Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta

PubMed Central

Lv, Xiaofei; Ma, Bin; Yu, Junbao; Chang, Scott X.; Xu, Jianming; Li, Yunzhao; Wang, Guangmei; Han, Guangxuan; Bo, Guan; Chu, Xiaojing

2016-01-01

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems. PMID:27824160

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta.

PubMed

Lv, Xiaofei; Ma, Bin; Yu, Junbao; Chang, Scott X; Xu, Jianming; Li, Yunzhao; Wang, Guangmei; Han, Guangxuan; Bo, Guan; Chu, Xiaojing

2016-11-08

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.

[Difference analysis among majors in medical parasitology exam papers by test item bank proposition].

PubMed

Jia, Lin-Zhi; Ya-Jun, Ma; Cao, Yi; Qian, Fen; Li, Xiang-Yu

2012-04-30

The quality index among "Medical Parasitology" exam papers and measured data for students in three majors from the university in 2010 were compared and analyzed. The exam papers were formed from the test item bank. The alpha reliability coefficients of the three exam papers were above 0.70. The knowledge structure and capacity structure of the exam papers were basically balanced. But the alpha reliability coefficients of the second major was the lowest, mainly due to quality of test items in the exam paper and the failure of revising the index of test item bank in time. This observation demonstrated that revising the test items and their index in the item bank according to the measured data can improve the quality of test item bank proposition and reduce the difference among exam papers.

An algorithm for optimal fusion of atlases with different labeling protocols

PubMed Central

Iglesias, Juan Eugenio; Sabuncu, Mert Rory; Aganj, Iman; Bhatt, Priyanka; Casillas, Christen; Salat, David; Boxer, Adam; Fischl, Bruce; Van Leemput, Koen

2014-01-01

In this paper we present a novel label fusion algorithm suited for scenarios in which different manual delineation protocols with potentially disparate structures have been used to annotate the training scans (hereafter referred to as “atlases”). Such scenarios arise when atlases have missing structures, when they have been labeled with different levels of detail, or when they have been taken from different heterogeneous databases. The proposed algorithm can be used to automatically label a novel scan with any of the protocols from the training data. Further, it enables us to generate new labels that are not present in any delineation protocol by defining intersections on the underling labels. We first use probabilistic models of label fusion to generalize three popular label fusion techniques to the multi-protocol setting: majority voting, semi-locally weighted voting and STAPLE. Then, we identify some shortcomings of the generalized methods, namely the inability to produce meaningful posterior probabilities for the different labels (majority voting, semi-locally weighted voting) and to exploit the similarities between the atlases (all three methods). Finally, we propose a novel generative label fusion model that can overcome these drawbacks. We use the proposed method to combine four brain MRI datasets labeled with different protocols (with a total of 102 unique labeled structures) to produce segmentations of 148 brain regions. Using cross-validation, we show that the proposed algorithm outperforms the generalizations of majority voting, semi-locally weighted voting and STAPLE (mean Dice score 83%, vs. 77%, 80% and 79%, respectively). We also evaluated the proposed algorithm in an aging study, successfully reproducing some well-known results in cortical and subcortical structures. PMID:25463466

Segmentation and Quantification for Angle-Closure Glaucoma Assessment in Anterior Segment OCT.

PubMed

Fu, Huazhu; Xu, Yanwu; Lin, Stephen; Zhang, Xiaoqin; Wong, Damon Wing Kee; Liu, Jiang; Frangi, Alejandro F; Baskaran, Mani; Aung, Tin

2017-09-01

Angle-closure glaucoma is a major cause of irreversible visual impairment and can be identified by measuring the anterior chamber angle (ACA) of the eye. The ACA can be viewed clearly through anterior segment optical coherence tomography (AS-OCT), but the imaging characteristics and the shapes and locations of major ocular structures can vary significantly among different AS-OCT modalities, thus complicating image analysis. To address this problem, we propose a data-driven approach for automatic AS-OCT structure segmentation, measurement, and screening. Our technique first estimates initial markers in the eye through label transfer from a hand-labeled exemplar data set, whose images are collected over different patients and AS-OCT modalities. These initial markers are then refined by using a graph-based smoothing method that is guided by AS-OCT structural information. These markers facilitate segmentation of major clinical structures, which are used to recover standard clinical parameters. These parameters can be used not only to support clinicians in making anatomical assessments, but also to serve as features for detecting anterior angle closure in automatic glaucoma screening algorithms. Experiments on Visante AS-OCT and Cirrus high-definition-OCT data sets demonstrate the effectiveness of our approach.

Interdisciplinary Studies at a Crossroads

ERIC Educational Resources Information Center

Kleinberg, Ethan

2008-01-01

In today's competitive college market, "interdisciplinary studies" are a major selling point for colleges and universities. Yet, on closer examination, it is apparent that the academic structure and place of the majority of interdisciplinary programs, departments, and centers are not substantially different from the academic disciplines,…

TRACE METAL CONTENT (Cu, Zn, Mn AND Fe) IN URTICA DIOICA L. AND PLANTAGO MAJOR L.

PubMed

Krolak, Elzbieta; Raczuk, Jolanta; Borkowska, Lidia

2016-11-01

The aim of the study was to compare the contents of Cu, Zn, Mn and Fe in the washed and unwashed leaves and roots of two plant species: Urica dioica L. and Plantago major L., used in herbal medicine. These two herb species occur in the same environmental habitats, yet their morphological structure is different. The soil and plant samples for analyses were collected from an uncontaminated area in Eastern Poland. In each habitat location, the samples were taken from sandy soils with slightly acidic and neutral pH values. The obtained results showed that U. dioica and P. major accumulated similar amounts of trace metals, such as: Cu, Zn and Fe, in leaves, despite the differences in the morphological structure of their overground parts. The content of Mn in leaves U. dioica was about twice as much as in P. major. Also, no differences in the metal content were observed between washed and unwashed leaves of both species. However, in the same habitat conditions, a significantly higher content of Cu, Zn and Mn was found in the roots of P. major than U. dioica. The content of Fe in the roots was similar in both species. P. major and U. dioica may be a valuable source of microelements, if they are obtained from unpolluted habitats.

A numerical study of slope and fuel structure effects on coupled wildfire behaviour

Treesearch

Rodman R. Linn; Judith L. Winterkamp; David R. Weise; Carleton Edminster

2010-01-01

Slope and fuel structure are commonly accepted as major factors affecting theway wildfires behave. However, it is possible that slope affects fire differently depending on the fuel bed. Six FIRETEC simulations using three different fuel beds on flat and upslope topography were used to examine this possibility. Fuel beds resembling grass, chaparral, and ponderosa pine...

The first mammalian aldehyde oxidase crystal structure: insights into substrate specificity.

PubMed

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T P; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-11-23

Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents. The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics. Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures. The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.

The structure of the casein micelle of milk and its changes during processing.

PubMed

Dalgleish, Douglas G; Corredig, Milena

2012-01-01

The majority of the protein in cow's milk is contained in the particles known as casein micelles. This review describes the main structural features of these particles and the different models that have been used to define the interior structures. The reactions of the micelles during processing operations are described in terms of the structural models.

Investigating elementary education and physical therapy majors' perceptions of an inquiry-based physics content course

NASA Astrophysics Data System (ADS)

Hilton, John Martin

This study investigates why physical therapy assistant majors engage and perform better than elementary education majors in an inquiry-based conceptual physics course at Mid-Atlantic Community College. The students from each major are demographically similar, both courses are similar in depth and structure, and each course supports the students' program. However, there is an observed difference in the levels of engagement with the curriculum and performance on writing-based assessments between the two groups. To explore possible explanations for the difference, I examine students' affinity for science, their beliefs about the nature of science and scientific knowledge in the classroom, and their perception of the usefulness of science to their program. During semi-structured interviews, students from both majors displayed nearly identical weak affinities for science, epistemological beliefs, and uncertainty about the usefulness of the class. However, the physical therapy majors' ability to see the relevance of the physics course experience to their program enhanced their interest and motivation. In contrast, the elementary education students do not see connections between the course and their program, and do not see a purpose for their learning of physics content. To improve the program, I propose a two-pronged approach - designing a faded-scaffolded-inquiry approach for both classes, and developing a field-based/seminar class for the elementary education majors. The scaffolded inquiry will help both groups develop better orientations toward lab activities, and the structured observations and reflection will help the elementary group connect the material to their program.

Atomic Force Microscopy Analysis of the Role of Major DNA-Binding Proteins in Organization of the Nucleoid in Escherichia coli

PubMed Central

Ohniwa, Ryosuke L.; Muchaku, Hiroki; Saito, Shinji; Wada, Chieko; Morikawa, Kazuya

2013-01-01

Bacterial genomic DNA is packed within the nucleoid of the cell along with various proteins and RNAs. We previously showed that the nucleoid in log phase cells consist of fibrous structures with diameters ranging from 30 to 80 nm, and that these structures, upon RNase A treatment, are converted into homogeneous thinner fibers with diameter of 10 nm. In this study, we investigated the role of major DNA-binding proteins in nucleoid organization by analyzing the nucleoid of mutant Escherichia coli strains lacking HU, IHF, H–NS, StpA, Fis, or Hfq using atomic force microscopy. Deletion of particular DNA-binding protein genes altered the nucleoid structure in different ways, but did not release the naked DNA even after the treatment with RNase A. This suggests that major DNA-binding proteins are involved in the formation of higher order structure once 10-nm fiber structure is built up from naked DNA. PMID:23951337

Structure-Specific Statistical Mapping of White Matter Tracts

PubMed Central

Yushkevich, Paul A.; Zhang, Hui; Simon, Tony; Gee, James C.

2008-01-01

We present a new model-based framework for the statistical analysis of diffusion imaging data associated with specific white matter tracts. The framework takes advantage of the fact that several of the major white matter tracts are thin sheet-like structures that can be effectively modeled by medial representations. The approach involves segmenting major tracts and fitting them with deformable geometric medial models. The medial representation makes it possible to average and combine tensor-based features along directions locally perpendicular to the tracts, thus reducing data dimensionality and accounting for errors in normalization. The framework enables the analysis of individual white matter structures, and provides a range of possibilities for computing statistics and visualizing differences between cohorts. The framework is demonstrated in a study of white matter differences in pediatric chromosome 22q11.2 deletion syndrome. PMID:18407524

Two distinct structures of alpha-conotoxin GI in aqueous solution.

PubMed

Maslennikov, I V; Sobol, A G; Gladky, K V; Lugovskoy, A A; Ostrovsky, A G; Tsetlin, V I; Ivanov, V T; Arseniev, A S

1998-06-01

The detailed analysis of conformational space of alpha-conotoxin GI in aqueous solution has been performed on the basis of two-dimensional NMR spectroscopy data using multiconformational approach. As the result, two topologically distinct interconvertible sets of GI conformations (populations of 78% and 22%) have been found. A common feature of the two sets is the Asn4-Cys7 beta-turn. The Gly8 to Tyrll region has a structure of right-handed helical turn in the major set and two sequential bends in the minor one. N-terminus and C-terminus also have different orientations, anti-parallel in the major conformational set and parallel in the minor one. An average pairwise rmsd for backbone heavy atoms is 0.56 A in the major set, 0.23 A in the minor, and 1.85 A between the structures of the two sets. The X-ray structure of GI [Guddat, L. W., Martin, J. A., Shan, L., Edmundson, A. B. & Gray, W. R. (1996) Biochemistry 35, 11329 - 11335] has the same folding pattern as the major NMR set, the average backbone rmsd between the two structures being 0.77 A.

Approach to prevention of obesity of Roma population in the Region of South Bohemia with focus on selected eating behaviors.

PubMed

Dolák, František; Šedová, Lenka; Nováková, Dita; Olišarová, Věra

2016-12-01

To survey obesity prevention methods for use in the Roma population with a focus on eating behaviors. A semi-structured interview was used to identify potentially useful obesity prevention methods. Basic anthropometric measurements were also gathered at the same time. This study was part of the "Obesity and overweight in the Roma minority in the Region of South Bohemia" research project (grant project 280-COST-LD14114). Participants consisted of members of the Roma minority (302 respondents) as well as the majority (Czech) population for comparisons. Differences in eating behaviors like irregular eating schedules and excessive consumption of fast food were observed. Statistically significant differences between the Roma minority and the majority (Czech/non-Roma) population were found in this area with the help of statistical significance tests. The Chi-square characteristic of independence (χ2) was, in case of this distribution, valued at 30.815 with 5 degrees of freedom, P < 0.001. The analyses, based on the second degree of classification, identified statistically significant differences between the Roma minority and the majority population. Members of the Roma minority attended preventive health check-ups statistically less often than members of the majority population. Differences between the majority and the Roma population were also found in the degree of patient cooperation with general practitioners. The results show that the Roma population is more likely to engage in eating behaviors that can contribute to overweight and obesity than the majority population. Based on the results of a semi-structured interview and on the results of anthropometric measurements, we can say that the Roma population is at a greater health risk, relative to overweight and obesity, than the majority population.

Structural design principles for delivery of bioactive components in nutraceuticals and functional foods.

PubMed

McClements, David Julian; Decker, Eric Andrew; Park, Yeonhwa; Weiss, Jochen

2009-06-01

There have been major advances in the design and fabrication of structured delivery systems for the encapsulation of nutraceutical and functional food components. A wide variety of delivery systems is now available, each with its own advantages and disadvantages for particular applications. This review begins by discussing some of the major nutraceutical and functional food components that need to be delivered and highlights the main limitations to their current utilization within the food industry. It then discusses the principles underpinning the rational design of structured delivery systems: the structural characteristics of the building blocks; the nature of the forces holding these building blocks together; and, the different ways of assembling these building blocks into structured delivery systems. Finally, we review the major types of structured delivery systems that are currently available to food scientists: lipid-based (simple, multiple, multilayer, and solid lipid particle emulsions); surfactant-based (simple micelles, mixed micelles, vesicles, and microemulsions) and biopolymer-based (soluble complexes, coacervates, hydrogel droplets, and particles). For each type of delivery system we describe its preparation, properties, advantages, and limitations.

Three-dimensional structure of Escherichia coli initiator tRNA/f//Met/

NASA Technical Reports Server (NTRS)

Woo, N. H.; Rich, A.; Roe, B. A.

1980-01-01

The crystal structure of Escherichia coli tRNA(f)(Met), an initiator transfer RNA, has been determined. While grossly similar to that of the chain-elongating yeast tRNA(Phe), there are three major differences. One involves the folding of the anticodon loop; in particular, the position of the constant uridine, U33. This difference was unexpected and may be of functional significance.

Solution structure of a DNA duplex containing a cis-diammineplatinum(II) 1,3-d(GTG) intrastrand cross-link, a major adduct in cells treated with the anticancer drug carboplatin.

PubMed

Teuben, J M; Bauer, C; Wang, A H; Reedijk, J

1999-09-21

The platinum 1,3-d(GXG) intrastrand cross-link is one of the adducts formed in the reaction of the antitumor drug cisplatin with DNA, and in fact the major adduct found in cells treated with the cisplatin analogue carboplatin. To determine the 3D structure of this adduct, the duplex d(CTCTGTGTCTC).d(GAGACACAGAG)], where GTG denotes a platinum 1,3-intrastrand cross-link, was prepared and studied with high-resolution (1)H NMR. The solution structure was determined using the SPEDREF protocol, which includes an iterative NOE-restrained refinement procedure. Calculated and recorded NOE spectra were found to be in good agreement (NMR R factor 22%). The studied duplex is more distorted from B-DNA than previously determined structures of the 1,2-d(GG) intrastrand adducts. The base pairing is lost for the 5'G-C and the central T-A base pair in the GTG lesion, and the central thymine is extruded from the minor groove. To accommodate this lesion, the minor groove is widened, and the 5'-guanine ribose adopts an N-type conformation. The helix is unwound locally and is significantly bent toward the major groove. Significant difference between the structural distortion of the 1, 3-d(GTG) cross-link and other Pt-DNA cross-links sheds new light on the observed differences in protein recognition of these lesions, and thus on the possible differences in mechanisms of action of the various Pt-DNA adducts formed in treatment with platinum anticancer complexes.

The structure of partially-premixed methane/air flames under varying premixing

NASA Astrophysics Data System (ADS)

Kluzek, Celine; Karpetis, Adonios

2008-11-01

The present work examines the spatial and scalar structure of laminar, partially premixed methane/air flames with the objective of developing flamelet mappings that capture the effect of varying premixture strength (air addition in fuel.) Experimental databases containing full thermochemistry measurements within laminar axisymmetric flames were obtained at Sandia National Laboratories, and the measurements of all major species and temperature are compared to opposed-jet one-dimensional flow simulation using Cantera and the full chemical kinetic mechanism of GRI 3.0. Particular emphasis is placed on the scalar structure of the laminar flames, and the formation of flamelet mappings that capture all of the salient features of thermochemistry in a conserved scalar representation. Three different premixture strengths were examined in detail: equivalence ratios of 1.8, 2.2, and 3.17 resulted in clear differences in the flame scalar structure, particularly in the position of the rich premixed flame zone and the attendant levels of major and intermediate species (carbon monoxide and hydrogen).

Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix.

PubMed

Sugimoto, Naoki

2014-01-01

How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described. © 2014 Elsevier Inc. All rights reserved.

Seeking Help in Domestic Violence Among Muslim Women in Muslim-Majority and Non-Muslim-Majority Countries: A Literature Review.

PubMed

Afrouz, Rojan; Crisp, Beth R; Taket, Ann

2018-01-01

Women from different backgrounds and cultures are at risk of domestic violence. Disclosing the abusive experience and seeking help is not straightforward and easy and might be a complicated and long-term process. Muslim women, like other groups of women, may face various barriers to disclose abusive relationships and for seeking help. Some of the barriers may be common for the majority of Muslim women in different contexts, while others might be related to women's situations and the wider society they live. To identify these barriers and make recommendations for future studies, this article reviews related papers conducted in both Muslim-majority and non-Muslim-majority countries. A critical systematic review of the literature was conducted for identifying Muslim women's barriers in disclosing abuse and seeking help. Twenty-one studies met the inclusion criteria. The main identified barriers are discussed into under four themes: social context, family context, individual factors, and expectations of service providers. Although the researchers tried to investigate various barriers in seeking help, many of them have not focused on structural obstacles. Besides, in many Muslim-majority countries, the issue has not been explored. Therefore, the results of the current article will not apply to those countries. Recommendation for future research comprises more qualitative research compatible with the women's cultures and backgrounds in different societies, focusing more on structural and cultural factors to explore and find women's barriers to seek help.

A Complete NMR Spectral Assignment of the Lipid-free Mouse Apolipoprotein A-I (ApoAI) C-terminal Truncation Mutant, ApoAI(1-216)

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

Yang, Yunhuang; Hoyt, David W.; Wang, Jianjun

2007-07-28

Apolipoprotein A-I (apoAI) is the major protein component of the high-density lipoprotein (HDL) that has been a hot subject of interests because of its anti-atherogenic properties. Upon lipid-binding, apoAI undergoes conformational changes from lipid-free to several different HDL-associated states (1). These different conformational states regulate HDL formation, maturation and transportation. Recent crystal structure of lipid-free human apoAI represents a major progress of structural study of lipid-free apoAI (2). However, no structural is available for lipid-free mouse apoAI (240-residues). Since mouse HDL is homogenous with only HDL2-like size, whereas human HDL is heterogeneous, containing HDL2/HDL3 as its main species, a structuralmore » comparison between human and mouse apoAI may allow us to identify structure basis of HDL size distribution difference between human and mouse. We carried out an NMR structure determination of lipid-free mouse apoAI (1-216) and completely assigned backbone atoms (except backbone amide proton and nitrogen atoms for residues D1, N48, W107, K108, K132, E135, F147, R148, M169 and K203). Secondary structure prediction using backbone NMR parameters indicates that lipid-free mouse apoAI consists of a four helical segments in the N-terminal domain, residues 1-180. In addition, two short helices are also observed between residues 190-195 and 210-215. The helix locations are significantly different from those in the crystal structure of human apoAI, suggesting that mouse apoAI may have a different conformational adaptation upon lipid-binding. BMRB deposit with accession number: 15091.« less

English Language Learners' Perceptions of Motivational Changes

ERIC Educational Resources Information Center

Lai, Hsuan-Yau Tony; Ting, Kuang-yun

2013-01-01

This study explores the changes in Taiwanese university students' English-learning motivation and the causes of these changes. The emphasis herein is on a comparison and contrast of both English major and non-major students in three different universities in Taiwan. In the study, a qualitative approach (20 semi-structured interviews) was used. The…

Structures of the major capsid proteins of the human Karolinska Institutet and Washington University polyomaviruses.

PubMed

Neu, Ursula; Wang, Jianbo; Macejak, Dennis; Garcea, Robert L; Stehle, Thilo

2011-07-01

The Karolinska Institutet and Washington University polyomaviruses (KIPyV and WUPyV, respectively) are recently discovered human viruses that infect the respiratory tract. Although they have not yet been linked to disease, they are prevalent in populations worldwide, with initial infection occurring in early childhood. Polyomavirus capsids consist of 72 pentamers of the major capsid protein viral protein 1 (VP1), which determines antigenicity and receptor specificity. The WUPyV and KIPyV VP1 proteins are distant in evolution from VP1 proteins of known structure such as simian virus 40 or murine polyomavirus. We present here the crystal structures of unassembled recombinant WUPyV and KIPyV VP1 pentamers at resolutions of 2.9 and 2.55 Å, respectively. The WUPyV and KIPyV VP1 core structures fold into the same β-sandwich that is a hallmark of all polyomavirus VP1 proteins crystallized to date. However, differences in sequence translate into profoundly different surface loop structures in KIPyV and WUPyV VP1 proteins. Such loop structures have not been observed for other polyomaviruses, and they provide initial clues about the possible interactions of these viruses with cell surface receptors.

On the Parity of Structural Persistence in Language Production and Comprehension

PubMed Central

Tooley, Kristen M.; Bock, Kathryn

2014-01-01

Structural priming creates structural persistence. That is, differences in experience with syntax can change subsequent language performance, and the changes can be observed in both language production and comprehension. However, the effects in comprehension and production appear to differ. In comprehension, persistence is typically found when the verbs are the same in primes and targets; in production, persistence occurs without verb overlap. The contrast suggests a theoretically important hypothesis: parsing in comprehension is lexically driven while formulation in production is structurally driven. A major weakness in this hypothesis about comprehension-production differences is that its empirical motivation rests on the outcomes of experiments in which the priming manipulations differ, the primed sentence structures differ, and the measures of priming differ. To sharpen the comparison, we examined structural persistence with and without verb overlap in both reading comprehension and spoken production, using the same prime presentation procedure, the same syntactic structures, the same sentences, and the same participants. These methods yielded abstract sructural persistence in comprehension as well as production. A measure of the strength of persistence revealed significant effects of priming and verb overlap without significant comprehension—production differences. This argues for uniformity in the structural mechanisms of language processing. PMID:24803423

Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar.

PubMed

Cárdenas, Constanza; Bidon-Chanal, Axel; Conejeros, Pablo; Arenas, Gloria; Marshall, Sergio; Luque, F Javier

2010-12-01

Knowledge of the 3D structure of the binding groove of major histocompatibility (MHC) molecules, which play a central role in the immune response, is crucial to shed light into the details of peptide recognition and polymorphism. This work reports molecular modeling studies aimed at providing 3D models for two class I and two class II MHC alleles from Salmo salar (Sasa), as the lack of experimental structures of fish MHC molecules represents a serious limitation to understand the specific preferences for peptide binding. The reliability of the structural models built up using bioinformatic tools was explored by means of molecular dynamics simulations of their complexes with representative peptides, and the energetics of the MHC-peptide interaction was determined by combining molecular mechanics interaction energies and implicit continuum solvation calculations. The structural models revealed the occurrence of notable differences in the nature of residues at specific positions in the binding groove not only between human and Sasa MHC proteins, but also between different Sasa alleles. Those differences lead to distinct trends in the structural features that mediate the binding of peptides to both class I and II MHC molecules, which are qualitatively reflected in the relative binding affinities. Overall, the structural models presented here are a valuable starting point to explore the interactions between MHC receptors and pathogen-specific interactions and to design vaccines against viral pathogens.

The structural evolution of the Ghadames and Illizi basins during the Paleozoic, Mesozoic and Cenozoic: Petroleum implications

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

Gauthier, F.J.; Boudjema, A.; Lounis, R.

1995-08-01

The Ghadames and Illizi basins cover the majority of the eastern Sahara of Algeria. Geologicaly, this part of the Central Saharan platform has been influenced by a series of structural arches and {open_quotes}moles{close_quotes} (continental highs) which controlled sedimentation and structure through geologic time. These features, resulting from and having been affected by nine major tectonic phases ranging from pre-Cambrian to Tertiary, completely bound the Ghadames and Illizi Basins. During the Paleozoic both basins formed one continuous depositional entity with the Ghadames basin being the distal portion of the continental sag basin where facies and thickness variations are observed over largemore » distances. It is during the Mesozoic-Cenozoic that the Ghadames basin starts to evolve differently from the Illizi Basin. Eustatic low-stand periods resulted in continental deposition yielding the major petroleum-bearing reservoir horizons (Cambrian, Ordovician, Siluro-Devonian and Carboniferous). High-stand periods corresponds to the major marine transgressions covering the majority of the Saharan platform. These transgressions deposited the principal source rock intervals of the Silurian and Middle to Upper Devonian. The main reservoirs of the Mesozoic and Cenozoic are Triassic sandstone sequences which are covered by a thick evaporite succession forming a super-seal. Structurally, the principal phases affecting this sequence are the extensional events related to the breakup of Pangea and the Alpine compressional events. The Ghadames and Illizi basins, therefore, have been controlled by a polphase tectonic history influenced by Pan African brittle basement fracturing which resulted in complex structures localized along the major basin bounding trends as well as several subsidiary trends within the basin. These trends, as demonstrated with key seismic data, have been found to contain the majority of hydrocarbons trapped.« less

Specificity of the trypanothione-dependent Leishmania major glyoxalase I: structure and biochemical comparison with the human enzyme.

PubMed

Ariza, Antonio; Vickers, Tim J; Greig, Neil; Armour, Kirsten A; Dixon, Mark J; Eggleston, Ian M; Fairlamb, Alan H; Bond, Charles S

2006-02-01

Trypanothione replaces glutathione in defence against cellular damage caused by oxidants, xenobiotics and methylglyoxal in the trypanosomatid parasites, which cause trypanosomiasis and leishmaniasis. In Leishmania major, the first step in methylglyoxal detoxification is performed by a trypanothione-dependent glyoxalase I (GLO1) containing a nickel cofactor; all other characterized eukaryotic glyoxalases use zinc. In kinetic studies L. major and human enzymes were active with methylglyoxal derivatives of several thiols, but showed opposite substrate selectivities: N1-glutathionylspermidine hemithioacetal is 40-fold better with L. major GLO1, whereas glutathione hemithioacetal is 300-fold better with human GLO1. Similarly, S-4-bromobenzylglutathionylspermidine is a 24-fold more potent linear competitive inhibitor of L. major than human GLO1 (Kis of 0.54 microM and 12.6 microM, respectively), whereas S-4-bromobenzylglutathione is >4000-fold more active against human than L. major GLO1 (Kis of 0.13 microM and >500 microM respectively). The crystal structure of L. major GLO1 reveals differences in active site architecture to both human GLO1 and the nickel-dependent Escherichia coli GLO1, including increased negative charge and hydrophobic character and truncation of a loop that may regulate catalysis in the human enzyme. These differences correlate with the differential binding of glutathione and trypanothione-based substrates, and thus offer a route to the rational design of L. major-specific GLO1 inhibitors.

Local structures around the substituted elements in mixed layered oxides

PubMed Central

Akama, Shota; Kobayashi, Wataru; Amaha, Kaoru; Niwa, Hideharu; Nitani, Hiroaki; Moritomo, Yutaka

2017-01-01

The chemical substitution of a transition metal (M) is an effective method to improve the functionality of a material, such as its electrochemical, magnetic, and dielectric properties. The substitution, however, causes local lattice distortion because the difference in the ionic radius (r) modifies the local interatomic distances. Here, we systematically investigated the local structures in the pure (x = 0.0) and mixed (x = 0.05 or 0.1) layered oxides, Na(M1−xM′x)O2 (M and M′ are the majority and minority transition metals, respectively), by means of extended X-ray absorption fine structure (EXAFS) analysis. We found that the local interatomic distance (dM-O) around the minority element approaches that around the majority element to reduces the local lattice distortion. We further found that the valence of the minority Mn changes so that its ionic radius approaches that of the majority M. PMID:28252008

Space Station truss structures and construction considerations

NASA Technical Reports Server (NTRS)

Mikulas, M. M., Jr.; Croomes, S. D.; Schneider, W.; Bush, H. G.; Nagy, K.; Pelischek, T.; Lake, M. S.; Wesselski, C.

1985-01-01

Although a specific configuration has not been selected for the Space Station, a gravity gradient stabilized station as a basis upon which to compare various structural and construction concepts is considered. The Space Station primary truss support structure is described in detail. Three approaches (see sketch A) which are believed to be representative of the major techniques for constructing large structures in space are also described in detail so that salient differences can be highlighted.

Metamorphic Proteins: Emergence of Dual Protein Folds from One Primary Sequence.

PubMed

Lella, Muralikrishna; Mahalakshmi, Radhakrishnan

2017-06-20

Every amino acid exhibits a different propensity for distinct structural conformations. Hence, decoding how the primary amino acid sequence undergoes the transition to a defined secondary structure and its final three-dimensional fold is presently considered predictable with reasonable certainty. However, protein sequences that defy the first principles of secondary structure prediction (they attain two different folds) have recently been discovered. Such proteins, aptly named metamorphic proteins, decrease the conformational constraint by increasing flexibility in the secondary structure and thereby result in efficient functionality. In this review, we discuss the major factors driving the conformational switch related both to protein sequence and to structure using illustrative examples. We discuss the concept of an evolutionary transition in sequence and structure, the functional impact of the tertiary fold, and the pressure of intrinsic and external factors that give rise to metamorphic proteins. We mainly focus on the major components of protein architecture, namely, the α-helix and β-sheet segments, which are involved in conformational switching within the same or highly similar sequences. These chameleonic sequences are widespread in both cytosolic and membrane proteins, and these folds are equally important for protein structure and function. We discuss the implications of metamorphic proteins and chameleonic peptide sequences in de novo peptide design.

Multidisciplinary study (CO2 flux, ERT, self-potential, permeability and structural surveys) in Fondi di Baia, Astroni and Agnano volcanoes: insights for the structural architecture of the Campi Flegrei caldera (southern Italy)

NASA Astrophysics Data System (ADS)

Isaia, Roberto; Carapezza, Maria Luisa; Conti, Eric; Giulia Di Giuseppe, Maria; Lucchetti, Carlo; Prinzi, Ernesto; Ranaldi, Massimo; Tarchini, Luca; Tramparulo, Francesco; Troiano, Antonio; Vitale, Stefano; Cascella, Enrico; Castello, Nicola; Cicatiello, Alessandro; Maiolino, Marco; Puzio, Domenico; Tazza, Lucia; Villani, Roberto

2017-04-01

Recent volcanism at Campi Flegrei caldera produced more than 70 eruptions in the last 15 ka formed different volcanic edifices. The vent distribution was related to the main volcano-tectonic structure active in the caldera along which also concentrated part of the present hydrothermal and fumarolic activity, such as in the Solfatara area. In order to define the role of major faults in the Campi Flegrei Caldera, we analyzed some volcanic craters (Fondi di Baia and Astroni) and the Agnano caldera, by means of different geochemical and geophysical technics including CO2 flux, electrical resistivity (ERT), self-potential and permeability surveys. We provided some ERT profiles and different maps of geochemical and geophysical features. Major fault planes were identified comparing ERT imaging with alignments of anomalies in maps. The results can improve the knowledge on the present state of these volcanoes actually not fully monitored though included in the area with high probability of future vent opening within the Campi Flegrei caldera.

A Comparison of Ethnic Minority and Majority Students: Social and Academic Integration, and Quality of Learning

ERIC Educational Resources Information Center

Severiens, Sabine; Wolff, Rick

2008-01-01

This article examines students from ethnic minorities and majorities with regard to the relationships between their social and academic integration and their quality of learning. A total of 523 students at four universities completed a questionnaire: analyses of variance were used to examine mean differences, and structural equation modelling…

Structure Determination of Glycogen Synthase Kinase-3 from Leishmania major and Comparative Inhibitor Structure-Activity Relationships with Trypanosoma brucei GSK-3

PubMed Central

Ojo, Kayode K.; Arakaki, Tracy L.; Napuli, Alberto J.; Inampudi, Krishna K.; Keyloun, Katelyn R.; Zhang, Li; Hol, Wim G.J.; Verlinde, Christophe L.M.J.; Merritt, Ethan A.; Van Voorhis, Wesley C.

2011-01-01

Glycogen synthase kinase-3 (GSK-3) is a drug target under intense investigation in pharmaceutical companies and constitutes an attractive piggyback target for eukaryotic pathogens. Two different GSKs are found in trypanosomatids, one about 150 residues shorter than the other. GSK-3 short (GeneDB: Tb927.10.13780) has previously been validated genetically as a drug target in Trypanosoma brucei by RNAi induced growth retardation; and chemically by correlation between enzyme and in vitro growth inhibition. Here, we report investigation of the equivalent GSK-3 short enzymes of L. major (LmjF18.0270) and L. infantum (LinJ18_V3.0270, identical in amino acid sequences to LdonGSK-3 short) and a crystal structure of LmajGSK-3 short at 2 Å resolution. The inhibitor structure-activity relationships (SARs) of L. major and L. infantum are virtually identical, suggesting that inhibitors could be useful for both cutaneous and visceral leishmaniasis. Leishmania spp. GSK-3 short has different inhibitor SARs than TbruGSK-3 short, which can be explained mostly by two variant residues in the ATP-binding pocket. Indeed, mutating these residues in the ATP-binding site of LmajGSK-3 short to the TbruGSK-3 short equivalents results in a mutant LmajGSK-3 short enzyme with SAR more similar to that of TbruGSK-3 short. The differences between human GSK-3β (HsGSK-3β) and LmajGSK-3 short SAR suggest that compounds which selectively inhibit LmajGSK-3 short may be found. PMID:21195115

EFFORTS TO EXPAND THE DSSTOX STRUCTURE-SEARCHABLE PUBLIC TOXICITY DATABASE NETWORK

EPA Science Inventory

A major goal of the DSSTox website is to improve the utility of published toxicity data across different fields of research. The largest barriers in the exploration of toxicity data by chemists and modelers are the lack of chemical structure annotation in the research literature ...

The neuro-muscular system in cercaria with different patterns of locomotion.

PubMed

Tolstenkov, Oleg O; Prokofiev, Vladimir V; Terenina, Nadezhda B; Gustafsson, Margaretha K S

2011-05-01

The neuro-muscular system (NMS) of cercariae with different swimming patterns was studied with immunocytochemical methods and confocal scanning laser microscopy. Specimens of the continuously swimming Cercaria parvicaudata, Maritrema subdolum and Himasthla elongata were compared with specimens of the intermittently swimming Cryptocotyle lingua and the attached Podocotyle atomon. The patterns of F-actin in the musculature, 5-HT immunoreactive (-IR), FMRFamide-IR neuronal elements, α-tubulin-IR elements in the nervous and sensory systems and DAPI-stained nuclei were investigated. The general plan of the NMS was similar in all cercariae studied. No major structural differences in the patterns of muscle fibres were observed. However, in the tail of C. lingua, transverse muscle fibres connecting the bands of longitudinal muscles were found. No major structural differences in the 5-HT- or FMRFamide-IR nervous systems were observed. The number of 5-HT-IR neurones in the cercarial bodies varied between 12 and 14. The number and distribution of the α-tubulin-IR processes on the cercarial bodies and tails differed from each other. The relation between the number and structure of the α-tubulin-IR processes and the host finding strategy of the cercariae is discussed. A detailed schematic picture of the NMS in the tails of C. lingua and M. subdolum is presented.

Synthesis of structurally diverse major groove DNA interstrand crosslinks using three different aldehyde precursors

PubMed Central

Mukherjee, Shivam; Guainazzi, Angelo; Schärer, Orlando D.

2014-01-01

DNA interstrand crosslinks (ICLs) are extremely cytotoxic lesions that block essential cellular processes, such as replication and transcription. Crosslinking agents are widely used in cancer chemotherapy and form an array of structurally diverse ICLs. Despite the clinical success of these agents, resistance of tumors to crosslinking agents, for example, through repair of these lesions by the cellular machinery remains a problem. We have previously reported the synthesis of site-specific ICLs mimicking those formed by nitrogen mustards to facilitate the studies of cellular responses to ICL formation. Here we extend these efforts and report the synthesis of structurally diverse major groove ICLs that induce severe, little or no distortion in the DNA. Our approach employs the incorporation of aldehyde precursors of different lengths into complementary strands and ICL formation using a double reductive amination with a variety of amines. Our studies provide insight into the structure and reactivity parameters of ICL formation by double reductive amination and yield a set of diverse ICLs that will be invaluable for exploring structure–activity relationships in ICL repair. PMID:24782532

Structure-property relationships in directionally solidified single crystal NiAl

NASA Technical Reports Server (NTRS)

Noebe, R. D.; Kim, J. T.; Gibala, R.

1987-01-01

The ordered intermetallic alloy NiAl is being considered as a potential high temperature structural material, but lack of ductility at ambient temperatures, especially in polycrystalline form, is presently a major obstacle in achieving this goal. Even general agreement of the intrinsic ductility that can be achieved in monocrystals is in dispute. In order to understand this problem, two directionally solidified ingots of NiAl which displayed known differences in ductility were characterized in sufficient detail to identify the corresponding microstructural differences. It was found that the type and size of casting defects, i.e., porosity, present in the material were the major factors in controlling ductility of NiAl single crystals and could explain the order of magnitude variance in fracture strains reported in the literature.

Structure and Mechanical Properties of the AlSi10Mg Alloy Samples Manufactured by Selective Laser Melting

NASA Astrophysics Data System (ADS)

Li, Xiaodan; Ni, Jiaqiang; Zhu, Qingfeng; Su, Hang; Cui, Jianzhong; Zhang, Yifei; Li, Jianzhong

2017-11-01

The AlSi10Mg alloy samples with the size of 14×14×91mm were produced by the selective laser melting (SLM) method in different building direction. The structures and the properties at -70°C of the sample in different direction were investigated. The results show that the structure in different building direction shows different morphology. The fish scale structures distribute on the side along the building direction, and the oval structures distribute on the side vertical to the building direction. Some pores in with the maximum size of 100 μm exist of the structure. And there is no major influence for the build orientation on the tensile properties. The tensile strength and the elongation of the sample in the building direction are 340 Mpa and 11.2 % respectively. And the tensile strength and the elongation of the sample vertical to building direction are 350 Mpa and 13.4 % respectively

Structure of the CCR5 Chemokine Receptor-HIV Entry Inhibitor Maraviroc Complex

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

Tan, Qiuxiang; Zhu, Ya; Li, Jian

2013-10-21

The CCR5 chemokine receptor acts as a co-receptor for HIV-1 viral entry. Here we report the 2.7 angstrom–resolution crystal structure of human CCR5 bound to the marketed HIV drug maraviroc. The structure reveals a ligand-binding site that is distinct from the proposed major recognition sites for chemokines and the viral glycoprotein gp120, providing insights into the mechanism of allosteric inhibition of chemokine signaling and viral entry. A comparison between CCR5 and CXCR4 crystal structures, along with models of co-receptor–gp120-V3 complexes, suggests that different charge distributions and steric hindrances caused by residue substitutions may be major determinants of HIV-1 co-receptor selectivity.more » These high-resolution insights into CCR5 can enable structure-based drug discovery for the treatment of HIV-1 infection.« less

Native fat globules of different sizes selected from raw milk: thermal and structural behavior.

PubMed

Michalski, Marie-Caroline; Ollivon, Michel; Briard, Valérie; Leconte, Nadine; Lopez, Christelle

2004-12-01

The aim of this study was to characterize differences in the thermal and structural behavior between different sized native milk fat globules. A novel microfiltration process permits the selection of native small fat globules (SFG, 1-3 microm) and large fat globules (LFG, >5 microm) in raw milk, that were analyzed by X-ray diffraction (XRD) coupled to differential scanning calorimetry (DSC). There were no major differences in triglyceride crystalline structures between SFG and LFG, after eliminating thermal history and the influence of cooling rates. The three main 3L and 2L crystalline structures appearing under slow cooling existed regardless of globule size. The supercooling increased for the SFG, mainly due to heterogeneous nucleation in winter milk, and also to compositional variations in spring milk. Differences appeared regarding stabilized crystalline forms at 20 degrees C and subsequent cooling: the SFG contained less 2L triglyceride structures than the LFG. These results can be important in dairy manufactures using tempering periods.

First Year Engineering Graphics Curricula in Major Engineering Colleges.

ERIC Educational Resources Information Center

Meyers, Frederick D.

2000-01-01

Investigates the commonalities and differences of graphics programs among nine universities in the United States by analyzing the course structure and reviewing attendance and course syllabi. (Author/YDS)

Health Diagnosis of Major Transportation Infrastructures in Shanghai Metropolis Using High-Resolution Persistent Scatterer Interferometry

PubMed Central

Qin, Xiaoqiong; Yang, Tianliang; Yang, Mengshi; Zhang, Lu; Liao, Mingsheng

2017-01-01

Since the Persistent Scatterer Synthetic Aperture Radar (SAR) Interferometry (PSI) technology allows the detection of ground subsidence with millimeter accuracy, it is becoming one of the most powerful and economical means for health diagnosis of major transportation infrastructures. However, structures of different types may suffer from various levels of localized subsidence due to the different structural characteristics and subsidence mechanisms. Moreover, in the complex urban scenery, some segments of these infrastructures may be sheltered by surrounding buildings in SAR images, obscuring the desirable signals. Therefore, the subsidence characteristics on different types of structures should be discussed separately and the accuracy of persistent scatterers (PSs) should be optimized. In this study, the PSI-based subsidence mapping over the entire transportation network of Shanghai (more than 10,000 km) is illustrated, achieving the city-wide monitoring specifically along the elevated roads, ground highways and underground subways. The precise geolocation and structural characteristics of infrastructures were combined to effectively guide more accurate identification and separation of PSs along the structures. The experimental results from two neighboring TerraSAR-X stacks from 2013 to 2016 were integrated by joint estimating the measurements in the overlapping area, performing large-scale subsidence mapping and were validated by leveling data, showing highly consistent in terms of subsidence velocities and time-series displacements. Spatial-temporal subsidence patterns on each type of infrastructures are strongly dependent on the operational durations and structural characteristics, as well as the variation of the foundation soil layers. PMID:29186039

Health Diagnosis of Major Transportation Infrastructures in Shanghai Metropolis Using High-Resolution Persistent Scatterer Interferometry.

PubMed

Qin, Xiaoqiong; Yang, Tianliang; Yang, Mengshi; Zhang, Lu; Liao, Mingsheng

2017-11-29

Since the Persistent Scatterer Synthetic Aperture Radar (SAR) Interferometry (PSI) technology allows the detection of ground subsidence with millimeter accuracy, it is becoming one of the most powerful and economical means for health diagnosis of major transportation infrastructures. However, structures of different types may suffer from various levels of localized subsidence due to the different structural characteristics and subsidence mechanisms. Moreover, in the complex urban scenery, some segments of these infrastructures may be sheltered by surrounding buildings in SAR images, obscuring the desirable signals. Therefore, the subsidence characteristics on different types of structures should be discussed separately and the accuracy of persistent scatterers (PSs) should be optimized. In this study, the PSI-based subsidence mapping over the entire transportation network of Shanghai (more than 10,000 km) is illustrated, achieving the city-wide monitoring specifically along the elevated roads, ground highways and underground subways. The precise geolocation and structural characteristics of infrastructures were combined to effectively guide more accurate identification and separation of PSs along the structures. The experimental results from two neighboring TerraSAR-X stacks from 2013 to 2016 were integrated by joint estimating the measurements in the overlapping area, performing large-scale subsidence mapping and were validated by leveling data, showing highly consistent in terms of subsidence velocities and time-series displacements. Spatial-temporal subsidence patterns on each type of infrastructures are strongly dependent on the operational durations and structural characteristics, as well as the variation of the foundation soil layers.

Disentangling environmental and spatial effects on phylogenetic structure of angiosperm tree communities in China.

PubMed

Qian, Hong; Chen, Shengbin; Zhang, Jin-Long

2017-07-17

Niche-based and neutrality-based theories are two major classes of theories explaining the assembly mechanisms of local communities. Both theories have been frequently used to explain species diversity and composition in local communities but their relative importance remains unclear. Here, we analyzed 57 assemblages of angiosperm trees in 0.1-ha forest plots across China to examine the effects of environmental heterogeneity (relevant to niche-based processes) and spatial contingency (relevant to neutrality-based processes) on phylogenetic structure of angiosperm tree assemblages distributed across a wide range of environment and space. Phylogenetic structure was quantified with six phylogenetic metrics (i.e., phylogenetic diversity, mean pairwise distance, mean nearest taxon distance, and the standardized effect sizes of these three metrics), which emphasize on different depths of evolutionary histories and account for different degrees of species richness effects. Our results showed that the variation in phylogenetic metrics explained independently by environmental variables was on average much greater than that explained independently by spatial structure, and the vast majority of the variation in phylogenetic metrics was explained by spatially structured environmental variables. We conclude that niche-based processes have played a more important role than neutrality-based processes in driving phylogenetic structure of angiosperm tree species in forest communities in China.

Eukaryotic major facilitator superfamily transporter modeling based on the prokaryotic GlpT crystal structure.

PubMed

Lemieux, M Joanne

2007-01-01

The major facilitator superfamily (MFS) of transporters represents the largest family of secondary active transporters and has a diverse range of substrates. With structural information for four MFS transporters, we can see a strong structural commonality suggesting, as predicted, a common architecture for MFS transporters. The rate for crystal structure determination of MFS transporters is slow, making modeling of both prokaryotic and eukaryotic transporters more enticing. In this review, models of eukaryotic transporters Glut1, G6PT, OCT1, OCT2 and Pho84, based on the crystal structures of the prokaryotic GlpT, based on the crystal structure of LacY are discussed. The techniques used to generate the different models are compared. In addition, the validity of these models and the strategy of using prokaryotic crystal structures to model eukaryotic proteins are discussed. For comparison, E. coli GlpT was modeled based on the E. coli LacY structure and compared to the crystal structure of GlpT demonstrating that experimental evidence is essential for accurate modeling of membrane proteins.

Boosting Completion at Community Colleges: Time, Choice, Structure and the Significant Role of States. Policy Brief

ERIC Educational Resources Information Center

Complete College America, 2010

2010-01-01

A new American majority of students is emerging on campuses, especially at community colleges. These students must delicately balance long hours at jobs they must have with the higher education they desire. Even though this emerging majority has fundamentally different needs, American higher education in general has been slow to change, continuing…

Populations of the Minor α-Conformation in AcGXGNH2 and the α-Helical Nucleation Propensities

NASA Astrophysics Data System (ADS)

Zhou, Yanjun; He, Liu; Zhang, Wenwen; Hu, Jingjing; Shi, Zhengshuang

2016-06-01

Intrinsic backbone conformational preferences of different amino acids are important for understanding the local structure of unfolded protein chains. Recent evidence suggests α-structure is relatively minor among three major backbone conformations for unfolded proteins. The α-helices are the dominant structures in many proteins. For these proteins, how could the α-structures occur from the least in unfolded to the most in folded states? Populations of the minor α-conformation in model peptides provide vital information. Reliable determination of populations of the α-conformers in these peptides that exist in multiple equilibriums of different conformations remains a challenge. Combined analyses on data from AcGXPNH2 and AcGXGNH2 peptides allow us to derive the populations of PII, β and α in AcGXGNH2. Our results show that on average residue X in AcGXGNH2 adopt PII, β, and α 44.7%, 44.5% and 10.8% of time, respectively. The contents of α-conformations for different amino acids define an α-helix nucleation propensity scale. With derived PII, β and α-contents, we can construct a free energy-conformation diagram on each AcGXGNH2 in aqueous solution for the three major backbone conformations. Our results would have broad implications on early-stage events of protein folding.

Interaction of SDS with β-galactosidase. A FT-IR study of the influence of detergent concentration and temperature.

NASA Astrophysics Data System (ADS)

Muga, A.; Castresana, J.; Arrondo, J. L. R.; López, S.; Bernabeu, C.

1988-05-01

The major structure of the enzyme β-galactosidase as studied by FT-IR is β-sheet with maxima in the amide I band at 1639 and 1655 cm -1 in H 2O and 1634 in D 2O. α-helix structure is also present with contribution from β-turns and less-ordered structure. Temperature induces a rearrangement of the structure producing a β-sheet-like conformation. In the presence of the surfactant SDS no big difference in structure is seen at 1% SDS (w:ww) concentration but there is a decrease of 5°C in the midpoint thermal denaturation. In the presence of 10% SDS a different picture is obtained with a higher random structure content.

The evolution of the Piedemonte Llanero petroleum system, Cordillera Oriental, Colombia (2) Reservoir petrography & petroleum geochemistry

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

Piggott, N.; Vear, A.; Warren, E.A.

1996-08-01

Detailed quantification of cements and rock texture, fluid inclusion microthermometry, thermal maturity data, oil-source rock correlations and structural restorations have been integrated to reveal the porosity and hydrocarbon charge evolution of reservoirs in the Piedemonte Llanero thrustbelt of Colombia. Active exploration of deeply buried structures in different thrust sheets of the Piedemonte Llanero has encountered quartz arenites of widely varying average porosities (4-15%). Porosity has been reduced by mechanical compaction and quartz cementation during burial, and by pressure solution during structural deformation. The relative importance and timing of these processes varies between thrust sheets controlling the observed porosity variation. Thermalmore » maturity data indicate that all thrust sheets have been deeply buried and uplifted in several stages of compression. Detailed structural restorations indicate significant differences in the burial histories of individual thrust sheets. Oil-source rock correlations suggest two major hydrocarbon components in the thrustbelt: a Late Cretaceous oil-prone source and a Tertiary oil- and gas-prone source. Initial generation charged early structures leading to partial inhibition of quartz cementation. For most structures quartz cementation predated major hydrocarbon migration. Average quartz cementation temperature is uniform within a structure, but varies between thrust sheets. These variations appear to reflect differences in burial depths during quartz cementation rather than variations in timing. Integration of all data reveals a complex but predictable evolution of porosity and hydrocarbon charge in both space and time which is being applied to current exploration in the Piedemonte Llanero and is relevant to thrustbelt exploration elsewhere.« less

Structural Maturation of HIV-1 Reverse Transcriptase—A Metamorphic Solution to Genomic Instability

PubMed Central

London, Robert E.

2016-01-01

Human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT)—a critical enzyme of the viral life cycle—undergoes a complex maturation process, required so that a pair of p66 precursor proteins can develop conformationally along different pathways, one evolving to form active polymerase and ribonuclease H (RH) domains, while the second forms a non-functional polymerase and a proteolyzed RH domain. These parallel maturation pathways rely on the structural ambiguity of a metamorphic polymerase domain, for which the sequence–structure relationship is not unique. Recent nuclear magnetic resonance (NMR) studies utilizing selective labeling techniques, and structural characterization of the p66 monomer precursor have provided important insights into the details of this maturation pathway, revealing many aspects of the three major steps involved: (1) domain rearrangement; (2) dimerization; and (3) subunit-selective RH domain proteolysis. This review summarizes the major structural changes that occur during the maturation process. We also highlight how mutations, often viewed within the context of the mature RT heterodimer, can exert a major influence on maturation and dimerization. It is further suggested that several steps in the RT maturation pathway may provide attractive targets for drug development. PMID:27690082

Composition and Dynamics of Bacterial Communities of a Drinking Water Supply System as Assessed by RNA- and DNA-Based 16S rRNA Gene Fingerprinting

PubMed Central

Eichler, Stefan; Christen, Richard; Höltje, Claudia; Westphal, Petra; Bötel, Julia; Brettar, Ingrid; Mehling, Arndt; Höfle, Manfred G.

2006-01-01

Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS revealed a significant influence of both source waters on the overall composition of the drinking water microflora and demonstrated the relevance of the raw water microflora for the drinking water microflora provided to the end user. PMID:16517632

Cortical abnormalities in adults and adolescents with major depression based on brain scans from 20 cohorts worldwide in the ENIGMA Major Depressive Disorder Working Group

PubMed Central

Schmaal, L; Hibar, D P; Sämann, P G; Hall, G B; Baune, B T; Jahanshad, N; Cheung, J W; van Erp, T G M; Bos, D; Ikram, M A; Vernooij, M W; Niessen, W J; Tiemeier, H; Hofman, A; Wittfeld, K; Grabe, H J; Janowitz, D; Bülow, R; Selonke, M; Völzke, H; Grotegerd, D; Dannlowski, U; Arolt, V; Opel, N; Heindel, W; Kugel, H; Hoehn, D; Czisch, M; Couvy-Duchesne, B; Rentería, M E; Strike, L T; Wright, M J; Mills, N T; de Zubicaray, G I; McMahon, K L; Medland, S E; Martin, N G; Gillespie, N A; Goya-Maldonado, R; Gruber, O; Krämer, B; Hatton, S N; Lagopoulos, J; Hickie, I B; Frodl, T; Carballedo, A; Frey, E M; van Velzen, L S; Penninx, B W J H; van Tol, M-J; van der Wee, N J; Davey, C G; Harrison, B J; Mwangi, B; Cao, B; Soares, J C; Veer, I M; Walter, H; Schoepf, D; Zurowski, B; Konrad, C; Schramm, E; Normann, C; Schnell, K; Sacchet, M D; Gotlib, I H; MacQueen, G M; Godlewska, B R; Nickson, T; McIntosh, A M; Papmeyer, M; Whalley, H C; Hall, J; Sussmann, J E; Li, M; Walter, M; Aftanas, L; Brack, I; Bokhan, N A; Thompson, P M; Veltman, D J

2017-01-01

The neuro-anatomical substrates of major depressive disorder (MDD) are still not well understood, despite many neuroimaging studies over the past few decades. Here we present the largest ever worldwide study by the ENIGMA (Enhancing Neuro Imaging Genetics through Meta-Analysis) Major Depressive Disorder Working Group on cortical structural alterations in MDD. Structural T1-weighted brain magnetic resonance imaging (MRI) scans from 2148 MDD patients and 7957 healthy controls were analysed with harmonized protocols at 20 sites around the world. To detect consistent effects of MDD and its modulators on cortical thickness and surface area estimates derived from MRI, statistical effects from sites were meta-analysed separately for adults and adolescents. Adults with MDD had thinner cortical gray matter than controls in the orbitofrontal cortex (OFC), anterior and posterior cingulate, insula and temporal lobes (Cohen's d effect sizes: −0.10 to −0.14). These effects were most pronounced in first episode and adult-onset patients (>21 years). Compared to matched controls, adolescents with MDD had lower total surface area (but no differences in cortical thickness) and regional reductions in frontal regions (medial OFC and superior frontal gyrus) and primary and higher-order visual, somatosensory and motor areas (d: −0.26 to −0.57). The strongest effects were found in recurrent adolescent patients. This highly powered global effort to identify consistent brain abnormalities showed widespread cortical alterations in MDD patients as compared to controls and suggests that MDD may impact brain structure in a highly dynamic way, with different patterns of alterations at different stages of life. PMID:27137745

Variability in Rheumatology day care hospitals in Spain: VALORA study.

PubMed

Hernández Miguel, María Victoria; Martín Martínez, María Auxiliadora; Corominas, Héctor; Sanchez-Piedra, Carlos; Sanmartí, Raimon; Fernandez Martinez, Carmen; García-Vicuña, Rosario

To describe the variability of the day care hospital units (DCHUs) of Rheumatology in Spain, in terms of structural resources and operating processes. Multicenter descriptive study with data from a self-completed questionnaire of DCHUs self-assessment based on DCHUs quality standards of the Spanish Society of Rheumatology. Structural resources and operating processes were analyzed and stratified by hospital complexity (regional, general, major and complex). Variability was determined using the coefficient of variation (CV) of the variable with clinical relevance that presented statistically significant differences when was compared by centers. A total of 89 hospitals (16 autonomous regions and Melilla) were included in the analysis. 11.2% of hospitals are regional, 22,5% general, 27%, major and 39,3% complex. A total of 92% of DCHUs were polyvalent. The number of treatments applied, the coordination between DCHUs and hospital pharmacy and the post graduate training process were the variables that showed statistically significant differences depending on the complexity of hospital. The highest rate of rheumatologic treatments was found in complex hospitals (2.97 per 1,000 population), and the lowest in general hospitals (2.01 per 1,000 population). The CV was 0.88 in major hospitals; 0.86 in regional; 0.76 in general, and 0.72 in the complex. there was variability in the number of treatments delivered in DCHUs, being greater in major hospitals and then in regional centers. Nonetheless, the variability in terms of structure and function does not seem due to differences in center complexity. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Reumatología y Colegio Mexicano de Reumatología. All rights reserved.

Cortical abnormalities in adults and adolescents with major depression based on brain scans from 20 cohorts worldwide in the ENIGMA Major Depressive Disorder Working Group.

PubMed

Schmaal, L; Hibar, D P; Sämann, P G; Hall, G B; Baune, B T; Jahanshad, N; Cheung, J W; van Erp, T G M; Bos, D; Ikram, M A; Vernooij, M W; Niessen, W J; Tiemeier, H; Hofman, A; Wittfeld, K; Grabe, H J; Janowitz, D; Bülow, R; Selonke, M; Völzke, H; Grotegerd, D; Dannlowski, U; Arolt, V; Opel, N; Heindel, W; Kugel, H; Hoehn, D; Czisch, M; Couvy-Duchesne, B; Rentería, M E; Strike, L T; Wright, M J; Mills, N T; de Zubicaray, G I; McMahon, K L; Medland, S E; Martin, N G; Gillespie, N A; Goya-Maldonado, R; Gruber, O; Krämer, B; Hatton, S N; Lagopoulos, J; Hickie, I B; Frodl, T; Carballedo, A; Frey, E M; van Velzen, L S; Penninx, B W J H; van Tol, M-J; van der Wee, N J; Davey, C G; Harrison, B J; Mwangi, B; Cao, B; Soares, J C; Veer, I M; Walter, H; Schoepf, D; Zurowski, B; Konrad, C; Schramm, E; Normann, C; Schnell, K; Sacchet, M D; Gotlib, I H; MacQueen, G M; Godlewska, B R; Nickson, T; McIntosh, A M; Papmeyer, M; Whalley, H C; Hall, J; Sussmann, J E; Li, M; Walter, M; Aftanas, L; Brack, I; Bokhan, N A; Thompson, P M; Veltman, D J

2017-06-01

The neuro-anatomical substrates of major depressive disorder (MDD) are still not well understood, despite many neuroimaging studies over the past few decades. Here we present the largest ever worldwide study by the ENIGMA (Enhancing Neuro Imaging Genetics through Meta-Analysis) Major Depressive Disorder Working Group on cortical structural alterations in MDD. Structural T1-weighted brain magnetic resonance imaging (MRI) scans from 2148 MDD patients and 7957 healthy controls were analysed with harmonized protocols at 20 sites around the world. To detect consistent effects of MDD and its modulators on cortical thickness and surface area estimates derived from MRI, statistical effects from sites were meta-analysed separately for adults and adolescents. Adults with MDD had thinner cortical gray matter than controls in the orbitofrontal cortex (OFC), anterior and posterior cingulate, insula and temporal lobes (Cohen's d effect sizes: -0.10 to -0.14). These effects were most pronounced in first episode and adult-onset patients (>21 years). Compared to matched controls, adolescents with MDD had lower total surface area (but no differences in cortical thickness) and regional reductions in frontal regions (medial OFC and superior frontal gyrus) and primary and higher-order visual, somatosensory and motor areas (d: -0.26 to -0.57). The strongest effects were found in recurrent adolescent patients. This highly powered global effort to identify consistent brain abnormalities showed widespread cortical alterations in MDD patients as compared to controls and suggests that MDD may impact brain structure in a highly dynamic way, with different patterns of alterations at different stages of life.

Sex differences in the pathways to major depression: a study of opposite-sex twin pairs.

PubMed

Kendler, Kenneth S; Gardner, Charles O

2014-04-01

The authors sought to clarify the nature of sex differences in the etiologic pathways to major depression. Retrospective and prospective assessments of 20 developmentally organized risk factors and the occurrence of past-year major depression were conducted at two waves of personal interviews at least 12 months apart in 1,057 opposite-sex dizygotic twin pairs from a population-based register. Analyses were conducted by structural modeling, examining within-pair differences. Sixty percent of all paths in the best-fit model exhibited sex differences. Eleven of the 20 risk factors differed across sexes in their impact on liability to major depression. Five had a greater impact in women: parental warmth, neuroticism, divorce, social support, and marital satisfaction. Six had a greater impact in men: childhood sexual abuse, conduct disorder, drug abuse, prior history of major depression, and distal and dependent proximal stressful life events. The life event categories responsible for the stronger effect in males were financial, occupational, and legal in nature. In a co-twin control design, which matches sisters and brothers on genetic and familial-environmental background, personality and failures in interpersonal relationships played a stronger etiologic role in major depression for women than for men. Externalizing psychopathology, prior depression, and specific "instrumental" classes of acute stressors were more important in the etiologic pathway to major depression for men. The results are consistent with previously proposed typologies of major depression that suggest two subtypes that differ in prevalence in women (deficiencies in caring relationships and interpersonal loss) and men (failures to achieve expected goals, with lowered self-worth).

Characterization of local complex structures in a recurrence plot to improve nonlinear dynamic discriminant analysis.

PubMed

Ding, Hang

2014-01-01

Structures in recurrence plots (RPs), preserving the rich information of nonlinear invariants and trajectory characteristics, have been increasingly analyzed in dynamic discrimination studies. The conventional analysis of RPs is mainly focused on quantifying the overall diagonal and vertical line structures through a method, called recurrence quantification analysis (RQA). This study extensively explores the information in RPs by quantifying local complex RP structures. To do this, an approach was developed to analyze the combination of three major RQA variables: determinism, laminarity, and recurrence rate (DLR) in a metawindow moving over a RP. It was then evaluated in two experiments discriminating (1) ideal nonlinear dynamic series emulated from the Lorenz system with different control parameters and (2) data sets of human heart rate regulations with normal sinus rhythms (n = 18) and congestive heart failure (n = 29). Finally, the DLR was compared with seven major RQA variables in terms of discriminatory power, measured by standardized mean difference (DSMD). In the two experiments, DLR resulted in the highest discriminatory power with DSMD = 2.53 and 0.98, respectively, which were 7.41 and 2.09 times the best performance from RQA. The study also revealed that the optimal RP structures for the discriminations were neither typical diagonal structures nor vertical structures. These findings indicate that local complex RP structures contain some rich information unexploited by RQA. Therefore, future research to extensively analyze complex RP structures would potentially improve the effectiveness of the RP analysis in dynamic discrimination studies.

The Effects of Individual Differences on Learner's Navigation in a Courseware

ERIC Educational Resources Information Center

Somyürek, Sibel; Güyer, Tolga; Atasoy, Bilal

2008-01-01

One of the major features of a computer based instruction (CBI) is its non-linear structure allowing learners the opportunity of flexible navigation to accommodate their own needs. However, this non-linear structure may cause problems such as inefficient navigation, being lost or cognitive overhead for some learners. The aim of this study is to…

Dimensions of Cultural Differences: Pancultural, ETIC/EMIC, and Ecological Approaches

ERIC Educational Resources Information Center

Stankov, Lazar; Lee, Jihyun

2009-01-01

We investigated the factorial structure of four major domains in social psychology (personality traits, social attitudes, values, and social norms) with an emphasis on cross-cultural differences. Three distinctive approaches--pancultural, multigroup, and multilevel--were applied to the data based on 22 measures that were collected from 2029…

Effects of Large-Scale Releases on the Genetic Structure of Red Sea Bream (Pagrus major, Temminck et Schlegel) Populations in Japan.

PubMed

Blanco Gonzalez, Enrique; Aritaki, Masato; Knutsen, Halvor; Taniguchi, Nobuhiko

2015-01-01

Large-scale hatchery releases are carried out for many marine fish species worldwide; nevertheless, the long-term effects of this practice on the genetic structure of natural populations remains unclear. The lack of knowledge is especially evident when independent stock enhancement programs are conducted simultaneously on the same species at different geographical locations, as occurs with red sea bream (Pagrus major, Temminck et Schlegel) in Japan. In this study, we examined the putative effects of intensive offspring releases on the genetic structure of red sea bream populations along the Japanese archipelago by genotyping 848 fish at fifteen microsatellite loci. Our results suggests weak but consistent patterns of genetic divergence (F(ST) = 0.002, p < 0.001). Red sea bream in Japan appeared spatially structured with several patches of distinct allelic composition, which corresponded to areas receiving an important influx of fish of hatchery origin, either released intentionally or from unintentional escapees from aquaculture operations. In addition to impacts upon local populations inhabiting semi-enclosed embayments, large-scale releases (either intentionally or from unintentional escapes) appeared also to have perturbed genetic structure in open areas. Hence, results of the present study suggest that independent large-scale marine stock enhancement programs conducted simultaneously on one species at different geographical locations may compromise native genetic structure and lead to patchy patterns in population genetic structure.

Replacement of the Endogenous Starch Debranching Enzymes ISA1 and ISA2 of Arabidopsis with the Rice Orthologs Reveals a Degree of Functional Conservation during Starch Synthesis

PubMed Central

Streb, Sebastian; Zeeman, Samuel C.

2014-01-01

This study tested the interchangeability of enzymes in starch metabolism between dicotyledonous and monocotyledonous plant species. Amylopectin - a branched glucose polymer - is the major component of starch and is responsible for its semi-crystalline property. Plants synthesize starch with distinct amylopectin structures, varying between species and tissues. The structure determines starch properties, an important characteristic for cooking and nutrition, and for the industrial uses of starch. Amylopectin synthesis involves at least three enzyme classes: starch synthases, branching enzymes and debranching enzymes. For all three classes, several enzyme isoforms have been identified. However, it is not clear which enzyme(s) are responsible for the large diversity of amylopectin structures. Here, we tested whether the specificities of the debranching enzymes (ISA1 and ISA2) are major determinants of species-dependent differences in amylopectin structure by replacing the dicotyledonous Arabidopsis isoamylases (AtISA1 and AtISA2) with the monocotyledonous rice (Oryza sativa) isoforms. We demonstrate that the ISA1 and ISA2 are sufficiently well conserved between these species to form heteromultimeric chimeric Arabidopsis/rice isoamylase enzymes. Furthermore, we were able to reconstitute the endosperm-specific rice OsISA1 homomultimeric complex in Arabidopsis isa1isa2 mutants. This homomultimer was able to facilitate normal rates of starch synthesis. The resulting amylopectin structure had small but significant differences in comparison to wild-type Arabidopsis amylopectin. This suggests that ISA1 and ISA2 have a conserved function between plant species with a major role in facilitating the crystallization of pre-amylopectin synthesized by starch synthases and branching enzymes, but also influencing the final structure of amylopectin. PMID:24642810

Multidecadal stability in tropical rain forest structure and dynamics across an old-growth landscape

PubMed Central

Clark, Deborah A.; Oberbauer, Steven F.; Kellner, James R.

2017-01-01

Have tropical rain forest landscapes changed directionally through recent decades? To answer this question requires tracking forest structure and dynamics through time and across within-forest environmental heterogeneity. While the impacts of major environmental gradients in soil nutrients, climate and topography on lowland tropical rain forest (TRF) structure and function have been extensively analyzed, the effects of the shorter environmental gradients typical of mesoscale TRF landscapes remain poorly understood. To evaluate multi-decadal performance of an old-growth TRF at the La Selva Biological Station, Costa Rica, we established 18 0.5-ha annually-censused forest inventory plots in a stratified-random design across major landscape edaphic gradients. Over the 17-year study period, there were moderate differences in stand dynamics and structure across these gradients but no detectable difference in woody productivity. We found large effects on forest structure and dynamics from the mega-Niño event at the outset of the study, with subdecadal recovery and subsequent stabilization. To extend the timeline to >40 years, we combined our findings with those from earlier studies at this site. While there were annual to multiannual variations in the structure and dynamics, particularly in relation to local disturbances and the mega-Niño event, at the longer temporal scale and broader spatial scale this landscape was remarkably stable. This stability contrasts notably with a current hypothesis of increasing biomass and dynamics of TRF, which we term the Bigger and Faster Hypothesis (B&FHo). We consider possible reasons for the contradiction and conclude that it is currently not possible to independently assess the vast majority of previously published B&FHo evidence due to restricted data access. PMID:28981502

Characterization of 17 chaperone-usher fimbriae encoded by Proteus mirabilis reveals strong conservation

PubMed Central

Kuan, Lisa; Schaffer, Jessica N.; Zouzias, Christos D.

2014-01-01

Proteus mirabilis is a Gram-negative enteric bacterium that causes complicated urinary tract infections, particularly in patients with indwelling catheters. Sequencing of clinical isolate P. mirabilis HI4320 revealed the presence of 17 predicted chaperone-usher fimbrial operons. We classified these fimbriae into three groups by their genetic relationship to other chaperone-usher fimbriae. Sixteen of these fimbriae are encoded by all seven currently sequenced P. mirabilis genomes. The predicted protein sequence of the major structural subunit for 14 of these fimbriae was highly conserved (≥95 % identity), whereas three other structural subunits (Fim3A, UcaA and Fim6A) were variable. Further examination of 58 clinical isolates showed that 14 of the 17 predicted major structural subunit genes of the fimbriae were present in most strains (>85 %). Transcription of the predicted major structural subunit genes for all 17 fimbriae was measured under different culture conditions designed to mimic conditions in the urinary tract. The majority of the fimbrial genes were induced during stationary phase, static culture or colony growth when compared to exponential-phase aerated culture. Major structural subunit proteins for six of these fimbriae were detected using MS of proteins sheared from the surface of broth-cultured P. mirabilis, demonstrating that this organism may produce multiple fimbriae within a single culture. The high degree of conservation of P. mirabilis fimbriae stands in contrast to uropathogenic Escherichia coli and Salmonella enterica, which exhibit greater variability in their fimbrial repertoires. These findings suggest there may be evolutionary pressure for P. mirabilis to maintain a large fimbrial arsenal. PMID:24809384

basement reservoir geometry and properties

NASA Astrophysics Data System (ADS)

Walter, bastien; Geraud, yves; Diraison, marc

2017-04-01

Basement reservoirs are nowadays frequently investigated for deep-seated fluid resources (e.g. geothermal energy, groundwater, hydrocarbons). The term 'basement' generally refers to crystalline and metamorphic formations, where matrix porosity is negligible in fresh basement rocks. Geothermal production of such unconventional reservoirs is controlled by brittle structures and altered rock matrix, resulting of a combination of different tectonic, hydrothermal or weathering phenomena. This work aims to characterize the petro-structural and petrophysical properties of two basement surface analogue case studies in geological extensive setting (the Albert Lake rift in Uganda; the Ifni proximal margin of the South West Morocco Atlantic coast). Different datasets, using field structural study, geophysical acquisition and laboratory petrophysical measurements, were integrated to describe the multi-scale geometry of the porous network of such fractured and weathered basement formations. This study points out the multi-scale distribution of all the features constituting the reservoir, over ten orders of magnitude from the pluri-kilometric scale of the major tectonics structures to the infra-millimetric scale of the secondary micro-porosity of fractured and weathered basements units. Major fault zones, with relatively thick and impermeable fault core structures, control the 'compartmentalization' of the reservoir by dividing it into several structural blocks. The analysis of these fault zones highlights the necessity for the basement reservoirs to be characterized by a highly connected fault and fracture system, where structure intersections represent the main fluid drainage areas between and within the reservoir's structural blocks. The suitable fluid storage areas in these reservoirs correspond to the damage zone of all the fault structures developed during the tectonic evolution of the basement and the weathered units of the basement roof developed during pre-rift exhumation phases. Macroscopic fracture density is highly dependent on the petrographic nature of the basement, with values up to 80 frac./m in fault damage zones of crystalline rocks. Dense micro-cracks associated to major fault structures can develop porosity and permeability up to 10% and 0.1 D. In some weathered horizons, alteration can develop matrix porosity up to 40% and the permeability reaches up to 1D. This study highlights therefore that basement reservoir properties are the result of the long geodynamic evolution of such formations, and the different fault zone compartments or weathering horizons have to be considered separately for reservoir understanding.

Integrating aeromagnetic and Landsat™ 8 data into subsurface structural mapping of Precambrian basement complex

NASA Astrophysics Data System (ADS)

Kayode, John Stephen; Nawawi, M. N. M.; Abdullah, Khiruddin B.; Khalil, Amin E.

2017-01-01

The integration of Aeromagnetic data and remotely sensed imagery with the intents of mapping the subsurface geological structures in part of the South-western basement complex of Nigeria was developed using the PCI Geomatica Software. 2013. The data obtained from the Nigerian Geological Survey Agency; was corrected using Regional Residual Separation of the Total Magnetic field anomalies enhanced, and International Geomagnetic Reference Field removed. The principal objective of this study is, therefore, to introduce a rapid and efficient method of subsurface structural depth estimate and structural index evaluation through the incorporation of the Euler Deconvolution technique into PCI Geomatica 2013 to prospect for subsurface geological structures. The shape and depth of burial helped to define these structures from the regional aeromagnetic map. The method enabled various structural indices to be automatically delineated for an index of between 0.5 SI and 3.0 SI at a maximum depth of 1.1 km that clearly showed the best depths estimate for all the structural indices. The results delineate two major magnetic belts in the area; the first belt shows an elongated ridge-like structure trending mostly along the NorthNortheast-SouthSouthwest and the other anomalies trends primarily in the Northeast, Northwest, Northeast-Southwest parts of the study area that could be attributed to basement complex granitic intrusions from the tectonic history of the area. The majority of the second structures showed various linear structures different from the first structure. Basically, a significant offset was delineated at the core segment of the study area, suggesting a major subsurface geological feature that controls mineralisation in this area.

Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization.

PubMed

Ibrahim, Tamer M; Bauer, Matthias R; Boeckler, Frank M

2015-01-01

Structure-based virtual screening techniques can help to identify new lead structures and complement other screening approaches in drug discovery. Prior to docking, the data (protein crystal structures and ligands) should be prepared with great attention to molecular and chemical details. Using a subset of 18 diverse targets from the recently introduced DEKOIS 2.0 benchmark set library, we found differences in the virtual screening performance of two popular docking tools (GOLD and Glide) when employing two different commercial packages (e.g. MOE and Maestro) for preparing input data. We systematically investigated the possible factors that can be responsible for the found differences in selected sets. For the Angiotensin-I-converting enzyme dataset, preparation of the bioactive molecules clearly exerted the highest influence on VS performance compared to preparation of the decoys or the target structure. The major contributing factors were different protonation states, molecular flexibility, and differences in the input conformation (particularly for cyclic moieties) of bioactives. In addition, score normalization strategies eliminated the biased docking scores shown by GOLD (ChemPLP) for the larger bioactives and produced a better performance. Generalizing these normalization strategies on the 18 DEKOIS 2.0 sets, improved the performances for the majority of GOLD (ChemPLP) docking, while it showed detrimental performances for the majority of Glide (SP) docking. In conclusion, we exemplify herein possible issues particularly during the preparation stage of molecular data and demonstrate to which extent these issues can cause perturbations in the virtual screening performance. We provide insights into what problems can occur and should be avoided, when generating benchmarks to characterize the virtual screening performance. Particularly, careful selection of an appropriate molecular preparation setup for the bioactive set and the use of score normalization for docking with GOLD (ChemPLP) appear to have a great importance for the screening performance. For virtual screening campaigns, we recommend to invest time and effort into including alternative preparation workflows into the generation of the master library, even at the cost of including multiple representations of each molecule. Graphical AbstractUsing DEKOIS 2.0 benchmark sets in structure-based virtual screening to probe the impact of molecular preparation and score normalization.

Differential co-localization with choline acetyltransferase in nervus terminalis suggests functional differences for GnRH isoforms in bonnethead sharks (Sphyrna tiburo)

PubMed Central

Moeller, John F.; Meredith, Michael

2010-01-01

The nervus terminalis (NT) is a vertebrate cranial nerve whose function in adults is unknown. In bonnethead sharks the nerve is anatomically independent of the olfactory system, with two major cell populations within one or more ganglia along its exposed length. Most cells are immunoreactive for either gonadotropin-releasing hormone (GnRH) or RFamide-like peptides. To define further the cell populations and connectivity, we used double-label immuno-cytochemistry with antisera to different isoforms of GnRH and to choline acetyltransferase (ChAT). The labeling patterns of two GnRH antisera revealed different populations of GnRH immunoreactive (ir) cell-profiles in the NT ganglion. One antiserum labeled a large group of cells and fibers, which likely contain mammalian GnRH (GnRH-I) as described in previous studies, and which were ChAT immunoreactive. The other antiserum labeled large club-like structures, which were anuclear, and a sparse number of fibers, but with no clear labeling of cell bodies in the ganglion. These club structures were choline acetyltrasferase (ChAT) negative, and preabsorption control tests suggest they may contain chicken-GnRH-II (GnRH-II) or dogfish GnRH. The second major NT ganglion cell-type was immunoreactive for RF-amides, which regulate GnRH release in other vertebrates, and may provide an intraganglionic influence on GnRH release. The immunocytochemical and anatomical differences between the two GnRH immunoreactive profile types indicate possible functional differences for these isoforms in the NT. The club-like structures may be sites of GnRH release into the general circulation since these structures were observed near blood vessels and resembled structures seen in the median eminence of rats. PMID:20950589

Differential co-localization with choline acetyltransferase in nervus terminalis suggests functional differences for GnRH isoforms in bonnethead sharks (Sphyrna tiburo).

PubMed

Moeller, John F; Meredith, Michael

2010-12-17

The nervus terminalis (NT) is a vertebrate cranial nerve whose function in adults is unknown. In bonnethead sharks, the nerve is anatomically independent of the olfactory system, with two major cell populations within one or more ganglia along its exposed length. Most cells are immunoreactive for either gonadotropin-releasing hormone (GnRH) or RF-amide-like peptides. To define further the cell populations and connectivity, we used double-label immunocytochemistry with antisera to different isoforms of GnRH and to choline acetyltransferase (ChAT). The labeling patterns of two GnRH antisera revealed different populations of GnRH-immunoreactive (ir) cell profiles in the NT ganglion. One antiserum labeled a large group of cells and fibers, which likely contain mammalian GnRH (GnRH-I) as described in previous studies and which were ChAT immunoreactive. The other antiserum labeled large club-like structures, which were anuclear, and a sparse number of fibers, but with no clear labeling of cell bodies in the ganglion. These club structures were choline acetyltrasferase (ChAT)-negative, and preabsorption control tests suggest they may contain chicken-GnRH-II (GnRH-II) or dogfish GnRH. The second major NT ganglion cell-type was immunoreactive for RF-amides, which regulate GnRH release in other vertebrates, and may provide an intraganglionic influence on GnRH release. The immunocytochemical and anatomical differences between the two GnRH-immunoreactive profile types indicate possible functional differences for these isoforms in the NT. The club-like structures may be sites of GnRH release into the general circulation since these structures were observed near blood vessels and resembled structures seen in the median eminence of rats. Copyright © 2010 Elsevier B.V. All rights reserved.

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

PubMed

Olechnovič, Kliment; Venclovas, Ceslovas

2014-07-01

The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Mechanical features of various silkworm crystalline considering hydration effect via molecular dynamics simulations.

PubMed

Kim, Yoonjung; Lee, Myeongsang; Choi, Hyunsung; Baek, Inchul; Kim, Jae In; Na, Sungsoo

2018-04-01

Silk materials are receiving significant attention as base materials for various functional nanomaterials and nanodevices, due to its exceptionally high mechanical properties, biocompatibility, and degradable characteristics. Although crystalline silk regions are composed of various repetitive motifs with differing amino acid sequences, how the effect of humidity works differently on each of the motifs and their structural characteristics remains unclear. We report molecular dynamics (MD) simulations on various silkworm fibroins composed of major motifs (i.e. (GAGAGS) n , (GAGAGA) n , and (GAGAGY) n ) at varying degrees of hydration, and reveal how each major motifs of silk fibroins change at each degrees of hydration using MD simulations and their structural properties in mechanical perspective via steered molecular dynamics simulations. Our results explain what effects humidity can have on nanoscale materials and devices consisting of crystalline silk materials.

Opportunities for healthier child feeding. Does ethnic position matter? - self-reported evaluation of family diet and impediments to change among parents with majority and minority status in Denmark.

PubMed

Nielsen, Annemette; Krasnik, Allan; Vassard, Ditte; Holm, Lotte

2014-07-01

Health inequality between ethnic groups is expressed in differences in the prevalence of diet related diseases. The aim of the study was to investigate and compare barriers toward eating healthier among ethnic majority and minority parents in Denmark. A postal survey was carried out among 2511 parents with either Danish or non-western ethnic minority descendant background, investigating barriers on cultural, structural, social, individual, and practical levels. The results showed that compared with parents of Danish origin, ethnic minority parents were more likely to evaluate their own diets negatively (OR 3.0, CI 1.7-5.3), and to evaluate their children's diets negatively (OR 4.6, CI 2.5-8.4). In addition, ethnic minority parents to a higher degree experienced barriers to eating healthier than Danish parents did. Most salient was ethnic minority parents' expression of a lack of control over their own food intake and the food given to their children in everyday life. Such a lack of control was identified on practical, social, structural and individual levels. Young age of the parents was found to explain some of the differences between ethnic groups. It is concluded that dietary interventions directed at parents of small children should address not only cultural background but also barriers operating on practical, social, structural, and individual levels, as some of these influence ethnic minorities and the majority population differently. Further exploration of the importance of young age and the interplay between structural and cultural factors in the lives of ethnic minority families is needed. Copyright © 2014. Published by Elsevier Ltd.

Concepts for Life Cycle Cost Control Required to Achieve Space Transportation Affordability and Sustainability

NASA Technical Reports Server (NTRS)

Rhodes, Russel E.; Zapata, Edgar; Levack, Daniel J. H.; Robinson, John W.; Donahue, Benjamin B.

2009-01-01

Cost control must be implemented through the establishment of requirements and controlled continually by managing to these requirements. Cost control of the non-recurring side of life cycle cost has traditionally been implemented in both commercial and government programs. The government uses the budget process to implement this control. The commercial approach is to use a similar process of allocating the non-recurring cost to major elements of the program. This type of control generally manages through a work breakdown structure (WBS) by defining the major elements of the program. If the cost control is to be applied across the entire program life cycle cost (LCC), the approach must be addressed very differently. A functional breakdown structure (FBS) is defined and recommended. Use of a FBS provides the visibifity to allow the choice of an integrated solution reducing the cost of providing many different elements of like function. The different functional solutions that drive the hardware logistics, quantity of documentation, operational labor, reliability and maintainability balance, and total integration of the entire system from DDT&E through the life of the program must be fully defined, compared, and final decisions made among these competing solutions. The major drivers of recurring cost have been identified and are presented and discussed. The LCC requirements must be established and flowed down to provide control of LCC. This LCC control will require a structured rigid process similar to the one traditionally used to control weight/performance for space transportation systems throughout the entire program. It has been demonstrated over the last 30 years that without a firm requirement and methodically structured cost control, it is unlikely that affordable and sustainable space transportation system LCC will be achieved.

Investigating Stratification within Higher Education through Examining the Status of Students in Different Academic Majors in Terms of Cultural, Social and Economic Capital

ERIC Educational Resources Information Center

Hassani, Mohammad; Ghasemi, Seyyed Jamal Mir

2016-01-01

This study was carried out in order to explore the status of stratification within higher education through measuring cultural, economic and social capital of students in major academic disciplines across universities in Urmia, Northwestern Iran. The findings indicate that there are stratification structures in the presence of students in…

Shining light on the differences in molecular structural chemical makeup and the cause of distinct degradation behavior between malting- and feed-type barley using synchrotron FTIR microspectroscopy: a novel approach.

PubMed

Yu, Peiqiang; Doiron, Kevin; Liu, Dasen

2008-05-14

The objective of this study was to use advanced synchrotron-sourced FTIR microspectroscopy (SFTIRM) as a novel approach to identify the differences in protein and carbohydrate molecular structure (chemical makeup) between these two varieties of barley and illustrate the exact causes for their significantly different degradation kinetics. Items assessed included (1) molecular structural differences in protein amide I to amide II intensities and their ratio within cellular dimensions, (2) molecular structural differences in protein secondary structure profile and their ratios, and (3) molecular structural differences in carbohydrate component peak profile. Our hypothesis was that molecular structure (chemical makeup) affects barley quality, fermentation, and degradation behavior in both humans and animals. Using SFTIRM, the protein and carbohydrate molecular structural chemical makeup of barley was revealed and identified. The protein molecular structural chemical makeup differed significantly between the two varieties of barleys. No difference in carbohydrate molecular structural chemical makeup was detected. Harrington was lower than Valier in protein amide I, amide II, and protein amide I to amide II ratio, while Harrington was relatively higher in model-fitted protein alpha-helix and beta-sheet, but lower in the others (beta-turn and random coil). These results indicated that it is the molecular structure of protein (chemical makeup) that may play a major role in the different degradation kinetics between the two varieties of barleys (not the molecular structure of carbohydrate). It is believed that use of the advanced synchrotron technology will make a significant step and an important contribution to research in examining the molecular structure (chemical makeup) of plant, feed, and seeds.

In situ AFM imaging of apolipoprotein A-I directly derived from plasma HDL.

PubMed

Gan, Chaoye; Wang, Zhexuan; Chen, Yong

2017-04-01

The major apolipoproteins of plasma lipoproteins play vital roles in the structural integrity and physiological functions of lipoproteins. More than ten structural models of apolipoprotein A-I (apoA-I), the major apolipoprotein of high-density lipoprotein (HDL), have been developed successively. In these models, apoA-I was supposed to organize in a ring-shaped form. To date, however, there is no direct evidence under physiological condition. Here, atomic force microscopy (AFM) was used to in situ visualize the organization of apoA-I, which was exposed via depletion of the lipid component of plasma HDL pre-immobilized on functionalized mica sheets. For the first time, the ring-shaped coarse structure and three detailed structures (crescent-shaped, gapped "O"-shaped, and parentheses-shaped structures, respectively) of apoA-I in plasma HDL, which have the ability of binding scavenger receptors, were directly observed and quantitatively measured by AFM. The three detailed structures probably represent the different extents to which the lipid component of HDL was depleted. Data on lipid depletion of HDL may provide clues to understand lipid insertion of HDL. These data provide important information for the understanding of the structure/maturation of plasma HDL. Moreover, they suggest a powerful method for directly visualizing the major apolipoproteins of plasma lipoproteins or the protein component of lipoprotein-like lipid-protein complexes. Copyright © 2017 Elsevier B.V. All rights reserved.

Behavior of road accidents: Structural time series approach

NASA Astrophysics Data System (ADS)

Junus, Noor Wahida Md; Ismail, Mohd Tahir; Arsad, Zainudin

2014-12-01

Road accidents become a major issue in contributing to the increasing number of deaths. Few researchers suggest that road accidents occur due to road structure and road condition. The road structure and condition may differ according to the area and volume of traffic of the location. Therefore, this paper attempts to look up the behavior of the road accidents in four main regions in Peninsular Malaysia by employing a structural time series (STS) approach. STS offers the possibility of modelling the unobserved component such as trends and seasonal component and it is allowed to vary over time. The results found that the number of road accidents is described by a different model. Perhaps, the results imply that the government, especially a policy maker should consider to implement a different approach in ways to overcome the increasing number of road accidents.

Detailed fetal anatomy assessment in the first trimester at 11, 12 and 13 weeks of gestation.

PubMed

Luchi, Carlo; Schifano, Martina; Sacchini, Clara; Nanini, Chiara; Sceusa, Francesca; Capriello, Patrizio; Genazzani, Andrea R

2012-06-01

The aim of the present observational study was to evaluate the feasibility of a morphological scan and determine the detection rate of fetal organs, structures and systems in the first trimester of pregnancy. 977 single pregnant women attending our Fetal Medicine Section to undergo first trimester screening for aneuploidies were enrolled and divided into three groups depending on gestational age and crown-rump-length measurement. Scans targeted on a total of 26 fetal anatomical structures were performed by a single operator. The overall detection rate was 96% at 11 weeks and reached 100% at 12 and 13 weeks, with a significant statistical difference between 11 and 12/13 weeks for the majority of the investigated fetal anatomical structures. Evaluation of most part of the fetal anatomical structures is feasible with high accuracy in the first trimester. Visualization of the majority of the targeted fetal organs improves from 11 to 13 weeks.

Inheritance of Adrenal Phenylethanolamine N-Methyltransferase Activity in the Rat

PubMed Central

Stolk, Jon M.; Vantini, Guido; Guchhait, Ras B.; Hurst, Jeffrey H.; Perry, Bruce D.; U'Prichard, David C.; Elston, Robert C.

1984-01-01

Phenylethanolamine N-methyltransferase (PNMT) is the enzyme that catalyzes the S-adenosyl-l-methionine-dependent methylation of (-)norepinephrine to (-)epinephrine in the adrenal medulla. Adrenal PNMT activity is markedly different in two highly inbred rat strains; enzyme activity in the F344 strain is more than fivefold greater than that in the Buf strain. Initial characterization of the enzyme in the two inbred strains reveals evidence for catalytic and structural differences, as reflected in dissimilar Km values for the cosubstrate (S-adenosyl-l-methionine) and prominent differences in thermal inactivation curves. To assess adrenal PNMT activity in an F344 x Buf pedigree, we employed a statistical procedure to test for one- and two-locus hypotheses in the presence of within-class correlations due to cage or litter effects. The PNMT data in the pedigree are best accounted for by segregation at a simple major locus superimposed upon a polygenic background; data obtained from the biochemical studies suggest that the major locus is a structural gene locus. PMID:6149973

Examining drivers of the emissions embodied in trade

PubMed Central

Wu, Leying; Wang, Zheng

2017-01-01

Emissions embodied in provincial trade (EEPT) have important effects on provinces’ responsibilities for carbon emission reductions. Based on a multi-regional input-output model, we calculated EEPT for China’s 30 provinces in 2002, 2007 and 2010, and we attempted to determine the drivers of EEPT. The results showed that, during this period, the ratio of EEPT to production-based emissions increased over time, reaching 40.24% in 2010. In consideration of its important role in carbon emissions, we analyzed the factors attributable to EEPT through structure decomposition analysis. The decomposition results showed that final demand and carbon emission intensity were two major factors in EEPT, while the final demand in other provinces and the carbon emission intensity in the local province were major factors for Emissions embodied in provincial exports and the final demand in the local province and the carbon emission intensity in other provinces were major factors for Emissions embodied in provincial imports. Regarding the differences among the EEPT of different provinces, changes in the structure of trade were the primary reason. PMID:28426769

Understanding the genetic diversity and population structure of yam (Dioscorea alata L.) using microsatellite markers

PubMed Central

Arnau, Gemma; MN, Sheela; Chair, Hana; Lebot, Vincent; K, Abraham; Perrier, Xavier; Petro, Dalila; Penet, Laurent; Pavis, Claudie

2017-01-01

Yams (Dioscorea sp.) are staple food crops for millions of people in tropical and subtropical regions. Dioscorea alata, also known as greater yam, is one of the major cultivated species and most widely distributed throughout the tropics. Despite its economic and cultural importance, very little is known about its origin, diversity and genetics. As a consequence, breeding efforts for resistance to its main disease, anthracnose, have been fairly limited. The objective of this study was to contribute to the understanding of D. alata genetic diversity by genotyping 384 accessions from different geographical regions (South Pacific, Asia, Africa and the Caribbean), using 24 microsatellite markers. Diversity structuration was assessed via Principal Coordinate Analysis, UPGMA analysis and the Bayesian approach implemented in STRUCTURE. Our results revealed the existence of a wide genetic diversity and a significant structuring associated with geographic origin, ploidy levels and morpho-agronomic characteristics. Seventeen major groups of genetically close cultivars have been identified, including eleven groups of diploid cultivars, four groups of triploids and two groups of tetraploids. STRUCTURE revealed the existence of six populations in the diploid genetic pool and a few admixed cultivars. These results will be very useful for rationalizing D. alata genetic resources in breeding programs across different regions and for improving germplasm conservation methods. PMID:28355293

Role of oxygen functionality on the band structure evolution and conductance of reduced graphene oxide

NASA Astrophysics Data System (ADS)

Roy, Rajarshi; Thapa, Ranjit; Chakrabarty, Soubhik; Jha, Arunava; Midya, Priyanka R.; Kumar, E. Mathan; Chattopadhyay, Kalyan K.

2017-06-01

Here we report, structural and electrical transport properties of reduced graphene oxide as a function of oxygen bonding configuration. We find that mainly epoxy (Csbnd Osbnd C) and carbonyl (Cdbnd O) functional groups remain as major residual components after reduction using three different reducing agents. We calculate the band structure in the presence of epoxy and carbonyl groups and defects. Finally, we calculate the theoretical band mobility and find that it is less for the carbonyl with epoxy system. We correlate the distortion of linear dispersion and opening of bandgap at K-point with conductance for different graphene system in presence of oxygen moieties.

The Latent Symptom Structure of the Beck Depression Inventory-II in Outpatients with Major Depression

ERIC Educational Resources Information Center

Quilty, Lena C.; Zhang, K. Anne; Bagby, R. Michael

2010-01-01

The Beck Depression Inventory-II (BDI-II) is a self-report instrument frequently used in clinical and research settings to assess depression severity. Although investigators have examined the factor structure of the BDI-II, a clear consensus on the best fitting model has not yet emerged, resulting in different recommendations regarding how to best…

Pectic oligosaccharide structure-function relationships: prebiotics, inhibitors of Escherichia coli O157:H7 adhesion and reduction of Shiga toxin cytotoxicity in HT29 cells

USDA-ARS?s Scientific Manuscript database

Shiga toxin (Stx)-producing, food-contaminating Escherichia coli (STEC) is a major health concern. Plant-derived pectin and pectic-oligosaccharides (POS) that are abundant in biomass have been considered as prebiotics and for the protection of humans from Stx intoxication. Five structurally differ...

Two different flavours of complexity in financial data

NASA Astrophysics Data System (ADS)

Buonocore, R. J.; Musmeci, N.; Aste, T.; Matteo, T. Di

2016-12-01

We discuss two elements that define the complexity of financial time series: one is the multiscaling property, which is linked to how the statistics of a single time-series changes with the time horizon; the second is the structure of dependency between time-series, which accounts for the collective behaviour, i.e. the market structure. Financial time-series have statistical properties which change with the time horizon and the quantification of such multiscaling property has been successful to distinguish among different degrees of development of markets, monitor the stability of firms and estimate risk. The study of the structure of dependency between time-series with the use of information filtering graphs can reveal important insight on the market structure highlighting risks, stress and portfolio management strategies. In this contribution we highlight achievements, major successes and discuss major challenges and open problems in the study of these two elements of complexity, hoping to attract the interest of more researchers in this research area. We indeed believe that with the advent of the Big Data era, the need and the further development of such approaches, designed to deal with systems with many degrees of freedom, have become more urgent.

The Myriad Properties of Pasteurella multocida Lipopolysaccharide

PubMed Central

Harper, Marina; Boyce, John Dallas

2017-01-01

Pasteurella multocida is a heterogeneous species that is a primary pathogen of many different vertebrates. This Gram-negative bacterium can cause a range of diseases, including fowl cholera in birds, haemorrhagic septicaemia in ungulates, atrophic rhinitis in swine, and lower respiratory tract infections in cattle and pigs. One of the primary virulence factors of P. multocida is lipopolysaccharide (LPS). Recent work has shown that this crucial surface molecule shows significant structural variability across different P. multocida strains, with many producing LPS structures that are highly similar to the carbohydrate component of host glycoproteins. It is likely that this LPS mimicry of host molecules plays a major role in the survival of P. multocida in certain host niches. P. multocida LPS also plays a significant role in resisting the action of chicken cathelicidins, and is a strong stimulator of host immune responses. The inflammatory response to the endotoxic lipid A component is a major contributor to the pathogenesis of certain infections. Recent work has shown that vaccines containing killed bacteria give protection only against other strains with identical, or nearly identical, surface LPS structures. Conversely, live attenuated vaccines give protection that is broadly protective, and their efficacy is independent of LPS structure. PMID:28825691

ATP regulation of the ligand-binding properties in temperate and cold-adapted haemoglobins. X-ray structure and ligand-binding kinetics in the sub-Antarctic fish Eleginops maclovinus.

PubMed

Coppola, Daniela; Abbruzzetti, Stefania; Nicoletti, Francesco; Merlino, Antonello; Gambacurta, Alessandra; Giordano, Daniela; Howes, Barry D; De Sanctis, Giampiero; Vitagliano, Luigi; Bruno, Stefano; di Prisco, Guido; Mazzarella, Lelio; Smulevich, Giulietta; Coletta, Massimo; Viappiani, Cristiano; Vergara, Alessandro; Verde, Cinzia

2012-10-30

The major haemoglobin of the sub-Antarctic fish Eleginops maclovinus was structurally and functionally characterised with the aim to compare molecular environmental adaptations in the O(2)-transport system of sub-Antarctic fishes of the suborder Notothenioidei with those of their high-latitude relatives. Ligand-binding kinetics of the major haemoglobin of E. maclovinus indicated strong stabilisation of the liganded quaternary T state, enhanced in the presence of the physiological allosteric effector ATP, compared to that of high-Antarctic Trematomus bernacchii. The activation enthalpy for O(2) dissociation was dramatically lower than that in T. bernacchii haemoglobin, suggesting remarkable differences in temperature sensitivity and structural changes associated with O(2) release and exit from the protein. The haemoglobin functional properties, together with the X-ray structure of the CO form at 1.49 Å resolution, the first of a temperate notothenioid, strongly support the hypothesis that in E. maclovinus, whose life-style varies according to changes in habitat, the mechanisms that regulate O(2) affinity and the ATP-induced Root effect differ from those of high-Antarctic Notothenioids.

Crystal structure and DNA repair activities of the AP endonuclease from Leishmania major.

PubMed

Vidal, Antonio E; Harkiolaki, Maria; Gallego, Claribel; Castillo-Acosta, Victor M; Ruiz-Pérez, Luis M; Wilson, Keith; González-Pacanowska, Dolores

2007-11-02

Apurinic/apyrimidinic endonucleases initiate the repair of abasic sites produced either spontaneously, from attack of bases by reactive oxygen species or as intermediates during base excision repair. The catalytic properties and crystal structure of Leishmania major apurinic/apyrimidinic endonuclease are described and compared with those of human APE1 and bacterial exonuclease III. The purified enzyme is shown to possess apurinic/apyrimidinic endonuclease activity of the same order as eukaryotic and prokaryotic counterparts and an equally robust 3'-phosphodiesterase activity. Consistent with this, expression of the L. major endonuclease confers resistance to both methyl methane sulphonate and H2O2 in Escherichia coli repair-deficient mutants while expression of the human homologue only reverts methyl methane sulphonate sensitivity. Structural analyses and modelling of the enzyme-DNA complex demonstrates a high degree of conservation to previously characterized homologues, although subtle differences in the active site geometry might account for the high 3'-phosphodiesterase activity. Our results confirm that the L. major's enzyme is a key element in mediating repair of apurinic/apyrimidinic sites and 3'-blocked termini and therefore must play an important role in the survival of kinetoplastid parasites after exposure to the highly oxidative environment within the host macrophage.

Two Growth Modes of Graphitic Carbon Nanofibers with Herring-Bone Structure

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

Merkulov, Igor A; Melechko, Anatoli Vasilievich; Wells, Jack C

2005-01-01

A simple mathematical model of the carbon nanofiber catalytic growth process is presented. Two major types of the fiber-catalyst interface shapes have been identified and described having qualitatively different structure in the center of a nanofiber. Presently, we discuss that the appearance of the irregular structure in the nanofiber central area is a result of curved-interface-growth kinematics. We suggest the method to determine the phenomenological parameters of the developed model from experimental data.

Two growth modes of graphitic carbon nanofibers with herring-bone structure

NASA Astrophysics Data System (ADS)

Merkulov, I. A.; Meleshko, A. V.; Wells, J. C.; Cui, H.; Merkulov, V. I.; Simpson, M. L.; Lowndes, D. H.

2005-07-01

A simple mathematical model of the carbon nanofiber catalytic growth process is presented. Two major types of the fiber-catalyst interface shapes have been identified and described having qualitatively different structure in the center of a nanofiber. Presently, we discuss that the appearance of the irregular structure in the nanofiber central area is a result of curved-interface-growth kinematics. We suggest the method to determine the phenomenological parameters of the developed model from experimental data.

Politics of the aged: orientations and behavior in major liberal democracies.

PubMed

Edinger, L J

1985-01-01

Do the political outlook and electoral behavior of the elderly differ notably from that of younger adults in leading capitalist democracies? A cross-national examination of poll data suggests that on the whole they do not. Among the aged certain cross-national differences in rates of political participation beyond voting may be related to differences in national socio-political structures as well as differences in individual attributes.

Structural features of cytochromes P450 and ligands that affect drug metabolism as revealed by X-ray crystallography and NMR.

PubMed

Gay, Sean C; Roberts, Arthur G; Halpert, James R

2010-09-01

Cytochromes P450 (P450s) play a major role in the clearance of drugs, toxins, and environmental pollutants. Additionally, metabolism by P450s can result in toxic or carcinogenic products. The metabolism of pharmaceuticals by P450s is a major concern during the design of new drug candidates. Determining the interactions between P450s and compounds of very diverse structures is complicated by the variability in P450-ligand interactions. Understanding the protein structural elements and the chemical attributes of ligands that dictate their orientation in the P450 active site will aid in the development of effective and safe therapeutic agents. The goal of this review is to describe P450-ligand interactions from two perspectives. The first is the various structural elements that microsomal P450s have at their disposal to assume the different conformations observed in X-ray crystal structures. The second is P450-ligand dynamics analyzed by NMR relaxation studies.

Determination of the cell wall polysaccharide and teichoic acid structures from Lactococcus lactis IL1403.

PubMed

Vinogradov, Evgeny; Sadovskaya, Irina; Courtin, Pascal; Kulakauskas, Saulius; Grard, Thierry; Mahony, Jennifer; van Sinderen, Douwe; Chapot-Chartier, Marie-Pierre

2018-06-15

In the lactic acid bacterium Lactococcus lactis, a cell wall polysaccharide (CWPS) is the bacterial receptor of the majority of infecting bacteriophages. The diversity of CWPS structures between strains explains, at least partially, the narrow host range of lactococcal phages. In the present work, we studied the polysaccharide components of the cell wall of the prototype L. lactis subsp. lactis strain IL1403. We identified a rhamnose-rich complex polysaccharide, carrying a glycerophosphate substitution, as the major component. Its structure was analyzed by 2D NMR spectroscopy, methylation analysis and MALDI-TOF MS and shown to be distinctly different from currently known lactococcal CWPS structures. It contains a linear backbone of repeated α-l-Rha disaccharide subunits, which is irregularly substituted with a trisaccharide occasionally bearing a glycerophosphate group. A poly (glycerol phosphate) teichoic acid, another important carbohydrate component of the IL1403 cell wall, was also isolated and structurally characterized. Copyright © 2018 Elsevier Ltd. All rights reserved.

Biochemistry for dietetic students: course content and format.

PubMed

Sirota, L H

1984-12-01

This article presents the results of a survey of the 251 undergraduate dietetic programs for course content and level of the biochemistry course most frequently used to satisfy competencies in biochemistry under Plan IV of the ADA in 1979-80. It showed that a common core of information was stressed by all biochemistry instructors, but there was great variability in content and level of material covered and the textbook chosen, depending on whether the biochemistry course was offered to dietetic majors only, in classes with other nonchemistry majors, or in classes with chemistry majors. Variability was also seen in the time allotted for biochemistry--39 to 280 hours (total lecture and required laboratory hours); laboratory requirements--only 71%; and departmental affiliation of the instructor--17 different departments, primarily of chemistry (80%), biology (8%), and home economics (4%). Topics given greatest emphasis were descriptive ones, such as definitions, simple structures, and reactions of intermediary metabolism in general terms. Topics given least emphasis were those involving mechanistic and quantitative biochemistry, such as respiratory quotient (RQ), enzyme kinetics, calculations of energy from fat and carbohydrates, and specific structures of vitamins, ketones, and metabolic intermediates. The lack of communication between biochemistry and nutrition instructors and the great differences in the preparation of dietetic majors in biochemistry are sources of concern.

Psychotherapy for Major Depressive Disorder and Generalized Anxiety Disorder: A Health Technology Assessment.

PubMed

2017-01-01

Major depressive disorder and generalized anxiety disorder are among the most commonly diagnosed mental illnesses in Canada; both are associated with a high societal and economic burden. Treatment for major depressive disorder and generalized anxiety disorder consists of pharmacological and psychological interventions. Three commonly used psychological interventions are cognitive behavioural therapy (CBT), interpersonal therapy, and supportive therapy. The objectives of this report were to assess the effectiveness and safety of these types of therapy for the treatment of adults with major depressive disorder and/or generalized anxiety disorder, to assess the cost-effectiveness of structured psychotherapy (CBT or interpersonal therapy), to calculate the budget impact of publicly funding structured psychotherapy, and to gain a greater understanding of the experiences of people with major depressive disorder and/or generalized anxiety disorder. We performed a literature search on October 27, 2016, for systematic reviews that compared CBT, interpersonal therapy, or supportive therapy with usual care, waitlist control, or pharmacotherapy in adult outpatients with major depressive disorder and/or generalized anxiety disorder. We developed an individual-level state-transition probabilistic model for a cohort of adult outpatients aged 18 to 75 years with a primary diagnosis of major depressive disorder to determine the cost-effectiveness of individual or group CBT (as a representative form of structured psychotherapy) versus usual care. We also estimated the 5-year budget impact of publicly funding structured psychotherapy in Ontario. Finally, we interviewed people with major depressive disorder and/or generalized anxiety disorder to better understand the impact of their condition on their daily lives and their experience with different treatment options, including psychotherapy. Interpersonal therapy compared with usual care reduced posttreatment major depressive disorder scores (standardized mean difference [SMD]: 0.24, 95% confidence interval [CI]: -0.47 to -0.02) and reduced relapse/recurrence in patients with major depressive disorder (relative risk [RR]: 0.41, 95% CI: 0.27-0.63). Supportive therapy compared with usual care improved major depressive disorder scores (SMD: 0.58, 95% CI: 0.45-0.72) and increased posttreatment recovery (odds ratio [OR]: 2.71, 95% CI: 1.19-6.16) in patients with major depressive disorder. CBT compared with usual care increased response (OR: 1.58, 95% CI: 1.11-2.26) and recovery (OR: 3.42, 95% CI: 1.98-5.93) in patients with major depressive disorder and decreased relapse/recurrence (RR: 0.68, 95% CI: 0.65-0.87]). For patients with generalized anxiety disorder, CBT improved symptoms posttreatment (SMD: 0.80, 95% CI: 0.67-0.93), improved clinical response posttreatment (RR: 0.64, 95% CI: 0.55-0.74), and improved quality-of-life scores (SMD: 0.44, 95% CI: 0.06-0.82). There was a significant difference in posttreatment recovery (OR: 1.98, 95% CI: 1.11-3.54) and mean major depressive disorder symptom scores (weighted mean difference: -3.07, 95% CI: -4.69 to -1.45) for patients who received individual versus group CBT. Details about the providers of psychotherapy were rarely reported in the systematic reviews we examined.In the base case probabilistic cost-utility analysis, compared with usual care, both group and individual CBT were associated with increased survival: 0.11 quality-adjusted life-years (QALYs) (95% credible interval [CrI]: 0.03-0.22) and 0.12 QALYs (95% CrI: 0.03-0.25), respectively.Group CBT provided by nonphysicians was associated with the smallest increase in discounted costs: $401 (95% CrI: $1,177 to 1,665). Group CBT provided by physicians, individual CBT provided by nonphysicians, and individual CBT provided by physicians were associated with the incremental costs of $1,805 (95% CrI: 65-3,516), $3,168 (95% CrI: 889-5,624), and $5,311 (95% CrI: 2,539-8,938), respectively. The corresponding incremental cost-effectiveness ratio (ICER) was lowest for group CBT provided by nonphysicians ($3,715/QALY gained) and highest for individual CBT provided by physicians ($43,443/QALY gained). In the analysis that ranked best strategies, individual CBT versus group CBT provided by nonphysicians yielded an ICER of $192,618 per QALY. The probability of group CBT provided by nonphysicians being cost-effective versus usual care was greater than 95% for all willingness-to-pay thresholds over $20,000 per QALY and was around 88% for individual CBT provided by physicians at a threshold of $100,000 per QALY.We estimated that adding structured psychotherapy to usual care over the next 5 years would result in a net budget impact of $68 million to $529 million, depending on a range of factors. We also estimated that to provide structured psychotherapy to all adults with major depressive disorder (alone or combined with generalized anxiety disorder) in Ontario by 2021, an estimated 500 therapists would be needed to provide group therapy, and 2,934 therapists would be needed to provide individual therapy.People with major depressive disorder and/or generalized anxiety disorder with whom we spoke reported finding psychotherapy effective, but they also reported experiencing a large number of barriers that prevented them from finding effective psychotherapy in a timely manner. Participants reported wanting more freedom to choose the type of psychotherapy they received. Compared with usual care, treatment with CBT, interpersonal therapy, or supportive therapy significantly reduces depression symptoms posttreatment. CBT significantly reduces anxiety symptoms posttreatment in patients with generalized anxiety disorder.Compared with usual care, treatment with structured psychotherapy (CBT or interpersonal therapy) represents good value for money for adults with major depressive disorder and/or generalized anxiety disorder. The most affordable option is group structured psychotherapy provided by nonphysicians, with the selective use of individual structured psychotherapy provided by nonphysicians or physicians for those who would benefit most from it (i.e., patients who are not engaging well with or adhering to group therapy).

In silico studies on tryparedoxin peroxidase of Leishmania infantum: structural aspects.

PubMed

Singh, Bishal Kumar; Dubey, Vikash Kumar

2009-09-01

Tryparedoxin peroxidase (TryP) is a key enzyme of the trypanothione-dependent metabolism for removal of oxidative stress in leishmania. These enzymes function as antioxidants through their peroxidase and peroxynitrite reductase activities. Inhibitors of this enzyme are presumed to be antilesihmania drugs and structural studies are prerequisite of rational drug design. We have constructed three dimensional structure of TryP of Leishmania infantum using comparative modeling. Structural analysis reveals several interesting features. Moreover, it shows remarkable structural difference with human host glutathione peroxidase, an enzyme involved in similar function and TryP from Leishmania major.

The structure of cross-cultural musical diversity.

PubMed

Rzeszutek, Tom; Savage, Patrick E; Brown, Steven

2012-04-22

Human cultural traits, such as languages, musics, rituals and material objects, vary widely across cultures. However, the majority of comparative analyses of human cultural diversity focus on between-culture variation without consideration for within-culture variation. In contrast, biological approaches to genetic diversity, such as the analysis of molecular variance (AMOVA) framework, partition genetic diversity into both within- and between-population components. We attempt here for the first time to quantify both components of cultural diversity by applying the AMOVA model to music. By employing this approach with 421 traditional songs from 16 Austronesian-speaking populations, we show that the vast majority of musical variability is due to differences within populations rather than differences between. This demonstrates a striking parallel to the structure of genetic diversity in humans. A neighbour-net analysis of pairwise population musical divergence shows a large amount of reticulation, indicating the pervasive occurrence of borrowing and/or convergent evolution of musical features across populations.

The structure of cross-cultural musical diversity

PubMed Central

Rzeszutek, Tom; Savage, Patrick E.; Brown, Steven

2012-01-01

Human cultural traits, such as languages, musics, rituals and material objects, vary widely across cultures. However, the majority of comparative analyses of human cultural diversity focus on between-culture variation without consideration for within-culture variation. In contrast, biological approaches to genetic diversity, such as the analysis of molecular variance (AMOVA) framework, partition genetic diversity into both within- and between-population components. We attempt here for the first time to quantify both components of cultural diversity by applying the AMOVA model to music. By employing this approach with 421 traditional songs from 16 Austronesian-speaking populations, we show that the vast majority of musical variability is due to differences within populations rather than differences between. This demonstrates a striking parallel to the structure of genetic diversity in humans. A neighbour-net analysis of pairwise population musical divergence shows a large amount of reticulation, indicating the pervasive occurrence of borrowing and/or convergent evolution of musical features across populations. PMID:22072606

Social structure of Facebook networks

NASA Astrophysics Data System (ADS)

Traud, Amanda L.; Mucha, Peter J.; Porter, Mason A.

2012-08-01

We study the social structure of Facebook “friendship” networks at one hundred American colleges and universities at a single point in time, and we examine the roles of user attributes-gender, class year, major, high school, and residence-at these institutions. We investigate the influence of common attributes at the dyad level in terms of assortativity coefficients and regression models. We then examine larger-scale groupings by detecting communities algorithmically and comparing them to network partitions based on user characteristics. We thereby examine the relative importance of different characteristics at different institutions, finding for example that common high school is more important to the social organization of large institutions and that the importance of common major varies significantly between institutions. Our calculations illustrate how microscopic and macroscopic perspectives give complementary insights on the social organization at universities and suggest future studies to investigate such phenomena further.

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.

PubMed

Hehir-Kwa, Jayne Y; Marschall, Tobias; Kloosterman, Wigard P; Francioli, Laurent C; Baaijens, Jasmijn A; Dijkstra, Louis J; Abdellaoui, Abdel; Koval, Vyacheslav; Thung, Djie Tjwan; Wardenaar, René; Renkens, Ivo; Coe, Bradley P; Deelen, Patrick; de Ligt, Joep; Lameijer, Eric-Wubbo; van Dijk, Freerk; Hormozdiari, Fereydoun; Uitterlinden, André G; van Duijn, Cornelia M; Eichler, Evan E; de Bakker, Paul I W; Swertz, Morris A; Wijmenga, Cisca; van Ommen, Gert-Jan B; Slagboom, P Eline; Boomsma, Dorret I; Schönhuth, Alexander; Ye, Kai; Guryev, Victor

2016-10-06

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.

Sex differences in human epilepsy.

PubMed

Savic, Ivanka

2014-09-01

In the majority of neuropsychiatric conditions, marked gender-based differences have been found in the epidemiology, clinical manifestations, and therapy of disease. Emerging data suggest that gender differences exist also in the epidemiology, and pathophysiology of epilepsy. The present review summarizes the current information regarding gender and epilepsy. These differences are regarded from the perspective of innate sex differences in cerebral morphology, structural and functional connections, and assuming that these differences may render men and women differently vulnerable to epileptogenicity. Copyright © 2014 Elsevier Inc. All rights reserved.

Multidrug efflux transporter, AcrB--the pumping mechanism.

PubMed

Murakami, Satoshi

2008-08-01

Resistance nodulation cell division (RND) transporters are one of the main causes of the bacterial multidrug resistance. They pump a wide range of antibiotics out of the cell by proton motive force. AcrB is the major RND transporter in Escherichia coli. Recently, the crystal structures of AcrB have been determined by different space groups. All these structures are consistent with asymmetric trimer. Each monomer has different conformation corresponding to one of the three functional states of the transport cycle. Transporting hydrophobic drug was bound in the periplasmic domain on one of the three monomers. The transport pathway with alternating access mechanism is located at the hydrophilic domain protruded into the periplasmic space while this mechanism of other transporter families like ATP binding cassette (ABC) and major facilitator superfamily (MFS) transporter is located in the membrane-embedded region. For the RND, protonation might also take place asymmetrically at the functionally important charged residues in the transmembrane (TM) region. The structures indicate that drugs are transported by a three-step functional rotation in which substrates undergo ordered binding change.

Trichomes: different regulatory networks lead to convergent structures.

PubMed

Serna, Laura; Martin, Cathie

2006-06-01

Sometimes, proteins, biological structures or even organisms have similar functions and appearances but have evolved through widely divergent pathways. There is experimental evidence to suggest that different developmental pathways have converged to produce similar outgrowths of the aerial plant epidermis, referred to as trichomes. The emerging picture suggests that trichomes in Arabidopsis thaliana and, perhaps, in cotton develop through a transcriptional regulatory network that differs from those regulating trichome formation in Antirrhinum and Solanaceous species. Several lines of evidence suggest that the duplication of a gene controlling anthocyanin production and subsequent divergence might be the major force driving trichome formation in Arabidopsis, whereas the multicellular trichomes of Antirrhinum and Solanaceous species appear to have a different regulatory origin.

Collagens--structure, function, and biosynthesis.

PubMed

Gelse, K; Pöschl, E; Aigner, T

2003-11-28

The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified so far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. This review focuses on the distribution and function of various collagen types in different tissues. It introduces their basic structural subunits and points out major steps in the biosynthesis and supramolecular processing of fibrillar collagens as prototypical members of this protein family. A final outlook indicates the importance of different collagen types not only for the understanding of collagen-related diseases, but also as a basis for the therapeutical use of members of this protein family discussed in other chapters of this issue.

Multi-centre diagnostic classification of individual structural neuroimaging scans from patients with major depressive disorder.

PubMed

Mwangi, Benson; Ebmeier, Klaus P; Matthews, Keith; Steele, J Douglas

2012-05-01

Quantitative abnormalities of brain structure in patients with major depressive disorder have been reported at a group level for decades. However, these structural differences appear subtle in comparison with conventional radiologically defined abnormalities, with considerable inter-subject variability. Consequently, it has not been possible to readily identify scans from patients with major depressive disorder at an individual level. Recently, machine learning techniques such as relevance vector machines and support vector machines have been applied to predictive classification of individual scans with variable success. Here we describe a novel hybrid method, which combines machine learning with feature selection and characterization, with the latter aimed at maximizing the accuracy of machine learning prediction. The method was tested using a multi-centre dataset of T(1)-weighted 'structural' scans. A total of 62 patients with major depressive disorder and matched controls were recruited from referred secondary care clinical populations in Aberdeen and Edinburgh, UK. The generalization ability and predictive accuracy of the classifiers was tested using data left out of the training process. High prediction accuracy was achieved (~90%). While feature selection was important for maximizing high predictive accuracy with machine learning, feature characterization contributed only a modest improvement to relevance vector machine-based prediction (~5%). Notably, while the only information provided for training the classifiers was T(1)-weighted scans plus a categorical label (major depressive disorder versus controls), both relevance vector machine and support vector machine 'weighting factors' (used for making predictions) correlated strongly with subjective ratings of illness severity. These results indicate that machine learning techniques have the potential to inform clinical practice and research, as they can make accurate predictions about brain scan data from individual subjects. Furthermore, machine learning weighting factors may reflect an objective biomarker of major depressive disorder illness severity, based on abnormalities of brain structure.

A Comparative Analysis of the Wages of Hispanic, Black, and Anglo Men.

ERIC Educational Resources Information Center

Reimers, Cordelia

This paper details the factors contributing to the wage structure of Hispanic men and compares the wages of Black and Anglo men. The major finding is that controlling for differences in observable personal characteristics--such as education and work experience--substantially reduces the wage differences between Hispanics and Anglos. For example,…

Self-Perceived Gains in Communication and Critical Thinking Skills: Are There Disciplinary Differences? AIR 1998 Annual Forum Paper.

ERIC Educational Resources Information Center

Li, Guihua; Long, Shawna; Simpson, Mary Ellen

This study sought to identify similarities and differences influencing students' self-perceived gains in communication and critical thinking skills. The study examined students' background characteristics and general college experiences, as well as their experiences in their major field of study. Structural equation modeling was used to examine…

[Features of the structure and parameters of the intra-alveolar septa in residents of Western Siberia].

PubMed

Shishkin, G S; Ustiuzhaninova, N V

1998-01-01

In inhabitants of Novosibirsk and Moscow district intraalveolar septum, the basic functional element of the lung consists of interstitial connective tissue and capillar network, limited with basement membranes, on which cells of epithelial lining are placed. There are no principal differences in septal structure between individuals from both regions. The majority of morphometric parameters are statistically similar, although certain peculiarities were noted in human subjects from Siberia, the most important of which is that air-blood barrier in them is 33% thinner than those in inhabitants of Moscow district. Majority of capillaries possess the air-blood barrier from both sides. This increases diffous capacity of the lungs and blood oxygenation level.

The Dynamic Process of Drug-GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics

PubMed Central

Schneider, Sebastian; Provasi, Davide; Filizola, Marta

2015-01-01

Major advances in G Protein-Coupled Receptor (GPCR) structural biology over the past few years have yielded a significant number of high-resolution crystal structures for several different receptor subtypes. This dramatic increase in GPCR structural information has underscored the use of automated docking algorithms for the discovery of novel ligands that can eventually be developed into improved therapeutics. However, these algorithms are often unable to discriminate between different, yet energetically similar, poses because of their relatively simple scoring functions. Here, we describe a metadynamics-based approach to study the dynamic process of ligand binding to/unbinding from GPCRs with a higher level of accuracy and yet satisfying efficiency. PMID:26260607

Determination of the relationship between major fault and zinc mineralization using fractal modeling in the Behabad fault zone, central Iran

NASA Astrophysics Data System (ADS)

Adib, Ahmad; Afzal, Peyman; Mirzaei Ilani, Shapour; Aliyari, Farhang

2017-10-01

The aim of this study is to determine a relationship between zinc mineralization and a major fault in the Behabad area, central Iran, using the Concentration-Distance to Major Fault (C-DMF), Area of Mineralized Zone-Distance to Major Fault (AMZ-DMF), and Concentration-Area (C-A) fractal models for Zn deposit/mine classification according to their distance from the Behabad fault. Application of the C-DMF and the AMZ-DMF models for Zn mineralization classification in the Behabad fault zone reveals that the main Zn deposits have a good correlation with the major fault in the area. The distance from the known zinc deposits/mines with Zn values higher than 29% and the area of the mineralized zone of more than 900 m2 to the major fault is lower than 1 km, which shows a positive correlation between Zn mineralization and the structural zone. As a result, the AMZ-DMF and C-DMF fractal models can be utilized for the delineation and the recognition of different mineralized zones in different types of magmatic and hydrothermal deposits.

Characterizing the Secondary Protein Structure of Black Widow Dragline Silk Using Solid-State NMR & X-ray Diffraction

PubMed Central

Jenkins, Janelle E.; Sampath, Sujatha; Butler, Emily; Kim, Jihyun; Henning, Robert W.; Holland, Gregory P.; Yarger, Jeffery L.

2013-01-01

This study provides a detailed secondary structural characterization of major ampullate dragline silk from Latrodectus hesperus (black widow) spiders. X-ray diffraction results show that the structure of black widow major ampullate silk fibers is comprised of stacked β-sheet nanocrystallites oriented parallel to the fiber axis and an amorphous region with oriented (anisotropic) and isotropic components. The combination of two-dimensional (2D) 13C-13C through-space and through-bond solid-state NMR experiments provide chemical shifts that are used to determine detailed information about amino acid motif secondary structure in black widow spider dragline silk. Individual amino acids are incorporated into different repetitive motifs that make up the majority of this protein-based biopolymer. From the solid-state NMR measurements, we assign distinct secondary conformations to each repetitive amino acid motif and hence to the amino acids that make up the motifs. Specifically, alanine is incorporated in β-sheet (poly(Alan) and poly(Gly-Ala)), 31-helix (poly(Gly-Gly-Xaa), and α-helix (poly(Gln-Gln-Ala-Tyr)) components. Glycine is determined to be in β-sheet (poly(Gly-Ala)) and 31-helical (poly(Gly-Gly-Xaa)) regions, while serine is present in β-sheet (poly(Gly-Ala-Ser)), 31-helix (poly(Gly-Gly-Ser)), and β-turn (poly(Gly-Pro-Ser)) structures. These various motif-specific secondary structural elements are quantitatively correlated to the primary amino acid sequence of major ampullate spidroin 1 and 2 (MaSp1 and MaSp2) and are shown to form a self-consistent model for black widow dragline silk. PMID:24024617

Raman and IR Spectroscopic Study of Hydrous Pyroxenes

NASA Astrophysics Data System (ADS)

Kung, J.; Li, C.; Stalder, R.; Inoue, T.; Chuang, S.; Balfan-Casanova, N.; Skogby, H.

2017-12-01

Pyroxene group is one of major composed minerals at upper mantle and is nominally anhydrous mineral (NAM), in terms of its crystal chemistry. The analysis of field specimens showed the mantle-derived pyroxene phase containing some amount of hydrogen within crystal structure, the major incorporation mechanism to be as hydroxyl, OH¯, which chemical component treats as `water', H2O. Compared with the other mantle-derived olivine and garnet, the crystal chemistry of pyroxene phases (opx and cpx) is more complex that can result in different OH¯ bonding environments that would greatly affect the geophysics-interested physical properties, for example, elasticity and transport properties. In order to understand how the hydroxyl bonding condition with different composition of opx and cpx in this study, IR and Raman spectroscopies were employed to investigate the lattice modes and hydroxyl-bonding environments with different composition and crystal structures. The studied pyroxene specimens included natural hydrous pyroxenes and synthesized hydrous orthoenstatite (OEN) at high pressure and temperature (4-7 GPa, 1300-1400°C). The measured IR band range was carried out from 2800 to 3600 cm-1 and the Raman range from 50 to 3600 cm-1. The analysis showed that the band of 3600 cm-1 is the major feature in natural opx specimens but its intensity would be varied in different crystal orientation. For synthesized OEN, the number of observed IR band is higher than that reported in previous studies. The common major bands observed in natural cpx are around 3500 cm-1. The Raman measurement of studied specimen is to characterize the variation of Raman mode as function of composition and possible Raman active hydroxyl-related modes. In this meeting the results will be presented and discussed.

Structural characterization of viral epitopes recognized by broadly cross-reactive antibodies.

PubMed

Lee, Peter S; Wilson, Ian A

2015-01-01

Influenza hemagglutinin (HA) is the major surface glycoprotein on influenza viruses and mediates viral attachment and subsequent fusion with host cells. The HA is the major target of the immune response, but due to its high level of variability, as evidenced by substantial antigenic diversity, it had been historically considered to elicit only a narrow, strain-specific antibody response. However, a recent explosion in the discovery of broadly neutralizing antibodies (bnAbs) to influenza virus has identified two major supersites of vulnerability on the HA through structural characterization of HA-antibody complexes. These commonly targeted epitopes are involved with receptor binding as well as the fusion machinery and, hence, are functionally conserved and less prone to mutation. These bnAbs can neutralize viruses by blocking infection or the spread of infection by preventing progeny release. Structural analyses of these bnAbs show they exhibit striking similarities and trends in recognition of the HA and use recurring recognition motifs, despite substantial differences in their germline genes. This information can be utilized in design of novel therapeutics as well as in immunogens for improved vaccines with greater breadth and efficacy.

A Bulky Rhodium Complex Bound to an Adenosine-Adenosine DNA Mismatch: General Architecture of the Metalloinsertion Binding Mode†

PubMed Central

Zeglis, Brian M.; Pierre, Valérie C.; Kaiser, Jens T.; Barton, Jacqueline K.

2009-01-01

Two crystal structures are determined for Δ-Rh(bpy)2(chrysi)3+ (chrysi = 5,6-chrysenequinone diimine) bound to the oligonucleotide duplex 5′-CGGAAATTACCG-3′ containing two adenosine-adenosine mismatches (italics) through metalloinsertion. Diffraction quality crystals with two different space groups (P3221 and P43212) were obtained under very similar crystallization conditions. In both structures, the bulky rhodium complex inserts into the two mismatched sites from the minor groove side, ejecting the mismatched bases into the major groove. The conformational changes are localized to the mismatched site; the metal complex replaces the mismatched base pair without an increase in base pair rise. The expansive metal complex is accommodated in the duplex by a slight opening in the phosphodiester backbone; all sugars retain a C2′-endo puckering, and flanking base pairs neither stretch nor shear. The structures differ, however, in that in one of the structures, an additional metal complex is bound by intercalation from the major groove at the central 5′-AT-3′ step. We conclude that this additional metal complex is intercalated into this central step because of crystal packing forces. The structures described here of Δ-Rh(bpy)2(chrysi)3+ bound to thermodynamically destabilized AA mismatches share critical features with binding by metalloinsertion in two other oligonucleotides containing different single base mismatches. These results underscore the generality of the metalloinsertion as a new mode of non-covalent binding by small molecules with a DNA duplex. PMID:19374348

Probing the chemical interaction space governed by 4-aminosubstituted benzenesulfonamides and carbonic anhydrase isoforms.

PubMed

Rasti, Behnam; Heravi, Yeganeh Entezari

2018-06-01

Isoform diversity, critical physiological roles and involvement in major diseases/disorders such as glaucoma, epilepsy, Alzheimer's disease, obesity, and cancers have made carbonic anhydrase (CA), one of the most interesting case studies in the field of computer aided drug design. Since applying non-selective inhibitors can result in major side effects, there have been considerable efforts so far to achieve selective inhibitors for different isoforms of CA. Using proteochemometrics approach, the chemical interaction space governed by a group of 4-amino-substituted benzenesulfonamides and human CAs has been explored in the present study. Several validation methods have been utilized to assess the validity, robustness and predictivity power of the proposed proteochemometric model. Our model has offered major structural information that can be applied to design new selective inhibitors for distinct isoforms of CA. To prove the applicability of the proposed model, new compounds have been designed based on the offered discriminative structural features.

Non-anticoagulant effects of low molecular weight heparins in inflammatory disorders: A review.

PubMed

Yan, Yishu; Ji, Yang; Su, Nan; Mei, Xiang; Wang, Yi; Du, Shanshan; Zhu, Wenming; Zhang, Chong; Lu, Yuan; Xing, Xin-Hui

2017-03-15

Low molecular weight heparins (LMWHs) are produced by chemical or enzymatic depolymerization of unfractionated heparin (UFH). Besides their well-known anticoagulant effects, LMWHs have also been reported to exhibit numerous anti-inflammatory properties. Previous studies have, however, shown that different production processes result in unique structural characteristics of LMWHs. The structural variations may help explain the different therapeutic spectrums in disease treatment for non-anticoagulant effects. In the present review, we summarize major advances in understanding and exploiting the anti-inflammatory disorder activities of LMWHs, based on mechanistic studies, preclinical experiments and clinical trials. We highlight differences in these activities of commercially available LMWHs produced using different manufacturing processes. We stress the importance of structure-activity relationship (SAR) studies on the non-anticoagulant effects of LMWHs and discuss strategies for exploring new clinical indications. Copyright © 2016 Elsevier Ltd. All rights reserved.

Surface and deep structures in graphics comprehension.

PubMed

Schnotz, Wolfgang; Baadte, Christiane

2015-05-01

Comprehension of graphics can be considered as a process of schema-mediated structure mapping from external graphics on internal mental models. Two experiments were conducted to test the hypothesis that graphics possess a perceptible surface structure as well as a semantic deep structure both of which affect mental model construction. The same content was presented to different groups of learners by graphics from different perspectives with different surface structures but the same deep structure. Deep structures were complementary: major features of the learning content in one experiment became minor features in the other experiment, and vice versa. Text was held constant. Participants were asked to read, understand, and memorize the learning material. Furthermore, they were either instructed to process the material from the perspective supported by the graphic or from an alternative perspective, or they received no further instruction. After learning, they were asked to recall the learning content from different perspectives by completing graphs of different formats as accurately as possible. Learners' recall was more accurate if the format of recall was the same as the learning format which indicates surface structure influences. However, participants also showed more accurate recall when they remembered the content from a perspective emphasizing the deep structure, regardless of the graphics format presented before. This included better recall of what they had not seen than of what they really had seen before. That is, deep structure effects overrode surface effects. Depending on context conditions, stimulation of additional cognitive processing by instruction had partially positive and partially negative effects.

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts

PubMed Central

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart EG; Robinson, Christopher T

2013-01-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning. PMID:23842653

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts.

PubMed

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E G; Robinson, Christopher T

2013-12-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.

Universal partitioning of the hierarchical fold network of 50-residue segments in proteins

PubMed Central

Ito, Jun-ichi; Sonobe, Yuki; Ikeda, Kazuyoshi; Tomii, Kentaro; Higo, Junichi

2009-01-01

Background Several studies have demonstrated that protein fold space is structured hierarchically and that power-law statistics are satisfied in relation between the numbers of protein families and protein folds (or superfamilies). We examined the internal structure and statistics in the fold space of 50 amino-acid residue segments taken from various protein folds. We used inter-residue contact patterns to measure the tertiary structural similarity among segments. Using this similarity measure, the segments were classified into a number (Kc) of clusters. We examined various Kc values for the clustering. The special resolution to differentiate the segment tertiary structures increases with increasing Kc. Furthermore, we constructed networks by linking structurally similar clusters. Results The network was partitioned persistently into four regions for Kc ≥ 1000. This main partitioning is consistent with results of earlier studies, where similar partitioning was reported in classifying protein domain structures. Furthermore, the network was partitioned naturally into several dozens of sub-networks (i.e., communities). Therefore, intra-sub-network clusters were mutually connected with numerous links, although inter-sub-network ones were rarely done with few links. For Kc ≥ 1000, the major sub-networks were about 40; the contents of the major sub-networks were conserved. This sub-partitioning is a novel finding, suggesting that the network is structured hierarchically: Segments construct a cluster, clusters form a sub-network, and sub-networks constitute a region. Additionally, the network was characterized by non-power-law statistics, which is also a novel finding. Conclusion Main findings are: (1) The universe of 50 residue segments found here was characterized by non-power-law statistics. Therefore, the universe differs from those ever reported for the protein domains. (2) The 50-residue segments were partitioned persistently and universally into some dozens (ca. 40) of major sub-networks, irrespective of the number of clusters. (3) These major sub-networks encompassed 90% of all segments. Consequently, the protein tertiary structure is constructed using the dozens of elements (sub-networks). PMID:19454039

Development of Working Day Weather Charts for Transportation Construction in South Dakota

DOT National Transportation Integrated Search

1998-05-01

Seasonal and daily weather events impact grading, surfacing and structure construction projects in various ways across the different climate regions of the state. When weather conditions prevent timely completion of major sequential components of a c...

Behavior of wet precast beam column connections under progressive collapse scenario: an experimental study

NASA Astrophysics Data System (ADS)

Nimse, Rohit B.; Joshi, Digesh D.; Patel, Paresh V.

2014-12-01

Progressive collapse denotes a failure of a major portion of a structure that has been initiated by failure of a relatively small part of the structure such as failure of any vertical load carrying element (typically columns). Failure of large part of any structure will results into substantial loss of human lives and natural resources. Therefore, it is important to prevent progressive collapse which is also known as disproportionate collapse. Nowadays, there is an increasing trend toward construction of buildings using precast concrete. In precast concrete construction, all the components of structures are produced in controlled environment and they are being transported to the site. At site such individual components are connected appropriately. Connections are the most critical elements of any precast structure, because in past major collapse of precast structure took place because of connection failure. In this study, behavior of three different 1/3rd scaled wet precast beam column connections under progressive collapse scenario are studied and its performance is compared with monolithic connection. Precast connections are constructed by adopting different connection detailing at the junction by considering reinforced concrete corbel for two specimens and steel billet for one specimen. Performance of specimen is evaluated on the basis of ultimate load carrying capacity, maximum deflection and deflection measured along the span of the beam. From the results, it is observed that load carrying capacity and ductility of precast connections considered in this study are more than that of monolithic connections.

Brain structure variation in great apes, with attention to the mountain gorilla (Gorilla beringei beringei).

PubMed

Sherwood, Chet C; Cranfield, Michael R; Mehlman, Patrick T; Lilly, Alecia A; Garbe, Jo Anne L; Whittier, Christopher A; Nutter, Felicia B; Rein, Thomas R; Bruner, Harlan J; Holloway, Ralph L; Tang, Cheuk Y; Naidich, Thomas P; Delman, Bradley N; Steklis, H Dieter; Erwin, Joseph M; Hof, Patrick R

2004-07-01

This report presents data regarding the brain structure of mountain gorillas (Gorilla beringei beringei) in comparison with other great apes. Magnetic resonance (MR) images of three mountain gorilla brains were obtained with a 3T scanner, and the volume of major neuroanatomical structures (neocortical gray matter, hippocampus, thalamus, striatum, and cerebellum) was measured. These data were included with our existing database that includes 23 chimpanzees, three western lowland gorillas, and six orangutans. We defined a multidimensional space by calculating the principal components (PCs) from the correlation matrix of brain structure fractions in the well-represented sample of chimpanzees. We then plotted data from all of the taxa in this space to examine phyletic variation in neural organization. Most of the variance in mountain gorillas, as well as other great apes, was contained within the chimpanzee range along the first two PCs, which accounted for 61.73% of the total variance. Thus, the majority of interspecific variation in brain structure observed among these ape taxa was no greater than the within-species variation seen in chimpanzees. The loadings on PCs indicated that the brain structure of great apes differs among taxa mostly in the relative sizes of the striatum, cerebellum, and hippocampus. These findings suggest possible functional differences among taxa in terms of neural adaptations for ecological and locomotor capacities. Importantly, these results fill a critical gap in current knowledge regarding great ape neuroanatomical diversity.

Text vectorization based on character recognition and character stroke modeling

NASA Astrophysics Data System (ADS)

Fan, Zhigang; Zhou, Bingfeng; Tse, Francis; Mu, Yadong; He, Tao

2014-03-01

In this paper, a text vectorization method is proposed using OCR (Optical Character Recognition) and character stroke modeling. This is based on the observation that for a particular character, its font glyphs may have different shapes, but often share same stroke structures. Like many other methods, the proposed algorithm contains two procedures, dominant point determination and data fitting. The first one partitions the outlines into segments and second one fits a curve to each segment. In the proposed method, the dominant points are classified as "major" (specifying stroke structures) and "minor" (specifying serif shapes). A set of rules (parameters) are determined offline specifying for each character the number of major and minor dominant points and for each dominant point the detection and fitting parameters (projection directions, boundary conditions and smoothness). For minor points, multiple sets of parameters could be used for different fonts. During operation, OCR is performed and the parameters associated with the recognized character are selected. Both major and minor dominant points are detected as a maximization process as specified by the parameter set. For minor points, an additional step could be performed to test the competing hypothesis and detect degenerated cases.

Reverse Aging of Composite Materials for Aeronautical Applications

NASA Astrophysics Data System (ADS)

lannone, Michele

2008-08-01

Hygro-thermal ageing of polymer matrix composite materials is a major issue for all the aeronautical structures. For carbon-epoxy composites generally used in aeronautical applications the major effect of ageing is the humidity absorption, which induces a plasticization effect, generally decreasing Tg and elastic moduli, and finally design allowables. A thermodynamical and kinetic study has been performed, aimed to establish a program of periodic heating of the composite part, able to reversing the ageing effect by inducing water desorption. The study was founded on a simple model based on Fick's law, coupled with a concept of "relative saturation coefficient" depending on the different temperature of the composite part and the environment. The behaviour of some structures exposed to humidity and "reverse aged" by heating has been virtually tested. The conclusion of the study allowed to issue a specific patent application for aeronautical structures to be designed on the basis of a "humidity free" concept which allows the use of higher design allowables; having as final results lighter composite structures with a simplified certification process.

Bacteriophage P23-77 Capsid Protein Structures Reveal the Archetype of an Ancient Branch from a Major Virus Lineage

PubMed Central

Rissanen, Ilona; Grimes, Jonathan M.; Pawlowski, Alice; Mäntynen, Sari; Harlos, Karl; Bamford, Jaana K.H.; Stuart, David I.

2013-01-01

Summary It has proved difficult to classify viruses unless they are closely related since their rapid evolution hinders detection of remote evolutionary relationships in their genetic sequences. However, structure varies more slowly than sequence, allowing deeper evolutionary relationships to be detected. Bacteriophage P23-77 is an example of a newly identified viral lineage, with members inhabiting extreme environments. We have solved multiple crystal structures of the major capsid proteins VP16 and VP17 of bacteriophage P23-77. They fit the 14 Å resolution cryo-electron microscopy reconstruction of the entire virus exquisitely well, allowing us to propose a model for both the capsid architecture and viral assembly, quite different from previously published models. The structures of the capsid proteins and their mode of association to form the viral capsid suggest that the P23-77-like and adeno-PRD1 lineages of viruses share an extremely ancient common ancestor. PMID:23623731

Different Sources, Different Answers: Aspects on Women's Work in Sundsvall, Sweden, 1860-1893

ERIC Educational Resources Information Center

Vikstrom, Lotta

2003-01-01

It is often hard to unravel the actual work of women in history. Generally few sources are able to give vital information on their occupational structure. What we know, though, is that a vast majority of women were engaged in domestic work. Servants frequently appear in quantitative data, such as parish registers, poll-taxes, or censuses.…

Automated protein NMR structure determination using wavelet de-noised NOESY spectra.

PubMed

Dancea, Felician; Günther, Ulrich

2005-11-01

A major time-consuming step of protein NMR structure determination is the generation of reliable NOESY cross peak lists which usually requires a significant amount of manual interaction. Here we present a new algorithm for automated peak picking involving wavelet de-noised NOESY spectra in a process where the identification of peaks is coupled to automated structure determination. The core of this method is the generation of incremental peak lists by applying different wavelet de-noising procedures which yield peak lists of a different noise content. In combination with additional filters which probe the consistency of the peak lists, good convergence of the NOESY-based automated structure determination could be achieved. These algorithms were implemented in the context of the ARIA software for automated NOE assignment and structure determination and were validated for a polysulfide-sulfur transferase protein of known structure. The procedures presented here should be commonly applicable for efficient protein NMR structure determination and automated NMR peak picking.

Crystal Structure of the Leishmania Major Phosphodiesterase LmjPDEB1 and Insight into the Design of hte Parasite-Selective Inhibitors

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

Wang,H.; Yan, Z.; Geng, J.

2007-01-01

Human leishmaniasis is a major public health problem in many countries, but chemotherapy is in an unsatisfactory state. Leishmania major phosphodiesterases (LmjPDEs) have been shown to play important roles in cell proliferation and apoptosis of the parasite. Thus LmjPDE inhibitors may potentially represent a novel class of drugs for the treatment of leishmaniasis. Reported here are the kinetic characterization of the LmjPDEB1 catalytic domain and its crystal structure as a complex with 3-isobutyl-1-methylxanthine (IBMX) at 1.55 Angstroms resolution. The structure of LmjPDEB1 is similar to that of human PDEs. IBMX stacks against the conserved phenylalanine and forms a hydrogen bondmore » with the invariant glutamine, in a pattern common to most inhibitors bound to human PDEs. However, an extensive structural comparison reveals subtle, but significant differences between the active sites of LmjPDEB1 and human PDEs. In addition, a pocket next to the inhibitor binding site is found to be unique to LmjPDEB1. This pocket is isolated by two gating residues in human PDE families, but constitutes a natural expansion of the inhibitor binding pocket in LmjPDEB1. The structure particularity might be useful for the development of parasite-selective inhibitors for the treatment of leishmaniasis.« less

The structure of a β-(1→3)-d-glucan from yeast cell walls

PubMed Central

Manners, David J.; Masson, Alan J.; Patterson, James C.

1973-01-01

Yeast glucan as normally prepared by various treatments of yeast (Saccharomyces cerevisiae) cell walls to remove mannan and glycogen is still heterogeneous. The major component (about 85%) is a branched β-(1→3)-glucan of high molecular weight (about 240000) containing 3% of β-(1→6)-glucosidic interchain linkages. The minor component is a branched β-(1→6)-glucan. A comparison of our results with those of other workers suggests that different glucan preparations may differ in the degree of heterogeneity and that the major β-(1→3)-glucan component may vary considerably in degree of branching. PMID:4359920

Geometry motivated alternative view on local protein backbone structures.

PubMed

Zacharias, Jan; Knapp, Ernst Walter

2013-11-01

We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (φ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, which is not possible for an R-plot, where structural regimes connected by periodicity appear disconnected. But there are other advantages, like a clear discrimination of the handedness of a local structure, a larger spread of the different local structure domains--the latter can yield a better separation of different local secondary structure motives--and many more. Compared to the R-plot we are not aware of any major disadvantage to classify local polypeptide structures with the (d, ϑ)-plot, except that it requires some elementary computations. To facilitate usage of the new (d, ϑ)-plot for protein structures we provide a web application (http://agknapp.chemie.fu-berlin.de/secsass), which shows the (d, ϑ)-plot side-by-side with the R-plot. © 2013 The Protein Society.

The Role of School in the Upward Mobility of Disadvantaged Immigrants’ Children

PubMed Central

HAO, LINGXIN; PONG, SUET-LING

2014-01-01

How can we explain exceptional advancement by disadvantaged immigrants’ children? Extending segmented assimilation theory, this article traces the structural and relational attributes of high schools attended by young adults who reached their late twenties in 2000. Hypotheses are derived from theories in sociology of education and tested with four waves of data from the National Educational Longitudinal Study (NELS). The authors offer three major findings. First, an overwhelming majority of disadvantaged students attend public schools; some relational attributes are typical in public schools attended by disadvantaged students. Second, children’s upward mobility is shaped by the structural and relational attributes of their high schools. Most school effects are the same for disadvantaged and advantaged youngsters, and student-educator bonds and curriculum structure have even stronger positive effects for the disadvantaged. Finally, mobility patterns differ widely among Chinese, Mexicans, and whites. Mexicans are less likely to be exposed to favorable school attributes. PMID:25418989

Perceptions of homelessness in older homeless veterans, VA homeless program staff liaisons, and housing intervention providers.

PubMed

Molinari, Victor A; Brown, Lisa M; Frahm, Kathryn A; Schinka, John A; Casey, Roger

2013-05-01

To understand the needs and challenges encountered by older homeless veterans. We conducted six focus groups of older veterans, two focus groups, and one semi-structured interview of VA staff liaisons, and two focus groups and one semi-structured interview of housing intervention providers. Major themes for older veterans: 1) negative homelessness experience; 2) benefits of the structured transitional housing program; 3) importance of peer outreach; and 4) need for age-tailored job placement programs. Major themes for VA staff liaison/housing intervention providers: 1) belief that the transitional housing program has made a positive change; 2) need for individualized criteria to address the unique needs of veterans; 3) distinct differences between older and younger homeless veterans; 4) outreach services; 5) permanent housing issues; and 6) coordination of services. Compared with younger veterans, older veterans have less social support, greater employment and health challenges, and, perhaps greater motivation to change.

Population genetic structure of critically endangered salamander (Hynobius amjiensis) in China: recommendations for conservation.

PubMed

Yang, J; Chen, C S; Chen, S H; Ding, P; Fan, Z Y; Lu, Y W; Yu, L P; Lin, H D

2016-06-10

Amji's salamander (Hynobius amjiensis) is a critically endangered species (IUCN Red List), which is endemic to mainland China. In the present study, five haplotypes were genotyped for the mtDNA cyt b gene in 45 specimens from three populations. Relatively low levels of haplotype diversity (h = 0.524) and nucleotide diversity (π = 0.00532) were detected. Analyses of the phylogenic structure of H. amjiensis showed no evidence of major geographic partitions or substantial barriers to historical gene flow throughout the species' range. Two major phylogenetic haplotype groups were revealed, and were estimated to have diverged about 1.262 million years ago. Mismatch distribution analysis, neutrality tests, and Bayesian skyline plots revealed no evidence of dramatic changes in the effective population size. According to the SAMOVA and STRUCTURE analyses, H. amjiensis should be regarded as two different management units.

Enzymatic synthesis of cocoa butter equivalent from olive oil and palmitic-stearic fatty acid mixture.

PubMed

Mohamed, Ibrahim O

2015-01-01

The main goal of the present research is to restructure olive oil triacylglycerol (TAG) using enzymatic acidolysis reaction to produce structured lipids that is close to cocoa butter in terms of TAG structure and melting characteristics. Lipase-catalyzed acidolysis of refined olive oil with a mixture of palmitic-stearic acids at different substrate ratios was performed in an agitated batch reactor maintained at constant temperature and agitation speed. The reaction attained steady-state conversion in about 5 h with an overall conversion of 92.6 % for the olive oil major triacylglycerol 1-palmitoy-2,3-dioleoyl glycerol (POO). The five major TAGs of the structured lipids produced with substrate mass ratio of 1:3 (olive oil/palmitic-stearic fatty acid mixture) were close to that of the cocoa butter with melting temperature between 32.6 and 37.7 °C. The proposed kinetics model used fits the experimental data very well.

Wanted: Good Leaders for Urban Schools

ERIC Educational Resources Information Center

Durden, Phyllis C.

2008-01-01

Differences in values and socio-economics, issues of diversity and equity, and changing educational expectations and structures challenge leadership preparation programs, particularly those in urban environments. This article focuses on discerning major urban education issues, defining constructs of leadership for urban schools, and identifying a…

Bibliographies without Tears: Bibliography-Managers Round-Up.

ERIC Educational Resources Information Center

Science Software Quarterly, 1984

1984-01-01

Reviews and compares "Sci-Mate,""Reference Manager," and "BIBLIOPHILE" software packages used for storage and retrieval tasks involving bibliographic data. Each program handles search tasks well; major differences are in the amount of flexibility in customizing the database structure, their import and export…

Psychotherapy for Major Depressive Disorder and Generalized Anxiety Disorder: A Health Technology Assessment

PubMed Central

McMartin, Kristen; Gajic-Veljanoski, Olga; Wells, David; Higgins, Caroline; Walter, Melissa

2017-01-01

Background Major depressive disorder and generalized anxiety disorder are among the most commonly diagnosed mental illnesses in Canada; both are associated with a high societal and economic burden. Treatment for major depressive disorder and generalized anxiety disorder consists of pharmacological and psychological interventions. Three commonly used psychological interventions are cognitive behavioural therapy (CBT), interpersonal therapy, and supportive therapy. The objectives of this report were to assess the effectiveness and safety of these types of therapy for the treatment of adults with major depressive disorder and/or generalized anxiety disorder, to assess the cost-effectiveness of structured psychotherapy (CBT or interpersonal therapy), to calculate the budget impact of publicly funding structured psychotherapy, and to gain a greater understanding of the experiences of people with major depressive disorder and/or generalized anxiety disorder. Methods We performed a literature search on October 27, 2016, for systematic reviews that compared CBT, interpersonal therapy, or supportive therapy with usual care, waitlist control, or pharmacotherapy in adult outpatients with major depressive disorder and/or generalized anxiety disorder. We developed an individual-level state-transition probabilistic model for a cohort of adult outpatients aged 18 to 75 years with a primary diagnosis of major depressive disorder to determine the cost-effectiveness of individual or group CBT (as a representative form of structured psychotherapy) versus usual care. We also estimated the 5-year budget impact of publicly funding structured psychotherapy in Ontario. Finally, we interviewed people with major depressive disorder and/or generalized anxiety disorder to better understand the impact of their condition on their daily lives and their experience with different treatment options, including psychotherapy. Results Interpersonal therapy compared with usual care reduced posttreatment major depressive disorder scores (standardized mean difference [SMD]: 0.24, 95% confidence interval [CI]: −0.47 to −0.02) and reduced relapse/recurrence in patients with major depressive disorder (relative risk [RR]: 0.41, 95% CI: 0.27–0.63). Supportive therapy compared with usual care improved major depressive disorder scores (SMD: 0.58, 95% CI: 0.45–0.72) and increased posttreatment recovery (odds ratio [OR]: 2.71, 95% CI: 1.19–6.16) in patients with major depressive disorder. CBT compared with usual care increased response (OR: 1.58, 95% CI: 1.11–2.26) and recovery (OR: 3.42, 95% CI: 1.98–5.93) in patients with major depressive disorder and decreased relapse/recurrence (RR: 0.68, 95% CI: 0.65–0.87]). For patients with generalized anxiety disorder, CBT improved symptoms posttreatment (SMD: 0.80, 95% CI: 0.67–0.93), improved clinical response posttreatment (RR: 0.64, 95% CI: 0.55–0.74), and improved quality-of-life scores (SMD: 0.44, 95% CI: 0.06–0.82). There was a significant difference in posttreatment recovery (OR: 1.98, 95% CI: 1.11–3.54) and mean major depressive disorder symptom scores (weighted mean difference: −3.07, 95% CI: −4.69 to −1.45) for patients who received individual versus group CBT. Details about the providers of psychotherapy were rarely reported in the systematic reviews we examined. In the base case probabilistic cost–utility analysis, compared with usual care, both group and individual CBT were associated with increased survival: 0.11 quality-adjusted life-years (QALYs) (95% credible interval [CrI]: 0.03–0.22) and 0.12 QALYs (95% CrI: 0.03–0.25), respectively. Group CBT provided by nonphysicians was associated with the smallest increase in discounted costs: $401 (95% CrI: $1,177 to 1,665). Group CBT provided by physicians, individual CBT provided by nonphysicians, and individual CBT provided by physicians were associated with the incremental costs of $1,805 (95% CrI: 65–3,516), $3,168 (95% CrI: 889–5,624), and $5,311 (95% CrI: 2,539–8,938), respectively. The corresponding incremental cost-effectiveness ratio (ICER) was lowest for group CBT provided by nonphysicians ($3,715/QALY gained) and highest for individual CBT provided by physicians ($43,443/QALY gained). In the analysis that ranked best strategies, individual CBT versus group CBT provided by nonphysicians yielded an ICER of $192,618 per QALY. The probability of group CBT provided by nonphysicians being cost-effective versus usual care was greater than 95% for all willingness-to-pay thresholds over $20,000 per QALY and was around 88% for individual CBT provided by physicians at a threshold of $100,000 per QALY. We estimated that adding structured psychotherapy to usual care over the next 5 years would result in a net budget impact of $68 million to $529 million, depending on a range of factors. We also estimated that to provide structured psychotherapy to all adults with major depressive disorder (alone or combined with generalized anxiety disorder) in Ontario by 2021, an estimated 500 therapists would be needed to provide group therapy, and 2,934 therapists would be needed to provide individual therapy. People with major depressive disorder and/or generalized anxiety disorder with whom we spoke reported finding psychotherapy effective, but they also reported experiencing a large number of barriers that prevented them from finding effective psychotherapy in a timely manner. Participants reported wanting more freedom to choose the type of psychotherapy they received. Conclusions Compared with usual care, treatment with CBT, interpersonal therapy, or supportive therapy significantly reduces depression symptoms posttreatment. CBT significantly reduces anxiety symptoms posttreatment in patients with generalized anxiety disorder. Compared with usual care, treatment with structured psychotherapy (CBT or interpersonal therapy) represents good value for money for adults with major depressive disorder and/or generalized anxiety disorder. The most affordable option is group structured psychotherapy provided by nonphysicians, with the selective use of individual structured psychotherapy provided by nonphysicians or physicians for those who would benefit most from it (i.e., patients who are not engaging well with or adhering to group therapy). PMID:29213344

Shear-lag effect and its effect on the design of high-rise buildings

NASA Astrophysics Data System (ADS)

Thanh Dat, Bui; Traykov, Alexander; Traykova, Marina

2018-03-01

For super high-rise buildings, the analysis and selection of suitable structural solutions are very important. The structure has not only to carry the gravity loads (self-weight, live load, etc.), but also to resist lateral loads (wind and earthquake loads). As the buildings become taller, the demand on different structural systems dramatically increases. The article considers the division of the structural systems of tall buildings into two main categories - interior structures for which the major part of the lateral load resisting system is located within the interior of the building, and exterior structures for which the major part of the lateral load resisting system is located at the building perimeter. The basic types of each of the main structural categories are described. In particular, the framed tube structures, which belong to the second main category of exterior structures, seem to be very efficient. That type of structure system allows tall buildings resist the lateral loads. However, those tube systems are affected by shear lag effect - a nonlinear distribution of stresses across the sides of the section, which is commonly found in box girders under lateral loads. Based on a numerical example, some general conclusions for the influence of the shear-lag effect on frequencies, periods, distribution and variation of the magnitude of the internal forces in the structure are presented.

Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.

PubMed

Roston, Daniel; Demapan, Darren; Cui, Qiang

2016-06-15

A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care.

Structure and Evolution of Insect Sperm: New Interpretations in the Age of Phylogenomics.

PubMed

Dallai, Romano; Gottardo, Marco; Beutel, Rolf Georg

2016-01-01

This comprehensive review of the structure of sperm in all orders of insects evaluates phylogenetic implications, with the background of a phylogeny based on transcriptomes. Sperm characters strongly support several major branches of the phylogeny of insects-for instance, Cercophora, Dicondylia, and Psocodea-and also different infraordinal groups. Some closely related taxa, such as Trichoptera and Lepidoptera (Amphiesmenoptera), differ greatly in sperm structure. Sperm characters are very conservative in some groups (Heteroptera, Odonata) but highly variable in others, including Zoraptera, a small and morphologically uniform group with a tremendously accelerated rate of sperm evolution. Unusual patterns such as sperm dimorphism, the formation of bundles, or aflagellate and immotile sperm have evolved independently in several groups.

Formation of propagation invariant laser beams with anamorphic optical systems

NASA Astrophysics Data System (ADS)

Soskind, Y. G.

2015-03-01

Propagation invariant structured laser beams play an important role in several photonics applications. A majority of propagation invariant beams are usually produced in the form of laser modes emanating from stable laser cavities. This work shows that anamorphic optical systems can be effectively employed to transform input propagation invariant laser beams and produce a variety of alternative propagation invariant structured laser beam distributions with different shapes and phase structures. This work also presents several types of anamorphic lens systems suitable for transforming the input laser modes into a variety of structured propagation invariant beams. The transformations are applied to different laser mode types, including Hermite-Gaussian, Laguerre-Gaussian, and Ince-Gaussian field distributions. The influence of the relative azimuthal orientation between the input laser modes and the anamorphic optical systems on the resulting transformed propagation invariant beams is presented as well.

Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation.

PubMed

Velazquez Camacho, Oscar; Galan, Carmen; Swist-Rosowska, Kalina; Ching, Reagan; Gamalinda, Michael; Karabiber, Fethullah; De La Rosa-Velazquez, Inti; Engist, Bettina; Koschorz, Birgit; Shukeir, Nicholas; Onishi-Seebacher, Megumi; van de Nobelen, Suzanne; Jenuwein, Thomas

2017-08-01

The Suv39h1 and Suv39h2 histone lysine methyltransferases are hallmark enzymes at mammalian heterochromatin. We show here that the mouse Suv39h2 enzyme differs from Suv39h1 by containing an N-terminal basic domain that facilitates retention at mitotic chromatin and provides an additional affinity for major satellite repeat RNA. To analyze an RNA-dependent interaction with chromatin, we purified native nucleosomes from mouse ES cells and detect that Suv39h1 and Suv39h2 exclusively associate with poly-nucleosomes. This association was attenuated upon RNaseH incubation and entirely lost upon RNaseA digestion of native chromatin. Major satellite repeat transcripts remain chromatin-associated and have a secondary structure that favors RNA:DNA hybrid formation. Together, these data reveal an RNA-mediated mechanism for the stable chromatin interaction of the Suv39h KMT and suggest a function for major satellite non-coding RNA in the organization of an RNA-nucleosome scaffold as the underlying structure of mouse heterochromatin.

Progress towards mapping the universe of protein folds

PubMed Central

Grant, Alastair; Lee, David; Orengo, Christine

2004-01-01

Although the precise aims differ between the various international structural genomics initiatives currently aiming to illuminate the universe of protein folds, many selectively target protein families for which the fold is unknown. How well can the current set of known protein families and folds be used to estimate the total number of folds in nature, and will structural genomics initiatives yield representatives for all the major protein families within a reasonable time scale? PMID:15128436

Stability Study of Anthropomorphic Robot Antares under External Load Action

NASA Astrophysics Data System (ADS)

Kodyakov, A. S.; Pavlyuk, N. A.; Budkov, V. Yu; Prakapovich, R. A.

2017-01-01

The paper presents the study of the behavior of the major structural elements of the lower limbs of anthropomorphic robot Antares under the influence of different types of loads (torsion, fracture). We have determined the required values for actuators torques for motion of the robot in space. The maximum values of torques are 5 Nm and 5.2 Nm respectively, and are able to withstand the upper and lower leg structures.

Invasive plants have different effects on trophic structure of green and brown food webs in terrestrial ecosystems: a meta-analysis.

PubMed

McCary, Matthew A; Mores, Robin; Farfan, Monica A; Wise, David H

2016-03-01

Although invasive plants are a major source of terrestrial ecosystem degradation worldwide, it remains unclear which trophic levels above the base of the food web are most vulnerable to plant invasions. We performed a meta-analysis of 38 independent studies from 32 papers to examine how invasive plants alter major groupings of primary and secondary consumers in three globally distributed ecosystems: wetlands, woodlands and grasslands. Within each ecosystem we examined if green (grazing) food webs are more sensitive to plant invasions compared to brown (detrital) food webs. Invasive plants have strong negative effects on primary consumers (detritivores, bacterivores, fungivores, and/or herbivores) in woodlands and wetlands, which become less abundant in both green and brown food webs in woodlands and green webs in wetlands. Plant invasions increased abundances of secondary consumers (predators and/or parasitoids) only in woodland brown food webs and green webs in wetlands. Effects of invasive plants on grazing and detrital food webs clearly differed between ecosystems. Overall, invasive plants had the most pronounced effects on the trophic structure of wetlands and woodlands, but caused no detectable changes to grassland trophic structure. © 2016 John Wiley & Sons Ltd/CNRS.

Deep Europe today: Geophysical synthesis of the upper mantle structure and lithospheric processes over 3.5 Ga

USGS Publications Warehouse

Artemieva, I.M.; Thybo, H.; Kaban, M.K.; ,

2006-01-01

We present a summary of geophysical models of the subcrustal lithosphere of Europe. This includes the results from seismic (reflection and refraction profiles, P- and S-wave tomography, mantle anisotropy), gravity, thermal, electromagnetic, elastic and petrological studies of the lithospheric mantle. We discuss major tectonic processes as reflected in the lithospheric structure of Europe, from Precambrian terrane accretion and subduction to Phanerozoic rifting, volcanism, subduction and continent-continent collision. The differences in the lithospheric structure of Precambrian and Phanerozoic Europe, as illustrated by a comparative analysis of different geophysical data, are shown to have both a compositional and a thermal origin. We propose an integrated model of physical properties of the European subcrustal lithosphere, with emphasis on the depth intervals around 150 and 250 km. At these depths, seismic velocity models, constrained by body-and surface-wave continent-scale tomography, are compared with mantle temperatures and mantle gravity anomalies. This comparison provides a framework for discussion of the physical or chemical origin of the major lithospheric anomalies and their relation to large-scale tectonic processes, which have formed the present lithosphere of Europe. ?? The Geological Society of London 2006.

The prevalence, clinical correlates and structure of phobic fears in Han Chinese women with recurrent major depression.

PubMed

Yang, Fuzhong; Qiu, Jianyin; Zhao, Hongsu; Wang, Zhoubing; Tao, Danhong; Xiao, Xue; Niu, Qihui; Wang, Qian; Li, Yajuan; Guo, Liyang; Li, Jianying; Li, Kan; Xia, Jing; Wang, Lina; Shang, Xiaofang; Sang, Wenhua; Gan, Zhaoyu; He, Kangmei; Zhao, Xiaochuan; Tian, Tian; Xu, Dan; Gu, Danhua; Weng, Xiaoqin; Li, Haimin; Tian, Jing; Yang, Lijun; Li, Qiang; Yang, Qingzhen; Wang, Hui; Dang, Yamei; Dai, Lei; Cui, Yanping; Ye, Dong; Cao, Juling; Guo, Li; Kang, Zhen; Liu, Jimeng; Chen, Bin; Liu, Jinhua; Zhang, Jinling; Yang, Donglin; Jiao, Bin; Yu, Fengyu; Geng, Feng; Li, Ling; Yang, Haiying; Dai, Hong; Wang, Hongli; Liu, Caixing; Liu, Haijun; Peng, Longyan; Wang, Xiaoping; Wei, Shaojun; Liu, Xiaojuan; Li, Chang; Liu, Zhengrong; Zhang, Qiwen; Di, Dongchuan; Shi, Shenxun; Flint, Jonathan; Kendler, Kenneth S

2014-03-01

Phobic fears are common in the general population and among individuals with major depression (MD). We know little about the prevalence, clinical correlates, and structure of phobic fears in Chinese women with MD. We assessed 22 phobic fears in 6017 Han Chinese women with MD. We used exploratory factor analysis to examine the structure of these phobic fears. We examined the relationship between individual phobic fears and the severity of MD, neuroticism, comorbid panic disorder, generalized anxiety disorder and dysthymia using logistic regression models. The frequency of phobic fears ranged from 3.0% (eating in public) to 36.0% (snakes). Phobic fears were significantly associated with more severe MD, high neuroticism, and co-morbid panic disorder, generalized anxiety disorder and dysthymia. Our factor analysis suggested four underlying subgroups of phobic fears which differed in their clinical correlates, severity and patterns of comorbidity. Data were collected retrospectively through interview and recall bias may have affected the results. Phobic fears are correlated with comorbid MD and more severe MD. These phobic fears clearly subdivide into four subgroups that differ meaningfully from each other. Copyright © 2014 Elsevier B.V. All rights reserved.

Topology of the correlation networks among major currencies using hierarchical structure methods

NASA Astrophysics Data System (ADS)

Keskin, Mustafa; Deviren, Bayram; Kocakaplan, Yusuf

2011-02-01

We studied the topology of correlation networks among 34 major currencies using the concept of a minimal spanning tree and hierarchical tree for the full years of 2007-2008 when major economic turbulence occurred. We used the USD (US Dollar) and the TL (Turkish Lira) as numeraires in which the USD was the major currency and the TL was the minor currency. We derived a hierarchical organization and constructed minimal spanning trees (MSTs) and hierarchical trees (HTs) for the full years of 2007, 2008 and for the 2007-2008 period. We performed a technique to associate a value of reliability to the links of MSTs and HTs by using bootstrap replicas of data. We also used the average linkage cluster analysis for obtaining the hierarchical trees in the case of the TL as the numeraire. These trees are useful tools for understanding and detecting the global structure, taxonomy and hierarchy in financial data. We illustrated how the minimal spanning trees and their related hierarchical trees developed over a period of time. From these trees we identified different clusters of currencies according to their proximity and economic ties. The clustered structure of the currencies and the key currency in each cluster were obtained and we found that the clusters matched nicely with the geographical regions of corresponding countries in the world such as Asia or Europe. As expected the key currencies were generally those showing major economic activity.

The Sharpless Asymmetric Dihydroxylation in the Organic Chemistry Majors Laboratory

ERIC Educational Resources Information Center

Nicholas, Christopher J.; Taylor, Melissa R.

2005-01-01

Sharpless asymmetric dihydroxylation is developed that focuses on the varying enantiomeric excess of the product diols based on the structures of the alkenes being oxidized. The experimental sequence enables investigation of this reaction in terms of the different chiral ligands being used.

Rebuilding a Research Ethics Committee

ERIC Educational Resources Information Center

Biggs, John S. G.; Marchesi, August

2013-01-01

The principal ethics committee in Australia's Capital, Canberra, underwent a major revision in the last three years based on changes debated in the literature. Committee or Board structure varies widely; regulations determining minimum size and membership differ between countries. Issues such as the effectiveness of committee management,…

An Integrated Geophysical and Tectonic Study of the Structure and Evolution of the Crust in the Snake River Plain Region, Pacific Northwest

NASA Astrophysics Data System (ADS)

Keller, G. R.; Khatiwada, M.

2016-12-01

The Snake River Plain region in the Pacific Northwest of North America has been the target of a number of recent studies that have revealed further complexities in its structure and tectonic evolution. Based on surface morphology and Late Cenozoic volcanic activity, the Snake River Plain consists of an eastern and western arm (ESRP and WSRP) that are similar in many respects but also quite different in other respects. Thus, its origin, evolution, structural complexities, the role of extension and magmatism in its formation, and the tectonic drivers are still subjects of debate. Numerous seismic studies have specifically focused on the structure of the ESRP and Yellowstone area. However, crustal-scale studies of the WSRP are limited. We added new gravity data to the existing coverage in the WSRP region and undertook a regional, integrated analysis approach that included magnetic, seismic reflection and refraction profiling, receiver function results, geological and geospatial data, and interpreted well logs. Our integrated geophysical modeling focused on the structure of the WSRP. We generated two crustal models across it at locations where the most existing geophysical and geological constraints were available. We observed both differences and similarities in the structure of the WSRP and ESRP. Although, the shallow crustal structures are different, a mid-crustal mafic intrusion is a major source of the high gravity anomaly values. Within the context of recent studies in the surrounding region, the intersection of the two arms of the Snake River Plain emerges as a major element of a complex tectonic intersection that includes the High Lava Plains of eastern Oregon, the Northern Nevada Rift, a southwestern extension of the ESRP into northern Nevada, as well as, faulting and volcanism extending northwestward to connect with the Columbia River Basalts region.

Deep learning of the sectional appearances of 3D CT images for anatomical structure segmentation based on an FCN voting method.

PubMed

Zhou, Xiangrong; Takayama, Ryosuke; Wang, Song; Hara, Takeshi; Fujita, Hiroshi

2017-10-01

We propose a single network trained by pixel-to-label deep learning to address the general issue of automatic multiple organ segmentation in three-dimensional (3D) computed tomography (CT) images. Our method can be described as a voxel-wise multiple-class classification scheme for automatically assigning labels to each pixel/voxel in a 2D/3D CT image. We simplify the segmentation algorithms of anatomical structures (including multiple organs) in a CT image (generally in 3D) to a majority voting scheme over the semantic segmentation of multiple 2D slices drawn from different viewpoints with redundancy. The proposed method inherits the spirit of fully convolutional networks (FCNs) that consist of "convolution" and "deconvolution" layers for 2D semantic image segmentation, and expands the core structure with 3D-2D-3D transformations to adapt to 3D CT image segmentation. All parameters in the proposed network are trained pixel-to-label from a small number of CT cases with human annotations as the ground truth. The proposed network naturally fulfills the requirements of multiple organ segmentations in CT cases of different sizes that cover arbitrary scan regions without any adjustment. The proposed network was trained and validated using the simultaneous segmentation of 19 anatomical structures in the human torso, including 17 major organs and two special regions (lumen and content inside of stomach). Some of these structures have never been reported in previous research on CT segmentation. A database consisting of 240 (95% for training and 5% for testing) 3D CT scans, together with their manually annotated ground-truth segmentations, was used in our experiments. The results show that the 19 structures of interest were segmented with acceptable accuracy (88.1% and 87.9% voxels in the training and testing datasets, respectively, were labeled correctly) against the ground truth. We propose a single network based on pixel-to-label deep learning to address the challenging issue of anatomical structure segmentation in 3D CT cases. The novelty of this work is the policy of deep learning of the different 2D sectional appearances of 3D anatomical structures for CT cases and the majority voting of the 3D segmentation results from multiple crossed 2D sections to achieve availability and reliability with better efficiency, generality, and flexibility than conventional segmentation methods, which must be guided by human expertise. © 2017 The Authors. Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Survey on Restoration of Endodontically Treated Anterior Teeth: A Questionnaire Based Study

PubMed Central

Ratnakar, P; Bhosgi, Rashmi; Metta, Kiran Kumar; Aggarwal, Kanika; Vinuta, S; Singh, Navneet

2014-01-01

Background: The aim of endodontic and restorative dentistry is the conservation of natural tooth structure. Endodontically treated tooth (ETT) undergoes loss of tooth structure and changes in physical characteristics. Therefore, proper selection of restoration for ETT is mandatory. The clinical approach of restoring ETT needs taking into considerations several issues. However, the best way to restore teeth after root canal treatment has long been and still a controversial subject to debate. Therefore, this study was carried out to detect the frequency of preferred methods of restoring ETT under different conditions. Materials and Methods: A questionnaire was framed and distributed among prosthodontists, endodontist and general practitioners of north India region to find out the frequency of best suitable material and method regarding restoration of ETT. 220 questionnaires were sent by electronic mail out of which 110 were received back. The questionnaire contained different methods of restoration of endodontically treated anterior teeth at different conditions (percentages) of remaining sound tooth structure. Respondents were asked to indicate their preferred method of restoration of those teeth. Results: Results showed that majority of respondents (51.82%) preferred to restore the tooth only with a tooth-color restorative material in condition A. In condition B, majority of respondents preferred to use tooth colored crown (44.55%) and prefabricated post and tooth colored restoration (24.5%). Whereas in condition C, most of the respondents preferred to use a cast post and core/crown (80.91%). Conclusion: From the findings of the present study, it can be concluded that the unrestored ETT is susceptible to fracture, which could lead to loss of tooth and that the maximum preservation of healthy tooth structure and use of restorative materials with mechanical properties similar to dental structure favor greater longevity of tooth restoration complex. PMID:25628482

Surgical management of tumors invading the aorta and major arterial structures.

PubMed

Carpenter, Susanne G; Stone, William M; Bower, Thomas C; Fowl, Richard J; Money, Samuel R

2011-11-01

This study investigates surgical management of tumors arising from or involving the aorta and major arterial structures. A retrospective single institutional review was conducted of patients undergoing arterial resection for tumors involving the aorta or major arterial structures between January 1992 and May 2009 at a tertiary care center. Patients with tumors abutting arteries without necessitating resection and those involving only venous structures were excluded. Patients were analyzed in groups by vessel involvement: aorta, carotid, external/common iliac, internal iliac, superficial femoral, and miscellaneous. Sixty patients were identified and included for review. The iliac arteries were most often resected, and sarcomatous pathology was most common (37 patients, 62%). Twelve patients underwent aortic resection, with eight (67%) of these undergoing graft reconstruction, one (8%) graft patch, and two (17%) primary repair. None of the 17 patients undergoing internal iliac resection underwent reconstruction, whereas the majority of patients in all other groups underwent reconstruction. Thirty-day mortality (TDM) was 0% in all groups, except the aortic (2/12, 17% TDM), and internal iliac arteries (1/17, 6% TDM). Estimated blood loss varied widely and was not significantly different between vessel groups (p = 0.280). Overall, 44 of 60 (73%) patients had negative margins. Fourteen patients (23%) returned to the operating room, most for wound infection or dehiscence. Mean follow-up was 20.25 months (range: 0.5-122.0 months, SD: 23 months). Forty patients were followed up for more than 1 year. Thus, with an overall median follow-up of 12.25 months, overall survival was 60% with disease-free survival of 40%. Resection of tumors involving the aorta and major arterial structures provides a reasonable option for treatment, but with significant perioperative morbidity. In selected patients, this aggressive intervention should be considered. Copyright © 2011 Annals of Vascular Surgery Inc. Published by Elsevier Inc. All rights reserved.

The response of epiphytic microbes to habitat and growth status of Potamogeton malaianus Miq. in Lake Taihu.

PubMed

Cai, Xianlei; Gao, Guang; Tang, Xiangming; Dong, Baili; Dai, Jiangyu; Chen, Dan; Song, Yuzhi

2013-10-01

To investigate the effects of different habitats and plant growth status on abundance, biomass and community structure of epiphytic microbes, Potamogeton malaianus Miq. at two different habitats (Gonghu Bay and East Taihu) in Lake Taihu were collected in June, August and November (corresponding to the period of development of submerged macrophytes). The relative abundance of major epiphytic algae groups was determined with high performance liquid chromatography (HPLC), and the structures and dynamics of epiphytic bacteria were assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. Results showed that the biomass of epiphytic microbes was not significant difference between the two sites, and the analysis of similarity found no significant intra-lake heterogeneity in community structure, but the temporal heterogeneity of epiphytic microbes was significant, which linked to the growth state of submerged macrophytes and water temperature. The difference in community structure between June and August was larger than that between August and November at each site, indicating that the growth status of submerged macrophytes has a greater impact on the community structure of epiphytic microbes than the seasonal variation of environmental conditions. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular dynamics simulations indicate that deoxyhemoglobin, oxyhemoglobin, carboxyhemoglobin, and glycated hemoglobin under compression and shear exhibit an anisotropic mechanical behavior.

PubMed

Yesudasan, Sumith; Wang, Xianqiao; Averett, Rodney D

2018-05-01

We developed a new mechanical model for determining the compression and shear mechanical behavior of four different hemoglobin structures. Previous studies on hemoglobin structures have focused primarily on overall mechanical behavior; however, this study investigates the mechanical behavior of hemoglobin, a major constituent of red blood cells, using steered molecular dynamics (SMD) simulations to obtain anisotropic mechanical behavior under compression and shear loading conditions. Four different configurations of hemoglobin molecules were considered: deoxyhemoglobin (deoxyHb), oxyhemoglobin (HbO 2 ), carboxyhemoglobin (HbCO), and glycated hemoglobin (HbA 1C ). The SMD simulations were performed on the hemoglobin variants to estimate their unidirectional stiffness and shear stiffness. Although hemoglobin is structurally denoted as a globular protein due to its spherical shape and secondary structure, our simulation results show a significant variation in the mechanical strength in different directions (anisotropy) and also a strength variation among the four different hemoglobin configurations studied. The glycated hemoglobin molecule possesses an overall higher compressive mechanical stiffness and shear stiffness when compared to deoxyhemoglobin, oxyhemoglobin, and carboxyhemoglobin molecules. Further results from the models indicate that the hemoglobin structures studied possess a soft outer shell and a stiff core based on stiffness.

Assessment of urban green space structures and their quality from a multidimensional perspective.

PubMed

Daniels, Benjamin; Zaunbrecher, Barbara S; Paas, Bastian; Ottermanns, Richard; Ziefle, Martina; Roß-Nickoll, Martina

2018-02-15

Facing the growing amount of people living in cities and, at the same time, the need for a compact and sustainable urban development to mitigate urban sprawl, it becomes increasingly important that green spaces in compact cities are designed to meet the various needs within an urban environment. Urban green spaces have a multitude of functions: Maintaining ecological processes and resulting services, e.g. providing habitat for animals and plants, providing a beneficial city microclimate as well as recreational space for citizens. Regarding these requirements, currently existing assessment procedures for green spaces have some major shortcomings, which are discussed in this paper. It is argued why a more detailed spatial level as well as a distinction between natural and artificial varieties of structural elements is justified and needed and how the assessment of urban green spaces benefits from the multidimensional perspective that is applied. By analyzing a selection of structural elements from an ecological, microclimatic and social perspective, indicator values are derived and a new, holistic metrics 1 is proposed. The results of the integrated analysis led to two major findings: first, that for some elements, the evaluation differs to a great extent between the different perspectives (disciplines) and second, that natural and artificial varieties are, in most cases, evaluated considerably different from each other. The differences between the perspectives call for an integrative planning policy which acknowledges the varying contribution of a structural element to different purposes (ecological, microclimatic, social) as well as a discussion about the prioritization of those purposes. The differences in the evaluation of natural vs. artificial elements verify the assumption that indicators which consider only generic elements fail to account for those refinements and are thus less suitable for planning and assessment purposes. Implications, challenges and scenarios for the application of such a metrics are finally discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Application of remote sensing data to structural analysis of the East Kalimantan, Indonesia

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

Moriya, Shunji; Nishidai, Takashi

1996-07-01

JERS-1 SAR and LANDSAT TM images of the northern Kutei Basin, East Kalimantan, Indonesia were geologically interpreted. The focus of the study is on the structural analysis of the Samarinda Anticlinorium located in the onshore area of the Kutei Basin. In the Samarinda Anticlinorium, N-S folds and thrusts are well developed in the Tertiary sediments. They are believed to have been formed during the Middle Miocene or later. In addition to the N-S structure, an extensive NW-SE lineament traversing the central part of the study area can be identified on the images. Image interpretation reveals that this lineament is amore » major fault formed before the Oligocene. Noticeable differences in the N-S structure are recognized at the north and south of this NW-SE fault, Lithology and thickness of the sediments overlying the basement are remarkably different at the north and south of the fault. These may be responsible for the differences in the N-S structure of the northern and southern Anticlinorium.« less

Defects in High Speed Growth of EFG Silicon Ribbon

NASA Technical Reports Server (NTRS)

Rao, C. V. H. N.; Cretella, M. C.

1984-01-01

Silicon ribbons grown by the Edge-defined Film-fed Growth (EFG) technique exhibit a characteristic defect structure typified by twins, dislocations, grain boundaries and silicon carbide inclusions. As growth speed is increased from less than 2.5 cm per minute, the structural details change. The major difference between the ribbons grown at speeds below and above 2.5 cm per minute is in the generation of a cellular structure at the higher growth speeds, observable in the ribbon cross section. The presence of the cross sectional structure leads, in general, to a reduction in cell performance. Models to explain the formation of such a cross sectional structure are presented and discussed.

Using multi-scale distribution and movement effects along a montane highway to identify optimal crossing locations for a large-bodied mammal community.

PubMed

Schuster, Richard; Römer, Heinrich; Germain, Ryan R

2013-01-01

Roads are a major cause of habitat fragmentation that can negatively affect many mammal populations. Mitigation measures such as crossing structures are a proposed method to reduce the negative effects of roads on wildlife, but the best methods for determining where such structures should be implemented, and how their effects might differ between species in mammal communities is largely unknown. We investigated the effects of a major highway through south-eastern British Columbia, Canada on several mammal species to determine how the highway may act as a barrier to animal movement, and how species may differ in their crossing-area preferences. We collected track data of eight mammal species across two winters, along both the highway and pre-marked transects, and used a multi-scale modeling approach to determine the scale at which habitat characteristics best predicted preferred crossing sites for each species. We found evidence for a severe barrier effect on all investigated species. Freely-available remotely-sensed habitat landscape data were better than more costly, manually-digitized microhabitat maps in supporting models that identified preferred crossing sites; however, models using both types of data were better yet. Further, in 6 of 8 cases models which incorporated multiple spatial scales were better at predicting preferred crossing sites than models utilizing any single scale. While each species differed in terms of the landscape variables associated with preferred/avoided crossing sites, we used a multi-model inference approach to identify locations along the highway where crossing structures may benefit all of the species considered. By specifically incorporating both highway and off-highway data and predictions we were able to show that landscape context plays an important role for maximizing mitigation measurement efficiency. Our results further highlight the need for mitigation measures along major highways to improve connectivity between mammal populations, and illustrate how multi-scale data can be used to identify preferred crossing sites for different species within a mammal community.

Probing the links between language and mathematical conceptualisation

NASA Astrophysics Data System (ADS)

Bell, Garry; Woo, Jeong Ho

1998-04-01

Although it is well known that the number-naming grammars of some Asian languages affect the number conceptualisation and operational capacity of the young children who use them, language structure in other fields of the mathematical register appears to have been underemphasised in explanations of the differential mathematical attainment of East Asian and western students. This study probed the conceptual structures which samples of Year 9 students in Korea and Australia had constructed for various geometrical terms. The two samples of students exhibited major differences in definition ranking preferences on angle, and in semantic profiles for parallelogram, triangle, square, circle, cylinder, trapezium and line. It is hypothesised that these differences may be due in part to the noun phrase grammar differences between Korean and English, and to the syntax and semantic transparency of some Korean geometrical names. Results indicated reinforcement for the Vygotskian view that culturally imposed language structures directly influence the cognitive development of the learner.

Investigation of methanogenic community structures in rural biogas digesters from different climatic regions in Yunnan, southwest China.

PubMed

Dong, Minghua; Wu, Yan; Li, Qiumin; Tian, Guangliang; Yang, Bin; Li, Yingjuan; Zhang, Lijuan; Wang, Yongxia; Xiao, Wei; Yin, Fang; Zhao, Xingling; Zhang, Wudi; Cui, Xiaolong

2015-05-01

Understanding of the microbial community structures of the biogas digesters in different climatic regions can help improve the methane production in the fermentation process. The methanogenic archaeal diversity in four rural biogas digesters (BNA, JSA, LJA, and XGA) was investigated by a culture-independent rRNA approach in different climatic regions in Yunnan. Community structure composed of 711 clones in the all libraries. A total of 33 operational taxonomic units (OTUs) were detected, and major groups of methanogens were the orders Methanosarcinales and Methanomicrobiales. 63.2 % of all archaeal OTUs belong to the order Methanosarcinales which mostly contain acetotrophic methanogens. Methanomicrobiales (19.5 % in all OTUs) were detected in considerable number. Additionally, there were minor rates of uncultured archaea. The principal component analysis indicated that the genus Methanosaeta was mainly affected by the fermentation temperatures.

Risk Behavior and Perception Among Youths Residing in Urban Public Housing Developments

PubMed Central

Li, Xiaoming; Stanton, Bonita; Black, Maureen M.; Romer, Daniel; Ricardo, Izabel; Kaljee, Linda

1994-01-01

The scientific literature and popular media suggest that variations in housing structure and neighborhood influence risk behaviors among youths living in low-income urban communities. To explore the importance of these factors on early sexual intercourse, substance use, drug trafficking, and school truancy, data from a community-based survey, conducted in six public housing developments in a major eastern metropolis, were analyzed. The survey group consisted of 300 youths aged 9 through 15 years. There were minimal differences in three potential mediators of risk behaviors (e.g., perceived social support, parenting style, and perceived risk exposure) and in self-reported adolescent risk behaviors among youths residing in different housing developments and between youths residing in high-rise and in low-rise structures. These findings do not support the hypothesis that within a risk-dense low-income environment, variations in building structure or in neighborhood are associated with differences in adolescent risk behaviors. PMID:19313105

The role of extracellular matrix components in pin bone attachments during storage-a comparison between farmed Atlantic salmon (Salmo salar) and cod (Gadus morhua L.).

PubMed

Rønning, Sissel B; Østbye, Tone-Kari; Krasnov, Aleksei; Vuong, Tram T; Veiseth-Kent, Eva; Kolset, Svein O; Pedersen, Mona E

2017-04-01

Pin bones represent a major problem for processing and quality of fish products. Development of methods of removal requires better knowledge of the pin bones' attachment to the muscle and structures involved in the breakdown during loosening. In this study, pin bones from cod and salmon were dissected from fish fillets after slaughter or storage on ice for 5 days, and thereafter analysed with molecular methods, which revealed major differences between these species before and after storage. The connective tissue (CT) attaches the pin bone to the muscle in cod, while the pin bones in salmon are embedded in adipose tissue. Collagens, elastin, lectin-binding proteins and glycosaminoglycans (GAGs) are all components of the attachment site, and this differ between salmon and cod, resulting in a CT in cod that is more resistant to enzymatic degradation compared to the CT in salmon. Structural differences are reflected in the composition of transcriptome. Microarray analysis comparing the attachment sites of the pin bones with a reference muscle sample showed limited differences in salmon. In cod, on the other hand, the variances were substantial, and the gene expression profiles suggested difference in myofibre structure, metabolism and cell processes between the pin bone attachment site and the reference muscle. Degradation of the connective tissue occurs closest to the pin bones and not in the neighbouring tissue, which was shown using light microscopy. This study shows that the attachment of the pin bones in cod and salmon is different; therefore, the development of methods for removal should be tailored to each individual species.

Matrix composition and community structure analysis of a novel bacterial pyrite leaching community.

PubMed

Ziegler, Sibylle; Ackermann, Sonia; Majzlan, Juraj; Gescher, Johannes

2009-09-01

Here we describe a novel bacterial community that is embedded in a matrix of carbohydrates and bio/geochemical products of pyrite (FeS(2)) oxidation. This community grows in stalactite-like structures--snottites--on the ceiling of an abandoned pyrite mine at pH values of 2.2-2.6. The aqueous phase in the matrix contains 200 mM of sulfate and total iron concentrations of 60 mM. Micro-X-ray diffraction analysis showed that jarosite [(K,Na,H(3)O)Fe(3)(SO(4))(2)(OH)(6)] is the major mineral embedded in the snottites. X-ray absorption near-edge structure experiments revealed three different sulfur species. The major signal can be ascribed to sulfate, and the other two features may correspond to thiols and sulfoxides. Arabinose was detected as the major sugar component in the extracellular polymeric substance. Via restriction fragment length polymorphism analysis, a community was found that mainly consists of iron oxidizing Leptospirillum and Ferrovum species but also of bacteria that could be involved in dissimilatory sulfate and dissimilatory iron reduction. Each snottite can be regarded as a complex, self-contained consortium of bacterial species fuelled by the decomposition of pyrite.

Structured-illumination reflectance imaging as a new modality for food quality detection

USDA-ARS?s Scientific Manuscript database

Uniform or diffuse illumination is the standard in implementing many different imaging modalities. This form of illumination, however, has some major limitations in acquisition of useful information from food products because reflectance from the food products is non-uniform due to irregular, curved...

Career Paths in Educational Leadership: Examining Principals' Narratives

ERIC Educational Resources Information Center

Parylo, Oksana; Zepeda, Sally J.; Bengtson, Ed

2012-01-01

This qualitative study analyzes the career path narratives of active principals. Structural narrative analysis was supplemented with sociolinguistic theory and thematic narrative analysis to discern the similarities and differences, as well as the patterns in the language used by participating principals. Thematic analysis found four major themes…

Assemblages of animals around urban structures: testing hypotheses of patterns in sediments under boat-mooring pontoons.

PubMed

Lindegarth, M

2001-05-01

Assemblages of animals in soft-sediments were studied in relation to pontoons for mooring private boats in two estuaries near Sydney, Australia. Based on previously observed patterns around other types of artificial structures, it was predicted that assemblages of animals under pontoons would be different from those in similar areas away from pontoons. Hypotheses about overall differences in average abundance and composition between sites with and without pontoons were tested, as were hypotheses about variable differences among and within estuaries. Analyses revealed that there were fewer crustaceans under pontoons in one estuary. The most conspicuous patterns related to pontoons were, however, differences in variability among sites with pontoons compared to sites without pontoons. Differences in spatial variability were found for the overall multivariate structure using Bray-Curtis dissimilarities and for abundances of most major taxa. Total abundance was approximately 60 times more variable among sites without pontoons and number of taxa were seven times more variable among sites with pontoons. Such patterns indicate that impacts of pontoons occur at some sites but not at others. This may be explained by intrinsic differences among sites or by differences in practices for maintenance. Predictions from these two contrasting models need to be tested in order to achieve efficient management of this type of structure.

Information-processing differences and laterality of students from different colleges and disciplines.

PubMed

Monfort, M; Martin, S A; Frederickson, W

1990-02-01

1023 college students were assessed for hemispheric brain dominance using the paper-and-pencil test, the Human Information Processing Survey. Analysis of scores of students majoring in Advertising, Interior Design, Music, Journalism, Art, Oral Communication, and Architecture suggested a preference for right-brain hemispheric processing, while scores of students majoring in Accounting, Management, Finance, Computer Science, Mathematics, Nursing, Funeral Service, Criminal Justice, and Elementary Education suggested a preference for left-hemispheric strategies for processing information. The differential effects of hemispheric processing in an educational system emphasizing the left-hemispheric activities of structured logic and sequential processing suggests repression of the intellectual development of those students who may be genetically favorable to right-hemispheric processing.

Fungal diversity in deep-sea sediments associated with asphalt seeps at the Sao Paulo Plateau

NASA Astrophysics Data System (ADS)

Nagano, Yuriko; Miura, Toshiko; Nishi, Shinro; Lima, Andre O.; Nakayama, Cristina; Pellizari, Vivian H.; Fujikura, Katsunori

2017-12-01

We investigated the fungal diversity in a total of 20 deep-sea sediment samples (of which 14 samples were associated with natural asphalt seeps and 6 samples were not associated) collected from two different sites at the Sao Paulo Plateau off Brazil by Ion Torrent PGM targeting ITS region of ribosomal RNA. Our results suggest that diverse fungi (113 operational taxonomic units (OTUs) based on clustering at 97% sequence similarity assigned into 9 classes and 31 genus) are present in deep-sea sediment samples collected at the Sao Paulo Plateau, dominated by Ascomycota (74.3%), followed by Basidiomycota (11.5%), unidentified fungi (7.1%), and sequences with no affiliation to any organisms in the public database (7.1%). However, it was revealed that only three species, namely Penicillium sp., Cadophora malorum and Rhodosporidium diobovatum, were dominant, with the majority of OTUs remaining a minor community. Unexpectedly, there was no significant difference in major fungal community structure between the asphalt seep and non-asphalt seep sites, despite the presence of mass hydrocarbon deposits and the high amount of macro organisms surrounding the asphalt seeps. However, there were some differences in the minor fungal communities, with possible asphalt degrading fungi present specifically in the asphalt seep sites. In contrast, some differences were found between the two different sampling sites. Classification of OTUs revealed that only 47 (41.6%) fungal OTUs exhibited >97% sequence similarity, in comparison with pre-existing ITS sequences in public databases, indicating that a majority of deep-sea inhabiting fungal taxa still remain undescribed. Although our knowledge on fungi and their role in deep-sea environments is still limited and scarce, this study increases our understanding of fungal diversity and community structure in deep-sea environments.

Amino acid and structural variability of Yersinia pestis LcrV protein

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

Anisimov, A P; Dentovskaya, S V; Panfertsev, E A

2009-11-09

The LcrV protein is a multifunctional virulence factor and protective antigen of the plague bacterium which is generally conserved between the epidemic strains of Yersinia pestis. They investigated the diversity in the LcrV sequences among non-epidemic Y. pestis strains which have a limited virulence in selected animal models and for humans. Sequencing of lcrV genes from ten Y. pestis strains belonging to different phylogenetic groups (subspecies) showed that the LcrV proteins possess four major variable hotspots at positions 18, 72, 273, and 324-326. These major variations, together with other minor substitutions in amino acid sequences, allowed them to classify themore » LcrV alleles into five sequence types (A-E). They observed that the strains of different Y. pestis subspecies can have the same typ of LcrV, and different types of LcrV can exist within the same natural plague focus. The LcrV polymorphisms were structurally analyzed by comparing the modeled structures of LcrV from all available strains. All changes except one occurred either in flexible regions or on the surface of the protein, but local chemical properties (i.e. those of a hydrophobic, hydrophilic, amphipathic, or charged nature) were conserved across all of the strains. Polymorphisms in flexible and surface regions are likely subject to less selective pressure, and have a limited impact on the structure. In contrast, the substitution of tryptophan at position 113 with either glutamic acid or glycine likely has a serious influence on the regional structure of the protein, and these mutations might have an effect on the function of LcrV. The polymorphisms at positions 18, 72 and 273 were accountable for differences in oligomerization of LcrV. The importance of the latter property in emergence of epidemic strains of Y. pestis during evolution of this pathogen will need to be further investigated.« less

Application of the Modular Command and Control Structure (MCES) to Marine Corps SINCGARS Allocation

DTIC Science & Technology

1991-07-01

The first goal is to delineate the difference between the system being analyzed and its environment . To bound the C3 system, the analyst should...hardware and software entities and structures, is related to the forces it controls and the environmental stimuli to which it responds, including the enemy...M CES represents the environmental facto:s that require explicit assumptions in the problem. This ring may be seen as including the major scenario

Development and application of a comprehensive simulation model to evaluate impacts of watershed structures and irrigation water use on streamflow and groundwater: The case of Wet Walnut Creek Watershed, Kansas, USA

USGS Publications Warehouse

Ramireddygari, S.R.; Sophocleous, M.A.; Koelliker, J.K.; Perkins, S.P.; Govindaraju, R.S.

2000-01-01

This paper presents the results of a comprehensive modeling study of surface and groundwater systems, including stream-aquifer interactions, for the Wet Walnut Creek Watershed in west-central Kansas. The main objective of this study was to assess the impacts of watershed structures and irrigation water use on streamflow and groundwater levels, which in turn affect availability of water for the Cheyenne Bottoms Wildlife Refuge Management area. The surface-water flow model, POTYLDR, and the groundwater flow model, MODFLOW, were combined into an integrated, watershed-scale, continuous simulation model. Major revisions and enhancements were made to the POTYLDR and MODFLOW models for simulating the detailed hydrologic budget for the Wet Walnut Creek Watershed. The computer simulation model was calibrated and verified using historical streamflow records (at Albert and Nekoma gaging stations), reported irrigation water use, observed water-level elevations in watershed structure pools, and groundwater levels in the alluvial aquifer system. To assess the impact of watershed structures and irrigation water use on streamflow and groundwater levels, a number of hypothetical management scenarios were simulated under various operational criteria for watershed structures and different annual limits on water use for irrigation. A standard 'base case' was defined to allow comparative analysis of the results of different scenarios. The simulated streamflows showed that watershed structures decrease both streamflows and groundwater levels in the watershed. The amount of water used for irrigation has a substantial effect on the total simulated streamflow and groundwater levels, indicating that irrigation is a major budget item for managing water resources in the watershed. (C) 2000 Elsevier Science B.V.This paper presents the results of a comprehensive modeling study of surface and groundwater systems, including stream-aquifer interactions, for the Wet Walnut Creek Watershed in west-central Kansas. The main objective of this study was to assess the impacts of watershed structures and irrigation water use on streamflow and groundwater levels, which in turn affect availability of water for the Cheyenne Bottoms Wildlife Refuge Management area. The surface-water flow model, POTYLDR, and the groundwater flow model, MODFLOW, were combined into an integrated, watershed-scale, continuous simulation model. Major revisions and enhancements were made to the POTYLDR and MODFLOW models for simulating the detailed hydrologic budget for the Wet Walnut Creek Watershed. The computer simulation model was calibrated and verified using historical streamflow records (at Albert and Nekoma gaging stations), reported irrigation water use, observed water-level elevations in watershed structure pools, and groundwater levels in the alluvial aquifer system. To assess the impact of watershed structures and irrigation water use on streamflow and groundwater levels, a number of hypothetical management scenarios were simulated under various operational criteria for watershed structures and different annual limits on water use for irrigation. A standard `base case' was defined to allow comparative analysis of the results of different scenarios. The simulated streamflows showed that watershed structures decrease both streamflows and groundwater levels in the watershed. The amount of water used for irrigation has a substantial effect on the total simulated streamflow and groundwater levels, indicating that irrigation is a major budget item for managing water resources in the watershed.A comprehensive simulation model that combines the surface water flow model POTYLDR and the groundwater flow model MODFLOW was used to study the impacts of watershed structures (e.g., dams) and irrigation water use (including stream-aquifer interactions) on streamflow and groundwater. The model was revised, enhanced, calibrated, and verified, then applied to evaluate the hydrologic budget for Wet Wal

Extrapolating subsurface geometry by surface expressions in transpressional strike slip fault, deduced from analogue experiments with settings of rheology and convergence angle

NASA Astrophysics Data System (ADS)

Hsieh, Shang Yu; Neubauer, Franz

2015-04-01

The internal structure of major strike-slip faults is still poorly understood, particularly how to extrapolate subsurface structures by surface expressions. Series of brittle analogue experiments by Leever et al., 2011 resulted the convergence angle is the most influential factor for surface structures. Further analogue models with different ductile settings allow a better understanding in extrapolating surface structures to the subsurface geometry of strike-slip faults. Fifteen analogue experiments were constructed to represent strike-slip faults in nature in different geological settings. As key parameters investigated in this study include: (a) the angle of convergence, (b) the thickness of brittle layer, (c) the influence of a rheological weak layer within the crust, and (d) influence of a thick and rheologically weak layer at the base of the crust. The experiments are aimed to explain first order structures along major transcurrent strike-slip faults such as the Altyn, Kunlun, San Andrea and Greendale (Darfield earthquake 2010) faults. The preliminary results show that convergence angle significantly influences the overall geometry of the transpressional system with greater convergence angles resulting in wider fault zones and higher elevation. Different positions, densities and viscosities of weak rheological layers have not only different surface expressions but also affect the fault geometry in the subsurface. For instance, rheological weak material in the bottom layer results in stretching when experiment reaches a certain displacement and a buildup of a less segmented, wide positive flower structure. At the surface, a wide fault valley in the middle of the fault zone is the reflection of stretching along the velocity discontinuity at depth. In models with a thin and rheologically weaker layer in the middle of the brittle layer, deformation is distributed over more faults and the geometry of the fault zone below and above the weak zone shows significant differences, suggesting that the correlation of structures across a weak layer has to be supported by geophysical data, which help constraining the geometry of the deep part. This latter experiment has significantly similar phenomena in reality, such as few pressure ridges along Altyn fault. The experimental results underline the need to understand the role of the convergence angle and the influence of rheology on fault evolution, in order to connect between surface deformation and subsurface geometry.

Structure-function relationship of avian eggshell matrix proteins: a comparative study of two major eggshell matrix proteins, ansocalcin and OC-17.

PubMed

Lakshminarayanan, Rajamani; Joseph, Jeremiah S; Kini, R Manjunatha; Valiyaveettil, Suresh

2005-01-01

The role of individual matrix proteins in avian eggshell calcification is poorly understood despite numerous attempts to characterize and localize their presence in the eggshell matrix. Ansocalcin, the major matrix protein from goose eggshell, was found to induce the formation of calcite crystal aggregates under in vitro. Owing to its high similarity with the chicken eggshell matrix protein ovocleidin 17 (OC-17), a comparative investigation has been carried out to understand the structure-function relationship. RP-HPLC shows that ansocalcin is the major component in extracts of goose eggshells before and after bleach treatment. However, OC-17 was observed in minute quantities in the extract of bleach-treated chicken eggshells. In vitro crystal growth experiments showed that OC-17 and ansocalcin interact differently with the calcite crystals formed. Circular dichroism, intrinsic tryptophan fluorescence, and dynamic light scattering studies showed that, under the conditions used in our experiments, OC-17 does not aggregate in solution or induce the nucleation of calcite aggregates in the concentration range used. These observations indicate that OC-17 and ansocalcin play different roles in the eggshell calcification. To our knowledge, this is the first report on the comparison of properties of homologous eggshell proteins that belong to the same phylogeny.

Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator

PubMed Central

Pierre, Valérie C.; Kaiser, Jens T.; Barton, Jacqueline K.

2007-01-01

We report the 1.1-Å resolution crystal structure of a bulky rhodium complex bound to two different DNA sites, mismatched and matched in the oligonucleotide 5′-(dCGGAAATTCCCG)2-3′. At the AC mismatch site, the structure reveals ligand insertion from the minor groove with ejection of both mismatched bases and elucidates how destabilized mispairs in DNA may be recognized. This unique binding mode contrasts with major groove intercalation, observed at a matched site, where doubling of the base pair rise accommodates stacking of the intercalator. Mass spectral analysis reveals different photocleavage products associated with the two binding modes in the crystal, with only products characteristic of mismatch binding in solution. This structure, illustrating two clearly distinct binding modes for a molecule with DNA, provides a rationale for the interrogation and detection of mismatches. PMID:17194756

Musculoskeletal pain symptoms among allied health professions' students: Prevalence rates and associated factors.

PubMed

Almhdawi, Khader A; Mathiowetz, Virgil; Al-Hourani, Zeid; Khader, Yousef; Kanaan, Saddam F; Alhasan, Mustafa

2017-11-06

Very few articles, comprehensively, investigated musculoskeletal pain symptoms (MPS) among wide variety of allied health professions (AHP) students. This study aimed to investigate the prevalence of MPS and their associated factors among different AHP majors' students. A cross-sectional design was conducted. A sample of AHP students from nine majors (n= 838, Mean age = 21.3 years) completed a validated structured self-administrated questionnaires including Nordic Musculoskeletal Questionnaire, Depression Anxiety Stress Scale (DASS 21), and specific questions regarding demographics and life style. MPS prevalence rate were compared between males and females and between majors. Logistic regression was conducted to identify predictors of MPS. MPS in neck, lower back, and shoulder 12-month were the most prevalent (67.1%, and 61.4%, 58.8% respectively). MPS prevalence was significantly higher in females and statistically different among majors. MPS were significantly associated with increased clinical training load, mental stress symptoms, and smartphone average use time. MPS in AHP students are prevalent and statistically higher among females. Students are advised to adhere to different conservative precautions and follow prevention programs. Future studies are needed to assess actual mechanisms causing MPS among AHP students and designing effective prevention programs specific to AHP students.

Dissolution of steel slags in aqueous media.

PubMed

Yadav, Shashikant; Mehra, Anurag

2017-07-01

Steel slag is a major industrial waste in steel industries, and its dissolution behavior in water needs to be characterized in the larger context of its potential use as an agent for sequestering CO 2 . For this purpose, a small closed system batch reactor was used to conduct the dissolution of steel slags in an aqueous medium under various dissolution conditions. In this study, two different types of steel slags were procured from steel plants in India, having diverse structural features, mineralogical compositions, and particle sizes. The experiment was performed at different temperatures for 240 h of dissolution at atmospheric pressure. The dissolution rates of major and minor slag elements were quantified through liquid-phase elemental analysis using an inductively coupled plasma atomic emission spectroscopy at different time intervals. Advanced analytical techniques such as field emission gun-scanning electron microscope, energy-dispersive X-ray, BET, and XRD were also used to analyze mineralogical and structural changes in the slag particles. High dissolution of slags was observed irrespective of the particle size distribution, which suggests high carbonation potential. Concentrations of toxic heavy metals in the leachate were far below maximum acceptable limits. Thus, the present study investigates the dissolution behavior of different mineral ions of steel slag in aqueous media in light of its potential application in CO 2 sequestration.

Folding a Protein with Equal Probability of Being Helix or Hairpin

PubMed Central

Lin, Chun-Yu; Chen, Nan-Yow; Mou, Chung Yu

2012-01-01

We explore the possibility for the native structure of a protein being inherently multiconformational in an ab initio coarse-grained model. Based on the Wang-Landau algorithm, the complete free energy landscape for the designed sequence 2DX4: INYWLAHAKAGYIVHWTA is constructed. It is shown that 2DX4 possesses two nearly degenerate native structures: one is a helix structure with the other a hairpinlike structure, and their free energy difference is <2% of that of local minima. Two degenerate native structures are stabilized by an energy barrier of ∼10 kcal/mol. Furthermore, the hydrogen-bond and dipole-dipole interactions are found to be two major competing interactions in transforming one conformation into the other. Our results indicate that two degenerate native structures are stabilized by subtle balance between different interactions in proteins. In particular, for small proteins, balance between the hydrogen-bond and dipole-dipole interactions happens for proteins of sizes being ∼18 amino acids and is shown to the main driving mechanism for the occurrence of degeneracy. These results provide important clues to the study of native structures of proteins. PMID:22828336

"Time Is Not Enough." Workload in Higher Education: A Student Perspective

ERIC Educational Resources Information Center

Kyndt, Eva; Berghmans, Inneke; Dochy, Filip; Bulckens, Lydwin

2014-01-01

Students' workload has been recognised as a major factor in the teaching and learning environment. This paper starts by structuring the different conceptualisations of workload described in the scientific literature. Besides the traditional distinction between objective and subjective or perceived workload, a distinction between conceptualisations…

Analysis of Relationships among Burnout, Academic Achievement, and Self-Regulation

ERIC Educational Resources Information Center

Duru, Erdinç; Duru, Sibel; Balkis, Murat

2014-01-01

This study examined the relationships among burnout, academic achievement, and self-regulation with two structural models. The participants were 383 undergraduates with different majors in a university in the western part of Turkey. The results showed that academic achievement was negatively associated with three dimensions of burnout and was…

Optimal Structures for Multimedia Instruction.

DTIC Science & Technology

1984-01-27

Adair 73] and [Carroll 80] studying the semiotic system of film, and (Barthes 571 studying cultural systems, such as the meaning of steak in French ... cuisine . 3.2.1 Saussure and Peirce Most work in semiotics derives from either Saussure or Peirce. A major difference in their approach [Eco 79] is that

Taxonomic profiling of bacterial community structure from coastal sediment of Alang-Sosiya shipbreaking yard near Bhavnagar, India.

PubMed

Patel, Vilas; Munot, Hitendra; Shah, Varun; Shouche, Yogesh S; Madamwar, Datta

2015-12-30

The Alang-Sosiya shipbreaking yard (ASSBY) is considered the largest of its kind in the world, and a major source of anthropogenic pollutants. The aim of this study was to investigate the impact of shipbreaking activities on the bacterial community structure with a combination of culture-dependent and culture-independent approaches. In the culture-dependent approach, 200 bacterial cultures were isolated and analyzed by molecular fingerprinting and 16S ribosomal RNA (r-RNA) gene sequencing, as well as being studied for degradation of polycyclic aromatic hydrocarbons (PAHs). In the culture-independent approach, operational taxonomic units (OTUs) were related to eight major phyla, of which Betaproteobacteria (especially Acidovorax) was predominantly found in the polluted sediments of ASSBY and Gammaproteobacteria in the pristine sediment sample. The statistical approaches showed a significant difference in the bacterial community structure between the pristine and polluted sediments. To the best of our knowledge, this is the first study investigating the effect of shipbreaking activity on the bacterial community structure of the coastal sediment at ASSBY. Copyright © 2015. Published by Elsevier Ltd.

Recombinant structures expand and contract inter and intragenic diversification at the KIR locus

PubMed Central

2013-01-01

Background The human KIR genes are arranged in at least six major gene-content haplotypes, all of which are combinations of four centromeric and two telomeric motifs. Several less frequent or minor haplotypes also exist, including insertions, deletions, and hybridization of KIR genes derived from the major haplotypes. These haplotype structures and their concomitant linkage disequilibrium among KIR genes suggest that more meaningful correlative data from studies of KIR genetics and complex disease may be achieved by measuring haplotypes of the KIR region in total. Results Towards that end, we developed a KIR haplotyping method that reports unambiguous combinations of KIR gene-content haplotypes, including both phase and copy number for each KIR. A total of 37 different gene content haplotypes were detected from 4,512 individuals and new sequence data was derived from haplotypes where the detailed structure was not previously available. Conclusions These new structures suggest a number of specific recombinant events during the course of KIR evolution, and add to an expanding diversity of potential new KIR haplotypes derived from gene duplication, deletion, and hybridization. PMID:23394822

Criteria for structural test

NASA Technical Reports Server (NTRS)

1973-01-01

The results of a study to define criteria and techniques of design, analysis and test which permit the use of a single major structural test article for performing dynamic, fatigue, and static testing are presented. The criteria developed is applicable to both space vehicles and aircraft structures operating in the subsonic or supersonic regime. The feasibility of such an approach was demonstrated by defining test interactions, compatibilities and incompatibilities between the three different types of tests. The results of the study indicate that the single test article concept is feasible with a testing sequence of dynamic test followed by a fatigue and static test.

In vivo trafficking and catabolism of IgG1 antibodies with Fc associated carbohydrates of differing structure.

PubMed

Wright, A; Sato, Y; Okada, T; Chang, K; Endo, T; Morrison, S

2000-12-01

We have now produced mouse-human chimeric IgG1 in wild-type Chinese hamster ovary (CHO) cell lines Pro-5 as well as in the glycosylation mutants Lec 2, Lec 8, and Lec 1. Analysis of the attached carbohydrates shows those present on IgG1-Lec 1 were mannose terminated. Carbohydrate present on IgG1-Lec8 was uniformly biantennary terminating in N-acetylglucosamine. The glycosylation profiles of IgG1-Lec 2 and IgG1-Pro-5 were heterogeneous. Only IgG1-Pro-5 was sialylated with sialic acid present on only a small percentage of the carbohydrate structures. When the in vivo fate of antibodies labeled with (125)I-lactotyramine was determined, it was found that the majority of all of the antibodies, irrespective of the structure of their attached carbohydrate, is catabolized in the skin and muscle. However, the attached carbohydrate structure does influence the amount that is catabolized in the liver and the liver serves as a major site for the catabolism of proteins bearing carbohydrate with the Lec2 (with terminal galactose) or Lec1(with terminal mannose) structure.

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data.

PubMed

Perczel, András; Jákli, Imre; McAllister, Michael A; Csizmadia, Imre G

2003-06-06

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.

Telemedicine at sea and onshore: divergences and convergences.

PubMed

Guitton, Matthieu J

2015-01-01

Telemedical Maritime Assistance Service (TMAS) is one of the fundamental components of medical assistance delivery at sea. However, while onshore telemedicine is undergoing a fast growth, these research and clinical investments unfortunately did not yet benefit for telemedicine at sea. While telemedicine aims at providing distant health care, telemedicine at sea and onshore bear major differences, particularly for merchant vessels, and to a lesser extent for passenger vessels, which can be divided between structural differences, differences of practices, and policy differences. Despite the existence of important divergences between telemedicine at sea and telemedicine onshore, these two major branches of distant health care delivery still converge in some respects. Identifying the convergences between telemedicine at sea and telemedicine onshore might contribute to increase and optimise the transfer from research on onshore telemedicine to maritime telemedicine, and to overcome the relatively low amount of research performed on telemedicine at sea compared to its onshore counterpart.

Comparison of Surgical Outcomes Between Teaching and Nonteaching Hospitals in the Department of Veterans Affairs

PubMed Central

Khuri, Shukri F.; Najjar, Samer F.; Daley, Jennifer; Krasnicka, Barbara; Hossain, Monir; Henderson, William G.; Aust, J. Bradley; Bass, Barbara; Bishop, Michael J.; Demakis, John; DePalma, Ralph; Fabri, Peter J.; Fink, Aaron; Gibbs, James; Grover, Frederick; Hammermeister, Karl; McDonald, Gerald; Neumayer, Leigh; Roswell, Robert H.; Spencer, Jeannette; Turnage, Richard H.

2001-01-01

Objective To determine whether the investment in postgraduate education and training places patients at risk for worse outcomes and higher costs than if medical and surgical care was delivered in nonteaching settings. Summary Background Data The Veterans Health Administration (VA) plays a major role in the training of medical students, residents, and fellows. Methods The database of the VA National Surgical Quality Improvement Program was analyzed for all major noncardiac operations performed during fiscal years 1997, 1998, and 1999. Teaching status of a hospital was determined on the basis of a background and structure questionnaire that was independently verified by a research fellow. Stepwise logistic regression was used to construct separate models predictive of 30-day mortality and morbidity for each of seven surgical specialties and eight operations. Based on these models, a severity index for each patient was calculated. Hierarchical logistic regression models were then created to examine the relationship between teaching versus nonteaching hospitals and 30-day postoperative mortality and morbidity, after adjusting for patient severity. Results Teaching hospitals performed 81% of the total surgical workload and 90% of the major surgery workload. In most specialties in teaching hospitals, the residents were the primary surgeons in more than 90% of the operations. Compared with nonteaching hospitals, the patient populations in teaching hospitals had a higher prevalence of risk factors, underwent more complex operations, and had longer operation times. Risk-adjusted mortality rates were not different between the teaching and nonteaching hospitals in the specialties and operations studied. The unadjusted complication rate was higher in teaching hospitals in six of seven specialties and four of eight operations. Risk adjustment did not eliminate completely these differences, probably reflecting the relatively poor predictive validity of some of the risk adjustment models for morbidity. Length of stay after major operations was not consistently different between teaching and nonteaching hospitals. Conclusion Compared with nonteaching hospitals, teaching hospitals in the VA perform the majority of complex and high-risk major procedures, with comparable risk-adjusted 30-day mortality rates. Risk-adjusted 30-day morbidity rates in teaching hospitals are higher in some specialties and operations than in nonteaching hospitals. Although this may reflect the weak predictive validity of some of the risk adjustment models for morbidity, it may also represent suboptimal processes and structures of care that are unique to teaching hospitals. Despite good quality of care in teaching hospitals, as evidenced by the 30-day mortality data, efforts should be made to examine further the structures and processes of surgical care prevailing in these hospitals. PMID:11524590

Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man.

PubMed

Kulski, Jerzy K; Shiina, Takashi; Anzai, Tatsuya; Kohara, Sakae; Inoko, Hidetoshi

2002-12-01

The major histocompatibility complex (MHC) genomic region is composed of a group of linked genes involved functionally with the adaptive and innate immune systems. The class I and class II genes are intrinsic features of the MHC and have been found in all the jawed vertebrates studied so far. The MHC genomic regions of the human and the chicken (B locus) have been fully sequenced and mapped, and the mouse MHC sequence is almost finished. Information on the MHC genomic structures (size, complexity, genic and intergenic composition and organization, gene order and number) of other vertebrates is largely limited or nonexistent. Therefore, we are mapping, sequencing and analyzing the MHC genomic regions of different human haplotypes and at least eight nonhuman species. Here, we review our progress with these sequences and compare the human MHC structure with that of the nonhuman primates (chimpanzee and rhesus macaque), other mammals (pigs, mice and rats) and nonmammalian vertebrates such as birds (chicken and quail), bony fish (medaka, pufferfish and zebrafish) and cartilaginous fish (nurse shark). This comparison reveals a complex MHC structure for mammals and a relatively simpler design for nonmammalian animals with a hypothetical prototypic structure for the shark. In the mammalian MHC, there are two to five different class I duplication blocks embedded within a framework of conserved nonclass I and/or nonclass II genes. With a few exceptions, the class I framework genes are absent from the MHC of birds, bony fish and sharks. Comparative genomics of the MHC reveal a highly plastic region with major structural differences between the mammalian and nonmammalian vertebrates. Additional genomic data are needed on animals of the reptilia, crocodilia and marsupial classes to find the origins of the class I framework genes and examples of structures that may be intermediate between the simple and complex MHC organizations of birds and mammals, respectively.

Determinants of the spatiotemporal dynamics of the 2009 H1N1 pandemic in Europe: implications for real-time modelling.

PubMed

Merler, Stefano; Ajelli, Marco; Pugliese, Andrea; Ferguson, Neil M

2011-09-01

Influenza pandemics in the last century were characterized by successive waves and differences in impact and timing between different regions, for reasons not clearly understood. The 2009 H1N1 pandemic showed rapid global spread, but with substantial heterogeneity in timing within each hemisphere. Even within Europe substantial variation was observed, with the UK being unique in experiencing a major first wave of transmission in early summer and all other countries having a single major epidemic in the autumn/winter, with a West to East pattern of spread. Here we show that a microsimulation model, parameterised using data about H1N1pdm collected by the beginning of June 2009, explains the occurrence of two waves in UK and a single wave in the rest of Europe as a consequence of timing of H1N1pdm spread, fluxes of travels from US and Mexico, and timing of school vacations. The model provides a description of pandemic spread through Europe, depending on intra-European mobility patterns and socio-demographic structure of the European populations, which is in broad agreement with observed timing of the pandemic in different countries. Attack rates are predicted to depend on the socio-demographic structure, with age dependent attack rates broadly agreeing with available serological data. Results suggest that the observed heterogeneity can be partly explained by the between country differences in Europe: marked differences in school calendars, mobility patterns and sociodemographic structures. Moreover, higher susceptibility of children to infection played a key role in determining the epidemiology of the 2009 pandemic. Our work shows that it would have been possible to obtain a broad-brush prediction of timing of the European pandemic well before the autumn of 2009, much more difficult to achieve with simpler models or pre-pandemic parameterisation. This supports the use of models accounting for the structure of complex modern societies for giving insight to policy makers.

Discrimination of tonal and atonal music in congenital amusia: The advantage of implicit tasks.

PubMed

Tillmann, Barbara; Lalitte, Philippe; Albouy, Philippe; Caclin, Anne; Bigand, Emmanuel

2016-05-01

Congenital amusia is a neurodevelopmental disorder of music perception and production, which has been attributed to a major deficit in pitch processing. While most studies and diagnosis tests have used explicit investigation methods, recent studies using implicit investigation approaches have revealed some unimpaired pitch structure processing in congenital amusia. The present study investigated amusic individuals' processing of tonal structures (e.g., musical structures respecting the Western tonal system) via three different questions. Amusic participants and their matched controls judged tonal versions (original musical excerpts) and atonal versions (with manipulated pitch content to remove tonal structures) of 12 musical pieces. For each piece, participants answered three questions that required judgments from different perspectives: an explicit structural one, a personal, emotional one and a more social one (judging the perception of others). Results revealed that amusic individuals' judgments differed between tonal and atonal versions. However, the question type influenced the extent of the revealed structure processing: while amusic individuals were impaired for the question requiring explicit structural judgments, they performed as well as their matched controls for the two other questions. Together with other recent studies, these findings suggest that congenital amusia might be related to a disorder of the conscious access to music processing rather than music processing per se. Copyright © 2016 Elsevier Ltd. All rights reserved.

Erythrocyte enzymes in groups of Rattus norvegicus with genetic differences in 2,3-diphosphoglycerate levels.

PubMed

Noble, N A; Tanaka, K R

1979-01-01

1. A major locus with two alleles is responsible for large differences in erythrocyte 2,3-diphosphoglycerate (DPG) levels in Rattus norvegicus. Blood from homozygous High-DPG, homozygous Low-DPG and heterozygous animals was used to measure blood indices and red cell enzyme activities. 2. Significant differences between groups were found in DPG levels, white blood cell counts and hemoglobin levels. 3. The results suggest that none of the red cell enzymes assayed is structurally or quantitatively different in the three groups.

Structure of N-linked oligosaccharides attached to chlorovirus PBCV-1 major capsid protein reveals unusual class of complex N-glycans

PubMed Central

De Castro, Cristina; Molinaro, Antonio; Piacente, Francesco; Gurnon, James R.; Sturiale, Luisa; Palmigiano, Angelo; Lanzetta, Rosa; Parrilli, Michelangelo; Garozzo, Domenico; Tonetti, Michela G.; Van Etten, James L.

2013-01-01

The major capsid protein Vp54 from the prototype chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1) contains four Asn-linked glycans. The structure of the four N-linked oligosaccharides and the type of substitution at each glycosylation site was determined by chemical, spectroscopic, and spectrometric analyses. Vp54 glycosylation is unusual in many ways, including: (i) unlike most viruses, PBCV-1 encodes most, if not all, of the machinery to glycosylate its major capsid protein; (ii) the glycans are attached to the protein by a β-glucose linkage; (iii) the Asn-linked glycans are not located in a typical N-X-(T/S) consensus site; and (iv) the process probably occurs in the cytoplasm. The four glycoforms share a common core structure, and the differences are related to the nonstoichiometric presence of two monosaccharides. The most abundant glycoform consists of nine neutral monosaccharide residues, organized in a highly branched fashion. Among the most distinctive features of the glycoforms are (i) a dimethylated rhamnose as the capping residue of the main chain, (ii) a hyperbranched fucose unit, and (iii) two rhamnose residues with opposite absolute configurations. These glycoforms differ from what has been reported so far in the three domains of life. Considering that chloroviruses and other members of the family Phycodnaviridae may have a long evolutionary history, we suggest that the chlorovirus glycosylation pathway is ancient, possibly existing before the development of the endoplasmic reticulum and Golgi pathway, and involves still unexplored mechanisms. PMID:23918378

Life comparative analysis of energy consumption and CO₂ emissions of different building structural frame types.

PubMed

Kim, Sangyong; Moon, Joon-Ho; Shin, Yoonseok; Kim, Gwang-Hee; Seo, Deok-Seok

2013-01-01

The objective of this research is to quantitatively measure and compare the environmental load and construction cost of different structural frame types. Construction cost also accounts for the costs of CO₂ emissions of input materials. The choice of structural frame type is a major consideration in construction, as this element represents about 33% of total building construction costs. In this research, four constructed buildings were analyzed, with these having either reinforced concrete (RC) or steel (S) structures. An input-output framework analysis was used to measure energy consumption and CO₂ emissions of input materials for each structural frame type. In addition, the CO₂ emissions cost was measured using the trading price of CO₂ emissions on the International Commodity Exchange. This research revealed that both energy consumption and CO₂ emissions were, on average, 26% lower with the RC structure than with the S structure, and the construction costs (including the CO₂ emissions cost) of the RC structure were about 9.8% lower, compared to the S structure. This research provides insights through which the construction industry will be able to respond to the carbon market, which is expected to continue to grow in the future.

Interspecific analysis of covariance structure in the masticatory apparatus of galagos.

PubMed

Vinyard, Christopher J

2007-01-01

The primate masticatory apparatus (MA) is a functionally integrated set of features, each of which performs important functions in biting, ingestive, and chewing behaviors. A comparison of morphological covariance structure among species for these MA features will help us to further understand the evolutionary history of this region. In this exploratory analysis, the covariance structure of the MA is compared across seven galago species to investigate 1) whether there are differences in covariance structure in this region, and 2) if so, how has this covariation changed with respect to size, MA form, diet, and/or phylogeny? Ten measurements of the MA functionally related to bite force production and load resistance were obtained from 218 adults of seven galago species. Correlation matrices were generated for these 10 dimensions and compared among species via matrix correlations and Mantel tests. Subsequently, pairwise covariance disparity in the MA was estimated as a measure of difference in covariance structure between species. Covariance disparity estimates were correlated with pairwise distances related to differences in body size, MA size and shape, genetic distance (based on cytochrome-b sequences) and percentage of dietary foods to determine whether one or more of these factors is linked to differences in covariance structure. Galagos differ in MA covariance structure. Body size appears to be a major factor correlated with differences in covariance structure among galagos. The largest galago species, Otolemur crassicaudatus, exhibits large differences in body mass and covariance structure relative to other galagos, and thus plays a primary role in creating this association. MA size and shape do not correlate with covariance structure when body mass is held constant. Diet also shows no association. Genetic distance is significantly negatively correlated with covariance disparity when body mass is held constant, but this correlation appears to be a function of the small body size and large genetic distance for Galagoides demidoff. These exploratory results indicate that changing body size may have been a key factor in the evolution of the galago MA.

Evolution of polyploidy and the diversification of plant-pollinator interactions.

PubMed

Thompson, John N; Merg, Kurt F

2008-08-01

One of the major mechanisms of plant diversification has been the evolution of polyploid populations that differ from their diploid progenitors in morphology, physiology, and environmental tolerances. Recent studies have indicated that polyploidy may also have major effects on ecological interactions with herbivores and pollinators. We evaluated pollination of sympatric diploid and tetraploid plants of the rhizomatous herb Heuchera grossulariifolia (Saxifragaceae) along the Selway and Salmon Rivers of northern Idaho, USA, during four consecutive years. Previous molecular and ecological analyses had indicated that the tetraploid populations along these two river systems are independently derived and differ from each other in multiple traits. In each region, we evaluated floral visitation rate by all insect visitors, pollination efficacy of all major visitors, and relative contribution of all major pollinators to seed set. In both regions, diploid and tetraploid plants attracted different suites of floral visitors. Most pollination was attributable to several bee species and the moth Greya politella. Lasioglossum bees preferentially visited diploid plants at Lower Salmon but not at Upper Selway, queen Bombus centralis preferentially visited tetraploids at both sites, and worker B. centralis differed between sites in their cytotype preference. Hence, diploid and autotetraploid H. grossulariifolia plants act essentially as separate ecological species and may experience partial reproductive isolation through differential visitation and pollination by their major floral visitors. Overall the results, together with recent results from other studies, suggest that the repeated evolution of polyploidy in plants may contribute importantly to the structure and diversification of ecological interactions in terrestrial communities.

Extracting and identifying concrete structural defects in GPR images

NASA Astrophysics Data System (ADS)

Ye, Qiling; Jiao, Liangbao; Liu, Chuanxin; Cao, Xuehong; Huston, Dryver; Xia, Tian

2018-03-01

Traditionally most GPR data interpretations are performed manually. With the advancement of computing technologies, how to automate GPR data interpretation to achieve high efficiency and accuracy has become an active research subject. In this paper, analytical characterizations of major defects in concrete structures, including delamination, air void and moisture in GPR images, are performed. In the study, the image features of different defects are compared. Algorithms are developed for defect feature extraction and identification. For validations, both simulation results and field test data are utilized.

Determination of Structural Parameters from EXAFS (Extended X-Ray Absorption Fine Structure): Application to Solutions and Catalysts.

DTIC Science & Technology

1984-05-23

the disorder was accurately known. Inverse Transform To isolate the EAFS contribution due to a single feature in the Fourier transform, the inverse ...is associated with setting the "fold" components to 27 zero in r-space. An inverse transform (real part) of the major feature of the Fig. 4 Fourier...phase of the resulting inverse transform represents only any differences between the material being studied and the reference. This residual is

Integrating and Assessing Structural Competency in an Innovative Prehealth Curriculum at Vanderbilt University

PubMed Central

Petty, JuLeigh

2017-01-01

Problem Structural competency is a framework for conceptualizing and addressing health-related social justice issues that emphasizes diagnostic recognition of economic and political conditions producing and racializing inequalities in health. Strategies are needed to teach prehealth undergraduate students concepts central to structural competency (e.g., structural inequity, structural racism, structural stigma) and to evaluate their impact. Approach The curriculum for Vanderbilt University’s innovative prehealth major in medicine, health, and society (MHS) was reshaped in 2013 to incorporate structural competency concepts and skills into undergraduate courses. The authors developed the Structural Foundations of Health (SFH) evaluation instrument, with closed- and open-ended questions designed to assess undergraduate students’ core structural competency skills. They piloted the SFH instrument in 2015 with MHS seniors. Outcomes Of the 85 students included in the analysis, most selected one or more structural factors as among the three most important in explaining U.S. regional childhood obesity rates (85%) and racial disparities in heart disease (92%). More than half described individual- or family-level structural factors (66%) or broad social and political factors (56%) as influencing geographic disparities in childhood obesity. Nearly two-thirds (66%) described racial disparities in heart disease as consequences of socioeconomic differences, discrimination/stereotypes, or policies with racial implications. Next Steps Preliminary data suggest that the MHS major trained students to identify and analyze relationships between structural factors and health outcomes. Future research will include a comparison of structural competency skills among MHS students and students in the traditional premedical track and assessment of these skills in incoming first-year students. PMID:28225732

Uriniferous tubule: structural and functional organization.

PubMed

Christensen, Erik Ilsø; Wagner, Carsten A; Kaissling, Brigitte

2012-04-01

The uriniferous tubule is divided into the proximal tubule, the intermediate (thin) tubule, the distal tubule and the collecting duct. The present chapter is based on the chapters by Maunsbach and Christensen on the proximal tubule, and by Kaissling and Kriz on the distal tubule and collecting duct in the 1992 edition of the Handbook of Physiology, Renal Physiology. It describes the fine structure (light and electron microscopy) of the entire mammalian uriniferous tubule, mainly in rats, mice, and rabbits. The structural data are complemented by recent data on the location of the major transport- and transport-regulating proteins, revealed by morphological means(immunohistochemistry, immunofluorescence, and/or mRNA in situ hybridization). The structural differences along the uriniferous tubule strictly coincide with the distribution of the major luminal and basolateral transport proteins and receptors and both together provide the basis for the subdivision of the uriniferous tubule into functional subunits. Data on structural adaptation to defined functional changes in vivo and to genetical alterations of specified proteins involved in transepithelial transport importantly deepen our comprehension of the correlation of structure and function in the kidney, of the role of each segment or cell type in the overall renal function,and our understanding of renal pathophysiology. © 2012 American Physiological Society. Compr Physiol 2:933-996, 2012.

Spatio-temporal patterns of major bacterial groups in alpine waters.

PubMed

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E G; Robinson, Christopher T

2014-01-01

Glacial alpine landscapes are undergoing rapid transformation due to changes in climate. The loss of glacial ice mass has directly influenced hydrologic characteristics of alpine floodplains. Consequently, hyporheic sediment conditions are likely to change in the future as surface waters fed by glacial water (kryal) become groundwater dominated (krenal). Such environmental shifts may subsequently change bacterial community structure and thus potential ecosystem functioning. We quantitatively investigated the structure of major bacterial groups in glacial and groundwater-fed streams in three alpine floodplains during different hydrologic periods. Our results show the importance of several physico-chemical variables that reflect local geological characteristics as well as water source in structuring bacterial groups. For instance, Alpha-, Betaproteobacteria and Cytophaga-Flavobacteria were influenced by pH, conductivity and temperature as well as by inorganic and organic carbon compounds, whereas phosphorous compounds and nitrate showed specific influence on single bacterial groups. These results can be used to predict future bacterial group shifts, and potential ecosystem functioning, in alpine landscapes under environmental transformation.

Physicochemical structural changes of cellulosic substrates during enzymatic saccharification

DOE PAGES

Meng, Xianzhi; Yoo, Chang Geun; Li, Mi; ...

2016-12-30

Enzymatic hydrolysis represents one of the major steps and barriers in the commercialization process of converting cellulosic substrates into biofuels and other value added products. It is usually achieved by a synergistic action of enzyme mixture typically consisting of multiple enzymes such as glucanase, cellobiohydrolase and β-glucosidase with different mode of actions. Due to the innate biomass recalcitrance, enzymatic hydrolysis normally starts with an initial fast rate of hydrolysis followed by a rapid decrease of rate toward the end of hydrolysis. With majority of literature studies focusing on the effect of key substrate characteristics on the initial rate or finalmore » yield of enzymatic hydrolysis, information about physicochemical structural changes of cellulosic substrates during enzymatic hydrolysis is still quite limited. Consequently, what slows down the reaction rate toward the end of hydrolysis is not well understood. Lastly, this review highlights recent advances in understanding the structural changes of cellulosic substrates during the hydrolysis process, to better understand the fundamental mechanisms of enzymatic hydrolysis.« less

Physicochemical structural changes of cellulosic substrates during enzymatic saccharification

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

Meng, Xianzhi; Yoo, Chang Geun; Li, Mi

Enzymatic hydrolysis represents one of the major steps and barriers in the commercialization process of converting cellulosic substrates into biofuels and other value added products. It is usually achieved by a synergistic action of enzyme mixture typically consisting of multiple enzymes such as glucanase, cellobiohydrolase and β-glucosidase with different mode of actions. Due to the innate biomass recalcitrance, enzymatic hydrolysis normally starts with an initial fast rate of hydrolysis followed by a rapid decrease of rate toward the end of hydrolysis. With majority of literature studies focusing on the effect of key substrate characteristics on the initial rate or finalmore » yield of enzymatic hydrolysis, information about physicochemical structural changes of cellulosic substrates during enzymatic hydrolysis is still quite limited. Consequently, what slows down the reaction rate toward the end of hydrolysis is not well understood. Lastly, this review highlights recent advances in understanding the structural changes of cellulosic substrates during the hydrolysis process, to better understand the fundamental mechanisms of enzymatic hydrolysis.« less

Structure of Black Male Students Academic Achievement in Science

NASA Astrophysics Data System (ADS)

Rascoe, Barbara

Educational policies and practices have been largely unsuccessful in closing the achievement gap between Black and White students "Schwartz, 2001". This achievement gap is especially problematic for Black students in science "Maton, Hrabrowski, - Schmitt, 2000. Given the fact that the Black-White achievement gap is still an enigma, the purpose of this article is to address the Black female-Black male academic achievement gap in science majors. Addressing barriers that Black male students may experience as college science and engineering majors, this article presents marketing strategies relative to politics, emotional intelligence, and issues with respect to how science teaching, and Black male students' responses to it, are different. Many Black male students may need to experience a paradigm shift, which structures and enhances their science achievement. Paradigm shifts are necessary because exceptional academic ability and motivation are not enough to get Black males from their first year in a science, technology, education, and mathematics "STEM" major to a bachelor's degree in science and engineering. The conclusions focus on the balance of truth-slippery slopes concerning the confluence of science teachers' further ado and Black male students' theories, methods, and values that position their academic achievement in science and engineering majors.

Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation

PubMed Central

Velazquez Camacho, Oscar; Galan, Carmen; Swist-Rosowska, Kalina; Ching, Reagan; Gamalinda, Michael; Karabiber, Fethullah; De La Rosa-Velazquez, Inti; Engist, Bettina; Koschorz, Birgit; Shukeir, Nicholas; Onishi-Seebacher, Megumi; van de Nobelen, Suzanne; Jenuwein, Thomas

2017-01-01

The Suv39h1 and Suv39h2 histone lysine methyltransferases are hallmark enzymes at mammalian heterochromatin. We show here that the mouse Suv39h2 enzyme differs from Suv39h1 by containing an N-terminal basic domain that facilitates retention at mitotic chromatin and provides an additional affinity for major satellite repeat RNA. To analyze an RNA-dependent interaction with chromatin, we purified native nucleosomes from mouse ES cells and detect that Suv39h1 and Suv39h2 exclusively associate with poly-nucleosomes. This association was attenuated upon RNaseH incubation and entirely lost upon RNaseA digestion of native chromatin. Major satellite repeat transcripts remain chromatin-associated and have a secondary structure that favors RNA:DNA hybrid formation. Together, these data reveal an RNA-mediated mechanism for the stable chromatin interaction of the Suv39h KMT and suggest a function for major satellite non-coding RNA in the organization of an RNA-nucleosome scaffold as the underlying structure of mouse heterochromatin. DOI: http://dx.doi.org/10.7554/eLife.25293.001 PMID:28760199

Differences between immigrant and non-immigrant groups in the use of primary medical care; a systematic review

PubMed Central

Uiters, Ellen; Devillé, Walter; Foets, Marleen; Spreeuwenberg, Peter; Groenewegen, Peter P

2009-01-01

Background Studies on differences between immigrant and non-immigrant groups in health care utilization vary with respect to the extent and direction of differences in use. Therefore, our study aimed to provide a systematic overview of the existing research on differences in primary care utilization between immigrant groups and the majority population. Methods For this review PubMed, PsycInfo, Cinahl, Sociofile, Web of Science and Current Contents were consulted. Study selection and quality assessment was performed using a predefined protocol by 2 reviewers independently of each other. Only original, quantitative, peer-reviewed papers were taken into account. To account for this hierarchical structure, logistic multilevel analyses were performed to examine the extent to which differences are found across countries and immigrant groups. Differences in primary care use were related to study characteristics, strength of the primary care system and methodological quality. Results A total of 37 studies from 7 countries met all inclusion criteria. Remarkably, studies performed within the US more often reported a significant lower use among immigrant groups as compared to the majority population than the other countries. As studies scored higher on methodological quality, the likelihood of reporting significant differences increased. Adjustment for health status and use of culture-/language-adjusted procedures during the data collection were negatively related to reporting significant differences in the studies. Conclusion Our review underlined the need for careful design in studies of differences in health care use between immigrant groups and the majority population. The results from studies concerning differences between immigrant and the majority population in primary health care use performed within the US might be interpreted as a reflection of a weaker primary care system in the US compared to Europe and Canada. PMID:19426567

Insights into the structure and function of membrane-integrated processive glycosyltransferases

DOE PAGES

Bi, Yunchen; Hubbard, Caitlin; Purushotham, Pallinti; ...

2015-09-02

Complex carbohydrates perform essential functions in life, including energy storage, cell signaling, protein targeting, quality control, as well as supporting cell structure and stability. Extracellular polysaccharides (EPS) represent mainly structural polymers and are found in essentially all kingdoms of life. For example, EPS are important biofilm and capsule components in bacteria, represent major constituents in cell walls of fungi, algae, arthropods and plants, and modulate the extracellular matrix in vertebrates. Different mechanisms evolved by which EPS are synthesized. In this paper, we review the structures and functions of membrane-integrated processive glycosyltransferases (GTs) implicated in the synthesis and secretion of chitin,more » alginate, hyaluronan and poly-N-acetylglucosamine (PNAG).« less

Comparison of the morphology, chemical composition and microstructure of cryptocrystalline graphite and carbon black

NASA Astrophysics Data System (ADS)

Quan, Ying; Liu, Qinfu; Zhang, Shilong; Zhang, Shuai

2018-07-01

The structures of cryptocrystalline graphite (CG) and carbon black (CB) have been analyzed using scanning electron microscopy (SEM), transmission electron microscopy (TEM), organic elemental analysis (OEA), X-ray diffraction (XRD), RAMAN and high-resolution transmission electron microscopy (HRTEM). These results indicate that CG has the same elemental composition as CB, with carbon being the major element present. SL sample (CG with low graphitization degree) and CB exhibit similar microcrystalline structures. CG was shown to contain a layered graphitic structure that was significantly different to the primary spherical particles present in CB. It is proposed that these CG sheets may potentially be reduced and delaminated to afford multilayer graphene structures with improved material properties.

Insights into the structure and function of membrane-integrated processive glycosyltransferases

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

Bi, Yunchen; Hubbard, Caitlin; Purushotham, Pallinti

Complex carbohydrates perform essential functions in life, including energy storage, cell signaling, protein targeting, quality control, as well as supporting cell structure and stability. Extracellular polysaccharides (EPS) represent mainly structural polymers and are found in essentially all kingdoms of life. For example, EPS are important biofilm and capsule components in bacteria, represent major constituents in cell walls of fungi, algae, arthropods and plants, and modulate the extracellular matrix in vertebrates. Different mechanisms evolved by which EPS are synthesized. In this paper, we review the structures and functions of membrane-integrated processive glycosyltransferases (GTs) implicated in the synthesis and secretion of chitin,more » alginate, hyaluronan and poly-N-acetylglucosamine (PNAG).« less

The structure and evolution of angiosperm nuclear genomes.

PubMed

Bennetzen, J L

1998-04-01

Despite several decades of investigation, the organization of angiosperm genomes remained largely unknown until very recently. Data describing the sequence composition of large segments of genomes, covering hundreds of kilobases of contiguous sequence, have only become available in the past two years. Recent results indicate commonalities in the characteristics of many plant genomes, including in the structure of chromosomal components like telomeres and centromeres, and in the order and content of genes. Major differences between angiosperms have been associated mainly with repetitive DNAs, both gene families and mobile elements. Intriguing new studies have begun to characterize the dynamic three-dimensional structures of chromosomes and chromatin, and the relationship between genome structure and co-ordinated gene function.

Structure and performance of different DRG classification systems for neonatal medicine.

PubMed

Muldoon, J H

1999-01-01

There are a number of Diagnosis-Related Group (DRG) classification systems that have evolved over the past 2 decades, each with their own strengths and weaknesses. DRG systems are used for case-mix trending, utilization management and quality improvement, comparative reporting, prospective payment, and price negotiations. For any of these applications it is essential to know the accuracy with which the DRG system classifies patients, specifically for predicting resource use and also mortality. The objective of this study was to assess the adequacy of the three most commonly used DRG systems for neonatal patients-Medicare DRGs, All Patient Diagnosis-Related Groups (AP-DRGs), and All Patient Refined Diagnosis-Related Groups (APR-DRGs). A 2-part methodology is used to assess adequacy. The first part is a descriptive analysis that examines the structural characteristics of each system. This provides a framework for understanding the inherent strengths and weaknesses of each system and for interpreting their statistical performance. The second part examines the statistical performance of each system on a large nationally representative hospital database. The analysis identifies major differences in the structure and statistical performance of the three DRG systems for neonates. The Medicare DRGs are structurally the least developed and yield the poorest overall statistical performance (cost R2 = 0.292; mortality R2 = 0.083). The APR-DRGs are structurally the most developed and yield the best statistical performance (cost R2 = 0.627; mortality R2 = 0.416). The AP-DRGs are intermediate to Medicare DRGs and APR-DRGs, although closer to APR-DRGs (cost R2 = 0.507; mortality R2 = 0.304). An analysis of payment impacts and systematic effects identifies there are major systematic biases with the Medicare DRGs. At the patient level, there is substantial underpayment for surgical neonates, transferred-in neonates, neonates discharged to home health services, and neonates who die. In contrast, there is substantial overpayment for normal newborns. At the facility level, there is substantial underpayment for freestanding acute children's hospitals and major teaching general hospitals. There is overpayment for other urban general hospitals but this pattern varies by hospital size. There is very substantial overpayment for other rural hospitals. The AP-DRGs remove the majority of the systematic effects but significant biases remain. The APR-DRGs remove most of the systematic effects but some biases remain.

Specificity Rendering ‘Hot-Spots’ for Aurora Kinase Inhibitor Design: The Role of Non-Covalent Interactions and Conformational Transitions

PubMed Central

Badrinarayan, Preethi; Sastry, G. Narahari

2014-01-01

The present study examines the conformational transitions occurring among the major structural motifs of Aurora kinase (AK) concomitant with the DFG-flip and deciphers the role of non-covalent interactions in rendering specificity. Multiple sequence alignment, docking and structural analysis of a repertoire of 56 crystal structures of AK from Protein Data Bank (PDB) has been carried out. The crystal structures were systematically categorized based on the conformational disposition of the DFG-loop [in (DI) 42, out (DO) 5 and out-up (DOU) 9], G-loop [extended (GE) 53 and folded (GF) 3] and αC-helix [in (CI) 42 and out (CO) 14]. The overlapping subsets on categorization show the inter-dependency among structural motifs. Therefore, the four distinct possibilities a) 2W1C (DI, CI, GE) b) 3E5A (DI, CI, GF) c) 3DJ6 (DI, CO, GF) d) 3UNZ (DOU, CO, GF) along with their co-crystals and apo-forms were subjected to molecular dynamics simulations of 40 ns each to evaluate the variations of individual residues and their impact on forming interactions. The non-covalent interactions formed by the 157 AK co-crystals with different regions of the binding site were initially studied with the docked complexes and structure interaction fingerprints. The frequency of the most prominent interactions was gauged in the AK inhibitors from PDB and the four representative conformations during 40 ns. Based on this study, seven major non-covalent interactions and their complementary sites in AK capable of rendering specificity have been prioritized for the design of different classes of inhibitors. PMID:25485544

Structural differences within negative and depressive syndrome dimensions in schizophrenia, organic brain disease, and major depression: A confirmatory factor analysis of the positive and negative syndrome scale.

PubMed

Eisenberg, Daniel P; Aniskin, Dmitry B; White, Leonard; Stein, Judith A; Harvey, Philip D; Galynker, Igor I

2009-01-01

The emerging dimensional approach to classification and treatment of psychiatric disorders calls for better understanding of diagnosis-related variations in psychiatric syndromes and for proper validation of psychometric scales used for the evaluation of those syndromes. This study tested the hypothesis that negative and depressive syndromes as measured by the Positive and Negative Syndrome Scale (PANSS) are consistent across different diagnoses. We administered the PANSS to subjects with schizophrenia (n = 305), organic brain disease (OBD, n = 66) and major depressive disorder (MDD, n = 75). Confirmatory factor analysis (CFA) was used to establish if the PANSS items for negative symptoms and for depression fit the hypothesized factor structure and if the item factor loadings were similar among the diagnostic groups. The negative and depressive symptom subscales fit well according to a variety of fit indexes for all groups individually after some modest model modification. However, multisample modeling procedures indicated that the pattern of factor loadings was significantly different among the groups in most cases. The results of this study indicate diagnosis-related variations in the negative and depressive syndrome dimensions in schizophrenia, OBD and MDD. These results also validate limited use of the PANSS for evaluation of negative and depressive syndromes in disorders other than schizophrenia. Larger studies are warranted to further evaluate clinical and nosologic significance of diagnostic categories, dimensions and structures of psychiatric syndromes. 2009 S. Karger AG, Basel.

Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid diversification in structure and function.

PubMed

Zhu, Xinyu; Ma, Hong; Chen, Zhiduan

2011-03-09

Plants contain numerous Su(var)3-9 homologues (SUVH) and related (SUVR) genes, some of which await functional characterization. Although there have been studies on the evolution of plant Su(var)3-9 SET genes, a systematic evolutionary study including major land plant groups has not been reported. Large-scale phylogenetic and evolutionary analyses can help to elucidate the underlying molecular mechanisms and contribute to improve genome annotation. Putative orthologs of plant Su(var)3-9 SET protein sequences were retrieved from major representatives of land plants. A novel clustering that included most members analyzed, henceforth referred to as core Su(var)3-9 homologues and related (cSUVHR) gene clade, was identified as well as all orthologous groups previously identified. Our analysis showed that plant Su(var)3-9 SET proteins possessed a variety of domain organizations, and can be classified into five types and ten subtypes. Plant Su(var)3-9 SET genes also exhibit a wide range of gene structures among different paralogs within a family, even in the regions encoding conserved PreSET and SET domains. We also found that the majority of SUVH members were intronless and formed three subclades within the SUVH clade. A detailed phylogenetic analysis of the plant Su(var)3-9 SET genes was performed. A novel deep phylogenetic relationship including most plant Su(var)3-9 SET genes was identified. Additional domains such as SAR, ZnF_C2H2 and WIYLD were early integrated into primordial PreSET/SET/PostSET domain organization. At least three classes of gene structures had been formed before the divergence of Physcomitrella patens (moss) from other land plants. One or multiple retroposition events might have occurred among SUVH genes with the donor genes leading to the V-2 orthologous group. The structural differences among evolutionary groups of plant Su(var)3-9 SET genes with different functions were described, contributing to the design of further experimental studies.

Effect of Topology Structure on the Output Performance of an Automobile Exhaust Thermoelectric Generator

NASA Astrophysics Data System (ADS)

Fang, W.; Quan, S. H.; Xie, C. J.; Ran, B.; Li, X. L.; Wang, L.; Jiao, Y. T.; Xu, T. W.

2017-05-01

The majority of the thermal energy released in an automotive internal combustion cycle is exhausted as waste heat through the tail pipe. This paper describes an automobile exhaust thermoelectric generator (AETEG), designed to recycle automobile waste heat. A model of the output characteristics of each thermoelectric device was established by testing their open circuit voltage and internal resistance, and combining the output characteristics. To better describe the relationship, the physical model was transformed into a topological model. The connection matrix was used to describe the relationship between any two thermoelectric devices in the topological structure. Different topological structures produced different power outputs; their output power was maximised by using an iterative algorithm to optimize the series-parallel electrical topology structure. The experimental results have shown that the output power of the optimal topology structure increases by 18.18% and 29.35% versus that of a pure in-series or parallel topology, respectively, and by 10.08% versus a manually defined structure (based on user experience). The thermoelectric conversion device increased energy efficiency by 40% when compared with a traditional car.

Chemistry of MOS-LSI radiation hardening

NASA Technical Reports Server (NTRS)

Grunthaner, P.

1985-01-01

The objective of this task was to obtain chemical information on MOS test samples. Toward this end, high resolution X-ray photoemission spectroscopy (XPS) has been the primary techniques used to characterize the chemistry and structure of the SiO2/Si interface for a variety of MOS structures with differing degrees of susceptibility to damage by ionizing radiation. The major accomplishments of this program are: (1) the identification of a structurally distinct region of SiO2 in the near-interfacial region of thermal SiO2 on Si; (2) the identification in the near-interfacial region of SiO2 structural differences between radiation hard and soft gate oxides; (3) the direct observation of radiation-induced damage sites in thermal SiO2 with XPS using in situ electron stress; (4) the correlation of suboxide state distributions at the SiO2/Si interface with processing parameters and radiation susceptibility; (5) the development of a chemical mechanism for radiation-induced interface state generation in SiO2/Si structures; and (6) the development benign chemical profiling techniques which permit the investigation of oxide/semiconductor structures using surface sensitive electron spectroscopic techniques.

Cell structures caused by settling particles in turbulent Rayleigh-Bénard convection

NASA Astrophysics Data System (ADS)

Lee, Changhoon; Park, Sangro

2016-11-01

Turbulent thermal convection is an important phenomenon frequently found in nature and industrial processes, often with laden particles. In the last several decades, the vast majority of studies have addressed single phase convective flow with focus on the scaling relation of flow parameters associated with heat transfer. Particle-laden Rayleigh-Bénard convection, however, has not been sufficiently studied. In this study, modulation of cell structures by settling particles in turbulent Rayleigh-Bénard convection in a doubly periodic square channel is investigated using direct numerical simulation with a point particle approach. Flow parameters are fixed at Rayleigh number=106, Prandtl number=0.7, the aspect ratio=6, and Froude number=0.19. We report from the simulations that settling heavy particles modulate irregular large-scale thermal plume structures into organized polygonal cell structures. Different shapes of flow structures are obtained for different particle diameters and mass loadings. We found that polygonal cell structures arise due to asymmetric feedback force exerted by particles onto hot and cold plumes. Increasing the number of particles augments the asymmetry and the polygonal cell structures become smaller, eventually going to the hexagonal structures.

Structural basis of unique ligand specificity of KAI2-like protein from parasitic weed Striga hermonthica.

PubMed

Xu, Yuqun; Miyakawa, Takuya; Nakamura, Hidemitsu; Nakamura, Akira; Imamura, Yusaku; Asami, Tadao; Tanokura, Masaru

2016-08-10

The perception of two plant germination inducers, karrikins and strigolactones, are mediated by the proteins KAI2 and D14. Recently, KAI2-type proteins from parasitic weeds, which are possibly related to seed germination induced by strigolactone, have been classified into three clades characterized by different responses to karrikin/strigolactone. Here we characterized a karrikin-binding protein in Striga (ShKAI2iB) that belongs to intermediate-evolving KAI2 and provided the structural bases for its karrikin-binding specificity. Binding assays showed that ShKAI2iB bound karrikins but not strigolactone, differing from other KAI2 and D14. The crystal structures of ShKAI2iB and ShKAI2iB-karrikin complex revealed obvious structural differences in a helix located at the entry of its ligand-binding cavity. This results in a smaller closed pocket, which is also the major cause of ShKAI2iB's specificity of binding karrikin. Our structural study also revealed that a few non-conserved amino acids led to the distinct ligand-binding profile of ShKAI2iB, suggesting that the evolution of KAI2 resulted in its diverse functions.

Differences in short-term memory span of social sciences, science and engineering, and business majors

NASA Astrophysics Data System (ADS)

Khan, Naeem Ullah

This study investigated the difference in the short-term memory span of students of three major groups, namely Social Sciences, Science and Engineering, and Business. This study was designed to answer the following two questions: (1) Is there a difference between short-term memory span, measured by digit span, among the students in or intended for Social Sciences, Science and Engineering, and Business majors? (2) Is there a difference of short-term memory span, measured by word span, among students in or intended for Social Sciences, Science and Engineering, and Business majors? For answering these two questions, inferential and descriptive statistics were used. Analysis of Variance (ANOVA) was used to compare the means of the scores of digit span and word span among the three major groups. The means of digit span and word span among the three groups were compared to find out if a statistically significant difference existed among them or not. The observations were recorded at the level of significance at alpha = .05, and highly significant at alpha = .01. The answer to the first question is yes. The results of this study showed a statistically significant difference in the means of the digit span of the three major groups of students in or intended for Social Sciences, Science and Engineering, and Business. The mean scaled score for digit span was 12.88 for Social Sciences, 14.27 for Science and Engineering, and 15.33 for Business majors, respectively. The means of the free recalls word span of the three groups was 7.23 for Social Sciences, 7.89 for Science and Engineering, and 7.12 for Business majors, respectively. No significant difference was observed in the means of the word span of the three groups. In general observations, it is noted that students want to stay in the subjects or majors in which they can perform well or feel comfortable. In addition to this, students are screened in the school system due to levels of performance or selection pressure. Students' academic performances are dependent on their academic environment and on their inherited construct of short-term and long-term memory span. The use of the memory in certain majors, such as Science and Engineering and Business, are more demanding as compared to Social Science majors. For example, for Science and Engineering majors, students need to memorize complex structures and also need to keep larger information at a stretch in their short-term memory to incorporate it into incoming and outgoing information. Of the other memory related constructs, the present study examined only the short-term memory of the students of different majors, and it was found that the students of the Social Sciences had a shorter digit span as compared to the Science and Engineering and Business majors. Business major students had the largest digit span as compared to the Social Sciences and Science and Engineering majors. This supports the idea that memory construct plays a role in the selection of student majors.

Comparison of benthic bacterial community composition in nine streams

Treesearch

Xueqing Gao; Ola A. Olapade; Laura G. Leff

2005-01-01

In this study, the abundance of major bacterial taxa (based on fluorescent in situ hybridization, FISH) and the structure of the bacterial community (based on denaturing gradient gel electrophoresis, DGGE) were determined in the benthos of 9 streams in the southeastern and midwestern United States and related to differences in environmental...

Camparison of benthic bacterial community composition in nine streams

Treesearch

Xuqing Gao; Ola A. Olapade; Laura G. Leff

2005-01-01

In this study, the abundance of major bacterial taxa (based on fluorescent in situ hybridization, FISH) and the structure of the bacterial community (based on denaturing gradient gel electrophoresis, DGGE) were determined in the benthos of 9 streams in the southeastern and midwestern United States and related to differences in environmental conditions. Taxa examined...

A Short Note on Rules and Higher Order Rules.

ERIC Educational Resources Information Center

Scandura, Joseph M.

This brief paper argues that structural analysis--an extended form of cognitive task analysis--demonstrates that both domain dependent and domain independent knowledge can be derived from specific content domains. It is noted that the major difference between the two is that lower order rules (specific knowledge) are derived directly from specific…

Introduction to Film.

ERIC Educational Resources Information Center

Burns, Gary

There are numerous ways to structure the introduction to film course so as to meet the needs of the different types of students who typically enroll. Assuming there is no production component in the course, the teacher is left with two major approaches to choose from--historical and aesthetic. The units in the course will typically be built around…

Advanced Bridge Capacity and Structural Integrity Assessment Methodology

DTIC Science & Technology

2013-03-01

following major drawbacks to working stress design: • inability to account for variability of loads and resistance • lack of knowledge of the level of...CERL TR-13-3 81 Early inclinometers were simple pendulums or tubes of water with buckets on each end where the difference in water level between to

Info/Information Theory: Speakers Choose Shorter Words in Predictive Contexts

ERIC Educational Resources Information Center

Mahowald, Kyle; Fedorenko, Evelina; Piantadosi, Steven T.; Gibson, Edward

2013-01-01

A major open question in natural language research is the role of communicative efficiency in the origin and on-line processing of language structures. Here, we use word pairs like "chimp/chimpanzee", which differ in length but have nearly identical meanings, to investigate the communicative properties of lexical systems and the communicative…

HARWI---A hard x-ray wiggler beam at DORIS

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

Graeff, W.; Bittner, L.; Brefeld, W.

1989-07-01

The construction of the wiggler W2 at DORIS is described together with the major components of the beamline. Details are given on the assembly and performance of the magnet structure. Three different monochromators are used in the beamline alternatively. One of them, a Laue--Bragg-type monochromator is described in more detail.

Effect of Sunlight on the Divergence of Community Structure of Fecal Bacteria in Cowpats Collected from Three Different Farms

EPA Science Inventory

Fecal pollution of environmental waters is a major concern for the general public because exposure to fecal-associated pathogens can have severe impacts on human health. In the last few years, numerous metagenomic studies applied next generation sequencing to understand the shift...

Clinical Presentation and Course of Depression in Youth: Does Onset in Childhood Differ from Onset in Adolescence?

ERIC Educational Resources Information Center

Birmaher, Boris; Williamson, Douglas E.; Dahl, Ronald E.; Axelson, David A.; Kaufman, Joan; Dorn, Lorah D.; Ryan, Neal D.

2004-01-01

Objective: To simultaneously and prospectively compare the clinical presentation, course, and parental psychiatric history between children and adolescents with major depressive disorder. Method: A group of prepubertal children (n = 46) and postpubertal adolescents (n = 22) were assessed with structured interviews for psychopathology and parental…

Divergence and Convergence within Greek Library Education: An Applied vs a Theoretical Approach

ERIC Educational Resources Information Center

Kyriaki-Manessi, Daphne

2008-01-01

This paper explores the differences and similarities of the three library schools educating librarians and information professionals in Greece. The structure of higher education in Greece has recently undergone major changes (2002) integrating technological institutions and universities under one umbrella that of higher education. As a result,…

The Effect of Overtly Categorizing Music on Preference for Popular Music Styles.

ERIC Educational Resources Information Center

Brittin, Ruth V.

1991-01-01

Presents results of a study that explored the effect of overt categorization on musical preference. Found no difference in choices of nonmusic majors when choices were structured as stipulated, unstipulated, or free form categories. Finds musical experience and gender affected preferences for pop and jazz, but not for rock music. (DK)

New Structures and Approaches for Teacher Preparation: Do They Make a Difference in Teacher Retention?

ERIC Educational Resources Information Center

Harris, Steven A.; Camp, William E.; Adkison, Judith

Low initial employment rates and high attrition among teachers are factors recognized as major contributors to the national teacher shortage. This research compared the effectiveness of three teacher preparation methods used in Texas: alternative certification programs (ACPs), Centers for Professional Development and Technology (CPDTs), and…

Clarifying the Conceptualization of Indicators within Different Models

ERIC Educational Resources Information Center

Wang, Jue; Engelhard, George, Jr.; Lu, Zhenqiu

2014-01-01

The authors of the focus article in this issue have emphasized the continuing confusion among some researchers regarding various indicators used in structural equation models (SEMs). Their major claim is that causal indicators are not inherently unstable, and even if they are unstable they are at least not more unstable than other types of…

Canadian Building Digests 1-100 (With Index).

ERIC Educational Resources Information Center

National Research Council of Canada, Ottawa (Ontario). Div. of Building Research.

One hundred different topics related to the technical aspects of building design and construction are discussed. The major areas of discussion are--(1) the effects of climate on building materials, (2) site and soil analysis, (3) acoustical and thermal design considerations, (4) fire and building design, (5) structural analysis and design, and (6)…

An Investigation of Lebanese G7-12 Students' Misconceptions and Difficulties in Genetics and Their Genetics Literacy

ERIC Educational Resources Information Center

Osman, Enja; BouJaoude, Saouma; Hamdan, Hiba

2017-01-01

Lebanese educators claim that middle and secondary school students exhibit poor understanding of genetics due to misconceptions and difficulties that hinder progression in conceptual understanding of major genetics concepts and phenomena across different grade levels. They attributed these problems to Lebanon's ill-structured genetics curriculum…

Bark And Its Possible Uses

Treesearch

J. M. Harkin; J. W. Rowe

1971-01-01

What to do with bark is a major question facing the wood conversion industries. Optimum utilization of bark residues demands appreciation of the complexity of bark and the extreme variation in chemical and physical properties between barks of different wood species. This report discusses bark structure, past and present utilization, and methods of upgrading bark both...

On "the Nurse Was a Doctor."

ERIC Educational Resources Information Center

Blaubergs, Maija S.

In this paper, the structure and the use of language are postulated as socializing agents influencing sex-role learning in three major ways: (1) sex differences occur in language use and parallel sex-role stereotypes; (2) the language that is addressed to children is usually the language of socialization which instructs the child what to do,…

Ti-doped ZnO Thin Films Prepared at Different Ambient Conditions: Electronic Structures and Magnetic Properties

PubMed Central

Yong, Zhihua; Liu, Tao; Uruga, Tomoya; Tanida, Hajime; Qi, Dongchen; Rusydi, Andrivo; Wee, Andrew T. S.

2010-01-01

We present a comprehensive study on Ti-doped ZnO thin films using X-ray Absorption Fine Structure (XAFS) spectroscopy. Ti K edge XAFS spectra were measured to study the electronic and chemical properties of Ti ions in the thin films grown under different ambient atmospheres. A strong dependence of Ti speciation, composition, and local structures upon the ambient conditions was observed. The XAFS results suggest a major tetrahedral coordination and a 4+ valence state. The sample grown in a mixture of 80% Ar and 20% O2 shows a portion of precipitates with higher coordination. A large distortion was observed by the Ti substitution in the ZnO lattice. Interestingly, the film prepared in 80% Ar, 20% O2 shows the largest saturation magnetic moment of 0.827 ± 0.013 µB/Ti.

Statistical learning and language acquisition

PubMed Central

Romberg, Alexa R.; Saffran, Jenny R.

2011-01-01

Human learners, including infants, are highly sensitive to structure in their environment. Statistical learning refers to the process of extracting this structure. A major question in language acquisition in the past few decades has been the extent to which infants use statistical learning mechanisms to acquire their native language. There have been many demonstrations showing infants’ ability to extract structures in linguistic input, such as the transitional probability between adjacent elements. This paper reviews current research on how statistical learning contributes to language acquisition. Current research is extending the initial findings of infants’ sensitivity to basic statistical information in many different directions, including investigating how infants represent regularities, learn about different levels of language, and integrate information across situations. These current directions emphasize studying statistical language learning in context: within language, within the infant learner, and within the environment as a whole. PMID:21666883

X-ray diffraction study of nanocrystalline and amorphous structure within major and minor ampullate dragline spider silks

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

Sampath, Sujatha; Isdebski, Thomas; Jenkins, Janelle E.

Synchrotron X-ray micro-diffraction experiments were carried out on Nephila clavipes (NC) and Argiope aurantia (AA) major (MA) and minor ampullate (MiA) fibers that make up dragline spider silk. The diffraction patterns show a semi-crystalline structure with {beta}-poly(L-alanine) nanocrystallites embedded in a partially oriented amorphous matrix. A superlattice reflection 'S' diffraction ring is observed, which corresponds to a crystalline component larger in size and is poorly oriented, when compared to the {beta}-poly(L-alanine) nanocrystallites that are commonly observed in dragline spider silks. Crystallite size, crystallinity and orientation about the fiber axis have been determined from the wide-angle X-ray diffraction (WAXD) patterns. Inmore » both NC and AA, the MiA silks are found to be more highly crystalline, when compared with the corresponding MA silks. Detailed analysis on the amorphous matrix shows considerable differences in the degree of order of the oriented amorphous component between the different silks studied and may play a crucial role in determining the mechanical properties of the silks.« less

Drivers of Macrofungi Community Structure Differ between Soil and Rotten-Wood Substrates in a Temperate Mountain Forest in China

PubMed Central

Chen, Yun; Svenning, Jens-Christian; Wang, Xueying; Cao, Ruofan; Yuan, Zhiliang; Ye, Yongzhong

2018-01-01

The effects of environmental and dispersal processes on macrofungi community assembly remain unclear. Further, it is not well understood if community assembly differs for different functional guilds of macrofungi, e.g., soil and rotten-wood macrofungi. In this study, using 2433 macrofungi sporocarps belonging to 217 species located within a forest dynamics plot in temperate mountain forest (China), we examined the explanatory power of topography, spatial eigenvectors (representing unknown spatial processes, e.g., dispersal), plant community, and light availability for local spatial variation in the macrofungi community through variance partitioning and partial least squares path modeling. We found spatial eigenvectors and light as the most important factors for explaining species richness and composition of macrofungi. Light was negatively correlated with species richness of macrofungi. Furthermore, species richness and composition of soil macrofungi were best explained by light, and species richness and composition of rotten-wood macrofungi were best explained by spatial eigenvectors. Woody plant community structure was not an important factor for species richness and composition of macrofungi. Our findings suggest that spatial processes, perhaps dispersal limitation, and light availability were the most important factors affecting macrofungi community in temperate deciduous broad-leaved forest. Major differences in influencing factors between soil and rotten-wood macrofungi were observed, with light as the major driver for soil macrofungi and unknown spatial processes as the major driver for rotten-wood macrofungi. These findings shed new light to the processes shaping community assembly in macrofungi in temperate deciduous broad-leaved forest and point to the potential importance of both intrinsic dynamics, such as dispersal, and external forcing, such as forest dynamics, via its effect on light availability. PMID:29410660

The Complete Set of Genes Encoding Major Intrinsic Proteins in Arabidopsis Provides a Framework for a New Nomenclature for Major Intrinsic Proteins in Plants1

PubMed Central

Johanson, Urban; Karlsson, Maria; Johansson, Ingela; Gustavsson, Sofia; Sjövall, Sara; Fraysse, Laure; Weig, Alfons R.; Kjellbom, Per

2001-01-01

Major intrinsic proteins (MIPs) facilitate the passive transport of small polar molecules across membranes. MIPs constitute a very old family of proteins and different forms have been found in all kinds of living organisms, including bacteria, fungi, animals, and plants. In the genomic sequence of Arabidopsis, we have identified 35 different MIP-encoding genes. Based on sequence similarity, these 35 proteins are divided into four different subfamilies: plasma membrane intrinsic proteins, tonoplast intrinsic proteins, NOD26-like intrinsic proteins also called NOD26-like MIPs, and the recently discovered small basic intrinsic proteins. In Arabidopsis, there are 13 plasma membrane intrinsic proteins, 10 tonoplast intrinsic proteins, nine NOD26-like intrinsic proteins, and three small basic intrinsic proteins. The gene structure in general is conserved within each subfamily, although there is a tendency to lose introns. Based on phylogenetic comparisons of maize (Zea mays) and Arabidopsis MIPs (AtMIPs), it is argued that the general intron patterns in the subfamilies were formed before the split of monocotyledons and dicotyledons. Although the gene structure is unique for each subfamily, there is a common pattern in how transmembrane helices are encoded on the exons in three of the subfamilies. The nomenclature for plant MIPs varies widely between different species but also between subfamilies in the same species. Based on the phylogeny of all AtMIPs, a new and more consistent nomenclature is proposed. The complete set of AtMIPs, together with the new nomenclature, will facilitate the isolation, classification, and labeling of plant MIPs from other species. PMID:11500536

Type II Heat-labile Enterotoxins: Structure, Function, and Immunomofdulatory Properties

PubMed Central

Hajishengallis, George; Connell, Terry D.

2012-01-01

The heat-labile enterotoxins (HLTs) of Escherichia coli and Vibrio cholerae are classified into two major types on the basis of genetic, biochemical, and immunological properties. Type I and Type II HLT have been intensively studied for their exceptionally strong adjuvant activities. Despite general structural similarities, these molecules, in intact or derivative (non-toxic) forms, display notable differences in their mode of immunomodulatory action. The molecular basis of these differences has remained largely uncharacterized until recently. This review focuses on the Type II HLTs and their immunomodulatory properties which depend largely on interactions with unique gangliosides and Toll-like receptors that are not utilized by the Type I HLTs. PMID:23137790

Characterization of the myoepithelial cells in the major salivary glands of the fruit bat Artibeus jamaicensis.

PubMed

Guerrero-Hernández, Julio; Moreno-Mendoza, Norma

2016-08-01

Bats constitute one of the most numerous mammalian species. Bats have a wide range of dietary habits and include carnivorous, haematophagous, insectivorous, frugivorous and nectivorous species. The salivary glands of these species have been of particular research interest due to their structural variability among chiropterans with different types of diets. Myoepithelial cells (MECs), which support and facilitate the expulsion of saliva from the secretory portions of salivary glands, are very important for their function; however, this cell type has not been extensively studied in the salivary glands of bats. In this study, we characterized the MECs in the major salivary glands of the fruit bat Artibeus jamaicensis. Herein, we describe the morphology of the parotid, submandibular and sublingual glands of A. jamaicensis at the light- and electro-microscopic level and the distribution of MECs in these glands, as defined by their expression of smooth-muscle markers such as α-smooth muscle actin (SMAα) and desmin, and of epithelial cell markers, such as KRT14. We found that the anatomical locations of the major salivary glands in this bat species are similar to those of humans, except that the bat sublingual gland appears to be unique, extending to join the contralateral homologous gland. Morphologically, the parotid gland has the characteristics of a mixed-secretory gland, whereas the submandibular and sublingual glands were identified as mucous-secretory glands. MECs positive for SMAα, KRT14 and desmin were found in all of the structural components of the three glands, except in their excretory ducts. Desmin is expressed at a lower level in the parotid gland than in the other glands. Our results suggest that the major salivary glands of A. jamaicensis, although anatomically and structurally similar to those of humans, play different physiological roles that can be attributed to the dietary habits of this species. © 2016 Anatomical Society.

Structural, functional and evolutionary characterization of major drought transcription factors families in maize

NASA Astrophysics Data System (ADS)

Mittal, Shikha; Banduni, Pooja; Mallikarjuna, Mallana G.; Rao, Atmakuri R.; Jain, Prashant A.; Dash, Prasanta K.; Thirunavukkarasu, Nepolean

2018-05-01

Drought is one of the major threats to maize production. In order to improve the production and to breed tolerant hybrids, understanding the genes and regulatory mechanisms during drought stress is important. Transcription factors (TFs) play a major role in gene regulation and many TFs have been identified in response to drought stress. In our experiment, a set of 15 major TF families comprising 1436 genes was structurally and functionally characterized using in-silico tools and a gene expression assay. All 1436 genes were mapped on 10 chromosome of maize. The functional annotation indicated the involvement of these genes in ABA signaling, ROS scavenging, photosynthesis, stomatal regulation, and sucrose metabolism. Duplication was identified as the primary force in divergence and expansion of TF families. Phylogenetic relationship was developed individually for each TF family as well as combined TF families. Phylogenetic analysis grouped the TF family of genes into TF-specific and mixed groups. Phylogenetic analysis of genes belonging to various TF families suggested that the origin of TFs occurred in the lineage of maize evolution. Gene structure analysis revealed that more number of genes were intron-rich as compared to intronless genes. Drought-responsive CRE’s such as ABREA, ABREB, DRE1 and DRECRTCOREAT have been identified. Expression and interaction analyses identified leaf-specific bZIP TF, GRMZM2G140355, as a potential contributor toward drought tolerance in maize. We also analyzed protein-protein interaction network of 269 drought-responsive genes belonging to different drought-related TFs. The information generated on structural and functional characteristics, expression and interaction of the drought-related TF families will be useful to decipher the drought tolerance mechanisms and to derive drought-tolerant genotypes in maize.

Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species.

PubMed

Oono, Ryoko; Lutzoni, François; Arnold, A Elizabeth; Kaye, Laurel; U'Ren, Jana M; May, Georgiana; Carbone, Ignazio

2014-08-01

• Fungal endophytes comprise one of the most ubiquitous groups of plant symbionts, inhabiting healthy leaves and stems of all major lineages of plants. Together, they comprise immense species richness, but little is known about the fundamental processes that generate their diversity. Exploration of their population structure is needed, especially with regard to geographic distributions and host affiliations.• We take a multilocus approach to examine genetic variation within and among populations of Lophodermium australe, an endophytic fungus commonly associated with healthy foliage of pines in the southeastern United States. Sampling focused on two pine species ranging from montane to coastal regions of North Carolina and Virginia.• Our sampling revealed two genetically distinct groups within Lophodermium australe. Our analysis detected less than one migrant per generation between them, indicating that they are distinct species. The species comprising the majority of isolates (major species) demonstrated a panmictic structure, whereas the species comprising the minority of isolates (cryptic species) demonstrated isolation by distance. Distantly related pine species hosted the same Lophodermium species, and host species did not influence genetic structure.• We present the first evidence for isolation by distance in a foliar fungal endophyte that is horizontally transmitted. Cryptic species may be common among microbial symbionts and are important to delimit when exploring their genetic structure and microevolutionary processes. The hyperdiversity of endophytic fungi may be explained in part by cryptic species without apparent ecological and morphological differences as well as genetic diversification within rare fungal species across large spatial scales. © 2014 Botanical Society of America, Inc.

Neural correlates of attention biases of people with major depressive disorder: a voxel-based morphometric study.

PubMed

Leung, K-K; Lee, T M C; Wong, M M C; Li, L S W; Yip, P S F; Khong, P-L

2009-07-01

Patients with major depressive disorder are found to show selective attention biases towards mood-congruent information. Although previous studies have identified various structural changes in the brains of these patients, it remains unclear whether the structural abnormalities are associated with these attention biases. In this study, we used voxel-based morphometry (VBM) to explore the structural correlates of attention biases towards depression-related stimuli. Seventeen female patients with major depressive disorder and 17 female healthy controls, matched on age and intelligence, underwent magnetic resonance imaging (MRI). They also performed positive-priming (PP) and negative-priming (NP) tasks involving neutral and negative words that assessed selective attention biases. The reaction time (RT) to a target word that had been attended to or ignored in a preceding trial was measured on the PP and NP tasks respectively. The structural differences between the two groups were correlated with the indexes of attention biases towards the negative words. The enhanced facilitation of attention to stimuli in the PP task by the negative valence was only found in the depressed patients, not in the healthy controls. Such attention biases towards negative stimuli were found to be associated with reduced gray-matter concentration (GMC) in the right superior frontal gyrus, the right anterior cingulate gyrus and the right fusiform gyrus. No differential effect in inhibition of attention towards negative stimuli in the NP task was found between the depressed patients and the healthy controls. Specific structural abnormalities in depression are associated with their attention biases towards mood-congruent information.

Vortex dynamics and wall shear stress behaviour associated with an elliptic jet impinging upon a flat plate

NASA Astrophysics Data System (ADS)

Long, J.; New, T. H.

2016-07-01

Vortical structures and dynamics of a Re h = 2100 elliptic jet impinging upon a flat plate were studied at H/ d h = 1, 2 and 4 jet-to-plate separation distances. Flow investigations were conducted along both its major and minor planes using laser-induced fluorescence and digital particle image velocimetry techniques. Results show that the impingement process along the major plane largely consists of primary jet ring-vortex and wall-separated secondary vortex formations, where they subsequently separate from the flat plate at smaller H/ d h = 1 and 2 separation distances. Key vortex formation locations occur closer to the impingement point as the separation distance increases. Interestingly, braid vortices and rib structures begin to take part in the impingement process at H/ d h = 4 and wave instabilities dominate the flow field. In contrast, significantly more coherent primary and secondary vortices with physically larger vortex core sizes and higher vortex strengths are observed along the minor plane, with no signs of braid vortices and rib structures. Lastly, influences of these different flow dynamics on the major and minor plane instantaneous and mean skin friction coefficient levels are investigated to shed light on the effects of separation distance on the wall shear stress distributions.

Structural characterization of the lipids A of three Bordetella bronchiseptica strains: variability of fatty acid substitution.

PubMed Central

Zarrouk, H; Karibian, D; Bodie, S; Perry, M B; Richards, J C; Caroff, M

1997-01-01

The structures of lipids A isolated from the lipopolysaccharides (LPSs; endotoxins) of three different pathogenic Bordetella bronchiseptica strains were investigated by chemical composition and methylation analysis, gas chromatography-mass spectrometry, nuclear magnetic resonance, and plasma desorption mass spectrometry (PDMS). The analyses revealed that the LPSs contain the classical lipid A bisphosphorylated beta-(1-->6)-linked D-glucosamine disaccharide with hydroxytetradecanoic acid in amide linkages. Their structures differ from that of the lipid A of Bordetella pertussis endotoxin by the replacement of hydroxydecanoic acid on the C-3 position with hydroxydodecanoic acid or dodecanoic acid and the presence of variable amounts of hexadecanoic acid. The dodecanoic acid is the first nonhydroxylated fatty acid to be found directly linked to a lipid A glucosamine. The lipids A were heterogeneous and composed of one to three major and several minor molecular species. The fatty acids in ester linkage were localized by PDMS of chemically modified lipids A. B. pertussis lipids A are usually hypoacylated with respect to those of enterobacterial lipids A. However, one of the three B. bronchiseptica strains had a major hexaacylated molecular species. C-4 and C-6' hydroxyl groups of the backbone disaccharide were unsubstituted, the latter being the proposed attachment site of the polysaccharide. The structural variability seen in these three lipids A was unusual for a single species and may have consequences for the pathogenicity of this Bordetella species. PMID:9171426

Structural characterization of the lipids A of three Bordetella bronchiseptica strains: variability of fatty acid substitution.

PubMed

Zarrouk, H; Karibian, D; Bodie, S; Perry, M B; Richards, J C; Caroff, M

1997-06-01

The structures of lipids A isolated from the lipopolysaccharides (LPSs; endotoxins) of three different pathogenic Bordetella bronchiseptica strains were investigated by chemical composition and methylation analysis, gas chromatography-mass spectrometry, nuclear magnetic resonance, and plasma desorption mass spectrometry (PDMS). The analyses revealed that the LPSs contain the classical lipid A bisphosphorylated beta-(1-->6)-linked D-glucosamine disaccharide with hydroxytetradecanoic acid in amide linkages. Their structures differ from that of the lipid A of Bordetella pertussis endotoxin by the replacement of hydroxydecanoic acid on the C-3 position with hydroxydodecanoic acid or dodecanoic acid and the presence of variable amounts of hexadecanoic acid. The dodecanoic acid is the first nonhydroxylated fatty acid to be found directly linked to a lipid A glucosamine. The lipids A were heterogeneous and composed of one to three major and several minor molecular species. The fatty acids in ester linkage were localized by PDMS of chemically modified lipids A. B. pertussis lipids A are usually hypoacylated with respect to those of enterobacterial lipids A. However, one of the three B. bronchiseptica strains had a major hexaacylated molecular species. C-4 and C-6' hydroxyl groups of the backbone disaccharide were unsubstituted, the latter being the proposed attachment site of the polysaccharide. The structural variability seen in these three lipids A was unusual for a single species and may have consequences for the pathogenicity of this Bordetella species.

A tale of two seas: contrasting patterns of population structure in the small-spotted catshark across Europe

PubMed Central

Gubili, Chrysoula; Sims, David W.; Veríssimo, Ana; Domenici, Paolo; Ellis, Jim; Grigoriou, Panagiotis; Johnson, Andrew F.; McHugh, Matthew; Neat, Francis; Satta, Andrea; Scarcella, Giuseppe; Serra-Pereira, Bárbara; Soldo, Alen; Genner, Martin J.; Griffiths, Andrew M.

2014-01-01

Elasmobranchs represent important components of marine ecosystems, but they can be vulnerable to overexploitation. This has driven investigations into the population genetic structure of large-bodied pelagic sharks, but relatively little is known of population structure in smaller demersal taxa, which are perhaps more representative of the biodiversity of the group. This study explores spatial population genetic structure of the small-spotted catshark (Scyliorhinus canicula), across European seas. The results show significant genetic differences among most of the Mediterranean sample collections, but no significant structure among Atlantic shelf areas. The data suggest the Mediterranean populations are likely to have persisted in a stable and structured environment during Pleistocene sea-level changes. Conversely, the Northeast Atlantic populations would have experienced major changes in habitat availability during glacial cycles, driving patterns of population reduction and expansion. The data also provide evidence of male-biased dispersal and female philopatry over large spatial scales, implying complex sex-determined differences in the behaviour of elasmobranchs. On the basis of this evidence, we suggest that patterns of connectivity are determined by trends of past habitat stability that provides opportunity for local adaptation in species exhibiting philopatric behaviour, implying that resilience of populations to fisheries and other stressors may differ across the range of species. PMID:26064555

Spatial and Temporal Variations of the K/T Boundary Record: Implications Concerning Possible Megaseiche in the Reworking Processes

NASA Astrophysics Data System (ADS)

Maurrasse, F. J.; Lamolda, M. A.

2004-05-01

Major physical disruptions characterize the sedimentary record of the K/T boundary (KTB) layer from different sites in the Southern Peninsula of Haiti as well as in diverse areas of the world. These disturbances are most important within the vicinity of the crater at Chicxulub, Yucatan, Mexico, and 65 million years ago that can be chronologically correlated with the bolide impact postulated by Alvarez et al (1981). At all sites the KTB layer shows spatial and temporal differences even within short distances, and the complexity of its characteristic signals includes serious micropaleontological inconsistencies with mixed biotic assemblages that perpetuate divergence of interpretations, thereby they raise doubts on the timing and real causal mechanisms of the biotic turnover that characterizes the boundary. Indeed, often the biostratigraphic signals are difficult to resolve because of hiatuses, or sediments are highly reworked, and distinct taxonomic successions are not clearly defined. Well defined as well as cryptic primary sedimentary structures within the boundary layer are constant at all outcrops, and they indicate complex, multiphase, subaqueous flow processes that affected sedimentation of the KTB layer at different times. The structures are known to characterize oscillatory wave processes that affect cohesionless sediments, and such water motion is only known to be associated with seiche as a modern analog that may have generated the amalgamation recorded at the KTB layer. We believe that "Megaseiche" associated with the KT impact event and its subsequent effects provides a plausible unifying mechanism to explain how various levels of the water column in different large basins can oscillate to develop the structures observed. Because of the magnitude of the bolide impact that generated initial tsunamis and large seismic waves worldwide, megaseiches of different frequencies and nodal modes must have developed in the oceans worldwide to leave different signatures in the mixing pattern. Most importantly, the heterogeneity must have been further intensified in subsequent times when more localized megaseiches developed in independent basins at different times during major crustal readjustment. These phenomena may explain the heterogeneity of patterns and apparent irreconcilable discrepancies observed at KTB sites worldwide, as the structures represent a record of water movement and resuspension of sediment of different intensities and at different timesat certain locations. As observed in smaller-scale modern seiche, various oscillatory modes controlled the duration and attenuation of the water movement, the magnitude of bottom traction and resuspension that led to complex sedimentary structures and reworking patterns of the sediments and microfossils.

Environmental drivers of differences in microbial community structure in crude oil reservoirs across a methanogenic gradient

USGS Publications Warehouse

Shelton, Jenna L.; Akob, Denise M.; McIntosh, Jennifer C.; Fierer, Noah; Spear, John R.; Warwick, Peter D.; McCray, John E.

2016-01-01

Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total Archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil) geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow, up-dip wells was different than the 17 deeper, down-dip wells. Also, the 17 down-dip wells had statistically similar microbial communities despite significant changes in environmental parameters between oil fields. Together, this implies that no single microbial population is a reliable indicator of a reservoir's ability to degrade crude oil to methane, and that geochemistry may be a more important indicator for selecting a reservoir suitable for microbial enhancement of natural gas generation.

Identification and classification of structural soil conservation measures based on very high resolution stereo satellite data.

PubMed

Eckert, Sandra; Tesfay Ghebremicael, Selamawit; Hurni, Hans; Kohler, Thomas

2017-05-15

Land degradation affects large areas of land around the globe, with grave consequences for those living off the land. Major efforts are being made to implement soil and water conservation measures that counteract soil erosion and help secure vital ecosystem services. However, where and to what extent such measures have been implemented is often not well documented. Knowledge about this could help to identify areas where soil and water conservation measures are successfully supporting sustainable land management, as well as areas requiring urgent rehabilitation of conservation structures such as terraces and bunds. This study explores the potential of the latest satellite-based remote sensing technology for use in assessing and monitoring the extent of existing soil and water conservation structures. We used a set of very high resolution stereo Geoeye-1 satellite data, from which we derived a detailed digital surface model as well as a set of other spectral, terrain, texture, and filtered information layers. We developed and applied an object-based classification approach, working on two segmentation levels. On the coarser level, the aim was to delimit certain landscape zones. Information about these landscape zones is useful in distinguishing different types of soil and water conservation structures, as each zone contains certain specific types of structures. On the finer level, the goal was to extract and identify different types of linear soil and water conservation structures. The classification rules were based mainly on spectral, textural, shape, and topographic properties, and included object relationships. This approach enabled us to identify and separate from other classes the majority (78.5%) of terraces and bunds, as well as most hillside terraces (81.25%). Omission and commission errors are similar to those obtained by the few existing studies focusing on the same research objective but using different types of remotely sensed data. Based on our results, we estimate that the construction of the conservation structures in our study area in Eritrea required over 300,000 person-days of work, which underlines the huge efforts involved in soil and water conservation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cesium vacancy ordering in phase-separated C s x F e 2 - y S e 2

DOE PAGES

Taddei, Keith M.; Sturza, M.; Chung, Duck -Yung; ...

2015-09-14

By simultaneously displaying magnetism and superconductivity in a single phase, the iron-based superconductors provide a model system for the study of magnetism's role in superconductivity. The class of intercalated iron selenide superconductors is unique among these in having the additional property of phase separation and coexistence of two distinct phases—one majority phase with iron vacancy ordering and strong antiferromagnetism, and the other a poorly understood minority microscopic phase with a contested structure. Adding to the intrigue, the majority phase has never been found to show superconductivity on its own while the minority phase has never been successfully synthesized separate frommore » the majority phase. In order to better understand this minority phase, a series of high-quality Cs xFe 2–ySe 2 single crystals with (0.8 ≤ x ≤ 1;0 ≤ y ≤ 0.3) were grown and studied. Neutron and x-ray powder diffraction performed on ground crystals show that the average I4/mmm structure of the minority phase is distinctly different from the high-temperature I4/mmm parent structure. Moreover, single-crystal diffraction reveals the presence of discrete superlattice reflections that remove the degeneracy of the Cs sites in both the majority and minority phases and reduce their structural symmetries from body centered to primitive. Group theoretical analysis in conjunction with structural modeling shows that the observed superlattice reflections originate from three-dimensional Cs vacancy ordering. This model predicts a 25% vacancy of the Cs site in the minority phase which is consistent with the site's refined occupancy. Magnetization measurements performed in tandem with neutron single-crystal diffraction provide evidence that the minority phase is the host of superconductivity. Lastly, our results also reveal a superconducting dome in which the superconducting transition temperature varies as a function of the nominal valence of iron.« less

Consequences of extinction in tropical peat-forming vegetation of the Middle to Late Pennsylvanian (Westphalian-Stephanian)

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

DiMichele, W.A.; Phillips, T.L.

1992-01-01

Peat-forming environments (coals) were major landscape elements of the Pennsylvanian tropics. Mires reached a pantropical zenith during the 9 Ma of the Westphalian when long intervals of similar vegetation were separated by short intervals of rapid change. Differences between successive vegetation types primarily reflect different proportions of several major habitat-specific subfloras within which species turnover occurred. A hierarchy of organizational levels is suggested in which biotic interactions helped structure and constrain patterns of species replacement. Lycopsids were the framework trees of nearly all Westphalian mires; tree ferns and pteridosperm were important subdominants by the late Westphalian. Environmental changes, largely climatic,more » during the Westphalian-Stephanian transition resulted in extinction of most mire species, particularly trees. Tree ferns dominated Stephanian mires following a short transitional period of small-lycopsid and fern abundance. Tree ferns were cheaply constructed opportunists and their rise in abundance coincided with an increase in species numbers throughout tropical lowlands. Within mires there was an increase in physical size of plants from several major lineages. The structure and dynamics of Stephanian mires differed from the Westphalian; previously sharp distinctions between mires and other lowland floras diminished. The Westphalian to Stephanian vegetational changes suggest that ecosystems can display a brittle'' response to environmental change. Such threshold responses are a likely consequences of levels of extinction high enough to disrupt ecosystem fabric. The success of opportunistic lineages following loss of indigenous mire vegetation constitutes a secondary replacement, with establishment of a new equilibrium within hundreds of thousands of years.« less

Moral values are associated with individual differences in regional brain volume

PubMed Central

Lewis, G. J.; Kanai, R.; Bates, T. C.; Rees, G.

2012-01-01

Moral sentiment has been hypothesized to reflect evolved adaptations to social living. If so, individual differences in moral values may relate to regional variation in brain structure. We tested this hypothesis in a sample of 70 young, healthy adults examining whether differences on two major dimensions of moral values were significantly associated with regional gray matter volume. The two clusters of moral values assessed were “individualizing” (values of harm/care and fairness), and “binding” (deference to authority, in-group loyalty, and purity/sanctity). Individualizing was positively associated with left dorsomedial prefrontal cortex volume, and negatively associated with bilateral precuneus volume. For binding, a significant positive association was found for bilateral subcallosal gyrus and a trend to significance for the left anterior insula volume. These findings demonstrate that variation in moral sentiment reflects individual differences in brain structure and suggest a biological basis for moral sentiment, distributed across multiple brain regions. PMID:22571458

Moral values are associated with individual differences in regional brain volume.

PubMed

Lewis, Gary J; Kanai, Ryota; Bates, Timothy C; Rees, Geraint

2012-08-01

Moral sentiment has been hypothesized to reflect evolved adaptations to social living. If so, individual differences in moral values may relate to regional variation in brain structure. We tested this hypothesis in a sample of 70 young, healthy adults examining whether differences on two major dimensions of moral values were significantly associated with regional gray matter volume. The two clusters of moral values assessed were "individualizing" (values of harm/care and fairness) and "binding" (deference to authority, in-group loyalty, and purity/sanctity). Individualizing was positively associated with left dorsomedial pFC volume and negatively associated with bilateral precuneus volume. For binding, a significant positive association was found for bilateral subcallosal gyrus and a trend to significance for the left anterior insula volume. These findings demonstrate that variation in moral sentiment reflects individual differences in brain structure and suggest a biological basis for moral sentiment, distributed across multiple brain regions.

The CD1 family: serving lipid antigens to T cells since the Mesozoic era.

PubMed

Zajonc, Dirk M

2016-08-01

Class I-like CD1 molecules are in a family of antigen-presenting molecules that bind lipids and lipopeptides, rather than peptides for immune surveillance by T cells. Since CD1 lacks the high degree of polymorphism found in their major histocompatibility complex (MHC) class I molecules, different species express different numbers of CD1 isotypes, likely to be able to present structurally diverse classes of lipid antigens. In this review, we will present a historical overview of the structures of the different human CD1 isotypes and also discuss species-specific adaptations of the lipid-binding groove. We will discuss how single amino acid changes alter the shape and volume of the CD1 binding groove, how these minor changes can give rise to different numbers of binding pockets, and how these pockets affect the lipid repertoire that can be presented by any given CD1 protein. We will compare the structures of various lipid antigens and finally, we will discuss recognition of CD1-presented lipid antigens by antigen receptors on T cells (TCRs).

Long live the axon. Parallels between ageing and pathology from a presynaptic point of view.

PubMed

Grillo, Federico W

2016-10-01

All animals have to find the right balance between investing resources into their reproductive cycle and protecting their tissues from age-related damage. In higher order organisms the brain is particularly vulnerable to ageing, as the great majority of post-mitotic neurons are there to stay for an entire life. While ageing is unavoidable, it may progress at different rates in different individuals of the same species depending on a variety of genetic and environmental factors. Inevitably though, ageing results in a cognitive and sensory-motor decline caused by changes in neuronal structure and function. Besides normal ageing, age-related pathological conditions can develop in a sizeable proportion of the population. While this wide array of diseases are considerably different compared to physiological ageing, the two processes share many similarities and are likely to interact. At the subcellular level, two key structures are involved in brain ageing: axons and their synapses. Here I highlight how the ageing process affects these structures in normal and neurodegenerative states in different brain areas. Copyright © 2016 Elsevier B.V. All rights reserved.

The CD1 family: serving lipid antigens to T cells since the Mesozoic era

PubMed Central

Zajonc, Dirk M.

2016-01-01

Class I-like CD1 molecules are in a family of antigen-presenting molecules that bind lipids and lipopeptides, rather than peptides for immune surveillance by T cells. Since CD1 lacks the high degree of polymorphism found in their major histocompatibility complex (MHC) class I molecules, different species express different numbers of CD1 isotypes, likely to be able to present structurally diverse classes of lipid antigens. In this review, we will present a historical overview of the structures of the different human CD1 isotypes and also discuss species-specific adaptations of the lipid-binding groove. We will discuss how single amino acid changes alter the shape and volume of the CD1 binding groove, how these minor changes can give rise to different numbers of binding pockets, and how these pockets affect the lipid repertoire that can be presented by any given CD1 protein. We will compare the structures of various lipid antigens and finally, we will discuss recognition of CD1-presented lipid antigens by antigen receptors on T cells (TCRs). PMID:27368414

Population genetic characterization and family reconstruction in brood bank collections of the Indian major carp Labeo rohita (Cyprinidae:Cypriniformes).

PubMed

Ullah, Ashraf; Basak, Abhisak; Islam, Md Nazrul; Alam, Md Samsul

2015-01-01

The founder stock of a captive breeding program is prone to changes in genetic structure due to inbreeding and genetic drift. Genetic characterization of the founder population using suitable molecular markers may help monitor periodic changes in the genetic structure in future. To develop benchmark information about the genetic structure we analyzed six microsatellite loci in the Brodbank collections of rohu (Labeo rohita) originated from three major rivers-the Jamuna, the Padma and the Halda. A total of 28 alleles were detected in 90 individuals with an average of 4.6 alleles per locus. The average observed heterozygosity ranged from 0.655 to 0.705 and the expected heterozygosity ranged from 0.702 to 0.725. The mean F IS values were 0.103, 0.106 and 0.018 for the Jamuna, Padma and Halda fishes respectively. The population pair-wise F ST values ranged from 0.0057 to 0.0278. Structure analysis grouped the fishes of the three rivers into two clusters. The numbers of half-sib families were 5, 5 and 4 and the numbers of full-sib families were 12, 10 and 18 for the Halda, Jamuna and the Padma samples respectively. Bottleneck was detected in all the river samples. We recommend to collect more fish from different locations of the major rivers to broaden the genetic variability of the founder stocks of the Brood bank.

Extrapolating surface structures to depth in transpressional systems: the role of rheology and convergence angle deduced from analogue experiments

NASA Astrophysics Data System (ADS)

Hsieh, Shang Yu; Neubauer, Franz; Cloetingh, Sierd; Willingshofer, Ernst; Sokoutis, Dimitrios

2014-05-01

The internal structure of major strike-slip faults is still poorly understood, particularly how the deep structure could be inferred from its surface expression (Molnar and Dayem, 2011 and references therein). Previous analogue experiments suggest that the convergence angle is the most influential factor (Leever et al., 2011). Further analogue modeling may allow a better understanding how to extrapolate surface structures to the subsurface geometry of strike-slip faults. Various scenarios of analogue experiments were designed to represent strike-slip faults in nature from different geological settings. As such key parameters, which are investigated in this study include: (a) the angle of convergence, (b) the thickness of brittle layer, (c) the influence of a rheological weak layer within the crust, and (d) influence of a thick and rheologically weak layer at the base of the crust. The latter aimed to simulate the effect of a hot metamorphic core complex or an alignment of uprising plutons bordered by a transtensional/transpressional strike-slip fault. The experiments are aimed to explain first order structures along major transcurrent strike-slip faults such as the Altyn, Kunlun, San Andrea and Greendale (Darfield earthquake 2010) faults. The preliminary results show that convergence angle significantly influences the overall geometry of the transpressive system with greater convergence angles resulting in wider fault zones and higher elevation. Different positions, densities and viscosities of weak rheological layers have not only different surface expressions but also affect the fault geometry in the subsurface. For instance, rheological weak material in the bottom layer results in stretching when experiment reaches a certain displacement and a buildup of a less segmented, wide positive flower structure. At the surface, a wide fault valley in the middle of the fault zone is the reflection of stretching along the velocity discontinuity at depth. In models with a thin and rheologically weaker layer in the middle of the brittle layer, deformation is distributed over more faults and the geometry of the fault zone below and above the weak zone shows significant differences, suggesting that the correlation of structures across a weak layer has to be supported by geophysical data, which help constraining the geometry of the deep part. This latter experiment has significantly similar phenomena in reality, such as few pressure ridges along Altyn fault. The experimental results underline the need to understand the role of the convergence angle and the influence of rheology on fault evolution, in order to connect between surface deformation and subsurface geometry. References Leever, K. A., Gabrielsen, R. H., Sokoutis, D., Willingshofer, E., 2011. The effect of convergence angle on the kinematic evolution of strain partitioning in transpressional brittle wedges: Insight from analog modeling and high-resolution digital image analysis. Tectonics, 30(2), TC2013. Molnar, P., Dayem, K.E., 2010. Major intracontinental strike-slip faults and contrasts in lithospheric strength. Geosphere, 6, 444-467.

Mixing Characteristics of Elliptical Jet Control with Crosswire

NASA Astrophysics Data System (ADS)

Manigandan, S.; Vijayaraja, K.

2018-02-01

The aerodynamic mixing efficiency of elliptical sonic jet flow with the effect of crosswire is studied computationally and experimentally at different range of nozzle pressure ratio with different orientation along the minor axis of the exit. The cross wire of different orientation is found to reduce the strength of the shock wave formation. Due to the presence of crosswire the pitot pressure oscillation is reduced fast, which weakens the shock cell structure. When the cross wire is placed at center position we see high mixing along the major axis. Similarly, when the cross wire is placed at ¼ and ¾ position we see high mixing promotion along minor axis. It also proves, as the position of the cross wire decreased along minor axis there will be increase in the mixing ratio. In addition to that we also found that, jet spread is high in major axis compared to minor axis due to bifurcation of jet along upstream

Spatial influence on breast muscle morphological structure, myofiber size, and gene expression associated with the wooden breast myopathy in broilers.

PubMed

Clark, D L; Velleman, S G

2016-12-01

The wooden breast (WB) myopathy is identified by the palpation of a rigid pectoralis major (p. major) muscle and is characterized as a fibrotic, necrotic p. major disorder in broilers. The objective of the current study was to determine spatial morphological and gene expression differences at 4 locations within WB affected muscle from different genetic lines. Morphology was evaluated in 2 broiler lines expressing the WB myopathy (Lines A and B) and a line without WB (Line C) at 3 ventral locations and one anterodorsal location in the p. major muscle. In WB affected muscle of Line A, fibrosis was greatest in the anterior locations of WB affected muscle. In Line B muscle, fibrosis was greatest in the anteroventral region and minimal in the anterodorsal or posterior regions. Average p. major myofiber diameter was 30% larger in Lines A and B compared to Line C. However, in Line A there were no differences between the percentage of large fibers (diameter >70 μm) in unaffected and WB affected muscles at any sampling region. The percentage of small fibers (diameter <10 μm), likely small regenerating fibers, and expression of myogenic determination factor 1 (MYOD1) and myogenin were increased in Line A WB affected muscle compared to unaffected muscle. In Line B, the percentage of small fibers and MYOD1 expression in WB affected muscle was not different from unaffected muscle. Connective tissue organization within WB affected muscle was also different in Lines A and B, which may be attributed to decorin, a proteoglycan that mediates collagen crosslinking, growth factor signaling, and cell growth. Decorin expression was increased at all locations within Line A. However, in Line B decorin was increased only in the fibrotic regions of the p. major. The compiled results provide evidence that the WB myopathy is not uniform throughout the entire p. major muscle and the anterior end of the p. major muscle was more affected by the condition. © 2016 Poultry Science Association Inc.

Analysis of the HIV-2 protease's adaptation to various ligands: characterization of backbone asymmetry using a structural alphabet.

PubMed

Triki, Dhoha; Cano Contreras, Mario Enrique; Flatters, Delphine; Visseaux, Benoit; Descamps, Diane; Camproux, Anne-Claude; Regad, Leslie

2018-01-15

The HIV-2 protease (PR2) is a homodimer of 99 residues with asymmetric assembly and binding various ligands. We propose an exhaustive study of the local structural asymmetry between the two monomers of all available PR2 structures complexed with various inhibitors using a structural alphabet approach. On average, PR2 exhibits asymmetry in 31% of its positions-i.e., exhibiting different backbone local conformations in the two monomers. This asymmetry was observed all along its structure, particularly in the elbow and flap regions. We first differentiated structural asymmetry conserved in most PR2 structures from the one specific to some PR2. Then, we explored the origin of the detected asymmetry in PR2. We localized asymmetry that could be induced by PR2's flexibility, allowing transition from the semi-open to closed conformations and the asymmetry potentially induced by ligand binding. This latter could be important for the PR2's adaptation to diverse ligands. Our results highlighted some differences between asymmetry of PR2 bound to darunavir and amprenavir that could explain their differences of affinity. This knowledge is critical for a better description of PR2's recognition and adaptation to various ligands and for a better understanding of the resistance of PR2 to most PR2 inhibitors, a major antiretroviral class.

Using multi-scale distribution and movement effects along a montane highway to identify optimal crossing locations for a large-bodied mammal community

PubMed Central

Römer, Heinrich; Germain, Ryan R.

2013-01-01

Roads are a major cause of habitat fragmentation that can negatively affect many mammal populations. Mitigation measures such as crossing structures are a proposed method to reduce the negative effects of roads on wildlife, but the best methods for determining where such structures should be implemented, and how their effects might differ between species in mammal communities is largely unknown. We investigated the effects of a major highway through south-eastern British Columbia, Canada on several mammal species to determine how the highway may act as a barrier to animal movement, and how species may differ in their crossing-area preferences. We collected track data of eight mammal species across two winters, along both the highway and pre-marked transects, and used a multi-scale modeling approach to determine the scale at which habitat characteristics best predicted preferred crossing sites for each species. We found evidence for a severe barrier effect on all investigated species. Freely-available remotely-sensed habitat landscape data were better than more costly, manually-digitized microhabitat maps in supporting models that identified preferred crossing sites; however, models using both types of data were better yet. Further, in 6 of 8 cases models which incorporated multiple spatial scales were better at predicting preferred crossing sites than models utilizing any single scale. While each species differed in terms of the landscape variables associated with preferred/avoided crossing sites, we used a multi-model inference approach to identify locations along the highway where crossing structures may benefit all of the species considered. By specifically incorporating both highway and off-highway data and predictions we were able to show that landscape context plays an important role for maximizing mitigation measurement efficiency. Our results further highlight the need for mitigation measures along major highways to improve connectivity between mammal populations, and illustrate how multi-scale data can be used to identify preferred crossing sites for different species within a mammal community. PMID:24244912

Multiscale pore structure and its effect on gas transport in organic-rich shale

NASA Astrophysics Data System (ADS)

Wu, Tianhao; Li, Xiang; Zhao, Junliang; Zhang, Dongxiao

2017-07-01

A systematic investigation of multiscale pore structure in organic-rich shale by means of the combination of various imaging techniques is presented, including the state-of-the-art Helium-Ion-Microscope (HIM). The study achieves insight into the major features at each scale and suggests the affordable techniques for specific objectives from the aspects of resolution, dimension, and cost. The pores, which appear to be isolated, are connected by smaller pores resolved by higher-resolution imaging. This observation provides valuable information, from the microscopic perspective of pore structure, for understanding how gas accumulates and transports from where it is generated. A comprehensive workflow is proposed based on the characteristics acquired from the multiscale pore structure analysis to simulate the gas transport process. The simulations are completed with three levels: the microscopic mechanisms should be taken into consideration at level I; the spatial distribution features of organic matter, inorganic matter, and macropores constitute the major issue at level II; and the microfracture orientation and topological structure are dominant factors at level III. The results of apparent permeability from simulations agree well with the values acquired from experiments. By means of the workflow, the impact of various gas transport mechanisms at different scales can be investigated more individually and precisely than conventional experiments.

Crystal structures of two tropinone reductases: Different reaction stereospecificities in the same protein fold

PubMed Central

Nakajima, Keiji; Yamashita, Atsuko; Akama, Hiroyuki; Nakatsu, Toru; Kato, Hiroaki; Hashimoto, Takashi; Oda, Jun’ichi; Yamada, Yasuyuki

1998-01-01

A pair of tropinone reductases (TRs) share 64% of the same amino acid residues and belong to the short-chain dehydrogenase/reductase family. In the synthesis of tropane alkaloids in several medicinal plants, the TRs reduce a carbonyl group of an alkaloid intermediate, tropinone, to hydroxy groups with different diastereomeric configurations. To clarify the structural basis for their different reaction stereospecificities, we determined the crystal structures of the two enzymes at 2.4- and 2.3-Å resolutions. The overall folding of the two enzymes was almost identical. The conservation was not confined within the core domains that are conserved within the protein family but extended outside the core domain where each family member has its characteristic structure. The binding sites for the cofactor and the positions of the active site residues were well conserved between the two TRs. The substrate binding site was composed mostly of hydrophobic amino acids in both TRs, but the presence of different charged residues conferred different electrostatic environments on the two enzymes. A modeling study indicated that these charged residues play a major role in controlling the binding orientation of tropinone within the substrate binding site, thereby determining the stereospecificity of the reaction product. The results obtained herein raise the possibility that in certain cases different stereospecificities can be acquired in enzymes by changing a few amino acid residues within substrate binding sites. PMID:9560196

Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight

PubMed Central

Chéron, Jean-Baptiste; Triki, Dhoha; Senac, Caroline; Flatters, Delphine; Camproux, Anne-Claude

2017-01-01

Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC), obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at http://www.mti.univ-paris-diderot.fr/recherche/plateformes/logiciels. PMID:28817602

Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight.

PubMed

Regad, Leslie; Chéron, Jean-Baptiste; Triki, Dhoha; Senac, Caroline; Flatters, Delphine; Camproux, Anne-Claude

2017-01-01

Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC), obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at http://www.mti.univ-paris-diderot.fr/recherche/plateformes/logiciels.

Visualizing Key Hinges and a Potential Major Source of Compliance in the Lever Arm of Myosin

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

J Brown; V Senthil Kumar; E ONeall-Hennessey

2011-12-31

We have determined the 2.3-{angstrom}-resolution crystal structure of a myosin light chain domain, corresponding to one type found in sea scallop catch ('smooth') muscle. This structure reveals hinges that may function in the 'on' and 'off' states of myosin. The molecule adopts two different conformations about the heavy chain 'hook' and regulatory light chain (RLC) helix D. This conformational change results in extended and compressed forms of the lever arm whose lengths differ by 10 {angstrom}. The heavy chain hook and RLC helix D hinges could thus serve as a potential major and localized source of cross-bridge compliance during themore » contractile cycle. In addition, in one of the molecules of the crystal, part of the RLC N-terminal extension is seen in atomic detail and forms a one-turn alpha-helix that interacts with RLC helix D. This extension, whose sequence is highly variable in different myosins, may thus modulate the flexibility of the lever arm. Moreover, the relative proximity of the phosphorylation site to the helix D hinge suggests a potential role for conformational changes about this hinge in the transition between the on and off states of regulated myosins.« less

Visualizing key hinges and a potential major source of compliance in the lever arm of myosin

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

Brown, J.H.; Robinson, H.; Senthil Kumar, V. S.

2011-01-04

We have determined the 2.3-{angstrom}-resolution crystal structure of a myosin light chain domain, corresponding to one type found in sea scallop catch ('smooth') muscle. This structure reveals hinges that may function in the 'on' and 'off' states of myosin. The molecule adopts two different conformations about the heavy chain 'hook' and regulatory light chain (RLC) helix D. This conformational change results in extended and compressed forms of the lever arm whose lengths differ by 10 {angstrom}. The heavy chain hook and RLC helix D hinges could thus serve as a potential major and localized source of cross-bridge compliance during themore » contractile cycle. In addition, in one of the molecules of the crystal, part of the RLC N-terminal extension is seen in atomic detail and forms a one-turn alpha-helix that interacts with RLC helix D. This extension, whose sequence is highly variable in different myosins, may thus modulate the flexibility of the lever arm. Moreover, the relative proximity of the phosphorylation site to the helix D hinge suggests a potential role for conformational changes about this hinge in the transition between the on and off states of regulated myosins.« less

Fine-scale population structure of Malays in Peninsular Malaysia and Singapore and implications for association studies.

PubMed

Hoh, Boon-Peng; Deng, Lian; Julia-Ashazila, Mat Jusoh; Zuraihan, Zakaria; Nur-Hasnah, Ma'amor; Nur-Shafawati, Ab Rajab; Hatin, Wan Isa; Endom, Ismail; Zilfalil, Bin Alwi; Khalid, Yusoff; Xu, Shuhua

2015-07-22

Fine scale population structure of Malays - the major population in Malaysia, has not been well studied. This may have important implications for both evolutionary and medical studies. Here, we investigated the population sub-structure of Malay involving 431 samples collected from all states from peninsular Malaysia and Singapore. We identified two major clusters of individuals corresponding to the north and south peninsular Malaysia. On an even finer scale, the genetic coordinates of the geographical Malay populations are in correlation with the latitudes (R(2) = 0.3925; P = 0.029). This finding is further supported by the pairwise FST of Malay sub-populations, of which the north and south regions showed the highest differentiation (FST [North-south] = 0.0011). The collective findings therefore suggest that population sub-structure of Malays are more heterogenous than previously expected even within a small geographical region, possibly due to factors like different genetic origins, geographical isolation, could result in spurious association as demonstrated in our analysis. We suggest that cautions should be taken during the stage of study design or interpreting the association signals in disease mapping studies which are expected to be conducted in Malay population in the near future.

Patterned biofilm formation reveals a mechanism for structural heterogeneity in bacterial biofilms.

PubMed

Gu, Huan; Hou, Shuyu; Yongyat, Chanokpon; De Tore, Suzanne; Ren, Dacheng

2013-09-03

Bacterial biofilms are ubiquitous and are the major cause of chronic infections in humans and persistent biofouling in industry. Despite the significance of bacterial biofilms, the mechanism of biofilm formation and associated drug tolerance is still not fully understood. A major challenge in biofilm research is the intrinsic heterogeneity in the biofilm structure, which leads to temporal and spatial variation in cell density and gene expression. To understand and control such structural heterogeneity, surfaces with patterned functional alkanthiols were used in this study to obtain Escherichia coli cell clusters with systematically varied cluster size and distance between clusters. The results from quantitative imaging analysis revealed an interesting phenomenon in which multicellular connections can be formed between cell clusters depending on the size of interacting clusters and the distance between them. In addition, significant differences in patterned biofilm formation were observed between wild-type E. coli RP437 and some of its isogenic mutants, indicating that certain cellular and genetic factors are involved in interactions among cell clusters. In particular, autoinducer-2-mediated quorum sensing was found to be important. Collectively, these results provide missing information that links cell-to-cell signaling and interaction among cell clusters to the structural organization of bacterial biofilms.

The Effect of Electronic Structure on the Phases Present in High Entropy Alloys

PubMed Central

Leong, Zhaoyuan; Wróbel, Jan S.; Dudarev, Sergei L.; Goodall, Russell; Todd, Iain; Nguyen-Manh, Duc

2017-01-01

Multicomponent systems, termed High Entropy Alloys (HEAs), with predominantly single solid solution phases are a current area of focus in alloy development. Although different empirical rules have been introduced to understand phase formation and determine what the dominant phases may be in these systems, experimental investigation has revealed that in many cases their structure is not a single solid solution phase, and that the rules may not accurately distinguish the stability of the phase boundaries. Here, a combined modelling and experimental approach that looks into the electronic structure is proposed to improve accuracy of the predictions of the majority phase. To do this, the Rigid Band model is generalised for magnetic systems in prediction of the majority phase most likely to be found. Good agreement is found when the predictions are confronted with data from experiments, including a new magnetic HEA system (CoFeNiV). This also includes predicting the structural transition with varying levels of constituent elements, as a function of the valence electron concentration, n, obtained from the integrated spin-polarised density of states. This method is suitable as a new predictive technique to identify compositions for further screening, in particular for magnetic HEAs. PMID:28059106

The Effect of Electronic Structure on the Phases Present in High Entropy Alloys.

PubMed

Leong, Zhaoyuan; Wróbel, Jan S; Dudarev, Sergei L; Goodall, Russell; Todd, Iain; Nguyen-Manh, Duc

2017-01-06

Multicomponent systems, termed High Entropy Alloys (HEAs), with predominantly single solid solution phases are a current area of focus in alloy development. Although different empirical rules have been introduced to understand phase formation and determine what the dominant phases may be in these systems, experimental investigation has revealed that in many cases their structure is not a single solid solution phase, and that the rules may not accurately distinguish the stability of the phase boundaries. Here, a combined modelling and experimental approach that looks into the electronic structure is proposed to improve accuracy of the predictions of the majority phase. To do this, the Rigid Band model is generalised for magnetic systems in prediction of the majority phase most likely to be found. Good agreement is found when the predictions are confronted with data from experiments, including a new magnetic HEA system (CoFeNiV). This also includes predicting the structural transition with varying levels of constituent elements, as a function of the valence electron concentration, n, obtained from the integrated spin-polarised density of states. This method is suitable as a new predictive technique to identify compositions for further screening, in particular for magnetic HEAs.

The physics and chemistry of graphene-on-surfaces.

PubMed

Zhao, Guoke; Li, Xinming; Huang, Meirong; Zhen, Zhen; Zhong, Yujia; Chen, Qiao; Zhao, Xuanliang; He, Yijia; Hu, Ruirui; Yang, Tingting; Zhang, Rujing; Li, Changli; Kong, Jing; Xu, Jian-Bin; Ruoff, Rodney S; Zhu, Hongwei

2017-07-31

Graphene has demonstrated great potential in next-generation electronics due to its unique two-dimensional structure and properties including a zero-gap band structure, high electron mobility, and high electrical and thermal conductivity. The integration of atom-thick graphene into a device always involves its interaction with a supporting substrate by van der Waals forces and other intermolecular forces or even covalent bonding, and this is critical to its real applications. Graphene films on different surfaces are expected to exhibit significant differences in their properties, which lead to changes in their morphology, electronic structure, surface chemistry/physics, and surface/interface states. Therefore, a thorough understanding of the surface/interface properties is of great importance. In this review, we describe the major "graphene-on-surface" structures and examine the roles of their properties and related phenomena in governing the overall performance for specific applications including optoelectronics, surface catalysis, anti-friction and superlubricity, and coatings and composites. Finally, perspectives on the opportunities and challenges of graphene-on-surface systems are discussed.

Probability of major depression diagnostic classification using semi-structured versus fully structured diagnostic interviews.

PubMed

Levis, Brooke; Benedetti, Andrea; Riehm, Kira E; Saadat, Nazanin; Levis, Alexander W; Azar, Marleine; Rice, Danielle B; Chiovitti, Matthew J; Sanchez, Tatiana A; Cuijpers, Pim; Gilbody, Simon; Ioannidis, John P A; Kloda, Lorie A; McMillan, Dean; Patten, Scott B; Shrier, Ian; Steele, Russell J; Ziegelstein, Roy C; Akena, Dickens H; Arroll, Bruce; Ayalon, Liat; Baradaran, Hamid R; Baron, Murray; Beraldi, Anna; Bombardier, Charles H; Butterworth, Peter; Carter, Gregory; Chagas, Marcos H; Chan, Juliana C N; Cholera, Rushina; Chowdhary, Neerja; Clover, Kerrie; Conwell, Yeates; de Man-van Ginkel, Janneke M; Delgadillo, Jaime; Fann, Jesse R; Fischer, Felix H; Fischler, Benjamin; Fung, Daniel; Gelaye, Bizu; Goodyear-Smith, Felicity; Greeno, Catherine G; Hall, Brian J; Hambridge, John; Harrison, Patricia A; Hegerl, Ulrich; Hides, Leanne; Hobfoll, Stevan E; Hudson, Marie; Hyphantis, Thomas; Inagaki, Masatoshi; Ismail, Khalida; Jetté, Nathalie; Khamseh, Mohammad E; Kiely, Kim M; Lamers, Femke; Liu, Shen-Ing; Lotrakul, Manote; Loureiro, Sonia R; Löwe, Bernd; Marsh, Laura; McGuire, Anthony; Mohd Sidik, Sherina; Munhoz, Tiago N; Muramatsu, Kumiko; Osório, Flávia L; Patel, Vikram; Pence, Brian W; Persoons, Philippe; Picardi, Angelo; Rooney, Alasdair G; Santos, Iná S; Shaaban, Juwita; Sidebottom, Abbey; Simning, Adam; Stafford, Lesley; Sung, Sharon; Tan, Pei Lin Lynnette; Turner, Alyna; van der Feltz-Cornelis, Christina M; van Weert, Henk C; Vöhringer, Paul A; White, Jennifer; Whooley, Mary A; Winkley, Kirsty; Yamada, Mitsuhiko; Zhang, Yuying; Thombs, Brett D

2018-06-01

Different diagnostic interviews are used as reference standards for major depression classification in research. Semi-structured interviews involve clinical judgement, whereas fully structured interviews are completely scripted. The Mini International Neuropsychiatric Interview (MINI), a brief fully structured interview, is also sometimes used. It is not known whether interview method is associated with probability of major depression classification.AimsTo evaluate the association between interview method and odds of major depression classification, controlling for depressive symptom scores and participant characteristics. Data collected for an individual participant data meta-analysis of Patient Health Questionnaire-9 (PHQ-9) diagnostic accuracy were analysed and binomial generalised linear mixed models were fit. A total of 17 158 participants (2287 with major depression) from 57 primary studies were analysed. Among fully structured interviews, odds of major depression were higher for the MINI compared with the Composite International Diagnostic Interview (CIDI) (odds ratio (OR) = 2.10; 95% CI = 1.15-3.87). Compared with semi-structured interviews, fully structured interviews (MINI excluded) were non-significantly more likely to classify participants with low-level depressive symptoms (PHQ-9 scores ≤6) as having major depression (OR = 3.13; 95% CI = 0.98-10.00), similarly likely for moderate-level symptoms (PHQ-9 scores 7-15) (OR = 0.96; 95% CI = 0.56-1.66) and significantly less likely for high-level symptoms (PHQ-9 scores ≥16) (OR = 0.50; 95% CI = 0.26-0.97). The MINI may identify more people as depressed than the CIDI, and semi-structured and fully structured interviews may not be interchangeable methods, but these results should be replicated.Declaration of interestDrs Jetté and Patten declare that they received a grant, outside the submitted work, from the Hotchkiss Brain Institute, which was jointly funded by the Institute and Pfizer. Pfizer was the original sponsor of the development of the PHQ-9, which is now in the public domain. Dr Chan is a steering committee member or consultant of Astra Zeneca, Bayer, Lilly, MSD and Pfizer. She has received sponsorships and honorarium for giving lectures and providing consultancy and her affiliated institution has received research grants from these companies. Dr Hegerl declares that within the past 3 years, he was an advisory board member for Lundbeck, Servier and Otsuka Pharma; a consultant for Bayer Pharma; and a speaker for Medice Arzneimittel, Novartis, and Roche Pharma, all outside the submitted work. Dr Inagaki declares that he has received grants from Novartis Pharma, lecture fees from Pfizer, Mochida, Shionogi, Sumitomo Dainippon Pharma, Daiichi-Sankyo, Meiji Seika and Takeda, and royalties from Nippon Hyoron Sha, Nanzando, Seiwa Shoten, Igaku-shoin and Technomics, all outside of the submitted work. Dr Yamada reports personal fees from Meiji Seika Pharma Co., Ltd., MSD K.K., Asahi Kasei Pharma Corporation, Seishin Shobo, Seiwa Shoten Co., Ltd., Igaku-shoin Ltd., Chugai Igakusha and Sentan Igakusha, all outside the submitted work. All other authors declare no competing interests. No funder had any role in the design and conduct of the study; collection, management, analysis and interpretation of the data; preparation, review or approval of the manuscript; and decision to submit the manuscript for publication.

A sampling-based method for ranking protein structural models by integrating multiple scores and features.

PubMed

Shi, Xiaohu; Zhang, Jingfen; He, Zhiquan; Shang, Yi; Xu, Dong

2011-09-01

One of the major challenges in protein tertiary structure prediction is structure quality assessment. In many cases, protein structure prediction tools generate good structural models, but fail to select the best models from a huge number of candidates as the final output. In this study, we developed a sampling-based machine-learning method to rank protein structural models by integrating multiple scores and features. First, features such as predicted secondary structure, solvent accessibility and residue-residue contact information are integrated by two Radial Basis Function (RBF) models trained from different datasets. Then, the two RBF scores and five selected scoring functions developed by others, i.e., Opus-CA, Opus-PSP, DFIRE, RAPDF, and Cheng Score are synthesized by a sampling method. At last, another integrated RBF model ranks the structural models according to the features of sampling distribution. We tested the proposed method by using two different datasets, including the CASP server prediction models of all CASP8 targets and a set of models generated by our in-house software MUFOLD. The test result shows that our method outperforms any individual scoring function on both best model selection, and overall correlation between the predicted ranking and the actual ranking of structural quality.

Life Comparative Analysis of Energy Consumption and CO2 Emissions of Different Building Structural Frame Types

PubMed Central

Kim, Sangyong; Moon, Joon-Ho; Shin, Yoonseok; Kim, Gwang-Hee; Seo, Deok-Seok

2013-01-01

The objective of this research is to quantitatively measure and compare the environmental load and construction cost of different structural frame types. Construction cost also accounts for the costs of CO2 emissions of input materials. The choice of structural frame type is a major consideration in construction, as this element represents about 33% of total building construction costs. In this research, four constructed buildings were analyzed, with these having either reinforced concrete (RC) or steel (S) structures. An input-output framework analysis was used to measure energy consumption and CO2 emissions of input materials for each structural frame type. In addition, the CO2 emissions cost was measured using the trading price of CO2 emissions on the International Commodity Exchange. This research revealed that both energy consumption and CO2 emissions were, on average, 26% lower with the RC structure than with the S structure, and the construction costs (including the CO2 emissions cost) of the RC structure were about 9.8% lower, compared to the S structure. This research provides insights through which the construction industry will be able to respond to the carbon market, which is expected to continue to grow in the future. PMID:24227998

Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors

PubMed Central

Wang, Jianwei; Zhang, Yong

2016-01-01

When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III–V, and II–VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain–low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side. PMID:27090430

First-principle modelling of forsterite surface properties: Accuracy of methods and basis sets.

PubMed

Demichelis, Raffaella; Bruno, Marco; Massaro, Francesco R; Prencipe, Mauro; De La Pierre, Marco; Nestola, Fabrizio

2015-07-15

The seven main crystal surfaces of forsterite (Mg2 SiO4 ) were modeled using various Gaussian-type basis sets, and several formulations for the exchange-correlation functional within the density functional theory (DFT). The recently developed pob-TZVP basis set provides the best results for all properties that are strongly dependent on the accuracy of the wavefunction. Convergence on the structure and on the basis set superposition error-corrected surface energy can be reached also with poorer basis sets. The effect of adopting different DFT functionals was assessed. All functionals give the same stability order for the various surfaces. Surfaces do not exhibit any major structural differences when optimized with different functionals, except for higher energy orientations where major rearrangements occur around the Mg sites at the surface or subsurface. When dispersions are not accounted for, all functionals provide similar surface energies. The inclusion of empirical dispersions raises the energy of all surfaces by a nearly systematic value proportional to the scaling factor s of the dispersion formulation. An estimation for the surface energy is provided through adopting C6 coefficients that are more suitable than the standard ones to describe O-O interactions in minerals. A 2 × 2 supercell of the most stable surface (010) was optimized. No surface reconstruction was observed. The resulting structure and surface energy show no difference with respect to those obtained when using the primitive cell. This result validates the (010) surface model here adopted, that will serve as a reference for future studies on adsorption and reactivity of water and carbon dioxide at this interface. © 2015 Wiley Periodicals, Inc.

Studies on a new class of organogelator containing 2-anthracenecarboxylic acid: influence of gelator and solvent on stereochemistry of the photodimers.

PubMed

Dawn, Arnab; Fujita, Norifumi; Haraguchi, Shuichi; Sada, Kazuki; Tamaru, Shun-ichi; Shinkai, Seiji

2009-11-07

A new class of binary organogelator (G1, G2 and G3) based on 2-anthracenecarboxylic acid (2Ac), attached noncovalently with the gelator counterpart containing a 3,4,5-tris(n-dodecyloxy)benzoylamide backbone has been developed. Among the three gelators, two (G2 and G3) are chiral containing D-alanine or L-2-phenylglycine moieties, respectively. They can act as efficient gelators of organic solvents with varying polarity depending upon the gelator systems. Gelator G1 even gelates chiral solvents. The photoirradiation of the gel samples produces photocyclodimers having different degrees of stereoselectivity for different systems. Gels with G1 and G2 produce head-to-head (h-h) photodimers as major products, whereas the stereoselectivity is reversed for the gels with G3 producing head-to-tail (h-t) photodimers as major products. Among those, G2/cyclohexane gel shows the highest degree of stereoselectivity, producing only h-h photodimers with some significant amount of chiral induction. Other chiral systems exhibit low to moderate chiral inductions. The gelator G1 can differentiate between the racemic and enantiomerically pure varieties of a solvent by exhibiting different gel melting temperatures (T(gel)). For different gel systems, T(gel) increases in all the cases as a consequence of photoreaction, except for the G2/cyclohexane gel, where a prominent gel-to-sol phase transition can be observed during the photoreaction. Hydrogen-bonding and pi-pi stacking interactions play the principal roles in constructing the gel structure. The morphologies of the gel systems vary between one-dimensional fibrils and a fibrillar network structure. In addition, the influences of the gelator and solvent polarity on the rate of photoreactions, photoproduct distributions as well as gel structures are investigated.

Exploring phylogenetic and functional signals in complex morphologies: the hamate of extant anthropoids as a test-case study.

PubMed

Almécija, Sergio; Orr, Caley M; Tocheri, Matthew W; Patel, Biren A; Jungers, William L

2015-01-01

Three-dimensional geometric morphometrics (3DGM) is a powerful tool for capturing and visualizing the "pure" shape of complex structures. However, these shape differences are sometimes difficult to interpret from a functional viewpoint, unless specific approaches (mostly based on biomechanical modeling) are employed. Here, we use 3DGM to explore the complex shape variation of the hamate, the disto-ulnar wrist bone, in anthropoid primates. Major trends of shape variation are explored using principal components analysis along with analyses of shape and size covariation. We also evaluate the phylogenetic patterning of hamate shape by plotting an anthropoid phylogenetic tree onto the shape space (i.e., phylomorphospace) and test against complete absence of phylogenetic signal using posterior permutation. Finally, the covariation of hamate shape and locomotor categories is explored by means of 2-block partial least squares (PLS) using shape coordinates and a matrix of data on arboreal locomotor behavior. Our results show that 3DGM is a valuable and versatile tool for characterizing the shape of complex structures such as wrist bones in anthropoids. For the hamate, a significant phylogenetic pattern is found in both hamate shape and size, indicating that closely related taxa are typically the most similar in hamate form. Our allometric analyses show that major differences in hamate shape among taxa are not a direct consequence of differences in hamate size. Finally, our PLS indicates a significant covariation of hamate shape and different types of arboreal locomotion, highlighting the relevance of this approach in future 3DGM studies seeking to capture a functional signal from complex biological structures. © 2014 Wiley Periodicals, Inc.

A morphometric analysis of cellular differentiation in caps of primary and lateral roots of Helianthus annuus

NASA Technical Reports Server (NTRS)

Moore, R.

1985-01-01

In order to determine if patterns of cell differentiation are similar in primary and lateral roots, I performed a morphometric analysis of the ultrastructure of calyptrogen, columella, and peripheral cells in primary and lateral roots of Helianthus annuus. Each cell type is characterized by a unique ultrastructure, and the ultrastructural changes characteristic of cellular differentiation in root caps are organelle specific. No major structural differences exist in the structures of the composite cell types, or in patterns of cell differentiation in caps of primary vs. lateral roots.

Structure-based drug design: docking and scoring.

PubMed

Kroemer, Romano T

2007-08-01

This review gives an introduction into ligand - receptor docking and illustrates the basic underlying concepts. An overview of different approaches and algorithms is provided. Although the application of docking and scoring has led to some remarkable successes, there are still some major challenges ahead, which are outlined here as well. Approaches to address some of these challenges and the latest developments in the area are presented. Some aspects of the assessment of docking program performance are discussed. A number of successful applications of structure-based virtual screening are described.

Effects of Hatchery Rearing on the Structure and Function of Salmonid Mechanosensory Systems.

PubMed

Brown, Andrew D; Sisneros, Joseph A; Jurasin, Tyler; Coffin, Allison B

2016-01-01

This paper reviews recent studies on the effects of hatchery rearing on the auditory and lateral line systems of salmonid fishes. Major conclusions are that (1) hatchery-reared juveniles exhibit abnormal lateral line morphology (relative to wild-origin conspecifics), suggesting that the hatchery environment affects lateral line structure, perhaps due to differences in the hydrodynamic conditions of hatcheries versus natural rearing environments, and (2) hatchery-reared salmonids have a high proportion of abnormal otoliths, a condition associated with reduced auditory sensitivity and suggestive of inner ear dysfunction.

[Application of the technique of analytical structure of project for the sub-project of websites catalog of the Virtual Health Library-Nursing].

PubMed

dos, Santos Luís Augusto; Marin, Heimar de Fátima; Marques, Isaac Rosa; Cunha, Isabel Cristina Kowal Olm

2007-01-01

This work intents, in a didactic form, to explain the benefits of use of a technique of project management, named Work Breakdown Structure: a graphical tool to identify the main results to be developed in a project. The real examples are applied to a sub-project of the Virtual Library in Health in Nursing (BVS-Enfermagem) to development of the Sites Catalogs. The benefits of graphical visualization for a major agreement between professionals of different expertise are presented.

Source Dependence and Story Production: A Comparison of Religion News Coverage by Specialists and Non-specialists at Three Newspapers.

ERIC Educational Resources Information Center

Buddenbaum, Judith M.

A study was conducted to compare the news reporting of religion specialists and nonspecialists at three major metropolitan newspapers. Representing different news policies and structural constraints, 1,164 religion news items from the "New York Times," Minneapolis "Star," and the Richmond (Virginia) "Times-Dispatch"…

UAE University Male Students' Interests Impact on Reading and Writing Performance and Improvement

ERIC Educational Resources Information Center

Al Murshidi, Ghadah

2014-01-01

The study examined the impact of the conjunction of structured journal writing and reading for pleasure on students' reading and writing skills. Forty male students from UAE University participated in the study. The participants are of different academic abilities, majors and nationalities. Many of them have little experience with reading for…

Psychometric Properties of Scores on the French and Korean Versions of the Hexaco Personality Inventory. Validity Studies

ERIC Educational Resources Information Center

Boies, Kathleen; Yoo, Tae-Yong; Ebacher, Annik; Lee, Kibeom; Ashton, Michael C.

2004-01-01

Recent lexical studies of personality structure suggest that there are six independent major dimensions of personality. The HEXACO Personality Inventory (HEXACO-PI), a new questionnaire that measures these six lexically derived personality constructs, was examined in two different cultural contexts using samples of 149 Francophone and 211 Korean…

Early Deterioration of Coarse Woody Debris

Treesearch

F.H. Tainter; J.W. McMinn

1999-01-01

Coarse woody debris (CWD) is an important structural component of southern forest ecosystems. CWD loading may be affected by different decomposition rates on sites of varying quality. Bolts of red oak and loblolly pine were placed on plots at each of three (hydric, mesic. and xeric) sites at the Savannah River Site and sampled over a 16-week period. Major changes...

The Views and Opinions of School Principals and Teachers on Positive Education

ERIC Educational Resources Information Center

Bas, Asli Uz; Firat, Necla Sahin

2017-01-01

The purpose of this study is to assess the views and opinions of school principals and teachers on positive education. The sample of the study includes 8 school principals and 12 teachers who attend different public schools in Izmir, Turkey. Data is collected through semi-structured interview technique. Findings show that majority of the…

Separation and structural analysis of saponins in a bark extract from Quillaja saponaria Molina.

PubMed

Nord, L I; Kenne, L

1999-07-20

Six major saponins were isolated from a bark extract from Quillaja saponaria Molina. Solid-phase extraction, followed by a two-step reversed-phase HPLC separation procedure with phosphate and ammonium acetate buffers of different pH values, was used. The compounds were characterised using NMR spectroscopy, mass spectrometry and chemical methods.

Can You Teach in a Normal Way? Examining Chinese and US Curricula's Approach to Teaching Fraction Divisions

ERIC Educational Resources Information Center

Feil, YingYing Crystal

2010-01-01

This dissertation presents two studies designed to examine the topic of fraction division in selected Chinese and US curricula. By comparing the structure and content of the Chinese and "Everyday Mathematics" textbooks and teacher's guides, Study 1 revealed many different features presented in the selected curricula. Major differences…

Examining the Relations among Student Motivation, Engagement, and Retention in a MOOC: A Structural Equation Modeling Approach

ERIC Educational Resources Information Center

Xiong, Yao; Li, Hongli; Kornhaber, Mindy L.; Suen, Hoi K.; Pursel, Barton; Goins, Deborah D.

2015-01-01

Students who are enrolled in MOOCs tend to have different motivational patterns than fee-paying college students. A majority of MOOC students demonstrate characteristics akin more to "tourists" than formal learners. As a consequence, MOOC students' completion rate is usually very low. The current study examines the relations among…

Do Differences in GPA Impact Attitudes about Group Work? A Comparison of Business and Non-Business Majors

ERIC Educational Resources Information Center

Grzimek, Volker; Marks, Melanie Beth; Kinnamon, Eric

2014-01-01

Using survey data the authors investigate the impact of grade point average (GPA) on students' preferences for classroom group work and its structure. Topics range from general attitudes and beliefs (benefits to grades, impact on mastery of material, professors' motives) to administration (group composition, grading, peer reviews, group…

Transfer of Learning from One Language to Another.

ERIC Educational Resources Information Center

Liu, Shirley

Can the way children learn Chinese help them to learn English? In this study, it is noted that there is a possibility that despite the structural differences between them, there is transference from the learning of Chinese to the learning of English. Skinner's four major reinforcement schedules were used in this study to promote this transference…

"I'm Good, but Not That Good": Digitally-Skilled Young People's Identity in Computing

ERIC Educational Resources Information Center

Wong, Billy

2017-01-01

Computers and information technology are fast becoming a part of young people's everyday life. However, there remains a difference between the majority who can use computers and the minority who are computer scientists or professionals. Drawing on 32 semi-structured interviews with digitally skilled young people (aged 13-19), we explore their…

Beginning School Math Competence: Minority and Majority Comparisons. Report No. 34.

ERIC Educational Resources Information Center

Entwisle, Doris R.; Alexander, Karl L.

This paper uses a structural model with a large random sample of urban children to explain children's competence in math concepts and computation at the time they begin first grade. These two aspects of math ability respond differently to environmental resources, with math concepts much more responsive to family factors before formal schooling…

Comparative study on histological structures of the vitelline membrane of hen and duck egg observed by cryo-scanning electron microscopy.

PubMed

Chung, Wen-Hsin; Lai, Kung-Ming; Hsu, Kuo-chiang

2010-02-10

The histological structures of the vitelline membranes (VM) of hen and duck eggs were observed by cryo-scanning electron microscopy (cryo-SEM), and the chemical characteristics were also compared. The outer layer surface (OLS) of duck egg VM showed networks constructed by fibrils and sheets (0.1-5.2 microm in width), and that of hen egg presented networks formed only by sheets (2-6 microm in width). Thicker fibrils (0.5-1.5 microm in width) with different arrangement were observed on the inner layer surface (ILS) of duck egg VM as compared to those (0.3-0.7 microm in width) of hen egg VM. Upon separation, the outer surface of the outer layer (OSOL) and the inner surface of the inner layer (ISIL) of hen and duck egg VMs were quite similar to fresh VM except that the OSOL of duck egg VM showed networks constructed only by sheets. Thin fibrils interlaced above a bumpy or flat structure were observed at the exposed surface of the outer layer (ESOL) of hen and duck egg VMs. The exposed surfaces of inner layers (ESIL) of hen and duck egg VMs showed similar structures of fibrils, which joined, branched, and ran in straight lines for long distances up to 30 microm; however, the widths of the fibrils shown in ESOL and ESIL of duck egg VM were 0.1 and 0.7-1.4 microm, respectively, and were greater than those (<0.1 and 0.5-0.8 microm) of hen egg VM. The continuous membranes of both hen and duck egg VMs were still attached to the outer layers when separated. The content of protein, the major component of VM, was higher in duck egg VM (88.6%) than in hen egg VM (81.6%). Four and six major SDS-soluble protein patterns with distinct localization were observed in hen and duck egg VMs, respectively. Overall, the different histological structures of hen and duck egg VMs were suggested to be majorly attributable to the diverse protein components.

Dioxygen Binding, Activation, and Reduction to H2O by Cu Enzymes.

PubMed

Solomon, Edward I

2016-07-05

Oxygen intermediates in copper enzymes exhibit unique spectroscopic features that reflect novel geometric and electronic structures that are key to reactivity. This perspective will describe: (1) the bonding origin of the unique spectroscopic features of the coupled binuclear copper enzymes and how this overcomes the spin forbiddenness of O2 binding and activates monooxygenase activity, (2) how the difference in exchange coupling in the non-coupled binuclear Cu enzymes controls the reaction mechanism, and (3) how the trinuclear Cu cluster present in the multicopper oxidases leads to a major structure/function difference in enabling the irreversible reductive cleavage of the O-O bond with little overpotential and generating a fully oxidized intermediate, different from the resting enzyme studied by crystallography, that is key in enabling fast PCET in the reductive half of the catalytic cycle.

Structure of Adeno-Associated Virus Type 4

PubMed Central

Padron, Eric; Bowman, Valorie; Kaludov, Nikola; Govindasamy, Lakshmanan; Levy, Hazel; Nick, Phillip; McKenna, Robert; Muzyczka, Nicholas; Chiorini, John A.; Baker, Timothy S.; Agbandje-McKenna, Mavis

2005-01-01

Adeno-associated virus (AAV) is a member of the Parvoviridae, belonging to the Dependovirus genus. Currently, several distinct isolates of AAV are in development for use in human gene therapy applications due to their ability to transduce different target cells. The need to manipulate AAV capsids for specific tissue delivery has generated interest in understanding their capsid structures. The structure of AAV type 4 (AAV4), one of the most antigenically distinct serotypes, was determined to 13-Å resolution by cryo-electron microscopy and image reconstruction. A pseudoatomic model was built for the AAV4 capsid by use of a structure-based sequence alignment of its major capsid protein, VP3, with that of AAV2, to which AAV4 is 58% identical and constrained by its reconstructed density envelope. The model showed variations in the surface loops that may account for the differences in receptor binding and antigenicity between AAV2 and AAV4. The AAV4 capsid surface topology also shows an unpredicted structural similarity to that of Aleutian mink disease virus and human parvovirus B19, autonomous members of the genus, despite limited sequence homology. PMID:15795290

Structural features of biomass in a hybrid MBBR reactor.

PubMed

Xiao, G Y; Ganczarczyk, J

2006-03-01

The structural features of biomass present in the hybrid MBBR (Moving Bed Biofilm Reactor) aeration tank were studied in two subsequent periods, which differed in hydraulic and substrate loads. The physical characteristics of attached-growth biomass, such as, biofilm thickness, density, porosity, inner and surface fractal dimensions, and those of suspended-growth biomass, such as, floc size distribution, density, porosity, inner and surface fractal dimensions, were investigated in each study period and then compared. The results indicated that biofilm always had a higher density, geometric porosity, and a larger boundary fractal dimension than flocs. Both types of biomass were found to exhibit at least two distinct Sierpinski fractal dimensions, indicating two major different pore space populations. With the increasing wastewater flow, both types of biomass were found to shift their structural properties to larger values, except porosity and surface roughness, which decreased. Floc density and biomass Sierpinski fractals were not affected much by the system loadings.

Chromosome ends: different sequences may provide conserved functions.

PubMed

Louis, Edward J; Vershinin, Alexander V

2005-07-01

The structures of specific chromosome regions, centromeres and telomeres, present a number of puzzles. As functions performed by these regions are ubiquitous and essential, their DNA, proteins and chromatin structure are expected to be conserved. Recent studies of centromeric DNA from human, Drosophila and plant species have demonstrated that a hidden universal centromere-specific sequence is highly unlikely. The DNA of telomeres is more conserved consisting of a tandemly repeated 6-8 bp Arabidopsis-like sequence in a majority of organisms as diverse as protozoan, fungi, mammals and plants. However, there are alternatives to short DNA repeats at the ends of chromosomes and for telomere elongation by telomerase. Here we focus on the similarities and diversity that exist among the structural elements, DNA sequences and proteins, that make up terminal domains (telomeres and subtelomeres), and how organisms use these in different ways to fulfil the functions of end-replication and end-protection. Copyright (c) 2005 Wiley Periodicals, Inc.

Information content of ozone retrieval algorithms

NASA Technical Reports Server (NTRS)

Rodgers, C.; Bhartia, P. K.; Chu, W. P.; Curran, R.; Deluisi, J.; Gille, J. C.; Hudson, R.; Mateer, C.; Rusch, D.; Thomas, R. J.

1989-01-01

The algorithms are characterized that were used for production processing by the major suppliers of ozone data to show quantitatively: how the retrieved profile is related to the actual profile (This characterizes the altitude range and vertical resolution of the data); the nature of systematic errors in the retrieved profiles, including their vertical structure and relation to uncertain instrumental parameters; how trends in the real ozone are reflected in trends in the retrieved ozone profile; and how trends in other quantities (both instrumental and atmospheric) might appear as trends in the ozone profile. No serious deficiencies were found in the algorithms used in generating the major available ozone data sets. As the measurements are all indirect in someway, and the retrieved profiles have different characteristics, data from different instruments are not directly comparable.

1,2-Di-2-quinolylethene

PubMed Central

Fun, Hoong-Kun; Kia, Reza; Maity, Annada C.; Chakrabarty, Rinku; Goswami, Shyamaprosad

2009-01-01

The title compound, C20H14N2, comprises two crystallographically independent centrosymmetric mol­ecules (A and B) with different conformations due to the disorder of molecule B. The whole of mol­ecule B is disordered over two sets of positions, corresponding to a 180° rotation of the molecule, with a site-occupancy ratio of 0.780 (6):0.220 (6). The minor component of the disordered part in B has the same configuration as mol­ecule A, but the major component is different. The dihedral angle between the planes of mol­ecule A and mol­ecule B (major component) is 63.22 (3)°. The crystal structure is stabilized by inter­molecular C—H⋯π inter­actions. PMID:21581953

Rural-Urban Differences in Consumer Governance at Community Health Centers

PubMed Central

Wright, David Bradley

2017-01-01

Context Community health centers (CHCs) are primary care clinics that serve mostly low-income patients in rural and urban areas. They are required to be governed by a consumer majority. What little is known about the structure and function of these boards in practice, suggests that CHC boards in rural areas may look and act differently than CHC boards in urban areas. Purpose To identify differences in the structure and function of consumer governance at CHCs in rural and urban areas. Methods Semi-structured telephone interviews were conducted with 30 CHC board members from 14 different states. Questions focused on board members’ perceptions of board composition and the role of consumers on the board. Findings CHCs in rural areas are more likely to have representative boards, are better able to convey confidence in the organization, and are better able to assess community needs than CHCs in urban areas. However, CHCs in rural areas often have problems achieving objective decision-making, and may have fewer means for objectively evaluating quality of care due to the lack of patient board member anonymity. Conclusions Consumer governance is implemented differently in rural and urban communities, and the advantages and disadvantages in each setting are unique. PMID:23551642

Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold

PubMed Central

Ribardo, Deborah A.; Brennan, Caitlin A.; Ruby, Edward G.; Jensen, Grant J.; Hendrixson, David R.

2016-01-01

Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, from Campylobacter and Vibrio species. For the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and show that diverse high-torque motors use variants of an ancestrally related family of structures to scaffold incorporation of additional stator complexes at wider radii from the axial driveshaft than in the model enteric motor. We identify the protein components of these additional scaffold structures and elucidate their sequential assembly, demonstrating that they are required for stator-complex incorporation. These proteins are widespread, suggesting that different bacteria have tailored torques to specific environments by scaffolding alternative stator placement and number. Our results quantitatively account for different motor torques, complete the assignment of the locations of the major flagellar components, and provide crucial constraints for understanding mechanisms of torque generation and the evolution of multiprotein complexes. PMID:26976588

Structural and Functional Differences Between Porcine Aorta and Vena Cava.

PubMed

Mattson, Jeffrey M; Zhang, Yanhang

2017-07-01

Elastin and collagen fibers are the major load-bearing extracellular matrix (ECM) constituents of the vascular wall. Arteries function differently than veins in the circulatory system; however as a result from several treatment options, veins are subjected to sudden elevated arterial pressure. It is thus important to recognize the fundamental structure and function differences between a vein and an artery. Our research compared the relationship between biaxial mechanical function and ECM structure of porcine thoracic aorta and inferior vena cava. Our study suggests that aorta contains slightly more elastin than collagen due to the cyclical extensibility, but vena cava contains almost four times more collagen than elastin to maintain integrity. Furthermore, multiphoton imaging of vena cava showed longitudinally oriented elastin and circumferentially oriented collagen that is recruited at supraphysiologic stress, but low levels of strain. However in aorta, elastin is distributed uniformly, and the primarily circumferentially oriented collagen is recruited at higher levels of strain than vena cava. These structural observations support the functional finding that vena cava is highly anisotropic with the longitude being more compliant and the circumference stiffening substantially at low levels of strain. Overall, our research demonstrates that fiber distributions and recruitment should be considered in addition to relative collagen and elastin contents. Also, the importance of accounting for the structural and functional differences between arteries and veins should be taken into account when considering disease treatment options.

Effect of sex on histological and histochemical structures of different parts of the kidney in Japanese quail.

PubMed

Mobini, Behzad; Abdollahi, MohammadHossein

2016-09-01

The aim of the present study was to investigate the effect of gender on the histological and histochemical structures of different anatomical regions of the kidney in Japanese quail (Coturnix japonica). Tissue samples from cranial, middle and caudal divisions of each kidney were obtained from 20 male and 20 female adult, healthy Japanese quail. The sections stained with hematoxylin & eosin ( H & E: ), Masson's trichrome, Verhoeff's, Alcian blue (pH 2.5), Periodic acid-Schiff, and Gomori's method for reticulum. Unusual findings of the kidney in Japanese quail were the presence of three types of nephrons, all the connective tissue fibers in capsule and interlobular septa and AB-reactions of the proximal convoluted cells. No significant sex-based differences were found. The various histological structures of the kidney showed no significant differences among different divisions of the left and right kidneys. It is concluded that the general histological and histochemical properties of the kidney in Japanese quail were similar to those of chickens and some other species, but that there were also some differences. One of the major differences was brush border of interdigitating microvilli on luminal surface of collecting ducts in Japanese quail. © 2016 Poultry Science Association Inc.

Effects of High-Intensity Interval Training versus Continuous Training on Physical Fitness, Cardiovascular Function and Quality of Life in Heart Failure Patients.

PubMed

Benda, Nathalie M M; Seeger, Joost P H; Stevens, Guus G C F; Hijmans-Kersten, Bregina T P; van Dijk, Arie P J; Bellersen, Louise; Lamfers, Evert J P; Hopman, Maria T E; Thijssen, Dick H J

2015-01-01

Physical fitness is an important prognostic factor in heart failure (HF). To improve fitness, different types of exercise have been explored, with recent focus on high-intensity interval training (HIT). We comprehensively compared effects of HIT versus continuous training (CT) in HF patients NYHA II-III on physical fitness, cardiovascular function and structure, and quality of life, and hypothesize that HIT leads to superior improvements compared to CT. Twenty HF patients (male:female 19:1, 64±8 yrs, ejection fraction 38±6%) were allocated to 12-weeks of HIT (10*1-minute at 90% maximal workload-alternated by 2.5 minutes at 30% maximal workload) or CT (30 minutes at 60-75% of maximal workload). Before and after intervention, we examined physical fitness (incremental cycling test), cardiac function and structure (echocardiography), vascular function and structure (ultrasound) and quality of life (SF-36, Minnesota living with HF questionnaire (MLHFQ)). Training improved maximal workload, peak oxygen uptake (VO2peak) related to the predicted VO2peak, oxygen uptake at the anaerobic threshold, and maximal oxygen pulse (all P<0.05), whilst no differences were present between HIT and CT (N.S.). We found no major changes in resting cardiovascular function and structure. SF-36 physical function score improved after training (P<0.05), whilst SF-36 total score and MLHFQ did not change after training (N.S.). Training induced significant improvements in parameters of physical fitness, although no evidence for superiority of HIT over CT was demonstrated. No major effect of training was found on cardiovascular structure and function or quality of life in HF patients NYHA II-III. Nederlands Trial Register NTR3671.

Structure of an Insecticide Sequestering Carboxylesterase from the Disease Vector Culex quinquefasciatus: What Makes an Enzyme a Good Insecticide Sponge?

PubMed

Hopkins, Davis H; Fraser, Nicholas J; Mabbitt, Peter D; Carr, Paul D; Oakeshott, John G; Jackson, Colin J

2017-10-17

Carboxylesterase (CBE)-mediated metabolic resistance to organophosphate and carbamate insecticides is a major problem for the control of insect disease vectors, such as the mosquito. The most common mechanism involves overexpression of CBEs that bind to the insecticide with high affinity, thereby sequestering them before they can interact with their target. However, the absence of any structure for an insecticide-sequestering CBE limits our understanding of the molecular basis for this process. We present the first structure of a CBE involved in sequestration, Cqestβ2 1 , from the mosquito disease vector Culex quinquefasciatus. Lysine methylation was used to obtain the crystal structure of Cqestβ2 1 , which adopts a canonical α/β-hydrolase fold that has high similarity to the target of organophosphate and carbamate insecticides, acetylcholinesterase. Sequence similarity networks of the insect carboxyl/cholinesterase family demonstrate that CBEs associated with metabolic insecticide resistance across many species share a level of similarity that distinguishes them from a variety of other classes. This is further emphasized by the structural similarities and differences in the binding pocket and active site residues of Cqestβ2 1 and other insect carboxyl/cholinesterases. Stopped-flow and steady-state inhibition studies support a major role for Cqestβ2 1 in organophosphate resistance and a minor role in carbamate resistance. Comparison with another isoform associated with insecticide resistance, Cqestβ1, showed both enzymes have similar affinity to insecticides, despite 16 amino acid differences between the two proteins. This provides a molecular understanding of pesticide sequestration by insect CBEs and could facilitate the design of CBE-specific inhibitors to circumvent this resistance mechanism in the future.

Association of polygenic risk for major psychiatric illness with subcortical volumes and white matter integrity in UK Biobank

PubMed Central

Reus, L. M.; Shen, X.; Gibson, J.; Wigmore, E.; Ligthart, L.; Adams, M. J.; Davies, G.; Cox, S. R.; Hagenaars, S. P.; Bastin, M. E.; Deary, I. J.; Whalley, H. C.; McIntosh, A. M.

2017-01-01

Major depressive disorder (MDD), schizophrenia (SCZ) and bipolar disorder (BP) are common, disabling and heritable psychiatric diseases with a complex overlapping polygenic architecture. Individuals with these disorders, as well as their unaffected relatives, show widespread structural differences in corticostriatal and limbic networks. Structural variation in many of these brain regions is also heritable and polygenic but whether their genetic architecture overlaps with that of major psychiatric disorders is unknown. We sought to address this issue by examining the impact of polygenic risk of MDD, SCZ, and BP on subcortical brain volumes and white matter (WM) microstructure in a large single sample of neuroimaging data; the UK Biobank Imaging study. The first release of UK Biobank imaging data comprised participants with overlapping genetic data and subcortical volumes (N = 978) and WM measures (N = 816). The calculation of polygenic risk scores was based on genome-wide association study results generated by the Psychiatric Genomics Consortium. Our findings indicated no statistically significant associations between either subcortical volumes or WM microstructure, and polygenic risk for MDD, SCZ or BP. These findings suggest that subcortical brain volumes and WM microstructure may not be closely linked to the genetic mechanisms of major psychiatric disorders. PMID:28186152

Association of polygenic risk for major psychiatric illness with subcortical volumes and white matter integrity in UK Biobank.

PubMed

Reus, L M; Shen, X; Gibson, J; Wigmore, E; Ligthart, L; Adams, M J; Davies, G; Cox, S R; Hagenaars, S P; Bastin, M E; Deary, I J; Whalley, H C; McIntosh, A M

2017-02-10

Major depressive disorder (MDD), schizophrenia (SCZ) and bipolar disorder (BP) are common, disabling and heritable psychiatric diseases with a complex overlapping polygenic architecture. Individuals with these disorders, as well as their unaffected relatives, show widespread structural differences in corticostriatal and limbic networks. Structural variation in many of these brain regions is also heritable and polygenic but whether their genetic architecture overlaps with that of major psychiatric disorders is unknown. We sought to address this issue by examining the impact of polygenic risk of MDD, SCZ, and BP on subcortical brain volumes and white matter (WM) microstructure in a large single sample of neuroimaging data; the UK Biobank Imaging study. The first release of UK Biobank imaging data comprised participants with overlapping genetic data and subcortical volumes (N = 978) and WM measures (N = 816). The calculation of polygenic risk scores was based on genome-wide association study results generated by the Psychiatric Genomics Consortium. Our findings indicated no statistically significant associations between either subcortical volumes or WM microstructure, and polygenic risk for MDD, SCZ or BP. These findings suggest that subcortical brain volumes and WM microstructure may not be closely linked to the genetic mechanisms of major psychiatric disorders.

Recent health sciences library building projects.

PubMed Central

Ludwig, L

1993-01-01

The Medical Library Association's third annual survey of recent health sciences library building projects identified fourteen libraries planning, expanding, or constructing new library facilities. Three of five new library buildings are freestanding structures where the library occupies all or a major portion of the space. The two other new facilities are for separately administered units where the library is a major tenant. Nine projects involve additions to or renovations of existing space. Six projects are in projected, predesign, or design stages or are awaiting funding approval. This paper describes four projects that illustrate technology's growing effect on librarians and libraries. They are designed to accommodate change, a plethora of electronic gear, and easy use of technology. Outwardly, they do not look much different than many other modern buildings. But, inside, the changes have been dramatic although they have evolved slowly as the building structure has been adapted to new conditions. Images PMID:8251970

Solid-phase extraction NMR studies of chromatographic fractions of saponins from Quillaja saponaria.

PubMed

Nyberg, Nils T; Baumann, Herbert; Kenne, Lennart

2003-01-15

The saponin mixture QH-B from the tree Quillaja saponaria var. Molina was fractionated by RP-HPLC in several steps. The fractions were analyzed by solid-phase extraction NMR (SPE-NMR), a technique combining the workup by solid-phase extraction with on-line coupling to an NMR flow probe. Together with MALDI-TOF mass spectrometry and comparison with chemical shifts of similar saponins, the structures of both major and minor components in QH-B could be obtained. The procedure described is a simple method to determine the structure of components in a complex mixture. The two major fractions of the mixture were found to contain at least 28 saponins, differing in the carbohydrate substructures. Eight of these have not previously been determined. The 28 saponins formed 14 equilibrium pairs by the migration of an O-acyl group between two adjacent positions on a fucosyl residue.

Structural and functional differences in the dio1 gene in mice with inherited type 1 deiodinase deficiency.

PubMed

Maia, A L; Berry, M J; Sabbag, R; Harney, J W; Larsen, P R

1995-08-01

The type 1 deiodinase (D1) provides the major portion of the circulating T3 in vertebrates. In C3H and certain other inbred mice, liver and kidney D1 activity is 5- to 10-fold lower than in the common phenotype, C57. The lower D1 levels are paralleled by a decreased normal-sized dio1 mRNA and hyperthyroxinemia. Low activity cosegregates with a restriction fragment length variant (RFLV) in both inbred and recombinant strains, indicating it is due to differences in the dio1 gene. The exonic structure and the deduced amino acid sequences are identical for both strains and highly homologous to that of the rat. The RFLV is due to an approximately 150-base pair expansion of repetitive sequences in the second intron of the C3H gene, but this segment does not differentially affect the transient expression of a human GH gene. The promoter and 5'-flanking regions of the C3H and C57 dio1 genes are very similar and are GC rich without TATA or CCAAT boxes. However, functional assays of 1.5-kilobase 5'-flanking dio1-CAT constructs showed 2- to 3-fold higher activity of the C57-CAT constructs. Deletion mutants showed that sequences between -705 and -162 were the cause of this. In this region, the only major difference between the two genes is a 21-base pair insert containing five CTG repeats in the C3H promoter. This difference also cosegregates with low D1 activity and the intron RFLV in four other mouse strains. The correlation of the CTG repeat insert with both in vitro and in vivo expression and the absence of other significant sequence differences in the 5'-flanking region argue that this is the major explanation for the impaired expression of the dio1 gene and the resulting hyperthyroxinemia of the C3H mouse.

Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase.

PubMed

Strajbl, Marek; Shurki, Avital; Warshel, Arieh

2003-12-09

F1-ATPase is the catalytic component of the ATP synthase molecular machine responsible for most of the uphill synthesis of ATP in living systems. The enormous advances in biochemical and structural studies of this machine provide an opportunity for detailed understanding of the nature of its rotary mechanism. However, further quantitative progress in this direction requires development of reliable ways of translating the observed structural changes to the corresponding energies. This requirement is particularly challenging because we are dealing with a large system that couples major structural changes with a chemical process. The present work provides such a structure-function correlation by using the linear response approximation to describe the rotary mechanism. This approach allows one to evaluate the energy of transitions between different conformational states by considering only the changes in the corresponding electrostatic energies of the ligands. The relevant energetics are also obtained by calculating the linear response approximation-based free energies of transferring the ligands from water to the different sites of F1-ATPase in their different conformational states. We also use the empirical valence bond approach to evaluate the actual free-energy profile for the ATP synthesis in the different conformational states of the system. Integrating the information from the different approaches provides a semiquantitative structure-function correlation for F1-ATPase. It is found that the conformational changes are converted to changes in the electrostatic interaction between the protein and its ligands, which drives the ATP synthesis.

Enhanced sampling of glutamate receptor ligand-binding domains.

PubMed

Lau, Albert Y

2018-04-14

The majority of excitatory synaptic transmission in the central nervous system is mediated by ionotropic glutamate receptors (iGluRs). These membrane-bound protein assemblies consist of modular domains that can be genetically isolated and expressed, which has resulted in a plethora of crystal structures of individual domains in different conformations bound to different ligands. These structures have presented opportunities for molecular dynamics (MD) simulation studies. To examine the free energies that govern molecular behavior, simulation strategies and algorithms have been developed, collectively called enhanced sampling methods This review focuses on the use of enhanced sampling MD simulations of isolated iGluR ligand-binding domains to characterize thermodynamic properties important to receptor function. Copyright © 2018 Elsevier B.V. All rights reserved.

The Structure of Medical Informatics Journal Literature

PubMed Central

Morris, Theodore A.; McCain, Katherine W.

1998-01-01

Abstract Objective: Medical informatics is an emergent interdisciplinary field described as drawing upon and contributing to both the health sciences and information sciences. The authors elucidate the disciplinary nature and internal structure of the field. Design: To better understand the field's disciplinary nature, the authors examine the intercitation relationships of its journal literature. To determine its internal structure, they examined its journal cocitation patterns. Measurements: The authors used data from the Science Citation Index (SCI) and Social Science Citation Index (SSCI) to perform intercitation studies among productive journal titles, and software routines from SPSS to perform multivariate data analyses on cocitation data for proposed core journals. Results: Intercitation network analysis suggests that a core literature exists, one mark of a separate discipline. Multivariate analyses of cocitation data suggest that major focus areas within the field include biomedical engineering, biomedical computing, decision support, and education. The interpretable dimensions of multidimensional scaling maps differed for the SCI and SSCI data sets. Strong links to information science literature were not found. Conclusion: The authors saw indications of a core literature and of several major research fronts. The field appears to be viewed differently by authors writing in journals indexed by SCI from those writing in journals indexed by SSCI, with more emphasis placed on computers and engineering versus decision making by the former and more emphasis on theory versus application (clinical practice) by the latter. PMID:9760393

Structure and phylogeography of two tropical predators, spinner (Stenella longirostris) and pantropical spotted (S. attenuata) dolphins, from SNP data

PubMed Central

Morin, Phillip A.

2018-01-01

Little is known about global patterns of genetic connectivity in pelagic dolphins, including how circumtropical pelagic dolphins spread globally following the rapid and recent radiation of the subfamily delphininae. In this study, we tested phylogeographic hypotheses for two circumtropical species, the spinner dolphin (Stenella longirostris) and the pantropical spotted dolphin (Stenella attenuata), using more than 3000 nuclear DNA single nucleotide polymorphisms (SNPs) in each species. Analyses for population structure indicated significant genetic differentiation between almost all subspecies and populations in both species. Bayesian phylogeographic analyses of spinner dolphins showed deep divergence between Indo-Pacific, Atlantic and eastern tropical Pacific Ocean (ETP) lineages. Despite high morphological variation, our results show very close relationships between endemic ETP spinner subspecies in relation to global diversity. The dwarf spinner dolphin is a monophyletic subspecies nested within a major clade of pantropical spinner dolphins from the Indian and western Pacific Ocean populations. Population-level division among the dwarf spinner dolphins was detected—with the northern Australia population being very different from that in Indonesia. In contrast to spinner dolphins, the major boundary for spotted dolphins is between offshore and coastal habitats in the ETP, supporting the current subspecies-level taxonomy. Comparing these species underscores the different scale at which population structure can arise, even in species that are similar in habitat (i.e. pelagic) and distribution. PMID:29765639

Can We Recognize an Innovation? Perspective from an Evolving Network Model

NASA Astrophysics Data System (ADS)

Jain, Sanjay; Krishna, Sandeep

"Innovations" are central to the evolution of societies and the evolution of life. But what constitutes an innovation? We can often agree after the event, when its consequences and impact over a long term are known, whether something was an innovation, and whether it was a "big" innovation or a "minor" one. But can we recognize an innovation "on the fly" as it appears? Successful entrepreneurs often can. Is it possible to formalize that intuition? We discuss this question in the setting of a mathematical model of evolving networks. The model exhibits self-organization , growth, stasis, and collapse of a complex system with many interacting components, reminiscent of real-world phenomena. A notion of "innovation" is formulated in terms of graph-theoretic constructs and other dynamical variables of the model. A new node in the graph gives rise to an innovation, provided it links up "appropriately" with existing nodes; in this view innovation necessarily depends upon the existing context. We show that innovations, as defined by us, play a major role in the birth, growth, and destruction of organizational structures. Furthermore, innovations can be categorized in terms of their graph-theoretic structure as they appear. Different structural classes of innovation have potentially different qualitative consequences for the future evolution of the system, some minor and some major. Possible general lessons from this specific model are briefly discussed.

Differing growth responses of major phylogenetic groups of marine bacteria to natural phytoplankton blooms in the western North Pacific Ocean.

PubMed

Tada, Yuya; Taniguchi, Akito; Nagao, Ippei; Miki, Takeshi; Uematsu, Mitsuo; Tsuda, Atsushi; Hamasaki, Koji

2011-06-01

Growth and productivity of phytoplankton substantially change organic matter characteristics, which affect bacterial abundance, productivity, and community structure in aquatic ecosystems. We analyzed bacterial community structures and measured activities inside and outside phytoplankton blooms in the western North Pacific Ocean by using bromodeoxyuridine immunocytochemistry and fluorescence in situ hybridization (BIC-FISH). Roseobacter/Rhodobacter, SAR11, Betaproteobacteria, Alteromonas, SAR86, and Bacteroidetes responded differently to changes in organic matter supply. Roseobacter/Rhodobacter bacteria remained widespread, active, and proliferating despite large fluctuations in organic matter and chlorophyll a (Chl-a) concentrations. The relative contribution of Bacteroidetes to total bacterial production was consistently high. Furthermore, we documented the unexpectedly large contribution of Alteromonas to total bacterial production in the bloom. Bacterial abundance, productivity, and growth potential (the proportion of growing cells in a population) were significantly correlated with Chl-a and particulate organic carbon concentrations. Canonical correspondence analysis showed that organic matter supply was critical for determining bacterial community structures. The growth potential of each bacterial group as a function of Chl-a concentration showed a bell-shaped distribution, indicating an optimal organic matter concentration to promote growth. The growth of Alteromonas and Betaproteobacteria was especially strongly correlated with organic matter supply. These data elucidate the distinctive ecological role of major bacterial taxa in organic matter cycling during open ocean phytoplankton blooms.

Differing Growth Responses of Major Phylogenetic Groups of Marine Bacteria to Natural Phytoplankton Blooms in the Western North Pacific Ocean ▿ †

PubMed Central

Tada, Yuya; Taniguchi, Akito; Nagao, Ippei; Miki, Takeshi; Uematsu, Mitsuo; Tsuda, Atsushi; Hamasaki, Koji

2011-01-01

Growth and productivity of phytoplankton substantially change organic matter characteristics, which affect bacterial abundance, productivity, and community structure in aquatic ecosystems. We analyzed bacterial community structures and measured activities inside and outside phytoplankton blooms in the western North Pacific Ocean by using bromodeoxyuridine immunocytochemistry and fluorescence in situ hybridization (BIC-FISH). Roseobacter/Rhodobacter, SAR11, Betaproteobacteria, Alteromonas, SAR86, and Bacteroidetes responded differently to changes in organic matter supply. Roseobacter/Rhodobacter bacteria remained widespread, active, and proliferating despite large fluctuations in organic matter and chlorophyll a (Chl-a) concentrations. The relative contribution of Bacteroidetes to total bacterial production was consistently high. Furthermore, we documented the unexpectedly large contribution of Alteromonas to total bacterial production in the bloom. Bacterial abundance, productivity, and growth potential (the proportion of growing cells in a population) were significantly correlated with Chl-a and particulate organic carbon concentrations. Canonical correspondence analysis showed that organic matter supply was critical for determining bacterial community structures. The growth potential of each bacterial group as a function of Chl-a concentration showed a bell-shaped distribution, indicating an optimal organic matter concentration to promote growth. The growth of Alteromonas and Betaproteobacteria was especially strongly correlated with organic matter supply. These data elucidate the distinctive ecological role of major bacterial taxa in organic matter cycling during open ocean phytoplankton blooms. PMID:21515719

Molecular, mesoscopic and microscopic structure evolution during amylase digestion of maize starch granules.

PubMed

Shrestha, Ashok K; Blazek, Jaroslav; Flanagan, Bernadine M; Dhital, Sushil; Larroque, Oscar; Morell, Matthew K; Gilbert, Elliot P; Gidley, Michael J

2012-09-01

Cereal starch granules with high (>50%) amylose content are a promising source of nutritionally desirable resistant starch, i.e. starch that escapes digestion in the small intestine, but the structural features responsible are not fully understood. We report the effects of partial enzyme digestion of maize starch granules on amylopectin branch length profiles, double and single helix contents, gelatinisation properties, crystallinity and lamellar periodicity. Comparing results for three maize starches (27, 57, and 84% amylose) that differ in both structural features and amylase-sensitivity allows conclusions to be drawn concerning the rate-determining features operating under the digestion conditions used. All starches are found to be digested by a side-by-side mechanism in which there is no major preference during enzyme attack for amylopectin branch lengths, helix form, crystallinity or lamellar organisation. We conclude that the major factor controlling enzyme susceptibility is granule architecture, with shorter length scales not playing a major role as inferred from the largely invariant nature of numerous structural measures during the digestion process (XRD, NMR, SAXS, DSC, FACE). Results are consistent with digestion rates being controlled by restricted diffusion of enzymes within densely packed granular structures, with an effective surface area for enzyme attack determined by external dimensions (57 or 84% amylose - relatively slow) or internal channels and pores (27% amylose - relatively fast). Although the process of granule digestion is to a first approximation non-discriminatory with respect to structure at molecular and mesoscopic length scales, secondary effects noted include (i) partial crystallisation of V-type helices during digestion of 27% amylose starch, (ii) preferential hydrolysis of long amylopectin branches during the early stage hydrolysis of 27% and 57% but not 84% amylose starches, linked with disruption of lamellar repeating structure and (iii) partial B-type recrystallisation after prolonged enzyme incubation for 57% and 84% amylose starches but not 27% amylose starch. Copyright © 2012 Elsevier Ltd. All rights reserved.

Impact of culture on autobiographical life structure in depression.

PubMed

Jobson, Laura; Miskon, Nazleen; Dalgleish, Tim; Hitchcock, Caitlin; Hill, Emma; Golden, Ann-Marie; Zulkefly, Nor Sheereen; Mukhtar, Firdaus

2018-03-23

Distortions in autobiographical memory have been implicated in major depressive disorder (MDD). Those with MDD demonstrate a 'depressogenic' autobiographical life structure. Research has not examined how culture influences this process. We investigated whether Malay individuals (members of an interdependent culture) with MDD demonstrated a 'depressogenic' autobiographical life structure similar to that of British individuals (members of an independent culture) with MDD. A 2 (Culture; Malay, British) × 2 (Mood; depressed, control) cross-sectional design using a card sort task and self-report measures was used. Malay individuals with MDD or no history of MDD completed the life-structure card-sorting task, which provided a novel method for investigating organizational structure of the life narrative. These data were compared to previously collected data in which British individuals with MDD or without MDD had completed the same task within the same experimental protocol. Pan-culturally those with MDD had greater negativity (i.e., used more negative attributes), negative redundancy (i.e., used the same negative attributes repeatedly across life chapters) and negative emodiversity (i.e., had greater variety and relative abundance of negative attributes), and reduced positive redundancy (i.e., used the same positive attributes repeatedly across chapters) in their structuring relative to controls. While the British MDD group had greater compartmentalization (i.e., the negative and positive attributes were clustered separately across different chapters) than British controls, the Malay MDD group had lower levels of compartmentalization than Malay controls. The findings suggest culture may shape aspects of the autobiographical life structure in MDD. The majority of the literature investigating depression pertains to individuals from European Western cultures, despite recognition that depression ranks as one of the most debilitating diseases worldwide. This raises questions as to whether current depression models and interventions can be applied universally or whether they are limited to European Western groups. The current study found that pan-culturally those with MDD had similar structuring of their life story relative to controls. However, there were some cultural differences that need to be considered (e.g., Malay individuals provided less detailed, less elaborate and less emotionally diverse life stories and while the British MDD group had greater compartmentalization than British controls, the Malay MDD group had lower levels of compartmentalization than Malay controls). Limitations of the study included group differences in gender and mood at the time of testing. Cultural differences in the number of attributes used may have influenced findings. Only the Malay group completed the individualism-collectivism measure. © 2018 The British Psychological Society.

Clostridium perfringens: insight into virulence evolution and population structure.

PubMed

Sawires, Youhanna S; Songer, J Glenn

2006-02-01

Clostridium perfringens is an important pathogen in veterinary and medical fields. Diseases caused by this organism are in many cases life threatening or fatal. At the same time, it is part of the ecological community of the intestinal tract of man and animals. Virulence in this species is not fully understood and it does seem that there is erratic distribution of the toxin/enzyme genes within C. perfringens population. We used the recently developed multiple-locus variable-number tandem repeat analysis (MLVA) scheme to investigate the evolution of virulence and population structure of this species. Analysis of the phylogenetic signal indicates that acquisition of the major toxin genes as well as other plasmid-borne toxin genes is a recent evolutionary event and their maintenance is essentially a function of the selective advantage they confer in certain niches under different conditions. In addition, it indicates the ability of virulent strains to cause disease in different host species. More interestingly, there is evidence that certain normal flora strains are virulent when they gain access to a different host species. Analysis of the population structure indicates that recombination events are the major tool that shapes the population and this panmixia is interrupted by frequent clonal expansion that mostly corresponds to disease processes. The signature of positive selection was detected in alpha toxin gene, suggesting the possibility of adaptive alleles on the other chromosomally encoded determinants. Finally, C. perfringens proved to have a dynamic population and availability of more genome sequences and use of comparative proteomics and animal modeling would provide more insight into the virulence of this organism.

Dispersion of Multidrug-Resistant Enterococcus faecium Isolates Belonging to Major Clonal Complexes in Different Portuguese Settings▿

PubMed Central

Freitas, Ana R.; Novais, Carla; Ruiz-Garbajosa, Patricia; Coque, Teresa M.; Peixe, Luísa

2009-01-01

The population structure of 56 Enterococcus faecium isolates selected from a collection of enterococci from humans, animals, and the environment in Portugal (1997 to 2007) was analyzed by multilocus sequence typing. We identified 41 sequence types clustering into CC17, CC5, CC9, CC22 and CC94, all clonal lineages comprising isolates from different hosts. Our findings highlight the role of community-associated hosts as reservoirs of enterococci able to cause human infections. PMID:19447948

[Dominant structural and functional adaptations of distant chemosensory systems in phylogenesis of Gastropoda].

PubMed

Zaĭtseva, O V

2000-08-01

The invasion of land by gastropods independent and repeated in the course of their evolution, was shown to be accompanied by appearance of organisationally similar olfactory tentacular organs and special integrative centres. The majority of primary and secondary water gastropods in different phylogenetic groups had a different, more primitive organisation of the tentacular sensory system as compared to the terrestrial species. Regularities of the phylogenetic adaptations of mollusks to the habitat media and lifestyle are discussed.

Phosphorylation of the budgerigar fledgling disease virus major capsid protein VP1

NASA Technical Reports Server (NTRS)

Haynes, J. I. 2nd; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

1992-01-01

The structural proteins of the budgerigar fledgling disease virus, the first known nonmammalian polyomavirus, were analyzed by isoelectric focusing and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The major capsid protein VP1 was found to be composed of at least five distinct species having isoelectric points ranging from pH 6.45 to 5.85. By analogy with the murine polyomavirus, these species apparently result from different modifications of an initial translation product. Primary chicken embryo cells were infected in the presence of 32Pi to determine whether the virus structural proteins were modified by phosphorylation. SDS-PAGE of the purified virus structural proteins demonstrated that VP1 (along with both minor capsid proteins) was phosphorylated. Two-dimensional analysis of the radiolabeled virus showed phosphorylation of only the two most acidic isoelectric species of VP1, indicating that this posttranslational modification contributes to VP1 species heterogeneity. Phosphoamino acid analysis of 32P-labeled VP1 revealed that phosphoserine is the only phosphoamino acid present in the VP1 protein.

Epitope mapping of the domains of human angiotensin converting enzyme.

PubMed

Kugaevskaya, Elena V; Kolesanova, Ekaterina F; Kozin, Sergey A; Veselovsky, Alexander V; Dedinsky, Ilya R; Elisseeva, Yulia E

2006-06-01

Somatic angiotensin converting enzyme (sACE), contains in its single chain two homologous domains (called N- and C-domains), each bearing a functional zinc-dependent active site. The present study aims to define the differences between two sACE domains and to localize experimentally revealed antigenic determinants (B-epitopes) in the recently determined three-dimensional structure of testicular tACE. The predicted linear antigenic determinants of human sACE were determined by peptide scanning ("PEPSCAN") approach. Essential difference was demonstrated between locations of the epitopes in the N- and C-domains. Comparison of arrangement of epitopes in the human domains with the corresponding sequences of some mammalian sACEs enabled to classify the revealed antigenic determinants as variable or conserved areas. The location of antigenic determinants with respect to various structural elements and to functionally important sites of the human sACE C-domain was estimated. The majority of antigenic sites of the C-domain were located at the irregular elements and at the boundaries of secondary structure elements. The data show structural differences between the sACE domains. The experimentally revealed antigenic determinants were in agreement with the recently determined crystal tACE structure. New potential applications are open to successfully produce mono-specific and group-specific antipeptide antibodies.

Structural basis of unique ligand specificity of KAI2-like protein from parasitic weed Striga hermonthica

PubMed Central

Xu, Yuqun; Miyakawa, Takuya; Nakamura, Hidemitsu; Nakamura, Akira; Imamura, Yusaku; Asami, Tadao; Tanokura, Masaru

2016-01-01

The perception of two plant germination inducers, karrikins and strigolactones, are mediated by the proteins KAI2 and D14. Recently, KAI2-type proteins from parasitic weeds, which are possibly related to seed germination induced by strigolactone, have been classified into three clades characterized by different responses to karrikin/strigolactone. Here we characterized a karrikin-binding protein in Striga (ShKAI2iB) that belongs to intermediate-evolving KAI2 and provided the structural bases for its karrikin-binding specificity. Binding assays showed that ShKAI2iB bound karrikins but not strigolactone, differing from other KAI2 and D14. The crystal structures of ShKAI2iB and ShKAI2iB-karrikin complex revealed obvious structural differences in a helix located at the entry of its ligand-binding cavity. This results in a smaller closed pocket, which is also the major cause of ShKAI2iB’s specificity of binding karrikin. Our structural study also revealed that a few non-conserved amino acids led to the distinct ligand-binding profile of ShKAI2iB, suggesting that the evolution of KAI2 resulted in its diverse functions. PMID:27507097

Use of satellite pictures for determining major shield fractures relevant for ore prospecting, northern Finland

NASA Technical Reports Server (NTRS)

Tuominen, H. V.; Aarnisalo, J. (Principal Investigator)

1976-01-01

The author has identified the following significant results. A combined analysis of LANDSAT 1 imagery, aeromagnetic and other maps, and aerial photos has revealed a dense network of bedrock fractures in northern Finland. They form several fracturing zones, which obviously represent surficial manifestations of major fractures. The fractures follow, in general, the eight main trends of crustal shear characteristics of the Baltic Shield, but show distinct deviations from them in detail. The major fracture zones divide the bedrock into a mosaic of polygonal blocks, which in many cases coincide with the main rock units of the area and are characterized by different patterns of internal fracturing. Known mineralizations show a tendency to concentrate along the fracture zones. Optical filtering of original LANDSAT images might provide a rapid tool for the analysis of major structural trends in extensive areas such as shields or entire continents.

Signal Transduction in Histidine Kinases: Insights from New Structures

PubMed Central

Bhate, Manasi P.; Molnar, Kathleen S.; Goulian, Mark; DeGrado, William F.

2015-01-01

Histidine kinases (HKs) are major players in bacterial signaling. There has been an explosion of new HK crystal structures in the last five years. We globally analyze the structures of HKs to yield insights into the mechanisms by which signals are transmitted to and across protein structures in this family. We interpret known enzymological data in the context of new structural data to show how asymmetry across the dimer interface is a key feature of signal transduction in HKs, and discuss how different HK domains undergo asymmetric-to-symmetric transitions during signal transduction and catalysis. A thermodynamic framework for signaling that encompasses these various properties is presented and the consequences of weak thermodynamic coupling are discussed. The synthesis of observations from enzymology, structural biology, protein engineering and thermodynamics paves the way for a deeper molecular understanding of histidine kinase signal transduction. PMID:25982528

Learning to Predict Combinatorial Structures

NASA Astrophysics Data System (ADS)

Vembu, Shankar

2009-12-01

The major challenge in designing a discriminative learning algorithm for predicting structured data is to address the computational issues arising from the exponential size of the output space. Existing algorithms make different assumptions to ensure efficient, polynomial time estimation of model parameters. For several combinatorial structures, including cycles, partially ordered sets, permutations and other graph classes, these assumptions do not hold. In this thesis, we address the problem of designing learning algorithms for predicting combinatorial structures by introducing two new assumptions: (i) The first assumption is that a particular counting problem can be solved efficiently. The consequence is a generalisation of the classical ridge regression for structured prediction. (ii) The second assumption is that a particular sampling problem can be solved efficiently. The consequence is a new technique for designing and analysing probabilistic structured prediction models. These results can be applied to solve several complex learning problems including but not limited to multi-label classification, multi-category hierarchical classification, and label ranking.

Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae)

PubMed Central

Zhang, Yong-Hua; Wang, Ian J.; Comes, Hans Peter; Peng, Hua; Qiu, Ying-Xiong

2016-01-01

Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels – phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important – climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors. PMID:27137438

Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae).

PubMed

Zhang, Yong-Hua; Wang, Ian J; Comes, Hans Peter; Peng, Hua; Qiu, Ying-Xiong

2016-05-03

Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels - phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important - climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors.

DISTRIBUTED STRUCTURE-SEARCHABLE TOXICITY ...

EPA Pesticide Factsheets

The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, SAR model development, or building of chemical relational databases (CRD). The Distributed Structure-Searchable Toxicity (DSSTox) Public Database Network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: 1) to adopt and encourage the use of a common standard file format (SDF) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; 2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure-toxicity data files, and that will effectively link knowledgeable toxicity data s

Structural and phase transition changes of sodium dodecyl sulfate micellar solution in alcohols probed by small-angle neutron scattering (SANS)

NASA Astrophysics Data System (ADS)

Putra, Edy Giri Rachman; Patriati, Arum

2015-04-01

Small-angle neutron scattering (SANS) measurements on 0.3M sodium dodecyl sulfate (SDS) micellar solutions have been performed in the presence of n-alcohols, from ethanol to decanol at different alcohol concentrations, 2-10 wt%. The ellipsoid micellar structure which occurred in the 0.3M SDS in aqueous solution with the size range of 30-50 Å has different behavior at various hydrocarbon chain length and concentration of alcohols. At low concentration and short chain-length of alcohols, such as ethanol, propanol, and butanol, the size of micelles reduced and had a spherical-like structure. The opposite effect occurred as medium to long chain alcohols, such as hexanol, octanol and decanol was added into the 0.3M SDS micellar solutions. The micelles structure changed to be more elongated in major axis and then crossed the critical phase transition from micellar solution into liquid crystal phase as lamellar structure emerged by further addition of alcohols. The inter-lamellar distances were also depending on the hydrocarbon chain length and concentration of alcohols. In the meantime, the persistent micellar structures occurred in addition of medium chain of n-alcohol, pentanol at all concentrations.

The crystal structure of human GDP-L-fucose synthase.

PubMed

Zhou, Huan; Sun, Lihua; Li, Jian; Xu, Chunyan; Yu, Feng; Liu, Yahui; Ji, Chaoneng; He, Jianhua

2013-09-01

Human GDP-l-fucose synthase, also known as FX protein, synthesizes GDP-l-fucose from its substrate GDP-4-keto-6-deoxy-d-mannose. The reaction involves epimerization at both C-3 and C-5 followed by an NADPH-dependent reduction of the carbonyl at C-4. In this paper, the first crystal structure of human FX protein was determined at 2.37 Å resolution. The asymmetric unit of the crystal structure contains four molecules which form two homodimers. Each molecule consists of two domains, a Rossmann-fold NADPH-binding motif and a carboxyl terminal domain. Compared with the Escherichia coli GDP-l-fucose synthase, the overall structures of these two enzymes have four major differences. There are four loops in the structure of human FX protein corresponding to two α-helices and two β-sheets in that of the E. coli enzyme. Besides, there are seven different amino acid residues binding with NAPDH comparing human FX protein with that from E. coli. The structure of human FX reveals the key catalytic residues and could be useful for the design of drugs for the treatment of inflammation, auto-immune diseases, and possibly certain types of cancer.

Effect of inherited structures on strike-slip plate boundaries: insight from analogue modelling of the central Levant Fracture System, Lebanon

NASA Astrophysics Data System (ADS)

Ghalayini, Ramadan; Daniel, Jean-Marc; Homberg, Catherine; Nader, Fadi

2015-04-01

Analogue sandbox modeling is a tool to simulate deformation style and structural evolution of sedimentary basins. The initial goal is to test what is the effect of inherited and crustal structures on the propagation, evolution, and final geometry of major strike-slip faults at the boundary between two tectonic plates. For this purpose, we have undertaken a series of analogue models to validate and reproduce the structures of the Levant Fracture System, a major NNE-SSW sinistral strike-slip fault forming the boundary between the Arabian and African plates. Onshore observations and recent high quality 3D seismic data in the Levant Basin offshore Lebanon demonstrated that Mesozoic ENE striking normal faults were reactivated into dextral strike-slip faults during the Late Miocene till present day activity of the plate boundary which shows a major restraining bend in Lebanon with a ~ 30°clockwise rotation in its trend. Experimental parameters consisted of a silicone layer at the base simulating the ductile crust, overlain by intercalated quartz sand and glass sand layers. Pre-existing structures were simulated by creating a graben in the silicone below the sand at an oblique (>60°) angle to the main throughgoing strike-slip fault. The latter contains a small stepover at depth to create transpression during sinistral strike-slip movement and consequently result in mountain building similarly to modern day Lebanon. Strike-slip movement and compression were regulated by steady-speed computer-controlled engines and the model was scanned using a CT-scanner continuously while deforming to have a final 4D model of the system. Results showed that existing normal faults were reactivated into dextral strike-slip faults as the sinistral movement between the two plates accumulated. Notably, the resulting restraining bend is asymmetric and segmented into two different compartments with differing geometries. One compartment shows a box fold anticline, while the second shows an asymmetric anticline. Thus, analogue modeling has validated observation in seismic data and onshore geology whereby Mount Lebanon and adjacent folds exhibit similar compartmentalization and geometric dissimilarities along the Levant Fracture System. We suggest that the presence of inherited structures will affect to a certain extent the geometry of restraining bends and control the evolution of large strike-slip faults passing through.

Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias

PubMed Central

2012-01-01

Background Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes. Results We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis. The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13 mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites. Conclusion The well-supported phylogenetic placement of pseudoscorpions as sister to Acariformes differs from some previous analyses based on morphology. However, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred tRNA and rRNA structures. PMID:22409411

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

Faham, S.; Watanabe, A.; Besserer, G.M.

Membrane transporters that use energy stored in sodium gradients to drive nutrients into cells constitute a major class of proteins. We report the crystal structure of a member of the solute sodium symporters (SSS), the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT). The -3.0 angstrom structure contains 14 transmembrane (TM) helices in an inward-facing conformation with a core structure of inverted repeats of 5 TM helices (TM2 to TM6 and TM7 to TM11). Galactose is bound in the center of the core, occluded from the outside solutions by hydrophobic residues. Surprisingly, the architecture of the core is similar to that of themore » leucine transporter (LeuT) from a different gene family. Modeling the outward-facing conformation based on the LeuT structure, in conjunction with biophysical data, provides insight into structural rearrangements for active transport.« less

Electrospray ionization of uranyl-citrate complexes

NASA Astrophysics Data System (ADS)

Somogyi, Árpád; Pasilis, Sofie P.; Pemberton, Jeanne E.

2007-09-01

Results presented here demonstrate the usefulness of electrospray ionization and gas-phase ion-molecule reactions to predict structural and electronic differences in complex inorganic ions. Electrospray ionization of uranyl citrate solutions generates positively and negatively charged ions that participate in further ion-molecule reactions in 3D ion trap and FT-ICR mass analyzers. Most ions observed are derived from the major solution uranyl-citrate complexes and involve species of {(UO2)2Cit2}2-, (UO2)3Cit2, and {(UO2)3Cit3}3-, where Cit indicates the citrate trianion, C6H5O73-. In a 3D ion trap operated at relatively high pressure, complex adducts containing solvent molecules, alkali and ammonium cations, and nitrate or chloride anions are dominant, and proton/alkali cation (Na+, K+) exchange is observed for up to six exchangeable protons in an excess of alkali cations. Adduct formation in a FT-ICR cell that is operated at lower pressures is less dominant, and direct detection of positive and negative ions of the major solution complexes is possible. Multiply charged ions are also detected, suggesting the presence of uranium in different oxidation states. Changes in uranium oxidation state are detected by He-CID and SORI-CID fragmentation, and certain fragments undergo association reactions in trapping analyzers, forming "exotic" species such as [(UO2)4O3]-, [(UO2)4O4]-, and [(UO2)4O5]-. Ion-molecule reactions with D2O in the FT-ICR cell indicate substantial differences in H/D exchange rate and D2O accommodation for different ion structures and charge states. Most notably, the positively charged ions [H2(UO2)2Cit2(H)]+ and [(UO2)2(Cit)]+ accommodate two and three D2O molecules, respectively, which reflects well the structural differences, i.e., tighter uranyl-citrate coordination in the former ion than in the latter. The corresponding negatively charged ions accommodate zero or two D2O molecules, which can be rationalized using suggested solution phase structures and charge state distributions.

Major Breeding Plumage Color Differences of Male Ruffs (Philomachus pugnax) Are Not Associated With Coding Sequence Variation in the MC1R Gene

PubMed Central

Küpper, Clemens; Burke, Terry; Lank, David B.

2015-01-01

Sequence variation in the melanocortin-1 receptor (MC1R) gene explains color morph variation in several species of birds and mammals. Ruffs (Philomachus pugnax) exhibit major dark/light color differences in melanin-based male breeding plumage which is closely associated with alternative reproductive behavior. A previous study identified a microsatellite marker (Ppu020) near the MC1R locus associated with the presence/absence of ornamental plumage. We investigated whether coding sequence variation in the MC1R gene explains major dark/light plumage color variation and/or the presence/absence of ornamental plumage in ruffs. Among 821bp of the MC1R coding region from 44 male ruffs we found 3 single nucleotide polymorphisms, representing 1 nonsynonymous and 2 synonymous amino acid substitutions. None were associated with major dark/light color differences or the presence/absence of ornamental plumage. At all amino acid sites known to be functionally important in other avian species with dark/light plumage color variation, ruffs were either monomorphic or the shared polymorphism did not coincide with color morph. Neither ornamental plumage color differences nor the presence/absence of ornamental plumage in ruffs are likely to be caused entirely by amino acid variation within the coding regions of the MC1R locus. Regulatory elements and structural variation at other loci may be involved in melanin expression and contribute to the extreme plumage polymorphism observed in this species. PMID:25534935

Multipole plasmons in graphene nanoellipses

NASA Astrophysics Data System (ADS)

Wang, Weihua; Song, Zhengyong

2018-02-01

We study multipole plasmons in graphene nanoellipses under the quasi-static approximation. The graphene is characterized by a homogeneous surface conductivity, and two coupled differential and integral equations are solved self-consistently to investigate the plasmonic modes in nanoellipses with a fixed area. With respect to the major axis, the symmetric and antisymmetric modes originally doubly degenerate in nanodisks will show different behavior as the semi-major axis increases. The eigen frequencies of the symmetric modes decrease, while those of the antisymmetric modes increase. At the edges, the phase changes of the symmetric dipole modes are linear and independent on structural changes; the phase changes of antisymmetric modes deviate from linear relationship, and the deviation depends on the semi-major axis. As a very large aspect ratio, they exhibit sharp peaks at the endpoints of the minor axis and zero phase changes at the endpoints of the major axis. The non-degenerate breathing mode shows its hot spots at the endpoints of the minor axis, and its eigen frequency gradually increases as the semi-major axis increases.

Persistent post-traumatic headache vs. migraine: an MRI study demonstrating differences in brain structure.

PubMed

Schwedt, Todd J; Chong, Catherine D; Peplinski, Jacob; Ross, Katherine; Berisha, Visar

2017-08-22

The majority of individuals with post-traumatic headache have symptoms that are indistinguishable from migraine. The overlap in symptoms amongst these individuals raises the question as to whether post-traumatic headache has a unique pathophysiology or if head trauma triggers migraine. The objective of this study was to compare brain structure in individuals with persistent post-traumatic headache (i.e. headache lasting at least 3 months following a traumatic brain injury) attributed to mild traumatic brain injury to that of individuals with migraine. Twenty-eight individuals with persistent post-traumatic headache attributed to mild traumatic brain injury and 28 individuals with migraine underwent brain magnetic resonance imaging on a 3 T scanner. Regional volumes, cortical thickness, surface area and curvature measurements were calculated from T1-weighted sequences and compared between subject groups using ANCOVA. MRI data from 28 healthy control subjects were used to interpret the differences in brain structure between migraine and persistent post-traumatic headache. Differences in regional volumes, cortical thickness, surface area and brain curvature were identified when comparing the group of individuals with persistent post-traumatic headache to the group with migraine. Structure was different between groups for regions within the right lateral orbitofrontal lobe, left caudal middle frontal lobe, left superior frontal lobe, left precuneus and right supramarginal gyrus (p < .05). Considering these regions only, there were differences between individuals with persistent post-traumatic headache and healthy controls within the right lateral orbitofrontal lobe, right supramarginal gyrus, and left superior frontal lobe and no differences when comparing the migraine cohort to healthy controls. In conclusion, persistent post-traumatic headache and migraine are associated with differences in brain structure, perhaps suggesting differences in their underlying pathophysiology. Additional studies are needed to further delineate similarities and differences in brain structure and function that are associated with post-traumatic headache and migraine and to determine their specificity for each of the headache types.

The Structure of Temperament in Preschoolers: A Two-Stage Factor Analytic Approach

PubMed Central

Dyson, Margaret W.; Olino, Thomas M.; Durbin, C. Emily; Goldsmith, H. Hill; Klein, Daniel N.

2012-01-01

The structure of temperament traits in young children has been the subject of extensive debate, with separate models proposing different trait dimensions. This research has relied almost exclusively on parent-report measures. The present study used an alternative approach, a laboratory observational measure, to explore the structure of temperament in preschoolers. A 2-stage factor analytic approach, exploratory factor analyses (n = 274) followed by confirmatory factor analyses (n = 276), was used. We retrieved an adequately fitting model that consisted of 5 dimensions: Sociability, Positive Affect/Interest, Dysphoria, Fear/Inhibition, and Constraint versus Impulsivity. This solution overlaps with, but is also distinct from, the major models derived from parent-report measures. PMID:21859196

A reflection on feelings and the history of science.

PubMed

Dror, Otniel E

2009-12-01

This reflection attends to Paul White's call in his introduction to this Focus section for a history of science that is informed by the history of emotions. It offers a succinct historical exemplification of the possibilities of studying the history of science in terms of the history of emotions. It draws on Raymond Williams's concept of "structure of feeling" in arguing for the emergence of an adrenaline structure of feeling during the early twentieth century. It provides a mosaic of different views of the immanence of the adrenaline structure of feeling in diverse scientific realms by broaching some of the major themes that appear in the individual essays in this Focus section.

Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

PubMed Central

de Oliveira Francisco, Flávio; Santiago, Leandro Rodrigues; Arias, Maria Cristina

2013-01-01

Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings. PMID:23569417

Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study.

PubMed

de Oliveira Francisco, Flávio; Santiago, Leandro Rodrigues; Arias, Maria Cristina

2013-03-01

Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.

Structure, coercive control, and autonomy promotion: A comparison of fathers' and mothers' food parenting strategies.

PubMed

Pratt, Mercedes; Hoffmann, Debra; Taylor, Maija; Musher-Eizenman, Dara

2017-05-01

This study explored differences in mothers' and fathers' food parenting strategies, specifically coercive control, structure, and autonomy promotion, and whether parenting style and parental responsibility for food parenting related to the use of these strategies. Parents of children aged 2.5-7.5 years ( N = 497) reported about their parenting practices and food parenting strategies. Parenting style accounted for the majority of the variance in food parenting. Fathers were more authoritarian than mothers. Authoritarian and permissive parenting practices were related to more coercive strategies. Mothers reported more food parenting responsibility. Responsibility was related to less coercive practices and more autonomy promotion and structure.

Trends in Reports on Climate Change in 2009-2011 in the Korean Press Based on Daily Newspapers' Ownership Structure

PubMed Central

Lee, Jihye; Kim, Hyunsook; Hong, Youngtak; Lee, Weonyoung

2013-01-01

Objectives The mass media play a crucial role in risk communication regarding climate change. The aim of this study was to investigate the trend in journalistic reports on climate change in the daily newspapers of Korea. Methods We selected 9 daily newspapers in Korea, which according to the ABC Association, represented 77% of newspaper circulation, out of a total of 44 Korean daily newspapers. The collected articles were from 2009 to 2011. All of the articles were sorted into the following 8 categories: greenhouse gas, climate change conventions, sea level rise, Intergovernmental Panel on Climate Change synthesis reports, expected damage and effect, use of fossil fuels, global warming, and mitigation or adaptation. A chi-squared test was done on the articles, which were counted and classified into cause, effect, and measurement of climate change according to the newspaper's majority or minority ownership structure. Results From the 9 selected newspapers, the number of articles on climate change by month was greatest in December 2009. Generally, the articles vague about climate change (lack of precise data, negative or skeptical tone, and improper use of terminology) were much more common than the articles presenting accurate knowledge. A statistical difference was found based on ownership structure: the majority-owned newspapers addressed the cause of climate change, while the minority-owned newspapers referred more to climate change measurement. Conclusions Our investigation revealed that generally Korean daily newspapers did not deliver accurate information about climate change. The coverage of the newspapers showed significant differences according to the ownership structure. PMID:23573375

Trends in reports on climate change in 2009-2011 in the Korean press based on daily newspapers' ownership structure.

PubMed

Lee, Jihye; Hong, Yeon-pyo; Kim, Hyunsook; Hong, Youngtak; Lee, Weonyoung

2013-03-01

The mass media play a crucial role in risk communication regarding climate change. The aim of this study was to investigate the trend in journalistic reports on climate change in the daily newspapers of Korea. We selected 9 daily newspapers in Korea, which according to the ABC Association, represented 77% of newspaper circulation, out of a total of 44 Korean daily newspapers. The collected articles were from 2009 to 2011. All of the articles were sorted into the following 8 categories: greenhouse gas, climate change conventions, sea level rise, Intergovernmental Panel on Climate Change synthesis reports, expected damage and effect, use of fossil fuels, global warming, and mitigation or adaptation. A chi-squared test was done on the articles, which were counted and classified into cause, effect, and measurement of climate change according to the newspaper's majority or minority ownership structure. From the 9 selected newspapers, the number of articles on climate change by month was greatest in December 2009. Generally, the articles vague about climate change (lack of precise data, negative or skeptical tone, and improper use of terminology) were much more common than the articles presenting accurate knowledge. A statistical difference was found based on ownership structure: the majority-owned newspapers addressed the cause of climate change, while the minority-owned newspapers referred more to climate change measurement. Our investigation revealed that generally Korean daily newspapers did not deliver accurate information about climate change. The coverage of the newspapers showed significant differences according to the ownership structure.

Apolipoprotein AI tertiary structures determine stability and phospholipid-binding activity of discoidal high-density lipoprotein particles of different sizes

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

Chen, Bin; Ren, Xuefeng; Neville, Tracey

2009-05-18

Human high-density lipoprotein (HDL) plays a key role in the reverse cholesterol transport pathway that delivers excess cholesterol back to the liver for clearance. In vivo, HDL particles vary in size, shape and biological function. The discoidal HDL is a 140-240 kDa, disk-shaped intermediate of mature HDL. During mature spherical HDL formation, discoidal HDLs play a key role in loading cholesterol ester onto the HDL particles by activating the enzyme, lecithin:cholesterol acyltransferase (LCAT). One of the major problems for high-resolution structural studies of discoidal HDL is the difficulty in obtaining pure and, foremost, homogenous sample. We demonstrate here that themore » commonly used cholate dialysis method for discoidal HDL preparation usually contains 5-10% lipid-poor apoAI that significantly interferes with the high-resolution structural analysis of discoidal HDL using biophysical methods. Using an ultracentrifugation method, we quickly removed lipid-poor apoAI. We also purified discoidal reconstituted HDL (rHDL) into two pure discoidal HDL species of different sizes that are amendable for high-resolution structural studies. A small rHDL has a diameter of 7.6 nm, and a large rHDL has a diameter of 9.8 nm. We show that these two different sizes of discoidal HDL particles display different stability and phospholipid-binding activity. Interestingly, these property/functional differences are independent from the apoAI -helical secondary structure, but are determined by the tertiary structural difference of apoAI on different discoidal rHDL particles, as evidenced by two-dimensional NMR and negative stain electron microscopy data. Our result further provides the first high-resolution NMR data, demonstrating a promise of structural determination of discoidal HDL at atomic resolution using a combination of NMR and other biophysical techniques.« less

Opisthobranchia (Mollusca, Gastropoda) – more than just slimy slugs. Shell reduction and its implications on defence and foraging

PubMed Central

Wägele, Heike; Klussmann-Kolb, Annette

2005-01-01

Background In general shell-less slugs are considered to be slimy animals with a rather dull appearance and a pest to garden plants. But marine slugs usually are beautifully coloured animals belonging to the less-known Opisthobranchia. They are characterized by a large array of interesting biological phenomena, usually related to foraging and/or defence. In this paper our knowledge of shell reduction, correlated with the evolution of different defensive and foraging strategies is reviewed, and new results on histology of different glandular systems are included. Results Based on a phylogeny obtained by morphological and histological data, the parallel reduction of the shell within the different groups is outlined. Major food sources are given and glandular structures are described as possible defensive structures in the external epithelia, and as internal glands. Conclusion According to phylogenetic analyses, the reduction of the shell correlates with the evolution of defensive strategies. Many different kinds of defence structures, like cleptocnides, mantle dermal formations (MDFs), and acid glands, are only present in shell-less slugs. In several cases, it is not clear whether the defensive devices were a prerequisite for the reduction of the shell, or reduction occurred before. Reduction of the shell and acquisition of different defensive structures had an implication on exploration of new food sources and therefore likely enhanced adaptive radiation of several groups. PMID:15715915

Phasins, Multifaceted Polyhydroxyalkanoate Granule-Associated Proteins

PubMed Central

Mezzina, Mariela P.

2016-01-01

Phasins are the major polyhydroxyalkanoate (PHA) granule-associated proteins. They promote bacterial growth and PHA synthesis and affect the number, size, and distribution of the granules. These proteins can be classified in 4 families with distinctive characteristics. Low-resolution structural studies and in silico predictions were performed in order to elucidate the structure of different phasins. Most of these proteins share some common structural features, such as a preponderant α-helix composition, the presence of disordered regions that provide flexibility to the protein, and coiled-coil interacting regions that form oligomerization domains. Due to their amphiphilic nature, these proteins play an important structural function, forming an interphase between the hydrophobic content of PHA granules and the hydrophilic cytoplasm content. Phasins have been observed to affect both PHA accumulation and utilization. Apart from their role as granule structural proteins, phasins have a remarkable variety of additional functions. Different phasins have been determined to (i) activate PHA depolymerization, (ii) increase the expression and activity of PHA synthases, (iii) participate in PHA granule segregation, and (iv) have both in vivo and in vitro chaperone activities. These properties suggest that phasins might play an active role in PHA-related stress protection and fitness enhancement. Due to their granule binding capacity and structural flexibility, several biotechnological applications have been developed using different phasins, increasing the interest in the study of these remarkable proteins. PMID:27287326

Phasins, Multifaceted Polyhydroxyalkanoate Granule-Associated Proteins.

PubMed

Mezzina, Mariela P; Pettinari, M Julia

2016-09-01

Phasins are the major polyhydroxyalkanoate (PHA) granule-associated proteins. They promote bacterial growth and PHA synthesis and affect the number, size, and distribution of the granules. These proteins can be classified in 4 families with distinctive characteristics. Low-resolution structural studies and in silico predictions were performed in order to elucidate the structure of different phasins. Most of these proteins share some common structural features, such as a preponderant α-helix composition, the presence of disordered regions that provide flexibility to the protein, and coiled-coil interacting regions that form oligomerization domains. Due to their amphiphilic nature, these proteins play an important structural function, forming an interphase between the hydrophobic content of PHA granules and the hydrophilic cytoplasm content. Phasins have been observed to affect both PHA accumulation and utilization. Apart from their role as granule structural proteins, phasins have a remarkable variety of additional functions. Different phasins have been determined to (i) activate PHA depolymerization, (ii) increase the expression and activity of PHA synthases, (iii) participate in PHA granule segregation, and (iv) have both in vivo and in vitro chaperone activities. These properties suggest that phasins might play an active role in PHA-related stress protection and fitness enhancement. Due to their granule binding capacity and structural flexibility, several biotechnological applications have been developed using different phasins, increasing the interest in the study of these remarkable proteins. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

A worldwide analysis of within-canopy variations in leaf structural, chemical and physiological traits across plant functional types

PubMed Central

Niinemets, Ülo; Keenan, Trevor F.; Hallik, Lea

2018-01-01

Summary Extensive within-canopy light gradients importantly affect photosynthetic productivity of leaves in different canopy positions and lead to light-dependent increases in foliage photosynthetic capacity per area (AA). However, the controls on AA variations by changes in underlying traits are poorly known. We constructed an unprecedented worldwide database including 831 within-canopy gradients with standardized light estimates for 304 species belonging to major vascular plant functional types, and analyzed within-canopy variations in 12 key foliage structural, chemical and physiological traits by quantitatively separating the contributions of different traits to photosynthetic acclimation. Although the light-dependent increase in AA is surprisingly similar in different plant functional types, they fundamentally differ in the share of the controls on AA by constituent traits. Species with high rates of canopy development and leaf turnover exhibiting highly dynamic light environments, actively change AA by nitrogen reallocation among and partitioning within leaves. In contrast, species with slow leaf turnover exhibit a passive AA acclimation response primarily determined by acclimation of leaf structure to growth light. This review emphasizes that different combinations of traits are responsible for within-canopy photosynthetic acclimation in different plant functional types and solves an old enigma of the role of mass- vs. area-based traits in vegetation acclimation. PMID:25318596

Antecedents and consequences of caregiving structure on young mothers and their infants.

PubMed

Arnold, Anna; Lewis, Jessica; Maximovich, Alexey; Ickovics, Jeannette; Kershaw, Trace

2011-10-01

This study describes the multigenerational caregiving structure of infants born to young women, the prenatal predictors of caregiving structure, and the effects of caregiving structure on the health of young mothers and their infants 6 months postpartum. The sample consisted of 784 young mothers involved in a longitudinal study in two U.S. cities. Women were classified into eight caregiving structure groups based on the mother's report of herself as a caregiver and her selection of the baby's father and/or grandparents as caregivers. ANCOVA analyses identified predictors and 6 month postpartum outcomes of caregiving structure. Planned comparisons explored the relationships among caregiving structure groups. A majority of women reported caregiving structures other than herself and the father as caregivers (87.1%). Grandparents were indicated as caregivers by most women (62.2%). Postpartum caregiving groups differed on prenatal social support, self-esteem, attachment avoidance and anxiety, relationship status, and living with the baby's father. While mother's self esteem significantly predicted father involvement, there were no differences on predictors between when the mother and father were caregivers, versus when the mother and grandparents were caregivers. Differences existed between groups on mother and child outcomes, including parenting stress, distress, and child dysfunction. Women reported significantly less parenting stress, child dysfunction, and negative child emotions when she and the father were caregivers, versus when she and grandparents were caregivers. The family system and the intergenerational dynamics within a multigenerational caregiving structure are critical to the health and well-being of both mothers and their children.

Antecedents and Consequences of Caregiving Structure on Young Mothers and Their Infants

PubMed Central

Lewis, Jessica; Maximovich, Alexey; Ickovics, Jeannette; Kershaw, Trace

2010-01-01

This study describes the multigenerational caregiving structure of infants born to young women, the prenatal predictors of caregiving structure, and the effects of caregiving structure on the health of young mothers and their infants 6 months postpartum. The sample consisted of 784 young mothers involved in a longitudinal study in two U.S. cities. Women were classified into eight caregiving structure groups based on the mother’s report of herself as a caregiver and her selection of the baby’s father and/or grandparents as caregivers. ANCOVA analyses identified predictors and 6 month postpartum outcomes of caregiving structure. Planned comparisons explored the relationships among caregiving structure groups. A majority of women reported caregiving structures other than herself and the father as caregivers (87.1%). Grandparents were indicated as caregivers by most women (62.2%). Postpartum caregiving groups differed on prenatal social support, self-esteem, attachment avoidance and anxiety, relationship status, and living with the baby’s father. While mother’s self esteem significantly predicted father involvement, there were no differences on predictors between when the mother and father were caregivers, versus when the mother and grandparents were caregivers. Differences existed between groups on mother and child outcomes, including parenting stress, distress, and child dysfunction. Women reported significantly less parenting stress, child dysfunction, and negative child emotions when she and the father were caregivers, versus when she and grandparents were caregivers. The family system and the intergenerational dynamics within a multigenerational caregiving structure are critical to the health and well-being of both mothers and their children. PMID:20680671

The Talent Development Middle School Model: Context, Components, and Initial Impacts on Students' Performance and Attendance

ERIC Educational Resources Information Center

Herlihy, Corinne M.; Kemple, James J.

2004-01-01

The Talent Development Middle School model was created to make a difference in struggling urban middle schools. The model is part of a trend in school improvement strategies whereby whole-school reform projects aim to improve performance and attendance outcomes for students through the use of major changes in both the organizational structure and…

Emergence of modern marine ecosystems.

PubMed

Hull, Pincelli M

2017-06-05

The structure and function of marine ecosystems are not fixed. Instead, major innovations - from the origin of oxygenic photosynthesis, to the evolution of reefs or of deep bioturbation, to the rise of pelagic calcifiers - have changed biogeochemical cycles and ecosystem dynamics. As a result, modern marine ecosystems are fundamentally different from those in the distant past. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Extreme Searcher's Guide to Web Search Engines: A Handbook for the Serious Searcher. 2nd Edition.

ERIC Educational Resources Information Center

Hock, Randolph

This book aims to facilitate more effective and efficient use of World Wide Web search engines by helping the reader: know the basic structure of the major search engines; become acquainted with those attributes (features, benefits, options, content, etc.) that search engines have in common and where they differ; know the main strengths and…

Reality Presentation and Communication: A Comparative Discussion of the Smithsonian Institution and The Washington Post as Communications Structures.

ERIC Educational Resources Information Center

Harvey, Lisa St. Clair

A comparative study of two types of media, a newspaper and a museum, reveals substantive differences in the ways each of these communications organizations alters the information which it presents to the public. Interviews conducted with spokespeople from the Washington Post and the Smithsonian Institution focused on three major theories of…

Stream Nitrate Response to Different Burning Treatments in Southern Appalachian Forests

Treesearch

Barton D. Clinton; James M. Vose; Jennifer D. Knoepp; Katherine J. Elliott

2003-01-01

Southern Appalachian forests are undergoing considerable change due to altered disturbance regimes. For example, fire exclusion has had a major impact on the structure and function of pine-hardwood ecosystems. Recently, fire has been prescribed for a variety of applications: 1) stand-replacement in the form of a mimicked wildfire, 2) site-preparation as part of a fell-...

Mathematical investigation of IP3-dependent calcium dynamics in astrocytes.

PubMed

Handy, Gregory; Taheri, Marsa; White, John A; Borisyuk, Alla

2017-06-01

We study evoked calcium dynamics in astrocytes, a major cell type in the mammalian brain. Experimental evidence has shown that such dynamics are highly variable between different trials, cells, and cell subcompartments. Here we present a qualitative analysis of a recent mathematical model of astrocyte calcium responses. We show how the major response types are generated in the model as a result of the underlying bifurcation structure. By varying key channel parameters, mimicking blockers used by experimentalists, we manipulate this underlying bifurcation structure and predict how the distributions of responses can change. We find that store-operated calcium channels, plasma membrane bound channels with little activity during calcium transients, have a surprisingly strong effect, underscoring the importance of considering these channels in both experiments and mathematical settings. Variation in the maximum flow in different calcium channels is also shown to determine the range of stable oscillations, as well as set the range of frequencies of the oscillations. Further, by conducting a randomized search through the parameter space and recording the resulting calcium responses, we create a database that can be used by experimentalists to help estimate the underlying channel distribution of their cells.

FIRE aircraft observations of horizontal and vertical transport in marine stratocumulus

NASA Technical Reports Server (NTRS)

Paluch, Ilga R.; Lenschow, Donald H.

1990-01-01

A major goal of research on marine stratocumulus is to try to understand the processes that generate and dissipate them. One approach to studying this problem is to investigate the boundary layer structure in the vicinity of a transition from a cloudy to a cloud-free region to document the differences in structure on each side of the transition. Since stratiform clouds have a major impact on the radiation divergence in the boundary layer, the transition from a cloudy to a clear boundary layer is a region of large horizontal inhomogeneity in air temperature and turbulence intensity. This leads to a considerable difference in horizontal and vertical transports between the cloudy and cloud-free regions. Measurements are used from the NCAR Electra aircraft during flights 5 (7 July 1987) and 10 (18 July 1987) of FIRE for this purpose. Flight 5 coincided with a LANDSAT overflight, and was designed to investigate the transition across a well-defined N-S cloud boundary, since the LANDSAT image can document the cloud cover in considerable detail. Turbulence legs were flown about 60 km on both sides of the cloud boundary. Flight 10 was flown at night in an area of scattered small cumuli and broken cloud patches.

Epigenetic regulation and chromatin remodeling in learning and memory.

PubMed

Kim, Somi; Kaang, Bong-Kiun

2017-01-13

Understanding the underlying mechanisms of memory formation and maintenance has been a major goal in the field of neuroscience. Memory formation and maintenance are tightly controlled complex processes. Among the various processes occurring at different levels, gene expression regulation is especially crucial for proper memory processing, as some genes need to be activated while some genes must be suppressed. Epigenetic regulation of the genome involves processes such as DNA methylation and histone post-translational modifications. These processes edit genomic properties or the interactions between the genome and histone cores. They then induce structural changes in the chromatin and lead to transcriptional changes of different genes. Recent studies have focused on the concept of chromatin remodeling, which consists of 3D structural changes in chromatin in relation to gene regulation, and is an important process in learning and memory. In this review, we will introduce three major epigenetic processes involved in memory regulation: DNA methylation, histone methylation and histone acetylation. We will also discuss general mechanisms of long-term memory storage and relate the epigenetic control of learning and memory to chromatin remodeling. Finally, we will discuss how epigenetic mechanisms can contribute to the pathologies of neurological disorders and cause memory-related symptoms.

1/f noise in titanium doped aluminum thin film deposited by electron beam evaporation method and its dependence on structural variation with temperature

NASA Astrophysics Data System (ADS)

Ananda, P.; Vedanayakam, S. Victor; Thyagarajan, K.; Nandakumar, N.

2018-05-01

A brief review of Titanium doped Aluminum film has many attractive properties such as thermal properties and 1/f noise is highlighted. The thin film devices of Titanium doped alluminium are specially used in aerospace technology, automotive, biomedical fields also in microelectronics. In this paper, we discus on 1/f noise and nonlinear effects in titanium doped alluminium thin films deposited on glass substrate using electron beam evaporation for different current densities on varying temperatures of the film. The plots are dawn for 1/f noise of the films at different temperatures ranging from 300°C to 450°C and the slopes are determined. The studies shows a higher order increment in FFT amplitude of low frequency 1/f noise in thin films at annealing temperature 400°C. In this technology used in aerospace has been the major field of application of titanium doped alluminium, being one of the major challenges of the development of new alloys with improved strength at high temperature, wide chord Titanium doped alluminium fan blades increases the efficiency while reducing 1/f noise. Structural properties of XRD is identified.

Lysozymes in the animal kingdom.

PubMed

Callewaert, Lien; Michiels, Chris W

2010-03-01

Lysozymes (EC 3.2.1.17) are hydrolytic enzymes, characterized by their ability to cleave the beta-(1,4)-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycan, the major bacterial cell wall polymer. In the animal kingdom, three major distinct lysozyme types have been identified--the c-type (chicken or conventional type), the g-type (goose-type) and the i-type (invertebrate type) lysozyme. Examination of the phylogenetic distribution of these lysozymes reveals that c-type lysozymes are predominantly present in the phylum of the Chordata and in different classes of the Arthropoda. Moreover, g-type lysozymes (or at least their corresponding genes) are found in members of the Chordata, as well as in some bivalve mollusks belonging to the invertebrates. In general, the latter animals are known to produce i-type lysozymes. Although the homology in primary structure for representatives of these three lysozyme types is limited, their three-dimensional structures show striking similarities. Nevertheless, some variation exists in their catalytic mechanisms and the genomic organization of their genes. Regarding their biological role, the widely recognized function of lysozymes is their contribution to antibacterial defence but, additionally, some lysozymes (belonging to different types) are known to function as digestive enzymes.

Structural heterogeneity leads to functional homogeneity in A. marina phycocyanin.

PubMed

Bar-Zvi, Shira; Lahav, Avital; Harris, Dvir; Niedzwiedzki, Dariusz M; Blankenship, Robert E; Adir, Noam

2018-07-01

The major light harvesting antenna in all cyanobacterial species is the phycobilisome (PBS). The smallest PBS identified to date is that of Acaryochloris marina (A. marina), composed of a single four-hexamer rod. We have determined the crystal structure of phycocyanin (AmPC), the major component of the A. marina PBS (AmPBS) to 2.1 Å. The basic unit of the AmPC is a heterodimer of two related subunits (α and β), and we show that the asymmetric unit contains a superposition of two α and two β isoforms, the products of the simultaneous expression of different genes. This is the first time to our knowledge that isolated proteins crystallized with such identifiable heterogeneity. We believe that the presence of the different isoforms allows the AmPBS to have a significant bathochromic shift in its fluorescence emission spectrum, allowing, in the total absence of allophycocyanin, a better overlap with absorption of the chlorophyll d-containing reaction centers. We show that this bathochromic shift exists in intact AmPBS as well as in its disassembled components, thus suggesting that AmPC can efficiently serve as the AmPBS terminal emitter. Copyright © 2018 Elsevier B.V. All rights reserved.

An integrated map of structural variation in 2,504 human genomes.

PubMed

Sudmant, Peter H; Rausch, Tobias; Gardner, Eugene J; Handsaker, Robert E; Abyzov, Alexej; Huddleston, John; Zhang, Yan; Ye, Kai; Jun, Goo; Fritz, Markus Hsi-Yang; Konkel, Miriam K; Malhotra, Ankit; Stütz, Adrian M; Shi, Xinghua; Casale, Francesco Paolo; Chen, Jieming; Hormozdiari, Fereydoun; Dayama, Gargi; Chen, Ken; Malig, Maika; Chaisson, Mark J P; Walter, Klaudia; Meiers, Sascha; Kashin, Seva; Garrison, Erik; Auton, Adam; Lam, Hugo Y K; Mu, Xinmeng Jasmine; Alkan, Can; Antaki, Danny; Bae, Taejeong; Cerveira, Eliza; Chines, Peter; Chong, Zechen; Clarke, Laura; Dal, Elif; Ding, Li; Emery, Sarah; Fan, Xian; Gujral, Madhusudan; Kahveci, Fatma; Kidd, Jeffrey M; Kong, Yu; Lameijer, Eric-Wubbo; McCarthy, Shane; Flicek, Paul; Gibbs, Richard A; Marth, Gabor; Mason, Christopher E; Menelaou, Androniki; Muzny, Donna M; Nelson, Bradley J; Noor, Amina; Parrish, Nicholas F; Pendleton, Matthew; Quitadamo, Andrew; Raeder, Benjamin; Schadt, Eric E; Romanovitch, Mallory; Schlattl, Andreas; Sebra, Robert; Shabalin, Andrey A; Untergasser, Andreas; Walker, Jerilyn A; Wang, Min; Yu, Fuli; Zhang, Chengsheng; Zhang, Jing; Zheng-Bradley, Xiangqun; Zhou, Wanding; Zichner, Thomas; Sebat, Jonathan; Batzer, Mark A; McCarroll, Steven A; Mills, Ryan E; Gerstein, Mark B; Bashir, Ali; Stegle, Oliver; Devine, Scott E; Lee, Charles; Eichler, Evan E; Korbel, Jan O

2015-10-01

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

Are major dissociative disorders characterized by a qualitatively different kind of dissociation?

PubMed

Rodewald, Frauke; Dell, Paul F; Wilhelm-Gossling, Claudia; Gast, Ursula

2011-01-01

A total of 66 patients with a major dissociative disorder, 54 patients with nondissociative disorders, and 30 nonclinical controls were administered the Structured Clinical Interview for DSM-IV Dissociative Disorders-Revised, the Dissociative Experiences Scale, the Multidimensional Inventory of Dissociation, and the Symptom Checklist 90-Revised. Dissociative patients reported significantly more dissociative and nondissociative symptoms than did nondissociative patients and nonclinical controls. When general psychopathology was controlled, the dissociation scores of dissociative patients were still significantly higher than those of both other groups, whereas the dissociation scores of nondissociative patients and nonclinical controls no longer differed. These findings appear to be congruent with a typological model of dissociation that distinguishes between 2 qualitatively different kinds of dissociation. Specifically, the results of this study suggest that the dissociation that occurs in major dissociative disorders (i.e., dissociative identity disorder [DID] and dissociative disorder not otherwise specified, Type 1 [DDNOS-1]) is qualitatively different from the dissociation that occurs in persons who do not have a dissociative disorder. In contrast to previous research, the dissociation of persons who do not have a dissociative disorder is not limited to absorption; it covers a much wider range of phenomena. The authors hypothesize that different mechanisms produce the dissociation of persons with DID and DDNOS-1 as opposed to the dissociation of persons who do not have a dissociative disorder.

Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand

PubMed Central

2011-01-01

Background The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure. Results A large fraction of genetic variation is observed within populations (about 80% and 90% for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2%) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern. Conclusions The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them. PMID:21672265

Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand.

PubMed

Kutanan, Wibhu; Kampuansai, Jatupol; Fuselli, Silvia; Nakbunlung, Supaporn; Seielstad, Mark; Bertorelle, Giorgio; Kangwanpong, Daoroong

2011-06-15

The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure. A large fraction of genetic variation is observed within populations (about 80% and 90% for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2%) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern. The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them. © 2011 Kutanan et al; licensee BioMed Central Ltd.

Communities of nirS-type denitrifiers in the water column of the oxygen minimum zone in the eastern South Pacific.

PubMed

Castro-González, Maribeb; Braker, Gesche; Farías, Laura; Ulloa, Osvaldo

2005-09-01

The major sites of water column denitrification in the ocean are oxygen minimum zones (OMZ), such as one in the eastern South Pacific (ESP). To understand the structure of denitrifying communities in the OMZ off Chile, denitrifier communities at two sites in the Chilean OMZ (Antofagasta and Iquique) and at different water depths were explored by terminal restriction fragment length polymorphism analysis and cloning of polymerase chain reaction (PCR)-amplified nirS genes. NirS is a functional marker gene for denitrification encoding cytochrome cd1-containing nitrite reductase, which catalyses the reduction of nitrite to nitric oxide, the key step in denitrification. Major differences were found between communities from the two geographic locations. Shifts in community structure occurred along a biogeochemical gradient at Antofagasta. Canonical correspondence analysis indicated that O2, NO3-, NO2- and depth were important environmental factors governing these communities along the biogeochemical gradient in the water column. Phylogenetic analysis grouped the majority of clones from the ESP in distinct clusters of genes from presumably novel and yet uncultivated denitrifers. These nirS clusters were distantly related to those found in the water column of the Arabian Sea but the phylogenetic distance was even higher compared with environmental sequences from marine sediments or any other habitat. This finding suggests similar environmental conditions trigger the development of denitrifiers with related nirS genotypes despite large geographic distances.

A Landscape Approach to Invasive Species Management.

PubMed

Lurgi, Miguel; Wells, Konstans; Kennedy, Malcolm; Campbell, Susan; Fordham, Damien A

2016-01-01

Biological invasions are not only a major threat to biodiversity, they also have major impacts on local economies and agricultural production systems. Once established, the connection of local populations into metapopulation networks facilitates dispersal at landscape scales, generating spatial dynamics that can impact the outcome of pest-management actions. Much planning goes into landscape-scale invasive species management. However, effective management requires knowledge on the interplay between metapopulation network topology and management actions. We address this knowledge gap using simulation models to explore the effectiveness of two common management strategies, applied across different extents and according to different rules for selecting target localities in metapopulations with different network topologies. These management actions are: (i) general population reduction, and (ii) reduction of an obligate resource. The reduction of an obligate resource was generally more efficient than population reduction for depleting populations at landscape scales. However, the way in which local populations are selected for management is important when the topology of the metapopulation is heterogeneous in terms of the distribution of connections among local populations. We tested these broad findings using real-world scenarios of European rabbits (Oryctolagus cuniculus) infesting agricultural landscapes in Western Australia. Although management strategies targeting central populations were more effective in simulated heterogeneous metapopulation structures, no difference was observed in real-world metapopulation structures that are highly homogeneous. In large metapopulations with high proximity and connectivity of neighbouring populations, different spatial management strategies yield similar outcomes. Directly considering spatial attributes in pest-management actions will be most important for metapopulation networks with heterogeneously distributed links. Our modelling framework provides a simple approach for identifying the best possible management strategy for invasive species based on metapopulation structure and control capacity. This information can be used by managers trying to devise efficient landscape-oriented management strategies for invasive species and can also generate insights for conservation purposes.

Comparative ultrastructure of the cuticle of trichostrongyle nematodes.

PubMed

Beveridge, I; Durette-Desset, M C

1994-09-01

The ultrastructure of the cuticle was examined in Austrostrongylus victoriensis, Patricialina birdi and Woolleya monodelphis (Herpetostrongylidae) from marsupials, Paraustrostrongylus ratti (Herpetostrongylidae) from rodents, Nippostrongylus magnus and Odilia bainae (Heligmonellidae) from rodents, Cooperia oncophora and Camelostrongylus mentulatus (Trichostrongylidae) from ruminants, and Nematodirus spathiger (Molineidae) from ruminants. The principal cuticular layers described previously were present in all species investigated. Major differences in the shape and composition of cuticular struts were observed as well as differences in components of the median zone of the cuticle, including the fluid-filled regions present in several species. Several different types of strut were observed. Although strut structure within the Heligmonellidae appeared to be constant, there were variations within both the Herpetostrongylidae and Trichostrongylidae. In Nem. spathiger the cuticular ridges lacked struts. The diversity of structures found in the species examined suggests that more extensive comparative studies of the trichostrongyle cuticle are warranted.

Steady State Structural Analysis of High Pressure Gas Turbine Blade using Finite Element Analysis

NASA Astrophysics Data System (ADS)

Mazarbhuiya, Hussain Mahamed Sahed Mostafa; Murari Pandey, Krishna

2017-08-01

In gas turbines the major portion of performance dependency lies upon turbine blade design. Turbine blades experience very high centrifugal, axial and tangential force during power generation. While withstanding these forces blades undergo elongation. Different methods have proposed for better enhancement of the mechanical properties of blade to withstand in extreme condition. Present paper describes the stress and elongation for blades having properties of different materials. Steady state structural analysis have performed in the present work for different materials (In 625, In 718, In 738, In 738 LC, MAR M246, Ni-Cr, Ti-alloy, Ti-Al, Ti-T6, U500). Remarkable finding is that the root of the blade is subjected to maximum stress for all blade materials and the blade made of MAR M246 has less stress and deformation among all other blade materials which can be selected as a suitable material for gas turbine blade.

SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data.

PubMed

Polishchuk, Maya; Paz, Inbal; Yakhini, Zohar; Mandel-Gutfreund, Yael

2018-05-25

Gene expression regulation is highly dependent on binding of RNA-binding proteins (RBPs) to their RNA targets. Growing evidence supports the notion that both RNA primary sequence and its local secondary structure play a role in specific Protein-RNA recognition and binding. Despite the great advance in high-throughput experimental methods for identifying sequence targets of RBPs, predicting the specific sequence and structure binding preferences of RBPs remains a major challenge. We present a novel webserver, SMARTIV, designed for discovering and visualizing combined RNA sequence and structure motifs from high-throughput RNA-binding data, generated from in-vivo experiments. The uniqueness of SMARTIV is that it predicts motifs from enriched k-mers that combine information from ranked RNA sequences and their predicted secondary structure, obtained using various folding methods. Consequently, SMARTIV generates Position Weight Matrices (PWMs) in a combined sequence and structure alphabet with assigned P-values. SMARTIV concisely represents the sequence and structure motif content as a single graphical logo, which is informative and easy for visual perception. SMARTIV was examined extensively on a variety of high-throughput binding experiments for RBPs from different families, generated from different technologies, showing consistent and accurate results. Finally, SMARTIV is a user-friendly webserver, highly efficient in run-time and freely accessible via http://smartiv.technion.ac.il/.

Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity.

PubMed

Carpenter, Danielle; Mitchell, Laura M; Armour, John A L

2017-02-20

Salivary amylase in humans is encoded by the copy variable gene AMY1 in the amylase gene cluster on chromosome 1. Although the role of salivary amylase is well established, the consequences of the copy number variation (CNV) at AMY1 on salivary amylase protein production are less well understood. The amylase gene cluster is highly structured with a fundamental difference between odd and even AMY1 copy number haplotypes. In this study, we aimed to explore, in samples from 119 unrelated individuals, not only the effects of AMY1 CNV on salivary amylase protein expression and amylase enzyme activity but also whether there is any evidence for underlying difference between the common haplotypes containing odd numbers of AMY1 and even copy number haplotypes. AMY1 copy number was significantly correlated with the variation observed in salivary amylase production (11.7% of variance, P < 0.0005) and enzyme activity (13.6% of variance, P < 0.0005) but did not explain the majority of observed variation between individuals. AMY1-odd and AMY1-even haplotypes showed a different relationship between copy number and expression levels, but the difference was not statistically significant (P = 0.052). Production of salivary amylase is correlated with AMY1 CNV, but the majority of interindividual variation comes from other sources. Long-range haplotype structure may affect expression, but this was not significant in our data.

Genomic Epidemiology of Salmonella enterica Serotype Enteritidis based on Population Structure of Prevalent Lineages

PubMed Central

Desai, Prerak T.; den Bakker, Henk C.; Mikoleit, Matthew; Tolar, Beth; Trees, Eija; Hendriksen, Rene S.; Frye, Jonathan G.; Porwollik, Steffen; Weimer, Bart C.; Wiedmann, Martin; Weinstock, George M.; Fields, Patricia I.; McClelland, Michael

2014-01-01

Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains from 2 different sequencing platforms. Five major genetic lineages were recognized, which revealed possible patterns of geographic and epidemiologic distribution. Analyses on the population dynamics and evolutionary history estimated that major lineages emerged during the 17th–18th centuries and diversified during the 1920s and 1950s. PMID:25147968

The College Mathematics Experience and Changes in Majors: A Structural Model Analysis.

ERIC Educational Resources Information Center

Whiteley, Meredith A.; Fenske, Robert H.

1990-01-01

Testing of a structural equation model with college mathematics experience as the focal variable in 745 students' final decisions concerning major or dropping out over 4 years of college yielded separate model estimates for 3 fields: scientific/technical, quantitative business, and business management majors. (Author/MSE)

Protein Delivery into Plant Cells: Toward In vivo Structural Biology

PubMed Central

Cedeño, Cesyen; Pauwels, Kris; Tompa, Peter

2017-01-01

Understanding the biologically relevant structural and functional behavior of proteins inside living plant cells is only possible through the combination of structural biology and cell biology. The state-of-the-art structural biology techniques are typically applied to molecules that are isolated from their native context. Although most experimental conditions can be easily controlled while dealing with an isolated, purified protein, a serious shortcoming of such in vitro work is that we cannot mimic the extremely complex intracellular environment in which the protein exists and functions. Therefore, it is highly desirable to investigate proteins in their natural habitat, i.e., within live cells. This is the major ambition of in-cell NMR, which aims to approach structure-function relationship under true in vivo conditions following delivery of labeled proteins into cells under physiological conditions. With a multidisciplinary approach that includes recombinant protein production, confocal fluorescence microscopy, nuclear magnetic resonance (NMR) spectroscopy and different intracellular protein delivery strategies, we explore the possibility to develop in-cell NMR studies in living plant cells. While we provide a comprehensive framework to set-up in-cell NMR, we identified the efficient intracellular introduction of isotope-labeled proteins as the major bottleneck. Based on experiments with the paradigmatic intrinsically disordered proteins (IDPs) Early Response to Dehydration protein 10 and 14, we also established the subcellular localization of ERD14 under abiotic stress. PMID:28469623

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

Perez-Miller, Samantha; Zou, Qin; Novotny, Milos V.

In mice, the major urinary proteins (MUP) play a key role in pheromonal communication by binding and transporting semiochemicals. MUP-IV is the only isoform known to be expressed in the vomeronasal mucosa. In comparison with the MUP isoforms that are abundantly excreted in the urine, MUP-IV is highly specific for the male mouse pheromone 2-sec-butyl-4,5-dihydrothiazole (SBT). To examine the structural basis of this ligand preference, we determined the X-ray crystal structure of MUP-IV bound to three mouse pheromones: SBT, 2,5-dimethylpyrazine, and 2-heptanone. We also obtained the structure of MUP-IV with 2-ethylhexanol bound in the cavity. These four structures show thatmore » relative to the major excreted MUP isoforms, three amino acid substitutions within the binding calyx impact ligand coordination. The F103 for A along with F54 for L result in a smaller cavity, potentially creating a more closely packed environment for the ligand. The E118 for G substitution introduces a charged group into a hydrophobic environment. The sidechain of E118 is observed to hydrogen bond to polar groups on all four ligands with nearly the same geometry as seen for the water-mediated hydrogen bond network in the MUP-I and MUP-II crystal structures. These differences in cavity size and interactions between the protein and ligand are likely to contribute to the observed specificity of MUP-IV.« less

Structural health monitoring methodology for aircraft condition-based maintenance

NASA Astrophysics Data System (ADS)

Saniger, Jordi; Reithler, Livier; Guedra-Degeorges, Didier; Takeda, Nobuo; Dupuis, Jean Pierre

2001-06-01

Reducing maintenance costs while keeping a constant level of safety is a major issue for Air Forces and airlines. The long term perspective is to implement condition based maintenance to guarantee a constant safety level while decreasing maintenance costs. On this purpose, the development of a generalized Structural Health Monitoring System (SHMS) is needed. The objective of such a system is to localize the damages and to assess their severity, with enough accuracy to allow low cost corrective actions. The present paper describes a SHMS based on acoustic emission technology. This choice was driven by its reliability and wide use in the aerospace industry. The described SHMS uses a new learning methodology which relies on the generation of artificial acoustic emission events on the structure and an acoustic emission sensor network. The calibrated acoustic emission events picked up by the sensors constitute the knowledge set that the system relies on. With this methodology, the anisotropy of composite structures is taken into account, thus avoiding the major cause of errors of classical localization methods. Moreover, it is adaptive to different structures as it does not rely on any particular model but on measured data. The acquired data is processed and the event's location and corrected amplitude are computed. The methodology has been demonstrated and experimental tests on elementary samples presented a degree of accuracy of 1cm.

Aberrant Global and Regional Topological Organization of the Fractional Anisotropy-weighted Brain Structural Networks in Major Depressive Disorder

PubMed Central

Chen, Jian-Huai; Yao, Zhi-Jian; Qin, Jiao-Long; Yan, Rui; Hua, Ling-Ling; Lu, Qing

2016-01-01

Background: Most previous neuroimaging studies have focused on the structural and functional abnormalities of local brain regions in major depressive disorder (MDD). Moreover, the exactly topological organization of networks underlying MDD remains unclear. This study examined the aberrant global and regional topological patterns of the brain white matter networks in MDD patients. Methods: The diffusion tensor imaging data were obtained from 27 patients with MDD and 40 healthy controls. The brain fractional anisotropy-weighted structural networks were constructed, and the global network and regional nodal metrics of the networks were explored by the complex network theory. Results: Compared with the healthy controls, the brain structural network of MDD patients showed an intact small-world topology, but significantly abnormal global network topological organization and regional nodal characteristic of the network in MDD were found. Our findings also indicated that the brain structural networks in MDD patients become a less strongly integrated network with a reduced central role of some key brain regions. Conclusions: All these resulted in a less optimal topological organization of networks underlying MDD patients, including an impaired capability of local information processing, reduced centrality of some brain regions and limited capacity to integrate information across different regions. Thus, these global network and regional node-level aberrations might contribute to understanding the pathogenesis of MDD from the view of the brain network. PMID:26960371

Massive Galaxies at z=2-3: A Large Population of Disky Star-Forming Systems?

NASA Astrophysics Data System (ADS)

Weinzirl, Tim; Jogee, S.; GOODS-NICMOS Collaboration

2011-01-01

The assembly modes via which galaxies develop their present-day mass and structure remain hotly debated. We explore this issue using one of the largest samples of massive galaxies (166 with stellar mass Mstar ≥ 5 × 1010 M⊙) at z=1-3 with NICMOS F160W observations from the GOODS NICMOS Survey (GNS), along with complementary ACS, Spitzer, and Chandra data. Our findings are: (1) The majority of the massive galaxies at z=2-3 have a disky structure (as characterized by the index of single-component Sersic profiles). Most are also compact with half-light radii less than 2 kpc. These massive galaxies at z=2-3 appear to be radically different in structure from their more massive descendants at z 0. Through artificial redshfiting experiments based on redshifted simulated NICMOS data of such massive z 0 elliptical, S0, and spiral galaxies, we show that most of this difference in structure is not due to cosmological or instrumental effects. This implies that significant structural evolution is needed to convert the massive z=2-3 systems into their z 0 elliptical and S0 descendants, and places important constraints on the associated evolutionary mechanisms (e.g., major mergers and cold accretion). (2) Using IR luminosities inferred from Spitzer detections, we find that over z=1-3, the mean star formation rate (SFR) rises substantially, even if AGN candidates are excluded. SFRs of several hundred solar masses per year or higher are common. The results imply a much higher average cold gas fraction than exists in z 0 galaxies. (3) We identify AGN candidates using a variety of techniques (X-ray properties, IR power-law, and IR-to-optical excess) and classify about one-third of the massive galaxies at z=1-3 as AGN hosts. The AGN fraction rises with redshift and is 40% at z=2-3. A significant fraction of the AGN candidates have disky structures although they host massive black holes.

Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales.

PubMed

Palumbi, S R; Baker, C S

1994-05-01

Powerful analyses of population structure require information from multiple genetic loci. To help develop a molecular toolbox for obtaining this information, we have designed universal oligonucleotide primers that span conserved intron-exon junctions in a wide variety of animal phyla. We test the utility of exon-primed, intron-crossing amplifications by analyzing the variability of actin intron sequences from humpback, blue, and bowhead whales and comparing the results with mitochondrial DNA (mtDNA) haplotype data. Humpback actin introns fall into two major clades that exist in different frequencies in different oceanic populations. It is surprising that Hawaii and California populations, which are very distinct in mtDNAs, are similar in actin intron alleles. This discrepancy between mtDNA and nuclear DNA results may be due either to differences in genetic drift in mitochondrial and nuclear genes or to preferential movement of males, which do not transmit mtDNA to offspring, between separate breeding grounds. Opposing mtDNA and nuclear DNA results can help clarify otherwise hidden patterns of structure in natural populations.

Force field-dependent structural divergence revealed during long time simulations of Calbindin d9k.

PubMed

Project, Elad; Nachliel, Esther; Gutman, Menachem

2010-07-15

The structural and the dynamic features of the Calbindin (CaB) protein in its holo and apo states are compared using molecular dynamics simulations under nine different force fields (FFs) (G43a1, G53a6, Opls-AA, Amber94, Amber99, Amber99p, AmberGS, AmberGSs, and Amber99sb). The results show that most FFs reproduce reasonably well the majority of the experimentally derived features of the CaB protein. However, in several cases, there are significant differences in secondary structure properties, root mean square deviations (RMSDs), root mean square fluctuations (RMSFs), and S(2) order parameters among the various FFs. What is more, in certain cases, these parameters differed from the experimentally derived values. Some of these deviations became noticeable only after 50 ns. A comparison with experimental data indicates that, for CaB, the Amber94 shows overall best agreement with the measured values, whereas several others seem to deviate from both crystal and nuclear magnetic resonance data. Copyright 2009 Wiley Periodicals, Inc.

Interactions of Multimodal Ligands with Proteins: Insights into Selectivity Using Molecular Dynamics Simulations.

PubMed

Parimal, Siddharth; Garde, Shekhar; Cramer, Steven M

2015-07-14

Fundamental understanding of protein-ligand interactions is important to the development of efficient bioseparations in multimodal chromatography. Here we employ molecular dynamics (MD) simulations to investigate the interactions of three different proteins--ubiquitin, cytochrome C, and α-chymotrypsinogen A, sampling a range of charge from +1e to +9e--with two multimodal chromatographic ligands containing similar chemical moieties--aromatic, carboxyl, and amide--in different structural arrangements. We use a spherical harmonic expansion to analyze ligand and individual moiety density profiles around the proteins. We find that the Capto MMC ligand, which contains an additional aliphatic group, displays stronger interactions than Nuvia CPrime ligand with all three proteins. Studying the ligand densities at the moiety level suggests that hydrophobic interactions play a major role in determining the locations of high ligand densities. Finally, the greater structural flexibility of the Capto MMC ligand compared to that of the Nuvia cPrime ligand allows for stronger structural complementarity and enables stronger hydrophobic interactions. These subtle and not-so-subtle differences in binding affinities and modalities for multimodal ligands can result in significantly different binding behavior towards proteins with important implications for bioprocessing.

Misalignment tolerable coil structure for biomedical applications with wireless power transfer.

PubMed

Chow, Jeff P W; Chen, Nan; Chung, Henry S H; Chan, Leanne L H

2013-01-01

Coil-misalignment is one of the major hurdles for inductively coupled wireless power transfer in applications like retinal prosthesis. Weak magnetic flux linkage due to coil misalignments would significantly impair the power efficiency. A novel receiver configuration with high misalignment tolerance is presented in this paper. The proposed receiver is composed of two receiver coils placed orthogonally, so as to reduce the variation of mutual inductance between transmitting and receiving coils under misalignment conditions. Three different receiver coil structures are analyzed and compared using the same length of wire. Theoretical predictions have been confirmed with measurement results.

[Advances in Parvovirus Non-structural Protein NS1 Induced Apoptosis].

PubMed

Tu, Mengyu; Liu, Fei; Chen, Shun; Wang, Mingshu; Cheng, Anchun

2015-11-01

Until now, more than seventeen parvovirus have been reported which can infect mammals and poultries. The infected cells appeared different properties of apoptosis and death, present a typical cytopathic effect. NS1 is a major nonstructural protein of parvovirus, with a conservative structure and function, which plays an important role in the viral life cycle. In addition to the influence on viral replication, the NS1 also participates in apoptosis induced by viruses. Parvovirus induced apoptosis which is mainly mediated by mitochondrial pathway, this review summarized the latest research progresses of parvovirus induced apoptosis.

Bacterial communities associated with an occurrence of colored water in an urban drinking water distribution system.

PubMed

Wu, Hui Ting; Mi, Zi Long; Zhang, Jing Xu; Chen, Chao; Xie, Shu Guang

2014-08-01

This study aimed to investigate bacterial community in an urban drinking water distribution system (DWDS) during an occurrence of colored water. Variation in the bacterial community diversity and structure was observed among the different waters, with the predominance of Proteobacteria. While Verrucomicrobia was also a major phylum group in colored water. Limnobacter was the major genus group in colored water, but Undibacterium predominated in normal tap water. The coexistence of Limnobacter as well as Sediminibacterium and Aquabacterium might contribute to the formation of colored water. Copyright © 2014 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Enantioselective potential of polysaccharide-based chiral stationary phases in supercritical fluid chromatography.

PubMed

Kucerova, Gabriela; Kalikova, Kveta; Tesarova, Eva

2017-06-01

The enantioselective potential of two polysaccharide-based chiral stationary phases for analysis of chiral structurally diverse biologically active compounds was evaluated in supercritical fluid chromatography using a set of 52 analytes. The chiral selectors immobilized on 2.5 μm silica particles were tris-(3,5-dimethylphenylcarmabate) derivatives of cellulose or amylose. The influence of the polysaccharide backbone, different organic modifiers, and different mobile phase additives on retention and enantioseparation was monitored. Conditions for fast baseline enantioseparation were found for the majority of the compounds. The success rate of baseline and partial enantioseparation with cellulose-based chiral stationary phase was 51.9% and 15.4%, respectively. Using amylose-based chiral stationary phase we obtained 76.9% of baseline enantioseparations and 9.6% of partial enantioseparations of the tested compounds. The best results on cellulose-based chiral stationary phase were achieved particularly with propane-2-ol and a mixture of isopropylamine and trifluoroacetic acid as organic modifier and additive to CO 2 , respectively. Methanol and basic additive isopropylamine were preferred on amylose-based chiral stationary phase. The complementary enantioselectivity of the cellulose- and amylose-based chiral stationary phases allows separation of the majority of the tested structurally different compounds. Separation systems were found to be directly applicable for analyses of biologically active compounds of interest. © 2017 Wiley Periodicals, Inc.

Phenolics and Terpenoids; the Promising New Search for Anthelmintics: A Critical Review.

PubMed

Mukherjee, Niladri; Mukherjee, Suprabhat; Saini, Prasanta; Roy, Priya; Sinha Babu, Santi P

2015-02-26

Ailments caused by helminth parasites are global causing different types of clinical complications with permanent and long term morbidity in humans. Although huge advances have been made in medical sciences the effectiveness of available anthelmintics are still quite limited. Starting from the 50's, most importance was given to synthetic compounds for developing remedies from them, however, the traditional knowledge of medicine of different countries continued to provide us clues against this widespread health problem. Natural products or structural analogs with diverse structures are always been the major sources for discovering new therapeutics and in recent past different active compounds have also been identified form these plant sources having anthelmintic properties. Although compounds of diverse chemical nature and classes were identified most active ones belong to either phenol or terpene in broad chemical nature. The mechanism of action of these phytotherapeutics is usually multi-targeted and can act against the helminth parasites through diverse spectrum of activities. In this reviewwe summarized the effective anthelmintics belong to either phenolics or terpenoids and highlighted the major way of their effectiveness. This also highlights the recent development of new therapeutic strategies against helminth parasites in the light of recent advances of knowledge. In addition, developing efficient strategies to promote apoptosis and disturbing redox status in them by natural products can provide us a clue in antifilarial drug developmental research and crucial unmet medical need.

Phenolics and Terpenoids; the Promising New Search for Anthelmintics: A Critical Review.

PubMed

Mukherjee, Niladri; Mukherjee, Suprabhat; Saini, Prasanta; Roy, Priya; Babu, Santi P Sinha

2016-01-01

Ailments caused by helminth parasites are global causing different types of clinical complications with permanent and long term morbidity in humans. Although huge advances have been made in medical sciences the effectiveness of available anthelmintics are still quite limited. Starting from the 50's, most importance was given to synthetic compounds for developing remedies from them, however, the traditional knowledge of medicine of different countries continued to provide us clues against this widespread health problem. Natural products or structural analogs with diverse structures are always been the major sources for discovering new therapeutics and in recent past different active compounds have also been identified form these plant sources having anthelmintic properties. Although compounds of diverse chemical nature and classes were identified, most active ones belong to either phenol or terpene in broad chemical nature. The mechanism of action of these phytotherapeutics is usually multi-targeted and can act against the helminth parasites through diverse spectrum of activities. In this review we summarized the effective anthelmintics belong to either phenolics or terpenoids and highlighted the major way of their effectiveness. This also highlights the recent development of new therapeutic strategies against helminth parasites in the light of recent advances of knowledge. In addition, developing efficient strategies to promote apoptosis and disturbing redox status in them by natural products can provide us a clue in antifilarial drug developmental research and crucial unmet medical need.

Synthesis and characterization of fac-Re(CO)3-aspartic-N-monoacetic acid, a structural analogue of a potential new renal tracer, fac-99mTc(CO)3(ASMA).

PubMed

Klenc, Jeffrey; Lipowska, Malgorzata; Taylor, Andrew T; Marzilli, Luigi G

2012-09-01

The reaction of an aminopolycarboxylate ligand, as partic- N - m onoacetic a cid (ASMA), with [Re(CO) 3 (H 2 O) 3 ] + was examined. The tridentate coordination of ASMA to this Re I tricarbonyl precursor yielded fac -Re(CO) 3 (ASMA) as a mixture of diastereomers. The chemistry is analogous to that of the Tc I tricarbonyl complex, which yields fac - 99m Tc(CO) 3 (ASMA) under similar conditions. The formation, structure, and isomerization of fac -Re(CO) 3 (ASMA) products were characterized by HPLC, 1 H NMR spectroscopy, and X-ray crystallography. The two major fac -Re(CO) 3 (ASMA) diastereomeric products each have a linear ONO coordination mode with two adjacent five-membered chelate rings, but they differ in the endo or exo orientation of the uncoordinated acetate group, in agreement with expectations based on previous studies. Conditions have been identified for the expedient isomerization of fac -Re(CO) 3 (ASMA) to a mixture consisting primarily of one major product. Because different isomeric species typically have different pharmacokinetic characteristics, these conditions may provide for the practical isolation of a single 99m Tc(CO) 3 (ASMA) species, thus allowing the isolation of the isomer that has optimal imaging and pharmacokinetic characteristics. This information will aid in the design of future 99m Tc radiopharmaceuticals.

Synthesis and characterization of fac-Re(CO)3-aspartic-N-monoacetic acid, a structural analogue of a potential new renal tracer, fac-99mTc(CO)3(ASMA)

PubMed Central

Klenc, Jeffrey; Lipowska, Malgorzata; Taylor, Andrew T.; Marzilli, Luigi G.

2013-01-01

The reaction of an aminopolycarboxylate ligand, aspartic-N-monoacetic acid (ASMA), with [Re(CO)3(H2O)3]+ was examined. The tridentate coordination of ASMA to this ReI tricarbonyl precursor yielded fac-Re(CO)3(ASMA) as a mixture of diastereomers. The chemistry is analogous to that of the TcI tricarbonyl complex, which yields fac-99mTc(CO)3(ASMA) under similar conditions. The formation, structure, and isomerization of fac-Re(CO)3(ASMA) products were characterized by HPLC, 1H NMR spectroscopy, and X-ray crystallography. The two major fac-Re(CO)3(ASMA) diastereomeric products each have a linear ONO coordination mode with two adjacent five-membered chelate rings, but they differ in the endo or exo orientation of the uncoordinated acetate group, in agreement with expectations based on previous studies. Conditions have been identified for the expedient isomerization of fac-Re(CO)3(ASMA) to a mixture consisting primarily of one major product. Because different isomeric species typically have different pharmacokinetic characteristics, these conditions may provide for the practical isolation of a single 99mTc(CO)3(ASMA) species, thus allowing the isolation of the isomer that has optimal imaging and pharmacokinetic characteristics. This information will aid in the design of future 99mTc radiopharmaceuticals. PMID:24273448

GlycomeDB – integration of open-access carbohydrate structure databases

PubMed Central

Ranzinger, René; Herget, Stephan; Wetter, Thomas; von der Lieth, Claus-Wilhelm

2008-01-01

Background Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource. PMID:18803830

Predicting structured metadata from unstructured metadata.

PubMed

Posch, Lisa; Panahiazar, Maryam; Dumontier, Michel; Gevaert, Olivier

2016-01-01

Enormous amounts of biomedical data have been and are being produced by investigators all over the world. However, one crucial and limiting factor in data reuse is accurate, structured and complete description of the data or data about the data-defined as metadata. We propose a framework to predict structured metadata terms from unstructured metadata for improving quality and quantity of metadata, using the Gene Expression Omnibus (GEO) microarray database. Our framework consists of classifiers trained using term frequency-inverse document frequency (TF-IDF) features and a second approach based on topics modeled using a Latent Dirichlet Allocation model (LDA) to reduce the dimensionality of the unstructured data. Our results on the GEO database show that structured metadata terms can be the most accurately predicted using the TF-IDF approach followed by LDA both outperforming the majority vote baseline. While some accuracy is lost by the dimensionality reduction of LDA, the difference is small for elements with few possible values, and there is a large improvement over the majority classifier baseline. Overall this is a promising approach for metadata prediction that is likely to be applicable to other datasets and has implications for researchers interested in biomedical metadata curation and metadata prediction. © The Author(s) 2016. Published by Oxford University Press.

Predicting structured metadata from unstructured metadata

PubMed Central

Posch, Lisa; Panahiazar, Maryam; Dumontier, Michel; Gevaert, Olivier

2016-01-01

Enormous amounts of biomedical data have been and are being produced by investigators all over the world. However, one crucial and limiting factor in data reuse is accurate, structured and complete description of the data or data about the data—defined as metadata. We propose a framework to predict structured metadata terms from unstructured metadata for improving quality and quantity of metadata, using the Gene Expression Omnibus (GEO) microarray database. Our framework consists of classifiers trained using term frequency-inverse document frequency (TF-IDF) features and a second approach based on topics modeled using a Latent Dirichlet Allocation model (LDA) to reduce the dimensionality of the unstructured data. Our results on the GEO database show that structured metadata terms can be the most accurately predicted using the TF-IDF approach followed by LDA both outperforming the majority vote baseline. While some accuracy is lost by the dimensionality reduction of LDA, the difference is small for elements with few possible values, and there is a large improvement over the majority classifier baseline. Overall this is a promising approach for metadata prediction that is likely to be applicable to other datasets and has implications for researchers interested in biomedical metadata curation and metadata prediction. Database URL: http://www.yeastgenome.org/ PMID:28637268

Membrane Transporters: Structure, Function and Targets for Drug Design

NASA Astrophysics Data System (ADS)

Ravna, Aina W.; Sager, Georg; Dahl, Svein G.; Sylte, Ingebrigt

Current therapeutic drugs act on four main types of molecular targets: enzymes, receptors, ion channels and transporters, among which a major part (60-70%) are membrane proteins. This review discusses the molecular structures and potential impact of membrane transporter proteins on new drug discovery. The three-dimensional (3D) molecular structure of a protein contains information about the active site and possible ligand binding, and about evolutionary relationships within the protein family. Transporters have a recognition site for a particular substrate, which may be used as a target for drugs inhibiting the transporter or acting as a false substrate. Three groups of transporters have particular interest as drug targets: the major facilitator superfamily, which includes almost 4000 different proteins transporting sugars, polyols, drugs, neurotransmitters, metabolites, amino acids, peptides, organic and inorganic anions and many other substrates; the ATP-binding cassette superfamily, which plays an important role in multidrug resistance in cancer chemotherapy; and the neurotransmitter:sodium symporter family, which includes the molecular targets for some of the most widely used psychotropic drugs. Recent technical advances have increased the number of known 3D structures of membrane transporters, and demonstrated that they form a divergent group of proteins with large conformational flexibility which facilitates transport of the substrate.

Relationships between structure, in vivo function and long-range axonal target of cortical pyramidal tract neurons.

PubMed

Rojas-Piloni, Gerardo; Guest, Jason M; Egger, Robert; Johnson, Andrew S; Sakmann, Bert; Oberlaender, Marcel

2017-10-11

Pyramidal tract neurons (PTs) represent the major output cell type of the neocortex. To investigate principles of how the results of cortical processing are broadcasted to different downstream targets thus requires experimental approaches, which provide access to the in vivo electrophysiology of PTs, whose subcortical target regions are identified. On the example of rat barrel cortex (vS1), we illustrate that retrograde tracer injections into multiple subcortical structures allow identifying the long-range axonal targets of individual in vivo recorded PTs. Here we report that soma depth and dendritic path lengths within each cortical layer of vS1, as well as spiking patterns during both periods of ongoing activity and during sensory stimulation, reflect the respective subcortical target regions of PTs. We show that these cellular properties result in a structure-function parameter space that allows predicting a PT's subcortical target region, without the need to inject multiple retrograde tracers.The major output cell type of the neocortex - pyramidal tract neurons (PTs) - send axonal projections to various subcortical areas. Here the authors combined in vivo recordings, retrograde tracings, and reconstructions of PTs in rat somatosensory cortex to show that PT structure and activity can predict specific subcortical targets.

Crystal structure of the zymogen form of the group A Streptococcus virulence factor SpeB: an integrin-binding cysteine protease.

PubMed

Kagawa, T F; Cooney, J C; Baker, H M; McSweeney, S; Liu, M; Gubba, S; Musser, J M; Baker, E N

2000-02-29

Pathogenic bacteria secrete protein toxins that weaken or disable their host, and thereby act as virulence factors. We have determined the crystal structure of streptococcal pyrogenic exotoxin B (SpeB), a cysteine protease that is a major virulence factor of the human pathogen Streptococcus pyogenes and participates in invasive disease episodes, including necrotizing fasciitis. The structure, determined for the 40-kDa precursor form of SpeB at 1.6-A resolution, reveals that the protein is a distant homologue of the papain superfamily that includes the mammalian cathepsins B, K, L, and S. Despite negligible sequence identity, the protease portion has the canonical papain fold, albeit with major loop insertions and deletions. The catalytic site differs from most other cysteine proteases in that it lacks the Asn residue of the Cys-His-Asn triad. The prosegment has a unique fold and inactivation mechanism that involves displacement of the catalytically essential His residue by a loop inserted into the active site. The structure also reveals the surface location of an integrin-binding Arg-Gly-Asp (RGD) motif that is a feature unique to SpeB among cysteine proteases and is linked to the pathogenesis of the most invasive strains of S. pyogenes.

Dissecting cross-impact on stock markets: an empirical analysis

NASA Astrophysics Data System (ADS)

Benzaquen, M.; Mastromatteo, I.; Eisler, Z.; Bouchaud, J.-P.

2017-02-01

The vast majority of market impact studies assess each product individually, and the interactions between the different order flows are disregarded. This strong approximation may lead to an underestimation of trading costs and possible contagion effects. Transactions in fact mediate a significant part of the correlation between different instruments. In turn, liquidity shares the sectorial structure of market correlations, which can be encoded as a set of eigenvalues and eigenvectors. We introduce a multivariate linear propagator model that successfully describes such a structure, and accounts for a significant fraction of the covariance of stock returns. We dissect the various dynamical mechanisms that contribute to the joint dynamics of assets. We also define two simplified models with substantially less parameters in order to reduce overfitting, and show that they have superior out-of-sample performance.

Studying the Formation and Development of Molecular Clouds: With the CCAT Heterodyne Array Instrument (CHAI)

NASA Technical Reports Server (NTRS)

Goldsmith, Paul F.

2012-01-01

Surveys of all different types provide basic data using different tracers. Molecular clouds have structure over a very wide range of scales. Thus, "high resolution" surveys and studies of selected nearby clouds add critical information. The combination of large-area and high resolution allows Increased spatial dynamic range, which in turn enables detection of new and perhaps critical morphology (e.g. filaments). Theoretical modeling has made major progress, and suggests that multiple forces are at work. Galactic-scale modeling also progressing - indicates that stellar feedback is required. Models must strive to reproduce observed cloud structure at all scales. Astrochemical observations are not unrelated to questions of cloud evolution and star formation but we are still learning how to use this capability.

Types of architectural structures and the use of smart materials

NASA Astrophysics Data System (ADS)

Tavşan, Cengiz; Sipahi, Serkan

2017-07-01

The developments in technology following the industrial revolution had their share of impact on both construction techniques, and material technologies. The change in the materials used by the construction industry brought along numerous innovations, which, in turn, took on an autonomous trend of development given the rise of nano-tech materials. Today, nano-tech materials are used extensively in numerous construction categories. Nano-tech materials, in general, are characterized by their reactionary nature, with the intent of repeating the reactions again and again under certain conditions. That is why nano-tech materials are often called smart materials. In construction industry, smart materials are categorized under 4 major perspectives: Shape-shifting smart materials, power generating smart materials, self-maintenance smart materials, and smart materials providing a high level of insulation. In architecture, various categories of construction often tend to exhibit their own approaches to design, materials, and construction techniques. This is a direct consequence of the need for different solutions for different functions. In this context, the use of technological materials should lead to the use of a set of smart materials for a given category of structures, while another category utilizes yet another set. In the present study, the smart materials used in specific categories of structures were reviewed with reference to nano-tech practices implemented in Europe, with a view to try and reveal the changes in the use of smart materials with reference to categories of structures. The study entails a discussion to test the hypothesis that nano-tech materials vary with reference to structure categories, on the basis of 18 examples from various structure categories, built by the construction firms with the highest level of potential in terms of doing business in Europe. The study comprises 3 major sections: The first section reiterates what the literature has to say about smart materials; the second discusses the types and characteristics of smart materials over the tables detailing their utilization and functions in the structures included in the set of examples. The final section of the study, on the other hand, elaborates on the findings, discussing them with reference to the types of structures.

The structures of cytosolic and plastid-located glutamine synthetases from Medicago truncatula reveal a common and dynamic architecture

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

Torreira, Eva; Seabra, Ana Rita; Marriott, Hazel

The experimental models of dicotyledonous cytoplasmic and plastid-located glutamine synthetases unveil a conserved eukaryotic-type decameric architecture, with subtle structural differences in M. truncatula isoenzymes that account for their distinct herbicide resistance. The first step of nitrogen assimilation in higher plants, the energy-driven incorporation of ammonia into glutamate, is catalyzed by glutamine synthetase. This central process yields the readily metabolizable glutamine, which in turn is at the basis of all subsequent biosynthesis of nitrogenous compounds. The essential role performed by glutamine synthetase makes it a prime target for herbicidal compounds, but also a suitable intervention point for the improvement of cropmore » yields. Although the majority of crop plants are dicotyledonous, little is known about the structural organization of glutamine synthetase in these organisms and about the functional differences between the different isoforms. Here, the structural characterization of two glutamine synthetase isoforms from the model legume Medicago truncatula is reported: the crystallographic structure of cytoplasmic GSII-1a and an electron cryomicroscopy reconstruction of plastid-located GSII-2a. Together, these structural models unveil a decameric organization of dicotyledonous glutamine synthetase, with two pentameric rings weakly connected by inter-ring loops. Moreover, rearrangement of these dynamic loops changes the relative orientation of the rings, suggesting a zipper-like mechanism for their assembly into a decameric enzyme. Finally, the atomic structure of M. truncatula GSII-1a provides important insights into the structural determinants of herbicide resistance in this family of enzymes, opening new avenues for the development of herbicide-resistant plants.« less

Mixing and Matching Detergents for Membrane Protein NMR Structure Determination

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

Columbus, Linda; Lipfert, Jan; Jambunathan, Kalyani

2009-10-21

One major obstacle to membrane protein structure determination is the selection of a detergent micelle that mimics the native lipid bilayer. Currently, detergents are selected by exhaustive screening because the effects of protein-detergent interactions on protein structure are poorly understood. In this study, the structure and dynamics of an integral membrane protein in different detergents is investigated by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy and small-angle X-ray scattering (SAXS). The results suggest that matching of the micelle dimensions to the protein's hydrophobic surface avoids exchange processes that reduce the completeness of the NMR observations. Based onmore » these dimensions, several mixed micelles were designed that improved the completeness of NMR observations. These findings provide a basis for the rational design of mixed micelles that may advance membrane protein structure determination by NMR.« less

Data from clinical notes: a perspective on the tension between structure and flexible documentation

PubMed Central

Denny, Joshua C; Xu, Hua; Lorenzi, Nancy; Stead, William W; Johnson, Kevin B

2011-01-01

Clinical documentation is central to patient care. The success of electronic health record system adoption may depend on how well such systems support clinical documentation. A major goal of integrating clinical documentation into electronic heath record systems is to generate reusable data. As a result, there has been an emphasis on deploying computer-based documentation systems that prioritize direct structured documentation. Research has demonstrated that healthcare providers value different factors when writing clinical notes, such as narrative expressivity, amenability to the existing workflow, and usability. The authors explore the tension between expressivity and structured clinical documentation, review methods for obtaining reusable data from clinical notes, and recommend that healthcare providers be able to choose how to document patient care based on workflow and note content needs. When reusable data are needed from notes, providers can use structured documentation or rely on post-hoc text processing to produce structured data, as appropriate. PMID:21233086

Investigation of Ion-Implanted Photosensitive Silicon Structures by Electrochemical Capacitance–Voltage Profiling

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

Yakovlev, G. E., E-mail: geyakovlev@etu.ru; Frolov, D. S.; Zubkova, A. V.

2016-03-15

The method of electrochemical capacitance–voltage profiling is used to study boron-implanted silicon structures for CCD matrices with backside illumination. A series of specially prepared structures with different energies and doses of ion implantation and also with various materials used for the coating layers (aluminum, silicon oxide, and their combinations) is studied. The profiles of the depth distribution of majority charge carriers of the studied structures are obtained experimentally. Also, using the Poisson equation and the Fredholm equation of the first kind, the distributions of the charge-carrier concentration and of the electric field in the structures are calculated. On the basismore » of the analysis and comparison of theoretical and experimental concentration profiles, recommendations concerning optimization of the structures’ parameters in order to increase the value of the pulling field and decrease the effect of the surface potential on the transport of charge carriers are suggested.« less

Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach.

PubMed

Paluch, Piotr; Pawlak, Tomasz; Oszajca, Marcin; Lasocha, Wieslaw; Potrzebowski, Marek J

2015-02-01

We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924. Copyright © 2014 Elsevier Inc. All rights reserved.

Similitude design for the vibration problems of plates and shells: A review

NASA Astrophysics Data System (ADS)

Zhu, Yunpeng; Wang, You; Luo, Zhong; Han, Qingkai; Wang, Deyou

2017-06-01

Similitude design plays a vital role in the analysis of vibration and shock problems encountered in large engineering equipment. Similitude design, including dimensional analysis and governing equation method, is founded on the dynamic similitude theory. This study reviews the application of similitude design methods in engineering practice and summarizes the major achievements of the dynamic similitude theory in structural vibration and shock problems in different fields, including marine structures, civil engineering structures, and large power equipment. This study also reviews the dynamic similitude design methods for thin-walled and composite material plates and shells, including the most recent work published by the authors. Structure sensitivity analysis is used to evaluate the scaling factors to attain accurate distorted scaling laws. Finally, this study discusses the existing problems and the potential of the dynamic similitude theory for the analysis of vibration and shock problems of structures.

Vibration suppression and slewing control of a flexible structure

NASA Technical Reports Server (NTRS)

Inman, Daniel J.; Garcia, Ephrahim; Pokines, Brett

1991-01-01

Examined here are the effects of motor dynamics and secondary piezoceramic actuators on vibration suppression during the slewing of flexible structures. The approach focuses on the interaction between the structure, the actuators, and the choice of control law. The results presented here are all simulated, but are based on experimentally determined parameters for the motor, structure, piezoceramic actuators, and piezofilm sensors. The simulation results clearly illustrate that the choice of motor inertia relative to beam inertia makes a critical difference in the performance of the system. In addition, the use of secondary piezoelectric actuators reduces the load requirements on the motor and also reduces the overshoot of the tip deflection. The structures considered here are a beam and a frame. The majority of results are based on a Euler Bernoulli beam model. The slewing frame introduces substantial torsional modes and a more realistic model. The slewing frame results are incomplete and represent work in progress.

Evaluation of Advanced Composite Structures Technologies for Application to NASA's Vision for Space Exploration

NASA Technical Reports Server (NTRS)

Tenney, Darrel R.

2008-01-01

AS&M performed a broad assessment survey and study to establish the potential composite materials and structures applications and benefits to the Constellation Program Elements. Trade studies were performed on selected elements to determine the potential weight or performance payoff from use of composites. Weight predictions were made for liquid hydrogen and oxygen tanks, interstage cylindrical shell, lunar surface access module, ascent module liquid methane tank, and lunar surface manipulator. A key part of this study was the evaluation of 88 different composite technologies to establish their criticality to applications for the Constellation Program. The overall outcome of this study shows that composites are viable structural materials which offer from 20% to 40% weight savings for many of the structural components that make up the Major Elements of the Constellation Program. NASA investment in advancing composite technologies for space structural applications is an investment in America's Space Exploration Program.

Relationships between cortical myeloarchitecture and electrophysiological networks

PubMed Central

Hunt, Benjamin A. E.; Tewarie, Prejaas K.; Mougin, Olivier E.; Geades, Nicolas; Singh, Krish D.; Morris, Peter G.; Gowland, Penny A.; Brookes, Matthew J.

2016-01-01

The human brain relies upon the dynamic formation and dissolution of a hierarchy of functional networks to support ongoing cognition. However, how functional connectivities underlying such networks are supported by cortical microstructure remains poorly understood. Recent animal work has demonstrated that electrical activity promotes myelination. Inspired by this, we test a hypothesis that gray-matter myelin is related to electrophysiological connectivity. Using ultra-high field MRI and the principle of structural covariance, we derive a structural network showing how myelin density differs across cortical regions and how separate regions can exhibit similar myeloarchitecture. Building upon recent evidence that neural oscillations mediate connectivity, we use magnetoencephalography to elucidate networks that represent the major electrophysiological pathways of communication in the brain. Finally, we show that a significant relationship exists between our functional and structural networks; this relationship differs as a function of neural oscillatory frequency and becomes stronger when integrating oscillations over frequency bands. Our study sheds light on the way in which cortical microstructure supports functional networks. Further, it paves the way for future investigations of the gray-matter structure/function relationship and its breakdown in pathology. PMID:27830650

Activation and desensitization of ionotropic glutamate receptors by selectively triggering pre-existing motions.

PubMed

Krieger, James; Lee, Ji Young; Greger, Ingo H; Bahar, Ivet

2018-02-23

Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that are key players in synaptic transmission and plasticity. They are composed of four subunits, each containing four functional domains, the quaternary packing and collective structural dynamics of which are important determinants of their molecular mechanism of function. With the explosion of structural studies on different members of the family, including the structures of activated open channels, the mechanisms of action of these central signaling machines are now being elucidated. We review the current state of computational studies on two major members of the family, AMPA and NMDA receptors, with focus on molecular simulations and elastic network model analyses that have provided insights into the coupled movements of extracellular and transmembrane domains. We describe the newly emerging mechanisms of activation, allosteric signaling and desensitization, as mainly a selective triggering of pre-existing soft motions, as deduced from computational models and analyses that leverage structural data on intact AMPA and NMDA receptors in different states. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Effect of silicide/silicon hetero-junction structure on thermal conductivity and Seebeck coefficient.

PubMed

Choi, Wonchul; Park, Young-Sam; Hyun, Younghoon; Zyung, Taehyoung; Kim, Jaehyeon; Kim, Soojung; Jeon, Hyojin; Shin, Mincheol; Jang, Moongyu

2013-12-01

We fabricated a thermoelectric device with a silicide/silicon laminated hetero-structure by using RF sputtering and rapid thermal annealing. The device was observed to have Ohmic characteristics by I-V measurement. The temperature differences and Seebeck coefficients of the proposed silicide/silicon laminated and bulk structure were measured. The laminated thermoelectric device shows suppression of heat flow from the hot to cold side. This is supported by the theory that the atomic mass difference between silicide and silicon creates a scattering center for phonons. The major impact of our work is that phonon transmission is suppressed at the interface between silicide and silicon without degrading electrical conductivity. The estimated thermal conductivity of the 3-layer laminated device is 126.2 +/- 3.7 W/m. K. Thus, by using the 3-layer laminated structure, thermal conductivity is reduced by around 16% compared to bulk silicon. However, the Seebeck coefficient of the thermoelectric device is degraded compared to that of bulk silicon. It is understood that electrical conductivity is improved by using silicide as a scattering center.

The complex and specific pMHC interactions with diverse HIV-1 TCR clonotypes reveal a structural basis for alterations in CTL function

NASA Astrophysics Data System (ADS)

Xia, Zhen; Chen, Huabiao; Kang, Seung-Gu; Huynh, Tien; Fang, Justin W.; Lamothe, Pedro A.; Walker, Bruce D.; Zhou, Ruhong

2014-02-01

Immune control of viral infections is modulated by diverse T cell receptor (TCR) clonotypes engaging peptide-MHC class I complexes on infected cells, but the relationship between TCR structure and antiviral function is unclear. Here we apply in silico molecular modeling with in vivo mutagenesis studies to investigate TCR-pMHC interactions from multiple CTL clonotypes specific for a well-defined HIV-1 epitope. Our molecular dynamics simulations of viral peptide-HLA-TCR complexes, based on two independent co-crystal structure templates, reveal that effective and ineffective clonotypes bind to the terminal portions of the peptide-MHC through similar salt bridges, but their hydrophobic side-chain packings can be very different, which accounts for the major part of the differences among these clonotypes. Non-specific hydrogen bonding to viral peptide also accommodates greater epitope variants. Furthermore, free energy perturbation calculations for point mutations on the viral peptide KK10 show excellent agreement with in vivo mutagenesis assays, with new predictions confirmed by additional experiments. These findings indicate a direct structural basis for heterogeneous CTL antiviral function.

Association of GSK3beta polymorphisms with brain structural changes in major depressive disorder.

PubMed

Inkster, Becky; Nichols, Thomas E; Saemann, Philipp G; Auer, Dorothee P; Holsboer, Florian; Muglia, Pierandrea; Matthews, Paul M

2009-07-01

Indirect evidence suggests that the glycogen synthase kinase-3beta (GSK3beta) gene might be implicated in major depressive disorder (MDD). We evaluated 15 GSK3beta single-nucleotide polymorphisms (SNPs) to test for associations with regional gray matter (GM) volume differences in patients with recurrent MDD. We then used the defined regions of interest based on significant associations to test for MDD x genotype interactions by including a matched control group without any psychiatric disorder, including MDD. General linear model with nonstationary cluster-based inference. Munich, Germany. Patients with recurrent MDD (n = 134) and age-, sex-, and ethnicity-matched healthy controls (n = 143). Associations between GSK3beta polymorphisms and regional GM volume differences. Variation in GM volume was associated with GSK3beta polymorphisms; the most significant associations were found for rs6438552, a putative functional intronic SNP that showed 3 significant GM clusters in the right and left superior temporal gyri and the right hippocampus (P < .001, P = .02, and P = .02, respectively, corrected for multiple comparisons across the whole brain). Similar results were obtained with rs12630592, an SNP in high linkage disequilibrium. A significant SNP x MDD status interaction was observed for the effect on GM volumes in the right hippocampus and superior temporal gyri (P < .001 and P = .01, corrected, respectively). The GSK3beta gene may have a role in determining regional GM volume differences of the right hippocampus and bilateral superior temporal gyri. The association between genotype and brain structure was specific to the patients with MDD, suggesting that GSK3beta genotypes might interact with MDD status. We speculate that this is a consequence of regional neocortical, glial, or neuronal growth or survival. In considering core cognitive features of MDD, the association of GSK3beta polymorphisms with structural variation in the temporal lobe and hippocampus is of particular interest in the context of other evidence for structural and functional abnormalities in the hippocampi of patients with MDD.

The structure of people's hair.

PubMed

Yang, Fei-Chi; Zhang, Yuchen; Rheinstädter, Maikel C

2014-01-01

Hair is a filamentous biomaterial consisting mainly of proteins in particular keratin. The structure of human hair is well known: the medulla is a loosely packed, disordered region near the centre of the hair surrounded by the cortex, which contains the major part of the fibre mass, mainly consisting of keratin proteins and structural lipids. The cortex is surrounded by the cuticle, a layer of dead, overlapping cells forming a protective layer around the hair. The corresponding structures have been studied extensively using a variety of different techniques, such as light, electron and atomic force microscopes, and also X-ray diffraction. We were interested in the question how much the molecular hair structure differs from person to person, between male and female hair, hair of different appearances such as colour and waviness. We included hair from parent and child, identical and fraternal twins in the study to see if genetically similar hair would show similar structural features. The molecular structure of the hair samples was studied using high-resolution X-ray diffraction, which covers length scales from molecules up to the organization of secondary structures. Signals due to the coiled-coil phase of α-helical keratin proteins, intermediate keratin filaments in the cortex and from the lipid layers in the cell membrane complex were observed in the specimen of all individuals, with very small deviations. Despite the relatively small number of individuals (12) included in this study, some conclusions can be drawn. While the general features were observed in all individuals and the corresponding molecular structures were almost identical, additional signals were observed in some specimen and assigned to different types of lipids in the cell membrane complex. Genetics seem to play a role in this composition as identical patterns were observed in hair from father and daughter and identical twins, however, not for fraternal twins. Identification and characterization of these features is an important step towards the detection of abnormalities in the molecular structure of hair as a potential diagnostic tool for certain diseases.

Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis.

PubMed

Tian, Li; Liu, Shijia; Wang, Shuai; Wang, Lushan

2016-03-24

Biomass can be converted into sugars by a series of lignocellulolytic enzymes, which belong to the glycoside hydrolase (GH) families summarized in CAZy databases. Here, using a structural bioinformatics method, we analyzed the active site architecture of the main lignocellulolytic enzyme families. The aromatic amino acids Trp/Tyr and polar amino acids Glu/Asp/Asn/Gln/Arg occurred at higher frequencies in the active site architecture than in the whole enzyme structure. And the number of potential subsites was significantly different among different families. In the cellulase and xylanase families, the conserved amino acids in the active site architecture were mostly found at the -2 to +1 subsites, while in β-glucosidase they were mainly concentrated at the -1 subsite. Families with more conserved binding amino acid residues displayed strong selectivity for their ligands, while those with fewer conserved binding amino acid residues often exhibited promiscuity when recognizing ligands. Enzymes with different activities also tended to bind different hydroxyl oxygen atoms on the ligand. These results may help us to better understand the common and unique structural bases of enzyme-ligand recognition from different families and provide a theoretical basis for the functional evolution and rational design of major lignocellulolytic enzymes.

Trace fossils as environment indicators in the Rocky Mountains

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

Shepard, B.

Throughout time, organisms have left various types of traces while engaged in different activities. The two major types of lebensspuren were made by suspension feeders found in turbulent water where organic matter is held in suspension, and by deposit feeders whose habitat is found in quiet, deeper waters where large quantities of organic matter settle from suspension. The different activities which occur in these two environments are the cause of the traces found in sediments. These include escape structures resulting from degradation or aggradation of sediments, feeding structures, dwelling structures, grazing traces, crawling traces, and resting traces. The use ofmore » trace fossils in hydrocarbon exploration is especially helpful in the Cretaceous sandstones of the Rocky Mountains because of the relative abundance of outcrops and the scarcity of body fossils. By combining the interpretation of physical processes with the biological traces, one more tool is made available in the determination of rock environments as an aid in hydrocarbon exploration. Materials exhibited include 8 x 10 color prints of different Cretaceous lebensspuren, hand-drawn cartoons of the six different trace activities, and a regional cross section of the Eagle sandstone illustrated by photographs of different traces near each location, as well as a variety of rock samples.« less

Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments.

PubMed

Hoffmann, Katy; Hassenrück, Christiane; Salman-Carvalho, Verena; Holtappels, Moritz; Bienhold, Christina

2017-01-01

Benthic deep-sea communities are largely dependent on particle flux from surface waters. In the Arctic Ocean, environmental changes occur more rapidly than in other ocean regions, and have major effects on the export of organic matter to the deep sea. Because bacteria constitute the majority of deep-sea benthic biomass and influence global element cycles, it is important to better understand how changes in organic matter input will affect bacterial communities at the Arctic seafloor. In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from the Long-Term Ecological Research Observatory HAUSGARTEN were supplemented with different types of habitat-related detritus (chitin, Arctic algae) and incubated for 23 days under in situ conditions. Chitin addition caused strong changes in community activity, while community structure remained similar to unfed control incubations. In contrast, the addition of phytodetritus resulted in strong changes in community composition, accompanied by increased community activity, indicating the need for adaptation in these treatments. High-throughput sequencing of the 16S rRNA gene and 16S rRNA revealed distinct taxonomic groups of potentially fast-growing, opportunistic bacteria in the different detritus treatments. Compared to the unfed control, Colwelliaceae, Psychromonadaceae , and Oceanospirillaceae increased in relative abundance in the chitin treatment, whereas Flavobacteriaceae, Marinilabiaceae , and Pseudoalteromonadaceae increased in the phytodetritus treatments. Hence, these groups may constitute indicator taxa for the different organic matter sources at this study site. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor, an important feedback mechanism to be considered in future climate change scenarios.

Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments

PubMed Central

Hoffmann, Katy; Hassenrück, Christiane; Salman-Carvalho, Verena; Holtappels, Moritz; Bienhold, Christina

2017-01-01

Benthic deep-sea communities are largely dependent on particle flux from surface waters. In the Arctic Ocean, environmental changes occur more rapidly than in other ocean regions, and have major effects on the export of organic matter to the deep sea. Because bacteria constitute the majority of deep-sea benthic biomass and influence global element cycles, it is important to better understand how changes in organic matter input will affect bacterial communities at the Arctic seafloor. In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from the Long-Term Ecological Research Observatory HAUSGARTEN were supplemented with different types of habitat-related detritus (chitin, Arctic algae) and incubated for 23 days under in situ conditions. Chitin addition caused strong changes in community activity, while community structure remained similar to unfed control incubations. In contrast, the addition of phytodetritus resulted in strong changes in community composition, accompanied by increased community activity, indicating the need for adaptation in these treatments. High-throughput sequencing of the 16S rRNA gene and 16S rRNA revealed distinct taxonomic groups of potentially fast-growing, opportunistic bacteria in the different detritus treatments. Compared to the unfed control, Colwelliaceae, Psychromonadaceae, and Oceanospirillaceae increased in relative abundance in the chitin treatment, whereas Flavobacteriaceae, Marinilabiaceae, and Pseudoalteromonadaceae increased in the phytodetritus treatments. Hence, these groups may constitute indicator taxa for the different organic matter sources at this study site. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor, an important feedback mechanism to be considered in future climate change scenarios. PMID:28286496

Effect of Discontinuities and Uncertainties on the Response and Failure of Composite Structures

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Perry, Ferman W.; Poteat, Marcia M. (Technical Monitor)

2000-01-01

The overall goal of this research was to assess the effect of discontinuities and uncertainties on the nonlinear response and failure of composite structures subjected to combined mechanical and thermal loads. The four key elements of the study were: (1) development of simple and efficient procedures for the accurate determination of transverse shear and transverse normal stresses in structural sandwiches as well as in unstiffened and stiffened composite panels and shells; (2) study the effects of transverse stresses on the response, damage initiation and propagation in composite and sandwich structures; (3) use of hierarchical sensitivity coefficients to identify the major parameters that affect the response and damage in each of the different levels in the hierarchy (micro-mechanical, layer, panel, subcomponent and component levels); and (4) application of fuzzy set techniques to identify the range and variation of possible responses. The computational models developed were used in conjunction with experiments, to understand the physical phenomena associated with the nonlinear response and failure of composite and sandwich structures. A toolkit was developed for use in conjunction with deterministic analysis programs to help the designer in assessing the effect of uncertainties in the different computational model parameters on the variability of the response quantities.

GTPase activity, structure, and mechanical properties of filaments assembled from bacterial cytoskeleton protein MreB.

PubMed

Esue, Osigwe; Wirtz, Denis; Tseng, Yiider

2006-02-01

MreB, a major component of the recently discovered bacterial cytoskeleton, displays a structure homologous to its eukaryotic counterpart actin. Here, we study the assembly and mechanical properties of Thermotoga maritima MreB in the presence of different nucleotides in vitro. We found that GTP, not ADP or GDP, can mediate MreB assembly into filamentous structures as effectively as ATP. Upon MreB assembly, both GTP and ATP release the gamma phosphate at similar rates. Therefore, MreB is an equally effective ATPase and GTPase. Electron microscopy and quantitative rheology suggest that the morphologies and micromechanical properties of filamentous ATP-MreB and GTP-MreB are similar. In contrast, mammalian actin assembly is favored in the presence of ATP over GTP. These results indicate that, despite high structural homology of their monomers, T. maritima MreB and actin filaments display different assembly, morphology, micromechanics, and nucleotide-binding specificity. Furthermore, the biophysical properties of T. maritima MreB filaments, including high rigidity and propensity to form bundles, suggest a mechanism by which MreB helical structure may be involved in imposing a cylindrical architecture on rod-shaped bacterial cells.

MEMS cantilever based magnetic field gradient sensor

NASA Astrophysics Data System (ADS)

Dabsch, Alexander; Rosenberg, Christoph; Stifter, Michael; Keplinger, Franz

2017-05-01

This paper describes major contributions to a MEMS magnetic field gradient sensor. An H-shaped structure supported by four arms with two circuit paths on the surface is designed for measuring two components of the magnetic flux density and one component of the gradient. The structure is produced from silicon wafers by a dry etching process. The gold leads on the surface carry the alternating current which interacts with the magnetic field component perpendicular to the direction of the current. If the excitation frequency is near to a mechanical resonance, vibrations with an amplitude within the range of 1-103 nm are expected. Both theoretical (simulations and analytic calculations) and experimental analysis have been carried out to optimize the structures for different strength of the magnetic gradient. In the same way the impact of the coupling structure on the resonance frequency and of different operating modes to simultaneously measure two components of the flux density were tested. For measuring the local gradient of the flux density the structure was operated at the first symmetrical and the first anti-symmetrical mode. Depending on the design, flux densities of approximately 2.5 µT and gradients starting from 1 µT mm-1 can be measured.

The Role of Life-Space, Social Activity, and Depression on the Subjective Memory Complaints of Community-Dwelling Filipino Elderly: A Structural Equation Model

ERIC Educational Resources Information Center

de Guzman, Allan B.; Lagdaan, Lovely France M.; Lagoy, Marie Lauren V.

2015-01-01

Subjective memory complaints are one of the major concerns of the elderly and remain a challenging area in gerontology. There are previous studies that identify different factors affecting subjective memory complaints. However, an extended model that correlates life-space on subjective memory complaints remains a blank spot. The objective of this…

Word Writing vs. Meaning Inferencing in Contextualized L2 Vocabulary Learning: Assessing the Effect of Different Vocabulary Learning Strategies

ERIC Educational Resources Information Center

Candry, Sarah; Elgort, Irina; Deconinck, Julie; Eyckmans, June

2017-01-01

The majority of L2 vocabulary studies concentrate on learning word meaning and provide learners with opportunities for semantic elaboration (i.e., focus on word meaning). However, in initial vocabulary learning, engaging in structural elaboration (i.e., focus on word form) with a view to acquiring L2 word form is equally important. The present…

Tilt-Pair Analysis of Images from a Range of Different Specimens in Single-Particle Electron Cryomicroscopy

PubMed Central

Henderson, Richard; Chen, Shaoxia; Chen, James Z.; Grigorieff, Nikolaus; Passmore, Lori A.; Ciccarelli, Luciano; Rubinstein, John L.; Crowther, R. Anthony; Stewart, Phoebe L.; Rosenthal, Peter B.

2011-01-01

The comparison of a pair of electron microscope images recorded at different specimen tilt angles provides a powerful approach for evaluating the quality of images, image-processing procedures, or three-dimensional structures. Here, we analyze tilt-pair images recorded from a range of specimens with different symmetries and molecular masses and show how the analysis can produce valuable information not easily obtained otherwise. We show that the accuracy of orientation determination of individual single particles depends on molecular mass, as expected theoretically since the information in each particle image increases with molecular mass. The angular uncertainty is less than 1° for particles of high molecular mass (∼ 50 MDa), several degrees for particles in the range 1–5 MDa, and tens of degrees for particles below 1 MDa. Orientational uncertainty may be the major contributor to the effective temperature factor (B-factor) describing contrast loss and therefore the maximum resolution of a structure determination. We also made two unexpected observations. Single particles that are known to be flexible showed a wider spread in orientation accuracy, and the orientations of the largest particles examined changed by several degrees during typical low-dose exposures. Smaller particles presumably also reorient during the exposure; hence, specimen movement is a second major factor that limits resolution. Tilt pairs thus enable assessment of orientation accuracy, map quality, specimen motion, and conformational heterogeneity. A convincing tilt-pair parameter plot, where 60% of the particles show a single cluster around the expected tilt axis and tilt angle, provides confidence in a structure determined using electron cryomicroscopy. PMID:21939668

Comparative phylogeography and demographic history of the wood lemming (Myopus schisticolor): implications for late Quaternary history of the taiga species in Eurasia.

PubMed

Fedorov, V B; Goropashnaya, A V; Boeskorov, G G; Cook, J A

2008-01-01

The association between demographic history, genealogy and geographical distribution of mitochondrial DNA cytochrome b haplotypes was studied in the wood lemming (Myopus schisticolor), a species that is closely associated with the boreal forest of the Eurasian taiga zone from Scandinavia to the Pacific coast. Except for a major phylogeographic discontinuity (0.9% nucleotide divergence) in southeastern Siberia, only shallow regional genetic structure was detected across northern Eurasia. Genetic signs of demographic expansions imply that successive range contractions and expansions on different spatial scales represented the primary historical events that shaped geographical patterns of genetic variation. Comparison of phylogeographic structure across a taxonomically diverse array of other species that are ecologically associated with the taiga forest revealed similar patterns and identified two general aspects. First, the major south-north phylogeographic discontinuity observed in five out of six species studied in southeastern Siberia and the Far East implies vicariant separation in two different refugial areas. The limited distribution range of the southeastern lineages provides no evidence of the importance of the putative southeastern refugial area for postglacial colonization of northern Eurasia by boreal forest species. Second, the lack of phylogeographic structure associated with significant reciprocal monophyly and genetic signatures of demographic expansion in all nine boreal forest animal species studied to date across most of northern Eurasia imply contraction of each species to a single refugial area during the late Pleistocene followed by range expansion on a continental scale. Similar phylogeographic patterns observed in this taxonomically diverse set of organisms with different life histories and dispersal potentials reflect the historical dynamics of their shared environment, the taiga forest in northern Eurasia.

Reduced frontal-subcortical white matter connectivity in association with suicidal ideation in major depressive disorder

PubMed Central

Myung, W; Han, C E; Fava, M; Mischoulon, D; Papakostas, G I; Heo, J-Y; Kim, K W; Kim, S T; Kim, D J H; Kim, D K; Seo, S W; Seong, J-K; Jeon, H J

2016-01-01

Major depressive disorder (MDD) and suicidal behavior have been associated with structural and functional changes in the brain. However, little is known regarding alterations of brain networks in MDD patients with suicidal ideation. We investigated whether or not MDD patients with suicidal ideation have different topological organizations of white matter networks compared with MDD patients without suicidal ideation. Participants consisted of 24 patients with MDD and suicidal ideation, 25 age- and gender-matched MDD patients without suicidal ideation and 31 healthy subjects. A network-based statistics (NBS) and a graph theoretical analysis were performed to assess differences in the inter-regional connectivity. Diffusion tensor imaging (DTI) was performed to assess topological changes according to suicidal ideation in MDD patients. The Scale for Suicide Ideation (SSI) and the Korean version of the Barrett Impulsiveness Scale (BIS) were used to assess the severity of suicidal ideation and impulsivity, respectively. Reduced structural connectivity in a characterized subnetwork was found in patients with MDD and suicidal ideation by utilizing NBS analysis. The subnetwork included the regions of the frontosubcortical circuits and the regions involved in executive function in the left hemisphere (rostral middle frontal, pallidum, superior parietal, frontal pole, caudate, putamen and thalamus). The graph theoretical analysis demonstrated that network measures of the left rostral middle frontal had a significant positive correlation with severity of SSI (r=0.59, P=0.02) and BIS (r=0.59, P=0.01). The total edge strength that was significantly associated with suicidal ideation did not differ between MDD patients without suicidal ideation and healthy subjects. Our findings suggest that the reduced frontosubcortical circuit of structural connectivity, which includes regions associated with executive function and impulsivity, appears to have a role in the emergence of suicidal ideation in MDD patients. PMID:27271861

Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

PubMed Central

Liu, Jun; Hua, Zheng-Shuang; Chen, Lin-Xing; Kuang, Jia-Liang; Li, Sheng-Jin; Shu, Wen-Sheng

2014-01-01

Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions. PMID:24727268

Regional grey matter structure differences between transsexuals and healthy controls--a voxel based morphometry study.

PubMed

Simon, Lajos; Kozák, Lajos R; Simon, Viktória; Czobor, Pál; Unoka, Zsolt; Szabó, Ádám; Csukly, Gábor

2013-01-01

Gender identity disorder (GID) refers to transsexual individuals who feel that their assigned biological gender is incongruent with their gender identity and this cannot be explained by any physical intersex condition. There is growing scientific interest in the last decades in studying the neuroanatomy and brain functions of transsexual individuals to better understand both the neuroanatomical features of transsexualism and the background of gender identity. So far, results are inconclusive but in general, transsexualism has been associated with a distinct neuroanatomical pattern. Studies mainly focused on male to female (MTF) transsexuals and there is scarcity of data acquired on female to male (FTM) transsexuals. Thus, our aim was to analyze structural MRI data with voxel based morphometry (VBM) obtained from both FTM and MTF transsexuals (n = 17) and compare them to the data of 18 age matched healthy control subjects (both males and females). We found differences in the regional grey matter (GM) structure of transsexual compared with control subjects, independent from their biological gender, in the cerebellum, the left angular gyrus and in the left inferior parietal lobule. Additionally, our findings showed that in several brain areas, regarding their GM volume, transsexual subjects did not differ significantly from controls sharing their gender identity but were different from those sharing their biological gender (areas in the left and right precentral gyri, the left postcentral gyrus, the left posterior cingulate, precuneus and calcarinus, the right cuneus, the right fusiform, lingual, middle and inferior occipital, and inferior temporal gyri). These results support the notion that structural brain differences exist between transsexual and healthy control subjects and that majority of these structural differences are dependent on the biological gender.

Soil fungi colony growth and community dynamics

NASA Astrophysics Data System (ADS)

Falconer, Ruth E.; Kravchenko, Alexandra; Otten, Wilfred

2010-05-01

Fungi are a major player in soil functioning, they contribute to soil structure formation and shaping of plant communities through their role in nutrient cycling, pathogenesis and symbiosis. Theoretical approaches which have emerged over the years and improved considerably our understanding of above ground plant communities are still lacking below ground. A theoretical framework is needed, such that links soil physics, fungal biology and mathematical biology in order to understand fungal community dynamics and diversity in undisturbed soils. Such a framework is essential if we are to understand how environmental change or soil manipulation impacts biodiversity. Different land use and management practices significantly affect soil environmental characteristics crucial for fungal communities by contributing different quantities and qualities of biomass inputs, generating different levels of soil disturbance, influencing soil temperature and moisture regimes, and affecting structure and geometry of soil pore space. Differences in pore structures generated by long-term differences in land use and management are reflected in notable changes in soil physical and hydraulic properties, including soil porosity, hydraulic conductivity and water retention (Brye and Pirani, 2005). Changes in numbers, shapes, and distributions of soil macropores have been often observed (e.g., Pachepsky et al., 1996; Giménez et al., 1997; Udawatta et al., 2008). However, specific implications of these differences in pore structure and geometries for ability of pathogenic as well as non-pathogenic fungi to colonize soil have not yet been addressed. Recent advances in computed tomography and microscopy facilitate detailed examination of the inner pore structures of undisturbed soil samples as well as visualization of fungal mycelia. Such tools together with modelling generate a new level of understanding of the mechanisms governing fungal behaviour at microscopic scales, and for the first time allow us to examine species interactions in a 3D soil environment.

Regional Grey Matter Structure Differences between Transsexuals and Healthy Controls—A Voxel Based Morphometry Study

PubMed Central

Simon, Lajos; Kozák, Lajos R.; Simon, Viktória; Czobor, Pál; Unoka, Zsolt; Szabó, Ádám; Csukly, Gábor

2013-01-01

Gender identity disorder (GID) refers to transsexual individuals who feel that their assigned biological gender is incongruent with their gender identity and this cannot be explained by any physical intersex condition. There is growing scientific interest in the last decades in studying the neuroanatomy and brain functions of transsexual individuals to better understand both the neuroanatomical features of transsexualism and the background of gender identity. So far, results are inconclusive but in general, transsexualism has been associated with a distinct neuroanatomical pattern. Studies mainly focused on male to female (MTF) transsexuals and there is scarcity of data acquired on female to male (FTM) transsexuals. Thus, our aim was to analyze structural MRI data with voxel based morphometry (VBM) obtained from both FTM and MTF transsexuals (n = 17) and compare them to the data of 18 age matched healthy control subjects (both males and females). We found differences in the regional grey matter (GM) structure of transsexual compared with control subjects, independent from their biological gender, in the cerebellum, the left angular gyrus and in the left inferior parietal lobule. Additionally, our findings showed that in several brain areas, regarding their GM volume, transsexual subjects did not differ significantly from controls sharing their gender identity but were different from those sharing their biological gender (areas in the left and right precentral gyri, the left postcentral gyrus, the left posterior cingulate, precuneus and calcarinus, the right cuneus, the right fusiform, lingual, middle and inferior occipital, and inferior temporal gyri). These results support the notion that structural brain differences exist between transsexual and healthy control subjects and that majority of these structural differences are dependent on the biological gender. PMID:24391851

Characterization of host-dependent mutations of apple fruit crinkle viroid replicating in newly identified experimental hosts suggests maintenance of stem-loop structures in the left-hand half of the molecule is important for replication.

PubMed

Suzuki, Takahiro; Fujibayashi, Misato; Hataya, Tatsuji; Taneda, Akito; He, Ying-Hong; Tsushima, Taro; Duraisamy, Ganesh Selvaraj; Siglová, Kristyna; Matoušek, Jaroslav; Sano, Teruo

2017-03-01

Apple fruit crinkle viroid (AFCVd) is a tentative member of the genus Apscaviroid, family Pospiviroidae. AFCVd has a narrow host range and is known to infect apple, hop and persimmon as natural hosts. In this study, tomato, cucumber and wild hop have been identified as new experimental herbaceous hosts. Foliar symptoms were very mild or virtually undetectable, but fruits of infected tomato were small, cracked and distorted. These symptoms resemble those observed on some AFCVd-sensitive apple cultivars. After transfer to tomato, cucumber and wild hop, sequence changes were detected in a natural AFCVd isolate from hop, and major variants in tomato, cucumber and wild hop differed in 10, 8 or 2 nucleotides, respectively, from the predominant one in the inoculum. The major variants in tomato and cucumber were almost identical, and the one in wild hop was very similar to the one in cultivated hop. Detailed analyses of the host-dependent sequence changes that appear in a naturally occurring AFCVd isolate from hop after transfer to tomato using small RNA deep sequence data and infectivity studies with dimeric RNA transcripts followed by progeny analysis indicate that the major AFCVd variant in tomato emerged by selection of a minor variant present in the inoculum (i.e. hop) followed by one to two host-dependent de novo mutations. Comparison of the secondary structures of major variants in hop, tomato and persimmon after transfer to tomato suggested that maintenance of stem-loop structures in the left-hand half of the molecule is critical for infection.

Interinstitutional review of slides for forensic pathology: types of inconsistencies.

PubMed

Ersoy, Gokhan; Akyildiz, Elif Ulker; Korkmaz, Gulay; Albek, Emre

2010-09-01

Because of the specific structure of forensic medicine in Turkey, reexamination of histopathologic specimens is a frequent practice. The aim of the present study is the assessment of microscopic diagnostic consistency in forensic pathology between different laboratories. Reports of the Council of Forensic Medicine between 2001 and 2004 were examined, and 150 cases with second pathologic examination were found. Results of histopathologic reports from peripheral laboratories were compared with those made by the Council pathologists with regard to diagnostic consistency. Consistency was assessed in 3 groups and 1 subgroup. Group 1, consistent and minor inconsistency; includes a major consistency subgroup. Group 2, major inconsistency, is the second diagnosis which is lethal; group 3, major inconsistency, is the first diagnosis which is lethal. The lung was found to be the organ with the highest frequency of diagnostic major inconsistency (group 2 and 3) and major consistency. Bronchopneumonia was the most common diagnosis. The brain had the highest frequency of intercenter diagnostic overall consistency (90.2%, group 1). Myocardial infarction was the diagnosis most frequently rejected on reevaluation (group 3). In conclusion, forensic pathology requires different experience than surgical ones. In cases of discrepancy between the anamnesis of the lethal event and pathologic findings, reevaluation of specimen is mandatory to avoid any diagnostic errors. Quality assurance systems with all include internal and external control mechanisms will improve the diagnostic reliability.

Morphology of the tracheal system of camel spiders (Chelicerata: Solifugae) based on micro-CT and 3D-reconstruction in exemplar species from three families.

PubMed

Franz-Guess, Sandra; Klußmann-Fricke, Bastian-Jesper; Wirkner, Christian S; Prendini, Lorenzo; Starck, J Matthias

2016-09-01

We studied the tracheal system of exemplar species representing three families of Solifugae Sundevall, 1833, i.e., Galeodes granti Pocock, 1903, Ammotrechula wasbaueri Muma, 1962 and Eremobates sp., using μCT-imaging and 3D-reconstruction. This is the first comparative study of the tracheal system of Solifugae in 85 years and the first using high-resolution nondestructive methods. The tracheal system was found to be structurally similar in all three species, with broad major tracheae predominantly in the prosoma as well as anastomoses (i.e., connections between tracheal branches from different stigmata) in the prosoma and opisthosoma. Differences among the three species were observed in the presence or absence of cheliceral air sacs, the number of tracheae supplying the heart, and the ramification of major tracheae in the opisthosoma. The structure of the tracheal system with its extensive branches and some anastomoses is assumed to aid rapid and efficient gas exchange in the respiratory tissues of these active predators. The large diameter of cheliceral tracheae (air sacs) of taxa with disproportionally heavier chelicerae suggests a role in weight reduction, enabling solifuges to reach greater speeds during predation. The air sacs may also permit more rapid and efficient gaseous exchange, necessary to operate the musculature of these structures, thereby improving their use for predation in an environment where prey is scarce. Copyright © 2016 Elsevier Ltd. All rights reserved.

The dynamics and control of large flexible space structures, 3. Part A: Shape and orientation control of a platform in orbit using point actuators

NASA Technical Reports Server (NTRS)

Bainum, P. M.; Reddy, A. S. S. R.; Krishna, R.; James, P. K.

1980-01-01

The dynamics, attitude, and shape control of a large thin flexible square platform in orbit are studied. Attitude and shape control are assumed to result from actuators placed perpendicular to the main surface and one edge and their effect on the rigid body and elastic modes is modelled to first order. The equations of motion are linearized about three different nominal orientations: (1) the platform following the local vertical with its major surface perpendicular to the orbital plane; (2) the platform following the local horizontal with its major surface normal to the local vertical; and (3) the platform following the local vertical with its major surface perpendicular to the orbit normal. The stability of the uncontrolled system is investigated analytically. Once controllability is established for a set of actuator locations, control law development is based on decoupling, pole placement, and linear optimal control theory. Frequencies and elastic modal shape functions are obtained using a finite element computer algorithm, two different approximate analytical methods, and the results of the three methods compared.

A Voxel-Based Morphometry Study of the Brain of University Students Majoring in Music and Nonmusic Disciplines.

PubMed

Sato, Kanako; Kirino, Eiji; Tanaka, Shoji

2015-01-01

The brain changes flexibly due to various experiences during the developmental stages of life. Previous voxel-based morphometry (VBM) studies have shown volumetric differences between musicians and nonmusicians in several brain regions including the superior temporal gyrus, sensorimotor areas, and superior parietal cortex. However, the reported brain regions depend on the study and are not necessarily consistent. By VBM, we investigated the effect of musical training on the brain structure by comparing university students majoring in music with those majoring in nonmusic disciplines. All participants were right-handed healthy Japanese females. We divided the nonmusic students into two groups and therefore examined three groups: music expert (ME), music hobby (MH), and nonmusic (NM) group. VBM showed that the ME group had the largest gray matter volumes in the right inferior frontal gyrus (IFG; BA 44), left middle occipital gyrus (BA 18), and bilateral lingual gyrus. These differences are considered to be caused by neuroplasticity during long and continuous musical training periods because the MH group showed intermediate volumes in these regions.

Using a structural competency framework to teach structural racism in pre-health education.

PubMed

Metzl, Jonathan M; Petty, JuLeigh; Olowojoba, Oluwatunmise V

2018-02-01

The inclusion of structural competency training in pre-health undergraduate programs may offer significant benefits to future healthcare professionals. This paper presents the results of a comparative study of an interdisciplinary pre-health curriculum based in structural competency with a traditional premedical curriculum. The authors describe the interdisciplinary pre-health curriculum, titled Medicine, Health, and Society (MHS) at Vanderbilt University. The authors then use a new survey tool, the Structural Foundations of Health Survey, to evaluate structural skills and sensibilities. The analysis compares MHS majors (n = 185) with premed science majors (n = 63) and first-semester freshmen (n = 91), with particular attention to understanding how structural factors shape health. Research was conducted from August 2015 to December 2016. Results suggest that MHS majors identified and analyzed relationships between structural factors and health outcomes at higher rates and in deeper ways than did premed science majors and freshmen, and also demonstrated higher understanding of structural and implicit racism and health disparities. The skills that MHS students exhibited represent proficiencies increasingly stressed by the MCAT, the AAMC, and other educational bodies that emphasize how contextual factors shape expressions of health and illness. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Self-Referential Processing, Rumination, and Cortical Midline Structures in Major Depression

PubMed Central

Nejad, Ayna Baladi; Fossati, Philippe; Lemogne, Cédric

2013-01-01

Major depression is associated with a bias toward negative emotional processing and increased self-focus, i.e., the process by which one engages in self-referential processing. The increased self-focus in depression is suggested to be of a persistent, repetitive and self-critical nature, and is conceptualized as ruminative brooding. The role of the medial prefrontal cortex in self-referential processing has been previously emphasized in acute major depression. There is increasing evidence that self-referential processing as well as the cortical midline structures play a major role in the development, course, and treatment response of major depressive disorder. However, the links between self-referential processing, rumination, and the cortical midline structures in depression are still poorly understood. Here, we reviewed brain imaging studies in depressed patients and healthy subjects that have examined these links. Self-referential processing in major depression seems associated with abnormally increased activity of the anterior cortical midline structures. Abnormal interactions between the lateralized task-positive network, and the midline cortical structures of the default mode network, as well as the emotional response network, may underlie the pervasiveness of ruminative brooding. Furthermore, targeting this maladaptive form of rumination and its underlying neural correlates may be key for effective treatment. PMID:24124416

The neural representation of social networks.

PubMed

Weaverdyck, Miriam E; Parkinson, Carolyn

2018-05-24

The computational demands associated with navigating large, complexly bonded social groups are thought to have significantly shaped human brain evolution. Yet, research on social network representation and cognitive neuroscience have progressed largely independently. Thus, little is known about how the human brain encodes the structure of the social networks in which it is embedded. This review highlights recent work seeking to bridge this gap in understanding. While the majority of research linking social network analysis and neuroimaging has focused on relating neuroanatomy to social network size, researchers have begun to define the neural architecture that encodes social network structure, cognitive and behavioral consequences of encoding this information, and individual differences in how people represent the structure of their social world. Copyright © 2018 Elsevier Ltd. All rights reserved.

Amelogenin and Enamel Biomimetics.

PubMed

Ruan, Qichao; Moradian-Oldak, Janet

Mature tooth enamel is acellular and does not regenerate itself. Developing technologies that rebuild tooth enamel and preserve tooth structure is therefore of great interest. Considering the importance of amelogenin protein in dental enamel formation, its ability to control apatite mineralization in vitro , and its potential to be applied in fabrication of future bio-inspired dental material this review focuses on two major subjects: amelogenin and enamel biomimetics. We review the most recent findings on amelogenin secondary and tertiary structural properties with a focus on its interactions with different targets including other enamel proteins, apatite mineral, and phospholipids. Following a brief overview of enamel hierarchical structure and its mechanical properties we will present the state-of-the-art strategies in the biomimetic reconstruction of human enamel.

Mysticism and schizophrenia: A phenomenological exploration of the structure of consciousness in the schizophrenia spectrum disorders.

PubMed

Parnas, Josef; Henriksen, Mads Gram

2016-07-01

Mysticism and schizophrenia are different categories of human existence and experience. Nonetheless, they exhibit important phenomenological affinities, which, however, remain largely unaddressed. In this study, we explore structural analogies between key features of mysticism and major clinical-phenomenological aspects of the schizophrenia spectrum disorders-i.e. attitudes, the nature of experience, and the 'other', mystical or psychotic reality. Not only do these features gravitate around the issue of the basic dimensions of consciousness, they crucially seem to implicate and presuppose a specific alteration of the very structure of consciousness. This finding has bearings for the understanding of consciousness and its psychopathological distortions. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Amelogenin and Enamel Biomimetics

PubMed Central

Ruan, Qichao; Moradian-Oldak, Janet

2015-01-01

Mature tooth enamel is acellular and does not regenerate itself. Developing technologies that rebuild tooth enamel and preserve tooth structure is therefore of great interest. Considering the importance of amelogenin protein in dental enamel formation, its ability to control apatite mineralization in vitro, and its potential to be applied in fabrication of future bio-inspired dental material this review focuses on two major subjects: amelogenin and enamel biomimetics. We review the most recent findings on amelogenin secondary and tertiary structural properties with a focus on its interactions with different targets including other enamel proteins, apatite mineral, and phospholipids. Following a brief overview of enamel hierarchical structure and its mechanical properties we will present the state-of-the-art strategies in the biomimetic reconstruction of human enamel. PMID:26251723

Introduction to the Wetland Book 1: Wetland structure and function, management, and nethods

USGS Publications Warehouse

Davidson, Nick C.; Middleton, Beth A.; McInnes, Robert J.; Everard, Mark; Irvine, Kenneth; Van Dam, Anne A.; Finlayson, C. Max; Finlayson, C. Max; Everard, Mark; Irvine, Kenneth; McInnes, Robert J.; Middleton, Beth A.; Van Dam, Anne A.; Davidson, Nick C.

2016-01-01

The Wetland Book 1 is designed as a ‘first port-of-call’ reference work for information on the structure and functions of wetlands, current approaches to wetland management, and methods for researching and understanding wetlands. Contributions by experts summarize key concepts, orient the reader to the major issues, and support further research on such issues by individuals and multidisciplinary teams. The Wetland Book 1 is organized in three parts - Wetland structure and function; Wetland management; and Wetland methods - each of which is divided into a number of thematic Sections. Each Section starts with one or more overview chapters, supported by chapters providing further information and case studies on different aspects of the theme.

Biological oscillations: Fluorescence monitoring by confocal microscopy

NASA Astrophysics Data System (ADS)

Chattoraj, Shyamtanu; Bhattacharyya, Kankan

2016-09-01

Fluctuations play a vital role in biological systems. Single molecule spectroscopy has recently revealed many new kinds of fluctuations in biological molecules. In this account, we focus on structural fluctuations of an antigen-antibody complex, conformational dynamics of a DNA quadruplex, effects of taxol on dynamics of microtubules, intermittent red-ox oscillations at different organelles in a live cell (mitochondria, lipid droplets, endoplasmic reticulum and cell membrane) and stochastic resonance in gene silencing. We show that there are major differences in these dynamics between a cancer cell and the corresponding non-cancer cell.

THE JOB DIMENSIONS OF ’WORKER ORIENTED’ JOB VARIABLES AND OF THEIR ATTRIBUTE PROFILES AS BASED ON DATA FROM THE POSITION ANALYSIS QUESTIONNAIRE.

DTIC Science & Technology

PAQ ). Two major data sources were developed and structured in terms of the behavioral job elements comprising the PAQ . One set of data consisted...of 536 jobs analyzed with the PAQ , while the second set of data consisted of the ratings of the relevance of 67 different human attributes to each of...the job activities and work situations described in the PAQ . Three different multivariate procedures were used to construct several sets of job

Molecular Modeling and Structural Stability of Wild-Type and Mutant CYP51 from Leishmania major: In Vitro and In Silico Analysis of a Laboratory Strain.

PubMed

Keighobadi, Masoud; Emami, Saeed; Lagzian, Milad; Fakhar, Mahdi; Rafiei, Alireza; Valadan, Reza

2018-03-19

Cutaneous leishmaniasis is a neglected tropical disease and a major public health in the most countries. Leishmania major is the most common cause of cutaneous leishmaniasis. In the Leishmania parasites, sterol 14α-demethylase (CYP51), which is involved in the biosynthesis of sterols, has been identified as an attractive target for development of new therapeutic agents. In this study, the sequence and structure of CYP51 in a laboratory strain (MRHO/IR/75/ER) of L. major were determined and compared to the wild-type strain. The results showed 19 mutations including seven non-synonymous and 12 synonymous ones in the CYP51 sequence of strain MRHO/IR/75/ER. Importantly, an arginine to lysine substitution at position of 474 resulted in destabilization of CYP51 (ΔΔG = 1.17 kcal/mol) in the laboratory strain; however, when the overall effects of all substitutions were evaluated by 100 ns molecular dynamics simulation, the final structure did not show any significant changes ( p -value < 0.05) in stability parameter of the strain MRHO/IR/75/ER compared to the wild-type protein. The energy level for the CYP51 of wild-type and MRHO/IR/75/ER strain were -40,027.1 and -39,706.48 Kcal/mol respectively. The overall Root-mean-square deviation (RMSD) deviation between two proteins was less than 1 Å throughout the simulation and Root-mean-square fluctuation (RMSF) plot also showed no substantial differences between amino acids fluctuation of the both protein. The results also showed that, these mutations were located on the protein periphery that neither interferes with protein folding nor with substrate/inhibitor binding. Therefore, L. major strain MRHO/IR/75/ER is suggested as a suitable laboratory model for studying biological role of CYP51 and inhibitory effects of sterol 14α-demethylase inhibitors.

Structural analysis of vimentin and keratin intermediate filaments by cryo-electron tomography.

PubMed

Norlén, Lars; Masich, Sergej; Goldie, Kenneth N; Hoenger, Andreas

2007-06-10

Intermediate filaments are a large and structurally diverse group of cellular filaments that are classified into five different groups. They are referred to as intermediate filaments (IFs) because they are intermediate in diameter between the two other cytoskeletal filament systems that is filamentous actin and microtubules. The basic building block of IFs is a predominantly alpha-helical rod with variable length globular N- and C-terminal domains. On the ultra-structural level there are two major differences between IFs and microtubules or actin filaments: IFs are non-polar, and they do not exhibit large globular domains. IF molecules associate via a coiled-coil interaction into dimers and higher oligomers. Structural investigations into the molecular building plan of IFs have been performed with a variety of biophysical and imaging methods such as negative staining and metal-shadowing electron microscopy (EM), mass determination by scanning transmission EM, X-ray crystallography on fragments of the IF stalk and low-angle X-ray scattering. The actual packing of IF dimers into a long filament varies between the different families. Typically the dimers form so called protofibrils that further assemble into a filament. Here we introduce new cryo-imaging methods for structural investigations of IFs in vitro and in vivo, i.e., cryo-electron microscopy and cryo-electron tomography, as well as associated techniques such as the preparation and handling of vitrified sections of cellular specimens.

Controlling major cellular processes of human mesenchymal stem cells using microwell structures.

PubMed

Xu, Xun; Wang, Weiwei; Kratz, Karl; Fang, Liang; Li, Zhengdong; Kurtz, Andreas; Ma, Nan; Lendlein, Andreas

2014-12-01

Directing stem cells towards a desired location and function by utilizing the structural cues of biomaterials is a promising approach for inducing effective tissue regeneration. Here, the cellular response of human adipose-derived mesenchymal stem cells (hADSCs) to structural signals from microstructured substrates comprising arrays of square-shaped or round-shaped microwells is explored as a transitional model between 2D and 3D systems. Microwells with a side length/diameter of 50 μm show advantages over 10 μm and 25 μm microwells for accommodating hADSCs within single microwells rather than in the inter-microwell area. The cell morphologies are three-dimensionally modulated by the microwell structure due to differences in focal adhesion and consequent alterations of the cytoskeleton. In contrast to the substrate with 50 μm round-shaped microwells, the substrate with 50 μm square-shaped microwells promotes the proliferation and osteogenic differentiation potential of hADSCs but reduces the cell migration velocity and distance. Such microwell shape-dependent modulatory effects are highly associated with Rho/ROCK signaling. Following ROCK inhibition, the differences in migration, proliferation, and osteogenesis between cells on different substrates are diminished. These results highlight the possibility to control stem cell functions through the use of structured microwells combined with the manipulation of Rho/ROCK signaling. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural Similarities and Differences between Two Functionally Distinct SecA Proteins, Mycobacterium tuberculosis SecA1 and SecA2

PubMed Central

Swanson, Stephanie; Ioerger, Thomas R.; Rigel, Nathan W.; Miller, Brittany K.; Braunstein, Miriam

2015-01-01

ABSTRACT While SecA is the ATPase component of the major bacterial secretory (Sec) system, mycobacteria and some Gram-positive pathogens have a second paralog, SecA2. In bacteria with two SecA paralogs, each SecA is functionally distinct, and they cannot compensate for one another. Compared to SecA1, SecA2 exports a distinct and smaller set of substrates, some of which have roles in virulence. In the mycobacterial system, some SecA2-dependent substrates lack a signal peptide, while others contain a signal peptide but possess features in the mature protein that necessitate a role for SecA2 in their export. It is unclear how SecA2 functions in protein export, and one open question is whether SecA2 works with the canonical SecYEG channel to export proteins. In this study, we report the structure of Mycobacterium tuberculosis SecA2 (MtbSecA2), which is the first structure of any SecA2 protein. A high level of structural similarity is observed between SecA2 and SecA1. The major structural difference is the absence of the helical wing domain, which is likely to play a role in how MtbSecA2 recognizes its unique substrates. Importantly, structural features critical to the interaction between SecA1 and SecYEG are preserved in SecA2. Furthermore, suppressor mutations of a dominant-negative secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG or the translocating polypeptide substrate. These results support a model in which the mycobacterial SecA2 works with SecYEG. IMPORTANCE SecA2 is a paralog of SecA1, which is the ATPase of the canonical bacterial Sec secretion system. SecA2 has a nonredundant function with SecA1, and SecA2 exports a distinct and smaller set of substrates than SecA1. This work reports the crystal structure of SecA2 of Mycobacterium tuberculosis (the first SecA2 structure reported for any organism). Many of the structural features of SecA1 are conserved in the SecA2 structure, including putative contacts with the SecYEG channel. Several structural differences are also identified that could relate to the unique function and selectivity of SecA2. Suppressor mutations of a secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG. PMID:26668263

Structural flexibility of a conserved antigenic region in hepatitis C virus glycoprotein E2 recognized by broadly neutralizing antibodies.

PubMed

Meola, Annalisa; Tarr, Alexander W; England, Patrick; Meredith, Luke W; McClure, C Patrick; Foung, Steven K H; McKeating, Jane A; Ball, Jonathan K; Rey, Felix A; Krey, Thomas

2015-02-01

Neutralizing antibodies (NAbs) targeting glycoprotein E2 are important for the control of hepatitis C virus (HCV) infection. One conserved antigenic site (amino acids 412 to 423) is disordered in the reported E2 structure, but a synthetic peptide mimicking this site forms a β-hairpin in complex with three independent NAbs. Our structure of the same peptide in complex with NAb 3/11 demonstrates a strikingly different extended conformation. We also show that residues 412 to 423 are essential for virus entry but not for E2 folding. Together with the neutralizing capacity of the 3/11 Fab fragment, this indicates an unexpected structural flexibility within this epitope. NAbs 3/11 and AP33 (recognizing the extended and β-hairpin conformations, respectively) display similar neutralizing activities despite converse binding kinetics. Our results suggest that HCV utilizes conformational flexibility as an immune evasion strategy, contributing to the limited immunogenicity of this epitope in patients, similar to the conformational flexibility described for other enveloped and nonenveloped viruses. Approximately 180 million people worldwide are infected with hepatitis C virus (HCV), and neutralizing antibodies play an important role in controlling the replication of this major human pathogen. We show here that one of the most conserved antigenic sites within the major glycoprotein E2 (amino acids 412 to 423), which is disordered in the recently reported crystal structure of an E2 core fragment, can adopt different conformations in the context of the infectious virus particle. Recombinant Fab fragments recognizing different conformations of this antigenic site have similar neutralization activities in spite of converse kinetic binding parameters. Of note, an antibody response targeting this antigenic region is less frequent than those targeting other more immunogenic regions in E2. Our results suggest that the observed conformational flexibility in this conserved antigenic region contributes to the evasion of the humoral host immune response, facilitating chronicity and the viral spread of HCV within an infected individual. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Evolution of land mammal diversity in North America during the Cenozoic

NASA Technical Reports Server (NTRS)

Stucky, Richard K.

1990-01-01

The North American continental patterns of generic richness, extinction, and origination have been reexamined and analyzed in the context of alpha and beta species diversity. The major models of diversity are discussed as well as primary concepts and theories based on studies of living organisms. The adequacy of the fossil record is considered and patterns of genetic richness and species level diversity are outlined. Major shifts in mammalian community structures are reviewed and hypotheses are presented on diversity origin, regulation, and maintenance for the North American record. Results demonstrate a complex relationship between continental alpha and beta diversity characterized by marked changes through time and differences in patterns at each level. It is clear that both biotic and abiotic factors have strongly influenced the evolution of North American species diversity and that major restructuring occurred in Cenozoic mammalian communities.

Plastoglobules in algae: A comprehensive comparative study of the presence of major structural and functional components in complex plastids.

PubMed

Lohscheider, Jens N; Río Bártulos, Carolina

2016-08-01

Plastoglobules (PG) are lipophilic droplets attached to thylakoid membranes in higher plants and green algae and are implicated in prenyl lipid biosynthesis. They might also represent a central hub for integration of plastid signals under stress and therefore the adaptation of the thylakoid membrane under such conditions. In Arabidopsis thaliana, PG contain around 30 specific proteins of which Fibrillins (FBN) and Activity of bc1 complex kinases (ABC1K) represent the majority with respect to both number and protein mass. However, nothing is known about the presence of PG in most algal species, which are responsible for about 50% of global primary production. Therefore, we searched the genomes of publicly available algal genomes for components of PG and the associated functional network in order to predict their presence and potential evolutionary conservation of physiological functions. We could identify homologous sequences for core components of PG, like FBN and ABC1K, in most investigated algal species. Furthermore, proteins at central and interesting positions within the PG functional coexpression network were identified. Phylogenetic sequence analysis revealed diversity within FBN and ABC1K sequences among algal species with complex plastids of the red lineage and large differences compared with green lineage species. Two types of FBN were detected that differ in their isoelectric point which seems to correlate with subcellular localization. Subgroups of FBN were shared between many investigated species and modeling of their 3D-structure implied a conserved structure. FBN and ABC1K are essential structural and functional components of PG. Their occurrence in investigated algal species suggests presence of PG therein and functions in prenyl lipid metabolism and adaptation of the thylakoid membrane that are conserved during evolution. Copyright © 2016 Elsevier B.V. All rights reserved.

Database-Guided Discovery of Potent Peptides to Combat HIV-1 or Superbugs

PubMed Central

Wang, Guangshun

2013-01-01

Antimicrobial peptides (AMPs), small host defense proteins, are indispensable for the protection of multicellular organisms such as plants and animals from infection. The number of AMPs discovered per year increased steadily since the 1980s. Over 2,000 natural AMPs from bacteria, protozoa, fungi, plants, and animals have been registered into the antimicrobial peptide database (APD). The majority of these AMPs (>86%) possess 11–50 amino acids with a net charge from 0 to +7 and hydrophobic percentages between 31–70%. This article summarizes peptide discovery on the basis of the APD. The major methods are the linguistic model, database screening, de novo design, and template-based design. Using these methods, we identified various potent peptides against human immunodeficiency virus type 1 (HIV-1) or methicillin-resistant Staphylococcus aureus (MRSA). While the stepwise designed anti-HIV peptide is disulfide-linked and rich in arginines, the ab initio designed anti-MRSA peptide is linear and rich in leucines. Thus, there are different requirements for antiviral and antibacterial peptides, which could kill pathogens via different molecular targets. The biased amino acid composition in the database-designed peptides, or natural peptides such as θ-defensins, requires the use of the improved two-dimensional NMR method for structural determination to avoid the publication of misleading structure and dynamics. In the case of human cathelicidin LL-37, structural determination requires 3D NMR techniques. The high-quality structure of LL-37 provides a solid basis for understanding its interactions with membranes of bacteria and other pathogens. In conclusion, the APD database is a comprehensive platform for storing, classifying, searching, predicting, and designing potent peptides against pathogenic bacteria, viruses, fungi, parasites, and cancer cells. PMID:24276259

Does white matter structure or hippocampal volume mediate associations between cortisol and cognitive ageing?

PubMed Central

Cox, Simon R.; MacPherson, Sarah E.; Ferguson, Karen J.; Royle, Natalie A.; Maniega, Susana Muñoz; Hernández, Maria del C. Valdés; Bastin, Mark E.; MacLullich, Alasdair M.J.; Wardlaw, Joanna M.; Deary, Ian J.

2015-01-01

Elevated glucocorticoid (GC) levels putatively damage specific brain regions, which in turn may accelerate cognitive ageing. However, many studies are cross-sectional or have relatively short follow-up periods, making it difficult to relate GCs directly to changes in cognitive ability with increasing age. Moreover, studies combining endocrine, MRI and cognitive variables are scarce, measurement methods vary considerably, and formal tests of the underlying causal hypothesis (cortisol → brain → cognition) are absent. In this study, 90 men, aged 73 years, provided measures of fluid intelligence, processing speed and memory, diurnal and reactive salivary cortisol and two measures of white matter (WM) structure (WM hyperintensity volume from structural MRI and mean diffusivity averaged across 12 major tracts from diffusion tensor MRI), hippocampal volume, and also cognitive ability at age 11. We tested whether negative relationships between cognitive ageing differences (over more than 60 years) and salivary cortisol were significantly mediated by WM and hippocampal volume. Significant associations between reactive cortisol at 73 and cognitive ageing differences between 11 and 73 (r = −.28 to −.36, p < .05) were partially mediated by both WM structural measures, but not hippocampal volume. Cortisol-WM relationships were modest, as was the degree to which WM structure attenuated cortisol–cognition associations (<15%). These data support the hypothesis that GCs contribute to cognitive ageing differences from childhood to the early 70s, partly via brain WM structure. PMID:26298692

Characterization of Aircraft Structural Damage Using Guided Wave Based Finite Element Analysis for In-Flight Structural Health Management

NASA Technical Reports Server (NTRS)

Seshadri, Banavara R.; Krishnamurthy, Thiagarajan; Ross, Richard W.

2016-01-01

The development of multidisciplinary Integrated Vehicle Health Management (IVHM) tools will enable accurate detection, diagnosis and prognosis of damage under normal and adverse conditions during flight. The adverse conditions include loss of control caused by environmental factors, actuator and sensor faults or failures, and structural damage conditions. A major concern is the growth of undetected damage/cracks due to fatigue and low velocity foreign object impact that can reach a critical size during flight, resulting in loss of control of the aircraft. To avoid unstable catastrophic propagation of damage during a flight, load levels must be maintained that are below the load-carrying capacity for damaged aircraft structures. Hence, a capability is needed for accurate real-time predictions of safe load carrying capacity for aircraft structures with complex damage configurations. In the present work, a procedure is developed that uses guided wave responses to interrogate damage. As the guided wave interacts with damage, the signal attenuates in some directions and reflects in others. This results in a difference in signal magnitude as well as phase shifts between signal responses for damaged and undamaged structures. Accurate estimation of damage size and location is made by evaluating the cumulative signal responses at various pre-selected sensor locations using a genetic algorithm (GA) based optimization procedure. The damage size and location is obtained by minimizing the difference between the reference responses and the responses obtained by wave propagation finite element analysis of different representative cracks, geometries and sizes.

Biomechanics of selected arborescent and shrubby monocotyledons

PubMed Central

Haushahn, Tobias; Fink, Samuel; Speck, Thomas

2016-01-01

Main aims of the study are a deepened understanding of the mechanically relevant (ultra-)structures and the mechanical behaviour of various arborescent and shrubby monocotyledons and obtaining the structure–function relationships of different structurally conspicuous parts in Dracaena marginata stems. The stems of five different “woody” monocotyledon species were dissected and the mechanical properties of the most noticeable tissues in the five monocotyledons and, additionally, of individual vascular bundles in D. marginata, were tested under tensile stress. Results for Young’s moduli and density of these tissues were assessed as well as the area, critical strain, Young’s modulus and tensile strength of the vascular bundles in Dracaena marginata. These analyses allowed for generating a model for the mechanical interaction of tissues and vascular bundles of the stem in D. marginata as well as filling major “white spots” in property charts for biological materials. Additionally we shortly discuss the potential significance of such studies for the development of branched and unbranched bio-inspired fibre-reinforced materials and structures with enhanced properties. PMID:28144511

Longitudinal distribution of Chironomidae (Diptera) downstream from a dam in a neotropical river.

PubMed

Pinha, G D; Aviz, D; Lopes Filho, D R; Petsch, D K; Marchese, M R; Takeda, A M

2013-08-01

The damming of a river causes dangerous consequences on structure of the environment downstream of the dam, modifying the sediment composition, which impose major adjustments in longitudinal distribution of benthic community. The construction of Engenheiro Sérgio Motta Dam in the Upper Paraná River has caused impacts on the aquatic communities, which are not yet fully known. This work aimed to provide more information about the effects of this impoundment on the structure of Chironomidae larvae assemblage. The analysis of data of physical and chemical variables in relation to biological data of 8 longitudinal sections in the Upper Paraná River showed that composition of Chironomidae larvae of stations near Engenheiro Sérgio Motta Dam differed of the other stations (farther of the Dam). The predominance of coarse sediments at stations upstream and finer sediments further downstream affected the choice of habitat by different morphotypes of Chironomidae and it caused a change in the structure of this assemblage in the longitudinal stretch.

Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient

PubMed Central

Vangestel, C; Mergeay, J; Dawson, D A; Callens, T; Vandomme, V; Lens, L

2012-01-01

House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients. PMID:22588131

Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient.

PubMed

Vangestel, C; Mergeay, J; Dawson, D A; Callens, T; Vandomme, V; Lens, L

2012-09-01

House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients.

Structural Heterogeneity and Functional Domains of Murine Immunoglobulin G Fc Receptors

NASA Astrophysics Data System (ADS)

Ravetch, Jeffrey V.; Luster, Andrew D.; Weinshank, Richard; Kochan, Jarema; Pavlovec, Amalia; Portnoy, Daniel A.; Hulmes, Jeffrey; Pan, Yu-Ching E.; Unkeless, Jay C.

1986-11-01

Binding of antibodies to effector cells by way of receptors to their constant regions (Fc receptors) is central to the pathway that leads to clearance of antigens by the immune system. The structure and function of this important class of receptors on immune cells is addressed through the molecular characterization of Fc receptors (FcR) specific for the murine immunoglobulin G isotype. Structural diversity is encoded by two genes that by alternative splicing result in expression of molecules with highly conserved extracellular domains and different transmembrane and intracytoplasmic domains. The proteins encoded by these genes are members of the immunoglobulin supergene family, most homologous to the major histocompatibility complex molecule Eβ. Functional reconstitution of ligand binding by transfection of individual FcR genes demonstrates that the requirements for ligand binding are encoded in a single gene. These studies demonstrate the molecular basis for the functional heterogeneity of FcR's, accounting for the possible transduction of different signals in response to a single ligand.

Discovery of Cellulose Surface Layer Conformation by Nonlinear Vibrational Spectroscopy

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

Zhang, Libing; Fu, Li; Wang, Hong-fei

2017-03-14

Significant questions remain with respect to the structure and polymorphs of cellulose. These include the cellulose surface layers and the bulk crystalline core as well as the conformational differences. The Total Internal Reflection Sum Frequency Generation Vibrational Spectroscopy (TIR-SFG-VS) combined with the conventional SFG-VS (non-TIR) can help to resolve these questions by selectively characterizing the molecular structures of surface layers and the crystalline core of cellulose. From the SFG spectra in the C-H and O-H regions, we found that the surface layers of Avicel are essentially amorphous; while the surface layers of Iβ cellulose are crystalline but with different structuralmore » and spectroscopic signatures than that of its crystalline core. This work demonstrates the capacity of TIR and Non-TIR SFG-VS tools in selectively studying the structures and polymorphs of cellulose. In addition, these results also suggest that the assignments of major vibrational peaks for cellulose need to be further determined.« less

Structural characterization of the exopolysaccharides from water kefir.

PubMed

Fels, Lea; Jakob, Frank; Vogel, Rudi F; Wefers, Daniel

2018-06-01

Water kefir is a beverage which is produced by initiating fermentation of a fruit extract/sucrose solution with insoluble kefir grains. Exopolysaccharides that are formed from sucrose play a major role in the kefir grain formation, but the exopolysaccharides in the kefir beverage and the detailed structural composition of the whole kefir grains have not been studied yet. Therefore, kefir grains and the corresponding kefir beverage were analyzed for exopolysaccharides by multiple chromatographic approaches and two-dimensional NMR spectroscopy. Furthermore, different fractionation techniques were applied to obtain further information about the exopolysaccharides. The exopolysaccharide-fraction of the investigated kefir beverage was predominantly composed of O3- and O2-branched dextrans as well as lower amounts of levans. The insoluble dextrans from the kefir grains were mostly O3-branched and contained an elevated portion of 1,3-linked glucose units compared to the soluble dextrans. The structurally different exopolysaccharides in water kefir suggest the involvement of multiple bacteria. Copyright © 2018 Elsevier Ltd. All rights reserved.

Exploration of multiple Sortase A protein conformations in virtual screening

NASA Astrophysics Data System (ADS)

Gao, Chunxia; Uzelac, Ivana; Gottfries, Johan; Eriksson, Leif A.

2016-02-01

Methicillin resistant Staphylococcus aureus (MRSA) has become a major health concern which has brought about an urgent need for new therapeutic agents. As the S. aureus Sortase A (SrtA) enzyme contributes to the adherence of the bacteria to the host cells, inhibition thereof by small molecules could be employed as potential antivirulence agents, also towards resistant strains. Albeit several virtual docking SrtA campaigns have been reported, no strongly inhibitatory non-covalent binders have as yet emerged therefrom. In order to better understand the binding modes of small molecules, and the effect of different receptor structures employed in the screening, we herein report on an exploratory study employing 10 known binders and 500 decoys on 100 SrtA structures generated from regular or steered molecular dynamics simulations on four different SrtA crystal/NMR structures. The results suggest a correlation between the protein structural flexibility and the virtual screening performance, and confirm the noted immobilization of the β6/β7 loop upon substrate binding. The NMR structures reported appear to perform slightly better than the Xray-crystal structures, but the binding modes fluctuate tremendously, and it might be suspected that the catalytic site is not necessarily the preferred site of binding for some of the reported active compounds.

Exploration of multiple Sortase A protein conformations in virtual screening

PubMed Central

Gao, Chunxia; Uzelac, Ivana; Gottfries, Johan; Eriksson, Leif A.

2016-01-01

Methicillin resistant Staphylococcus aureus (MRSA) has become a major health concern which has brought about an urgent need for new therapeutic agents. As the S. aureus Sortase A (SrtA) enzyme contributes to the adherence of the bacteria to the host cells, inhibition thereof by small molecules could be employed as potential antivirulence agents, also towards resistant strains. Albeit several virtual docking SrtA campaigns have been reported, no strongly inhibitatory non-covalent binders have as yet emerged therefrom. In order to better understand the binding modes of small molecules, and the effect of different receptor structures employed in the screening, we herein report on an exploratory study employing 10 known binders and 500 decoys on 100 SrtA structures generated from regular or steered molecular dynamics simulations on four different SrtA crystal/NMR structures. The results suggest a correlation between the protein structural flexibility and the virtual screening performance, and confirm the noted immobilization of the β6/β7 loop upon substrate binding. The NMR structures reported appear to perform slightly better than the Xray-crystal structures, but the binding modes fluctuate tremendously, and it might be suspected that the catalytic site is not necessarily the preferred site of binding for some of the reported active compounds. PMID:26846342

Structural and phase transition changes of sodium dodecyl sulfate micellar solution in alcohols probed by small-angle neutron scattering (SANS)

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

Putra, Edy Giri Rachman; Patriati, Arum; Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Gadjah Mada, Bulaksumur, Yogyakarta 55281, Indonesia giri@batan.go.id

2015-04-16

Small-angle neutron scattering (SANS) measurements on 0.3M sodium dodecyl sulfate (SDS) micellar solutions have been performed in the presence of n-alcohols, from ethanol to decanol at different alcohol concentrations, 2–10 wt%. The ellipsoid micellar structure which occurred in the 0.3M SDS in aqueous solution with the size range of 30–50 Å has different behavior at various hydrocarbon chain length and concentration of alcohols. At low concentration and short chain-length of alcohols, such as ethanol, propanol, and butanol, the size of micelles reduced and had a spherical-like structure. The opposite effect occurred as medium to long chain alcohols, such as hexanol,more » octanol and decanol was added into the 0.3M SDS micellar solutions. The micelles structure changed to be more elongated in major axis and then crossed the critical phase transition from micellar solution into liquid crystal phase as lamellar structure emerged by further addition of alcohols. The inter-lamellar distances were also depending on the hydrocarbon chain length and concentration of alcohols. In the meantime, the persistent micellar structures occurred in addition of medium chain of n-alcohol, pentanol at all concentrations.« less

Intracellular origin and ultrastructure of platelet-derived microparticles.

PubMed

Ponomareva, A A; Nevzorova, T A; Mordakhanova, E R; Andrianova, I A; Rauova, L; Litvinov, R I; Weisel, J W

2017-08-01

Essentials Platelet microparticles play a major role in pathologies, including hemostasis and thrombosis. Platelet microparticles have been analyzed and classified based on their ultrastructure. The structure and intracellular origin of microparticles depend on the cell-activating stimulus. Thrombin-treated platelets fall apart and form microparticles that contain cellular organelles. Background Platelet-derived microparticles comprise the major population of circulating blood microparticles that play an important role in hemostasis and thrombosis. Despite numerous studies on the (patho)physiological roles of platelet-derived microparticles, mechanisms of their formation and structural details remain largely unknown. Objectives Here we studied the formation, ultrastructure and composition of platelet-derived microparticles from isolated human platelets, either quiescent or stimulated with one of the following activators: arachidonic acid, ADP, collagen, thrombin or calcium ionophore A23187. Methods Using flow cytometry, transmission and scanning electron microscopy, we analyzed the intracellular origin, structural diversity and size distributions of the subcellular particles released from platelets. Results The structure, dimensions and intracellular origin of microparticles depend on the cell-activating stimulus. The main structural groups include a vesicle surrounded by one thin membrane or multivesicular structures. Thrombin, unlike other stimuli, induced formation of microparticles not only from the platelet plasma membrane and cytoplasm but also from intracellular structures. A fraction of these vesicular particles having an intracellular origin contained organelles, such as mitochondria, glycogen granules and vacuoles. The size of platelet-derived microparticles depended on the nature of the cell-activating stimulus. Conclusion The results obtained provide a structural basis for the qualitative differences of various platelet activators, for specific physiological and pathological effects of microparticles, and for development of advanced assays. © 2017 International Society on Thrombosis and Haemostasis.

Magnitude and nature of carbohydrate-aromatic interactions in fucose-phenol and fucose-indole complexes: CCSD(T) level interaction energy calculations.

PubMed

Tsuzuki, Seiji; Uchimaru, Tadafumi; Mikami, Masuhiro

2011-10-20

The CH/π contact structures of the fucose-phenol and fucose-indole complexes and the stabilization energies by formation of the complexes (E(form)) were studied by ab initio molecular orbital calculations. The three types of interactions (CH/π and OH/π interactions and OH/O hydrogen bonds) were compared and evaluated in a single molecular system and at the same level of theory. The E(form) calculated for the most stable CH/π contact structure of the fucose-phenol complex at the CCSD(T) level (-4.9 kcal/mol) is close to that for the most stable CH/π contact structure of the fucose-benzene complex (-4.5 kcal/mol). On the other hand the most stable CH/π contact structure of the fucose-indole complex has substantially larger E(form) (-6.5 kcal/mol). The dispersion interaction is the major source of the attraction in the CH/π contact structures of the fucose-phenol and fucose-indole complexes as in the case of the fucose-benzene complex. The electrostatic interactions in the CH/π contact structures are small (less than 1.5 kcal/mol). The nature of the interactions between the nonpolar surface of the carbohydrate and aromatic rings is completely different from that of the conventional hydrogen bonds where the electrostatic interaction is the major source of the attraction. The distributed multipole analysis and DFT-SATP analysis show that the dispersion interactions in the CH/π contact structure of fucose-indole complex are substantially larger than those in the CH/π contact structures of fucose-benzene and fucose-phenol complexes. The large dispersion interactions are responsible for the large E(form) for the fucose-indole complex.

Structural development of the Dieppe-Hampshire Basin (Eastern English Channel): Contribution of new seismic data

NASA Astrophysics Data System (ADS)

Jollivet-Castelot, Martin; Gaullier, Virginie; Paquet, Fabien; Chanier, Frank; Thinon, Isabelle; Lasseur, Eric; Averbuch, Olivier

2017-04-01

The Dieppe-Hampshire Basin is a Cenozoic basin crossing the eastern English Channel, between SE of England and the French coast. This basin and its borders developed during the Cenozoic, a period of overall tectonic inversion, in response to the opening of the North Atlantic Ocean and Pyrenean-alpine deformation episodes. Both extensional and subsequent compressional deformations within this area involve the reactivation of older major regional structures, inherited from the Variscan Orogeny. However, the detailed structural development of the Dieppe-Hampshire Basin still remains poorly constrained, as well as the detailed stratigraphic framework of Cenozoic series, notably in terms of seismic stratigraphy and sequence stratigraphy. New very high resolution seismic data, acquired during the oceanographic cruise "TREMOR" (R/V "Côtes de la Manche", 2014, 1800 kilometers of Sparker profiles), and bathymetric data from SHOM and UKHO, have allowed to image the sedimentary filling and tectonic structures of the Dieppe-Hampshire Basin and adjacent areas. The interpretation was first focused on a seismic facies analysis that led to evidence numerous unconformities and seismic units ranging from the Upper Cretaceous to the Bartonian (Late Eocene). The interpretation of the seismic profiles also allowed to map precisely many tectonic features, as faults, folds and monoclinal flexures. Thanks to the new data, we especially imaged the complexity of the deformation within the highest tectonized zones of the region, along the Nord-Baie de Seine Basin and offshore the Boulonnais coast with an unprecedented resolution. The expression of the deformation appears to be very different between the Mesozoic and the Cenozoic series, with prevailing folding affecting the Cenozoic strata whereas the Mesozoic series are predominantly faulted. This deformation pattern illustrates two major structural trends, respectively E-W and NW-SE directed, both syn- to post-Bartonian in age. The first one is consistent in age and orientation with a late Pyrenean or early Alpine deformation phase, while the second one appears to have a different origin, in regards to the overall geodynamic framework. We suggest that the major heterogeneities of crustal blocks underlying the basin played an important role on the development and orientations of these deformations. These preliminary results will be improved soon thanks to a new cruise, "TREMOR 2" (2017), which will be focused on the acquisition of new VHR seismic lines, bathymetric data and coring.

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

PubMed

Park, Hahnbeom; Lee, Gyu Rie; Heo, Lim; Seok, Chaok

2014-01-01

Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function.

Three-dimensional lithospheric electrical structure of Southern Granulite Terrain, India and its tectonic implications

NASA Astrophysics Data System (ADS)

Patro, Prasanta K.; Sarma, S. V. S.; Naganjaneyulu, K.

2014-01-01

crustal as well as the upper mantle lithospheric electrical structure of the Southern Granulite Terrain (SGT) is evaluated, using the magnetotelluric (MT) data from two parallel traverses: one is an 500 km long N-S trending traverse across SGT and another a 200 km long traverse. Data space Occam 3-D inversion was used to invert the MT data. The electrical characterization of lithospheric structure in SGT shows basically a highly resistive (several thousands of Ohm meters) upper crustal layer overlying a moderately resistive (a few hundred Ohm meters) lower crustal layer which in turn is underlain by the upper mantle lithosphere whose resistivity shows significant changes along the traverse. The highly resistive upper crustal layer is interspersed with four major conductive features with three of them cutting across the crustal column, bringing out a well-defined crustal block structure in SGT with individual highly resistive blocks showing correspondence to the geologically demarcated Salem, Madurai, and Trivandrum blocks. The 3-D model also brought out a well-defined major crustal conductor located in the northern half of the Madurai block. The electrical characteristics of this south dipping conductor and its close spatial correlation with two of the major structural elements, viz., Karur-Oddanchatram-Kodaikanal Shear Zone and Karur-Kamban-Painavu-Trichur Shear Zone, suggest that this conductive feature is closely linked to the subduction-collision tectonic processes in the SGT, and it is inferred that the Archean Dharwar craton/neoproterozoic SGT terrain boundary lies south of the Palghat-Cauvery shear zone. The results also showed that the Achankovil shear zone is characterized by a well-defined north dipping conductive feature. The resistive block adjoining this conductor on the southern side, representing the Trivandrum block, is shown to be downthrown along this north dipping crustal conductor relative to the Madurai block, suggesting a northward movement of Trivandrum block colliding against the Madurai block. The lithospheric upper mantle electrical structure of the SGT up to a depth of 100 km may be broadly divided into two distinctly different segments, viz., northern and southern segments. The northern lithospheric segment, over a major part, is characterized by a thick resistive upper mantle, while the southern one is characterized by a dominantly conductive medium suggesting a relatively thinned lithosphere in the southern segment.