predict the entire fragmentation size distribution, taking into account intact and joints rock properties, the type and properties of explosives and the drilling pattern. Results produced by this simulator were quite favorable when compared with real fragmentation data obtained from a blast quarry. It is anticipated that the use of Monte Carlo simulation will increase our understanding of the effects of rock mass and explosive properties on the rock fragmentation by blasting, as well as increase our confidence in these empirical models. This understanding will translate into improvements in blasting operations, its corresponding costs and the overall economics of open pit mines and rock quarries.