Extrinsic factors regulate partial agonist efficacy of strychnine-sensitive glycine receptors

PubMed Central

Farroni, Jeffrey S; McCool, Brian A

2004-01-01

Background Strychnine-sensitive glycine receptors in many adult forebrain regions consist of alpha2 + beta heteromeric channels. This subunit composition is distinct from the alpha1 + beta channels found throughout the adult spinal cord. Unfortunately, the pharmacology of forebrain alpha2beta receptors are poorly defined compared to 'neonatal' alpha2 homomeric channels or 'spinal' alpha1beta heteromers. In addition, the pharmacologic properties of native alpha2beta glycine receptors have been generally distinct from receptors produced by heterologous expression. To identify subtype-specific pharmacologic tools for the forebrain alpha2beta receptors, it is important to identify a heterologous expression system that closely resembles these native glycine-gated chloride channels. Results While exploring pharmacological properties of alpha2beta glycine receptors compared to alpha2-homomers, we found that distinct heterologous expression systems appeared to differentially influence partial agonist pharmacology. The β-amino acid taurine possessed 30–50% efficacy for alpha2-containing receptor isoforms when expressed in HEK 293 cells. However, taurine efficacy was dramatically reduced in L-cell fibroblasts. Similar results were obtained for β-alanine. The efficacy of these partial agonists was also strongly reduced by the beta subunit. There were no significant differences in apparent strychnine affinity values calculated from concentration-response data between expression systems or subunit combinations. Nor did relative levels of expression correlate with partial agonist efficacy when compared within or between several different expression systems. Finally, disruption of the tubulin cytoskeleton reduced the efficacy of partial agonists in a subunit-dependent, but system-independent, fashion. Conclusions Our results suggest that different heterologous expression systems can dramatically influence the agonist pharmacology of strychnine-sensitive glycine receptors. In the systems examine here, these effects are independent of both absolute expression level and any system-related alterations in the agonist binding site. We conclude that complex interactions between receptor composition and extrinsic factors may play a significant role in determining strychnine-sensitive glycine receptor partial agonist pharmacology. PMID:15301692

Extrinsic factors regulate partial agonist efficacy of strychnine-sensitive glycine receptors.

PubMed

Farroni, Jeffrey S; McCool, Brian A

2004-08-09

Strychnine-sensitive glycine receptors in many adult forebrain regions consist of alpha2 + beta heteromeric channels. This subunit composition is distinct from the alpha1 + beta channels found throughout the adult spinal cord. Unfortunately, the pharmacology of forebrain alpha2beta receptors are poorly defined compared to 'neonatal' alpha2 homomeric channels or 'spinal' alpha1beta heteromers. In addition, the pharmacologic properties of native alpha2beta glycine receptors have been generally distinct from receptors produced by heterologous expression. To identify subtype-specific pharmacologic tools for the forebrain alpha2beta receptors, it is important to identify a heterologous expression system that closely resembles these native glycine-gated chloride channels. While exploring pharmacological properties of alpha2beta glycine receptors compared to alpha2-homomers, we found that distinct heterologous expression systems appeared to differentially influence partial agonist pharmacology. The beta-amino acid taurine possessed 30-50% efficacy for alpha2-containing receptor isoforms when expressed in HEK 293 cells. However, taurine efficacy was dramatically reduced in L-cell fibroblasts. Similar results were obtained for beta-alanine. The efficacy of these partial agonists was also strongly reduced by the beta subunit. There were no significant differences in apparent strychnine affinity values calculated from concentration-response data between expression systems or subunit combinations. Nor did relative levels of expression correlate with partial agonist efficacy when compared within or between several different expression systems. Finally, disruption of the tubulin cytoskeleton reduced the efficacy of partial agonists in a subunit-dependent, but system-independent, fashion. Our results suggest that different heterologous expression systems can dramatically influence the agonist pharmacology of strychnine-sensitive glycine receptors. In the systems examine here, these effects are independent of both absolute expression level and any system-related alterations in the agonist binding site. We conclude that complex interactions between receptor composition and extrinsic factors may play a significant role in determining strychnine-sensitive glycine receptor partial agonist pharmacology.

Structural Analysis of HMGD-DNA Complexes Reveal Influence of Intercalation on Sequence Selectivity and DNA Bending

PubMed Central

Churchill, Mair E.A.; Klass, Janet; Zoetewey, David L.

2010-01-01

The ubiquitous eukaryotic High-Mobility-Group-Box (HMGB) chromosomal proteins promote many chromatin-mediated cellular activities through their non-sequence-specific binding and bending of DNA. Minor groove DNA binding by the HMG box results in substantial DNA bending toward the major groove owing to electrostatic interactions, shape complementarity and DNA intercalation that occurs at two sites. Here, the structures of the complexes formed with DNA by a partially DNA intercalation-deficient mutant of Drosophila melanogaster HMGD have been determined by X-ray crystallography at a resolution of 2.85 Å. The six proteins and fifty base pairs of DNA in the crystal structure revealed a variety of bound conformations. All of the proteins bound in the minor groove, bridging DNA molecules, presumably because these DNA regions are easily deformed. The loss of the primary site of DNA intercalation decreased overall DNA bending and shape complementarity. However, DNA bending at the secondary site of intercalation was retained and most protein-DNA contacts were preserved. The mode of binding resembles the HMGB1-boxA-cisplatin-DNA complex, which also lacks a primary intercalating residue. This study provides new insights into the binding mechanisms used by HMG boxes to recognize varied DNA structures and sequences as well as modulate DNA structure and DNA bending. PMID:20800069

Partial melting of the Allende (CV3) meteorite - Implications for origins of basaltic meteorites

NASA Technical Reports Server (NTRS)

Jurewicz, A. J. G.; Mittlefehldt, D. W.; Jones, J. H.

1991-01-01

Eucrites and angrites are distinct types of basaltic meteorites whose origins are poorly known. Experiments in which samples of the Allende (CV3) carbonaceous chondrite were partially melted indicate that partial melts can resemble either eucrites or angrites, depending only on the oxygen fugacity. Melts are eucritic if this variable is below that of the iron-wuestite buffer or angritic if above it. With changing pressure, the graphite-oxygen redox reaction can produce oxygen fugacities that are above or below those of the iron-wuestite buffer. Therefore, a single, homogeneous, carbonaceous planetoid greater than 110 kilometers in radius could produce melts of drastically different composition, depending on the depth of melting.

The Zhamanshin impact feature: A new class of complex crater?

NASA Technical Reports Server (NTRS)

Garvin, J. B.; Schnetzler, C. C.

1992-01-01

The record of 10-km-scale impact events of Quaternary age includes only two 'proven' impact structures: the Zhamanshin Impact Feature (ZIF) and the Bosumtwi Impact Crater (BIC). What makes these impact landforms interesting from the standpoint of recent Earth history is their almost total lack of morphologic similarity, in spite of similar absolute ages and dimensions. The BIC resembles pristine complex craters on the Moon to first order (i.e., 'U'-shaped topographic cross section with preserved rim), while the ZIF displays virtually none of the typical morphologic elements of a 13- to 14-km-diameter complex crater. Indeed, this apparent lack of a craterlike surficial topographic expression initially led Soviet geologists to conclude that the structure was only 5.5 to 6 km in diameter and at least 4.5 Ma in age. However, more recent drilling and geophysical observations at the ZIF have indicated that its pre-erosional diameter is at least 13.5 km, and that its age is most probably 0.87 Ma. Why the present topographic expression of a 13.5-km complex impact crater less than 1 m.y. old most closely resembles heavily degraded Mesozoic shield craters such as Lappajarvi is a question of considerable debate. Hypotheses for the lack of a clearly defined craterlike form at the ZIF include a highly oblique impact, a low-strength 'cometary' projectile, weak or water-saturated target materials, and anomalous erosion patterns. The problem remains unresolved because typical erosion rates within the arid sedimentary platform environment of central Kazakhstan in which the ZIF is located are typically low; it would require at least a factor of 10 greater erosion at the ZIF in order to degrade the near-rim ejecta typical of a 13.5-km complex crater by hundreds of meters in only 0.87 Ma, and to partially infill an inner cavity with 27 cu km (an equivalent uniform thickness of infill of 166 m). Our analysis of the degree of erosion and infill at the ZIF calls for rates in the 0.19 to 0.38 mm/yr range over the lifetime of the landform, which are a factor of 10 to 20 in excess of typical rates for the Kazakhstan semidesert.

The Sounds of Nanoscience: Acoustic STM Analogues

ERIC Educational Resources Information Center

Euler, Manfred

2013-01-01

A hands-on model of scanning tunnelling microscopy (STM) is presented. It uses near-field imaging with sound and computer assisted visualization to create acoustic mappings of resonator arrangements. Due to the (partial) analogy of matter and sound waves the images closely resemble STM scans of atoms. Moreover, the method can be extended to build…

Eating Patterns and Disorders in a College Population: Are College Women's Eating Problems a New Phenomenon?

ERIC Educational Resources Information Center

Hesse-Biber, Sharlene

1989-01-01

Analysis of questionnaires returned by 395 sophomores reveals that the eating difficulties of college women may be a problem that only partially resembles clinical eating disorders. They displayed the behavioral symptoms but not the psychological traits associated with anorexia and bulimia. Diagnosis and treatment issues, and sociocultural…

Genetics Home Reference: Meier-Gorlin syndrome

MedlinePlus

... ORC1, encoding the largest subunit of the origin recognition complex, cause microcephalic primordial dwarfism resembling Meier-Gorlin ... M, Skidmore DL, Samuels ME. Mutations in origin recognition complex gene ORC4 cause Meier-Gorlin syndrome. Nat ...

New cryptic species of the 'revolutum' group of Echinostoma (Digenea: Echinostomatidae) revealed by molecular and morphological data.

PubMed

Georgieva, Simona; Selbach, Christian; Faltýnková, Anna; Soldánová, Miroslava; Sures, Bernd; Skírnisson, Karl; Kostadinova, Aneta

2013-03-13

The digenean species of Echinostoma (Echinostomatidae) with 37 collar spines that comprise the so-called 'revolutum' species complex, qualify as cryptic due to the interspecific homogeneity of characters used to differentiate species. Only five species were considered valid in the most recent revision of the group but recent molecular studies have demonstrated a higher diversity within the group. In a study of the digeneans parasitising molluscs in central and northern Europe we found that Radix auricularia, R. peregra and Stagnicola palustris were infected with larval stages of two cryptic species of the 'revolutum' complex, one resembling E. revolutum and one undescribed species, Echinostoma sp. IG. This paper provides morphological and molecular evidence for their delimitation. Totals of 2,030 R. auricularia, 357 R. peregra and 577 S. palustris were collected in seven reservoirs of the River Ruhr catchment area in Germany and a total of 573 R. peregra was collected in five lakes in Iceland. Cercariae were examined and identified live and fixed in molecular grade ethanol for DNA isolation and in hot/cold 4% formaldehyde solution for obtaining measurements from fixed materials. Partial fragments of the mitochondrial gene nicotinamide adenine dinucleotide dehydrogenase subunit 1 (nad1) were amplified for 14 isolates. Detailed examination of cercarial morphology allowed us to differentiate the cercariae of the two Echinostoma spp. of the 'revolutum' species complex. A total of 14 partial nad1 sequences was generated and aligned with selected published sequences for eight species of the 'revolutum' species complex. Both NJ and BI analyses resulted in consensus trees with similar topologies in which the isolates from Europe formed strongly supported reciprocally monophyletic lineages. The analyses also provided evidence that North American isolates identified as E. revolutum represent another cryptic species of the 'revolutum' species complex. Our findings highlight the need for further analyses of patterns of interspecific variation based on molecular and morphological evidence to enhance the re-evaluation of the species and advance our understanding of the relationships within the 'revolutum' group of Echinostoma.

New cryptic species of the ‘revolutum’ group of Echinostoma (Digenea: Echinostomatidae) revealed by molecular and morphological data

PubMed Central

2013-01-01

Background The digenean species of Echinostoma (Echinostomatidae) with 37 collar spines that comprise the so-called ‘revolutum’ species complex, qualify as cryptic due to the interspecific homogeneity of characters used to differentiate species. Only five species were considered valid in the most recent revision of the group but recent molecular studies have demonstrated a higher diversity within the group. In a study of the digeneans parasitising molluscs in central and northern Europe we found that Radix auricularia, R. peregra and Stagnicola palustris were infected with larval stages of two cryptic species of the ‘revolutum’ complex, one resembling E. revolutum and one undescribed species, Echinostoma sp. IG. This paper provides morphological and molecular evidence for their delimitation. Methods Totals of 2,030 R. auricularia, 357 R. peregra and 577 S. palustris were collected in seven reservoirs of the River Ruhr catchment area in Germany and a total of 573 R. peregra was collected in five lakes in Iceland. Cercariae were examined and identified live and fixed in molecular grade ethanol for DNA isolation and in hot/cold 4% formaldehyde solution for obtaining measurements from fixed materials. Partial fragments of the mitochondrial gene nicotinamide adenine dinucleotide dehydrogenase subunit 1 (nad1) were amplified for 14 isolates. Results Detailed examination of cercarial morphology allowed us to differentiate the cercariae of the two Echinostoma spp. of the ‘revolutum’ species complex. A total of 14 partial nad1 sequences was generated and aligned with selected published sequences for eight species of the ‘revolutum’ species complex. Both NJ and BI analyses resulted in consensus trees with similar topologies in which the isolates from Europe formed strongly supported reciprocally monophyletic lineages. The analyses also provided evidence that North American isolates identified as E. revolutum represent another cryptic species of the ‘revolutum’ species complex. Conclusion Our findings highlight the need for further analyses of patterns of interspecific variation based on molecular and morphological evidence to enhance the re-evaluation of the species and advance our understanding of the relationships within the ‘revolutum’ group of Echinostoma. PMID:23497579

Effects of parenting quality on adolescents' personality resemblance to their parents. The TRAILS study.

PubMed

Langenhof, M Rohaa; Komdeur, Jan; Oldehinkel, Albertine J

2016-08-01

This study considers the development of resemblance between 741 adolescents and their biological parents, across six NEO-PI-R personality traits known to be important in psychological problems: anger-hostility, impulsiveness, vulnerability, assertiveness, excitement-seeking, and self-discipline. We modelled the association between perceived parental warmth and rejection at age eleven and personality resemblance to parents at about age sixteen. Parenting experienced during early adolescence was related to the degree and direction in which adolescents resembled their parents five years later in life. Rejection, especially from fathers, significantly predicted a smaller resemblance to both the parents. Girls were more strongly affected by parental quality than boys, and there was some indication that adolescents responded in opposite ways to parenting from mothers and fathers. This study is a first step in uncovering the complex interplay between parenting, gender, and the current generation's ability to develop personality traits independent from the previous generation. Copyright © 2016 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

Age-related differences in complex monitoring performance.

DOT National Transportation Integrated Search

1981-04-01

The present study examined the effect of age on the ability to sustain attention to a complex monitoring task. The visual display was designed to resemble an air traffic control radar display containing alphanumeric symbols. Subjects in age groups 18...

Who Resembles Whom? Mimetic and Coincidental Look-Alikes among Tropical Reef Fishes

PubMed Central

Robertson, D. Ross

2013-01-01

Studies of mimicry among tropical reef-fishes usually give little or no consideration to alternative explanations for behavioral associations between unrelated, look-alike species that benefit the supposed mimic. I propose and assess such an alternative explanation. With mimicry the mimic resembles its model, evolved to do so in response to selection by the mimicry target, and gains evolved benefits from that resemblance. In the alternative, the social-trap hypothesis, a coincidental resemblance of the model to the “mimic” inadvertently attracts the latter to it, and reinforcement of this social trapping by learned benefits leads to the “mimic” regularly associating with the model. I examine three well known cases of supposed aggressive mimicry among reef-fishes in relation to nine predictions from these hypotheses, and assess which hypothesis offers a better explanation for each. One case, involving precise and complex morphological and behavioral resemblance, is strongly consistent with mimicry, one is inconclusive, and one is more consistent with a social-trap based on coincidental, imprecise resemblance. Few cases of supposed interspecific mimicry among tropical reef fishes have been examined in depth, and many such associations may involve social traps arising from generalized, coincidental resemblance. Mimicry may be much less common among these fishes than is generally thought. PMID:23372795

Lassomycin, a ribosomally synthesized cyclic peptide, kills mycobacterium tuberculosis by targeting the ATP-dependent protease ClpC1P1P2.

PubMed

Gavrish, Ekaterina; Sit, Clarissa S; Cao, Shugeng; Kandror, Olga; Spoering, Amy; Peoples, Aaron; Ling, Losee; Fetterman, Ashley; Hughes, Dallas; Bissell, Anthony; Torrey, Heather; Akopian, Tatos; Mueller, Andreas; Epstein, Slava; Goldberg, Alfred; Clardy, Jon; Lewis, Kim

2014-04-24

Languishing antibiotic discovery and flourishing antibiotic resistance have prompted the development of alternative untapped sources for antibiotic discovery, including previously uncultured bacteria. Here, we screen extracts from uncultured species against Mycobacterium tuberculosis and identify lassomycin, an antibiotic that exhibits potent bactericidal activity against both growing and dormant mycobacteria, including drug-resistant forms of M. tuberculosis, but little activity against other bacteria or mammalian cells. Lassomycin is a highly basic, ribosomally encoded cyclic peptide with an unusual structural fold that only partially resembles that of other lasso peptides. We show that lassomycin binds to a highly acidic region of the ClpC1 ATPase complex and markedly stimulates its ATPase activity without stimulating ClpP1P2-catalyzed protein breakdown, which is essential for viability of mycobacteria. This mechanism, uncoupling ATPase from proteolytic activity, accounts for the bactericidal activity of lassomycin. Copyright © 2014 Elsevier Ltd. All rights reserved.

An exploratory investigation of various assessment instruments as correlates of complex visual monitoring performance.

DOT National Transportation Integrated Search

1980-10-01

The present study examined a variety of possible predictors of complex monitoring performance. The criterion task was designed to resemble that of a highly automated air traffic control radar system containing computer-generated alphanumeric displays...

The Recognition without Cued Recall Phenomenon: Support for a Feature-Matching Theory over a Partial Recollection Account

ERIC Educational Resources Information Center

Ryals, Anthony J.; Cleary, Anne M.

2012-01-01

Among cues that fail to elicit successful recall, participants can still discriminate between cues that do and do not resemble studied items. This ability is referred to as recognition without cued recall (RWCR). We hypothesized that whereas recognition with cued recall is at least partly based on recalled studied information, RWCR results from a…

Biological adaptations for functional features of language in the face of cultural evolution.

PubMed

Christiansen, Morten H; Reali, Florencia; Chater, Nick

2011-04-01

Although there may be no true language universals, it is nonetheless possible to discern several family resemblance patterns across the languages of the world. Recent work on the cultural evolution of language indicates the source of these patterns is unlikely to be an innate universal grammar evolved through biological adaptations for arbitrary linguistic features. Instead, it has been suggested that the patterns of resemblance emerge because language has been shaped by the brain, with individual languages representing different but partially overlapping solutions to the same set of nonlinguistic constraints. Here, we use computational simulations to investigate whether biological adaptation for functional features of language, deriving from cognitive and communicative constraints, may nonetheless be possible alongside rapid cultural evolution. Specifically, we focus on the Baldwin effect as an evolutionary mechanism by which previously learned linguistic features might become innate through natural selection across many generations of language users. The results indicate that cultural evolution of language does not necessarily prevent functional features of language from becoming genetically fixed, thus potentially providing a particularly informative source of constraints on cross-linguistic resemblance patterns.

Partial co-option of the appendage patterning pathway in the development of abdominal appendages in the sepsid fly Themira biloba

PubMed Central

Nijhout, H. Frederik

2014-01-01

The abdominal appendages on male Themira biloba (Diptera: Sepsidae) are complex novel structures used during mating. These abdominal appendages superficially resemble the serially homologous insect appendages in that they have a joint and a short segment that can be rotated. Non-genital appendages do not occur in adult pterygote insects, so these abdominal appendages are novel structures with no obvious ancestry. We investigated whether the genes that pattern the serially homologous insect appendages have been co-opted to pattern these novel abdominal appendages. Immunohistochemistry was used to determine the expression patterns of the genes extradenticle (exd), Distal-less (Dll), engrailed (en), Notch, and the Bithorax Complex in the appendages of T. biloba during pupation. The expression patterns of Exd, En, and Notch were consistent with the hypothesis that a portion of the patterning pathway that establishes the coxopodite has been co-opted to pattern the developing abdominal appendages. However, Dll was only expressed in the bristles of the developing appendages and not the proximal–distal axis of the appendage itself. The lack of Dll expression indicates the absence of a distal domain of the appendage suggesting that sepsid abdominal appendages only use genes that normally pattern the base of segmental appendages. PMID:20182886

Structure and thermotropic phase behavior of sodium and potassium carboxylate ionomers

NASA Astrophysics Data System (ADS)

Mantsch, H. H.; Weng, S. F.; Yang, P. W.; Eysel, H. H.

1994-07-01

A molecular complex is formed between long-chain carboxylic acids and their alkali salts in a 1 : 1 mixture. These so-called "acid soaps" or carboxylate ionomers have multilamellar bilayer-type structures in solid state, which are retained in the presence of excess water, resembling the dispersions (gels) formed by typical two-chain amphiphiles, e.g. lipids. The special arrangement of hydrogen-bonded pairs of carboxylic acid and carboxylate groups into a unique "head-group" is supported by frequency shifts and partial or total disappearance of the characteristic vibrations of carboxylic acid dimers and of carboxylate groups. The existence of well-ordered hydrocarbon chains is demonstrated by the existence and polarization properties of the methylene rocking and wagging propagation modes. The gel to liquid-crystal phase transition of the hydrated acid soaps shows practically no cation dependence, unlike the corresponding phase transition in neutral soaps which varies considerably with the nature of the counterion. There is spectroscopic evidence to suggest a cooperative process that involves "melting" of the alkyl chains and disintegration of the hydrogen-bonded carboxylate—carboxylic acid complex, followed by a cation-dependent equilibrium that favors the formation of acid dimers at elevated temperatures and some form of hydrogen-bonded ion pair aggregates at intermediate temperatures.

Cemento-ossifying fibroma of mandible mimicking complex composite odontome.

PubMed

Dewan, Hitesh Sudarshan; Dewan, Sudarshan Kumar; Bahl, Sumit; Tushar Parekh, Parth

2016-10-19

Cemento-ossifying fibroma (COF) is a fibro-osseous lesion or non-odontogenic tumour that affects craniofacial bones. These lesions are included in the spectrum of fibro-osseous lesions arising from periodontal ligament cells, which can deposit combination of cementum and bone surrounded by fibrous tissue. It clinically, macroscopically and radiologically resembles complex composite odontome and can be differentiated only on the basis of histopathology. They usually occur solitarily as a painless and expansile spherical or ovoid jawbone mass that may displace the roots of adjacent teeth. They predominantly occur in females in third and fourth decades of life. We present a case report of a 20-year-old man, with a mildly painful swelling in the mandible which was successfully treated with enucleation and diagnosed as COF. Its resemblance to complex composite odontome and unique surgical approach are highlighted in this paper. 2016 BMJ Publishing Group Ltd.

Slow Feature Analysis on Retinal Waves Leads to V1 Complex Cells

PubMed Central

Dähne, Sven; Wilbert, Niko; Wiskott, Laurenz

2014-01-01

The developing visual system of many mammalian species is partially structured and organized even before the onset of vision. Spontaneous neural activity, which spreads in waves across the retina, has been suggested to play a major role in these prenatal structuring processes. Recently, it has been shown that when employing an efficient coding strategy, such as sparse coding, these retinal activity patterns lead to basis functions that resemble optimal stimuli of simple cells in primary visual cortex (V1). Here we present the results of applying a coding strategy that optimizes for temporal slowness, namely Slow Feature Analysis (SFA), to a biologically plausible model of retinal waves. Previously, SFA has been successfully applied to model parts of the visual system, most notably in reproducing a rich set of complex-cell features by training SFA with quasi-natural image sequences. In the present work, we obtain SFA units that share a number of properties with cortical complex-cells by training on simulated retinal waves. The emergence of two distinct properties of the SFA units (phase invariance and orientation tuning) is thoroughly investigated via control experiments and mathematical analysis of the input-output functions found by SFA. The results support the idea that retinal waves share relevant temporal and spatial properties with natural visual input. Hence, retinal waves seem suitable training stimuli to learn invariances and thereby shape the developing early visual system such that it is best prepared for coding input from the natural world. PMID:24810948

Molecular characterization of putative Hepatozoon sp. from the sedge warbler (Acrocephalus schoenobaenus).

PubMed

Biedrzycka, Aleksandra; Kloch, Agnieszka; Migalska, Magdalena; Bielański, Wojciech

2013-05-01

We characterized partial sequences of 18S rDNA from sedge warblers infected with a parasite described previously as Hepatozoon kabeeni. Prevalence was 47% in sampled birds.We detected 3 parasite haplotypes in 62 sequenced samples from infected animals. In phylogenetic analyses, 2 of the putative Hepatozoon haplotypes closely resembled Lankesterella minima and L. valsainensis. The third haplotype grouped in a wider clade composed of Caryospora and Eimeria. None of the haplotypes showed resemblance to sequences of Hepatozoon from reptiles and mammals. Molecular detection results were consistent with those from microscopy of stained blood smears, confirming that the primers indeed amplified the parasite sequences. Here we provide evidence that the avian Hepatozoon-like parasites are most likely Lankesterella, supporting the suggestion that the systematic position of avian Hepatozoon-like species needs to be revised.

Six species of Acanthobothrium (Eucestoda: Tetraphyllidea) in stingrays (Chondrichthyes: Rajiformes: Myliobatoidei) from Ecuador.

PubMed

Marguee, F; Brooks, D R; Barriga, R

1997-06-01

Six species of Acanthobothrium, 4 described as new, are reported in stingrays from southern Ecuador. Acanthobothrium atahualpai n. sp. in Gymnura afuerae most closely resembles Acanthobothrium fogeli and Acanthobothrium parviuncinatum by having bothridial hooks with recurved prongs and short handles. It differs from A. fogeli by having bothridial hooks 163-195 microns vs. 78-114 microns long and averaging 25 vs. 32 testes per pruglottis: it differs from A. parviuncinatum by having bothridial hooks 163-195 microns vs. 87 microns long and averaging 25 vs. 13 testes per proglottis. Acanthobothrium minusculus n. sp. in Urolophus tumbesensis most resembles Acanthobothrium campbelli and Acanthobothrium vargasi by being no more than 3 mm long and having 6-30 testes per proglottis. It can be distinguished from them by having bothridial hooks averaging 86 microns vs. 108-111 microns and 130-133 microns long, and 6-10 vs. 15-23 and 22-29 testes per proglottis, respectively. Acanthobothrium monksi n. sp. in Aetobatus narinari resembles Acanthobothrium tasajerasi from Himantura schmardae by having a prominent genital atrium and a large globose cirrus sac; it differs by averaging 21 vs. 35 testes per proglottis and having bothridial hooks averaging 150 microns vs. 165 microns long. Acanthobothrium obuncus n. sp. in Dasyatis longus resembles a group of species characterized by wider than long to square immature and mature proglottides, bothridia at least partially fused to the scolex at their posterior ends, and asymmetrical ovarian arms with aporal arms extending anteriorly to the vaginal level. It resembles Acanthobothrium americanum by averaging 73 vs. 72 testes per proglottis, but differs by having bothridial hooks averaging 120-131 microns vs. 151 microns long; it resembles Acanthobothrium chilensis by having bothridial hooks averaging 120-131 microns vs. 130 microns long, but differs by averaging 73 vs. 90 testes per proglottis. Acanthobothrium campbelli in Urotrygon chilensis and Acanthobothrium costarricense in Dasyatis longus, previously known in those hosts from the Pacific coast of Costa Rica, are reported from Ecuador for the first time.

Stress Corrosion Cracking Control Plans. 3. Copper Alloys

DTIC Science & Technology

1975-06-01

convenience intended to include amines and all other species which can react with copper to produce the cupric -ammonium complex ion or perhap...capability of forming complexes even resembling the cupric -ammonium complex should be considered as potentially causative of SCC as ammonia unless...nitrate, acetate, tartrate , or citrate which also contain copper ions. There is some evidence that oxides of nitrogen (generating ammoniacal species

Multilocus Genotyping and Molecular Phylogenetics Resolve a Novel Head Blight Pathogen within the Fusarium graminearum Species Complex from Ethiopia

USDA-ARS?s Scientific Manuscript database

A survey of Fusarium head blight (FHB)-contaminated wheat in Ethiopia recovered 31 isolates resembling members of the Fusarium graminearum species complex. Results of a multilocus genotyping (MLGT) assay for FHB species and trichothecene chemotype determination suggested that 22 of these isolates m...

Identification of phosphates involved in catalysis by the ribozyme RNase P RNA.

PubMed Central

Harris, M E; Pace, N R

1995-01-01

The RNA subunit of ribonuclease P (RNase P RNA) is a catalytic RNA that cleaves precursor tRNAs to generate mature tRNA 5' ends. Little is known concerning the identity and arrangement of functional groups that constitute the active site of this ribozyme. We have used an RNase P RNA-substrate conjugate that undergoes rapid, accurate, and efficient self-cleavage in vitro to probe, by phosphorothioate modification-interference, functional groups required for catalysis. We identify four phosphate oxygens where substitution by sulfur significantly reduces the catalytic rate (50-200-fold). Interference at one site was partially rescued in the presence of manganese, suggesting a direct involvement in binding divalent metal ion cofactors required for catalysis. All sites are located in conserved sequence and secondary structure, and positioned adjacent to the substrate phosphate in a tertiary structure model of the ribozyme-substrate complex. The spatial arrangement of phosphorothioate-sensitive sites in RNase P RNA was found to resemble the distribution of analogous positions in the secondary and potential tertiary structures of other large catalytic RNAs. PMID:7585250

The transitional behaviour of avalanches in cohesive granular materials

NASA Astrophysics Data System (ADS)

Quintanilla, M. A. S.; Valverde, J. M.; Castellanos, A.

2006-07-01

We present a statistical analysis of avalanches of granular materials that partially fill a slowly rotated horizontal drum. For large sized noncohesive grains the classical coherent oscillation is reproduced, consisting of a quasi-periodic succession of regularly sized avalanches. As the powder cohesiveness is increased by decreasing the particle size, we observe a gradual crossover to a complex dynamics that resembles the transitional behaviour observed in fusion plasmas. For particle size below ~50 µm, avalanches lose a characteristic size, retain a short term memory and turn gradually decorrelated in the long term as described by a Markov process. In contrast, large grains made cohesive by coating them with adhesive microparticles display a distinct phenomenology, characterized by a quasi-regular succession of well defined small precursors and large relaxation events. The transition from a one-peaked distribution (noncohesive large beads) to a flattened distribution (fine cohesive beads) passing through the two-peaked distribution of cohesive large beads had already been predicted using a coupled-map lattice model, as the relaxation mechanism of grain reorganization becomes dominant to the detriment of inertia.

Generalization of the Activated Complex Theory of Reaction Rates. I. Quantum Mechanical Treatment

DOE R&D Accomplishments Database

Marcus, R. A.

1964-01-01

In its usual form activated complex theory assumes a quasi-equilibrium between reactants and activated complex, a separable reaction coordinate, a Cartesian reaction coordinate, and an absence of interaction of rotation with internal motion in the complex. In the present paper a rate expression is derived without introducing the Cartesian assumption. The expression bears a formal resemblance to the usual one and reduces to it when the added assumptions of the latter are introduced.

Characterization of Early Partial Seizure Onset: Frequency, Complexity and Entropy

PubMed Central

Jouny, Christophe C.; Bergey, Gregory K.

2011-01-01

Objective A clear classification of partial seizures onset features is not yet established. Complexity and entropy have been very widely used to describe dynamical systems, but a systematic evaluation of these measures to characterize partial seizures has never been performed. Methods Eighteen different measures including power in frequency bands up to 300Hz, Gabor atom density (GAD), Higuchi fractal dimension (HFD), Lempel-Ziv complexity, Shannon entropy, sample entropy, and permutation entropy, were selected to test sensitivity to partial seizure onset. Intracranial recordings from forty-five patients with mesial temporal, neocortical temporal and neocortical extratemporal seizure foci were included (331 partial seizures). Results GAD, Lempel-Ziv complexity, HFD, high frequency activity, and sample entropy were the most reliable measures to assess early seizure onset. Conclusions Increases in complexity and occurrence of high-frequency components appear to be commonly associated with early stages of partial seizure evolution from all regions. The type of measure (frequency-based, complexity or entropy) does not predict the efficiency of the method to detect seizure onset. Significance Differences between measures such as GAD and HFD highlight the multimodal nature of partial seizure onsets. Improved methods for early seizure detection may be achieved from a better understanding of these underlying dynamics. PMID:21872526

CorMatrix valved conduit in a porcine model: long-term remodelling and biomechanical characterization.

PubMed

Mosala Nezhad, Zahra; Poncelet, Alain; de Kerchove, Laurent; Fervaille, Caroline; Banse, Xavier; Bollen, Xavier; Dehoux, Jean-Paul; El Khoury, Gebrine; Gianello, Pierre

2017-01-01

Porcine small intestinal submucosa extracellular matrix (CorMatrix; CorMatrix Cardiovascular, Rosewell, GA) is a relatively novel tissue substitute used in cardiovascular applications. We investigated the biological reaction and remodelling of CorMatrix as a tri-leaflet valved conduit in a pig model. We hypothesized that CorMatrix maintains a durable architecture as a valved conduit and remodels to resemble surrounding tissues. We fashioned the valved conduit using a 7 × 10 cm 4-ply CorMatrix sheet and placed it in the thoracic aorta of seven landrace pigs for 3, 4, 5 and 6 months. Biodegradation, replacement by native tissue, strength and durability were examined by histology, immunohistochemistry and mechanical testing. Four pigs, one per time frame, completed the study. The conduit lost its original architecture as a tri-leaflet valve due to cusp immobility, subsequent attachment to the wall segment and consequent maintenance of a thick arterial wall-like structure. Scaffold resorption was incomplete, with disorganized inconsistent spatial and temporal degradation even at 6 months. Fibrosis, scarring and calcification started at 4 months and chronic inflammation persisted. The partially remodelled scaffold did not resemble the aortic wall, suggesting impaired remodelling. Mechanical testing showed progressive weakening of the tissues over time, which were liable to breakage. CorMatrix is biodegradable; however, it failed to remodel in a structured and anatomical fashion in an arterial environment. Progressive mechanical and remodelling failure in this scenario might be explained by the complexity of the conduit design and the host's chronic inflammatory response, leading to early fibrosis and calcification. © The Author 2016. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Complex matrix multiplication operations with data pre-conditioning in a high performance computing architecture

DOEpatents

Eichenberger, Alexandre E; Gschwind, Michael K; Gunnels, John A

2014-02-11

Mechanisms for performing a complex matrix multiplication operation are provided. A vector load operation is performed to load a first vector operand of the complex matrix multiplication operation to a first target vector register. The first vector operand comprises a real and imaginary part of a first complex vector value. A complex load and splat operation is performed to load a second complex vector value of a second vector operand and replicate the second complex vector value within a second target vector register. The second complex vector value has a real and imaginary part. A cross multiply add operation is performed on elements of the first target vector register and elements of the second target vector register to generate a partial product of the complex matrix multiplication operation. The partial product is accumulated with other partial products and a resulting accumulated partial product is stored in a result vector register.

Primary Mucinous Cystadenocarcinoma of the Breast: Cytologic Finding and Expression of MUC5 Are Different from Mucinous Carcinoma.

PubMed

Kim, Sung Eun; Park, Ji Hye; Hong, Soonwon; Koo, Ja Seung; Jeong, Joon; Jung, Woo-Hee

2012-12-01

Mucinous cystadenocarcinoma (MCA) in the breast is a rare neoplasm. There have been 13 cases of primary breast MCA reported. The MCA presents as a large, partially cystic mass in postmenopausal woman with a good prognosis. The microscopic findings resemble those of ovarian, pancreatic, or appendiceal MCA. The aspiration findings showed mucin-containing cell clusters in the background of mucin and necrotic material. The cell clusters had intracytoplasmic mucin displacing atypical nuclei to the periphery. Histologically, the tumor revealed an abundant mucin pool with small floating clusters of mucin-containing tumor cells. There were also small cysts lined by a single layer of tall columnar mucinous cells, resembling those of the uterine endocervix. The cancer cells were positive for mucin (MUC) 5 and negative for MUC2 and MUC6. This mucin profile is different from ordinary mucinous carcinoma and may be a unique characteristic of breast MCA.

Changes in the immune system during and after spaceflight

NASA Technical Reports Server (NTRS)

Taylor, G. R.; Konstantinova, I.; Sonnenfeld, G.; Jennings, R.

1997-01-01

The results of immunological analyses before, during and after spaceflight, have established the fact that spaceflight can result in a blunting of the immune mechanisms of human crew members and animal test species. There is some evidence that the immune function changes in short-term flights resemble those occurring after acute stress, while the changes during long-term flights resemble those caused by chronic stress. In addition, this blunting of the immune function occurs concomitant with a relative increase in potentially infectious microorganisms in the space cabin environment. This combination of events results in an increased probability of inflight infectious events. The realization of this probability has been shown to be partially negated by the judicious use of a preflight health stabilization program and other operational countermeasures. The continuation of these countermeasures, as well as microbial and immunological monitoring, are recommended for continued spaceflight safety.

Petrography, geochemistry, and U-Pb geochronology of pegmatites and aplites associated with the Alvand intrusive complex in the Hamedan region, Sanandaj-Sirjan zone, Zagros orogen (Iran)

NASA Astrophysics Data System (ADS)

Sepahi, Ali Asghar; Salami, Sedigheh; Lentz, David; McFarlane, Christopher; Maanijou, Mohammad

2018-04-01

The Alvand intrusive complex in the Hamedan area in Iran is in the Sanandaj-Sirjan zone of the Zagros orogen. It consists of a wide range of plutonic rocks, mainly gabbro, diorite, granodiorite, granite, and leucogranites that were intruded by aplitic and pegmatitic dykes. At least three successive magmatic episodes generated an older gabbro-diorite-tonalite assemblage, followed by a voluminous granodiorite-granite association, which was then followed by minor leucocratic granitoids. Aplitic and pegmatitic dykes and bodies have truncated both plutonic rocks of the Alvand intrusive complex and its metamorphic aureole. Chemically they belong to peraluminous LCT (Li-, Cs-, and Ta-bearing) family of pegmatites. Mineralogically, they resemble Muscovite (MS) and Muscovite Rare Element (MSREL) classes of pegmatites. High amounts of some elements, such as Sn (up to 10,000 ppm), Rb (up to 936 ppm), Ba (up to 706 ppm), and LREE (up to 404 ppm) indicate the highly fractionated nature of some of these aplites and pegmatites. U-Pb dating of monazite, zircon, and allanite by LA-ICPMS indicate the following ages: monazite-bearing aplites of Heydareh-e-Poshteshahr and Barfejin areas, southwest of Hamedan, give an age range of 162-172 Ma; zircon in Heydareh-e-Poshteshar gives an average age of 165 Ma and for allanite-bearing pegmatites of Artiman area, north of Tuyserkan, an age of 154.1 ± 3.7 Ma was determined. These overlap with previously reported ages (ca. 167-153 Ma) for the plutonic rocks of the Alvand complex. Therefore, these data reveal that the Jurassic was a period of magmatism in the Hamedan region and adjacent areas in the Sanandaj-Sirjan zone, which was situated at the southern edge of the central Iranian micro-plate (southern Eurasian plate) at this time. Our results also suggest that advective heating in a continental arc setting has caused melting of fertile supracrustal lithologies, such as meta-pelites. These partial melts were then emplaced at much higher crustal levels, but within a thermally anomalous environment, which, therefore, leads to formation of evolved felsic rocks, such as the studied LCT aplite-pegmatite suite and their parental granitic rocks. This is a new result that indicates the role of syn-subduction crustal partial melting in the region as part of Zagros orogeny.

Dynamic Interaction of cBid with Detergents, Liposomes and Mitochondria

PubMed Central

Bleicken, Stephanie; García-Sáez, Ana J.; Conte, Elena; Bordignon, Enrica

2012-01-01

The BH3-only protein Bid plays a key role in the induction of mitochondrial apoptosis, but its mechanism of action is still not completely understood. Here we studied the two main activation events of Bid: Caspase-8 cleavage and interaction with the membrane bilayer. We found a striking reversible behaviour of the dissociation-association events between the Bid fragments p15 and p7. Caspase-8 cleavage does not induce per se separation of the two Bid fragments, which remain in a stable complex resembling the full length Bid. Detergents trigger a complete dissociation, which can be fully reversed by detergent removal in a range of protein concentrations from 100 µM down to 500 nM. Incubation of cBid with cardiolipin-containing liposomes leads to partial dissociation of the complex. Only p15 (tBid) fragments are found at the membrane, while p7 shows no tendency to interact with the bilayer, but complete removal of p7 strongly increases the propensity of tBid to become membrane-associated. Despite the striking structural similarities of inactive Bid and Bax, Bid does not form oligomers and reacts differently in the presence of detergents and membranes, highlighting clear differences in the modes of action of the two proteins. The partial dissociation of cBid triggered by the membrane is suggested to depend on the strong and specific interaction between p15 and p7. The reversible disassembly and re-assembly of the cBid molecules at the membrane was as well proven by EPR using spin labeled cBid in the presence of isolated mitochondria. The observed dynamic dissociation of the two Bid fragments could allow the assistance to the pore-forming Bax to occur repeatedly and may explain the proposed “hit-and-run" mode of action of Bid at the bilayer. PMID:22540011

Encapsulation of atmospheric CO2 by a self-assembled decanuclear cadmium complex via unfamiliar perchlorato and carbonato bridges.

PubMed

García-Deibe, Ana M; Portela-García, Cristina; Fondo, Matilde; Mota, Antonio J; Sanmartín-Matalobos, Jesús

2012-10-11

A decanuclear Cd complex has been found as a carbonate-containing capsule. The structure strongly resembles a ten-blade waterwheel with a central carbonate ligand surrounded by two superimposed Cd(5)O(5) crowns with a pentagonal antiprism-like disposition. The capsule is doubly capped by two pentadentate perchlorate anions.

Complex partial status epilepticus: a recurrent problem.

PubMed Central

Cockerell, O C; Walker, M C; Sander, J W; Shorvon, S D

1994-01-01

Twenty patients with complex partial status epilepticus were identified retrospectively from a specialist neurology hospital. Seventeen patients experienced recurrent episodes of complex partial status epilepticus, often occurring at regular intervals, usually over many years, and while being treated with effective anti-epileptic drugs. No unifying cause for the recurrences, and no common epilepsy aetiologies, were identified. In spite of the frequency of recurrence and length of history, none of the patients showed any marked evidence of cognitive or neurological deterioration. Complex partial status epilepticus is more common than is generally recognised, should be differentiated from other forms of non-convulsive status, and is often difficult to treat. PMID:8021671

Carbohydrate recognition: A minimalistic approach to binding

NASA Astrophysics Data System (ADS)

Kubik, Stefan

2012-09-01

Synthetic receptors with properties resembling those of carbohydrate-binding proteins are known, but they are structurally rather complex. Elaborate structures are, however, not always required to bind carbohydrates in water -- much simpler compounds can be just as effective.

Effect of Gravity Waves from Small Islands in the Southern Ocean on the Southern Hemisphere Atmospheric Circulation

NASA Technical Reports Server (NTRS)

Garfinkel, C. I.; Oman, L. D.

2018-01-01

The effect of small islands in the Southern Ocean on the atmospheric circulation in the Southern Hemisphere is considered with a series of simulations using the NASA Goddard Earth Observing System Chemistry-Climate Model in which the gravity wave stress generated by these islands is increased to resemble observed values. The enhanced gravity wave drag leads to a 2 K warming of the springtime polar stratosphere, partially ameliorating biases in this region. Resolved wave drag declines in the stratospheric region in which the added orographic gravity waves deposit their momentum, such that changes in gravity waves are partially compensated by changes in resolved waves, though resolved wave drag increases further poleward. The orographic drag from these islands has impacts for surface climate, as biases in tropospheric jet position are also partially ameliorated. These results suggest that these small islands are likely contributing to the missing drag near 60 degrees S in the upper stratosphere evident in many data assimilation products.

Craters Near Nilokeras Scopulus

NASA Image and Video Library

2015-03-04

This image from NASA Mars Reconnaissance Orbiter of craters near Nilokeras Scopulus shows two pits partially filled with lumpy material, probably trapped dust that blew in from the atmosphere. This image shows two pits partially filled with lumpy material, probably trapped dust that blew in from the atmosphere. The pits themselves resemble impact craters, but they are part of a chain of similar features aligned with nearby faults, so they could be collapse features instead. Note also the tracks left by rolling boulders at the bottom of the craters. Nilokeras Scopulus is the name for the cliff, about 756 kilometers long, in the northern hemisphere of Mars where these craters are located. It was named based on an albedo (brightness) feature mapped by astronomer E. M. Antoniadi in 1930. http://photojournal.jpl.nasa.gov/catalog/PIA19304

Myxoid stroma and delicate vasculature of a superficial angiomyxoma give rise to the red planet sign.

PubMed

Green, Margaret; Logemann, Nichola; Sulit, Daryl J

2014-09-16

Superficial angiomyxomas are uncommon benign mesenchymal tumors. They often recur locally if partially removed. This case report demonstrates not only the characteristic pathological findings of a superficial angiomyxoma in a 33- year-old man, but also shows a unique dermatoscopic image, which in our estimation resembles a celestial red planet such as the blood moon seen during a lunar eclipse. We propose to call this the "red planet" sign for a superficial angiomyxoma on dermoscopic examination.

Mutations in ORC1, encoding the largest subunit of the origin recognition complex, cause microcephalic primordial dwarfism resembling Meier-Gorlin syndrome.

PubMed

Bicknell, Louise S; Walker, Sarah; Klingseisen, Anna; Stiff, Tom; Leitch, Andrea; Kerzendorfer, Claudia; Martin, Carol-Anne; Yeyati, Patricia; Al Sanna, Nouriya; Bober, Michael; Johnson, Diana; Wise, Carol; Jackson, Andrew P; O'Driscoll, Mark; Jeggo, Penny A

2011-02-27

Studies into disorders of extreme growth failure (for example, Seckel syndrome and Majewski osteodysplastic primordial dwarfism type II) have implicated fundamental cellular processes of DNA damage response signaling and centrosome function in the regulation of human growth. Here we report that mutations in ORC1, encoding a subunit of the origin recognition complex, cause microcephalic primordial dwarfism resembling Meier-Gorlin syndrome. We establish that these mutations disrupt known ORC1 functions including pre-replicative complex formation and origin activation. ORC1 deficiency perturbs S-phase entry and S-phase progression. Additionally, we show that Orc1 depletion in zebrafish is sufficient to markedly reduce body size during rapid embryonic growth. Our data suggest a model in which ORC1 mutations impair replication licensing, slowing cell cycle progression and consequently impeding growth during development, particularly at times of rapid proliferation. These findings establish a novel mechanism for the pathogenesis of microcephalic dwarfism and show a surprising but important developmental impact of impaired origin licensing.

Galactic Behavior for the Outer B Ring

NASA Image and Video Library

2010-11-01

Keeping a close watch on the outer portion of Saturn B ring, NASA Cassini spacecraft records the complex inward and outward movement of the edge of the ring. This ring movement resembles the suspected behavior of spiral disk galaxies.

Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation

PubMed Central

Mihalik, Ágoston; Csermely, Peter

2011-01-01

Network analysis became a powerful tool giving new insights to the understanding of cellular behavior. Heat shock, the archetype of stress responses, is a well-characterized and simple model of cellular dynamics. S. cerevisiae is an appropriate model organism, since both its protein-protein interaction network (interactome) and stress response at the gene expression level have been well characterized. However, the analysis of the reorganization of the yeast interactome during stress has not been investigated yet. We calculated the changes of the interaction-weights of the yeast interactome from the changes of mRNA expression levels upon heat shock. The major finding of our study is that heat shock induced a significant decrease in both the overlaps and connections of yeast interactome modules. In agreement with this the weighted diameter of the yeast interactome had a 4.9-fold increase in heat shock. Several key proteins of the heat shock response became centers of heat shock-induced local communities, as well as bridges providing a residual connection of modules after heat shock. The observed changes resemble to a ‘stratus-cumulus’ type transition of the interactome structure, since the unstressed yeast interactome had a globally connected organization, similar to that of stratus clouds, whereas the heat shocked interactome had a multifocal organization, similar to that of cumulus clouds. Our results showed that heat shock induces a partial disintegration of the global organization of the yeast interactome. This change may be rather general occurring in many types of stresses. Moreover, other complex systems, such as single proteins, social networks and ecosystems may also decrease their inter-modular links, thus develop more compact modules, and display a partial disintegration of their global structure in the initial phase of crisis. Thus, our work may provide a model of a general, system-level adaptation mechanism to environmental changes. PMID:22022244

Silver Nanoparticle Transport and Interactions in Partially Saturated Sand and Soil

NASA Astrophysics Data System (ADS)

Yecheskel, Y.; Dror, I.; Berkowitz, B.

2016-12-01

The growing applications of engineered nanoparticles (ENPs), included in numerous products and industrial processes, are expected to spread in the near future on a global level. Along with the properties that make ENPs so appealing, the concern that they may act as a new class of persistent and toxic contaminants also arises. The post-use release of ENPs to the environment is inevitable and soil appears to be one of the largest sinks of these potential contaminants. To date, despite the significant attention that ENP behavior in the environment has received, only a few studies have considered the fate and transport of ENPs in partially saturated systems. In this study, we focus on the transport and fate of silver NPs (Ag-NPs) in partially saturated sand and soil columns. Experimental results reveal significant differences between sand and soil with respect to ENP transport, and emphasize the importance of employing natural porous media in experiments. Breakthrough curves (BTCs), retention profiles, ENP mass balance and modeling were applied to characterize Ag-NP transport and gain insights into the mechanisms of retardation. The effect of initial Ag-NP concentration, Ag-NP size, saturation level, flow rate, and solution chemistry were found to affect Ag-NP transport behavior. Unlike transport of Ag-NP in sand columns, where the BTC pattern resembles that of a conservative tracer, Ag-NP transport in soil columns shows moderate mobility and complex BTC patterns. In general, the BTC shape consists of two steps, which imply two retention mechanisms. The influence of each mechanism is affected by the physicochemical conditions. In all cases, a two kinetic site model was shown to fit the experimental BTC results, with time-dependent and depth-dependent attachment-detachment mechanisms. Overall, Ag-NP mobility decreases with the presence of Ca2+ and Cl- ions, and increases with the presence of humic acid, increased saturation levels, and higher input concentrations of Ag-NPs.

Selective self-assembly of adenine-silver nanoparticles forms rings resembling the size of cells

NASA Astrophysics Data System (ADS)

Choi, Sungmoon; Park, Soonyoung; Yang, Seon-Ah; Jeong, Yujin; Yu, Junhua

2015-12-01

Self-assembly has played critical roles in the construction of functional nanomaterials. However, the structure of the macroscale multicomponent materials built by the self-assembly of nanoscale building blocks is hard to predict due to multiple intermolecular interactions of great complexity. Evaporation of solvents is usually an important approach to induce kinetically stable assemblies of building blocks with a large-scale specific arrangement. During such a deweting process, we tried to monitor the possible interactions between silver nanoparticles and nucleobases at a larger scale by epifluorescence microscopy, thanks to the doping of silver nanoparticles with luminescent silver nanodots. ssDNA oligomer-stabilized silver nanoparticles and adenine self-assemble to form ring-like compartments similar to the size of modern cells. However, the silver ions only dismantle the self-assembly of adenine. The rings are thermodynamically stable as the drying process only enrich the nanoparticles-nucleobase mixture to a concentration that activates the self-assembly. The permeable membrane-like edge of the ring is composed of adenine filaments glued together by silver nanoparticles. Interestingly, chemicals are partially confined and accumulated inside the ring, suggesting that this might be used as a microreactor to speed up chemical reactions during a dewetting process.

Primary Mucinous Cystadenocarcinoma of the Breast: Cytologic Finding and Expression of MUC5 Are Different from Mucinous Carcinoma

PubMed Central

Kim, Sung Eun; Park, Ji Hye; Hong, SoonWon; Koo, Ja Seung; Jeong, Joon

2012-01-01

Mucinous cystadenocarcinoma (MCA) in the breast is a rare neoplasm. There have been 13 cases of primary breast MCA reported. The MCA presents as a large, partially cystic mass in postmenopausal woman with a good prognosis. The microscopic findings resemble those of ovarian, pancreatic, or appendiceal MCA. The aspiration findings showed mucin-containing cell clusters in the background of mucin and necrotic material. The cell clusters had intracytoplasmic mucin displacing atypical nuclei to the periphery. Histologically, the tumor revealed an abundant mucin pool with small floating clusters of mucin-containing tumor cells. There were also small cysts lined by a single layer of tall columnar mucinous cells, resembling those of the uterine endocervix. The cancer cells were positive for mucin (MUC) 5 and negative for MUC2 and MUC6. This mucin profile is different from ordinary mucinous carcinoma and may be a unique characteristic of breast MCA. PMID:23323116

Template optimization and transfer in perceptual learning.

PubMed

Kurki, Ilmari; Hyvärinen, Aapo; Saarinen, Jussi

2016-08-01

We studied how learning changes the processing of a low-level Gabor stimulus, using a classification-image method (psychophysical reverse correlation) and a task where observers discriminated between slight differences in the phase (relative alignment) of a target Gabor in visual noise. The method estimates the internal "template" that describes how the visual system weights the input information for decisions. One popular idea has been that learning makes the template more like an ideal Bayesian weighting; however, the evidence has been indirect. We used a new regression technique to directly estimate the template weight change and to test whether the direction of reweighting is significantly different from an optimal learning strategy. The subjects trained the task for six daily sessions, and we tested the transfer of training to a target in an orthogonal orientation. Strong learning and partial transfer were observed. We tested whether task precision (difficulty) had an effect on template change and transfer: Observers trained in either a high-precision (small, 60° phase difference) or a low-precision task (180°). Task precision did not have an effect on the amount of template change or transfer, suggesting that task precision per se does not determine whether learning generalizes. Classification images show that training made observers use more task-relevant features and unlearn some irrelevant features. The transfer templates resembled partially optimized versions of templates in training sessions. The template change direction resembles ideal learning significantly but not completely. The amount of template change was highly correlated with the amount of learning.

Unliganded Thyroid Hormone Receptor Regulates Metamorphic Timing via the Recruitment of Histone Deacetylase Complexes

PubMed Central

2014-01-01

Anuran metamorphosis involves a complex series of tissue transformations that change an aquatic tadpole to a terrestrial frog and resembles the postembryonic perinatal period in mammals. Thyroid hormone (TH) plays a causative role in amphibian metamorphosis and its effect is mediated by TH receptors (TRs). Molecular analyses during Xenopus development have shown that unliganded TR recruits histone deacetylase (HDAC)-containing N-CoR/SMRT complexes and causes histone deacetylation at target genes while liganded TR leads to increased histone acetylations and altered histone methylations at target genes. Transgenic studies involving mutant TR-cofactors have shown that corepressor recruitment by unliganded TR is required to ensure proper timing of the onset of metamorphosis while coactivator levels influence the rate of metamorphic progression. In addition, a number of factors that can influence cellular free TH levels appear to contribute the timing of metamorphic transformations of different organs by regulating the levels of unliganded vs. liganded TR in an organ-specific manner. Thus, the recruitment of HDAC-containing corepressor complexes by unliganded TR likely controls both the timing of the initiation of metamorphosis and the temporal regulation of organ-specific transformations. Similar mechanisms likely mediate TR function in mammals as the maturation of many organs during postembryonic development is dependent upon TH and resembles organ metamorphosis in amphibians. PMID:23962846

Neural coding in graphs of bidirectional associative memories.

PubMed

Bouchain, A David; Palm, Günther

2012-01-24

In the last years we have developed large neural network models for the realization of complex cognitive tasks in a neural network architecture that resembles the network of the cerebral cortex. We have used networks of several cortical modules that contain two populations of neurons (one excitatory, one inhibitory). The excitatory populations in these so-called "cortical networks" are organized as a graph of Bidirectional Associative Memories (BAMs), where edges of the graph correspond to BAMs connecting two neural modules and nodes of the graph correspond to excitatory populations with associative feedback connections (and inhibitory interneurons). The neural code in each of these modules consists essentially of the firing pattern of the excitatory population, where mainly it is the subset of active neurons that codes the contents to be represented. The overall activity can be used to distinguish different properties of the patterns that are represented which we need to distinguish and control when performing complex tasks like language understanding with these cortical networks. The most important pattern properties or situations are: exactly fitting or matching input, incomplete information or partially matching pattern, superposition of several patterns, conflicting information, and new information that is to be learned. We show simple simulations of these situations in one area or module and discuss how to distinguish these situations based on the overall internal activation of the module. This article is part of a Special Issue entitled "Neural Coding". Copyright © 2011 Elsevier B.V. All rights reserved.

Novel test of motor and other dysfunctions in mouse neurological disease models.

PubMed

Barth, Albert M I; Mody, Istvan

2014-01-15

Just like human neurological disorders, corresponding mouse models present multiple deficiencies. Estimating disease progression or potential treatment effectiveness in such models necessitates the use of time consuming and multiple tests usually requiring a large number of scarcely available genetically modified animals. Here we present a novel and simple single camera arrangement and analysis software for detailed motor function evaluation in mice walking on a wire mesh that provides complex 3D information (instantaneous position, speed, distance traveled, foot fault depth, duration, location, relationship to speed of movement, etc.). We investigated 3 groups of mice with various neurological deficits: (1) unilateral motor cortical stroke; (2) effects of moderate ethanol doses; and (3) aging (96-99 weeks old). We show that post stroke recovery can be divided into separate stages based on strikingly different characteristics of motor function deficits, some resembling the human motor neglect syndrome. Mice treated with moderate dose of alcohol and aged mice showed specific motor and exploratory deficits. Other tests rely either partially or entirely on manual video analysis introducing a significant subjective component into the analysis, and analyze a single aspect of motor function. Our novel experimental approach provides qualitatively new, complex information about motor impairments and locomotor/exploratory activity. It should be useful for the detailed characterization of a broad range of human neurological disease models in mice, and for the more accurate assessment of disease progression or treatment effectiveness. Copyright © 2013 Elsevier B.V. All rights reserved.

Mantle ingredients for making the fingerprint of Etna alkaline magmas: implications for shallow partial melting within the complex geodynamic framework of Eastern Sicily

NASA Astrophysics Data System (ADS)

Viccaro, Marco; Zuccarello, Francesco

2017-09-01

Mantle ingredients responsible for the signature of Etnean Na- and K-alkaline magmas and their relationships with short-term geochemical changes of the erupted volcanic rocks have been constrained through a partial melting model that considers major, trace elements and water contents in the produced liquids. Characteristics of the Etnean source for alkaline magmas have been supposed similar to those of the mantle accessible at a regional scale, namely below the Hyblean Plateau. The assumption that the Etnean mantle resembles the one beneath the Hyblean Plateau is justified by the large geochemical affinities of the Etnean hawaiites/K-trachybasalts and the Hyblean hawaiites/alkali basalts for what concerns both trace elements and isotope systematics. We have modeled partial melting of a composite source constituted by two rock types, inferred by lithological and geochemical features of the Hyblean xenoliths: 1) a spinel lherzolite bearing metasomatic, hydrous phases and 2) a garnet pyroxenite in form of veins intruded into the spinel lherzolite. The partial melting modeling has been applied to each rock type and the resulting primary liquids have been then mixed in various proportions. These compositions have been compared with some Etnean alkaline magmas of the post ∼60 ka activity, which were firstly re-equilibrated to mantle conditions through mass balance calculations. Our results put into evidence that concentrations of major and trace elements along with the water obtained from the modeling are remarkably comparable with those of Etnean melts re-equilibrated at primary conditions. Different proportions of the spinel lherzolite with variable modal contents of metasomatic phases and of the garnet pyroxenite can therefore account for the signature of a large spectrum of Etnean alkaline magmas and for their geochemical variability through time, emphasizing the crucial role played by compositional small-scale heterogeneity of the source. These heterogeneities are able to produce magmas with variable compositions and volatile contents, which can then undergo distinct histories of ascent and evolution, leading to the wide range of eruptive styles observed at Mt. Etna volcano. Being partial melting confined in the spinel facies of the mantle, our model implies that the source of Mt. Etna magmas might be rather shallow (<2 GPa; i.e., lesser than ca. 60 km), excluding the presence of deep, plume-like mantle structures responsible for magma generation. Partial melting should occur consequently as a response of mantle decompression within the framework of regional tectonics affecting the Eastern Sicily, which could be triggered by extensional tectonics and/or subduction-induced mantle upwelling.

Partial connectivity increases cultural accumulation within groups.

PubMed

Derex, Maxime; Boyd, Robert

2016-03-15

Complex technologies used in most human societies are beyond the inventive capacities of individuals. Instead, they result from a cumulative process in which innovations are gradually added to existing cultural traits across many generations. Recent work suggests that a population's ability to develop complex technologies is positively affected by its size and connectedness. Here, we present a simple computer-based experiment that compares the accumulation of innovations by fully and partially connected groups of the same size in a complex fitness landscape. We find that the propensity to learn from successful individuals drastically reduces cultural diversity within fully connected groups. In comparison, partially connected groups produce more diverse solutions, and this diversity allows them to develop complex solutions that are never produced in fully connected groups. These results suggest that explanations of ancestral patterns of cultural complexity may need to consider levels of population fragmentation and interaction patterns between partially isolated groups.

Partial connectivity increases cultural accumulation within groups

PubMed Central

Boyd, Robert

2016-01-01

Complex technologies used in most human societies are beyond the inventive capacities of individuals. Instead, they result from a cumulative process in which innovations are gradually added to existing cultural traits across many generations. Recent work suggests that a population’s ability to develop complex technologies is positively affected by its size and connectedness. Here, we present a simple computer-based experiment that compares the accumulation of innovations by fully and partially connected groups of the same size in a complex fitness landscape. We find that the propensity to learn from successful individuals drastically reduces cultural diversity within fully connected groups. In comparison, partially connected groups produce more diverse solutions, and this diversity allows them to develop complex solutions that are never produced in fully connected groups. These results suggest that explanations of ancestral patterns of cultural complexity may need to consider levels of population fragmentation and interaction patterns between partially isolated groups. PMID:26929364

The decay widths, the decay constants, and the branching fractions of a resonant state

NASA Astrophysics Data System (ADS)

de la Madrid, Rafael

2015-08-01

We introduce the differential and the total decay widths of a resonant (Gamow) state decaying into a continuum of stable states. When the resonance has several decay modes, we introduce the corresponding partial decay widths and branching fractions. In the approximation that the resonance is sharp, the expressions for the differential, partial and total decay widths of a resonant state bear a close resemblance with the Golden Rule. In such approximation, the branching fractions of a resonant state are the same as the standard branching fractions obtained by way of the Golden Rule. We also introduce dimensionless decay constants along with their associated differential decay constants, and we express experimentally measurable quantities such as the branching fractions and the energy distributions of decay events in terms of those dimensionless decay constants.

Apoptosis and tumor cell death in response to HAMLET (human alpha-lactalbumin made lethal to tumor cells).

PubMed

Hallgren, Oskar; Aits, Sonja; Brest, Patrick; Gustafsson, Lotta; Mossberg, Ann-Kristin; Wullt, Björn; Svanborg, Catharina

2008-01-01

HAMLET (human alpha-lactalbumin made lethal to tumor cells) is a molecular complex derived from human milk that kills tumor cells by a process resembling programmed cell death. The complex consists of partially unfolded alpha-lactalbumin and oleic acid, and both the protein and the fatty acid are required for cell death. HAMLET has broad antitumor activity in vitro, and its therapeutic effect has been confirmed in vivo in a human glioblastoma rat xenograft model, in patients with skin papillomas and in patients with bladder cancer. The mechanisms of tumor cell death remain unclear, however. Immediately after the encounter with tumor cells, HAMLET invades the cells and causes mitochondrial membrane depolarization, cytochrome c release, phosphatidyl serine exposure, and a low caspase response. A fraction of the cells undergoes morphological changes characteristic of apoptosis, but caspase inhibition does not rescue the cells and Bcl-2 overexpression or altered p53 status does not influence the sensitivity of tumor cells to HAMLET. HAMLET also creates a state of unfolded protein overload and activates 20S proteasomes, which contributes to cell death. In parallel, HAMLET translocates to tumor cell nuclei, where high-affinity interactions with histones cause chromatin disruption, loss of transcription, and nuclear condensation. The dying cells also show morphological changes compatible with macroautophagy, and recent studies indicate that macroautophagy is involved in the cell death response to HAMLET. The results suggest that HAMLET, like a hydra with many heads, may interact with several crucial cellular organelles, thereby activating several forms of cell death, in parallel. This complexity might underlie the rapid death response of tumor cells and the broad antitumor activity of HAMLET.

Comparison of the Manganese Cluster in Oxygen-Evolving Photosystem II with Distorted Cubane Manganese Compounds through X-ray Absorption Spectroscopy

PubMed Central

Cinco, Roehl M.; Rompel, Annette; Visser, Hendrik; Aromí, Guillem; Christou, George; Sauer, Kenneth; Klein, Melvin P.; Yachandra, Vittal K.

2014-01-01

X-ray absorption spectroscopy has been employed to assess the degree of similarity between the oxygen-evolving complex (OEC) in photosystem II (PS II) and a family of synthetic manganese complexes containing the distorted cubane [Mn4O3X] core (X = benzoate, acetate, methoxide, hydroxide, azide, fluoride, chloride, or bromide). These [Mn4(μ3-O)3(μ3-X)] cubanes possess C3v symmetry except for the X = benzoate species, which is slightly more distorted with only Cs symmetry. In addition, Mn4O3Cl complexes containing three or six terminal Cl ligands at three of the Mn were included in this study. The Mn K-edge X-ray absorption near edge structure (XANES) from the oxygen-ligated complexes begin to resemble general features of the PS II (S1 state) spectrum, although the second derivatives are distinct from those in PS II. The extended X-ray absorption fine structure (EXAFS) of these Mn compounds also displays superficial resemblance to that of PS II, but major differences emerge on closer examination of the phases and amplitudes. The most obvious distinction is the smaller magnitude of the Fourier transform (FT) of the PS II EXAFS compared to the FTs from the distorted cubanes. Curve fitting of the Mn EXAFS spectra verifies the known core structures of the Mn cubanes, and shows that the number of the crucial 2.7 and 3.3 Å Mn–Mn distances differs from that observed in the OEC. The EXAFS method detects small changes in the core structures as X is varied in this series, and serves to exclude the distorted cubane of C3v symmetry as a topological model for the Mn catalytic cluster of the OEC. Instead, the method shows that even more distortion of the cubane framework, altering the ratio of the Mn–Mn distances, is required to resemble the Mn cluster in PS II. PMID:11671305

Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures

NASA Astrophysics Data System (ADS)

Shock, Everetr L.; Koretsky, Carla M.

1995-04-01

Regression of standard state equilibrium constants with the revised Helgeson-Kirkham-Flowers (HKF) equation of state allows evaluation of standard partial molal entropies ( overlineSo) of aqueous metal-organic complexes involving monovalent organic acid ligands. These values of overlineSo provide the basis for correlations that can be used, together with correlation algorithms among standard partial molal properties of aqueous complexes and equation-of-state parameters, to estimate thermodynamic properties including equilibrium constants for complexes between aqueous metals and several monovalent organic acid ligands at the elevated pressures and temperatures of many geochemical processes which involve aqueous solutions. Data, parameters, and estimates are given for 270 formate, propanoate, n-butanoate, n-pentanoate, glycolate, lactate, glycinate, and alanate complexes, and a consistent algorithm is provided for making other estimates. Standard partial molal entropies of association ( Δ -Sro) for metal-monovalent organic acid ligand complexes fall into at least two groups dependent upon the type of functional groups present in the ligand. It is shown that isothermal correlations among equilibrium constants for complex formation are consistent with one another and with similar correlations for inorganic metal-ligand complexes. Additional correlations allow estimates of standard partial molal Gibbs free energies of association at 25°C and 1 bar which can be used in cases where no experimentally derived values are available.

Apparent complex partial seizures in a bipolar patient after withdrawal of carbamazepine.

PubMed

Garbutt, J C; Gillette, G M

1988-10-01

A 64-year-old woman with long-standing bipolar illness was treated with carbamazepine and clonazepam with minimal success. Discontinuation of carbamazepine and clonazepam was followed by episodic amnesia, purposeless behavior, déjà vu, and confusion. Although her EEG was normal, the episodes were compatible with complex partial seizures and ceased after carbamazepine and clonazepam were reinstituted. This case raises the question of whether discontinuing carbamazepine and clonazepam can induce complex partial seizures in bipolar patients.

Photoelectric charging of partially sunlit dielectric surfaces in space

NASA Technical Reports Server (NTRS)

De, B. R.; Criswell, D. R.

1977-01-01

Sunlight-shadow effects may substantially alter the charging situation for a dielectric surface. The sunlight-shadow boundary tends to be the site of intense multipole electric fields. Charges on a sunlit dielectric surface have a finite effective mobility. The charge distribution tends to resemble that on a conducting surface. A boundary between a conducting and a dielectric surface may not represent a conductivity discontinuity when this boundary is sunlit; charges may migrate at a nontrivial rate across the boundary. A contracting or expanding sunlit area may experience a supercharging.

Aldose Reductase-Deficient Mice Develop Nephrogenic Diabetes Insipidus

PubMed Central

Ho, Horace T. B.; Chung, Sookja K.; Law, Janice W. S.; Ko, Ben C. B.; Tam, Sidney C. F.; Brooks, Heddwen L.; Knepper, Mark A.; Chung, Stephen S. M.

2000-01-01

Aldose reductase (ALR2) is thought to be involved in the pathogenesis of various diseases associated with diabetes mellitus, such as cataract, retinopathy, neuropathy, and nephropathy. However, its physiological functions are not well understood. We developed mice deficient in this enzyme and found that they had no apparent developmental or reproductive abnormality except that they drank and urinated significantly more than their wild-type littermates. These ALR2-deficient mice exhibited a partially defective urine-concentrating ability, having a phenotype resembling that of nephrogenic diabetes insipidus. PMID:10913167

The Common Ancestor of Archaea and Eukarya Was Not an Archaeon

PubMed Central

Forterre, Patrick

2013-01-01

It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other. PMID:24348094

The common ancestor of archaea and eukarya was not an archaeon.

PubMed

Forterre, Patrick

2013-01-01

It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the "prokaryotic" phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.

Effects of asynchrony and ear of presentation on the pitch of mistuned partials in harmonic and frequency-shifted complex tones.

PubMed

Brunstrom, J M; Roberts, B

2001-07-01

When a partial of a periodic complex is mistuned, its change in pitch is greater than expected. Two experiments examined whether these partial-pitch shifts are related to the computation of global pitch. In experiment 1, stimuli were either harmonic or frequency-shifted (25% of F0) complexes. One partial was mistuned by +/- 4% and played with leading and lagging portions of 500 ms each, relative to the other components (1 s), in both monaural and dichotic contexts. Subjects indicated whether the mistuned partial was higher or lower in pitch when concurrent with the other components. Responses were positively correlated with the direction of mistuning in all conditions. In experiment 2, stimuli from each condition were compared with synchronous equivalents. Subjects matched a pure tone to the pitch of the mistuned partial (component 4). The results showed that partial-pitch shifts are not reduced in size by asynchrony. Similar asynchronies are known to produce a near-exclusion of a mistuned partial from the global-pitch computation. This mismatch indicates that global and partial pitch are derived from different processes. The similarity of the partial-pitch shifts observed for harmonic and frequency-shifted stimuli suggests that they arise from a grouping mechanism that is sensitive to spectral regularity.

Cryptic Speciation Patterns in Iranian Rock Lizards Uncovered by Integrative Taxonomy

PubMed Central

Ahmadzadeh, Faraham; Flecks, Morris; Carretero, Miguel A.; Mozaffari, Omid; Böhme, Wolfgang; Harris, D. James; Freitas, Susana; Rödder, Dennis

2013-01-01

While traditionally species recognition has been based solely on morphological differences either typological or quantitative, several newly developed methods can be used for a more objective and integrative approach on species delimitation. This may be especially relevant when dealing with cryptic species or species complexes, where high overall resemblance between species is coupled with comparatively high morphological variation within populations. Rock lizards, genus Darevskia, are such an example, as many of its members offer few diagnostic morphological features. Herein, we use a combination of genetic, morphological and ecological criteria to delimit cryptic species within two species complexes, D. chlorogaster and D. defilippii, both distributed in northern Iran. Our analyses are based on molecular information from two nuclear and two mitochondrial genes, morphological data (15 morphometric, 16 meristic and four categorical characters) and eleven newly calculated spatial environmental predictors. The phylogeny inferred for Darevskia confirmed monophyly of each species complex, with each of them comprising several highly divergent clades, especially when compared to other congeners. We identified seven candidate species within each complex, of which three and four species were supported by Bayesian species delimitation within D. chlorogaster and D. defilippii, respectively. Trained with genetically determined clades, Ecological Niche Modeling provided additional support for these cryptic species. Especially those within the D. defilippii-complex exhibit well-differentiated niches. Due to overall morphological resemblance, in a first approach PCA with mixed variables only showed the separation between the two complexes. However, MANCOVA and subsequent Discriminant Analysis performed separately for both complexes allowed for distinction of the species when sample size was large enough, namely within the D. chlorogaster-complex. In conclusion, the results support four new species, which are described herein. PMID:24324611

Growth responses of Neurospora crassa to increased partial pressures of the noble gases and nitrogen.

PubMed

Buchheit, R G; Schreiner, H R; Doebbler, G F

1966-02-01

Buchheit, R. G. (Union Carbide Corp., Tonawanda, N.Y.), H. R. Schreiner, and G. F. Doebbler. Growth responses of Neurospora crassa to increased partial pressures of the noble gases and nitrogen. J. Bacteriol. 91:622-627. 1966.-Growth rate of the fungus Neurospora crassa depends in part on the nature of metabolically "inert gas" present in its environment. At high partial pressures, the noble gas elements (helium, neon, argon, krypton, and xenon) inhibit growth in the order: Xe > Kr> Ar > Ne > He. Nitrogen (N(2)) closely resembles He in inhibitory effectiveness. Partial pressures required for 50% inhibition of growth were: Xe (0.8 atm), Kr (1.6 atm), Ar (3.8 atm), Ne (35 atm), and He ( approximately 300 atm). With respect to inhibition of growth, the noble gases and N(2) differ qualitatively and quantitatively from the order of effectiveness found with other biological effects, i.e., narcosis, inhibition of insect development, depression of O(2)-dependent radiation sensitivity, and effects on tissue-slice glycolysis and respiration. Partial pressures giving 50% inhibition of N. crassa growth parallel various physical properties (i.e., solubilities, solubility ratios, etc.) of the noble gases. Linear correlation of 50% inhibition pressures to the polarizability and of the logarithm of pressure to the first and second ionization potentials suggests the involvement of weak intermolecular interactions or charge-transfer in the biological activity of the noble gases.

Helical unwinding and side-chain unlocking unravel the outward open conformation of the melibiose transporter

NASA Astrophysics Data System (ADS)

Wang, Li-Ying; Ravi, Vidhya M.; Leblanc, Gérard; Padrós, Esteve; Cladera, Josep; Perálvarez-Marín, Alex

2016-09-01

Molecular dynamics simulations have been used to study the alternate access mechanism of the melibiose transporter from Escherichia coli. Starting from the outward-facing partially occluded form, 2 out of 12 simulations produced an outward full open form and one partially open, whereas the rest yielded fully or partially occluded forms. The shape of the outward-open form resembles other outward-open conformations of secondary transporters. During the transporter opening, conformational changes in some loops are followed by changes in the periplasm region of transmembrane helix 7. Helical curvature relaxation and unlocking of hydrophobic and ionic locks promote the outward opening of the transporter making accessible the substrate binding site. In particular, FRET studies on mutants of conserved aromatic residues of extracellular loop 4 showed lack of substrate binding, emphasizing the importance of this loop for making crucial interactions that control the opening of the periplasmic side. This study indicates that the alternate access mechanism for the melibiose transporter fits better into a flexible gating mechanism rather than the archetypical helical rigid-body rocker-switch mechanism.

Axelrod models of social influence with cultural repulsion

NASA Astrophysics Data System (ADS)

Radillo-Díaz, Alejandro; Pérez, Luis A.; Del Castillo-Mussot, Marcelo

2009-12-01

Since both attractive and repulsive effects among agents are important in social systems, we present simulations of two models based on Axelrod’s homogenization mechanism that includes repulsion. These models are the repulsive model, where all individuals can repel, and the partially repulsive model where only a fraction of repelling agents are considered. In these two models, attractive dynamics is implemented for agents with the ability to repel each other only if the number of features shared by them is greater than a threshold parameter. Otherwise, repelling dynamics is used. In the repulsive model, the transition from a monocultural state to a fragmented one often occurs abruptly from one cultural-variability value to the next one and a second transition emerges. For the partially repulsive model, there are also two different transitions present: the initial one being as abrupt as the one found for the repulsive model, whereas the second one follows a less abrupt behavior and resembles that of the original Axelrod model. However, the second transition for this model occurrs from a partially fragmented state and not from a monocultural one.

Effects of noise exposure on performance of a simulated radar task.

DOT National Transportation Integrated Search

1979-11-01

The present study examined the effect of noise (radar control room sounds, 80 dBA) on the ability to sustain attention to a complex monitoring task. The visual display was designed to resemble that of a highly automated air traffic control radar syst...

Drilling into Rhyolitic Magma at Shallow depth at Krafla Volcanic Complex, NE-Iceland

NASA Astrophysics Data System (ADS)

Mortensen, A. K.; Markússon, S. H.; Gudmundsson, Á.; Pálsson, B.

2017-12-01

Krafla volcanic complex in NE-Iceland is an active volcano but the latest eruption was the Krafla Fires in 1975-1984. Though recent volcanic activity has consisted of basaltic fissure eruptions, then it is rhyolitic magma that has been intercepted on at least two occasions while drilling geothermal production wells in the geothermal field suggesting a layered magma plumbing system beneath the Krafla volcanic complex. In 2008 quenched rhyolitic glass was retrieved from the bottom of well KJ-39, which is 2865 m deep ( 2571 m true vertical depth). In 2009 magma was again encountered at an even shallower depth and in more than 2,5 km distance from the bottom of well KJ-39, but in 2009 well IDDP-1 was drilled into magma three times just below 2100 m depth. Only on the last occasion was quenched glass retrieved to confirm that magma had been encountered. In well KJ-39 the quenched glass was rhyolitic in composition. The glass contained resorbed minerals of plagioclase, clinopyroxene and titanomagnetite, but the composition of the glass resembles magma that has formed by partial melting of hydrated basalt. The melt was encountered among cuttings from impermeable, coarse basaltic intrusives at a depth, where the well was anticipated to penetrate the Hólseldar volcanic fissure. In IDDP-1 the quenched glass was also rhyolitic in composition. The glass contained less than 5% of phenocrysts, but the phenocryst assemblage included andesine plagioclase, augite, pigeonite, and titanomagnetite. At IDDP-1 the melt was encountered below a permeable zone composed of fine to coarse grained felsite and granophyre. The disclosure of magma in two wells at Krafla volcanic complex verify that rhyolitic magma can be encountered at shallow depth across a larger area within the caldera. The encounter of magma at shallow depth conforms with that superheated conditions have been found at >2000 m depth in large parts of Krafla geothermal field.

Newborn infants detect cues of concurrent sound segregation.

PubMed

Bendixen, Alexandra; Háden, Gábor P; Németh, Renáta; Farkas, Dávid; Török, Miklós; Winkler, István

2015-01-01

Separating concurrent sounds is fundamental for a veridical perception of one's auditory surroundings. Sound components that are harmonically related and start at the same time are usually grouped into a common perceptual object, whereas components that are not in harmonic relation or have different onset times are more likely to be perceived in terms of separate objects. Here we tested whether neonates are able to pick up the cues supporting this sound organization principle. We presented newborn infants with a series of complex tones with their harmonics in tune (creating the percept of a unitary sound object) and with manipulated variants, which gave the impression of two concurrently active sound sources. The manipulated variant had either one mistuned partial (single-cue condition) or the onset of this mistuned partial was also delayed (double-cue condition). Tuned and manipulated sounds were presented in random order with equal probabilities. Recording the neonates' electroencephalographic responses allowed us to evaluate their processing of the sounds. Results show that, in both conditions, mistuned sounds elicited a negative displacement of the event-related potential (ERP) relative to tuned sounds from 360 to 400 ms after sound onset. The mistuning-related ERP component resembles the object-related negativity (ORN) component in adults, which is associated with concurrent sound segregation. Delayed onset additionally led to a negative displacement from 160 to 200 ms, which was probably more related to the physical parameters of the sounds than to their perceptual segregation. The elicitation of an ORN-like response in newborn infants suggests that neonates possess the basic capabilities of segregating concurrent sounds by detecting inharmonic relations between the co-occurring sounds. © 2015 S. Karger AG, Basel.

A three-parameter two-state model of receptor function that incorporates affinity, efficacy, and signal amplification.

PubMed

Buchwald, Peter

2017-06-01

A generalized model of receptor function is proposed that relies on the essential assumptions of the minimal two-state receptor theory (i.e., ligand binding followed by receptor activation), but uses a different parametrization and allows nonlinear response (transduction) for possible signal amplification. For the most general case, three parameters are used: K d , the classic equilibrium dissociation constant to characterize binding affinity; ε , an intrinsic efficacy to characterize the ability of the bound ligand to activate the receptor (ranging from 0 for an antagonist to 1 for a full agonist); and γ , a gain (amplification) parameter to characterize the nonlinearity of postactivation signal transduction (ranging from 1 for no amplification to infinity). The obtained equation, E/Emax=εγLεγ+1-εL+Kd, resembles that of the operational (Black and Leff) or minimal two-state (del Castillo-Katz) models, E/Emax=τLτ+1L+Kd, with εγ playing a role somewhat similar to that of the τ efficacy parameter of those models, but has several advantages. Its parameters are more intuitive as they are conceptually clearly related to the different steps of binding, activation, and signal transduction (amplification), and they are also better suited for optimization by nonlinear regression. It allows fitting of complex data where receptor binding and response are measured separately and the fractional occupancy and response are mismatched. Unlike the previous models, it is a true generalized model as simplified forms can be reproduced with special cases of its parameters. Such simplified forms can be used on their own to characterize partial agonism, competing partial and full agonists, or signal amplification.

An unusual case of iron deficiency anemia is associated with extremely low level of transferrin receptor.

PubMed

Hao, Shuangying; Li, Huihui; Sun, Xiaoyan; Li, Juan; Li, Kuanyu

2015-01-01

A case study of a female patient, diagnosed with iron deficiency anemia, was unresponsive to oral iron treatment and only partially responsive to parenteral iron therapy, a clinical profile resembling the iron-refractory iron deficiency anemia (IRIDA) disorder. However, the patient failed to exhibit microcytic phenotype, one of the IRIDA hallmarks. Biochemical assays revealed that serum iron, hepcidin, interluekin 6, and transferrin saturation were within the normal range of references or were comparable to her non-anemic offspring. Iron contents in serum and red blood cells and hemoglobin levels were measured, which confirmed the partial improvement of anemia after parenteral iron therapy. Strikingly, serum transferrin receptor in patient was almost undetectable, reflecting the very low activity of bone-marrow erythropoiesis. Our data demonstrate that this is not a case of systemic iron deficiency, but rather cellular iron deficit due to the low level of transferrin receptor, particularly in erythroid tissue.

Multilevel modelling of somatotype components: the Portuguese sibling study on growth, fitness, lifestyle and health.

PubMed

Pereira, Sara; Katzmarzyk, Peter T; Gomes, Thayse Natacha; Souza, Michele; Chaves, Raquel N; Santos, Fernanda K Dos; Santos, Daniel; Hedeker, Donald; Maia, José A R

2017-06-01

Somatotype is a complex trait influenced by different genetic and environmental factors as well as by other covariates whose effects are still unclear. To (1) estimate siblings' resemblance in their general somatotype; (2) identify sib-pair (brother-brother (BB), sister-sister (SS), brother-sister (BS)) similarities in individual somatotype components; (3) examine the degree to which between and within variances differ among sib-ships; and (4) investigate the effects of physical activity (PA) and family socioeconomic status (SES) on these relationships. The sample comprises 1058 Portuguese siblings (538 females) aged 9-20 years. Somatotype was calculated using the Health-Carter method, while PA and SES information was obtained by questionnaire. Multi-level modelling was done in SuperMix software. Older subjects showed the lowest values for endomorphy and mesomorphy, but the highest values for ectomorphy; and more physically active subjects showed the highest values for mesomorphy. In general, the familiality of somatotype was moderate (ρ = 0.35). Same-sex siblings had the strongest resemblance (endomorphy: ρ SS > ρ BB > ρ BS ; mesomorphy: ρ BB = ρ SS > ρ BS ; ectomorphy: ρ BB > ρ SS > ρ BS ). For the ectomorphy and mesomorphy components, BS pairs showed the highest between sib-ship variance, but the lowest within sib-ship variance; while for endomorphy BS showed the lowest between and within sib-ship variances. These results highlight the significant familial effects on somatotype and the complexity of the role of familial resemblance in explaining variance in somatotypes.

Characterization of class II β chain major histocompatibility complex genes in a family of Hawaiian honeycreepers: 'amakihi (Hemignathus virens).

PubMed

Jarvi, Susan I; Bianchi, Kiara R; Farias, Margaret Em; Txakeeyang, Ann; McFarland, Thomas; Belcaid, Mahdi; Asano, Ashley

2016-07-01

Hawaiian honeycreepers (Drepanidinae) have evolved in the absence of mosquitoes for over five million years. Through human activity, mosquitoes were introduced to the Hawaiian archipelago less than 200 years ago. Mosquito-vectored diseases such as avian malaria caused by Plasmodium relictum and Avipoxviruses have greatly impacted these vulnerable species. Susceptibility to these diseases is variable among and within species. Due to their function in adaptive immunity, the role of major histocompatibility complex genes (Mhc) in disease susceptibility is under investigation. In this study, we evaluate gene organization and levels of diversity of Mhc class II β chain genes (exon 2) in a captive-reared family of Hawaii 'amakihi (Hemignathus virens). A total of 233 sequences (173 bp) were obtained by PCR+1 amplification and cloning, and 5720 sequences were generated by Roche 454 pyrosequencing. We report a total of 17 alleles originating from a minimum of 14 distinct loci. We detected three linkage groups that appear to represent three distinct haplotypes. Phylogenetic analysis revealed one variable cluster resembling classical Mhc sequences (DAB) and one highly conserved, low variability cluster resembling non-classical Mhc sequences (DBB). High net evolutionary divergence values between DAB and DBB resemble that seen between chicken BLB system and YLB system genes. High amino acid identity among non-classical alleles from 12 species of passerines (DBB) and four species of Galliformes (YLB) was found, suggesting that these non-classical passerine sequences may be related to the Galliforme YLB sequences.

Avoiding the "It's a Small World" Effect: A Lesson Plan to Explore Diversity

ERIC Educational Resources Information Center

Endacott, Jason L.; Bowles, Freddie A.

2013-01-01

Classroom instruction about other cultures all too often resembles the Disney version of "It's a Small World" with Fantasyland-like cultural stereotypes, ceremonial activities, and traditional dress that can lead to serious misunderstandings about the depth and complexity of global societies. Social studies instruction presents the…

Hands-on Force Spectroscopy: Weird Springs and Protein Folding

ERIC Educational Resources Information Center

Euler, Manfred

2008-01-01

A force spectroscopy model experiment is presented using a low-cost tensile apparatus described earlier. Force-extension measurements of twisted rubber bands are obtained. They exhibit a complex nonlinear elastic behaviour that resembles atomic force spectroscopy investigations of molecules of titin, a muscle protein. The model experiments open up…

Streaming Media

ERIC Educational Resources Information Center

Pulley, John

2009-01-01

At a time when the evolutionary pace of new media resembles the real-time mutation of certain microorganisms, the age-old question of how best to connect with constituents can seem impossibly complex--even for an elite institution plugged into the motherboard of Silicon Valley. Identifying the most effective vehicle for reaching a particular…

Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids

PubMed Central

Eisenberg, Bob; Hyon, YunKyong; Liu, Chun

2010-01-01

Ionic solutions are mixtures of interacting anions and cations. They hardly resemble dilute gases of uncharged noninteracting point particles described in elementary textbooks. Biological and electrochemical solutions have many components that interact strongly as they flow in concentrated environments near electrodes, ion channels, or active sites of enzymes. Interactions in concentrated environments help determine the characteristic properties of electrodes, enzymes, and ion channels. Flows are driven by a combination of electrical and chemical potentials that depend on the charges, concentrations, and sizes of all ions, not just the same type of ion. We use a variational method EnVarA (energy variational analysis) that combines Hamilton’s least action and Rayleigh’s dissipation principles to create a variational field theory that includes flow, friction, and complex structure with physical boundary conditions. EnVarA optimizes both the action integral functional of classical mechanics and the dissipation functional. These functionals can include entropy and dissipation as well as potential energy. The stationary point of the action is determined with respect to the trajectory of particles. The stationary point of the dissipation is determined with respect to rate functions (such as velocity). Both variations are written in one Eulerian (laboratory) framework. In variational analysis, an “extra layer” of mathematics is used to derive partial differential equations. Energies and dissipations of different components are combined in EnVarA and Euler–Lagrange equations are then derived. These partial differential equations are the unique consequence of the contributions of individual components. The form and parameters of the partial differential equations are determined by algebra without additional physical content or assumptions. The partial differential equations of mixtures automatically combine physical properties of individual (unmixed) components. If a new component is added to the energy or dissipation, the Euler–Lagrange equations change form and interaction terms appear without additional adjustable parameters. EnVarA has previously been used to compute properties of liquid crystals, polymer fluids, and electrorheological fluids containing solid balls and charged oil droplets that fission and fuse. Here we apply EnVarA to the primitive model of electrolytes in which ions are spheres in a frictional dielectric. The resulting Euler–Lagrange equations include electrostatics and diffusion and friction. They are a time dependent generalization of the Poisson–Nernst–Planck equations of semiconductors, electrochemistry, and molecular biophysics. They include the finite diameter of ions. The EnVarA treatment is applied to ions next to a charged wall, where layering is observed. Applied to an ion channel, EnVarA calculates a quick transient pile-up of electric charge, transient and steady flow through the channel, stationary “binding” in the channel, and the eventual accumulation of salts in “unstirred layers” near channels. EnVarA treats electrolytes in a unified way as complex rather than simple fluids. Ad hoc descriptions of interactions and flow have been used in many areas of science to deal with the nonideal properties of electrolytes. It seems likely that the variational treatment can simplify, unify, and perhaps derive and improve those descriptions. PMID:20849161

Mullerian papilloma-like proliferation arising in cystic pelvic endosalpingiosis.

PubMed

McCluggage, W Glenn; O'Rourke, Declan; McElhenney, Clodagh; Crooks, Michael

2002-09-01

This report describes an unusual epithelial proliferation occurring in pelvic cystic endosalpingiosis. A cyst mass lined by a layer of ciliated epithelial cells involved the posterior surface of the cervix and vagina. The epithelial proliferation within the wall resembled a mullerian papilloma with fibrous and fibrovascular cores lined by bland cuboidal epithelial cells. Other areas had a microglandular growth pattern resembling cervical microglandular hyperplasia, and focally there was a solid growth pattern. Foci of typical endosalpingiosis involved the surface of both ovaries and pelvic soft tissues. The cystic lesion recurred after partial cystectomy and drainage and was followed up radiologically and with periodic fine-needle aspiration. Part of the wall of the cyst removed 11 years after the original surgery showed an identical epithelial proliferation. MIB1 staining showed a proliferation index of less than 5%, contrasting with the higher proliferation index of a typical serous borderline tumor. The differential diagnosis is discussed. As far as we are aware, this is the first report of such a benign epithelial proliferation involving cystic endosalpingiosis. Copyright 2002, Elsevier Science (USA). All rights reserved.

The Preparation of an Ultrastable Mesoporous Cr(III)-MOF via Reductive Labilization

DTIC Science & Technology

2015-09-02

of metal clusters from a template MOF with a known structure. Fe(III)-MOFs can serve as practical structural templates because iron resembles chromium ...clusters in PCN-333 are able to accommodate both di- and trivalent metal ions by varying the charges of the terminal ligands, the bridging oxygen atoms, and...molecules in trivalent aqua complexes27 Inert complexes Labile complexes M(OH2) Cr(OH2)6 3+ Ir(OH2)6 3+ V(OH2)6 3+ Fe(OH2)6 3+ Ti(OH2)6 3+ k (s1) 2.4 10

Retrograde renal hilar dissection and segmental arterial clamping: a simple modification to achieve super-selective robotic partial nephrectomy.

PubMed

Greene, Richard N; Sutherland, Douglas E; Tausch, Timothy J; Perez, Deo S

2014-03-01

Super-selective vascular control prior to robotic partial nephrectomy (also known as 'zero-ischemia') is a novel surgical technique that promises to reduce warm ischemia time. The technique has been shown to be feasible but adds substantial technical complexity and cost to the procedure. We present a simplified retrograde dissection of the renal hilum to achieve selective vascular control during robotic partial nephrectomy. Consecutive patients with stage 1 solid and complex cystic renal masses underwent robotic partial nephrectomies with selective vascular control using a modification to previously described super-selective robotic partial nephrectomy. In each case, the renal arterial branch supplying the mass and surrounding parenchyma was dissected in a retrograde fashion from the tumor. Intra-renal dissection of the interlobular artery was not performed. Intra-operative immunofluorescence was not utilized as assessment of parenchymal ischemia was documented before partial nephrectomy. Data was prospectively collected in an IRB-approved partial nephrectomy database. Operative variables between patients undergoing super-selective versus standard robotic partial nephrectomy were compared. Super-selective partial nephrectomy with retrograde hilar dissection was successfully completed in five consecutive patients. There were no complications or conversions to traditional partial nephrectomy. All were diagnosed with renal cell carcinoma and surgical margins were all negative. Estimated blood loss, warm ischemia time, operative time and length of stay were all comparable between patients undergoing super-selective and standard robotic partial nephrectomy. Retrograde hilar dissection appears to be a feasible and safe approach to super-selective partial nephrectomy without adding complex renovascular surgical techniques or cost to the procedure.

A computational approach to achieve situational awareness from limited observations of a complex system

NASA Astrophysics Data System (ADS)

Sherwin, Jason

At the start of the 21st century, the topic of complexity remains a formidable challenge in engineering, science and other aspects of our world. It seems that when disaster strikes it is because some complex and unforeseen interaction causes the unfortunate outcome. Why did the financial system of the world meltdown in 2008--2009? Why are global temperatures on the rise? These questions and other ones like them are difficult to answer because they pertain to contexts that require lengthy descriptions. In other words, these contexts are complex. But we as human beings are able to observe and recognize this thing we call 'complexity'. Furthermore, we recognize that there are certain elements of a context that form a system of complex interactions---i.e., a complex system. Many researchers have even noted similarities between seemingly disparate complex systems. Do sub-atomic systems bear resemblance to weather patterns? Or do human-based economic systems bear resemblance to macroscopic flows? Where do we draw the line in their resemblance? These are the kinds of questions that are asked in complex systems research. And the ability to recognize complexity is not only limited to analytic research. Rather, there are many known examples of humans who, not only observe and recognize but also, operate complex systems. How do they do it? Is there something superhuman about these people or is there something common to human anatomy that makes it possible to fly a plane? Or to drive a bus? Or to operate a nuclear power plant? Or to play Chopin's etudes on the piano? In each of these examples, a human being operates a complex system of machinery, whether it is a plane, a bus, a nuclear power plant or a piano. What is the common thread running through these abilities? The study of situational awareness (SA) examines how people do these types of remarkable feats. It is not a bottom-up science though because it relies on finding general principles running through a host of varied human activities. Nevertheless, since it is not constrained by computational details, the study of situational awareness provides a unique opportunity to approach complex tasks of operation from an analytical perspective. In other words, with SA, we get to see how humans observe, recognize and react to complex systems on which they exert some control. Reconciling this perspective on complexity with complex systems research, it might be possible to further our understanding of complex phenomena if we can probe the anatomical mechanisms by which we, as humans, do it naturally. At this unique intersection of two disciplines, a hybrid approach is needed. So in this work, we propose just such an approach. In particular, this research proposes a computational approach to the situational awareness (SA) of complex systems. Here we propose to implement certain aspects of situational awareness via a biologically-inspired machine-learning technique called Hierarchical Temporal Memory (HTM). In doing so, we will use either simulated or actual data to create and to test computational implementations of situational awareness. This will be tested in two example contexts, one being more complex than the other. The ultimate goal of this research is to demonstrate a possible approach to analyzing and understanding complex systems. By using HTM and carefully developing techniques to analyze the SA formed from data, it is believed that this goal can be obtained.

Abstraction of complex concepts with a refined partial-area taxonomy of SNOMED

PubMed Central

Wang, Yue; Halper, Michael; Wei, Duo; Perl, Yehoshua; Geller, James

2012-01-01

An algorithmically-derived abstraction network, called the partial-area taxonomy, for a SNOMED hierarchy has led to the identification of concepts considered complex. The designation “complex” is arrived at automatically on the basis of structural analyses of overlap among the constituent concept groups of the partial-area taxonomy. Such complex concepts, called overlapping concepts, constitute a tangled portion of a hierarchy and can be obstacles to users trying to gain an understanding of the hierarchy’s content. A new methodology for partitioning the entire collection of overlapping concepts into singly-rooted groups, that are more manageable to work with and comprehend, is presented. Different kinds of overlapping concepts with varying degrees of complexity are identified. This leads to an abstract model of the overlapping concepts called the disjoint partial-area taxonomy, which serves as a vehicle for enhanced, high-level display. The methodology is demonstrated with an application to SNOMED’s Specimen hierarchy. Overall, the resulting disjoint partial-area taxonomy offers a refined view of the hierarchy’s structural organization and conceptual content that can aid users, such as maintenance personnel, working with SNOMED. The utility of the disjoint partial-area taxonomy as the basis for a SNOMED auditing regimen is presented in a companion paper. PMID:21878396

Safety assessment for the postictal confusional phase following complex partial seizure.

PubMed

Tucker, C

1985-06-01

Misunderstanding of the postictal confusional state that follows the complex partial seizure has caused emotional and physical harm to patients. Concern about this phenomenon and its effects upon the patient prompted this study to explore, describe, and document one method of intervention to lessen these harmful effects. An evaluative descriptive research design was employed to assess patient safety during and after the postictal confusional phase following a complex partial seizure. A closed-structured questionnaire and participant observation were the methods used to collect data for this study. A Level of Safety Tool was specifically designed for this study.

Molecular mechanism of NDMA formation from N,N-dimethylsulfamide during ozonation: quantum chemical insights into a bromide-catalyzed pathway.

PubMed

Trogolo, Daniela; Mishra, Brijesh Kumar; Heeb, Michèle B; von Gunten, Urs; Arey, J Samuel

2015-04-07

During ozonation of drinking water, the fungicide metabolite N,N-dimethylsulfamide (DMS) can be transformed into a highly toxic product, N-nitrosodimethylamine (NDMA). We used quantum chemical computations and stopped-flow experiments to evaluate a chemical mechanism proposed previously to describe this transformation. Stopped-flow experiments indicate a pK(a) = 10.4 for DMS. Experiments show that hypobromous acid (HOBr), generated by ozone oxidation of naturally occurring bromide, brominates the deprotonated DMS(-) anion with a near-diffusion controlled rate constant (7.1 ± 0.6 × 10(8) M(-1) s(-1)), forming Br-DMS(-) anion. According to quantum chemical calculations, Br-DMS has a pK(a) ∼ 9.0 and thus remains partially deprotonated at neutral pH. The anionic Br-DMS(-) bromamine can react with ozone with a high rate constant (10(5 ± 2.5) M(-1) s(-1)), forming the reaction intermediate (BrNO)(SO2)N(CH3)2(-). This intermediate resembles a loosely bound complex between an electrophilic nitrosyl bromide (BrNO) molecule and an electron-rich dimethylaminosulfinate ((SO2)N(CH3)2(-)) fragment, based on inspection of computed natural charges and geometric parameters. This fragile complex undergoes immediate (10(10 ± 2.5) s(-1)) reaction by two branches: an exothermic channel that produces NDMA, and an entropy-driven channel giving non-NDMA products. Computational results bring new insights into the electronic nature, chemical equilibria, and kinetics of the elementary reactions of this pathway, enabled by computed energies of structures that are not possible to access experimentally.

Anatomy of a new B-cell-specific enhancer.

PubMed Central

Koch, W; Benoist, C; Mathis, D

1989-01-01

The major histocompatibility complex class II molecules, like the immunoglobulins, are prominent B-lymphocyte markers. Herein, we describe a B-cell-specific enhancer associated with the murine class II gene, Ek alpha. This enhancer has a complex anatomy that suggests interactions between remotely spaced elements. Of particular interest is the finding that two CCAAT boxes spaced one kilobase apart are important for enhancer activity. Somewhat surprisingly, the E alpha and immunoglobulin enhancers seem to show little resemblance. Images PMID:2467189

Note on the coefficient of variations of neuronal spike trains.

PubMed

Lengler, Johannes; Steger, Angelika

2017-08-01

It is known that many neurons in the brain show spike trains with a coefficient of variation (CV) of the interspike times of approximately 1, thus resembling the properties of Poisson spike trains. Computational studies have been able to reproduce this phenomenon. However, the underlying models were too complex to be examined analytically. In this paper, we offer a simple model that shows the same effect but is accessible to an analytic treatment. The model is a random walk model with a reflecting barrier; we give explicit formulas for the CV in the regime of excess inhibition. We also analyze the effect of probabilistic synapses in our model and show that it resembles previous findings that were obtained by simulation.

Selective self-assembly of adenine-silver nanoparticles forms rings resembling the size of cells

PubMed Central

Choi, Sungmoon; Park, Soonyoung; Yang, Seon-Ah; Jeong, Yujin; Yu, Junhua

2015-01-01

Self-assembly has played critical roles in the construction of functional nanomaterials. However, the structure of the macroscale multicomponent materials built by the self-assembly of nanoscale building blocks is hard to predict due to multiple intermolecular interactions of great complexity. Evaporation of solvents is usually an important approach to induce kinetically stable assemblies of building blocks with a large-scale specific arrangement. During such a deweting process, we tried to monitor the possible interactions between silver nanoparticles and nucleobases at a larger scale by epifluorescence microscopy, thanks to the doping of silver nanoparticles with luminescent silver nanodots. ssDNA oligomer-stabilized silver nanoparticles and adenine self-assemble to form ring-like compartments similar to the size of modern cells. However, the silver ions only dismantle the self-assembly of adenine. The rings are thermodynamically stable as the drying process only enrich the nanoparticles-nucleobase mixture to a concentration that activates the self-assembly. The permeable membrane-like edge of the ring is composed of adenine filaments glued together by silver nanoparticles. Interestingly, chemicals are partially confined and accumulated inside the ring, suggesting that this might be used as a microreactor to speed up chemical reactions during a dewetting process. PMID:26643504

A Structural Basis for the Regulatory Inactivation of DnaA

PubMed Central

Xu, Qingping; McMullan, Daniel; Abdubek, Polat; Astakhova, Tamara; Carlton, Dennis; Chen, Connie; Chiu, Hsiu-Ju; Clayton, Thomas; Das, Debanu; Deller, Marc C.; Duan, Lian; Elsliger, Marc-Andre; Feuerhelm, Julie; Hale, Joanna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Johnson, Hope A.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Trame, Christine; van den Bedem, Henry; Weekes, Dana; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

2009-01-01

Summary Regulatory inactivation of DnaA is dependent on Hda, a protein homologous to the AAA+ ATPase region of the replication initiator DnaA. When bound to the sliding clamp loaded onto duplex DNA, Hda can stimulate the transformation of active DnaA-ATP into inactive DnaA-ADP. The crystal structure of Hda from Shewanella amazonensis SB2B at 1.75 Å resolution reveals that Hda resembles typical AAA+ ATPases. The arrangement of the two subdomains in Hda (residues 1-174, 175-241) differs dramatically from that of DnaA. A CDP molecule anchors the Hda domains in a conformation which promotes dimer formation. The Hda dimer adopts a novel oligomeric assembly for AAA+ proteins in which the arginine finger, crucial for ATP hydrolysis, is fully exposed and available to hydrolyze DnaA-ATP through a typical AAA+ type mechanism. The sliding clamp binding motifs at the N-terminus of each Hda monomer are partially buried and combine to form an antiparallel β-sheet at the dimer interface. The inaccessibility of the clamp binding motifs in the CDP bound structure of Hda suggests that conformational changes are required for Hda to form a functional complex with the clamp. Thus, the CDP-bound Hda dimer likely represents an inactive form of Hda. PMID:19000695

Identifying product order with restricted Boltzmann machines

NASA Astrophysics Data System (ADS)

Rao, Wen-Jia; Li, Zhenyu; Zhu, Qiong; Luo, Mingxing; Wan, Xin

2018-03-01

Unsupervised machine learning via a restricted Boltzmann machine is a useful tool in distinguishing an ordered phase from a disordered phase. Here we study its application on the two-dimensional Ashkin-Teller model, which features a partially ordered product phase. We train the neural network with spin configuration data generated by Monte Carlo simulations and show that distinct features of the product phase can be learned from nonergodic samples resulting from symmetry breaking. Careful analysis of the weight matrices inspires us to define a nontrivial machine-learning motivated quantity of the product form, which resembles the conventional product order parameter.

Identification of Ccr4-Not Complex Components as Regulators of Transition from Partial to Genuine Induced Pluripotent Stem Cells

PubMed Central

Kamon, Masayoshi; Katano, Miyuki; Hiraki-Kamon, Keiko; Hishida, Tomoaki; Nakachi, Yutaka; Mizuno, Yosuke; Okazaki, Yasushi; Suzuki, Ayumu; Hirasaki, Masataka; Ueda, Atsushi; Nishimoto, Masazumi; Kato, Hidemasa

2014-01-01

Somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) by defined factors. However, substantial cell numbers subjected to iPSC induction stray from the main reprogramming route and are immortalized as partial iPSCs. These partial iPSCs can become genuine iPSCs by exposure to the ground state condition. However, such conversion is only possible for mouse partial iPSCs, and it is not applicable to human cells. Moreover, the molecular basis of this conversion is completely unknown. Therefore, we performed genome-wide screening with a piggyBac vector to identify genes involved in conversion from partial to genuine iPSCs. This screening led to identification of Cnot2, one of the core components of the Ccr4-Not complex. Subsequent analyses revealed that other core components, Cnot1 and Cnot3, also contributed to the conversion. Thus, our data have uncovered a novel role of core components of the Ccr4-Not complex as regulators of transition from partial to genuine iPSCs. PMID:24200330

Growth Responses of Neurospora crassa to Increased Partial Pressures of the Noble Gases and Nitrogen

PubMed Central

Buchheit, R. G.; Schreiner, H. R.; Doebbler, G. F.

1966-01-01

Buchheit, R. G. (Union Carbide Corp., Tonawanda, N.Y.), H. R. Schreiner, and G. F. Doebbler. Growth responses of Neurospora crassa to increased partial pressures of the noble gases and nitrogen. J. Bacteriol. 91:622–627. 1966.—Growth rate of the fungus Neurospora crassa depends in part on the nature of metabolically “inert gas” present in its environment. At high partial pressures, the noble gas elements (helium, neon, argon, krypton, and xenon) inhibit growth in the order: Xe > Kr> Ar ≫ Ne ≫ He. Nitrogen (N2) closely resembles He in inhibitory effectiveness. Partial pressures required for 50% inhibition of growth were: Xe (0.8 atm), Kr (1.6 atm), Ar (3.8 atm), Ne (35 atm), and He (∼ 300 atm). With respect to inhibition of growth, the noble gases and N2 differ qualitatively and quantitatively from the order of effectiveness found with other biological effects, i.e., narcosis, inhibition of insect development, depression of O2-dependent radiation sensitivity, and effects on tissue-slice glycolysis and respiration. Partial pressures giving 50% inhibition of N. crassa growth parallel various physical properties (i.e., solubilities, solubility ratios, etc.) of the noble gases. Linear correlation of 50% inhibition pressures to the polarizability and of the logarithm of pressure to the first and second ionization potentials suggests the involvement of weak intermolecular interactions or charge-transfer in the biological activity of the noble gases. PMID:5883104

How partial reinforcement of food cues affects the extinction and reacquisition of appetitive responses. A new model for dieting success?

PubMed

van den Akker, Karolien; Havermans, Remco C; Bouton, Mark E; Jansen, Anita

2014-10-01

Animals and humans can easily learn to associate an initially neutral cue with food intake through classical conditioning, but extinction of learned appetitive responses can be more difficult. Intermittent or partial reinforcement of food cues causes especially persistent behaviour in animals: after exposure to such learning schedules, the decline in responding that occurs during extinction is slow. After extinction, increases in responding with renewed reinforcement of food cues (reacquisition) might be less rapid after acquisition with partial reinforcement. In humans, it may be that the eating behaviour of some individuals resembles partial reinforcement schedules to a greater extent, possibly affecting dieting success by interacting with extinction and reacquisition. Furthermore, impulsivity has been associated with less successful dieting, and this association might be explained by impulsivity affecting the learning and extinction of appetitive responses. In the present two studies, the effects of different reinforcement schedules and impulsivity on the acquisition, extinction, and reacquisition of appetitive responses were investigated in a conditioning paradigm involving food rewards in healthy humans. Overall, the results indicate both partial reinforcement schedules and, possibly, impulsivity to be associated with worse extinction performance. A new model of dieting success is proposed: learning histories and, perhaps, certain personality traits (impulsivity) can interfere with the extinction and reacquisition of appetitive responses to food cues and they may be causally related to unsuccessful dieting. Copyright © 2014 Elsevier Ltd. All rights reserved.

Hurleyella, a new genus of Nearctic Dolichopodidae (Diptera)

Treesearch

Justin Runyon; Harold Robinson

2010-01-01

The new micro-dolichopodid genus Hurleyella and two new species, H. cumberlandensis and H. brooksi are described from the Nearctic. Hurleyella resembles the subfamily Medeterinae in having the legs bare of major setae, a depressed posterior mesonotum, and concave dorsal postcranium, but the complex male genitalia is unlike the relatively simple structure of...

A Semantic Navigation Model for Video Games

NASA Astrophysics Data System (ADS)

van Driel, Leonard; Bidarra, Rafael

Navigational performance of artificial intelligence (AI) characters in computer games is gaining an increasingly important role in the perception of their behavior. While recent games successfully solve some complex navigation problems, there is little known or documented on the underlying approaches, often resembling a primitive conglomerate of ad-hoc algorithms for specific situations.

Identification and Analysis of Partial Shading Breakdown Sites in CuIn xGa (1-x)Se 2 Modules

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

Palmiotti, Elizabeth; Johnston, Steven; Gerber, Andreas

In this paper, CuIn xGa (1-x) (CIGS) mini-modules are stressed under reverse bias, resembling partial shading conditions, to predict and characterize where failures occur. Partial shading can cause permanent damage in the form of 'wormlike' defects on thin-film modules due to thermal runaway. This results in module-scale power losses. We have used dark lock-in thermography (DLIT) to spatially observe localized heating when reverse-bias breakdown occurs on various CIGS mini-modules. For better understanding of how and where these defects originated and propagated, we have developed techniques where the current is limited during reverse-bias stressing. This allows for DLIT-based detection and detailedmore » studying of the region where breakdown is initiated before thermal runaway leads to permanent damage. Statistics of breakdown sites using current-limited conditions has allowed for reasonable identification of the as-grown defects where permanent breakdown will likely originate. Scanning electron microscope results and wormlike defect analysis show that breakdown originates in defects such as small pits, craters, or cracks in the CIGS layer, and the wormlike defects propagate near the top CIGS interface.« less

Long persistence of rigor mortis at constant low temperature.

PubMed

Varetto, Lorenzo; Curto, Ombretta

2005-01-06

We studied the persistence of rigor mortis by using physical manipulation. We tested the mobility of the knee on 146 corpses kept under refrigeration at Torino's city mortuary at a constant temperature of +4 degrees C. We found a persistence of complete rigor lasting for 10 days in all the cadavers we kept under observation; and in one case, rigor lasted for 16 days. Between the 11th and the 17th days, a progressively increasing number of corpses showed a change from complete into partial rigor (characterized by partial bending of the articulation). After the 17th day, all the remaining corpses showed partial rigor and in the two cadavers that were kept under observation "à outrance" we found the absolute resolution of rigor mortis occurred on the 28th day. Our results prove that it is possible to find a persistence of rigor mortis that is much longer than the expected when environmental conditions resemble average outdoor winter temperatures in temperate zones. Therefore, this datum must be considered when a corpse is found in those environmental conditions so that when estimating the time of death, we are not misled by the long persistence of rigor mortis.

Identification and Analysis of Partial Shading Breakdown Sites in CuIn xGa (1-x)Se 2 Modules

DOE PAGES

Palmiotti, Elizabeth; Johnston, Steven; Gerber, Andreas; ...

2017-12-20

In this paper, CuIn xGa (1-x) (CIGS) mini-modules are stressed under reverse bias, resembling partial shading conditions, to predict and characterize where failures occur. Partial shading can cause permanent damage in the form of 'wormlike' defects on thin-film modules due to thermal runaway. This results in module-scale power losses. We have used dark lock-in thermography (DLIT) to spatially observe localized heating when reverse-bias breakdown occurs on various CIGS mini-modules. For better understanding of how and where these defects originated and propagated, we have developed techniques where the current is limited during reverse-bias stressing. This allows for DLIT-based detection and detailedmore » studying of the region where breakdown is initiated before thermal runaway leads to permanent damage. Statistics of breakdown sites using current-limited conditions has allowed for reasonable identification of the as-grown defects where permanent breakdown will likely originate. Scanning electron microscope results and wormlike defect analysis show that breakdown originates in defects such as small pits, craters, or cracks in the CIGS layer, and the wormlike defects propagate near the top CIGS interface.« less

NADH-ubiquinone oxidoreductase activity in the kinetoplasts of the plant trypanosomatid Phytomonas serpens.

PubMed

González-Halphen, Diego; Maslov, Dmitri A

2004-03-01

NADH-ubiquinone oxidoreductase activity is present in mitochondrial lysates of Phytomonas serpens. Rotenone at 2-10 microM inhibited the activity 50-75%, indicating that it belongs to respiratory complex I. The activity was also inhibited 50-60% in the presence of 10-30 nM atovaquone suggesting that inhibition of complex I represents a likely mechanism of the known antileishmanial activity of this drug. The complex was partially purified by chromatography on DEAE-Sepharose CL-6B and gel-filtration on Sepharose CL-2B. The NADH:ubiquinone oxidoreductase activity in this preparation was completely inactivated by 20 nM atovaquone. The partially purified complex was present in a low amount and its subunits could not be discerned by staining with Coomassie. However, one of its components, a homologue of the 39 kDa subunit of the bovine complex I, was identified immunochemically in the original lysate and in the partially purified material.

Cadmium-sulfide crystallites in Cd-. gamma. -glutamyl peptide complexes from Lycopersicon and Daucus

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

Reese, R.N.; Winge, D.R.

1989-04-01

Hydroponically-grown tomato plants (Lycopersicon esculentum P. Mill. cv stone) and suspension-cultured carrot cells (Daucus carota L.) exposed to 100 {mu}M cadmium salts produced metal-{gamma}-glutamyl peptide complexes containing acid labile sulfur. The properties of the complexes resemble the Cd-{gamma}-glutamyl complexes from Schizosaccharomyces pombe and Candida glabrata, known to contain a CdS crystallite core. The crystallite core is stabilized by a coating of peptides of the general structure ({gamma}-Glu-Cys){sub n}-Gly. The Cd-peptide complexes contain predominantly peptides of n{sub 2}, n{sub 3}, n{sub 4} and n{sub 3}desGly. Zn-peptide complexes were also isolated from carrot cultures grown in MS medium supplemented with 2 mMmore » Zn and cysteine. Results of preliminary characterization of these complexes are consistent with the presence of a colloidal particle similar to that of the Cd-complexes.« less

ARC-1989-A89-7030

NASA Image and Video Library

1989-08-25

P-34692 Range : 500 km. ( 300 miles ) Smallest Resolvable Feature : 900 m. or 2,700 ft. Part of Triton's complex geological history canbe seen in this image, shot by Voyager 2. Part of a sequence, it shows a surface dominated by many roughly circular, polygonal, and arcuate features between 30 and 50 km (18 and 30 miles ) across. Some resemble degraded impact craters of Mars, while others resemble the 'palimpsest' features of Jupiter's satellite Ganymede. Peculiar intersecting, double ridged lines are 15 to 20 km. or 9 to 12 miles wide and hundreds of kilometers long. Theyresemble some deformational belts of Ganymede. Patches of plainsforming material tend to occur in local depressions. The geologic features of Triton and spectroscopic information indicates that the surface of Triton is underlain by a mixture of ices.

Frustration across the periodic table: heterolytic cleavage of dihydrogen by metal complexes

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

Bullock, R. Morris; Chambers, Geoffrey M.

2017-07-24

This Perspective examines the field of Frustrated Lewis Pairs (FLPs) in the context of transition metal mediated heterolytic cleavage of H2, with a particular emphasis on molecular complexes bearing an intramolecular Lewis base. FLPs have traditionally been associated with group compounds, yet many transition metal reactions support a broader classification of FLPs to include certain types of transition metal complexes with reactivity resembling main group based FLPs. This article surveys transition metal complexes that heterolytically cleave H2, which vary in the degree that the Lewis pairs within these systems interact. Particular attention is focused on complexes bearing a pendant aminemore » function as the base. Consideration of transition metal compounds in the context of FLPs can inspire new innovations and improvements in transition metal catalysis.« less

Spatial Distribution of Overstory Retention Influences Resources and Growth of Longleaf Pine Seedlings

Treesearch

Brian Palik; Robert J. Mitchell; Stephen Pecot; Mike Battaglia; Mou Pu

2003-01-01

Increasingly, overstory retention is being used in forests traditionally managed for single-cohort structure. One rationale for retention is that residual stand structure better resembles the complex structure of forests after natural disturbance, helping to perpetuate ecosystem fuctions dependent on that structure. The benefits of retention come at the cost of reduced...

Robotic partial nephrectomy for complex renal tumors: surgical technique.

PubMed

Rogers, Craig G; Singh, Amar; Blatt, Adam M; Linehan, W Marston; Pinto, Peter A

2008-03-01

Laparoscopic partial nephrectomy requires advanced training to accomplish tumor resection and renal reconstruction while minimizing warm ischemia times. Complex renal tumors add an additional challenge to a minimally invasive approach to nephron-sparing surgery. We describe our technique, illustrated with video, of robotic partial nephrectomy for complex renal tumors, including hilar, endophytic, and multiple tumors. Robotic assistance was used to resect 14 tumors in eight patients (mean age: 50.3 yr; range: 30-68 yr). Three patients had hereditary kidney cancer. All patients had complex tumor features, including hilar tumors (n=5), endophytic tumors (n=4), and/or multiple tumors (n=3). Robotic partial nephrectomy procedures were performed successfully without complications. Hilar clamping was used with a mean warm ischemia time of 31 min (range: 24-45 min). Mean blood loss was 230 ml (range: 100-450 ml). Histopathology confirmed clear-cell renal cell carcinoma (n=3), hybrid oncocytic tumor (n=2), chromophobe renal cell carcinoma (n=2), and oncocytoma (n=1). All patients had negative surgical margins. Mean index tumor size was 3.6 cm (range: 2.6-6.4 cm). Mean hospital stay was 2.6 d. At 3-mo follow-up, no patients experienced a statistically significant change in serum creatinine or estimated glomerular filtration rate and there was no evidence of tumor recurrence. Robotic partial nephrectomy is safe and feasible for select patients with complex renal tumors, including hilar, endophytic, and multiple tumors. Robotic assistance may facilitate a minimally invasive, nephron-sparing approach for select patients with complex renal tumors who might otherwise require open surgery or total nephrectomy.

Cadmium-sulfide crystallites in Cd-(. gamma. EC) sub n G peptide complexes from tomato. [Lycopersicon esculentum

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

Reese, R.N.; White, C.A.; Winge, D.R.

Hydroponically grown tomato plants (Lycopersicon esculentum P. Mill cv Golden Boy) exposed to 100 micromolar cadmium sulfate produced metal-({gamma}EC){sub n}G peptide complexes containing acid-labile sulfur. The properties of the complexes resemble those of the cadmium-({gamma}EC){sub n}G peptide complexes from Schizo-saccharomyces pombe and Candida glabrata known to contain a cadmium sulfide crystallite core. The crystallite is stabilized by a sheath of peptides of general structure ({gamma}Glu-Cys){sub n}-Gly. The cadmium-peptide complexes of tomato contained predominantly peptides of n{sub 3}, n{sub 4}, and n{sub 5}. Spectroscopic analyses indicated that the tomato cadmium-sulfide-peptide complex contained CdS crystallite core particles smaller than 2.0 nanometers inmore » diameter.« less

Hydraulic effects in a radiative atmosphere with ionization

NASA Astrophysics Data System (ADS)

Bhat, P.; Brandenburg, A.

2016-03-01

Context. In his 1978 paper, Eugene Parker postulated the need for hydraulic downward motion to explain magnetic flux concentrations at the solar surface. A similar process has also recently been seen in simplified (e.g., isothermal) models of flux concentrations from the negative effective magnetic pressure instability (NEMPI). Aims: We study the effects of partial ionization near the radiative surface on the formation of these magnetic flux concentrations. Methods: We first obtain one-dimensional (1D) equilibrium solutions using either a Kramers-like opacity or the H- opacity. The resulting atmospheres are then used as initial conditions in two-dimensional (2D) models where flows are driven by an imposed gradient force that resembles a localized negative pressure in the form of a blob. To isolate the effects of partial ionization and radiation, we ignore turbulence and convection. Results: Because of partial ionization, an unstable stratification always forms near the surface. We show that the extrema in the specific entropy profiles correspond to the extrema in the degree of ionization. In the 2D models without partial ionization, strong flux concentrations form just above the height where the blob is placed. Interestingly, in models with partial ionization, such flux concentrations always form at the surface well above the blob. This is due to the corresponding negative gradient in specific entropy. Owing to the absence of turbulence, the downflows reach transonic speeds. Conclusions: We demonstrate that, together with density stratification, the imposed source of negative pressure drives the formation of flux concentrations. We find that the inclusion of partial ionization affects the entropy profile dramatically, causing strong flux concentrations to form closer to the surface. We speculate that turbulence effects are needed to limit the strength of flux concentrations and homogenize the specific entropy to a stratification that is close to marginal.

Frustration across the periodic table: heterolytic cleavage of dihydrogen by metal complexes.

PubMed

Bullock, R Morris; Chambers, Geoffrey M

2017-08-28

This perspective examines frustrated Lewis pairs (FLPs) in the context of heterolytic cleavage of H 2 by transition metal complexes, with an emphasis on molecular complexes bearing an intramolecular Lewis base. FLPs have traditionally been associated with main group compounds, yet many reactions of transition metal complexes support a broader classification of FLPs that includes certain types of transition metal complexes with reactivity resembling main group-based FLPs. This article surveys transition metal complexes that heterolytically cleave H 2 , which vary in the degree that the Lewis pairs within these systems interact. Many of the examples include complexes bearing a pendant amine functioning as the base with the metal functioning as the hydride acceptor. Consideration of transition metal compounds in the context of FLPs can inspire new innovations and improvements in transition metal catalysis.This article is part of the themed issue 'Frustrated Lewis pair chemistry'. © 2017 The Author(s).

Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota.

PubMed

Cignarella, Francesca; Cantoni, Claudia; Ghezzi, Laura; Salter, Amber; Dorsett, Yair; Chen, Lei; Phillips, Daniel; Weinstock, George M; Fontana, Luigi; Cross, Anne H; Zhou, Yanjiao; Piccio, Laura

2018-06-05

Multiple sclerosis (MS) is more common in western countries with diet being a potential contributing factor. Here we show that intermittent fasting (IF) ameliorated clinical course and pathology of the MS model, experimental autoimmune encephalomyelitis (EAE). IF led to increased gut bacteria richness, enrichment of the Lactobacillaceae, Bacteroidaceae, and Prevotellaceae families and enhanced antioxidative microbial metabolic pathways. IF altered T cells in the gut with a reduction of IL-17 producing T cells and an increase in regulatory T cells. Fecal microbiome transplantation from mice on IF ameliorated EAE in immunized recipient mice on a normal diet, suggesting that IF effects are at least partially mediated by the gut flora. In a pilot clinical trial in MS patients, intermittent energy restriction altered blood adipokines and the gut flora resembling protective changes observed in mice. In conclusion, IF has potent immunomodulatory effects that are at least partially mediated by the gut microbiome. Copyright © 2018 Elsevier Inc. All rights reserved.

The so-called "Spanish model" - tobacco industry strategies and its impact in Europe and Latin America.

PubMed

Schneider, Nick K; Sebrié, Ernesto M; Fernández, Esteve

2011-12-07

To demonstrate the tobacco industry rationale behind the "Spanish model" on non-smokers' protection in hospitality venues and the impact it had on some European and Latin American countries between 2006 and 2011. Tobacco industry documents research triangulated against news and media reports. As an alternative to the successful implementation of 100% smoke-free policies, several European and Latin American countries introduced partial smoking bans based on the so-called "Spanish model", a legal framework widely advocated by parts of the hospitality industry with striking similarities to "accommodation programmes" promoted by the tobacco industry in the late 1990s. These developments started with the implementation of the Spanish tobacco control law (Ley 28/2005) in 2006 and have increased since then. The Spanish experience demonstrates that partial smoking bans often resemble tobacco industry strategies and are used to spread a failed approach on international level. Researchers, advocates and policy makers should be aware of this ineffective policy.

The so-called "Spanish model" - Tobacco industry strategies and its impact in Europe and Latin America

PubMed Central

2011-01-01

Background To demonstrate the tobacco industry rationale behind the "Spanish model" on non-smokers' protection in hospitality venues and the impact it had on some European and Latin American countries between 2006 and 2011. Methods Tobacco industry documents research triangulated against news and media reports. Results As an alternative to the successful implementation of 100% smoke-free policies, several European and Latin American countries introduced partial smoking bans based on the so-called "Spanish model", a legal framework widely advocated by parts of the hospitality industry with striking similarities to "accommodation programmes" promoted by the tobacco industry in the late 1990s. These developments started with the implementation of the Spanish tobacco control law (Ley 28/2005) in 2006 and have increased since then. Conclusion The Spanish experience demonstrates that partial smoking bans often resemble tobacco industry strategies and are used to spread a failed approach on international level. Researchers, advocates and policy makers should be aware of this ineffective policy. PMID:22151884

A novel protein-protein interaction in the RES (REtention and Splicing) complex.

PubMed

Tripsianes, Konstantinos; Friberg, Anders; Barrandon, Charlotte; Brooks, Mark; van Tilbeurgh, Herman; Seraphin, Bertrand; Sattler, Michael

2014-10-10

The retention and splicing (RES) complex is a conserved spliceosome-associated module that was shown to enhance splicing of a subset of transcripts and promote the nuclear retention of unspliced pre-mRNAs in yeast. The heterotrimeric RES complex is organized around the Snu17p protein that binds to both the Bud13p and Pml1p subunits. Snu17p exhibits an RRM domain that resembles a U2AF homology motif (UHM) and Bud13p harbors a Trp residue reminiscent of an UHM-ligand motif (ULM). It has therefore been proposed that the interaction between Snu17p and Bud13p resembles canonical UHM-ULM complexes. Here, we have used biochemical and NMR structural analysis to characterize the structure of the yeast Snu17p-Bud13p complex. Unlike known UHMs that sequester the Trp residue of the ULM ligand in a hydrophobic pocket, Snu17p and Bud13p utilize a large interaction surface formed around the two helices of the Snu17p domain. In total 18 residues of the Bud13p ligand wrap around the Snu17p helical surface in an U-turn-like arrangement. The invariant Trp(232) in Bud13p is located in the center of the turn, and contacts surface residues of Snu17p. The structural data are supported by mutational analysis and indicate that Snu17p provides an extended binding surface with Bud13p that is notably distinct from canonical UHM-ULM interactions. Our data highlight structural diversity in RRM-protein interactions, analogous to the one seen for nucleic acid interactions. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Predatory Dinosaurs from the Sahara and Late Cretaceous Faunal Differentiation

PubMed

Sereno; Dutheil; Iarochene; Larsson; Lyon; Magwene; Sidor; Varricchio; Wilson

1996-05-17

Late Cretaceous (Cenomanian) fossils discovered in the Kem Kem region of Morocco include large predatory dinosaurs that inhabited Africa as it drifted into geographic isolation. One, represented by a skull approximately 1.6 meters in length, is an advanced allosauroid referable to the African genus Carcharodontosaurus. Another, represented by a partial skeleton with slender proportions, is a new basal coelurosaur closely resembling the Egyptian genus Bahariasaurus. Comparisons with Cretaceous theropods from other continents reveal a previously unrecognized global radiation of carcharodontosaurid predators. Substantial geographic differentiation of dinosaurian faunas in response to continental drift appears to have arisen abruptly at the beginning of the Late Cretaceous.

Wetting and spreading at the molecular scale

NASA Technical Reports Server (NTRS)

Koplik, Joel; Banavar, Jayanth R.

1994-01-01

We have studied the microscopic aspects of the spreading of liquid drops on a solid surface by molecular dynamics simulations of coexisting three-phase Lennard-Jones systems of liquid, vapor and solid. We consider both spherically symmetric atoms and chain-like molecules, and a range of interaction strengths. As the attraction between liquid and solid increases we observed a smooth transition in spreading regimes, from partial to complete to terraced wetting. In the terraced case, where distinct monomolecular layers spread with different velocities, the layers are ordered but not solid, with qualitative behavior resembling recent experimental findings, but with interesting differences in the spreading rate.

Asymmetric peer selections among Blacks, Asians, and Whites in a virtual environment: Preliminary evidence for triangulated threat theory.

PubMed

Tawa, John

2017-01-01

Black, Asian, and White participants (N = 210) created self-resembling avatars and engaged in peer-selection tasks during social events in the virtual world, Second Life, that were designed to simulate various types of resource competition. Participants in merit-based resource competition settings had less diversity in their peer groups compared to participants in settings where no resource competition was present, and Asian participants had lower preference for Black peers. Furthermore, these relationships were mediated by out-group discomfort. Results are discussed in relation to partial support for triangulated threat theory of group relations among Blacks, Asians, and Whites.

Patterns of human local cerebral glucose metabolism during epileptic seizures

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

Engel, J. Jr.; Kuhl, D.E.; Phelps, M.E.

1982-10-01

Ictal patterns of local cerebral metabolic rate have been studied in epileptic patients by positron computed tomography with /sup 18/F-labeled 2-fluoro-2-deoxy-D-glucose. Partial seizures were associated with activation of anatomic structures unique to each patient studied. Ictal increases and decreases in local cerebral metabolism were observed. Scans performed during generalized convulsions induced by electroshock demonstrated a diffuse ictal increase and postictal decrease in cerebral metabolism. Petit mal absences were associated with a diffuse increase in cerebral metabolic rate. The ictal fluorodeoxyglucose patterns obtained from patients do not resemble autoradiographic patterns obtained from common experimental animal models of epilepsy.

Application of a disturbance-rejection controller for robotic-enhanced limb rehabilitation trainings.

PubMed

Madoński, R; Kordasz, M; Sauer, P

2014-07-01

The paper presents an application of a special case of an Active Disturbance Rejection Controller (ADRC) in governing a proper realization of basic limb rehabilitation trainings. The experimental study is performed on a model of a flexible joint manipulator, whose behavior resembles a real robotic rehabilitation device. The multidimensional character of the considered assisting mechanism makes it a nontrivial modeling and control problem. However, by the use of the ADRC approach, the modeling uncertainty in the plant is partially decoupled from the system, which increases the robustness of the whole control framework against both internal and external disturbances. © 2013 ISA. Published by ISA. All rights reserved.

An Individual-Oriented Model on the Emergence of Support in Fights, Its Reciprocation and Exchange

PubMed Central

Hemelrijk, Charlotte K.; Puga-Gonzalez, Ivan

2012-01-01

Complex social behaviour of primates has usually been attributed to the operation of complex cognition. Recently, models have shown that constraints imposed by the socio-spatial structuring of individuals in a group may result in an unexpectedly high number of patterns of complex social behaviour, resembling the dominance styles of egalitarian and despotic species of macaques and the differences between them. This includes affiliative patterns, such as reciprocation of grooming, grooming up the hierarchy, and reconciliation. In the present study, we show that the distribution of support in fights, which is the social behaviour that is potentially most sophisticated in terms of cognitive processes, may emerge in the same way. The model represents the spatial grouping of individuals and their social behaviour, such as their avoidance of risks during attacks, the self-reinforcing effects of winning and losing their fights, their tendency to join in fights of others that are close by (social facilitation), their tendency to groom when they are anxious, the reduction of their anxiety by grooming, and the increase of anxiety when involved in aggression. Further, we represent the difference in intensity of aggression apparent in egalitarian and despotic macaques. The model reproduces many aspects of support in fights, such as its different types, namely, conservative, bridging and revolutionary, patterns of choice of coalition partners attributed to triadic awareness, those of reciprocation of support and ‘spiteful acts’ and of exchange between support and grooming. This work is important because it suggests that behaviour that seems to result from sophisticated cognition may be a side-effect of spatial structure and dominance interactions and it shows that partial correlations fail to completely omit these effects of spatial structure. Further, the model is falsifiable, since it results in many patterns that can easily be tested in real primates by means of existing data. PMID:22666348

H-atom addition and abstraction reactions in mixed CO, H2CO and CH3OH ices - an extended view on complex organic molecule formation

NASA Astrophysics Data System (ADS)

Chuang, K.-J.; Fedoseev, G.; Ioppolo, S.; van Dishoeck, E. F.; Linnartz, H.

2016-01-01

Complex organic molecules (COMs) have been observed not only in the hot cores surrounding low- and high-mass protostars, but also in cold dark clouds. Therefore, it is interesting to understand how such species can be formed without the presence of embedded energy sources. We present new laboratory experiments on the low-temperature solid state formation of three complex molecules - methyl formate (HC(O)OCH3), glycolaldehyde (HC(O)CH2OH) and ethylene glycol (H2C(OH)CH2OH) - through recombination of free radicals formed via H-atom addition and abstraction reactions at different stages in the CO→H2CO→CH3OH hydrogenation network at 15 K. The experiments extend previous CO hydrogenation studies and aim at resembling the physical-chemical conditions typical of the CO freeze-out stage in dark molecular clouds, when H2CO and CH3OH form by recombination of accreting CO molecules and H-atoms on ice grains. We confirm that H2CO, once formed through CO hydrogenation, not only yields CH3OH through ongoing H-atom addition reactions, but is also subject to H-atom-induced abstraction reactions, yielding CO again. In a similar way, H2CO is also formed in abstraction reactions involving CH3OH. The dominant methanol H-atom abstraction product is expected to be CH2OH, while H-atom additions to H2CO should at least partially proceed through CH3O intermediate radicals. The occurrence of H-atom abstraction reactions in ice mantles leads to more reactive intermediates (HCO, CH3O and CH2OH) than previously thought, when assuming sequential H-atom addition reactions only. This enhances the probability to form COMs through radical-radical recombination without the need of UV photolysis or cosmic rays as external triggers.

Auditing complex concepts of SNOMED using a refined hierarchical abstraction network.

PubMed

Wang, Yue; Halper, Michael; Wei, Duo; Gu, Huanying; Perl, Yehoshua; Xu, Junchuan; Elhanan, Gai; Chen, Yan; Spackman, Kent A; Case, James T; Hripcsak, George

2012-02-01

Auditors of a large terminology, such as SNOMED CT, face a daunting challenge. To aid them in their efforts, it is essential to devise techniques that can automatically identify concepts warranting special attention. "Complex" concepts, which by their very nature are more difficult to model, fall neatly into this category. A special kind of grouping, called a partial-area, is utilized in the characterization of complex concepts. In particular, the complex concepts that are the focus of this work are those appearing in intersections of multiple partial-areas and are thus referred to as overlapping concepts. In a companion paper, an automatic methodology for identifying and partitioning the entire collection of overlapping concepts into disjoint, singly-rooted groups, that are more manageable to work with and comprehend, has been presented. The partitioning methodology formed the foundation for the development of an abstraction network for the overlapping concepts called a disjoint partial-area taxonomy. This new disjoint partial-area taxonomy offers a collection of semantically uniform partial-areas and is exploited herein as the basis for a novel auditing methodology. The review of the overlapping concepts is done in a top-down order within semantically uniform groups. These groups are themselves reviewed in a top-down order, which proceeds from the less complex to the more complex overlapping concepts. The results of applying the methodology to SNOMED's Specimen hierarchy are presented. Hypotheses regarding error ratios for overlapping concepts and between different kinds of overlapping concepts are formulated. Two phases of auditing the Specimen hierarchy for two releases of SNOMED are reported on. With the use of the double bootstrap and Fisher's exact test (two-tailed), the auditing of concepts and especially roots of overlapping partial-areas is shown to yield a statistically significant higher proportion of errors. Copyright © 2011 Elsevier Inc. All rights reserved.

Homologies between the amino acid sequences of some vertebrate peptide hormones and peptides isolated from invertebrate sources.

PubMed

De Loof, A; Schoofs, L

1990-01-01

1. The 4K-prothoracicotropic hormone (PTTH) or bombyxin and the melanization-reddish coloration hormone of the silkworm Bombyx mori resemble insulin and insulin-like growth factors. 2. The family of adipokinetic/red pigment concentrating hormones has some similarity with glucagon. 3. Members of the FMRFamide family are found in vertebrates as well as in invertebrates. 4. In Locusta, a molecule immunologically and biologically related to amphibian melanophore stimulating hormone has been partially characterized. 5. Enkephalins and enkephalin-related peptides occur in insects and other invertebrates. 6. Peptides belonging to the tachykinin family have been isolated from molluscan (Octopus) salivary glands and from insect nervous tissue (Locusta migratoria). 7. Invertebrate arginine-vasotocin homologs have been isolated from an insect (Locusta migratoria) and from a mollusc (Conus). 8. In Leucophaea, Locusta and Drosophila, peptides resembling those of the vertebrate gastrin/cholecystokinin family have been identified. 9. As the number of different neuro-/gut peptides with possible function(s) as hormone, neurotransmitter or neuromodulator is now estimated to be of the order of a few hundred, more similarities will probably show up in the near future.

Cassandra retrotransposons carry independently transcribed 5S RNA

PubMed Central

Kalendar, Ruslan; Tanskanen, Jaakko; Chang, Wei; Antonius, Kristiina; Sela, Hanan; Peleg, Ofer; Schulman, Alan H.

2008-01-01

We report a group of TRIMs (terminal-repeat retrotransposons in miniature), which are small nonautonomous retrotransposons. These elements, named Cassandra, universally carry conserved 5S RNA sequences and associated RNA polymerase (pol) III promoters and terminators in their long terminal repeats (LTRs). They were found in all vascular plants investigated. Uniquely for LTR retrotransposons, Cassandra produces noncapped, polyadenylated transcripts from the 5S pol III promoter. Capped, read-through transcripts containing Cassandra sequences can also be detected in RNA and in EST databases. The predicted Cassandra RNA 5S secondary structures resemble those for cellular 5S rRNA, with high information content specifically in the pol III promoter region. Genic integration sites are common for Cassandra, an unusual feature for abundant retrotransposons. The 5S in each LTR produces a tandem 5S arrangement with an inter-5S spacing resembling that of cellular 5S. The distribution of 5S genes is very variable in flowering plants and may be partially explained by Cassandra activity. Cassandra thus appears both to have adapted a ubiquitous cellular gene for ribosomal RNA for use as a promoter and to parasitize an as-yet-unidentified group of retrotransposons for the proteins needed in its lifecycle. PMID:18408163

Using instrumental variables to estimate a Cox's proportional hazards regression subject to additive confounding

PubMed Central

Tosteson, Tor D.; Morden, Nancy E.; Stukel, Therese A.; O'Malley, A. James

2014-01-01

The estimation of treatment effects is one of the primary goals of statistics in medicine. Estimation based on observational studies is subject to confounding. Statistical methods for controlling bias due to confounding include regression adjustment, propensity scores and inverse probability weighted estimators. These methods require that all confounders are recorded in the data. The method of instrumental variables (IVs) can eliminate bias in observational studies even in the absence of information on confounders. We propose a method for integrating IVs within the framework of Cox's proportional hazards model and demonstrate the conditions under which it recovers the causal effect of treatment. The methodology is based on the approximate orthogonality of an instrument with unobserved confounders among those at risk. We derive an estimator as the solution to an estimating equation that resembles the score equation of the partial likelihood in much the same way as the traditional IV estimator resembles the normal equations. To justify this IV estimator for a Cox model we perform simulations to evaluate its operating characteristics. Finally, we apply the estimator to an observational study of the effect of coronary catheterization on survival. PMID:25506259

Using instrumental variables to estimate a Cox's proportional hazards regression subject to additive confounding.

PubMed

MacKenzie, Todd A; Tosteson, Tor D; Morden, Nancy E; Stukel, Therese A; O'Malley, A James

2014-06-01

The estimation of treatment effects is one of the primary goals of statistics in medicine. Estimation based on observational studies is subject to confounding. Statistical methods for controlling bias due to confounding include regression adjustment, propensity scores and inverse probability weighted estimators. These methods require that all confounders are recorded in the data. The method of instrumental variables (IVs) can eliminate bias in observational studies even in the absence of information on confounders. We propose a method for integrating IVs within the framework of Cox's proportional hazards model and demonstrate the conditions under which it recovers the causal effect of treatment. The methodology is based on the approximate orthogonality of an instrument with unobserved confounders among those at risk. We derive an estimator as the solution to an estimating equation that resembles the score equation of the partial likelihood in much the same way as the traditional IV estimator resembles the normal equations. To justify this IV estimator for a Cox model we perform simulations to evaluate its operating characteristics. Finally, we apply the estimator to an observational study of the effect of coronary catheterization on survival.

Human endomembrane H+ pump strongly resembles the ATP-synthetase of Archaebacteria.

PubMed Central

Südhof, T C; Fried, V A; Stone, D K; Johnston, P A; Xie, X S

1989-01-01

Preparations of mammalian H+ pumps that acidify intracellular vesicles contain eight or nine polypeptides, ranging in size from 116 to 17 kDa. Biochemical analysis indicates that the 70- and 58-kDa polypeptides are subunits critical for ATP hydrolysis. The amino acid sequences of the major catalytic subunits (58 and 70 kDa) of the endomembrane H+ pump are unknown from animal cells. We report here the complete sequence of the 58-kDa subunit derived from a human kidney cDNA clone and partial sequences of the 70- and 58-kDa subunits purified from clathrin-coated vesicles of bovine brain. The amino acid sequences of both proteins strongly resemble the sequences of the corresponding subunits of the vacuolar H+ pumps of Archaebacteria, plants, and fungi. The archaebacterial enzyme is believed to use a H+ gradient to synthesize ATP. Thus, a common ancestral protein has given rise to a H+ pump that synthesizes ATP in one organism and hydrolyzes it in another and is highly conserved from prokaryotes to humans. The same pump appears to mediate the acidification of intracellular organelles, including coated vesicles, lysosomes, and secretory granules, as well as extracellular fluids such as urine. PMID:2527371

Intrinsically Disordered Energy Landscapes

PubMed Central

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

2015-01-01

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

Primary Follicular Dystrophy with Scarring Dermatitis in C57BL/6 Mouse Substrains Resembles Central Centrifugal Cicatricial Alopecia in Humans

PubMed Central

Sundberg, John P.; Taylor, Douglas; Lorch, Gwendolen; Miller, Jim; Silva, Kathleen A.; Sundberg, Beth A.; Roopenian, Derry; Sperling, Leonard; Ong, David; King, Lloyd E.; Everts, Helen

2011-01-01

A number of C57BL/6 (B6) substrains are commonly used by scientists for basic biomedical research. One of several B6 strain specific background diseases is focal alopecia that may resolve or progress to severe, ulcerative dermatitis. Clinical and progressive histologic changes of skin disease commonly observed in C57BL/6J and preliminary studies in other closely related substrains are presented. Lesions develop due to a primary follicular dystrophy with rupture of severely affected follicles leading to formation of secondary foreign body granulomas (trichogranulomas) in affected B6 substrains of mice. Histologically these changes resemble the human disease called central centrifugal cicatrical alopecia (CCCA). Four B6 substrains tested have a polymorphism in alcohol dehydrogenase 4 (Adh4) that reduces its activity and potentially affects removal of excess retinol. Using immunohistochemistry, differential expression of epithelial retinol dehydrogenase (DHRS9) was detected which may partially explain anecdotal reports of frequency differences between B6 substrains. The combination of these two defects have the potential to make high dietary vitamin A levels toxic in some B6 substrains while not affecting most other commonly used inbred strains. PMID:20861494

Immunolocalization of a Histidine-Rich Epidermal Differentiation Protein in the Chicken Supports the Hypothesis of an Evolutionary Developmental Link between the Embryonic Subperiderm and Feather Barbs and Barbules

PubMed Central

Alibardi, Lorenzo; Holthaus, Karin Brigit; Sukseree, Supawadee; Hermann, Marcela; Tschachler, Erwin

2016-01-01

The morphogenesis of feathers is a complex process that depends on a tight spatiotemporal regulation of gene expression and assembly of the protein components of mature feathers. Recent comparative genomics and gene transcription studies have indicated that genes within the epidermal differentiation complex (EDC) encode numerous structural proteins of cornifying skin cells in amniotes including birds. Here, we determined the localization of one of these proteins, termed EDMTFH (Epidermal Differentiation Protein starting with a MTF motif and rich in Histidine), which belongs to a group of EDC-encoded proteins rich in aromatic amino acid residues. We raised an antibody against an EDMTFH-specific epitope and performed immunohistochemical investigations by light microscopy and immunogold labeling by electron microscopy of chicken embryos at days 14–18 of development. EDMTFH was specifically present in the subperiderm, a transient layer of the embryonic epidermis, and in barbs and barbules of feathers. In the latter, it partially localized to bundles of so-called feather beta-keratins (corneous beta-proteins, CBPs). Cells of the embryonic periderm, the epidermis proper, and the feather sheath were immunonegative for EDMTFH. The results of this study indicate that EDMTFH may contribute to the unique mechanical properties of feathers and define EDMTFH as a common marker of the subperiderm and the feather barbules. This expression pattern of EDMTFH resembles that of epidermal differentiation cysteine-rich protein (EDCRP) and feather CBPs and is in accordance with the hypothesis that a major part of the cyclically regenerating feather follicle is topologically, developmentally and evolutionarily related to the embryonic subperiderm. PMID:27936131

Academic Achievement and Behavioral Ratings in Children with Absence and Complex Partial Epilepsy.

ERIC Educational Resources Information Center

Williams, Jane; And Others

1996-01-01

Assessment of 84 children diagnosed with controlled or uncontrolled complex partial or absence seizures but no documented learning or emotional disorders found no influence of seizure type on achievement test scores or behavioral ratings. A main effect was found for degree of control, with poorly controlled seizures correlating with lower reading…

Autism in Two Females with Duplications Involving Xp11.22-p11.23

ERIC Educational Resources Information Center

Edens, Anna C.; Lyons, Michael J.; Duron, Reyna M.; DuPont, Barbara R.; Holden, Kenton R.

2011-01-01

We present two phenotypically similar females with Xp duplication who have autism and epilepsy. Case 1 is a 14-year-old Honduran female with autism and medically refractory complex partial, secondarily generalized epilepsy. Case 2 is a 3-year-old Austrian female with autism and medically refractory complex partial epilepsy. Both patients also…

Mathematical Methods for Physics and Engineering Third Edition Paperback Set

NASA Astrophysics Data System (ADS)

Riley, Ken F.; Hobson, Mike P.; Bence, Stephen J.

2006-06-01

Prefaces; 1. Preliminary algebra; 2. Preliminary calculus; 3. Complex numbers and hyperbolic functions; 4. Series and limits; 5. Partial differentiation; 6. Multiple integrals; 7. Vector algebra; 8. Matrices and vector spaces; 9. Normal modes; 10. Vector calculus; 11. Line, surface and volume integrals; 12. Fourier series; 13. Integral transforms; 14. First-order ordinary differential equations; 15. Higher-order ordinary differential equations; 16. Series solutions of ordinary differential equations; 17. Eigenfunction methods for differential equations; 18. Special functions; 19. Quantum operators; 20. Partial differential equations: general and particular; 21. Partial differential equations: separation of variables; 22. Calculus of variations; 23. Integral equations; 24. Complex variables; 25. Application of complex variables; 26. Tensors; 27. Numerical methods; 28. Group theory; 29. Representation theory; 30. Probability; 31. Statistics; Index.

Possible induction of West syndrome by oxcarbazepine therapy in a patient with complex partial seizures.

PubMed

Veerapandiyan, Aravindhan; Singh, Piyush; Mikati, Mohamad A

2012-03-01

Oxcarbazepine has been reported to precipitate myoclonic, generalised tonic-clonic, absence, and complex partial seizures, and carbamazepine to precipitate absences, myoclonic seizures and spasms. Here, we report a one-year, six-month-old girl with complex partial seizures who developed infantile spasms, developmental regression, and hypsarrhythmia during the two weeks directly following initiation of oxcarbazepine (14 mg/kg/day). All of these resolved within a few days after discontinuation of this medication. Although we cannot rule out that the above association may have been coincidental, or that the improvement may have been due to concurrent therapy, this case raises the possibility that oxcarbazepine, like carbamazepine, may precipitate infantile spasms and West syndrome.

Scombroid poisoning.

PubMed

Lange, W R

1988-04-01

The symptoms of scombroid poisoning resemble an acute allergic reaction. Tuna, albacore, mackerel and bonito are implicated, as are nonscombroid fish such as mahi-mahi and bluefish. The histamine content of affected fish is high, but the pathophysiology is more complex than the mere ingestion of histamine. Antihistamines and cimetidine appear to be effective in controlling symptoms. Prevention consists of prompt and adequate refrigeration of dark-meated fish.

Isotopic characteristics of simulated meteoritic organic matter. I - Kerogen-like material

NASA Technical Reports Server (NTRS)

Kerridge, John F.; Mariner, Ruth; Flores, Jose; Chang, Sherwood

1989-01-01

Carbonaceous residues from a variety of laboratory syntheses yield release patterns for C and H isotopes during stepwise combustion that fail to mimic the striking patterns characteristic of meteoritic kerogen-like residues that otherwise superficially resemble them. It seems likely that the meteoritic material comprises a complex mixture of substances having different origins and/or synthesis conditions.

Representing and Enacting Movement: The Body as an Instructional Resource in a Simulator-Based Environment

ERIC Educational Resources Information Center

Sellberg, Charlott

2017-01-01

Simulators are used to practice in a safe setting before training in a safety-critical environment. Since the nature of situations encountered in high-risk domains is complex and dynamic, it is considered important for the simulation to resemble conditions of real world tasks. For this reason, simulation-based training is often discussed in terms…

[Generation of Superoxide Radicals by Complex III in Heart Mitochondria and Antioxidant Effect of Dinitrosyl Iron Complexes at Different Partial Pressure of Oxygen].

PubMed

Dudylina, A L; Ivanova, M V; Shumaev, K B; Ruuge, E K

2016-01-01

The EPR spin-trapping technique and EPR-oximetry were used to study generation of superoxide radicals in heart mitochondria isolated from Wistar rats under conditions of variable oxygen concentration. Lithium phthalocyanine and TEMPONE-15N-D16 were chosen to determine oxygen content in a gas-permeable capillary tube containing mitochondria. TIRON was used as a spin trap. We investigated the influence of different oxygen concentrations in incubation mixture and demonstrated that heart mitochondria can generate superoxide in complex III at different partial pressure of oxygen as well as under the conditions of deep hypoxia (< 5% O2). Dinitrosyl iron complexes with glutathione (the pharmaceutical drug "Oxacom") exerted an antioxidant effect, regardless of the value of the partial pressure of oxygen, but the magnitude and kinetic characteristics of the effect depended on the concentration of the drug.

Active-State Model of a Dopamine D2 Receptor - Gαi Complex Stabilized by Aripiprazole-Type Partial Agonists

PubMed Central

Kling, Ralf C.; Tschammer, Nuska; Lanig, Harald; Clark, Timothy; Gmeiner, Peter

2014-01-01

Partial agonists exhibit a submaximal capacity to enhance the coupling of one receptor to an intracellular binding partner. Although a multitude of studies have reported different ligand-specific conformations for a given receptor, little is known about the mechanism by which different receptor conformations are connected to the capacity to activate the coupling to G-proteins. We have now performed molecular-dynamics simulations employing our recently described active-state homology model of the dopamine D2 receptor-Gαi protein-complex coupled to the partial agonists aripiprazole and FAUC350, in order to understand the structural determinants of partial agonism better. We have compared our findings with our model of the D2R-Gαi-complex in the presence of the full agonist dopamine. The two partial agonists are capable of inducing different conformations of important structural motifs, including the extracellular loop regions, the binding pocket and, in particular, intracellular G-protein-binding domains. As G-protein-coupling to certain intracellular epitopes of the receptor is considered the key step of allosterically triggered nucleotide-exchange, it is tempting to assume that impaired coupling between the receptor and the G-protein caused by distinct ligand-specific conformations is a major determinant of partial agonist efficacy. PMID:24932547

Loss of 'complexity' and aging. Potential applications of fractals and chaos theory to senescence

NASA Technical Reports Server (NTRS)

Lipsitz, L. A.; Goldberger, A. L.

1992-01-01

The concept of "complexity," derived from the field of nonlinear dynamics, can be adapted to measure the output of physiologic processes that generate highly variable fluctuations resembling "chaos." We review data suggesting that physiologic aging is associated with a generalized loss of such complexity in the dynamics of healthy organ system function and hypothesize that such loss of complexity leads to an impaired ability to adapt to physiologic stress. This hypothesis is supported by observations showing an age-related loss of complex variability in multiple physiologic processes including cardiovascular control, pulsatile hormone release, and electroencephalographic potentials. If further research supports this hypothesis, measures of complexity based on chaos theory and the related geometric concept of fractals may provide new ways to monitor senescence and test the efficacy of specific interventions to modify the age-related decline in adaptive capacity.

Data-based discharge extrapolation: estimating annual discharge for a partially gauged large river basin from its small sub-basins

NASA Astrophysics Data System (ADS)

Gong, L.

2013-12-01

Large-scale hydrological models and land surface models are by far the only tools for accessing future water resources in climate change impact studies. Those models estimate discharge with large uncertainties, due to the complex interaction between climate and hydrology, the limited quality and availability of data, as well as model uncertainties. A new purely data-based scale-extrapolation method is proposed, to estimate water resources for a large basin solely from selected small sub-basins, which are typically two-orders-of-magnitude smaller than the large basin. Those small sub-basins contain sufficient information, not only on climate and land surface, but also on hydrological characteristics for the large basin In the Baltic Sea drainage basin, best discharge estimation for the gauged area was achieved with sub-basins that cover 2-4% of the gauged area. There exist multiple sets of sub-basins that resemble the climate and hydrology of the basin equally well. Those multiple sets estimate annual discharge for gauged area consistently well with 5% average error. The scale-extrapolation method is completely data-based; therefore it does not force any modelling error into the prediction. The multiple predictions are expected to bracket the inherent variations and uncertainties of the climate and hydrology of the basin. The method can be applied in both un-gauged basins and un-gauged periods with uncertainty estimation.

Purification, partial characterization and role in lipid transport to developing oocytes of a novel lipophorin from the cowpea weevil, Callosobruchus maculatus.

PubMed

Ximenes, A A; Oliveira, G A; Bittencourt-Cunha, P; Tomokyo, M; Leite, D B; Folly, E; Golodne, D M; Atella, G C

2008-01-01

Lipid transport in arthropods is achieved by highly specialized lipoproteins, which resemble those described in vertebrate blood. Here we describe purification and characterization of the lipid-apolipoprotein complex, lipophorin (Lp), from adults and larvae of the cowpea weevil Callosobruchus maculatus. We also describe the Lp-mediated lipid transfer to developing oocytes. Lps were isolated from homogenates of C. maculatus larvae and adults by potassio bromide gradient and characterized with respect to physicochemical properties and lipid content. The weevil Lp (465 kDa) and larval Lp (585 kDa), with hydrated densities of 1.22 and 1.14 g/mL, contained 34 and 56% lipids and 9 and 7% carbohydrates, respectively. In both Lps, mannose was the predominant monosaccharide detected by paper chromatography. SDS-PAGE revealed two apolipoproteins in each Lp with molecular masses of 225 kDa (apolipoprotein-I) and 79 kDa (apolipoprotein-II). The lipids were extracted and analyzed by thin-layer chromatography. The major phospholipids found were phosphatidylserine, phosphatidylcholine and phosphatidylethanolamine in adult Lp, and phosphatidylcholine, phosphatidylethanolamine and sphingomyelin in larval Lp. Hydrocarbons, fatty acids and triacylglycerol were the major neutral lipids found in both Lps. Lps labeled in the protein moiety with radioactive iodine (125I-iodine) or in the lipid moiety with fluorescent lipids revealed direct evidence of endocytic uptake of Lps in live oocytes of C. maculatus.

Sleep, Torpor and Memory Impairment

NASA Astrophysics Data System (ADS)

Palchykova, S.; Tobler, I.

It is now well known that daily torpor induces a sleep deficit. Djungarian hamsters emerging from this hypometabolic state spend most of the time in sleep. This sleep is characterized by high initial values of EEG slow-wave activity (SWA) that monotonically decline during recovery sleep. These features resemble the changes seen in numerous species during recovery after prolonged wakefulness or sleep deprivation (SD). When hamsters are totally or partially sleep deprived immediately after emerging from torpor, an additional increase in SWA can be induced. It has been therefore postulated, that these slow- waves are homeostatically regulated, as predicted by the two-process model of sleep regulation, and that during daily torpor a sleep deficit is accumulated as it is during prolonged waking. The predominance of SWA in the frontal EEG observed both after SD and daily torpor provides further evidence for the similarity of these conditions. It has been shown in several animal and human studies that sleep can enhance memory consolidation, and that SD leads to memory impairment. Preliminary data obtained in the Djungarian hamster showed that both SD and daily torpor result in object recognition deficits. Thus, animals subjected to SD immediately after learning, or if they underwent an episode of daily torpor between learning and retention, displayed impaired recognition memory for complex object scenes. The investigation of daily torpor can reveal mechanisms that could have important implications for hypometabolic state induction in other mammalian species, including humans.

A structural basis for the regulatory inactivation of DnaA.

PubMed

Xu, Qingping; McMullan, Daniel; Abdubek, Polat; Astakhova, Tamara; Carlton, Dennis; Chen, Connie; Chiu, Hsiu-Ju; Clayton, Thomas; Das, Debanu; Deller, Marc C; Duan, Lian; Elsliger, Marc-Andre; Feuerhelm, Julie; Hale, Joanna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K; Johnson, Hope A; Klock, Heath E; Knuth, Mark W; Kozbial, Piotr; Sri Krishna, S; Kumar, Abhinav; Marciano, David; Miller, Mitchell D; Morse, Andrew T; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L; Sefcovic, Natasha; Trame, Christine; van den Bedem, Henry; Weekes, Dana; Hodgson, Keith O; Wooley, John; Deacon, Ashley M; Godzik, Adam; Lesley, Scott A; Wilson, Ian A

2009-01-16

Regulatory inactivation of DnaA is dependent on Hda (homologous to DnaA), a protein homologous to the AAA+ (ATPases associated with diverse cellular activities) ATPase region of the replication initiator DnaA. When bound to the sliding clamp loaded onto duplex DNA, Hda can stimulate the transformation of active DnaA-ATP into inactive DnaA-ADP. The crystal structure of Hda from Shewanella amazonensis SB2B at 1.75 A resolution reveals that Hda resembles typical AAA+ ATPases. The arrangement of the two subdomains in Hda (residues 1-174 and 175-241) differs dramatically from that of DnaA. A CDP molecule anchors the Hda domains in a conformation that promotes dimer formation. The Hda dimer adopts a novel oligomeric assembly for AAA+ proteins in which the arginine finger, crucial for ATP hydrolysis, is fully exposed and available to hydrolyze DnaA-ATP through a typical AAA+ type of mechanism. The sliding clamp binding motifs at the N-terminus of each Hda monomer are partially buried and combine to form an antiparallel beta-sheet at the dimer interface. The inaccessibility of the clamp binding motifs in the CDP-bound structure of Hda suggests that conformational changes are required for Hda to form a functional complex with the clamp. Thus, the CDP-bound Hda dimer likely represents an inactive form of Hda.

Modeling ligand recognition at the P2Y12 receptor in light of X-ray structural information

NASA Astrophysics Data System (ADS)

Paoletta, Silvia; Sabbadin, Davide; von Kügelgen, Ivar; Hinz, Sonja; Katritch, Vsevolod; Hoffmann, Kristina; Abdelrahman, Aliaa; Straßburger, Jens; Baqi, Younis; Zhao, Qiang; Stevens, Raymond C.; Moro, Stefano; Müller, Christa E.; Jacobson, Kenneth A.

2015-08-01

The G protein-coupled P2Y12 receptor (P2Y12R) is an important antithrombotic target and of great interest for pharmaceutical discovery. Its recently solved, highly divergent crystallographic structures in complex either with nucleotides (full or partial agonist) or with a nonnucleotide antagonist raise the question of which structure is more useful to understand ligand recognition. Therefore, we performed extensive molecular modeling studies based on these structures and mutagenesis, to predict the binding modes of major classes of P2Y12R ligands previously reported. Various nucleotide derivatives docked readily to the agonist-bound P2Y12R, but uncharged nucleotide-like antagonist ticagrelor required a hybrid receptor resembling the agonist-bound P2Y12R except for the top portion of TM6. Supervised molecular dynamics (SuMD) of ticagrelor binding indicated interactions with the extracellular regions of P2Y12R, defining possible meta-binding sites. Ureas, sulfonylureas, sulfonamides, anthraquinones and glutamic acid piperazines docked readily to the antagonist-bound P2Y12R. Docking dinucleotides at both agonist- and antagonist-bound structures suggested interactions with two P2Y12R pockets. Thus, our structure-based approach consistently rationalized the main structure-activity relationships within each ligand class, giving useful information for designing improved ligands.

Two-photon excitation spectroscopy of carotenoid-containing and carotenoid-depleted LH2 complexes from purple bacteria.

PubMed

Stepanenko, Ilya; Kompanetz, Viktor; Makhneva, Zoya; Chekalin, Sergey; Moskalenko, Andrei; Razjivin, Andrei

2009-08-27

We applied two-photon fluorescence excitation spectroscopy to LH2 complex from purple bacteria Allochromatium minutissimum and Rhodobacter sphaeroides . Bacteriochlorophyll fluorescence was measured under two-photon excitation of the samples within the 1200-1500 nm region. Spectra were obtained for both carotenoid-containing and -depleted complexes of each bacterium to allow their direct comparison. The depletion of carotenoids did not alter the two-photon excitation spectra of either bacteria. The spectra featured a wide excitation band around 1350 nm (2x675 nm, 14,800 cm(-1)) which strongly resembled two-photon fluorescence excitation spectra of similar complexes published by other authors. We consider obtained experimental data to be evidence of direct two-photon excitation of bacteriochlorophyll excitonic states in this spectral region.

NonMarkov Ito Processes with 1- state memory

NASA Astrophysics Data System (ADS)

McCauley, Joseph L.

2010-08-01

A Markov process, by definition, cannot depend on any previous state other than the last observed state. An Ito process implies the Fokker-Planck and Kolmogorov backward time partial differential eqns. for transition densities, which in turn imply the Chapman-Kolmogorov eqn., but without requiring the Markov condition. We present a class of Ito process superficially resembling Markov processes, but with 1-state memory. In finance, such processes would obey the efficient market hypothesis up through the level of pair correlations. These stochastic processes have been mislabeled in recent literature as 'nonlinear Markov processes'. Inspired by Doob and Feller, who pointed out that the ChapmanKolmogorov eqn. is not restricted to Markov processes, we exhibit a Gaussian Ito transition density with 1-state memory in the drift coefficient that satisfies both of Kolmogorov's partial differential eqns. and also the Chapman-Kolmogorov eqn. In addition, we show that three of the examples from McKean's seminal 1966 paper are also nonMarkov Ito processes. Last, we show that the transition density of the generalized Black-Scholes type partial differential eqn. describes a martingale, and satisfies the ChapmanKolmogorov eqn. This leads to the shortest-known proof that the Green function of the Black-Scholes eqn. with variable diffusion coefficient provides the so-called martingale measure of option pricing.

Electrospun Fibrous Scaffolds for Tissue Engineering: Viewpoints on Architecture and Fabrication.

PubMed

Jun, Indong; Han, Hyung-Seop; Edwards, James R; Jeon, Hojeong

2018-03-06

Electrospinning has been used for the fabrication of extracellular matrix (ECM)-mimicking fibrous scaffolds for several decades. Electrospun fibrous scaffolds provide nanoscale/microscale fibrous structures with interconnecting pores, resembling natural ECM in tissues, and showing a high potential to facilitate the formation of artificial functional tissues. In this review, we summarize the fundamental principles of electrospinning processes for generating complex fibrous scaffold geometries that are similar in structural complexity to the ECM of living tissues. Moreover, several approaches for the formation of three-dimensional fibrous scaffolds arranged in hierarchical structures for tissue engineering are also presented.

Emerging properties of financial time series in the ``Game of Life''

NASA Astrophysics Data System (ADS)

Hernández-Montoya, A. R.; Coronel-Brizio, H. F.; Stevens-Ramírez, G. A.; Rodríguez-Achach, M.; Politi, M.; Scalas, E.

2011-12-01

We explore the spatial complexity of Conway’s “Game of Life,” a prototypical cellular automaton by means of a geometrical procedure generating a two-dimensional random walk from a bidimensional lattice with periodical boundaries. The one-dimensional projection of this process is analyzed and it turns out that some of its statistical properties resemble the so-called stylized facts observed in financial time series. The scope and meaning of this result are discussed from the viewpoint of complex systems. In particular, we stress how the supposed peculiarities of financial time series are, often, overrated in their importance.

Emerging properties of financial time series in the "Game of Life".

PubMed

Hernández-Montoya, A R; Coronel-Brizio, H F; Stevens-Ramírez, G A; Rodríguez-Achach, M; Politi, M; Scalas, E

2011-12-01

We explore the spatial complexity of Conway's "Game of Life," a prototypical cellular automaton by means of a geometrical procedure generating a two-dimensional random walk from a bidimensional lattice with periodical boundaries. The one-dimensional projection of this process is analyzed and it turns out that some of its statistical properties resemble the so-called stylized facts observed in financial time series. The scope and meaning of this result are discussed from the viewpoint of complex systems. In particular, we stress how the supposed peculiarities of financial time series are, often, overrated in their importance.

Student Solution Manual for Mathematical Methods for Physics and Engineering Third Edition

NASA Astrophysics Data System (ADS)

Riley, K. F.; Hobson, M. P.

2006-03-01

Preface; 1. Preliminary algebra; 2. Preliminary calculus; 3. Complex numbers and hyperbolic functions; 4. Series and limits; 5. Partial differentiation; 6. Multiple integrals; 7. Vector algebra; 8. Matrices and vector spaces; 9. Normal modes; 10. Vector calculus; 11. Line, surface and volume integrals; 12. Fourier series; 13. Integral transforms; 14. First-order ordinary differential equations; 15. Higher-order ordinary differential equations; 16. Series solutions of ordinary differential equations; 17. Eigenfunction methods for differential equations; 18. Special functions; 19. Quantum operators; 20. Partial differential equations: general and particular; 21. Partial differential equations: separation of variables; 22. Calculus of variations; 23. Integral equations; 24. Complex variables; 25. Application of complex variables; 26. Tensors; 27. Numerical methods; 28. Group theory; 29. Representation theory; 30. Probability; 31. Statistics.

Nestin expression in the retina of rats with inherited retinal degeneration.

PubMed

Valamanesh, Fatemeh; Monnin, Julie; Morand-Villeneuve, Nadège; Michel, Germaine; Zaher, Murhaf; Miloudi, Sofiane; Chemouni, Deborah; Jeanny, Jean-Claude; Versaux-Botteri, Claudine

2013-05-01

Nestin is found in radial glia and neuronal/glial progenitor cells during retinal development, and is re-expressed after acute damage in the retina of adult mammals. We have investigated nestin expression in the retina of the Royal College of Surgeons (RCS) rat model of human inherited blindness, Retinitis pigmentosa (RP). During the first postnatal week, nestin immunoreactivity was located in elongated processes resembling radial glia in both control and dystrophic animals. During the second postnatal week, the density of nestin immunoreactive radial processes decreased progressively starting in the outer retina. At postnatal day 20 (PNd20), Nestin immunoreactive radial processes were no longer visible, with immunoreactivity restricted to structures resembling Müller end-feet and/or astrocytes located in the ganglion cell layer (GCL) in both control and dystrophic rats. These morphological results were confirmed by Western blotting and qPCR analysis. The level of nestin remained low in control animals at different time points up to 1 year, but we observed a re-expression of this protein from PNd30 in the dystrophic animals. The morphology of cells re-expressing nestin resembled that of radial glia and/or Muller cells, but co-localization of nestin and glutamine synthetase (GS: a marker of mature Müller cells) was only partial. Interestingly, whereas Western blot analysis confirmed the increase in protein levels from PNd30 onwards, mRNA levels remained low in dystrophic rats. Additional studies demonstrated that the discrepancy between protein and mRNA contents could be due to a dysfunction in proteasome activity as often observed in neurodegenerative pathologies. In conclusion, because of its localization in astrocytes and in radial processes resembling radial glia in the pathologic adult retina, nestin may be involved in mechanisms such as cell migration, generation of new neurons or glial cells and/or in retinal (re)modeling in dystrophic adult animals. The lack of concomitant up-regulation of mRNAs in adult dystrophic animals suggests that the pathology could lead to transcriptional and/or metabolic changes involving the stabilization of the half-life and/or dysregulation of degradation processes of nestin protein. Copyright © 2013 Elsevier Ltd. All rights reserved.

Molecular mechanisms of serotonergic action of the HIV-1 antiretroviral efavirenz.

PubMed

Dalwadi, Dhwanil A; Kim, Seongcheol; Amdani, Shahnawaz M; Chen, Zhenglan; Huang, Ren-Qi; Schetz, John A

2016-08-01

Efavirenz is highly effective at suppressing HIV-1, and the WHO guidelines list it as a component of the first-line antiretroviral (ARV) therapies for treatment-naïve patients. Though the pharmacological basis is unclear, efavirenz is commonly associated with a risk for neuropsychiatric adverse events (NPAEs) when taken at the prescribed dose. In many patients these NPAEs appear to subside after several weeks of treatment, though long-term studies show that in some patients the NPAEs persist. In a recent study focusing on the abuse potential of efavirenz, its receptor psychopharmacology was reported to include interactions with a number of established molecular targets for known drugs of abuse, and it displayed a prevailing behavioral profile in rodents resembling an LSD-like activity. In this report, we discovered interactions with additional serotonergic targets that may be associated with efavirenz-induced NPAEs. The most robust interactions were with 5-HT3A and 5-HT6 receptors, with more modest interactions noted for the 5-HT2B receptor and monoamine oxidase A. From a molecular mechanistic perspective, efavirenz acts as a 5-HT6 receptor inverse agonist of Gs-signaling, 5-HT2A and 5-HT2C antagonist of Gq-signaling, and a blocker of the 5-HT3A receptor currents. Efavirenz also completely or partially blocks agonist stimulation of the M1 and M3 muscarinic receptors, respectively. Schild analysis suggests that efavirenz competes for the same site on the 5-HT2A receptor as two known hallucinogenic partial agonists (±)-DOI and LSD. Prolonged exposure to efavirenz reduces 5-HT2A receptor density and responsiveness to 5-HT. Other ARVs such as zidovudine, nevirapine and emtricitabine did not share the same complex pharmacological profile as efavirenz, though some of them weakly interact with the 5-HT6 receptor or modestly block GABAA currents. Published by Elsevier Ltd.

Auditing Complex Concepts of SNOMED using a Refined Hierarchical Abstraction Network

PubMed Central

Wang, Yue; Halper, Michael; Wei, Duo; Gu, Huanying; Perl, Yehoshua; Xu, Junchuan; Elhanan, Gai; Chen, Yan; Spackman, Kent A.; Case, James T.; Hripcsak, George

2012-01-01

Auditors of a large terminology, such as SNOMED CT, face a daunting challenge. To aid them in their efforts, it is essential to devise techniques that can automatically identify concepts warranting special attention. “Complex” concepts, which by their very nature are more difficult to model, fall neatly into this category. A special kind of grouping, called a partial-area, is utilized in the characterization of complex concepts. In particular, the complex concepts that are the focus of this work are those appearing in intersections of multiple partial-areas and are thus referred to as overlapping concepts. In a companion paper, an automatic methodology for identifying and partitioning the entire collection of overlapping concepts into disjoint, singly-rooted groups, that are more manageable to work with and comprehend, has been presented. The partitioning methodology formed the foundation for the development of an abstraction network for the overlapping concepts called a disjoint partial-area taxonomy. This new disjoint partial-area taxonomy offers a collection of semantically uniform partial-areas and is exploited herein as the basis for a novel auditing methodology. The review of the overlapping concepts is done in a top-down order within semantically uniform groups. These groups are themselves reviewed in a top-down order, which proceeds from the less complex to the more complex overlapping concepts. The results of applying the methodology to SNOMED’s Specimen hierarchy are presented. Hypotheses regarding error ratios for overlapping concepts and between different kinds of overlapping concepts are formulated. Two phases of auditing the Specimen hierarchy for two releases of SNOMED are reported on. With the use of the double bootstrap and Fisher’s exact test (two-tailed), the auditing of concepts and especially roots of overlapping partial-areas is shown to yield a statistically significant higher proportion of errors. PMID:21907827

Complexation of imidazopyridine-based cations with a 24-crown-8 ether host: [2]pseudorotaxane and partially threaded structures.

PubMed

Moreno-Olivares, Surisadai I; Cervantes, Ruy; Tiburcio, Jorge

2013-11-01

A new series of linear molecules derived from 1,2-bis(imidazopyridin-2-yl)ethane can fully or partially penetrate the cavity of the dibenzo-24-crown-8 macrocycle to produce a new family of host-guest complexes. Protonation or alkylation of the nitrogen atoms on the pyridine rings led to an increase in the guest total positive charge up to 4+ and simultaneously generated two new recognition sites (pyridinium motifs) that are in competition with the 1,2-bis(benzimidazole)ethane motif for the crown ether. The relative position of the pyridine ring and the chemical nature of the N-substituent determined the preferred motif and the host-guest complex geometry: (i) for linear guests with relatively bulky groups (i.e., a benzyl substituent), the 1,2-bis(benzimidazole)ethane motif is favored, leading to a fully threaded complex with a [2]pseudorotaxane geometry; (ii) for small substituents, such as -H and -CH3 groups, regardless of the guest shape, the pyridinium motifs are preferred, leading to external partially threaded complexes in a 2:1 host to guest stoichiometry.

An unexpected semi-hydrogenation of a ligand in the complexation of 2,7-bispyridinyl-1,8-naphthyridine with Ru3(CO)12.

PubMed

Liao, Bei-Sih; Liu, Yi-Hung; Peng, Shie-Ming; Reddy, K Rajender; Liu, Shin-Hung; Chou, Pi-Tai; Liu, Shiuh-Tzung

2014-03-07

Thermal reaction of 2,7-bis(2-pyridinyl)-l,8-naphthyridine () with Ru3(CO)12 in the presence of moisture resulted in the formation of a formate-bridged diruthenium complex [(-H3)Ru2(μ-HCOO)(CO)4] (), in which the ligand was partially hydrogenated. Complex was fully characterized by spectroscopic analyses and X-ray single crystal determination. Regarding the partially reduced ligand in , it occurs through a water-gas shift type reduction. The bridging formate ligand can be substituted by other carboxylate ligands. Physical and chemical properties of the newly prepared complexes were investigated.

The cnidarian origin of the proto-oncogenes NF-κB/STAT and WNT-like oncogenic pathway drives the ctenophores (Review)

PubMed Central

SINKOVICS, JOSEPH G.

2015-01-01

The cell survival pathways of the diploblastic early multicellular eukaryotic hosts contain and operate the molecular machinery resembling those of malignantly transformed individual cells of highly advanced multicellular hosts (including Homo). In the present review, the STAT/NF-κB pathway of the cnidarian Nematostella vectensis is compared with that of human tumors (malignant lymphomas, including Reed-Sternberg cells) pointing out similarities, including possible viral initiation in both cases. In the ctenophore genome and proteome, β-catenin gains intranuclear advantages due to a physiologically weak destructive complex in the cytoplasm, and lack of natural inhibitors (the Dickkopfs). Thus, a scenario similar to what tumor cells initiate and achieve is presented through several constitutive loss-of-function type mutations in the destructive complex and in the elimination of inhibitors. Vice versa, malignantly transformed individual cells of advanced multicellular hosts assume pheno-genotypic resemblance to cells of unicellular or early multicellular hosts, and presumably to their ancient predecessors, by returning to the semblance of immortality and to the resumption of the state of high degree of resistance to physicochemical insults. Human leukemogenic and oncogenic pathways are presented for comparisons. The supreme bioengineers RNA/DNA complex encoded both the malignantly transformed immortal cell and the human cerebral cortex. The former generates molecules for the immortality of cellular life in the Universe. The latter invents the inhibitors of the process in order to gain control over it. PMID:26239915

The cnidarian origin of the proto-oncogenes NF-κB/STAT and WNT-like oncogenic pathway drives the ctenophores (Review).

PubMed

Sinkovics, Joseph G

2015-10-01

The cell survival pathways of the diploblastic early multicellular eukaryotic hosts contain and operate the molecular machinery resembling those of malignantly transformed individual cells of highly advanced multicellular hosts (including Homo). In the present review, the STAT/NF-κB pathway of the cnidarian Nematostella vectensis is compared with that of human tumors (malignant lymphomas, including Reed-Sternberg cells) pointing out similarities, including possible viral initiation in both cases. In the ctenophore genome and proteome, β-catenin gains intranuclear advantages due to a physiologically weak destructive complex in the cytoplasm, and lack of natural inhibitors (the dickkopfs). Thus, a scenario similar to what tumor cells initiate and achieve is presented through several constitutive loss-of-function type mutations in the destructive complex and in the elimination of inhibitors. Vice versa, malignantly transformed individual cells of advanced multicellular hosts assume pheno-genotypic resemblance to cells of unicellular or early multicellular hosts, and presumably to their ancient predecessors, by returning to the semblance of immortality and to the resumption of the state of high degree of resistance to physicochemical insults. Human leukemogenic and oncogenic pathways are presented for comparisons. The supreme bioengineers RNA/DNA complex encoded both the malignantly transformed immortal cell and the human cerebral cortex. The former generates molecules for the immortality of cellular life in the Universe. The latter invents the inhibitors of the process in order to gain control over it.

Rare earth element contents and multiple mantle sources of the transform-related Mount Edgecumbe basalts, southeastern Alaska

USGS Publications Warehouse

Riehle, J.R.; Budahn, J.R.; Lanphere, M.A.; Brew, D.A.

1994-01-01

Pleistocene basalt of the Mount Edgecumbe volcanic field (MEF) is subdivided into a plagioclase type and an olivine type. Th/La ratios of plagioclase basalt are similar to those of mid-ocean-ridge basalt (MORB), whereas those of olivine basalt are of continental affinity. Rare earth element (REE) contents of the olivine basalt, which resemble those of transitional MORB, are modelled by 10-15% partial melting of fertile spinel-plagioclase lherzolite followed by removal of 8-13% olivine. It is concluded that olivine basalt originated in subcontinental spinel lherzolite and that plagioclase basalt may have originated in suboceanic lithosphere of the Pacific plate. -from Authors

Parquet: Regions of areal plastic dislocations (on Venus)

NASA Technical Reports Server (NTRS)

Sukhanov, A. L.

1986-01-01

The extensive flat elevations of the Northern Hemisphere of Venus are covered with frequently intersecting lines of dislocations, resembling the outline of a giant parquet. In the internal sections of these regions we find grabens and regions of extension, and on the periphery lobe-shaped flow structures. The parquet was formed after the beginning of the formation of the lava plains, but covered by the youngest lava. These structures apparently arose partly because of the dragging of blocks of crust by the asthenospheric flows, and partly in the gravitational sliding of such heated blocks in the partial melting of their base. It is possible that these elevations occupy on Venus the place of the Earth's rift systems.

Acetate and succinate production in amoebae, helminths, diplomonads, trichomonads and trypanosomatids: common and diverse metabolic strategies used by parasitic lower eukaryotes.

PubMed

Bringaud, F; Ebikeme, C; Boshart, M

2010-08-01

Parasites that often grow anaerobically in their hosts have adopted a fermentative strategy relying on the production of partially oxidized end products, including lactate, glycerol, ethanol, succinate and acetate. This review focuses on recent progress in understanding acetate production in protist parasites, such as amoebae, diplomonads, trichomonads, trypanosomatids and in the metazoan parasites helminths, as well as the succinate production pathway(s) present in some of them. We also describe the unconventional organisation of the tricarboxylic acid cycle associated with the fermentative strategy adopted by the procyclic trypanosomes, which may resemble the probable structure of the primordial TCA cycle in prokaryotes.

Defect-Induced Hedgehog Polarization States in Multiferroics

NASA Astrophysics Data System (ADS)

Li, Linze; Cheng, Xiaoxing; Jokisaari, Jacob R.; Gao, Peng; Britson, Jason; Adamo, Carolina; Heikes, Colin; Schlom, Darrell G.; Chen, Long-Qing; Pan, Xiaoqing

2018-03-01

Continuous developments in nanotechnology require new approaches to materials synthesis that can produce novel functional structures. Here, we show that nanoscale defects, such as nonstoichiometric nanoregions (NSNRs), can act as nano-building blocks for creating complex electrical polarization structures in the prototypical multiferroic BiFeO3 . An array of charged NSNRs are produced in BiFeO3 thin films by tuning the substrate temperature during film growth. Atomic-scale scanning transmission electron microscopy imaging reveals exotic polarization rotation patterns around these NSNRs. These polarization patterns resemble hedgehog or vortex topologies and can cause local changes in lattice symmetries leading to mixed-phase structures resembling the morphotropic phase boundary with high piezoelectricity. Phase-field simulations indicate that the observed polarization configurations are mainly induced by charged states at the NSNRs. Engineering defects thus may provide a new route for developing ferroelectric- or multiferroic-based nanodevices.

Defect-Induced Hedgehog Polarization States in Multiferroics.

PubMed

Li, Linze; Cheng, Xiaoxing; Jokisaari, Jacob R; Gao, Peng; Britson, Jason; Adamo, Carolina; Heikes, Colin; Schlom, Darrell G; Chen, Long-Qing; Pan, Xiaoqing

2018-03-30

Continuous developments in nanotechnology require new approaches to materials synthesis that can produce novel functional structures. Here, we show that nanoscale defects, such as nonstoichiometric nanoregions (NSNRs), can act as nano-building blocks for creating complex electrical polarization structures in the prototypical multiferroic BiFeO_{3}. An array of charged NSNRs are produced in BiFeO_{3} thin films by tuning the substrate temperature during film growth. Atomic-scale scanning transmission electron microscopy imaging reveals exotic polarization rotation patterns around these NSNRs. These polarization patterns resemble hedgehog or vortex topologies and can cause local changes in lattice symmetries leading to mixed-phase structures resembling the morphotropic phase boundary with high piezoelectricity. Phase-field simulations indicate that the observed polarization configurations are mainly induced by charged states at the NSNRs. Engineering defects thus may provide a new route for developing ferroelectric- or multiferroic-based nanodevices.

PubMed Central

Maziade, Jean; Théorêt, Johanne

2004-01-01

OBJECTIVE: To describe the patients residents see in one hospital's family medicine unit and to determine whether these patients resemble family medicine patients in other Quebec hospitals. DESIGN: Descriptive study. SETTING: Urban teaching hospital. PARTICIPANTS: Patients 20 years and older who were admitted to the family medicine unit at Hôpital du St-Sacrement between April 1, 1999, and March 31, 2000, were compared with all patients admitted in general medicine to Quebec hospitals during this period. MAIN OUTCOME MEASURES: Sex, age, main diagnosis, secondary diagnoses, types of diseases, length of stay, number of consultations and specialties involved, referral after hospitalization. RESULTS: Patients hospitalized in this unit were older, had more secondary diagnoses, and stayed in hospital slightly longer than patients hospitalized in general medicine in Quebec as a whole. Residents were, therefore, exposed to patients who were more medically complex. CONCLUSION: Patients to whom residents were exposed resemble patients they will see in future hospital practice. PMID:15648384

Embracing chaos and complexity: a quantum change for public health.

PubMed

Resnicow, Kenneth; Page, Scott E

2008-08-01

Public health research and practice have been guided by a cognitive, rational paradigm where inputs produce linear, predictable changes in outputs. However, the conceptual and statistical assumptions underlying this paradigm may be flawed. In particular, this perspective does not adequately account for nonlinear and quantum influences on human behavior. We propose that health behavior change is better understood through the lens of chaos theory and complex adaptive systems. Key relevant principles include that behavior change (1) is often a quantum event; (2) can resemble a chaotic process that is sensitive to initial conditions, highly variable, and difficult to predict; and (3) occurs within a complex adaptive system with multiple components, where results are often greater than the sum of their parts.

Intact functional fourteen-subunit respiratory membrane-bound [NiFe]-hydrogenase complex of the hyperthermophilic archaeon Pyrococcus furiosus.

PubMed

McTernan, Patrick M; Chandrayan, Sanjeev K; Wu, Chang-Hao; Vaccaro, Brian J; Lancaster, W Andrew; Yang, Qingyuan; Fu, Dax; Hura, Greg L; Tainer, John A; Adams, Michael W W

2014-07-11

The archaeon Pyrococcus furiosus grows optimally at 100 °C by converting carbohydrates to acetate, CO2, and H2, obtaining energy from a respiratory membrane-bound hydrogenase (MBH). This conserves energy by coupling H2 production to oxidation of reduced ferredoxin with generation of a sodium ion gradient. MBH is encoded by a 14-gene operon with both hydrogenase and Na(+)/H(+) antiporter modules. Herein a His-tagged MBH was expressed in P. furiosus and the detergent-solubilized complex purified under anaerobic conditions by affinity chromatography. Purified MBH contains all 14 subunits by electrophoretic analysis (13 subunits were also identified by mass spectrometry) and had a measured iron:nickel ratio of 15:1, resembling the predicted value of 13:1. The as-purified enzyme exhibited a rhombic EPR signal characteristic of the ready nickel-boron state. The purified and membrane-bound forms of MBH both preferentially evolved H2 with the physiological donor (reduced ferredoxin) as well as with standard dyes. The O2 sensitivities of the two forms were similar (half-lives of ∼ 15 h in air), but the purified enzyme was more thermolabile (half-lives at 90 °C of 1 and 25 h, respectively). Structural analysis of purified MBH by small angle x-ray scattering indicated a Z-shaped structure with a mass of 310 kDa, resembling the predicted value (298 kDa). The angle x-ray scattering analyses reinforce and extend the conserved sequence relationships of group 4 enzymes and complex I (NADH quinone oxidoreductase). This is the first report on the properties of a solubilized form of an intact respiratory MBH complex that is proposed to evolve H2 and pump Na(+) ions. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Microwave-assisted synthesis and crystal structure of oxo(diperoxo)(4,4'-di-tert-butyl-2,2'-bipyridine)-molybdenum(VI).

PubMed

Amarante, Tatiana R; Almeida Paz, Filipe A; Gago, Sandra; Gonçalves, Isabel S; Pillinger, Martyn; Rodrigues, Alírio E; Abrantes, Marta

2009-09-16

The oxodiperoxo complex MoO(O2)(2)(tbbpy) (tbbpy = 4,4'-di-tert-butyl-2,2'- bipyridine) was isolated from the reaction of MoO2Cl(2)(tbbpy) in water under microwaveassisted heating at 120 masculineC for 4 h. The structure of the oxodiperoxo complex was determined by single crystal X-ray diffraction. The Mo(VI) centre is seven-coordinated with a geometry which strongly resembles a highly distorted bipyramid. Individual MoO(O2)(2)(tbbpy) complexes are interdigitated along the [010] direction to form a column. The crystal structure is formed by the close packing of the columnar-stacked complexes. Interactions between neighbouring columns are essentially of van der Waals type mediated by the need to effectively fill the available space.

Hydrous partial melting in the sheeted dike complex at fast spreading ridges: experimental and natural observations

NASA Astrophysics Data System (ADS)

France, Lydéric; Koepke, Juergen; Ildefonse, Benoit; Cichy, Sarah B.; Deschamps, Fabien

2010-11-01

In ophiolites and in present-day oceanic crust formed at fast spreading ridges, oceanic plagiogranites are commonly observed at, or close to the base of the sheeted dike complex. They can be produced either by differentiation of mafic melts, or by hydrous partial melting of the hydrothermally altered sheeted dikes. In addition, the hydrothermally altered base of the sheeted dike complex, which is often infiltrated by plagiogranitic veins, is usually recrystallized into granoblastic dikes that are commonly interpreted as a result of prograde granulitic metamorphism. To test the anatectic origin of oceanic plagiogranites, we performed melting experiments on a natural hydrothermally altered dike, under conditions that match those prevailing at the base of the sheeted dike complex. All generated melts are water saturated, transitional between tholeiitic and calc-alkaline, and match the compositions of oceanic plagiogranites observed close to the base of the sheeted dike complex. Newly crystallized clinopyroxene and plagioclase have compositions that are characteristic of the same minerals in granoblastic dikes. Published silicic melt compositions obtained in classical MORB fractionation experiments also broadly match the compositions of oceanic plagiogranites; however, the compositions of the coexisting experimental minerals significantly deviate from those of the granoblastic dikes. Our results demonstrate that hydrous partial melting is a likely common process in the root zone of the sheeted dike complex, starting at temperatures exceeding 850°C. The newly formed melt can either crystallize to form oceanic plagiogranites or may be recycled within the melt lens resulting in hybridized and contaminated MORB melts. It represents the main MORB crustal contamination process. The residue after the partial melting event is represented by the granoblastic dikes. Our results support a model with a dynamic melt lens that has the potential to trigger hydrous partial melting reactions in the previously hydrothermally altered sheeted dikes. A new thermometer using the Al content of clinopyroxene is also elaborated.

El Hierro's floating stones as messengers of crust-magma interaction at depth

NASA Astrophysics Data System (ADS)

Burchardt, S.; Troll, V. R.; Schmeling, H.; Koyi, H.; Blythe, L. S.; Longpré, M. A.; Deegan, F. M.

2012-04-01

During the early stages of the submarine eruption that started on October 10 2011 south of El Hierro, Canary Islands, Spain, peculiar eruption products were found floating on the sea surface. These centimetre- to decimetre-sized "bombs" have been termed "restingolites" after the nearby village La Restinga and consist of a basaltic rind and a white to light grey core that resembles pumice in texture. According to Troll et al. (2011; see also Troll et al. EGU 2012 Abstracts), this material consists of a glassy matrix hosting extensive vesicle networks, which results in extremely low densities allowing these rocks to float on sea water. Mineralogical and geochemical analyses reveal that the "restingolites" originate from the sedimentary rocks (sand-, silt-, and mudstones) that form layer 1 of the oceanic crust beneath El Hierro. During the onset and early stages of the eruption, magma ponded at the base of this sedimentary sequence, breaking its way through the sedimentary rocks to the ocean floor. The textures of the "restingolites" reveal that crust-magma interaction during fragmentation and transport of the xenoliths involved rapid partial melting and volatile exsolution. Xenoliths strikingly similar to those from El Hierro are known from eruptions on other Canary Islands (e.g. La Palma, Gran Canaria, and Lanzarote). In fact, they resemble in texture xenoliths of various protoliths from volcanic areas worldwide (e.g. Krakatao, Indonesia, Cerro Quemado, Guatemala, Laacher See, Germany). This indicates that the process of partial melting and volatile exsolution, which the "restingolites" bear witness of, is probably occurring frequently during shallow crustal magma emplacement. Thermomechanical numerical models of the effect of the density decrease associated with the formation of vesicle networks in partially molten xenoliths show that xenoliths of crustal rocks initially sink in a magma chamber, but may start to float to the chamber roof once they start to heat up and vesiculate. The "floating stones" from El Hierro thus represent the products of crust-magma interaction beneath the Canary Islands, but is probably relevant in most volcanic areas and tectonic settings. In addition, xenolith devolatilisation has important general implications for the mechanics of crustal recycling, magma emplacement into the upper crust and volatile release from active volcanic systems.

Resonance behavior of atomic and molecular photoionization amplitudes

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

Cherepkov, N. A.; Kuznetsov, V. V.; Semenov, S. K.

The behavior of the partial photoionization amplitudes with a given orbital angular momentum l in the complex plane in resonances is studied. In the autoionization resonances the trajectory of the amplitude in the complex plane corresponds to a circle. With increasing photoelectron energy the amplitude moves about a circle in the counterclockwise direction. The new expressions for the partial amplitudes in the resonance are proposed which are similar to the Fano form but contain the 'partial' profile parameters which are connected with the Fano parameter q by a simple relation. In the giant dipole resonances the amplitudes in the complexmore » plane also move about a circle in the counterclockwise direction provided the Coulomb phase is excluded from the amplitude. In the correlational resonances created by channel interactions with the giant dipole resonance the trajectories of the amplitudes acquire a loop about which the amplitudes move in the counterclockwise direction. Very similar behavior of partial photoionization amplitudes in the complex plane is demonstrated also for the dipole transitions from the K shells of the N{sub 2} molecule in the {sigma}* shape resonance.« less

Activation of a chloroplast type of fructose bisphosphatase from Chlamydomonas reinhardtii by light-mediated agents

NASA Technical Reports Server (NTRS)

Huppe, H. C.; Buchanan, B. B.

1989-01-01

A chloroplast type of fructose-1,6-bisphosphatase, a central regulatory enzyme of photosynthetic carbon metabolism, has been partially purified from Chlamydomonas reinhardtii. Unlike its counterpart from spinach chloroplasts, the algal FBPase showed a strict requirement for a dithiol reductant irrespective of Mg2+ concentration. The enzymes from the two sources resembled each other immunologically, in subunit molecular mass and response to pH. In the presence of dithiothreitol, the pH optimum for both the algal and spinach enzymes shifted from 8.5 to a more physiologic value of 8.0 as the Mg2+ concentration was increased from 1 to 16 mM. At 1 mM Mg2+, a concentration estimated to be close to physiological, the Chlamydomonas FBPase was active only in the presence of reduced thioredoxin and was most active with Chlamydomonas thioredoxin f. Under these conditions, the enzyme showed a pH optimum of 8.0. The data suggest that the Chlamydomonas enzyme resembles its spinach counterpart in most respects, but it has a stricter requirement for reduction and less strict reductant specificity. A comparison of the properties of the FBPases from Chlamydomonas and spinach will be helpful for elucidating the mechanism of the reductive activation of this enzyme.

Crystal Structure of a Human IκB Kinase β Asymmetric Dimer

PubMed Central

Liu, Shenping; Misquitta, Yohann R.; Olland, Andrea; Johnson, Mark A.; Kelleher, Kerry S.; Kriz, Ron; Lin, Laura L.; Stahl, Mark; Mosyak, Lidia

2013-01-01

Phosphorylation of inhibitor of nuclear transcription factor κB (IκB) by IκB kinase (IKK) triggers the degradation of IκB and migration of cytoplasmic κB to the nucleus where it promotes the transcription of its target genes. Activation of IKK is achieved by phosphorylation of its main subunit, IKKβ, at the activation loop sites. Here, we report the 2.8 Å resolution crystal structure of human IKKβ (hIKKβ), which is partially phosphorylated and bound to the staurosporine analog K252a. The hIKKβ protomer adopts a trimodular structure that closely resembles that from Xenopus laevis (xIKKβ): an N-terminal kinase domain (KD), a central ubiquitin-like domain (ULD), and a C-terminal scaffold/dimerization domain (SDD). Although hIKKβ and xIKKβ utilize a similar dimerization mode, their overall geometries are distinct. In contrast to the structure resembling closed shears reported previously for xIKKβ, hIKKβ exists as an open asymmetric dimer in which the two KDs are further apart, with one in an active and the other in an inactive conformation. Dimer interactions are limited to the C-terminal six-helix bundle that acts as a hinge between the two subunits. The observed domain movements in the structures of IKKβ may represent trans-phosphorylation steps that accompany IKKβ activation. PMID:23792959

A magnesium-induced triplex pre-organizes the SAM-II riboswitch

PubMed Central

Roy, Susmita; Lammert, Heiko; Dayie, T. Kwaku; Sanbonmatsu, Karissa Y.

2017-01-01

Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state. Our CEST and SAXS experiments, at different magnesium ion concentrations, quantitatively confirm our simulation results, demonstrating that magnesium ions induce collapse and pre-organization. Agreement between theory and experiment bolsters microscopic interpretation of our simulations, which shows that triplex formation between helix P2b and loop L1 is highly sensitive to magnesium and plays a key role in pre-organization. Pre-organization of the SAM-II riboswitch allows rapid detection of ligand with high selectivity, which is important for biological function. PMID:28248966

Including pride and its group-based, relational, and contextual features in theories of contempt.

PubMed

Sullivan, Gavin Brent

2017-01-01

Sentiment includes emotional and enduring attitudinal features of contempt, but explaining contempt as a mixture of basic emotion system affects does not adequately address the family resemblance structure of the concept. Adding forms of individual, group-based, and widely shared arrogance and contempt is necessary to capture the complex mixed feelings of proud superiority when "looking down upon" and acting harshly towards others.

The subgenual organ complex in the cave cricket Troglophilus neglectus (Orthoptera: Rhaphidophoridae): comparative innervation and sensory evolution

PubMed Central

Strauß, Johannes; Stritih, Nataša; Lakes-Harlan, Reinhard

2014-01-01

Comparative studies of the organization of nervous systems and sensory organs can reveal their evolution and specific adaptations. In the forelegs of some Ensifera (including crickets and tettigoniids), tympanal hearing organs are located in close proximity to the mechanosensitive subgenual organ (SGO). In the present study, the SGO complex in the non-hearing cave cricket Troglophilus neglectus (Rhaphidophoridae) is investigated for the neuronal innervation pattern and for organs homologous to the hearing organs in related taxa. We analyse the innervation pattern of the sensory organs (SGO and intermediate organ (IO)) and its variability between individuals. In T. neglectus, the IO consists of two major groups of closely associated sensilla with different positions. While the distal-most sensilla superficially resemble tettigoniid auditory sensilla in location and orientation, the sensory innervation does not show these two groups to be distinct organs. Though variability in the number of sensory nerve branches occurs, usually either organ is supplied by a single nerve branch. Hence, no sensory elements clearly homologous to the auditory organ are evident. In contrast to other non-hearing Ensifera, the cave cricket sensory structures are relatively simple, consistent with a plesiomorphic organization resembling sensory innervation in grasshoppers and stick insects. PMID:26064547

The role of redundant information in cultural transmission and cultural stabilization.

PubMed

Acerbi, Alberto; Tennie, Claudio

2016-02-01

Redundant copying has been proposed as a manner to achieve the high-fidelity necessary to pass on and preserve complex traits in human cultural transmission. There are at least 2 ways to define redundant copying. One refers to the possibility of copying repeatedly the same trait over time, and another to the ability to exploit multiple layers of information pointing to the same trait during a single copying event. Using an individual-based model, we explore how redundant copying (defined as in the latter way) helps to achieve successful transmission. The authors show that increasing redundant copying increases the likelihood of accurately transmitting a behavior more than either augmenting the number of copying occasions across time or boosting the general accuracy of social learning. They also investigate how different cost functions, deriving, for example, from the need to invest more energy in cognitive processing, impact the evolution of redundant copying. The authors show that populations converge either to high-fitness/high-costs states (with high redundant copying and complex culturally transmitted behaviors; resembling human culture) or to low-fitness/low-costs states (with low redundant copying and simple transmitted behaviors; resembling social learning forms typical of nonhuman animals). This outcome may help to explain why cumulative culture is rare in the animal kingdom. (c) 2016 APA, all rights reserved).

Evolution of heliobacteria: implications for photosynthetic reaction center complexes

NASA Technical Reports Server (NTRS)

Vermaas, W. F.; Blankenship, R. E. (Principal Investigator)

1994-01-01

The evolutionary position of the heliobacteria, a group of green photosynthetic bacteria with a photosynthetic apparatus functionally resembling Photosystem I of plants and cyanobacteria, has been investigated with respect to the evolutionary relationship to Gram-positive bacteria and cyanobacteria. On the basis of 16S rRNA sequence analysis, the heliobacteria appear to be most closely related to Gram-positive bacteria, but also an evolutionary link to cyanobacteria is evident. Interestingly, a 46-residue domain including the putative sixth membrane-spanning region of the heliobacterial reaction center protein show rather strong similarity (33% identity and 72% similarity) to a region including the sixth membrane-spanning region of the CP47 protein, a chlorophyll-binding core antenna polypeptide of Photosystem II. The N-terminal half of the heliobacterial reaction center polypeptide shows a moderate sequence similarity (22% identity over 232 residues) with the CP47 protein, which is significantly more than the similarity with the Photosystem I core polypeptides in this region. An evolutionary model for photosynthetic reaction center complexes is discussed, in which an ancestral homodimeric reaction center protein (possibly resembling the heliobacterial reaction center protein) with 11 membrane-spanning regions per polypeptide has diverged to give rise to the core of Photosystem I, Photosystem II, and of the photosynthetic apparatus in green, purple, and heliobacteria.

Magnetic Evidence for a Partially Differentiated Carbonaceous Chondrite Parent Body and Possible Implications for Asteroid 21 Lutetia

NASA Astrophysics Data System (ADS)

Weiss, Benjamin; Carporzen, L.; Elkins-Tanton, L.; Shuster, D. L.; Ebel, D. S.; Gattacceca, J.; Binzel, R. P.

2010-10-01

The origin of remanent magnetization in the CV carbonaceous chondrite Allende has been a longstanding mystery. The possibility of a core dynamo like that known for achondrite parent bodies has been discounted because chondrite parent bodies are assumed to be undifferentiated. Here we report that Allende's magnetization was acquired over several million years (Ma) during metasomatism on the parent planetesimal in a > 20 microtesla field 8-9 Ma after solar system formation. This field was present too recently and directionally stable for too long to have been the generated by the protoplanetary disk or young Sun. The field intensity is in the range expected for planetesimal core dynamos (Weiss et al. 2010), suggesting that CV chondrites are derived from the outer, unmelted layer of a partially differentiated body with a convecting metallic core (Elkins-Tanton et al. 2010). This suggests that asteroids with differentiated interiors could be present today but masked under chondritic surfaces. In fact, CV chondrites are spectrally similar to many members of the Eos asteroid family whose spectral diversity has been interpreted as evidence for a partially differentiated parent asteroid (Mothe-Diniz et al. 2008). CV chondrite spectral and polarimetric data also resemble those of asteroid 21 Lutetia (e.g., Belskaya et al. 2010), recently encountered by the Rosetta spacecraft. Ground-based measurements of Lutetia indicate a high density of 2.4-5.1 g cm-3 (Drummond et al. 2010), while radar data seem to rule out a metallic surface composition (Shepard et al. 2008). If Rosetta spacecraft measurements confirm a high density and a CV-like surface composition for Lutetia, then we propose Lutetia may be an example of a partially differentiated carbonaceous chondrite parent body. Regardless, the very existence of primitive achondrites, which contain evidence of both relict chondrules and partial melting, are prima facie evidence for the formation of partially differentiated bodies.

Appearance and partial purification of a high molecular weight protein in crabs exposed to saxitoxin.

PubMed

Barber, K G; Kitts, D D; Townsley, P M; Smith, D S

1988-01-01

This paper provides evidence for a protein component which appears to be involved in the seasonal resistance of small shore crabs, Hemigrapsus oregonesis and Hemigrapsus nudus to saxitoxin, a principle neurotoxin involved in paralytic shellfish poisoning (PSP). This unique protein complex was isolated and partially purified by ion exchange chromatography using DEAE-cellulose from visceral tissue extracts of resistant crabs. The complex was absent in control crabs that were sensitive to saxitoxin. In addition, the protein complex was induced in the crab after acute administration of low doses of saxitoxin. Results indicate that the protein complex is acidic in nature and has an apparent mol. wt of 145,000.

Label-free imaging to study phenotypic behavioural traits of cells in complex co-cultures

NASA Astrophysics Data System (ADS)

Suman, Rakesh; Smith, Gabrielle; Hazel, Kathryn E. A.; Kasprowicz, Richard; Coles, Mark; O'Toole, Peter; Chawla, Sangeeta

2016-02-01

Time-lapse imaging is a fundamental tool for studying cellular behaviours, however studies of primary cells in complex co-culture environments often requires fluorescent labelling and significant light exposure that can perturb their natural function over time. Here, we describe ptychographic phase imaging that permits prolonged label-free time-lapse imaging of microglia in the presence of neurons and astrocytes, which better resembles in vivo microenvironments. We demonstrate the use of ptychography as an assay to study the phenotypic behaviour of microglial cells in primary neuronal co-cultures through the addition of cyclosporine A, a potent immune-modulator.

A complex baleen whale call recorded in the Mariana Trench Marine National Monument.

PubMed

Nieukirk, Sharon L; Fregosi, Selene; Mellinger, David K; Klinck, Holger

2016-09-01

In fall 2014 and spring 2015, passive acoustic data were collected via autonomous gliders east of Guam in an area that included the Mariana Trench Marine National Monument. A short (2-4 s), complex sound was recorded that features a ∼38 Hz moan with both harmonics and amplitude modulation, followed by broad-frequency metallic-sounding sweeps up to 7.5 kHz. This sound was recorded regularly during both fall and spring surveys. Aurally, the sound is quite unusual and most resembles the minke whale "Star Wars" call. It is likely this sound is biological and produced by a baleen whale.

Exchange coupling in the complex magnetic multilayers

NASA Astrophysics Data System (ADS)

Uzdin, V. M.; Adamowicz, L.; Kocinski, P.

1996-06-01

Exchange coupling in the complex magnetic sandwich structures containing nonmagnetic (NM) and ferromagnetic (FM) layers composed of two different ferromagnetic metals has been studied within the framework of the quantum wells model. The strength of the exchange coupling in the multilayer structure with thin layers of a second ferromagnetic material inserted at the interface of FM/NM/FM sandwich was calculated at various physical situations. In one case the exponential dependence of the exchange coupling on the thickness of the interface ferromagnetic layer has been obtained in striking resemblance to the Parkin experimental results for magnetoresistance (S. S. P. Parkin, Phys. Rev. Lett., 71 (1993) 1641).

Evolution of the transcription complex during sporulation of Bacillus subtilis.

PubMed

Brevet, J

1976-01-01

Ribonucleic acid polymerase activity in partially purified extract of cells of Bacillus subtilis harvested at different times (t-1, to, t1, and t2) was studied by zone centrifugation. During the course of sporulation, vegetative sigma-factor activity decreased and the transcription complex lost some of its affinity for active sigma factor. The complex underwent a two-stage change in sedimentation value, from 14.5S in vegetative growth phase to a 13S species very early in sporulation to a 16S species at later times. Two SpoO mutants have been studied by zone centrifugation. One strain, a rifampin-resistant (RfmR) mutant, failed to show any modification of the transcription complex, whereas the other, a Rfms strain, underwent a partial evolution of the transcription complex after to.

Joint Intelligence Analysis Complex: DOD Partially Used Best Practices for Analyzing Alternatives and Should Do So Fully for Future Military Construction Decisions

DTIC Science & Technology

2016-09-01

Military Construction Decisions Report to Congressional Requesters September 2016 GAO-16-853 United States Government Accountability Office...ANALYSIS COMPLEX DOD Partially Used Best Practices for Analyzing Alternatives and Should Do So Fully for Future Military Construction Decisions What...a set of AOA best practices for military construction decisions. Without guidance for using AOA best practices during certain military construction

On the solution of the complex eikonal equation in acoustic VTI media: A perturbation plus optimization scheme

NASA Astrophysics Data System (ADS)

Huang, Xingguo; Sun, Jianguo; Greenhalgh, Stewart

2018-04-01

We present methods for obtaining numerical and analytic solutions of the complex eikonal equation in inhomogeneous acoustic VTI media (transversely isotropic media with a vertical symmetry axis). The key and novel point of the method for obtaining numerical solutions is to transform the problem of solving the highly nonlinear acoustic VTI eikonal equation into one of solving the relatively simple eikonal equation for the background (isotropic) medium and a system of linear partial differential equations. Specifically, to obtain the real and imaginary parts of the complex traveltime in inhomogeneous acoustic VTI media, we generalize a perturbation theory, which was developed earlier for solving the conventional real eikonal equation in inhomogeneous anisotropic media, to the complex eikonal equation in such media. After the perturbation analysis, we obtain two types of equations. One is the complex eikonal equation for the background medium and the other is a system of linearized partial differential equations for the coefficients of the corresponding complex traveltime formulas. To solve the complex eikonal equation for the background medium, we employ an optimization scheme that we developed for solving the complex eikonal equation in isotropic media. Then, to solve the system of linearized partial differential equations for the coefficients of the complex traveltime formulas, we use the finite difference method based on the fast marching strategy. Furthermore, by applying the complex source point method and the paraxial approximation, we develop the analytic solutions of the complex eikonal equation in acoustic VTI media, both for the isotropic and elliptical anisotropic background medium. Our numerical results demonstrate the effectiveness of our derivations and illustrate the influence of the beam widths and the anisotropic parameters on the complex traveltimes.

Premalignant lesions in the kidney.

PubMed

Kirkali, Z; Yorukoglu, K

2001-12-07

Renal cell carcinoma (RCC) is the most malignant urologic disease. Different lesions, such as dysplasia in the tubules adjacent to RCC, atypical hyperplasia in the cyst epithelium of von Hippel-Lindau syndrome, and adenoma have been described for a number of years as possible premalignant changes or precursor lesions of RCC. In two recent papers, kidneys adjacent to RCC or removed from other causes were analyzed, and dysplastic lesions were identified and defined in detail. Currently renal intraepithelial neoplasia (RIN) is the proposed term for classification. The criteria for a lesion to be defined as premalignant are (1) morphological similarity; (2) spatial association; (3) development of microinvasive carcinoma; (4) higher frequency, severity, and extent then invasive carcinoma; (5) progression to invasive cancer; and (6) similar genetic alterations. RIN resembles the neoplastic cells of RCC. There is spatial association. Progression to invasive carcinoma is described in experimental cancer models, and in some human renal tumors. Similar molecular alterations are found in some putative premalignant changes. The treatment for RCC is radical or partial nephrectomy. Preneoplastic lesions may remain in the renal remnant in patients treated by partial nephrectomy and may be the source of local recurrences. RIN seems to be a biologic precursor of some RCCs and warrants further investigation. Interpretation and reporting of these lesions would reveal important resources for the biological nature and clinical significance. The management of RIN diagnosed in a renal biopsy and partial nephrectomy needs to be answered.

Exploring the Photoreduction of Au(III) Complexes in the Gas-Phase

NASA Astrophysics Data System (ADS)

Marcum, Jesse C.; Kaufman, Sydney H.; Weber, J. Mathias

2010-06-01

We have used photodissociation spectroscopy to probe the electronic structure and photoreduction of Au(III) in gas-phase complexes containing Cl- and OH-. The gas-phase electronic spectrum of [AuCl_4]- closely resembles the aqueous solution spectrum, showing a lack of strong solvatochromic shifts. Substitution of Cl- ligands with OH- results in a strong blue shift, in agreement with ligand-field theory. Upon excitation, [AuCl_4]- can dissociate by loss of either one or two neutral Cl atoms, resulting in the reduction of gold from Au(III) to Au(II) and Au(I) respectively. The hydroxide substituted complex, [AuCl_2(OH)_2]-, demonstrates similar behavior but the only observable fragment channel is the loss of two neutral OH ligands, leading only to Au(I).

Long-range electron transport of ruthenium-centered multilayer films via a stepping-stone mechanism.

PubMed

Terada, Kei-ichi; Nakamura, Hisao; Kanaizuka, Katsuhiko; Haga, Masa-aki; Asai, Yoshihiro; Ishida, Takao

2012-03-27

We studied electron transport of Ru complex multilayer films, whose structure resembles redox-active complex films known in the literature to have long-range electron transport abilities. Hydrogen bond formation in terms of pH control was used to induce spontaneous growth of a Ru complex multilayer. We made a cross-check between electrochemical measurements and I-V measurements using PEDOT:PSS to eliminate the risk of pinhole contributions to the mechanism and have found small β values of 0.012-0.021 Å(-1). Our Ru complex layers exhibit long-range electron transport but with low conductance. On the basis of the results of our theoretical-experimental collaboration, we propose a modified tunneling mechanism named the "stepping-stone mechanism", where the alignment of site potentials forms a narrow band around E(F), making resonant tunneling possible. Our observations may support Tuccito et al.'s proposed mechanism. © 2012 American Chemical Society

Speech recognition against harmonic and inharmonic complexes: Spectral dips and periodicity

PubMed Central

Deroche, Mickael L. D.; Culling, John F.; Chatterjee, Monita; Limb, Charles J.

2014-01-01

Speech recognition in a complex masker usually benefits from masker harmonicity, but there are several factors at work. The present study focused on two of them, glimpsing spectrally in between masker partials and periodicity within individual frequency channels. Using both a theoretical and an experimental approach, it is demonstrated that when inharmonic complexes are generated by jittering partials from their harmonic positions, there are better opportunities for spectral glimpsing in inharmonic than in harmonic maskers, and this difference is enhanced as fundamental frequency (F0) increases. As a result, measurements of masking level difference between the two maskers can be reduced, particularly at higher F0s. Using inharmonic maskers that offer similar glimpsing opportunity to harmonic maskers, it was found that the masking level difference between the two maskers varied little with F0, was influenced by periodicity of the first four partials, and could occur in low-, mid-, or high-frequency regions. Overall, the present results suggested that both spectral glimpsing and periodicity contribute to speech recognition under masking by harmonic complexes, and these effects seem independent from one another. PMID:24815268

Establishment and characterization of Macaca fascicularis lymphoblastoid cell lines.

PubMed

Manning, C H; Heise, E R

1992-01-01

A panel of cynomolgus macaque lymphoblastoid cell lines (LCL) was established by transforming peripheral blood mononuclear cells (PBMC) with Herpesvirus papio (HVP), and selected lines were examined by flow cytometry. Results indicate that HVP-transformed macaque LCL are phenotypically heterogeneous and resemble human Epstein-Barr virus (EBV)-transformed LCL in the abundant expression of major histocompatibility complex (MHC) class I and class II molecules. At least some lines are of B cell origin.

Purification of a novel, nucleoplasmin-like protein from somatic nuclei.

PubMed Central

Cotten, M; Chalkley, R

1987-01-01

We have purified a nucleoplasmin-like protein from the nuclei of somatic Xenopus laevis cells. This protein possesses a number of the distinctive features of nucleoplasmin isolated from oocytes or unfertilized eggs. The protein is recognized by both monoclonal and polyclonal antisera raised against egg nucleoplasmin. The protein has an oligomeric structure, which must be heated in SDS to completely dissociate, is acidic, phosphorylated and efficiently promotes the in vitro formation of chromatin. We have partially characterized this novel protein and because of its resemblance to nucleoplasmin isolated from oocytes or unfertilized eggs we have named this protein nucleoplasmin S. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. Fig. 8. PMID:3443097

Are effects of emotion expression on trait impressions mediated by babyfaceness? Evidence from connectionist modeling.

PubMed

Zebrowitz, Leslie A; Kikuchi, Masako; Fellous, Jean-Marc

2007-05-01

Two studies provided evidence that bolsters the Marsh, Adams, and Kleck hypothesis that the morphology of certain emotion expressions reflects an evolved adaptation to mimic babies or mature adults. Study 1 found differences in emotion expressions' resemblance to babies using objective indices of babyfaceness provided by connectionist models that are impervious to overlapping cultural stereotypes about babies and the emotions. Study 2 not only replicated parallels between impressions of certain emotions and babies versus adults but also showed that objective indices of babyfaceness partially mediated impressions of the emotion expressions. babyface effects were independent of strong effects of attractiveness, and babyfaceness did not mediate impressions of happy expressions, to which the evolutionary hypothesis would not apply.

Scimitar Syndrome and H-type Tracheo-esophageal Fistula in a Newborn Infant.

PubMed

Lastinger, Allison; El Yaman, Malek; Gustafson, Robert; Yossuck, Panitan

2016-06-01

Scimitar syndrome is a rare congenital anomaly characterized by partial anomalous pulmonary venous drainage of the right lung to the inferior vena cava (IVC) creating a tubular opacity paralleling the right cardiac border on chest radiography which resembles a curved Turkish sword or scimitar. Associated pulmonary and vascular anomalies have been reported in cases of Scimitar syndrome, most commonly hypoplasia of right lung, dextroposition of the heart, hypoplasia of the right pulmonary artery, and aberrant arterial supply from the descending aorta to the affected lobe of the right lung. To the best of our knowledge, this is the first case of Scimitar syndrome with an H-type tracheoesophageal fistula that has ever been reported. Copyright © 2013. Published by Elsevier B.V.

In-Source Fragmentation and the Sources of Partially Tryptic Peptides in Shotgun Proteomics

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

Kim, Jong-Seo; Monroe, Matthew E.; Camp, David G.

2013-02-01

Partially tryptic peptides are often identified in shotgun proteomics using trypsin as the proteolytic enzyme; however, it has been controversial regarding the sources of such partially tryptic peptides. Herein we investigate the impact of in-source fragmentation on shotgun proteomics using three biological samples, including a standard protein mixture, a mouse brain tissue homogenate, and a mouse plasma sample. Since the in-source fragments of a peptide retain the same elution time with its parent fully tryptic peptide, the partially tryptic peptides from in-source fragmentation can be distinguished from the other partially tryptic peptides by plotting the observed retention times against themore » computationally predicted retention times. Most partially tryptic in-source fragmentation artifacts were misaligned from the linear distribution of fully tryptic peptides. The impact of in-source fragmentation on peptide identifications was clearly significant in a less complex sample such as a standard protein digest, where ~60 % of unique peptides were observed as partially tryptic peptides from in-source fragmentation. In mouse brain or mouse plasma samples, in-source fragmentation contributed to 1-3 % of all identified peptides. The other major source of partially tryptic peptides in complex biological samples is presumably proteolytic processing by endogenous proteases in the samples. By filtering out the in-source fragmentation artifacts from the identified partially tryptic or non-tryptic peptides, it is possible to directly survey in-vivo proteolytic processing in biological samples such as blood plasma.« less

On the formation of continental silicic melts in thermochemical mantle convection models: implications for early Earth

NASA Astrophysics Data System (ADS)

van Thienen, P.; van den Berg, A. P.; Vlaar, N. J.

2004-12-01

Important constituents of Archean cratons, formed in the early and hot history of the Earth, are Tonalite-Trondhjemite-Granodiorite (TTG) plutons and greenstone belts. The formation of these granite-greenstone terrains is often ascribed to plate-tectonic processes. Buoyancy considerations, however, do not allow plate tectonics to take place in a significantly hotter Earth. We therefore propose an alternative mechanism for the coeval and proximate production of TTG plutons and greenstone-like crustal successions. That is, when a locally anomalously thick basaltic crust has been produced by continued addition of extrusive or intrusive basalts due to partial melting of the underlying convecting mantle, the transition of a sufficient amount of basalt in the lower crust to eclogite may trigger a resurfacing event, in which a complete crustal section of over 1000 km long sinks into the mantle in less than 2 million years. Pressure release partial melting in the complementary upwelling mantle produces large volumes of basaltic material replacing the original crust. Partial melting at the base of this newly produced crust may generate felsic melts which are added as intrusives and/or extrusives to the generally mafic crustal succession, adding to what resembles a greenstone belt. Partial melting of metabasalt in the sinking crustal section produces a significant volume of TTG melt which is added to the crust directly above the location of 'subduction', presumably in the form of a pluton. This scenario is self-consistently produced by numerical thermochemical mantle convection models, presented in this paper, including partial melting of mantle peridotite and crustal (meta)basalt. The metamorphic p, T conditions under which partial melting of metabasalt takes place in this scenario are consistent with geochemical trace element data for TTGs, which indicate melting under amphibolite rather than eclogite facies. Other geodynamical settings which we have also investigated, including partial melting in small scale delaminations of the lower crust, at the base of a anomalously thick crust and due to the influx of a lower mantle diapir fail to reproduce this behavior unequivocally and mostly show melting of metabasalt in the eclogite stability field instead.

Propagation of partially coherent controllable dark hollow beams with various symmetries in turbulent atmosphere

NASA Astrophysics Data System (ADS)

Wang, Haiyan; Li, Xiangyin

2010-01-01

Normalized intensity distribution, the complex degree of coherence and power in the bucket for partially coherent controllable dark hollow beams (DHBs) with various symmetries propagating in atmospheric turbulence are derived using tensor method and investigated in detail. Analytical results show that, after sufficient propagation distance, partially coherent DHBs with various symmetries eventually become circular Gaussian beam (without dark hollow) in turbulent atmosphere, which is different from its propagation properties in free space. The partially coherent DHBs return to a circular Gaussian beam rapidly for stronger turbulence, higher coherence, lower beam order, smaller p or smaller beam waist width. Another interesting observation is that the profile of the complex degree of coherence attains a similar profile to that of the average intensity of the related beam propagating in a turbulent atmosphere. Besides the laser power focusablity of DHBs are better than that of Gaussian beam propagating in turbulent atmosphere.

An introduction to the partial credit model for developing nursing assessments.

PubMed

Fox, C

1999-11-01

The partial credit model, which is a special case of the Rasch measurement model, was presented as a useful way to develop and refine complex nursing assessments. The advantages of the Rasch model over the classical psychometric model were presented including the lack of bias in the measurement process, the ability to highlight those items in need of refinement, the provision of information on congruence between the data and the model, and feedback on the usefulness of the response categories. The partial credit model was introduced as a way to develop complex nursing assessments such as performance-based assessments, because of the model's ability to accommodate a variety of scoring procedures. Finally, an application of the partial credit model was illustrated using the Practical Knowledge Inventory for Nurses, a paper-and-pencil instrument that measures on-the-job decision-making for nurses.

Volcanic Constructs on Ganymede and Enceladus: Topographic Evidence from Stereo Images and Photoclinometry

NASA Technical Reports Server (NTRS)

Schenk, Paul M.; Moore, Jeffrey M.

1995-01-01

The morphology of volcanic features on Ganymede differs significantly from that on the terrestrial planets. Few if any major volcanic landforms, such as thick flows or shield volcanoes, have been identified to date. Using new stereo Voyager images, we have searched Ganymede for relief-generating volcanic constructs. We observed seven major types of volcanic structures, including several not previously recognized. The oldest are broad flat-topped domes partially filling many older craters in dark terrain. Similar domes occur on Enceladus. Together with smooth dark deposits, these domes indicate that the volcanic history of the dark terrain is complex. Bright terrain covers vast areas, although the style of emplacement remains unclear. Smooth bright materials embay and flood older terrains, and may have been emplaced as low- viscosity fluids. Associated with smooth bright material are a number of scalloped-shaped, semi- enclosed scarps that cut into preexisting terrain. In planform these structures resemble terrestrial calderas. The youngest volcanic materials identified are a series of small flows that may have flooded the floor of the multiring impact structure Gilgamesh, forming a broad dome, The identification of volcanic constructs up to I km thick is the first evidence for extrusion of moderate-to-high viscosity material on Ganymede. Viscosity and yield strength estimates for these materials span several orders of magnitude, indicating that volcanic materials on Ganymede have a range of compositions and/or were extruded under a wide range of conditions and/or eruptive styles.

Succinyl-CoA:(R)-Benzylsuccinate CoA-Transferase: an Enzyme of the Anaerobic Toluene Catabolic Pathway in Denitrifying Bacteria†

PubMed Central

Leutwein, Christina; Heider, Johann

2001-01-01

Anaerobic microbial toluene catabolism is initiated by addition of fumarate to the methyl group of toluene, yielding (R)-benzylsuccinate as first intermediate, which is further metabolized via β-oxidation to benzoyl-coenzyme A (CoA) and succinyl-CoA. A specific succinyl-CoA:(R)-benzylsuccinate CoA-transferase activating (R)-benzylsuccinate to the CoA-thioester was purified and characterized from Thauera aromatica. The enzyme is fully reversible and forms exclusively the 2-(R)-benzylsuccinyl-CoA isomer. Only some close chemical analogs of the substrates are accepted by the enzyme: succinate was partially replaced by maleate or methylsuccinate, and (R)-benzylsuccinate was replaced by methylsuccinate, benzylmalonate, or phenylsuccinate. In contrast to all other known CoA-transferases, the enzyme consists of two subunits of similar amino acid sequences and similar sizes (44 and 45 kDa) in an α2β2 conformation. Identity of the subunits with the products of the previously identified toluene-induced bbsEF genes was confirmed by determination of the exact masses via electrospray-mass spectrometry. The deduced amino acid sequences resemble those of only two other characterized CoA-transferases, oxalyl-CoA:formate CoA-transferase and (E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase, which represent a new family of CoA-transferases. As suggested by kinetic analysis, the reaction mechanism of enzymes of this family apparently involves formation of a ternary complex between the enzyme and the two substrates. PMID:11418570

A complex of Cardicola Short, 1953 (Digenea: Aporocotylidae) species infecting the milkfish Chanos chanos Forsskål (Gonorynchiformes), with descriptions of two new species.

PubMed

Yong, Russell Q-Y; Cutmore, Scott C; Miller, Terrence L; Wee, Nicholas Q-X; Cribb, Thomas H

2016-11-01

Two new species of Cardicola Short, 1953 are described from the milkfish, Chanos chanos Forsskål (Gonorynchiformes: Chanidae), obtained from off Lizard Island on the northern Great Barrier Reef (GBR) and North Stradbroke Island in southeast Queensland. These are the first known blood flukes from this order of fishes. Cardicola suni n. sp. differs from all other Cardicola spp. by a combination of a large ovoid oral sucker surrounding a subterminal mouth, recurved tegumental spines up to 16 μm long, anterior caeca occupying 25.1-31.3% (28.7%) of total body length and a mostly-intercaecal ovary. Cardicola jiigurru n. sp. differs from C. suni n. sp. and all other species of Cardicola by a combination of a narrowly lanceolate body, weakly-muscularised and poorly-demarcated oral sucker, minute tegumental spines <1 µm in length, and anterior caeca occupying 15.9-22.0% (19.4%) of total body length, an almost entirely post-caecal ovary and the male genital pore terminal on a dorsolateral protuberance. A third species, closely resembling C. suni n. sp., was also discovered off Wangetti Beach, north Queensland, but is not described due to lack of material. Molecular phylogenetic analysis, based on both ITS2 and partial 28S rDNA regions, shows that these three species form a clade nested within that formed by existing species of Cardicola.

Mdt1 Facilitates Efficient Repair of Blocked DNA Double-Strand Breaks and Recombinational Maintenance of Telomeres▿

PubMed Central

Pike, Brietta L.; Heierhorst, Jörg

2007-01-01

DNA recombination plays critical roles in DNA repair and alternative telomere maintenance. Here we show that absence of the SQ/TQ cluster domain-containing protein Mdt1 (Ybl051c) renders Saccharomyces cerevisiae particularly hypersensitive to bleomycin, a drug that causes 3′-phospho-glycolate-blocked DNA double-strand breaks (DSBs). mdt1Δ also hypersensitizes partially recombination-defective cells to camptothecin-induced 3′-phospho-tyrosyl protein-blocked DSBs. Remarkably, whereas mdt1Δ cells are unable to restore broken chromosomes after bleomycin treatment, they efficiently repair “clean” endonuclease-generated DSBs. Epistasis analyses indicate that MDT1 acts in the repair of bleomycin-induced DSBs by regulating the efficiency of the homologous recombination pathway as well as telomere-related functions of the KU complex. Moreover, mdt1Δ leads to severe synthetic growth defects with a deletion of the recombination facilitator and telomere-positioning factor gene CTF18 already in the absence of exogenous DNA damage. Importantly, mdt1Δ causes a dramatic shift from the usually prevalent type II to the less-efficient type I pathway of recombinational telomere maintenance in the absence of telomerase in liquid senescence assays. As telomeres resemble protein-blocked DSBs, the results indicate that Mdt1 acts in a novel blocked-end-specific recombination pathway that is required for the efficiency of both drug-induced DSB repair and telomerase-independent telomere maintenance. PMID:17636027

The Bacteroides sp. 3_1_23 Pif1 protein is a multifunctional helicase.

PubMed

Liu, Na-Nv; Duan, Xiao-Lei; Ai, Xia; Yang, Yan-Tao; Li, Ming; Dou, Shuo-Xing; Rety, Stephane; Deprez, Eric; Xi, Xu-Guang

2015-10-15

ScPif1 DNA helicase is the prototypical member of a 5'-to-3' helicase superfamily conserved from bacteria to human and plays various roles in the maintenance of genomic homeostasis. While many studies have been performed with eukaryotic Pif1 helicases, including yeast and human Pif1 proteins, the potential functions and biochemical properties of prokaryotic Pif1 helicases remain largely unknown. Here, we report the expression, purification and biochemical analysis of Pif1 helicase from Bacteroides sp. 3_1_23 (BsPif1). BsPif1 binds to a large panel of DNA substrates and, in particular, efficiently unwinds partial duplex DNAs with 5'-overhang, fork-like substrates, D-loop and flap-like substrates, suggesting that BsPif1 may act at stalled DNA replication forks and enhance Okazaki fragment maturation. Like its eukaryotic homologues, BsPif1 resolves R-loop structures and unwinds DNA-RNA hybrids. Furthermore, BsPif1 efficiently unfolds G-quadruplexes and disrupts nucleoprotein complexes. Altogether, these results highlight that prokaryotic Pif1 helicases may resolve common issues that arise during DNA transactions. Interestingly, we found that BsPif1 is different from yeast Pif1, but resembles more human Pif1 with regard to substrate specificity, helicase activity and mode of action. These findings are discussed in the context of the possible functions of prokaryotic Pif1 helicases in vivo. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Resemblance of actin-binding protein/actin gels to covalently crosslinked networks

NASA Astrophysics Data System (ADS)

Janmey, Paul A.; Hvidt, Søren; Lamb, Jennifer; Stossel, Thomas P.

1990-05-01

THE maintainance of the shape of cells is often due to their surface elasticity, which arises mainly from an actin-rich cytoplasmic cortex1,2. On locomotion, phagocytosis or fission, however, these cells become partially fluid-like. The finding of proteins that can bind to actin and control the assembly of, or crosslink, actin filaments, and of intracellular messages that regulate the activities of some of these actin-binding proteins, indicates that such 'gel sol' transformations result from the rearrangement of cortical actin-rich networks3. Alternatively, on the basis of a study of the mechanical properties of mixtures of actin filaments and an Acanthamoeba actin-binding protein, α-actinin, it has been proposed that these transformations can be accounted for by rapid exchange of crosslinks between actin filaments4: the cortical network would be solid when the deformation rate is greater than the rate of crosslink exchange, but would deform or 'creep' when deformation is slow enough to permit crosslinker molecules to rearrange. Here we report, however, that mixtures of actin filaments and actin-binding protein (ABP), an actin crosslinking protein of many higher eukaryotes, form gels Theologically equivalent to covalently crosslinked networks. These gels do not creep in response to applied stress on a time scale compatible with most cell-surface movements. These findings support a more complex and controlled mechanism underlying the dynamic mechanical properties of cortical cytoplasm, and can explain why cells do not collapse under the constant shear forces that often exist in tissues.

Hydrogen sulfide interacts with calcium signaling to enhance the chromium tolerance in Setaria italica.

PubMed

Fang, Huihui; Jing, Tao; Liu, Zhiqiang; Zhang, Liping; Jin, Zhuping; Pei, Yanxi

2014-12-01

The oscillation of intracellular calcium (Ca(2+)) concentration is a primary event in numerous biological processes in plants, including stress response. Hydrogen sulfide (H2S), an emerging gasotransmitter, was found to have positive effects in plants responding to chromium (Cr(6+)) stress through interacting with Ca(2+) signaling. While Ca(2+) resemblances H2S in mediating biotic and abiotic stresses, crosstalk between the two pathways remains unclear. In this study, Ca(2+) signaling interacted with H2S to produce a complex physiological response, which enhanced the Cr(6+) tolerance in foxtail millet (Setaria italica). Results indicate that Cr(6+) stress activated endogenous H2S synthesis as well as Ca(2+) signaling. Moreover, toxic symptoms caused by Cr(6+) stress were strongly moderated by 50μM H2S and 20mM Ca(2+). Conversely, treatments with H2S synthesis inhibitor and Ca(2+) chelators prior to Cr(6+)-exposure aggravated these toxic symptoms. Interestingly, Ca(2+) upregulated expression of two important factors in metal metabolism, MT3A and PCS, which participated in the biosynthesis of heavy metal chelators, in a H2S-dependent manner to cope with Cr(6+) stress. These findings also suggest that the H2S dependent pathway is a component of the Ca(2+) activating antioxidant system and H2S partially contributes Ca(2+)-activating antioxidant system. Copyright © 2014 Elsevier Ltd. All rights reserved.

Are SCN1A gene mutations responsible for genetic susceptibility to subacute sclerosing panencephalitis?

PubMed

Garg, Ravindra Kumar

2012-02-01

Dravet syndrome, characterized predominantly by myoclonus, has a striking clinical resemblance to subacute sclerosing panencephalitis (SSPE). Patients with Dravet syndrome develop significant mental decline with advancing age of affected child like in SSPE. It is well established that SCN1A gene mutations are associated with Dravet syndrome. Even periodic EEG complexes have been described in Dravet syndrome. In addition to Dravet syndrome, several other types of acute and subacute encephalopathic syndromes having clinical and electroencephalographic resemblance to SSPE are associated with SCN1A gene mutations. SSPE is a devastating progressive inflammatory disorder of the central nervous system. It is caused by persistent infection of the brain by an aberrant measles virus. Only a few of a vast number of measles infected pediatric population develop SSPE. There are several reports describing presence of SSPE is close relatives and it has been described previously in sibling and twin pairs. A genetic susceptibility for development of SSPE is likely. In fact, a variety of genetic abnormalities have already been described in patients with SSPE. It can also be argued that because of striking clinical resemblance between Dravet and various epileptic and encephalopathic syndromes associated with SCN1A gene mutations and SSPE, SCN1A gene abnormalities may also be responsible for susceptibility to SSPE in measles infected children. Copyright © 2011 Elsevier Ltd. All rights reserved.

Termination Patterns of Complex Partial Seizures: An Intracranial EEG Study

PubMed Central

Afra, Pegah; Jouny, Christopher C.; Bergey, Gregory K.

2015-01-01

Purpose While seizure onset patterns have been the subject of many reports, there have been few studies of seizure termination. In this study we report the incidence of synchronous and asynchronous termination patterns of partial seizures recorded with intracranial arrays. Methods Data were collected from patients with intractable complex partial seizures undergoing presurgical evaluations with intracranial electrodes. Patients with seizures originating from mesial temporal and neocortical regions were grouped into three groups based on patterns of seizure termination: synchronous only (So), asynchronous only (Ao), or mixed (S/A, with both synchronous and asynchronous termination patterns). Results 88% of the patients in the MT group had seizures with a synchronous pattern of termination exclusively (38%) or mixed (50%). 82% of the NC group had seizures with synchronous pattern of termination exclusively (52%) or mixed (30%). In the NC group, there was a significant difference of the range of seizure durations between So and Ao groups, with Ao exhibiting higher variability. Seizures with synchronous termination had low variability in both groups. Conclusions Synchronous seizure termination is a common pattern for complex partial seizures of both mesial temporal or neocortical onset. This may reflect stereotyped network behavior or dynamics at the seizure focus. PMID:26552555

Feasibility for direct rapid energy dispersive X-ray fluorescence (EDXRF) and scattering analysis of complex matrix liquids by partial least squares.

PubMed

Angeyo, K H; Gari, S; Mustapha, A O; Mangala, J M

2012-11-01

The greatest challenge to material characterization by XRF technique is encountered in direct trace analysis of complex matrices. We exploited partial least squares (PLS) in conjunction with energy dispersive X-ray fluorescence and scattering (EDXRFS) spectrometry to rapidly (200 s) analyze lubricating oils. The PLS-EDXRFS method affords non-invasive quality assurance (QA) analysis of complex matrix liquids as it gave optimistic results for both heavy- and low-Z metal additives. Scatter peaks may further be used for QA characterization via the light elements. Copyright © 2012 Elsevier Ltd. All rights reserved.

A Lamellar Complex of Lecithin and Poly-l-Tyrosine

PubMed Central

Giannoni, G.; Padden, F. J.; Roe, R. J.

1971-01-01

Complexes of poly-L-tyrosine (PT) with dipalmitoyllecithin, synthetic, (DPL) and with egg lecithin (EL) have been obtained by precipitation from methanol-water solutions. Chemical analysis indicates that both lecithins bind PT up to a limiting ratio of about 4 tyrosine residues/lecithin molecule. DPL-PT complexes have a lamellar structure closely resembling lecithin itself. In fact, DPL and DPL-PT lamellae have very nearly the same thickness as precipitated from methanol-water, although their swelling behavior on resuspension in pure water is different. The complexes crystallize in the form of hexagonal platelets, some monolayers and some with terraced spiral growths, with a thickness of 50-55 A. In X-ray and electron diffraction they yield sharp reflections at 4.14 A which are characteristic of hexagonal packing of phospholipid paraffinic chains. The order-disorder transition temperature of this crystalline lattice, determined by differential scanning calorimetry, is somewhat higher in the complex than in pure DPL. Physical models consistent with these observations are discussed. ImagesFIGURE 1 aFIGURE 1 b PMID:5134208

10. PARTIAL VIEW OF SOUTH FACE OF MST AND BRIDGE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

10. PARTIAL VIEW OF SOUTH FACE OF MST AND BRIDGE CRANE MOVED TO ITS SOUTHERN LIMIT - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 West, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

11. PARTIAL VIEW OF NORTH FACE OF MST AND BRIDGE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

11. PARTIAL VIEW OF NORTH FACE OF MST AND BRIDGE CRANE MOVED TO ITS NORTHERN LIMIT - Vandenberg Air Force Base, Space Launch Complex 3, Launch Pad 3 West, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

Clinical, pathological and functional characterization of riboflavin-responsive neuropathy

PubMed Central

Manole, Andreea; Jaunmuktane, Zane; Hargreaves, Iain; Ludtmann, Marthe H R; Salpietro, Vincenzo; Bello, Oscar D; Pope, Simon; Pandraud, Amelie; Horga, Alejandro; Scalco, Renata S; Li, Abi; Ashokkumar, Balasubramaniem; Lourenço, Charles M; Heales, Simon; Horvath, Rita; Chinnery, Patrick F; Toro, Camilo; Singleton, Andrew B; Jacques, Thomas S; Abramov, Andrey Y; Muntoni, Francesco; Hanna, Michael G; Reilly, Mary M; Revesz, Tamas; Kullmann, Dimitri M

2017-01-01

Abstract Brown-Vialetto-Van Laere syndrome represents a phenotypic spectrum of motor, sensory, and cranial nerve neuropathy, often with ataxia, optic atrophy and respiratory problems leading to ventilator-dependence. Loss-of-function mutations in two riboflavin transporter genes, SLC52A2 and SLC52A3, have recently been linked to Brown-Vialetto-Van Laere syndrome. However, the genetic frequency, neuropathology and downstream consequences of riboflavin transporter mutations are unclear. By screening a large cohort of 132 patients with early-onset severe sensory, motor and cranial nerve neuropathy we confirmed the strong genetic link between riboflavin transporter mutations and Brown-Vialetto-Van Laere syndrome, identifying 22 pathogenic mutations in SLC52A2 and SLC52A3, 14 of which were novel. Brain and spinal cord neuropathological examination of two cases with SLC52A3 mutations showed classical symmetrical brainstem lesions resembling pathology seen in mitochondrial disease, including severe neuronal loss in the lower cranial nerve nuclei, anterior horns and corresponding nerves, atrophy of the spinothalamic and spinocerebellar tracts and posterior column–medial lemniscus pathways. Mitochondrial dysfunction has previously been implicated in an array of neurodegenerative disorders. Since riboflavin metabolites are critical components of the mitochondrial electron transport chain, we hypothesized that reduced riboflavin transport would result in impaired mitochondrial activity, and confirmed this using in vitro and in vivo models. Electron transport chain complex I and complex II activity were decreased in SLC52A2 patient fibroblasts, while global knockdown of the single Drosophila melanogaster riboflavin transporter homologue revealed reduced levels of riboflavin, downstream metabolites, and electron transport chain complex I activity. This in turn led to abnormal mitochondrial membrane potential, respiratory chain activity and morphology. Riboflavin transporter knockdown in Drosophila also resulted in severely impaired locomotor activity and reduced lifespan, mirroring patient pathology, and these phenotypes could be partially rescued using a novel esterified derivative of riboflavin. Our findings expand the genetic, clinical and neuropathological features of Brown-Vialetto-Van Laere syndrome, implicate mitochondrial dysfunction as a downstream consequence of riboflavin transporter gene defects, and validate riboflavin esters as a potential therapeutic strategy. PMID:29053833

Clinical, pathological and functional characterization of riboflavin-responsive neuropathy.

PubMed

Manole, Andreea; Jaunmuktane, Zane; Hargreaves, Iain; Ludtmann, Marthe H R; Salpietro, Vincenzo; Bello, Oscar D; Pope, Simon; Pandraud, Amelie; Horga, Alejandro; Scalco, Renata S; Li, Abi; Ashokkumar, Balasubramaniem; Lourenço, Charles M; Heales, Simon; Horvath, Rita; Chinnery, Patrick F; Toro, Camilo; Singleton, Andrew B; Jacques, Thomas S; Abramov, Andrey Y; Muntoni, Francesco; Hanna, Michael G; Reilly, Mary M; Revesz, Tamas; Kullmann, Dimitri M; Jepson, James E C; Houlden, Henry

2017-11-01

Brown-Vialetto-Van Laere syndrome represents a phenotypic spectrum of motor, sensory, and cranial nerve neuropathy, often with ataxia, optic atrophy and respiratory problems leading to ventilator-dependence. Loss-of-function mutations in two riboflavin transporter genes, SLC52A2 and SLC52A3, have recently been linked to Brown-Vialetto-Van Laere syndrome. However, the genetic frequency, neuropathology and downstream consequences of riboflavin transporter mutations are unclear. By screening a large cohort of 132 patients with early-onset severe sensory, motor and cranial nerve neuropathy we confirmed the strong genetic link between riboflavin transporter mutations and Brown-Vialetto-Van Laere syndrome, identifying 22 pathogenic mutations in SLC52A2 and SLC52A3, 14 of which were novel. Brain and spinal cord neuropathological examination of two cases with SLC52A3 mutations showed classical symmetrical brainstem lesions resembling pathology seen in mitochondrial disease, including severe neuronal loss in the lower cranial nerve nuclei, anterior horns and corresponding nerves, atrophy of the spinothalamic and spinocerebellar tracts and posterior column-medial lemniscus pathways. Mitochondrial dysfunction has previously been implicated in an array of neurodegenerative disorders. Since riboflavin metabolites are critical components of the mitochondrial electron transport chain, we hypothesized that reduced riboflavin transport would result in impaired mitochondrial activity, and confirmed this using in vitro and in vivo models. Electron transport chain complex I and complex II activity were decreased in SLC52A2 patient fibroblasts, while global knockdown of the single Drosophila melanogaster riboflavin transporter homologue revealed reduced levels of riboflavin, downstream metabolites, and electron transport chain complex I activity. This in turn led to abnormal mitochondrial membrane potential, respiratory chain activity and morphology. Riboflavin transporter knockdown in Drosophila also resulted in severely impaired locomotor activity and reduced lifespan, mirroring patient pathology, and these phenotypes could be partially rescued using a novel esterified derivative of riboflavin. Our findings expand the genetic, clinical and neuropathological features of Brown-Vialetto-Van Laere syndrome, implicate mitochondrial dysfunction as a downstream consequence of riboflavin transporter gene defects, and validate riboflavin esters as a potential therapeutic strategy. © The Author (2017). Published by Oxford University Press on behalf of the Guarantors of Brain.

Complexation- and ligand-induced metal release from 316L particles: importance of particle size and crystallographic structure.

PubMed

Hedberg, Yolanda; Hedberg, Jonas; Liu, Yi; Wallinder, Inger Odnevall

2011-12-01

Iron, chromium, nickel, and manganese released from gas-atomized AISI 316L stainless steel powders (sized <45 and <4 μm) were investigated in artificial lysosomal fluid (ALF, pH 4.5) and in solutions of its individual inorganic and organic components to determine its most aggressive component, elucidate synergistic effects, and assess release mechanisms, in dependence of surface changes using atomic absorption spectroscopy, Raman, XPS, and voltammetry. Complexation is the main reason for metal release from 316L particles immersed in ALF. Iron was mainly released, while manganese was preferentially released as a consequence of the reduction of manganese oxide on the surface. These processes resulted in highly complexing media in a partial oxidation of trivalent chromium to hexavalent chromium on the surface. The extent of metal release was partially controlled by surface properties (e.g., availability of elements on the surface and structure of the outermost surface) and partially by the complexation capacity of the different metals with the complexing agents of the different media. In general, compared to the coarse powder (<45 μm), the fine (<4 μm) powder displayed significantly higher released amounts of metals per surface area, increased with increased solution complexation capacity, while less amounts of metals were released into non-complexing solutions. Due to the ferritic structure of lower solubility for nickel of the fine powder, more nickel was released into all solutions compared with the coarser powder.

Architecture and ssDNA interaction of the Timeless-Tipin-RPA complex

PubMed Central

Witosch, Justine; Wolf, Eva; Mizuno, Naoko

2014-01-01

The Timeless-Tipin (Tim-Tipin) complex, also referred to as the fork protection complex, is involved in coordination of DNA replication. Tim-Tipin is suggested to be recruited to replication forks via Replication Protein A (RPA) but details of the interaction are unknown. Here, using cryo-EM and biochemical methods, we characterized complex formation of Tim-Tipin, RPA and single-stranded DNA (ssDNA). Tim-Tipin and RPA form a 258 kDa complex with a 1:1:1 stoichiometry. The cryo-EM 3D reconstruction revealed a globular architecture of the Tim-Tipin-RPA complex with a ring-like and a U-shaped domain covered by a RPA lid. Interestingly, RPA in the complex adopts a horse shoe-like shape resembling its conformation in the presence of long ssDNA (>30 nucleotides). Furthermore, the recruitment of the Tim-Tipin-RPA complex to ssDNA is modulated by the RPA conformation and requires RPA to be in the more compact 30 nt ssDNA binding mode. The dynamic formation and disruption of the Tim-Tipin-RPA-ssDNA complex implicates the RPA-based recruitment of Tim-Tipin to the replication fork. PMID:25348395

Symptomatic complex partial status epilepticus manifesting as utilization behavior of a mobile phone.

PubMed

Carota, Antonio; Novy, Jan; Rossetti, Andrea O

2009-03-01

Utilization behavior (UB) consists of reaching out and using objects in the environment in an automatic manner and out of context. This behavior has been correlated to frontal lobe dysfunction, especially of the right hemisphere. We describe a 60-year-old woman, affected by a glioblastoma located in the right frontal region, who presented with intermittent UB of the mobile phone as the main clinical manifestation of partial complex status epilepticus. Video/EEG studies showed a striking correlation between mobile phone utilization and ictal epileptic activity. Clinical and EEG findings were markedly reduced after the introduction of antiepileptic drugs. This case study suggests that UB may be added to the symptoms described for partial seizures originating from frontal areas.

Temporal precision in the visual pathway through the interplay of excitation and stimulus-driven suppression.

PubMed

Butts, Daniel A; Weng, Chong; Jin, Jianzhong; Alonso, Jose-Manuel; Paninski, Liam

2011-08-03

Visual neurons can respond with extremely precise temporal patterning to visual stimuli that change on much slower time scales. Here, we investigate how the precise timing of cat thalamic spike trains-which can have timing as precise as 1 ms-is related to the stimulus, in the context of both artificial noise and natural visual stimuli. Using a nonlinear modeling framework applied to extracellular data, we demonstrate that the precise timing of thalamic spike trains can be explained by the interplay between an excitatory input and a delayed suppressive input that resembles inhibition, such that neuronal responses only occur in brief windows where excitation exceeds suppression. The resulting description of thalamic computation resembles earlier models of contrast adaptation, suggesting a more general role for mechanisms of contrast adaptation in visual processing. Thus, we describe a more complex computation underlying thalamic responses to artificial and natural stimuli that has implications for understanding how visual information is represented in the early stages of visual processing.

Transcriptome analysis of the phytobacterium Xylella fastidiosa growing under xylem-based chemical conditions.

PubMed

Ciraulo, Maristela Boaceff; Santos, Daiene Souza; Rodrigues, Ana Claudia de Freitas Oliveira; de Oliveira, Marcus Vinícius; Rodrigues, Tiago; de Oliveira, Regina Costa; Nunes, Luiz R

2010-01-01

Xylella fastidiosa is a xylem-limited bacterium responsible for important plant diseases, like citrus-variegated chlorosis (CVC) and grapevine Pierce's disease (PD). Interestingly, in vitro growth of X. fastidiosa in chemically defined media that resemble xylem fluid has been achieved, allowing studies of metabolic processes used by xylem-dwelling bacteria to thrive in such nutrient-poor conditions. Thus, we performed microarray hybridizations to compare transcriptomes of X. fastidiosa cells grown in 3G10-R, a medium that resembles grape sap, and in Periwinkle Wilt (PW), the complex medium traditionally used to cultivate X. fastidiosa. We identified 299 transcripts modulated in response to growth in these media. Some 3G10R-overexpressed genes have been shown to be upregulated in cells directly isolated from infected plants and may be involved in plant colonization, virulence and environmental competition. In contrast, cells cultivated in PW show a metabolic switch associated with increased aerobic respiration and enhanced bacterial growth rates.

Transcriptome Analysis of the Phytobacterium Xylella fastidiosa Growing under Xylem-Based Chemical Conditions

PubMed Central

Ciraulo, Maristela Boaceff; Santos, Daiene Souza; Rodrigues, Ana Claudia de Freitas Oliveira; de Oliveira, Marcus Vinícius; Rodrigues, Tiago; de Oliveira, Regina Costa; Nunes, Luiz R.

2010-01-01

Xylella fastidiosa is a xylem-limited bacterium responsible for important plant diseases, like citrus-variegated chlorosis (CVC) and grapevine Pierce's disease (PD). Interestingly, in vitro growth of X. fastidiosa in chemically defined media that resemble xylem fluid has been achieved, allowing studies of metabolic processes used by xylem-dwelling bacteria to thrive in such nutrient-poor conditions. Thus, we performed microarray hybridizations to compare transcriptomes of X. fastidiosa cells grown in 3G10-R, a medium that resembles grape sap, and in Periwinkle Wilt (PW), the complex medium traditionally used to cultivate X. fastidiosa. We identified 299 transcripts modulated in response to growth in these media. Some 3G10R-overexpressed genes have been shown to be upregulated in cells directly isolated from infected plants and may be involved in plant colonization, virulence and environmental competition. In contrast, cells cultivated in PW show a metabolic switch associated with increased aerobic respiration and enhanced bacterial growth rates. PMID:20625415

Macrofaunal recolonization of copper-contaminated sediments in San Diego Bay.

PubMed

Neira, Carlos; Mendoza, Guillermo; Porrachia, Magali; Stransky, Chris; Levin, Lisa A

2015-12-30

Effects of Cu-loading on macrofaunal recolonization were examined in Shelter Island Yacht Basin (San Diego Bay, California). Sediments with high and low Cu levels were defaunated and Cu-spiked, translocated, and then placed back into the environment. These demonstrated that the alteration observed in benthic communities associated with Cu contamination occurs during initial recolonization. After a 3-month exposure to sediments with varying Cu levels, two primary colonizing communities were identified: (1) a "mouth assemblage" resembling adjacent background fauna associated with low-Cu levels that was more diverse and predominantly dominated by surface- and subsurface-deposit feeders, burrowers, and tube builders, and (2) a "head assemblage" resembling adjacent background fauna associated with high-Cu concentrations, with few dominant species and an increasing importance of carnivores and mobile epifauna. Cu loading can cause reduced biodiversity and lower structural complexity that may last several months if high concentrations persist, with a direct effect on community functioning. Copyright © 2015 Elsevier Ltd. All rights reserved.

Silica deposits on Mars with features resembling hot spring biosignatures at El Tatio in Chile

PubMed Central

Ruff, Steven W.; Farmer, Jack D.

2016-01-01

The Mars rover Spirit encountered outcrops and regolith composed of opaline silica (amorphous SiO2·nH2O) in an ancient volcanic hydrothermal setting in Gusev crater. An origin via either fumarole-related acid-sulfate leaching or precipitation from hot spring fluids was suggested previously. However, the potential significance of the characteristic nodular and mm-scale digitate opaline silica structures was not recognized. Here we report remarkably similar features within active hot spring/geyser discharge channels at El Tatio in northern Chile, where halite-encrusted silica yields infrared spectra that are the best match yet to spectra from Spirit. Furthermore, we show that the nodular and digitate silica structures at El Tatio that most closely resemble those on Mars include complex sedimentary structures produced by a combination of biotic and abiotic processes. Although fully abiotic processes are not ruled out for the Martian silica structures, they satisfy an a priori definition of potential biosignatures. PMID:27853166

3-D Object Pose Determination Using Complex EGI

DTIC Science & Technology

1990-10-01

the length of edges of the polyhedron from the EGI. Dane and Bajcsy [4] make use of the Gaussian Image to spatially segment a group of range points...involving real range data of two smooth objects were conducted. The two smooth objects are the torus and ellipsoid, whose databases have been created...in the simulations earlier. 5.0.1 Implementational Issues The torus and ellipsoid were crafted out of clay to resemble the models whose databases were

Eukaryotic-Like Virus Budding in Archaea

PubMed Central

Quemin, Emmanuelle R. J.; Chlanda, Petr; Sachse, Martin; Forterre, Patrick

2016-01-01

ABSTRACT Similar to many eukaryotic viruses (and unlike bacteriophages), viruses infecting archaea are often encased in lipid-containing envelopes. However, the mechanisms of their morphogenesis and egress remain unexplored. Here, we used dual-axis electron tomography (ET) to characterize the morphogenesis of Sulfolobus spindle-shaped virus 1 (SSV1), the prototype of the family Fuselloviridae and representative of the most abundant archaea-specific group of viruses. Our results show that SSV1 assembly and egress are concomitant and occur at the cellular cytoplasmic membrane via a process highly reminiscent of the budding of enveloped viruses that infect eukaryotes. The viral nucleoprotein complexes are extruded in the form of previously unknown rod-shaped intermediate structures which have an envelope continuous with the host membrane. Further maturation into characteristic spindle-shaped virions takes place while virions remain attached to the cell surface. Our data also revealed the formation of constricted ring-like structures which resemble the budding necks observed prior to the ESCRT machinery-mediated membrane scission during egress of various enveloped viruses of eukaryotes. Collectively, we provide evidence that archaeal spindle-shaped viruses contain a lipid envelope acquired upon budding of the viral nucleoprotein complex through the host cytoplasmic membrane. The proposed model bears a clear resemblance to the egress strategy employed by enveloped eukaryotic viruses and raises important questions as to how the archaeal single-layered membrane composed of tetraether lipids can undergo scission. PMID:27624130

Reconstitution of the Light Harvesting Chlorophyll a/b Pigment-Protein Complex into Developing Chloroplast Membranes Using a Dialyzable Detergent 1

PubMed Central

Darr, Sylvia C.; Arntzen, Charles J.

1986-01-01

Conditions were developed to isolate the light-harvesting chlorophyll-protein complex serving photosystem II (LHC-II) using a dialyzable detergent, octylpolyoxyethylene. This LHC-II was successfully reconstituted into partially developed chloroplast thylakoids of Hordeum vulgare var Morex (barley) seedlings which were deficient in LHC-II. Functional association of LHC-II with the photosystem II (PSII) core complex was measured by two independent functional assays of PSII sensitization by LHC-II. A 3-fold excess of reconstituted LHC-II was required to equal the activity of LHC developing in vivo. We suggest that a linker component may be absent in the partially developed membranes which is required for specific association of the PSII core complex and LHC-II. Images Fig. 1 PMID:16664744

Geochemistry and petrogenesis of the Laramie anorthosite complex, Wyoming

USGS Publications Warehouse

Fountain, J.C.; Hodge, D.S.; Allan, Hills F.

1981-01-01

A geochemical investigation of the Laramie anorthosite complex determined that monsonite associated with the complex are characterized by positive Eu anomalies and display a regular variation in composition with distance from the monzonite/county rock contact. Anorthositic rocks have major and trace element abundance typical of similar complexes. The internal variations in the monzonite were produced by in situ fractionation and contamination. The data indicate that anorthosite and monzonite cannot be comagmatic. It is proposed that the anorthosite and monzonite of the complex evolved from two distinct magmas, and that two stages of anatectic melting contributed to the evolution of the monzonite. An initial stage of partial melting was induced by intrusion of a gabbroic anorthosite magma into the lower crust; a second partial melting event occurred after emplacement where heat from the intrusions melted country rocks resulting in extensive contamination ofthe monzonite. ?? 1981.

Identification of Clinical Isolates of Actinomyces Species by Amplified 16S Ribosomal DNA Restriction Analysis

PubMed Central

Hall, Val; Talbot, P. R.; Stubbs, S. L.; Duerden, B. I.

2001-01-01

Amplified 16S ribosomal DNA (rDNA) restriction analysis (ARDRA), using enzymes HaeIII and HpaII, was applied to 176 fresh and 299 stored clinical isolates of putative Actinomyces spp. referred to the Anaerobe Reference Unit of the Public Health Laboratory Service for confirmation of identity. Results were compared with ARDRA results obtained previously for reference strains and with conventional phenotypic reactions. Identities of some strains were confirmed by analysis of partial 16S rDNA sequences. Of the 475 isolates, 331 (70%) were clearly assigned to recognized Actinomyces species, including 94 isolates assigned to six recently described species. A further 52 isolates in 12 ARDRA profiles were designated as apparently resembling recognized species, and 44 isolates, in 18 novel profiles, were confirmed as members of genera other than Actinomyces. The identities of 48 isolates in nine profiles remain uncertain, and they may represent novel species of Actinomyces. For the majority of species, phenotypic results, published reactions for the species, and ARDRA profiles concurred. However, of 113 stored isolates originally identified as A. meyeri or resembling A. meyeri by phenotypic tests, only 21 were confirmed as A. meyeri by ARDRA; 63 were reassigned as A. turicensis, 7 as other recognized species, and 22 as unidentified actinomycetes. Analyses of incidence and clinical associations of Actinomyces spp. add to the currently sparse knowledge of some recently described species. PMID:11574572

Severity of mutant phenotype in a series of chlorophyll-deficient wheat mutants depends on light intensity and the severity of the block in chlorophyll synthesis.

PubMed

Falbel, T G; Meehl, J B; Staehelin, L A

1996-10-01

Analyses of a series of allelic chlorina mutants of wheat (Triticum aestivum L.), which have partial blocks in chlorophyll (Chl) synthesis and, therefore, a limited Chl supply, reinforce the principle that Chl is required for the stable accumulation of Chl-binding proteins and that only reaction centers accumulate when the supply of Chl is severely limited. Depending on the rate of Chl accumulation (determined by the severity of the mutation) and on the rate of turnover of Chl and its precursors (determined by the environment in which the plant is grown), the mutants each reach an equilibrium of Chl synthesis and degradation. Together these mutants generate a spectrum of phenotypes. Under the harshest conditions (high illumination), plants with moderate blocks in Chl synthesis have membranes with very little Chl and Chl-proteins and membrane stacks resembling the thylakoids of the lethal xantha mutants of barely grown at low to medium light intensities (which have more severe blocks). In contrast, when grown under low-light conditions the same plants with moderate blocks have thylakoids resembling those of the wild type. The wide range of phenotypes of Chl b-deficient mutants has historically produced more confusion than enlightenment, but incomparable growth conditions can now explain the discrepancies reported in the literature.

Severity of mutant phenotype in a series of chlorophyll-deficient wheat mutants depends on light intensity and the severity of the block in chlorophyll synthesis.

PubMed Central

Falbel, T G; Meehl, J B; Staehelin, L A

1996-01-01

Analyses of a series of allelic chlorina mutants of wheat (Triticum aestivum L.), which have partial blocks in chlorophyll (Chl) synthesis and, therefore, a limited Chl supply, reinforce the principle that Chl is required for the stable accumulation of Chl-binding proteins and that only reaction centers accumulate when the supply of Chl is severely limited. Depending on the rate of Chl accumulation (determined by the severity of the mutation) and on the rate of turnover of Chl and its precursors (determined by the environment in which the plant is grown), the mutants each reach an equilibrium of Chl synthesis and degradation. Together these mutants generate a spectrum of phenotypes. Under the harshest conditions (high illumination), plants with moderate blocks in Chl synthesis have membranes with very little Chl and Chl-proteins and membrane stacks resembling the thylakoids of the lethal xantha mutants of barely grown at low to medium light intensities (which have more severe blocks). In contrast, when grown under low-light conditions the same plants with moderate blocks have thylakoids resembling those of the wild type. The wide range of phenotypes of Chl b-deficient mutants has historically produced more confusion than enlightenment, but incomparable growth conditions can now explain the discrepancies reported in the literature. PMID:8883392

Inferior Cerebellar Hypoplasia Resembling a Dandy-Walker-Like Malformation in Purebred Eurasier Dogs with Familial Non-Progressive Ataxia: A Retrospective and Prospective Clinical Cohort Study

PubMed Central

Bernardino, Filipa; Rentmeister, Kai; Schmidt, Martin J.; Bruehschwein, Andreas; Matiasek, Kaspar; Matiasek, Lara A.; Lauda, Alexander; Schoon, Heinz A.; Fischer, Andrea

2015-01-01

Cerebellar malformations can be inherited or caused by insults during cerebellar development. To date, only sporadic cases of cerebellar malformations have been reported in dogs, and the genetic background has remained obscure. Therefore, this study`s objective was to describe the clinical characteristics, imaging features and pedigree data of a familial cerebellar hypoplasia in purebred Eurasier dogs. A uniform cerebellar malformation characterized by consistent absence of the caudal portions of the cerebellar vermis and, to a lesser degree, the caudal portions of the cerebellar hemispheres in association with large retrocerebellar fluid accumulations was recognized in 14 closely related Eurasier dogs. Hydrocephalus was an additional feature in some dogs. All dogs displayed non-progressive ataxia, which had already been noted when the dogs were 5 – 6 weeks old. The severity of the ataxia varied between dogs, from mild truncal sway, subtle dysmetric gait, dysequilibrium and pelvic limb ataxia to severe cerebellar ataxia in puppies and episodic falling or rolling. Follow-up examinations in adult dogs showed improvement of the cerebellar ataxia and a still absent menace response. Epileptic seizures occurred in some dogs. The association of partial vermis agenesis with an enlarged fourth ventricle and an enlarged caudal (posterior) fossa resembled a Dandy-Walker-like malformation in some dogs. Pedigree analyses were consistent with autosomal recessive inheritance. PMID:25668516

Secular trends of infectious disease mortality in The Netherlands, 1911-1978: quantitative estimates of changes coinciding with the introduction of antibiotics.

PubMed

Mackenbach, J P; Looman, C W

1988-09-01

Secular trends of mortality from 21 infectious diseases in the Netherlands were studied by inspection of age/sex-standardized mortality curves and by log-linear regression analysis. An attempt was made to obtain quantitative estimates for changes coinciding with the introduction of antibiotics. Two possible types of effect were considered: a sharp reduction of mortality at the moment of the introduction of antibiotics, and a longer lasting (acceleration of) mortality decline after the introduction. Changes resembling the first type of effect were possibly present for many infectious diseases, but were difficult to measure exactly, due to late effects on mortality of World War II. Changes resembling the second type of effect were present in 16 infectious diseases and were sometimes quite large. For example, estimated differences in per cent per annum mortality change were 10% or larger for puerperal fever, scarlet fever, rheumatic fever, erysipelas, otitis media, tuberculosis, and bacillary dysentery. No acceleration of mortality decline after the introduction of antibiotics was present in mortality from 'all other diseases'. Although the exact contribution of antibiotics to the observed changes cannot be inferred from this time trend analysis, the quantitative estimates of the changes show that even a partial contribution would represent a substantial effect of antibiotics on mortality from infectious diseases in the Netherlands.

Chemical Zoning of Feldspars in Lunar Granitoids: Implications for the Origins of Lunar Silicic Magmas

NASA Technical Reports Server (NTRS)

Mills, R. D; Simon, J. I.; Alexander, C.M. O'D.; Wang, J.; Christoffersen, R.; Rahman, Z..

2014-01-01

Fine-scale chemical and textural measurements of alkali and plagioclase feldspars in the Apollo granitoids (ex. Fig. 1) can be used to address their petrologic origin(s). Recent findings suggest that these granitoids may hold clues of global importance, rather than of only local significance for small-scale fractionation. Observations of morphological features that resemble silicic domes on the unsampled portion of the Moon suggest that local, sizable net-works of high-silica melt (>65 wt % SiO2) were present during crust-formation. Remote sensing data from these regions suggest high concentrations of Si and heat-producing elements (K, U, and Th). To help under-stand the role of high-silica melts in the chemical differentiation of the Moon, three questions must be answered: (1) when were these magmas generated?, (2) what was the source material?, and (3) were these magmas produced from internal differentiation. or impact melting and crystallization? Here we focus on #3. It is difficult to produce high-silica melts solely by fractional crystallization. Partial melting of preexisting crust may therefore also have been important and pos-sibly the primary mechanism that produced the silicic magmas on the Moon. Experimental studies demonstrate that partial melting of gabbroic rock under mildly hydrated conditions can produce high-silica compositions and it has been suggested by that partial melting by basaltic underplating is the mechanism by which high-silica melts were produced on the Moon. TEM and SIMS analyses, coordinated with isotopic dating and tracer studies, can help test whether the minerals in the Apollo granitoids formed in a plutonic setting or were the result of impact-induced partial melting. We analyzed granitoid clasts from 3 Apollo samples: polymict breccia 12013,141, crystalline-matrix breccia 14303,353, and breccia 15405,78

Developing a Comparative Docking Protocol for the Prediction of Peptide Selectivity Profiles: Investigation of Potassium Channel Toxins

PubMed Central

Chen, Po-Chia; Kuyucak, Serdar

2012-01-01

During the development of selective peptides against highly homologous targets, a reliable tool is sought that can predict information on both mechanisms of binding and relative affinities. These tools must first be tested on known profiles before application on novel therapeutic candidates. We therefore present a comparative docking protocol in HADDOCK using critical motifs, and use it to “predict” the various selectivity profiles of several major αKTX scorpion toxin families versus Kv1.1, Kv1.2 and Kv1.3. By correlating results across toxins of similar profiles, a comprehensive set of functional residues can be identified. Reasonable models of channel-toxin interactions can be then drawn that are consistent with known affinity and mutagenesis. Without biological information on the interaction, HADDOCK reproduces mechanisms underlying the universal binding of αKTX-2 toxins, and Kv1.3 selectivity of αKTX-3 toxins. The addition of constraints encouraging the critical lysine insertion confirms these findings, and gives analogous explanations for other families, including models of partial pore-block in αKTX-6. While qualitatively informative, the HADDOCK scoring function is not yet sufficient for accurate affinity-ranking. False minima in low-affinity complexes often resemble true binding in high-affinity complexes, despite steric/conformational penalties apparent from visual inspection. This contamination significantly complicates energetic analysis, although it is usually possible to obtain correct ranking via careful interpretation of binding-well characteristics and elimination of false positives. Aside from adaptations to the broader potassium channel family, we suggest that this strategy of comparative docking can be extended to other channels of interest with known structure, especially in cases where a critical motif exists to improve docking effectiveness. PMID:22474570

Unravelling the binding mechanism and protein stability of human serum albumin while interacting with nefopam analogues: a biophysical and insilico approach.

PubMed

Gokara, Mahesh; Narayana, Vidadala V; Sadarangani, Vineet; Chowdhury, Shatabdi Roy; Varkala, Sreelaxmi; Ramachary, Dhevalapally B; Subramanyam, Rajagopal

2017-08-01

In this study, molecular binding affinity was investigated for Nefopam analogues (NFs), a functionalized benzoxazocine, with human serum albumin (HSA), a major transport protein in the blood. Its binding affinity and concomitant changes in its conformation, binding site and simulations were also studied. Fluorescence data revealed that the fluorescence quenching of HSA upon binding of NFs analogues is based on a static mechanism. The three analogues of NFs binding constants (K A ) are in the order of NF3 > NF2 > NF1 with values of 1.53 ± .057 × 10 4 , 2.16 ± .071 × 10 4 and 3.6 ± .102 × 10 5  M -1 , respectively. Concurrently, thermodynamic parameters indicate that the binding process was spontaneous, and the complexes were stabilized mostly by hydrophobic interactions, except for NF2 has one hydrogen bond stabilizes it along with hydrophobic interactions. Circular dichroism (CD) studies revealed that there is a decrease in α-helix with an increase in β-sheets and random coils signifying partial unfolding of the protein upon binding of NFs, which might be due to the formation of NFs-HSA complexes. Further, molecular docking studies showed that NF1, NF2 and NF3 bound to subdomains IIIA, IB and IIA through hydrophobic interactions. However, NF1 have additionally formed a single hydrogen bond with LYS 413. Furthermore, molecular simulations unveiled that NFs binding was in support with the structural perturbation observed in CD, which is evident from the root mean square deviation and R g fluctuations. We hope our insights will provide ample scope for engineering new drugs based on the resemblances with NFs for enhanced efficacy with HSA.

Rubredoxin-related Maturation Factor Guarantees Metal Cofactor Integrity during Aerobic Biosynthesis of Membrane-bound [NiFe] Hydrogenase*

PubMed Central

Fritsch, Johannes; Siebert, Elisabeth; Priebe, Jacqueline; Zebger, Ingo; Lendzian, Friedhelm; Teutloff, Christian; Friedrich, Bärbel; Lenz, Oliver

2014-01-01

The membrane-bound [NiFe] hydrogenase (MBH) supports growth of Ralstonia eutropha H16 with H2 as the sole energy source. The enzyme undergoes a complex biosynthesis process that proceeds during cell growth even at ambient O2 levels and involves 14 specific maturation proteins. One of these is a rubredoxin-like protein, which is essential for biosynthesis of active MBH at high oxygen concentrations but dispensable under microaerobic growth conditions. To obtain insights into the function of HoxR, we investigated the MBH protein purified from the cytoplasmic membrane of hoxR mutant cells. Compared with wild-type MBH, the mutant enzyme displayed severely decreased hydrogenase activity. Electron paramagnetic resonance and infrared spectroscopic analyses revealed features resembling those of O2-sensitive [NiFe] hydrogenases and/or oxidatively damaged protein. The catalytic center resided partially in an inactive Niu-A-like state, and the electron transfer chain consisting of three different Fe-S clusters showed marked alterations compared with wild-type enzyme. Purification of HoxR protein from its original host, R. eutropha, revealed only low protein amounts. Therefore, recombinant HoxR protein was isolated from Escherichia coli. Unlike common rubredoxins, the HoxR protein was colorless, rather unstable, and essentially metal-free. Conversion of the atypical iron-binding motif into a canonical one through genetic engineering led to a stable reddish rubredoxin. Remarkably, the modified HoxR protein did not support MBH-dependent growth at high O2. Analysis of MBH-associated protein complexes points toward a specific interaction of HoxR with the Fe-S cluster-bearing small subunit. This supports the previously made notion that HoxR avoids oxidative damage of the metal centers of the MBH, in particular the unprecedented Cys6[4Fe-3S] cluster. PMID:24448806

Bayesian Model Selection under Time Constraints

NASA Astrophysics Data System (ADS)

Hoege, M.; Nowak, W.; Illman, W. A.

2017-12-01

Bayesian model selection (BMS) provides a consistent framework for rating and comparing models in multi-model inference. In cases where models of vastly different complexity compete with each other, we also face vastly different computational runtimes of such models. For instance, time series of a quantity of interest can be simulated by an autoregressive process model that takes even less than a second for one run, or by a partial differential equations-based model with runtimes up to several hours or even days. The classical BMS is based on a quantity called Bayesian model evidence (BME). It determines the model weights in the selection process and resembles a trade-off between bias of a model and its complexity. However, in practice, the runtime of models is another weight relevant factor for model selection. Hence, we believe that it should be included, leading to an overall trade-off problem between bias, variance and computing effort. We approach this triple trade-off from the viewpoint of our ability to generate realizations of the models under a given computational budget. One way to obtain BME values is through sampling-based integration techniques. We argue with the fact that more expensive models can be sampled much less under time constraints than faster models (in straight proportion to their runtime). The computed evidence in favor of a more expensive model is statistically less significant than the evidence computed in favor of a faster model, since sampling-based strategies are always subject to statistical sampling error. We present a straightforward way to include this misbalance into the model weights that are the basis for model selection. Our approach follows directly from the idea of insufficient significance. It is based on a computationally cheap bootstrapping error estimate of model evidence and is easy to implement. The approach is illustrated in a small synthetic modeling study.

4. VAL PARTIAL ELEVATION SHOWING LAUNCHER BRIDGE ON SUPPORTS, LAUNCHER ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

4. VAL PARTIAL ELEVATION SHOWING LAUNCHER BRIDGE ON SUPPORTS, LAUNCHER SLAB, SUPPORT CARRIAGE, CONCRETE 'A' FRAME STRUCTURE AND CAMERA TOWER LOOKING SOUTHEAST. - Variable Angle Launcher Complex, Variable Angle Launcher, CA State Highway 39 at Morris Reservior, Azusa, Los Angeles County, CA

Sparse orthogonal population representation of spatial context in the retrosplenial cortex.

PubMed

Mao, Dun; Kandler, Steffen; McNaughton, Bruce L; Bonin, Vincent

2017-08-15

Sparse orthogonal coding is a key feature of hippocampal neural activity, which is believed to increase episodic memory capacity and to assist in navigation. Some retrosplenial cortex (RSC) neurons convey distributed spatial and navigational signals, but place-field representations such as observed in the hippocampus have not been reported. Combining cellular Ca 2+ imaging in RSC of mice with a head-fixed locomotion assay, we identified a population of RSC neurons, located predominantly in superficial layers, whose ensemble activity closely resembles that of hippocampal CA1 place cells during the same task. Like CA1 place cells, these RSC neurons fire in sequences during movement, and show narrowly tuned firing fields that form a sparse, orthogonal code correlated with location. RSC 'place' cell activity is robust to environmental manipulations, showing partial remapping similar to that observed in CA1. This population code for spatial context may assist the RSC in its role in memory and/or navigation.Neurons in the retrosplenial cortex (RSC) encode spatial and navigational signals. Here the authors use calcium imaging to show that, similar to the hippocampus, RSC neurons also encode place cell-like activity in a sparse orthogonal representation, partially anchored to the allocentric cues on the linear track.

Plastic and Heritable Components of Phenotypic Variation in Nucella lapillus: An Assessment Using Reciprocal Transplant and Common Garden Experiments

PubMed Central

Pascoal, Sonia; Carvalho, Gary; Creer, Simon; Rock, Jenny; Kawaii, Kei; Mendo, Sonia; Hughes, Roger

2012-01-01

Assessment of plastic and heritable components of phenotypic variation is crucial for understanding the evolution of adaptive character traits in heterogeneous environments. We assessed the above in relation to adaptive shell morphology of the rocky intertidal snail Nucella lapillus by reciprocal transplantation of snails between two shores differing in wave action and rearing snails of the same provenance in a common garden. Results were compared with those reported for similar experiments conducted elsewhere. Microsatellite variation indicated limited gene flow between the populations. Intrinsic growth rate was greater in exposed-site than sheltered-site snails, but the reverse was true of absolute growth rate, suggesting heritable compensation for reduced foraging opportunity at the exposed site. Shell morphology of reciprocal transplants partially converged through plasticity toward that of native snails. Shell morphology of F2s in the common garden partially retained characteristics of the P-generation, suggesting genetic control. A maternal effect was revealed by greater resemblance of F1s than F2s to the P-generation. The observed synergistic effects of plastic, maternal and genetic control of shell-shape may be expected to maximise fitness when environmental characteristics become unpredictable through dispersal. PMID:22299035

Plastic and heritable components of phenotypic variation in Nucella lapillus: an assessment using reciprocal transplant and common garden experiments.

PubMed

Pascoal, Sonia; Carvalho, Gary; Creer, Simon; Rock, Jenny; Kawaii, Kei; Mendo, Sonia; Hughes, Roger

2012-01-01

Assessment of plastic and heritable components of phenotypic variation is crucial for understanding the evolution of adaptive character traits in heterogeneous environments. We assessed the above in relation to adaptive shell morphology of the rocky intertidal snail Nucella lapillus by reciprocal transplantation of snails between two shores differing in wave action and rearing snails of the same provenance in a common garden. Results were compared with those reported for similar experiments conducted elsewhere. Microsatellite variation indicated limited gene flow between the populations. Intrinsic growth rate was greater in exposed-site than sheltered-site snails, but the reverse was true of absolute growth rate, suggesting heritable compensation for reduced foraging opportunity at the exposed site. Shell morphology of reciprocal transplants partially converged through plasticity toward that of native snails. Shell morphology of F(2)s in the common garden partially retained characteristics of the P-generation, suggesting genetic control. A maternal effect was revealed by greater resemblance of F(1)s than F(2)s to the P-generation. The observed synergistic effects of plastic, maternal and genetic control of shell-shape may be expected to maximise fitness when environmental characteristics become unpredictable through dispersal.

Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR

PubMed Central

Surana, Parag

2016-01-01

Abstract The study of intermediates in the protein folding pathway provides a wealth of information about the energy landscape. The intermediates also frequently initiate pathogenic fibril formations. While observing the intermediates is difficult due to their transient nature, extreme conditions can partially unfold the proteins and provide a glimpse of the intermediate states. Here, we observe the high resolution structure of a hydrophobic core mutant of Ubiquitin at an extreme acidic pH by nuclear magnetic resonance (NMR) spectroscopy. In the structure, the native secondary and tertiary structure is conserved for a major part of the protein. However, a long loop between the beta strands β3 and β5 is partially unfolded. The altered structure is supported by fluorescence data and the difference in free energies between the native state and the intermediate is reflected in the denaturant induced melting curves. The unfolded region includes amino acids that are critical for interaction with cofactors as well as for assembly of poly‐Ubiquitin chains. The structure at acidic pH resembles a late folding intermediate of Ubiquitin and indicates that upon stabilization of the protein's core, the long loop converges on the core in the final step of the folding process. PMID:27111887

Developing silvicultural systems based on partial cutting in western hemlock–Sitka spruce stands of southeast Alaska.

Treesearch

Robert L. Deal; J.C. Tappeiner; Paul E. Hennon

2002-01-01

The effects of partial cutting on species composition, stand structure and growth, tree size distribution, and tree disease and mortality were evaluated on 73 plots in 18 stands that were harvested 12–96 years ago in southeast Alaska. Partially-cut stands had diverse and highly complex stand structures similar to uncut stands. Sitka spruce was maintained in mixed...

Structure and Activity of the Flagellar Rotor Protein FliY

PubMed Central

Sircar, Ria; Greenswag, Anna R.; Bilwes, Alexandrine M.; Gonzalez-Bonet, Gabriela; Crane, Brian R.

2013-01-01

Rotating flagella propel bacteria toward favorable environments. Sense of rotation is determined by the intracellular response regulator CheY, which when phosphorylated (CheY-P) interacts directly with the flagellar motor. In many different types of bacteria, the CheC/CheX/FliY (CXY) family of phosphatases terminates the CheY-P signal. Unlike CheC and CheX, FliY is localized in the flagellar switch complex, which also contains the stator-coupling protein FliG and the target of CheY-P, FliM. The 2.5 Å resolution crystal structure of the FliY catalytic domain from Thermotoga maritima bears strong resemblance to the middle domain of FliM. Regions of FliM that mediate contacts within the rotor compose the phosphatase active sites in FliY. Despite the similarity between FliY and FliM, FliY does not bind FliG and thus is unlikely to be a substitute for FliM in the center of the switch complex. Solution studies indicate that FliY dimerizes through its C-terminal domains, which resemble the Escherichia coli switch complex component FliN. FliY differs topologically from the E. coli chemotaxis phosphatase CheZ but appears to utilize similar structural motifs for CheY dephosphorylation in close analogy to CheX. Recognition properties and phosphatase activities of site-directed mutants identify two pseudosymmetric active sites in FliY (Glu35/Asn38 and Glu132/Asn135), with the second site (Glu132/Asn135) being more active. A putative N-terminal CheY binding domain conserved with FliM is not required for binding CheY-P or phosphatase activity. PMID:23532838

Facial resemblance to emotions: group differences, impression effects, and race stereotypes.

PubMed

Zebrowitz, Leslie A; Kikuchi, Masako; Fellous, Jean-Marc

2010-02-01

The authors used connectionist modeling to extend previous research on emotion overgeneralization effects. Study 1 demonstrated that neutral expression male faces objectively resemble angry expressions more than female faces do, female faces objectively resemble surprise expressions more than male faces do, White faces objectively resemble angry expressions more than Black or Korean faces do, and Black faces objectively resemble happy and surprise expressions more than White faces do. Study 2 demonstrated that objective resemblance to emotion expressions influences trait impressions even when statistically controlling possible confounding influences of attractiveness and babyfaceness. It further demonstrated that emotion overgeneralization is moderated by face race and that racial differences in emotion resemblance contribute to White perceivers' stereotypes of Blacks and Asians. These results suggest that intergroup relations may be strained not only by cultural stereotypes but also by adaptive responses to emotion expressions that are overgeneralized to groups whose faces subtly resemble particular emotions. Copyright 2009 APA, all rights reserved

Net (ERP/SAP2) one of the Ras-inducible TCFs, has a novel inhibitory domain with resemblance to the helix-loop-helix motif.

PubMed Central

Maira, S M; Wurtz, J M; Wasylyk, B

1996-01-01

The three ternary complex factors (TCFs), Net (ERP/ SAP-2), ELK-1 and SAP-1, are highly related ets oncogene family members that participate in the response of the cell to Ras and growth signals. Understanding the different roles of these factors will provide insights into how the signals result in coordinate regulation of the cell. We show that Net inhibits transcription under basal conditions, in which SAP-1a is inactive and ELK-1 stimulates. Repression is mediated by the NID, the Net Inhibitory Domain of about 50 amino acids, which autoregulates the Net protein and also inhibits when it is isolated in a heterologous fusion protein. Net is particularly sensitive to Ras activation. Ras activates Net through the C-domain, which is conserved between the three TCFs, and the NID is an efficient inhibitor of Ras activation. The NID, as well as more C-terminal sequences, inhibit DNA binding. Net is more refractory to DNA binding than the other TCFs, possibly due to the presence of multiple inhibitory elements. The NID may adopt a helix-loop-helix (HLH) structure, as evidenced by homology to other HLH motifs, structure predictions, model building and mutagenesis of critical residues. The sequence resemblance with myogenic factors suggested that Net may form complexes with the same partners. Indeed, we found that Net can interact in vivo with the basic HLH factor, E47. We propose that Net is regulated at the level of its latent DNA-binding activity by protein interactions and/or phosphorylation. Net may form complexes with HLH proteins as well as SRF on specific promotor sequences. The identification of the novel inhibitory domain provides a new inroad into exploring the different roles of the ternary complex factors in growth control and transformation. Images PMID:8918463

Net (ERP/SAP2) one of the Ras-inducible TCFs, has a novel inhibitory domain with resemblance to the helix-loop-helix motif.

PubMed

Maira, S M; Wurtz, J M; Wasylyk, B

1996-11-01

The three ternary complex factors (TCFs), Net (ERP/ SAP-2), ELK-1 and SAP-1, are highly related ets oncogene family members that participate in the response of the cell to Ras and growth signals. Understanding the different roles of these factors will provide insights into how the signals result in coordinate regulation of the cell. We show that Net inhibits transcription under basal conditions, in which SAP-1a is inactive and ELK-1 stimulates. Repression is mediated by the NID, the Net Inhibitory Domain of about 50 amino acids, which autoregulates the Net protein and also inhibits when it is isolated in a heterologous fusion protein. Net is particularly sensitive to Ras activation. Ras activates Net through the C-domain, which is conserved between the three TCFs, and the NID is an efficient inhibitor of Ras activation. The NID, as well as more C-terminal sequences, inhibit DNA binding. Net is more refractory to DNA binding than the other TCFs, possibly due to the presence of multiple inhibitory elements. The NID may adopt a helix-loop-helix (HLH) structure, as evidenced by homology to other HLH motifs, structure predictions, model building and mutagenesis of critical residues. The sequence resemblance with myogenic factors suggested that Net may form complexes with the same partners. Indeed, we found that Net can interact in vivo with the basic HLH factor, E47. We propose that Net is regulated at the level of its latent DNA-binding activity by protein interactions and/or phosphorylation. Net may form complexes with HLH proteins as well as SRF on specific promotor sequences. The identification of the novel inhibitory domain provides a new inroad into exploring the different roles of the ternary complex factors in growth control and transformation.

Spatial complexity of solutions of higher order partial differential equations

NASA Astrophysics Data System (ADS)

Kukavica, Igor

2004-03-01

We address spatial oscillation properties of solutions of higher order parabolic partial differential equations. In the case of the Kuramoto-Sivashinsky equation ut + uxxxx + uxx + u ux = 0, we prove that for solutions u on the global attractor, the quantity card {x epsi [0, L]:u(x, t) = lgr}, where L > 0 is the spatial period, can be bounded by a polynomial function of L for all \\lambda\\in{\\Bbb R} . A similar property is proven for a general higher order partial differential equation u_t+(-1)^{s}\\partial_x^{2s}u+ \\sum_{k=0}^{2s-1}v_k(x,t)\\partial_x^k u =0 .

Termination patterns of complex partial seizures: An intracranial EEG study.

PubMed

Afra, Pegah; Jouny, Christopher C; Bergey, Gregory K

2015-11-01

While seizure onset patterns have been the subject of many reports, there have been few studies of seizure termination. In this study we report the incidence of synchronous and asynchronous termination patterns of partial seizures recorded with intracranial arrays. Data were collected from patients with intractable complex partial seizures undergoing presurgical evaluations with intracranial electrodes. Patients with seizures originating from mesial temporal and neocortical regions were grouped into three groups based on patterns of seizure termination: synchronous only (So), asynchronous only (Ao), or mixed (S/A, with both synchronous and asynchronous termination patterns). 88% of the patients in the MT group had seizures with a synchronous pattern of termination exclusively (38%) or mixed (50%). 82% of the NC group had seizures with synchronous pattern of termination exclusively (52%) or mixed (30%). In the NC group, there was a significant difference of the range of seizure durations between So and Ao groups, with Ao exhibiting higher variability. Seizures with synchronous termination had low variability in both groups. Synchronous seizure termination is a common pattern for complex partials seizures of both mesial temporal or neocortical onset. This may reflect stereotyped network behavior or dynamics at the seizure focus. Copyright © 2015 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

Evaluating the effects of trophic complexity on a keystone predator by disassembling a partial intraguild predation food web.

PubMed

Davenport, Jon M; Chalcraft, David R

2012-01-01

1. Many taxa can be found in food webs that differ in trophic complexity, but it is unclear how trophic complexity affects the performance of particular taxa. In pond food webs, larvae of the salamander Ambystoma opacum occupy the intermediate predator trophic position in a partial intraguild predation (IGP) food web and can function as keystone predators. Larval A. opacum are also found in simpler food webs lacking either top predators or shared prey. 2. We conducted an experiment where a partial IGP food web was simplified, and we measured the growth and survival of larval A. opacum in each set of food webs. Partial IGP food webs that had either a low abundance or high abundance of total prey were also simplified by independently removing top predators and/or shared prey. 3. Removing top predators always increased A. opacum survival, but removal of shared prey had no effect on A. opacum survival, regardless of total prey abundance. 4. Surprisingly, food web simplification had no effect on the growth of A. opacum when present in food webs with a low abundance of prey but had important effects on A. opacum growth in food webs with a high abundance of prey. Simplifying a partial IGP food web with a high abundance of prey reduced A. opacum growth when either top predators or shared prey were removed from the food web and the loss of top predators and shared prey influenced A. opacum growth in a non-additive fashion. 5. The non-additive response in A. opacum growth appears to be the result of supplemental prey availability augmenting the beneficial effects of top predators. Top predators had a beneficial effect on A. opacum populations by reducing the abundance of A. opacum present and thereby reducing the intensity of intraspecific competition. 6. Our study indicates that the effects of food web simplification on the performance of A. opacum are complex and depend on both how a partial IGP food web is simplified and how abundant prey are in the food web. These findings are important because they demonstrate how trophic complexity can create variation in the performance of intermediate predators that play important roles in temporary pond food webs. © 2011 The Authors. Journal of Animal Ecology © 2011 British Ecological Society.

Design, synthesis and exploring the quantitative structure-activity relationship of some antioxidant flavonoid analogues.

PubMed

Das, Sreeparna; Mitra, Indrani; Batuta, Shaikh; Niharul Alam, Md; Roy, Kunal; Begum, Naznin Ara

2014-11-01

A series of flavonoid analogues were synthesized and screened for the in vitro antioxidant activity through their ability to quench 1,1-diphenyl-2-picryl hydrazyl (DPPH) radical. The activity of these compounds, measured in comparison to the well-known standard antioxidants (29-32), their precursors (38-42) and other bioactive moieties (38-42) resembling partially the flavone skeleton was analyzed further to develop Quantitative Structure-Activity Relationship (QSAR) models using the Genetic Function Approximation (GFA) technique. Based on the essential structural requirements predicted by the QSAR models, some analogues were designed, synthesized and tested for activity. The predicted and experimental activities of these compounds were well correlated. Flavone analogue 20 was found to be the most potent antioxidant. Copyright © 2014 Elsevier Ltd. All rights reserved.

Discovery of a radio nebula around PSR J0855-4644

NASA Astrophysics Data System (ADS)

Maitra, C.; Roy, S.; Acero, F.; Gupta, Y.

2018-06-01

We report the discovery of a diffuse radio emission around PSR J0855-4644 using an upgraded GMRT (uGMRT) observation at 1.35 GHz. The radio emission is spatially coincident with the diffuse X-ray pulsar wind nebula (PWN) seen with XMM-Newton but is much larger in extent compared to the compact axisymmetric PWN seen with Chandra. The morphology of the emission, with a bright partial ring-like structure and two faint tail-like features strongly resembles a bow shock nebula, and indicates a velocity of 100 km s-1 through the ambient medium. We conclude that the emission is most likely to be associated with the radio PWN of PSR J0855-4644. From the integrated flux density, we estimate the energetics of the PWN.

Causal nature of neighborhood deprivation on individual risk of coronary heart disease or ischemic stroke: A prospective national Swedish co-relative control study in men and women.

PubMed

Forsberg, Per-Ola; Ohlsson, Henrik; Sundquist, Kristina

2018-03-01

We studied the association between neighborhood socioeconomic status (SES) and incidence of coronary heart disease (CHD) or ischemic stroke in the total population and in full- and half-siblings to determine whether these associations are causal or a result from familial confounding. Data were retrieved from nationwide Swedish registers containing individual clinical data linked to neighborhood of residence. After adjustment for individual SES, the association between neighborhood SES and CHD showed no decrease with increasing genetic resemblance, particularly in women. This indicates that the association between neighborhood SES and CHD incidence is partially causal among women, which represents a novel finding. Copyright © 2018 Elsevier Ltd. All rights reserved.

Schizophrenia and the corpus callosum: developmental, structural and functional relationships.

PubMed

David, A S

1994-10-20

Several empirical and theoretical connections exist between schizophrenia and the corpus callosum: (1) disconnection symptoms resemble certain psychotic phenomena; (2) abnormal interhemispheric transmission could explain typically schizophrenic phenomena; (3) cases of psychosis have been found in association with complete and partial agenesis of the callosum; (4) experimental neuropsychology with schizophrenic patients has revealed abnormal patterns of interhemispheric transfer; (5) studies using magnetic resonance imaging have shown abnormal callosal dimensions in schizophrenic patients. The evidence in support of these links is discussed critically. Novel neuropsychological approaches in the study of information transfer in the visual modality between the cerebral hemispheres, consistent with callosal hyperconnectivity in schizophrenic patients but not matched psychiatric controls are highlighted. Some suggestions for further work including integrating functional and structural measures are offered.

Does Facial Resemblance Enhance Cooperation?

PubMed Central

Giang, Trang; Bell, Raoul; Buchner, Axel

2012-01-01

Facial self-resemblance has been proposed to serve as a kinship cue that facilitates cooperation between kin. In the present study, facial resemblance was manipulated by morphing stimulus faces with the participants' own faces or control faces (resulting in self-resemblant or other-resemblant composite faces). A norming study showed that the perceived degree of kinship was higher for the participants and the self-resemblant composite faces than for actual first-degree relatives. Effects of facial self-resemblance on trust and cooperation were tested in a paradigm that has proven to be sensitive to facial trustworthiness, facial likability, and facial expression. First, participants played a cooperation game in which the composite faces were shown. Then, likability ratings were assessed. In a source memory test, participants were required to identify old and new faces, and were asked to remember whether the faces belonged to cooperators or cheaters in the cooperation game. Old-new recognition was enhanced for self-resemblant faces in comparison to other-resemblant faces. However, facial self-resemblance had no effects on the degree of cooperation in the cooperation game, on the emotional evaluation of the faces as reflected in the likability judgments, and on the expectation that a face belonged to a cooperator rather than to a cheater. Therefore, the present results are clearly inconsistent with the assumption of an evolved kin recognition module built into the human face recognition system. PMID:23094095

Experimental generation of partially coherent beams with different complex degrees of coherence.

PubMed

Wang, Fei; Liu, Xianlong; Yuan, Yangsheng; Cai, Yangjian

2013-06-01

We established an experimental setup for generating partially coherent beams with different complex degrees of coherence, and we report experimental generation of an elliptical Gaussian Schell-model (GSM) beam and a Laguerre-GSM beam for the first time. It has been demonstrated experimentally that an elliptical GSM beam and a Laguerre-GSM beam produce an elliptical beam spot and a dark hollow beam spot in the focal plane (or in the far field), respectively, which agrees with theoretical predictions. Our results are useful for beam shaping and particle trapping.

The Design of Molecular Hosts, Guests, and Their Complexes.

ERIC Educational Resources Information Center

Cram, Donald J.

1988-01-01

Describes the origins, definitions, tools, and principles of host-guest chemistry. Gives examples of chiral recognition in complexation, of partial transacylase mimics, of caviplexes, and of a synthetic molecular cell. (Author/RT)

Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature.

PubMed

Roux, Fabrice; Colomé-Tatché, Maria; Edelist, Cécile; Wardenaar, René; Guerche, Philippe; Hospital, Frédéric; Colot, Vincent; Jansen, Ritsert C; Johannes, Frank

2011-08-01

We extensively phenotyped 6000 Arabidopsis plants with experimentally perturbed DNA methylomes as well as a diverse panel of natural accessions in a common garden. We found that alterations in DNA methylation not only caused heritable phenotypic diversity but also produced heritability patterns closely resembling those of the natural accessions. Our findings indicate that epigenetically induced and naturally occurring variation in complex traits share part of their polygenic architecture and may offer complementary adaptation routes in ecological settings.

DDT: participation in ultraviolet-detectable, charge-transfer complexation.

PubMed

Wilson, W E; Fishbein, L; Clements, S T

1971-01-15

The chlorophenyl groups of DDT and several of its metabolites are capable of participating in a charge-transfer interaction with tetracyanoethylene detectable in the ultraviolet region of the spectrum. In addition, during a change of state DDT undergoes ultraviolet spectral alterations that closely resemble those previously claimed to support the hypothesis suggesting charge-transfer interaction between this pesticide and a component of insect nerve tissue. The pesticide DDT possesses structural characteristics that would permit it to participate in several types of molecular association.

A family study of dermatoglyphic traits in India: segregation analysis of accessory palmar triradii and the atd angle.

PubMed

Gilligan, S B; Borecki, I B; Mathew, S; Vijaykumar, M; Malhotra, K C; Rao, D C

1987-09-01

Accessory triradii and the atd angle were examined via complex segregation analysis in order to evaluate possible genetic effects on these dermatoglyphic traits, measured in an endogamous Brahmin caste of peninsular India. The phenotypes considered included: presence of accessory palmar triradii a' and d', associated with the interdigital areas II and IV, respectively; presence of an accessory axial triradius tt' associated with the proximal margin of the palm; and an arctanh-transformation of the atd angle measurement. For all accessory triradii considered in the present investigation familial resemblance was evident. The most parsimonious model which could account for the observed resemblance was a multifactorial model that includes polygenic effects as well as transmissible environmental effects that are inherited in the same pattern as polygenes. Evidence of familial resemblance was also found for the arctanh-transformed atd angle, which could be attributed, initially, to both a major effect and a multifactorial component. Tests of transmission of a putative major gene were performed which yielded results consistent with Mendelian transmission, although an alternative test of no transmission of the major effect also fit the data. In light of these contrasting results we are precluded from accepting with confidence the notion of a major gene influence on the atd angle. We have concluded that the accessory triradii a', d', and tt', and the atd angle are influenced by multifactorial effects, including additive polygenes and possible environmental factors, such as intrauterine effects.

Propagation and coherence properties of higher order partially coherent dark hollow beams in turbulence

NASA Astrophysics Data System (ADS)

Eyyuboğlu, Halil Tanyer

2008-02-01

We formulate and evaluate in terms of graphical outputs, source and receiver plane expressions, the complex degree of coherence, beam size variation and power in bucket performance for higher order partially coherent dark hollow beams propagating in turbulent atmosphere. Our formulation is able to cover square, rectangular, circular, elliptical geometries for dark hollow and flat-topped beams in one single expression. From the graphical outputs of the receiver plane, it is observed that higher order partially coherent dark hollow beams will initially develop an outer ring around a central lobe, but will eventually evolve towards a Gaussian shape as the propagation distance is extended. It is further observed that stronger turbulence levels and greater partial coherence have similar effects on beam profile. During propagation, modulus of complex degree of coherence of partially coherent dark hollow beams appears to rise above that of the source plane values, reaching as high as near unity. Beam size analysis shows that, among the types examined, (nearly) flat-topped beam experiences the least beam expansion. Power in bucket analysis indicates that lowest order square fully coherent dark beam offers the best power capturing.

Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease.

PubMed

Nakae, Setsu; Hijikata, Atsushi; Tsuji, Toshiyuki; Yonezawa, Kouki; Kouyama, Ken-Ichi; Mayanagi, Kouta; Ishino, Sonoko; Ishino, Yoshizumi; Shirai, Tsuyoshi

2016-11-01

Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway. Copyright © 2016 Elsevier Ltd. All rights reserved.

Electron and Ion Reactions in Molecular Solids: from astrochemistry to radiobiology

NASA Astrophysics Data System (ADS)

Huels, Michael A.

2001-05-01

Wherever ionizing radiation interacts with matter, it initiates reaction cascades involving ions, radicals, and ballistic secondary electrons; these reactions occur on fs time-scales, and may lead to substantial physical and chemical modifications of a medium. Here I present measurements of 0-80 eV electron and ion reactions in condensed films ranging from simple to complex, and astrophysical to biological in nature. Targets contain either: small molecules, hydrocarbons of increasing complexity (incl. bases, sugars, single/double stranded DNA), molecules on rare gas matrices, or mixed cryogenic films resembling astrophysical or planetary surface ices containing O2, H2O, methane, and aromatic hydrocarbons. The basic electron or ion reaction mechanisms and pathways are found to be fundamentally universal, but are modulated by the physical and chemical nature of the medium; depending on the latter, a reaction cascade may lead to different end-points, e.g. a decrease in molecular complexity via molecular fragmentations, or increases in complexity via secondary ion collision induced synthesis of larger molecules in hydrocarbon rich surface ices.

Pigment organization in the photosynthetic apparatus of Roseiflexus castenholzii.

PubMed

Collins, Aaron M; Xin, Yueyong; Blankenship, Robert E

2009-08-01

The light-harvesting-reaction center (LHRC) complex from the chlorosome-lacking filamentous anoxygenic phototroph (FAP), Roseiflexus castenholzii (R. castenholzii) was purified and characterized for overall pigment organization. The LHRC is a single complex that is comprised of light harvesting (LH) and reaction center (RC) polypeptides as well as an attached c-type cytochrome. The dominant carotenoid found in the LHRC is keto-gamma-carotene, which transfers excitation to the long wavelength antenna band with 35% efficiency. Linear dichroism and fluorescence polarization measurements indicate that the long wavelength antenna pigments absorbing around 880 nm are perpendicular to the membrane plane, with the corresponding Q(y) transition dipoles in the plane of the membrane. The antenna pigments absorbing around 800 nm, as well as the bound carotenoid, are oriented at a large angle with respect to the membrane. The antenna pigments spectroscopically resemble the well-studied LH2 complex from purple bacteria, however the close association with the RC makes the light harvesting component of this complex functionally more like LH1.

Studying light-harvesting models with superconducting circuits.

PubMed

Potočnik, Anton; Bargerbos, Arno; Schröder, Florian A Y N; Khan, Saeed A; Collodo, Michele C; Gasparinetti, Simone; Salathé, Yves; Creatore, Celestino; Eichler, Christopher; Türeci, Hakan E; Chin, Alex W; Wallraff, Andreas

2018-03-02

The process of photosynthesis, the main source of energy in the living world, converts sunlight into chemical energy. The high efficiency of this process is believed to be enabled by an interplay between the quantum nature of molecular structures in photosynthetic complexes and their interaction with the environment. Investigating these effects in biological samples is challenging due to their complex and disordered structure. Here we experimentally demonstrate a technique for studying photosynthetic models based on superconducting quantum circuits, which complements existing experimental, theoretical, and computational approaches. We demonstrate a high degree of freedom in design and experimental control of our approach based on a simplified three-site model of a pigment protein complex with realistic parameters scaled down in energy by a factor of 10 5 . We show that the excitation transport between quantum-coherent sites disordered in energy can be enabled through the interaction with environmental noise. We also show that the efficiency of the process is maximized for structured noise resembling intramolecular phononic environments found in photosynthetic complexes.

Crystal structure of plant light-harvesting complex shows the active, energy-transmitting state

PubMed Central

Barros, Tiago; Royant, Antoine; Standfuss, Jörg; Dreuw, Andreas; Kühlbrandt, Werner

2009-01-01

Plants dissipate excess excitation energy as heat by non-photochemical quenching (NPQ). NPQ has been thought to resemble in vitro aggregation quenching of the major antenna complex, light harvesting complex of photosystem II (LHC-II). Both processes are widely believed to involve a conformational change that creates a quenching centre of two neighbouring pigments within the complex. Using recombinant LHC-II lacking the pigments implicated in quenching, we show that they have no particular role. Single crystals of LHC-II emit strong, orientation-dependent fluorescence with an emission maximum at 680 nm. The average lifetime of the main 680 nm crystal emission at 100 K is 1.31 ns, but only 0.39 ns for LHC-II aggregates under identical conditions. The strong emission and comparatively long fluorescence lifetimes of single LHC-II crystals indicate that the complex is unquenched, and that therefore the crystal structure shows the active, energy-transmitting state of LHC-II. We conclude that quenching of excitation energy in the light-harvesting antenna is due to the molecular interaction with external pigments in vitro or other pigment–protein complexes such as PsbS in vivo, and does not require a conformational change within the complex. PMID:19131972

Eight new species of Cestrum (Solanaceae) from Mesoamerica

PubMed Central

Monro, Alex K.

2012-01-01

Abstract As part of the preparation of a taxonomic revision of Cestrum (Solanaceae) for Flora Mesoamericana eight hitherto undescribed species from Mexico, Guatemala, Costa Rica and Panama were identified. These eight new species are described and illustrated. Affinities of the species are discussed and Global Species Conservation Assessments presented.The new species are Cestrum amistadense A.K. Monro, sp. nov. (Vulnerable) which most closely resembles Cestrum longiflorum Ruiz & Pav., Cestrum contrerasianum A.K. Monro, sp. nov. (Vulnerable) which most closely resembles Cestrum formosum C.V.Morton, Cestrum darienense A.K. Monro, sp. nov. (Near Threatened) which most closely resembles Cestrum morae Hunz., Cestrum gilliae A.K. Monro, sp. nov. (Near Threatened) which most closely resembles Cestrum morae, Cestrum haberii A.K. Monro, sp. nov. (Vulnerable) which most closely resembles Cestrum poasanum Donn.Sm., Cestrum knappiae A.K. Monro, sp. nov. (Near Threatened) which most closely resembles Cestrum acuminatum Francey, Cestrum lentii A.K. Monro, sp. nov. (Near Threatened) which most closely resembles Cestrum johnniegentrianum D’Arcy and Cestrum talamancaense A.K. Monro (Least Concern) which most closely resembles Cestrum laxum Benth. PMID:22287930

Eukaryotes first: how could that be?

PubMed

Mariscal, Carlos; Doolittle, W Ford

2015-09-26

In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such 'eukaryotes first' (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier 'progenotic' period or RNA world. Bacteria and Archaea thus must have lost these complex features secondarily, through 'streamlining'. If the canonical three-domain tree in which Archaea and Eukarya are sisters is accepted, EF entails that Bacteria and Archaea are convergently prokaryotic. We ask what this means and how it might be tested. © 2015 The Author(s).

Evidence for hot Mississippi Valley-type brines in the Reelfoot Rift complex, south-central United States, in Late Pennsylvanian-Early Permian

USGS Publications Warehouse

Leach, D.L.; Apodaca, L.E.; Repetski, J.E.; Powell, J.W.; Rowan, E.L.

1997-01-01

Petrographic and fluid inclusion studies of sparry dolomite cement from Upper Cambrian to Lower Ordovician rocks and conodont thermal-alteration indices provide evidence that hot mississippi valley-type brines were once present in the Reelfoot Rift complex. The cathodoluminescent microstratigraphy of sparry dolomite cement in the Reelfoot Rift resembles that of sparry dolomite cement associated with widespread mississippi valley-type deposition in the Ozark region. If correlative cathodoluminescent zones in the sparry dolomite from the Ozark and Reelfoot Rift regions indicate broadly contemporaneous dolomite deposition, then the results show that the Ozark MVT-type hydrothermal system extended into the Reelfoot region and onto the western flank of the Nashville Dome. Independent evidence supports migration of MVT-type brines into the Ozark region from the Reelfoot Rift complex in late Paleozoic time.

Self-assembly of a double-helical complex of sodium.

PubMed

Bell, T W; Jousselin, H

1994-02-03

Spontaneous self-organization of helical and multiple-helical molecular structures occurs on several levels in living organisms. Key examples are alpha-helical polypeptides, double-helical nucleic acids and helical protein structures, including F-actin, microtubules and the protein sheath of the tobacco mosaic virus. Although the self-assembly of double-helical transition-metal complexes bears some resemblance to the molecular organization of double-stranded DNA, selection between monohelical, double-helical and triple-helical structures is determined largely by the size and geometrical preference of the tightly bound metal. Here we present an example of double-helical assembly induced by the weaker and non-directional interactions of an alkali-metal ion with an organic ligand that is pre-organized into a coil. We have characterized the resulting complex by two-dimensional NMR and fast-atom-bombardment mass spectrometry. These results provide a step toward the creation of molecular tubes or ion channels consisting of intertwined coils.

Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements

PubMed Central

Liu, Pengfei; Erez, Ayelet; Sreenath Nagamani, Sandesh C.; Dhar, Shweta U.; Kołodziejska, Katarzyna E.; Dharmadhikari, Avinash V.; Cooper, M. Lance; Wiszniewska, Joanna; Zhang, Feng; Withers, Marjorie A.; Bacino, Carlos A.; Campos-Acevedo, Luis Daniel; Delgado, Mauricio R.; Freedenberg, Debra; Garnica, Adolfo; Grebe, Theresa A.; Hernández-Almaguer, Dolores; Immken, LaDonna; Lalani, Seema R.; McLean, Scott D.; Northrup, Hope; Scaglia, Fernando; Strathearn, Lane; Trapane, Pamela; Kang, Sung-Hae L.; Patel, Ankita; Cheung, Sau Wai; Hastings, P. J.; Stankiewicz, Paweł; Lupski, James R.; Bi, Weimin

2011-01-01

SUMMARY Complex genomic rearrangements (CGR) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, a chromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated we observed localization and multiple copy number changes including deletions, duplications and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism’s life cycle. PMID:21925314

Structure of a group II intron in complex with its reverse transcriptase.

PubMed

Qu, Guosheng; Kaushal, Prem Singh; Wang, Jia; Shigematsu, Hideki; Piazza, Carol Lyn; Agrawal, Rajendra Kumar; Belfort, Marlene; Wang, Hong-Wei

2016-06-01

Bacterial group II introns are large catalytic RNAs related to nuclear spliceosomal introns and eukaryotic retrotransposons. They self-splice, yielding mature RNA, and integrate into DNA as retroelements. A fully active group II intron forms a ribonucleoprotein complex comprising the intron ribozyme and an intron-encoded protein that performs multiple activities including reverse transcription, in which intron RNA is copied into the DNA target. Here we report cryo-EM structures of an endogenously spliced Lactococcus lactis group IIA intron in its ribonucleoprotein complex form at 3.8-Å resolution and in its protein-depleted form at 4.5-Å resolution, revealing functional coordination of the intron RNA with the protein. Remarkably, the protein structure reveals a close relationship between the reverse transcriptase catalytic domain and telomerase, whereas the active splicing center resembles the spliceosomal Prp8 protein. These extraordinary similarities hint at intricate ancestral relationships and provide new insights into splicing and retromobility.

The sensitivity of gas-phase models of dense interstellar clouds to changes in dissociative recombination branching ratios

NASA Technical Reports Server (NTRS)

Millar, T. J.; Defrees, D. J.; Mclean, A. D.; Herbst, E.

1988-01-01

The approach of Bates to the determination of neutral product branching ratios in ion-electron dissociative recombination reactions has been utilized in conjunction with quantum chemical techniques to redetermine branching ratios for a wide variety of important reactions of this class in dense interstellar clouds. The branching ratios have then been used in a pseudo time-dependent model calculation of the gas phase chemistry of a dark cloud resembling TMC-1 and the results compared with an analogous model containing previously used branching ratios. In general, the changes in branching ratios lead to stronger effects on calculated molecular abundances at steady state than at earlier times and often lead to reductions in the calculated abundances of complex molecules. However, at the so-called 'early time' when complex molecule synthesis is most efficient, the abundances of complex molecules are hardly affected by the newly used branching ratios.

Complex lasso: new entangled motifs in proteins

NASA Astrophysics Data System (ADS)

Niemyska, Wanda; Dabrowski-Tumanski, Pawel; Kadlof, Michal; Haglund, Ellinor; Sułkowski, Piotr; Sulkowska, Joanna I.

2016-11-01

We identify new entangled motifs in proteins that we call complex lassos. Lassos arise in proteins with disulfide bridges (or in proteins with amide linkages), when termini of a protein backbone pierce through an auxiliary surface of minimal area, spanned on a covalent loop. We find that as much as 18% of all proteins with disulfide bridges in a non-redundant subset of PDB form complex lassos, and classify them into six distinct geometric classes, one of which resembles supercoiling known from DNA. Based on biological classification of proteins we find that lassos are much more common in viruses, plants and fungi than in other kingdoms of life. We also discuss how changes in the oxidation/reduction potential may affect the function of proteins with lassos. Lassos and associated surfaces of minimal area provide new, interesting and possessing many potential applications geometric characteristics not only of proteins, but also of other biomolecules.

3D Bioprinting of Tissue/Organ Models.

PubMed

Pati, Falguni; Gantelius, Jesper; Svahn, Helene Andersson

2016-04-04

In vitro tissue/organ models are useful platforms that can facilitate systematic, repetitive, and quantitative investigations of drugs/chemicals. The primary objective when developing tissue/organ models is to reproduce physiologically relevant functions that typically require complex culture systems. Bioprinting offers exciting prospects for constructing 3D tissue/organ models, as it enables the reproducible, automated production of complex living tissues. Bioprinted tissues/organs may prove useful for screening novel compounds or predicting toxicity, as the spatial and chemical complexity inherent to native tissues/organs can be recreated. In this Review, we highlight the importance of developing 3D in vitro tissue/organ models by 3D bioprinting techniques, characterization of these models for evaluating their resemblance to native tissue, and their application in the prioritization of lead candidates, toxicity testing, and as disease/tumor models. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identifying partial topology of complex dynamical networks via a pinning mechanism

NASA Astrophysics Data System (ADS)

Zhu, Shuaibing; Zhou, Jin; Lu, Jun-an

2018-04-01

In this paper, we study the problem of identifying the partial topology of complex dynamical networks via a pinning mechanism. By using the network synchronization theory and the adaptive feedback controlling method, we propose a method which can greatly reduce the number of nodes and observers in the response network. Particularly, this method can also identify the whole topology of complex networks. A theorem is established rigorously, from which some corollaries are also derived in order to make our method more cost-effective. Several numerical examples are provided to verify the effectiveness of the proposed method. In the simulation, an approach is also given to avoid possible identification failure caused by inner synchronization of the drive network.

[Effects of creating a tunnel through intercondylar fossa under arthroscopy for the treatment of complex tears at the medial meniscus posterior horn].

PubMed

Dong, Ling-Dai; Bing, Chang-Jian; Li, Jian-Lin; Cai, Yue

2017-04-25

To discuss the advantages of the arthroscopic treatment for complex tears of the medial meniscus posterior horn by creating a tunnel passageway through the intercondylar fossa. All 127 patients including 24 males and 103 females with complex tears at the medial meniscus posterior horn were reviewed. The age of all patients ranged from 45 to 78 years old, with an average of 67 years old. All 127 patients were treated with partial meniscectomy, in which 112 patients were treated with partial meniscectomy smoothly with three incisions (anterior medial incision, anterior lateral incision, high anterior lateral incision), and 15 patients were treated with four incisions (anterior medial incision, anterior lateral incision, high anterior lateral incision, posterior medial incision). Four aspects were estimated:whether the meniscus posterior horns could be observed totally and conveniently, whether tools could be pushed to target area conveniently, the damage of adjacent cartilages, operation time(the operation time of partial meniscectomy). Posterior horns of all patients were totally and conveniently observed, tools were conveniently pushed to the target area in all cases, and all the cases had no iatrogenic injuries at adjacent cartilages. The operation time of partial meniscectomy at posterior horns with three incisions ranged from 5 to 10 minutes, and it ranged from 10 to 30 minutes with four incisions. It is very convenient and fast of the arthroscopy to treat complex tears of the medial meniscus posterior horn by creating a tunnel through the intercondylor fossa. Iatrogenic injuries of the adjacent cartilages were prevented to the greatest extent.

Reversible exposure of hydrophobic residues on albumin as a novel strategy for formulation of nanodelivery vehicles for taxanes

PubMed Central

Garro, AG; Beltramo, DM; Alasino, RV; Leonhard, V; Heredia, V; Bianco, ID

2011-01-01

Background: We report herein a novel strategy for the preparation of protein-based nanode-livery vehicles for hydrophobic active pharmaceutical ingredients. Methods: The procedure consisted of three steps, ie, exposure of hydrophobic residues of a protein to a pH-induced partial unfolding: interaction between hydrophobic residues on the protein and the hydrophobic active pharmaceutical ingredient, and a final step where the structure of the protein was reversed to a native-like state by returning to neutral pH. As proof of concept, the interaction of paclitaxel with partially unfolded states of human serum albumin was evaluated as a potential method for the preparation of water-soluble complexes of the taxane with albumin. Results: We found that paclitaxel readily binds to pH-induced partially unfolded albumin, leading to the formation of optically clear water-soluble complexes. The complexes thus formed were more stable in solution when the albumin native state was at least partially restored by neutralization of the solution to a pH around 7. It was also observed that the hydrodynamic radius of human serum albumin was only slightly increased after the cycle of pH changes, remaining in a monomeric state with a size according to paclitaxel binding. Furthermore, paclitaxel binding did not affect the overall exposure of charged groups of human serum albumin, as evaluated by its interaction with an ionic exchange resin. Conclusion: The in vitro biological activity of the complexes formed was qualitatively equivalent to that of a Cremophor®-based formulation. PMID:21822381

Scaffolding Learning by Modelling: The Effects of Partially Worked-out Models

ERIC Educational Resources Information Center

Mulder, Yvonne G.; Bollen, Lars; de Jong, Ton; Lazonder, Ard W.

2016-01-01

Creating executable computer models is a potentially powerful approach to science learning. Learning by modelling is also challenging because students can easily get overwhelmed by the inherent complexities of the task. This study investigated whether offering partially worked-out models can facilitate students' modelling practices and promote…

Architecture and ssDNA interaction of the Timeless-Tipin-RPA complex.

PubMed

Witosch, Justine; Wolf, Eva; Mizuno, Naoko

2014-11-10

The Timeless-Tipin (Tim-Tipin) complex, also referred to as the fork protection complex, is involved in coordination of DNA replication. Tim-Tipin is suggested to be recruited to replication forks via Replication Protein A (RPA) but details of the interaction are unknown. Here, using cryo-EM and biochemical methods, we characterized complex formation of Tim-Tipin, RPA and single-stranded DNA (ssDNA). Tim-Tipin and RPA form a 258 kDa complex with a 1:1:1 stoichiometry. The cryo-EM 3D reconstruction revealed a globular architecture of the Tim-Tipin-RPA complex with a ring-like and a U-shaped domain covered by a RPA lid. Interestingly, RPA in the complex adopts a horse shoe-like shape resembling its conformation in the presence of long ssDNA (>30 nucleotides). Furthermore, the recruitment of the Tim-Tipin-RPA complex to ssDNA is modulated by the RPA conformation and requires RPA to be in the more compact 30 nt ssDNA binding mode. The dynamic formation and disruption of the Tim-Tipin-RPA-ssDNA complex implicates the RPA-based recruitment of Tim-Tipin to the replication fork. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Comparative outcomes and assessment of trifecta in 500 robotic and laparoscopic partial nephrectomy cases: a single surgeon experience.

PubMed

Khalifeh, Ali; Autorino, Riccardo; Hillyer, Shahab P; Laydner, Humberto; Eyraud, Remi; Panumatrassamee, Kamol; Long, Jean-Alexandre; Kaouk, Jihad H

2013-04-01

We report a comparative analysis of a large series of laparoscopic and robotic partial nephrectomies performed by a high volume single surgeon at a tertiary care institution. We retrospectively reviewed the medical charts of 500 patients treated with minimally invasive partial nephrectomy by a single surgeon between March 2002 and February 2012. Demographic and perioperative data were collected and statistically analyzed. R.E.N.A.L. (radius, exophytic/endophytic properties, nearness of tumor to the collecting system or sinus in mm, anterior/posterior and location relative to polar lines) nephrometry score was used to score tumors. Those scored as moderate and high complexity were designated as complex. Trifecta was defined as a combination of warm ischemia time less than 25 minutes, negative surgical margins and no perioperative complications. Two groups were identified, including 261 patients with robotic and 231 with laparoscopic partial nephrectomy. Demographics were similar in the groups. The robotic group was significantly more morbid (Charlson comorbidity index 3.75 vs 1.26), included more complex tumors (R.E.N.A.L. score 5.98 vs 7.2), and had lower operative (169.9 vs 191.7 minutes) and warm ischemia (17.9 vs 25.2 minutes) time, intraoperative (2.6% vs 5.6%, each p <0.001) and postoperative (24.53% vs 32.03%, p = 0.004) complications, and positive margin rate (2.9% vs 5.6%, p <0.001). Thus, a higher overall trifecta rate was observed for robotic partial nephrectomy (58.7% vs 31.6%, p <0.001). The laparoscopic group had longer followup (3.43 vs 1.51 years, p <0.001) and no significant difference in postoperative changes in renal function. Main study limitations were the retrospective nature, arbitrary definition of trifecta and shorter followup in the RPN group. Our large comparative analysis shows that robotic partial nephrectomy offers a wider range of indications, better operative outcomes and lower perioperative morbidity than laparoscopic partial nephrectomy. Overall, the quest for trifecta seems to be better accomplished by robotic partial nephrectomy, which is likely to become the new standard for minimally invasive partial nephrectomy. Copyright © 2013 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

The vertebral remains of the late Miocene great ape Hispanopithecus laietanus from Can Llobateres 2 (Vallès-Penedès Basin, NE Iberian Peninsula).

PubMed

Susanna, Ivette; Alba, David M; Almécija, Sergio; Moyà-Solà, Salvador

2014-08-01

Here we describe the vertebral fragments from the partial skeleton IPS18800 of the fossil great ape Hispanopithecus laietanus (Hominidae: Dryopithecinae) from the late Miocene (9.6 Ma) of Can Llobateres 2 (Vallès-Penedès Basin, Catalonia, Spain). The eight specimens (IPS18800.5-IPS18800.12) include a fragment of thoracic vertebral body, three partial bodies and four neural arch fragments of lumbar vertebrae. Despite the retention of primitive features (moderately long lumbar vertebral bodies with slightly concave ventrolateral sides), these specimens display a suite of derived, modern hominoid-like features: thoracic vertebrae with dorsally-situated costal foveae; lumbar vertebrae with non-ventrally-oriented transverse processes originating from a robust pedicle, caudally-long laminae with caudally-oriented spinous process, elliptical end-plates, and moderately stout bodies reduced in length and with no ventral keel. These features, functionally related to orthograde behaviors, are indicative of a broad and shallow thorax with a moderately short and stiff lumbar region in Hispanopithecus. Despite its large body mass (ca. 39-40 kg), its vertebral morphology is more comparable to that of hylobatids and Ateles than to extant great apes. This is confirmed by our morphometric analyses, also indicating that Hispanopithecus most closely resembles Pierolapithecus and Morotopithecus among Miocene apes, whereas Proconsul and Nacholapithecus resemble pronograde monkeys. Only in a few features (craniocaudally short and transversely wide pedicles, transverse processes situated on the pedicle, and slight ventral wedging), Hispanopithecus is more derived towards the extant great ape condition than other Miocene apes. Overall, the vertebral morphology of Hispanopithecus supports previous inferences of an orthograde body plan with suspensory and climbing adaptations. However, given similarities with Ateles and the retention of a longer and more flexible spine than in extant great apes, the Hispanopithecus morphology is also consistent with some degree of above-branch quadrupedalism, as previously inferred from other anatomical regions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Cross-couplings in the elaboration of luminescent bis-terpyridyl iridium complexes: the effect of extended or inhibited conjugation on emission.

PubMed

Leslie, Wendy; Batsanov, Andrei S; Howard, Judith A K; Williams, J A Gareth

2004-02-21

The utility of Suzuki cross-coupling methodology for the in situ elaboration of bromo-functionalised bis-terpyridyl iridium(III) complexes has been explored. The complex [Ir(tpy)(tpy-phi-Br)]3+ [tpy-phi-Br = 4'-(4-bromophenyl)-2,2':6',2''-terpyridine] undergoes palladium-catalysed cross-coupling with aryl boronic acids to yield biaryl-substituted complexes directly. The biphenyl and 4-cyanobiphenyl-substituted products display relatively intense, long-lived (tau > 100 mus) yellow emission in degassed aqueous solution at room temperature, assigned to a 3pi-pi* state. A 4-aminobiphenyl-substituted analogue displays an additional low energy absorbance band, attributed to an intraligand charge-transfer (ILCT) excited state, and is scarcely emissive under the same conditions. The iridium(III) complex of 4'-mesityl-terpyridine is also reported. Its emission is much shorter-lived, with a spectral profile resembling that of unsubstituted [Ir(tpy)2]3+, confirming the need for the attainment of a roughly coplanar geometry for stabilisation of the 3pi-pi* excited state.

Structural basis for basal activity and autoactivation of abscisic acid (ABA) signaling SnRK2 kinases

PubMed Central

Ng, Ley-Moy; Soon, Fen-Fen; Zhou, X. Edward; West, Graham M.; Kovach, Amanda; Suino-Powell, Kelly M.; Chalmers, Michael J.; Li, Jun; Yong, Eu-Leong; Zhu, Jian-Kang; Griffin, Patrick R.; Melcher, Karsten; Xu, H. Eric

2011-01-01

Abscisic acid (ABA) is an essential hormone that controls plant growth, development, and responses to abiotic stresses. Central for ABA signaling is the ABA-mediated autoactivation of three monomeric Snf1-related kinases (SnRK2.2, -2.3, and -2.6). In the absence of ABA, SnRK2s are kept in an inactive state by forming physical complexes with type 2C protein phosphatases (PP2Cs). Upon relief of this inhibition, SnRK2 kinases can autoactivate through unknown mechanisms. Here, we report the crystal structures of full-length Arabidopsis thaliana SnRK2.3 and SnRK2.6 at 1.9- and 2.3-Å resolution, respectively. The structures, in combination with biochemical studies, reveal a two-step mechanism of intramolecular kinase activation that resembles the intermolecular activation of cyclin-dependent kinases. First, release of inhibition by PP2C allows the SnRK2s to become partially active because of an intramolecular stabilization of the catalytic domain by a conserved helix in the kinase regulatory domain. This stabilization enables SnRK2s to gain full activity by activation loop autophosphorylation. Autophosphorylation is more efficient in SnRK2.6, which has higher stability than SnRK2.3 and has well-structured activation loop phosphate acceptor sites that are positioned next to the catalytic site. Together, these data provide a structural framework that links ABA-mediated release of PP2C inhibition to activation of SnRK2 kinases. PMID:22160701

Genetic analysis reveals the identity of the photoreceptor for phototaxis in hormogonium filaments of Nostoc punctiforme.

PubMed

Campbell, Elsie L; Hagen, Kari D; Chen, Rui; Risser, Douglas D; Ferreira, Daniela P; Meeks, John C

2015-02-15

In cyanobacterial Nostoc species, substratum-dependent gliding motility is confined to specialized nongrowing filaments called hormogonia, which differentiate from vegetative filaments as part of a conditional life cycle and function as dispersal units. Here we confirm that Nostoc punctiforme hormogonia are positively phototactic to white light over a wide range of intensities. N. punctiforme contains two gene clusters (clusters 2 and 2i), each of which encodes modular cyanobacteriochrome-methyl-accepting chemotaxis proteins (MCPs) and other proteins that putatively constitute a basic chemotaxis-like signal transduction complex. Transcriptional analysis established that all genes in clusters 2 and 2i, plus two additional clusters (clusters 1 and 3) with genes encoding MCPs lacking cyanobacteriochrome sensory domains, are upregulated during the differentiation of hormogonia. Mutational analysis determined that only genes in cluster 2i are essential for positive phototaxis in N. punctiforme hormogonia; here these genes are designated ptx (for phototaxis) genes. The cluster is unusual in containing complete or partial duplicates of genes encoding proteins homologous to the well-described chemotaxis elements CheY, CheW, MCP, and CheA. The cyanobacteriochrome-MCP gene (ptxD) lacks transmembrane domains and has 7 potential binding sites for bilins. The transcriptional start site of the ptx genes does not resemble a sigma 70 consensus recognition sequence; moreover, it is upstream of two genes encoding gas vesicle proteins (gvpA and gvpC), which also are expressed only in the hormogonium filaments of N. punctiforme. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

MDMA (3,4-Methylenedioxymethamphetamine) Analogues as Tools to Characterize MDMA-Like Effects: An Approach to Understand Entactogen Pharmacology

PubMed Central

Sáez-Briones, P.; Hernández, A.

2013-01-01

Besides stimulants and hallucinogens, whose psychotropic effects are shared by many structurally related molecules exhibiting different efficacies and potencies in humans, the phenylisopropylamine MDMA (3,4-methylenedioxymethamphetamine, XTC, “Ecstasy”) is the prototypical representative of a separate class of psychotropic substance, able to elicit the so-called entactogenic syndrome in healthy humans. This reversible altered state of consciousness, usually described as an “open mind state”, may have relevant therapeutic applications, both in psychotherapy and as a pharmacological support in many neuropsychiatric disorders with a high rate of treatment failure. Nevertheless, a comprehensive and systematic exploration of the structure-activity relationships associated with entactogenic activity has remained incomplete and controversial, highlighting the possibility that MDMA might represent a pharmacological rarity in the field of psychotropics. As the latter is still an open question, the pharmacological characterization of MDMA analogues remains the logical strategy to attempt the elucidation of the structural requirements needed to elicit typical MDMA-like effects. Intriguingly, almost no experimental evidence supports the existence of actual MDMA analogues that truly resemble the whole pharmacological profile of MDMA, probably due to its complex (and partially not fully understood) mechanism of action that includes a disruption of monoaminergic neurotransmission. The present review presents a brief summary of the pharmacology of MDMA, followed by the evidence accumulated over the years regarding the characterization of classical structurally related MDMA analogues in different models and how this state of the art highlights the need to develop new and better MDMA analogues. PMID:24403876

Purification and partial characterization of the major outer membrane protein of Chlamydia trachomatis

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

Caldwell, H.D.; Kromhout, J.; Schachter, J.

1981-03-01

Elementary bodies (EB) of Chlamydia trachomatis serotypes C, E, and L2 were extrinsically radioiodinated, and whole-cell lysates of these serotypes were compared by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Autoradiography of the polypeptide profiles identified a major surface protein with an apparent subunit molecular weight of 39,500 that was common to each C. trachomatis serotype. The abilities of nonionic (Triton X-100), dipolar ionic (Zwittergent TM-314), mild (sodium deoxycholate and sodium N-lauroyl sarcosine), and strongly anionic (SDS) detergents to extract this protein from intact EB of the L2 serotype were investigated by SDS-PAGE analysis of the soluble and insoluble fractions obtainedmore » after each detergent treatment. Only SDS readily extracted this protein from intact EB. Sarkosyl treatment selectively solubilized the majority of other EB proteins, leaving the 39,500-dalton protein associated with the Sarkosyl-insoluble fraction. Ultrastructural studies of the Sarkosyl-insoluble EB pellet showed it to consist of empty EB particles possessing an apparently intact outer membrane. No structural evidence for a peptidoglycan-like cell wall was found. Morphologically these chlamydial outer membrane complexes (COMC) resembled intact chlamydial EB outer membranes. The 39,500-dalton outer membrane protein was quantitatively extracted from COMC by treating them with 2% SDS at 60 degrees C. This protein accounted for 61% of the total COMC-associated protein, and its extraction resulted in a concomitant loss of the COMC membrane structure and morphology. The 39,500-dalton major outer membrane protein is a serogroup antigen of C. trachomatis organisms.« less

Aposematism and crypsis are not enough to explain dorsal polymorphism in the Iberian adder

NASA Astrophysics Data System (ADS)

Martínez-Freiría, Fernando; Pérez i de Lanuza, Guillem; Pimenta, António A.; Pinto, Tiago; Santos, Xavier

2017-11-01

Aposematic organisms can show phenotypic variability across their distributional ranges. The ecological advantages of this variability have been scarcely studied in vipers. We explored this issue in Vipera seoanei, a species that exhibits five geographically structured dorsal colour phenotypes across Northern Iberia: two zigzag patterned (Classic and Cantabrica), one dorsal-strip patterned (Bilineata), one even grey (Uniform), and one melanistic (Melanistic). We compared predation rates (raptors and mammals) on plasticine models resembling each colour phenotype in three localities. Visual modelling techniques were used to infer detectability (i.e. conspicuousness) of each model type for visually guided predators (i.e. diurnal raptors). We hypothesize that predation rates will be lower for the two zigzag models (aposematism hypothesis) and that models with higher detectability would show higher predation rates (detectability hypothesis). Classic and Bilineata models were the most conspicuous, while Cantabrica and Uniform were the less. Melanistic presented an intermediate conspicuousness. Predation rate was low (3.24% of models) although there was variation in attack frequency among models. Zigzag models were scarcely predated supporting the aposematic role of the zigzag pattern in European vipers to reduce predation (aposematism hypothesis). From the non-zigzag models, high predation occurred on Bilineata and Melanistic models, and low on Uniform models, partially supporting our detectability hypothesis. These results suggest particular evolutionary advantages for non-zigzag phenotypes such as better performance of Melanistic phenotypes in cold environments or better crypsis of Uniform phenotypes. Polymorphism in V. seoanei may respond to a complex number of forces acting differentially across an environmental gradient.

Na+ Influx Induced by New Antimalarials Causes Rapid Alterations in the Cholesterol Content and Morphology of Plasmodium falciparum

PubMed Central

Das, Sudipta; Bhatanagar, Suyash; Morrisey, Joanne M.; Daly, Thomas M.; Burns, James M.; Coppens, Isabelle; Vaidya, Akhil B.

2016-01-01

Among the several new antimalarials discovered over the past decade are at least three clinical candidate drugs, each with a distinct chemical structure, that disrupt Na+ homeostasis resulting in a rapid increase in intracellular Na+ concentration ([Na+]i) within the erythrocytic stages of Plasmodium falciparum. At present, events triggered by Na+ influx that result in parasite demise are not well-understood. Here we report effects of two such drugs, a pyrazoleamide and a spiroindolone, on intraerythrocytic P. falciparum. Within minutes following the exposure to these drugs, the trophozoite stage parasite, which normally contains little cholesterol, was made permeant by cholesterol-dependent detergents, suggesting it acquired a substantial amount of the lipid. Consistently, the merozoite surface protein 1 and 2 (MSP1 and MSP2), glycosylphosphotidylinositol (GPI)-anchored proteins normally uniformly distributed in the parasite plasma membrane, coalesced into clusters. These alterations were not observed following drug treatment of P. falciparum parasites adapted to grow in a low [Na+] growth medium. Both cholesterol acquisition and MSP1 coalescence were reversible upon the removal of the drugs, implicating an active process of cholesterol exclusion from trophozoites that we hypothesize is inhibited by high [Na+]i. Electron microscopy of drug-treated trophozoites revealed substantial morphological changes normally seen at the later schizont stage including the appearance of partial inner membrane complexes, dense organelles that resemble “rhoptries” and apparent nuclear division. Together these results suggest that [Na+]i disruptor drugs by altering levels of cholesterol in the parasite, dysregulate trophozoite to schizont development and cause parasite demise. PMID:27227970

Web server to identify similarity of amino acid motifs to compounds (SAAMCO).

PubMed

Casey, Fergal P; Davey, Norman E; Baran, Ivan; Varekova, Radka Svobodova; Shields, Denis C

2008-07-01

Protein-protein interactions are fundamental in mediating biological processes including metabolism, cell growth, and signaling. To be able to selectively inhibit or induce protein activity or complex formation is a key feature in controlling disease. For those situations in which protein-protein interactions derive substantial affinity from short linear peptide sequences, or motifs, we can develop search algorithms for peptidomimetic compounds that resemble the short peptide's structure but are not compromised by poor pharmacological properties. SAAMCO is a Web service ( http://bioware.ucd.ie/ approximately saamco) that facilitates the screening of motifs with known structures against bioactive compound databases. It is built on an algorithm that defines compound similarity based on the presence of appropriate amino acid side chain fragments and a favorable Root Mean Squared Deviation (RMSD) between compound and motif structure. The methodology is efficient as the available compound databases are preprocessed and fast regular expression searches filter potential matches before time-intensive 3D superposition is performed. The required input information is minimal, and the compound databases have been selected to maximize the availability of information on biological activity. "Hits" are accompanied with a visualization window and links to source database entries. Motif matching can be defined on partial or full similarity which will increase or reduce respectively the number of potential mimetic compounds. The Web server provides the functionality for rapid screening of known or putative interaction motifs against prepared compound libraries using a novel search algorithm. The tabulated results can be analyzed by linking to appropriate databases and by visualization.

Crystal structure at 2.8Å of Huntingtin-interacting protein 1 (HIP1) coiled-coil domain reveals a charged surface suitable for HIP-protein interactor (HIPPI)

PubMed Central

Niu, Qian; Ybe, Joel A.

2008-01-01

Summary Huntington’s disease is a genetic neurological disorder that is triggered by the dissociation of the huntingtin protein (htt) from its obligate interaction partner Huntingtin-interacting protein 1 (HIP1). The release of htt permits HIP-protein interactor (HIPPI) to bind to its recognition site on HIP1 to form a HIPPI/HIP1 complex that recruits Procaspase-8 to begin the process of apoptosis. The interaction module between HIPPI and HIP1 was predicted to resemble a death-effector domain (DED). Our 2.8 Å crystal structure of the HIP1 371-481 sub-fragment that includes F432 and K474 important for HIPPI binding is not a DED, but is a partially opened coiled-coil. The HIP1 371-481 model reveals a basic surface we hypothesize is suitable for binding HIPPI. There is an opened region next to the putative HIPPI site that is highly negatively charged. The acidic residues in this region are highly conserved in HIP1 and a related protein, HIP1R from different organisms, but are not conserved in the yeast homolog of HIP1, sla2p. We have modeled ∼85% of the coiled-coil domain by joining our new HIP1 371-481 structure to the HIP1 482-586 model (PDB code: 2NO2). Finally, the middle of this coiled-coil domain may be intrinsically flexible and suggests a new interaction model where HIPPI binds to a “U” shaped HIP1 molecule. PMID:18155047

Two cases of childhood narcolepsy mimicking epileptic seizures in video-EEG/EMG.

PubMed

Yanagishita, Tomoe; Ito, Susumu; Ohtani, Yui; Eto, Kaoru; Kanbayashi, Takashi; Oguni, Hirokazu; Nagata, Satoru

2018-06-06

Narcolepsy is characterized by excessive sleepiness, hypnagogic hallucinations, and sleep paralysis, and can occur with or without cataplexy. Here, we report two children with narcolepsy presenting with cataplexy mimicking epileptic seizures as determined by long-term video-electroencephalography (EEG) and electromyography (EMG) monitoring. Case 1 was a 15-year-old girl presenting with recurrent episodes of "convulsions" and loss of consciousness, who was referred to our hospital with a diagnosis of epilepsy showing "convulsions" and "complex partial seizures". The long-term video-polygraph showed a clonic attack lasting for 15 s, which corresponded to 1-2 Hz with interruption of mentalis EMG discharges lasting for 70-300 ms without any EEG changes. Narcolepsy was suspected due to the attack induced by hearty laughs and the presence of sleep attacks, and confirmed by low orexin levels in cerebrospinal fluid (CSF). Case 2 was an 11-year-old girl presenting with recurrent episodes of myoclonic attacks simultaneously with dropping objects immediately after hearty laughs, in addition to sleep attacks, hypnagogic hallucinations, and sleep paralysis. The long-term video-polygraph showed a subtle attack, characterized by dropping chopsticks from her hand, which corresponded to an interruption of ongoing deltoid EMG discharges lasting 140 ms without any EEG changes. A diagnosis of narcolepsy was confirmed by the low orexin levels in CSF. These cases demonstrate that children with narcolepsy may have attacks of cataplexy that resemble clonic or myoclonic seizures. Copyright © 2018 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

Surgical Management of Complex Lower-Extremity Trauma With a Long Hindfoot Fusion Nail: A Case Report.

PubMed

Jain, Nickul S; Lopez, Gregory D; Bederman, S Samuel; Wirth, Garrett A; Scolaro, John A

2016-08-01

High-energy injuries can result in complete or partial loss of the talus. Ipsilateral fractures to the lower limb increase the complexity of surgical management, and treatment is guided by previous case reports of similar injuries. A case of complex lower-extremity trauma with extruded and missing talar body and ipsilateral type IIIB open tibia fracture is presented. Surgical limb reconstruction and salvage was performed successfully with a single orthopaedic implant in a manner not described previously in the literature. The purpose of this case report is to present the novel use of a single orthopaedic implant for treatment of a complex, open traumatic injury. Previous case reports in the literature have described the management of complete or partial talar loss. We describe the novel use of a long hindfoot fusion nail and staged bone grafting to achieve tibiocalcaneal arthrodesis for the treatment of complex lower-extremity trauma. Therapeutic, Level IV: Case study. © 2015 The Author(s).

Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor.

PubMed Central

Aghajari, N.; Feller, G.; Gerday, C.; Haser, R.

1998-01-01

Alteromonas haloplanctis is a bacterium that flourishes in Antarctic sea-water and it is considered as an extreme psychrophile. We have determined the crystal structures of the alpha-amylase (AHA) secreted by this bacterium, in its native state to 2.0 angstroms resolution as well as in complex with Tris to 1.85 angstroms resolution. The structure of AHA, which is the first experimentally determined three-dimensional structure of a psychrophilic enzyme, resembles those of other known alpha-amylases of various origins with a surprisingly greatest similarity to mammalian alpha-amylases. AHA contains a chloride ion which activates the hydrolytic cleavage of substrate alpha-1,4-glycosidic bonds. The chloride binding site is situated approximately 5 angstroms from the active site which is characterized by a triad of acid residues (Asp 174, Glu 200, Asp 264). These are all involved in firm binding of the Tris moiety. A reaction mechanism for substrate hydrolysis is proposed on the basis of the Tris inhibitor binding and the chloride activation. A trio of residues (Ser 303, His 337, Glu 19) having a striking spatial resemblance with serine-protease like catalytic triads was found approximately 22 angstroms from the active site. We found that this triad is equally present in other chloride dependent alpha-amylases, and suggest that it could be responsible for autoproteolytic events observed in solution for this cold adapted alpha-amylase. PMID:9541387

Bile duct adenoma and von Meyenburg complex-like duct arising in hepatitis and cirrhosis: pathogenesis and histological characteristics.

PubMed

Aishima, Shinichi; Tanaka, Yuki; Kubo, Yuichiro; Shirabe, Ken; Maehara, Yoshihiko; Oda, Yoshinao

2014-11-01

Morphologic features and neoplastic potentials of bile duct adenoma (BDA) and von Meyenburg complex (VMC)-like duct arising in chronic liver disease were unknown. Thirty-five BDAs and 12 VMC-like duct lesions were observed in 39 cases with chronic liver disease. BDAs were divided into the EMA-cytoplasmic type (n = 14) and EMA-luminal type (n = 21). EMA-cytoplasmic BDA composed of a proliferation of cuboidal to low-columnar cells forming an open lumen with NCAM(+)/MUC6(-), resembling an interlobular bile duct. EMA-luminal BDA showed uniform cuboidal cells with narrow lumen, and NCAM(++)/MUC6(++), resembling a ductular reaction. VMC-like duct showed positive MUC1 expression and negative MUC6. The expression of S100P, glucose transporter-1 (GLUT-1) and insulin-like growth factor II mRNA-binding protein 3 (IMP-3) were not detected in three lesions. p16 expression was higher than those of the ductular reaction, and the Ki67 and p53 indexes were very low (<1.0%). Large-sized EMA-luminal BDA shows sclerotic stroma. We classified small nodular lesions of ductal or ductular cells in chronic hepatitis and cirrhosis into the following groups: BDA, interlobular bile duct type; BDA, ductular/peribiliary gland type; and VMC-like duct. They may be reactive proliferation rather than neoplastic lesions. © 2014 Japanese Society of Pathology and Wiley Publishing Asia Pty Ltd.

Fetuin-A/Albumin-Mineral Complexes Resembling Serum Calcium Granules and Putative Nanobacteria: Demonstration of a Dual Inhibition-Seeding Concept

PubMed Central

Young, David; Young, John D.

2009-01-01

Serum-derived granulations and purported nanobacteria (NB) are pleomorphic apatite structures shown to resemble calcium granules widely distributed in nature. They appear to be assembled through a dual inhibitory-seeding mechanism involving proteinaceous factors, as determined by protease (trypsin and chymotrypsin) and heat inactivation studies. When inoculated into cell culture medium, the purified proteins fetuin-A and albumin fail to induce mineralization, but they will readily combine with exogenously added calcium and phosphate, even in submillimolar amounts, to form complexes that will undergo morphological transitions from nanoparticles to spindles, films, and aggregates. As a mineralization inhibitor, fetuin-A is much more potent than albumin, and it will only seed particles at higher mineral-to-protein concentrations. Both proteins display a bell-shaped, dose-dependent relationship, indicative of the same dual inhibitory-seeding mechanism seen with whole serum. As ascertained by both seeding experiments and gel electrophoresis, fetuin-A is not only more dominant but it appears to compete avidly for nanoparticle binding at the expense of albumin. The nanoparticles formed in the presence of fetuin-A are smaller than their albumin counterparts, and they have a greater tendency to display a multi-layered ring morphology. In comparison, the particles seeded by albumin appear mostly incomplete, with single walls. Chemically, spectroscopically, and morphologically, the protein-mineral particles resemble closely serum granules and NB. These particles are thus seen to undergo an amorphous to crystalline transformation, the kinetics and completeness of which depend on the protein-to-mineral ratios, with low ratios favoring faster conversion to crystals. Our results point to a dual inhibitory-seeding, de-repression model for the assembly of particles in supersaturated solutions like serum. The presence of proteins and other inhibitory factors tend to block apatite nuclei formation or to stabilize the nascent nuclei as amorphous or semi-crystalline spherical nanoparticles, until the same inhibitory influences are overwhelmed or de-repressed, whereby the apatite nuclei grow in size to coalesce into crystalline spindles and films—a mechanism that may explain not only the formation of calcium granules in nature but also normal or ectopic calcification in the body. PMID:19956594

Effect of amylopectin on the rheological properties of aqueous dispersions of starch-sodium palmitate complexes

USDA-ARS?s Scientific Manuscript database

Aqueous dispersions of normal and high-amylose corn starch were steam jet cooked and blended with aqueous solutions of sodium palmitate to form amylose inclusion complexes. Partial conversion of complexed sodium palmitate to palmitic acid by addition of acetic acid led to the formation of gels. Bl...

Embedding and partial resolution of complex cones over Fano threefolds

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

Dwivedi, Siddharth, E-mail: sdwivedi@iitk.ac.in

2016-12-15

This work deals with the study of embeddings of toric Calabi–Yau fourfolds which are complex cones over the smooth Fano threefolds. In particular, we focus on finding various embeddings of Fano threefolds inside other Fano threefolds and study the partial resolution of the latter in hope to find new toric dualities. We find many diagrams possible for many of these Fano threefolds, but unfortunately, none of them are consistent quiver theories. We also obtain a quiver Chern–Simons theory which matches a theory known to the literature, thus providing an alternate method of obtaining it.

Complexity of parallel implementation of domain decomposition techniques for elliptic partial differential equations

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

Gropp, W.D.; Keyes, D.E.

1988-03-01

The authors discuss the parallel implementation of preconditioned conjugate gradient (PCG)-based domain decomposition techniques for self-adjoint elliptic partial differential equations in two dimensions on several architectures. The complexity of these methods is described on a variety of message-passing parallel computers as a function of the size of the problem, number of processors and relative communication speeds of the processors. They show that communication startups are very important, and that even the small amount of global communication in these methods can significantly reduce the performance of many message-passing architectures.

Family values in the age of genomics: comparative analyses of temperate bacteriophage HK022.

PubMed

Weisberg, R A; Gottesmann, M E; Hendrix, R W; Little, J W

1999-01-01

HK022 is a temperate coliphage related to phage lambda. Its chromosome has been completely sequenced, and several aspects of its life cycle have been intensively studied. In the overall arrangement, expression, and function of most of its genes, HK022 broadly resembles lambda and other members of the lambda family. Upon closer view, significant differences emerge. The differences reveal alternative strategies used by related phages to cope with similar problems and illuminate previously unknown regulatory and structural motifs. HK022 prophages protect lysogens from superinfection by producing a sequence-specific RNA binding protein that prematurely terminates nascent transcripts of infecting phage. It uses a novel RNA-based mechanism to antiterminate its own early transcription. The HK022 protein shell is strengthened by a complex pattern of covalent subunit interlinking to form a unitary structure that resembles chain-mail armour. Its integrase and repressor proteins are similar to those of lambda, but the differences provide insights into the evolution of biological specificity and the elements needed for construction of a stable genetic switch.

Flavonols and ellagic acid derivatives in peels of different species of jabuticaba (Plinia spp.) identified by HPLC-DAD-ESI/MSn.

PubMed

Neves, Nathália de Andrade; Stringheta, Paulo César; Gómez-Alonso, Sergio; Hermosín-Gutiérrez, Isidro

2018-06-30

Extracts of jabuticaba peels show complex chromatographic profiles at 360 nm, with some peaks presenting UV-Vis spectra resembling those of flavonol glycosides and others resembling that of ellagic acid. The presence and tentative identification of these phenolic compounds were comprehensively studied in four species of Brazilian jabuticaba fruit - Plinia trunciflora, variety 'jabuticaba de cabinho'; P. caulifora, varieties 'jabuticaba paulista' and 'jabuticaba canaã-açu'; P. jaboticaba, variety 'jabuticaba sabará'; and P. phitrantha, variety 'jabuticaba branca-vinho' - using HPLC-DAD-ESI-MS n . Seventeen flavonols derived from quercetin and three from myricetin and eighteen derivatives of ellagic acid and eleven of methyl ellagic acid were detected. Most of them were newly described and mainly occurred in glycosylated and acylglycosylated forms. Some compounds were missing in one variety, such as the absence of methyl ellagic acid derivatives in 'jabuticaba branca-vinho', and others only appeared in one variety, thus suggesting potential capacity for varietal differentiation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Here Looking at You, Tethys

NASA Image and Video Library

2017-01-23

Tethys, one of Saturn's larger icy moons, vaguely resembles an eyeball staring off into space in this view from NASA's Cassini spacecraft. The resemblance is due to the enormous crater, Odysseus, and its complex of central peaks. Like any solar system moon, Tethys (660 miles or 1,062 kilometers across) has suffered many impacts. These impacts are a prime shaper of the appearance of a moon's surface , especially when the moon has no active geological processes. In this case, a large impact not only created a crater known as Odysseus, but the rebound of the impact caused the mountainous peaks, named Scheria Montes, to form in the center of the crater. This view looks toward the leading side of Tethys. North on Tethys is up and rotated 1 degree to the left. The image was taken in green light with the Cassini spacecraft narrow-angle camera on Nov. 10, 2016. The view was acquired at a distance of approximately 228,000 miles (367,000 kilometers) from Tethys. Image scale is 1.2 miles (2 kilometers) per pixel. http://photojournal.jpl.nasa.gov/catalog/PIA20518

Links between quantum physics and thought.

PubMed

Robson, Barry

2009-01-01

Quantum mechanics (QM) provides a variety of ideas that can assist in developing Artificial Intelligence for healthcare, and opens the possibility of developing a unified system of Best Practice for inference that will embrace both QM and classical inference. Of particular interest is inference in the hyperbolic-complex plane, the counterpart of the normal i-complex plane of basic QM. There are two reasons. First, QM appears to rotate from i-complex Hilbert space to hyperbolic-complex descriptions when observations are made on wave functions as particles, yielding classical results, and classical laws of probability manipulation (e.g. the law of composition of probabilities) then hold, whereas in the i-complex plane they do not. Second, i-complex Hilbert space is not the whole story in physics. Hyperbolic complex planes arise in extension from the Dirac-Clifford calculus to particle physics, in relativistic correction thereby, and in regard to spinors and twisters. Generalization of these forms resemble grammatical constructions and promote the idea that probability-weighted algebraic elements can be used to hold dimensions of syntactic and semantic meaning. It is also starting to look as though when a solution is reached by an inference system in the hyperbolic-complex, the hyperbolic-imaginary values disappear, while conversely hyperbolic-imaginary values are associated with the un-queried state of a system and goal seeking behavior.

A Partial Theory of Executive Succession.

ERIC Educational Resources Information Center

Thiemann, Francis C.

This study has two purposes: (1) To construct a partial theory of succession, and (2) to utilize a method of theory construction which combines some of the concepts of Hans Zetterberg with the principles of formal symbolic logic. A bibliography on succession in complex organizations with entries on descriptive and empirical studies from various…

Understanding Rasch Measurement: Partial Credit Model and Pivot Anchoring.

ERIC Educational Resources Information Center

Bode, Rita K.

2001-01-01

Describes the Rasch measurement partial credit model, what it is, how it differs from other Rasch models, and when and how to use it. Also describes the calibration of instruments with increasingly complex items. Explains pivot anchoring and illustrates its use and describes the effect of pivot anchoring on step calibrations, item hierarchy, and…

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

Lu, Jun; Byrne, Noel; Wang, John

Clinical studies indicate that partial agonists of the G-protein-coupled, free fatty acid receptor 1 GPR40 enhance glucose-dependent insulin secretion and represent a potential mechanism for the treatment of type 2 diabetes mellitus. Full allosteric agonists (AgoPAMs) of GPR40 bind to a site distinct from partial agonists and can provide additional efficacy. We report the 3.2-Å crystal structure of human GPR40 (hGPR40) in complex with both the partial agonist MK-8666 and an AgoPAM, which exposes a novel lipid-facing AgoPAM-binding pocket outside the transmembrane helical bundle. Comparison with an additional 2.2-Å structure of the hGPR40–MK-8666 binary complex reveals an induced-fit conformational couplingmore » between the partial agonist and AgoPAM binding sites, involving rearrangements of the transmembrane helices 4 and 5 (TM4 and TM5) and transition of the intracellular loop 2 (ICL2) into a short helix. These conformational changes likely prime GPR40 to a more active-like state and explain the binding cooperativity between these ligands.« less

Self-assembly of discrete metal complexes in aqueous solution via block copolypeptide amphiphiles.

PubMed

Kuroiwa, Keita; Masaki, Yoshitaka; Koga, Yuko; Deming, Timothy J

2013-01-21

The integration of discrete metal complexes has been attracting significant interest due to the potential of these materials for soft metal-metal interactions and supramolecular assembly. Additionally, block copolypeptide amphiphiles have been investigated concerning their capacity for self-assembly into structures such as nanoparticles, nanosheets and nanofibers. In this study, we combined these two concepts by investigating the self-assembly of discrete metal complexes in aqueous solution using block copolypeptides. Normally, discrete metal complexes such as [Au(CN)(2)]-, when molecularly dispersed in water, cannot interact with one another. Our results demonstrated, however, that the addition of block copolypeptide amphiphiles such as K(183)L(19) to [Au(CN)(2)]- solutions induced one-dimensional integration of the discrete metal complex, resulting in photoluminescence originating from multinuclear complexes with metal-metal interactions. Transmission electron microscopy (TEM) showed a fibrous nanostructure with lengths and widths of approximately 100 and 20 nm, respectively, which grew to form advanced nanoarchitectures, including those resembling the weave patterns of Waraji (traditional Japanese straw sandals). This concept of combining block copolypeptide amphiphiles with discrete coordination compounds allows the design of flexible and functional supramolecular coordination systems in water.

A new species of Pristimantis (Amphibia, Anura, Craugastoridae) from the foothills of the Andes in Manu National Park, southeastern Peru.

PubMed

Shepack, Alexander; von May, Rudolf; Ttito, Alex; Catenazzi, Alessandro

2016-01-01

We describe a new species of Pristimantis from the humid sub-montane forest of the Región Cusco in Peru. Pristimantis pluvialis sp. n. was collected in the Kosñipata and Entoro valleys at elevations from 740 to 1110 m a.s.l., near the borders of Manu National Park and within the Huachiperi Haramba Queros Conservation Concession. The new species can be distinguished from other members of the genus Pristimantis by its rostral tubercle, smooth dorsal skin, and by its advertisement call. Pristimantis lacrimosus and Pristimantis waoranii superficially most resemble the new species, but Pristimantis pluvialis sp. n. differs from both species by having a rostral tubercle (absent in Pristimantis waoranii and variable in Pristimantis lacrimosus) and larger size, from Pristimantis lacrimosus by its call emitted at a lower frequency, and from Pristimantis waoranii for its dorsal coloration with dark markings. Two other species have partially overlapping distributions and resemble the new species, Pristimantis mendax and Pristimantis olivaceus, but they produce advertisement calls with much higher dominant frequencies than the advertisement call of the new species. Furthermore, Pristimantis mendax differs from the new species by lacking a rostral tubercle and by having a sigmoid inner tarsal fold, whereas Pristimantis olivaceus differs by being smaller and by having dorsal skin shagreen with scattered tubercles. The new species has snout-vent length of 21.8-26.9 mm in males (n = 12) and 28.8 mm in a single female.

Behavioural properties of chick somitic mesoderm and lateral plate when explanted in vitro.

PubMed

Bellairs, R; Sanders, E J; Portch, P A

1980-04-01

Tissue culture, time-lapse cinematographic and electron microscopic techniques have been used to study the properties of chick mesoderm at several stages of differentiation. Lateral plate, unsegmented mesoderm (segmental plate), and newly formed somites were dissected from stage-12 embryos, whilst dermo-myotomes and sclerotomes were dissected from stage-18 embryos. Each type of mesoderm was found to exhibit a characteristic pattern of behaviour. The explants from the unsegmented mesoderm from the newly formed somites and from the older embryos could be placed in a developmental sequence; with increasing differentiation they settled and spread on the substrate more readily, whether explanted as pieces of tissue or as individual cells, and it was concluded that this implied an increased adhesion to the substrate. Similarly, with increasing differentiation, the cells segmented at a faster rate. No significant differences could be discerned in the internal structure of the different types of cells, although differences in the general shape were apparent. The lateral plate mesoderm cells, which bear some resemblances to the unsegmented mesoderm cells in the embryo, also show some morphological resemblances to them in vitro. However, the lateral plate cells had a much greater success in attaching to glass or platic substrates. They were also found to have the highest speed of locomotion of all the tissues studied, whereas the unsegmented had the lowest. It is concluded therefore, that although cells may look similar to one another morphologically, their behaviour may differ greatly, probably because they are already partially determined.

Chiral copper(II) complex-catalyzed reactions of partially protected carbohydrates.

PubMed

Allen, C Liana; Miller, Scott J

2013-12-20

Catalyst-controlled regioselective functionalization of partially protected saccharide molecules is a highly important yet under-developed area of carbohydrate chemistry. Such reactions allow for the reduction of protecting group manipulation steps required in syntheses involving sugars. Herein, an approach to these processes using enantiopure copper-bis(oxazoline) catalysts to control couplings of electrophiles to various partially protected sugars is reported. In a number of cases, divergent regioselectivity was observed as a function of the enantiomer of catalyst that is used.

Molecular and morphological characterization of the cercariae of Lecithodendrium linstowi (Dollfus, 1931), a trematode of bats, and incrimination of the first intermediate snail host, Radix balthica.

PubMed

Enabulele, Egie E; Lawton, Scott P; Walker, Anthony J; Kirk, Ruth S

2018-03-01

Lecithodendrium linstowi is one of the most prevalent and abundant trematodes of bats, but the larval stages and intermediate hosts have not been identified. We present the first molecular and morphological characterization of the cercariae of L. linstowi based on a phylogenetic analysis of partial fragments of LSU and ITS2 rDNA. The first intermediate host was incriminated as Radix balthica by DNA barcoding using cox1 and ITS2 sequences, although the snail morphologically resembled Radix peregra, emphasizing the requirement for molecular identification of lymnaeids as important intermediate hosts of medical and veterinary impact. The application of molecular data in this study has enabled linkage of life cycle stages and accurate incrimination of the first intermediate host.

Evolution and End Point of the Black String Instability: Large D Solution.

PubMed

Emparan, Roberto; Suzuki, Ryotaku; Tanabe, Kentaro

2015-08-28

We derive a simple set of nonlinear, (1+1)-dimensional partial differential equations that describe the dynamical evolution of black strings and branes to leading order in the expansion in the inverse of the number of dimensions D. These equations are easily solved numerically. Their solution shows that thin enough black strings are unstable to developing inhomogeneities along their length, and at late times they asymptote to stable nonuniform black strings. This proves an earlier conjecture about the end point of the instability of black strings in a large enough number of dimensions. If the initial black string is very thin, the final configuration is highly nonuniform and resembles a periodic array of localized black holes joined by short necks. We also present the equations that describe the nonlinear dynamics of anti-de Sitter black branes at large D.

Terraced spreading of simple liquids on solid surfaces

NASA Technical Reports Server (NTRS)

Yang, Ju-Xing; Koplik, Joel; Banavar, Jayanth R.

1992-01-01

We have studied the spreading of liquid drops on a solid surface by molecular-dynamics simulations of coexisting three-phase Lennard-Jones systems of liquid, vapor, and solid. We consider both spherically symmetric atoms and diatomic molecules, and a range of interaction strengths. As the attraction between liquid and solid increases we observe a smooth transition in spreading regimes, from partial to complete to terraced wetting. In the terraced case, where distinct monomolecular layers spread with different velocities, the layers are ordered but not solid, with substantial molecular diffusion both within and between layers. The quantitative behavior resembles recent experimental findings, but the detailed dynamics differ. In particular, the layers exhibit an unusual spreading law, where their radii vary in time as R-squared approximately equal to log10t, which disagrees with experiments on polymeric liquids as well as recent calculations.

Peptide-specific recognition of human cytomegalovirus strains controls adaptive natural killer cells.

PubMed

Hammer, Quirin; Rückert, Timo; Borst, Eva Maria; Dunst, Josefine; Haubner, André; Durek, Pawel; Heinrich, Frederik; Gasparoni, Gilles; Babic, Marina; Tomic, Adriana; Pietra, Gabriella; Nienen, Mikalai; Blau, Igor Wolfgang; Hofmann, Jörg; Na, Il-Kang; Prinz, Immo; Koenecke, Christian; Hemmati, Philipp; Babel, Nina; Arnold, Renate; Walter, Jörn; Thurley, Kevin; Mashreghi, Mir-Farzin; Messerle, Martin; Romagnani, Chiara

2018-05-01

Natural killer (NK) cells are innate lymphocytes that lack antigen-specific rearranged receptors, a hallmark of adaptive lymphocytes. In some people infected with human cytomegalovirus (HCMV), an NK cell subset expressing the activating receptor NKG2C undergoes clonal-like expansion that partially resembles anti-viral adaptive responses. However, the viral ligand that drives the activation and differentiation of adaptive NKG2C + NK cells has remained unclear. Here we found that adaptive NKG2C + NK cells differentially recognized distinct HCMV strains encoding variable UL40 peptides that, in combination with pro-inflammatory signals, controlled the population expansion and differentiation of adaptive NKG2C + NK cells. Thus, we propose that polymorphic HCMV peptides contribute to shaping of the heterogeneity of adaptive NKG2C + NK cell populations among HCMV-seropositive people.

Summer declines in activity and body temperature offer polar bears limited energy savings

USGS Publications Warehouse

Whiteman, J.P.; Harlow, H.J.; Durner, George M.; Anderson-Sprecher, R.; Albeke, Shannon E.; Regehr, Eric V.; Amstrup, Steven C.; Ben-David, M.

2015-01-01

Polar bears (Ursus maritimus) summer on the sea ice or, where it melts, on shore. Although the physiology of “ice” bears in summer is unknown, “shore” bears purportedly minimize energy losses by entering a hibernation-like state when deprived of food. Such a strategy could partially compensate for the loss of on-ice foraging opportunities caused by climate change. However, here we report gradual, moderate declines in activity and body temperature of both shore and ice bears in summer, resembling energy expenditures typical of fasting, nonhibernating mammals. Also, we found that to avoid unsustainable heat loss while swimming, bears employed unusual heterothermy of the body core. Thus, although well adapted to seasonal ice melt, polar bears appear susceptible to deleterious declines in body condition during the lengthening period of summer food deprivation.

Hodgkin's-like lymphoma in a ferret (Mustela putorius furo).

PubMed

Matsumoto, Isao; Uchida, Kazuyuki; Chambers, James Kenn; Nibe, Kazumi; Sato, Yu; Hamasu, Taku; Nakayama, Hiroyuki

2017-10-07

A 7-year-old castrated male ferret developed unilateral cervical lymphadenomegaly over a 1-month period. Histological examination revealed proliferation of tumor cells in a diffuse and partially nodular pattern. The tumor cells were predominantly Hodgkin cells and binucleated Reed-Sternberg cells, characterized by abundant, clear, vacuolated cytoplasm, pleomorphic, ovoid nuclei with thick nuclear membranes and distinct nucleoli. Multinucleated cells, resembling lymphocytic and histiocytic (L&H) cells, were also observed. Immunohistochemically, the tumor cells expressed Pax-5, BLA-36 and vimentin. A small population of the tumor cells expressed CD20. This case showed proliferation of Hodgkin/Reed-Sternberg cells in conjunction with L&H cells that were histologically analogous to feline Hodgkin's-like lymphoma. However, Pax-5 and BLA-36 expression along with rare CD20 expression were consistent with classical Hodgkin's lymphoma in humans.

A new species of Cacatuocotyle (Monogenea, Dactylogyridae) parasitizing Astyanax spp. (Characiformes, Characidae) from Brazil, including molecular data and a key to species identification.

PubMed

Zago, Aline Cristina; Franceschini, Lidiane; Müller, Maria Isabel; Silva, Reinaldo José da

2018-06-26

The present study describes Cacatuocotyle papilionis n. sp. (Monogenea, Dactylogyridae) from the skin of the characid fishes Astyanax lacustris (Lütken, 1875) (=Astyanax altiparanae Garutti & Britski, 2000) and Astyanax fasciatus (Cuvier, 1819) (Characiformes, Characidae) from the Southeast of Brazil, supported by morphological and molecular data. The new species differs from all congeners, mainly due to the morphology of the ventral bar (resembling a butterfly), accessory piece, and the number of rings of the male copulatory organ (MCO), comprising a coiled tube with 4.5-5.5 counterclockwise rings. The first molecular data for this monogenean genus is provided in this study, using the partial sequences of the ribosomal gene (28S), as well as providing an identification key to the species.

Temporal chaos in Boussinesq magnetoconvection

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

Bekki, Naoaki; Moriguchi, Hirofumi; Fundamental Science, Gifu National College of Technology, Motosu, Gifu 501-0495

2007-01-15

Two-dimensional Boussinesq magnetoconvection with idealized stress-free boundary conditions is numerically investigated in order to make clear the difference between chaos and turbulence. It is shown that the long-term behavior of magnetoconvection exhibits spatially coherent and temporally chaotic rolls in marked contrast to highly turbulent fluids. It is also shown that heat transport becomes larger anomalously when the polarity reversal of the magnetic field occurs intermittently in the case of temporally chaotic magnetoconvection. It is found that the Poincare return map of the relative maximum temperature fluctuation of partial differential equations as a function of the preceding maximum resembles the famousmore » Lorenz plot in narrow rolls of magnetoconvection. The chaotic behavior of narrow rolls for individual parameter values robustly persists up to rolls about one fifth as wide as they are high near the codimension-two bifurcation point.« less

Determination of five active compounds in Artemisia princeps and A. capillaris based on UPLC-DAD and discrimination of two species with multivariate analysis.

PubMed

Yang, Heejung; Lee, Dong Young; Jeon, Minji; Suh, Youngbae; Sung, Sang Hyun

2014-05-01

Five active compounds, chlorogenic acid, 3,5-di-O-caffeoylquinic acid, 4,5-di-O-caffeoylquinic acid, jaceosidin, and eupatilin, in Artemisia princeps (Compositae) were simultaneously determined by ultra-performance liquid chromatography connected to diode array detector. The morphological resemblance between A. princeps and A. capillaris makes it difficult to properly identify species properly. It occasionally leads to misuse or misapplication in Korean traditional medicine. In the study, the discrimination between A. princeps and A. capillaris was optimally performed by the developed validation method, which resulted in definitely a difference between two species. Also, it was developed the most reliable markers contributing to the discrimination of two species by the multivariate analysis methods, such as a principal component analysis and a partial least squares discrimination analysis.

Sparse distributed memory

NASA Technical Reports Server (NTRS)

Denning, Peter J.

1989-01-01

Sparse distributed memory was proposed be Pentti Kanerva as a realizable architecture that could store large patterns and retrieve them based on partial matches with patterns representing current sensory inputs. This memory exhibits behaviors, both in theory and in experiment, that resemble those previously unapproached by machines - e.g., rapid recognition of faces or odors, discovery of new connections between seemingly unrelated ideas, continuation of a sequence of events when given a cue from the middle, knowing that one doesn't know, or getting stuck with an answer on the tip of one's tongue. These behaviors are now within reach of machines that can be incorporated into the computing systems of robots capable of seeing, talking, and manipulating. Kanerva's theory is a break with the Western rationalistic tradition, allowing a new interpretation of learning and cognition that respects biology and the mysteries of individual human beings.

Localisation of deformations of the midfacial complex in subjects with class III malocclusions employing thin-plate spline analysis

PubMed Central

SINGH, G. D.; McNAMARA JR, J. A.; LOZANOFF, S.

1997-01-01

This study determines deformations of the midface that contribute to a class III appearance, employing thin-plate spline analysis. A total of 135 lateral cephalographs of prepubertal children of European-American descent with either class III malocclusions or a class I molar occlusion were compared. The cephalographs were traced and checked, and 7 homologous landmarks of the midface were identified and digitised. The data sets were scaled to an equivalent size and subjected to Procrustes analysis. These statistical tests indicated significant differences (P<0.05) between the averaged class I and class III morphologies. Thin-plate spline analysis indicated that both affine and nonaffine transformations contribute towards the total spline for the averaged midfacial configuration. For nonaffine transformations, partial warp 3 had the highest magnitude, indicating the large scale deformations of the midfacial configuration. These deformations affected the palatal landmarks, and were associated with compression of the midfacial complex in the anteroposterior plane predominantly. Partial warp 4 produced some vertical compression of the posterior aspect of the midfacial complex whereas partial warps 1 and 2 indicated localised shape changes of the maxillary alveolus region. Large spatial-scale deformations therefore affect the midfacial complex in an anteroposterior axis, in combination with vertical compression and localised distortions. These deformations may represent a developmental diminution of the palatal complex anteroposteriorly that, allied with vertical shortening of midfacial height posteriorly, results in class III malocclusions with a retrusive midfacial profile. PMID:9449078

Localisation of deformations of the midfacial complex in subjects with class III malocclusions employing thin-plate spline analysis.

PubMed

Singh, G D; McNamara, J A; Lozanoff, S

1997-11-01

This study determines deformations of the midface that contribute to a class III appearance, employing thinplate spline analysis. A total of 135 lateral cephalographs of prepubertal children of European-American descent with either class III malocclusions or a class I molar occlusion were compared. The cephalographs were traced and checked, and 7 homologous landmarks of the midface were identified and digitised. The data sets were scaled to an equivalent size and subjected to Procrustes analysis. These statistical tests indicated significant differences (P < 0.05) between the averaged class I and class III morphologies. Thinplate spline analysis indicated that both affine and nonaffine transformations contribute towards the total spline for the averaged midfacial configuration. For nonaffine transformations, partial warp 3 had the highest magnitude, indicating the large scale deformations of the midfacial configuration. These deformations affected the palatal landmarks, and were associated with compression of the midfacial complex in the anteroposterior plane predominantly. Partial warp 4 produced some vertical compression of the posterior aspect of the midfacial complex whereas partial warps 1 and 2 indicated localised shape changes of the maxillary alveolus region. large spatial-scale deformations therefore affect the midfacial complex in an anteroposterior axis, in combination with vertical compression and localised distortions. These deformations may represent a developmental diminution of the palatal complex anteroposteriorly that, allied with vertical shortening of midfacial height posteriorly, results in class III malocclusions with a retrusive midfacial profile.

The SMS4 cryptographic system design based on dynamic partial self-reconfiguration technology

NASA Astrophysics Data System (ADS)

Wang, Jianxin; Gao, Xianwei; Li, Xiuying; Sui, Meili

2013-03-01

This paper describes SMS4 algorithm by using dynamic partial self-reconfiguration. The design is implemented on Xilinx VirtexII-Pro XC2VP30 FPGA devices. The partial self-reconfiguration encryption/decryption module data throughput is up to 50Mb/s, key expansion and encryption/decryption modules use 1606 and 1570 slices respectively, and the resource utilization ratio of the key expansion by using partial self-reconfiguration technology is less 32.03% and slices are less 757 than the non-reconfiguration technology. SMS4 implementation gets a good balance between high performance and low complexity in area. The theoretical and practical research of dynamic partial self-reconfiguration has a broad space for development and application prospect.

New Abstraction Networks and a New Visualization Tool in Support of Auditing the SNOMED CT Content

PubMed Central

Geller, James; Ochs, Christopher; Perl, Yehoshua; Xu, Junchuan

2012-01-01

Medical terminologies are large and complex. Frequently, errors are hidden in this complexity. Our objective is to find such errors, which can be aided by deriving abstraction networks from a large terminology. Abstraction networks preserve important features but eliminate many minor details, which are often not useful for identifying errors. Providing visualizations for such abstraction networks aids auditors by allowing them to quickly focus on elements of interest within a terminology. Previously we introduced area taxonomies and partial area taxonomies for SNOMED CT. In this paper, two advanced, novel kinds of abstraction networks, the relationship-constrained partial area subtaxonomy and the root-constrained partial area subtaxonomy are defined and their benefits are demonstrated. We also describe BLUSNO, an innovative software tool for quickly generating and visualizing these SNOMED CT abstraction networks. BLUSNO is a dynamic, interactive system that provides quick access to well organized information about SNOMED CT. PMID:23304293

New abstraction networks and a new visualization tool in support of auditing the SNOMED CT content.

PubMed

Geller, James; Ochs, Christopher; Perl, Yehoshua; Xu, Junchuan

2012-01-01

Medical terminologies are large and complex. Frequently, errors are hidden in this complexity. Our objective is to find such errors, which can be aided by deriving abstraction networks from a large terminology. Abstraction networks preserve important features but eliminate many minor details, which are often not useful for identifying errors. Providing visualizations for such abstraction networks aids auditors by allowing them to quickly focus on elements of interest within a terminology. Previously we introduced area taxonomies and partial area taxonomies for SNOMED CT. In this paper, two advanced, novel kinds of abstraction networks, the relationship-constrained partial area subtaxonomy and the root-constrained partial area subtaxonomy are defined and their benefits are demonstrated. We also describe BLUSNO, an innovative software tool for quickly generating and visualizing these SNOMED CT abstraction networks. BLUSNO is a dynamic, interactive system that provides quick access to well organized information about SNOMED CT.

Discriminating males and unpredictable females: males differentiate self-similar facial cues more than females in the judgment of opposite-sex attractiveness.

PubMed

Zhuang, Jin-Ying; Zhang, Sen; Xu, Jing; Hu, Die

2014-01-01

Attractiveness judgment in the context of mate preferences is thought to reflect an assessment of mate quality in relation to an absolute scale of genetic fitness and a relative scale of self-similarity. In this study, subjects judged the attractiveness and trustworthiness of faces in composite images that were manipulated to produce self-similar (self-resemblance) and dissimilar (other-resemblance) images. Males differentiated between self- and other-resemblance as well as among different degrees of self-resemblance in their attractiveness ratings; females did not. Specifically, in Experiment 1, using a morphing technique, we created previously unseen face images possessing different degrees (0%, 30%, 40%, or 50%) of incorporation of the subject's images (different degrees of self-resemblance) and found that males preferred images that were closer to average (0%) rather than more self-similar, whereas females showed no preference for any degree of self-similarity. In Experiment 2, we added a pro-social question about trustworthiness. We replicated the Experiment 1 attractiveness rating results and further found that males differentiated between self- and other-resemblance for the same degree of composites; women did not. Both males and females showed a similar preference for self-resemblances when judging trustworthiness. In conclusion, only males factored self-resemblance into their attractiveness ratings of opposite-sex individuals in a manner consistent with cues of reproductive fitness, although both sexes favored self-resemblance when judging trustworthiness.

Alterations of neurochemical expression of the coeliac-superior mesenteric ganglion complex (CSMG) neurons supplying the prepyloric region of the porcine stomach following partial stomach resection.

PubMed

Palus, Katarzyna; Całka, Jarosław

2016-03-01

The purpose of the present study was to determine the response of the porcine coeliac-superior mesenteric ganglion complex (CSMG) neurons projecting to the prepyloric area of the porcine stomach to peripheral neuronal damage following partial stomach resection. To identify the sympathetic neurons innervating the studied area of stomach, the neuronal retrograde tracer Fast Blue (FB) was applied to control and partial stomach resection (RES) groups. On the 22nd day after FB injection, following laparotomy, the partial resection of the previously FB-injected stomach prepyloric area was performed in animals of RES group. On the 28th day, all animals were re-anaesthetized and euthanized. The CSMG complex was then collected and processed for double-labeling immunofluorescence. In control animals, retrograde-labelled perikarya were immunoreactive to tyrosine hydroxylase (TH), dopamine β-hydroxylase (DβH), neuropeptide Y (NPY) and galanin (GAL). Partial stomach resection decreased the numbers of FB-positive neurons immunopositive for TH and DβH. However, the strong increase of NPY and GAL expression, as well as de novo-synthesis of neuronal nitric oxide synthase (nNOS) and leu5-Enkephalin (LENK) was noted in studied neurons. Furthermore, FB-positive neurons in all pigs were surrounded by a network of cocaine- and amphetamine-regulated transcript peptide (CART)-, calcitonin gene-related peptide (CGRP)-, and substance P (SP)-, vasoactive intestinal peptide (VIP)-, LENK- and nNOS- immunoreactive nerve fibers. This may suggest neuroprotective contribution of these neurotransmitters in traumatic responses of sympathetic neurons to peripheral axonal damage. Copyright © 2015 Elsevier B.V. All rights reserved.

Effects of stress on human mating preferences: stressed individuals prefer dissimilar mates

PubMed Central

Lass-Hennemann, Johanna; Deuter, Christian E.; Kuehl, Linn K.; Schulz, André; Blumenthal, Terry D.; Schachinger, Hartmut

2010-01-01

Although humans usually prefer mates that resemble themselves, mating preferences can vary with context. Stress has been shown to alter mating preferences in animals, but the effects of stress on human mating preferences are unknown. Here, we investigated whether stress alters men's preference for self-resembling mates. Participants first underwent a cold-pressor test (stress induction) or a control procedure. Then, participants viewed either neutral pictures or pictures of erotic female nudes whose facial characteristics were computer-modified to resemble either the participant or another participant, or were not modified, while startle eyeblink responses were elicited by noise probes. Erotic pictures were rated as being pleasant, and reduced startle magnitude compared with neutral pictures. In the control group, startle magnitude was smaller during foreground presentation of photographs of self-resembling female nudes compared with other-resembling female nudes and non-manipulated female nudes, indicating a higher approach motivation to self-resembling mates. In the stress group, startle magnitude was larger during foreground presentation of self-resembling female nudes compared with other-resembling female nudes and non-manipulated female nudes, indicating a higher approach motivation to dissimilar mates. Our findings show that stress affects human mating preferences: unstressed individuals showed the expected preference for similar mates, but stressed individuals seem to prefer dissimilar mates. PMID:20219732

Crystal structure of casein kinase-1, a phosphate-directed protein kinase.

PubMed Central

Xu, R M; Carmel, G; Sweet, R M; Kuret, J; Cheng, X

1995-01-01

The structure of a truncated variant of casein kinase-1 from Schizosaccharomyces pombe, has been determined in complex with MgATP at 2.0 A resolution. The model resembles the 'closed', ATP-bound conformations of the cyclin-dependent kinase 2 and the cAMP-dependent protein kinase, with clear differences in the structure of surface loops that impart unique features to casein kinase-1. The structure is of unphosphorylated, active conformation of casein kinase-1 and the peptide-binding site is fully accessible to substrate. Images PMID:7889932

Viroid Pathogenicity: One Process, Many Faces

PubMed Central

Owens, Robert A.; Hammond, Rosemarie W.

2009-01-01

Despite the non-coding nature of their small RNA genomes, the visible symptoms of viroid infection resemble those associated with many plant virus diseases. Recent evidence indicates that viroid-derived small RNAs acting through host RNA silencing pathways play a key role in viroid pathogenicity. Host responses to viroid infection are complex, involving signaling cascades containing host-encoded protein kinases and crosstalk between hormonal and defense-signaling pathways. Studies of viroid-host interaction in the context of entire biochemical or developmental pathways are just beginning, and many working hypotheses have yet to be critically tested. PMID:21994551

Metal-organic complexes in geochemical processes: temperature dependence of the standard thermodynamic properties of aqueous complexes between metal cations and dicarboxylate ligands

NASA Astrophysics Data System (ADS)

Prapaipong, Panjai; Shock, Everett L.; Koretsky, Carla M.

1999-10-01

By combining results from regression and correlation methods, standard state thermodynamic properties for aqueous complexes between metal cations and divalent organic acid ligands (oxalate, malonate, succinate, glutarate, and adipate) are evaluated and applied to geochemical processes. Regression of experimental standard-state equilibrium constants with the revised Helgeson-Kirkham-Flowers (HKF) equation of state yields standard partial molal entropies (S¯°) of aqueous metal-organic complexes, which allow determination of thermodynamic properties of the complexes at elevated temperatures. In cases where S¯° is not available from either regression or calorimetric measurement, the values of S¯° can be estimated from a linear correlation between standard partial molal entropies of association (ΔS¯°r) and standard partial molal entropies of aqueous cations (S¯°M). The correlation is independent of cation charge, which makes it possible to predict S¯° for complexes between divalent organic acids and numerous metal cations. Similarly, correlations between standard Gibbs free energies of association of metal-organic complexes (ΔḠ°r) and Gibbs free energies of formation (ΔḠ°f) for divalent metal cations allow estimates of standard-state equilibrium constants where experimental data are not available. These correlations are found to be a function of ligand structure and cation charge. Predicted equilibrium constants for dicarboxylate complexes of numerous cations were included with those for inorganic and other organic complexes to study the effects of dicarboxylate complexes on the speciation of metals and organic acids in oil-field brines. Relatively low concentrations of oxalic and malonic acids affect the speciation of cations more than similar concentrations of succinic, glutaric, and adipic acids. However, the extent to which metal-dicarboxylate complexes contribute to the speciation of dissolved metals depends on the type of dicarboxylic acid ligand; relative concentration of inorganic, mono-, and dicarboxylate ligands; and the type of metal cation. As an example, in the same solution, dicarboxylic acids have a greater influence on the speciation of Fe+2 and Mg+2 than on the speciation of Zn+2 and Mn+2.

Sudbury Igneous Complex: Impact melt or igneous rock? Implications for lunar magmatism

NASA Technical Reports Server (NTRS)

Norman, Marc D.

1992-01-01

The recent suggestion that the Sudbury Igneous Complex (SIC) is a fractionated impact melt may have profound implications for understanding the lunar crust and the magmatic history of the Moon. A cornerstone of much current thought on the Moon is that the development of the lunar crust can be traced through the lineage of 'pristine' igneous rocks. However, if rocks closely resembling those from layered igneous intrusions can be produced by differentiation of a large impact melt sheet, then much of what is thought to be known about the Moon may be called into question. This paper presents a brief evaluation of the SIC as a differentiated impact melt vs. endogenous igneous magma and possible implications for the magmatic history of the lunar crust.

Down-Regulation of TM29, a Tomato SEPALLATA Homolog, Causes Parthenocarpic Fruit Development and Floral Reversion1

PubMed Central

Ampomah-Dwamena, Charles; Morris, Bret A.; Sutherland, Paul; Veit, Bruce; Yao, Jia-Long

2002-01-01

We have characterized the tomato (Lycopersicon esculentum Mill.) MADS box gene TM29 that shared a high amino acid sequence homology to the Arabidopsis SEP1, 2, and 3 (SEPALLATA1, 2, and 3) genes. TM29 showed similar expression profiles to SEP1, with accumulation of mRNA in the primordia of all four whorls of floral organs. In addition, TM29 mRNA was detected in inflorescence and vegetative meristems. To understand TM29 function, we produced transgenic tomato plants in which TM29 expression was down-regulated by either cosuppression or antisense techniques. These transgenic plants produced aberrant flowers with morphogenetic alterations in the organs of the inner three whorls. Petals and stamens were green rather than yellow, suggesting a partial conversion to a sepalloid identity. Stamens and ovaries were infertile, with the later developing into parthenocarpic fruit. Ectopic shoots with partially developed leaves and secondary flowers emerged from the fruit. These shoots resembled the primary transgenic flowers and continued to produce parthenocarpic fruit and additional ectopic shoots. Based on the temporal and spatial expression pattern and transgenic phenotypes, we propose that TM29 functions in floral organ development, fruit development, and maintenance of floral meristem identity in tomato. PMID:12376628

Target identification using Zernike moments and neural networks

NASA Astrophysics Data System (ADS)

Azimi-Sadjadi, Mahmood R.; Jamshidi, Arta A.; Nevis, Andrew J.

2001-10-01

The development of an underwater target identification algorithm capable of identifying various types of underwater targets, such as mines, under different environmental conditions pose many technical problems. Some of the contributing factors are: targets have diverse sizes, shapes and reflectivity properties. Target emplacement environment is variable; targets may be proud or partially buried. Environmental properties vary significantly from one location to another. Bottom features such as sand, rocks, corals, and vegetation can conceal a target whether it is partially buried or proud. Competing clutter with responses that closely resemble those of the targets may lead to false positives. All the problems mentioned above contribute to overly difficult and challenging conditions that could lead to unreliable algorithm performance with existing methods. In this paper, we developed and tested a shape-dependent feature extraction scheme that provides features invariant to rotation, size scaling and translation; properties that are extremely useful for any target classification problem. The developed schemes were tested on an electro-optical imagery data set collected under different environmental conditions with variable background, range and target types. The electro-optic data set was collected using a Laser Line Scan (LLS) sensor by the Coastal Systems Station (CSS), located in Panama City, Florida. The performance of the developed scheme and its robustness to distortion, rotation, scaling and translation was also studied.

Formation of Partially and Fully Elaborated Generalized Equivalence Classes

ERIC Educational Resources Information Center

Fields, Lanny; Moss, Patricia

2008-01-01

Most complex categories observed in real-world settings consist of perceptually disparate stimuli, such as a picture of a person's face, the person's name as written, and the same name as heard, as well as dimensional variants of some or all of these stimuli. The stimuli function as members of a single partially or fully elaborated generalized…

Computing the Partial Fraction Decomposition of Rational Functions with Irreducible Quadratic Factors in the Denominators

ERIC Educational Resources Information Center

Man, Yiu-Kwong

2012-01-01

In this note, a new method for computing the partial fraction decomposition of rational functions with irreducible quadratic factors in the denominators is presented. This method involves polynomial divisions and substitutions only, without having to solve for the complex roots of the irreducible quadratic polynomial or to solve a system of linear…

Balance and sustainability in multi-aged stands: a northern conifer case study

Treesearch

Robert S. Seymour; Laura S. Kenefic

1998-01-01

Foresters in the Northeast are both blessed and cursed by the inherent complexity of the region's forests. Thousands of years may pass between natural stand-replacing disturbances, though partial disturbances, such as blowdown, defoliating insects, and various forms of partial cutting, are common (Seymour 1995). Foresters in the region typically deal with...

Evaluation of partial coherence correction in X-ray ptychography

DOE PAGES

Burdet, Nicolas; Shi, Xiaowen; Parks, Daniel; ...

2015-02-23

Coherent X-ray Diffraction Imaging (CDI) and X-ray ptychography both heavily rely on the high degree of spatial coherence of the X-ray illumination for sufficient experimental data quality for reconstruction convergence. Nevertheless, the majority of the available synchrotron undulator sources have a limited degree of partial coherence, leading to reduced data quality and a lower speckle contrast in the coherent diffraction patterns. It is still an open question whether experimentalists should compromise the coherence properties of an X-ray source in exchange for a higher flux density at a sample, especially when some materials of scientific interest are relatively weak scatterers. Amore » previous study has suggested that in CDI, the best strategy for the study of strong phase objects is to maintain a high degree of coherence of the illuminating X-rays because of the broadening of solution space resulting from the strong phase structures. In this article, we demonstrate the first systematic analysis of the effectiveness of partial coherence correction in ptychography as a function of the coherence properties, degree of complexity of illumination (degree of phase diversity of the probe) and sample phase complexity. We have also performed analysis of how well ptychographic algorithms refine X-ray probe and complex coherence functions when those variables are unknown at the start of reconstructions, for noise-free simulated data, in the case of both real-valued and highly-complex objects.« less

Can misfolded proteins be beneficial? The HAMLET case.

PubMed

Pettersson-Kastberg, Jenny; Aits, Sonja; Gustafsson, Lotta; Mossberg, Anki; Storm, Petter; Trulsson, Maria; Persson, Filip; Mok, K Hun; Svanborg, Catharina

2009-01-01

By changing the three-dimensional structure, a protein can attain new functions, distinct from those of the native protein. Amyloid-forming proteins are one example, in which conformational change may lead to fibril formation and, in many cases, neurodegenerative disease. We have proposed that partial unfolding provides a mechanism to generate new and useful functional variants from a given polypeptide chain. Here we present HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) as an example where partial unfolding and the incorporation of cofactor create a complex with new, beneficial properties. Native alpha-lactalbumin functions as a substrate specifier in lactose synthesis, but when partially unfolded the protein binds oleic acid and forms the tumoricidal HAMLET complex. When the properties of HAMLET were first described they were surprising, as protein folding intermediates and especially amyloid-forming protein intermediates had been regarded as toxic conformations, but since then structural studies have supported functional diversity arising from a change in fold. The properties of HAMLET suggest a mechanism of structure-function variation, which might help the limited number of human protein genes to generate sufficient structural diversity to meet the diverse functional demands of complex organisms.

Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex.

PubMed

Numata, Tomoyuki; Inanaga, Hideko; Sato, Chikara; Osawa, Takuo

2015-01-30

Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. Here, we show that the Csm1, Csm3, and Csm4 proteins from Methanocaldococcus jannaschii form a stable subcomplex. We also report the crystal structure of the M. jannaschii Csm3-Csm4 subcomplex at 3.1Å resolution. The complex structure revealed the presence of a basic concave surface around their interface, suggesting the RNA and/or DNA binding ability of the complex. A gel retardation analysis showed that the Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Based on bioinformatics, we constructed a model structure of the Csm1-Csm4-Csm3 ternary complex, which provides insights into its role in the Csm interference complex. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Tim9p–Tim10p complex binds to the transmembrane domains of the ADP/ATP carrier

PubMed Central

Curran, Sean P.; Leuenberger, Danielle; Oppliger, Wolfgang; Koehler, Carla M.

2002-01-01

The soluble Tim9p–Tim10p (Tim, translocase of inner membrane) complex of the mitochondrial intermembrane space mediates the import of the carrier proteins and is a component of the TIM22 import system. The mechanism by which the Tim9p–Tim10p complex assembles and binds the carriers is not well understood, but previous studies have proposed that the conserved cysteine residues in the ‘twin CX3C’ motif coordinate zinc and potentially generate a zinc-finger-like structure that binds to the matrix loops of the carrier proteins. Here we have purified the native and recombinant Tim9p–Tim10p complex, and show that both complexes resemble each other and consist of three Tim9p and three Tim10p. Results from inductively coupled plasma–mass spectrometry studies failed to detect zinc in the Tim9p–Tim10p complex. Instead, the cysteine residues seemingly formed disulfide linkages. The Tim9p–Tim10p complex bound specifically to the transmembrane domains of the ADP/ATP carrier, but had no affinity for Tim23p, an inner membrane protein that is inserted via the TIM22 complex. The chaperone-like Tim9p–Tim10p complex thus may prevent aggregation of the unfolded carrier proteins in the aqueous intermembrane space. PMID:11867522

The Set1/COMPASS histone H3 methyltransferase helps regulate mitosis with the CDK1 and NIMA mitotic kinases in Aspergillus nidulans.

PubMed

Govindaraghavan, Meera; Anglin, Sarah Lea; Osmani, Aysha H; Osmani, Stephen A

2014-08-01

Mitosis is promoted and regulated by reversible protein phosphorylation catalyzed by the essential NIMA and CDK1 kinases in the model filamentous fungus Aspergillus nidulans. Protein methylation mediated by the Set1/COMPASS methyltransferase complex has also been shown to regulate mitosis in budding yeast with the Aurora mitotic kinase. We uncover a genetic interaction between An-swd1, which encodes a subunit of the Set1 protein methyltransferase complex, with NIMA as partial inactivation of nimA is poorly tolerated in the absence of swd1. This genetic interaction is additionally seen without the Set1 methyltransferase catalytic subunit. Importantly partial inactivation of NIMT, a mitotic activator of the CDK1 kinase, also causes lethality in the absence of Set1 function, revealing a functional relationship between the Set1 complex and two pivotal mitotic kinases. The main target for Set1-mediated methylation is histone H3K4. Mutational analysis of histone H3 revealed that modifying the H3K4 target residue of Set1 methyltransferase activity phenocopied the lethality seen when either NIMA or CDK1 are partially functional. We probed the mechanistic basis of these genetic interactions and find that the Set1 complex performs functions with CDK1 for initiating mitosis and with NIMA during progression through mitosis. The studies uncover a joint requirement for the Set1 methyltransferase complex with the CDK1 and NIMA kinases for successful mitosis. The findings extend the roles of the Set1 complex to include the initiation of mitosis with CDK1 and mitotic progression with NIMA in addition to its previously identified interactions with Aurora and type 1 phosphatase in budding yeast. Copyright © 2014 by the Genetics Society of America.

Conspicuousness, color resemblance, and toxicity in geographically diverging mimicry: The pan-Amazonian frog Allobates femoralis.

PubMed

Amézquita, Adolfo; Ramos, Óscar; González, Mabel Cristina; Rodríguez, Camilo; Medina, Iliana; Simões, Pedro Ivo; Lima, Albertina Pimentel

2017-04-01

Predation risk is allegedly reduced in Batesian and Müllerian mimics, because their coloration resembles the conspicuous coloration of unpalatable prey. The efficacy of mimicry is thought to be affected by variation in the unpalatability of prey, the conspicuousness of the signals, and the visual system of predators that see them. Many frog species exhibit small colorful patches contrasting against an otherwise dark body. By measuring toxicity and color reflectance in a geographically variable frog species and the syntopic toxic species, we tested whether unpalatability was correlated with between-species color resemblance and whether resemblance was highest for the most conspicuous components of coloration pattern. Heterospecific resemblance in colorful patches was highest between species at the same locality, but unrelated to concomitant variation in toxicity. Surprisingly, resemblance was lower for the conspicuous femoral patches compared to the inconspicuous dorsum. By building visual models, we further tested whether resemblance was affected by the visual system of model predators. As predicted, mimic-model resemblance was higher under the visual system of simulated predators compared to no visual system at all. Our results indicate that femoral patches are aposematic signals and support a role of mimicry in driving phenotypic divergence or mimetic radiation between localities. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

You Need to Know: There Is a Causal Relationship between Structural Knowledge and Control Performance in Complex Problem Solving Tasks

ERIC Educational Resources Information Center

Goode, Natassia; Beckmann, Jens F.

2010-01-01

This study investigates the relationships between structural knowledge, control performance and fluid intelligence in a complex problem solving (CPS) task. 75 participants received either complete, partial or no information regarding the underlying structure of a complex problem solving task, and controlled the task to reach specific goals.…

Arachnoid membranes in the posterior half of the incisural space: an inverted Liliequist membrane-like arachnoid complex.

PubMed

Zhang, Xi-An; Qi, Song-Tao; Fan, Jun; Huang, Guang-Long; Peng, Jun-Xiang

2014-08-01

The aim of this study was to describe the similarity of configuration between the arachnoid complex in the posterior half of the incisural space and the Liliequist membrane. Microsurgical dissection and anatomical observation were performed in 20 formalin-fixed adult cadaver heads. The origin, distribution, and configuration of the arachnoid membranes and their relationships with the vascular structures in the posterior half of the incisural space were examined. The posterior perimesencephalic membrane and the cerebellar precentral membrane have a common origin at the tentorial edge and form an arachnoid complex strikingly resembling an inverted Liliequist membrane. Asymmetry between sides is not uncommon. If the cerebellar precentral membrane is hypoplastic on one side or both, the well-developed quadrigeminal membrane plays a prominent part in partitioning the subarachnoid space in the posterior half of the incisural space. The arachnoid complex in the posterior half of the incisural space can be regarded as an inverted Liliequist membrane. This concept can help neurosurgeons to gain better understanding of the surgical anatomy at the level of the tentorial incisura.

Endosymbiosis and the design of eukaryotic electron transport.

PubMed

Berry, Stephan

2003-09-30

The bioenergetic organelles of eukaryotic cells, mitochondria and chloroplasts, are derived from endosymbiotic bacteria. Their electron transport chains (ETCs) resemble those of free-living bacteria, but were tailored for energy transformation within the host cell. Parallel evolutionary processes in mitochondria and chloroplasts include reductive as well as expansive events: On one hand, bacterial complexes were lost in eukaryotes with a concomitant loss of metabolic flexibility. On the other hand, new subunits have been added to the remaining bacterial complexes, new complexes have been introduced, and elaborate folding patterns of the thylakoid and mitochondrial inner membranes have emerged. Some bacterial pathways were reinvented independently by eukaryotes, such as parallel routes for quinol oxidation or the use of various anaerobic electron acceptors. Multicellular organization and ontogenetic cycles in eukaryotes gave rise to further modifications of the bioenergetic organelles. Besides mitochondria and chloroplasts, eukaryotes have ETCs in other membranes, such as the plasma membrane (PM) redox system, or the cytochrome P450 (CYP) system. These systems have fewer complexes and simpler branching patterns than those in energy-transforming organelles, and they are often adapted to non-bioenergetic functions such as detoxification or cellular defense.

Electronic structural changes of Mn in the oxygen-evolving complex of photosystem II during the catalytic cycle.

PubMed

Glatzel, Pieter; Schroeder, Henning; Pushkar, Yulia; Boron, Thaddeus; Mukherjee, Shreya; Christou, George; Pecoraro, Vincent L; Messinger, Johannes; Yachandra, Vittal K; Bergmann, Uwe; Yano, Junko

2013-05-20

The oxygen-evolving complex (OEC) in photosystem II (PS II) was studied in the S0 through S3 states using 1s2p resonant inelastic X-ray scattering spectroscopy. The spectral changes of the OEC during the S-state transitions are subtle, indicating that the electrons are strongly delocalized throughout the cluster. The result suggests that, in addition to the Mn ions, ligands are also playing an important role in the redox reactions. A series of Mn(IV) coordination complexes were compared, particularly with the PS II S3 state spectrum to understand its oxidation state. We find strong variations of the electronic structure within the series of Mn(IV) model systems. The spectrum of the S3 state best resembles those of the Mn(IV) complexes Mn3(IV)Ca2 and saplnMn2(IV)(OH)2. The current result emphasizes that the assignment of formal oxidation states alone is not sufficient for understanding the detailed electronic structural changes that govern the catalytic reaction in the OEC.

Topics in Complexity: From Physical to Life Science Systems

NASA Astrophysics Data System (ADS)

Charry, Pedro David Manrique

Complexity seeks to unwrap the mechanisms responsible for collective phenomena across the physical, biological, chemical, economic and social sciences. This thesis investigates real-world complex dynamical systems ranging from the quantum/natural domain to the social domain. The following novel understandings are developed concerning these systems' out-of-equilibrium and nonlinear behavior. Standard quantum techniques show divergent outcomes when a quantum system comprising more than one subunit is far from thermodynamic equilibrium. Abnormal photon inter-arrival times help fulfill the metabolic needs of a terrestrial photosynthetic bacterium. Spatial correlations within incident light can act as a driving mechanism for an organism's adaptation toward more ordered structures. The group dynamics of non-identical objects, whose assembly rules depend on mutual heterogeneity, yield rich transition dynamics between isolation and cohesion, with the cohesion regime reproducing a particular universal pattern commonly found in many real-world systems. Analyses of covert networks reveal collective gender superiority in the connectivity that provides benefits for system robustness and survival. Nodal migration in a network generates complex contagion profiles that lie beyond traditional approaches and yet resemble many modern-day outbreaks.

Constitutional Chromoanagenesis of Distal 13q in a Young Adult with Recurrent Strokes.

PubMed

Burnside, Rachel D; Harris, April; Speyer, Darrow; Burgin, W Scott; Rose, David Z; Sanchez-Valle, Amarilis

2016-01-01

Constitutional chromoanagenesis events, which include chromoanasynthesis and chromothripsis and result in highly complex rearrangements, have been reported for only a few individuals. While rare, these phenomena have likely been underestimated in a constitutional setting as technologies that can accurately detect such complexity are relatively new to the mature field of clinical cytogenetics. G-banding is not likely to accurately identify chromoanasynthesis or chromothripsis, since the banding patterns of chromosomes are likely to be misidentified or oversimplified due to a much lower resolution. We describe a patient who was initially referred for cytogenetic testing as a child for speech delay. As a young adult, he was referred again for recurrent strokes. Chromosome analysis was performed, and the rearrangement resembled a simple duplication of 13q32q34. However, SNP microarray analysis showed a complex pattern of copy number gains and a loss consistent with chromoanasynthesis involving distal 13q (13q32.1q34). This report emphasizes the value of performing microarray analysis for individuals with abnormal or complex chromosome rearrangements. © 2016 S. Karger AG, Basel.

Pre-attentive processing of spectrally complex sounds with asynchronous onsets: an event-related potential study with human subjects.

PubMed

Tervaniemi, M; Schröger, E; Näätänen, R

1997-05-23

Neuronal mechanisms involved in the processing of complex sounds with asynchronous onsets were studied in reading subjects. The sound onset asynchrony (SOA) between the leading partial and the remaining complex tone was varied between 0 and 360 ms. Infrequently occurring deviant sounds (in which one out of 10 harmonics was different in pitch relative to the frequently occurring standard sound) elicited the mismatch negativity (MMN), a change-specific cortical event-related potential (ERP) component. This indicates that the pitch of standard stimuli had been pre-attentively coded by sensory-memory traces. Moreover, when the complex-tone onset fell within temporal integration window initiated by the leading-partial onset, the deviants elicited the N2b component. This indexes that involuntary attention switch towards the sound change occurred. In summary, the present results support the existence of pre-perceptual integration mechanism of 100-200 ms duration and emphasize its importance in switching attention towards the stimulus change.

Role of antisense RNAs in evolution of yeast regulatory complexity.

PubMed

Lin, Chih-Hsu; Tsai, Zing Tsung-Yeh; Wang, Daryi

2013-01-01

Antisense RNAs (asRNAs) are known to regulate gene expression. However, a genome-wide mechanism of asRNA regulation is unclear, and there is no good explanation why partial asRNAs are not functional. To explore its regulatory role, we investigated asRNAs using an evolutionary approach, as genome-wide experimental data are limited. We found that the percentage of genes coupling with asRNAs in Saccharomyces cerevisiae is negatively associated with regulatory complexity and evolutionary age. Nevertheless, asRNAs evolve more slowly when their sense genes are under more complex regulation. Older genes coupling with asRNAs are more likely to demonstrate inverse expression, reflecting the role of these asRNAs as repressors. Our analyses provide novel evidence, suggesting a minor contribution of asRNAs in developing regulatory complexity. Although our results support the leaky hypothesis for asRNA transcription, our evidence also suggests that partial asRNAs may have evolved as repressors. Our study deepens the understanding of asRNA regulatory evolution. Copyright © 2013 Elsevier Inc. All rights reserved.

Dynamics of Metamorphic Core Complexes Inferred From Modeling and Metamorphic Petrology

NASA Astrophysics Data System (ADS)

Whitney, D. L.; Rey, P.; Teyssier, C.

2008-12-01

Orogenic collapse involves extension and thinning of thick, hot, and in some cases partially molten, crust, leading to the formation of metamorphic core complexes (MCC) that are commonly cored by migmatite domes. 2D numerical modeling predicts that the geometry and P-T-t history of MCC varies as a function of the presence/absence of a partially molten layer in the deep crust; the nature of heterogeneities that localize the MCC (e.g. normal fault in upper crust vs. point-like anomaly in the deep crust); and extensional strain rate. The presence of melt in particular has a significant effect on the thermal and structural history of MCC because the presence of partially molten crust or magma bodies at depth enhances upward advection of material and heat. At high extension rate (cm/year in the region of the MCC), partially molten crust crystallizes as migmatite and cools along a high geothermal gradient (35-65 C/km); material remains partially molten during ascent, forming a migmatite dome when it crystallizes at shallower crustal levels (e.g. cordierite/sillimanite stability field). At low strain rate (mm/yr in the MCC region), the partially molten crust crystallizes at high pressure (e.g. kyanite zone); this material is subsequently deformed in the solid-state along a cooler geothermal gradient (20-35 C/km) during ascent. MCC that develop during extension of partially molten crust may therefore record distinct crystallization versus exhumation histories as a function of extensional strain rate. The mineral assemblages, metamorphic reaction histories, and structures of migmatite-cored (Mc) MCC can therefore be used to interpret the dynamics of MCC formation, e.g. "fast" McMCC in the northern N American Cordillera and Aegean regions.

Competitive sorption of carbonate and arsenic to hematite: combined ATR-FTIR and batch experiments.

PubMed

Brechbühl, Yves; Christl, Iso; Elzinga, Evert J; Kretzschmar, Ruben

2012-07-01

The competitive sorption of carbonate and arsenic to hematite was investigated in closed-system batch experiments. The experimental conditions covered a pH range of 3-7, arsenate concentrations of 3-300 μM, and arsenite concentrations of 3-200 μM. Dissolved carbonate concentrations were varied by fixing the CO(2) partial pressure at 0.39 (atmospheric), 10, or 100 hPa. Sorption data were modeled with a one-site three plane model considering carbonate and arsenate surface complexes derived from ATR-FTIR spectroscopy analyses. Macroscopic sorption data revealed that in the pH range 3-7, carbonate was a weak competitor for both arsenite and arsenate. The competitive effect of carbonate increased with increasing CO(2) partial pressure and decreasing arsenic concentrations. For arsenate, sorption was reduced by carbonate only at slightly acidic to neutral pH values, whereas arsenite sorption was decreased across the entire pH range. ATR-FTIR spectra indicated the predominant formation of bidentate binuclear inner-sphere surface complexes for both sorbed arsenate and sorbed carbonate. Surface complexation modeling based on the dominant arsenate and carbonate surface complexes indicated by ATR-FTIR and assuming inner-sphere complexation of arsenite successfully described the macroscopic sorption data. Our results imply that in natural arsenic-contaminated systems where iron oxide minerals are important sorbents, dissolved carbonate may increase aqueous arsenite concentrations, but will affect dissolved arsenate concentrations only at neutral to alkaline pH and at very high CO(2) partial pressures. Copyright © 2012 Elsevier Inc. All rights reserved.

Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

PubMed

Bapteste, Eric; Lopez, Philippe; Bouchard, Frédéric; Baquero, Fernando; McInerney, James O; Burian, Richard M

2012-11-06

All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.

Early events in xenograft development from the human embryonic stem cell line HS181--resemblance with an initial multiple epiblast formation.

PubMed

Gertow, Karin; Cedervall, Jessica; Jamil, Seema; Ali, Rouknuddin; Imreh, Marta P; Gulyas, Miklos; Sandstedt, Bengt; Ahrlund-Richter, Lars

2011-01-01

Xenografting is widely used for assessing in vivo pluripotency of human stem cell populations. Here, we report on early to late events in the development of mature experimental teratoma from a well-characterized human embryonic stem cell (HESC) line, HS181. The results show an embryonic process, increasingly chaotic. Active proliferation of the stem cell derived cellular progeny was detected already at day 5, and characterized by the appearance of multiple sites of engraftment, with structures of single or pseudostratified columnar epithelium surrounding small cavities. The striking histological resemblance to developing embryonic ectoderm, and the formation of epiblast-like structures was supported by the expression of the markers OCT4, NANOG, SSEA-4 and KLF4, but a lack of REX1. The early neural marker NESTIN was uniformly expressed, while markers linked to gastrulation, such as BMP-4, NODAL or BRACHYURY were not detected. Thus, observations on day 5 indicated differentiation comparable to the most early transient cell populations in human post implantation development. Confirming and expanding on previous findings from HS181 xenografts, these early events were followed by an increasingly chaotic development, incorporated in the formation of a benign teratoma with complex embryonic components. In the mature HS181 teratomas not all types of organs/tissues were detected, indicating a restricted differentiation, and a lack of adequate spatial developmental cues during the further teratoma formation. Uniquely, a kinetic alignment of rare complex structures was made to human embryos at diagnosed gestation stages, showing minor kinetic deviations between HS181 teratoma and the human counterpart.

Role of glutamate-104 in generating a transition state analogue inhibitor at the active site of cytidine deaminase.

PubMed

Carlow, D C; Short, S A; Wolfenden, R

1996-01-23

The 19F-NMR resonance of 5-[19F]fluoropyrimidin-2-one ribonucleoside moves upfield when it is bound by wild-type cytidine deaminase from Escherichia coli, in agreement with UV and X-ray spectroscopic indications that this inhibitor is bound as the rate 3,4-hydrated species 5-fluoro-3,4-dihydrouridine, a transition state analogue inhibitor resembling an intermediate in direct water attack on 5-fluorocytidine. Comparison of pKa values of model compounds indicates that the equilibrium constant for 3,4-hydration of this inhibitor in free solution is 3.5 x 10(-4) M, so that the corrected dissociation constant of 5-fluoro-3,4-dihydrouridine from the wild-type enzyme is 3.9 x 10(-11) M. Very different behavior is observed for a mutant enzyme in which alanine replaces Glu-104 at the active site, and kcat has been reduced by a factor of 10(8). 5-[19F]Fluoropyrimidin-2-one ribonucleoside is strongly fluorescent, making it possible to observe that the mutant enzyme binds this inhibitor even more tightly (Kd = 4.4 x 10(-8) M) than does the native enzyme (Kd = 1.1 x 10(-7) M). 19F-NMR indicates, however, that the E104A mutant enzyme binds the inhibitor without modification, in a form that resembles the substrate in the ground state. These results are consistent with a major role for Glu-104, not only in stabilizing the ES++ complex in the transition state, but also in destabilizing the ES complex in the ground state.

Hidden physics models: Machine learning of nonlinear partial differential equations

NASA Astrophysics Data System (ADS)

Raissi, Maziar; Karniadakis, George Em

2018-03-01

While there is currently a lot of enthusiasm about "big data", useful data is usually "small" and expensive to acquire. In this paper, we present a new paradigm of learning partial differential equations from small data. In particular, we introduce hidden physics models, which are essentially data-efficient learning machines capable of leveraging the underlying laws of physics, expressed by time dependent and nonlinear partial differential equations, to extract patterns from high-dimensional data generated from experiments. The proposed methodology may be applied to the problem of learning, system identification, or data-driven discovery of partial differential equations. Our framework relies on Gaussian processes, a powerful tool for probabilistic inference over functions, that enables us to strike a balance between model complexity and data fitting. The effectiveness of the proposed approach is demonstrated through a variety of canonical problems, spanning a number of scientific domains, including the Navier-Stokes, Schrödinger, Kuramoto-Sivashinsky, and time dependent linear fractional equations. The methodology provides a promising new direction for harnessing the long-standing developments of classical methods in applied mathematics and mathematical physics to design learning machines with the ability to operate in complex domains without requiring large quantities of data.

Condensin-driven remodelling of X chromosome topology during dosage compensation

NASA Astrophysics Data System (ADS)

Crane, Emily; Bian, Qian; McCord, Rachel Patton; Lajoie, Bryan R.; Wheeler, Bayly S.; Ralston, Edward J.; Uzawa, Satoru; Dekker, Job; Meyer, Barbara J.

2015-07-01

The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure. Here we perform genome-wide chromosome conformation capture analysis, fluorescent in situ hybridization (FISH), and RNA-seq to obtain comprehensive three-dimensional (3D) maps of the Caenorhabditis elegans genome and to dissect X chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (~1 Mb) resembling mammalian topologically associating domains (TADs). TADs on X chromosomes have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X chromosomes coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X chromosomes by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a distinct higher-order structure onto X chromosomes while regulating gene expression chromosome-wide.

Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation

PubMed Central

Crane, Emily; Bian, Qian; McCord, Rachel Patton; Lajoie, Bryan R.; Wheeler, Bayly S.; Ralston, Edward J.; Uzawa, Satoru; Dekker, Job; Meyer, Barbara J.

2015-01-01

The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure1,2. Here we perform genome-wide chromosome conformation capture analysis, FISH, and RNA-seq to obtain comprehensive 3D maps of the Caenorhabditis elegans genome and to dissect X-chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half3–7. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes5,6. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (~1 Mb) resembling mammalian Topologically Associating Domains (TADs)8,9. TADs on X have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a distinct higher-order structure onto X while regulating gene expression chromosome wide. PMID:26030525

Filling the Assurance Gap on Complex Electronics

NASA Technical Reports Server (NTRS)

Plastow, Richard A.

2007-01-01

Many of the methods used to develop software bare a close resemblance to Complex Electronics (CE) development. CE are now programmed to perform tasks that were previously handled by software, such as communication protocols. For example, the James Webb Space Telescope will use Field Programmable Gate Arrays (FPGAs), which can have over a million logic gates, to send telemetry. System-on-chip (SoC) devices, another type of complex electronics, can combine a microprocessor, input and output channels, and sometimes an FPGA for programmability. With this increased intricacy, the possibility of software-like bugs such as incorrect design, logic, and unexpected interactions within the logic is great. Since CE devices are obscuring the hardware/software boundary, mature software methodologies have been proposed, with slight modifications, to develop these devices. By using standardized S/W Engineering methods such as checklists, missing requirements and bugs can be detected earlier in the development cycle, thus creating a development process for CE that can be easily maintained and configurable based on the device used.

Software Process Assurance for Complex Electronics

NASA Technical Reports Server (NTRS)

Plastow, Richard A.

2007-01-01

Complex Electronics (CE) now perform tasks that were previously handled in software, such as communication protocols. Many methods used to develop software bare a close resemblance to CE development. Field Programmable Gate Arrays (FPGAs) can have over a million logic gates while system-on-chip (SOC) devices can combine a microprocessor, input and output channels, and sometimes an FPGA for programmability. With this increased intricacy, the possibility of software-like bugs such as incorrect design, logic, and unexpected interactions within the logic is great. With CE devices obscuring the hardware/software boundary, we propose that mature software methodologies may be utilized with slight modifications in the development of these devices. Software Process Assurance for Complex Electronics (SPACE) is a research project that used standardized S/W Assurance/Engineering practices to provide an assurance framework for development activities. Tools such as checklists, best practices and techniques were used to detect missing requirements and bugs earlier in the development cycle creating a development process for CE that was more easily maintained, consistent and configurable based on the device used.

The Nubian Complex of Dhofar, Oman: an African middle stone age industry in Southern Arabia.

PubMed

Rose, Jeffrey I; Usik, Vitaly I; Marks, Anthony E; Hilbert, Yamandu H; Galletti, Christopher S; Parton, Ash; Geiling, Jean Marie; Cerný, Viktor; Morley, Mike W; Roberts, Richard G

2011-01-01

Despite the numerous studies proposing early human population expansions from Africa into Arabia during the Late Pleistocene, no archaeological sites have yet been discovered in Arabia that resemble a specific African industry, which would indicate demographic exchange across the Red Sea. Here we report the discovery of a buried site and more than 100 new surface scatters in the Dhofar region of Oman belonging to a regionally-specific African lithic industry--the late Nubian Complex--known previously only from the northeast and Horn of Africa during Marine Isotope Stage 5, ∼128,000 to 74,000 years ago. Two optically stimulated luminescence age estimates from the open-air site of Aybut Al Auwal in Oman place the Arabian Nubian Complex at ∼106,000 years ago, providing archaeological evidence for the presence of a distinct northeast African Middle Stone Age technocomplex in southern Arabia sometime in the first half of Marine Isotope Stage 5.

Mechanism suppressing glycogen synthesis in neurons and its demise in progressive myoclonus epilepsy.

PubMed

Vilchez, David; Ros, Susana; Cifuentes, Daniel; Pujadas, Lluís; Vallès, Jordi; García-Fojeda, Belén; Criado-García, Olga; Fernández-Sánchez, Elena; Medraño-Fernández, Iria; Domínguez, Jorge; García-Rocha, Mar; Soriano, Eduardo; Rodríguez de Córdoba, Santiago; Guinovart, Joan J

2007-11-01

Glycogen synthesis is normally absent in neurons. However, inclusion bodies resembling abnormal glycogen accumulate in several neurological diseases, particularly in progressive myoclonus epilepsy or Lafora disease. We show here that mouse neurons have the enzymatic machinery for synthesizing glycogen, but that it is suppressed by retention of muscle glycogen synthase (MGS) in the phosphorylated, inactive state. This suppression was further ensured by a complex of laforin and malin, which are the two proteins whose mutations cause Lafora disease. The laforin-malin complex caused proteasome-dependent degradation both of the adaptor protein targeting to glycogen, PTG, which brings protein phosphatase 1 to MGS for activation, and of MGS itself. Enforced expression of PTG led to glycogen deposition in neurons and caused apoptosis. Therefore, the malin-laforin complex ensures a blockade of neuronal glycogen synthesis even under intense glycogenic conditions. Here we explain the formation of polyglucosan inclusions in Lafora disease by demonstrating a crucial role for laforin and malin in glycogen synthesis.

Models and observations of Arctic melt ponds

NASA Astrophysics Data System (ADS)

Golden, K. M.

2016-12-01

During the Arctic melt season, the sea ice surface undergoes a striking transformation from vast expanses of snow covered ice to complex mosaics of ice and melt ponds. Sea ice albedo, a key parameter in climate modeling, is largely determined by the complex evolution of melt pond configurations. In fact, ice-albedo feedback has played a significant role in the recent declines of the summer Arctic sea ice pack. However, understanding melt pond evolution remains a challenge to improving climate projections. It has been found that as the ponds grow and coalesce, the fractal dimension of their boundaries undergoes a transition from 1 to about 2, around a critical length scale of 100 square meters in area. As the ponds evolve they take complex, self-similar shapes with boundaries resembling space-filling curves. I will outline how mathematical models of composite materials and statistical physics, such as percolation and Ising models, are being used to describe this evolution and predict key geometrical parameters that agree very closely with observations.

The Nubian Complex of Dhofar, Oman: An African Middle Stone Age Industry in Southern Arabia

PubMed Central

Rose, Jeffrey I.; Usik, Vitaly I.; Marks, Anthony E.; Hilbert, Yamandu H.; Galletti, Christopher S.; Parton, Ash; Geiling, Jean Marie; Černý, Viktor; Morley, Mike W.; Roberts, Richard G.

2011-01-01

Despite the numerous studies proposing early human population expansions from Africa into Arabia during the Late Pleistocene, no archaeological sites have yet been discovered in Arabia that resemble a specific African industry, which would indicate demographic exchange across the Red Sea. Here we report the discovery of a buried site and more than 100 new surface scatters in the Dhofar region of Oman belonging to a regionally-specific African lithic industry - the late Nubian Complex - known previously only from the northeast and Horn of Africa during Marine Isotope Stage 5, ∼128,000 to 74,000 years ago. Two optically stimulated luminescence age estimates from the open-air site of Aybut Al Auwal in Oman place the Arabian Nubian Complex at ∼106,000 years ago, providing archaeological evidence for the presence of a distinct northeast African Middle Stone Age technocomplex in southern Arabia sometime in the first half of Marine Isotope Stage 5. PMID:22140561

Evaluation of the cognitive effects of travel technique in complex real and virtual environments.

PubMed

Suma, Evan A; Finkelstein, Samantha L; Reid, Myra; V Babu, Sabarish; Ulinski, Amy C; Hodges, Larry F

2010-01-01

We report a series of experiments conducted to investigate the effects of travel technique on information gathering and cognition in complex virtual environments. In the first experiment, participants completed a non-branching multilevel 3D maze at their own pace using either real walking or one of two virtual travel techniques. In the second experiment, we constructed a real-world maze with branching pathways and modeled an identical virtual environment. Participants explored either the real or virtual maze for a predetermined amount of time using real walking or a virtual travel technique. Our results across experiments suggest that for complex environments requiring a large number of turns, virtual travel is an acceptable substitute for real walking if the goal of the application involves learning or reasoning based on information presented in the virtual world. However, for applications that require fast, efficient navigation or travel that closely resembles real-world behavior, real walking has advantages over common joystick-based virtual travel techniques.

Crystal structure of the conserved herpesvirus fusion regulator complex gH—gL

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

Chowdary, Tirumala K.; Cairns, Tina M.; Atanasiu, Doina

2015-02-09

Herpesviruses, which cause many incurable diseases, infect cells by fusing viral and cellular membranes. Whereas most other enveloped viruses use a single viral catalyst called a fusogen, herpesviruses, inexplicably, require two conserved fusion-machinery components, gB and the heterodimer gH–gL, plus other nonconserved components. gB is a class III viral fusogen, but unlike other members of its class, it does not function alone. We determined the crystal structure of the gH ectodomain bound to gL from herpes simplex virus 2. gH–gL is an unusually tight complex with a unique architecture that, unexpectedly, does not resemble any known viral fusogen. Instead, wemore » propose that gH–gL activates gB for fusion, possibly through direct binding. Formation of a gB–gH–gL complex is critical for fusion and is inhibited by a neutralizing antibody, making the gB–gH–gL interface a promising antiviral target.« less

Crystal structure of the conserved herpes virus fusion regulator complex gH-gL

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

Chowdary, Tirumala K; Cairns, Tina M; Atanasiu, Doina

2010-09-13

Herpesviruses, which cause many incurable diseases, infect cells by fusing viral and cellular membranes. Whereas most other enveloped viruses use a single viral catalyst called a fusogen, herpesviruses, inexplicably, require two conserved fusion-machinery components, gB and the heterodimer gH-gL, plus other nonconserved components. gB is a class III viral fusogen, but unlike other members of its class, it does not function alone. We determined the crystal structure of the gH ectodomain bound to gL from herpes simplex virus 2. gH-gL is an unusually tight complex with a unique architecture that, unexpectedly, does not resemble any known viral fusogen. Instead, wemore » propose that gH-gL activates gB for fusion, possibly through direct binding. Formation of a gB-gH-gL complex is critical for fusion and is inhibited by a neutralizing antibody, making the gB-gH-gL interface a promising antiviral target.« less

Crystal Structure of the Conserved Herpes Virus Fusion Regulator Complex gH–gL

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

Chowdary, T.; Cairns, T; Atanasiu, D

2010-01-01

Herpesviruses, which cause many incurable diseases, infect cells by fusing viral and cellular membranes. Whereas most other enveloped viruses use a single viral catalyst called a fusogen, herpesviruses, inexplicably, require two conserved fusion-machinery components, gB and the heterodimer gH-gL, plus other nonconserved components. gB is a class III viral fusogen, but unlike other members of its class, it does not function alone. We determined the crystal structure of the gH ectodomain bound to gL from herpes simplex virus 2. gH-gL is an unusually tight complex with a unique architecture that, unexpectedly, does not resemble any known viral fusogen. Instead, wemore » propose that gH-gL activates gB for fusion, possibly through direct binding. Formation of a gB-gH-gL complex is critical for fusion and is inhibited by a neutralizing antibody, making the gB-gH-gL interface a promising antiviral target.« less

Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA–protein interactions

PubMed Central

Khanova, Elena; Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S.

2012-01-01

Eukaryotic ribonuclease (RNase) P and RNase MRP are closely related ribonucleoprotein complexes involved in the metabolism of various RNA molecules including tRNA, rRNA, and some mRNAs. While evolutionarily related to bacterial RNase P, eukaryotic enzymes of the RNase P/MRP family are much more complex. Saccharomyces cerevisiae RNase P consists of a catalytic RNA component and nine essential proteins; yeast RNase MRP has an RNA component resembling that in RNase P and 10 essential proteins, most of which are shared with RNase P. The structural organizations of eukaryotic RNases P/MRP are not clear. Here we present the results of RNA–protein UV crosslinking studies performed on RNase P and RNase MRP holoenzymes isolated from yeast. The results indicate locations of specific protein-binding sites in the RNA components of RNase P and RNase MRP and shed light on the structural organizations of these large ribonucleoprotein complexes. PMID:22332141

Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA-protein interactions.

PubMed

Khanova, Elena; Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S

2012-04-01

Eukaryotic ribonuclease (RNase) P and RNase MRP are closely related ribonucleoprotein complexes involved in the metabolism of various RNA molecules including tRNA, rRNA, and some mRNAs. While evolutionarily related to bacterial RNase P, eukaryotic enzymes of the RNase P/MRP family are much more complex. Saccharomyces cerevisiae RNase P consists of a catalytic RNA component and nine essential proteins; yeast RNase MRP has an RNA component resembling that in RNase P and 10 essential proteins, most of which are shared with RNase P. The structural organizations of eukaryotic RNases P/MRP are not clear. Here we present the results of RNA-protein UV crosslinking studies performed on RNase P and RNase MRP holoenzymes isolated from yeast. The results indicate locations of specific protein-binding sites in the RNA components of RNase P and RNase MRP and shed light on the structural organizations of these large ribonucleoprotein complexes.

Cristispira from oyster styles: complex morphology of large symbiotic spirochetes

NASA Technical Reports Server (NTRS)

Margulis, L.; Nault, L.; Sieburth, J. M.

1991-01-01

Crystalline styles (digestive organs) of bivalve mollusks provide the habitat for highly motile bacteria. Styles from freshly-collected oysters, Crassostrea virginica, were studied by electron microscopy; Cristispira spirochetes were abundant in these organs. Detailed study reveals these spirochetes to be among the most complex prokaryotic cells known. More than 600 periplasmic flagella and an adhering outer lipoprotein membrane (e.g., a 270 degrees sillon) form the ultrastructural basis for the "crista," first described by light microscopy. Unique rosette structures corresponding to the "chambers" or "ovoid inclusions" of light microscopy were detected at the periphery of all protoplasmic cylinders. Polar organelles and linearly aligned flagellar insertions are conspicuous. In size and complexity, Cristispira more resembles Pillotina, Diplocalyx, Clevelandina and Hollandina (large spirochetes symbiotic in termites) than it does Treponema. Cristispira pectinis (Gross, 1910), the type species; Spirillum ostrea (Noguchi, 1921); and another, less frequent bacterial symbiont are the predominant inhabitants of the dense style matrix. The ultrastructure of the spirillum and an electron micrograph of the third bacterium are shown.

Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms.

PubMed

Kloosterman, Wigard P; Tavakoli-Yaraki, Masoumeh; van Roosmalen, Markus J; van Binsbergen, Ellen; Renkens, Ivo; Duran, Karen; Ballarati, Lucia; Vergult, Sarah; Giardino, Daniela; Hansson, Kerstin; Ruivenkamp, Claudia A L; Jager, Myrthe; van Haeringen, Arie; Ippel, Elly F; Haaf, Thomas; Passarge, Eberhard; Hochstenbach, Ron; Menten, Björn; Larizza, Lidia; Guryev, Victor; Poot, Martin; Cuppen, Edwin

2012-06-28

Chromothripsis represents a novel phenomenon in the structural variation landscape of cancer genomes. Here, we analyze the genomes of ten patients with congenital disease who were preselected to carry complex chromosomal rearrangements with more than two breakpoints. The rearrangements displayed unanticipated complexity resembling chromothripsis. We find that eight of them contain hallmarks of multiple clustered double-stranded DNA breaks (DSBs) on one or more chromosomes. In addition, nucleotide resolution analysis of 98 breakpoint junctions indicates that break repair involves nonhomologous or microhomology-mediated end joining. We observed that these eight rearrangements are balanced or contain sporadic deletions ranging in size between a few hundred base pairs and several megabases. The two remaining complex rearrangements did not display signs of DSBs and contain duplications, indicative of rearrangement processes involving template switching. Our work provides detailed insight into the characteristics of chromothripsis and supports a role for clustered DSBs driving some constitutional chromothripsis rearrangements. Copyright © 2012 The Authors. Published by Elsevier Inc. All rights reserved.

Designing To Learn about Complex Systems.

ERIC Educational Resources Information Center

Hmelo, Cindy E.; Holton, Douglas L.; Kolodner, Janet L.

2000-01-01

Indicates the presence of complex structural, behavioral, and functional relations to understanding. Reports on a design experiment in which 6th grade children learned about the human respiratory system by designing artificial lungs and building partial working models. Makes suggestions for successful learning from design activities. (Contains 44…

Efficacy and tolerability of nitric-zinc complex in the treatment of external genital warts and "difficult-to-treat" warts: a "proof of concept", prospective, multicentre, open study.

PubMed

Cusini, M; Micali, G; Lacarrubba, F; Puviani, M; Barcella, A; Milani, M

2015-12-01

Treatment of plantar and periungueal warts (so called "difficult-to-treat" warts, DTW) and external genital warts (EGW) remains unsatisfactory. Medical or invasive procedures are partially effective and/or painful. Furthermore recurrences rates after treatments are still a relevant problem for all the available therapies. Nitric-zinc complex is a solution for topical application containing nitric acid, zinc, copper and organic acids able to induce a caustic effect of the wart trough mummification and proteins denaturation/coagulation action. Nitric-zinc complex has been shown to be an effective and well tolerated treatment of common warts. We evaluated in a prospective open label 4-centre trial, the efficacy and local tolerability of nitric-zinc complex in the treatment of EGW and DTW. A total of 37 immunocompetent subjects (20 men and 17 women; mean age: 45 years) with single or multiple lesions, were enrolled, after their informed consent. A total of 30 subjects had EGW, 2 subjects had plantar warts, 2 warts of the hand and 3 periungueal lesions. Nitric-zinc aqueous solution was applied topically using a 30 mL capillary tube over the lesions until a whitening/yellowish reaction appeared. A second (or more, if needed) application was performed at two-week interval until a complete clinical cure rate was observed. Primary outcome of the study was the clinical evaluation with picture documentation of the evolution of lesions classified as total cure, partial disappearance or no effect. Topical tolerability was evaluated through patient's reported adverse events. All subjects completed the study. A complete cure of lesions was observed in 31 subjects (90%) after one and up to four applications. Three patients with EGW (8%) showed a partial disappearance of lesions and one (2%) subject was no responder to four nitric-zinc complex applications. The product was well tolerated. No serious adverse events were observed or recorded. Nitric-zinc complex topical solution has shown to be an effective and well tolerated treatment of EGW and "difficult-to-treat" warts with a 90% of subjects with a total cure after one or up to four applications. A total or partial response was observed in 99% of the subjects. Nitric-zinc complex could be considered an easy-to-use effective treatment strategy of "difficult-to-treat" warts and external genital warts. Additional studies comparing nitric-zinc complex to other strategies are warranted.

Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates

PubMed Central

Dibrova, Daria V.; Cherepanov, Dmitry A.; Galperin, Michael Y.; Skulachev, Vladimir P.; Mulkidjanian, Armen Y.

2013-01-01

This review traces the evolution of the cytochrome bc complexes from their early spread among prokaryotic lineages and up to the mitochondrial cytochrome bc1 complex (complex III) and its role in apoptosis. The results of phylogenomic analysis suggest that the bacterial cytochrome b6f-type complexes with short cytochromes b were the ancient form that preceded in evolution the cytochrome bc1-type complexes with long cytochromes b. The common ancestor of the b6f-type and the bc1-type complexes probably resembled the b6f-type complexes found in Heliobacteriaceae and in some Planctomycetes. Lateral transfers of cytochrome bc operons could account for the several instances of acquisition of different types of bacterial cytochrome bc complexes by archaea. The gradual oxygenation of the atmosphere could be the key evolutionary factor that has driven further divergence and spread of the cytochrome bc complexes. On one hand, oxygen could be used as a very efficient terminal electron acceptor. On the other hand, auto-oxidation of the components of the bc complex results in the generation of reactive oxygen species (ROS), which necessitated diverse adaptations of the b6f-type and bc1-type complexes, as well as other, functionally coupled proteins. A detailed scenario of the gradual involvement of the cardiolipin-containing mitochondrial cytochrome bc1 complex into the intrinsic apoptotic pathway is proposed, where the functioning of the complex as an apoptotic trigger is viewed as a way to accelerate the elimination of the cells with irreparably damaged, ROS-producing mitochondria. PMID:23871937

A new genus of horse from Pleistocene North America

PubMed Central

Zazula, Grant D; MacPhee, Ross DE; Scott, Eric; Cahill, James A; McHorse, Brianna K; Kapp, Joshua D; Stiller, Mathias; Wooller, Matthew J; Orlando, Ludovic; Southon, John; Froese, Duane G

2017-01-01

The extinct ‘New World stilt-legged’, or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here, we report complete mitochondrial and partial nuclear genomes from NWSL equids from across their geographic range. Although multiple NWSL equid species have been named, our palaeogenomic and morphometric analyses support the idea that there was only a single species of middle to late Pleistocene NWSL equid, and demonstrate that it falls outside of crown group Equus. We therefore propose a new genus, Haringtonhippus, for the sole species H. francisci. Our combined genomic and phenomic approach to resolving the systematics of extinct megafauna will allow for an improved understanding of the full extent of the terminal Pleistocene extinction event. PMID:29182148

Context generalization in Drosophila visual learning requires the mushroom bodies

NASA Astrophysics Data System (ADS)

Liu, Li; Wolf, Reinhard; Ernst, Roman; Heisenberg, Martin

1999-08-01

The world is permanently changing. Laboratory experiments on learning and memory normally minimize this feature of reality, keeping all conditions except the conditioned and unconditioned stimuli as constant as possible. In the real world, however, animals need to extract from the universe of sensory signals the actual predictors of salient events by separating them from non-predictive stimuli (context). In principle, this can be achieved ifonly those sensory inputs that resemble the reinforcer in theirtemporal structure are taken as predictors. Here we study visual learning in the fly Drosophila melanogaster, using a flight simulator,, and show that memory retrieval is, indeed, partially context-independent. Moreover, we show that the mushroom bodies, which are required for olfactory but not visual or tactile learning, effectively support context generalization. In visual learning in Drosophila, it appears that a facilitating effect of context cues for memory retrieval is the default state, whereas making recall context-independent requires additional processing.

Probing the symmetry of the potential of localized surface plasmon resonances with phase-shaped electron beams.

PubMed

Guzzinati, Giulio; Béché, Armand; Lourenço-Martins, Hugo; Martin, Jérôme; Kociak, Mathieu; Verbeeck, Jo

2017-04-12

Plasmonics, the science and technology of the interaction of light with metallic objects, is fundamentally changing the way we can detect, generate and manipulate light. Although the field is progressing swiftly, thanks to the availability of nanoscale manufacturing and analysis methods, fundamental properties such as the plasmonic excitations' symmetries cannot be accessed directly, leading to a partial, sometimes incorrect, understanding of their properties. Here we overcome this limitation by deliberately shaping the wave function of an electron beam to match a plasmonic excitations' symmetry in a modified transmission electron microscope. We show experimentally and theoretically that this offers selective detection of specific plasmon modes within metallic nanoparticles, while excluding modes with other symmetries. This method resembles the widespread use of polarized light for the selective excitation of plasmon modes with the advantage of locally probing the response of individual plasmonic objects and a far wider range of symmetry selection criteria.

Species of Phaeoacremonium Associated with Infections in Humans and Environmental Reservoirs in Infected Woody Plants

PubMed Central

Mostert, Lizel; Groenewald, Johannes Z.; Summerbell, Richard C.; Robert, Vincent; Sutton, Deanna A.; Padhye, Arvind A.; Crous, Pedro W.

2005-01-01

To date, three species of Phaeoacremonium have been associated with phaeohyphomycosis. These are P. parasiticum (formerly Phialophora parasitica), P. inflatipes, and P. rubrigenum. Numerous unknown isolates resembling Phaeoacremonium spp. have in recent years been isolated from human patients as well as from woody plants that appear to be the main environmental source of these fungi. Nine new Phaeoacremonium species, of which six were obtained as etiologic agents of human opportunistic infection, are reported. They can be identified based on their cultural and morphological characters, and the identifications are strongly supported in phylogenetic analyses of partial sequences of the actin, β-tubulin, and calmodulin genes. A multiple-entry electronic key based on morphological, cultural, and β-tubulin sequence data was developed to facilitate routine species identification. Reexamination of all isolates of P. inflatipes associated with human disease showed them to be misidentified and to belong to the new taxa described here. PMID:15814996

Spontaneous parasitic leiomyoma in a post-partum woman.

PubMed

Iida, Mana; Ishikawa, Hiroshi; Shozu, Makio

2016-12-01

We report a case of spontaneous parasitic leiomyoma in a 30-year-old post-partum woman. A subserosal leiomyoma had been noted at the first trimester screening, and she had experienced persistent abdominal pain during her previous pregnancy. She was referred to hospital with severe abdominal pain at 7 months after delivery. We detected a homogenous solid tumor that resembled the subserosal leiomyoma but was completely detached from the uterus. On laparoscopy the vascularization of the tumor was supplied from the omentum, which was tightly adherent to the tumor. Histopathologically, the tumor was surrounded by a fibrous vascular capsule, and broadly hyalinized and partially calcified, consistent with a degenerated uterine leiomyoma. Detachment of a pedunculated subserosal leiomyoma from the uterus following adhesion to other pelvic structures throughout pregnancy may result in a parasitic leiomyoma, a rare subtype of uterine leiomyoma. © 2016 Japan Society of Obstetrics and Gynecology.

Simple and fast polydimethylsiloxane (PDMS) patterning using a cutting plotter and vinyl adhesives to achieve etching results.

PubMed

Hyun Kim; Sun-Young Yoo; Ji Sung Kim; Zihuan Wang; Woon Hee Lee; Kyo-In Koo; Jong-Mo Seo; Dong-Il Cho

2017-07-01

Inhibition of polydimethylsiloxane (PDMS) polymerization could be observed when spin-coated over vinyl substrates. The degree of polymerization, partially curing or fully curing, depended on the PDMS thickness coated over the vinyl substrate. This characteristic was exploited to achieve simple and fast PDMS patterning method using a vinyl adhesive layer patterned through a cutting plotter. The proposed patterning method showed results resembling PDMS etching. Therefore, patterning PDMS over PDMS, glass, silicon, and gold substrates were tested to compare the results with conventional etching methods. Vinyl stencils with widths ranging from 200μm to 1500μm were used for the procedure. To evaluate the accuracy of the cutting plotter, stencil designed on the AutoCAD software and the actual stencil widths were compared. Furthermore, this method's accuracy was also evaluated by comparing the widths of the actual stencils and etched PDMS results.

Mobility of pyroclastic flows and surges at the Soufriere Hills Volcano, Montserrat

USGS Publications Warehouse

Calder, E.S.; Cole, P.D.; Dade, W.B.; Druitt, T.H.; Hoblitt, R.P.; Huppert, H.E.; Ritchie, L.; Sparks, R.S.J.; Young, S.R.

1999-01-01

The Soufriere Hills Volcano on Montserrat has produced avalanche-like pyroclastic flows formed by collapse of the unstable lava dome or explosive activity. Pyroclastic flows associated with dome collapse generate overlying dilute surges which detach from and travel beyond their parent flows. The largest surges partially transform by rapid sedimentation into dense secondary pyroclastic flows that pose significant hazards to distal areas. Different kinds of pyroclastic density currents display contrasting mobilities indicated by ratios of total height of fall H, run-out distance L, area inundated A and volume transported V. Dome-collapse flow mobilities (characterised by either L/H or A/V 2/3) resemble those of terrestrial and extraterrestrial cold-rockfalls (Dade and Huppert, 1998). In contrast, fountain-fed pumice flows and fine-grained, secondary pyroclastic flows travel slower but, for comparable initial volumes and heights, can inundate greater areas.

Hippocampal Processing of Ambiguity Enhances Fear Memory

PubMed Central

Amadi, Ugwechi; Lim, Seh Hong; Liu, Elizabeth; Baratta, Michael V.; Goosens, Ki Ann

2016-01-01

Despite the ubiquitous use of Pavlovian fear conditioning as a model for fear learning, the highly predictable conditions used in the laboratory do not resemble real-world conditions, where dangerous situations can lead to unpleasant outcomes in unpredictable ways. Here we varied the timing of aversive events following predictive cues in rodents and discovered that temporal ambiguity of aversive events greatly enhances fear. During fear conditioning with unpredictably timed aversive events, pharmacological inactivation of the dorsal hippocampus or optogenetic silencing of CA1 cells during aversive negative prediction errors prevented this enhancement of fear without impacting fear learning for predictable events. Dorsal hippocampal inactivation also prevented ambiguity-related enhancement of fear during auditory fear conditioning under a partial reinforcement schedule. These results reveal that information about the timing and occurrence of aversive events is rapidly acquired and that unexpectedly timed or omitted aversive events generate hippocampal signals to enhance fear learning. PMID:28182526

Fragment approach to the electronic structure of τ -boron allotrope

NASA Astrophysics Data System (ADS)

Karmodak, Naiwrit; Jemmis, Eluvathingal D.

2017-04-01

The presence of nonconventional bonding features is an intriguing part of elemental boron. The recent addition of τ boron to the family of three-dimensional boron allotropes is no exception. We provide an understanding of the electronic structure of τ boron using a fragment molecular approach, where the effect of symmetry reduction on skeletal bands of B12 and the B57 fragments are examined qualitatively by analyzing the projected density of states of these fragments. In spite of the structural resemblance to β boron, the reduction of symmetry from a rhombohedral space group to the orthorhombic one destabilizes the bands and reduces the electronic requirements. This suggests the presence of the partially occupied boron sites, as seen for a β boron unit cell, and draws the possibility for the existence of different energetically similar polymorphs. τ boron has a lower binding energy than β boron.

Supernatural beliefs, natural kinds, and conceptual structure.

PubMed

Walker, S J

1992-11-01

This article presents cross-cultural evidence in support of the notion that adults' natural kind concepts are theory based but may be informed by knowledge/belief systems other than the biological. Three groups of subjects from western Nigeria--rural, urban, and elite--participated in the study. Subjects heard stories describing alterations of appearance; that is, one natural kind was made to resemble another in both ritual and nonritual contexts. Subjects then were required to judge the identity of the altered item and to give an explanation for the category judgment. It was predicted that subjects would make more nonpreservation-of-identity category judgments supported by supernatural explanations in the ritual contexts and that subjects' use of supernatural explanations would reflect the extent of their engagement with the supernatural. The first prediction was borne out; the second prediction was only partially supported. Discussion of the results emphasizes the importance of exploring the role of sociocultural factors in conceptual structure.

Coproduction of healthcare service

PubMed Central

Batalden, Maren; Batalden, Paul; Margolis, Peter; Seid, Michael; Armstrong, Gail; Opipari-Arrigan, Lisa; Hartung, Hans

2016-01-01

Efforts to ensure effective participation of patients in healthcare are called by many names—patient centredness, patient engagement, patient experience. Improvement initiatives in this domain often resemble the efforts of manufacturers to engage consumers in designing and marketing products. Services, however, are fundamentally different than products; unlike goods, services are always ‘coproduced’. Failure to recognise this unique character of a service and its implications may limit our success in partnering with patients to improve health care. We trace a partial history of the coproduction concept, present a model of healthcare service coproduction and explore its application as a design principle in three healthcare service delivery innovations. We use the principle to examine the roles, relationships and aims of this interdependent work. We explore the principle's implications and challenges for health professional development, for service delivery system design and for understanding and measuring benefit in healthcare services. PMID:26376674

Degenerate R-S perturbation theory

NASA Technical Reports Server (NTRS)

Hirschfelder, J. O.; Certain, P. R.

1973-01-01

A concise, systematic procedure is given for determining the Rayleigh-Schrodinger energies and wave functions of degenerate states to arbitrarily high orders even when the degeneracies of the various states are resolved in arbitrary orders. The procedure is expressed in terms of an iterative cycle in which the energy through the (2n+1)st order is expressed in terms of the partially determined wave function through the n-th order. Both a direct and an operator derivation are given. The two approaches are equivalent and can be transcribed into each other. The direct approach deals with the wave functions (without the use of formal operators) and has the advantage that it resembles the usual treatment of nondegenerate perturbations and maintains close contact with the basic physics. In the operator approach, the wave functions are expressed in terms of infinite order operators which are determined by the successive resolution of the space of the zeroth order functions.

A FEniCS-based programming framework for modeling turbulent flow by the Reynolds-averaged Navier-Stokes equations

NASA Astrophysics Data System (ADS)

Mortensen, Mikael; Langtangen, Hans Petter; Wells, Garth N.

2011-09-01

Finding an appropriate turbulence model for a given flow case usually calls for extensive experimentation with both models and numerical solution methods. This work presents the design and implementation of a flexible, programmable software framework for assisting with numerical experiments in computational turbulence. The framework targets Reynolds-averaged Navier-Stokes models, discretized by finite element methods. The novel implementation makes use of Python and the FEniCS package, the combination of which leads to compact and reusable code, where model- and solver-specific code resemble closely the mathematical formulation of equations and algorithms. The presented ideas and programming techniques are also applicable to other fields that involve systems of nonlinear partial differential equations. We demonstrate the framework in two applications and investigate the impact of various linearizations on the convergence properties of nonlinear solvers for a Reynolds-averaged Navier-Stokes model.

Hippocampal Processing of Ambiguity Enhances Fear Memory.

PubMed

Amadi, Ugwechi; Lim, Seh Hong; Liu, Elizabeth; Baratta, Michael V; Goosens, Ki A

2017-02-01

Despite the ubiquitous use of Pavlovian fear conditioning as a model for fear learning, the highly predictable conditions used in the laboratory do not resemble real-world conditions, in which dangerous situations can lead to unpleasant outcomes in unpredictable ways. In the current experiments, we varied the timing of aversive events after predictive cues in rodents and discovered that temporal ambiguity of aversive events greatly enhances fear. During fear conditioning with unpredictably timed aversive events, pharmacological inactivation of the dorsal hippocampus or optogenetic silencing of cornu ammonis 1 cells during aversive negative prediction errors prevented this enhancement of fear without affecting fear learning for predictable events. Dorsal hippocampal inactivation also prevented ambiguity-related enhancement of fear during auditory fear conditioning under a partial-reinforcement schedule. These results reveal that information about the timing and occurrence of aversive events is rapidly acquired and that unexpectedly timed or omitted aversive events generate hippocampal signals to enhance fear learning.

Molecular phylogeny of moth-specialized spider sub-family Cyrtarachninae, which includes bolas spiders.

PubMed

Tanikawa, Akio; Shinkai, Akira; Miyashita, Tadashi

2014-11-01

The evolutionary process of the unique web architectures of spiders of the sub-family Cyrtarachninae, which includes the triangular web weaver, bolas spider, and webless spider, is thought to be derived from reduction of orbicular 'spanning-thread webs' resembling ordinal orb webs. A molecular phylogenetic analysis was conducted to explore this hypothesis using orbicular web spiders Cyrtarachne, Paraplectana, Poecilopachys, triangular web spider Pasilobus, bolas spiders Ordgarius and Mastophora, and webless spider Celaenia. The phylogeny inferred from partial sequences of mt-COI, nuclear 18S-rRNA and 28S-rRNA showed that the common ancestor of these spiders diverged into two clades: a spanning-thread web clade and a bolas or webless clade. This finding suggests that the triangular web evolved by reduction of an orbicular spanning web, but that bolas spiders evolved in the early stage, which does not support the gradual web reduction hypothesis.

Morphological evidence for phages in Xylella fastidiosa

PubMed Central

Chen, Jianchi; Civerolo, Edwin L

2008-01-01

Presumptive phage particles associated with Xylella fastidiosa strain Temecula-1 grown in PW broth were observed by transmission electron microscopy (TEM) in ultrathin sections of bacterial cell-containing low speed centrifugation pellets and in partially purified preparations from CsCl equilibrium centrifugation density gradients. Ultrathin-sectioned cell pellets contained icosahedral particles of about 45 nm in diameter. Samples collected from CsCl density gradients revealed mostly non-tailed icosahedral but also tailed particles. The icosahedral particles could be divided into two types: a large type (about 45 nm) and a small type (about 30 nm). Filamentous phage-like particles (17 × 120 to 6,300 nm) were also observed. The presence of different types of phage-like particles resembling to those in several bacteriophage families provides new physical evidence, in addition to X. fastidiosa genomic information, that X. fastidiosa possesses active phages. This is the first report of phage particles released in X. fastidiosa cultures. PMID:18538030

Degenerate RS perturbation theory. [Rayleigh-Schroedinger energies and wave functions

NASA Technical Reports Server (NTRS)

Hirschfelder, J. O.; Certain, P. R.

1974-01-01

A concise, systematic procedure is given for determining the Rayleigh-Schroedinger energies and wave functions of degenerate states to arbitrarily high orders even when the degeneracies of the various states are resolved in arbitrary orders. The procedure is expressed in terms of an iterative cycle in which the energy through the (2n + 1)-th order is expressed in terms of the partially determined wave function through the n-th order. Both a direct and an operator derivation are given. The two approaches are equivalent and can be transcribed into each other. The direct approach deals with the wave functions (without the use of formal operators) and has the advantage that it resembles the usual treatment of nondegenerate perturbations and maintains close contact with the basic physics. In the operator approach, the wave functions are expressed in terms of infinite-order operators which are determined by the successive resolution of the space of the zeroth-order functions.

Animal physiology. Summer declines in activity and body temperature offer polar bears limited energy savings.

PubMed

Whiteman, J P; Harlow, H J; Durner, G M; Anderson-Sprecher, R; Albeke, S E; Regehr, E V; Amstrup, S C; Ben-David, M

2015-07-17

Polar bears (Ursus maritimus) summer on the sea ice or, where it melts, on shore. Although the physiology of "ice" bears in summer is unknown, "shore" bears purportedly minimize energy losses by entering a hibernation-like state when deprived of food. Such a strategy could partially compensate for the loss of on-ice foraging opportunities caused by climate change. However, here we report gradual, moderate declines in activity and body temperature of both shore and ice bears in summer, resembling energy expenditures typical of fasting, nonhibernating mammals. Also, we found that to avoid unsustainable heat loss while swimming, bears employed unusual heterothermy of the body core. Thus, although well adapted to seasonal ice melt, polar bears appear susceptible to deleterious declines in body condition during the lengthening period of summer food deprivation. Copyright © 2015, American Association for the Advancement of Science.

Pathophysiology of immobilization osteoporosis

NASA Technical Reports Server (NTRS)

Doty, S. B.; DiCarlo, E. F.

1995-01-01

The reduction of gravity-related forces on the skeleton creates a type of osteoporosis that is unique because its severity is dependent on the mechanical stress bearing function of the skeleton as well as the length of time that the forces are absent or reduced. Bones that bear weight under normal conditions are more affected than bones that normally do not bear weight. The cytokine environment and the cells in the affected bones are altered in time so that stem cells produce fewer new cells and the differentiated cells tend to be less active. These alterations in the local environment of the affected parts appear to resemble those of age- and disease-associated systemic forms of osteoporosis. The osteoporosis produced as a result of the loss of normal activity however, appears to be at least partially reversible through remobilization, strenuous exercise, and--possibly in the future--cytokine therapy.

Sibling earthquakes generated within a persistent rupture barrier on the Sunda megathrust under Simeulue Island

NASA Astrophysics Data System (ADS)

Morgan, Paul M.; Feng, Lujia; Meltzner, Aron J.; Lindsey, Eric O.; Tsang, Louisa L. H.; Hill, Emma M.

2017-03-01

A section of the Sunda megathrust underneath Simeulue is known to persistently halt rupture propagation of great earthquakes, including those in 2004 (Mw 9.2) and 2005 (Mw 8.6). Yet the same section generated large earthquakes in 2002 (Mw 7.3) and 2008 (Mw 7.4). To date, few studies have investigated the 2002 and 2008 events, and none have satisfactorily located or explained them. Using near-field InSAR, GPS, and coral geodetic data, we find that the slip distributions of the two events are not identical but do show a close resemblance and largely overlap. We thus consider these earthquakes "siblings" that were generated by an anomalous "parent" feature of the megathrust. We suggest that this parent feature is a locked asperity surrounded by the otherwise partially creeping Simeulue section, perhaps structurally controlled by a broad morphological high on the megathrust.

Zebrafish cdc6 hypomorphic mutation causes Meier-Gorlin syndrome-like phenotype.

PubMed

Yao, Likun; Chen, Jing; Wu, Xiaotong; Jia, Shunji; Meng, Anming

2017-11-01

Cell Division Cycle 6 (Cdc6) is a component of pre-replicative complex (preRC) forming on DNA replication origins in eukaryotes. Recessive mutations in ORC1, ORC4, ORC6, CDT1 or CDC6 of the preRC in human cause Meier-Gorlin syndrome (MGS) that is characterized by impaired post-natal growth, short stature and microcephaly. However, vertebrate models of MGS have not been reported. Through N-ethyl-N-nitrosourea mutagenesis and Cas9 knockout, we generate several cdc6 mutant lines in zebrafish. Loss-of-function mutations of cdc6, as manifested by cdc6tsu4305 and cdc6tsu7cd mutants, lead to embryonic lethality due to cell cycle arrest at the S phase and extensive apoptosis. Embryos homozygous for a cdc6 hypomorphic mutation, cdc6tsu21cd, develop normally during embryogenesis. Later on, compared with their wild-type (WT) siblings, cdc6tsu21cd mutant fish show growth retardation, and their body weight and length in adulthood are greatly reduced, which resemble human MGS. Surprisingly, cdc6tsu21cd mutant fish become males with a short life and fail to mate with WT females, suggesting defective reproduction. Overexpression of Cdc6 mutant forms, which mimic human CDC6(T323R) mutation found in a MGS patient, in zebrafish cdc6tsu4305 mutant embryos partially represses cell death phenotype, suggesting that the human CDC6(T323R) mutation is a hypomorph. cdc6tsu21cd mutant fish will be useful to detect more tissue defects and develop medical treatment strategies for MGS patients. © The Author 2017. Published by Oxford University Press.

Structural changes in the ageing periosteum using collagen III immuno-staining and chromium labelling as indicators.

PubMed

Al-Qtaitat, A; Shore, R C; Aaron, J E

2010-03-01

The periosteum and Sharpey's fibre extensions occupy the musculoskeletal interface and may be strategic in age-related deterioration. Because of its exceptionally powerful insertions the porcine mandible is an ideal model and its periosteal system was compared in 4 separate regions of adult young (1 year) and older (3 year) animals. These were examined by undecalcified histology, collagen immunohistochemistry and mineral histochemistry using polarization, epifluorescence and laser confocal microscopy; mineral ultrastructure was facilitated by chromium labelling with EDX microanalysis. Birefringent Sharpey's fibres were coarse (>8 microm) or fine and classified as horizontal (more common with age), oblique (most common in youth) or vertical (least common); in addition they were designated "superficial", "transcortical" and "intertrabecular" (the latter being deep, coarse and vertical). Their specific affinity for collagen type III FITC-labelled antibody demonstrated 3-dimensional arrays of bone-permeating fibres. With age at each region the cortical thickness rose (e.g. 4.9 mm to 9.3 mm), the periosteum thinned (e.g. 180-/+7 microm to 129-/+8 microm; p<0.001), and the periosteum: bone ratio diminished (e.g. 3.65-/+0.36 to 1.40-/+0.14; p<0.001) while Sharpey's fibres became fewer, fragmented, superficial and shortened (e.g. 226-/+27 microm to 55-/+6 microm; p<0.001). Accompanying was the sporadic encroachment of calcified particles, 1 microm diameter, in irregular periosteal aggregates or interlinked around Sharpey bundles (resembling calcifying turkey leg tendon). EDX microanalysis confirmed prominent chromium spectral peaks in the older periosteum only, coincident with chromium-labelled mineral "ghosts". It was concluded that the periosteum and Sharpey's fibres, deep-penetrating and complex in youth, partially hardens and regresses with age with implications for its functional properties.

Naturalistic FMRI mapping reveals superior temporal sulcus as the hub for the distributed brain network for social perception.

PubMed

Lahnakoski, Juha M; Glerean, Enrico; Salmi, Juha; Jääskeläinen, Iiro P; Sams, Mikko; Hari, Riitta; Nummenmaa, Lauri

2012-01-01

Despite the abundant data on brain networks processing static social signals, such as pictures of faces, the neural systems supporting social perception in naturalistic conditions are still poorly understood. Here we delineated brain networks subserving social perception under naturalistic conditions in 19 healthy humans who watched, during 3-T functional magnetic resonance imaging (fMRI), a set of 137 short (approximately 16 s each, total 27 min) audiovisual movie clips depicting pre-selected social signals. Two independent raters estimated how well each clip represented eight social features (faces, human bodies, biological motion, goal-oriented actions, emotion, social interaction, pain, and speech) and six filler features (places, objects, rigid motion, people not in social interaction, non-goal-oriented action, and non-human sounds) lacking social content. These ratings were used as predictors in the fMRI analysis. The posterior superior temporal sulcus (STS) responded to all social features but not to any non-social features, and the anterior STS responded to all social features except bodies and biological motion. We also found four partially segregated, extended networks for processing of specific social signals: (1) a fronto-temporal network responding to multiple social categories, (2) a fronto-parietal network preferentially activated to bodies, motion, and pain, (3) a temporo-amygdalar network responding to faces, social interaction, and speech, and (4) a fronto-insular network responding to pain, emotions, social interactions, and speech. Our results highlight the role of the pSTS in processing multiple aspects of social information, as well as the feasibility and efficiency of fMRI mapping under conditions that resemble the complexity of real life.

Weekly infusional high-dose 5-fluorouracil and leucovorin and biweekly cisplatin: a convenient treatment option in advanced gastric cancer.

PubMed

Kundel, Yulia; Purim, Ofer; Figer, Arie; Stemmer, Salomon M; Tichler, Thomas; Sulkes, Jaqueline; Sulkes, Aaron; Brenner, Baruch

2008-04-01

To summarize our experience using a regimen of weekly 5-FU and leucovorin (LV) and biweekly cisplatin (CDDP) in advanced gastric cancer (AGC). Patients had previously untreated histologically confirmed AGC. Treatment consisted of intravenous weekly infusional 5-FU and LV and biweekly CDDP, given for 6 weeks followed by a 2-week rest. Initially, a lower dose level was used (5-FU 2000 mg/m(2), LV 500 mg/m(2), CDDP 40 mg/m(2)), which was later increased (5-FU 2600 mg/m(2), LV 500 mg/m(2), CDDP 50 mg/m(2)). Forty-five patients were treated, 18 at the lower dose level and 27 at the higher dose level. The median age was 67 years and 55% were male. Grade > or =3 toxicity was documented in 37% of patients but toxicity related hospitalizations or treatment discontinuation occurred in only 22% and 13%, respectively. There were no toxic deaths. The most common hematological toxicities were anemia and neutropenia and the most common non-hematological toxicities were nausea, vomiting and fatigue. Of the 39 patients evaluable for response, 13 (33%) had partial response (PR) and 11 (28%) had stable disease (SD). Control of disease (PR+SD) was achieved in 61%. The higher dose level was associated with a higher response rate (p=0.07) and an increased toxicity (p=0.01), mostly hematological and gastrointestinal. Median progression-free survival and overall survival were 3.5 and 9.2 months, respectively. This regimen appears safe, with a manageable toxicity profile. Efficacy data resemble those reported for more complex and toxic regimens. The higher dose level had enhanced activity, at the expense of increased toxicity.

Nipbl and mediator cooperatively regulate gene expression to control limb development.

PubMed

Muto, Akihiko; Ikeda, Shingo; Lopez-Burks, Martha E; Kikuchi, Yutaka; Calof, Anne L; Lander, Arthur D; Schilling, Thomas F

2014-09-01

Haploinsufficiency for Nipbl, a cohesin loading protein, causes Cornelia de Lange Syndrome (CdLS), the most common "cohesinopathy". It has been proposed that the effects of Nipbl-haploinsufficiency result from disruption of long-range communication between DNA elements. Here we use zebrafish and mouse models of CdLS to examine how transcriptional changes caused by Nipbl deficiency give rise to limb defects, a common condition in individuals with CdLS. In the zebrafish pectoral fin (forelimb), knockdown of Nipbl expression led to size reductions and patterning defects that were preceded by dysregulated expression of key early limb development genes, including fgfs, shha, hand2 and multiple hox genes. In limb buds of Nipbl-haploinsufficient mice, transcriptome analysis revealed many similar gene expression changes, as well as altered expression of additional classes of genes that play roles in limb development. In both species, the pattern of dysregulation of hox-gene expression depended on genomic location within the Hox clusters. In view of studies suggesting that Nipbl colocalizes with the mediator complex, which facilitates enhancer-promoter communication, we also examined zebrafish deficient for the Med12 Mediator subunit, and found they resembled Nipbl-deficient fish in both morphology and gene expression. Moreover, combined partial reduction of both Nipbl and Med12 had a strongly synergistic effect, consistent with both molecules acting in a common pathway. In addition, three-dimensional fluorescent in situ hybridization revealed that Nipbl and Med12 are required to bring regions containing long-range enhancers into close proximity with the zebrafish hoxda cluster. These data demonstrate a crucial role for Nipbl in limb development, and support the view that its actions on multiple gene pathways result from its influence, together with Mediator, on regulation of long-range chromosomal interactions.

Zebrafish cdc6 hypomorphic mutation causes Meier-Gorlin syndrome-like phenotype

PubMed Central

Yao, Likun; Chen, Jing; Wu, Xiaotong; Jia, Shunji; Meng, Anming

2017-01-01

Abstract Cell Division Cycle 6 (Cdc6) is a component of pre-replicative complex (preRC) forming on DNA replication origins in eukaryotes. Recessive mutations in ORC1, ORC4, ORC6, CDT1 or CDC6 of the preRC in human cause Meier-Gorlin syndrome (MGS) that is characterized by impaired post-natal growth, short stature and microcephaly. However, vertebrate models of MGS have not been reported. Through N-ethyl-N-nitrosourea mutagenesis and Cas9 knockout, we generate several cdc6 mutant lines in zebrafish. Loss-of-function mutations of cdc6, as manifested by cdc6tsu4305 and cdc6tsu7cd mutants, lead to embryonic lethality due to cell cycle arrest at the S phase and extensive apoptosis. Embryos homozygous for a cdc6 hypomorphic mutation, cdc6tsu21cd, develop normally during embryogenesis. Later on, compared with their wild-type (WT) siblings, cdc6tsu21cd mutant fish show growth retardation, and their body weight and length in adulthood are greatly reduced, which resemble human MGS. Surprisingly, cdc6tsu21cd mutant fish become males with a short life and fail to mate with WT females, suggesting defective reproduction. Overexpression of Cdc6 mutant forms, which mimic human CDC6(T323R) mutation found in a MGS patient, in zebrafish cdc6tsu4305 mutant embryos partially represses cell death phenotype, suggesting that the human CDC6(T323R) mutation is a hypomorph. cdc6tsu21cd mutant fish will be useful to detect more tissue defects and develop medical treatment strategies for MGS patients. PMID:28985365

Crystal structure at 2.8 A of Huntingtin-interacting protein 1 (HIP1) coiled-coil domain reveals a charged surface suitable for HIP1 protein interactor (HIPPI).

PubMed

Niu, Qian; Ybe, Joel A

2008-02-01

Huntington's disease is a genetic neurological disorder that is triggered by the dissociation of the huntingtin protein (htt) from its obligate interaction partner Huntingtin-interacting protein 1 (HIP1). The release of the huntingtin protein permits HIP1 protein interactor (HIPPI) to bind to its recognition site on HIP1 to form a HIPPI/HIP1 complex that recruits procaspase-8 to begin the process of apoptosis. The interaction module between HIPPI and HIP1 was predicted to resemble a death-effector domain. Our 2.8-A crystal structure of the HIP1 371-481 subfragment that includes F432 and K474, which is important for HIPPI binding, is not a death-effector domain but is a partially opened coiled coil. The HIP1 371-481 model reveals a basic surface that we hypothesize to be suitable for binding HIPPI. There is an opened region next to the putative HIPPI site that is highly negatively charged. The acidic residues in this region are highly conserved in HIP1 and a related protein, HIP1R, from different organisms but are not conserved in the yeast homologue of HIP1, sla2p. We have modeled approximately 85% of the coiled-coil domain by joining our new HIP1 371-481 structure to the HIP1 482-586 model (Protein Data Bank code: 2NO2). Finally, the middle of this coiled-coil domain may be intrinsically flexible and suggests a new interaction model where HIPPI binds to a U-shaped HIP1 molecule.

Engineering Approaches Toward Deconstructing and Controlling the Stem Cell Environment

PubMed Central

Edalat, Faramarz; Bae, Hojae; Manoucheri, Sam; Cha, Jae Min; Khademhosseini, Ali

2012-01-01

Stem cell-based therapeutics have become a vital component in tissue engineering and regenerative medicine. The microenvironment within which stem cells reside, i.e. the niche, plays a crucial role in regulating stem cell self-renewal and differentiation. However, current biological techniques lack the means to recapitulate the complexity of this microenvironment. Nano- and microengineered materials offer innovative methods to: (1) deconstruct the stem cell niche to understand the effects of individual elements; (2) construct complex tissue-like structures resembling the niche to better predict and control cellular processes; and (3) transplant stem cells or activate endogenous stem cell populations for regeneration of aged or diseased tissues. Here, we highlight some of the latest advances in this field and discuss future applications and directions of the use of nano- and microtechnologies for stem cell engineering. PMID:22101755

RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution.

PubMed

Venkataraman, Sangita; Prasad, Burra V L S; Selvarajan, Ramasamy

2018-02-10

RNA dependent RNA polymerase (RdRp) is one of the most versatile enzymes of RNA viruses that is indispensable for replicating the genome as well as for carrying out transcription. The core structural features of RdRps are conserved, despite the divergence in their sequences. The structure of RdRp resembles that of a cupped right hand and consists of fingers, palm and thumb subdomains. The catalysis involves the participation of conserved aspartates and divalent metal ions. Complexes of RdRps with substrates, inhibitors and metal ions provide a comprehensive view of their functional mechanism and offer valuable insights regarding the development of antivirals. In this article, we provide an overview of the structural aspects of RdRps and their complexes from the Group III, IV and V viruses and their structure-based phylogeny.

RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution

PubMed Central

Venkataraman, Sangita; Prasad, Burra V L S; Selvarajan, Ramasamy

2018-01-01

RNA dependent RNA polymerase (RdRp) is one of the most versatile enzymes of RNA viruses that is indispensable for replicating the genome as well as for carrying out transcription. The core structural features of RdRps are conserved, despite the divergence in their sequences. The structure of RdRp resembles that of a cupped right hand and consists of fingers, palm and thumb subdomains. The catalysis involves the participation of conserved aspartates and divalent metal ions. Complexes of RdRps with substrates, inhibitors and metal ions provide a comprehensive view of their functional mechanism and offer valuable insights regarding the development of antivirals. In this article, we provide an overview of the structural aspects of RdRps and their complexes from the Group III, IV and V viruses and their structure-based phylogeny. PMID:29439438

Assembly of micro/nanomaterials into complex, three-dimensional architectures by compressive buckling

NASA Astrophysics Data System (ADS)

Xu, Sheng; Yan, Zheng; Jang, Kyung-In; Huang, Wen; Fu, Haoran; Kim, Jeonghyun; Wei, Zijun; Flavin, Matthew; McCracken, Joselle; Wang, Renhan; Badea, Adina; Liu, Yuhao; Xiao, Dongqing; Zhou, Guoyan; Lee, Jungwoo; Chung, Ha Uk; Cheng, Huanyu; Ren, Wen; Banks, Anthony; Li, Xiuling; Paik, Ungyu; Nuzzo, Ralph G.; Huang, Yonggang; Zhang, Yihui; Rogers, John A.

2015-01-01

Complex three-dimensional (3D) structures in biology (e.g., cytoskeletal webs, neural circuits, and vasculature networks) form naturally to provide essential functions in even the most basic forms of life. Compelling opportunities exist for analogous 3D architectures in human-made devices, but design options are constrained by existing capabilities in materials growth and assembly. We report routes to previously inaccessible classes of 3D constructs in advanced materials, including device-grade silicon. The schemes involve geometric transformation of 2D micro/nanostructures into extended 3D layouts by compressive buckling. Demonstrations include experimental and theoretical studies of more than 40 representative geometries, from single and multiple helices, toroids, and conical spirals to structures that resemble spherical baskets, cuboid cages, starbursts, flowers, scaffolds, fences, and frameworks, each with single- and/or multiple-level configurations.

Engineering approaches toward deconstructing and controlling the stem cell environment.

PubMed

Edalat, Faramarz; Bae, Hojae; Manoucheri, Sam; Cha, Jae Min; Khademhosseini, Ali

2012-06-01

Stem cell-based therapeutics have become a vital component in tissue engineering and regenerative medicine. The microenvironment within which stem cells reside, i.e., the niche, plays a crucial role in regulating stem cell self-renewal and differentiation. However, current biological techniques lack the means to recapitulate the complexity of this microenvironment. Nano- and microengineered materials offer innovative methods to (1) deconstruct the stem cell niche to understand the effects of individual elements; (2) construct complex tissue-like structures resembling the niche to better predict and control cellular processes; and (3) transplant stem cells or activate endogenous stem cell populations for regeneration of aged or diseased tissues. In this article, we highlight some of the latest advances in this field and discuss future applications and directions of the use of nano- and microtechnologies for stem cell engineering.

Modelling radiation fluxes in simple and complex environments: basics of the RayMan model.

PubMed

Matzarakis, Andreas; Rutz, Frank; Mayer, Helmut

2010-03-01

Short- and long-wave radiation flux densities absorbed by people have a significant influence on their energy balance. The heat effect of the absorbed radiation flux densities is parameterised by the mean radiant temperature. This paper presents the physical basis of the RayMan model, which simulates the short- and long-wave radiation flux densities from the three-dimensional surroundings in simple and complex environments. RayMan has the character of a freely available radiation and human-bioclimate model. The aim of the RayMan model is to calculate radiation flux densities, sunshine duration, shadow spaces and thermo-physiologically relevant assessment indices using only a limited number of meteorological and other input data. A comparison between measured and simulated values for global radiation and mean radiant temperature shows that the simulated data closely resemble measured data.

Electrostatic interactions guide the active site face of a structure-specific ribonuclease to its RNA substrate.

PubMed

Plantinga, Matthew J; Korennykh, Alexei V; Piccirilli, Joseph A; Correll, Carl C

2008-08-26

Restrictocin, a member of the alpha-sarcin family of site-specific endoribonucleases, uses electrostatic interactions to bind to the ribosome and to RNA oligonucleotides, including the minimal specific substrate, the sarcin/ricin loop (SRL) of 23S-28S rRNA. Restrictocin binds to the SRL by forming a ground-state E:S complex that is stabilized predominantly by Coulomb interactions and depends on neither the sequence nor structure of the RNA, suggesting a nonspecific complex. The 22 cationic residues of restrictocin are dispersed throughout this protein surface, complicating a priori identification of a Coulomb interacting surface. Structural studies have identified an enzyme-substrate interface, which is expected to overlap with the electrostatic E:S interface. Here, we identified restrictocin residues that contribute to binding in the E:S complex by determining the salt dependence [partial differential log(k 2/ K 1/2)/ partial differential log[KCl

Generic strategies for chemical space exploration.

PubMed

Andersen, Jakob L; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F

2014-01-01

The chemical universe of molecules reachable from a set of start compounds by iterative application of a finite number of reactions is usually so vast, that sophisticated and efficient exploration strategies are required to cope with the combinatorial complexity. A stringent analysis of (bio)chemical reaction networks, as approximations of these complex chemical spaces, forms the foundation for the understanding of functional relations in Chemistry and Biology. Graphs and graph rewriting are natural models for molecules and reactions. Borrowing the idea of partial evaluation from functional programming, we introduce partial applications of rewrite rules. A framework for the specification of exploration strategies in graph-rewriting systems is presented. Using key examples of complex reaction networks from carbohydrate chemistry we demonstrate the feasibility of this high-level strategy framework. While being designed for chemical applications, the framework can also be used to emulate higher-level transformation models such as illustrated in a small puzzle game.

Cancer vulnerabilities unveiled by genomic loss

PubMed Central

Nijhawan, Deepak; Zack, Travis I.; Ren, Yin; Strickland, Matthew R.; Lamothe, Rebecca; Schumacher, Steven E.; Tsherniak, Aviad; Besche, Henrike C.; Rosenbluh, Joseph; Shehata, Shyemaa; Cowley, Glenn S.; Weir, Barbara A.; Goldberg, Alfred L.; Mesirov, Jill P.; Root, David E.; Bhatia, Sangeeta N.; Beroukhim, Rameen; Hahn, William C.

2012-01-01

Summary Due to genome instability, most cancers exhibit loss of regions containing tumor suppressor genes and collateral loss of other genes. To identify cancer-specific vulnerabilities that are the result of copy-number losses, we performed integrated analyses of genome-wide copy-number and RNAi profiles and identified 56 genes for which gene suppression specifically inhibited the proliferation of cells harboring partial copy-number loss of that gene. These CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes are enriched for spliceosome, proteasome and ribosome components. One CYCLOPS gene, PSMC2, encodes an essential member of the 19S proteasome. Normal cells express excess PSMC2, which resides in a complex with PSMC1, PSMD2, and PSMD5 and acts as a reservoir protecting cells from PSMC2 suppression. Cells harboring partial PSMC2 copy-number loss lack this complex and die after PSMC2 suppression. These observations define a distinct class of cancer-specific liabilities resulting from genome instability. PMID:22901813

Electronic structure and partial charge distribution of Doxorubicin in different molecular environments.

PubMed

Poudel, Lokendra; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Podgornik, Rudolf; Steinmetz, Nicole F; Ching, Wai-Yim

2015-05-18

The electronic structure and partial charge of doxorubicin (DOX) in three different molecular environments-isolated, solvated, and intercalated in a DNA complex-are studied by first-principles density functional methods. It is shown that the addition of solvating water molecules to DOX, together with the proximity to and interaction with DNA, has a significant impact on the electronic structure as well as on the partial charge distribution. Significant improvement in estimating the DOX-DNA interaction energy is achieved. The results are further elucidated by resolving the total density of states and surface charge density into different functional groups. It is concluded that the presence of the solvent and the details of the interaction geometry matter greatly in determining the stability of DOX complexation. Ab initio calculations on realistic models are an important step toward a more accurate description of the long-range interactions in biomolecular systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three dimensional multi-cellular muscle-like tissue engineering in perfusion-based bioreactors.

PubMed

Cerino, Giulia; Gaudiello, Emanuele; Grussenmeyer, Thomas; Melly, Ludovic; Massai, Diana; Banfi, Andrea; Martin, Ivan; Eckstein, Friedrich; Grapow, Martin; Marsano, Anna

2016-01-01

Conventional tissue engineering strategies often rely on the use of a single progenitor cell source to engineer in vitro biological models; however, multi-cellular environments can better resemble the complexity of native tissues. Previous described co-culture models used skeletal myoblasts, as parenchymal cell source, and mesenchymal or endothelial cells, as stromal component. Here, we propose instead the use of adipose tissue-derived stromal vascular fraction cells, which include both mesenchymal and endothelial cells, to better resemble the native stroma. Percentage of serum supplementation is one of the crucial parameters to steer skeletal myoblasts toward either proliferation (20%) or differentiation (5%) in two-dimensional culture conditions. On the contrary, three-dimensional (3D) skeletal myoblast culture often simply adopts the serum content used in monolayer, without taking into account the new cell environment. When considering 3D cultures of mm-thick engineered tissues, homogeneous and sufficient oxygen supply is paramount to avoid formation of necrotic cores. Perfusion-based bioreactor culture can significantly improve the oxygen access to the cells, enhancing the viability and the contractility of the engineered tissues. In this study, we first investigated the influence of different serum supplementations on the skeletal myoblast ability to proliferate and differentiate during 3D perfusion-based culture. We tested percentages of serum promoting monolayer skeletal myoblast-proliferation (20%) and differentiation (5%) and suitable for stromal cell culture (10%) with a view to identify the most suitable condition for the subsequent co-culture. The 10% serum medium composition resulted in the highest number of mature myotubes and construct functionality. Co-culture with stromal vascular fraction cells at 10% serum also supported the skeletal myoblast differentiation and maturation, hence providing a functional engineered 3D muscle model that resembles the native multi-cellular environment. © 2015 Wiley Periodicals, Inc.

Development of Potent Antiviral Drugs Inspired by Viral Hexameric DNA-Packaging Motors with Revolving Mechanism

PubMed Central

Pi, Fengmei; Zhao, Zhengyi; Chelikani, Venkata; Yoder, Kristine; Kvaratskhelia, Mamuka

2016-01-01

The intracellular parasitic nature of viruses and the emergence of antiviral drug resistance necessitate the development of new potent antiviral drugs. Recently, a method for developing potent inhibitory drugs by targeting biological machines with high stoichiometry and a sequential-action mechanism was described. Inspired by this finding, we reviewed the development of antiviral drugs targeting viral DNA-packaging motors. Inhibiting multisubunit targets with sequential actions resembles breaking one bulb in a series of Christmas lights, which turns off the entire string. Indeed, studies on viral DNA packaging might lead to the development of new antiviral drugs. Recent elucidation of the mechanism of the viral double-stranded DNA (dsDNA)-packaging motor with sequential one-way revolving motion will promote the development of potent antiviral drugs with high specificity and efficiency. Traditionally, biomotors have been classified into two categories: linear and rotation motors. Recently discovered was a third type of biomotor, including the viral DNA-packaging motor, beside the bacterial DNA translocases, that uses a revolving mechanism without rotation. By analogy, rotation resembles the Earth's rotation on its own axis, while revolving resembles the Earth's revolving around the Sun (see animations at http://rnanano.osu.edu/movie.html). Herein, we review the structures of viral dsDNA-packaging motors, the stoichiometries of motor components, and the motion mechanisms of the motors. All viral dsDNA-packaging motors, including those of dsDNA/dsRNA bacteriophages, adenoviruses, poxviruses, herpesviruses, mimiviruses, megaviruses, pandoraviruses, and pithoviruses, contain a high-stoichiometry machine composed of multiple components that work cooperatively and sequentially. Thus, it is an ideal target for potent drug development based on the power function of the stoichiometries of target complexes that work sequentially. PMID:27356896

Distribution of Thelastomatoid Nematodes (Nematoda: Oxyurida) in Endemic and Introduced Cockroaches on the Galápagos Island Archipelago, Ecuador.

PubMed

Sinnott, Devinn; Carreno, Ramon A; Herrera, Henri

2015-08-01

The thelastomatoid pinworm fauna (Nematoda: Oxyurida: Thelastomatoidea) was surveyed in 3 endemic species and 6 introduced species of cockroach hosts (Insecta: Blattaria) in the Galápagos Islands, Ecuador. A total of 658 host specimens were examined from preserved collections that had been collected between 1966 and 2003 from 7 islands in the archipelago. Eight species of pinworms were identified from these cockroach hosts, including the dominant species Cephalobellus ovumglutinosus and a Severianoia sp. as well as Leidynema appendiculata, Hammerschmidtiella diesingi, an unidentified Cephalobellus species resembling Cephalobellus magalhaesi, an unidentified Protrellus species closely resembling Protrellus shamimi, and an undescribed Blattophila sp. Five new host records are identified for C. ovumglutinosus including the endemic Galápagos cockroaches Chorisoneura carpenteri, Ischnoptera snodgrassii, and Ischnoptera santacruzensis. These endemics were also infected with an undescribed Blatticola sp. Other species recorded resemble known pinworms from other hosts around the world. Prevalence between islands and between host species was variable, but total prevalence for individual pinworm species was consistently low (<10%). A single host specimen examined was infected with more than 1 pinworm species; otherwise only a single species was observed in each infected host. At least 1 introduced pinworm species carried to the islands via invasive cockroach hosts was present in endemic host species, but several globally widespread introduced pinworm species were absent from endemic cockroaches. Santa Cruz was inhabited by the greatest number of pinworm species, likely due to a higher rate of invasive host introduction. This survey, the first from this region, showed that the distribution and transmission of pinworms in the Galápagos Islands is complex and may provide future models of invertebrate dispersal and speciation in an ecosystem already rich with examples of evolution.

Two-dimensional receptive-field organization in striate cortical neurons of the cat.

PubMed

Sun, M; Bonds, A B

1994-01-01

The two-dimensional organization of receptive fields (RFs) of 44 cells in the cat visual cortex and four cells from the cat LGN was measured by stimulation with either dots or bars of light. The light bars were presented in different positions and orientations centered on the RFs. The RFs found were arbitrarily divided into four general types: Punctate, resembling DOG filters (11%); those resembling Gabor filters (9%); elongate (36%); and multipeaked-type (44%). Elongate RFs, usually found in simple cells, could show more than one excitatory band or bifurcation of excitatory regions. Although regions inhibitory to a given stimulus transition (e.g. ON) often coincided with regions excitatory to the opposite transition (e.g. OFF), this was by no means the rule. Measurements were highly repeatable and stable over periods of at least 1 h. A comparison between measurements made with dots and with bars showed reasonable matches in about 40% of the cases. In general, bar-based measurements revealed larger RFs with more structure, especially with respect to inhibitory regions. Inactivation of lower cortical layers (V-VI) by local GABA injection was found to reduce sharpness of detail and to increase both receptive-field size and noise in upper layer cells, suggesting vertically organized RF mechanisms. Across the population, some cells bore close resemblance to theoretically proposed filters, while others had a complexity that was clearly not generalizable, to the extent that they seemed more suited to detection of specific structures. We would speculate that the broadly varying forms of cat cortical receptive fields result from developmental processes akin to those that form ocular-dominance columns, but on a smaller scale.

Asymmetrical Gene Flow in a Hybrid Zone of Hawaiian Schiedea (Caryophyllaceae) Species with Contrasting Mating Systems

PubMed Central

Wallace, Lisa E.; Culley, Theresa M.; Weller, Stephen G.; Sakai, Ann K.; Kuenzi, Ashley; Roy, Tilottama; Wagner, Warren L.; Nepokroeff, Molly

2011-01-01

Asymmetrical gene flow, which has frequently been documented in naturally occurring hybrid zones, can result from various genetic and demographic factors. Understanding these factors is important for determining the ecological conditions that permitted hybridization and the evolutionary potential inherent in hybrids. Here, we characterized morphological, nuclear, and chloroplast variation in a putative hybrid zone between Schiedea menziesii and S. salicaria, endemic Hawaiian species with contrasting breeding systems. Schiedea menziesii is hermaphroditic with moderate selfing; S. salicaria is gynodioecious and wind-pollinated, with partially selfing hermaphrodites and largely outcrossed females. We tested three hypotheses: 1) putative hybrids were derived from natural crosses between S. menziesii and S. salicaria, 2) gene flow via pollen is unidirectional from S. salicaria to S. menziesii and 3) in the hybrid zone, traits associated with wind pollination would be favored as a result of pollen-swamping by S. salicaria. Schiedea menziesii and S. salicaria have distinct morphologies and chloroplast genomes but are less differentiated at the nuclear loci. Hybrids are most similar to S. menziesii at chloroplast loci, exhibit nuclear allele frequencies in common with both parental species, and resemble S. salicaria in pollen production and pollen size, traits important to wind pollination. Additionally, unlike S. menziesii, the hybrid zone contains many females, suggesting that the nuclear gene responsible for male sterility in S. salicaria has been transferred to hybrid plants. Continued selection of nuclear genes in the hybrid zone may result in a population that resembles S. salicaria, but retains chloroplast lineage(s) of S. menziesii. PMID:21949765

A new species of Pristimantis (Amphibia, Anura, Craugastoridae) from the foothills of the Andes in Manu National Park, southeastern Peru

PubMed Central

Shepack, Alexander; von May, Rudolf; Ttito, Alex; Catenazzi, Alessandro

2016-01-01

Abstract We describe a new species of Pristimantis from the humid sub-montane forest of the Región Cusco in Peru. Pristimantis pluvialis sp. n. was collected in the Kosñipata and Entoro valleys at elevations from 740 to 1110 m a.s.l., near the borders of Manu National Park and within the Huachiperi Haramba Queros Conservation Concession. The new species can be distinguished from other members of the genus Pristimantis by its rostral tubercle, smooth dorsal skin, and by its advertisement call. Pristimantis lacrimosus and Pristimantis waoranii superficially most resemble the new species, but Pristimantis pluvialis sp. n. differs from both species by having a rostral tubercle (absent in Pristimantis waoranii and variable in Pristimantis lacrimosus) and larger size, from Pristimantis lacrimosus by its call emitted at a lower frequency, and from Pristimantis waoranii for its dorsal coloration with dark markings. Two other species have partially overlapping distributions and resemble the new species, Pristimantis mendax and Pristimantis olivaceus, but they produce advertisement calls with much higher dominant frequencies than the advertisement call of the new species. Furthermore, Pristimantis mendax differs from the new species by lacking a rostral tubercle and by having a sigmoid inner tarsal fold, whereas Pristimantis olivaceus differs by being smaller and by having dorsal skin shagreen with scattered tubercles. The new species has snout-vent length of 21.8–26.9 mm in males (n = 12) and 28.8 mm in a single female. PMID:27408563

Primordial odontogenic tumor: Subepithelial expression of Syndecan-1 and Ki-67 suggests origin during early odontogenesis.

PubMed

Bologna-Molina, R; Mikami, T; Pereira-Prado, V; Tapia-Repetto, G; Pires, F R; Carlos, R; Mosqueda-Taylor, A

2018-03-01

Primordial odontogenic tumor (POT) is composed of variably cellular myxoid connective tissue, surrounded by cuboidal to columnar odontogenic epithelium resembling the inner epithelium of the enamel organ, which often invaginates into the underlying connective tissue. The tumor is delimited at least partially by a thin fibrous capsule. It derives from the early stages of tooth development. Syndecan-1 is a heparan sulfate proteoglycan that has a physiological role in several cellular functions, including maintenance of the epithelial architecture, cell-to-cell adhesion and interaction of cells with extracellular matrix, and with diverse growth factors, stimulating cell proliferation. Ki-67 is considered the gold standard as a cell proliferation marker. The aim of this study was to examine the expression of Syndecan-1 and Ki-67 proliferation index in POT and normal tooth germs to better understand the biological behavior of this tumor. Results showed that Syndecan-1 was more intensely expressed in subepithelial mesenchymal areas of POT, in a pattern that resembles the early stages of tooth development. The cell proliferation index (4.1%) suggests that POT is a slow growing tumor. Syndecan-1 expression in tooth germs in late cap and early bell stages was similar to POT, showing immunopositivity in subepithelial mesenchymal condensed areas. The immunohistochemical findings showed a pattern in which the population of subepithelial mesenchymal cells exhibited greater proliferative activity than the central portion of the dental papilla. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd. All rights reserved.

Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase.

PubMed

Li de La Sierra-Gallay, Ines; Collinet, Bruno; Graille, Marc; Quevillon-Cheruel, Sophie; Liger, Dominique; Minard, Philippe; Blondeau, Karine; Henckes, Gilles; Aufrère, Robert; Leulliot, Nicolas; Zhou, Cong-Zhao; Sorel, Isabelle; Ferrer, Jean-Luc; Poupon, Anne; Janin, Joël; van Tilbeurgh, Herman

2004-03-01

The protein product of the YGR205w gene of Saccharomyces cerevisiae was targeted as part of our yeast structural genomics project. YGR205w codes for a small (290 amino acids) protein with unknown structure and function. The only recognizable sequence feature is the presence of a Walker A motif (P loop) indicating a possible nucleotide binding/converting function. We determined the three-dimensional crystal structure of Se-methionine substituted protein using multiple anomalous diffraction. The structure revealed a well known mononucleotide fold and strong resemblance to the structure of small metabolite phosphorylating enzymes such as pantothenate and phosphoribulo kinase. Biochemical experiments show that YGR205w binds specifically ATP and, less tightly, ADP. The structure also revealed the presence of two bound sulphate ions, occupying opposite niches in a canyon that corresponds to the active site of the protein. One sulphate is bound to the P-loop in a position that corresponds to the position of beta-phosphate in mononucleotide protein ATP complex, suggesting the protein is indeed a kinase. The nature of the phosphate accepting substrate remains to be determined. Copyright 2004 Wiley-Liss, Inc.

Analysis of Students' Aptitude to Provide Meaning to Images that Represent Cellular Components at the Molecular Level

PubMed Central

Dahmani, Hassen-Reda; Schneeberger, Patricia

2009-01-01

The number of experimentally derived structures of cellular components is rapidly expanding, and this phenomenon is accompanied by the development of a new semiotic system for teaching. The infographic approach is shifting from a schematic toward a more realistic representation of cellular components. By realistic we mean artist-prepared or computer graphic images that closely resemble experimentally derived structures and are characterized by a low level of styling and simplification. This change brings about a new challenge for teachers: designing course instructions that allow students to interpret these images in a meaningful way. To determine how students deal with this change, we designed several image-based, in-course assessments. The images were highly relevant for the cell biology course but did not resemble any of the images in the teaching documents. We asked students to label the cellular components, describe their function, or both. What we learned from these tests is that realistic images, with a higher apparent level of complexity, do not deter students from investigating their meaning. When given a choice, the students do not necessarily choose the most simplified representation, and they were sensitive to functional indications embedded in realistic images. PMID:19723817

Computational studies of complexation of nitrous oxide by borane-phosphine frustrated Lewis pairs.

PubMed

Gilbert, Thomas M

2012-08-14

Computational studies of complexes Ar(3)B-ONN-PR(3) derived from reactions between borane-phosphine frustrated Lewis pairs and N(2)O reveal several interesting facets. Natural resonance theory calculations support a change in the preferred resonance structure as the Lewis acidity of the borane increases. Potential constitutional isomers where phosphorus binds to oxygen and boron to nitrogen are predicted to be unstable with respect to loss of phosphine oxide and free N(2). Other constitutional isomers represent stationary points on the potential energy surface; most are considerably less stable than the observed complexes, but one is predicted to be as stable. This arises because the dominant resonance form combines alternating charge with the presence of a stabilizing NO double bond. The relationship between Lewis acidity and complex formation for a variety of boranes was explored; the results are consistent with the idea that greater Lewis acidity stabilizes both classical and frustrated Lewis acid-base pairs, but to differing degrees such that both types can entrap N(2)O. Calculations addressing the mechanism of complex formation suggest that N(2)O binds first through the nitrogen to the phosphine phosphorus of the FLP, whereupon boron coordinates the oxygen atom. Studies of the mechanism of the degenerate exchange reaction between (4-F-H(4)C(6))(3)B-ONN-P(t-Bu)(3) and B(C(6)H(4)-4-F)(3), involves a "transition state", with relatively short B-O distances, and so resembles a classical I(a) process. The process involves two barriers, one associated with bringing the incoming borane into proximity with the oxygen, and the other associated with isomerising from a ladle-shaped cis-trans ct conformer to the observed trans-trans tt-type structure. The overall barrier for degenerate exchange was predicted to be between 65 and 110 kJ mol(-1), in fair agreement with experiment. Similar studies of the reaction between (4-F-H(4)C(6))(3)B-ONN-P(t-Bu)(3) and B(C(6)F(5))(3) indicate that this process more closely resembles a classical I(d) process, in that the "transition state" involves long B-O distances. Derivatization of the complexed NNO fragment appears possible; interaction between (F(5)C(6))(3)B-ONN-P(t-Bu)(3) and MeLi suggests stability for the ion pairs (F(5)C(6))(3)B-ON(Me)N-P(t-Bu)(3)(-)/Li(+) and (F(5)C(6))(3)B-ONN(Me)-P(t-Bu)(3)(-)/Li(+).

Cocowood Fibrovascular Tissue System—Another Wonder of Plant Evolution

PubMed Central

González, Oswaldo M.; Nguyen, Khoi A.

2016-01-01

The coconut palm (Cocos nucifera L.) stem tissue (referred to as cocowood in this study) is a complex fibrovascular system that is made up of fibrovascular bundles embedded into a parenchymatous ground tissue. The complex configuration of fibrovascular bundles along with the non-uniform distribution of the material properties likely allow senile coconut stems to optimize their biomechanical performance per unit mass (i.e., mechanical efficiency) and grow into tall, slender, and very flexible plants with minimum resources of biomass and water. For the first time, to the best of the authors' knowledge, this paper examines, from the integral (i.e., stem structure) and macroscopic (i.e., tissue structure) levels of hierarchy, the characteristic triple helix formation depicted by the fibrovascular bundles within the monocotyledon cocowood. The natural course of the tangential orientation of the axial fibrovascular bundles is mapped for the whole cocowood structure by quantifying 264 cocowood discs, corresponding to 41 senile coconut palms estimated to be >70 years old. The observed variations were modeled in this paper by simple equations that partially enabled characterization of the cocowood fibrovascular tissue system. Furthermore, 11 finite element analyses (FEA) were performed over a three dimensional (3D) finite element (FE) model resembling a characteristic coconut palm stem of 25 m in height to analyze the biomaterial reactions produced by the progressive deviation of the tangential fibrovascular bundles on the cocowood mechanical response (i.e., on the material compressive strength and the bending stiffness). The analyses in this study were carried out for the critical wind speed of 23 m/s (i.e., Gale tornado according to the Fujita tornado scale). For each analysis, the characteristic average maxima degree of orientation of the cocowood fibrovascular bundles was varied from 0° to 51°. The acquired results provided a deep understanding of the cocowood optimum fibrovascular tissue system that denotes the natural evolution of the material through millions of years. The knowledge advanced from this study may also serve as concept generators for innovative biomimetic applications to improve current engineered wood products. PMID:27555849

Exp-function method for solving fractional partial differential equations.

PubMed

Zheng, Bin

2013-01-01

We extend the Exp-function method to fractional partial differential equations in the sense of modified Riemann-Liouville derivative based on nonlinear fractional complex transformation. For illustrating the validity of this method, we apply it to the space-time fractional Fokas equation and the nonlinear fractional Sharma-Tasso-Olver (STO) equation. As a result, some new exact solutions for them are successfully established.

The Persistence of Erroneous Familiarity in an Epileptic Male: Challenging Perceptual Theories of Deja Vu Activation

ERIC Educational Resources Information Center

O'Connor, Akira R.; Moulin, Christopher J. A.

2008-01-01

We report the case of a 39-year-old, temporal lobe epileptic male, MH. Prior to complex partial seizure, experienced up to three times a day, MH often experiences an aura experienced as a persistent sensation of deja vu. Data-driven theories of deja vu formation suggest that partial familiarity for the perceived stimulus is responsible for the…

Preliminary study of the interactions caused by crossing shock waves and a turbulent boundary layer

NASA Technical Reports Server (NTRS)

Ketchum, A. C.; Bogdonoff, S. M.; Fernando, E. M.; Batcho, P. F.

1989-01-01

The subject research, the first phase of an extended study of the interaction of crossing shock waves with a turbulent boundary layer, has revealed the complexity of the resulting flow. Detailed surface visualization and mean wall static pressure distributions show little resemblance to the inviscid flow approximation, and the exploratory high frequency measurements show that the flow downstream of the theoretical inviscid shock crossing position has a significant unsteady characteristic. Further developments of the (unsteady) high frequency measurements are required to fully characterize the unsteadiness and the requirements to include this component in flowfield modeling.

Complex discrete dynamics from simple continuous population models.

PubMed

Gamarra, Javier G P; Solé, Ricard V

2002-05-01

Nonoverlapping generations have been classically modelled as difference equations in order to account for the discrete nature of reproductive events. However, other events such as resource consumption or mortality are continuous and take place in the within-generation time. We have realistically assumed a hybrid ODE bidimensional model of resources and consumers with discrete events for reproduction. Numerical and analytical approaches showed that the resulting dynamics resembles a Ricker map, including the doubling route to chaos. Stochastic simulations with a handling-time parameter for indirect competition of juveniles may affect the qualitative behaviour of the model.

Electronic Chemotherapy Order Entry: A Major Cancer Center's Implementation

PubMed Central

Sklarin, Nancy T.; Granovsky, Svetlana; O'Reilly, Eileen M.; Zelenetz, Andrew D.

2011-01-01

Implementation of a computerized provider order entry system for complex chemotherapy regimens at a large cancer center required intense effort from a multidisciplinary team of clinical and systems experts with experience in all facets of the chemotherapy process. The online tools had to resemble the paper forms used at the time and parallel the successful established process as well as add new functionality. Close collaboration between the institution and the vendor was necessary. This article summarizes the institutional efforts, challenges, and collaborative processes that facilitated universal chemotherapy computerized electronic order entry across multiple sites during a period of several years. PMID:22043182

Electronic Chemotherapy Order Entry: A Major Cancer Center's Implementation.

PubMed

Sklarin, Nancy T; Granovsky, Svetlana; O'Reilly, Eileen M; Zelenetz, Andrew D

2011-07-01

Implementation of a computerized provider order entry system for complex chemotherapy regimens at a large cancer center required intense effort from a multidisciplinary team of clinical and systems experts with experience in all facets of the chemotherapy process. The online tools had to resemble the paper forms used at the time and parallel the successful established process as well as add new functionality. Close collaboration between the institution and the vendor was necessary. This article summarizes the institutional efforts, challenges, and collaborative processes that facilitated universal chemotherapy computerized electronic order entry across multiple sites during a period of several years.

Dimensionality-Driven Metal-Insulator Transition in Spin-Orbit-Coupled SrIrO3

NASA Astrophysics Data System (ADS)

Schütz, P.; Di Sante, D.; Dudy, L.; Gabel, J.; Stübinger, M.; Kamp, M.; Huang, Y.; Capone, M.; Husanu, M.-A.; Strocov, V. N.; Sangiovanni, G.; Sing, M.; Claessen, R.

2017-12-01

Upon reduction of the film thickness we observe a metal-insulator transition in epitaxially stabilized, spin-orbit-coupled SrIrO3 ultrathin films. By comparison of the experimental electronic dispersions with density functional theory at various levels of complexity we identify the leading microscopic mechanisms, i.e., a dimensionality-induced readjustment of octahedral rotations, magnetism, and electronic correlations. The astonishing resemblance of the band structure in the two-dimensional limit to that of bulk Sr2 IrO4 opens new avenues to unconventional superconductivity by "clean" electron doping through electric field gating.

Electrostatic formation of liquid marbles and agglomerates

NASA Astrophysics Data System (ADS)

Liyanaarachchi, K. R.; Ireland, P. M.; Webber, G. B.; Galvin, K. P.

2013-07-01

We report observations of a sudden, explosive release of electrostatically charged 100 μm glass beads from a particle bed. These cross an air gap of several millimeters, are engulfed by an approaching pendant water drop, and form a metastable spherical agglomerate on the bed surface. The stability transition of the particle bed is explained by promotion of internal friction by in-plane electrostatic stresses. The novel agglomerates formed this way resemble the "liquid marbles" formed by coating a drop with hydrophobic particles. Complex multi-layered agglomerates may also be produced by this method, with potential industrial, pharmaceutical, environmental, and biological applications.

Detrended Partial-Cross-Correlation Analysis: A New Method for Analyzing Correlations in Complex System

PubMed Central

Yuan, Naiming; Fu, Zuntao; Zhang, Huan; Piao, Lin; Xoplaki, Elena; Luterbacher, Juerg

2015-01-01

In this paper, a new method, detrended partial-cross-correlation analysis (DPCCA), is proposed. Based on detrended cross-correlation analysis (DCCA), this method is improved by including partial-correlation technique, which can be applied to quantify the relations of two non-stationary signals (with influences of other signals removed) on different time scales. We illustrate the advantages of this method by performing two numerical tests. Test I shows the advantages of DPCCA in handling non-stationary signals, while Test II reveals the “intrinsic” relations between two considered time series with potential influences of other unconsidered signals removed. To further show the utility of DPCCA in natural complex systems, we provide new evidence on the winter-time Pacific Decadal Oscillation (PDO) and the winter-time Nino3 Sea Surface Temperature Anomaly (Nino3-SSTA) affecting the Summer Rainfall over the middle-lower reaches of the Yangtze River (SRYR). By applying DPCCA, better significant correlations between SRYR and Nino3-SSTA on time scales of 6 ~ 8 years are found over the period 1951 ~ 2012, while significant correlations between SRYR and PDO on time scales of 35 years arise. With these physically explainable results, we have confidence that DPCCA is an useful method in addressing complex systems. PMID:25634341

Cerebral blood flow during paroxysmal EEG activation induced by sleep in patients with complex partial seizures

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

Gozukirmizi, E.; Meyer, J.S.; Okabe, T.

1982-01-01

Cerebral blood flow (CBF) measurements were combined with sleep polysomnography in nine patients with complex partial seizures. Two methods were used: the 133Xe method for measuring regional (rCBF) and the stable xenon CT method for local (LCBF). Compared to nonepileptic subjects, who show diffuse CBF decreases during stages I-II, non-REM sleep onset, patients with complex partial seizures show statistically significant increases in CBF which are maximal in regions where the EEG focus is localized and are predominantly seen in one temporal region but are also propagated to other cerebral areas. Both CBF methods gave comparable results, but greater statistical significancemore » was achieved by stable xenon CT methodology. CBF increases are more diffuse than predicted by EEG paroxysmal activity recorded from scalp electrodes. An advantage of the 133Xe inhalation method was achievement of reliable data despite movement of the head. This was attributed to the use of a helmet which maintained the probes approximated to the scalp. Disadvantages were poor resolution (7 cm3) and two-dimensional information. The advantage of stable xenon CT method is excellent resolution (80 mm3) in three dimensions, but a disadvantage is that movement of the head in patients with seizure disorders may limit satisfactory measurements.« less

Online sequential Monte Carlo smoother for partially observed diffusion processes

NASA Astrophysics Data System (ADS)

Gloaguen, Pierre; Étienne, Marie-Pierre; Le Corff, Sylvain

2018-12-01

This paper introduces a new algorithm to approximate smoothed additive functionals of partially observed diffusion processes. This method relies on a new sequential Monte Carlo method which allows to compute such approximations online, i.e., as the observations are received, and with a computational complexity growing linearly with the number of Monte Carlo samples. The original algorithm cannot be used in the case of partially observed stochastic differential equations since the transition density of the latent data is usually unknown. We prove that it may be extended to partially observed continuous processes by replacing this unknown quantity by an unbiased estimator obtained for instance using general Poisson estimators. This estimator is proved to be consistent and its performance are illustrated using data from two models.

Effect of facial self-resemblance on the startle response and subjective ratings of erotic stimuli in heterosexual men.

PubMed

Lass-Hennemann, Johanna; Deuter, Christian E; Kuehl, Linn K; Schulz, Andre; Blumenthal, Terry D; Schachinger, Hartmut

2011-10-01

Cues of kinship are predicted to increase prosocial behavior due to the benefits of inclusive fitness, but to decrease approach motivation due to the potential costs of inbreeding. Previous studies have shown that facial resemblance, a putative cue of kinship, increases prosocial behavior. However, the effects of facial resemblance on mating preferences are equivocal, with some studies finding that facial resemblance decreases sexual attractiveness ratings, while other studies show that individuals choose mates partly on the basis of similarity. To further investigate this issue, a psychophysiological measure of affective processing, the startle response, was used in this study, assuming that differences in approach motivation to erotic pictures will modulate startle. Male volunteers (n = 30) viewed 30 pictures of erotic female nudes while startle eyeblink responses were elicited by acoustic noise probes. The female nude pictures were digitally altered so that the face either resembled the male participant or another participant, or were not altered. Non-nude neutral pictures were also included. Importantly, the digital alteration was undetected by the participants. Erotic pictures were rated as being pleasant and clearly reduced startle eyeblink magnitude as compared to neutral pictures. Participants showed greater startle inhibition to self-resembling than to other-resembling or non-manipulated female nude pictures, but subjective pleasure and arousal ratings did not differ among the three erotic picture categories. Our data suggest that visual facial resemblance of opposite-sex nudes increases approach motivation in men, and that this effect was not due to their conscious evaluation of the erotic stimuli.

Subpopulation of store-operated Ca2+ channels regulate Ca2+-induced Ca2+ release in non-excitable cells.

PubMed

Yao, Jian; Li, Qin; Chen, Jin; Muallem, Shmuel

2004-05-14

Ca2+-induced Ca2+ release (CICR) is a well characterized activity in skeletal and cardiac muscles mediated by the ryanodine receptors. The present study demonstrates CICR in the non-excitable parotid acinar cells, which resembles the mechanism described in cardiac myocytes. Partial depletion of internal Ca2+ stores leads to a minimal activation of Ca2+ influx. Ca2+ influx through this pathway results in an explosive mobilization of Ca2+ from the majority of the stores by CICR. Thus, stimulation of parotid acinar cells in Ca2+ -free medium with 0.5 microm carbachol releases approximately 5% of the Ca2+ mobilizable by 1 mm carbachol. Addition of external Ca2+ induced the same Ca2+ release observed in maximally stimulated cells. Similar results were obtained by a short treatment with 2.5-10 microm cyclopiazonic acid, an inhibitor of the sarco/endoplasmic reticulum Ca2+ ATPase pump. The Ca2+ release induced by the addition of external Ca2+ was largely independent of IP(3)Rs because it was reduced by only approximately 30% by the inhibition of the inositol 1,4,5-trisphosphate receptors with caffeine or heparin. Measurements of Ca2+ -activated outward current and [Ca2+](i) suggested that most CICR triggered by Ca2+ influx occurred away from the plasma membrane. Measurement of the response to several concentrations of cyclopiazonic acid revealed that Ca2+ influx that regulates CICR is associated with a selective portion of the internal Ca2+ pool. The minimal activation of Ca2+ influx by partial store depletion was confirmed by the measurement of Mn2+ influx. Inhibition of Ca2+ influx with SKF96365 or 2-aminoethoxydiphenyl borate prevented activation of CICR observed on addition of external Ca2+. These findings provide evidence for activation of CICR by Ca2+ influx in non-excitable cells, demonstrate a previously unrecognized role for Ca2+ influx in triggering CICR, and indicate that CICR in non-excitable cells resembles CICR in cardiac myocytes with the exception that in cardiac cells Ca2+ influx is mediated by voltage-regulated Ca2+ channels whereas in non-excitable cells Ca2+ influx is mediated by store-operated channels.

Microglomerular Synaptic Complexes in the Sky-Compass Network of the Honeybee Connect Parallel Pathways from the Anterior Optic Tubercle to the Central Complex.

PubMed

Held, Martina; Berz, Annuska; Hensgen, Ronja; Muenz, Thomas S; Scholl, Christina; Rössler, Wolfgang; Homberg, Uwe; Pfeiffer, Keram

2016-01-01

While the ability of honeybees to navigate relying on sky-compass information has been investigated in a large number of behavioral studies, the underlying neuronal system has so far received less attention. The sky-compass pathway has recently been described from its input region, the dorsal rim area (DRA) of the compound eye, to the anterior optic tubercle (AOTU). The aim of this study is to reveal the connection from the AOTU to the central complex (CX). For this purpose, we investigated the anatomy of large microglomerular synaptic complexes in the medial and lateral bulbs (MBUs/LBUs) of the lateral complex (LX). The synaptic complexes are formed by tubercle-lateral accessory lobe neuron 1 (TuLAL1) neurons of the AOTU and GABAergic tangential neurons of the central body's (CB) lower division (TL neurons). Both TuLAL1 and TL neurons strongly resemble neurons forming these complexes in other insect species. We further investigated the ultrastructure of these synaptic complexes using transmission electron microscopy. We found that single large presynaptic terminals of TuLAL1 neurons enclose many small profiles (SPs) of TL neurons. The synaptic connections between these neurons are established by two types of synapses: divergent dyads and divergent tetrads. Our data support the assumption that these complexes are a highly conserved feature in the insect brain and play an important role in reliable signal transmission within the sky-compass pathway.

Alpha-lactalbumin unfolding is not sufficient to cause apoptosis, but is required for the conversion to HAMLET (human alpha-lactalbumin made lethal to tumor cells).

PubMed

Svensson, Malin; Fast, Jonas; Mossberg, Ann-Kristin; Düringer, Caroline; Gustafsson, Lotta; Hallgren, Oskar; Brooks, Charles L; Berliner, Lawrence; Linse, Sara; Svanborg, Catharina

2003-12-01

HAMLET (human alpha-lactalbumin made lethal to tumor cells) is a complex of human alpha-lactalbumin and oleic acid (C18:1:9 cis) that kills tumor cells by an apoptosis-like mechanism. Previous studies have shown that a conformational change is required to form HAMLET from alpha-lactalbumin, and that a partially unfolded conformation is maintained in the HAMLET complex. This study examined if unfolding of alpha-lactalbumin is sufficient to induce cell death. We used the bovine alpha-lactalbumin Ca(2+) site mutant D87A, which is unable to bind Ca(2+), and thus remains partially unfolded regardless of solvent conditions. The D87A mutant protein was found to be inactive in the apoptosis assay, but could readily be converted to a HAMLET-like complex in the presence of oleic acid. BAMLET (bovine alpha-lactalbumin made lethal to tumor cells) and D87A-BAMLET complexes were both able to kill tumor cells. This activity was independent of the Ca(2+)site, as HAMLET maintained a high affinity for Ca(2+) but D87A-BAMLET was active with no Ca(2+) bound. We conclude that partial unfolding of alpha-lactalbumin is necessary but not sufficient to trigger cell death, and that the activity of HAMLET is defined both by the protein and the lipid cofactor. Furthermore, a functional Ca(2+)-binding site is not required for conversion of alpha-lactalbumin to the active complex or to cause cell death. This suggests that the lipid cofactor stabilizes the altered fold without interfering with the Ca(2+)site.

EzyAmp signal amplification cascade enables isothermal detection of nucleic acid and protein targets.

PubMed

Linardy, Evelyn M; Erskine, Simon M; Lima, Nicole E; Lonergan, Tina; Mokany, Elisa; Todd, Alison V

2016-01-15

Advancements in molecular biology have improved the ability to characterize disease-related nucleic acids and proteins. Recently, there has been an increasing desire for tests that can be performed outside of centralised laboratories. This study describes a novel isothermal signal amplification cascade called EzyAmp (enzymatic signal amplification) that is being developed for detection of targets at the point of care. EzyAmp exploits the ability of some restriction endonucleases to cleave substrates containing nicks within their recognition sites. EzyAmp uses two oligonucleotide duplexes (partial complexes 1 and 2) which are initially cleavage-resistant as they lack a complete recognition site. The recognition site of partial complex 1 can be completed by hybridization of a triggering oligonucleotide (Driver Fragment 1) that is generated by a target-specific initiation event. Binding of Driver Fragment 1 generates a completed complex 1, which upon cleavage, releases Driver Fragment 2. In turn, binding of Driver Fragment 2 to partial complex 2 creates completed complex 2 which when cleaved releases additional Driver Fragment 1. Each cleavage event separates fluorophore quencher pairs resulting in an increase in fluorescence. At this stage a cascade of signal production becomes independent of further target-specific initiation events. This study demonstrated that the EzyAmp cascade can facilitate detection and quantification of nucleic acid targets with sensitivity down to aM concentration. Further, the same cascade detected VEGF protein with a sensitivity of 20nM showing that this universal method for amplifying signal may be linked to the detection of different types of analytes in an isothermal format. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Neutral complexes as oxidants for the reduced form of parsley (Petroselinum crispum) [2Fe--2S] ferredoxin. Evidence for partial blocking by redox-inactive Cr(III) complexes.

PubMed Central

Adzamli, I K; Kim, H O; Sykes, A G

1982-01-01

The 1 : 1 reactions of three neutral Co(III) oxidants, Co(acac)3, Co(NH3)3(NO2)3 and Co(acac)2(NH3)(NO2), with reduced parsley (Petroselinum crispum) [2Fe--2S] ferredoxin (which carries a substantial negative charge), have been studied at 25 degrees C, pH 8.0 (Tris/HCl), I0.10 (NaCl). Whereas it has previously been demonstrated that with Co(NH3)6+ as oxidant the reaction if completely blocked by redox-inactive Cr(NH3)63+, the neutral oxidants are only partially blocked by this same complex. The effects of three Cr(III) complexes, Cr(NH3)63+%, Cr(en)33+ and (en)2Cr . mu(OH,O2CCH3) . CR(en)24+ have been investigated. Kinetic data for the response of 3+, neutral, as well as 1--oxidants to the presence of 3+ (and 4+) Cr(III) complexes can now be rationalized in terms of a single functional site on the protein for electron transfer. Electrostatics have a significant influence on association at this site. PMID:7115307

Phenomenology of hallucinations, illusions, and delusions as part of seizure semiology.

PubMed

Kasper, B S; Kasper, E M; Pauli, E; Stefan, H

2010-05-01

In partial epilepsy, a localized hypersynchronous neuronal discharge evolving into a partial seizure affecting a particular cortical region or cerebral subsystem can give rise to subjective symptoms, which are perceived by the affected person only, that is, ictal hallucinations, illusions, or delusions. When forming the beginning of a symptom sequence leading to impairment of consciousness and/or a classic generalized seizure, these phenomena are referred to as an epileptic aura, but they also occur in isolation. They often manifest in the fully awake state, as part of simple partial seizures, but they also can be associated to different degrees of disturbed consciousness. Initial ictal symptoms often are closely related to the physiological functions of the cortical circuit involved and, therefore, can provide localizing information. When brain regions related to sensory integration are involved, the seizure discharge can cause specific kinds of hallucinations, for example, visual, auditory, gustatory, olfactory, and cutaneous sensory sensations. In addition to these elementary sensory perceptions, quite complex hallucinations related to a partial seizure can arise, for example, perception of visual scenes or hearing music. By involving psychic and emotional spheres of human perception, many seizures also give rise to hallucinatory emotional states (e.g., fear or happiness) or even more complex hallucinations (e.g., visuospatial phenomena), illusions (e.g., déjà vu, out-of-body experience), or delusional beliefs (e.g., identity change) that often are not easily recognized as epileptic. Here we suggest a classification into elementary sensory, complex sensory, and complex integratory seizure symptoms. Epileptic hallucinations, illusions, and delusions shine interesting light on the physiology and functional anatomy of brain regions involved and their functions in the human being. This article, in which 10 cases are described, introduces the fascinating phenomenology of subjective seizure symptoms. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Consciousness and epilepsy: why are complex-partial seizures complex?

PubMed Central

Englot, Dario J.; Blumenfeld, Hal

2010-01-01

Why do complex-partial seizures in temporal lobe epilepsy (TLE) cause a loss of consciousness? Abnormal function of the medial temporal lobe is expected to cause memory loss, but it is unclear why profoundly impaired consciousness is so common in temporal lobe seizures. Recent exciting advances in behavioral, electrophysiological, and neuroimaging techniques spanning both human patients and animal models may allow new insights into this old question. While behavioral automatisms are often associated with diminished consciousness during temporal lobe seizures, impaired consciousness without ictal motor activity has also been described. Some have argued that electrographic lateralization of seizure activity to the left temporal lobe is most likely to cause impaired consciousness, but the evidence remains equivocal. Other data correlates ictal consciousness in TLE with bilateral temporal lobe involvement of seizure spiking. Nevertheless, it remains unclear why bilateral temporal seizures should impair responsiveness. Recent evidence has shown that impaired consciousness during temporal lobe seizures is correlated with large-amplitude slow EEG activity and neuroimaging signal decreases in the frontal and parietal association cortices. This abnormal decreased function in the neocortex contrasts with fast polyspike activity and elevated cerebral blood flow in limbic and other subcortical structures ictally. Our laboratory has thus proposed the “network inhibition hypothesis,” in which seizure activity propagates to subcortical regions necessary for cortical activation, allowing the cortex to descend into an inhibited state of unconsciousness during complex-partial temporal lobe seizures. Supporting this hypothesis, recent rat studies during partial limbic seizures have shown that behavioral arrest is associated with frontal cortical slow waves, decreased neuronal firing, and hypometabolism. Animal studies further demonstrate that cortical deactivation and behavioral changes depend on seizure spread to subcortical structures including the lateral septum. Understanding the contributions of network inhibition to impaired consciousness in TLE is an important goal, as recurrent limbic seizures often result in cortical dysfunction during and between epileptic events that adversely affects patients’ quality of life. PMID:19818900

Episodic growth of a Late Cretaceous and Paleogene intrusive complex of pegmatitic leucogranite, Ruby Mountains core complex, Nevada, USA

USGS Publications Warehouse

Howard, Keith A.; Wooden, J.L.; Barnes, C.G.; Premo, W.R.; Snoke, A.W.; Lee, S.-Y.

2011-01-01

Gneissic pegmatitic leucogranite forms a dominant component (>600 km3) of the midcrustal infrastructure of the Ruby Mountains–East Humboldt Range core complex (Nevada, USA), and was assembled and modified episodically into a batholithic volume by myriad small intrusions from ca. 92 to 29 Ma. This injection complex consists of deformed sheets and other bodies emplaced syntectonically into a stratigraphic framework of marble, calc-silicate rocks, quartzite, schist, and other granitoids. Bodies of pegmatitic granite coalesce around host-rock remnants, which preserve relict or ghost stratigraphy, thrusts, and fold nappes. Intrusion inflated but did not disrupt the host-rock structure. The pegmatitic granite increases proportionally downward from structurally high positions to the bottoms of 1-km-deep canyons where it constitutes 95%–100% of the rock. Zircon and monazite dated by U-Pb (sensitive high-resolution ion microprobe, SHRIMP) for this rock type cluster diffusely at ages near 92, 82(?), 69, 38, and 29 Ma, and indicate successive or rejuvenated igneous crystallization multiple times over long periods of the Late Cretaceous and the Paleogene. Initial partial melting of unexposed pelites may have generated granite forerunners, which were remobilized several times in partial melting events. Sources for the pegmatitic granite differed isotopically from sources of similar-aged interleaved equigranular granites. Dominant Late Cretaceous and fewer Paleogene ages recorded from some pegmatitic granite samples, and Paleogene-only ages from the two structurally deepest samples, together with varying zircon trace element contents, suggest several disparate ages of final emplacement or remobilization of various small bodies. Folded sills that merge with dikes that cut the same folds suggest that there may have been in situ partial remobilization. The pegmatitic granite intrusions represent prolonged and recurrent generation, assembly, and partial melting modification of a batholithic volume even while the regional tectonic environment varied dramatically from contractile thickening to extension and mafic underplating.

Zircon U-Pb ages and Hf-O isotopic composition of migmatites from the Zanjan-Takab complex, NW Iran: Constraints on partial melting of metasediments

NASA Astrophysics Data System (ADS)

Moghadam, Hadi Shafaii; Li, Xian-Hua; Stern, Robert J.; Ghorbani, Ghasem; Bakhshizad, Farzaneh

2016-01-01

We study migmatites and other metamorphic rocks in the Zanjan-Takab region of NW Iran and use these results to report the first evidence of Oligocene core complex formation in Iran. Four samples of migmatites associated with paragneisses, including leucosomes and associated para-amphibolite melanosomes were selected for U-Pb dating and Hf-O isotopic analysis. Zircon cores - interpreted as originally detrital zircons - have variable ages that peak at ca. 100-110 Ma, but their sedimentation age - indicated by the youngest 206Pb/238U ages - is ca. 35-40 Ma. New zircons associated with incipient melting occur as overgrowths around zircon cores and/or as newly grown grains. Morphologies and internal structures suggest that rim growth and formation of new zircons were associated with partial melting. All four samples contain zircons with rims that yield 206Pb/238U ages of 28-25 Ma, indicating that partial melting occurred in Late Oligocene time. δ18O values for zircon rims vary between 8.2 and 12.3‰, significantly higher than expected for mantle inputs (δ18O 6‰) and consistent with equilibrium with surface materials. Zircon rims yield εHf(t) between 2.2 and 12.4 and two-stage Hf model ages of 448-562 Ma, indicating that the region is underlain by Cadomian-Caledonian crust. According to the Hf-O isotopic values, the main mechanism forming zircon rims was dissolution of pre-existing detrital zircons with reprecipitation of new zircon shortly thereafter. Oligocene ages indicate that partial melting accompanied core complex formation in the Zanjan-Takab region. Extension, melting, and core complex formation in south-central Iran are Eocene in age, but younger ages of Oligocene-Miocene in NW Iran and Turkey indicate that extension was distributed throughout the region during Cenozoic time.

Older Adults' Trait Impressions of Faces Are Sensitive to Subtle Resemblance to Emotions

PubMed Central

Zebrowitz, Leslie A.

2013-01-01

Younger adults (YA) attribute emotion-related traits to people whose neutral facial structure resembles an emotion (emotion overgeneralization). The fact that older adults (OA) show deficits in accurately labeling basic emotions suggests that they may be relatively insensitive to variations in the emotion resemblance of neutral expression faces that underlie emotion overgeneralization effects. On the other hand, the fact that OA, like YA, show a ‘pop-out’ effect for anger, more quickly locating an angry than a happy face in a neutral array, suggests that both age groups may be equally sensitive to emotion resemblance. We used computer modeling to assess the degree to which neutral faces objectively resembled emotions and assessed whether that resemblance predicted trait impressions. We found that both OA and YA showed anger and surprise overgeneralization in ratings of danger and naiveté, respectively, with no significant differences in the strength of the effects for the two age groups. These findings suggest that well-documented OA deficits on emotion recognition tasks may be more due to processing demands than to an insensitivity to the social affordances of emotion expressions. PMID:24058225

Custom-Molded Foot-Orthosis Intervention and Multisegment Medial Foot Kinematics During Walking

PubMed Central

Cobb, Stephen C.; Tis, Laurie L.; Johnson, Jeffrey T.; Wang, Yong “Tai”; Geil, Mark D.

2011-01-01

Context: Foot-orthosis (FO) intervention to prevent and treat numerous lower extremity injuries is widely accepted clinically. However, the results of quantitative gait analyses have been equivocal. The foot models used, participants receiving intervention, and orthoses used might contribute to the variability. Objective: To investigate the effect of a custom-molded FO intervention on multisegment medial foot kinematics during walking in participants with low-mobile foot posture. Design: Crossover study. Setting: University biomechanics and ergonomics laboratory. Patients or Other Participants: Sixteen participants with low-mobile foot posture (7 men, 9 women) were assigned randomly to 1 of 2 FO groups. Interventions : After a 2-week period to break in the FOs, individuals participated in a gait analysis that consisted of 5 successful walking trials (1.3 to 1.4 m/s) during no-FO and FO conditions. Main Outcome Measure(s): Three-dimensional displacements during 4 subphases of stance (loading response, mid-stance, terminal stance, preswing) were computed for each multisegment foot model articulation. Results: Repeated-measures analyses of variance (ANOVAs) revealed that rearfoot complex dorsiflexion displacement during midstance was greater in the FO than the no-FO condition (F1,14 = 5.24, P = .04, partial η2 = 0.27). Terminal stance repeated-measures ANOVA results revealed insert-by-insert condition interactions for the first metatarsophalangeal joint complex (F1,14 = 7.87, P = .01, partial η2 = 0.36). However, additional follow-up analysis did not reveal differences between the no-FO and FO conditions for the balanced traditional orthosis (F1,14 = 4.32, P = .08, partial η2 = 0.38) or full-contact orthosis (F1,14 = 4.10, P = .08, partial η2 = 0.37). Conclusions: Greater rearfoot complex dorsiflexion during midstance associated with FO intervention may represent improved foot kinematics in people with low-mobile foot postures. Furthermore, FO intervention might partially correct dys-functional kinematic patterns associated with low-mobile foot postures. PMID:21944067

A new routing enhancement scheme based on node blocking state advertisement in wavelength-routed WDM networks

NASA Astrophysics Data System (ADS)

Hu, Peigang; Jin, Yaohui; Zhang, Chunlei; He, Hao; Hu, WeiSheng

2005-02-01

The increasing switching capacity brings the optical node with considerable complexity. Due to the limitation in cost and technology, an optical node is often designed with partial switching capability and partial resource sharing. It means that the node is of blocking to some extent, for example multi-granularity switching node, which in fact is a structure using pass wavelength to reduce the dimension of OXC, and partial sharing wavelength converter (WC) OXC. It is conceivable that these blocking nodes will have great effects on the problem of routing and wavelength assignment. Some previous works studied the blocking case, partial WC OXC, using complicated wavelength assignment algorithm. But the complexities of these schemes decide them to be not in practice in real networks. In this paper, we propose a new scheme based on the node blocking state advertisement to reduce the retry or rerouting probability and improve the efficiency of routing in the networks with blocking nodes. In the scheme, node blocking state are advertised to the other nodes in networks, which will be used for subsequent route calculation to find a path with lowest blocking probability. The performance of the scheme is evaluated using discrete event model in 14-node NSFNET, all the nodes of which employ a kind of partial sharing WC OXC structure. In the simulation, a simple First-Fit wavelength assignment algorithm is used. The simulation results demonstrate that the new scheme considerably reduces the retry or rerouting probability in routing process.

Multiple subpial transection for intractable partial epilepsy: an international meta-analysis.

PubMed

Spencer, Susan S; Schramm, Johannes; Wyler, Allen; O'Connor, Michael; Orbach, Darren; Krauss, Gregory; Sperling, Michael; Devinsky, Orrin; Elger, Christian; Lesser, Ronald; Mulligan, Lisa; Westerveld, Michael

2002-02-01

Because the number and variety of patients at any single facility is not sufficient for clinical or statistical analysis, data from six major epilepsy centers that performed multiple subpial transections (MSTs) for medically intractable epilepsy were collected. A meta-analysis was performed to elucidate the indications and outcome, and to assess the results of the procedure. Overall, 211 patients were represented with data regarding preoperative evaluation, procedures, seizure types and frequencies before and after surgery, postoperative deficits, and demographic information. Fifty-three patients underwent MST without resection. In patients with MST plus resection, excellent outcome (>95% reduction in seizure frequency) was obtained in 87% of patients for generalized seizures, 68% for complex partial seizures, and 68% for simple partial seizures. For the patients who underwent MST without resection, the rate of excellent outcome was only slightly lower, at 71% for generalized, 62% for complex partial, and 63% for simple partial seizures. EEG localization, age at epilepsy onset, duration of epilepsy, and location of MST were not significant predictors of outcome for any kinds of seizures after MST, with or without resection. New neurologic deficits were found in 47 patients overall, comparable in MST with resection (23%) or without (19%). These preliminary results suggest that MST has efficacy by itself, with minimal neurologic compromise, in cases in which resective surgery cannot be used to treat uncontrolled epilepsy. MST should be investigated as a stand-alone procedure to allow further development of criteria and predictive factors for outcome.

The ATRX syndrome protein forms a chromatin-remodeling complex with Daxx and localizes in promyelocytic leukemia nuclear bodies.

PubMed

Xue, Yutong; Gibbons, Richard; Yan, Zhijiang; Yang, Dafeng; McDowell, Tarra L; Sechi, Salvatore; Qin, Jun; Zhou, Sharleen; Higgs, Doug; Wang, Weidong

2003-09-16

ATRX syndrome is characterized by X-linked mental retardation associated with alpha-thalassemia. The gene mutated in this disease, ATRX, encodes a plant homeodomain-like finger and a SWI2/SNF2-like ATPase motif, both of which are often found in chromatin-remodeling enzymes, but ATRX has not been characterized biochemically. By immunoprecipitation from HeLa extract, we found that ATRX is in a complex with transcription cofactor Daxx. The following evidence supports that ATRX and Daxx are components of an ATP-dependent chromatin-remodeling complex: (i) Daxx and ATRX can be coimmunoisolated by antibodies specific for each protein; (ii) a proportion of Daxx cofractionates with ATRX as a complex of 1 MDa by gel-filtration analysis; (iii) in extract from cells of a patient with ATRX syndrome, the level of the Daxx-ATRX complex is correspondingly reduced; (iv) a proportion of ATRX and Daxx colocalize in promyelocytic leukemia nuclear bodies, with which Daxx had previously been located; and (v) the ATRX complex displays ATP-dependent activities that resemble those of other chromatin-remodeling complexes, including triple-helix DNA displacement and alteration of mononucleosome disruption patterns. But unlike the previously described SWI/SNF or NURD complexes, the ATRX complex does not randomize DNA phasing of the mononucleosomes, suggesting that it may remodel chromatin differently. Taken together, the results suggest that ATRX functions in conjunction with Daxx in a novel chromatin-remodeling complex. The defects in ATRX syndrome may result from inappropriate expression of genes controlled by this complex.

Molding cork sheets to complex shapes

NASA Technical Reports Server (NTRS)

Sharpe, M. H.; Simpson, W. G.; Walker, H. M.

1977-01-01

Partially cured cork sheet is easily formed to complex shapes and then final-cured. Temperature and pressure levels required for process depend upon resin system used and final density and strength desired. Sheet can be bonded to surface during final cure, or can be first-formed in mold and bonded to surface in separate step.

Computer-Based Assessment of Complex Problem Solving: Concept, Implementation, and Application

ERIC Educational Resources Information Center

Greiff, Samuel; Wustenberg, Sascha; Holt, Daniel V.; Goldhammer, Frank; Funke, Joachim

2013-01-01

Complex Problem Solving (CPS) skills are essential to successfully deal with environments that change dynamically and involve a large number of interconnected and partially unknown causal influences. The increasing importance of such skills in the 21st century requires appropriate assessment and intervention methods, which in turn rely on adequate…

Infrared Photodissociation Spectroscopy of Metal Ion -WATER Complexes

NASA Astrophysics Data System (ADS)

Bandyopadhyay, B.; Carnegie, P. D.; Duncan, M. A.

2011-06-01

Metal ion-water complexes are produced in a supersonic expansion cluster source via laser vaporization technique. Infrared photodissociation spectroscopy has been performed in the O-H stretch region. DFT calculations have also been carried out to obtain the structures and vibrational frequencies. Infrared spectra show partially resolved rotational structures which will be analyzed.

Chemical modification of projectile residues and target material in a MEMIN cratering experiment

NASA Astrophysics Data System (ADS)

Ebert, Matthias; Hecht, Lutz; Deutsch, Alexander; Kenkmann, Thomas

2013-01-01

In the context of the MEMIN project, a hypervelocity cratering experiment has been performed using a sphere of the iron meteorite Campo del Cielo as projectile accelerated to 4.56 km s-1, and a block of Seeberger sandstone as target material. The ejecta, collected in a newly designed catcher, are represented by (1) weakly deformed, (2) highly deformed, and (3) highly shocked material. The latter shows shock-metamorphic features such as planar deformation features (PDF) in quartz, formation of diaplectic quartz glass, partial melting of the sandstone, and partially molten projectile, mixed mechanically and chemically with target melt. During mixing of projectile and target melts, the Fe of the projectile is preferentially partitioned into target melt to a greater degree than Ni and Co yielding a Fe/Ni that is generally higher than Fe/Ni in the projectile. This fractionation results from the differing siderophile properties, specifically from differences in reactivity of Fe, Ni, and Co with oxygen during projectile-target interaction. Projectile matter was also detected in shocked quartz grains. The average Fe/Ni of quartz with PDF (about 20) and of silica glasses (about 24) are in contrast to the average sandstone ratio (about 422), but resembles the Fe/Ni-ratio of the projectile (about 14). We briefly discuss possible reasons of projectile melting and vaporization in the experiment, in which the calculated maximum shock pressure does not exceed 55 GPa.

Next Generation Real-Time Systems: Investigating the Potential of Partial-Solution Tasks.

DTIC Science & Technology

1994-12-01

insufficient for dealing with the complexities of next-generation real - time systems . New methods of intelligent control must be developed for guaranteeing...on-time task completion for real - time systems that are faced with unpredictable and dynamically changing requirements. Implementing real-time...tasks by experimentally measuring the change in performance of 11 simulated real - time systems when converted from all-or-nothing tasks to partial

Some partial-unit-memory convolutional codes

NASA Technical Reports Server (NTRS)

Abdel-Ghaffar, K.; Mceliece, R. J.; Solomon, G.

1991-01-01

The results of a study on a class of error correcting codes called partial unit memory (PUM) codes are presented. This class of codes, though not entirely new, has until now remained relatively unexplored. The possibility of using the well developed theory of block codes to construct a large family of promising PUM codes is shown. The performance of several specific PUM codes are compared with that of the Voyager standard (2, 1, 6) convolutional code. It was found that these codes can outperform the Voyager code with little or no increase in decoder complexity. This suggests that there may very well be PUM codes that can be used for deep space telemetry that offer both increased performance and decreased implementational complexity over current coding systems.

Partial trisomy 16p in an adolescent with autistic disorder and Tourette`s syndrome

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

Hebebrand, J.; Martin, M.; Remschmidt, H.

A partial trisomy 16p was identified in a 14-year-old male adolescent with autistic disorder. He additionally showed complex motor and vocal phenomena, including some simple tics which had first appeared in childhood. Whereas these simple tics were of subclinical significance, an additional diagnosis of Tourette`s syndrome (TS) appears justified. The case report illustrates the diagnostic difficulties in assessing psychiatric symptomatology associated with both disorders, especially complex motor and vocal phenomena. The cytogenetic finding is discussed critically in the light of other chromosome abnormalities reported in both TS and autistic disorder. Chromosome 16p should be considered as a candidate region especiallymore » for autistic disorder. 21 refs.« less

Robot-assisted laparoscopic partial nephrectomy versus laparoscopic partial nephrectomy: A propensity score-matched comparative analysis of surgical outcomes and preserved renal parenchymal volume.

PubMed

Tachibana, Hidekazu; Takagi, Toshio; Kondo, Tsunenori; Ishida, Hideki; Tanabe, Kazunari

2018-04-01

To compare surgical outcomes, including renal function and the preserved renal parenchymal volume, between robot-assisted laparoscopic partial nephrectomy and laparoscopic partial nephrectomy using propensity score-matched analyses. In total, 253 patients, with a normal contralateral kidney, who underwent laparoscopic partial nephrectomy (n = 131) or robot-assisted laparoscopic partial nephrectomy (n = 122) with renal arterial clamping between 2010 and 2015, were included. Patients' background and tumor factors were adjusted by propensity score matching. Surgical outcomes, including postoperative renal function, complications, warm ischemia time and preserved renal parenchymal volume, evaluated by volumetric analysis, were compared between the surgical procedures. After matching, 64 patients were assigned to each group. The mean age was 56-57 years, and the mean tumor size was 22 mm. Approximately 50% of patients had low complexity tumors (RENAL nephrometry score 4-7). The incidence rate of acute kidney failure was significantly lower in the robot-assisted laparoscopic partial nephrectomy (11%) than laparoscopic partial nephrectomy (23%) group (P = 0.049), and warm ischemia time shorter in the robot-assisted laparoscopic partial nephrectomy (17 min) than laparoscopic partial nephrectomy (25 min) group (P < 0.0001). The preservation rate of renal function, measured by the estimated glomerular filtration rate, at 6 months post-surgery was 96% for robot-assisted laparoscopic partial nephrectomy and 90% for laparoscopic partial nephrectomy (P < 0.0001). The preserved renal parenchymal volume was higher for robot-assisted laparoscopic partial nephrectomy (89%) than laparoscopic partial nephrectomy (77%; P < 0.0001). The rate of perioperative complications, surgical margin status and length of hospital stay were equivalent for both techniques. Robot-assisted laparoscopic partial nephrectomy allows to achieve better preservation of renal function and parenchymal volume than laparoscopic partial nephrectomy. © 2018 The Japanese Urological Association.

CUMULATE ROCKS ASSOCIATED WITH CARBONATE ASSIMILATION, HORTAVÆR COMPLEX, NORTH-CENTRAL NORWAY

NASA Astrophysics Data System (ADS)

Barnes, C. G.; Prestvik, T.; Li, Y.

2009-12-01

The Hortavær igneous complex intruded high-grade metamorphic rocks of the Caledonian Helgeland Nappe Complex at ca. 466 Ma. The complex is an unusual mafic-silicic layered intrusion (MASLI) because the principal felsic rock type is syenite and because the syenite formed in situ rather than by deep-seated partial melting of crustal rocks. Magma differentiation in the complex was by assimilation, primarily of calc-silicate rocks and melts with contributions from marble and semi-pelites, plus fractional crystallization. The effect of assimilation of calcite-rich rocks was to enhance stability of fassaitic clinopyroxene at the expense of olivine, which resulted in alkali-rich residual melts and lowering of silica activity. This combination of MASLI-style emplacement and carbonate assimilation produced three types of cumulate rocks: (1) Syenitic cumulates formed by liquid-crystal separation. As sheets of mafic magma were loaded on crystal-rich syenitic magma, residual liquid was expelled, penetrating the overlying mafic sheets in flame structures, and leaving a cumulate syenite. (2) Reaction cumulates. Carbonate assimilation, illustrated by a simple assimilation reaction: olivine + calcite + melt = clinopyroxene + CO2 resulted in cpx-rich cumulates such as clinopyroxenite, gabbro, and mela-monzodiorite, many of which contain igneous calcite. (3) Magmatic skarns. Calc-silicate host rocks underwent partial melting during assimilation, yielding a Ca-rich melt as the principal assimilated material and permitting extensive reaction with surrounding magma to form Kspar + cpx + garnet-rich ‘cumulate’ rocks. Cumulate types (2) and (3) do not reflect traditional views of cumulate rocks but instead result from a series of melt-present discontinuous (peritectic) reactions and partial melting of calc-silicate xenoliths. In the Hortavær complex, such cumulates are evident because of the distinctive peritectic cumulate assemblages. It is unclear whether assimilation of ‘normal’ silicate rocks results in peritectic assemblages, or whether they could be identified as such if they exist.

Lanthanide complexes as luminogenic probes to measure sulfide levels in industrial samples.

PubMed

Thorson, Megan K; Ung, Phuc; Leaver, Franklin M; Corbin, Teresa S; Tuck, Kellie L; Graham, Bim; Barrios, Amy M

2015-10-08

A series of lanthanide-based, azide-appended complexes were investigated as hydrogen sulfide-sensitive probes. Europium complex 1 and Tb complex 3 both displayed a sulfide-dependent increase in luminescence, while Tb complex 2 displayed a decrease in luminescence upon exposure to NaHS. The utility of the complexes for monitoring sulfide levels in industrial oil and water samples was investigated. Complex 3 provided a sensitive measure of sulfide levels in petrochemical water samples (detection limit ∼ 250 nM), while complex 1 was capable of monitoring μM levels of sulfide in partially refined crude oil. Copyright © 2015 Elsevier B.V. All rights reserved.

Wireless rake-receiver using adaptive filter with a family of partial update algorithms in noise cancellation applications

NASA Astrophysics Data System (ADS)

Fayadh, Rashid A.; Malek, F.; Fadhil, Hilal A.; Aldhaibani, Jaafar A.; Salman, M. K.; Abdullah, Farah Salwani

2015-05-01

For high data rate propagation in wireless ultra-wideband (UWB) communication systems, the inter-symbol interference (ISI), multiple-access interference (MAI), and multiple-users interference (MUI) are influencing the performance of the wireless systems. In this paper, the rake-receiver was presented with the spread signal by direct sequence spread spectrum (DS-SS) technique. The adaptive rake-receiver structure was shown with adjusting the receiver tap weights using least mean squares (LMS), normalized least mean squares (NLMS), and affine projection algorithms (APA) to support the weak signals by noise cancellation and mitigate the interferences. To minimize the data convergence speed and to reduce the computational complexity by the previous algorithms, a well-known approach of partial-updates (PU) adaptive filters were employed with algorithms, such as sequential-partial, periodic-partial, M-max-partial, and selective-partial updates (SPU) in the proposed system. The simulation results of bit error rate (BER) versus signal-to-noise ratio (SNR) are illustrated to show the performance of partial-update algorithms that have nearly comparable performance with the full update adaptive filters. Furthermore, the SPU-partial has closed performance to the full-NLMS and full-APA while the M-max-partial has closed performance to the full-LMS updates algorithms.

Amplitude and frequency modulation control of sound production in a mechanical model of the avian syrinx.

PubMed

Elemans, Coen P H; Muller, Mees; Larsen, Ole Naesbye; van Leeuwen, Johan L

2009-04-01

Birdsong has developed into one of the important models for motor control of learned behaviour and shows many parallels with speech acquisition in humans. However, there are several experimental limitations to studying the vocal organ - the syrinx - in vivo. The multidisciplinary approach of combining experimental data and mathematical modelling has greatly improved the understanding of neural control and peripheral motor dynamics of sound generation in birds. Here, we present a simple mechanical model of the syrinx that facilitates detailed study of vibrations and sound production. Our model resembles the 'starling resistor', a collapsible tube model, and consists of a tube with a single membrane in its casing, suspended in an external pressure chamber and driven by various pressure patterns. With this design, we can separately control 'bronchial' pressure and tension in the oscillating membrane and generate a wide variety of 'syllables' with simple sweeps of the control parameters. We show that the membrane exhibits high frequency, self-sustained oscillations in the audio range (>600 Hz fundamental frequency) using laser Doppler vibrometry, and systematically explore the conditions for sound production of the model in its control space. The fundamental frequency of the sound increases with tension in three membranes with different stiffness and mass. The lower-bound fundamental frequency increases with membrane mass. The membrane vibrations are strongly coupled to the resonance properties of the distal tube, most likely because of its reflective properties to sound waves. Our model is a gross simplification of the complex morphology found in birds, and more closely resembles mathematical models of the syrinx. Our results confirm several assumptions underlying existing mathematical models in a complex geometry.

Mimicking a p53-MDM2 interaction based on a stable immunoglobulin-like domain scaffold.

PubMed

Jimenez-Sandoval, Pedro; Madrigal-Carrillo, Ezequiel A; Santamaría-Suárez, Hugo A; Maturana, Daniel; Rentería-González, Itzel; Benitez-Cardoza, Claudia G; Torres-Larios, Alfredo; Brieba, Luis G

2018-04-26

Antibodies recognize protein targets with great affinity and specificity. However, posttranslational modifications and the presence of intrinsic disulfide-bonds pose difficulties for their industrial use. The immunoglobulin fold is one of the most ubiquitous folds in nature and it is found in many proteins besides antibodies. An example of a protein family with an immunoglobulin-like fold is the Cysteine Protease Inhibitors (ICP) family I42 of the MEROPs database for protease and protease inhibitors. Members of this protein family are thermostable and do not present internal disulfide bonds. Crystal structures of several ICPs indicate that they resemble the Ig-like domain of the human T cell co-receptor CD8α As ICPs present 2 flexible recognition loops that vary accordingly to their targeted protease, we hypothesize that members of this protein family would be ideal to design peptide aptamers that mimic protein-protein interactions. Herein, we use an ICP variant from Entamoeba histolytica (EhICP1) to mimic the interaction between p53 and MDM2. We found that a 13 amino-acid peptide derived from p53 can be introduced in 2 variable loops (DE, FG) but not the third (BC). Chimeric EhICP1-p53 form a stable complex with MDM2 at a micromolar range. Crystal structure of the EhICP1-p53(FG)-loop variant in complex with MDM2 reveals a swapping subdomain between 2 chimeric molecules, however, the p53 peptide interacts with MDM2 as in previous crystal structures. The structural details of the EhICP1-p53(FG) interaction with MDM2 resemble the interaction between an antibody and MDM2. © 2018 Wiley Periodicals, Inc.

Adaptations in the structure and innervation of follicle-sinus complexes to an aquatic environment as seen in the Florida manatee (Trichechus manatus latirostris).

PubMed

Sarko, Diana K; Reep, Roger L; Mazurkiewicz, Joseph E; Rice, Frank L

2007-09-20

Florida manatees are large-bodied aquatic herbivores that use large tactile vibrissae for several purposes. Facial vibrissae are used to forage in a turbid water environment, and the largest perioral vibrissae can also grasp and manipulate objects. Other vibrissae distributed over the entire postfacial body appear to function as a lateral line system. All manatee vibrissae emanate from densely innervated follicle-sinus complexes (FSCs) like those in other mammals, although proportionately larger commensurate with the caliber of the vibrissae. As revealed by immunofluorescence, all manatee FSCs have many types of C, Adelta and Abeta innervation including Merkel, club, and longitudinal lanceolate endings at the level of the ring sinus, but they lack other types such as reticular and spiny endings at the level of the cavernous sinus. As in non-whisking terrestrial species, the inner conical bodies of facial FSCs are well innervated but lack Abeta-fiber terminals. Importantly, manatee FSCs have two unique types of Abeta-fiber endings. First, all of the FSCs have exceptionally large-caliber axons that branch to terminate as novel, gigantic spindle-like endings located at the upper ring sinus. Second, facial FSCs have smaller caliber Abeta fibers that terminate in the trabeculae of the cavernous sinus as an ending that resembles a Golgi tendon organ. In addition, the largest perioral vibrissae, which are used for grasping, have exceptionally well-developed medullary cores that have a structure and dense small-fiber innervation resembling that of tooth pulp. Other features of the epidermis and upper dermis structure and innervation differ from that seen in terrestrial mammals. Copyright (c) 2007 Wiley-Liss, Inc.

ANIMAL ANALOGIES IN FIRST IMPRESSIONS OF FACES.

PubMed

Zebrowitz, Leslie A; Wadlinger, Heather A; Luevano, Victor X; White, Benjamin M; Xing, Cai; Zhang, Yi

2011-08-01

Analogies between humans and animals based on facial resemblance have a long history. We report evidence for reverse anthropomorphism and the extension of facial stereotypes to lions, foxes, and dogs. In the stereotype extension, more positive traits were attributed to animals judged more attractive than con-specifics; more childlike traits were attributed to those judged more babyfaced. In the reverse anthropomorphism, human faces with more resemblance to lions, ascertained by connectionist modeling of facial metrics, were judged more dominant, cold, and shrewd, controlling attractiveness, babyfaceness, and sex. Faces with more resemblance to Labradors were judged warmer and less shrewd. Resemblance to foxes did not predict impressions. Results for lions and dogs were consistent with trait impressions of these animals and support the species overgeneralization hypothesis that evolutionarily adaptive reactions to particular animals are overgeneralized, with people perceived to have traits associated with animals their faces resemble. Other possible explanations are discussed.

ANIMAL ANALOGIES IN FIRST IMPRESSIONS OF FACES

PubMed Central

Zebrowitz, Leslie A.; Wadlinger, Heather A.; Luevano, Victor X.; White, Benjamin M.; Xing, Cai; Zhang, Yi

2013-01-01

Analogies between humans and animals based on facial resemblance have a long history. We report evidence for reverse anthropomorphism and the extension of facial stereotypes to lions, foxes, and dogs. In the stereotype extension, more positive traits were attributed to animals judged more attractive than con-specifics; more childlike traits were attributed to those judged more babyfaced. In the reverse anthropomorphism, human faces with more resemblance to lions, ascertained by connectionist modeling of facial metrics, were judged more dominant, cold, and shrewd, controlling attractiveness, babyfaceness, and sex. Faces with more resemblance to Labradors were judged warmer and less shrewd. Resemblance to foxes did not predict impressions. Results for lions and dogs were consistent with trait impressions of these animals and support the species overgeneralization hypothesis that evolutionarily adaptive reactions to particular animals are overgeneralized, with people perceived to have traits associated with animals their faces resemble. Other possible explanations are discussed. PMID:25339791

Glutathione, Glutaredoxins, and Iron.

PubMed

Berndt, Carsten; Lillig, Christopher Horst

2017-11-20

Glutathione (GSH) is the most abundant cellular low-molecular-weight thiol in the majority of organisms in all kingdoms of life. Therefore, functions of GSH and disturbed regulation of its concentration are associated with numerous physiological and pathological situations. Recent Advances: The function of GSH as redox buffer or antioxidant is increasingly being questioned. New functions, especially functions connected to the cellular iron homeostasis, were elucidated. Via the formation of iron complexes, GSH is an important player in all aspects of iron metabolism: sensing and regulation of iron levels, iron trafficking, and biosynthesis of iron cofactors. The variety of GSH coordinated iron complexes and their functions with a special focus on FeS-glutaredoxins are summarized in this review. Interestingly, GSH analogues that function as major low-molecular-weight thiols in organisms lacking GSH resemble the functions in iron homeostasis. Since these iron-related functions are most likely also connected to thiol redox chemistry, it is difficult to distinguish between mechanisms related to either redox or iron metabolisms. The ability of GSH to coordinate iron in different complexes with or without proteins needs further investigation. The discovery of new Fe-GSH complexes and their physiological functions will significantly advance our understanding of cellular iron homeostasis. Antioxid. Redox Signal. 27, 1235-1251.

Molecular-orbital models for the catalytic activity and selectivity of coordinatively unsaturated platinum surfaces and complexes

NASA Astrophysics Data System (ADS)

Balazs, A. C.; Johnson, K. H.

1982-01-01

Electronic structures have been calculated for 5-, 6-, and 10-atom Pt clusters, as well as for a Pt(PH 3) 4 coordination complex, using the self-consistent-field X-alpha scattered-wave (SCF-Xα-SW) molecular-orbital technique. The 10-atom cluster models the local geometry of a flat, unreconstructed Pt(100) surface, while the 5- and 6-atom clusters show features of a stepped Pt surface. Pt(PH 3) 4 resembles the chemically similar homogeneous catalyst Pt(PPh 3) 4. Common to all these coordinatively unsaturated complexes are orbitals lying near or coinciding with the highest occupied molecular orbital ("Fermi level") which show pronounced d lobes pointing directly into the vacuum. Under the hypothesis that these molecular orbitals are mainly responsible for the chemical activities of the above species, one can account for the relative similarities and differences in catalytic activity and selectivity displayed by unreconstructed Pt(100) surfaces, stepped Pt surfaces or particles, and isolated Pt(PPh 3) 4 coordination complexes. The relevance of these findings to catalyst-support interactions is also discussed. Finally, relativistic corrections to the electronic structures are calculated and their implications on catalytic properties discussed.

Numerical and Experimental Methods for Wake Flow Analysis in Complex Terrain

NASA Astrophysics Data System (ADS)

Castellani, Francesco; Astolfi, Davide; Piccioni, Emanuele; Terzi, Ludovico

2015-06-01

Assessment and interpretation of the quality of wind farms power output is a non-trivial task, which poses at least three main challenges: reliable comprehension of free wind flow, which is stretched to the limit on very complex terrains, realistic model of how wake interactions resemble on the wind flow, awareness of the consequences on turbine control systems, including alignment patterns to the wind and, consequently, power output. The present work deals with an onshore wind farm in southern Italy, which has been a test case of IEA- Task 31 Wakebench project: 17 turbines, with 2.3 MW of rated power each, are sited on a very complex terrain. A cluster of machines is investigated through numerical and experimental methods: CFD is employed for simulating wind fields and power extraction, as well as wakes, are estimated through the Actuator Disc model. SCADA data mining techniques are employed for comparison between models and actual performances. The simulations are performed both on the real terrain and on flat terrain, in order to disentangle the effects of complex flow and wake effects. Attention is devoted to comparison between actual alignment patterns of the cluster of turbines and predicted flow deviation.

The coordination chemistry of dipyridylbenzene: N-deficient terpyridine or panacea for brightly luminescent metal complexes?

PubMed

Williams, J A Gareth

2009-06-01

1,3-Di(2-pyridyl)benzene (dpybH) structurally resembles the widely-used ligand terpyridine (tpy), with which it is isoelectronic. In this critical review, following a brief overview of synthetic strategies for dpybH and derivatives, we survey the different types of complex that are possible with these ligands. Whilst metals such as ruthenium(ii), osmium(ii) and platinum(ii) give a terdentate N--C--N binding mode in which cyclometallation occurs at C(2), the ions iridium(iii), rhodium(iii) and palladium(ii) favour C(4) metallation. The latter process can be blocked by appropriate ligand modification, to allow the N--C--N mode to be accessed with these metal ions too. The luminescence properties of the complexes are discussed. A huge range of emission efficiencies are encountered amongst Ir(iii) complexes containing dpyb derivatives, according to the other ligands present. Trends can be rationalised with the aid of simple frontier-orbital considerations. The Pt(ii) complexes of dipyridylbenzenes are also intensely luminescent. Their application to contemporary organic light-emitting device (OLED) technology is discussed, including white light emitters exploiting excimer emission. Their potential as cell imaging agents amenable to time-resolved detection procedures on the microsecond timescale has also been demonstrated (118 references).

Controlled molecular self-assembly of complex three-dimensional structures in soft materials

PubMed Central

Huang, Changjin; Quinn, David; Suresh, Subra

2018-01-01

Many applications in tissue engineering, flexible electronics, and soft robotics call for approaches that are capable of producing complex 3D architectures in soft materials. Here we present a method using molecular self-assembly to generate hydrogel-based 3D architectures that resembles the appealing features of the bottom-up process in morphogenesis of living tissues. Our strategy effectively utilizes the three essential components dictating living tissue morphogenesis to produce complex 3D architectures: modulation of local chemistry, material transport, and mechanics, which can be engineered by controlling the local distribution of polymerization inhibitor (i.e., oxygen), diffusion of monomers/cross-linkers through the porous structures of cross-linked polymer network, and mechanical constraints, respectively. We show that oxygen plays a role in hydrogel polymerization which is mechanistically similar to the role of growth factors in tissue growth, and the continued growth of hydrogel enabled by diffusion of monomers/cross-linkers into the porous hydrogel similar to the mechanisms of tissue growth enabled by material transport. The capability and versatility of our strategy are demonstrated through biomimetics of tissue morphogenesis for both plants and animals, and its application to generate other complex 3D architectures. Our technique opens avenues to studying many growth phenomena found in nature and generating complex 3D structures to benefit diverse applications. PMID:29255037

Peptide Fragmentation by Corona Discharge Induced Electrochemical Ionization

PubMed Central

Lloyd, John R.; Hess, Sonja

2010-01-01

Fundamental studies have greatly improved our understanding of electrospray, including the underlying electrochemical reactions. Generally regarded as disadvantageous, we have recently shown that corona discharge (CD) can be used as an effective method to create a radical cation species [M]+•, thus optimizing the electrochemical reactions that occur on the surface of the stainless steel (SS) electrospray capillary tip. This technique is known as CD initiated electrochemical ionization (CD-ECI). Here, we report on the fundamental studies using CD-ECI to induce analytically useful in-source fragmentation of a range of molecules that complex transition metals. Compounds that have been selectively fragmented using CD-ECI include enolate forming phenylglycine containing peptides, glycopeptides, nucleosides and phosphopeptides. Collision induced dissociation (CID) or other activation techniques were not necessary for CD-ECI fragmentation. A four step mechanism was proposed: 1. Complexation using either Fe in the SS capillary tip material or Cu(II) as an offline complexation reagent; 2. Electrochemical oxidation of the complexed metal and thus formation of a radical cation (e.g.; Fe - e− → Fe +•); 3. Radical fragmentation of the complexed compound. 4. Electrospray ionization of the fragmented neutrals. Fragmentation patterns resembling b- and y-type ions were observed and allowed the localization of the phosphorylation sites. PMID:20869880

Complexity analysis of spontaneous brain activity in mood disorders: A magnetoencephalography study of bipolar disorder and major depression.

PubMed

Fernández, Alberto; Al-Timemy, Ali H; Ferre, Francisco; Rubio, Gabriel; Escudero, Javier

2018-04-26

The lack of a biomarker for Bipolar Disorder (BD) causes problems in the differential diagnosis with other mood disorders such as major depression (MD), and misdiagnosis frequently occurs. Bearing this in mind, we investigated non-linear magnetoencephalography (MEG) patterns in BD and MD. Lempel-Ziv Complexity (LZC) was used to evaluate the resting-state MEG activity in a cross-sectional sample of 60 subjects, including 20 patients with MD, 16 patients with BD type-I, and 24 control (CON) subjects. Particular attention was paid to the role of age. The results were aggregated by scalp region. Overall, MD patients showed significantly higher LZC scores than BD patients and CONs. Linear regression analyses demonstrated distinct tendencies of complexity progression as a function of age, with BD patients showing a divergent tendency as compared with MD and CON groups. Logistic regressions confirmed such distinct relationship with age, which allowed the classification of diagnostic groups. The patterns of neural complexity in BD and MD showed not only quantitative differences in their non-linear MEG characteristics but also divergent trajectories of progression as a function of age. Moreover, neural complexity patterns in BD patients resembled those previously observed in schizophrenia, thus supporting preceding evidence of common neuropathological processes. Copyright © 2018 Elsevier Inc. All rights reserved.

A fossil biting midge (Diptera: Ceratopogonidae) from early Eocene Indian amber with a complex pheromone evaporator

NASA Astrophysics Data System (ADS)

Stebner, Frauke; Szadziewski, Ryszard; Rühr, Peter T.; Singh, Hukam; Hammel, Jörg U.; Kvifte, Gunnar Mikalsen; Rust, Jes

2016-10-01

The life-like fidelity of organisms captured in amber is unique among all kinds of fossilization and represents an invaluable source for different fields of palaeontological and biological research. One of the most challenging aspects in amber research is the study of traits related to behaviour. Here, indirect evidence for pheromone-mediated mating behaviour is recorded from a biting midge (Ceratopogonidae) in 54 million-year-old Indian amber. Camptopterohelea odora n. sp. exhibits a complex, pocket shaped structure on the wings, which resembles the wing folds of certain moth flies (Diptera: Psychodidae) and scent organs that are only known from butterflies and moths (Lepidoptera) so far. Our studies suggests that pheromone releasing structures on the wings have evolved independently in biting midges and might be much more widespread in fossil as well as modern insects than known so far.

3D Printed Robotic Hand

NASA Technical Reports Server (NTRS)

Pizarro, Yaritzmar Rosario; Schuler, Jason M.; Lippitt, Thomas C.

2013-01-01

Dexterous robotic hands are changing the way robots and humans interact and use common tools. Unfortunately, the complexity of the joints and actuations drive up the manufacturing cost. Some cutting edge and commercially available rapid prototyping machines now have the ability to print multiple materials and even combine these materials in the same job. A 3D model of a robotic hand was designed using Creo Parametric 2.0. Combining "hard" and "soft" materials, the model was printed on the Object Connex350 3D printer with the purpose of resembling as much as possible the human appearance and mobility of a real hand while needing no assembly. After printing the prototype, strings where installed as actuators to test mobility. Based on printing materials, the manufacturing cost of the hand was $167, significantly lower than other robotic hands without the actuators since they have more complex assembly processes.

Light-driven solute transport in Halobacterium halobium

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1979-01-01

The cell membrane of Halobacterium halobium exhibits differential regions which contain crystalline arrays of a single kind of protein, termed bacteriorhodopsin. This bacterial retinal-protein complex resembles the visual pigment and, after the absorption of protons, translocates H(+) across the cell membrane, leading to an electrochemical gradient for protons between the inside and the outside of the cell. Thus, light is an alternate source of energy in these bacteria, in addition to terminal oxidation. The paper deals with work on light-driven transport in H. halobium with cell envelope vesicles. The discussion covers light-driven movements of H(+), Na(+), and K(+); light-driven amino acid transport; and apparent allosteric control of amino acid transport. The scheme of energy coupling in H. halobium vesicles appears simple, its quantitative details are quite complex and reveal regulatory phenomena. More knowledge is required of the way the coupling components are regulated by the ion gradients present.

Visual analysis of geocoded twin data puts nature and nurture on the map.

PubMed

Davis, O S P; Haworth, C M A; Lewis, C M; Plomin, R

2012-09-01

Twin studies allow us to estimate the relative contributions of nature and nurture to human phenotypes by comparing the resemblance of identical and fraternal twins. Variation in complex traits is a balance of genetic and environmental influences; these influences are typically estimated at a population level. However, what if the balance of nature and nurture varies depending on where we grow up? Here we use statistical and visual analysis of geocoded data from over 6700 families to show that genetic and environmental contributions to 45 childhood cognitive and behavioral phenotypes vary geographically in the United Kingdom. This has implications for detecting environmental exposures that may interact with the genetic influences on complex traits, and for the statistical power of samples recruited for genetic association studies. More broadly, our experience demonstrates the potential for collaborative exploratory visualization to act as a lingua franca for large-scale interdisciplinary research.

Presentation of lipid antigens to T cells.

PubMed

Mori, Lucia; De Libero, Gennaro

2008-04-15

T cells specific for lipid antigens participate in regulation of the immune response during infections, tumor immunosurveillance, allergy and autoimmune diseases. T cells recognize lipid antigens as complexes formed with CD1 antigen-presenting molecules, thus resembling recognition of MHC-peptide complexes. The biophysical properties of lipids impose unique mechanisms for their delivery, internalization into antigen-presenting cells, membrane trafficking, processing, and loading of CD1 molecules. Each of these steps is controlled at molecular and celular levels and determines lipid immunogenicity. Lipid antigens may derive from microbes and from the cellular metabolism, thus allowing the immune system to survey a large repertoire of immunogenic molecules. Recognition of lipid antigens facilitates the detection of infectious agents and the initiation of responses involved in immunoregulation and autoimmunity. This review focuses on the presentation mechanisms and specific recognition of self and bacterial lipid antigens and discusses the important open issues.

Molecular propulsion: chemical sensing and chemotaxis of DNA driven by RNA polymerase.

PubMed

Yu, Hua; Jo, Kyubong; Kounovsky, Kristy L; de Pablo, Juan J; Schwartz, David C

2009-04-29

Living cells sense extracellular signals and direct their movements in response to stimuli in environment. Such autonomous movement allows these machines to sample chemical change over a distance, leading to chemotaxis. Synthetic catalytic rods have been reported to chemotax toward hydrogen peroxide fuel. Nevertheless individualized autonomous control of movement of a population of biomolecules under physiological conditions has not been demonstrated. Here we show the first experimental evidence that a molecular complex consisting of a DNA template and associating RNA polymerases (RNAPs) displays chemokinetic motion driven by transcription substrates nucleoside triphosphates (NTPs). Furthermore this molecular complex exhibits a biased migration into a concentration gradient of NTPs, resembling chemotaxis. We describe this behavior as "Molecular Propulsion", in which RNAP transcriptional actions deform DNA template conformation engendering measurable enhancement of motility. Our results provide new opportunities for designing and directing nanomachines by imposing external triggers within an experimental system.

A feasibility study of the use of bounded beams resembling the shape of evanescent and inhomogeneous waves.

PubMed

Declercq, Nico F; Leroy, Oswald

2011-08-01

Plane waves are solutions of the visco-elastic wave equation. Their wave vector can be real for homogeneous plane waves or complex for inhomogeneous and evanescent plane waves. Although interesting from a theoretical point of view, complex wave vectors normally only emerge naturally when propagation or scattering is studied of sound under the appearance of damping effects. Because of the particular behavior of inhomogeneous and evanescent waves and their estimated efficiency for surface wave generation, bounded beams, experimentally mimicking their infinite counterparts similar to (wide) Gaussian beams imitating infinite harmonic plane waves, are of special interest in this report. The study describes the behavior of bounded inhomogeneous and bounded evanescent waves in terms of amplitude and phase distribution as well as energy flow direction. The outcome is of importance to the applicability of bounded inhomogeneous ultrasonic waves for nondestructive testing. Copyright © 2011. Published by Elsevier B.V.

Structural mechanism of Smad4 recognition by the nuclear oncoprotein Ski: insights on Ski-mediated repression of TGF-beta signaling.

PubMed

Wu, Jia Wei; Krawitz, Ariel R; Chai, Jijie; Li, Wenyu; Zhang, Fangjiu; Luo, Kunxin; Shi, Yigong

2002-11-01

The Ski family of nuclear oncoproteins represses TGF-beta signaling through interactions with the Smad proteins. The crystal structure of the Smad4 binding domain of human c-Ski in complex with the MH2 domain of Smad4 reveals specific recognition of the Smad4 L3 loop region by a highly conserved interaction loop (I loop) from Ski. The Ski binding surface on Smad4 significantly overlaps with that required for binding of the R-Smads. Indeed, Ski disrupts the formation of a functional complex between the Co- and R-Smads, explaining how it could lead to repression of TGF-beta, activin, and BMP responses. Intriguingly, the structure of the Ski fragment, stabilized by a bound zinc atom, resembles the SAND domain, in which the corresponding I loop is responsible for DNA binding.

Assurance of Complex Electronics. What Path Do We Take?

NASA Technical Reports Server (NTRS)

Plastow, Richard A.

2007-01-01

Many of the methods used to develop software bare a close resemblance to Complex Electronics (CE) development. CE are now programmed to perform tasks that were previously handled in software, such as communication protocols. For instance, Field Programmable Gate Arrays (FPGAs) can have over a million logic gates while system-on-chip (SOC) devices can combine a microprocessor, input and output channels, and sometimes an FPGA for programmability. With this increased intricacy, the possibility of "software-like" bugs such as incorrect design, logic, and unexpected interactions within the logic is great. Since CE devices are obscuring the hardware/software boundary, we propose that mature software methodologies may be utilized with slight modifications to develop these devices. By using standardized S/W Engineering methods such as checklists, missing requirements and "bugs" can be detected earlier in the development cycle, thus creating a development process for CE that will be easily maintained and configurable based on the device used.

Interrogating viral capsid assembly with ion mobility-mass spectrometry

NASA Astrophysics Data System (ADS)

Uetrecht, Charlotte; Barbu, Ioana M.; Shoemaker, Glen K.; van Duijn, Esther; Heck, Albert J. R.

2011-02-01

Most proteins fulfil their function as part of large protein complexes. Surprisingly, little is known about the pathways and regulation of protein assembly. Several viral coat proteins can spontaneously assemble into capsids in vitro with morphologies identical to the native virion and thus resemble ideal model systems for studying protein complex formation. Even for these systems, the mechanism for self-assembly is still poorly understood, although it is generally thought that smaller oligomeric structures form key intermediates. This assembly nucleus and larger viral assembly intermediates are typically low abundant and difficult to monitor. Here, we characterised small oligomers of Hepatitis B virus (HBV) and norovirus under equilibrium conditions using native ion mobility mass spectrometry. This data in conjunction with computational modelling enabled us to elucidate structural features of these oligomers. Instead of more globular shapes, the intermediates exhibit sheet-like structures suggesting that they are assembly competent. We propose pathways for the formation of both capsids.

Materials science. Assembly of micro/nanomaterials into complex, three-dimensional architectures by compressive buckling.

PubMed

Xu, Sheng; Yan, Zheng; Jang, Kyung-In; Huang, Wen; Fu, Haoran; Kim, Jeonghyun; Wei, Zijun; Flavin, Matthew; McCracken, Joselle; Wang, Renhan; Badea, Adina; Liu, Yuhao; Xiao, Dongqing; Zhou, Guoyan; Lee, Jungwoo; Chung, Ha Uk; Cheng, Huanyu; Ren, Wen; Banks, Anthony; Li, Xiuling; Paik, Ungyu; Nuzzo, Ralph G; Huang, Yonggang; Zhang, Yihui; Rogers, John A

2015-01-09

Complex three-dimensional (3D) structures in biology (e.g., cytoskeletal webs, neural circuits, and vasculature networks) form naturally to provide essential functions in even the most basic forms of life. Compelling opportunities exist for analogous 3D architectures in human-made devices, but design options are constrained by existing capabilities in materials growth and assembly. We report routes to previously inaccessible classes of 3D constructs in advanced materials, including device-grade silicon. The schemes involve geometric transformation of 2D micro/nanostructures into extended 3D layouts by compressive buckling. Demonstrations include experimental and theoretical studies of more than 40 representative geometries, from single and multiple helices, toroids, and conical spirals to structures that resemble spherical baskets, cuboid cages, starbursts, flowers, scaffolds, fences, and frameworks, each with single- and/or multiple-level configurations. Copyright © 2015, American Association for the Advancement of Science.

A fossil biting midge (Diptera: Ceratopogonidae) from early Eocene Indian amber with a complex pheromone evaporator.

PubMed

Stebner, Frauke; Szadziewski, Ryszard; Rühr, Peter T; Singh, Hukam; Hammel, Jörg U; Kvifte, Gunnar Mikalsen; Rust, Jes

2016-10-04

The life-like fidelity of organisms captured in amber is unique among all kinds of fossilization and represents an invaluable source for different fields of palaeontological and biological research. One of the most challenging aspects in amber research is the study of traits related to behaviour. Here, indirect evidence for pheromone-mediated mating behaviour is recorded from a biting midge (Ceratopogonidae) in 54 million-year-old Indian amber. Camptopterohelea odora n. sp. exhibits a complex, pocket shaped structure on the wings, which resembles the wing folds of certain moth flies (Diptera: Psychodidae) and scent organs that are only known from butterflies and moths (Lepidoptera) so far. Our studies suggests that pheromone releasing structures on the wings have evolved independently in biting midges and might be much more widespread in fossil as well as modern insects than known so far.