Atomic structures of corkscrew-forming segments of SOD1 reveal varied oligomer conformations.

PubMed

Sangwan, Smriti; Sawaya, Michael R; Murray, Kevin A; Hughes, Michael P; Eisenberg, David S

2018-02-17

The aggregation cascade of disease-related amyloidogenic proteins, terminating in insoluble amyloid fibrils, involves intermediate oligomeric states. The structural and biochemical details of these oligomers have been largely unknown. Here we report crystal structures of variants of the cytotoxic oligomer-forming segment residues 28-38 of the ALS-linked protein, SOD1. The crystal structures reveal three different architectures: corkscrew oligomeric structure, nontwisting curved sheet structure and a steric zipper proto-filament structure. Our work highlights the polymorphism of the segment 28-38 of SOD1 and identifies the molecular features of amyloidogenic entities. © 2018 The Protein Society.

Earth observations during STS-58

NASA Image and Video Library

1993-10-22

STS058-88-017 (18 Oct-1 Nov 1993) --- The eye-catching "bullseye" of the Richat Structure adds interest to the barren Gres de Chinguetti Plateau in central Mauretania, northwest Africa. It represents domally uplifted, layered (sedimentary) rocks that have been eroded by water and wind into the present shape. Desert sands have invaded the feature from the south. The origin of the structure is unknown. It is not an impact structure, because field work showed that strata are undisturbed and flat-lying in the middle of the feature, and no shock-altered rock could be found. There is no evidence for a salt dome or shale diapir, nor is there any geophysical evidence for an underlying dome of dense igneous rock having about the same density as the sedimentary layers.

Structure-activity relationship of karrikin germination stimulants.

PubMed

Flematti, Gavin R; Scaffidi, Adrian; Goddard-Borger, Ethan D; Heath, Charles H; Nelson, David C; Commander, Lucy E; Stick, Robert V; Dixon, Kingsley W; Smith, Steven M; Ghisalberti, Emilio L

2010-08-11

Karrikins (2H-furo[2,3-c]pyran-2-ones) are potent smoke-derived germination promoters for a diverse range of plant species but, to date, their mode of action remains unknown. This paper reports the structure-activity relationship of numerous karrikin analogues to increase understanding of the key structural features of the molecule that are required for biological activity. The results demonstrate that modification at the C5 position is preferred over modification at the C3, C4, or C7 positions for retaining the highest bioactivity.

Unique Structural Features and Sequence Motifs of Proline Utilization A (PutA)

PubMed Central

Singh, Ranjan K.; Tanner, John J.

2013-01-01

Proline utilization A proteins (PutAs) are bifunctional enzymes that catalyze the oxidation of proline to glutamate using spatially separated proline dehydrogenase and pyrroline-5-carboxylate dehydrogenase active sites. Here we use the crystal structure of the minimalist PutA from Bradyrhizobium japonicum (BjPutA) along with sequence analysis to identify unique structural features of PutAs. This analysis shows that PutAs have secondary structural elements and domains not found in the related monofunctional enzymes. Some of these extra features are predicted to be important for substrate channeling in BjPutA. Multiple sequence alignment analysis shows that some PutAs have a 17-residue conserved motif in the C-terminal 20–30 residues of the polypeptide chain. The BjPutA structure shows that this motif helps seal the internal substrate-channeling cavity from the bulk medium. Finally, it is shown that some PutAs have a 100–200 residue domain of unknown function in the C-terminus that is not found in minimalist PutAs. Remote homology detection suggests that this domain is homologous to the oligomerization beta-hairpin and Rossmann fold domain of BjPutA. PMID:22201760

MODAL TRACKING of A Structural Device: A Subspace Identification Approach

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

Candy, J. V.; Franco, S. N.; Ruggiero, E. L.

Mechanical devices operating in an environment contaminated by noise, uncertainties, and extraneous disturbances lead to low signal-to-noise-ratios creating an extremely challenging processing problem. To detect/classify a device subsystem from noisy data, it is necessary to identify unique signatures or particular features. An obvious feature would be resonant (modal) frequencies emitted during its normal operation. In this report, we discuss a model-based approach to incorporate these physical features into a dynamic structure that can be used for such an identification. The approach we take after pre-processing the raw vibration data and removing any extraneous disturbances is to obtain a representation ofmore » the structurally unknown device along with its subsystems that capture these salient features. One approach is to recognize that unique modal frequencies (sinusoidal lines) appear in the estimated power spectrum that are solely characteristic of the device under investigation. Therefore, the objective of this effort is based on constructing a black box model of the device that captures these physical features that can be exploited to “diagnose” whether or not the particular device subsystem (track/detect/classify) is operating normally from noisy vibrational data. Here we discuss the application of a modern system identification approach based on stochastic subspace realization techniques capable of both (1) identifying the underlying black-box structure thereby enabling the extraction of structural modes that can be used for analysis and modal tracking as well as (2) indicators of condition and possible changes from normal operation.« less

Complete fold annotation of the human proteome using a novel structural feature space.

PubMed

Middleton, Sarah A; Illuminati, Joseph; Kim, Junhyong

2017-04-13

Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example. We demonstrate the utility of this method by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into potential biological function, such as prediction of RNA-binding ability. Our method can be applied to de novo fold prediction of entire proteomes and identify candidate novel fold families.

The puzzling Venusian polar atmospheric structure reproduced by a general circulation model

PubMed Central

Ando, Hiroki; Sugimoto, Norihiko; Takagi, Masahiro; Kashimura, Hiroki; Imamura, Takeshi; Matsuda, Yoshihisa

2016-01-01

Unlike the polar vortices observed in the Earth, Mars and Titan atmospheres, the observed Venus polar vortex is warmer than the midlatitudes at cloud-top levels (∼65 km). This warm polar vortex is zonally surrounded by a cold latitude band located at ∼60° latitude, which is a unique feature called ‘cold collar' in the Venus atmosphere. Although these structures have been observed in numerous previous observations, the formation mechanism is still unknown. Here we perform numerical simulations of the Venus atmospheric circulation using a general circulation model, and succeed in reproducing these puzzling features in close agreement with the observations. The cold collar and warm polar region are attributed to the residual mean meridional circulation enhanced by the thermal tide. The present results strongly suggest that the thermal tide is crucial for the structure of the Venus upper polar atmosphere at and above cloud levels. PMID:26832195

Surface Proteins of Gram-Positive Pathogens: Using Crystallography to Uncover Novel Features in Drug and Vaccine Candidates

NASA Astrophysics Data System (ADS)

Baker, Edward N.; Proft, Thomas; Kang, Haejoo

Proteins displayed on the cell surfaces of pathogenic organisms are the front-line troops of bacterial attack, playing critical roles in colonization, infection and virulence. Although such proteins can often be recognized from genome sequence data, through characteristic sequence motifs, their functions are often unknown. One such group of surface proteins is attached to the cell surface of Gram-positive pathogens through the action of sortase enzymes. Some of these proteins are now known to form pili: long filamentous structures that mediate attachment to human cells. Crystallographic analyses of these and other cell surface proteins have uncovered novel features in their structure, assembly and stability, including the presence of inter- and intramolecular isopeptide crosslinks. This improved understanding of structures on the bacterial cell surface offers opportunities for the development of some new drug targets and for novel approaches to vaccine design.

Complete fold annotation of the human proteome using a novel structural feature space

PubMed Central

Middleton, Sarah A.; Illuminati, Joseph; Kim, Junhyong

2017-01-01

Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example. We demonstrate the utility of this method by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into potential biological function, such as prediction of RNA-binding ability. Our method can be applied to de novo fold prediction of entire proteomes and identify candidate novel fold families. PMID:28406174

Drosophila transposon insertions as unknowns for structured inquiry recombination mapping exercises in an undergraduate genetics course.

PubMed

Marcus, Jeffrey M; Hughes, Tia M

2009-06-01

Structured inquiry approaches, in which students receive a Drosophila strain of unknown genotype to analyze and map the constituent mutations, are a common feature of many genetics teaching laboratories. The required crosses frustrate many students because they are aware that they are participating in a fundamentally trivial exercise, as the map locations of the genes are already established and have been recalculated thousands of times by generations of students. We modified the traditional structured inquiry approach to include a novel research experience for the students in our undergraduate genetics laboratories. Students conducted crosses with Drosophila strains carrying P[lacW] transposon insertions in genes without documented recombination map positions, representing a large number of unique, but equivalent genetic unknowns. Using the eye color phenotypes associated with the inserts as visible markers, it is straightforward to calculate recombination map positions for the interrupted loci. Collectively, our students mapped 95 genetic loci on chromosomes 2 and 3. In most cases, the calculated 95% confidence interval for meiotic map location overlapped with the predicted map position based on cytology. The research experience evoked positive student responses and helped students better understand the nature of scientific research for little additional cost or instructor effort.

Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis

PubMed Central

Chakrabarti, Kausik; Pearson, Michael; Grate, Leslie; Sterne-Weiler, Timothy; Deans, Jonathan; Donohue, John Paul; Ares, Manuel

2007-01-01

As the genomes of more eukaryotic pathogens are sequenced, understanding how molecular differences between parasite and host might be exploited to provide new therapies has become a major focus. Central to cell function are RNA-containing complexes involved in gene expression, such as the ribosome, the spliceosome, snoRNAs, RNase P, and telomerase, among others. In this article we identify by comparative genomics and validate by RNA analysis numerous previously unknown structural RNAs encoded by the Plasmodium falciparum genome, including the telomerase RNA, U3, 31 snoRNAs, as well as previously predicted spliceosomal snRNAs, SRP RNA, MRP RNA, and RNAse P RNA. Furthermore, we identify six new RNA coding genes of unknown function. To investigate the relationships of the RNA coding genes to other genomic features in related parasites, we developed a genome browser for P. falciparum (http://areslab.ucsc.edu/cgi-bin/hgGateway). Additional experiments provide evidence supporting the prediction that snoRNAs guide methylation of a specific position on U4 snRNA, as well as predicting an snRNA promoter element particular to Plasmodium sp. These findings should allow detailed structural comparisons between the RNA components of the gene expression machinery of the parasite and its vertebrate hosts. PMID:17901154

Automated prediction of protein function and detection of functional sites from structure.

PubMed

Pazos, Florencio; Sternberg, Michael J E

2004-10-12

Current structural genomics projects are yielding structures for proteins whose functions are unknown. Accordingly, there is a pressing requirement for computational methods for function prediction. Here we present PHUNCTIONER, an automatic method for structure-based function prediction using automatically extracted functional sites (residues associated to functions). The method relates proteins with the same function through structural alignments and extracts 3D profiles of conserved residues. Functional features to train the method are extracted from the Gene Ontology (GO) database. The method extracts these features from the entire GO hierarchy and hence is applicable across the whole range of function specificity. 3D profiles associated with 121 GO annotations were extracted. We tested the power of the method both for the prediction of function and for the extraction of functional sites. The success of function prediction by our method was compared with the standard homology-based method. In the zone of low sequence similarity (approximately 15%), our method assigns the correct GO annotation in 90% of the protein structures considered, approximately 20% higher than inheritance of function from the closest homologue.

Semi-automated surface mapping via unsupervised classification

NASA Astrophysics Data System (ADS)

D'Amore, M.; Le Scaon, R.; Helbert, J.; Maturilli, A.

2017-09-01

Due to the increasing volume of the returned data from space mission, the human search for correlation and identification of interesting features becomes more and more unfeasible. Statistical extraction of features via machine learning methods will increase the scientific output of remote sensing missions and aid the discovery of yet unknown feature hidden in dataset. Those methods exploit algorithm trained on features from multiple instrument, returning classification maps that explore intra-dataset correlation, allowing for the discovery of unknown features. We present two applications, one for Mercury and one for Vesta.

Pilot study to establish a nasal tip prediction method from unknown human skeletal remains for facial reconstruction and skull photo superimposition as applied to a Japanese male populations.

PubMed

Utsuno, Hajime; Kageyama, Toru; Uchida, Keiichi; Kibayashi, Kazuhiko; Sakurada, Koichi; Uemura, Koichi

2016-02-01

Skull-photo superimposition is a technique used to identify the relationship between the skull and a photograph of a target person: and facial reconstruction reproduces antemortem facial features from an unknown human skull, or identifies the facial features of unknown human skeletal remains. These techniques are based on soft tissue thickness and the relationships between soft tissue and the skull, i.e., the position of the ear and external acoustic meatus, pupil and orbit, nose and nasal aperture, and lips and teeth. However, the ear and nose region are relatively difficult to identify because of their structure, as the soft tissues of these regions are lined with cartilage. We attempted to establish a more accurate method to determine the position of the nasal tip from the skull. We measured the height of the maxilla and mid-lower facial region in 55 Japanese men and generated a regression equation from the collected data. We obtained a result that was 2.0±0.99mm (mean±SD) distant from the true nasal tip, when applied to a validation set consisting of another 12 Japanese men. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

[Fast discrimination of edible vegetable oil based on Raman spectroscopy].

PubMed

Zhou, Xiu-Jun; Dai, Lian-Kui; Li, Sheng

2012-07-01

A novel method to fast discriminate edible vegetable oils by Raman spectroscopy is presented. The training set is composed of different edible vegetable oils with known classes. Based on their original Raman spectra, baseline correction and normalization were applied to obtain standard spectra. Two characteristic peaks describing the unsaturated degree of vegetable oil were selected as feature vectors; then the centers of all classes were calculated. For an edible vegetable oil with unknown class, the same pretreatment and feature extraction methods were used. The Euclidian distances between the feature vector of the unknown sample and the center of each class were calculated, and the class of the unknown sample was finally determined by the minimum distance. For 43 edible vegetable oil samples from seven different classes, experimental results show that the clustering effect of each class was more obvious and the class distance was much larger with the new feature extraction method compared with PCA. The above classification model can be applied to discriminate unknown edible vegetable oils rapidly and accurately.

Human Hippocampal Structure: A Novel Biomarker Predicting Mnemonic Vulnerability to, and Recovery from, Sleep Deprivation

PubMed Central

Goldstein-Piekarski, Andrea N.; Greer, Stephanie M.; Stark, Shauna; Stark, Craig E.

2016-01-01

Sleep deprivation impairs the formation of new memories. However, marked interindividual variability exists in the degree to which sleep loss compromises learning, the mechanistic reasons for which are unclear. Furthermore, which physiological sleep processes restore learning ability following sleep deprivation are similarly unknown. Here, we demonstrate that the structural morphology of human hippocampal subfields represents one factor determining vulnerability (and conversely, resilience) to the impact of sleep deprivation on memory formation. Moreover, this same measure of brain morphology was further associated with the quality of nonrapid eye movement slow wave oscillations during recovery sleep, and by way of such activity, determined the success of memory restoration. Such findings provide a novel human biomarker of cognitive susceptibility to, and recovery from, sleep deprivation. Moreover, this metric may be of special predictive utility for professions in which memory function is paramount yet insufficient sleep is pervasive (e.g., aviation, military, and medicine). SIGNIFICANCE STATEMENT Sleep deprivation does not impact all people equally. Some individuals show cognitive resilience to the effects of sleep loss, whereas others express striking vulnerability, the reasons for which remain largely unknown. Here, we demonstrate that structural features of the human brain, specifically those within the hippocampus, accurately predict which individuals are susceptible (or conversely, resilient) to memory impairments caused by sleep deprivation. Moreover, this same structural feature determines the success of memory restoration following subsequent recovery sleep. Therefore, structural properties of the human brain represent a novel biomarker predicting individual vulnerability to (and recovery from) the effects of sleep loss, one with occupational relevance in professions where insufficient sleep is pervasive yet memory function is paramount. PMID:26911684

Recognition of the geologic framework of porphyry deposits on ERTS-1 imagery

NASA Technical Reports Server (NTRS)

Wilson, J. C. (Principal Investigator)

1973-01-01

The author has identified the following significant results. Photointerpretation methods have been most successfully applied in the less vegetated test sites where several previously unknown geologic features have been recognized and known ones extended. Northwest mid-Tertiary faults in the ELY, Nevada area are observed to offset north-trending ranges and abruptly terminate older Mesozoic structures. In the Ray, Arizona area the observed patterns of fault and fracture systems appear to be related to the locations of known porphyry copper deposits. In the Tanacross, Alaska area a number of regional circular features observed may represent near surface intrusions and, therefore, permissive environments for copper porphyries.

Metabolomics and Prostate Cancer

DTIC Science & Technology

2013-05-01

features indicated in pairwise analysis molecular identification revealed Caprolactam, L- Phosphatidic acid , and Peptide (Tyr-Lys-Thr) as possibly...10-8 Unknown – Caprolactam 4 – 1 595.4_153 – 443.3_275 4.2 x 10-8 Unknown – Unknown 4 – 4 597.4_306 - 595.4_153 7.1 x 10-8 L- Phosphatidic acid ...three of the seven additional features implicated including caprolactam, L- Phosphatidic acid and the peptide Tyr-Lys-Thr. Each of these molecules was

Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins.

PubMed

Hsing, Michael; Cherkasov, Artem

2008-06-25

Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown that the presence of sizable indels in protein sequences may be indicative of protein essentiality and their role in protein interaction networks. Examples of utilization of indels for structure-based drug design have also been recently demonstrated. Nonetheless many structural and functional characteristics of indels remain less researched or unknown. We have created a web-based resource, Indel PDB, representing a structural database of insertions/deletions identified from the sequence alignments of highly similar proteins found in the Protein Data Bank (PDB). Indel PDB utilized large amounts of available structural information to characterize 1-, 2- and 3-dimensional features of indel sites. Indel PDB contains 117,266 non-redundant indel sites extracted from 11,294 indel-containing proteins. Unlike loop databases, Indel PDB features more indel sequences with secondary structures including alpha-helices and beta-sheets in addition to loops. The insertion fragments have been characterized by their sequences, lengths, locations, secondary structure composition, solvent accessibility, protein domain association and three dimensional structures. By utilizing the data available in Indel PDB, we have studied and presented here several sequence and structural features of indels. We anticipate that Indel PDB will not only enable future functional studies of indels, but will also assist protein modeling efforts and identification of indel-directed drug binding sites.

Complete fold annotation of the human proteome using a novel structural feature space

DOE PAGES

Middleton, Sarah A.; Illuminati, Joseph; Kim, Junhyong

2017-04-13

Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example. We demonstrate the utility of this methodmore » by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into potential biological function, such as prediction of RNA-binding ability. Finally, our method can be applied to de novo fold prediction of entire proteomes and identify candidate novel fold families.« less

DetectTLC: Automated Reaction Mixture Screening Utilizing Quantitative Mass Spectrometry Image Feature

PubMed Central

Kaddi, Chanchala D.; Bennett, Rachel V.; Paine, Martin R. L.; Banks, Mitchel D.; Weber, Arthur L.; Fernández, Facundo M.; Wang, May D.

2016-01-01

Full characterization of complex reaction mixtures is necessary to understand mechanisms, optimize yields, and elucidate secondary reaction pathways. Molecular-level information for species in such mixtures can be readily obtained by coupling mass spectrometry imaging (MSI) with thin layer chromatography (TLC) separations. User-guided investigation of imaging data for mixture components with known m/z values is generally straightforward; however, spot detection for unknowns is highly tedious, and limits the applicability of MSI in conjunction with TLC. To accelerate imaging data mining, we developed DetectTLC, an approach that automatically identifies m/z values exhibiting TLC spot-like regions in MS molecular images. Furthermore, DetectTLC can also spatially match m/z values for spots acquired during alternating high and low collision-energy scans, pairing product ions with precursors to enhance structural identification. As an example, DetectTLC is applied to the identification and structural confirmation of unknown, yet significant, products of abiotic pyrazinone and aminopyrazine nucleoside analog synthesis. PMID:26508443

Anomalous High-Energy Waterfall-Like Electronic Structure in 5 d Transition Metal Oxide Sr2IrO4 with a Strong Spin-Orbit Coupling

NASA Astrophysics Data System (ADS)

Liu, Yan; Yu, Li; Jia, Xiaowen; Zhao, Jianzhou; Weng, Hongming; Peng, Yingying; Chen, Chaoyu; Xie, Zhuojin; Mou, Daixiang; He, Junfeng; Liu, Xu; Feng, Ya; Yi, Hemian; Zhao, Lin; Liu, Guodong; He, Shaolong; Dong, Xiaoli; Zhang, Jun; Xu, Zuyan; Chen, Chuangtian; Cao, Gang; Dai, Xi; Fang, Zhong; Zhou, X. J.

2015-08-01

The low energy electronic structure of Sr2IrO4 has been well studied and understood in terms of an effective Jeff = 1/2 Mott insulator model. However, little work has been done in studying its high energy electronic behaviors. Here we report a new observation of the anomalous high energy electronic structure in Sr2IrO4. By taking high-resolution angle-resolved photoemission measurements on Sr2IrO4 over a wide energy range, we have revealed for the first time that the high energy electronic structures show unusual nearly-vertical bands that extend over a large energy range. Such anomalous high energy behaviors resemble the high energy waterfall features observed in the cuprate superconductors. While strong electron correlation plays an important role in producing high energy waterfall features in the cuprate superconductors, the revelation of the high energy anomalies in Sr2IrO4, which exhibits strong spin-orbit coupling and a moderate electron correlation, points to an unknown and novel route in generating exotic electronic excitations.

Anomalous High-Energy Waterfall-Like Electronic Structure in 5 d Transition Metal Oxide Sr2IrO4 with a Strong Spin-Orbit Coupling.

PubMed

Liu, Yan; Yu, Li; Jia, Xiaowen; Zhao, Jianzhou; Weng, Hongming; Peng, Yingying; Chen, Chaoyu; Xie, Zhuojin; Mou, Daixiang; He, Junfeng; Liu, Xu; Feng, Ya; Yi, Hemian; Zhao, Lin; Liu, Guodong; He, Shaolong; Dong, Xiaoli; Zhang, Jun; Xu, Zuyan; Chen, Chuangtian; Cao, Gang; Dai, Xi; Fang, Zhong; Zhou, X J

2015-08-12

The low energy electronic structure of Sr2IrO4 has been well studied and understood in terms of an effective Jeff = 1/2 Mott insulator model. However, little work has been done in studying its high energy electronic behaviors. Here we report a new observation of the anomalous high energy electronic structure in Sr2IrO4. By taking high-resolution angle-resolved photoemission measurements on Sr2IrO4 over a wide energy range, we have revealed for the first time that the high energy electronic structures show unusual nearly-vertical bands that extend over a large energy range. Such anomalous high energy behaviors resemble the high energy waterfall features observed in the cuprate superconductors. While strong electron correlation plays an important role in producing high energy waterfall features in the cuprate superconductors, the revelation of the high energy anomalies in Sr2IrO4, which exhibits strong spin-orbit coupling and a moderate electron correlation, points to an unknown and novel route in generating exotic electronic excitations.

Free energy landscape of activation in a signaling protein at atomic resolution

PubMed Central

Pontiggia, F.; Pachov, D.V.; Clarkson, M.W.; Villali, J.; Hagan, M.F.; Pande, V.S.; Kern, D.

2015-01-01

The interconversion between inactive and active protein states, traditionally described by two static structures, is at the heart of signaling. However, how folded states interconvert is largely unknown due to the inability to experimentally observe transition pathways. Here we explore the free energy landscape of the bacterial response regulator NtrC by combining computation and NMR, and discover unexpected features underlying efficient signaling. We find that functional states are defined purely in kinetic and not structural terms. The need of a well-defined conformer, crucial to the active state, is absent in the inactive state, which comprises a heterogeneous collection of conformers. The transition between active and inactive states occurs through multiple pathways, facilitated by a number of nonnative transient hydrogen bonds, thus lowering the transition barrier through both entropic and enthalpic contributions. These findings may represent general features for functional conformational transitions within the folded state. PMID:26073309

Experience improves feature extraction in Drosophila.

PubMed

Peng, Yueqing; Xi, Wang; Zhang, Wei; Zhang, Ke; Guo, Aike

2007-05-09

Previous exposure to a pattern in the visual scene can enhance subsequent recognition of that pattern in many species from honeybees to humans. However, whether previous experience with a visual feature of an object, such as color or shape, can also facilitate later recognition of that particular feature from multiple visual features is largely unknown. Visual feature extraction is the ability to select the key component from multiple visual features. Using a visual flight simulator, we designed a novel protocol for visual feature extraction to investigate the effects of previous experience on visual reinforcement learning in Drosophila. We found that, after conditioning with a visual feature of objects among combinatorial shape-color features, wild-type flies exhibited poor ability to extract the correct visual feature. However, the ability for visual feature extraction was greatly enhanced in flies trained previously with that visual feature alone. Moreover, we demonstrated that flies might possess the ability to extract the abstract category of "shape" but not a particular shape. Finally, this experience-dependent feature extraction is absent in flies with defective MBs, one of the central brain structures in Drosophila. Our results indicate that previous experience can enhance visual feature extraction in Drosophila and that MBs are required for this experience-dependent visual cognition.

Sequential structural damage diagnosis algorithm using a change point detection method

NASA Astrophysics Data System (ADS)

Noh, H.; Rajagopal, R.; Kiremidjian, A. S.

2013-11-01

This paper introduces a damage diagnosis algorithm for civil structures that uses a sequential change point detection method. The general change point detection method uses the known pre- and post-damage feature distributions to perform a sequential hypothesis test. In practice, however, the post-damage distribution is unlikely to be known a priori, unless we are looking for a known specific type of damage. Therefore, we introduce an additional algorithm that estimates and updates this distribution as data are collected using the maximum likelihood and the Bayesian methods. We also applied an approximate method to reduce the computation load and memory requirement associated with the estimation. The algorithm is validated using a set of experimental data collected from a four-story steel special moment-resisting frame and multiple sets of simulated data. Various features of different dimensions have been explored, and the algorithm was able to identify damage, particularly when it uses multidimensional damage sensitive features and lower false alarm rates, with a known post-damage feature distribution. For unknown feature distribution cases, the post-damage distribution was consistently estimated and the detection delays were only a few time steps longer than the delays from the general method that assumes we know the post-damage feature distribution. We confirmed that the Bayesian method is particularly efficient in declaring damage with minimal memory requirement, but the maximum likelihood method provides an insightful heuristic approach.

The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials

PubMed Central

McDougall, Carmel; Woodcroft, Ben J.

2016-01-01

In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs) identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the construction of biological materials with diverse morphologies. The SilkSlider predictor software developed here is available at https://github.com/wwood/SilkSlider. PMID:27415783

An anti-disturbing real time pose estimation method and system

NASA Astrophysics Data System (ADS)

Zhou, Jian; Zhang, Xiao-hu

2011-08-01

Pose estimation relating two-dimensional (2D) images to three-dimensional (3D) rigid object need some known features to track. In practice, there are many algorithms which perform this task in high accuracy, but all of these algorithms suffer from features lost. This paper investigated the pose estimation when numbers of known features or even all of them were invisible. Firstly, known features were tracked to calculate pose in the current and the next image. Secondly, some unknown but good features to track were automatically detected in the current and the next image. Thirdly, those unknown features which were on the rigid and could match each other in the two images were retained. Because of the motion characteristic of the rigid object, the 3D information of those unknown features on the rigid could be solved by the rigid object's pose at the two moment and their 2D information in the two images except only two case: the first one was that both camera and object have no relative motion and camera parameter such as focus length, principle point, and etc. have no change at the two moment; the second one was that there was no shared scene or no matched feature in the two image. Finally, because those unknown features at the first time were known now, pose estimation could go on in the followed images in spite of the missing of known features in the beginning by repeating the process mentioned above. The robustness of pose estimation by different features detection algorithms such as Kanade-Lucas-Tomasi (KLT) feature, Scale Invariant Feature Transform (SIFT) and Speed Up Robust Feature (SURF) were compared and the compact of the different relative motion between camera and the rigid object were discussed in this paper. Graphic Processing Unit (GPU) parallel computing was also used to extract and to match hundreds of features for real time pose estimation which was hard to work on Central Processing Unit (CPU). Compared with other pose estimation methods, this new method can estimate pose between camera and object when part even all known features are lost, and has a quick response time benefit from GPU parallel computing. The method present here can be used widely in vision-guide techniques to strengthen its intelligence and generalization, which can also play an important role in autonomous navigation and positioning, robots fields at unknown environment. The results of simulation and experiments demonstrate that proposed method could suppress noise effectively, extracted features robustly, and achieve the real time need. Theory analysis and experiment shows the method is reasonable and efficient.

Use of Small Angle Neutron Scattering to Study Various Properties of Wool and Mohair Fibres

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

Franklyn, C. B.; Toeroek, Gy.

2011-12-13

To maintain a competitive edge in the wool and mohair industry, a detailed knowledge and understanding of the properties of wool fibres is essential. Standard techniques are used to determine fibre diameter, length and strength; however, properties such as hydroscopicity, lustre and changes in fibre structure following chemical or mechanical treatment are not so well understood. The unique capabilities of small angle neutron scattering to study changes in the supermolecular structure of wool fibres, particularly at the level of the microfibril-matrix complex, have been used to provide previously unknown features of the fibres. The results of these studies are presented.

Structural analysis of behavioral networks from the Internet

NASA Astrophysics Data System (ADS)

Meiss, M. R.; Menczer, F.; Vespignani, A.

2008-06-01

In spite of the Internet's phenomenal growth and social impact, many aspects of the collective communication behavior of its users are largely unknown. Understanding the structure and dynamics of the behavioral networks that connect users with each other and with services across the Internet is key to modeling the network and designing future applications. We present a characterization of the properties of the behavioral networks generated by several million users of the Abilene (Internet2) network. Structural features of these networks offer new insights into scaling properties of network activity and ways of distinguishing particular patterns of traffic. For example, we find that the structure of the behavioral network associated with Web activity is characterized by such extreme heterogeneity as to challenge any simple attempt to model Web server traffic.

Protein–DNA Interactions: The Story so Far and a New Method for Prediction

DOE PAGES

Jones, Susan; Thornton, Janet M.

2003-01-01

This review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one-third of DNAbinding protein families. A library of 3D structural templates of HTH motifs was derived from proteins in the PDB. Templates were scanned against complete protein structures and the optimal superposition of a template on a structure calculated. Significance thresholds in terms of a minimum root mean squared deviation (rmsd) of an optimal superposition, and a minimum motif accessible surface area (ASA), have been calculated. Inmore » this way, it is possible to scan the template library against proteins of unknown function to make predictions about DNA-binding functionality.« less

Crystal Structure of Cocosin, A Potential Food Allergen from Coconut (Cocos nucifera).

PubMed

Jin, Tengchuan; Wang, Cheng; Zhang, Caiying; Wang, Yang; Chen, Yu-Wei; Guo, Feng; Howard, Andrew; Cao, Min-Jie; Fu, Tong-Jen; McHugh, Tara H; Zhang, Yuzhu

2017-08-30

Coconut (Cocos nucifera) is an important palm tree. Coconut fruit is widely consumed. The most abundant storage protein in coconut fruit is cocosin (a likely food allergen), which belongs to the 11S globulin family. Cocosin was crystallized near a century ago, but its structure remains unknown. By optimizing crystallization conditions and cryoprotectant solutions, we were able to obtain cocosin crystals that diffracted to 1.85 Å. The cocosin gene was cloned from genomic DNA isolated from dry coconut tissue. The protein sequence deduced from the predicted cocosin coding sequence was used to guide model building and structure refinement. The structure of cocosin was determined for the first time, and it revealed a typical 11S globulin feature of a double layer doughnut-shaped hexamer.

Online feature selection with streaming features.

PubMed

Wu, Xindong; Yu, Kui; Ding, Wei; Wang, Hao; Zhu, Xingquan

2013-05-01

We propose a new online feature selection framework for applications with streaming features where the knowledge of the full feature space is unknown in advance. We define streaming features as features that flow in one by one over time whereas the number of training examples remains fixed. This is in contrast with traditional online learning methods that only deal with sequentially added observations, with little attention being paid to streaming features. The critical challenges for Online Streaming Feature Selection (OSFS) include 1) the continuous growth of feature volumes over time, 2) a large feature space, possibly of unknown or infinite size, and 3) the unavailability of the entire feature set before learning starts. In the paper, we present a novel Online Streaming Feature Selection method to select strongly relevant and nonredundant features on the fly. An efficient Fast-OSFS algorithm is proposed to improve feature selection performance. The proposed algorithms are evaluated extensively on high-dimensional datasets and also with a real-world case study on impact crater detection. Experimental results demonstrate that the algorithms achieve better compactness and higher prediction accuracy than existing streaming feature selection algorithms.

Efficacy of function specific 3D-motifs in enzyme classification according to their EC-numbers.

PubMed

Rahimi, Amir; Madadkar-Sobhani, Armin; Touserkani, Rouzbeh; Goliaei, Bahram

2013-11-07

Due to the increasing number of protein structures with unknown function originated from structural genomics projects, protein function prediction has become an important subject in bioinformatics. Among diverse function prediction methods, exploring known 3D-motifs, which are associated with functional elements in unknown protein structures is one of the most biologically meaningful methods. Homologous enzymes inherit such motifs in their active sites from common ancestors. However, slight differences in the properties of these motifs, results in variation in the reactions and substrates of the enzymes. In this study, we examined the possibility of discriminating highly related active site patterns according to their EC-numbers by 3D-motifs. For each EC-number, the spatial arrangement of an active site, which has minimum average distance to other active sites with the same function, was selected as a representative 3D-motif. In order to characterize the motifs, various points in active site elements were tested. The results demonstrated the possibility of predicting full EC-number of enzymes by 3D-motifs. However, the discriminating power of 3D-motifs varies among different enzyme families and depends on selecting the appropriate points and features. © 2013 Elsevier Ltd. All rights reserved.

Isotropic and Anisotropic Growth of Metal-Organic Framework (MOF) on MOF: Logical Inference on MOF Structure Based on Growth Behavior and Morphological Feature.

PubMed

Choi, Sora; Kim, Taeho; Ji, Hoyeon; Lee, Hee Jung; Oh, Moonhyun

2016-11-02

The growth of one metal-organic framework (MOF) on another MOF for constructing a heterocompositional hybrid MOF is an interesting research topic because of the curiosity regarding the occurrence of this phenomenon and the value of hybrid MOFs as multifunctional materials or routes for fine-tuning MOF properties. In particular, the anisotropic growth of MOF on MOF is fascinating for the development of MOFs possessing atypical shapes and heterostructures or abnormal properties. Herein, we clarify the understanding of growth behavior of a secondary MOF on an initial MOF template, such as isotropic or anisotropic ways associated with their cell parameters. The isotropic growth of MIL-68-Br on the MIL-68 template results in the formation of core-shell-type MIL-68@MIL-68-Br. However, the unique anisotropic growth of a secondary MOF (MOF-NDC) on the MIL-68 template results in semitubular particles, and structural features of this unknown secondary MOF are successfully speculated for the first time on the basis of its unique growth behavior and morphological characteristics. Finally, the validation of this structural speculation is verified by the powder X-ray diffraction and the selected area electron diffraction studies. The results suggests that the growth behavior and morphological features of MOFs should be considered to be important factors for understanding the MOFs' structures.

Bayesian nonlinear structural FE model and seismic input identification for damage assessment of civil structures

NASA Astrophysics Data System (ADS)

Astroza, Rodrigo; Ebrahimian, Hamed; Li, Yong; Conte, Joel P.

2017-09-01

A methodology is proposed to update mechanics-based nonlinear finite element (FE) models of civil structures subjected to unknown input excitation. The approach allows to jointly estimate unknown time-invariant model parameters of a nonlinear FE model of the structure and the unknown time histories of input excitations using spatially-sparse output response measurements recorded during an earthquake event. The unscented Kalman filter, which circumvents the computation of FE response sensitivities with respect to the unknown model parameters and unknown input excitations by using a deterministic sampling approach, is employed as the estimation tool. The use of measurement data obtained from arrays of heterogeneous sensors, including accelerometers, displacement sensors, and strain gauges is investigated. Based on the estimated FE model parameters and input excitations, the updated nonlinear FE model can be interrogated to detect, localize, classify, and assess damage in the structure. Numerically simulated response data of a three-dimensional 4-story 2-by-1 bay steel frame structure with six unknown model parameters subjected to unknown bi-directional horizontal seismic excitation, and a three-dimensional 5-story 2-by-1 bay reinforced concrete frame structure with nine unknown model parameters subjected to unknown bi-directional horizontal seismic excitation are used to illustrate and validate the proposed methodology. The results of the validation studies show the excellent performance and robustness of the proposed algorithm to jointly estimate unknown FE model parameters and unknown input excitations.

Hallerman-Streiff-like syndrome presenting with laterality and cardiac defects.

PubMed

Morice-Picard, Fanny; Marlin, Sandrine; Rooryck, Caroline; Fayon, Mickael; Thambo, Jeao-Benoît; Demarquez, Jean-Louis; Fauroux, Brigitte; Denoyelle, Francoise; Lacombe, Didier

2009-04-01

We report two patients considered to have an atypical presentation of Hallerman-Streiff syndrome (HSS) associated with laterality and cardiac defects. Clinical features include typical facial gestalt, atrophy of the skin, and hypotrichosis. Ophthalmologic abnormalities, normally present in HSS, are only found in one of the two patients. Both of them have respiratory problems secondary to the classical narrow upper airway described in this syndrome. Both these patients have laterality defects and one has additional structural cardiac malformations. Cardiac defects have occasionally been reported in the HSS literature, but are not considered as a classical feature of the syndrome. Situs inversus has never been reported in this syndrome. Almost all HSS cases have been sporadic and their origin and inheritance pattern remain unknown.

Autonomous exploration and mapping of unknown environments

NASA Astrophysics Data System (ADS)

Owens, Jason; Osteen, Phil; Fields, MaryAnne

2012-06-01

Autonomous exploration and mapping is a vital capability for future robotic systems expected to function in arbitrary complex environments. In this paper, we describe an end-to-end robotic solution for remotely mapping buildings. For a typical mapping system, an unmanned system is directed to enter an unknown building at a distance, sense the internal structure, and, barring additional tasks, while in situ, create a 2-D map of the building. This map provides a useful and intuitive representation of the environment for the remote operator. We have integrated a robust mapping and exploration system utilizing laser range scanners and RGB-D cameras, and we demonstrate an exploration and metacognition algorithm on a robotic platform. The algorithm allows the robot to safely navigate the building, explore the interior, report significant features to the operator, and generate a consistent map - all while maintaining localization.

Morphometric analysis of astrocytes in brainstem respiratory regions.

PubMed

Sheikhbahaei, Shahriar; Morris, Brian; Collina, Jared; Anjum, Sommer; Znati, Sami; Gamarra, Julio; Zhang, Ruli; Gourine, Alexander V; Smith, Jeffrey C

2018-06-11

Astrocytes, the most abundant and structurally complex glial cells of the central nervous system, are proposed to play an important role in modulating the activities of neuronal networks, including respiratory rhythm-generating circuits of the preBötzinger complex (preBötC) located in the ventrolateral medulla of the brainstem. However, structural properties of astrocytes residing within different brainstem regions are unknown. In this study astrocytes in the preBötC, an intermediate reticular formation (IRF) region with respiratory-related function, and a region of the nucleus tractus solitarius (NTS) in adult rats were reconstructed and their morphological features were compared. Detailed morphological analysis revealed that preBötC astrocytes are structurally more complex than those residing within the functionally distinct neighboring IRF region, or the NTS, located at the dorsal aspect of the medulla oblongata. Structural analyses of the brainstem microvasculature indicated no significant regional differences in vascular properties. We hypothesize that high morphological complexity of preBötC astrocytes reflects their functional role in providing structural/metabolic support and modulation of the key neuronal circuits essential for breathing, as well as constraints imposed by arrangements of associated neurons and/or other local structural features of the brainstem parenchyma. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

Identification of DNA-Binding Proteins Using Structural, Electrostatic and Evolutionary Features

PubMed Central

Nimrod, Guy; Szilágyi, András; Leslie, Christina; Ben-Tal, Nir

2009-01-01

Summary DNA binding proteins (DBPs) often take part in various crucial processes of the cell's life cycle. Therefore, the identification and characterization of these proteins are of great importance. We present here a random forests classifier for identifying DBPs among proteins with known three-dimensional structures. First, clusters of evolutionarily conserved regions (patches) on the protein's surface are detected using the PatchFinder algorithm; previous studies showed that these regions are typically the proteins' functionally important regions. Next, we train a classifier using features like the electrostatic potential, cluster-based amino acid conservation patterns and the secondary structure content of the patches, as well as features of the whole protein including its dipole moment. Using 10-fold cross validation on a dataset of 138 DNA-binding proteins and 110 proteins which do not bind DNA, the classifier achieved a sensitivity and a specificity of 0.90, which is overall better than the performance of previously published methods. Furthermore, when we tested 5 different methods on 11 new DBPs which did not appear in the original dataset, only our method annotated all correctly. The resulting classifier was applied to a collection of 757 proteins of known structure and unknown function. Of these proteins, 218 were predicted to bind DNA, and we anticipate that some of them interact with DNA using new structural motifs. The use of complementary computational tools supports the notion that at least some of them do bind DNA. PMID:19233205

Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.

PubMed

Nimrod, Guy; Szilágyi, András; Leslie, Christina; Ben-Tal, Nir

2009-04-10

DNA-binding proteins (DBPs) participate in various crucial processes in the life-cycle of the cells, and the identification and characterization of these proteins is of great importance. We present here a random forests classifier for identifying DBPs among proteins with known 3D structures. First, clusters of evolutionarily conserved regions (patches) on the surface of proteins were detected using the PatchFinder algorithm; earlier studies showed that these regions are typically the functionally important regions of proteins. Next, we trained a classifier using features like the electrostatic potential, cluster-based amino acid conservation patterns and the secondary structure content of the patches, as well as features of the whole protein, including its dipole moment. Using 10-fold cross-validation on a dataset of 138 DBPs and 110 proteins that do not bind DNA, the classifier achieved a sensitivity and a specificity of 0.90, which is overall better than the performance of published methods. Furthermore, when we tested five different methods on 11 new DBPs that did not appear in the original dataset, only our method annotated all correctly. The resulting classifier was applied to a collection of 757 proteins of known structure and unknown function. Of these proteins, 218 were predicted to bind DNA, and we anticipate that some of them interact with DNA using new structural motifs. The use of complementary computational tools supports the notion that at least some of them do bind DNA.

Temporal evolution of the spatial covariability of rainfall in South America

NASA Astrophysics Data System (ADS)

Ciemer, Catrin; Boers, Niklas; Barbosa, Henrique M. J.; Kurths, Jürgen; Rammig, Anja

2017-10-01

The climate of South America exhibits pronounced differences between rainy and dry seasons, associated with specific synoptic features such as the establishment of the South Atlantic convergence zone. Here, we analyze the spatiotemporal correlation structure and in particular teleconnections of daily rainfall associated with these features by means of evolving complex networks. A modification of Pearson's correlation coefficient is introduced to handle the intricate statistical properties of daily rainfall. On this basis, spatial correlation networks are constructed, and new appropriate network measures are introduced in order to analyze the temporal evolution of the networks' characteristics. We particularly focus on the identification of coherent areas of similar rainfall patterns and previously unknown teleconnection structures between remote areas. We show that the monsoon onset is characterized by an abrupt transition from erratic to organized regional connectivity that prevails during the monsoon season, while only the onset times themselves exhibit anomalous large-scale organization of teleconnections. Furthermore, we reveal that the two mega-droughts in the Amazon basin were already announced in the previous year by an anomalous behavior of the connectivity structure.

Insights into structural features determining odorant affinities to honey bee odorant binding protein 14.

PubMed

Schwaighofer, Andreas; Pechlaner, Maria; Oostenbrink, Chris; Kotlowski, Caroline; Araman, Can; Mastrogiacomo, Rosa; Pelosi, Paolo; Knoll, Wolfgang; Nowak, Christoph; Larisika, Melanie

2014-04-18

Molecular interactions between odorants and odorant binding proteins (OBPs) are of major importance for understanding the principles of selectivity of OBPs towards the wide range of semiochemicals. It is largely unknown on a structural basis, how an OBP binds and discriminates between odorant molecules. Here we examine this aspect in greater detail by comparing the C-minus OBP14 of the honey bee (Apis mellifera L.) to a mutant form of the protein that comprises the third disulfide bond lacking in C-minus OBPs. Affinities of structurally analogous odorants featuring an aromatic phenol group with different side chains were assessed based on changes of the thermal stability of the protein upon odorant binding monitored by circular dichroism spectroscopy. Our results indicate a tendency that odorants show higher affinity to the wild-type OBP suggesting that the introduced rigidity in the mutant protein has a negative effect on odorant binding. Furthermore, we show that OBP14 stability is very sensitive to the position and type of functional groups in the odorant. Copyright © 2014 Elsevier Inc. All rights reserved.

On the Structure of Neuronal Population Activity under Fluctuations in Attentional State

PubMed Central

Denfield, George H.; Bethge, Matthias; Tolias, Andreas S.

2016-01-01

Attention is commonly thought to improve behavioral performance by increasing response gain and suppressing shared variability in neuronal populations. However, both the focus and the strength of attention are likely to vary from one experimental trial to the next, thereby inducing response variability unknown to the experimenter. Here we study analytically how fluctuations in attentional state affect the structure of population responses in a simple model of spatial and feature attention. In our model, attention acts on the neural response exclusively by modulating each neuron's gain. Neurons are conditionally independent given the stimulus and the attentional gain, and correlated activity arises only from trial-to-trial fluctuations of the attentional state, which are unknown to the experimenter. We find that this simple model can readily explain many aspects of neural response modulation under attention, such as increased response gain, reduced individual and shared variability, increased correlations with firing rates, limited range correlations, and differential correlations. We therefore suggest that attention may act primarily by increasing response gain of individual neurons without affecting their correlation structure. The experimentally observed reduction in correlations may instead result from reduced variability of the attentional gain when a stimulus is attended. Moreover, we show that attentional gain fluctuations, even if unknown to a downstream readout, do not impair the readout accuracy despite inducing limited-range correlations, whereas fluctuations of the attended feature can in principle limit behavioral performance. SIGNIFICANCE STATEMENT Covert attention is one of the most widely studied examples of top-down modulation of neural activity in the visual system. Recent studies argue that attention improves behavioral performance by shaping of the noise distribution to suppress shared variability rather than by increasing response gain. Our work shows, however, that latent, trial-to-trial fluctuations of the focus and strength of attention lead to shared variability that is highly consistent with known experimental observations. Interestingly, fluctuations in the strength of attention do not affect coding performance. As a consequence, the experimentally observed changes in response variability may not be a mechanism of attention, but rather a side effect of attentional allocation strategies in different behavioral contexts. PMID:26843656

Splicing-Related Features of Introns Serve to Propel Evolution

PubMed Central

Luo, Yuping; Li, Chun; Gong, Xi; Wang, Yanlu; Zhang, Kunshan; Cui, Yaru; Sun, Yi Eve; Li, Siguang

2013-01-01

The role of spliceosomal intronic structures played in evolution has only begun to be elucidated. Comparative genomic analyses of fungal snoRNA sequences, which are often contained within introns and/or exons, revealed that about one-third of snoRNA-associated introns in three major snoRNA gene clusters manifested polymorphisms, likely resulting from intron loss and gain events during fungi evolution. Genomic deletions can clearly be observed as one mechanism underlying intron and exon loss, as well as generation of complex introns where several introns lie in juxtaposition without intercalating exons. Strikingly, by tracking conserved snoRNAs in introns, we found that some introns had moved from one position to another by excision from donor sites and insertion into target sties elsewhere in the genome without needing transposon structures. This study revealed the origin of many newly gained introns. Moreover, our analyses suggested that intron-containing sequences were more prone to sustainable structural changes than DNA sequences without introns due to intron's ability to jump within the genome via unknown mechanisms. We propose that splicing-related structural features of introns serve as an additional motor to propel evolution. PMID:23516505

Anomalous High-Energy Waterfall-Like Electronic Structure in 5 d Transition Metal Oxide Sr2IrO4 with a Strong Spin-Orbit Coupling

PubMed Central

Liu, Yan; Yu, Li; Jia, Xiaowen; Zhao, Jianzhou; Weng, Hongming; Peng, Yingying; Chen, Chaoyu; Xie, Zhuojin; Mou, Daixiang; He, Junfeng; Liu, Xu; Feng, Ya; Yi, Hemian; Zhao, Lin; Liu, Guodong; He, Shaolong; Dong, Xiaoli; Zhang, Jun; Xu, Zuyan; Chen, Chuangtian; Cao, Gang; Dai, Xi; Fang, Zhong; Zhou, X. J.

2015-01-01

The low energy electronic structure of Sr2IrO4 has been well studied and understood in terms of an effective Jeff = 1/2 Mott insulator model. However, little work has been done in studying its high energy electronic behaviors. Here we report a new observation of the anomalous high energy electronic structure in Sr2IrO4. By taking high-resolution angle-resolved photoemission measurements on Sr2IrO4 over a wide energy range, we have revealed for the first time that the high energy electronic structures show unusual nearly-vertical bands that extend over a large energy range. Such anomalous high energy behaviors resemble the high energy waterfall features observed in the cuprate superconductors. While strong electron correlation plays an important role in producing high energy waterfall features in the cuprate superconductors, the revelation of the high energy anomalies in Sr2IrO4, which exhibits strong spin-orbit coupling and a moderate electron correlation, points to an unknown and novel route in generating exotic electronic excitations. PMID:26267653

Comparative study of methods for recognition of an unknown person's action from a video sequence

NASA Astrophysics Data System (ADS)

Hori, Takayuki; Ohya, Jun; Kurumisawa, Jun

2009-02-01

This paper proposes a Tensor Decomposition Based method that can recognize an unknown person's action from a video sequence, where the unknown person is not included in the database (tensor) used for the recognition. The tensor consists of persons, actions and time-series image features. For the observed unknown person's action, one of the actions stored in the tensor is assumed. Using the motion signature obtained from the assumption, the unknown person's actions are synthesized. The actions of one of the persons in the tensor are replaced by the synthesized actions. Then, the core tensor for the replaced tensor is computed. This process is repeated for the actions and persons. For each iteration, the difference between the replaced and original core tensors is computed. The assumption that gives the minimal difference is the action recognition result. For the time-series image features to be stored in the tensor and to be extracted from the observed video sequence, the human body silhouette's contour shape based feature is used. To show the validity of our proposed method, our proposed method is experimentally compared with Nearest Neighbor rule and Principal Component analysis based method. Experiments using 33 persons' seven kinds of action show that our proposed method achieves better recognition accuracies for the seven actions than the other methods.

Investigations into an unknown organism on the martian meteorite Allan Hills 84001

NASA Technical Reports Server (NTRS)

Steele, A.; Goddard, D. T.; Stapleton, D.; Toporski, J. K.; Peters, V.; Bassinger, V.; Sharples, G.; Wynn-Williams, D. D.; McKay, D. S.

2000-01-01

Examination of fracture surfaces near the fusion crust of the martian meteorite Allan Hills (ALH) 84001 have been conducted using scanning electron microscopy (SEM) and atomic force microscopy (AFM) and has revealed structures strongly resembling mycelium. These structures were compared with similar structures found in Antarctic cryptoendolithic communities. On morphology alone, we conclude that these features are not only terrestrial in origin but probably belong to a member of the Actinomycetales, which we consider was introduced during the Antarctic residency of this meteorite. If true, this is the first documented account of terrestrial microbial activity within a meteorite from the Antarctic blue ice fields. These structures, however, do not bear any resemblance to those postulated to be martian biota, although they are a probable source of the organic contaminants previously reported in this meteorite.

Titan's "Hot Cross Bun": A Titan Laccolith?

NASA Astrophysics Data System (ADS)

Lopes, Rosaly M. C.; Stofan, E. R.; Wall, S. D.; Wood, C.; Kirk, R. L.; Lucas, A.; Mitchell, K. L.; Lunine, J. I.; Turtle, E. P.; Radebaugh, J.; Malaska, M.; Cassini RADAR Team

2012-10-01

Cassini’s RADAR instrument acquired Synthetic Aperture Radar data during the T83 flyby on May 22, 2012. The data showed a feature centered at 38.5N, 203W that resembles a “hot cross bun”. This type of feature has not been seen on Titan before, even though 52% of Titan’s surface has been imaged using SAR. The feature, approximately 100 km across, is mostly radar bright but the cross pattern, interpreted to be extensional fractures, located roughly at the center of the brighter area, appears darker at radar wavelengths (2.3 cm). Radar illumination of the image indicates that the fractures are lower in elevation than the surrounding bright region. The morphology of the region is markedly similar to that of a 30-km dome-shaped feature on Venus that lies at the summit of the Kunapipi volcano. The Venus feature is interpreted to be the result of intrusion of magma at the summit of the volcano [1]. A similar feature, interpreted as a laccolith, is seen on the Moon near the crater Ramsden [2]. The lunar feature, imaged by the Lunar Reconnaissance Orbiter, shows the cross-shaped depression over a 300 m high rise. No topographic data for the feature on Titan are available at this time, but the morphology seen by the SAR data suggests that the feature may have been formed by material pushing up from below. Laccoliths form when an igneous intrusion splits apart two strata, resulting in a domeline structure. This previously unknown type of structure on Titan may be yet another indication of cryovolcanism. [1] Stofan, E.R., et al, Icarus, 152, 75-95, 2001. [2] Wichman, R.W. and Schultz, P. H. (1996). Icarus, 122, Issue 1, July 1996, pages 193-199. doi:10.1006/icar.1996.0118

Environmental structure and competitive scoring advantages in team competitions.

PubMed

Merritt, Sears; Clauset, Aaron

2013-10-29

In most professional sports, playing field structure is kept neutral so that scoring imbalances may be attributed to differences in team skill. It thus remains unknown what impact environmental heterogeneities can have on scoring dynamics or competitive advantages. Applying a novel generative model of scoring dynamics to roughly 10 million team competitions drawn from an online game, we quantify the relationship between the structure within a competition and its scoring dynamics, while controlling the impact of chance. Despite wide structural variations, we observe a common three-phase pattern in the tempo of events. Tempo and balance are highly predictable from a competition's structural features alone and teams exploit environmental heterogeneities for sustained competitive advantage. Surprisingly, the most balanced competitions are associated with specific environmental heterogeneities, not from equally skilled teams. These results shed new light on the design principles of balanced competition, and illustrate the potential of online game data for investigating social dynamics and competition.

Method for removing atomic-model bias in macromolecular crystallography

DOEpatents

Terwilliger, Thomas C [Santa Fe, NM

2006-08-01

Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

Environmental structure and competitive scoring advantages in team competitions

NASA Astrophysics Data System (ADS)

Merritt, Sears; Clauset, Aaron

2013-10-01

In most professional sports, playing field structure is kept neutral so that scoring imbalances may be attributed to differences in team skill. It thus remains unknown what impact environmental heterogeneities can have on scoring dynamics or competitive advantages. Applying a novel generative model of scoring dynamics to roughly 10 million team competitions drawn from an online game, we quantify the relationship between the structure within a competition and its scoring dynamics, while controlling the impact of chance. Despite wide structural variations, we observe a common three-phase pattern in the tempo of events. Tempo and balance are highly predictable from a competition's structural features alone and teams exploit environmental heterogeneities for sustained competitive advantage. Surprisingly, the most balanced competitions are associated with specific environmental heterogeneities, not from equally skilled teams. These results shed new light on the design principles of balanced competition, and illustrate the potential of online game data for investigating social dynamics and competition.

Study of nanoscale structural biology using advanced particle beam microscopy

NASA Astrophysics Data System (ADS)

Boseman, Adam J.

This work investigates developmental and structural biology at the nanoscale using current advancements in particle beam microscopy. Typically the examination of micro- and nanoscale features is performed using scanning electron microscopy (SEM), but in order to decrease surface charging, and increase resolution, an obscuring conductive layer is applied to the sample surface. As magnification increases, this layer begins to limit the ability to identify nanoscale surface structures. A new technology, Helium Ion Microscopy (HIM), is used to examine uncoated surface structures on the cuticle of wild type and mutant fruit flies. Corneal nanostructures observed with HIM are further investigated by FIB/SEM to provide detailed three dimensional information about internal events occurring during early structural development. These techniques are also used to reconstruct a mosquito germarium in order to characterize unknown events in early oogenesis. Findings from these studies, and many more like them, will soon unravel many of the mysteries surrounding the world of developmental biology.

Fast Markerless Tracking for Augmented Reality in Planar Environment

NASA Astrophysics Data System (ADS)

Basori, Ahmad Hoirul; Afif, Fadhil Noer; Almazyad, Abdulaziz S.; AbuJabal, Hamza Ali S.; Rehman, Amjad; Alkawaz, Mohammed Hazim

2015-12-01

Markerless tracking for augmented reality should not only be accurate but also fast enough to provide a seamless synchronization between real and virtual beings. Current reported methods showed that a vision-based tracking is accurate but requires high computational power. This paper proposes a real-time hybrid-based method for tracking unknown environments in markerless augmented reality. The proposed method provides collaboration of vision-based approach with accelerometers and gyroscopes sensors as camera pose predictor. To align the augmentation relative to camera motion, the tracking method is done by substituting feature-based camera estimation with combination of inertial sensors with complementary filter to provide more dynamic response. The proposed method managed to track unknown environment with faster processing time compared to available feature-based approaches. Moreover, the proposed method can sustain its estimation in a situation where feature-based tracking loses its track. The collaboration of sensor tracking managed to perform the task for about 22.97 FPS, up to five times faster than feature-based tracking method used as comparison. Therefore, the proposed method can be used to track unknown environments without depending on amount of features on scene, while requiring lower computational cost.

Cerebral vascular amyloid seeds drive amyloid β-protein fibril assembly with a distinct anti-parallel structure

PubMed Central

Xu, Feng; Fu, Ziao; Dass, Sharmila; Kotarba, AnnMarie E.; Davis, Judianne; Smith, Steven O.; Van Nostrand, William E.

2016-01-01

Cerebrovascular accumulation of amyloid β-protein (Aβ), a condition known as cerebral amyloid angiopathy (CAA), is a common pathological feature of patients with Alzheimer's disease. Familial Aβ mutations, such as Dutch-E22Q and Iowa-D23N, can cause severe cerebrovascular accumulation of amyloid that serves as a potent driver of vascular cognitive impairment and dementia. The distinctive features of vascular amyloid that underlie its unique pathological properties remain unknown. Here, we use transgenic mouse models producing CAA mutants (Tg-SwDI) or overproducing human wild-type Aβ (Tg2576) to demonstrate that CAA-mutant vascular amyloid influences wild-type Aβ deposition in brain. We also show isolated microvascular amyloid seeds from Tg-SwDI mice drive assembly of human wild-type Aβ into distinct anti-parallel β-sheet fibrils. These findings indicate that cerebrovascular amyloid can serve as an effective scaffold to promote rapid assembly and strong deposition of Aβ into a unique structure that likely contributes to its distinctive pathology. PMID:27869115

Evolution of plant cell wall: Arabinogalactan-proteins from three moss genera show structural differences compared to seed plants.

PubMed

Bartels, Desirée; Baumann, Alexander; Maeder, Malte; Geske, Thomas; Heise, Esther Marie; von Schwartzenberg, Klaus; Classen, Birgit

2017-05-01

Arabinogalactan-proteins (AGPs) are important proteoglycans of plant cell walls. They seem to be present in most, if not all seed plants, but their occurrence and structure in bryophytes is widely unknown and actually the focus of AGP research. With regard to evolution of plant cell wall, we isolated AGPs from the three mosses Sphagnum sp., Physcomitrella patens and Polytrichastrum formosum. The moss AGPs show structural characteristics common for AGPs of seed plants, but also unique features, especially 3-O-methyl-rhamnose (trivial name acofriose) as terminal monosaccharide not found in arabinogalactan-proteins of angiosperms and 1,2,3-linked galactose as branching point never found in arabinogalactan-proteins before. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multiple conformations of the cytidine repressor DNA-binding domain coalesce to one upon recognition of a specific DNA surface.

PubMed

Moody, Colleen L; Tretyachenko-Ladokhina, Vira; Laue, Thomas M; Senear, Donald F; Cocco, Melanie J

2011-08-09

The cytidine repressor (CytR) is a member of the LacR family of bacterial repressors with distinct functional features. The Escherichia coli CytR regulon comprises nine operons whose palindromic operators vary in both sequence and, most significantly, spacing between the recognition half-sites. This suggests a strong likelihood that protein folding would be coupled to DNA binding as a mechanism to accommodate the variety of different operator architectures to which CytR is targeted. Such coupling is a common feature of sequence-specific DNA-binding proteins, including the LacR family repressors; however, there are no significant structural rearrangements upon DNA binding within the three-helix DNA-binding domains (DBDs) studied to date. We used nuclear magnetic resonance (NMR) spectroscopy to characterize the CytR DBD free in solution and to determine the high-resolution structure of a CytR DBD monomer bound specifically to one DNA half-site of the uridine phosphorylase (udp) operator. We find that the free DBD populates multiple distinct conformations distinguished by up to four sets of NMR peaks per residue. This structural heterogeneity is previously unknown in the LacR family. These stable structures coalesce into a single, more stable udp-bound form that features a three-helix bundle containing a canonical helix-turn-helix motif. However, this structure differs from all other LacR family members whose structures are known with regard to the packing of the helices and consequently their relative orientations. Aspects of CytR activity are unique among repressors; we identify here structural properties that are also distinct and that might underlie the different functional properties. © 2011 American Chemical Society

Automated adaptive inference of phenomenological dynamical models.

PubMed

Daniels, Bryan C; Nemenman, Ilya

2015-08-21

Dynamics of complex systems is often driven by large and intricate networks of microscopic interactions, whose sheer size obfuscates understanding. With limited experimental data, many parameters of such dynamics are unknown, and thus detailed, mechanistic models risk overfitting and making faulty predictions. At the other extreme, simple ad hoc models often miss defining features of the underlying systems. Here we develop an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the available data. Such adaptive models produce accurate predictions even when microscopic details are unknown. The approach is computationally tractable, even for a relatively large number of dynamical variables. Using simulated data, it correctly infers the phase space structure for planetary motion, avoids overfitting in a biological signalling system and produces accurate predictions for yeast glycolysis with tens of data points and over half of the interacting species unobserved.

Weak signal transmission in complex networks and its application in detecting connectivity.

PubMed

Liang, Xiaoming; Liu, Zonghua; Li, Baowen

2009-10-01

We present a network model of coupled oscillators to study how a weak signal is transmitted in complex networks. Through both theoretical analysis and numerical simulations, we find that the response of other nodes to the weak signal decays exponentially with their topological distance to the signal source and the coupling strength between two neighboring nodes can be figured out by the responses. This finding can be conveniently used to detect the topology of unknown network, such as the degree distribution, clustering coefficient and community structure, etc., by repeatedly choosing different nodes as the signal source. Through four typical networks, i.e., the regular one dimensional, small world, random, and scale-free networks, we show that the features of network can be approximately given by investigating many fewer nodes than the network size, thus our approach to detect the topology of unknown network may be efficient in practical situations with large network size.

Automated adaptive inference of phenomenological dynamical models

PubMed Central

Daniels, Bryan C.; Nemenman, Ilya

2015-01-01

Dynamics of complex systems is often driven by large and intricate networks of microscopic interactions, whose sheer size obfuscates understanding. With limited experimental data, many parameters of such dynamics are unknown, and thus detailed, mechanistic models risk overfitting and making faulty predictions. At the other extreme, simple ad hoc models often miss defining features of the underlying systems. Here we develop an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the available data. Such adaptive models produce accurate predictions even when microscopic details are unknown. The approach is computationally tractable, even for a relatively large number of dynamical variables. Using simulated data, it correctly infers the phase space structure for planetary motion, avoids overfitting in a biological signalling system and produces accurate predictions for yeast glycolysis with tens of data points and over half of the interacting species unobserved. PMID:26293508

First ERTS-1 results in southeastern France: Geology, sedimentology, pollution at sea

NASA Technical Reports Server (NTRS)

Fontanel, A.; Guillemot, J.; Guy, M.

1973-01-01

Results obtained by four ERTS projects in southeastern France are summarized. With regard to geology, ERTS photos of Western Alps are very useful for tectonic interpretation because large features are clearly visible on these photographs even though they are often hidden by small complicated structures if studied on large scale documents. The 18-day repetition coverage was not obtained, and time-varying sedimentological surveys were impossible. Nevertheless, it was possible to delineate the variations of the shorelines in the Rhone Delta for a period covering the least 8,000 years. Some instances of industries discharging pollutant products at sea were detected, as well as very large anomalies of unknown origin. Some examples of coherent optical processing have been made in order to bring out tectonic features in the Alps mountains.

Correlation between the sub-structure parameters and the manufacturing technologies of metal threads in historical textiles using X-ray line profile analysis

NASA Astrophysics Data System (ADS)

Csiszár, Gábor; Ungár, Tamás; Járó, Márta

2013-06-01

Micro-structure can talk when documentation is missing. In ancient Roman or medieval periods, kings, queens, or just rich people decorated their clothes or even their horse covers richly with miniature jewels or metal threads. The origin or the fabrication techniques of these ancient threads is often unknown. Thirteen thread samples made of gold or gilt silver manufactured during the last sixteen hundred years are investigated for the micro-structure in terms of dislocation density, crystallite size, and planar defects. In a few cases, these features are compared with sub-structure of similar metallic threads prepared in modern, twentieth century workshops. The sub-structure is determined by X-ray line profile analysis, using high resolution diffractograms with negligible instrumental broadening. On the basis of the sub-structure parameters, we attempt to assess the metal-threads manufacturing procedures on samples stemming from the fourth century A.D. until now.

Structural Prediction and In Silico Physicochemical Characterization for Mouse Caltrin I and Bovine Caltrin Proteins

PubMed Central

Grasso, Ernesto J.; Sottile, Adolfo E.; Coronel, Carlos E.

2016-01-01

It is known that caltrin (calcium transport inhibitor) protein binds to sperm cells during ejaculation and inhibits extracellular Ca2+ uptake. Although the sequence and some biological features of mouse caltrin I and bovine caltrin are known, their physicochemical properties and tertiary structure are mainly unknown. We predicted the 3D structures of mouse caltrin I and bovine caltrin by molecular homology modeling and threading. Surface electrostatic potentials and electric fields were calculated using the Poisson–Boltzmann equation. Several different bioinformatics tools and available web servers were used to thoroughly analyze the physicochemical characteristics of both proteins, such as their Kyte and Doolittle hydropathy scores and helical wheel projections. The results presented in this work significantly aid further understanding of the molecular mechanisms of caltrin proteins modulating physiological processes associated with fertilization. PMID:27812283

Structural and Functional Dissection of the Heterocyclic Peptide Cytotoxin Streptolysin S*S⃞

PubMed Central

Mitchell, Douglas A.; Lee, Shaun W.; Pence, Morgan A.; Markley, Andrew L.; Limm, Joyce D.; Nizet, Victor; Dixon, Jack E.

2009-01-01

The human pathogen Streptococcus pyogenes secretes a highly cytolytic toxin known as streptolysin S (SLS). SLS is a key virulence determinant and responsible for the β-hemolytic phenotype of these bacteria. Despite over a century of research, the chemical structure of SLS remains unknown. Recent experiments have revealed that SLS is generated from an inactive precursor peptide that undergoes extensive post-translational modification to an active form. In this work, we address outstanding questions regarding the SLS biosynthetic process, elucidating the features of substrate recognition and sites of posttranslational modification to the SLS precursor peptide. Further, we exploit these findings to guide the design of artificial cytolytic toxins that are recognized by the SLS biosynthetic enzymes and others that are intrinsically cytolytic. This new structural information has ramifications for future antimicrobial therapies. PMID:19286651

Ultra structural changes occurring in duct ectasia and periductal mastitis and their significance in etiopathogenesis.

PubMed

Ramalingam, Kirithiga; Vuthaluru, Seenu; Srivastava, Anurag; Dinda, Amit Kumar; Dhar, Anita

2017-01-01

Duct ectasia (DE) and periductal mastitis (PDM) are the most common benign breast conditions seen in women. The etiopathogenesis of these entities is still not clear and most of the theories regarding the causation are based on the histological features as seen on light microscopy. The ultramicroscopic features associated with these conditions that may give more insight to the etiopathogenesis are unknown. To study the ultrastructural changes occurring in mammary duct cones in patients with DE and PDM using Transmission Electron Microscopic (TEM). Major ducts removed by radical duct excision from 21 patients with final histopathological diagnosis of DE and PDM were subjected to TEM study with 2 normal duct samples as controls. The TEM features of DE were denudation of the epithelial cells with focal loss of microvilli, widening of the inter-epithelial junctions with focal disruption of the T bars, periductal collagenisation without inflammation, and features suggestive of Epithelial Mesenchymal Transition (EMT). PDM features are intact epithelial lining with proliferative epithelium and periductal collagenisation with inflammation. Based on the TEM findings, we suggest that DE and PDM are two different entities. EMT a novel finding observed in DE in this study.

Ultra structural changes occurring in duct ectasia and periductal mastitis and their significance in etiopathogenesis

PubMed Central

Ramalingam, Kirithiga; Vuthaluru, Seenu; Srivastava, Anurag; Dinda, Amit Kumar; Dhar, Anita

2017-01-01

Introduction Duct ectasia (DE) and periductal mastitis (PDM) are the most common benign breast conditions seen in women. The etiopathogenesis of these entities is still not clear and most of the theories regarding the causation are based on the histological features as seen on light microscopy. The ultramicroscopic features associated with these conditions that may give more insight to the etiopathogenesis are unknown. Aim To study the ultrastructural changes occurring in mammary duct cones in patients with DE and PDM using Transmission Electron Microscopic (TEM). Method Major ducts removed by radical duct excision from 21 patients with final histopathological diagnosis of DE and PDM were subjected to TEM study with 2 normal duct samples as controls. Results The TEM features of DE were denudation of the epithelial cells with focal loss of microvilli, widening of the inter-epithelial junctions with focal disruption of the T bars, periductal collagenisation without inflammation, and features suggestive of Epithelial Mesenchymal Transition (EMT). PDM features are intact epithelial lining with proliferative epithelium and periductal collagenisation with inflammation. Conclusions Based on the TEM findings, we suggest that DE and PDM are two different entities. EMT a novel finding observed in DE in this study. PMID:28273122

The structure of the inner arcsecond of R Aquarii observed with the Hubble Space Telescope

NASA Technical Reports Server (NTRS)

Burgarella, Denis; Paresce, Francesco

1992-01-01

The inner arcsec of R Aquarii has been observed with the Faint Object Camera on the Hubble Space Telescope. A simple and reliable linear deconvolution method is used to resolve the two features, designated C1 and C2 from radio observations, into several condensations. C1 is composed of four objects, designated C1a, C1b located at 0.099 arcsec from C1a, C3 at 0.162 arcsec from C1a, and C4 at 0.137 arcsec from C1a. The source C3, detected at 2 cm in the radio and in H-alpha, might be the V = 6-11 Mira variable. The nature of feature C4 is still unknown. Features C1a and C1b have not been resolved by another instrument, and it might be possible that the hot star is one of the two or a nearby nondetected object.

The contribution of local features to familiarity judgments in music.

PubMed

Bigand, Emmanuel; Gérard, Yannick; Molin, Paul

2009-07-01

The contributions of local and global features to object identification depend upon the context. For example, while local features play an essential role in identification of words and objects, the global features are more influential in face recognition. In order to evaluate the respective strengths of local and global features for face recognition, researchers usually ask participants to recognize human faces (famous or learned) in normal and scrambled pictures. In this paper, we address a similar issue in music. We present the results of an experiment in which musically untrained participants were asked to differentiate famous from unknown musical excerpts that were presented in normal or scrambled ways. Manipulating the size of the temporal window on which the scrambling procedure was applied allowed us to evaluate the minimal length of time necessary for participants to make a familiarity judgment. Quite surprisingly, the minimum duration for differentiation of famous from unknown pieces is extremely short. This finding highlights the contribution of very local features to music memory.

Synchrotron x-ray microdiffraction reveals intrinsic structural features of amyloid deposits in situ.

PubMed

Briki, Fatma; Vérine, Jérôme; Doucet, Jean; Bénas, Philippe; Fayard, Barbara; Delpech, Marc; Grateau, Gilles; Riès-Kautt, Madeleine

2011-07-20

Amyloidoses are increasingly recognized as a major public health concern in Western countries. All amyloidoses share common morphological, structural, and tinctorial properties. These consist of staining by specific dyes, a fibrillar aspect in electron microscopy and a typical cross-β folding in x-ray diffraction patterns. Most studies that aim at deciphering the amyloid structure rely on fibers generated in vitro or extracted from tissues using protocols that may modify their intrinsic structure. Therefore, the fine details of the in situ architecture of the deposits remain unknown. Here, we present to our knowledge the first data obtained on ex vivo human renal tissue sections using x-ray microdiffraction. The typical cross-β features from fixed paraffin-embedded samples are similar to those formed in vitro or extracted from tissues. Moreover, the fiber orientation maps obtained across glomerular sections reveal an intrinsic texture that is correlated with the glomerulus morphology. These results are of the highest importance to understanding the formation of amyloid deposits and are thus expected to trigger new incentives for tissue investigation. Moreover, the access to intrinsic structural parameters such as fiber size and orientation using synchrotron x-ray microdiffraction, could provide valuable information concerning in situ mechanisms and deposit formation with potential benefits for diagnostic and therapeutic purposes. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mutational robustness accelerates the origin of novel RNA phenotypes through phenotypic plasticity.

PubMed

Wagner, Andreas

2014-02-18

Novel phenotypes can originate either through mutations in existing genotypes or through phenotypic plasticity, the ability of one genotype to form multiple phenotypes. From molecules to organisms, plasticity is a ubiquitous feature of life, and a potential source of exaptations, adaptive traits that originated for nonadaptive reasons. Another ubiquitous feature is robustness to mutations, although it is unknown whether such robustness helps or hinders the origin of new phenotypes through plasticity. RNA is ideal to address this question, because it shows extensive plasticity in its secondary structure phenotypes, a consequence of their continual folding and unfolding, and these phenotypes have important biological functions. Moreover, RNA is to some extent robust to mutations. This robustness structures RNA genotype space into myriad connected networks of genotypes with the same phenotype, and it influences the dynamics of evolving populations on a genotype network. In this study I show that both effects help accelerate the exploration of novel phenotypes through plasticity. My observations are based on many RNA molecules sampled at random from RNA sequence space, and on 30 biological RNA molecules. They are thus not only a generic feature of RNA sequence space but are relevant for the molecular evolution of biological RNA. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Exploration and discovery in Yellowstone Lake: Results from high-resolution sonar imaging, seismic reflection profiling, and submersible studies

USGS Publications Warehouse

Morgan, L.A.; Shanks, Wayne C.; Lovalvo, D.A.; Johnson, S.Y.; Stephenson, W.J.; Pierce, K.L.; Harlan, S.S.; Finn, C.A.; Lee, G.; Webring, M.; Schulze, B.; Duhn, J.; Sweeney, R.; Balistrieri, L.

2003-01-01

Discoveries from multi-beam sonar mapping and seismic reflection surveys of the northern, central, and West Thumb basins of Yellowstone Lake provide new insight into the extent of post-collapse volcanism and active hydrothermal processes occurring in a large lake environment above a large magma chamber. Yellowstone Lake has an irregular bottom covered with dozens of features directly related to hydrothermal, tectonic, volcanic, and sedimentary processes. Detailed bathymetric, seismic reflection, and magnetic evidence reveals that rhyolitic lava flows underlie much of Yellowstone Lake and exert fundamental control on lake bathymetry and localization of hydrothermal activity. Many previously unknown features have been identified and include over 250 hydrothermal vents, several very large (>500 m diameter) hydrothermal explosion craters, many small hydrothermal vent craters (???1-200 m diameter), domed lacustrine sediments related to hydrothermal activity, elongate fissures cutting post-glacial sediments, siliceous hydrothermal spire structures, sublacustrine landslide deposits, submerged former shorelines, and a recently active graben. Sampling and observations with a submersible remotely operated vehicle confirm and extend our understanding of the identified features. Faults, fissures, hydrothermally inflated domal structures, hydrothermal explosion craters, and sublacustrine landslides constitute potentially significant geologic hazards. Toxic elements derived from hydrothermal processes also may significantly affect the Yellowstone ecosystem. Published by Elsevier Science B.V.

Network analysis of named entity co-occurrences in written texts

NASA Astrophysics Data System (ADS)

Amancio, Diego Raphael

2016-06-01

The use of methods borrowed from statistics and physics to analyze written texts has allowed the discovery of unprecedent patterns of human behavior and cognition by establishing links between models features and language structure. While current models have been useful to unveil patterns via analysis of syntactical and semantical networks, only a few works have probed the relevance of investigating the structure arising from the relationship between relevant entities such as characters, locations and organizations. In this study, we represent entities appearing in the same context as a co-occurrence network, where links are established according to a null model based on random, shuffled texts. Computational simulations performed in novels revealed that the proposed model displays interesting topological features, such as the small world feature, characterized by high values of clustering coefficient. The effectiveness of our model was verified in a practical pattern recognition task in real networks. When compared with traditional word adjacency networks, our model displayed optimized results in identifying unknown references in texts. Because the proposed representation plays a complementary role in characterizing unstructured documents via topological analysis of named entities, we believe that it could be useful to improve the characterization of written texts (and related systems), specially if combined with traditional approaches based on statistical and deeper paradigms.

Structural Pituitary Abnormalities Associated With CHARGE Syndrome

PubMed Central

Gregory, Louise C.; Gevers, Evelien F.; Baker, Joanne; Kasia, Tessa; Chong, Kling; Josifova, Dragana J.; Caimari, Maria; Bilan, Frederic; McCabe, Mark J.

2013-01-01

Introduction: CHARGE syndrome is a multisystem disorder that, in addition to Kallmann syndrome/isolated hypogonadotrophic hypogonadism, has been associated with anterior pituitary hypoplasia (APH). However, structural abnormalities such as an ectopic posterior pituitary (EPP) have not yet been described in such patients. Objective: The aims of the study were: 1) to describe the association between CHARGE syndrome and a structurally abnormal pituitary gland; and 2) to investigate whether CHD7 variants, which are identified in 65% of CHARGE patients, are common in septo-optic dysplasia /hypopituitarism. Methods: We describe 2 patients with features of CHARGE and EPP. CHD7 was sequenced in these and other patients with septo-optic dysplasia/hypopituitarism. Results: EPP, APH, and GH, TSH, and probable LH/FSH deficiency were present in 1 patient, and EPP and APH with GH, TSH, LH/FSH, and ACTH deficiency were present in another patient, both of whom had features of CHARGE syndrome. Both had variations in CHD7 that were novel and undetected in control cohorts or in the international database of CHARGE patients, but were also present in their unaffected mothers. No CHD7 variants were detected in the patients with septo-optic dysplasia/hypopituitarism without additional CHARGE features. Conclusion: We report a novel association between CHARGE syndrome and structural abnormalities of the pituitary gland in 2 patients with variations in CHD7 that are of unknown significance. However, CHD7 mutations are an uncommon cause of septo-optic dysplasia or hypopituitarism. Our data suggest the need for evaluation of pituitary function/anatomy in patients with CHARGE syndrome. PMID:23526466

Thermal infrared emission spectroscopy of the pyroxene mineral series

NASA Astrophysics Data System (ADS)

Hamilton, Victoria E.

2000-04-01

The thermal infrared emissivity spectra of coarse particulate samples of compositions in the pyroxene series display reststrahlen features (absorptions) that distinguish not only orthorhombic from monoclinic structures, but also major end-members within the two structural groups, as well as minerals within solid solution series. The exact number of reststrahlen features observed and their positions are dependent on mineral structure and cation occupancy of the M1 and M2 sites. End-member quadrilateral pyroxenes (Mg2Si2O6-Fe2Si2O6-Ca[Mg,Fe]Si2O6) are easily distinguished from each other and from minerals in the nonquadrilateral series (NaFeSi2O6-Na[Al,Fe]Si2O6-LiAlSi2O6). Furthermore, among quadrilateral pyroxenes, variations in Mg/(Mg+Fe) are linearly correlated with several band locations, as are variations in Ca content in high-Ca clinopyroxenes. In both quadrilateral and nonquadrilateral compositions, Christiansen feature positions are also diagnostic. No correlations with minor constituents (of the order of 0.05 atoms per formula unit) were observed. The detailed spectral characteristics of pyroxenes and their variability as a function of structure and cation occupancy are presented here with determinative curves for the identification of pyroxene composition. These data have important implications for the interpretation of spectral data from both laboratory and remote sensing instruments because they should permit a more detailed determination of pyroxene composition in measured unknown pure mineral and bulk compositions dominated by surface scattering, i.e., all particulates greater than ~65 μm, and solid samples.

The Function of Embryonic Stem Cell-expressed RAS (E-RAS), a Unique RAS Family Member, Correlates with Its Additional Motifs and Its Structural Properties.

PubMed

Nakhaei-Rad, Saeideh; Nakhaeizadeh, Hossein; Kordes, Claus; Cirstea, Ion C; Schmick, Malte; Dvorsky, Radovan; Bastiaens, Philippe I H; Häussinger, Dieter; Ahmadian, Mohammad Reza

2015-06-19

E-RAS is a member of the RAS family specifically expressed in embryonic stem cells, gastric tumors, and hepatic stellate cells. Unlike classical RAS isoforms (H-, N-, and K-RAS4B), E-RAS has, in addition to striking and remarkable sequence deviations, an extended 38-amino acid-long unique N-terminal region with still unknown functions. We investigated the molecular mechanism of E-RAS regulation and function with respect to its sequence and structural features. We found that N-terminal extension of E-RAS is important for E-RAS signaling activity. E-RAS protein most remarkably revealed a different mode of effector interaction as compared with H-RAS, which correlates with deviations in the effector-binding site of E-RAS. Of all these residues, tryptophan 79 (arginine 41 in H-RAS), in the interswitch region, modulates the effector selectivity of RAS proteins from H-RAS to E-RAS features. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Mechanical Characterization of Polysilicon MEMS: A Hybrid TMCMC/POD-Kriging Approach.

PubMed

Mirzazadeh, Ramin; Eftekhar Azam, Saeed; Mariani, Stefano

2018-04-17

Microscale uncertainties related to the geometry and morphology of polycrystalline silicon films, constituting the movable structures of micro electro-mechanical systems (MEMS), were investigated through a joint numerical/experimental approach. An on-chip testing device was designed and fabricated to deform a compliant polysilicon beam. In previous studies, we showed that the scattering in the input–output characteristics of the device can be properly described only if statistical features related to the morphology of the columnar polysilicon film and to the etching process adopted to release the movable structure are taken into account. In this work, a high fidelity finite element model of the device was used to feed a transitional Markov chain Monte Carlo (TMCMC) algorithm for the estimation of the unknown parameters governing the aforementioned statistical features. To reduce the computational cost of the stochastic analysis, a synergy of proper orthogonal decomposition (POD) and kriging interpolation was adopted. Results are reported for a batch of nominally identical tested devices, in terms of measurement error-affected probability distributions of the overall Young’s modulus of the polysilicon film and of the overetch depth.

19. Photographer unknown, circa 1950 'THE LOOP OVER' BRIDGE WAS ...

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

19. Photographer unknown, circa 1950 'THE LOOP OVER' BRIDGE WAS CONSTRUCTED ON NEWFOUND GAP ROAD TO REPLACE A SERIES OF DANGEROUS SWITCHBACKS. THIS ENGINEERING FEATURE QUICKLY BECAME A POPULAR TOURIST ATTRACTION. - Great Smoky Mountains National Park Roads & Bridges, Gatlinburg, Sevier County, TN

Levothyroxine sodium revisited: A wholistic structural elucidation approach of new impurities via HPLC-HRMS/MS, on-line H/D exchange, NMR spectroscopy and chemical synthesis.

PubMed

Ruggenthaler, M; Grass, J; Schuh, W; Huber, C G; Reischl, R J

2017-02-20

The structural elucidation of unknown pharmaceutical impurities plays an important role in the quality control of newly developed and well-established active pharmaceutical ingredients (APIs). The United States Pharmacopeia (USP) monograph for the API Levothyroxine Sodium, a synthetic thyroid hormone, features two high pressure liquid chromatography (HPLC) methods using UV-VIS absorption detection to determine organic impurities in the drug substance. The impurity profile of the first USP method ("Procedure 1") has already been extensively studied, however for the second method ("Procedure 2"), which exhibits a significantly different impurity profile, no wholistic structural elucidation of impurities has been performed yet. Applying minor modifications to the chromatographic parameters of USP "Procedure 2" and using various comprehensive structural elucidation methods such as high resolution tandem mass spectrometry with on-line hydrogen-deuterium (H/D) exchange or two-dimensional nuclear magnetic resonance spectroscopy (NMR) we gained new insights about the complex impurity profile of the synthetic thyroid hormone. This resulted in the characterization of 24 compounds previously unknown to literature and the introduction of two new classes of Levothyroxine Sodium impurities. Five novel compounds were unambiguously identified via isolation or synthesis of reference substances and subsequent NMR spectroscopic investigation. Additionally, Collision-Induced Dissociation (CID)-type fragmentation of identified major impurities as well as neutral loss fragmentation patterns of many characterized impurities were discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket.

PubMed

Keiper, Sonja; Bebenroth, Dirk; Seelig, Burckhard; Westhof, Eric; Jäschke, Andres

2004-09-01

Artificial ribozymes catalyze a variety of chemical reactions. Their structures and reaction mechanisms are largely unknown. We have analyzed a ribozyme catalyzing Diels-Alder cycloaddition reactions by comprehensive mutation analysis and a variety of probing techniques. New tertiary interactions involving base pairs between nucleotides of the 5' terminus and a large internal loop forming a pseudoknot fold were identified. The probing data indicate a preformed tertiary structure that shows no major changes on substrate or product binding. Based on these observations, a molecular architecture featuring a Y-shaped arrangement is proposed. The tertiary structure is formed in a rather unusual way; that is, the opposite sides of the asymmetric internal loop are clamped by the four 5'-terminal nucleotides, forming two adjacent two base-pair helices. It is proposed that the catalytic pocket is formed by a wedge within one of these helices.

Structured Post-IQ Domain Governs Selectivity of Myosin X for Fascin-Actin Bundles*

PubMed Central

Nagy, Stanislav; Rock, Ronald S.

2010-01-01

Without guidance cues, cytoskeletal motors would traffic components to the wrong destination with disastrous consequences for the cell. Recently, we identified a motor protein, myosin X, that identifies bundled actin filaments for transport. These bundles direct myosin X to a unique destination, the tips of cellular filopodia. Because the structural and kinetic features that drive bundle selection are unknown, we employed a domain-swapping approach with the nonselective myosin V to identify the selectivity module of myosin X. We found a surprising role of the myosin X tail region (post-IQ) in supporting long runs on bundles. Moreover, the myosin X head is adapted for initiating processive runs on bundles. We found that the tail is structured and biases the orientation of the two myosin X heads because a targeted insertion that introduces flexibility in the tail abolishes selectivity. Together, these results suggest how myosin motors may manage to read cellular addresses. PMID:20538587

Structural character of the Ghost Dance fault, Yucca Mountain, Nevada

USGS Publications Warehouse

Spengler, R.W.; Braun, C.A.; Linden, R.M.; Martin, L.G.; Ross-Brown, D. M.; Blackburn, R.L.

1993-01-01

Detailed structural mapping of an area that straddles the southern part of the Ghost Dance Fault has revealed the presence of several additional subparallel to anastomosing faults. These faults, mapped at a scale of 1:240, are: 1) dominantly north trending, 2) present on both the upthrown and downthrown sides of the surface trace of the Ghost Dance fault, 3) near-vertical features that commonly offset strata down to the west by 3 to 6 m (10 to 20 ft), and 4) commonly spaced 15 to 46 m (50 to 150 ft) apart. The zone also exhibits a structural fabric, containing an abundance of northwest-trending fractures. The width of the zone appears to be at least 213 m (700 ft) near the southernmost boundary of the study area but remains unknown near the northern extent of the study area, where the width of the study area is only 183 m (600 ft).

Natural products as an inspiration in the diversity-oriented synthesis of bioactive compound libraries

PubMed Central

Cordier, Christopher; Morton, Daniel; Murrison, Sarah; O'Leary-Steele, Catherine

2008-01-01

The purpose of diversity-oriented synthesis is to drive the discovery of small molecules with previously unknown biological functions. Natural products necessarily populate biologically relevant chemical space, since they bind both their biosynthetic enzymes and their target macromolecules. Natural product families are, therefore, libraries of pre-validated, functionally diverse structures in which individual compounds selectively modulate unrelated macromolecular targets. This review describes examples of diversity-oriented syntheses which have, to some extent, been inspired by the structures of natural products. Particular emphasis is placed on innovations that allow the synthesis of compound libraries that, like natural products, are skeletally diverse. Mimicking the broad structural features of natural products may allow the discovery of compounds that modulate the functions of macromolecules for which ligands are not known. The ability of innovations in diversity-oriented synthesis to deliver such compounds is critically assessed. PMID:18663392

The fundamentals behind solving for unknown molecular structures using computer-assisted structure elucidation: a free software package at the undergraduate and graduate levels.

PubMed

Moser, Arvin; Pautler, Brent G

2016-05-15

The successful elucidation of an unknown compound's molecular structure often requires an analyst with profound knowledge and experience of advanced spectroscopic techniques, such as Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. The implementation of Computer-Assisted Structure Elucidation (CASE) software in solving for unknown structures, such as isolated natural products and/or reaction impurities, can serve both as elucidation and teaching tools. As such, the introduction of CASE software with 112 exercises to train students in conjunction with the traditional pen and paper approach will strengthen their overall understanding of solving unknowns and explore of various structural end points to determine the validity of the results quickly. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Arsia Mons Ripples

NASA Image and Video Library

2012-02-17

This image captured by NASA 2001 Mars Odyssey spacecraft shows a series of low, concentric ridges is located to the west of Arsia Mons. The origin of these features is unknown, and there are no similar features at the other Tharsis volcanoes.

Tasks and premises in quantum state determination

NASA Astrophysics Data System (ADS)

Carmeli, Claudio; Heinosaari, Teiko; Schultz, Jussi; Toigo, Alessandro

2014-02-01

The purpose of quantum tomography is to determine an unknown quantum state from measurement outcome statistics. There are two obvious ways to generalize this setting. First, our task need not be the determination of any possible input state but only some input states, for instance pure states. Second, we may have some prior information, or premise, which guarantees that the input state belongs to some subset of states, for instance the set of states with rank less than half of the dimension of the Hilbert space. We investigate state determination under these two supplemental features, concentrating on the cases where the task and the premise are statements about the rank of the unknown state. We characterize the structure of quantum observables (positive operator valued measures) that are capable of fulfilling these type of determination tasks. After the general treatment we focus on the class of covariant phase space observables, thus providing physically relevant examples of observables both capable and incapable of performing these tasks. In this context, the effect of noise is discussed.

Caregiver Strain and Sensory Features in Children with Autism Spectrum Disorder and Other Developmental Disabilities

ERIC Educational Resources Information Center

Kirby, Anne V.; White, Tamira J.; Baranek, Grace T.

2015-01-01

Caring for children with disabilities contributes to increased levels of parent stress or caregiver strain. However, the potential relationship of sensory features to strain among caregivers of children with autism spectrum disorder (ASD) and other developmental disabilities (DD) is unknown. Sensory features include overreactions, underreactions,…

Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments.

PubMed

Zani, Carlos L; Carroll, Anthony R

2017-06-23

The discovery of novel and/or new bioactive natural products from biota sources is often confounded by the reisolation of known natural products. Dereplication strategies that involve the analysis of NMR and MS spectroscopic data to infer structural features present in purified natural products in combination with database searches of these substructures provide an efficient method to rapidly identify known natural products. Unfortunately this strategy has been hampered by the lack of publically available and comprehensive natural product databases and open source cheminformatics tools. A new platform, DEREP-NP, has been developed to help solve this problem. DEREP-NP uses the open source cheminformatics program DataWarrior to generate a database containing counts of 65 structural fragments present in 229 358 natural product structures derived from plants, animals, and microorganisms, published before 2013 and freely available in the nonproprietary Universal Natural Products Database (UNPD). By counting the number of times one or more of these structural features occurs in an unknown compound, as deduced from the analysis of its NMR ( 1 H, HSQC, and/or HMBC) and/or MS data, matching structures carrying the same numeric combination of searched structural features can be retrieved from the database. Confirmation that the matching structure is the same compound can then be verified through literature comparison of spectroscopic data. This methodology can be applied to both purified natural products and fractions containing a small number of individual compounds that are often generated as screening libraries. The utility of DEREP-NP has been verified through the analysis of spectra derived from compounds (and fractions containing two or three compounds) isolated from plant, marine invertebrate, and fungal sources. DEREP-NP is freely available at https://github.com/clzani/DEREP-NP and will help to streamline the natural product discovery process.

Time drawings: Spatial representation of temporal concepts.

PubMed

Leone, María Juliana; Salles, Alejo; Pulver, Alejandro; Golombek, Diego Andrés; Sigman, Mariano

2018-03-01

Time representation is a fundamental property of human cognition. Ample evidence shows that time (and numbers) are represented in space. However, how the conceptual mapping varies across individuals, scales, and temporal structures remains largely unknown. To investigate this issue, we conducted a large online study consisting in five experiments that addressed different time scales and topology: Zones of time, Seasons, Days of the week, Parts of the day and Timeline. Participants were asked to map different kinds of time events to a location in space and to determine their size and color. Results showed that time is organized in space in a hierarchical progression: some features appear to be universal (i.e. selection order), others are shaped by how time is organized in distinct cultures (i.e. location order) and, finally, some aspects vary depending on individual features such as age, gender, and chronotype (i.e. size and color). Copyright © 2018 Elsevier Inc. All rights reserved.

Keywords and Co-Occurrence Patterns in the Voynich Manuscript: An Information-Theoretic Analysis

PubMed Central

Montemurro, Marcelo A.; Zanette, Damián H.

2013-01-01

The Voynich manuscript has remained so far as a mystery for linguists and cryptologists. While the text written on medieval parchment -using an unknown script system- shows basic statistical patterns that bear resemblance to those from real languages, there are features that suggested to some researches that the manuscript was a forgery intended as a hoax. Here we analyse the long-range structure of the manuscript using methods from information theory. We show that the Voynich manuscript presents a complex organization in the distribution of words that is compatible with those found in real language sequences. We are also able to extract some of the most significant semantic word-networks in the text. These results together with some previously known statistical features of the Voynich manuscript, give support to the presence of a genuine message inside the book. PMID:23805215

Cornelia de Lange syndrome: a case study.

PubMed

Kalal, Goud Iravathy; Raina, Vimarsh P; Nayak, Veerabhadra S; Teotia, Pooja; Gupta, Bhushan V

2009-02-01

Cornelia de Lange syndrome (CDLS) is a relatively common multiple congenital anomaly/mental retardation disorder with an unknown genetic and molecular pathogenesis. The essential features of this developmental malformation syndrome are retardation in growth, developmental delay, various structural limb abnormalities, and distinctive facial features. Most cases are sporadic and are thought to result from a new dominant mutation. Consequently, hypotheses regarding the pathogenetic mechanisms underlying the two distinct phenotypes, classic and mild, are purely speculative. The recent discovery of molecular techniques and identification of the NIPBL gene has allowed etiologic diagnosis of this disorder. In this article, we describe a patient with CDLS in whom conventional cytogenetics, fluorescence in situ hybridization, and NIPBL gene mutation analysis determined an etiologic diagnosis, providing precise genetic counseling and facilitated the family to make an evidence-based decision for conception and also alleviated the extreme degree of anxiety associated with the thought of having a second child in this set of circumstances.

[The age-specific features of palm dermatoglyphics in the adults subjects].

PubMed

Teplov, K V; Bozhchenko, A P; Tolmachev, I A; Moiseenko, S A

2016-01-01

This article was designed to consider the congenital age-specific features of palm dermatoglyphics in the adults subjects (including the type of the papillary patterns, axial tri-radii, the termini of palmar main lines, the rudiments of palmar lines, the dermatoglyphic ridge count between the stable anatomical structures). The objective of the study was to look for the new diagnostic markers of the biological age. It included the identification of the palm prints obtained from 180 Caucasoid men and 120 women at the age varying from 16 to 80 years. The results of the mathematical and statistical analysis provided the basis for drawing up the list of 18 attributes of palm dermatoglyphics significantly (p<0.05) differing in the frequency of occurrence between the representatives of individual age groups. The methods are proposed allowing to use these findings for the expert evaluation of the age of unknown subjects.

A new method for constructing networks from binary data

NASA Astrophysics Data System (ADS)

van Borkulo, Claudia D.; Borsboom, Denny; Epskamp, Sacha; Blanken, Tessa F.; Boschloo, Lynn; Schoevers, Robert A.; Waldorp, Lourens J.

2014-08-01

Network analysis is entering fields where network structures are unknown, such as psychology and the educational sciences. A crucial step in the application of network models lies in the assessment of network structure. Current methods either have serious drawbacks or are only suitable for Gaussian data. In the present paper, we present a method for assessing network structures from binary data. Although models for binary data are infamous for their computational intractability, we present a computationally efficient model for estimating network structures. The approach, which is based on Ising models as used in physics, combines logistic regression with model selection based on a Goodness-of-Fit measure to identify relevant relationships between variables that define connections in a network. A validation study shows that this method succeeds in revealing the most relevant features of a network for realistic sample sizes. We apply our proposed method to estimate the network of depression and anxiety symptoms from symptom scores of 1108 subjects. Possible extensions of the model are discussed.

Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling

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

Ren, Xiaoming; Gelinas, Amy D.; von Carlowitz, Ira

IL-1α is an essential cytokine that contributes to inflammatory responses and is implicated in various forms of pathogenesis and cancer. Here we report a naphthyl modified DNA aptamer that specifically binds IL-1α and inhibits its signaling pathway. By solving the crystal structure of the IL-1α/aptamer, we provide a high-resolution structure of this critical cytokine and we reveal its functional interaction interface with high-affinity ligands. The non-helical aptamer, which represents a highly compact nucleic acid structure, contains a wealth of new conformational features, including an unknown form of G-quadruplex. The IL-1α/aptamer interface is composed of unusual polar and hydrophobic elements, alongmore » with an elaborate hydrogen bonding network that is mediated by sodium ion. IL-1α uses the same interface to interact with both the aptamer and its cognate receptor IL-1RI, thereby suggesting a novel route to immunomodulatory therapeutics.« less

Single-crystal Raman spectroscopy and X-ray crystallography at beamline X26-C of the NSLS

PubMed Central

Stoner-Ma, Deborah; Skinner, John M.; Schneider, Dieter K.; Cowan, Matt; Sweet, Robert M.; Orville, Allen M.

2011-01-01

Three-dimensional structures derived from X-ray diffraction of protein crystals provide a wealth of information. Features and interactions important for the function of macromolecules can be deduced and catalytic mechanisms postulated. Still, many questions can remain, for example regarding metal oxidation states and the interpretation of ‘mystery density’, i.e. ambiguous or unknown features within the electron density maps, especially at ∼2 Å resolutions typical of most macromolecular structures. Beamline X26-C at the National Synchrotron Light Source (NSLS), Brookhaven National Laboratory (BNL), provides researchers with the opportunity to not only determine the atomic structure of their samples but also to explore the electronic and vibrational characteristics of the sample before, during and after X-ray diffraction data collection. When samples are maintained under cryo-conditions, an opportunity to promote and follow photochemical reactions in situ as a function of X-ray exposure is also provided. Plans are in place to further expand the capabilities at beamline X26-C and to develop beamlines at NSLS-II, currently under construction at BNL, which will provide users access to a wide array of complementary spectroscopic methods in addition to high-quality X-ray diffraction data. PMID:21169688

XAFS study of copper(II) complexes with square planar and square pyramidal coordination geometries

NASA Astrophysics Data System (ADS)

Gaur, A.; Klysubun, W.; Nitin Nair, N.; Shrivastava, B. D.; Prasad, J.; Srivastava, K.

2016-08-01

X-ray absorption fine structure of six Cu(II) complexes, Cu2(Clna)4 2H2O (1), Cu2(ac)4 2H2O (2), Cu2(phac)4 (pyz) (3), Cu2(bpy)2(na)2 H2O (ClO4) (4), Cu2(teen)4(OH)2(ClO4)2 (5) and Cu2(tmen)4(OH)2(ClO4)2 (6) (where ac, phac, pyz, bpy, na, teen, tmen = acetate, phenyl acetate, pyrazole, bipyridine, nicotinic acid, tetraethyethylenediamine, tetramethylethylenediamine, respectively), which were supposed to have square pyramidal and square planar coordination geometries have been investigated. The differences observed in the X-ray absorption near edge structure (XANES) features of the standard compounds having four, five and six coordination geometry points towards presence of square planar and square pyramidal geometry around Cu centre in the studied complexes. The presence of intense pre-edge feature in the spectra of four complexes, 1-4, indicates square pyramidal coordination. Another important XANES feature, present in complexes 5 and 6, is prominent shoulder in the rising part of edge whose intensity decreases in the presence of axial ligands and thus indicates four coordination in these complexes. Ab initio calculations were carried out for square planar and square pyramidal Cu centres to observe the variation of 4p density of states in the presence and absence of axial ligands. To determine the number and distance of scattering atoms around Cu centre in the complexes, EXAFS analysis has been done using the paths obtained from Cu(II) oxide model and an axial Cu-O path from model of a square pyramidal complex. The results obtained from EXAFS analysis have been reported which confirmed the inference drawn from XANES features. Thus, it has been shown that these paths from model of a standard compound can be used to determine the structural parameters for complexes having unknown structure.

A new look at Togo through the eyes of a SLAR

NASA Technical Reports Server (NTRS)

Dellwig, L. F.

1980-01-01

Imaging of Togo in 1977 with SLAR provided the data required for the production of map controlled radar mosaics at a scale of 1:200,000 with 95 percent of all control points at that scale within + or - 4.0 millimeters of true positions. The moasics served as the base for the generation of a revised geologic map of Togo. Aided by two looks, numerous revisions resulted, not only with the addition of previously unknown structural features, a revision of age relationships, and the refinement of unit boundaries, but also with the repositioning of rock units and the reorientation of major faults.

The crystal structure of mammalian inositol 1,3,4,5,6-pentakisphosphate 2-kinase reveals a new zinc-binding site and key features for protein function

PubMed Central

Franco-Echevarría, Elsa; Sanz-Aparicio, Julia; Brearley, Charles A.; González-Rubio, Juana M.; González, Beatriz

2017-01-01

Inositol 1,3,4,5,6-pentakisphosphate 2-kinases (IP5 2-Ks) are part of a family of enzymes in charge of synthesizing inositol hexakisphosphate (IP6) in eukaryotic cells. This protein and its product IP6 present many roles in cells, participating in mRNA export, embryonic development, and apoptosis. We reported previously that the full-length IP5 2-K from Arabidopsis thaliana is a zinc metallo-enzyme, including two separated lobes (the N- and C-lobes). We have also shown conformational changes in IP5 2-K and have identified the residues involved in substrate recognition and catalysis. However, the specific features of mammalian IP5 2-Ks remain unknown. To this end, we report here the first structure for a murine IP5 2-K in complex with ATP/IP5 or IP6. Our structural findings indicated that the general folding in N- and C-lobes is conserved with A. thaliana IP5 2-K. A helical scaffold in the C-lobe constitutes the inositol phosphate-binding site, which, along with the participation of the N-lobe, endows high specificity to this protein. However, we also noted large structural differences between the orthologues from these two eukaryotic kingdoms. These differences include a novel zinc-binding site and regions unique to the mammalian IP5 2-K, as an unexpected basic patch on the protein surface. In conclusion, our findings have uncovered distinct features of a mammalian IP5 2-K and set the stage for investigations into protein-protein or protein-RNA interactions important for IP5 2-K function and activity. PMID:28450399

A scanning acoustic microscope discriminates cancer cells in fluid

NASA Astrophysics Data System (ADS)

Miura, Katsutoshi; Yamamoto, Seiji

2015-10-01

Scanning acoustic microscopy (SAM) discriminates lesions in sections by assessing the speed of sound (SOS) or attenuation of sound (AOS) through tissues within a few minutes without staining; however, its clinical use in cytological diagnosis is unknown. We applied a thin layer preparation method to observe benign and malignant effusions using SAM. Although SAM is inferior in detecting nuclear features than light microscopy, it can differentiate malignant from benign cells using the higher SOS and AOS values and large irregular cell clusters that are typical features of carcinomas. Moreover, each single malignant cell exhibits characteristic cytoplasmic features such as a large size, irregular borders and secretory or cytoskeletal content. By adjusting the observation range, malignant cells are differentiated from benign cells easily using SAM. Subtle changes in the functional and structural heterogeneity of tumour cells were pursuable with a different digital data of SAM. SAM can be a useful tool for screening malignant cells in effusions before light microscopic observation. Higher AOS values in malignant cells compared with those of benign cells support the feasibility of a novel sonodynamic therapy for malignant effusions.

MSSA de-noising of horizon time structure to improve the curvature attribute analysis

NASA Astrophysics Data System (ADS)

Tiwari, R. K.; Rekapalli, R.; Vedanti, N.

2017-12-01

Although the seismic attributes are useful for identifying sub-surface structural features like faults, fractures, lineaments and sharp stratigraphy etc., the different kinds of noises arising from unknown physical sources during the data acquisition and processing creates acute problems in physical interpretation of complex crustal structures. Hence, we propose to study effect of noise on curvature attribute analysis of seismic time structure data. We propose here Multichannel Singular Spectrum Analysis (MSSA) de-noising algorithm as a pre filtering scheme to reduce effect of noise. To demonstrate the procedure, first, we compute the most positive and negative curvature on a synthetic time structure with surface features resembling anticlines, synclines and faults and then adding the known percentage of noise. We noticed that the curvatures estimated from the noisy data reveal considerable deviations from the curvature of pure synthetic data. This suggests that there is a strong impact of noise on the curvature estimates. Further, we have employed 2D median filter and MSSA methods to filter the noisy time structure and then computed the curvatures. The comparisons of curvatures estimated from de-noised data suggest that the results obtained from MSSA de-noised data match well with the curvatures of pure synthetic data. Finally, we present an example of real data analysis from Utsira Top (UT) horizon of Southern Viking Graben, Norway to identify the time-lapse changes in UT horizon after CO2 injection. We applied the MSSA de-noising algorithm on UT horizon time structure and amplitude data of pre and post CO2 injection. Our analyses suggest modest but clearly visible, structural changes in the UT horizon after CO2 injection at a few locations, which seem to be associated with the locations of change in seismic amplitudes. Thus, the results from both the synthetic and real field data suggest that the MSSA based de-noising algorithm is robust for filtering the horizon time structures for accurate curvature attributes analysis and better interpretation of structural changes in geological features. Key Words: Curvature attributes, MSSA, Seismic Horizon, 2D-median filter, Utsira Horizon.

iEzy-Drug: A Web Server for Identifying the Interaction between Enzymes and Drugs in Cellular Networking

PubMed Central

Min, Jian-Liang; Chou, Kuo-Chen

2013-01-01

With the features of extremely high selectivity and efficiency in catalyzing almost all the chemical reactions in cells, enzymes play vitally important roles for the life of an organism and hence have become frequent targets for drug design. An essential step in developing drugs by targeting enzymes is to identify drug-enzyme interactions in cells. It is both time-consuming and costly to do this purely by means of experimental techniques alone. Although some computational methods were developed in this regard based on the knowledge of the three-dimensional structure of enzyme, unfortunately their usage is quite limited because three-dimensional structures of many enzymes are still unknown. Here, we reported a sequence-based predictor, called “iEzy-Drug,” in which each drug compound was formulated by a molecular fingerprint with 258 feature components, each enzyme by the Chou's pseudo amino acid composition generated via incorporating sequential evolution information and physicochemical features derived from its sequence, and the prediction engine was operated by the fuzzy K-nearest neighbor algorithm. The overall success rate achieved by iEzy-Drug via rigorous cross-validations was about 91%. Moreover, to maximize the convenience for the majority of experimental scientists, a user-friendly web server was established, by which users can easily obtain their desired results. PMID:24371828

Exploration and discovery in Yellowstone Lake: results from high-resolution sonar imaging, seismic reflection profiling, and submersible studies

NASA Astrophysics Data System (ADS)

Morgan, L. A.; Shanks, W. C.; Lovalvo, D. A.; Johnson, S. Y.; Stephenson, W. J.; Pierce, K. L.; Harlan, S. S.; Finn, C. A.; Lee, G.; Webring, M.; Schulze, B.; Dühn, J.; Sweeney, R.; Balistrieri, L.

2003-04-01

'No portion of the American continent is perhaps so rich in wonders as the Yellow Stone' (F.V. Hayden, September 2, 1874) Discoveries from multi-beam sonar mapping and seismic reflection surveys of the northern, central, and West Thumb basins of Yellowstone Lake provide new insight into the extent of post-collapse volcanism and active hydrothermal processes occurring in a large lake environment above a large magma chamber. Yellowstone Lake has an irregular bottom covered with dozens of features directly related to hydrothermal, tectonic, volcanic, and sedimentary processes. Detailed bathymetric, seismic reflection, and magnetic evidence reveals that rhyolitic lava flows underlie much of Yellowstone Lake and exert fundamental control on lake bathymetry and localization of hydrothermal activity. Many previously unknown features have been identified and include over 250 hydrothermal vents, several very large (>500 m diameter) hydrothermal explosion craters, many small hydrothermal vent craters (˜1-200 m diameter), domed lacustrine sediments related to hydrothermal activity, elongate fissures cutting post-glacial sediments, siliceous hydrothermal spire structures, sublacustrine landslide deposits, submerged former shorelines, and a recently active graben. Sampling and observations with a submersible remotely operated vehicle confirm and extend our understanding of the identified features. Faults, fissures, hydrothermally inflated domal structures, hydrothermal explosion craters, and sublacustrine landslides constitute potentially significant geologic hazards. Toxic elements derived from hydrothermal processes also may significantly affect the Yellowstone ecosystem.

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

PubMed Central

McDaniell, Ryan; Lee, Bum-Kyu; Song, Lingyun; Liu, Zheng; Boyle, Alan P.; Erdos, Michael R.; Scott, Laura J.; Morken, Mario A.; Kucera, Katerina S.; Battenhouse, Anna; Keefe, Damian; Collins, Francis S.; Willard, Huntington F.; Lieb, Jason D.; Furey, Terrence S.; Crawford, Gregory E.; Iyer, Vishwanath R.; Birney, Ewan

2010-01-01

The extent to which variation in chromatin structure and transcription factor binding may influence gene expression, and thus underlie or contribute to variation in phenotype, is unknown. To address this question, we cataloged both individual-to-individual variation and differences between homologous chromosomes within the same individual (allele-specific variation) in chromatin structure and transcription factor binding in lymphoblastoid cells derived from individuals of geographically diverse ancestry. Ten percent of active chromatin sites were individual-specific; a similar proportion were allele-specific. Both individual-specific and allele-specific sites were commonly transmitted from parent to child, which suggests that they are heritable features of the human genome. Our study shows that heritable chromatin status and transcription factor binding differ as a result of genetic variation and may underlie phenotypic variation in humans. PMID:20299549

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.

A conserved αβ transmembrane interface forms the core of a compact T-cell receptor–CD3 structure within the membrane

PubMed Central

Krshnan, Logesvaran; Park, Soohyung; Im, Wonpil; Call, Melissa J.; Call, Matthew E.

2016-01-01

The T-cell antigen receptor (TCR) is an assembly of eight type I single-pass membrane proteins that occupies a central position in adaptive immunity. Many TCR-triggering models invoke an alteration in receptor complex structure as the initiating event, but both the precise subunit organization and the pathway by which ligand-induced alterations are transferred to the cytoplasmic signaling domains are unknown. Here, we show that the receptor complex transmembrane (TM) domains form an intimately associated eight-helix bundle organized by a specific interhelical TCR TM interface. The salient features of this core structure are absolutely conserved between αβ and γδ TCR sequences and throughout vertebrate evolution, and mutations at key interface residues caused defects in the formation of stable TCRαβ:CD3δε:CD3γε:ζζ complexes. These findings demonstrate that the eight TCR–CD3 subunits form a compact and precisely organized structure within the membrane and provide a structural basis for further investigation of conformationally regulated models of transbilayer TCR signaling. PMID:27791034

Experimental and Imaging Techniques for Examining Fibrin Clot Structures in Normal and Diseased States

PubMed Central

Fan, Natalie K.; Keegan, Philip M.; Platt, Manu O.; Averett, Rodney D.

2015-01-01

Fibrin is an extracellular matrix protein that is responsible for maintaining the structural integrity of blood clots. Much research has been done on fibrin in the past years to include the investigation of synthesis, structure-function, and lysis of clots. However, there is still much unknown about the morphological and structural features of clots that ensue from patients with disease. In this research study, experimental techniques are presented that allow for the examination of morphological differences of abnormal clot structures due to diseased states such as diabetes and sickle cell anemia. Our study focuses on the preparation and evaluation of fibrin clots in order to assess morphological differences using various experimental assays and confocal microscopy. In addition, a method is also described that allows for continuous, real-time calculation of lysis rates in fibrin clots. The techniques described herein are important for researchers and clinicians seeking to elucidate comorbid thrombotic pathologies such as myocardial infarctions, ischemic heart disease, and strokes in patients with diabetes or sickle cell disease. PMID:25867016

A conserved αβ transmembrane interface forms the core of a compact T-cell receptor-CD3 structure within the membrane.

PubMed

Krshnan, Logesvaran; Park, Soohyung; Im, Wonpil; Call, Melissa J; Call, Matthew E

2016-10-25

The T-cell antigen receptor (TCR) is an assembly of eight type I single-pass membrane proteins that occupies a central position in adaptive immunity. Many TCR-triggering models invoke an alteration in receptor complex structure as the initiating event, but both the precise subunit organization and the pathway by which ligand-induced alterations are transferred to the cytoplasmic signaling domains are unknown. Here, we show that the receptor complex transmembrane (TM) domains form an intimately associated eight-helix bundle organized by a specific interhelical TCR TM interface. The salient features of this core structure are absolutely conserved between αβ and γδ TCR sequences and throughout vertebrate evolution, and mutations at key interface residues caused defects in the formation of stable TCRαβ:CD3δε:CD3γε:ζζ complexes. These findings demonstrate that the eight TCR-CD3 subunits form a compact and precisely organized structure within the membrane and provide a structural basis for further investigation of conformationally regulated models of transbilayer TCR signaling.

Solution Structure and Membrane Interaction of the Cytoplasmic Tail of HIV-1 gp41 Protein.

PubMed

Murphy, R Elliot; Samal, Alexandra B; Vlach, Jiri; Saad, Jamil S

2017-11-07

The cytoplasmic tail of gp41 (gp41CT) remains the last HIV-1 domain with an unknown structure. It plays important roles in HIV-1 replication such as mediating envelope (Env) intracellular trafficking and incorporation into assembling virions, mechanisms of which are poorly understood. Here, we present the solution structure of gp41CT in a micellar environment and characterize its interaction with the membrane. We show that the N-terminal 45 residues are unstructured and not associated with the membrane. However, the C-terminal 105 residues form three membrane-bound amphipathic α helices with distinctive structural features such as variable degree of membrane penetration, hydrophobic and basic surfaces, clusters of aromatic residues, and a network of cation-π interactions. This work fills a major gap by providing the structure of the last segment of HIV-1 Env, which will provide insights into the mechanisms of Gag-mediated Env incorporation as well as the overall Env mobility and conformation on the virion surface. Copyright © 2017 Elsevier Ltd. All rights reserved.

Swit_4259, an acetoacetate decarboxylase-like enzyme from Sphingomonas wittichii RW1

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

Mydy, Lisa S.; Mashhadi, Zahra; Knight, T. William

The Gram-negative bacteriumSphingomonas wittichiiRW1 is notable for its ability to metabolize a variety of aromatic hydrocarbons. Not surprisingly, theS. wittichiigenome contains a number of putative aromatic hydrocarbon-degrading gene clusters. One of these includes an enzyme of unknown function, Swit_4259, which belongs to the acetoacetate decarboxylase-like superfamily (ADCSF). Here, it is reported that Swit_4259 is a small (28.8 kDa) tetrameric ADCSF enzyme that, unlike the prototypical members of the superfamily, does not have acetoacetate decarboxylase activity. Structural characterization shows that the tertiary structure of Swit_4259 is nearly identical to that of the true decarboxylases, but there are important differences in themore » fine structure of the Swit_4259 active site that lead to a divergence in function. In addition, it is shown that while it is a poor substrate, Swit_4259 can catalyze the hydration of 2-oxo-hex-3-enedioate to yield 2-oxo-4-hydroxyhexanedioate. It is also demonstrated that Swit_4259 has pyruvate aldolase-dehydratase activity, a feature that is common to all of the family V ADCSF enzymes studied to date. The enzymatic activity, together with the genomic context, suggests that Swit_4259 may be a hydratase with a role in the metabolism of an as-yet-unknown hydrocarbon. These data have implications for engineering bioremediation pathways to degrade specific pollutants, as well as structure–function relationships within the ADCSF in general.« less

Structural control and health monitoring of building structures with unknown ground excitations: Experimental investigation

NASA Astrophysics Data System (ADS)

He, Jia; Xu, You-Lin; Zhan, Sheng; Huang, Qin

2017-03-01

When health monitoring system and vibration control system both are required for a building structure, it will be beneficial and cost-effective to integrate these two systems together for creating a smart building structure. Recently, on the basis of extended Kalman filter (EKF), a time-domain integrated approach was proposed for the identification of structural parameters of the controlled buildings with unknown ground excitations. The identified physical parameters and structural state vectors were then utilized to determine the control force for vibration suppression. In this paper, the possibility of establishing such a smart building structure with the function of simultaneous damage detection and vibration suppression was explored experimentally. A five-story shear building structure equipped with three magneto-rheological (MR) dampers was built. Four additional columns were added to the building model, and several damage scenarios were then simulated by symmetrically cutting off these columns in certain stories. Two sets of earthquakes, i.e. Kobe earthquake and Northridge earthquake, were considered as seismic input and assumed to be unknown during the tests. The structural parameters and the unknown ground excitations were identified during the tests by using the proposed identification method with the measured control forces. Based on the identified structural parameters and system states, a switching control law was employed to adjust the current applied to the MR dampers for the purpose of vibration attenuation. The experimental results show that the presented approach is capable of satisfactorily identifying structural damages and unknown excitations on one hand and significantly mitigating the structural vibration on the other hand.

Structure Determination of Unknown Organic Liquids Using NMR and IR Spectroscopy: A General Chemistry Laboratory

ERIC Educational Resources Information Center

Pavel, John T.; Hyde, Erin C.; Bruch, Martha D.

2012-01-01

This experiment introduced general chemistry students to the basic concepts of organic structures and to the power of spectroscopic methods for structure determination. Students employed a combination of IR and NMR spectroscopy to perform de novo structure determination of unknown alcohols, without being provided with a list of possible…

Temporal resolution for the perception of features and conjunctions.

PubMed

Bodelón, Clara; Fallah, Mazyar; Reynolds, John H

2007-01-24

The visual system decomposes stimuli into their constituent features, represented by neurons with different feature selectivities. How the signals carried by these feature-selective neurons are integrated into coherent object representations is unknown. To constrain the set of possible integrative mechanisms, we quantified the temporal resolution of perception for color, orientation, and conjunctions of these two features. We find that temporal resolution is measurably higher for each feature than for their conjunction, indicating that time is required to integrate features into a perceptual whole. This finding places temporal limits on the mechanisms that could mediate this form of perceptual integration.

Experimental shock deformation in zircon: a transmission electron microscopic study

NASA Astrophysics Data System (ADS)

Leroux, H.; Reimold, W. U.; Koeberl, C.; Hornemann, U.; Doukhan, J.-C.

1999-06-01

In recent years, apparently shock-induced and, thus, impact-characteristic microdeformations, in the form of planar microdeformation features and so-called strawberry (granular) texture, have been observed in zircons in rocks from confirmed impact structures and from the K/ T boundary. The nature of the planar microdeformations in this mineral is, however, still unknown, and critical information is needed regarding the shock pressure range in which these deformation effects are produced. We experimentally shock deformed two series of thin zircon (ZrSiO 4) target plates, cut perpendicular to the c-axis, at shock pressures of 20, 40, and 60 GPa. The recovered samples were characterized by optical and scanning electron microscopy. In addition, one sample series was studied by transmission electron microscopy (TEM). Microdeformation effects observed at 20 GPa include pervasive micro-cleavage and dislocation patterns. Plastic deformation is indicated by a high density of straight dislocations in glide configuration. The dominant glide systems are <100>{010}. Micro-cleavages, induced by shear stresses during the compression stage, occur mostly in the {100} planes. The large density of dislocations at crack tips shows that plastic deformation was initiated by the micro-cracking processs. At 40 GPa, the sample was partly transformed from the zircon (z) to a scheelite (CaWO 4)-type (s) structure. Planar deformation features (PDFs) containing an amorphous phase of zircon composition are present in the not yet transformed zircon relics. The phase with scheelite structure, initiated in the {100} planes of zircon, consists of thin (0.1 to several μm) bands that crosscut the zircon matrix. The phase transformation is displacive (martensitic) and can be related by {100} z // {112} s and [001] z // <110> s. The scheelite structure phase is densely twinned, with twins in the (112) plane. The 60-GPa sample consists completely of the scheelite structure phase. Crosscutting and displacing relationships between twins and PDFs demonstrate that PDFs are formed in the zircon structure, i.e., before the phase transformation to the scheelite structure occurred, most likely at the shock front. Crystallographic orientations of optically visible planar features in zircon, in comparison with orientations of planar defects at the TEM scale, suggest that the optically visible features are more likely planar microfractures than PDFs.

Synthesis and Characterization of 1,4-Dihydro-3,1-Benzoxazines and 1,2,3,4-Tetrahydroquinazolines: An Unknown Structure Determination Experiment

ERIC Educational Resources Information Center

Bendorf, Holly D.; Vebrosky, Emily N.; Eck, Brian J.

2016-01-01

In this experiment for an upper-division course in organic structure determination, each student prepares an unknown compound and characterizes the product using multiple spectroscopic techniques. The unknowns, 2-aryl-substituted 1,4-dihydro-3,1-benzoxazines and 1,2,3,4-tetrahydroquinazolines, are prepared in a single step by the condensation of…

17. Photographic copy of photograph. Location unknown but assumed to ...

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

17. Photographic copy of photograph. Location unknown but assumed to be uper end of canal. Features no longer extant. (Source: U.S. Department of Interior. Office of Indian Affairs. Indian Irrigation service. Annual Report, Fiscal Year 1925. Vol. I, Narrative and Photographs, Irrigation District #4, California and Southern Arizona, RG 75, Entry 655, Box 28, National Archives, Washington, DC.) Photographer unknown. MAIN (TITLED FLORENCE) CANAL, WASTEWAY, SLUICEWAY, & BRIDGE, 1/26/25. - San Carlos Irrigation Project, Marin Canal, Amhurst-Hayden Dam to Picacho Reservoir, Coolidge, Pinal County, AZ

Structural features and lipid binding domain of tubulin on biomimetic mitochondrial membranes

PubMed Central

Hoogerheide, David P.; Noskov, Sergei Y.; Jacobs, Daniel; Bergdoll, Lucie; Silin, Vitalii; Worcester, David L.; Abramson, Jeff; Nanda, Hirsh; Rostovtseva, Tatiana K.; Bezrukov, Sergey M.

2017-01-01

Dimeric tubulin, an abundant water-soluble cytosolic protein known primarily for its role in the cytoskeleton, is routinely found to be associated with mitochondrial outer membranes, although the structure and physiological role of mitochondria-bound tubulin are still unknown. There is also no consensus on whether tubulin is a peripheral membrane protein or is integrated into the outer mitochondrial membrane. Here the results of five independent techniques—surface plasmon resonance, electrochemical impedance spectroscopy, bilayer overtone analysis, neutron reflectometry, and molecular dynamics simulations—suggest that α-tubulin’s amphipathic helix H10 is responsible for peripheral binding of dimeric tubulin to biomimetic “mitochondrial” membranes in a manner that differentiates between the two primary lipid headgroups found in mitochondrial membranes, phosphatidylethanolamine and phosphatidylcholine. The identification of the tubulin dimer orientation and membrane-binding domain represents an essential step toward our understanding of the complex mechanisms by which tubulin interacts with integral proteins of the mitochondrial outer membrane and is important for the structure-inspired design of tubulin-targeting agents. PMID:28420794

Structure and reactivity of a mononuclear gold(II) complex

NASA Astrophysics Data System (ADS)

Preiß, Sebastian; Förster, Christoph; Otto, Sven; Bauer, Matthias; Müller, Patrick; Hinderberger, Dariush; Hashemi Haeri, Haleh; Carella, Luca; Heinze, Katja

2017-12-01

Mononuclear gold(II) complexes are very rare labile species. Transient gold(II) species have been suggested in homogeneous catalysis and in medical applications, but their geometric and electronic structures have remained essentially unexplored: even fundamental data, such as the ionic radius of gold(II), are unknown. Now, an unprecedentedly stable neutral gold(II) complex of a porphyrin derivative has been isolated, and its structural and spectroscopic features determined. The gold atom adopts a 2+2 coordination mode in between those of gold(III) (four-coordinate square planar) and gold(I) (two-coordinate linear), owing to a second-order Jahn-Teller distortion enabled by the relativistically lowered 6s orbital of gold. The reactivity of this gold(II) complex towards dioxygen, nitrosobenzene and acids is discussed. This study provides insight on the ionic radius of gold(II), and allows it to be placed within the homologous series of nd9 Cu/Ag/Au divalent ions and the 5d8/9/10 Pt/Au/Hg 'relativistic' triad in the periodic table.

Genetically Encoded Chemical Probes In Cells Reveal the Binding Path of Urocortin-I to CRF Class B GPCR

PubMed Central

Coin, Irene; Katritch, Vsevolod; Sun, Tingting; Xiang, Zheng; Siu, Fai Yiu; Beyermann, Michael; Stevens, Raymond C.; Wang, Lei

2014-01-01

SUMMARY Molecular determinants regulating the activation of class B G-protein coupled receptors (GPCRs) by native peptide agonists are largely unknown. We have investigated here the interaction between the corticotropin releasing factor receptor type 1 (CRF1R) and its native 40-mer peptide ligand Urocortin-I directly in mammalian cells. By incorporating unnatural amino acid photo-chemical and new click-chemical probes into the receptor, 44 inter-molecular spatial constraints have been derived for the ligand-receptor interaction. The data were analyzed in the context of the recently resolved crystal structure of CRF1R transmembrane domain and existing extracellular domain structures, yielding a complete conformational model for the peptide-receptor complex. Structural features of the receptor-ligand complex yield molecular insights on the mechanism of receptor activation. The experimental strategy provides unique information on full-length post-translationally modified GPCRs in the native membrane of the live cell, complementing in vitro biophysical reductionist approaches. PMID:24290358

Structural character of the Ghost Dance Fault, Yucca Mountain, Nevada

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

Spengler, R.W.; Braun, C.A.; Linden, R.M.

1993-12-31

Detailed structural mapping of an area that straddles the southern part of the Ghost Dance Fault has revealed the presence of several additional subparallel to anastomosing faults. These faults, mapped at a scale of 1:240, are: (1) dominantly north-trending, (2) present on both the upthrown and downthrown sides of the surface trace of the Ghost Dance fault, (3) near-vertical features that commonly offset strata down to the west by 3 to 6 m (10 to 20 ft), and (4) commonly spaced 15 to 46 m (50 to 150 ft) apart. The zone also exhibits a structural fabric, containing an abundancemore » of northwest-trending fractures. The width of the zone appears to be at least 213 m (700 ft) near the southernmost boundary of the study area but remains unknown near the northern extent of the study area, where the width of the study area is only 183 m (600 ft).« less

Structural Insights into the Allosteric Operation of the Lon AAA+ Protease.

PubMed

Lin, Chien-Chu; Su, Shih-Chieh; Su, Ming-Yuan; Liang, Pi-Hui; Feng, Chia-Cheng; Wu, Shih-Hsiung; Chang, Chung-I

2016-05-03

The Lon AAA+ protease (LonA) is an evolutionarily conserved protease that couples the ATPase cycle into motion to drive substrate translocation and degradation. A hallmark feature shared by AAA+ proteases is the stimulation of ATPase activity by substrates. Here we report the structure of LonA bound to three ADPs, revealing the first AAA+ protease assembly where the six protomers are arranged alternately in nucleotide-free and bound states. Nucleotide binding induces large coordinated movements of conserved pore loops from two pairs of three non-adjacent protomers and shuttling of the proteolytic groove between the ATPase site and a previously unknown Arg paddle. Structural and biochemical evidence supports the roles of the substrate-bound proteolytic groove in allosteric stimulation of ATPase activity and the conserved Arg paddle in driving substrate degradation. Altogether, this work provides a molecular framework for understanding how ATP-dependent chemomechanical movements drive allosteric processes for substrate degradation in a major protein-destruction machine. Copyright © 2016 Elsevier Ltd. All rights reserved.

The intriguing nature of dorsal root ganglion neurons: linking structure with polarity and function.

PubMed

Nascimento, Ana Isabel; Mar, Fernando Milhazes; Sousa, Mónica Mendes

2018-05-02

Dorsal root ganglion (DRG) neurons are the first neurons of the sensory pathway. They are activated by a variety of sensory stimuli that are then transmitted to the central nervous system. An important feature of DRG neurons is their unique morphology where a single process -the stem axon- bifurcates into a peripheral and a central axonal branch, with different functions and cellular properties. Distinctive structural aspects of the two DRG neuron branches may have important implications for their function in health and disease. However, the link between DRG axonal branch structure, polarity and function has been largely neglected in the field, and relevant information is rather scattered across the literature. In particular, ultrastructural differences between the two axonal branches are likely to account for the higher transport and regenerative ability of the peripheral DRG neuron axon when compared to the central one. Nevertheless, the cell intrinsic factors contributing to this central-peripheral asymmetry are still unknown. Here we critically review the factors that may underlie the functional asymmetry between the peripheral and central DRG axonal branches. Also, we discuss the hypothesis that DRG neurons may assemble a structure resembling the axon initial segment that may be responsible, at least in part, for their polarity and electrophysiological features. Ultimately, we suggest that the clarification of the axonal ultrastructure of DRG neurons using state-of-the-art techniques will be crucial to understand the physiology of this peculiar cell type. Copyright © 2018. Published by Elsevier Ltd.

Visualization of HIV T Cell Virological Synapses and Virus-Containing Compartments by Three-Dimensional Correlative Light and Electron Microscopy

PubMed Central

Wang, Lili; Eng, Edward T.; Law, Kenneth; Gordon, Ronald E.; Rice, William J.

2016-01-01

ABSTRACT Virological synapses (VS) are adhesive structures that form between infected and uninfected cells to enhance the spread of HIV-1. During T cell VS formation, viral proteins are actively recruited to the site of cell-cell contact where the viral material is efficiently translocated to target cells into heterogeneous, protease-resistant, antibody-inaccessible compartments. Using correlative light and electron microscopy (CLEM), we define the membrane topography of the virus-containing compartments (VCC) where HIV is found following VS-mediated transfer. Focused ion beam scanning electron microscopy (FIB-SEM) and serial sectioning transmission electron microscopy (SS-TEM) were used to better resolve the fluorescent Gag-containing structures within the VCC. We found that small punctate fluorescent signals correlated with single viral particles in enclosed vesicular compartments or surface-localized virus particles and that large fluorescent signals correlated with membranous Gag-containing structures with unknown pathological function. CLEM imaging revealed distinct pools of newly deposited viral proteins within endocytic and nonendocytic compartments in VS target T cells. IMPORTANCE This study directly correlates individual virus-associated objects observed in light microscopy with ultrastructural features seen by electron microscopy in the HIV-1 virological synapse. This approach elucidates which infection-associated ultrastructural features represent bona fide HIV protein complexes. We define the morphology of some HIV cell-to-cell transfer intermediates as true endocytic compartments and resolve unique synapse-associated viral structures created by transfer across virological synapses. PMID:27847357

396. Delineator Unknown Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF ...

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

396. Delineator Unknown Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; EAST BAY CROSSING; CANTILEVER STRUCTURE; DETAILS I; DRG. NO. 68 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

397. Delineator Unknown Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF ...

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

397. Delineator Unknown Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; EAST BAY CROSSING; CANTILEVER STRUCTURE; DETAILS II; DRG. NO. 69 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

Identification of input variables for feature based artificial neural networks-saccade detection in EOG recordings.

PubMed

Tigges, P; Kathmann, N; Engel, R R

1997-07-01

Though artificial neural networks (ANN) are excellent tools for pattern recognition problems when signal to noise ratio is low, the identification of decision relevant features for ANN input data is still a crucial issue. The experience of the ANN designer and the existing knowledge and understanding of the problem seem to be the only links for a specific construction. In the present study a backpropagation ANN based on modified raw data inputs showed encouraging results. Investigating the specific influences of prototypical input patterns on a specially designed ANN led to a new sparse and efficient input data presentation. This data coding obtained by a semiautomatic procedure combining existing expert knowledge and the internal representation structures of the raw data based ANN yielded a list of feature vectors, each representing the relevant information for saccade identification. The feature based ANN produced a reduction of the error rate of nearly 40% compared with the raw data ANN. An overall correct classification of 92% of so far unknown data was realized. The proposed method of extracting internal ANN knowledge for the production of a better input data representation is not restricted to EOG recordings, and could be used in various fields of signal analysis.

Inductively coupled plasma mass spectrometry (ICP MS): a versatile tool.

PubMed

Ammann, Adrian A

2007-04-01

Inductively coupled plasma (ICP) mass spectrometry (MS) is routinely used in many diverse research fields such as earth, environmental, life and forensic sciences and in food, material, chemical, semiconductor and nuclear industries. The high ion density and the high temperature in a plasma provide an ideal atomizer and element ionizer for all types of samples and matrices introduced by a variety of specialized devices. Outstanding properties such as high sensitivity (ppt-ppq), relative salt tolerance, compound-independent element response and highest quantitation accuracy lead to the unchallenged performance of ICP MS in efficiently detecting, identifying and reliably quantifying trace elements. The increasing availability of relevant reference compounds and high separation selectivity extend the molecular identification capability of ICP MS hyphenated to species-specific separation techniques. While molecular ion source MS is specialized in determining the structure of unknown molecules, ICP MS is an efficient and highly sensitive tool for target-element orientated discoveries of relevant and unknown compounds. This special-feature, tutorial article presents the principle and advantages of ICP MS, highlighting these using examples from recently published investigations. Copyright 2007 John Wiley & Sons, Ltd.

Simple robust control laws for robot manipulators. Part 2: Adaptive case

NASA Technical Reports Server (NTRS)

Bayard, D. S.; Wen, J. T.

1987-01-01

A new class of asymptotically stable adaptive control laws is introduced for application to the robotic manipulator. Unlike most applications of adaptive control theory to robotic manipulators, this analysis addresses the nonlinear dynamics directly without approximation, linearization, or ad hoc assumptions, and utilizes a parameterization based on physical (time-invariant) quantities. This approach is made possible by using energy-like Lyapunov functions which retain the nonlinear character and structure of the dynamics, rather than simple quadratic forms which are ubiquitous to the adaptive control literature, and which have bound the theory tightly to linear systems with unknown parameters. It is a unique feature of these results that the adaptive forms arise by straightforward certainty equivalence adaptation of their nonadaptive counterparts found in the companion to this paper (i.e., by replacing unknown quantities by their estimates) and that this simple approach leads to asymptotically stable closed-loop adaptive systems. Furthermore, it is emphasized that this approach does not require convergence of the parameter estimates (i.e., via persistent excitation), invertibility of the mass matrix estimate, or measurement of the joint accelerations.

A flexible model for correlated medical costs, with application to medical expenditure panel survey data.

PubMed

Chen, Jinsong; Liu, Lei; Shih, Ya-Chen T; Zhang, Daowen; Severini, Thomas A

2016-03-15

We propose a flexible model for correlated medical cost data with several appealing features. First, the mean function is partially linear. Second, the distributional form for the response is not specified. Third, the covariance structure of correlated medical costs has a semiparametric form. We use extended generalized estimating equations to simultaneously estimate all parameters of interest. B-splines are used to estimate unknown functions, and a modification to Akaike information criterion is proposed for selecting knots in spline bases. We apply the model to correlated medical costs in the Medical Expenditure Panel Survey dataset. Simulation studies are conducted to assess the performance of our method. Copyright © 2015 John Wiley & Sons, Ltd.

Geophysical surveys and archaeological insights at Fort Pierre Chouteau, a frontier trading post on the Middle Missouri

NASA Astrophysics Data System (ADS)

Patton, Margaret Maurine

Fort Pierre Chouteau in present day South Dakota was the most important fur trading post of the American Fur Company in the 1830s, serving as a regional hub for the fur trade. The Fort was sold to the U.S. Military in 1855 for use as a base in the Sioux Wars but was abandoned in 1856. Geophysical surveys and previous excavations indicate evidence of both occupations. Geophysics is an important tool for determining the extent of archaeological sites, yet the relationships between geophysical anomalies and excavation features may not be readily evident. Initial geophysical surveys (Kvamme 2007) were completed to determine the extent of the fur trading Fort, and additional surveys in August 2012 used magnetometry and electrical resistance to determine if evidence of military structures exists outside of the Fort. This study examines connections between excavation features and geophysical anomalies in order to better interpret anomalies inside the Fort palisade. The palisade builder's trench, adobe pavement, post holes, and unknown structures are characterized through the analysis of the excavations and anomalies. The location of one of the military structures outside of the palisade is also identified. As many sites have histories of excavations prior to any geophysical surveys, combining the two sets of information is important in order to more fully understand site layout and the archaeological causes of geophysical anomalies.

Identification of a motor to auditory pathway important for vocal learning

PubMed Central

Roberts, Todd F.; Hisey, Erin; Tanaka, Masashi; Kearney, Matthew; Chattree, Gaurav; Yang, Cindy F.; Shah, Nirao M.; Mooney, Richard

2017-01-01

Summary Learning to vocalize depends on the ability to adaptively modify the temporal and spectral features of vocal elements. Neurons that convey motor-related signals to the auditory system are theorized to facilitate vocal learning, but the identity and function of such neurons remain unknown. Here we identify a previously unknown neuron type in the songbird brain that transmits vocal motor signals to the auditory cortex. Genetically ablating these neurons in juveniles disrupted their ability to imitate features of an adult tutor’s song. Ablating these neurons in adults had little effect on previously learned songs, but interfered with their ability to adaptively modify the duration of vocal elements and largely prevented the degradation of song’s temporal features normally caused by deafening. These findings identify a motor to auditory circuit essential to vocal imitation and to the adaptive modification of vocal timing. PMID:28504672

Scale-free networks of the earth’s surface

NASA Astrophysics Data System (ADS)

Liu, Gang; He, Jing; Luo, Kaitian; Gao, Peichao; Ma, Lei

2016-06-01

Studying the structure of real complex systems is of paramount importance in science and engineering. Despite our understanding of lots of real systems, we hardly cognize our unique living environment — the earth. The structural complexity of the earth’s surface is, however, still unknown in detail. Here, we define the modeling of graph topology for the earth’s surface, using the satellite images of the earth’s surface under different spatial resolutions derived from Google Earth. We find that the graph topologies of the earth’s surface are scale-free networks regardless of the spatial resolutions. For different spatial resolutions, the exponents of power-law distributions and the modularity are both quite different; however, the average clustering coefficient is approximately equal to a constant. We explore the morphology study of the earth’s surface, which enables a comprehensive understanding of the morphological feature of the earth’s surface.

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

Ma, Xiang; Zhang, Shuai; Jiao, Fang

Two-step nucleation pathways in which disordered, amorphous, or dense liquid states precede appearance of crystalline phases have been reported for a wide range of materials, but the dynamics of such pathways are poorly understood. Moreover, whether these pathways are general features of crystallizing systems or a consequence of system-specific structural details that select for direct vs two-step processes is unknown. Using atomic force microscopy to directly observe crystallization of sequence-defined polymers, we show that crystallization pathways are indeed sequence dependent. When a short hydrophobic region is added to a sequence that directly forms crystalline particles, crystallization instead follows a two-stepmore » pathway that begins with creation of disordered clusters of 10-20 molecules and is characterized by highly non-linear crystallization kinetics in which clusters transform into ordered structures that then enter the growth phase. The results shed new light on non-classical crystallization mechanisms and have implications for design of self-assembling polymer systems.« less

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

Middleton, Sarah A.; Illuminati, Joseph; Kim, Junhyong

Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example. We demonstrate the utility of this methodmore » by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into potential biological function, such as prediction of RNA-binding ability. Finally, our method can be applied to de novo fold prediction of entire proteomes and identify candidate novel fold families.« less

In situ architecture of the algal nuclear pore complex.

PubMed

Mosalaganti, Shyamal; Kosinski, Jan; Albert, Sahradha; Schaffer, Miroslava; Strenkert, Daniela; Salomé, Patrice A; Merchant, Sabeeha S; Plitzko, Jürgen M; Baumeister, Wolfgang; Engel, Benjamin D; Beck, Martin

2018-06-18

Nuclear pore complexes (NPCs) span the nuclear envelope and mediate nucleocytoplasmic exchange. They are a hallmark of eukaryotes and deeply rooted in the evolutionary origin of cellular compartmentalization. NPCs have an elaborate architecture that has been well studied in vertebrates. Whether this architecture is unique or varies significantly in other eukaryotic kingdoms remains unknown, predominantly due to missing in situ structural data. Here, we report the architecture of the algal NPC from the early branching eukaryote Chlamydomonas reinhardtii and compare it to the human NPC. We find that the inner ring of the Chlamydomonas NPC has an unexpectedly large diameter, and the outer rings exhibit an asymmetric oligomeric state that has not been observed or predicted previously. Our study provides evidence that the NPC is subject to substantial structural variation between species. The divergent and conserved features of NPC architecture provide insights into the evolution of the nucleocytoplasmic transport machinery.

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

Strickland, Madeleine; Stanley, Ann Marie; Wang, Guangshun

Paralogous enzymes arise from gene duplication events that confer a novel function, although it is unclear how cross-reaction between the original and duplicate protein interaction network is minimized. We investigated HPr:EIsugar and NPr:EINtr, the initial complexes of paralogous phosphorylation cascades involved in sugar import and nitrogen regulation in bacteria, respectively. Although the HPr:EIsugar interaction has been well characterized, involving multiple complexes and transient interactions, the exact nature of the NPr:EINtr complex was unknown. We set out to identify the key features of the interaction by performing binding assays and elucidating the structure of NPr in complex with the phosphorylation domainmore » of EINtr (EINNtr), using a hybrid approach involving X-ray, homology, and sparse nuclear magnetic resonance. We found that the overall fold and active-site structure of the two complexes are conserved in order to maintain productive phosphorylation, however, the interface surface potential differs between the two complexes, which prevents cross-reaction.« less

Centromeric Barrier Disruption Leads to Mitotic Defects in Schizosaccharomyces pombe

PubMed Central

Gaither, Terilyn L.; Merrett, Stephanie L.; Pun, Matthew J.; Scott, Kristin C.

2014-01-01

Centromeres are cis-acting chromosomal domains that direct kinetochore formation, enabling faithful chromosome segregation and preserving genome stability. The centromeres of most eukaryotic organisms are structurally complex, composed of nonoverlapping, structurally and functionally distinct chromatin subdomains, including the specialized core chromatin that underlies the kinetochore and pericentromeric heterochromatin. The genomic and epigenetic features that specify and preserve the adjacent chromatin subdomains critical to centromere identity are currently unknown. Here we demonstrate that chromatin barriers regulate this process in Schizosaccharomyces pombe. Reduced fitness and mitotic chromosome segregation defects occur in strains that carry exogenous DNA inserted at centromere 1 chromatin barriers. Abnormal phenotypes are accompanied by changes in the structural integrity of both the centromeric core chromatin domain, containing the conserved CENP-ACnp1 protein, and the flanking pericentric heterochromatin domain. Barrier mutant cells can revert to wild-type growth and centromere structure at a high frequency after the spontaneous excision of integrated exogenous DNA. Our results reveal a previously undemonstrated role for chromatin barriers in chromosome segregation and in the prevention of genome instability. PMID:24531725

Reconstruction of financial networks for robust estimation of systemic risk

NASA Astrophysics Data System (ADS)

Mastromatteo, Iacopo; Zarinelli, Elia; Marsili, Matteo

2012-03-01

In this paper we estimate the propagation of liquidity shocks through interbank markets when the information about the underlying credit network is incomplete. We show that techniques such as maximum entropy currently used to reconstruct credit networks severely underestimate the risk of contagion by assuming a trivial (fully connected) topology, a type of network structure which can be very different from the one empirically observed. We propose an efficient message-passing algorithm to explore the space of possible network structures and show that a correct estimation of the network degree of connectedness leads to more reliable estimations for systemic risk. Such an algorithm is also able to produce maximally fragile structures, providing a practical upper bound for the risk of contagion when the actual network structure is unknown. We test our algorithm on ensembles of synthetic data encoding some features of real financial networks (sparsity and heterogeneity), finding that more accurate estimations of risk can be achieved. Finally we find that this algorithm can be used to control the amount of information that regulators need to require from banks in order to sufficiently constrain the reconstruction of financial networks.

Determination of the structural properties of the aqueous electrolyte LiCl6H 2 O at the supercooled state using the Reverse Monte Carlo (RMC) simulation

NASA Astrophysics Data System (ADS)

ZIANE, M.; HABCHI, M.; DEROUICHE, A.; MESLI, S. M.; BENZOUINE, F.; KOTBI, M.

2017-03-01

A structural study of an aqueous electrolyte whose experimental results are available. It is a solution of A structural study of an aqueous electrolyte whose experimental results are available. It is a solution LiCl6H 2 O type at supercooled state (162K) contrasted with pure water at room temperature by means of Partial Distribution Functions (PDF) issue from neutron scattering technique. The aqueous electrolyte solution of the chloride lithium LiCl presents interesting properties which is studied by different methods at different concentration and thermodynamical states: This system possesses the property to become a glass through a metastable supercooled state when the temperature decreases. Based on these partial functions, the Reverse Monte Carlo method (RMC) computes radial correlation functions which allow exploring a number of structural features of the system. The purpose of the RMC is to produce a consistent configuration with the experimental data. They are usually the most important in the limit of systematic errors (of unknown distribution).

Using airborne LiDAR in geoarchaeological contexts: Assessment of an automatic tool for the detection and the morphometric analysis of grazing archaeological structures (French Massif Central).

NASA Astrophysics Data System (ADS)

Roussel, Erwan; Toumazet, Jean-Pierre; Florez, Marta; Vautier, Franck; Dousteyssier, Bertrand

2014-05-01

Airborne laser scanning (ALS) of archaeological regions of interest is nowadays a widely used and established method for accurate topographic and microtopographic survey. The penetration of the vegetation cover by the laser beam allows the reconstruction of reliable digital terrain models (DTM) of forested areas where traditional prospection methods are inefficient, time-consuming and non-exhaustive. The ALS technology provides the opportunity to discover new archaeological features hidden by vegetation and provides a comprehensive survey of cultural heritage sites within their environmental context. However, the post-processing of LiDAR points clouds produces a huge quantity of data in which relevant archaeological features are not easily detectable with common visualizing and analysing tools. Undoubtedly, there is an urgent need for automation of structures detection and morphometric extraction techniques, especially for the "archaeological desert" in densely forested areas. This presentation deals with the development of automatic detection procedures applied to archaeological structures located in the French Massif Central, in the western forested part of the Puy-de-Dôme volcano between 950 and 1100 m a.s.l.. These unknown archaeological sites were discovered by the March 2011 ALS mission and display a high density of subcircular depressions with a corridor access. The spatial organization of these depressions vary from isolated to aggregated or aligned features. Functionally, they appear to be former grazing constructions built from the medieval to the modern period. Similar grazing structures are known in other locations of the French Massif Central (Sancy, Artense, Cézallier) where the ground is vegetation-free. In order to develop a reliable process of automatic detection and mapping of these archaeological structures, a learning zone has been delineated within the ALS surveyed area. The grazing features were mapped and typical morphometric attributes were calculated based on 2 methods: (i) The mapping of the archaeological structures by a human operator using common visualisation tools (DTM, multi-direction hillshading & local relief models) within a GIS environment; (ii) The automatic detection and mapping performed by a recognition algorithm based on a user defined geometric pattern of the grazing structures. The efficiency of the automatic tool has been assessed by comparing the number of structures detected and the morphometric attributes calculated by the two methods. Our results indicate that the algorithm is efficient for the detection and the location of grazing structures. Concerning the morphometric results, there is still a discrepancy between automatic and expert calculations, due to both the expert mapping choices and the algorithm calibration.

Joint deconvolution and classification with applications to passive acoustic underwater multipath.

PubMed

Anderson, Hyrum S; Gupta, Maya R

2008-11-01

This paper addresses the problem of classifying signals that have been corrupted by noise and unknown linear time-invariant (LTI) filtering such as multipath, given labeled uncorrupted training signals. A maximum a posteriori approach to the deconvolution and classification is considered, which produces estimates of the desired signal, the unknown channel, and the class label. For cases in which only a class label is needed, the classification accuracy can be improved by not committing to an estimate of the channel or signal. A variant of the quadratic discriminant analysis (QDA) classifier is proposed that probabilistically accounts for the unknown LTI filtering, and which avoids deconvolution. The proposed QDA classifier can work either directly on the signal or on features whose transformation by LTI filtering can be analyzed; as an example a classifier for subband-power features is derived. Results on simulated data and real Bowhead whale vocalizations show that jointly considering deconvolution with classification can dramatically improve classification performance over traditional methods over a range of signal-to-noise ratios.

Application of ground-penetrating radar to investigation of near-surface fault properties in the San Francisco Bay region

USGS Publications Warehouse

Cai, J.; McMechan, G.A.; Fisher, M.A.

1996-01-01

In many geologic environments, ground-penetrating radar (GPR) provides high-resolution images of near-surface Earth structure. GPR data collection is nondestructive and very economical. The scale of features detected by GPR lies between those imaged by high-resolution seismic reflection surveys and those exposed in trenches and is therefore potentially complementary to traditional techniques for fault location and mapping. Sixty-two GPR profiles were collected at 12 sites in the San Francisco Bay region. Results show that GPR data correlate with large-scale features in existing trench observations, can be used to locate faults where they are buried or where their positions are not well known, and can identify previously unknown fault segments. The best data acquired were on a profile across the San Andreas fault, traversing Pleistocene terrace deposits south of Olema in Marin County; this profile shows a complicated multi-branched fault system from the ground surface down to about 40 m, the maximum depth for which data were recorded.

Uncertain viscoelastic models with fractional order: A new spectral tau method to study the numerical simulations of the solution

NASA Astrophysics Data System (ADS)

Ahmadian, A.; Ismail, F.; Salahshour, S.; Baleanu, D.; Ghaemi, F.

2017-12-01

The analysis of the behaviors of physical phenomena is important to discover significant features of the character and the structure of mathematical models. Frequently the unknown parameters involve in the models are assumed to be unvarying over time. In reality, some of them are uncertain and implicitly depend on several factors. In this study, to consider such uncertainty in variables of the models, they are characterized based on the fuzzy notion. We propose here a new model based on fractional calculus to deal with the Kelvin-Voigt (KV) equation and non-Newtonian fluid behavior model with fuzzy parameters. A new and accurate numerical algorithm using a spectral tau technique based on the generalized fractional Legendre polynomials (GFLPs) is developed to solve those problems under uncertainty. Numerical simulations are carried out and the analysis of the results highlights the significant features of the new technique in comparison with the previous findings. A detailed error analysis is also carried out and discussed.

Unified analysis of optical absorption spectra of carotenoids based on a stochastic model.

PubMed

Uragami, Chiasa; Saito, Keisuke; Yoshizawa, Masayuki; Molnár, Péter; Hashimoto, Hideki

2018-05-03

The chemical structures of the carotenoid molecules are very simple and one might think that the electronic feature of it is easily predicted. However, it still has so much unknown information except the correlation between the electronic energy state and the length of effective conjugation chain of carotenoids. To investigate the electronic feature of the carotenoids, the most essential method is measuring the optical absorption spectra, but simulating it from the resonance Raman spectra is also the effective way. From this reason, we studied the optical absorption spectra as well as resonance Raman spectra of 15 different kinds of cyclic carotenoid molecules, recorded in tetrahydrofuran (THF) solutions at room temperature. The whole band shapes of the absorption spectra of all these carotenoid molecules were successfully simulated based on a stochastic model using Brownian oscillators. The parameters obtained from the simulation made it possible to discuss the intermolecular interaction between carotenoids and solvent THF molecules quantitatively. Copyright © 2018. Published by Elsevier Inc.

High temperature structure in cool binary stars

NASA Technical Reports Server (NTRS)

Dupree, A. K.; Brickhouse, Nancy S.; Hanson, G. J.

1995-01-01

Strong high temperature emission lines in the EUVE spectra of binary stars containing cool components (Alpha Aur (Capella), 44 iota Boo, Lambda And, and VY Ari) provide the basis to define reliably the differential emission measure of hot plasma. The emission measure distributions for the short-period (P less than or equal to 13 d) binary systems show a high temperature enhancement over a relatively narrow temperature region similar to that originally found in Capella (Dupree et al. 1993). The emission measure distributions of rapidly rotating single stars 31 Com and AB Dor also contain a local enhancement of the emission measure although at different temperatures and width from Capella, suggesting that the enhancement in these objects may be characteristic of rapid rotation of a stellar corona. This feature might be identified with a (polar) active region, although its density and absolute size are unknown; in the binaries Capella and VY Ari, the feature is narrow and it may arise from an interaction region between the components.

Epidemiologic features of child unintentional injury in rural PuCheng, China.

PubMed

Li, Shaohua; Tang, Zhiru; Zhang, Xiujun; Yan, Lilun; Wang, Shidong; Liu, Guoqi; Zhang, Guo; Zhu, Mingxing; Schwebel, David C; Sun, Yehuan

2013-07-01

Epidemiologic features of unintentional injuries among children in rural China are unknown. Using a stratified sampling method, we conducted a retrospective study of injury reports over a year-long period. Structured oral questionnaires were administered to parents of 2551 children ages 0 to 14. The annual incidence of unintentional injuries was 15.6%, with boys (16.7%) having a slightly higher rate than girls (14.5%; p greater than .05). The four leading causes of injury for both genders were falls (5.1% annual incidence), burns (2.9%), animal-related injuries (1.7%), and traffic injuries (1.6%). Unintentional injuries have substantial negative effects on children and their families. In rural PuCheng, China, the incidence of unintentional injury among children is extremely high compared to other regions of the world. The types of injuries incurred are somewhat different from those reported in other geographic areas. Injury prevention programs targeting the issues specific to this region, and similar rural regions of China, are needed.

A Stable, Magnetic, and Metallic Li3O4 Compound as a Discharge Product in a Li-Air Battery.

PubMed

Yang, Guochun; Wang, Yanchao; Ma, Yanming

2014-08-07

The Li-air battery with the specific energy exceeding that of a Li ion battery has been aimed as the next-generation battery. The improvement of the performance of the Li-air battery needs a full resolution of the actual discharge products. Li2O2 has been long recognized as the main discharge product, with which, however, there are obvious failures on the understanding of various experimental observations (e.g., magnetism, oxygen K-edge spectrum, etc.) on discharge products. There is a possibility of the existence of other Li-O compounds unknown thus far. Here, a hitherto unknown Li3O4 compound as a discharge product of the Li-air battery was predicted through first-principles swarm structure searching calculations. The new compound has a unique structure featuring the mixture of superoxide O2(-) and peroxide O2(2-), the first such example in the Li-O system. The existence of superoxide O2(-) creates magnetism and hole-doped metallicity. Findings of Li3O4 gave rise to direct explanations of the unresolved experimental magnetism, triple peaks of oxygen K-edge spectra, and the Raman peak at 1125 cm(-1) of the discharge products. Our work enables an opportunity for the performance of capacity, charge overpotential, and round-trip efficiency of the Li-air battery.

Putative Monofunctional Type I Polyketide Synthase Units: A Dinoflagellate-Specific Feature?

PubMed Central

Eichholz, Karsten; Beszteri, Bánk; John, Uwe

2012-01-01

Marine dinoflagellates (alveolata) are microalgae of which some cause harmful algal blooms and produce a broad variety of most likely polyketide synthesis derived phycotoxins. Recently, novel polyketide synthesase (PKS) transcripts have been described from the Florida red tide dinoflagellate Karenia brevis (gymnodiniales) which are evolutionarily related to Type I PKS but were apparently expressed as monofunctional proteins, a feature typical of Type II PKS. Here, we investigated expression units of PKS I-like sequences in Alexandrium ostenfeldii (gonyaulacales) and Heterocapsa triquetra (peridiniales) at the transcript and protein level. The five full length transcripts we obtained were all characterized by polyadenylation, a 3′ UTR and the dinoflagellate specific spliced leader sequence at the 5′end. Each of the five transcripts encoded a single ketoacylsynthase (KS) domain showing high similarity to K. brevis KS sequences. The monofunctional structure was also confirmed using dinoflagellate specific KS antibodies in Western Blots. In a maximum likelihood phylogenetic analysis of KS domains from diverse PKSs, dinoflagellate KSs formed a clade placed well within the protist Type I PKS clade between apicomplexa, haptophytes and chlorophytes. These findings indicate that the atypical PKS I structure, i.e., expression as putative monofunctional units, might be a dinoflagellate specific feature. In addition, the sequenced transcripts harbored a previously unknown, apparently dinoflagellate specific conserved N-terminal domain. We discuss the implications of this novel region with regard to the putative monofunctional organization of Type I PKS in dinoflagellates. PMID:23139807

The Peculiar Light Curve of J1415+1320: A Case Study in Extreme Scattering Events

NASA Astrophysics Data System (ADS)

Vedantham, H. K.; Readhead, A. C. S.; Hovatta, T.; Koopmans, L. V. E.; Pearson, T. J.; Blandford, R. D.; Gurwell, M. A.; Lähteenmäki, A.; Max-Moerbeck, W.; Pavlidou, V.; Ravi, V.; Reeves, R. A.; Richards, J. L.; Tornikoski, M.; Zensus, J. A.

2017-08-01

The radio light curve of J1415+1320 (PKS 1413+135) shows time-symmetric and recurring U-shaped features across the centimeter-wave and millimeter-wave bands. The symmetry of these features points to lensing by an intervening object as the cause. U-shaped events in radio light curves in the centimeter-wave band have previously been attributed to Extreme scattering events (ESE). ESEs are thought to be the result of lensing by compact plasma structures in the Galactic interstellar medium, but the precise nature of these plasma structures remains unknown. Since the strength of a plasma lens evolves with wavelength λ as {λ }2, the presence of correlated variations at over a wide wavelength range casts doubt on the canonical ESE interpretation for J1415+1320. In this paper, we critically examine the evidence for plasma lensing in J1415+1320. We compute limits on the lensing strength and the associated free-free opacity of the putative plasma lenses. We compare the observed and model ESE light curves, and also derive a lower limit on the lens distance based on the effects of parallax due to the Earth’s orbit around the Sun. We conclude that plasma lensing is not a viable interpretation for J1415+1320's light curves and that symmetric U-shaped features in the radio light curves of extragalactic sources do not present prima facie evidence for ESEs. The methodology presented here is generic enough to be applicable to any plasma-lensing candidate.

Structural hierarchy as a key to complex phase selection in Al-Sm

NASA Astrophysics Data System (ADS)

Ye, Z.; Zhang, F.; Sun, Y.; Nguyen, M. C.; Zhou, S. H.; Zhou, L.; Meng, F.; Ott, R. T.; Park, E.; Besser, M. F.; Kramer, M. J.; Ding, Z. J.; Mendelev, M. I.; Wang, C. Z.; Napolitano, R. E.; Ho, K. M.

2017-10-01

Investigating the unknown structure of the complex cubic phase, previously observed to crystallize from melt-spun amorphous Al-10 at.% Sm alloy, we determine the structure in full site-occupancy detail, highlighting several critical structural features that govern the far-from-equilibrium phase selection pathway. Using an efficient genetic algorithm combining molecular dynamics, density functional theory, and x-ray diffraction, the structure is clearly identified as body-centered cubic I m 3 ¯m (No. 229) with ˜140 atoms per cubic unit cell and a lattice parameter of 1.4 nm. The complex structure is further refined to elucidate the detailed site occupancy, revealing full Sm occupancy on 6b sites and split Sm/Al occupancy on 16f sites. Based on the refined site occupancy associated with the experimentally observed phase, we term this phase ɛ -A l60S m11 (bcc), corresponding to the limiting situation when all 16f sites are occupied by Sm. However, it should be recognized that the range of solubility enabled by split occupancy at Sm sites is an important feature in phase selection under experimental conditions, permitting an avenue for transition with little or no chemical partitioning. Our analysis shows that the ɛ -A l60S m11 (bcc) exhibits a "3-6-6-1" first-shell packing around Sm centers on 16f sites, the same dominant motif exhibited by the undercooled liquid. The coincident motif supports the notion that liquid/glass ordering at high undercooling may give rise to topological invariants between the noncrystalline and crystalline states that provide kinetic pathways to metastable phases that are not accessible during near-equilibrium processing.

Structural hierarchy as a key to complex phase selection in Al-Sm

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

Ye, Z.; Zhang, F.; Sun, Y.

Investigating the unknown structure of the complex cubic phase, previously observed to crystallize from melt-spun amorphous Al–10 at.% Sm alloy, we determine the structure in full site-occupancy detail, highlighting several critical structural features that govern the far-from-equilibrium phase selection pathway. Using an efficient genetic algorithm combining molecular dynamics, density functional theory, and x-ray diffraction, the structure is clearly identified as body-centered cubic Im¯3m (No. 229) with ~140 atoms per cubic unit cell and a lattice parameter of 1.4 nm. The complex structure is further refined to elucidate the detailed site occupancy, revealing full Sm occupancy on 6b sites and splitmore » Sm/Al occupancy on 16f sites. Based on the refined site occupancy associated with the experimentally observed phase, we term this phase ε–Al 60Sm 11(bcc), corresponding to the limiting situation when all 16f sites are occupied by Sm. However, it should be recognized that the range of solubility enabled by split occupancy at Sm sites is an important feature in phase selection under experimental conditions, permitting an avenue for transition with little or no chemical partitioning. Our analysis shows that the ε–Al 60Sm 11(bcc) exhibits a “3-6-6-1” first-shell packing around Sm centers on 16f sites, the same dominant motif exhibited by the undercooled liquid. Here, the coincident motif supports the notion that liquid/glass ordering at high undercooling may give rise to topological invariants between the noncrystalline and crystalline states that provide kinetic pathways to metastable phases that are not accessible during near-equilibrium processing.« less

Structural and functional studies of a 50 kDa antigenic protein from Salmonella enterica serovar Typhi.

PubMed

Choong, Yee Siew; Lim, Theam Soon; Chew, Ai Lan; Aziah, Ismail; Ismail, Asma

2011-04-01

The high typhoid incidence rate in developing and under-developed countries emphasizes the need for a rapid, affordable and accessible diagnostic test for effective therapy and disease management. TYPHIDOT®, a rapid dot enzyme immunoassay test for typhoid, was developed from the discovery of a ∼50 kDa protein specific for Salmonella enterica serovar Typhi. However, the structure of this antigen remains unknown till today. Studies on the structure of this antigen are important to elucidate its function, which will in turn increase the efficiency of the development and improvement of the typhoid detection test. This paper described the predictive structure and function of the antigenically specific protein. The homology modeling approach was employed to construct the three-dimensional structure of the antigen. The built structure possesses the features of TolC-like outer membrane protein. Molecular docking simulation was also performed to further probe the functionality of the antigen. Docking results showed that hexamminecobalt, Co(NH(3))(6)(3+), as an inhibitor of TolC protein, formed favorable hydrogen bonds with D368 and D371 of the antigen. The single point (D368A, D371A) and double point (D368A and D371A) mutations of the antigen showed a decrease (single point mutation) and loss (double point mutations) of binding affinity towards hexamminecobalt. The architecture features of the built model and the docking simulation reinforced and supported that this antigen is indeed the variant of outer membrane protein, TolC. As channel proteins are important for the virulence and survival of bacteria, therefore this ∼50 kDa channel protein is a good specific target for typhoid detection test. Copyright © 2011 Elsevier Inc. All rights reserved.

Structural hierarchy as a key to complex phase selection in Al-Sm

DOE PAGES

Ye, Z.; Zhang, F.; Sun, Y.; ...

2017-10-12

Investigating the unknown structure of the complex cubic phase, previously observed to crystallize from melt-spun amorphous Al–10 at.% Sm alloy, we determine the structure in full site-occupancy detail, highlighting several critical structural features that govern the far-from-equilibrium phase selection pathway. Using an efficient genetic algorithm combining molecular dynamics, density functional theory, and x-ray diffraction, the structure is clearly identified as body-centered cubic Im¯3m (No. 229) with ~140 atoms per cubic unit cell and a lattice parameter of 1.4 nm. The complex structure is further refined to elucidate the detailed site occupancy, revealing full Sm occupancy on 6b sites and splitmore » Sm/Al occupancy on 16f sites. Based on the refined site occupancy associated with the experimentally observed phase, we term this phase ε–Al 60Sm 11(bcc), corresponding to the limiting situation when all 16f sites are occupied by Sm. However, it should be recognized that the range of solubility enabled by split occupancy at Sm sites is an important feature in phase selection under experimental conditions, permitting an avenue for transition with little or no chemical partitioning. Our analysis shows that the ε–Al 60Sm 11(bcc) exhibits a “3-6-6-1” first-shell packing around Sm centers on 16f sites, the same dominant motif exhibited by the undercooled liquid. Here, the coincident motif supports the notion that liquid/glass ordering at high undercooling may give rise to topological invariants between the noncrystalline and crystalline states that provide kinetic pathways to metastable phases that are not accessible during near-equilibrium processing.« less

Predicting DNA binding proteins using support vector machine with hybrid fractal features.

PubMed

Niu, Xiao-Hui; Hu, Xue-Hai; Shi, Feng; Xia, Jing-Bo

2014-02-21

DNA-binding proteins play a vitally important role in many biological processes. Prediction of DNA-binding proteins from amino acid sequence is a significant but not fairly resolved scientific problem. Chaos game representation (CGR) investigates the patterns hidden in protein sequences, and visually reveals previously unknown structure. Fractal dimensions (FD) are good tools to measure sizes of complex, highly irregular geometric objects. In order to extract the intrinsic correlation with DNA-binding property from protein sequences, CGR algorithm, fractal dimension and amino acid composition are applied to formulate the numerical features of protein samples in this paper. Seven groups of features are extracted, which can be computed directly from the primary sequence, and each group is evaluated by the 10-fold cross-validation test and Jackknife test. Comparing the results of numerical experiments, the group of amino acid composition and fractal dimension (21-dimension vector) gets the best result, the average accuracy is 81.82% and average Matthew's correlation coefficient (MCC) is 0.6017. This resulting predictor is also compared with existing method DNA-Prot and shows better performances. © 2013 The Authors. Published by Elsevier Ltd All rights reserved.

The modal surface interpolation method for damage localization

NASA Astrophysics Data System (ADS)

Pina Limongelli, Maria

2017-05-01

The Interpolation Method (IM) has been previously proposed and successfully applied for damage localization in plate like structures. The method is based on the detection of localized reductions of smoothness in the Operational Deformed Shapes (ODSs) of the structure. The IM can be applied to any type of structure provided the ODSs are estimated accurately in the original and in the damaged configurations. If the latter circumstance fails to occur, for example when the structure is subjected to an unknown input(s) or if the structural responses are strongly corrupted by noise, both false and missing alarms occur when the IM is applied to localize a concentrated damage. In order to overcome these drawbacks a modification of the method is herein investigated. An ODS is the deformed shape of a structure subjected to a harmonic excitation: at resonances the ODS are dominated by the relevant mode shapes. The effect of noise at resonance is usually lower with respect to other frequency values hence the relevant ODS are estimated with higher reliability. Several methods have been proposed to reliably estimate modal shapes in case of unknown input. These two circumstances can be exploited to improve the reliability of the IM. In order to reduce or eliminate the drawbacks related to the estimation of the ODSs in case of noisy signals, in this paper is investigated a modified version of the method based on a damage feature calculated considering the interpolation error relevant only to the modal shapes and not to all the operational shapes in the significant frequency range. Herein will be reported the comparison between the results of the IM in its actual version (with the interpolation error calculated summing up the contributions of all the operational shapes) and in the new proposed version (with the estimation of the interpolation error limited to the modal shapes).

Vegetative anatomy and relationships of Setchellanthus caeruleus (Setchellanthaceae)

Treesearch

Sherwin Carlquist; Regis B. Miller

1999-05-01

On account of its distinctive features, Setchellanthus cannot be included within any of the families of glucosinolate-producing plants. Features unknown in any of these families include abundant vasicentric tracheids, abaxial axial parenchyma, and only short uniseriate rays (composed of upright cells) in wood: and the presence of wide-helix tracheary elements in leaves...

The Development of Invariant Object Recognition Requires Visual Experience with Temporally Smooth Objects

ERIC Educational Resources Information Center

Wood, Justin N.; Wood, Samantha M. W.

2018-01-01

How do newborns learn to recognize objects? According to temporal learning models in computational neuroscience, the brain constructs object representations by extracting smoothly changing features from the environment. To date, however, it is unknown whether newborns depend on smoothly changing features to build invariant object representations.…

Style consistent classification of isogenous patterns.

PubMed

Sarkar, Prateek; Nagy, George

2005-01-01

In many applications of pattern recognition, patterns appear together in groups (fields) that have a common origin. For example, a printed word is usually a field of character patterns printed in the same font. A common origin induces consistency of style in features measured on patterns. The features of patterns co-occurring in a field are statistically dependent because they share the same, albeit unknown, style. Style constrained classifiers achieve higher classification accuracy by modeling such dependence among patterns in a field. Effects of style consistency on the distributions of field-features (concatenation of pattern features) can be modeled by hierarchical mixtures. Each field derives from a mixture of styles, while, within a field, a pattern derives from a class-style conditional mixture of Gaussians. Based on this model, an optimal style constrained classifier processes entire fields of patterns rendered in a consistent but unknown style. In a laboratory experiment, style constrained classification reduced errors on fields of printed digits by nearly 25 percent over singlet classifiers. Longer fields favor our classification method because they furnish more information about the underlying style.

Intraluminal fibrosis in interstitial lung disorders.

PubMed Central

Basset, F.; Ferrans, V. J.; Soler, P.; Takemura, T.; Fukuda, Y.; Crystal, R. G.

1986-01-01

The histopathologic and ultrastructural features of intraluminal organizing and fibrotic changes were studied in open lung biopsies and autopsy specimens from 373 patients with interstitial lung disorders, including hypersensitivity pneumonitis (n = 44), idiopathic pulmonary fibrosis (n = 92), collagen-vascular diseases (n = 20), chronic eosinophilic pneumonia (n = 10), pulmonary histiocytosis X (n-90), pulmonary sarcoidosis (n = 62), pneumoconioses (n = 25), Legionnaire's disease (n = 5), drug- and toxin-induced pneumonitis (n = 4), radiation-induced pneumonitis (n = 2), lymphangioleiomyomatosis (n = 11), and chronic organizing pneumonia of unknown cause (n = 8). Three patterns of intraluminal organization and fibrosis were recognized: 1) intraluminal buds, which partially filled the alveoli, alveolar ducts and/or distal bronchioles; 2) obliterative changes, in which loose connective tissue masses obliterated the lumens of alveoli, alveolar ducts or distal bronchioles, and 3) mural incorporation of previously intraluminal connective tissue masses, which fused with alveolar, alveolar ductal, or bronchiolar structures and frequently became reepithelialized. All three patterns had common morphologic features, suggesting that, regardless of their severity, they resulted from a common pathogenetic mechanism, ie, the migration of activated connective tissue cells, through defects in the epithelial lining and its basement membrane, from the interstitial into the intraluminal compartment. Intraluminal buds were observed most frequently in hypersensitivity pneumonitis, chronic eosinophilic pneumonia, and organizing pneumonia of unknown cause. Mural incorporation and, to a lesser extent, obliterative changes were observed in most interstitial disorders and were very prominent in idiopathic pulmonary fibrosis. Mural incorporation and obliterative changes play an important role in pulmonary remodeling, especially when several adjacent alveoli and/or other air spaces are involved. Under these circumstances, intraluminal organization can mediate the fusion of adjacent alveolar structures by intraluminal connective tissue. Images Figure 15 Figure 9 Figure 10 Figure 16 Figure 17 Figure 1 Figure 2 Figure 3 Figure 4 Figure 18 Figure 5 Figure 6 Figure 7 Figure 8 Figure 19 Figure 20 Figure 11 Figure 12 Figure 13 Figure 14 PMID:3953768

Biosignatures observed by Raman mapping in silicified materials

NASA Astrophysics Data System (ADS)

Foucher, F.; Westall, F.; Knoll, A.

2012-04-01

Establishing the biogenicity of ancient microbial remains is relatively difficult due to their simple shape and small size (micrometric-submicrometric). Potential biosignatures that remain in the rocks are related to morphological aspects of the potential microfossils, their chemical composition (carbon and associated elements), and evidence for metabolic activity (elemental isotopic signature, biominerals, corrosion/leaching features). Detection of biosignatures related to each of these microbial characteristics will increase the confidence with which biogenicity can be assigned to an unknown structure. However, given the small size of the microfossils and the consequent faint organic/geochemical traces, sophisticated instrumentation, such as mass spectrometers, electron microscopes, proton probes, nano-SIMS or even synchrotrons is generally required. In this study, we demonstrate the usefulness of Raman spectroscopy, and in particular Raman mapping, as a very powerful tool for the study of both organic and minerals biosignatures. Our investigations concern silicified, carbonaceous-walled microfossils from the Precambrian (700-800 Ma) Draken Formation, Spitsbergen (Svalbard). The microfossils consist of filamentous cyanobacterial mats containing trapped coccoidal planktonic microorganisms. The filaments are generally ~5 µm in width and the coccoidal structures are ~10µm in diameter. The Raman spectrometer used (WITec Alpha500 RA) allows compositional 2D/3D mapping at a sub-micrometric resolution of fossilised microorganisms, whose biogenicity had been previously established on the basis of their morphological characteristics and carbonaceous composition [1]. Complementary features were revealed by the micro-Raman mapping that may aid interpretation of biogenicity in an unknown structure. They included detection of opaline silica, titanium dioxide (anatase), pyrite and hydroxyapatite associated with the microfossils. Opaline silica is metastable and normally converts to quartz but, in this case where the rocks are very poorly metamorphosed, conversion seems to have been inhibited by the kerogen matrix within which the opal precipitated. Both anatase and pyrite may be formed abiogenically but their intimate association with the remnants of microorganisms suggests a link between the diagenesis of the dead organisms and the precipitation of these minerals. Interestingly, the Raman maps of the Draken microfossils also document differences in the D/G peak ratios within a particular microfossil structure. Thus, we demonstrate that mapping using micro-Raman spectrometry is a rapid method of investigation of potential biosignatures and an excellent complement to other methods of biosignature detection. Reference: [1] Knoll, A. H., Swett, K., and Mark, J., 1991, Journal of Paleontology 65, 531-569.

Navigation in GPS Denied Environments: Feature-Aided Inertial Systems

DTIC Science & Technology

2010-03-01

21] Brown , R. G. and Hwang , P. Y. C., Introduction to Random Signals and Applied Kalman Filtering, Third Edition, John Wiley & Sons, Inc., New York...knowledge is provided in [17]. An online (extended Kalman filter-based) method for calculating a trajectory by tracking features at an unknown location on...Finally, the trajectory error is estimated using these associated features in a Kalman estimator. The next couple of paragraphs will explain these

Functional and Structural Characterization of Zebrafish ASC.

PubMed

Li, Yajuan; Huang, Yi; Cao, Xiaocong; Yin, Xueying; Jin, Xiangyu; Liu, Sheng; Jiang, Jiansheng; Jiang, Wei; Xiao, Tsan Sam; Zhou, Rongbin; Cai, Gang; Hu, Bing; Jin, Tengchuan

2018-05-23

The zebrafish genome encodes homologs for most of the proteins involved in inflammatory pathways; however, the molecular components and activation mechanisms of fish inflammasomes are largely unknown. ASC (apoptosis-associated speck-like protein containing a caspase-recruitment domain (CARD)) is the only adaptor involved in the formation of multiple types of inflammasomes. Here, we demonstrate that zASC is also involved in inflammasome activation in zebrafish. When overexpressed in vitro and in vivo in zebrafish, both the zASC and zASC pyrin domain (PYD) proteins form speck and filament structures. Importantly, the crystal structures of the N-terminal PYD and C-terminal CARD of zebrafish ASC were determined independently as two separate entities fused to maltose-binding protein (MBP). Structure-guided mutagenesis revealed the functional relevance of the PYD hydrophilic surface found in the crystal lattice. Finally, the fish caspase-1 homolog Caspy, but not the caspase-4/11 homolog Caspy2, interacts with zASC through homotypic PYD-PYD interactions, which differ from those in mammals. These observations establish the conserved and unique structural/functional features of the zASC-dependent inflammasome pathway. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Identification and classification of cathinone unknowns by statistical analysis processing of direct analysis in real time-high resolution mass spectrometry-derived "neutral loss" spectra.

PubMed

Fowble, Kristen L; Shepard, Jason R E; Musah, Rabi A

2018-03-01

An approach to the rapid determination of the structures of novel synthetic cathinone designer drugs, also known as bath salts, is reported. While cathinones fragment so extensively by electron impact mass spectrometry that their mass spectra often cannot be used to identify the structure, collision-induced dissociation (CID) direct analysis in real time-high resolution mass spectrometry (DART-HRMS) experiments furnished spectra that provided diagnostic fragmentation patterns for the analyzed cathinones. From this data, neutral loss spectra, which reflect the presence of specific chemical moieties, could be acquired. These spectra showed striking similarities between cathinones sharing structural features such as pyrrolidine rings and methylenedioxy moieties. Principle component analysis (PCA) of the neutral loss spectra of nine synthetic cathinones of various types including ethcathinones, those containing a methylenedioxy moiety appended to the benzene ring, and pyrrolidine-containing structures, illustrated that cathinones falling within the same class clustered together and could be distinguished from those of other classes. Furthermore, hierarchical clustering analysis of the neutral loss data of a model set derived from 44 synthetic cathinones, furnished a dendrogram in which structurally similar cathinones clustered together. The ability of this model system to facilitate structure determination was tested using 4-fluoroethcathinone, 3,4-methylenedioxy-α-pyrrolidinohexanophenone (MDPHP), and ethylone, which fall into the ethcathinone, pyrrolidine-containing, and methylenedioxy-containing subclasses respectively. The results showed that their neutral loss spectra correctly fell within the ethcathinone, pyrrolidine-containing and methylenedioxy-containing cathinone clades of the dendrogram, and that the neutral loss information could be used to infer the structures of these compounds. The analysis and data processing steps are rapid and samples can be analyzed in their native form without any sample processing steps. The robustness of the dendrogram dataset can be readily increased by continued addition of newly discovered structures. The approach can be broadly applied to structure determination of unknowns, and would be particularly useful for analyses where sample amounts are limited. Copyright © 2017 Elsevier B.V. All rights reserved.

The role of chemistry and pH of solid surfaces for specific adsorption of biomolecules in solution--accurate computational models and experiment.

PubMed

Heinz, Hendrik

2014-06-18

Adsorption of biomolecules and polymers to inorganic nanostructures plays a major role in the design of novel materials and therapeutics. The behavior of flexible molecules on solid surfaces at a scale of 1-1000 nm remains difficult and expensive to monitor using current laboratory techniques, while playing a critical role in energy conversion and composite materials as well as in understanding the origin of diseases. Approaches to implement key surface features and pH in molecular models of solids are explained, and distinct mechanisms of peptide recognition on metal nanostructures, silica and apatite surfaces in solution are described as illustrative examples. The influence of surface energies, specific surface features and protonation states on the structure of aqueous interfaces and selective biomolecular adsorption is found to be critical, comparable to the well-known influence of the charge state and pH of proteins and surfactants on their conformations and assembly. The representation of such details in molecular models according to experimental data and available chemical knowledge enables accurate simulations of unknown complex interfaces in atomic resolution in quantitative agreement with independent experimental measurements. In this context, the benefits of a uniform force field for all material classes and of a mineral surface structure database are discussed.

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

PubMed Central

Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian

2015-01-01

Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually rely on tandem MS to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. We present a method for searching molecular structure databases using tandem MS data of small molecules. Our method computes a fragmentation tree that best explains the fragmentation spectrum of an unknown molecule. We use the fragmentation tree to predict the molecular structure fingerprint of the unknown compound using machine learning. This fingerprint is then used to search a molecular structure database such as PubChem. Our method is shown to improve on the competing methods for computational metabolite identification by a considerable margin. PMID:26392543

The Use of a Modified Semantic Features Analysis Approach in Aphasia

ERIC Educational Resources Information Center

Hashimoto, Naomi; Frome, Amber

2011-01-01

Several studies have reported improved naming using the semantic feature analysis (SFA) approach in individuals with aphasia. Whether the SFA can be modified and still produce naming improvements in aphasia is unknown. The present study was designed to address this question by using a modified version of the SFA approach. Three, rather than the…

Social relationship difficulties in autism and reactive attachment disorder: Improving diagnostic validity through structured assessment.

PubMed

Davidson, Claire; O'Hare, Anne; Mactaggart, Fiona; Green, Jonathan; Young, David; Gillberg, Christopher; Minnis, Helen

2015-05-01

Autism Spectrum Disorder (ASD) versus Reactive Attachment Disorder (RAD) is a common diagnostic challenge for clinicians due to overlapping difficulties with social relationships. RAD is associated with neglect or maltreatment whereas ASD is not: accurate differential diagnosis is therefore critical. Very little research has investigated the relationship between the two, and it is unknown if standardised measures are able to discriminate between ASD and RAD. The current study aimed to address these issues. Fifty eight children with ASD, and no history of maltreatment, were group matched on age with 67 children with RAD. Group profiles on multi-informant measures of RAD were investigated and group differences explored. Discriminant function analysis determined assessment features that best discriminated between the two groups. Although, according to parent report, children with ASD presented with significantly fewer indiscriminate friendliness behaviours compared to the RAD group (p<0.001), 36 children with ASD appeared to meet core RAD criteria. However, structured observation clearly demonstrated that features were indicative of ASD and not RAD for all but 1 of these 36 children. Children with RAD and children with ASD may demonstrate similar social relationship difficulties but there appears to be a difference in the social quality of the interactions between the groups. In most cases it was possible to differentiate between children with ASD and children with RAD via structured observation. Nevertheless, for a small proportion of children with ASD, particularly those whose difficulties may be more subtle, our current standardised measures, including structured observation, may not be effective in differentiating RAD from ASD. Copyright © 2015. Published by Elsevier Ltd.

[Melorheostosis of the hand in a pediatric patient].

PubMed

Masquijo, Julio Javier; Allende, Victoria

2010-12-01

Melorheostosis is a rare benign sclerosing bone dysplasia. Its etiology is unknown. Both sexes can be affected. Sites most frequently involved are the long bones of the lower limbs and the adjacent soft tissue structures. The disease is unusual in the upper limbs, and few cases have been reported in the hand. We report the case of a 7-year-old girl who had typical features of melorheostosis in the right hand. Diagnosis was made by conventional radiography and bone scintigraphy. Magnetic resonance contributed to the assessment of soft tissue lesions. Medical treatment allowed pain relief and range of motion improvement. Because melorheostosis has a variable tendency towards progression and association with tumors, a close follow-up of these patients is recommended.

Parameter discovery in stochastic biological models using simulated annealing and statistical model checking.

PubMed

Hussain, Faraz; Jha, Sumit K; Jha, Susmit; Langmead, Christopher J

2014-01-01

Stochastic models are increasingly used to study the behaviour of biochemical systems. While the structure of such models is often readily available from first principles, unknown quantitative features of the model are incorporated into the model as parameters. Algorithmic discovery of parameter values from experimentally observed facts remains a challenge for the computational systems biology community. We present a new parameter discovery algorithm that uses simulated annealing, sequential hypothesis testing, and statistical model checking to learn the parameters in a stochastic model. We apply our technique to a model of glucose and insulin metabolism used for in-silico validation of artificial pancreata and demonstrate its effectiveness by developing parallel CUDA-based implementation for parameter synthesis in this model.

Aluminium X-ray absorption Near Edge Structure in model compounds and Earth's surface minerals

NASA Astrophysics Data System (ADS)

Ildefonse, P.; Cabaret, D.; Sainctavit, P.; Calas, G.; Flank, A.-M.; Lagarde, P.

Aluminium K-edge X-ray absorption near edge spectra (XANES) of a suite of silicate and oxides minerals consist of electronic excitations occurring in the edge region, and multiple scattering resonances at higher energies. The main XANES feature for four-fold Al is at around 2 eV lower energy than the main XANES feature for six-fold Al. This provides a useful probe for coordination numbers in clay minerals, gels, glasses or material with unknown Al-coordination number. Six-fold aluminium yields a large variety of XANES features which can be correlated with octahedral point symmetry, number of aluminium sites and distribution of Al-O distances. These three parameters may act together, and the quantitative interpretation of XANES spectra is difficult. For a low point symmetry (1), variations are mainly related to the number of Al sites and distribution of Al-O distances: pyrophyllite, one Al site, is clearly distinguished from kaolinite and gibbsite presenting two Al sites. For a given number of Al-site (1), variations are controlled by changes in point symmetry, the number of XANES features being increased as point symmetry decreases. For a given point symmetry (1) and a given number of Al site (1), variations are related to second nearest neighbours (gibbsite versus kaolinite). The amplitude of the XANES feature at about 1566 eV is a useful probe for the assessment of AlIV/Altotal ratios in 2/1 phyllosilicates. Al-K XANES has been performed on synthetic Al-bearing goethites which cannot be studied by 27Al NMR. At low Al content, Al-K XANES is very different from that of α-AlOOH but at the highest level, XANES spectrum tends to that of diaspore. Al-K XAS is thus a promising tool for the structural study of poorly ordered materials such as clay minerals and natural alumino-silicate gels together with Al-subsituted Fe-oxyhydroxides.

High-Resolution Structural Monitoring of Ionospheric Absorption Events

DTIC Science & Technology

2013-07-01

ionospheric plasma conductivity 5 . This results in enhanced absorption of the cosmic high frequency (HF; typically 10 – 60 MHz) radio background ...7 riometry. Incorporation of an outrigger site, to enable treatment of the unknown structure of the celestial background and the effects of...riometry. Incorporation of an outrigger site, to enable treatment of the unknown structure of the celestial background and the effects of confusion

Detecting Precontact Anthropogenic Microtopographic Features in a Forested Landscape with Lidar: A Case Study from the Upper Great Lakes Region, AD 1000-1600

PubMed Central

Howey, Meghan C. L.; Sullivan, Franklin B.; Tallant, Jason; Kopple, Robert Vande; Palace, Michael W.

2016-01-01

Forested settings present challenges for understanding the full extent of past human landscape modifications. Field-based archaeological reconnaissance in forests is low-efficiency and most remote sensing techniques are of limited utility, and together, this means many past sites and features in forests are unknown. Archaeologists have increasingly used light detection and ranging (lidar), a remote sensing tool that uses pulses of light to measure reflecting surfaces at high spatial resolution, to address these limitations. Archaeology studies using lidar have made significant progress identifying permanent structures built by large-scale complex agriculturalist societies. Largely unaccounted for, however, are numerous small and more practical modifications of landscapes by smaller-scale societies. Here we show these may also be detectable with lidar by identifying remnants of food storage pits (cache pits) created by mobile hunter-gatherers in the upper Great Lakes during Late Precontact (ca. AD 1000–1600) that now only exist as subtle microtopographic features. Years of intensive field survey identified 69 cache pit groups between two inland lakes in northern Michigan, almost all of which were located within ~500 m of a lakeshore. Applying a novel series of image processing techniques and statistical analyses to a high spatial resolution DTM we created from commercial-grade lidar, our detection routine identified 139 high potential cache pit clusters. These included most of the previously known clusters as well as several unknown clusters located >1500 m from either lakeshore, much further from lakeshores than all previously identified cultural sites. Food storage is understood to have emerged regionally as a risk-buffering strategy after AD 1000 but our results indicate the current record of hunter-gatherer cache pit food storage is markedly incomplete and this practice and its associated impact on the landscape may be greater than anticipated. Our study also demonstrates the potential of harnessing commercial-grade lidar for other fine-grained archaeology applications. PMID:27584031

Detecting Precontact Anthropogenic Microtopographic Features in a Forested Landscape with Lidar: A Case Study from the Upper Great Lakes Region, AD 1000-1600.

PubMed

Howey, Meghan C L; Sullivan, Franklin B; Tallant, Jason; Kopple, Robert Vande; Palace, Michael W

2016-01-01

Forested settings present challenges for understanding the full extent of past human landscape modifications. Field-based archaeological reconnaissance in forests is low-efficiency and most remote sensing techniques are of limited utility, and together, this means many past sites and features in forests are unknown. Archaeologists have increasingly used light detection and ranging (lidar), a remote sensing tool that uses pulses of light to measure reflecting surfaces at high spatial resolution, to address these limitations. Archaeology studies using lidar have made significant progress identifying permanent structures built by large-scale complex agriculturalist societies. Largely unaccounted for, however, are numerous small and more practical modifications of landscapes by smaller-scale societies. Here we show these may also be detectable with lidar by identifying remnants of food storage pits (cache pits) created by mobile hunter-gatherers in the upper Great Lakes during Late Precontact (ca. AD 1000-1600) that now only exist as subtle microtopographic features. Years of intensive field survey identified 69 cache pit groups between two inland lakes in northern Michigan, almost all of which were located within ~500 m of a lakeshore. Applying a novel series of image processing techniques and statistical analyses to a high spatial resolution DTM we created from commercial-grade lidar, our detection routine identified 139 high potential cache pit clusters. These included most of the previously known clusters as well as several unknown clusters located >1500 m from either lakeshore, much further from lakeshores than all previously identified cultural sites. Food storage is understood to have emerged regionally as a risk-buffering strategy after AD 1000 but our results indicate the current record of hunter-gatherer cache pit food storage is markedly incomplete and this practice and its associated impact on the landscape may be greater than anticipated. Our study also demonstrates the potential of harnessing commercial-grade lidar for other fine-grained archaeology applications.

Synthesis and structural characterization of the Zintl phases Na{sub 3}Ca{sub 3}TrPn{sub 4}, Na{sub 3}Sr{sub 3}TrPn{sub 4}, and Na{sub 3}Eu{sub 3}TrPn{sub 4} (Tr=Al, Ga, In; Pn=P, As, Sb)

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

Wang, Yi; Suen, Nian-Tzu; College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002

15 new quaternary Zintl phases have been synthesized by solid-state reactions from the respective elements, and their structures have been determined by single-crystal X-ray diffraction. Na{sub 3}E{sub 3}TrPn{sub 4} (E=Ca, Sr, Eu; Tr=Al, Ga, In; Pn=P, As, Sb) crystallize in the hexagonal crystal system with the non-centrosymmetric space group P6{sub 3}mc (No. 186). The structure represents a variant of the K{sub 6}HgS{sub 4} structure type (Pearson index hP22) and features [TrPn{sub 4}]{sup 9–} tetrahedral units, surrounded by Na{sup +} and Ca{sup 2+}, Sr{sup 2+}, Eu{sup 2+} cations. The nominal formula rationalization [Na{sup +}]{sub 3}[E{sup 2+}]{sub 3}[TrPn{sub 4}]{sup 9–} follows themore » octet rule, suggesting closed-shell configurations for all atoms and intrinsic semiconducting behavior. However, structure refinements for several members hint at disorder and mixing of cations that potentially counteract the optimal valence electron count. - Graphical abstract: The hexagonal, non-centrosymmetric structure of Na{sub 3}E{sub 3}TrPn{sub 4} (E=Ca, Sr, Eu; Tr=Al, Ga, In; Pn=P, As, Sb) features [TrPn{sub 4}]{sup 9–} tetrahedral units, surrounded by Na{sup +} and Ca{sup 2+}, Sr{sup 2+}, Eu{sup 2+} cations. - Highlights: • 15 quaternary phosphides, arsenides, and antimonides are synthesized and structurally characterized. • The structure is a variant of the hexagonal K{sub 6}HgS{sub 4}-type, with distinctive pattern for the cations. • Occupational and/or positional disorder of yet unknown origin exists for some members of the series.« less

Archaeogeophysical investigations of early Caddo settlement patterning at the Crenshaw site (3MI6)

NASA Astrophysics Data System (ADS)

Samuelsen, John R.

The Teran map, made during Don Domingo Teran de los Rios' expedition for New Spain, shows a Caddo settlement in 1691 with a vacant mound center and many small farmsteads dispersed across the countryside along both banks of the Red River. This map, combined with the 19th Century photographs taken by William Soule, provides a testable model for the settlement pattern of the Caddo people called the Teran-Soule model. This model states that large numbers of people besides a small caretaker population did not inhabit the mound centers, supporting a vacant mound center hypothesis. Recent studies have begun to challenge this hypothesis, using archaeogeophysical techniques to find structures near Middle to Late Caddo mounds. An archaeogeophysical survey of the Crenshaw site along the Great Bend of the Red River was conducted to determine if structures could be found there. Is the settlement pattern at this early Caddo site, occupied between A.D. 700 and 1400, consistent with the late historic model of a vacant mound center? Is there evidence that both Caddo and Fourche Maline occupations existed in horizontally distinct components? The 3.2 hectare survey identified more than 100 possible structures, of which more than 50 are probably structures associated with the Fourche Maline or early Caddo occupations of the site. Several structures were found in linear patterns, including an oval series of possible structures measuring 90 x 85 m in diameter. While cultural affiliation was not determined for most of these features, some can be attributed to Caddo origin based on architectural attributes, such as extended entranceways. This suggests that Crenshaw was not literally vacant, but the presence of extended entranceways suggests that some of the identified features were special use structures, which does not conflict with the vacant mound center hypothesis. However, the large number of possible structures present with unknown cultural affiliations provides ample opportunities for testing the model.

Invisible Colors of the Moon

NASA Image and Video Library

2009-09-24

Data from NASA Moon Mineralogy Mapper instrument on the Indian Space Research Organization Chandrayaan-1 spacecraft reveal subtle and previously unknown lunar diversity and features. Animation available at the Photojournal.

Reconstruction of phonon relaxation times from systems featuring interfaces with unknown properties

NASA Astrophysics Data System (ADS)

Forghani, Mojtaba; Hadjiconstantinou, Nicolas G.

2018-05-01

We present a method for reconstructing the phonon relaxation-time function τω=τ (ω ) (including polarization) and associated phonon free-path distribution from thermal spectroscopy data for systems featuring interfaces with unknown properties. Our method does not rely on the effective thermal-conductivity approximation or a particular physical model of the interface behavior. The reconstruction is formulated as an optimization problem in which the relaxation times are determined as functions of frequency by minimizing the discrepancy between the experimentally measured temperature profiles and solutions of the Boltzmann transport equation for the same system. Interface properties such as transmissivities are included as unknowns in the optimization; however, because for the thermal spectroscopy problems considered here the reconstruction is not very sensitive to the interface properties, the transmissivities are only approximately reconstructed and can be considered as byproducts of the calculation whose primary objective is the accurate determination of the relaxation times. The proposed method is validated using synthetic experimental data obtained from Monte Carlo solutions of the Boltzmann transport equation. The method is shown to remain robust in the presence of uncertainty (noise) in the measurement.

Principales lignes structurales du Maroc nord-oriental : apport de la gravimétrie

NASA Astrophysics Data System (ADS)

Chennouf, Touria; Khattach, Driss; Milhi, Abdellah; Andrieux, Pierre; Keating, Pierre

2007-05-01

The present work is based on various filtered maps (horizontal derivative, upward continuation) and Euler deconvolution of the gravity data from northeastern Morocco. These results allow the delineation of many geological structures, such as faults, basins, or diapirs. Some of these structures are hidden totally or partially by the Mesozoic and Cenozoic cover. The results were used to make a structural map of the study area; this map confirms the existence of several faults, localised or inferred, from former geological studies. It complements information on some of them and outlines a great number of deep or near-surface faults that had remained unknown until the present time. The major features show two principal directions: N080°-085° and N055°-065°, with a predominance of the latter, and their depth can reach 4500 m. The N080°-085° directions correspond to the Kebdana, Sidi Bouhouria, Naima, and Guefait faults, and the N055°-065° directions correspond to a fault parallel to the Mediterranean coast and the Moulouya, Madagh, Angad, and Zekkara faults.

Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens.

PubMed

Pan, Joshua; Meyers, Robin M; Michel, Brittany C; Mashtalir, Nazar; Sizemore, Ann E; Wells, Jonathan N; Cassel, Seth H; Vazquez, Francisca; Weir, Barbara A; Hahn, William C; Marsh, Joseph A; Tsherniak, Aviad; Kadoch, Cigall

2018-05-23

Protein complexes are assemblies of subunits that have co-evolved to execute one or many coordinated functions in the cellular environment. Functional annotation of mammalian protein complexes is critical to understanding biological processes, as well as disease mechanisms. Here, we used genetic co-essentiality derived from genome-scale RNAi- and CRISPR-Cas9-based fitness screens performed across hundreds of human cancer cell lines to assign measures of functional similarity. From these measures, we systematically built and characterized functional similarity networks that recapitulate known structural and functional features of well-studied protein complexes and resolve novel functional modules within complexes lacking structural resolution, such as the mammalian SWI/SNF complex. Finally, by integrating functional networks with large protein-protein interaction networks, we discovered novel protein complexes involving recently evolved genes of unknown function. Taken together, these findings demonstrate the utility of genetic perturbation screens alone, and in combination with large-scale biophysical data, to enhance our understanding of mammalian protein complexes in normal and disease states. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii

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

Qiu, Wei; Wernimont, Amy; Tang, Keliang

2009-09-29

Serine/threonine kinases secreted from rhoptry organelles constitute important virulence factors of Toxoplasma gondii. Rhoptry kinases are highly divergent and their structures and regulatory mechanism are hitherto unknown. Here, we report the X-ray crystal structures of two related pseudokinases named ROP2 and ROP8, which differ primarily in their substrate-binding site. ROP kinases contain a typical bilobate kinase fold and a novel N-terminal extension that both stabilizes the N-lobe and provides a unique means of regulation. Although ROP2 and ROP8 were catalytically inactive, they provided a template for homology modelling of the active kinase ROP18, a major virulence determinant of T. gondii.more » Autophosphorylation of key residues in the N-terminal extension resulted in ROP18 activation, which in turn phosphorylated ROP2 and ROP8. Mutagenesis and mass spectrometry experiments revealed that ROP18 was maximally activated when this phosphorylated N-terminus relieved autoinhibition resulting from extension of aliphatic side chains into the ATP-binding pocket. This novel means of regulation governs ROP kinases implicated in parasite virulence.« less

Reevaluation of the Dentary Structures of Caenagnathid Oviraptorosaurs (Dinosauria, Theropoda).

PubMed

Wang, Shuo; Zhang, Qiyue; Yang, Rui

2018-01-10

Among the characters of caenagnathid oviraptorosaurians, the lateral occlusal grooves and ridges on the occlusal surface of the jaw bones often receive special attention. Recent studies demonstrated that ontogenetic edentulism is present in caenagnathids, and therefore the lateral occlusal grooves and ridges are vestigial alveoli and interdental septa, respectively. In the present paper, the dentary structures of caenagnathids were reevaluated based on CT images of Caenagnathiasia sp. IVPP V20377. Several previously unknown features including crateriform vestigial alveoli, the morphology of the dentary interior hollow space, and the paired blind tubes beneath the dentary symphyseal shelf are recognized. Current lines of evidence suggest different jaw bone morphologies are likely produced by various tooth reduction patterns, which indicates ontogenetic dietary shift, if once presented in caenagnathids and Sapeornis, may have been different from the condition seen in Limusaurus. The 3D images of dentary interior spaces suggest that while tooth reduction progresses, the empty alveoli are partially modified into structures accommodating blood vessels that nourish the rhamphotheca, probably representing a functional compensation for the insufficient blood supply in toothed jaw bones.

Identification of a novel box C/D snoRNA from mouse nucleolar cDNA library.

PubMed

Zhou, Hui; Zhao, Jin; Yu, Chuan-He; Luo, Qing-Jun; Chen, Yue-Qin; Xiao, Yu; Qu, Liang-Hu

2004-02-18

By construction and screen of mouse nucleolar cDNA library, a novel mammalian small nucleolar RNAs (snoRNA) was identified. The novel snoRNA, 70 nt in length, displays structural features typical of C/D box snoRNA family. The snoRNA possesses an 11-nt-long rRNA antisense element and is predicted to guide the 2'-O-methylation of mouse 28S rRNA at G4043, a site unknown so far to be modified in vertebrates. The comparison of functional element of snoRNA guides among eukaryotes reveals that the novel snoRNA is a mammalian counterpart of yeast snR38 despite highly divergent sequence between them. Mouse and human snR38 and other cognates in distant vertebrates were positively detected with slight length variability. As expected, the rRNA ribose-methylation site predicted by mouse snR38 was precisely mapped by specific-primer extension assay. Furthermore, our analyses show that mouse and human snR38 gene have multiple variants and are nested in the introns of different host genes with unknown function. Thus, snR38 is a phylogenetically conserved methylation guide but exhibits different genomic organization in eukaryotes.

Epileptic encephalopathy with continuous spike-waves during sleep: the need for transition from childhood to adulthood medical care appears to be related to etiology.

PubMed

de Saint-Martin, Anne; Rudolf, Gabrielle; Seegmuller, Caroline; Valenti-Hirsch, Maria Paola; Hirsch, Edouard

2014-08-01

Epileptic encephalopathy with continuous diffuse spike-waves during slow-wave sleep (ECSWS) presents clinically with infrequent nocturnal focal seizures, atypical absences related to secondary bilateral synchrony, negative myoclonia, and atonic and rare generalized tonic-clonic seizures. The unique electroencephalography (EEG) pattern found in ECSWS consists of continuous, diffuse, bilateral spike-waves during slow-wave sleep. Despite the eventual disappearance of clinical seizures and EEG abnormalities by adolescence, the prognosis is guarded in most cases because of neuropsychological and behavioral deficits. ECSWS has a heterogeneous etiology (genetic, structural, and unknown). Because epilepsy and electroencephalography (EEG) abnormalities in epileptic encephalopathy with continuous diffuse spike-waves during slow-wave sleep (ECSWS) are self-limited and age related, the need for ongoing medical care and transition to adult care might be questioned. For adolescents in whom etiology remains unknown (possibly genetic) and who experience the disappearance of seizures and EEG abnormalities, there is rarely need for long-term neurologic follow-up, because often a relatively normal cognitive and social evolution follows. However, the majority of patients with structural and possibly "genetic syndromic" etiologies will have persistent cognitive deficits and will need suitable socioeducative care. Therefore, the transition process in ECSWS will depend mainly on etiology and its related features (epileptic active phase duration, and cognitive and behavioral evolution) and revolve around neuropsychological and social support rather than medical and pharmacologic follow-up. Wiley Periodicals, Inc. © 2014 International League Against Epilepsy.

Damage detection and quantification in a structural model under seismic excitation using time-frequency analysis

NASA Astrophysics Data System (ADS)

Chan, Chun-Kai; Loh, Chin-Hsiung; Wu, Tzu-Hsiu

2015-04-01

In civil engineering, health monitoring and damage detection are typically carry out by using a large amount of sensors. Typically, most methods require global measurements to extract the properties of the structure. However, some sensors, like LVDT, cannot be used due to in situ limitation so that the global deformation remains unknown. An experiment is used to demonstrate the proposed algorithms: a one-story 2-bay reinforce concrete frame under weak and strong seismic excitation. In this paper signal processing techniques and nonlinear identification are used and applied to the response measurements of seismic response of reinforced concrete structures subject to different level of earthquake excitations. Both modal-based and signal-based system identification and feature extraction techniques are used to study the nonlinear inelastic response of RC frame using both input and output response data or output only measurement. From the signal-based damage identification method, which include the enhancement of time-frequency analysis of acceleration responses and the estimation of permanent deformation using directly from acceleration response data. Finally, local deformation measurement from dense optical tractor is also use to quantify the damage of the RC frame structure.

Spatio-Temporal EEG Models for Brain Interfaces

PubMed Central

Gonzalez-Navarro, P.; Moghadamfalahi, M.; Akcakaya, M.; Erdogmus, D.

2016-01-01

Multichannel electroencephalography (EEG) is widely used in non-invasive brain computer interfaces (BCIs) for user intent inference. EEG can be assumed to be a Gaussian process with unknown mean and autocovariance, and the estimation of parameters is required for BCI inference. However, the relatively high dimensionality of the EEG feature vectors with respect to the number of labeled observations lead to rank deficient covariance matrix estimates. In this manuscript, to overcome ill-conditioned covariance estimation, we propose a structure for the covariance matrices of the multichannel EEG signals. Specifically, we assume that these covariances can be modeled as a Kronecker product of temporal and spatial covariances. Our results over the experimental data collected from the users of a letter-by-letter typing BCI show that with less number of parameter estimations, the system can achieve higher classification accuracies compared to a method that uses full unstructured covariance estimation. Moreover, in order to illustrate that the proposed Kronecker product structure could enable shortening the BCI calibration data collection sessions, using Cramer-Rao bound analysis on simulated data, we demonstrate that a model with structured covariance matrices will achieve the same estimation error as a model with no covariance structure using fewer labeled EEG observations. PMID:27713590

Structural Characterization of New Peptide Variants Produced by Cyanobacteria from the Brazilian Atlantic Coastal Forest Using Liquid Chromatography Coupled to Quadrupole Time-of-Flight Tandem Mass Spectrometry

PubMed Central

Sanz, Miriam; Andreote, Ana Paula Dini; Fiore, Marli Fatima; Dörr, Felipe Augusto; Pinto, Ernani

2015-01-01

Cyanobacteria from underexplored and extreme habitats are attracting increasing attention in the search for new bioactive substances. However, cyanobacterial communities from tropical and subtropical regions are still largely unknown, especially with respect to metabolite production. Among the structurally diverse secondary metabolites produced by these organisms, peptides are by far the most frequently described structures. In this work, liquid chromatography/electrospray ionization coupled to high resolution quadrupole time-of-flight tandem mass spectrometry with positive ion detection was applied to study the peptide profile of a group of cyanobacteria isolated from the Southeastern Brazilian coastal forest. A total of 38 peptides belonging to three different families (anabaenopeptins, aeruginosins, and cyanopeptolins) were detected in the extracts. Of the 38 peptides, 37 were detected here for the first time. New structural features were proposed based on mass accuracy data and isotopic patterns derived from full scan and MS/MS spectra. Interestingly, of the 40 surveyed strains only nine were confirmed to be peptide producers; all of these strains belonged to the order Nostocales (three Nostoc sp., two Desmonostoc sp. and four Brasilonema sp.). PMID:26096276

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

Osipiuk, J.; Gornicki, P.; Maj, L.

The structure of the YlxR protein of unknown function from Streptococcus pneumonia was determined to 1.35 Angstroms. YlxR is expressed from the nusA/infB operon in bacteria and belongs to a small protein family (COG2740) that shares a conserved sequence motif GRGA(Y/W). The family shows no significant amino-acid sequence similarity with other proteins. Three-wavelength diffraction MAD data were collected to 1.7 Angstroms from orthorhombic crystals using synchrotron radiation and the structure was determined using a semi-automated approach. The YlxR structure resembles a two-layer {alpha}/{beta} sandwich with the overall shape of a cylinder and shows no structural homology to proteins of knownmore » structure. Structural analysis revealed that the YlxR structure represents a new protein fold that belongs to the {alpha}-{beta} plait superfamily. The distribution of the electrostatic surface potential shows a large positively charged patch on one side of the protein, a feature often found in nucleic acid-binding proteins. Three sulfate ions bind to this positively charged surface. Analysis of potential binding sites uncovered several substantial clefts, with the largest spanning 3/4 of the protein. A similar distribution of binding sites and a large sharply bent cleft are observed in RNA-binding proteins that are unrelated in sequence and structure. It is proposed that YlxR is an RNA-binding protein.« less

Streptococcus pneumonia YlxR at 1.35 A shows a putative new fold.

PubMed

Osipiuk, J; Górnicki, P; Maj, L; Dementieva, I; Laskowski, R; Joachimiak, A

2001-11-01

The structure of the YlxR protein of unknown function from Streptococcus pneumonia was determined to 1.35 A. YlxR is expressed from the nusA/infB operon in bacteria and belongs to a small protein family (COG2740) that shares a conserved sequence motif GRGA(Y/W). The family shows no significant amino-acid sequence similarity with other proteins. Three-wavelength diffraction MAD data were collected to 1.7 A from orthorhombic crystals using synchrotron radiation and the structure was determined using a semi-automated approach. The YlxR structure resembles a two-layer alpha/beta sandwich with the overall shape of a cylinder and shows no structural homology to proteins of known structure. Structural analysis revealed that the YlxR structure represents a new protein fold that belongs to the alpha-beta plait superfamily. The distribution of the electrostatic surface potential shows a large positively charged patch on one side of the protein, a feature often found in nucleic acid-binding proteins. Three sulfate ions bind to this positively charged surface. Analysis of potential binding sites uncovered several substantial clefts, with the largest spanning 3/4 of the protein. A similar distribution of binding sites and a large sharply bent cleft are observed in RNA-binding proteins that are unrelated in sequence and structure. It is proposed that YlxR is an RNA-binding protein.

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

PubMed Central

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

A novel sensitivity-based method for damage detection of structures under unknown periodic excitations

NASA Astrophysics Data System (ADS)

Naseralavi, S. S.; Salajegheh, E.; Fadaee, M. J.; Salajegheh, J.

2014-06-01

This paper presents a technique for damage detection in structures under unknown periodic excitations using the transient displacement response. The method is capable of identifying the damage parameters without finding the input excitations. We first define the concept of displacement space as a linear space in which each point represents displacements of structure under an excitation and initial condition. Roughly speaking, the method is based on the fact that structural displacements under free and forced vibrations are associated with two parallel subspaces in the displacement space. Considering this novel geometrical viewpoint, an equation called kernel parallelization equation (KPE) is derived for damage detection under unknown periodic excitations and a sensitivity-based algorithm for solving KPE is proposed accordingly. The method is evaluated via three case studies under periodic excitations, which confirm the efficiency of the proposed method.

Glycosyltransferase-mediated Sweet Modification in Oral Streptococci.

PubMed

Zhu, F; Zhang, H; Wu, H

2015-05-01

Bacterial glycosyltransferases play important roles in bacterial fitness and virulence. Oral streptococci have evolved diverse strategies to survive and thrive in the carbohydrate-rich oral cavity. In this review, we discuss 2 important biological processes mediated by 2 distinct groups of glycosyltransferases in oral streptococci that are important for bacterial colonization and virulence. The first process is the glycosylation of highly conserved serine-rich repeat adhesins by a series of glycosyltransferases. Using Streptococcus parasanguinis as a model, we highlight new features of several glycosyltransferases that sequentially modify the serine-rich glycoprotein Fap1. Distinct features of a novel glycosyltransferase fold from a domain of unknown function 1792 are contrasted with common properties of canonical glycosyltransferases. The second biological process we cover is involved in building sticky glucan matrix to establish cariogenic biofilms by an important opportunistic pathogen Streptococcus mutans through the action of a family of 3 glucosyltransferases. We focus on discussing the structural feature of this family as a glycoside hydrolase family of enzymes. While the 2 processes are distinct, they all produce carbohydrate-coated biomolecules, which enable bacteria to stick better in the complex oral microbiome. Understanding the making of the sweet modification presents a unique opportunity to develop novel antiadhesion and antibiofilm strategies to fight infections by oral streptococci and beyond. © International & American Associations for Dental Research 2015.

Glycosyltransferase-mediated Sweet Modification in Oral Streptococci

PubMed Central

Zhu, F.; Zhang, H.

2015-01-01

Bacterial glycosyltransferases play important roles in bacterial fitness and virulence. Oral streptococci have evolved diverse strategies to survive and thrive in the carbohydrate-rich oral cavity. In this review, we discuss 2 important biological processes mediated by 2 distinct groups of glycosyltransferases in oral streptococci that are important for bacterial colonization and virulence. The first process is the glycosylation of highly conserved serine-rich repeat adhesins by a series of glycosyltransferases. Using Streptococcus parasanguinis as a model, we highlight new features of several glycosyltransferases that sequentially modify the serine-rich glycoprotein Fap1. Distinct features of a novel glycosyltransferase fold from a domain of unknown function 1792 are contrasted with common properties of canonical glycosyltransferases. The second biological process we cover is involved in building sticky glucan matrix to establish cariogenic biofilms by an important opportunistic pathogen Streptococcus mutans through the action of a family of 3 glucosyltransferases. We focus on discussing the structural feature of this family as a glycoside hydrolase family of enzymes. While the 2 processes are distinct, they all produce carbohydrate-coated biomolecules, which enable bacteria to stick better in the complex oral microbiome. Understanding the making of the sweet modification presents a unique opportunity to develop novel antiadhesion and antibiofilm strategies to fight infections by oral streptococci and beyond. PMID:25755271

Evaluating the Small-World-Ness of a Sampled Network: Functional Connectivity of Entorhinal-Hippocampal Circuitry

NASA Astrophysics Data System (ADS)

She, Qi; Chen, Guanrong; Chan, Rosa H. M.

2016-02-01

The amount of publicly accessible experimental data has gradually increased in recent years, which makes it possible to reconsider many longstanding questions in neuroscience. In this paper, an efficient framework is presented for reconstructing functional connectivity using experimental spike-train data. A modified generalized linear model (GLM) with L1-norm penalty was used to investigate 10 datasets. These datasets contain spike-train data collected from the entorhinal-hippocampal region in the brains of rats performing different tasks. The analysis shows that entorhinal-hippocampal network of well-trained rats demonstrated significant small-world features. It is found that the connectivity structure generated by distance-dependent models is responsible for the observed small-world features of the reconstructed networks. The models are utilized to simulate a subset of units recorded from a large biological neural network using multiple electrodes. Two metrics for quantifying the small-world-ness both suggest that the reconstructed network from the sampled nodes estimates a more prominent small-world-ness feature than that of the original unknown network when the number of recorded neurons is small. Finally, this study shows that it is feasible to adjust the estimated small-world-ness results based on the number of neurons recorded to provide a more accurate reference of the network property.

The effect of wall thickness distribution on mechanical reliability and strength in unidirectional porous ceramics.

PubMed

Seuba, Jordi; Deville, Sylvain; Guizard, Christian; Stevenson, Adam J

2016-01-01

Macroporous ceramics exhibit an intrinsic strength variability caused by the random distribution of defects in their structure. However, the precise role of microstructural features, other than pore volume, on reliability is still unknown. Here, we analyze the applicability of the Weibull analysis to unidirectional macroporous yttria-stabilized-zirconia (YSZ) prepared by ice-templating. First, we performed crush tests on samples with controlled microstructural features with the loading direction parallel to the porosity. The compressive strength data were fitted using two different fitting techniques, ordinary least squares and Bayesian Markov Chain Monte Carlo, to evaluate whether Weibull statistics are an adequate descriptor of the strength distribution. The statistical descriptors indicated that the strength data are well described by the Weibull statistical approach, for both fitting methods used. Furthermore, we assess the effect of different microstructural features (volume, size, densification of the walls, and morphology) on Weibull modulus and strength. We found that the key microstructural parameter controlling reliability is wall thickness. In contrast, pore volume is the main parameter controlling the strength. The highest Weibull modulus ([Formula: see text]) and mean strength (198.2 MPa) were obtained for the samples with the smallest and narrowest wall thickness distribution (3.1 [Formula: see text]m) and lower pore volume (54.5%).

The effect of wall thickness distribution on mechanical reliability and strength in unidirectional porous ceramics

NASA Astrophysics Data System (ADS)

Seuba, Jordi; Deville, Sylvain; Guizard, Christian; Stevenson, Adam J.

2016-01-01

Macroporous ceramics exhibit an intrinsic strength variability caused by the random distribution of defects in their structure. However, the precise role of microstructural features, other than pore volume, on reliability is still unknown. Here, we analyze the applicability of the Weibull analysis to unidirectional macroporous yttria-stabilized-zirconia (YSZ) prepared by ice-templating. First, we performed crush tests on samples with controlled microstructural features with the loading direction parallel to the porosity. The compressive strength data were fitted using two different fitting techniques, ordinary least squares and Bayesian Markov Chain Monte Carlo, to evaluate whether Weibull statistics are an adequate descriptor of the strength distribution. The statistical descriptors indicated that the strength data are well described by the Weibull statistical approach, for both fitting methods used. Furthermore, we assess the effect of different microstructural features (volume, size, densification of the walls, and morphology) on Weibull modulus and strength. We found that the key microstructural parameter controlling reliability is wall thickness. In contrast, pore volume is the main parameter controlling the strength. The highest Weibull modulus (?) and mean strength (198.2 MPa) were obtained for the samples with the smallest and narrowest wall thickness distribution (3.1 ?m) and lower pore volume (54.5%).

Intrahaplotypic Variants Differentiate Complex Linkage Disequilibrium within Human MHC Haplotypes

PubMed Central

Lam, Tze Hau; Tay, Matthew Zirui; Wang, Bei; Xiao, Ziwei; Ren, Ee Chee

2015-01-01

Distinct regions of long-range genetic fixation in the human MHC region, known as conserved extended haplotypes (CEHs), possess unique genomic characteristics and are strongly associated with numerous diseases. While CEHs appear to be homogeneous by SNP analysis, the nature of fine variations within their genomic structure is unknown. Using multiple, MHC-homozygous cell lines, we demonstrate extensive sequence conservation in two common Asian MHC haplotypes: A33-B58-DR3 and A2-B46-DR9. However, characterization of phase-resolved MHC haplotypes revealed unique intra-CEH patterns of variation and uncovered 127 single nucleotide variants (SNVs) which are missing from public databases. We further show that the strong linkage disequilibrium structure within the human MHC that typically confounds precise identification of genetic features can be resolved using intra-CEH variants, as evidenced by rs3129063 and rs448489, which affect expression of ZFP57, a gene important in methylation and epigenetic regulation. This study demonstrates an improved strategy that can be used towards genetic dissection of diseases. PMID:26593880

New tricks for the glycyl radical enzyme family

PubMed Central

Backman, Lindsey R.F.; Funk, Michael A.; Dawson, Christopher D.; Drennan, Catherine. L.

2018-01-01

Glycyl radical enzymes (GREs) are important biological catalysts in both strict and facultative anaerobes, playing key roles both in the human microbiota and in the environment. GREs contain a backbone glycyl radical that is post-translationally installed, enabling radical-based mechanisms. GREs function in several metabolic pathways including mixed acid fermentation, ribonucleotide reduction, and the anaerobic breakdown of the nutrient choline and the pollutant toluene. By generating a substrate-based radical species within the active site, GREs enable C-C, C-O, and C-N bond breaking and formation steps that are otherwise challenging for non-radical enzymes. Identification of previously unknown family members from genomic data and the determination of structures of well-characterized GREs have expanded the scope of GRE-catalyzed reactions as well as defined key features that enable radical catalysis. Here we review the structures and mechanisms of characterized GREs, classifying members into five categories. We consider the open questions about each of the five GRE classes and evaluate the tools available to interrogate uncharacterized GREs. PMID:28901199

The Sagatu Ridge dike swarm, Ethiopian rift margin. [tectonic evolution

NASA Technical Reports Server (NTRS)

Mohr, P. A.; Potter, E. C.

1976-01-01

A swarm of dikes forms the core of the Sagatu Ridge, a 70-km-long topographic feature elevated to more than 4000 m above sea level and 1500 m above the level of the Eastern (Somalian) plateau. The ridge trends NNE and lies about 50 km east of the northeasterly trending rift-valley margin. Intrusion of the dikes and buildup of the flood-lava pile, largely hawaiitic but with trachyte preponderant in the final stages, occurred during the late Pliocene-early Pleistocene and may have been contemporaneous with downwarping of the protorift trough to the west. The ensuing faulting that formed the present rift margin, however, bypassed the ridge. The peculiar situation and orientation of the Sagatu Ridge, and its temporary existence as a line of crustal extension and voluminous magmatism, are considered related to a powerful structural control by a major line of Precambrian crustal weakness, well exposed further south. Transverse rift structures of unknown type appear to have limited the development of the ridge to the north and south.

Unravelling Some of the Structure-Property Relationships in Graphene Oxide at Low Degree of Oxidation.

PubMed

Savazzi, Filippo; Risplendi, Francesca; Mallia, Giuseppe; Harrison, Nicholas M; Cicero, Giancarlo

2018-04-05

Graphene oxide (GO) is a versatile 2D material whose properties can be tuned by changing the type and concentration of oxygen-containing functional groups attached to its surface. However, a detailed knowledge of the dependence of the chemo/physical features of this material on its chemical composition is largely unknown. We combine classical molecular dynamics and density functional theory simulations to predict the structural and electronic properties of GO at low degree of oxidation and suggest a revision of the Lerf-Klinowski model. We find that layer deformation is larger for samples containing high concentrations of epoxy groups and that correspondingly the band gap increases. Targeted chemical modification of the GO surface appears to be an effective route to tailor the electronic properties of the monolayer for given applications. Our simulations also show that the chemical shift of the C-1s XPS peak allows one to unambiguously characterize GO composition, resolving the peak attribution  uncertainty often encountered in experiments.

Simulation-based hypothesis testing of high dimensional means under covariance heterogeneity.

PubMed

Chang, Jinyuan; Zheng, Chao; Zhou, Wen-Xin; Zhou, Wen

2017-12-01

In this article, we study the problem of testing the mean vectors of high dimensional data in both one-sample and two-sample cases. The proposed testing procedures employ maximum-type statistics and the parametric bootstrap techniques to compute the critical values. Different from the existing tests that heavily rely on the structural conditions on the unknown covariance matrices, the proposed tests allow general covariance structures of the data and therefore enjoy wide scope of applicability in practice. To enhance powers of the tests against sparse alternatives, we further propose two-step procedures with a preliminary feature screening step. Theoretical properties of the proposed tests are investigated. Through extensive numerical experiments on synthetic data sets and an human acute lymphoblastic leukemia gene expression data set, we illustrate the performance of the new tests and how they may provide assistance on detecting disease-associated gene-sets. The proposed methods have been implemented in an R-package HDtest and are available on CRAN. © 2017, The International Biometric Society.

Super-resolution microscopy reveals cell wall dynamics and peptidoglycan architecture in ovococcal bacteria.

PubMed

Wheeler, Richard; Mesnage, Stéphane; Boneca, Ivo G; Hobbs, Jamie K; Foster, Simon J

2011-12-01

Cell morphology and viability in Eubacteria is dictated by the architecture of peptidoglycan, the major and essential structural component of the cell wall. Although the biochemical composition of peptidoglycan is well understood, how the peptidoglycan architecture can accommodate the dynamics of growth and division while maintaining cell shape remains largely unknown. Here, we elucidate the peptidoglycan architecture and dynamics of bacteria with ovoid cell shape (ovococci), which includes a number of important pathogens, by combining biochemical analyses with atomic force and super-resolution microscopies. Atomic force microscopy analysis showed preferential orientation of the peptidoglycan network parallel to the short axis of the cell, with distinct architectural features associated with septal and peripheral wall synthesis. Super-resolution three-dimensional structured illumination fluorescence microscopy was applied for the first time in bacteria to unravel the dynamics of peptidoglycan assembly in ovococci. The ovococci have a unique peptidoglycan architecture and growth mode not observed in other model organisms. © 2011 Blackwell Publishing Ltd.

Right Ventricular Myocardial Ischemia with Arrhythmia in an Asphyxiated Newborn

PubMed Central

Solevåg, Anne Lee; Schmölzer, Georg M.; Cheung, Po-Yin

2016-01-01

Background Infant and neonatal myocardial infarction (MI) has been described in association with congenital heart disease, coronary artery abnormalities, myocarditis, and tumors. MI in the perinatal period in a structurally normal heart and with ventricular arrhythmia as a presenting feature has not been thoroughly described. Published case reports describe treatment methods extrapolated from adult MI. However, due to the rare occurrence, the most appropriate acute treatment for both MI and ventricular arrhythmia in newborn infants remains unknown. Case A male term infant with perinatal asphyxia and need for extensive cardiopulmonary resuscitation at birth had ventricular tachyarrhythmia and ST-elevations on electrocardiogram. Four hours after birth, he died from cardiogenic failure. A thrombus at the right coronary artery was found on autopsy. Conclusion MI in the perinatal period in a structurally normal heart is very rare and mortality is high. Although acute treatments extrapolated from adult MI has been described to result in favorable outcomes in newborn infants, guidelines are lacking on how to manage acute MI and associated ventricular arrhythmia. PMID:27280062

Ubiquitin Utilizes an Acidic Surface Patch to Alter Chromatin Structure

PubMed Central

Debelouchina, Galia T.; Gerecht, Karola; Muir, Tom W.

2016-01-01

Ubiquitylation of histone H2B, associated with gene activation, leads to chromatin decompaction through an unknown mechanism. We used a hydrogen-deuterium exchange strategy coupled with nuclear magnetic resonance spectroscopy to map the ubiquitin surface responsible for its structural effects on chromatin. Our studies revealed that a previously uncharacterized acidic patch on ubiquitin comprising residues Glu16 and Glu18 is essential for decompaction. These residues mediate promiscuous electrostatic interactions with the basic histone proteins, potentially positioning the ubiquitin moiety as a dynamic “wedge” that prevents the intimate association of neighboring nucleosomes. Using two independent cross-linking strategies and an oligomerization assay, we also showed that ubiquitin-ubiquitin contacts occur in the chromatin environment and are important for the solubilization of the chromatin polymers. Our work highlights a novel, chromatin-related aspect of the “ubiquitin code”, and sheds light on how the information rich ubiquitin modification can orchestrate different biochemical outcomes using different surface features. PMID:27870837

[Myofibrillar myopaathy].

PubMed

Hayashi, Yukiko

2013-01-01

Myofibrillar myopathy (MFM) is a group of hereditary disorders pathologically characterized by focal disorganizations of myofibril structures with cytoplasmic inclusions. Most of the diseases so-called desmin-related or storage myopathy, cytoplasmic body myopathy, spheroid body myopathy, reducing body myopathy, and hyaline body myopathy are included in MFM. Several causative genes have been identified such as DES, CRYAB, MYOT, ZASP, BAG3, FLNC, DNAJB6, FHL1, TTN, and VCP. Most of these genes encode Z-line related proteins or proteins associated with protein quality control. Since MFM is the name from pathological characteristics, clinical features of the patients including the age at disease onset, affected muscles, disease course, and complications are quite variable. In this paper, characteristic clinical and pathological features of each causative gene are summarized. Unexpectedly, hereditary myopathy with early respiratory failure (HMERF) caused by mutation in the A-band region of TTN is the most common cause of MFM in our cohort. Despite of intensive mutation screening, the causative gene of more than 60% of MFM patients is still unknown. Further identification of novel causative genes and elucidate pathomechanisms of protein aggregation in necessary.

Systematic drug repositioning for a wide range of diseases with integrative analyses of phenotypic and molecular data.

PubMed

Iwata, Hiroaki; Sawada, Ryusuke; Mizutani, Sayaka; Yamanishi, Yoshihiro

2015-02-23

Drug repositioning, or the application of known drugs to new indications, is a challenging issue in pharmaceutical science. In this study, we developed a new computational method to predict unknown drug indications for systematic drug repositioning in a framework of supervised network inference. We defined a descriptor for each drug-disease pair based on the phenotypic features of drugs (e.g., medicinal effects and side effects) and various molecular features of diseases (e.g., disease-causing genes, diagnostic markers, disease-related pathways, and environmental factors) and constructed a statistical model to predict new drug-disease associations for a wide range of diseases in the International Classification of Diseases. Our results show that the proposed method outperforms previous methods in terms of accuracy and applicability, and its performance does not depend on drug chemical structure similarity. Finally, we performed a comprehensive prediction of a drug-disease association network consisting of 2349 drugs and 858 diseases and described biologically meaningful examples of newly predicted drug indications for several types of cancers and nonhereditary diseases.

Arctic Ocean Gravity Field Derived From ERS-1 Satellite Altimetry.

PubMed

Laxon, S; McAdoo, D

1994-07-29

The derivation of a marine gravity field from satellite altimetry over permanently ice-covered regions of the Arctic Ocean provides much new geophysical information about the structure and development of the Arctic sea floor. The Arctic Ocean, because of its remote location and perpetual ice cover, remains from a tectonic point of view the most poorly understood ocean basin on Earth. A gravity field has been derived with data from the ERS-1 radar altimeter, including permanently ice-covered regions. The gravity field described here clearly delineates sections of the Arctic Basin margin along with the tips of the Lomonosov and Arctic mid-ocean ridges. Several important tectonic features of the Amerasia Basin are clearly expressed in this gravity field. These include the Mendeleev Ridge; the Northwind Ridge; details of the Chukchi Borderland; and a north-south trending, linear feature in the middle of the Canada Basin that apparently represents an extinct spreading center that "died" in the Mesozoic. Some tectonic models of the Canada Basin have proposed such a failed spreading center, but its actual existence and location were heretofore unknown.

Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthesis

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

Stefely, Jonathan A.; Reidenbach, Andrew G.; Ulbrich, Arne

The ancient UbiB protein kinase-like family is involved in isoprenoid lipid biosynthesis and is implicated in human diseases, but demonstration of UbiB kinase activity has remained elusive for unknown reasons. In this paper, we quantitatively define UbiB-specific sequence motifs and reveal their positions within the crystal structure of a UbiB protein, ADCK3. We find that multiple UbiB-specific features are poised to inhibit protein kinase activity, including an N-terminal domain that occupies the typical substrate binding pocket and a unique A-rich loop that limits ATP binding by establishing an unusual selectivity for ADP. A single alanine-to-glycine mutation of this loop flipsmore » this coenzyme selectivity and enables autophosphorylation but inhibits coenzyme Q biosynthesis in vivo, demonstrating functional relevance for this unique feature. Finally, our work provides mechanistic insight into UbiB enzyme activity and establishes a molecular foundation for further investigation of how UbiB family proteins affect diseases and diverse biological pathways.« less

The Sleep Disorder in Anti-lgLON5 Disease.

PubMed

Gaig, Carles; Iranzo, Alex; Santamaria, Joan; Graus, Francesc

2018-05-23

To review the clinical and polysomnographic features of the sleep disorder occurring in the recently described anti-IgLON5 disease. The hallmark of the disease is the presence of antibodies against IgLON5, a neural cell adhesion molecule of unknown function. The disease presents a robust HLA association, and the neuropathological examination shows a novel neuronal tauopathy with predominant hypothalamic and brainstem involvement. Most patients (> 80%) present sleep-related vocalizations with movements and behaviors and sleep-disordered breathing. Polysomnographic studies show (1) a complex NREM sleep parasomnia at sleep initiation characterized by undifferentiated NREM or poorly structured N2 sleep with sleep-talking or mumbling, and simple or finalistic movements followed by normal periods of N3 or N2 NREM sleep, (2) REM sleep behavior disorder (RBD), and (3) obstructive sleep apnea with stridor. The last two features appear mainly in periods where NREM sleep normalizes. Identification of the anti-IgLON5 sleep disorder is important to suspect the disease. The combination of abnormal NREM sleep initiation, followed by normal periods of NREM sleep and RBD, represents a novel parasomnia.

Urban sprawl and fragmentation in Latin America: a dynamic quantification and characterization of spatial patterns.

PubMed

Inostroza, Luis; Baur, Rolf; Csaplovics, Elmar

2013-01-30

South America is one of the most urbanized continents in the world, where almost 84% of the total population lives in cities, more urbanized than North America (82%) and Europe (73%). Spatial dynamics, their structure, main features, land consumption rates, spatial arrangement, fragmentation degrees and comparability, remain mostly unknown for most Latin American cities. Using satellite imagery the main parameters of sprawl are quantified for 10 Latin American cities over a period of 20 years by monitoring growth patterns and identifying spatial metrics to characterize urban development and sprawling features measured with GIS tools. This quantification contributes to a better understanding of urban form in Latin America. A pervasive spatial expansion has been observed, where most of the studied cities are expanding at fast rates with falling densities trend. Although important differences in the rates of land consumption and densities exist, there is an underlying fragmentation trend towards increasing sprawl. These trends of spatial discontinuity may eventually be intensified by further economic development. Urban Sprawl/Latin America/GIS metrics/spatial development. Copyright © 2012 Elsevier Ltd. All rights reserved.

A new gonad-infecting species of Philometra (Nematoda: Philometridae) from the Atlantic Spanish mackerel Scomberomorus maculatus (Scombridae) off the Atlantic Coast of Florida and South Carolina.

PubMed

Moravec, František; Bakenhaster, Micah; de Buron, Isaure

2013-04-01

A new nematode species, Philometra atlantica n. sp. (Philometridae), is described from male and female specimens found in the ovary of the Atlantic Spanish mackerel, Scomberomorus maculatus (Mitchill) (Scombridae, Perciformes), off the Atlantic coast of Florida and South Carolina. Based on light and scanning electron microscopy examination, the new species differs from most other gonad-infecting Philometra spp. in the length of spicules (111-126 μm), number and arrangement of genital papillae, and a U-shaped, dorsally interrupted caudal mound in the male. A unique feature among all gonad-infecting philometrids is the presence of 2 reflexed dorsal barbs on the distal end of the gubernaculum. From a few congeneric, gonad-infecting species with unknown males, it can be distinguished by some morphological and biometrical features found in gravid females (body length, length of first-stage larvae or esophagus, structure of caudal end) and by the host type (fish family) and geographical distribution. Philometra atlantica is the fourth valid gonad-infecting species of Philometra reported from fishes of the family Scombridae.

Combined measurement system for double shield tunnel boring machine guidance based on optical and visual methods.

PubMed

Lin, Jiarui; Gao, Kai; Gao, Yang; Wang, Zheng

2017-10-01

In order to detect the position of the cutting shield at the head of a double shield tunnel boring machine (TBM) during the excavation, this paper develops a combined measurement system which is mainly composed of several optical feature points, a monocular vision sensor, a laser target sensor, and a total station. The different elements of the combined system are mounted on the TBM in suitable sequence, and the position of the cutting shield in the reference total station frame is determined by coordinate transformations. Subsequently, the structure of the feature points and matching technique for them are expounded, the position measurement method based on monocular vision is presented, and the calibration methods for the unknown relationships among different parts of the system are proposed. Finally, a set of experimental platforms to simulate the double shield TBM is established, and accuracy verification experiments are conducted. Experimental results show that the mean deviation of the system is 6.8 mm, which satisfies the requirements of double shield TBM guidance.

Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthesis

DOE PAGES

Stefely, Jonathan A.; Reidenbach, Andrew G.; Ulbrich, Arne; ...

2014-12-11

The ancient UbiB protein kinase-like family is involved in isoprenoid lipid biosynthesis and is implicated in human diseases, but demonstration of UbiB kinase activity has remained elusive for unknown reasons. In this paper, we quantitatively define UbiB-specific sequence motifs and reveal their positions within the crystal structure of a UbiB protein, ADCK3. We find that multiple UbiB-specific features are poised to inhibit protein kinase activity, including an N-terminal domain that occupies the typical substrate binding pocket and a unique A-rich loop that limits ATP binding by establishing an unusual selectivity for ADP. A single alanine-to-glycine mutation of this loop flipsmore » this coenzyme selectivity and enables autophosphorylation but inhibits coenzyme Q biosynthesis in vivo, demonstrating functional relevance for this unique feature. Finally, our work provides mechanistic insight into UbiB enzyme activity and establishes a molecular foundation for further investigation of how UbiB family proteins affect diseases and diverse biological pathways.« less

A Class of Population Covariance Matrices in the Bootstrap Approach to Covariance Structure Analysis

ERIC Educational Resources Information Center

Yuan, Ke-Hai; Hayashi, Kentaro; Yanagihara, Hirokazu

2007-01-01

Model evaluation in covariance structure analysis is critical before the results can be trusted. Due to finite sample sizes and unknown distributions of real data, existing conclusions regarding a particular statistic may not be applicable in practice. The bootstrap procedure automatically takes care of the unknown distribution and, for a given…

1. Drop Structure on the Arizona Crosscut Canal. Photographer unknown, ...

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

1. Drop Structure on the Arizona Crosscut Canal. Photographer unknown, no date. Note that caption is incorrect: in relation to Camelback Mountain (rear), this can only be the Old Crosscut. Source: reprinted from the 13th Annual Report of the U.S. Geological Survey, 1893. - Old Crosscut Canal, North Side of Salt River, Phoenix, Maricopa County, AZ

Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites

PubMed Central

Piazza, Aurèle; Adrian, Michael; Samazan, Frédéric; Heddi, Brahim; Hamon, Florian; Serero, Alexandre; Lopes, Judith; Teulade-Fichou, Marie-Paule; Phan, Anh Tuân; Nicolas, Alain

2015-01-01

G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids, with various biological roles. However, structural features dictating their formation and/or functionin vivo are unknown. InS. cerevisiae, the pathological persistency of G4 within the CEB1 minisatellite induces its rearrangement during leading-strand replication. We now show that several other G4-forming sequences remain stable. Extensive mutagenesis of the CEB25 minisatellite motif reveals that only variants with very short (≤ 4 nt) G4 loops preferentially containing pyrimidine bases trigger genomic instability. Parallel biophysical analyses demonstrate that shortening loop length does not change the monomorphic G4 structure of CEB25 variants but drastically increases its thermal stability, in correlation with thein vivo instability. Finally, bioinformatics analyses reveal that the threat for genomic stability posed by G4 bearing short pyrimidine loops is conserved inC. elegans and humans. This work provides a framework explanation for the heterogeneous instability behavior of G4-forming sequencesin vivo, highlights the importance of structure thermal stability, and questions the prevailing assumption that G4 structures with short or longer loops are as likely to formin vivo. PMID:25956747

Structure elucidation of metabolite x17299 by interpretation of mass spectrometric data.

PubMed

Zhang, Qibo; Ford, Lisa A; Evans, Anne M; Toal, Douglas R

2017-01-01

A major bottleneck in metabolomic studies is metabolite identification from accurate mass spectrometric data. Metabolite x17299 was identified in plasma as an unknown in a metabolomic study using a compound-centric approach where the associated ion features of the compound were used to determine the true molecular mass. The aim of this work is to elucidate the chemical structure of x17299, a new compound by de novo interpretation of mass spectrometric data. An Orbitrap Elite mass spectrometer was used for acquisition of mass spectra up to MS 4 at high resolution. Synthetic standards of N,N,N -trimethyl-l-alanyl-l-proline betaine (l,l-TMAP), a diastereomer, and an enantiomer were chemically prepared. The planar structure of x17299 was successfully proposed by de novo mechanistic interpretation of mass spectrometric data without any laborious purification and nuclear magnetic resonance spectroscopic analysis. The proposed structure was verified by deuterium exchanged mass spectrometric analysis and confirmed by comparison to a synthetic standard. Relative configuration of x17299 was determined by direct chromatographic comparison to a pair of synthetic diastereomers. Absolute configuration was assigned after derivatization of x17299 with a chiral auxiliary group followed by its chromatographic comparison to a pair of synthetic standards. The chemical structure of metabolite x17299 was determined to be l,l-TMAP.

Euglena gracilis chloroplast DNA: analysis of a 1.6 kb intron of the psb C gene containing an open reading frame of 458 codons.

PubMed

Montandon, P E; Vasserot, A; Stutz, E

1986-01-01

We retrieved a 1.6 kbp intron separating two exons of the psb C gene which codes for the 44 kDa reaction center protein of photosystem II. This intron is 3 to 4 times the size of all previously sequenced Euglena gracilis chloroplast introns. It contains an open reading frame of 458 codons potentially coding for a basic protein of 54 kDa of yet unknown function. The intron boundaries follow consensus sequences established for chloroplast introns related to class II and nuclear pre-mRNA introns. Its 3'-terminal segment has structural features similar to class II mitochondrial introns with an invariant base A as possible branch point for lariat formation.

[Skin fibrosis in hyperthyroidism treated by sotalol and radioactive iodine (author's transl)].

PubMed

Bonnetblanc, J M; Michel, J P; Catanzano, G; Gualde, N; Loubet, A; Leboutet, J M; Liozon, F; Roux, J

1979-01-01

The authors present detailed data about skin fibrosis appearing in hyperthyroidism treated by Sotalol and radioactive iodine. Cutaneous thickening is discovered quite rapidly when the patient is monitored daily (as in case 4). It is asymptomatic and no other features of scleroderma are found. Regression occurs within 4-10 months. Histologically, fibrosis is located in the entire dermis. Dermal appendages are normal and no inflammatory changes occur. No anomalies of collagen structure and fibroblasts have been observed ultrastructurally. Immunological studies (direct immunofluorescence of the skin, lymphocyte transformation and leucocyte migration tests with Sotalol) were normal. The mechanism is unknown, but an immunological or a toxic one is excluded; however a pharmacological action is possible. The role of other betablockers must be assessed by a randomised study.

The Structural Architecture of an Infectious Mammalian Prion Using Electron Cryomicroscopy.

PubMed

Vázquez-Fernández, Ester; Vos, Matthijn R; Afanasyev, Pavel; Cebey, Lino; Sevillano, Alejandro M; Vidal, Enric; Rosa, Isaac; Renault, Ludovic; Ramos, Adriana; Peters, Peter J; Fernández, José Jesús; van Heel, Marin; Young, Howard S; Requena, Jesús R; Wille, Holger

2016-09-01

The structure of the infectious prion protein (PrPSc), which is responsible for Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy, has escaped all attempts at elucidation due to its insolubility and propensity to aggregate. PrPSc replicates by converting the non-infectious, cellular prion protein (PrPC) into the misfolded, infectious conformer through an unknown mechanism. PrPSc and its N-terminally truncated variant, PrP 27-30, aggregate into amorphous aggregates, 2D crystals, and amyloid fibrils. The structure of these infectious conformers is essential to understanding prion replication and the development of structure-based therapeutic interventions. Here we used the repetitive organization inherent to GPI-anchorless PrP 27-30 amyloid fibrils to analyze their structure via electron cryomicroscopy. Fourier-transform analyses of averaged fibril segments indicate a repeating unit of 19.1 Å. 3D reconstructions of these fibrils revealed two distinct protofilaments, and, together with a molecular volume of 18,990 Å3, predicted the height of each PrP 27-30 molecule as ~17.7 Å. Together, the data indicate a four-rung β-solenoid structure as a key feature for the architecture of infectious mammalian prions. Furthermore, they allow to formulate a molecular mechanism for the replication of prions. Knowledge of the prion structure will provide important insights into the self-propagation mechanisms of protein misfolding.

Skin and scales of teleost fish: Simple structure but high performance and multiple functions

NASA Astrophysics Data System (ADS)

Vernerey, Franck J.; Barthelat, Francois

2014-08-01

Natural and man-made structural materials perform similar functions such as structural support or protection. Therefore they rely on the same types of properties: strength, robustness, lightweight. Nature can therefore provide a significant source of inspiration for new and alternative engineering designs. We report here some results regarding a very common, yet largely unknown, type of biological material: fish skin. Within a thin, flexible and lightweight layer, fish skins display a variety of strain stiffening and stabilizing mechanisms which promote multiple functions such as protection, robustness and swimming efficiency. We particularly discuss four important features pertaining to scaled skins: (a) a strongly elastic tensile behavior that is independent from the presence of rigid scales, (b) a compressive response that prevents buckling and wrinkling instabilities, which are usually predominant for thin membranes, (c) a bending response that displays nonlinear stiffening mechanisms arising from geometric constraints between neighboring scales and (d) a robust structure that preserves the above characteristics upon the loss or damage of structural elements. These important properties make fish skin an attractive model for the development of very thin and flexible armors and protective layers, especially when combined with the high penetration resistance of individual scales. Scaled structures inspired by fish skin could find applications in ultra-light and flexible armor systems, flexible electronics or the design of smart and adaptive morphing structures for aerospace vehicles.

Impact-Basin Formation on Mercury: Current Observations and Outstanding Questions

NASA Astrophysics Data System (ADS)

Baker, D. M. H.; Head, J. W.; Fassett, C. I.

2018-05-01

Mercury provides an important laboratory for understanding impact-basin formation on planetary bodies. MESSENGER observations improved our understanding, but much is still unknown about the formation and evolution of basin features.

Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants1[W][OA

PubMed Central

Jiang, Wen-kai; Liu, Yun-long; Xia, En-hua; Gao, Li-zhi

2013-01-01

The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs. PMID:23396833

Effect of silhouetting and inversion on view invariance in the monkey inferotemporal cortex

PubMed Central

2017-01-01

We effortlessly recognize objects across changes in viewpoint, but we know relatively little about the features that underlie viewpoint invariance in the brain. Here, we set out to characterize how viewpoint invariance in monkey inferior temporal (IT) neurons is influenced by two image manipulations—silhouetting and inversion. Reducing an object into its silhouette removes internal detail, so this would reveal how much viewpoint invariance depends on the external contours. Inverting an object retains but rearranges features, so this would reveal how much viewpoint invariance depends on the arrangement and orientation of features. Our main findings are 1) view invariance is weakened by silhouetting but not by inversion; 2) view invariance was stronger in neurons that generalized across silhouetting and inversion; 3) neuronal responses to natural objects matched early with that of silhouettes and only later to that of inverted objects, indicative of coarse-to-fine processing; and 4) the impact of silhouetting and inversion depended on object structure. Taken together, our results elucidate the underlying features and dynamics of view-invariant object representations in the brain. NEW & NOTEWORTHY We easily recognize objects across changes in viewpoint, but the underlying features are unknown. Here, we show that view invariance in the monkey inferotemporal cortex is driven mainly by external object contours and is not specialized for object orientation. We also find that the responses to natural objects match with that of their silhouettes early in the response, and with inverted versions later in the response—indicative of a coarse-to-fine processing sequence in the brain. PMID:28381484

Effect of silhouetting and inversion on view invariance in the monkey inferotemporal cortex.

PubMed

Ratan Murty, N Apurva; Arun, S P

2017-07-01

We effortlessly recognize objects across changes in viewpoint, but we know relatively little about the features that underlie viewpoint invariance in the brain. Here, we set out to characterize how viewpoint invariance in monkey inferior temporal (IT) neurons is influenced by two image manipulations-silhouetting and inversion. Reducing an object into its silhouette removes internal detail, so this would reveal how much viewpoint invariance depends on the external contours. Inverting an object retains but rearranges features, so this would reveal how much viewpoint invariance depends on the arrangement and orientation of features. Our main findings are 1 ) view invariance is weakened by silhouetting but not by inversion; 2 ) view invariance was stronger in neurons that generalized across silhouetting and inversion; 3 ) neuronal responses to natural objects matched early with that of silhouettes and only later to that of inverted objects, indicative of coarse-to-fine processing; and 4 ) the impact of silhouetting and inversion depended on object structure. Taken together, our results elucidate the underlying features and dynamics of view-invariant object representations in the brain. NEW & NOTEWORTHY We easily recognize objects across changes in viewpoint, but the underlying features are unknown. Here, we show that view invariance in the monkey inferotemporal cortex is driven mainly by external object contours and is not specialized for object orientation. We also find that the responses to natural objects match with that of their silhouettes early in the response, and with inverted versions later in the response-indicative of a coarse-to-fine processing sequence in the brain. Copyright © 2017 the American Physiological Society.

A Tephra Database With an Intelligent Correlation System, Mono-Inyo Volcanic Chain, CA

NASA Astrophysics Data System (ADS)

Bursik, M.; Rogova, G.

2004-12-01

We are assembling a web-accessible, relational database of information on past eruptions of the Mono-Inyo volcanic chain, eastern California. The PostgreSQL database structure follows the North American Data Model and CordLink. The database allows us to extract the features diagnostic of particular pyroclastic layers, as well as lava domes and flows. The features include depth in the section, layer thickness and internal stratigraphy, mineral assemblage, major and trace element composition, tephra componentry and granulometry, and radiocarbon age. Our working hypotheses are that 1) the database will prove useful for unraveling the complex recent volcanic history of the Mono-Inyo chain 2) aided by the use of an intelligent correlation system integrated into the database system. The Mono-Inyo chain consists of domes, craters and flows that stretch for 50 km north-south, subparallel to the Sierran range front fault system. Almost all eruptions within the chain probably occurred less than 50,000 years ago. Because of the variety of magma and eruption types, and the migration of source regions in time and space, it is nontrivial to discern patterns of behaviour. We have explored the use of multiple artificial neural networks combined within the framework of the Dempster-Shafer theory of evidence to construct a hybrid information processing system as an aid in the correlation of Mono-Inyo pyroclastic layers. It is hoped that such a system could provide information useful to discerning eruptive patterns that would otherwise be difficult to sort and categorize. In a test case on tephra layers at known sites, the intelligent correlation system was able to categorize observations correctly 96% of the time. In a test case with layers at one unknown site, and using a pairwise comparison of the unknown site with the known sites, a one-to-one correlation between the unknown site and the known sites was found to sometimes be poor. Such a result could be used to aid a stratigrapher in rethinking or questioning a proposed correlation. This rethinking might not happen without the input from the intelligent system.

Encephalocraniocutaneous lipomatosis with calvarial exostosis - Case report and review of literature

PubMed Central

Thakur, Shruti; Thakur, Vijay; Sood, Ram Gopal; Thakur, Charu Smita; Khanna, Shweta

2013-01-01

Encephalocraniocutaneous lipomatosis (ECCL), also known as Haberland syndrome, is a rare syndrome with unknown etiology. The syndrome is characterized by a triad of unique cutaneous, ocular, and central nervous system (CNS) manifestations. The cutaneous hallmark, nevus psiloliparus (NP), along with overlying alopecia is a constant feature. Choristoma of the eyelid is the most common ocular manifestation, while intracranial lipoma is the predominant CNS finding. Genetic counseling is required to emphasize that the disorder, although congenital, is not inheritable. We present a 21-year-old female with cutaneous, ocular, and CNS features satisfying the diagnostic criteria for ECCL. To our knowledge, this is the first case of ECCL having a large temporal exostosis. The objective of this article is to better understand the phenotypic spectrum of this syndrome whose molecular basis is still unknown. PMID:24604937

Radar target classification method with high accuracy and decision speed performance using MUSIC spectrum vectors and PCA projection

NASA Astrophysics Data System (ADS)

Secmen, Mustafa

2011-10-01

This paper introduces the performance of an electromagnetic target recognition method in resonance scattering region, which includes pseudo spectrum Multiple Signal Classification (MUSIC) algorithm and principal component analysis (PCA) technique. The aim of this method is to classify an "unknown" target as one of the "known" targets in an aspect-independent manner. The suggested method initially collects the late-time portion of noise-free time-scattered signals obtained from different reference aspect angles of known targets. Afterward, these signals are used to obtain MUSIC spectrums in real frequency domain having super-resolution ability and noise resistant feature. In the final step, PCA technique is applied to these spectrums in order to reduce dimensionality and obtain only one feature vector per known target. In the decision stage, noise-free or noisy scattered signal of an unknown (test) target from an unknown aspect angle is initially obtained. Subsequently, MUSIC algorithm is processed for this test signal and resulting test vector is compared with feature vectors of known targets one by one. Finally, the highest correlation gives the type of test target. The method is applied to wire models of airplane targets, and it is shown that it can tolerate considerable noise levels although it has a few different reference aspect angles. Besides, the runtime of the method for a test target is sufficiently low, which makes the method suitable for real-time applications.

Proof-of-Concept Studies in Novel Guided Wave Methods for Metallic Structural Condition

DTIC Science & Technology

2009-03-01

stiffness tensor which is general can be complex (viscoelastic behavior). More details on the compatibility operator can be found in (Gopalakrishnan...structure was in when these AR coefficients were recorded is scored as the " vote " for the unknown condition using that particular input signal. This...signals that are imparted to the structure in its unknown state. The votes for each condition are then summed and the condition with the plurality of

Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry.

PubMed

Wang, Cheng; He, Lidong; Li, Da-Wei; Bruschweiler-Li, Lei; Marshall, Alan G; Brüschweiler, Rafael

2017-10-06

Metabolite identification in metabolomics samples is a key step that critically impacts downstream analysis. We recently introduced the SUMMIT NMR/mass spectrometry (MS) hybrid approach for the identification of the molecular structure of unknown metabolites based on the combination of NMR, MS, and combinatorial cheminformatics. Here, we demonstrate the feasibility of the approach for an untargeted analysis of both a model mixture and E. coli cell lysate based on 2D/3D NMR experiments in combination with Fourier transform ion cyclotron resonance MS and MS/MS data. For 19 of the 25 model metabolites, SUMMIT yielded complete structures that matched those in the mixture independent of database information. Of those, seven top-ranked structures matched those in the mixture, and four of those were further validated by positive ion MS/MS. For five metabolites, not part of the 19 metabolites, correct molecular structural motifs could be identified. For E. coli, SUMMIT MS/NMR identified 20 previously known metabolites with three or more 1 H spins independent of database information. Moreover, for 15 unknown metabolites, molecular structural fragments were determined consistent with their spin systems and chemical shifts. By providing structural information for entire metabolites or molecular fragments, SUMMIT MS/NMR greatly assists the targeted or untargeted analysis of complex mixtures of unknown compounds.

Photocopy of photograph. Photographer unknown. Poster from the World War ...

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

Photocopy of photograph. Photographer unknown. Poster from the World War II period. During drives to encourage purchase of war bonds, posters featuring female shipyard workers were widely distributed purchasers were allowed one vote for each bond bought. Votes were cast and the woman who got the most votes was named "War Bond Girl." The contest was won by Kay McGinty, 4th row, 2nd column. - Naval Base Philadelphia-Philadelphia Naval Shipyard, League Island, Philadelphia, Philadelphia County, PA

Tracking problem for electromechanical system under influence of external perturbations

NASA Astrophysics Data System (ADS)

Kochetkov, Sergey A.; Krasnova, Svetlana A.; Utkin, Victor A.

2017-01-01

For electromechanical objects the new control algorithms (vortex algprithms) are developed on the base of discontinuous functions. The distinctive feature of these algorithms is providing of asymptotical convergence of the output variables to zero under influence of unknown bounded disturbances of prescribed class. The advantages of proposed approach is demonstrated for direct current motor with permanent excitation. It is shown that inner variables of the system converge to unknown bounded disturbances and guarantee asymptotical convergence of output variables to zero.

Echolocating bats rely on audiovocal feedback to adapt sonar signal design.

PubMed

Luo, Jinhong; Moss, Cynthia F

2017-10-10

Many species of bat emit acoustic signals and use information carried by echoes reflecting from nearby objects to navigate and forage. It is widely documented that echolocating bats adjust the features of sonar calls in response to echo feedback; however, it remains unknown whether audiovocal feedback contributes to sonar call design. Audiovocal feedback refers to the monitoring of one's own vocalizations during call production and has been intensively studied in nonecholocating animals. Audiovocal feedback not only is a necessary component of vocal learning but also guides the control of the spectro-temporal structure of vocalizations. Here, we show that audiovocal feedback is directly involved in the echolocating bat's control of sonar call features. As big brown bats tracked targets from a stationary position, we played acoustic jamming signals, simulating calls of another bat, timed to selectively perturb audiovocal feedback or echo feedback. We found that the bats exhibited the largest call-frequency adjustments when the jamming signals occurred during vocal production. By contrast, bats did not show sonar call-frequency adjustments when the jamming signals coincided with the arrival of target echoes. Furthermore, bats rapidly adapted sonar call design in the first vocalization following the jamming signal, revealing a response latency in the range of 66 to 94 ms. Thus, bats, like songbirds and humans, rely on audiovocal feedback to structure sonar signal design.

A new application of the phase-field method for understanding the mechanisms of nuclear architecture reorganization.

PubMed

Lee, S Seirin; Tashiro, S; Awazu, A; Kobayashi, R

2017-01-01

Specific features of nuclear architecture are important for the functional organization of the nucleus, and chromatin consists of two forms, heterochromatin and euchromatin. Conventional nuclear architecture is observed when heterochromatin is enriched at nuclear periphery, and it represents the primary structure in the majority of eukaryotic cells, including the rod cells of diurnal mammals. In contrast to this, inverted nuclear architecture is observed when the heterochromatin is distributed at the center of the nucleus, which occurs in the rod cells of nocturnal mammals. The inverted architecture found in the rod cells of the adult mouse is formed through the reorganization of conventional architecture during terminal differentiation. Although a previous experimental approach has demonstrated the relationship between these two nuclear architecture types at the molecular level, the mechanisms underlying long-range reorganization processes remain unknown. The details of nuclear structures and their spatial and temporal dynamics remain to be elucidated. Therefore, a comprehensive approach, using mathematical modeling, is required, in order to address these questions. Here, we propose a new mathematical approach to the understanding of nuclear architecture dynamics using the phase-field method. We successfully recreated the process of nuclear architecture reorganization, and showed that it is robustly induced by physical features, independent of a specific genotype. Our study demonstrates the potential of phase-field method application in the life science fields.

Organic Spectroscopy Laboratory: Utilizing IR and NMR in the Identification of an Unknown Substance

ERIC Educational Resources Information Center

Glagovich, Neil M.; Shine, Timothy D.

2005-01-01

A laboratory experiment that emphasizes the interpretation of both infrared (IR) and nuclear magnetic resonance (NMR) spectra in the elucidation of the structure of an unknown compound was developed. The method helps students determine [to the first power]H- and [to the thirteenth power]C-NMR spectra from the structures of compounds and to…

The crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1: Implications to protein function and drug design.

PubMed

Ronin, Céline; Costa, David Mendes; Tavares, Joana; Faria, Joana; Ciesielski, Fabrice; Ciapetti, Paola; Smith, Terry K; MacDougall, Jane; Cordeiro-da-Silva, Anabela; Pemberton, Iain K

2018-01-01

The de novo crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSir2rp1) has been solved at 1.99Å in complex with an acetyl-lysine peptide substrate. The structure is broadly commensurate with Hst2/SIRT2 proteins of yeast and human origin, reproducing many of the structural features common to these sirtuin deacetylases, including the characteristic small zinc-binding domain, and the larger Rossmann-fold domain involved in NAD+-binding interactions. The two domains are linked via a cofactor binding loop ordered in open conformation. The peptide substrate binds to the LiSir2rp1 protein via a cleft formed between the small and large domains, with the acetyl-lysine side chain inserting further into the resultant hydrophobic tunnel. Crystals were obtained only with recombinant LiSir2rp1 possessing an extensive internal deletion of a proteolytically-sensitive region unique to the sirtuins of kinetoplastid origin. Deletion of 51 internal amino acids (P253-E303) from LiSir2rp1 did not appear to alter peptide substrate interactions in deacetylation assays, but was indispensable to obtain crystals. Removal of this potentially flexible region, that otherwise extends from the classical structural elements of the Rossmann-fold, specifically the β8-β9 connector, appears to result in lower accumulation of the protein when expressed from episomal vectors in L. infantum SIR2rp1 single knockout promastigotes. The biological function of the large serine-rich insertion in kinetoplastid/trypanosomatid sirtuins, highlighted as a disordered region with strong potential for post-translational modification, remains unknown but may confer additional cellular functions that are distinct from their human counterparts. These unique molecular features, along with the resolution of the first kinetoplastid sirtuin deacetylase structure, present novel opportunities for drug design against a protein target previously established as essential to parasite survival and proliferation.

Multivariate Bayesian modeling of known and unknown causes of events--an application to biosurveillance.

PubMed

Shen, Yanna; Cooper, Gregory F

2012-09-01

This paper investigates Bayesian modeling of known and unknown causes of events in the context of disease-outbreak detection. We introduce a multivariate Bayesian approach that models multiple evidential features of every person in the population. This approach models and detects (1) known diseases (e.g., influenza and anthrax) by using informative prior probabilities and (2) unknown diseases (e.g., a new, highly contagious respiratory virus that has never been seen before) by using relatively non-informative prior probabilities. We report the results of simulation experiments which support that this modeling method can improve the detection of new disease outbreaks in a population. A contribution of this paper is that it introduces a multivariate Bayesian approach for jointly modeling both known and unknown causes of events. Such modeling has general applicability in domains where the space of known causes is incomplete. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking.

PubMed

Jayaseelan, Kalai Vanii; Steinbeck, Christoph

2014-07-05

In metabolomics experiments, spectral fingerprints of metabolites with no known structural identity are detected routinely. Computer-assisted structure elucidation (CASE) has been used to determine the structural identities of unknown compounds. It is generally accepted that a single 1D NMR spectrum or mass spectrum is usually not sufficient to establish the identity of a hitherto unknown compound. When a suite of spectra from 1D and 2D NMR experiments supplemented with a molecular formula are available, the successful elucidation of the chemical structure for candidates with up to 30 heavy atoms has been reported previously by one of the authors. In high-throughput metabolomics, usually 1D NMR or mass spectrometry experiments alone are conducted for rapid analysis of samples. This method subsequently requires that the spectral patterns are analyzed automatically to quickly identify known and unknown structures. In this study, we investigated whether additional existing knowledge, such as the fact that the unknown compound is a natural product, can be used to improve the ranking of the correct structure in the result list after the structure elucidation process. To identify unknowns using as little spectroscopic information as possible, we implemented an evolutionary algorithm-based CASE mechanism to elucidate candidates in a fully automated fashion, with input of the molecular formula and 13C NMR spectrum of the isolated compound. We also tested how filters like natural product-likeness, a measure that calculates the similarity of the compounds to known natural product space, might enhance the performance and quality of the structure elucidation. The evolutionary algorithm is implemented within the SENECA package for CASE reported previously, and is available for free download under artistic license at http://sourceforge.net/projects/seneca/. The natural product-likeness calculator is incorporated as a plugin within SENECA and is available as a GUI client and command-line executable. Significant improvements in candidate ranking were demonstrated for 41 small test molecules when the CASE system was supplemented by a natural product-likeness filter. In spectroscopically underdetermined structure elucidation problems, natural product-likeness can contribute to a better ranking of the correct structure in the results list.

Topographic and sedimentary features in the Yap subduction zone and their implications for the Caroline Ridge subduction

NASA Astrophysics Data System (ADS)

Dong, Dongdong; Zhang, Zhengyi; Bai, Yongliang; Fan, Jianke; Zhang, Guangxu

2018-01-01

The Yap subduction zone in the western Pacific presents some unique features compared to normal intra-oceanic subduction zones such as the subduction of an oceanic plateau. However, due to the relative paucity of geophysical data, the detailed structure remains unknown in this area. In this study, we present the latest high-quality swath bathymetry and multi-channel seismic data acquired synchronously in 2015 across the Yap subduction zone. The topographic and sedimentary features are intensively investigated and a modified evolutionary model of the Yap subduction zone is proposed. The two-stage evolution of the Parece Vela Basin (PVB) produced fabrics that are N-S trending and NW-SE trending. Our seismic data clearly reveal landslide deposits at the upper slope break of the forearc, to the north of the Yap Island, which was identified as the fault notch denoting a lithological boundary in previous work. The swath bathymetry and seismic profile reveal detailed horst and graben structures, including a crescent-shaped fault zone near the contact between the Yap Trench and the Caroline Ridge. A simple geometric model is proposed to explain the structure formation, indicating that the higher topography of the Caroline Ridge resulted in enhanced bending-related extension. A seismic angular unconformity (named R1) is identified in the Sorol Trough, marking the onset of rifting in the trough. Based on the sequence thickness and deposition rate by Deep Sea Drilling Project (DSDP), it is deduced that the Sorol Trough formed at 10 Ma or even earlier. A modified model for the Yap subduction zone evolution is proposed, incorporating three major tectonic events: the proto-Yap Arc rupture in the Oligocene, the collision of the Caroline Ridge and the Yap Trench in the late Oligocene or middle Miocene, and the onset of the Sorol Trough rifting in the late Miocene.

Early diagnosis of regional odontodysplasia in an infant.

PubMed

Canela, Alfredo Hiram Carrillo; Rezende, Karla Mayra Pinto E Carvalho; Benitez, Mirtha; Bönecker, Marcelo

2012-03-01

Regional odontodysplasia is a rare and significant dental malformation. It is a dental alteration of unknown etiology, involving both mesodermal and ectodermal dental components, which present clinical, radiographic, and histologic features. This article reports a clinical case of a 10-month-old child who was diagnosed with regional odontodysplasia in the maxilla, confirmed by radiographic examination, with a follow-up of 5 years. The clinical, radiographic, and histologic features were reviewed.

Pragmatic Language Features of Mothers with the "FMR1" Premutation Are Associated with the Language Outcomes of Adolescents and Young Adults with Fragile X Syndrome

ERIC Educational Resources Information Center

Klusek, Jessica; McGrath, Sara E.; Abbeduto, Leonard; Roberts, Jane E.

2016-01-01

Purpose: Pragmatic language difficulties have been documented as part of the FMR1 premutation phenotype, yet the interplay between these features in mothers and the language outcomes of their children with fragile X syndrome is unknown. This study aimed to determine whether pragmatic language difficulties in mothers with the "FMR1"…

Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction.

PubMed

Chira, Camelia; Horvath, Dragos; Dumitrescu, D

2011-07-30

Proteins are complex structures made of amino acids having a fundamental role in the correct functioning of living cells. The structure of a protein is the result of the protein folding process. However, the general principles that govern the folding of natural proteins into a native structure are unknown. The problem of predicting a protein structure with minimum-energy starting from the unfolded amino acid sequence is a highly complex and important task in molecular and computational biology. Protein structure prediction has important applications in fields such as drug design and disease prediction. The protein structure prediction problem is NP-hard even in simplified lattice protein models. An evolutionary model based on hill-climbing genetic operators is proposed for protein structure prediction in the hydrophobic - polar (HP) model. Problem-specific search operators are implemented and applied using a steepest-ascent hill-climbing approach. Furthermore, the proposed model enforces an explicit diversification stage during the evolution in order to avoid local optimum. The main features of the resulting evolutionary algorithm - hill-climbing mechanism and diversification strategy - are evaluated in a set of numerical experiments for the protein structure prediction problem to assess their impact to the efficiency of the search process. Furthermore, the emerging consolidated model is compared to relevant algorithms from the literature for a set of difficult bidimensional instances from lattice protein models. The results obtained by the proposed algorithm are promising and competitive with those of related methods.

Structure Biology of Membrane Bound Enzymes

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

Fu, Dax

The overall goal of the proposed research is to understand the membrane-associated active processes catalyzed by an alkanemore » $$\\square$$-hydroxylase (AlkB) from eubacterium Pseudomonase oleovorans. AlkB performs oxygenation of unactivated hydrocarbons found in crude oils. The enzymatic reaction involves energy-demanding steps in the membrane with the uses of structurally unknown metal active sites featuring a diiron [FeFe] center. At present, a critical barrier to understanding the membrane-associated reaction mechanism is the lack of structural information. The structural biology efforts have been challenged by technical difficulties commonly encountered in crystallization and structural determination of membrane proteins. The specific aims of the current budget cycle are to crystalize AlkB and initiate X-ray analysis to set the stage for structural determination. The long-term goals of our structural biology efforts are to provide an atomic description of AlkB structure, and to uncover the mechanisms of selective modification of hydrocarbons. The structural information will help elucidating how the unactivated C-H bonds of saturated hydrocarbons are oxidized to initiate biodegradation and biotransformation processes. The knowledge gained will be fundamental to biotechnological applications to biofuel transformation of non-edible oil feedstock. Renewable biodiesel is a promising energy carry that can be used to reduce fossil fuel dependency. The proposed research capitalizes on prior BES-supported efforts on over-expression and purification of AlkB to explore the inner workings of a bioenergy-relevant membrane-bound enzyme.« less

Modeling photoacoustic spectral features of micron-sized particles

NASA Astrophysics Data System (ADS)

Strohm, Eric M.; Gorelikov, Ivan; Matsuura, Naomi; Kolios, Michael C.

2014-10-01

The photoacoustic signal generated from particles when irradiated by light is determined by attributes of the particle such as the size, speed of sound, morphology and the optical absorption coefficient. Unique features such as periodically varying minima and maxima are observed throughout the photoacoustic signal power spectrum, where the periodicity depends on these physical attributes. The frequency content of the photoacoustic signals can be used to obtain the physical attributes of unknown particles by comparison to analytical solutions of homogeneous symmetric geometric structures, such as spheres. However, analytical solutions do not exist for irregularly shaped particles, inhomogeneous particles or particles near structures. A finite element model (FEM) was used to simulate photoacoustic wave propagation from four different particle configurations: a homogeneous particle suspended in water, a homogeneous particle on a reflecting boundary, an inhomogeneous particle with an absorbing shell and non-absorbing core, and an irregularly shaped particle such as a red blood cell. Biocompatible perfluorocarbon droplets, 3-5 μm in diameter containing optically absorbing nanoparticles were used as the representative ideal particles, as they are spherical, homogeneous, optically translucent, and have known physical properties. The photoacoustic spectrum of micron-sized single droplets in suspension and on a reflecting boundary were measured over the frequency range of 100-500 MHz and compared directly to analytical models and the FEM. Good agreement between the analytical model, FEM and measured values were observed for a droplet in suspension, where the spectral minima agreed to within a 3.3 MHz standard deviation. For a droplet on a reflecting boundary, spectral features were correctly reproduced using the FEM but not the analytical model. The photoacoustic spectra from other common particle configurations such as particle with an absorbing shell and a biconcave-shaped red blood cell were also investigated, where unique features in the power spectrum could be used to identify them.

MACSIMS : multiple alignment of complete sequences information management system

PubMed Central

Thompson, Julie D; Muller, Arnaud; Waterhouse, Andrew; Procter, Jim; Barton, Geoffrey J; Plewniak, Frédéric; Poch, Olivier

2006-01-01

Background In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the vast amount of heterogeneous data available. Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family. Results MACSIMS is a multiple alignment-based information management program that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is retrieved automatically from the public databases. In the multiple alignment, homologous regions are identified and the retrieved data is evaluated and propagated from known to unknown sequences with these reliable regions. In a large-scale evaluation, the specificity of the propagated sequence features is estimated to be >99%, i.e. very few false positive predictions are made. MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases. The number of sequence features associated with these proteins was increased by 60%, compared to the features available in the public databases. An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis. Conclusion MACSIMS is a new information management system that incorporates detailed analyses of protein families at the structural, functional and evolutionary levels. MACSIMS thus provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. A web server and the source code are available at . PMID:16792820

The location and nature of the Telemzan High Ghadames basin boundary in southern Tunisia based on gravity and magnetic anomalies

NASA Astrophysics Data System (ADS)

Gabtni, H.; Jallouli, C.; Mickus, K. L.; Zouari, H.; Turki, M. M.

2006-03-01

Gravity and magnetic data were analyzed to add constraints on the location and nature of the Telemzan-Ghadames boundary (TGB) and structure of the Ghadames basin in southern Tunisia. TGB is the boundary between the thick sedimentary cover of the intracratonic Ghadames basin to the south and the thin sedimentary cover of the Saharan platform to the north. The upward continuation of the Bouguer gravity anomalies showed that the TGB is a regional geophysical feature that may have controlled the amount of sediment being deposited both north and south of the boundary and the tectonic environment in the region since Paleozoic time. To emphasize the shorter wavelength gravity and magnetic anomalies, a series of gray scale images of the directional horizontal gradients were constructed that determined a series of previously unknown east-west-trending gravity and magnetic anomalies south of 31.6°N that correspond to lineaments seen on a Landsat 7 image and the location of the TGB. Also, an edge-enhancement analysis illustrated the same linear gravity anomalies and showed the subbasins and uplifts within the Ghadames basin had source depths of between 0.5 and 3.4 km. A north-south trending gravity model showed that the TGB is a relatively gradual feature (possibly basement stepped down by relatively low-displacement faulting) controlling the subsidence of the main Ghadames basin and confirms the edge-enhancement analysis that subbasin S3 and uplift U1 are the main structural features within the Ghadames basin. The knowledge of basement architecture of the Ghadames basin is important for future petroleum exploration within this intracratonic basin.

Small Mounds in Chryse Planitia

NASA Image and Video Library

2011-07-15

The suggested area in this observation from NASA Mars Reconnaissance Orbiter is characterized by a group of cones, shield-like features, and round mounds. They are a few hundred meters to kilometers in diameter but their heights are unknown.

Familial polycystic ovarian disease.

PubMed

Givens, J R

1988-12-01

Emphasis is placed on the heterogeneity of the phenotypic presentation of PCOD. It is the common expression of an unknown number of disorders and thus is a sign and not a specific diagnosis. Two essential features are arrested follicular maturation and atresia of follicles. Normal folliculogenesis is described, emphasizing that a large number of areas could be subject to derangement causing PCOD. Any interference of the finely balanced sequence of events can lead to PCOD. The genetic defect causing familial PCOD is unknown and the initiating event remains undefined. Three families are described that illustrate four features of familial PCOD. A number of associated disorders such as diabetes, hyperinsulinemia, obesity, and hypertension are described. The potential importance of agents that modulate the LH and FSH activity that may cause PCOD is emphasized. The theoretic means by which similar male and female gonadal abnormalities may be coupled in families through growth factors EGF and alpha TGF are presented.

Structural violence and chronic kidney disease of unknown etiology in Sri Lanka.

PubMed

de Silva, M W Amarasiri; Albert, Steven M; Jayasekara, J M K B

2017-04-01

Research published on Chronic Kidney Disease of Unknown Etiology (CKDu) in Sri Lanka has been undertaken largely from biomedical and epidemiological perspectives. The main objective of these studies has been to identify the etiology of the disease, which affects as much as 15-21% of the population in some regions and is associated with kidney failure. Few studies have sought to address how CKDu is socially and behaviorally situated in the affected districts. The present study, informed by structural violence theory, utilized a mixed-method approach that analyzed primary and secondary data for Medawachchiya District Secretariat Division in Anuradhapura District for 2010 and 2015, and examined CKDu as a manifestation of social inequality and exclusion and the creation of a marginalized group of agricultural laborers. Data include historical analyses, a case-control study, ecologic analysis of features of communities and CKDu prevalence, and direct observations and interviews with people in affected communities. In 2010, the most important factor associated with CKDu was private dug wells that were used for supplying water to homes. In 2015, when the number of patients had increased, CKDu was more closely linked to occupation, especially male wage labor. The male wage laborer, being the poorest of the poor, has become a particularly vulnerable social category in agricultural settlements in Medawachchiya. The co-occurrence of this social category and CKDu can be regarded as unintended consequences of the official agricultural colonization policy that started during British colonial times and has continued since independence. Copyright © 2017 Elsevier Ltd. All rights reserved.

AN ENIGMATIC POINT-LIKE FEATURE WITHIN THE HD 169142 TRANSITIONAL DISK ,

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

Biller, Beth A.; Males, Jared; Morzinski, Katie

2014-09-01

We report the detection of a faint point-like feature possibly related to ongoing planet-formation in the disk of the transition disk star HD 169142. The point-like feature has a Δmag(L) ∼ 6.4, at a separation of ∼0.''11 and position angle ∼0°. Given its lack of an H or K{sub S} counterpart despite its relative brightness, this candidate cannot be explained by purely photospheric emission and must be a disk feature heated by an as yet unknown source. Its extremely red colors make it highly unlikely to be a background object, but future multi-wavelength follow up is necessary for confirmation and characterization ofmore » this feature.« less

Characterizing Functional Domains for TIM-Mediated Enveloped Virus Entry

PubMed Central

Moller-Tank, Sven; Albritton, Lorraine M.; Rennert, Paul D.

2014-01-01

ABSTRACT T-cell immunoglobulin and mucin domain 1 (TIM-1) and other TIM family members were recently identified as phosphatidylserine (PtdSer)-mediated virus entry-enhancing receptors (PVEERs). These proteins enhance entry of Ebola virus (EBOV) and other viruses by binding PtdSer on the viral envelope, concentrating virus on the cell surface, and promoting subsequent internalization. The PtdSer-binding activity of the immunoglobulin-like variable (IgV) domain is essential for both virus binding and internalization by TIM-1. However, TIM-3, whose IgV domain also binds PtdSer, does not effectively enhance virus entry, indicating that other domains of TIM proteins are functionally important. Here, we investigate the domains supporting enhancement of enveloped virus entry, thereby defining the features necessary for a functional PVEER. Using a variety of chimeras and deletion mutants, we found that in addition to a functional PtdSer-binding domain PVEERs require a stalk domain of sufficient length, containing sequences that promote an extended structure. Neither the cytoplasmic nor the transmembrane domain of TIM-1 is essential for enhancing virus entry, provided the protein is still plasma membrane bound. Based on these defined characteristics, we generated a mimic lacking TIM sequences and composed of annexin V, the mucin-like domain of α-dystroglycan, and a glycophosphatidylinositol anchor that functioned as a PVEER to enhance transduction of virions displaying Ebola, Chikungunya, Ross River, or Sindbis virus glycoproteins. This identification of the key features necessary for PtdSer-mediated enhancement of virus entry provides a basis for more effective recognition of unknown PVEERs. IMPORTANCE T-cell immunoglobulin and mucin domain 1 (TIM-1) and other TIM family members are recently identified phosphatidylserine (PtdSer)-mediated virus entry-enhancing receptors (PVEERs). These proteins enhance virus entry by binding the phospholipid, PtdSer, present on the viral membrane. While it is known that the PtdSer binding is essential for the PVEER function of TIM-1, TIM-3 shares this binding activity but does not enhance virus entry. No comprehensive studies have been done to characterize the other domains of TIM-1. In this study, using a variety of chimeric proteins and deletion mutants, we define the features necessary for a functional PVEER. With these features in mind, we generated a TIM-1 mimic using functionally similar domains from other proteins. This mimic, like TIM-1, effectively enhanced transduction. These studies provide insight into the key features necessary for PVEERs and will allow for more effective identification of unknown PVEERs. PMID:24696470

Modulation of a Pore in the Capsid of JC Polyomavirus Reduces Infectivity and Prevents Exposure of the Minor Capsid Proteins

PubMed Central

Nelson, Christian D. S.; Ströh, Luisa J.; Gee, Gretchen V.; O'Hara, Bethany A.; Stehle, Thilo

2015-01-01

ABSTRACT JC polyomavirus (JCPyV) infection of immunocompromised individuals results in the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML). The viral capsid of JCPyV is composed primarily of the major capsid protein virus protein 1 (VP1), and pentameric arrangement of VP1 monomers results in the formation of a pore at the 5-fold axis of symmetry. While the presence of this pore is conserved among polyomaviruses, its functional role in infection or assembly is unknown. Here, we investigate the role of the 5-fold pore in assembly and infection of JCPyV by generating a panel of mutant viruses containing amino acid substitutions of the residues lining this pore. Multicycle growth assays demonstrated that the fitness of all mutants was reduced compared to that of the wild-type virus. Bacterial expression of VP1 pentamers containing substitutions to residues lining the 5-fold pore did not affect pentamer assembly or prevent association with the VP2 minor capsid protein. The X-ray crystal structures of selected pore mutants contained subtle changes to the 5-fold pore, and no other changes to VP1 were observed. Pore mutant pseudoviruses were not deficient in assembly, packaging of the minor capsid proteins, or binding to cells or in transport to the host cell endoplasmic reticulum. Instead, these mutant viruses were unable to expose VP2 upon arrival to the endoplasmic reticulum, a step that is critical for infection. This study demonstrated that the 5-fold pore is an important structural feature of JCPyV and that minor modifications to this structure have significant impacts on infectious entry. IMPORTANCE JCPyV is an important human pathogen that causes a severe neurological disease in immunocompromised individuals. While the high-resolution X-ray structure of the major capsid protein of JCPyV has been solved, the importance of a major structural feature of the capsid, the 5-fold pore, remains poorly understood. This pore is conserved across polyomaviruses and suggests either that these viruses have limited structural plasticity in this region or that this pore is important in infection or assembly. Using a structure-guided mutational approach, we showed that modulation of this pore severely inhibits JCPyV infection. These mutants do not appear deficient in assembly or early steps in infectious entry and are instead reduced in their ability to expose a minor capsid protein in the host cell endoplasmic reticulum. Our work demonstrates that the 5-fold pore is an important structural feature for JCPyV. PMID:25609820

Metastatic Neuroendocrine Carcinoma of Unknown Origin Arising in the Femoral Nerve Sheath.

PubMed

Candy, Nicholas; Young, Adam; Allinson, Kieren; Carr, Oliver; McMillen, Jason; Trivedi, Rikin

2017-08-01

Metastatic neuroendocrine carcinoma of unknown origin is a rare condition, usually presenting with lesions in the liver and/or lung. We present the first reported case of a metastatic neuroendocrine carcinoma of unknown origin arising in the femoral nerve sheath. Magnetic resonance imaging demonstrated what was thought to be a schwannoma in the left femoral nerve sheath in the proximal femoral triangle, immediately inferior to the anterior inferior iliac spine. At the time of operation, the tumor capsule was invading surrounding tissue, as well as three trunks of the femoral nerve. The patient underwent a subtotal resection, preserving the integrity of the residual functioning femoral nerve trunks. Histologic evaluation determined that the tumor had features consistent with a metastatic neuroendocrine carcinoma of unknown primary origin. The patient recovered well postoperatively, and subsequent radiologic evaluation failed to demonstrate a potential primary site. Unfortunately, the patient re-presented with disease progression and was subsequently referred to palliative care. We recommend that there is a definite role for surgery in the management of solitary neuroendocrine carcinoma of unknown origin. Copyright © 2017 Elsevier Inc. All rights reserved.

Tick receptor for outer surface protein A from Ixodes ricinus — the first intrinsically disordered protein involved in vector-microbe recognition

NASA Astrophysics Data System (ADS)

Urbanowicz, Anna; Lewandowski, Dominik; Szpotkowski, Kamil; Figlerowicz, Marek

2016-04-01

The tick receptor for outer surface protein A (TROSPA) is the only identified factor involved in tick gut colonization by various Borrelia species. TROSPA is localized in the gut epithelium and can recognize and bind the outer surface bacterial protein OspA via an unknown mechanism. Based on earlier reports and our latest observations, we considered that TROSPA would be the first identified intrinsically disordered protein (IDP) involved in the interaction between a vector and a pathogenic microbe. To verify this hypothesis, we performed structural studies of a TROSPA mutant from Ixodes ricinus using both computational and experimental approaches. Irrespective of the method used, we observed that the secondary structure content of the TROSPA polypeptide chain is low. In addition, the collected SAXS data indicated that this protein is highly extended and exists in solution as a set of numerous conformers. These features are all commonly considered hallmarks of IDPs. Taking advantage of our SAXS data, we created structural models of TROSPA and proposed a putative mechanism for the TROSPA-OspA interaction. The disordered nature of TROSPA may explain the ability of a wide spectrum of Borrelia species to colonize the tick gut.

Structure and Orientation of a Voltage-Sensor Toxin in Lipid Membranes

PubMed Central

Jung, Hyun Ho; Jung, Hoi Jong; Milescu, Mirela; Lee, Chul Won; Lee, Seungkyu; Lee, Ju Yeon; Eu, Young-Jae; Kim, Ha Hyung; Swartz, Kenton J.; Kim, Jae Il

2010-01-01

Abstract Amphipathic protein toxins from tarantula venom inhibit voltage-activated potassium (Kv) channels by binding to a critical helix-turn-helix motif termed the voltage sensor paddle. Although these toxins partition into membranes to bind the paddle motif, their structure and orientation within the membrane are unknown. We investigated the interaction of a tarantula toxin named SGTx with membranes using both fluorescence and NMR spectroscopy. Depth-dependent fluorescence-quenching experiments with brominated lipids suggest that Trp30 in SGTx is positioned ∼9 Å from the center of the bilayer. NMR spectra reveal that the inhibitor cystine knot structure of the toxin does not radically change upon membrane partitioning. Transferred cross-saturation NMR experiments indicate that the toxin's hydrophobic protrusion contacts the hydrophobic core of the membrane, whereas most surrounding polar residues remain at interfacial regions of the bilayer. The inferred orientation of the toxin reveals a twofold symmetry in the arrangement of basic and hydrophobic residues, a feature that is conserved among tarantula toxins. These results have important implications for regions of the toxin involved in recognizing membranes and voltage-sensor paddles, and for the mechanisms by which tarantula toxins alter the activity of different types of ion channels. PMID:20643084

Co-altered functional networks and brain structure in unmedicated patients with bipolar and major depressive disorders.

PubMed

He, Hao; Sui, Jing; Du, Yuhui; Yu, Qingbao; Lin, Dongdong; Drevets, Wayne C; Savitz, Jonathan B; Yang, Jian; Victor, Teresa A; Calhoun, Vince D

2017-12-01

Bipolar disorder (BD) and major depressive disorder (MDD) share similar clinical characteristics that often obscure the diagnostic distinctions between their depressive conditions. Both functional and structural brain abnormalities have been reported in these two disorders. However, the direct link between altered functioning and structure in these two diseases is unknown. To elucidate this relationship, we conducted a multimodal fusion analysis on the functional network connectivity (FNC) and gray matter density from MRI data from 13 BD, 40 MDD, and 33 matched healthy controls (HC). A data-driven fusion method called mCCA+jICA was used to identify the co-altered FNC and gray matter components. Comparing to HC, BD exhibited reduced gray matter density in the parietal and occipital cortices, which correlated with attenuated functional connectivity within sensory and motor networks, as well as hyper-connectivity in regions that are putatively engaged in cognitive control. In addition, lower gray matter density was found in MDD in the amygdala and cerebellum. High accuracy in discriminating across groups was also achieved by trained classification models, implying that features extracted from the fusion analysis hold the potential to ultimately serve as diagnostic biomarkers for mood disorders.

Mammalian translation elongation factor eEF1A2: X-ray structure and new features of GDP/GTP exchange mechanism in higher eukaryotes

PubMed Central

Crepin, Thibaut; Shalak, Vyacheslav F.; Yaremchuk, Anna D.; Vlasenko, Dmytro O.; McCarthy, Andrew; Negrutskii, Boris S.; Tukalo, Michail A.; El'skaya, Anna V.

2014-01-01

Eukaryotic elongation factor eEF1A transits between the GTP- and GDP-bound conformations during the ribosomal polypeptide chain elongation. eEF1A*GTP establishes a complex with the aminoacyl-tRNA in the A site of the 80S ribosome. Correct codon–anticodon recognition triggers GTP hydrolysis, with subsequent dissociation of eEF1A*GDP from the ribosome. The structures of both the ‘GTP’- and ‘GDP’-bound conformations of eEF1A are unknown. Thus, the eEF1A-related ribosomal mechanisms were anticipated only by analogy with the bacterial homolog EF-Tu. Here, we report the first crystal structure of the mammalian eEF1A2*GDP complex which indicates major differences in the organization of the nucleotide-binding domain and intramolecular movements of eEF1A compared to EF-Tu. Our results explain the nucleotide exchange mechanism in the mammalian eEF1A and suggest that the first step of eEF1A*GDP dissociation from the 80S ribosome is the rotation of the nucleotide-binding domain observed after GTP hydrolysis. PMID:25326326

Protein Structure Determination using Metagenome sequence data

PubMed Central

Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A.; Kim, David E.; Kamisetty, Hetunandan; Kyrpides, Nikos C.; Baker, David

2017-01-01

Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families, and that metagenome sequence data more than triples the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact based structure matching and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the PDB. This approach provides the representative models for large protein families originally envisioned as the goal of the protein structure initiative at a fraction of the cost. PMID:28104891

Multistationarity in mass action networks with applications to ERK activation.

PubMed

Conradi, Carsten; Flockerzi, Dietrich

2012-07-01

Ordinary Differential Equations (ODEs) are an important tool in many areas of Quantitative Biology. For many ODE systems multistationarity (i.e. the existence of at least two positive steady states) is a desired feature. In general establishing multistationarity is a difficult task as realistic biological models are large in terms of states and (unknown) parameters and in most cases poorly parameterized (because of noisy measurement data of few components, a very small number of data points and only a limited number of repetitions). For mass action networks establishing multistationarity hence is equivalent to establishing the existence of at least two positive solutions of a large polynomial system with unknown coefficients. For mass action networks with certain structural properties, expressed in terms of the stoichiometric matrix and the reaction rate-exponent matrix, we present necessary and sufficient conditions for multistationarity that take the form of linear inequality systems. Solutions of these inequality systems define pairs of steady states and parameter values. We also present a sufficient condition to identify networks where the aforementioned conditions hold. To show the applicability of our results we analyse an ODE system that is defined by the mass action network describing the extracellular signal-regulated kinase (ERK) cascade (i.e. ERK-activation).

Off-Policy Actor-Critic Structure for Optimal Control of Unknown Systems With Disturbances.

PubMed

Song, Ruizhuo; Lewis, Frank L; Wei, Qinglai; Zhang, Huaguang

2016-05-01

An optimal control method is developed for unknown continuous-time systems with unknown disturbances in this paper. The integral reinforcement learning (IRL) algorithm is presented to obtain the iterative control. Off-policy learning is used to allow the dynamics to be completely unknown. Neural networks are used to construct critic and action networks. It is shown that if there are unknown disturbances, off-policy IRL may not converge or may be biased. For reducing the influence of unknown disturbances, a disturbances compensation controller is added. It is proven that the weight errors are uniformly ultimately bounded based on Lyapunov techniques. Convergence of the Hamiltonian function is also proven. The simulation study demonstrates the effectiveness of the proposed optimal control method for unknown systems with disturbances.

Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development

PubMed Central

Moraes, Gleiciane Leal; Gomes, Guelber Cardoso; de Sousa, Paulo Robson Monteiro; Alves, Cláudio Nahum; Govender, Thavendran; Kruger, Hendrik G.; Maguire, Glenn E.M.; Lamichhane, Gyanu; Lameira, Jerônimo

2015-01-01

SUMMARY Tuberculosis (TB) is the second leading cause of human mortality from infectious diseases worldwide. The WHO reported 1.3 million deaths and 8.6 million new cases of TB in 2012. Mycobacterium tuberculosis (M. tuberculosis), the infectious bacteria that causes TB, is encapsulated by a thick and robust cell wall. The innermost segment of the cell wall is comprised of peptidoglycan, a layer that is required for survival and growth of the pathogen. Enzymes that catalyse biosynthesis of the peptidoglycan are essential and are therefore attractive targets for discovery of novel antibiotics as humans lack similar enzymes making it possible to selectively target bacteria only. In this paper, we have reviewed the structures and functions of enzymes GlmS, GlmM, GlmU, MurA, MurB, MurC, MurD, MurE and MurF from M. tuberculosis that are involved in peptidoglycan biosynthesis. In addition, we report homology modelled 3D structures of those key enzymes from M. tuberculosis of which the structures are still unknown. We demonstrated that natural substrates can be successfully docked into the active sites of the GlmS and GlmU respectively. It is therefore expected that the models and the data provided herein will facilitate translational research to develop new drugs to treat TB. PMID:25701501

Polymeric assembly of gluten proteins in an aqueous ethanol solvent.

PubMed

Dahesh, Mohsen; Banc, Amélie; Duri, Agnès; Morel, Marie-Hélène; Ramos, Laurence

2014-09-25

The supramolecular organization of wheat gluten proteins is largely unknown due to the intrinsic complexity of this family of proteins and their insolubility in water. We fractionate gluten in a water/ethanol mixture (50/50 v/v) and obtain a protein extract which is depleted in gliadin, the monomeric part of wheat gluten proteins, and enriched in glutenin, the polymeric part of wheat gluten proteins. We investigate the structure of the proteins in the solvent used for extraction over a wide range of concentration, by combining X-ray scattering and multiangle static and dynamic light scattering. Our data show that, in the ethanol/water mixture, the proteins display features characteristic of flexible polymer chains in a good solvent. In the dilute regime, the proteins form very loose structures of characteristic size 150 nm, with an internal dynamics which is quantitatively similar to that of branched polymer coils. In more concentrated regimes, data highlight a hierarchical structure with one characteristic length scale of the order of a few nm, which displays the scaling with concentration expected for a semidilute polymer in good solvent, and a fractal arrangement at a much larger length scale. This structure is strikingly similar to that of polymeric gels, thus providing some factual knowledge to rationalize the viscoelastic properties of wheat gluten proteins and their assemblies.

Muscular Dystrophy with Ribitol-Phosphate Deficiency: A Novel Post-Translational Mechanism in Dystroglycanopathy

PubMed Central

Kanagawa, Motoi; Toda, Tatsushi

2017-01-01

Muscular dystrophy is a group of genetic disorders characterized by progressive muscle weakness. In the early 2000s, a new classification of muscular dystrophy, dystroglycanopathy, was established. Dystroglycanopathy often associates with abnormalities in the central nervous system. Currently, at least eighteen genes have been identified that are responsible for dystroglycanopathy, and despite its genetic heterogeneity, its common biochemical feature is abnormal glycosylation of alpha-dystroglycan. Abnormal glycosylation of alpha-dystroglycan reduces its binding activities to ligand proteins, including laminins. In just the last few years, remarkable progress has been made in determining the sugar chain structures and gene functions associated with dystroglycanopathy. The normal sugar chain contains tandem structures of ribitol-phosphate, a pentose alcohol that was previously unknown in humans. The dystroglycanopathy genes fukutin, fukutin-related protein (FKRP), and isoprenoid synthase domain-containing protein (ISPD) encode essential enzymes for the synthesis of this structure: fukutin and FKRP transfer ribitol-phosphate onto sugar chains of alpha-dystroglycan, and ISPD synthesizes CDP-ribitol, a donor substrate for fukutin and FKRP. These findings resolved long-standing questions and established a disease subgroup that is ribitol-phosphate deficient, which describes a large population of dystroglycanopathy patients. Here, we review the history of dystroglycanopathy, the properties of the sugar chain structure of alpha-dystroglycan, dystroglycanopathy gene functions, and therapeutic strategies. PMID:29081423

Assembly of the outermost spore layer: pieces of the puzzle are coming together.

PubMed

Stewart, George C

2017-05-01

Certain endospore-forming soil dwelling bacteria are important human, animal or insect pathogens. These organisms produce spores containing an outer layer, the exosporium. The exosporium is the site of interactions between the spore and the soil environment and between the spore and the infected host during the initial stages of infection. The composition and assembly process of the exosporium are poorly understood. This is partly due to the extreme stability of the exosporium that has proven to be refractive to existing methods to deconstruct the intact structure into its component parts. Although more than 20 proteins have been identified as exosporium-associated, their abundance, relationship to other proteins and the processes by which they are assembled to create the exosporium are largely unknown. In this issue of Molecular Microbiology, Terry, Jiang, and colleagues in Per Bullough's laboratory show that the ExsY protein is a major structural protein of the exosporium basal layer of B. cereus family spores and that it can self-assemble into complex structures that possess many of the structural features characteristic of the exosporium basal layer. The authors refined a model for exosporium assembly. Their findings may have implications for exosporium formation in other spore forming bacteria, including Clostridium species. © 2017 John Wiley & Sons Ltd.

Infectious causes of fever of unknown origin.

PubMed

McGregor, Alastair C; Moore, David A

2015-06-01

The causes of fever of unknown origin (FUO) are changing because advances in clinical practice and diagnostics have facilitated the identification of some infections. A variety of bacterial infections can cause FUO, and these can be divided into those that are easy to identify using culture and those that require serological or molecular tests for identification. A number of viral, parasitic and fungal infections can also cause prolonged fever. This article summarises the clinical features and diagnostic strategy of these infections. © Royal College of Physicians 2015. All rights reserved.

Total Synthesis of Purported Cephalosporolides H and I, Penisporolide B, and Their Stereoisomers.

PubMed

Wang, Jian; Tong, Rongbiao

2016-05-20

Development of a unified, bioinspired synthetic strategy to access four possible diastereomers of unique 2,2-dimethyl-[5,5]-spiroacetal-cis-fused-γ-lactone (Me2SAFL) is reported, featuring pyridinium chlorochromate (PCC)-promoted oxidative ring expansion of β-hydroxy cyclic ethers and dehydrative ring-contraction rearrangement of 10-membered lactones. Synthetic utility of this strategy was demonstrated by total syntheses of 12 Me2SAFLs, corresponding to the purported cephalosporolide H (CesH), cephalosporolide I (CesI), and penisporolide B (PenB) and their possible diastereomers. Comprehensive NMR data analysis suggested that the tricyclic Me2SAFL core of CesH, CesI, and PenB should be revised to the same relative (3R*, 4R*, 6S*, 9R*) configuration and that the side chains required an unknown constitutional structure revision.

Mobile robots IV; Proceedings of the Meeting, Philadelphia, PA, Nov. 6, 7, 1989

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

Wolfe, W.J.; Chun, W.H.

1990-01-01

The present conference on mobile robot systems discusses high-speed machine perception based on passive sensing, wide-angle optical ranging, three-dimensional path planning for flying/crawling robots, navigation of autonomous mobile intelligence in an unstructured natural environment, mechanical models for the locomotion of a four-articulated-track robot, a rule-based command language for a semiautonomous Mars rover, and a computer model of the structured light vision system for a Mars rover. Also discussed are optical flow and three-dimensional information for navigation, feature-based reasoning trail detection, a symbolic neural-net production system for obstacle avoidance and navigation, intelligent path planning for robot navigation in an unknown environment,more » behaviors from a hierarchical control system, stereoscopic TV systems, the REACT language for autonomous robots, and a man-amplifying exoskeleton.« less

A novel visual-inertial monocular SLAM

NASA Astrophysics Data System (ADS)

Yue, Xiaofeng; Zhang, Wenjuan; Xu, Li; Liu, JiangGuo

2018-02-01

With the development of sensors and computer vision research community, cameras, which are accurate, compact, wellunderstood and most importantly cheap and ubiquitous today, have gradually been at the center of robot location. Simultaneous localization and mapping (SLAM) using visual features, which is a system getting motion information from image acquisition equipment and rebuild the structure in unknown environment. We provide an analysis of bioinspired flights in insects, employing a novel technique based on SLAM. Then combining visual and inertial measurements to get high accuracy and robustness. we present a novel tightly-coupled Visual-Inertial Simultaneous Localization and Mapping system which get a new attempt to address two challenges which are the initialization problem and the calibration problem. experimental results and analysis show the proposed approach has a more accurate quantitative simulation of insect navigation, which can reach the positioning accuracy of centimeter level.

Genetics Home Reference: Fryns syndrome

MedlinePlus

... are some genetic conditions more common in particular ethnic groups? Genetic Changes The cause of Fryns syndrome is unknown. The disorder is thought to be genetic because it tends to run in families and has features similar to those of other ...

Hitherto unknown shear rupture mechanism as a source of instability in intact hard rocks at highly confined compression

NASA Astrophysics Data System (ADS)

Tarasov, Boris G.

2014-05-01

Today, frictional shear resistance along pre-existing faults is considered to be the lower limit on rock shear strength for confined conditions corresponding to the seismogenic layer. This paper introduces a recently identified shear rupture mechanism providing a paradoxical feature of hard rocks - the possibility of shear rupture propagation through the highly confined intact rock mass at shear stress levels significantly less than frictional strength. In the new mechanism, the rock failure associated with consecutive creation of small slabs (known as ‘domino-blocks') from the intact rock in the rupture tip is driven by a fan-shaped domino structure representing the rupture head. The fan-head combines such unique features as: extremely low shear resistance, self-sustaining stress intensification, and self-unbalancing conditions. Due to this the failure process caused by the mechanism is very dynamic and violent. This makes it impossible to directly observe and study the mechanism and can explain why the mechanism has not been detected before. This paper provides physical motivation for the mechanism, based upon side effects accompanying the failure process. Physical and mathematical models of the mechanism presented in the paper explain unique and paradoxical features of the mechanism. The new shear rupture mechanism allows a novel point of view for understanding the nature of spontaneous failure processes in hard rocks including earthquakes.

Common and Distant Structural Characteristics of Feruloyl Esterase Families from Aspergillus oryzae

PubMed Central

Udatha, D. B. R. K. Gupta; Mapelli, Valeria; Panagiotou, Gianni; Olsson, Lisbeth

2012-01-01

Background Feruloyl esterases (FAEs) are important biomass degrading accessory enzymes due to their capability of cleaving the ester links between hemicellulose and pectin to aromatic compounds of lignin, thus enhancing the accessibility of plant tissues to cellulolytic and hemicellulolytic enzymes. FAEs have gained increased attention in the area of biocatalytic transformations for the synthesis of value added compounds with medicinal and nutritional applications. Following the increasing attention on these enzymes, a novel descriptor based classification system has been proposed for FAEs resulting into 12 distinct families and pharmacophore models for three FAE sub-families have been developed. Methodology/Principal Findings The feruloylome of Aspergillus oryzae contains 13 predicted FAEs belonging to six sub-families based on our recently developed descriptor-based classification system. The three-dimensional structures of the 13 FAEs were modeled for structural analysis of the feruloylome. The three genes coding for three enzymes, viz., A.O.2, A.O.8 and A.O.10 from the feruloylome of A. oryzae, representing sub-families with unknown functional features, were heterologously expressed in Pichia pastoris, characterized for substrate specificity and structural characterization through CD spectroscopy. Common feature-based pharamacophore models were developed according to substrate specificity characteristics of the three enzymes. The active site residues were identified for the three expressed FAEs by determining the titration curves of amino acid residues as a function of the pH by applying molecular simulations. Conclusions/Significance Our findings on the structure-function relationships and substrate specificity of the FAEs of A. oryzae will be instrumental for further understanding of the FAE families in the novel classification system. The developed pharmacophore models could be applied for virtual screening of compound databases for short listing the putative substrates prior to docking studies or for post-processing docking results to remove false positives. Our study exemplifies how computational predictions can complement to the information obtained through experimental methods. PMID:22745763

Common and distant structural characteristics of feruloyl esterase families from Aspergillus oryzae.

PubMed

Udatha, D B R K Gupta; Mapelli, Valeria; Panagiotou, Gianni; Olsson, Lisbeth

2012-01-01

Feruloyl esterases (FAEs) are important biomass degrading accessory enzymes due to their capability of cleaving the ester links between hemicellulose and pectin to aromatic compounds of lignin, thus enhancing the accessibility of plant tissues to cellulolytic and hemicellulolytic enzymes. FAEs have gained increased attention in the area of biocatalytic transformations for the synthesis of value added compounds with medicinal and nutritional applications. Following the increasing attention on these enzymes, a novel descriptor based classification system has been proposed for FAEs resulting into 12 distinct families and pharmacophore models for three FAE sub-families have been developed. The feruloylome of Aspergillus oryzae contains 13 predicted FAEs belonging to six sub-families based on our recently developed descriptor-based classification system. The three-dimensional structures of the 13 FAEs were modeled for structural analysis of the feruloylome. The three genes coding for three enzymes, viz., A.O.2, A.O.8 and A.O.10 from the feruloylome of A. oryzae, representing sub-families with unknown functional features, were heterologously expressed in Pichia pastoris, characterized for substrate specificity and structural characterization through CD spectroscopy. Common feature-based pharamacophore models were developed according to substrate specificity characteristics of the three enzymes. The active site residues were identified for the three expressed FAEs by determining the titration curves of amino acid residues as a function of the pH by applying molecular simulations. Our findings on the structure-function relationships and substrate specificity of the FAEs of A. oryzae will be instrumental for further understanding of the FAE families in the novel classification system. The developed pharmacophore models could be applied for virtual screening of compound databases for short listing the putative substrates prior to docking studies or for post-processing docking results to remove false positives. Our study exemplifies how computational predictions can complement to the information obtained through experimental methods.

Combined infrared and ultraviolet-visible spectroscopy matrix-isolated carbon vapor

NASA Technical Reports Server (NTRS)

Kurtz, Joe; Huffman, Donald R.

1990-01-01

Infrared and UV-visible absorption spectra have been measured on the same sample of matrix-isolated carbon vapor in order to establish correlations between absorption intensities of vibrational and electronic transitions as a function of sample annealing. A high degree of correlation has been found between the IR feature at 1998/cm recently assigned to C8 and a UV absorption feature at about 3100 A. Thus, for the first time, direct evidence is given for the assignment of one of the unknown UV-visible features of the long-studied matrix-isolated carbon vapor spectrum.

A keyword spotting model using perceptually significant energy features

NASA Astrophysics Data System (ADS)

Umakanthan, Padmalochini

The task of a keyword recognition system is to detect the presence of certain words in a conversation based on the linguistic information present in human speech. Such keyword spotting systems have applications in homeland security, telephone surveillance and human-computer interfacing. General procedure of a keyword spotting system involves feature generation and matching. In this work, new set of features that are based on the psycho-acoustic masking nature of human speech are proposed. After developing these features a time aligned pattern matching process was implemented to locate the words in a set of unknown words. A word boundary detection technique based on frame classification using the nonlinear characteristics of speech is also addressed in this work. Validation of this keyword spotting model was done using widely acclaimed Cepstral features. The experimental results indicate the viability of using these perceptually significant features as an augmented feature set in keyword spotting.

Conjunctive Coding of Complex Object Features

PubMed Central

Erez, Jonathan; Cusack, Rhodri; Kendall, William; Barense, Morgan D.

2016-01-01

Critical to perceiving an object is the ability to bind its constituent features into a cohesive representation, yet the manner by which the visual system integrates object features to yield a unified percept remains unknown. Here, we present a novel application of multivoxel pattern analysis of neuroimaging data that allows a direct investigation of whether neural representations integrate object features into a whole that is different from the sum of its parts. We found that patterns of activity throughout the ventral visual stream (VVS), extending anteriorly into the perirhinal cortex (PRC), discriminated between the same features combined into different objects. Despite this sensitivity to the unique conjunctions of features comprising objects, activity in regions of the VVS, again extending into the PRC, was invariant to the viewpoints from which the conjunctions were presented. These results suggest that the manner in which our visual system processes complex objects depends on the explicit coding of the conjunctions of features comprising them. PMID:25921583

New Infrared Emission Features and Spectral Variations in Ngc 7023

NASA Technical Reports Server (NTRS)

Werner, M. W.; Uchida, K. I.; Sellgren, K.; Marengo, M.; Gordon, K. D.; Morris, P. W.; Houck, J. R.; Stansberry, J. A.

2004-01-01

We observed the reflection nebula NGC 7023, with the Short-High module and the long-slit Short-Low and Long-Low modules of the Infrared Spectrograph on the Spitzer Space Telescope. We also present Infrared Array Camera (IRAC) and Multiband Imaging Photometer for Spitzer (MIPS) images of NGC 7023 at 3.6, 4.5, 8.0, and 24 m. We observe the aromatic emission features (AEFs) at 6.2, 7.7, 8.6, 11.3, and 12.7 m, plus a wealth of weaker features. We find new unidentified interstellar emission features at 6.7, 10.1, 15.8, 17.4, and 19.0 m. Possible identifications include aromatic hydrocarbons or nanoparticles of unknown mineralogy. We see variations in relative feature strengths, central wavelengths, and feature widths, in the AEFs and weaker emission features, depending on both distance from the star and nebular position (southeast vs. northwest).

Conceptualization of the Unknown by 6-, 9-, and 14-Year-Old Children in a Story-Telling Context: In Search of a "Heffalump."

ERIC Educational Resources Information Center

Pramling, Niklas; Norlander, Torsten; Archer, Trevor

2003-01-01

Examined 6-, 9-, and 14-year-olds' imagination of the unknown within a storytelling context. Performed phenomenological analysis of the two youngest groups' drawings and the oldest group's story on the "heffalump" theme. Derived eight categories providing an image-analysis of the concept of the "unknown" structured as "something-otherwise," that…

Convergent structural responses of tropical forests to diverse disturbance regimes.

PubMed

Kellner, James R; Asner, Gregory P

2009-09-01

Size frequency distributions of canopy gaps are a hallmark of forest dynamics. But it remains unknown whether legacies of forest disturbance are influencing vertical size structure of landscapes, or space-filling in the canopy volume. We used data from LiDAR remote sensing to quantify distributions of canopy height and sizes of 434,501 canopy gaps in five tropical rain forest landscapes in Costa Rica and Hawaii. The sites represented a wide range of variation in structure and natural disturbance history, from canopy gap dynamics in lowland Costa Rica and Hawaii, to stages and types of stand-level dieback on upland Mauna Kea and Kohala volcanoes. Large differences in vertical canopy structure characterized these five tropical rain forest landscapes, some of which were related to known disturbance events. Although there were quantitative differences in the values of scaling exponents within and among sites, size frequency distributions of canopy gaps followed power laws at all sites and in all canopy height classes. Scaling relationships in gap size at different heights in the canopy were qualitatively similar at all sites, revealing a remarkable similarity despite clearly defined differences in species composition and modes of prevailing disturbance. These findings indicate that power-law gap-size frequency distributions are ubiquitous features of these five tropical rain forest landscapes, and suggest that mechanisms of forest disturbance may be secondary to other processes in determining vertical and horizontal size structure in canopies.

Making an unknown unknown a known unknown: Missing data in longitudinal neuroimaging studies.

PubMed

Matta, Tyler H; Flournoy, John C; Byrne, Michelle L

2017-10-28

The analysis of longitudinal neuroimaging data within the massively univariate framework provides the opportunity to study empirical questions about neurodevelopment. Missing outcome data are an all-to-common feature of any longitudinal study, a feature that, if handled improperly, can reduce statistical power and lead to biased parameter estimates. The goal of this paper is to provide conceptual clarity of the issues and non-issues that arise from analyzing incomplete data in longitudinal studies with particular focus on neuroimaging data. This paper begins with a review of the hierarchy of missing data mechanisms and their relationship to likelihood-based methods, a review that is necessary not just for likelihood-based methods, but also for multiple-imputation methods. Next, the paper provides a series of simulation studies with designs common in longitudinal neuroimaging studies to help illustrate missing data concepts regardless of interpretation. Finally, two applied examples are used to demonstrate the sensitivity of inferences under different missing data assumptions and how this may change the substantive interpretation. The paper concludes with a set of guidelines for analyzing incomplete longitudinal data that can improve the validity of research findings in developmental neuroimaging research. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Knowledge Discovery in Literature Data Bases

NASA Astrophysics Data System (ADS)

Albrecht, Rudolf; Merkl, Dieter

The concept of knowledge discovery as defined through ``establishing previously unknown and unsuspected relations of features in a data base'' is, cum grano salis, relatively easy to implement for data bases containing numerical data. Increasingly we find at our disposal data bases containing scientific literature. Computer assisted detection of unknown relations of features in such data bases would be extremely valuable and would lead to new scientific insights. However, the current representation of scientific knowledge in such data bases is not conducive to computer processing. Any correlation of features still has to be done by the human reader, a process which is plagued by ineffectiveness and incompleteness. On the other hand we note that considerable progress is being made in an area where reading all available material is totally prohibitive: the World Wide Web. Robots and Web crawlers mine the Web continuously and construct data bases which allow the identification of pages of interest in near real time. An obvious step is to categorize and classify the documents in the text data base. This can be used to identify papers worth reading, or which are of unexpected cross-relevance. We show the results of first experiments using unsupervised classification based on neural networks.

Chemistry by Computer.

ERIC Educational Resources Information Center

Garmon, Linda

1981-01-01

Describes the features of various computer chemistry programs. Utilization of computer graphics, color, digital imaging, and other innovations are discussed in programs including those which aid in the identification of unknowns, predict whether chemical reactions are feasible, and predict the biological activity of xenobiotic compounds. (CS)

Identifying known unknowns using the US EPA's CompTox Chemistry Dashboard

EPA Science Inventory

Chemical features observed using high-resolution mass spectrometry can be tentatively identified using online chemical reference databases by searching molecular formulae and monoisotopic masses and then rank-ordering of the hits using appropriate relevance criteria. The most li...

Where and what is the paralaminar nucleus? A review on a unique and frequently overlooked area of the primate amygdala

PubMed Central

deCampo, Danielle; Fudge, Julie

2011-01-01

The primate amygdala is composed of multiple subnuclei that play distinct roles in amygdala function. While some nuclei have been areas of focused investigation, others remain virtually unknown. One of the more obscure regions of the amygdala is the paralaminar nucleus (PL). The PL in humans and non-human primates is relatively expanded compared to lower species. Long considered to be part of the basal nucleus, the PL has several interesting features that make it unique. These features include a dense concentration of small cells, high concentrations of receptors for corticotropin releasing hormone and benzodiazepines, and dense innervation of serotonergic fibers. More recently, high concentrations of immature-appearing cells have been noted in the primate PL, suggesting special mechanisms of neural plasticity. Following a brief overview of amygdala structure and function, this review will provide an introduction to the history, embryology, anatomical connectivity, immunohistochemical and cytoarchitectural properties of the PL. Our conclusion based on the following information, is that the PL is a unique subregion of the amygdala that may yield important clues about the normal growth and function of the amygdala, particularly in higher species. PMID:21906624

Computational intelligence techniques for biological data mining: An overview

NASA Astrophysics Data System (ADS)

Faye, Ibrahima; Iqbal, Muhammad Javed; Said, Abas Md; Samir, Brahim Belhaouari

2014-10-01

Computational techniques have been successfully utilized for a highly accurate analysis and modeling of multifaceted and raw biological data gathered from various genome sequencing projects. These techniques are proving much more effective to overcome the limitations of the traditional in-vitro experiments on the constantly increasing sequence data. However, most critical problems that caught the attention of the researchers may include, but not limited to these: accurate structure and function prediction of unknown proteins, protein subcellular localization prediction, finding protein-protein interactions, protein fold recognition, analysis of microarray gene expression data, etc. To solve these problems, various classification and clustering techniques using machine learning have been extensively used in the published literature. These techniques include neural network algorithms, genetic algorithms, fuzzy ARTMAP, K-Means, K-NN, SVM, Rough set classifiers, decision tree and HMM based algorithms. Major difficulties in applying the above algorithms include the limitations found in the previous feature encoding and selection methods while extracting the best features, increasing classification accuracy and decreasing the running time overheads of the learning algorithms. The application of this research would be potentially useful in the drug design and in the diagnosis of some diseases. This paper presents a concise overview of the well-known protein classification techniques.

MonoSLAM: real-time single camera SLAM.

PubMed

Davison, Andrew J; Reid, Ian D; Molton, Nicholas D; Stasse, Olivier

2007-06-01

We present a real-time algorithm which can recover the 3D trajectory of a monocular camera, moving rapidly through a previously unknown scene. Our system, which we dub MonoSLAM, is the first successful application of the SLAM methodology from mobile robotics to the "pure vision" domain of a single uncontrolled camera, achieving real time but drift-free performance inaccessible to Structure from Motion approaches. The core of the approach is the online creation of a sparse but persistent map of natural landmarks within a probabilistic framework. Our key novel contributions include an active approach to mapping and measurement, the use of a general motion model for smooth camera movement, and solutions for monocular feature initialization and feature orientation estimation. Together, these add up to an extremely efficient and robust algorithm which runs at 30 Hz with standard PC and camera hardware. This work extends the range of robotic systems in which SLAM can be usefully applied, but also opens up new areas. We present applications of MonoSLAM to real-time 3D localization and mapping for a high-performance full-size humanoid robot and live augmented reality with a hand-held camera.

Exceptionally Preserved Cambrian Trilobite Digestive System Revealed in 3D by Synchrotron-Radiation X-Ray Tomographic Microscopy

PubMed Central

Eriksson, Mats E.; Terfelt, Fredrik

2012-01-01

The Cambrian ‘Orsten’ fauna comprises exceptionally preserved and phosphatised microscopic arthropods. The external morphology of these fossils is well known, but their internal soft-tissue anatomy has remained virtually unknown. Here, we report the first non-biomineralised tissues from a juvenile polymerid trilobite, represented by digestive structures, glands, and connective strands harboured in a hypostome from the Swedish ‘Orsten’ fauna. Synchrotron-radiation X-ray tomographic microscopy enabled three-dimensional internal recordings at sub-micrometre resolution. The specimen provides the first unambiguous evidence for a J-shaped anterior gut and the presence of a crop with a constricted alimentary tract in the Trilobita. Moreover, the gut is Y-shaped in cross section, probably due to a collapsed lumen of that shape, another feature which has not previously been observed in trilobites. The combination of anatomical features suggests that the trilobite hypostome is functionally analogous to the labrum of euarthropods and that it was a sophisticated element closely integrated with the digestive system. This study also briefly addresses the preservational bias of the ‘Orsten’ fauna, particularly the near-absence of polymerid trilobites, and the taphonomy of the soft-tissue-harbouring hypostome. PMID:22558180

Exceptionally preserved Cambrian trilobite digestive system revealed in 3D by synchrotron-radiation X-ray tomographic microscopy.

PubMed

Eriksson, Mats E; Terfelt, Fredrik

2012-01-01

The Cambrian 'Orsten' fauna comprises exceptionally preserved and phosphatised microscopic arthropods. The external morphology of these fossils is well known, but their internal soft-tissue anatomy has remained virtually unknown. Here, we report the first non-biomineralised tissues from a juvenile polymerid trilobite, represented by digestive structures, glands, and connective strands harboured in a hypostome from the Swedish 'Orsten' fauna. Synchrotron-radiation X-ray tomographic microscopy enabled three-dimensional internal recordings at sub-micrometre resolution. The specimen provides the first unambiguous evidence for a J-shaped anterior gut and the presence of a crop with a constricted alimentary tract in the Trilobita. Moreover, the gut is Y-shaped in cross section, probably due to a collapsed lumen of that shape, another feature which has not previously been observed in trilobites. The combination of anatomical features suggests that the trilobite hypostome is functionally analogous to the labrum of euarthropods and that it was a sophisticated element closely integrated with the digestive system. This study also briefly addresses the preservational bias of the 'Orsten' fauna, particularly the near-absence of polymerid trilobites, and the taphonomy of the soft-tissue-harbouring hypostome.

Designing lymphocyte functional structure for optimal signal detection: voilà, T cells.

PubMed

Noest, A J

2000-11-21

One basic task of immune systems is to detect signals from unknown "intruders" amidst a noisy background of harmless signals. To clarify the functional importance of many observed lymphocyte properties, I ask: What properties would a cell have if one designed it according to the theory of optimal detection, with minimal regard for biological constraints? Sparse and reasonable assumptions about the statistics of available signals prove sufficient for deriving many features of the optimal functional structure, in an incremental and modular design. The use of one common formalism guarantees that all parts of the design collaborate to solve the detection task. Detection performance is computed at several stages of the design. Comparison between design variants reveals e.g. the importance of controlling the signal integration time. This predicts that an appropriate control mechanism should exist. Comparing the design to reality, I find a striking similarity with many features of T cells. For example, the formalism dictates clonal specificity, serial receptor triggering, (grades of) anergy, negative and positive selection, co-stimulation, high-zone tolerance, and clonal production of cytokines. Serious mismatches should be found if T cells were hindered by mechanistic constraints or vestiges of their (co-)evolutionary history, but I have not found clear examples. By contrast, fundamental mismatches abound when comparing the design to immune systems of e.g. invertebrates. The wide-ranging differences seem to hinge on the (in)ability to generate a large diversity of receptors. Copyright 2000 Academic Press.

Genomic Structure of an Economically Important Cyanobacterium, Arthrospira (Spirulina) platensis NIES-39

PubMed Central

Fujisawa, Takatomo; Narikawa, Rei; Okamoto, Shinobu; Ehira, Shigeki; Yoshimura, Hidehisa; Suzuki, Iwane; Masuda, Tatsuru; Mochimaru, Mari; Takaichi, Shinichi; Awai, Koichiro; Sekine, Mitsuo; Horikawa, Hiroshi; Yashiro, Isao; Omata, Seiha; Takarada, Hiromi; Katano, Yoko; Kosugi, Hiroki; Tanikawa, Satoshi; Ohmori, Kazuko; Sato, Naoki; Ikeuchi, Masahiko; Fujita, Nobuyuki; Ohmori, Masayuki

2010-01-01

A filamentous non-N2-fixing cyanobacterium, Arthrospira (Spirulina) platensis, is an important organism for industrial applications and as a food supply. Almost the complete genome of A. platensis NIES-39 was determined in this study. The genome structure of A. platensis is estimated to be a single, circular chromosome of 6.8 Mb, based on optical mapping. Annotation of this 6.7 Mb sequence yielded 6630 protein-coding genes as well as two sets of rRNA genes and 40 tRNA genes. Of the protein-coding genes, 78% are similar to those of other organisms; the remaining 22% are currently unknown. A total 612 kb of the genome comprise group II introns, insertion sequences and some repetitive elements. Group I introns are located in a protein-coding region. Abundant restriction-modification systems were determined. Unique features in the gene composition were noted, particularly in a large number of genes for adenylate cyclase and haemolysin-like Ca2+-binding proteins and in chemotaxis proteins. Filament-specific genes were highlighted by comparative genomic analysis. PMID:20203057

Problems in understanding the structure and assembly of viruses

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

King, J.

1997-12-01

Though viruses infect the cells of all groups of animals, plants, and microorganisms, their structures follow a limited number of general themes; spherical or cylindrical shells built of hundreds of repeated protein subunits enclosing a nucleic acid - DNA or RNA - genome. Since the 1960s it has been known that the protein shells of spherical viruses in fact conform to icosahedral symmetry or to subtle deviations from icosahedral symmetry. The construction of the shell lattices and the transformations they go through in the different stages of the viral life cycle are not fully understood. The shells contain the nucleicmore » in a highly condensed state, of unknown coiling/organization. Features of the well studied bacterial viruses will be reviewed, with examples from adenoviruses, herpesviruses, poliovirus, and HIV. The emergence of new viral disease has led to increased interest in the development of agents which interfere with virus reproduction at the level of the assembly or function of the organized particle. Recently computational approaches to the problem of virus assembly have made important contributions to clarifying shell assembly processes. 1 ref.« less

Alzheimer’s disease: biological aspects, therapeutic perspectives and diagnostic tools

NASA Astrophysics Data System (ADS)

Di Carlo, M.; Giacomazza, D.; San Biagio, P. L.

2012-06-01

Alzheimer’s disease (AD) is the most common form of dementia among older people. Dementia is an irreversible brain disorder that seriously affects a person’s ability to carry out daily activities. It is characterized by loss of cognitive functioning and behavioral abilities, to such an extent that it interferes with the daily life and activities of the affected patients. Although it is still unknown how the disease process begins, it seems that brain damage starts a decade or more before problems become evident. Scientific data seem to indicate that changes in the generation or the degradation of the amyloid-b peptide (Aβ) lead to the formation of aggregated structures that are the triggering molecular events in the pathogenic cascade of AD. This review summarizes some characteristic features of Aβ misfolding and aggregation and how cell damage and death mechanisms are induced by these supramolecular and toxic structures. Further, some interventions for the early diagnosis of AD are described and in the last part the potential therapeutic strategies adoptable to slow down, or better block, the progression of the pathology are reported.

Early diagnosis of genital mucosal melanoma: how good are our dermoscopic criteria?

PubMed

Rogers, Tova; Pulitzer, Melissa; Marino, Maria L; Marghoob, Ashfaq A; Zivanovic, Oliver; Marchetti, Michael A

2016-10-01

There are limited studies on the dermoscopic features of mucosal melanoma, particularly early-stage lesions. Described criteria include the presence of blue, gray, or white colors, with a reported sensitivity of 100%. It is unclear if these features will aid in the detection of early mucosal melanoma or improve diagnostic accuracy compared to naked-eye examination alone. An Asian female in her fifties was referred for evaluation of an asymptomatic, irregularly pigmented patch of the clitoral hood and labia minora of unknown duration. Her past medical history was notable for Stage IV non-small cell lung cancer. She denied a personal or family history of skin cancer. Dermoscopic evaluation of the vulvar lesion revealed heterogeneous brown and black pigmentation mostly composed of thick lines. There were no other colors or structures present. As the differential diagnosis included vulvar melanosis and mucosal melanoma, the patient was recommended to undergo biopsy, which was delayed due to complications from her underlying lung cancer. Repeat dermoscopic imaging performed three months later revealed significant changes concerning for melanoma, including increase in size, asymmetric darkening, and the appearance of structureless areas and central blue and pink colors. Histopathological examination of a biopsy and subsequent resection confirmed the diagnosis of melanoma in situ. Previously described dermoscopic features for mucosal melanoma may not have high sensitivity for early melanomas. Additional studies are needed to define the dermoscopic characteristics of mucosal melanomas that aid in early detection. Health care providers should have a low threshold for biopsy of mucosal lesions that show any clinical or dermoscopic features of melanoma, especially in older women.

Universal dynamical properties preclude standard clustering in a large class of biochemical data.

PubMed

Gomez, Florian; Stoop, Ralph L; Stoop, Ruedi

2014-09-01

Clustering of chemical and biochemical data based on observed features is a central cognitive step in the analysis of chemical substances, in particular in combinatorial chemistry, or of complex biochemical reaction networks. Often, for reasons unknown to the researcher, this step produces disappointing results. Once the sources of the problem are known, improved clustering methods might revitalize the statistical approach of compound and reaction search and analysis. Here, we present a generic mechanism that may be at the origin of many clustering difficulties. The variety of dynamical behaviors that can be exhibited by complex biochemical reactions on variation of the system parameters are fundamental system fingerprints. In parameter space, shrimp-like or swallow-tail structures separate parameter sets that lead to stable periodic dynamical behavior from those leading to irregular behavior. We work out the genericity of this phenomenon and demonstrate novel examples for their occurrence in realistic models of biophysics. Although we elucidate the phenomenon by considering the emergence of periodicity in dependence on system parameters in a low-dimensional parameter space, the conclusions from our simple setting are shown to continue to be valid for features in a higher-dimensional feature space, as long as the feature-generating mechanism is not too extreme and the dimension of this space is not too high compared with the amount of available data. For online versions of super-paramagnetic clustering see http://stoop.ini.uzh.ch/research/clustering. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Disrupted white matter connectivity underlying developmental dyslexia: A machine learning approach.

PubMed

Cui, Zaixu; Xia, Zhichao; Su, Mengmeng; Shu, Hua; Gong, Gaolang

2016-04-01

Developmental dyslexia has been hypothesized to result from multiple causes and exhibit multiple manifestations, implying a distributed multidimensional effect on human brain. The disruption of specific white-matter (WM) tracts/regions has been observed in dyslexic children. However, it remains unknown if developmental dyslexia affects the human brain WM in a multidimensional manner. Being a natural tool for evaluating this hypothesis, the multivariate machine learning approach was applied in this study to compare 28 school-aged dyslexic children with 33 age-matched controls. Structural magnetic resonance imaging (MRI) and diffusion tensor imaging were acquired to extract five multitype WM features at a regional level: white matter volume, fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity. A linear support vector machine (LSVM) classifier achieved an accuracy of 83.61% using these MRI features to distinguish dyslexic children from controls. Notably, the most discriminative features that contributed to the classification were primarily associated with WM regions within the putative reading network/system (e.g., the superior longitudinal fasciculus, inferior fronto-occipital fasciculus, thalamocortical projections, and corpus callosum), the limbic system (e.g., the cingulum and fornix), and the motor system (e.g., the cerebellar peduncle, corona radiata, and corticospinal tract). These results were well replicated using a logistic regression classifier. These findings provided direct evidence supporting a multidimensional effect of developmental dyslexia on WM connectivity of human brain, and highlighted the involvement of WM tracts/regions beyond the well-recognized reading system in dyslexia. Finally, the discriminating results demonstrated a potential of WM neuroimaging features as imaging markers for identifying dyslexic individuals. © 2016 Wiley Periodicals, Inc.

Top-down attention based on object representation and incremental memory for knowledge building and inference.

PubMed

Kim, Bumhwi; Ban, Sang-Woo; Lee, Minho

2013-10-01

Humans can efficiently perceive arbitrary visual objects based on an incremental learning mechanism with selective attention. This paper proposes a new task specific top-down attention model to locate a target object based on its form and color representation along with a bottom-up saliency based on relativity of primitive visual features and some memory modules. In the proposed model top-down bias signals corresponding to the target form and color features are generated, which draw the preferential attention to the desired object by the proposed selective attention model in concomitance with the bottom-up saliency process. The object form and color representation and memory modules have an incremental learning mechanism together with a proper object feature representation scheme. The proposed model includes a Growing Fuzzy Topology Adaptive Resonance Theory (GFTART) network which plays two important roles in object color and form biased attention; one is to incrementally learn and memorize color and form features of various objects, and the other is to generate a top-down bias signal to localize a target object by focusing on the candidate local areas. Moreover, the GFTART network can be utilized for knowledge inference which enables the perception of new unknown objects on the basis of the object form and color features stored in the memory during training. Experimental results show that the proposed model is successful in focusing on the specified target objects, in addition to the incremental representation and memorization of various objects in natural scenes. In addition, the proposed model properly infers new unknown objects based on the form and color features of previously trained objects. Copyright © 2013 Elsevier Ltd. All rights reserved.

Improving link prediction in complex networks by adaptively exploiting multiple structural features of networks

NASA Astrophysics Data System (ADS)

Ma, Chuang; Bao, Zhong-Kui; Zhang, Hai-Feng

2017-10-01

So far, many network-structure-based link prediction methods have been proposed. However, these methods only highlight one or two structural features of networks, and then use the methods to predict missing links in different networks. The performances of these existing methods are not always satisfied in all cases since each network has its unique underlying structural features. In this paper, by analyzing different real networks, we find that the structural features of different networks are remarkably different. In particular, even in the same network, their inner structural features are utterly different. Therefore, more structural features should be considered. However, owing to the remarkably different structural features, the contributions of different features are hard to be given in advance. Inspired by these facts, an adaptive fusion model regarding link prediction is proposed to incorporate multiple structural features. In the model, a logistic function combing multiple structural features is defined, then the weight of each feature in the logistic function is adaptively determined by exploiting the known structure information. Last, we use the "learnt" logistic function to predict the connection probabilities of missing links. According to our experimental results, we find that the performance of our adaptive fusion model is better than many similarity indices.

Morphological analysis of hummocks in debris avalanche deposits using UAS-derived high-definition topographic data

NASA Astrophysics Data System (ADS)

Hayakawa, Yuichi S.; Obanawa, Hiroyuki; Yoshida, Hidetsugu; Naruhashi, Ryutaro; Okumura, Koji; Zaiki, Masumi

2016-04-01

Debris avalanche caused by sector collapse of a volcanic mountain often forms depositional landforms with characteristic surface morphology comprising hummocks. Geomorphological and sedimentological analyses of debris avalanche deposits (DAD) at the northeastern face of Mt. Erciyes in central Turkey have been performed to investigate the mechanisms and processes of the debris avalanche. The morphometry of hummocks provides an opportunity to examine the volumetric and kinematic characteristics of the DAD. Although the exact age has been unknown, the sector collapse of this DAD was supposed to have occurred in the late Pleistocene (sometime during 90-20 ka), and subsequent sediment supply from the DAD could have affected ancient human activities in the downstream basin areas. In order to measure detailed surface morphology and depositional structures of the DAD, we apply structure-from-motion multi-view stereo (SfM-MVS) photogrammetry using unmanned aerial system (UAS) and a handheld camera. The UAS, including small unmanned aerial vehicle (sUAV) and a digital camera, provides low-altitude aerial photographs to capture surface morphology for an area of several square kilometers. A high-resolution topographic data, as well as an orthorectified image, of the hummocks were then obtained from the digital elevation model (DEM), and the geometric features of the hummocks were examined. A handheld camera is also used to obtain photographs of outcrop face of the DAD along a road to support the seimentological investigation. The three-dimensional topographic models of the outcrop, with a panoramic orthorectified image projected on a vertical plane, were obtained. This data enables to effectively describe sedimentological structure of the hummock in DAD. The detailed map of the DAD is also further examined with a regional geomorphological map to be compared with other geomorphological features including fluvial valleys, terraces, lakes and active faults.

Experimental identification and computational characterization of a novel extracellular metalloproteinase produced by Clostridium sordellii † †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6ra27654g Click here for additional data file.

PubMed Central

Tao, Aoxiang; Heeney, Dustin D.; McIndoo, Eric R.; French, John M.

2017-01-01

Clostridium sordellii is a lethal pathogen for both animals and humans. Severe capillary leakage, toxic shock syndrome, and an extreme leukemoid reaction (LR), are hallmark features of C. sordellii infections and contribute to its high mortality rate. Here we report the discovery of a previously unknown and uncharacterized metalloproteinase of C. sordellii (referred as Mcs1) that cleaves human vascular cell adhesion molecule (VCAM)-1 in vitro, an adhesion molecule critical to hematopoietic precursor retention and leukocyte diapedesis. We successfully identified the open reading frame encoding Mcs1 within the ATCC 9714 genome and developed an Δmcs1 mutant strain using the ClosTron mutagenesis technology. No VCAM-1 proteolysis was observed from exotoxins collected from mutant strain cultures. Using advanced protein structural modeling and molecular dynamics simulation techniques, the 3D molecular structure and conformational features of Mcs1 were also characterized. Our data demonstrates that Mcs1 proteolytic activity is controlled by the electrostatic interactions between Glu113 and Arg227 residues and the gating motions within its cleft region. This pilot interdisciplinary investigation provided crucial experimental evidence of the existence of Mcs1 in C. sordellii and molecular insights into its 3D structure and proteolytic activity. These findings have the potential to help advance new therapeutics and diagnostics against deadly C. sordellii infections. Follow-up in vitro and in vivo work is under way to further characterize Mcs1 enzymatic kinetics and its role in C. sordellii pathogenesis. PMID:28515901

Comparative morphology of spermatozoa and reproductive systems of zorapteran species from different world regions (Insecta, Zoraptera).

PubMed

Dallai, Romano; Gottardo, Marco; Mercati, David; Machida, Ryuichiro; Mashimo, Yuta; Matsumura, Yoko; Rafael, José Albertino; Beutel, Rolf Georg

2014-07-01

The male and female reproductive apparatus of Zorotypus magnicaudelli (Malaysia), Zorotypus huxleyi (Ecuador) and Zorotypus weidneri (Brazil) were examined and documented in detail. The genital apparatus and sperm of the three species show only minor differences. The testes are larger in Z. magnicaudelli. Z. huxleyi lacks the helical appendage in the accessory glands. A long cuticular flagellum is present in Z. magnicaudelli and in the previously studied Zorotypus caudelli like in several other species, whereas it is absent in Z. weidneri, Z. huxleyi, Zorotypus hubbardi, Zorotypus impolitus and Zorotypus guineensis. Characteristic features of the very similar sperm are the presence of: a) two dense arches above the axoneme; b) a 9 + 9+2 axoneme with detached subtubules A and B of doublets 1 and 6; c) the axonemal end degenerating with enlarging accessory tubules; d) accessory tubules with 17 protofilaments; e) three accessory bodies beneath the axoneme; and f) two mitochondrial derivatives of equal shape. The first characteristic (a) is unknown outside of Zoraptera and possibly autapomorphic. The sperm structure differs distinctly in Z. impolitus and Z. hubbardi, which produce giant sperm and possess a huge spermatheca. The presence of the same sperm type in species either provided with a sclerotized coiled flagellum in males or lacking this structure indicates that a different organization of the genital apparatus does not necessarily affect the sperm structure. The flagellum and its pouch has probably evolved within Zoraptera, but it cannot be excluded that it is a groundplan feature and was reduced several times. The fossil evidence and our findings suggest that distinct modifications in the genital apparatus occurred before the fragmentation of the Gondwanan landmass in the middle Cretaceous. Copyright © 2014 Elsevier Ltd. All rights reserved.

EuroForMix: An open source software based on a continuous model to evaluate STR DNA profiles from a mixture of contributors with artefacts.

PubMed

Bleka, Øyvind; Storvik, Geir; Gill, Peter

2016-03-01

We have released a software named EuroForMix to analyze STR DNA profiles in a user-friendly graphical user interface. The software implements a model to explain the allelic peak height on a continuous scale in order to carry out weight-of-evidence calculations for profiles which could be from a mixture of contributors. Through a properly parameterized model we are able to do inference on mixture proportions, the peak height properties, stutter proportion and degradation. In addition, EuroForMix includes models for allele drop-out, allele drop-in and sub-population structure. EuroForMix supports two inference approaches for likelihood ratio calculations. The first approach uses maximum likelihood estimation of the unknown parameters. The second approach is Bayesian based which requires prior distributions to be specified for the parameters involved. The user may specify any number of known and unknown contributors in the model, however we find that there is a practical computing time limit which restricts the model to a maximum of four unknown contributors. EuroForMix is the first freely open source, continuous model (accommodating peak height, stutter, drop-in, drop-out, population substructure and degradation), to be reported in the literature. It therefore serves an important purpose to act as an unrestricted platform to compare different solutions that are available. The implementation of the continuous model used in the software showed close to identical results to the R-package DNAmixtures, which requires a HUGIN Expert license to be used. An additional feature in EuroForMix is the ability for the user to adapt the Bayesian inference framework by incorporating their own prior information. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Mass-forming cholangiocarcinoma and adenocarcinoma of unknown primary: can they be distinguished on liver MRI?

PubMed

Al Ansari, Najwa; Kim, Bong Soo; Srirattanapong, Saowanee; Semelka, Charles T A; Ramalho, Miguel; Altun, Ersan; Woosley, John T; Calvo, Benjamin; Semelka, Richard C

2014-12-01

To determine MR features suggestive of mass-forming cholangiocarcinoma (CCA) or liver metastases of adenocarcinoma of unknown primary (AUP), and to compare the ability of two experienced radiologists to establish the correct diagnosis. 61 patients with CCA or AUP, with MRIs were placed into two groups: population 1, 28 patients with certain diagnosis of either CCA or AUP; and population 2, 33 patients with uncertain diagnosis. Using population 1 with known diagnosis, two investigators formulated imaging criteria for CCA or AUP, which represented phase 1 of the study. In phase 2, two independent radiologists categorized the patients in populations 1 and 2 as CCA or AUP using the formulated criteria. This categorization was compared with the patient medical records and pathologist review. Findings were tested for statistical significance. In phase 1, solitary lesion, multifocal lesions with dominant lesion, capsule retraction, and porta hepatis lymphadenopathy were features of CCA; multifocal lesions with similar size, and ring enhancement were features of AUP. The number of lesions, capsule retraction, and early tumor enhancement pattern were observed to be significant features (P < 0.05). In phase 2, agreement between the two radiologists was good (k = 0.663). For population 1, the agreement was good (k = 0.659), and was fair for population 2 (k = 0.293). Concordance between the two radiologists, medical record, and the pathologist was found in 41/61 (67%) patients. Distinctive features of CCA and AUP are identifiable on MRI images, which may aid the radiologist to establish the correct diagnosis.

Learning the 3-D structure of objects from 2-D views depends on shape, not format

PubMed Central

Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

2016-01-01

Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

The sequence, structure and evolutionary features of HOTAIR in mammals

PubMed Central

2011-01-01

Background An increasing number of long noncoding RNAs (lncRNAs) have been identified recently. Different from all the others that function in cis to regulate local gene expression, the newly identified HOTAIR is located between HoxC11 and HoxC12 in the human genome and regulates HoxD expression in multiple tissues. Like the well-characterised lncRNA Xist, HOTAIR binds to polycomb proteins to methylate histones at multiple HoxD loci, but unlike Xist, many details of its structure and function, as well as the trans regulation, remain unclear. Moreover, HOTAIR is involved in the aberrant regulation of gene expression in cancer. Results To identify conserved domains in HOTAIR and study the phylogenetic distribution of this lncRNA, we searched the genomes of 10 mammalian and 3 non-mammalian vertebrates for matches to its 6 exons and the two conserved domains within the 1800 bp exon6 using Infernal. There was just one high-scoring hit for each mammal, but many low-scoring hits were found in both mammals and non-mammalian vertebrates. These hits and their flanking genes in four placental mammals and platypus were examined to determine whether HOTAIR contained elements shared by other lncRNAs. Several of the hits were within unknown transcripts or ncRNAs, many were within introns of, or antisense to, protein-coding genes, and conservation of the flanking genes was observed only between human and chimpanzee. Phylogenetic analysis revealed discrete evolutionary dynamics for orthologous sequences of HOTAIR exons. Exon1 at the 5' end and a domain in exon6 near the 3' end, which contain domains that bind to multiple proteins, have evolved faster in primates than in other mammals. Structures were predicted for exon1, two domains of exon6 and the full HOTAIR sequence. The sequence and structure of two fragments, in exon1 and the domain B of exon6 respectively, were identified to robustly occur in predicted structures of exon1, domain B of exon6 and the full HOTAIR in mammals. Conclusions HOTAIR exists in mammals, has poorly conserved sequences and considerably conserved structures, and has evolved faster than nearby HoxC genes. Exons of HOTAIR show distinct evolutionary features, and a 239 bp domain in the 1804 bp exon6 is especially conserved. These features, together with the absence of some exons and sequences in mouse, rat and kangaroo, suggest ab initio generation of HOTAIR in marsupials. Structure prediction identifies two fragments in the 5' end exon1 and the 3' end domain B of exon6, with sequence and structure invariably occurring in various predicted structures of exon1, the domain B of exon6 and the full HOTAIR. PMID:21496275

Use of designed sequences in protein structure recognition.

PubMed

Kumar, Gayatri; Mudgal, Richa; Srinivasan, Narayanaswamy; Sandhya, Sankaran

2018-05-09

Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is provided for part or full-length proteins of 7726 families. For the remaining 52% of the families, information on 3-D structure is not yet available. We use the computationally designed sequences that are intermediately related to two protein domain families, which are already known to share the same fold. These strategically designed sequences enable detection of distant relationships and here, we have employed them for the purpose of structure recognition of protein families of yet unknown structure. We first measured the success rate of our approach using a dataset of protein families of known fold and achieved a success rate of 88%. Next, for 1392 families of yet unknown structure, we made structural assignments for part/full length of the proteins. Fold association for 423 domains of unknown function (DUFs) are provided as a step towards functional annotation. The results indicate that knowledge-based filling of gaps in protein sequence space is a lucrative approach for structure recognition. Such sequences assist in traversal through protein sequence space and effectively function as 'linkers', where natural linkers between distant proteins are unavailable. This article was reviewed by Oliviero Carugo, Christine Orengo and Srikrishna Subramanian.

The hypothalamus and pituitary in cerebral gigantism. A clinicopathologic and immunocytochemical study.

PubMed

Whitaker, M D; Scheithauer, B W; Hayles, A B; Okazaki, H

1985-07-01

Cerebral gigantism, or Sotos' disease, is a rare disorder of unknown cause characterized by the early onset of excessive growth, acromegalic features, and some degree of mental retardation. Although several endocrinologic abnormalities have been described in such patients, none has been specific or sufficient to explain the clinical features. Our report of the endocrinologic and pathologic aspects in a young woman with Sotos' disease includes the first microanatomic study of the hypothalamus and immunocytochemical examination of the pituitary gland in this disorder.

Low-rank matrix fitting based on subspace perturbation analysis with applications to structure from motion.

PubMed

Jia, Hongjun; Martinez, Aleix M

2009-05-01

The task of finding a low-rank (r) matrix that best fits an original data matrix of higher rank is a recurring problem in science and engineering. The problem becomes especially difficult when the original data matrix has some missing entries and contains an unknown additive noise term in the remaining elements. The former problem can be solved by concatenating a set of r-column matrices that share a common single r-dimensional solution space. Unfortunately, the number of possible submatrices is generally very large and, hence, the results obtained with one set of r-column matrices will generally be different from that captured by a different set. Ideally, we would like to find that solution that is least affected by noise. This requires that we determine which of the r-column matrices (i.e., which of the original feature points) are less influenced by the unknown noise term. This paper presents a criterion to successfully carry out such a selection. Our key result is to formally prove that the more distinct the r vectors of the r-column matrices are, the less they are swayed by noise. This key result is then combined with the use of a noise model to derive an upper bound for the effect that noise and occlusions have on each of the r-column matrices. It is shown how this criterion can be effectively used to recover the noise-free matrix of rank r. Finally, we derive the affine and projective structure-from-motion (SFM) algorithms using the proposed criterion. Extensive validation on synthetic and real data sets shows the superiority of the proposed approach over the state of the art.

Pose-free structure from motion using depth from motion constraints.

PubMed

Zhang, Ji; Boutin, Mireille; Aliaga, Daniel G

2011-10-01

Structure from motion (SFM) is the problem of recovering the geometry of a scene from a stream of images taken from unknown viewpoints. One popular approach to estimate the geometry of a scene is to track scene features on several images and reconstruct their position in 3-D. During this process, the unknown camera pose must also be recovered. Unfortunately, recovering the pose can be an ill-conditioned problem which, in turn, can make the SFM problem difficult to solve accurately. We propose an alternative formulation of the SFM problem with fixed internal camera parameters known a priori. In this formulation, obtained by algebraic variable elimination, the external camera pose parameters do not appear. As a result, the problem is better conditioned in addition to involving much fewer variables. Variable elimination is done in three steps. First, we take the standard SFM equations in projective coordinates and eliminate the camera orientations from the equations. We then further eliminate the camera center positions. Finally, we also eliminate all 3-D point positions coordinates, except for their depths with respect to the camera center, thus obtaining a set of simple polynomial equations of degree two and three. We show that, when there are merely a few points and pictures, these "depth-only equations" can be solved in a global fashion using homotopy methods. We also show that, in general, these same equations can be used to formulate a pose-free cost function to refine SFM solutions in a way that is more accurate than by minimizing the total reprojection error, as done when using the bundle adjustment method. The generalization of our approach to the case of varying internal camera parameters is briefly discussed. © 2011 IEEE

Mode of action and resistance studies unveil new roles for tropodithietic acid as an anticancer agent and the γ-glutamyl cycle as a proton sink.

PubMed

Wilson, Maxwell Z; Wang, Rurun; Gitai, Zemer; Seyedsayamdost, Mohammad R

2016-02-09

While we have come to appreciate the architectural complexity of microbially synthesized secondary metabolites, far less attention has been paid to linking their structural features with possible modes of action. This is certainly the case with tropodithietic acid (TDA), a broad-spectrum antibiotic generated by marine bacteria that engage in dynamic symbioses with microscopic algae. TDA promotes algal health by killing unwanted marine pathogens; however, its mode of action (MoA) and significance for the survival of an algal-bacterial miniecosystem remains unknown. Using cytological profiling, we herein determine the MoA of TDA and surprisingly find that it acts by a mechanism similar to polyether antibiotics, which are structurally highly divergent. We show that like polyether drugs, TDA collapses the proton motive force by a proton antiport mechanism, in which extracellular protons are exchanged for cytoplasmic cations. The α-carboxy-tropone substructure is ideal for this purpose as the proton can be carried on the carboxyl group, whereas the basicity of the tropylium ion facilitates cation export. Based on similarities to polyether anticancer agents we have further examined TDA's cytotoxicity and find it to exhibit potent, broad-spectrum anticancer activities. These results highlight the power of MoA-profiling technologies in repurposing old drugs for new targets. In addition, we identify an operon that confers TDA resistance to the producing marine bacteria. Bioinformatic and biochemical analyses of these genes lead to a previously unknown metabolic link between TDA/acid resistance and the γ-glutamyl cycle. The implications of this resistance mechanism in the context of the algal-bacterial symbiosis are discussed.

Mode of action and resistance studies unveil new roles for tropodithietic acid as an anticancer agent and the γ-glutamyl cycle as a proton sink

PubMed Central

Wilson, Maxwell Z.; Wang, Rurun; Gitai, Zemer; Seyedsayamdost, Mohammad R.

2016-01-01

While we have come to appreciate the architectural complexity of microbially synthesized secondary metabolites, far less attention has been paid to linking their structural features with possible modes of action. This is certainly the case with tropodithietic acid (TDA), a broad-spectrum antibiotic generated by marine bacteria that engage in dynamic symbioses with microscopic algae. TDA promotes algal health by killing unwanted marine pathogens; however, its mode of action (MoA) and significance for the survival of an algal–bacterial miniecosystem remains unknown. Using cytological profiling, we herein determine the MoA of TDA and surprisingly find that it acts by a mechanism similar to polyether antibiotics, which are structurally highly divergent. We show that like polyether drugs, TDA collapses the proton motive force by a proton antiport mechanism, in which extracellular protons are exchanged for cytoplasmic cations. The α-carboxy-tropone substructure is ideal for this purpose as the proton can be carried on the carboxyl group, whereas the basicity of the tropylium ion facilitates cation export. Based on similarities to polyether anticancer agents we have further examined TDA’s cytotoxicity and find it to exhibit potent, broad-spectrum anticancer activities. These results highlight the power of MoA-profiling technologies in repurposing old drugs for new targets. In addition, we identify an operon that confers TDA resistance to the producing marine bacteria. Bioinformatic and biochemical analyses of these genes lead to a previously unknown metabolic link between TDA/acid resistance and the γ-glutamyl cycle. The implications of this resistance mechanism in the context of the algal-bacterial symbiosis are discussed. PMID:26802120

A second RNA-binding protein is essential for ethanol tolerance provided by the bacterial OLE ribonucleoprotein complex.

PubMed

Harris, Kimberly A; Zhou, Zhiyuan; Peters, Michelle L; Wilkins, Sarah G; Breaker, Ronald R

2018-06-18

OLE (ornate, large, extremophilic) RNAs comprise a class of structured noncoding RNAs (ncRNAs) found in many extremophilic bacteria species. OLE RNAs constitute one of the longest and most widespread bacterial ncRNA classes whose major biochemical function remains unknown. In the Gram-positive alkaliphile Bacillus halodurans , OLE RNA is abundant, and localizes to the cell membrane by association with the transmembrane OLE-associated protein called OapA (formerly OAP). These characteristics, along with the well-conserved sequence and structural features of OLE RNAs, suggest that the OLE ribonucleoprotein (RNP) complex performs important biological functions. B. halodurans strains lacking OLE RNA ( ∆ole ) or OapA ( ∆oapA ) are less tolerant of cold (20 °C) and short-chain alcohols (e.g., ethanol). Here, we describe the effects of a mutant OapA (called PM1) that more strongly inhibits growth under cold or ethanol stress compared with strains lacking the oapA gene, even when wild-type OapA is present. This dominant-negative effect of PM1 is reversed by mutations that render OLE RNA nonfunctional. This finding demonstrates that the deleterious PM1 phenotype requires an intact RNP complex, and suggests that the complex has one or more additional undiscovered components. A genetic screen uncovered PM1 phenotype suppressor mutations in the ybzG gene, which codes for a putative RNA-binding protein of unknown biological function. We observe that YbzG protein (also called OapB) selectively binds OLE RNA in vitro, whereas a mutant version of the protein is not observed to bind OLE RNA. Thus, YbzG/OapB is an important component of the functional OLE RNP complex in B. halodurans .

Developmental Features of Exploration.

ERIC Educational Resources Information Center

Vandenberg, Brian

1984-01-01

Analyzes the exploratory patterns of 112 children ages 4 to 12, using visual and auditory stimuli and toy preference and toy exploration tasks. Finds that a preference for complexity and for unknown toys increases with age and notes age differences in exploratory patterns and question-asking behavior. (Author/CB)

Circular RNA biogenesis can proceed through an exon-containing lariat precursor.

PubMed

Barrett, Steven P; Wang, Peter L; Salzman, Julia

2015-06-09

Pervasive expression of circular RNA is a recently discovered feature of eukaryotic gene expression programs, yet its function remains largely unknown. The presumed biogenesis of these RNAs involves a non-canonical 'backsplicing' event. Recent studies in mammalian cell culture posit that backsplicing is facilitated by inverted repeats flanking the circularized exon(s). Although such sequence elements are common in mammals, they are rare in lower eukaryotes, making current models insufficient to describe circularization. Through systematic splice site mutagenesis and the identification of splicing intermediates, we show that circular RNA in Schizosaccharomyces pombe is generated through an exon-containing lariat precursor. Furthermore, we have performed high-throughput and comprehensive mutagenesis of a circle-forming exon, which enabled us to discover a systematic effect of exon length on RNA circularization. Our results uncover a mechanism for circular RNA biogenesis that may account for circularization in genes that lack noticeable flanking intronic secondary structure.

Vision guided landing of an an autonomous helicopter in hazardous terrain

NASA Technical Reports Server (NTRS)

Johnson, Andrew E.; Montgomery, Jim

2005-01-01

Future robotic space missions will employ a precision soft-landing capability that will enable exploration of previously inaccessible sites that have strong scientific significance. To enable this capability, a fully autonomous onboard system that identifies and avoids hazardous features such as steep slopes and large rocks is required. Such a system will also provide greater functionality in unstructured terrain to unmanned aerial vehicles. This paper describes an algorithm for landing hazard avoidance based on images from a single moving camera. The core of the algorithm is an efficient application of structure from motion to generate a dense elevation map of the landing area. Hazards are then detected in this map and a safe landing site is selected. The algorithm has been implemented on an autonomous helicopter testbed and demonstrated four times resulting in the first autonomous landing of an unmanned helicopter in unknown and hazardous terrain.

A thermodynamic unification of jamming

NASA Astrophysics Data System (ADS)

Lu, Kevin; Brodsky, E. E.; Kavehpour, H. P.

2008-05-01

Fragile materials ranging from sand to fire retardant to toothpaste are able to exhibit both solid and fluid-like properties across the jamming transition. Unlike ordinary fusion, systems of grains, foams and colloids jam and cease to flow under conditions that still remain unknown. Here, we quantify jamming using a thermodynamic approach by accounting for the structural ageing and the shear-induced compressibility of dry sand. Specifically, the jamming threshold is defined using a non-thermal temperature that measures the `fluffiness' of a granular mixture. The thermodynamic model, cast in terms of pressure, temperature and free volume, also successfully predicts the entropic data of five molecular glasses. Notably, the predicted configurational entropy averts the Kauzmann paradox-an unresolved crisis where the configurational entropy becomes negative-entirely. Without any free parameters, the proposed equation-of-state also governs the mechanism of shear banding and the associated features of shear softening and thickness invariance.

Children's sequential information search is sensitive to environmental probabilities.

PubMed

Nelson, Jonathan D; Divjak, Bojana; Gudmundsdottir, Gudny; Martignon, Laura F; Meder, Björn

2014-01-01

We investigated 4th-grade children's search strategies on sequential search tasks in which the goal is to identify an unknown target object by asking yes-no questions about its features. We used exhaustive search to identify the most efficient question strategies and evaluated the usefulness of children's questions accordingly. Results show that children have good intuitions regarding questions' usefulness and search adaptively, relative to the statistical structure of the task environment. Search was especially efficient in a task environment that was representative of real-world experiences. This suggests that children may use their knowledge of real-world environmental statistics to guide their search behavior. We also compared different related search tasks. We found positive transfer effects from first doing a number search task on a later person search task. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Sensory experience modifies feature map relationships in visual cortex

PubMed Central

Cloherty, Shaun L; Hughes, Nicholas J; Hietanen, Markus A; Bhagavatula, Partha S

2016-01-01

The extent to which brain structure is influenced by sensory input during development is a critical but controversial question. A paradigmatic system for studying this is the mammalian visual cortex. Maps of orientation preference (OP) and ocular dominance (OD) in the primary visual cortex of ferrets, cats and monkeys can be individually changed by altered visual input. However, the spatial relationship between OP and OD maps has appeared immutable. Using a computational model we predicted that biasing the visual input to orthogonal orientation in the two eyes should cause a shift of OP pinwheels towards the border of OD columns. We then confirmed this prediction by rearing cats wearing orthogonally oriented cylindrical lenses over each eye. Thus, the spatial relationship between OP and OD maps can be modified by visual experience, revealing a previously unknown degree of brain plasticity in response to sensory input. DOI: http://dx.doi.org/10.7554/eLife.13911.001 PMID:27310531

Mind the gap: Neural coding of species identity in birdsong prosody.

PubMed

Araki, Makoto; Bandi, M M; Yazaki-Sugiyama, Yoko

2016-12-09

Juvenile songbirds learn vocal communication from adult tutors of the same species but not from adults of other species. How species-specific learning emerges from the basic features of song prosody remains unknown. In the zebra finch auditory cortex, we discovered a class of neurons that register the silent temporal gaps between song syllables and are distinct from neurons encoding syllable morphology. Behavioral learning and neuronal coding of temporal gap structure resisted song tutoring from other species: Zebra finches fostered by Bengalese finch parents learned Bengalese finch song morphology transposed onto zebra finch temporal gaps. During the vocal learning period, temporal gap neurons fired selectively to zebra finch song. The innate temporal coding of intersyllable silent gaps suggests a neuronal barcode for conspecific vocal learning and social communication in acoustically diverse environments. Copyright © 2016, American Association for the Advancement of Science.

Coding of navigational affordances in the human visual system

PubMed Central

Epstein, Russell A.

2017-01-01

A central component of spatial navigation is determining where one can and cannot go in the immediate environment. We used fMRI to test the hypothesis that the human visual system solves this problem by automatically identifying the navigational affordances of the local scene. Multivoxel pattern analyses showed that a scene-selective region of dorsal occipitoparietal cortex, known as the occipital place area, represents pathways for movement in scenes in a manner that is tolerant to variability in other visual features. These effects were found in two experiments: One using tightly controlled artificial environments as stimuli, the other using a diverse set of complex, natural scenes. A reconstruction analysis demonstrated that the population codes of the occipital place area could be used to predict the affordances of novel scenes. Taken together, these results reveal a previously unknown mechanism for perceiving the affordance structure of navigable space. PMID:28416669

The topography of mutational processes in breast cancer genomes.

PubMed

Morganella, Sandro; Alexandrov, Ludmil B; Glodzik, Dominik; Zou, Xueqing; Davies, Helen; Staaf, Johan; Sieuwerts, Anieta M; Brinkman, Arie B; Martin, Sancha; Ramakrishna, Manasa; Butler, Adam; Kim, Hyung-Yong; Borg, Åke; Sotiriou, Christos; Futreal, P Andrew; Campbell, Peter J; Span, Paul N; Van Laere, Steven; Lakhani, Sunil R; Eyfjord, Jorunn E; Thompson, Alastair M; Stunnenberg, Hendrik G; van de Vijver, Marc J; Martens, John W M; Børresen-Dale, Anne-Lise; Richardson, Andrea L; Kong, Gu; Thomas, Gilles; Sale, Julian; Rada, Cristina; Stratton, Michael R; Birney, Ewan; Nik-Zainal, Serena

2016-05-02

Somatic mutations in human cancers show unevenness in genomic distribution that correlate with aspects of genome structure and function. These mutations are, however, generated by multiple mutational processes operating through the cellular lineage between the fertilized egg and the cancer cell, each composed of specific DNA damage and repair components and leaving its own characteristic mutational signature on the genome. Using somatic mutation catalogues from 560 breast cancer whole-genome sequences, here we show that each of 12 base substitution, 2 insertion/deletion (indel) and 6 rearrangement mutational signatures present in breast tissue, exhibit distinct relationships with genomic features relating to transcription, DNA replication and chromatin organization. This signature-based approach permits visualization of the genomic distribution of mutational processes associated with APOBEC enzymes, mismatch repair deficiency and homologous recombinational repair deficiency, as well as mutational processes of unknown aetiology. Furthermore, it highlights mechanistic insights including a putative replication-dependent mechanism of APOBEC-related mutagenesis.

Genesis and growth of extracellular vesicle-derived microcalcification in atherosclerotic plaques

PubMed Central

Hutcheson, Joshua D.; Goettsch, Claudia; Bertazzo, Sergio; Maldonado, Natalia; Ruiz, Jessica L.; Goh, Wilson; Yabusaki, Katsumi; Faits, Tyler; Bouten, Carlijn; Franck, Gregory; Quillard, Thibaut; Libby, Peter; Aikawa, Masanori; Weinbaum, Sheldon; Aikawa, Elena

2015-01-01

Clinical evidence links arterial calcification and cardiovascular risk. Finite-element modelling of the stress distribution within atherosclerotic plaques has suggested that subcellular microcalcifications in the fibrous cap may promote material failure of the plaque, but that large calcifications can stabilize it. Yet the physicochemical mechanisms underlying such mineral formation and growth in atheromata remain unknown. Here, by using three-dimensional collagen hydrogels that mimic structural features of the atherosclerotic fibrous cap, and high-resolution microscopic and spectroscopic analyses of both the hydrogels and of calcified human plaques, we demonstrate that calcific mineral formation and maturation results from a series of events involving the aggregation of calcifying extracellular vesicles, and the formation of microcalcifications and ultimately large calcification zones. We also show that calcification morphology and the plaque’s collagen content – two determinants of atherosclerotic plaque stability - are interlinked. PMID:26752654

Near-island biological hotspots in barren ocean basins.

PubMed

Gove, Jamison M; McManus, Margaret A; Neuheimer, Anna B; Polovina, Jeffrey J; Drazen, Jeffrey C; Smith, Craig R; Merrifield, Mark A; Friedlander, Alan M; Ehses, Julia S; Young, Charles W; Dillon, Amanda K; Williams, Gareth J

2016-02-16

Phytoplankton production drives marine ecosystem trophic-structure and global fisheries yields. Phytoplankton biomass is particularly influential near coral reef islands and atolls that span the oligotrophic tropical oceans. The paradoxical enhancement in phytoplankton near an island-reef ecosystem--Island Mass Effect (IME)--was first documented 60 years ago, yet much remains unknown about the prevalence and drivers of this ecologically important phenomenon. Here we provide the first basin-scale investigation of IME. We show that IME is a near-ubiquitous feature among a majority (91%) of coral reef ecosystems surveyed, creating near-island 'hotspots' of phytoplankton biomass throughout the upper water column. Variations in IME strength are governed by geomorphic type (atoll vs island), bathymetric slope, reef area and local human impacts (for example, human-derived nutrient input). These ocean oases increase nearshore phytoplankton biomass by up to 86% over oceanic conditions, providing basal energetic resources to higher trophic levels that support subsistence-based human populations.

Cutaneous Collagenous Vasculopathy

PubMed Central

Ortleb, Melanie; Boyd, Alan S.; Powers, Jennifer

2015-01-01

Cutaneous collagenous vasculopathy is a rare microangiopathy of dermal blood vessels. Clinically indistinguishable from generalized essential telangiectasia, this condition is diagnosed by its unique histological appearance. In contrast to other primary telangiectatic processes, cutaneous collagenous vasculopathy has dilated vascular structures that contain deposits of eosinophilic hyaline material within the vessel walls. To date, cutaneous collagenous vasculopathy has been described in a total of 19 cases in the medical literature. The first several cases were described exclusively in middle-aged to elderly men. Though it has now been described in both men and women, cutaneous collagenous vasculopathy is still most often described in middle-aged to older adults. No particular disease or medication has been linked to the development of cutaneous collagenous vasculopathy, and the etiology remains unknown. In this case series, the authors present three additional patients diagnosed with cutaneous collagenous vasculopathy and discuss their clinical and histopathologic features. PMID:26705441

Mushroom tumor: a new disease on Flammulina velutipes caused by Ochrobactrum pseudogrignonense.

PubMed

Wu, Zhipeng; Peng, Weihong; He, Xiaolan; Wang, Bo; Gan, Bingcheng; Zhang, Xiaoping

2016-01-01

Mushroom tumor on Flammulina velutipes has become the main disease during the off-season cultivation of F. velutipes while the causal organism has remained unknown. The present study was aimed at identifying the pathogen confirming its pathogenisity following Koch's Postulates, characterizing it using morphological, physiological, biochemical and molecular features, and studying its current distribution. We determined that mushroom tumor is a new bacterial infection disease caused by Ochrobactrum pseudogrignonense. It produces tumor-like structures on the surface of the substrate, and inhibits the formation of primordia and fruiting of F. velutipes. The molecular studies showed that this new pathogen is closely related to Ochrobactrum based on 16S rRNA sequences. This is the first time that Ochrobactrum has been shown to be a pathogen of a mushroom. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Forging Unsupported Metal-Boryl Bonds with Icosahedral Carboranes.

PubMed

Saleh, Liban M A; Dziedzic, Rafal M; Khan, Saeed I; Spokoyny, Alexander M

2016-06-13

In contrast to the plethora of metal-catalyzed cross-coupling methods available for the installation of functional groups on aromatic hydrocarbons, a comparable variety of methods are currently not available for icosahedral carboranes, which are boron-rich three-dimensional aromatic analogues of aryl groups. Part of this is due to the limited understanding of the elementary steps for cross-coupling involving carboranes. Here, we report our efforts in isolating metal-boryl complexes to further our understanding of one of these elementary steps, oxidative addition. Structurally characterized examples of group 10 M-B bonds featuring icosahedral carboranes are completely unknown. Use of mercurocarboranes as a reagent to deliver M-B bonds saw divergent reactivity for platinum and palladium, with a Pt-B bond being isolated for the former, and a rare Pd-Hg bond being formed for the latter. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

HHsvm: fast and accurate classification of profile–profile matches identified by HHsearch

PubMed Central

Dlakić, Mensur

2009-01-01

Motivation: Recently developed profile–profile methods rival structural comparisons in their ability to detect homology between distantly related proteins. Despite this tremendous progress, many genuine relationships between protein families cannot be recognized as comparisons of their profiles result in scores that are statistically insignificant. Results: Using known evolutionary relationships among protein superfamilies in SCOP database, support vector machines were trained on four sets of discriminatory features derived from the output of HHsearch. Upon validation, it was shown that the automatic classification of all profile–profile matches was superior to fixed threshold-based annotation in terms of sensitivity and specificity. The effectiveness of this approach was demonstrated by annotating several domains of unknown function from the Pfam database. Availability: Programs and scripts implementing the methods described in this manuscript are freely available from http://hhsvm.dlakiclab.org/. Contact: mdlakic@montana.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19773335

FBRDLR: Fast blind reconstruction approach with dictionary learning regularization for infrared microscopy spectra

NASA Astrophysics Data System (ADS)

Liu, Tingting; Liu, Hai; Chen, Zengzhao; Chen, Yingying; Wang, Shengming; Liu, Zhi; Zhang, Hao

2018-05-01

Infrared (IR) spectra are the fingerprints of the molecules, and the spectral band location closely relates to the structure of a molecule. Thus, specimen identification can be performed based on IR spectroscopy. However, spectrally overlapping components prevent the specific identification of hyperfine molecular information of different substances. In this paper, we propose a fast blind reconstruction approach for IR spectra, which is based on sparse and redundant representations over a dictionary. The proposed method recovers the spectrum with the discrete wavelet transform dictionary on its content. The experimental results demonstrate that the proposed method is superior because of the better performance when compared with other state-of-the-art methods. The method the authors used remove the instrument aging issue to a large extent, thus leading the reconstruction IR spectra a more convenient tool for extracting features of an unknown material and interpreting it.

Deep Direct Reinforcement Learning for Financial Signal Representation and Trading.

PubMed

Deng, Yue; Bao, Feng; Kong, Youyong; Ren, Zhiquan; Dai, Qionghai

2017-03-01

Can we train the computer to beat experienced traders for financial assert trading? In this paper, we try to address this challenge by introducing a recurrent deep neural network (NN) for real-time financial signal representation and trading. Our model is inspired by two biological-related learning concepts of deep learning (DL) and reinforcement learning (RL). In the framework, the DL part automatically senses the dynamic market condition for informative feature learning. Then, the RL module interacts with deep representations and makes trading decisions to accumulate the ultimate rewards in an unknown environment. The learning system is implemented in a complex NN that exhibits both the deep and recurrent structures. Hence, we propose a task-aware backpropagation through time method to cope with the gradient vanishing issue in deep training. The robustness of the neural system is verified on both the stock and the commodity future markets under broad testing conditions.

Endogenous vs Exogenous Allosteric Modulators in GPCRs: A dispute for shuttling CB1 among different membrane microenvironments

NASA Astrophysics Data System (ADS)

Stornaiuolo, Mariano; Bruno, Agostino; Botta, Lorenzo; Regina, Giuseppe La; Cosconati, Sandro; Silvestri, Romano; Marinelli, Luciana; Novellino, Ettore

2015-10-01

A Cannabinoid Receptor 1 (CB1) binding site for the selective allosteric modulator ORG27569 is here identified through an integrate approach of consensus pocket prediction, mutagenesis studies and Mass Spectrometry. This unprecedented ORG27569 pocket presents the structural features of a Cholesterol Consensus Motif, a cholesterol interacting region already found in other GPCRs. ORG27569 and cholesterol affects oppositely CB1 affinity for orthosteric ligands. Moreover, the rise in cholesterol intracellular level results in CB1 trafficking to the axonal region of neuronal cells, while, on the contrary, ORG27568 binding induces CB1 enrichment at the soma. This control of receptor migration among functionally different membrane regions of the cell further contributes to downstream signalling and adds a previously unknown mechanism underpinning CB1 modulation by ORG27569 , that goes beyond a mere control of receptor affinity for orthosteric ligands.

Immunogold Localization of Key Metabolic Enzymes in the Anammoxosome and on the Tubule-Like Structures of Kuenenia stuttgartiensis.

PubMed

de Almeida, Naomi M; Neumann, Sarah; Mesman, Rob J; Ferousi, Christina; Keltjens, Jan T; Jetten, Mike S M; Kartal, Boran; van Niftrik, Laura

2015-07-01

Anaerobic ammonium-oxidizing (anammox) bacteria oxidize ammonium with nitrite as the terminal electron acceptor to form dinitrogen gas in the absence of oxygen. Anammox bacteria have a compartmentalized cell plan with a central membrane-bound "prokaryotic organelle" called the anammoxosome. The anammoxosome occupies most of the cell volume, has a curved membrane, and contains conspicuous tubule-like structures of unknown identity and function. It was suggested previously that the catalytic reactions of the anammox pathway occur in the anammoxosome, and that proton motive force was established across its membrane. Here, we used antibodies raised against five key enzymes of the anammox catabolism to determine their cellular location. The antibodies were raised against purified native hydroxylamine oxidoreductase-like protein kustc0458 with its redox partner kustc0457, hydrazine dehydrogenase (HDH; kustc0694), hydroxylamine oxidase (HOX; kustc1061), nitrite oxidoreductase (NXR; kustd1700/03/04), and hydrazine synthase (HZS; kuste2859-61) of the anammox bacterium Kuenenia stuttgartiensis. We determined that all five protein complexes were exclusively located inside the anammoxosome matrix. Four of the protein complexes did not appear to form higher-order protein organizations. However, the present data indicated for the first time that NXR is part of the tubule-like structures, which may stretch the whole length of the anammoxosome. These findings support the anammoxosome as the locus of catabolic reactions of the anammox pathway. Anammox bacteria are environmentally relevant microorganisms that contribute significantly to the release of fixed nitrogen in nature. Furthermore, the anammox process is applied for nitrogen removal from wastewater as an environment-friendly and cost-effective technology. These microorganisms feature a unique cellular organelle, the anammoxosome, which was proposed to contain the energy metabolism of the cell and tubule-like structures with hitherto unknown function. Here, we purified five native enzymes catalyzing key reactions in the anammox metabolism and raised antibodies against these in order to localize them within the cell. We showed that all enzymes were located within the anammoxosome, and nitrite oxidoreductase was located exclusively at the tubule-like structures, providing the first insights into the function of these subcellular structures. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

The role of invasive and non-invasive procedures in diagnosing fever of unknown origin.

PubMed

Mete, Bilgul; Vanli, Ersin; Yemisen, Mucahit; Balkan, Ilker Inanc; Dagtekin, Hilal; Ozaras, Resat; Saltoglu, Nese; Mert, Ali; Ozturk, Recep; Tabak, Fehmi

2012-01-01

The etiology of fever of unknown origin has changed because of the recent advances in and widespread use of invasive and non-invasive diagnostic tools. However, undiagnosed patients still constitute a significant number. To determine the etiological distribution and role of non-invasive and invasive diagnostic tools in the diagnosis of fever of unknown origin. One hundred patients who were hospitalized between June 2001 and 2009 with a fever of unknown origin were included in this study. Clinical and laboratory data were collected from the patients' medical records retrospectively. Fifty three percent of the patients were male, with a mean age of 45 years. The etiology of fever was determined to be infectious diseases in 26, collagen vascular diseases in 38, neoplastic diseases in 14, miscellaneous in 2 and undiagnosed in 20 patients. When the etiologic distribution was analyzed over time, it was noted that the rate of infectious diseases decreased, whereas the rate of rheumatological and undiagnosed diseases relatively increased because of the advances in imaging and microbiological studies. Seventy patients had a definitive diagnosis, whereas 10 patients had a possible diagnosis. The diagnoses were established based on clinical features and non-invasive tests for 61% of the patients and diagnostic benefit was obtained for 49% of the patients undergoing invasive tests. Biopsy procedures contributed a rate of 42% to diagnoses in patients who received biopsies. Clinical features (such as detailed medical history-taking and physical examination) may contribute to diagnoses, particularly in cases of collagen vascular diseases. Imaging studies exhibit certain pathologies that guide invasive studies. Biopsy procedures contribute greatly to diagnoses, particularly for malignancies and infectious diseases that are not diagnosed by non-invasive procedures.

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.

PubMed

Neuwald, Andrew F; Altschul, Stephen F

2016-12-01

Over evolutionary time, members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches. At the sequence level, such divergence appears as correlations that arise from residue patterns distinct to each subgroup. Such a superfamily may be viewed as a population of sequences corresponding to a complex, high-dimensional probability distribution. Here we model this distribution as hierarchical interrelated hidden Markov models (hiHMMs), which describe these sequence correlations implicitly. By characterizing such correlations one may hope to obtain information regarding functionally-relevant properties that have thus far evaded detection. To do so, we infer a hiHMM distribution from sequence data using Bayes' theorem and Markov chain Monte Carlo (MCMC) sampling, which is widely recognized as the most effective approach for characterizing a complex, high dimensional distribution. Other routines then map correlated residue patterns to available structures with a view to hypothesis generation. When applied to N-acetyltransferases, this reveals sequence and structural features indicative of functionally important, yet generally unknown biochemical properties. Even for sets of proteins for which nothing is known beyond unannotated sequences and structures, this can lead to helpful insights. We describe, for example, a putative coenzyme-A-induced-fit substrate binding mechanism mediated by arginine residue switching between salt bridge and π-π stacking interactions. A suite of programs implementing this approach is available (psed.igs.umaryland.edu).

Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development.

PubMed

Moraes, Gleiciane Leal; Gomes, Guelber Cardoso; Monteiro de Sousa, Paulo Robson; Alves, Cláudio Nahum; Govender, Thavendran; Kruger, Hendrik G; Maguire, Glenn E M; Lamichhane, Gyanu; Lameira, Jerônimo

2015-03-01

Tuberculosis (TB) is the second leading cause of human mortality from infectious diseases worldwide. The WHO reported 1.3 million deaths and 8.6 million new cases of TB in 2012. Mycobacterium tuberculosis (M. tuberculosis), the infectious bacteria that causes TB, is encapsulated by a thick and robust cell wall. The innermost segment of the cell wall is comprised of peptidoglycan, a layer that is required for survival and growth of the pathogen. Enzymes that catalyse biosynthesis of the peptidoglycan are essential and are therefore attractive targets for discovery of novel antibiotics as humans lack similar enzymes making it possible to selectively target bacteria only. In this paper, we have reviewed the structures and functions of enzymes GlmS, GlmM, GlmU, MurA, MurB, MurC, MurD, MurE and MurF from M. tuberculosis that are involved in peptidoglycan biosynthesis. In addition, we report homology modelled 3D structures of those key enzymes from M. tuberculosis of which the structures are still unknown. We demonstrated that natural substrates can be successfully docked into the active sites of the GlmS and GlmU respectively. It is therefore expected that the models and the data provided herein will facilitate translational research to develop new drugs to treat TB. Copyright © 2015. Published by Elsevier Ltd.

Utilization of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for structural studies related to biology and disease

NASA Astrophysics Data System (ADS)

Costello, Catherine E.; Helin, Jari; Ngoka, Lambert C. M.

1996-04-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), because of its high sensitivity and relatively straightforward requirements for sample preparation, is contributing to the solution of structural problems in biology and to the development of therapeutic approaches through increased understanding of pharmacology and enhanced capabilities for quality control of pharmaceuticals. We are using a reflectron TOF- MS for the determination of molecular weights of individual compounds and the components of mixtures that are naturally occurring or are generated through enzymic digests, and employing the post-source decay mode to elucidate structural details. To maximize the sensitivity and information content of the spectra, varied matrices, derivative, and stepwise degradation procedures are being explored. Present studies include investigations of oligosaccharides, neutral glycolipids, gangliosides, glycoproteins, neuropeptides and proteins. Rules for fragmentation are being developed with model compounds and used for the structural elucidation of unknowns. When adequate sample amounts are available, the results are compared with low- and high-energy collision-induced decomposition spectra obtained with tandem MS in order to provide a data base for the correlation of spectral features and guidance in selection of approaches for scarce biological samples. Current projects include biophysical studies of glycoplipids, glycoproteins and oligosaccharides and investigations of the substance P receptor, transthyretin genetic variants and cisplatin-DNA interactions.

A versatile approach to the study of the transient response of a submerged thin shell

NASA Astrophysics Data System (ADS)

Leblond, C.; Sigrist, J.-F.

2010-01-01

The transient response of submerged two-dimensional thin shell subjected to weak acoustical or mechanical excitations is addressed in this paper. The proposed approach is first exposed in a detailed manner: it is based on Laplace transform in time, in vacuo eigenvector expansion with time-dependent coefficients for the structural dynamics and boundary-integral formulation for the fluid. The projection of the fluid pressure on the in vacuo eigenvectors leads to a fully coupled system involving the modal time-dependent displacement coefficients, which are the problem unknowns. They are simply determined by matrix inversion in the Laplace domain. Application of the method to the response of a two-dimensional immersed shell to a weak acoustical excitation is then exposed: the proposed test-case corresponds to the design of immersed structures subjected to underwater explosions, which is of paramount importance in naval shipbuilding. Comparison of a numerical calculation based on the proposed approach with an analytical solution is exposed; versatility of the method is also highlighted by referring to "classical" FEM/FEM or FEM/BEM simulations. As a conspicuous feature of the method, calculation of the fluid response functions corresponding to a given geometry has to be performed once, allowing various simulations for different material properties of the structure, as well as for various excitations on the structure. This versatile approach can therefore be efficiently and extensively used for design purposes.

Comparing large covariance matrices under weak conditions on the dependence structure and its application to gene clustering.

PubMed

Chang, Jinyuan; Zhou, Wen; Zhou, Wen-Xin; Wang, Lan

2017-03-01

Comparing large covariance matrices has important applications in modern genomics, where scientists are often interested in understanding whether relationships (e.g., dependencies or co-regulations) among a large number of genes vary between different biological states. We propose a computationally fast procedure for testing the equality of two large covariance matrices when the dimensions of the covariance matrices are much larger than the sample sizes. A distinguishing feature of the new procedure is that it imposes no structural assumptions on the unknown covariance matrices. Hence, the test is robust with respect to various complex dependence structures that frequently arise in genomics. We prove that the proposed procedure is asymptotically valid under weak moment conditions. As an interesting application, we derive a new gene clustering algorithm which shares the same nice property of avoiding restrictive structural assumptions for high-dimensional genomics data. Using an asthma gene expression dataset, we illustrate how the new test helps compare the covariance matrices of the genes across different gene sets/pathways between the disease group and the control group, and how the gene clustering algorithm provides new insights on the way gene clustering patterns differ between the two groups. The proposed methods have been implemented in an R-package HDtest and are available on CRAN. © 2016, The International Biometric Society.

Dynamics of the metal binding domains and regulation of the human copper transporters ATP7B and ATP7A.

PubMed

Yu, Corey H; Dolgova, Natalia V; Dmitriev, Oleg Y

2017-04-01

Copper transporters ATP7A and ATP7B regulate copper levels in the human cells and deliver copper to the biosynthetic pathways. ATP7A and ATP7B belong to the P-type ATPases and share much of the domain architecture and the mechanism of ATP hydrolysis with the other, well-studied, enzymes of this type. A unique structural feature of the copper ATPases is the chain of six cytosolic metal-binding domains (MBDs), which are believed to be involved in copper-dependent regulation of the activity and intracellular localization of these enzymes. Although the structures of all the MBDs have been solved, the mechanism of copper-dependent regulation of ATP7B and ATP7A, the roles of individual MBDs, and the relationship between the regulatory and catalytic copper binding are still unknown. We describe the structure and dynamics of the MBDs, review the current knowledge about their functional roles and propose a mechanism of regulation of ATP7B by copper-dependent changes in the dynamics and conformation of the MBD chain. Transient interactions between the MBDs, rather than transitions between distinct static conformations are likely to form the structural basis of regulation of the ATP-dependent copper transporters in human cells. © 2016 IUBMB Life, 69(4):226-235, 2017. © 2017 International Union of Biochemistry and Molecular Biology.

Insights into RNA binding by the anticancer drug cisplatin from the crystal structure of cisplatin-modified ribosome

PubMed Central

Melnikov, Sergey V.; Söll, Dieter; Steitz, Thomas A.

2016-01-01

Abstract Cisplatin is a widely prescribed anticancer drug, which triggers cell death by covalent binding to a broad range of biological molecules. Among cisplatin targets, cellular RNAs remain the most poorly characterized molecules. Although cisplatin was shown to inactivate essential RNAs, including ribosomal, spliceosomal and telomeric RNAs, cisplatin binding sites in most RNA molecules are unknown, and therefore it remains challenging to study how modifications of RNA by cisplatin contributes to its toxicity. Here we report a 2.6Å-resolution X-ray structure of cisplatin-modified 70S ribosome, which describes cisplatin binding to the ribosome and provides the first nearly atomic model of cisplatin–RNA complex. We observe nine cisplatin molecules bound to the ribosome and reveal consensus structural features of the cisplatin-binding sites. Two of the cisplatin molecules modify conserved functional centers of the ribosome—the mRNA-channel and the GTPase center. In the mRNA-channel, cisplatin intercalates between the ribosome and the messenger RNA, suggesting that the observed inhibition of protein synthesis by cisplatin is caused by impaired mRNA-translocation. Our structure provides an insight into RNA targeting and inhibition by cisplatin, which can help predict cisplatin-binding sites in other cellular RNAs and design studies to elucidate a link between RNA modifications by cisplatin and cisplatin toxicity. PMID:27079977

Automatically measuring the effect of strategy drawing features on pupils' handwriting and gender

NASA Astrophysics Data System (ADS)

Tabatabaey-Mashadi, Narges; Sudirman, Rubita; Guest, Richard M.; Khalid, Puspa Inayat

2013-12-01

Children's dynamic drawing strategies have been recently recognized as indicators of handwriting ability. However the influence of each feature in predicting handwriting is unknown due to lack of a measuring system. An automated measuring algorithm suitable for psychological assessment and non-subjective scoring is presented here. Using the weight vector and classification rate of a machine learning algorithm, an overall feature's effect is calculated which is comparable in different groupings. In this study thirteen previously detected drawing strategy features are measured for their influence on handwriting and gender. Features are extracted from drawing a triangle, Beery VMI and Bender Gestalt tangent patterns. Samples are related to 203 pupils (77 below average writers, and 101 female). The results show that the number of strokes in drawing the triangle pattern plays a major role in both groupings; however Left Tendency flag feature is affected by children's handwriting about 2.5 times greater than their gender. Experiments indicate that different forms of a feature sometimes show different influences.

Blind Bayesian restoration of adaptive optics telescope images using generalized Gaussian Markov random field models

NASA Astrophysics Data System (ADS)

Jeffs, Brian D.; Christou, Julian C.

1998-09-01

This paper addresses post processing for resolution enhancement of sequences of short exposure adaptive optics (AO) images of space objects. The unknown residual blur is removed using Bayesian maximum a posteriori blind image restoration techniques. In the problem formulation, both the true image and the unknown blur psf's are represented by the flexible generalized Gaussian Markov random field (GGMRF) model. The GGMRF probability density function provides a natural mechanism for expressing available prior information about the image and blur. Incorporating such prior knowledge in the deconvolution optimization is crucial for the success of blind restoration algorithms. For example, space objects often contain sharp edge boundaries and geometric structures, while the residual blur psf in the corresponding partially corrected AO image is spectrally band limited, and exhibits while the residual blur psf in the corresponding partially corrected AO image is spectrally band limited, and exhibits smoothed, random , texture-like features on a peaked central core. By properly choosing parameters, GGMRF models can accurately represent both the blur psf and the object, and serve to regularize the deconvolution problem. These two GGMRF models also serve as discriminator functions to separate blur and object in the solution. Algorithm performance is demonstrated with examples from synthetic AO images. Results indicate significant resolution enhancement when applied to partially corrected AO images. An efficient computational algorithm is described.

Facile hydrothermal crystallization of NaLn(WO4)2 (Ln=La-Lu, and Y), phase/morphology evolution, and photoluminescence

NASA Astrophysics Data System (ADS)

Shi, Xiaofei; Li, Ji-Guang; Wang, Xuejiao; Zhu, Qi; Kim, Byung-Nam; Sun, Xudong

2017-12-01

Hydrothermal reaction of Ln nitrate and Na2WO4 at pH=8 and 200 °C for 24 hours, in the absence of any additive, has directly produced the scheelite-type sodium lanthanide tungstate of NaLn(WO4)2 for the larger Ln3+ of Ln=La-Dy (including Y, Group I) and an unknown compound that can be transformed into NaLn(WO4)2 by calcination at the low temperature of 600 °C for the smaller Ln3+ of Ln=Ho-Lu (Group II). With the successful synthesis of NaLn(WO4)2 for the full spectrum of Ln, the effects of lanthanide contraction on the structural features, crystal morphology, and IR responses of the compounds were clarified. The temperature- and time-course phase/morphology evolutions and the phase conversion upon calcination were thoroughly studied for the Group I and Group II compounds with Ln=La and Lu for example, respectively. Unknown intermediates were characterized by elemental analysis, IR absorption, thermogravimetry, and differential scanning calorimetry to better understand their chemical composition and coordination. The photoluminescence properties of NaEu(WO4)2 and NaTb(WO4)2, including excitation, emission, fluorescence decay, and quantum efficiency of luminescence, were also comparatively studied for the as-synthesized and calcination products.

381. J.H.E., Delineator Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF ...

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

381. J.H.E., Delineator Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; WEST BAY CROSSING; SUSPENDED STRUCTURE; ERECTION; DRG. NO. 43 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

Childhood Ependymoma Treatment (PDQ®)—Health Professional Version

Cancer.gov

In childhood ependymoma, cancer forms in the tissues of the brain and spinal cord. The cause of ependymoma is unknown. Find out about the molecular and clinical features, diagnosis, prognosis, treatment, and clinical trials for pediatric ependymoma, subependymoma, myxopapillary ependymoma, anaplastic ependymoma, and RELA fusion–positive ependymoma.

Open access: a closed shop?

NASA Astrophysics Data System (ADS)

Bradford, Rick

2013-01-01

Your December 2012 issue contains both a short news article on the progress of the open-access movement ("UK open access gains ground", p11) and a lengthy feature about the visionary Irish physicist Edward Hutchinson Synge ("Unknown genius", pp26-29). I find the combination of these articles ironic.

Filimonas endophytica sp. nov., isolated from surface-sterilized root of Cosmos bipinnatus.

PubMed

Han, Ji-Hye; Kim, Tae-Su; Joung, Yochan; Kim, Seung Bum

2015-12-01

A Gram-stain-negative, yellow, motile by gliding, filamentous bacterium, designated SR 2-06T, was isolated from surface-sterilized root of garden cosmos. 16S rRNA gene sequence analysis indicated that SR 2-06T was related most closely to Filimonas lacunae YT21T of the family Chitinophagaceae at a sequence similarity of 96.90 %, while levels of similarity to other related taxa were less than 93.08 %. Strain SR 2-06T exhibited similar features to F. lacunae in that it contained MK-7 as the major respiratory quinone, and iso-C15 : 1 G, iso-C15 : 0 and a summed feature consisting of C16 : 1ω6c and/or C16 : 1ω7c as the major fatty acids. However, strain SR 2-06T was distinguished from F. lacunae using a combination of physiological and biochemical properties. The cellular polar lipids were phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids, an unknown phospholipid and unidentified polar lipids. The DNA G+C content was 46.0 mol%. The phenotypic and phylogenetic evidence clearly indicates that strain SR 2-06T represents a novel species of the genus Filimonas, for which the name Filimonas endophytica sp. nov. is proposed. The type strain is SR 2-06T ( = KCTC 42060T = JCM 19844T).

Synthetic cannabinoids: In silico prediction of the cannabinoid receptor 1 affinity by a quantitative structure-activity relationship model.

PubMed

Paulke, Alexander; Proschak, Ewgenij; Sommer, Kai; Achenbach, Janosch; Wunder, Cora; Toennes, Stefan W

2016-03-14

The number of new synthetic psychoactive compounds increase steadily. Among the group of these psychoactive compounds, the synthetic cannabinoids (SCBs) are most popular and serve as a substitute of herbal cannabis. More than 600 of these substances already exist. For some SCBs the in vitro cannabinoid receptor 1 (CB1) affinity is known, but for the majority it is unknown. A quantitative structure-activity relationship (QSAR) model was developed, which allows the determination of the SCBs affinity to CB1 (expressed as binding constant (Ki)) without reference substances. The chemically advance template search descriptor was used for vector representation of the compound structures. The similarity between two molecules was calculated using the Feature-Pair Distribution Similarity. The Ki values were calculated using the Inverse Distance Weighting method. The prediction model was validated using a cross validation procedure. The predicted Ki values of some new SCBs were in a range between 20 (considerably higher affinity to CB1 than THC) to 468 (considerably lower affinity to CB1 than THC). The present QSAR model can serve as a simple, fast and cheap tool to get a first hint of the biological activity of new synthetic cannabinoids or of other new psychoactive compounds. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Mammalian translation elongation factor eEF1A2: X-ray structure and new features of GDP/GTP exchange mechanism in higher eukaryotes.

PubMed

Crepin, Thibaut; Shalak, Vyacheslav F; Yaremchuk, Anna D; Vlasenko, Dmytro O; McCarthy, Andrew; Negrutskii, Boris S; Tukalo, Michail A; El'skaya, Anna V

2014-11-10

Eukaryotic elongation factor eEF1A transits between the GTP- and GDP-bound conformations during the ribosomal polypeptide chain elongation. eEF1A*GTP establishes a complex with the aminoacyl-tRNA in the A site of the 80S ribosome. Correct codon-anticodon recognition triggers GTP hydrolysis, with subsequent dissociation of eEF1A*GDP from the ribosome. The structures of both the 'GTP'- and 'GDP'-bound conformations of eEF1A are unknown. Thus, the eEF1A-related ribosomal mechanisms were anticipated only by analogy with the bacterial homolog EF-Tu. Here, we report the first crystal structure of the mammalian eEF1A2*GDP complex which indicates major differences in the organization of the nucleotide-binding domain and intramolecular movements of eEF1A compared to EF-Tu. Our results explain the nucleotide exchange mechanism in the mammalian eEF1A and suggest that the first step of eEF1A*GDP dissociation from the 80S ribosome is the rotation of the nucleotide-binding domain observed after GTP hydrolysis. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Reversible Nerve Conduction Block Using Kilohertz Frequency Alternating Current

PubMed Central

Kilgore, Kevin L.; Bhadra, Niloy

2013-01-01

Objectives The features and clinical applications of balanced-charge kilohertz frequency alternating currents (KHFAC) are reviewed. Preclinical studies of KHFAC block have demonstrated that it can produce an extremely rapid and reversible block of nerve conduction. Recent systematic analysis and experimentation utilizing KHFAC block has resulted in a significant increase in interest in KHFAC block, both scientifically and clinically. Materials and Methods We review the history and characteristics of KHFAC block, the methods used to investigate this type of block, the experimental evaluation of block, and the electrical parameters and electrode designs needed to achieve successful block. We then analyze the existing clinical applications of high frequency currents, comparing the early results with the known features of KHFAC block. Results Although many features of KHFAC block have been characterized, there is still much that is unknown regarding the response of neural structures to rapidly fluctuating electrical fields. The clinical reports to date do not provide sufficient information to properly evaluate the mechanisms that result in successful or unsuccessful treatment. Conclusions KHFAC nerve block has significant potential as a means of controlling nerve activity for the purpose of treating disease. However, early clinical studies in the use of high frequency currents for the treatment of pain have not been designed to elucidate mechanisms or allow direct comparisons to preclinical data. We strongly encourage the careful reporting of the parameters utilized in these clinical studies, as well as the development of outcome measures that could illuminate the mechanisms of this modality. PMID:23924075

Hashimoto thyroiditis: clinical and diagnostic criteria.

PubMed

Caturegli, P; De Remigis, A; Rose, N R

2014-01-01

Hashimoto thyroiditis (HT), now considered the most common autoimmune disease, was described over a century ago as a pronounced lymphoid goiter affecting predominantly women. In addition to this classic form, several other clinico-pathologic entities are now included under the term HT: fibrous variant, IgG4-related variant, juvenile form, Hashitoxicosis, and painless thyroiditis (sporadic or post-partum). All forms are characterized pathologically by the infiltration of hematopoietic mononuclear cells, mainly lymphocytes, in the interstitium among the thyroid follicles, although specific features can be recognized in each variant. Thyroid cells undergo atrophy or transform into a bolder type of follicular cell rich in mitochondria called Hürthle cell. Most HT forms ultimately evolve into hypothyroidism, although at presentation patients can be euthyroid or even hyperthyroid. The diagnosis of HT relies on the demonstration of circulating antibodies to thyroid antigens (mainly thyroperoxidase and thyroglobulin) and reduced echogenicity on thyroid sonogram in a patient with proper clinical features. The treatment remains symptomatic and based on the administration of synthetic thyroid hormones to correct the hypothyroidism as needed. Surgery is performed when the goiter is large enough to cause significant compression of the surrounding cervical structures, or when some areas of the thyroid gland mimic the features of a nodule whose cytology cannot be ascertained as benign. HT remains a complex and ever expanding disease of unknown pathogenesis that awaits prevention or novel forms of treatment. Copyright © 2014 Elsevier B.V. All rights reserved.

Dissolution-Enlarged Fractures Imaging Using Electrical Resistivity Tomography (ERT)

NASA Astrophysics Data System (ADS)

Siami-Irdemoosa, Elnaz

In recent years the electrical imaging techniques have been largely applied to geotechnical and environmental investigations. These techniques have proven to be the best geophysical methods for site investigations in karst terrain, particularly when the overburden soil is clay-dominated. Karst is terrain with a special landscape and distinctive hydrological system developed by dissolution of rocks, particularly carbonate rocks such as limestone and dolomite, made by enlarging fractures into underground conduits that can enlarge into caverns, and in some cases collapse to form sinkholes. Bedding planes, joints, and faults are the principal structural guides for underground flow and dissolution in almost all karstified rocks. Despite the important role of fractures in karst development, the geometry of dissolution-enlarged fractures remain poorly unknown. These features are characterized by an strong contrast with the surrounding formations in terms of physical properties, such as electrical resistivity. Electrical resistivity tomography (ERT) was used as the primary geophysical tool to image the subsurface in a karst terrain in Greene County, Missouri. Pattern, orientation and density of the joint sets were interpreted from ERT data in the investigation site. The Multi-channel Analysis of Surface Wave (MASW) method and coring were employed to validate the interpretation results. Two sets of orthogonal visually prominent joints have been identified in the investigation site: north-south trending joint sets and west-east trending joint sets. However, most of the visually prominent joint sets are associated with either cultural features that concentrate runoff, natural surface drainage features or natural surface drainage.

Effective Moment Feature Vectors for Protein Domain Structures

PubMed Central

Shi, Jian-Yu; Yiu, Siu-Ming; Zhang, Yan-Ning; Chin, Francis Yuk-Lun

2013-01-01

Imaging processing techniques have been shown to be useful in studying protein domain structures. The idea is to represent the pairwise distances of any two residues of the structure in a 2D distance matrix (DM). Features and/or submatrices are extracted from this DM to represent a domain. Existing approaches, however, may involve a large number of features (100–400) or complicated mathematical operations. Finding fewer but more effective features is always desirable. In this paper, based on some key observations on DMs, we are able to decompose a DM image into four basic binary images, each representing the structural characteristics of a fundamental secondary structure element (SSE) or a motif in the domain. Using the concept of moments in image processing, we further derive 45 structural features based on the four binary images. Together with 4 features extracted from the basic images, we represent the structure of a domain using 49 features. We show that our feature vectors can represent domain structures effectively in terms of the following. (1) We show a higher accuracy for domain classification. (2) We show a clear and consistent distribution of domains using our proposed structural vector space. (3) We are able to cluster the domains according to our moment features and demonstrate a relationship between structural variation and functional diversity. PMID:24391828

Enterocolic lymphocytic phlebitis: clinicopathologic features and review of the literature.

PubMed

Ngo, Nyethane; Chang, Fuju

2007-07-01

Enterocolic lymphocytic phlebitis (ELP) is a recently described entity and is of unknown etiology and pathogenesis. It is characterized by phlebitis of the bowel wall and mesentery, without arterial involvement or evidence of systemic vasculitis. The clinical presentation of ELP is varied, but it most commonly manifests with signs of an acute abdomen. Clinical, radiologic, and endoscopic findings are often conflicting and misdiagnosis is common as venous thrombosis is not suspected. The diagnosis of ELP is obtained histologically. There is a spectrum of histologic features associated with ELP, which includes lymphocytic phlebitis, necrotizing phlebitis, granulomatous phlebitis, and myointimal hyperplasia. Other features include venous thrombi and acute ischemic changes of the intestine. Surgical resection of the affected bowel is usually curative and recurrences are rare. The clinical and histopathologic features of ELP are reviewed.

The Intra-Americas Sea low-level jet: overview and future research.

PubMed

Amador, Jorge A

2008-12-01

A relevant climate feature of the Intra-Americas Sea (IAS) is the low-level jet (IALLJ) dominating the IAS circulation, both in summer and winter; and yet it is practically unknown with regard to its nature, structure, interactions with mid-latitude and tropical phenomena, and its role in regional weather and climate. This paper updates IALLJ current knowledge and its contribution to IAS circulation-precipitation patterns and presents recent findings about the IALLJ based on first in situ observations during Phase 3 of the Experimento Climático en las Albercas de Agua Cálida (ECAC), an international field campaign to study IALLJ dynamics during July 2001. Nonhydrostatic fifth-generation Pennsylvania State University National Center for Atmospheric Research Mesoscale Model (MM5) simulations were compared with observations and reanalysis. Large-scale circulation patterns of the IALLJ northern hemisphere summer and winter components suggest that trades, and so the IALLJ, are responding to land-ocean thermal contrasts during the summer season of each continent. The IALLJ is a natural component of the American monsoons as a result of the continent's approximate north-south land distribution. During warm (cold) El Niño-Southern Oscillation phases, winds associated with the IALLJ core (IALLJC) are stronger (weaker) than normal, so precipitation anomalies are positive (negative) in the western Caribbean near Central America and negative (positive) in the central IAS. During the ECAC Phase 3, strong surface winds associated with the IALLJ induced upwelling, cooling down the sea surface temperature by 1-2 degrees C. The atmospheric mixed layer height reached 1 km near the surface wind maximum below the IALLJC. Observations indicate that primary water vapor advection takes place in a shallow layer between the IALLJC and the ocean surface. Latent heat flux peaked below the IALLJC. Neither the reanalysis nor MM5 captured the observed thermodynamic and kinematic IALLJ structure. So far, IALLJ knowledge is based on either dynamically initialized data or simulations of global (regional) models, which implies that a more systematic and scientific approach is needed to improve it. The Intra-Americas Study of Climate Processes is a great regional opportunity to address trough field work, modeling, and process studies, many of the IALLJ unknown features.

Early Cambrian Pentamerous Cubozoan Embryos from South China

PubMed Central

Han, Jian; Kubota, Shin; Li, Guoxiang; Yao, Xiaoyong; Yang, Xiaoguang; Shu, Degan; Li, Yong; Kinoshita, Shunichi; Sasaki, Osamu; Komiya, Tsuyoshi; Yan, Gang

2013-01-01

Background Extant cubozoans are voracious predators characterized by their square shape, four evenly spaced outstretched tentacles and well-developed eyes. A few cubozoan fossils are known from the Middle Cambrian Marjum Formation of Utah and the well-known Carboniferous Mazon Creek Formation of Illinois. Undisputed cubozoan fossils were previously unknown from the early Cambrian; by that time probably all representatives of the living marine phyla, especially those of basal animals, should have evolved. Methods Microscopic fossils were recovered from a phosphatic limestone in the Lower Cambrian Kuanchuanpu Formation of South China using traditional acetic-acid maceration. Seven of the pre-hatched pentamerous cubozoan embryos, each of which bears five pairs of subumbrellar tentacle buds, were analyzed in detail through computed microtomography (Micro-CT) and scanning electron microscopy (SEM) without coating. Results The figured microscopic fossils are unequivocal pre-hatching embryos based on their spherical fertilization envelope and the enclosed soft-tissue that has preserved key anatomical features arranged in perfect pentaradial symmetry, allowing detailed comparison with modern cnidarians, especially medusozoans. A combination of features, such as the claustrum, gonad-lamella, suspensorium and velarium suspended by the frenula, occur exclusively in the gastrovascular system of extant cubozoans, indicating a cubozoan affinity for these fossils. Additionally, the interior anatomy of these embryonic cubozoan fossils unprecedentedly exhibits the development of many new septum-derived lamellae and well-partitioned gastric pockets unknown in living cubozoans, implying that ancestral cubozoans had already evolved highly specialized structures displaying unexpected complexity at the dawn of the Cambrian. The well-developed endodermic lamellae and gastric pockets developed in the late embryonic stages of these cubozoan fossils are comparable with extant pelagic juvenile cubomedusae rather than sessile cubopolyps, whcih indicates a direct development in these fossil taxa, lacking characteristic stages of a typical cnidarian metagenesis such as planktonic planula and sessile polyps. PMID:23950993

Trispyrazolylborate Complexes: An Advanced Synthesis Experiment Using Paramagnetic NMR, Variable-Temperature NMR, and EPR Spectroscopies

ERIC Educational Resources Information Center

Abell, Timothy N.; McCarrick, Robert M.; Bretz, Stacey Lowery; Tierney, David L.

2017-01-01

A structured inquiry experiment for inorganic synthesis has been developed to introduce undergraduate students to advanced spectroscopic techniques including paramagnetic nuclear magnetic resonance and electron paramagnetic resonance. Students synthesize multiple complexes with unknown first row transition metals and identify the unknown metals by…

389. J.H.E., Delineator Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF ...

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

389. J.H.E., Delineator Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; WEST BAY CROSSING; SUSPENDED STRUCTURE; TYPICAL DETAILS; DRG. NO. 42 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

ShiftNMFk 1.2

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

Alexandrov, Boian S.; Vesselinov, Velimir V.; Stanev, Valentin

The ShiftNMFk1.2 code, or as we call it, GreenNMFk, represents a hybrid algorithm combining unsupervised adaptive machine learning and Green's function inverse method. GreenNMFk allows an efficient and high performance de-mixing and feature extraction of a multitude of nonnegative signals that change their shape propagating through the medium. The signals are mixed and recorded by a network of uncorrelated sensors. The code couples Non-negative Matrix Factorization (NMF) and inverse-analysis Green's functions method. GreenNMF synergistically performs decomposition of the recorded mixtures, finds the number of the unknown sources and uses the Green's function of the governing partial differential equation to identifymore » the unknown sources and their charecteristics. GreenNMF can be applied directly to any problem controlled by a known partial-differential parabolic equation where mixtures of an unknown number of sources are measured at multiple locations. Full GreenNMFk method is a subject LANL U.S. Patent application S133364.000 August, 2017. The ShiftNMFk 1.2 version here is a toy version of this method that can work with a limited number of unknown sources (4 or less).« less

Computational and Experimental Characterization of Ribosomal DNA and RNA G-Quadruplexes

NASA Astrophysics Data System (ADS)

Cho, Samuel

DNA G-quadruplexes in human telomeres and gene promoters are being extensively studied for their role in controlling the growth of cancer cells. Recent studies strongly suggest that guanine (G)-rich genes encoding pre-ribosomal RNA (pre-rRNA) are a potential anticancer target through the inhibition of RNA polymerase I (Pol I) in ribosome biogenesis. However, the structures of ribosomal G-quadruplexes at atomic resolution are unknown, and very little biophysical characterization has been performed on them to date. Here, we have modeled two putative rDNA G-quadruplex structures, NUC 19P and NUC 23P, which we observe via circular dichroism (CD) spectroscopy to adopt a predominantly parallel topology, and their counterpart rRNA. To validate and refine the putative ribosomal G-quadruplex structures, we performed all-atom molecular dynamics (MD) simulations using the CHARMM36 force field in the presence and absence of stabilizing K + or Na + ions. We optimized the CHARMM36 force field K + parameters to be more consistent with quantum mechanical calculations (and the polarizable Drude model force field) so that the K + ion is predominantly in the G-quadruplex channel. Our MD simulations show that the rDNA G-quadruplex have more well-defined, predominantly parallel-topology structures than rRNA and NUC 19P is more structured than NUC 23P, which features extended loops. Our study demonstrates that they are both potential targets for the design of novel chemotherapeutics.

Structural basis for the initiation of eukaryotic transcription-coupled DNA repair.

PubMed

Xu, Jun; Lahiri, Indrajit; Wang, Wei; Wier, Adam; Cianfrocco, Michael A; Chong, Jenny; Hare, Alissa A; Dervan, Peter B; DiMaio, Frank; Leschziner, Andres E; Wang, Dong

2017-11-30

Eukaryotic transcription-coupled repair (TCR) is an important and well-conserved sub-pathway of nucleotide excision repair that preferentially removes DNA lesions from the template strand that block translocation of RNA polymerase II (Pol II). Cockayne syndrome group B (CSB, also known as ERCC6) protein in humans (or its yeast orthologues, Rad26 in Saccharomyces cerevisiae and Rhp26 in Schizosaccharomyces pombe) is among the first proteins to be recruited to the lesion-arrested Pol II during the initiation of eukaryotic TCR. Mutations in CSB are associated with the autosomal-recessive neurological disorder Cockayne syndrome, which is characterized by progeriod features, growth failure and photosensitivity. The molecular mechanism of eukaryotic TCR initiation remains unclear, with several long-standing unanswered questions. How cells distinguish DNA lesion-arrested Pol II from other forms of arrested Pol II, the role of CSB in TCR initiation, and how CSB interacts with the arrested Pol II complex are all unknown. The lack of structures of CSB or the Pol II-CSB complex has hindered our ability to address these questions. Here we report the structure of the S. cerevisiae Pol II-Rad26 complex solved by cryo-electron microscopy. The structure reveals that Rad26 binds to the DNA upstream of Pol II, where it markedly alters its path. Our structural and functional data suggest that the conserved Swi2/Snf2-family core ATPase domain promotes the forward movement of Pol II, and elucidate key roles for Rad26 in both TCR and transcription elongation.

Crystal structure of a feruloyl esterase belonging to the tannase family: a disulfide bond near a catalytic triad.

PubMed

Suzuki, Kentaro; Hori, Akane; Kawamoto, Kazusa; Thangudu, Ratna Rajesh; Ishida, Takuya; Igarashi, Kiyohiko; Samejima, Masahiro; Yamada, Chihaya; Arakawa, Takatoshi; Wakagi, Takayoshi; Koseki, Takuya; Fushinobu, Shinya

2014-10-01

Feruloyl esterase (FAE) catalyzes the hydrolysis of the ferulic and diferulic acids present in plant cell wall polysaccharides, and tannase catalyzes the hydrolysis of tannins to release gallic acid. The fungal tannase family in the ESTHER database contains various enzymes, including FAEs and tannases. Despite the importance of FAEs and tannases in bioindustrial applications, three-dimensional structures of the fungal tannase family members have been unknown. Here, we determined the crystal structure of FAE B from Aspergillus oryzae (AoFaeB), which belongs to the fungal tannase family, at 1.5 Å resolution. AoFaeB consists of a catalytic α/β-hydrolase fold domain and a large lid domain, and the latter has a novel fold. To estimate probable binding models of substrates in AoFaeB, an automated docking analysis was performed. In the active site pocket of AoFaeB, residues responsible for the substrate specificity of the FAE activity were identified. The catalytic triad of AoFaeB comprises Ser203, Asp417, and His457, and the serine and histidine residues are directly connected by a disulfide bond of the neighboring cysteine residues, Cys202 and Cys458. This structural feature, the "CS-D-HC motif," is unprecedented in serine hydrolases. A mutational analysis indicated that the novel structural motif plays essential roles in the function of the active site. © 2014 Wiley Periodicals, Inc.

Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation

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

Xiao, Xiao; Yang, Hanjing; Arutiunian, Vagan

The catalytic activity of human cytidine deaminase APOBEC3B (A3B) has been correlated with kataegic mutational patterns within multiple cancer types. The molecular basis of how the N-terminal non-catalytic CD1 regulates the catalytic activity and consequently, biological function of A3B remains relatively unknown. Here, we report the crystal structure of a soluble human A3B-CD1 variant and delineate several structural elements of CD1 involved in molecular assembly, nucleic acid interactions and catalytic regulation of A3B. We show that (i) A3B expressed in human cells exists in hypoactive high-molecular-weight (HMW) complexes, which can be activated without apparent dissociation into low-molecular-weight (LMW) species aftermore » RNase A treatment. (ii) Multiple surface hydrophobic residues of CD1 mediate the HMW complex assembly and affect the catalytic activity, including one tryptophan residue W127 that likely acts through regulating nucleic acid binding. (iii) One of the highly positively charged surfaces on CD1 is involved in RNA-dependent attenuation of A3B catalysis. (iv) Surface hydrophobic residues of CD1 are involved in heterogeneous nuclear ribonucleoproteins (hnRNPs) binding to A3B. The structural and biochemical insights described here suggest that unique structural features on CD1 regulate the molecular assembly and catalytic activity of A3B through distinct mechanisms.« less

Abnormalities in the structural covariance of emotion regulation networks in major depressive disorder.

PubMed

Wu, Huawang; Sun, Hui; Wang, Chao; Yu, Lin; Li, Yilan; Peng, Hongjun; Lu, Xiaobing; Hu, Qingmao; Ning, Yuping; Jiang, Tianzi; Xu, Jinping; Wang, Jiaojian

2017-01-01

Major depressive disorder (MDD) is a common psychiatric disorder that is characterized by cognitive deficits and affective symptoms. To date, an increasing number of neuroimaging studies have focused on emotion regulation and have consistently shown that emotion dysregulation is one of the central features and underlying mechanisms of MDD. Although gray matter morphological abnormalities in regions within emotion regulation networks have been identified in MDD, the interactions and relationships between these gray matter structures remain largely unknown. Thus, in this study, we adopted a structural covariance method based on gray matter volume to investigate the brain morphological abnormalities within the emotion regulation networks in a large cohort of 65 MDD patients and 65 age- and gender-matched healthy controls. A permutation test with p < 0.05 was used to identify the significant changes in covariance connectivity strengths between MDD patients and healthy controls. The structural covariance analysis revealed an increased correlation strength of gray matter volume between the left angular gyrus and the left amygdala and between the right angular gyrus and the right amygdala, as well as a decreased correlation strength of the gray matter volume between the right angular gyrus and the posterior cingulate cortex in MDD. Our findings support the notion that emotion dysregulation is an underlying mechanism of MDD by revealing disrupted structural covariance patterns in the emotion regulation network. Copyright © 2016 Elsevier Ltd. All rights reserved.

The structure of Medicago truncatula δ 1-pyrroline-5-carboxylate reductase provides new insights into regulation of proline biosynthesis in plants

DOE PAGES

Ruszkowski, Milosz; Nocek, Boguslaw; Forlani, Giuseppe; ...

2015-10-30

The two pathways for proline biosynthesis in higher plants share the last step, the conversion of δ 1-pyrroline-5-carboxylate (P5C) to L-proline, which is catalyzed by P5C reductase (P5CR, EC 1.5.1.2) with the use of NAD(P)H as a coenzyme. There is increasing amount of evidence to suggest a complex regulation of P5CR activity at the post-translational level, yet the molecular basis of these mechanisms is unknown. Here we report the three-dimensional structure of the P5CR enzyme from the model legume Medicago truncatula (Mt). The crystal structures of unliganded MtP5CR decamer, and its complexes with the products NAD +, NADP +, andmore » L-proline were refined using x-ray diffraction data (at 1.7, 1.85, 1.95, and 2.1 Å resolution, respectively). Based on the presented structural data, the coenzyme preference for NADPH over NADH was explained, and NADPH is suggested to be the only coenzyme used by MtP5CR in vivo. Moreover, the insensitivity of MtP5CR to feed-back inhibition by proline, revealed by enzymatic analysis, was correlated with structural features. Additionally, a mechanism for the modulation of enzyme activity by chloride anions is discussed, as well as the rationale for the possible development of effective enzyme inhibitors.« less

The structure of the cysteine protease and lectin-like domains of Cwp84, a surface layer-associated protein from Clostridium difficile

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

Bradshaw, William J.; Public Health England, Porton Down, Salisbury SP4 0JG; Kirby, Jonathan M.

2014-07-01

The crystal structure of Cwp84, an S-layer protein from Clostridium difficile is presented for the first time. The cathepsin L-like fold of cysteine protease domain, a newly observed ‘lectin-like’ domain and several other features are described. Clostridium difficile is a major problem as an aetiological agent for antibiotic-associated diarrhoea. The mechanism by which the bacterium colonizes the gut during infection is poorly understood, but undoubtedly involves a myriad of components present on the bacterial surface. The mechanism of C. difficile surface-layer (S-layer) biogenesis is also largely unknown but involves the post-translational cleavage of a single polypeptide (surface-layer protein A; SlpA)more » into low- and high-molecular-weight subunits by Cwp84, a surface-located cysteine protease. Here, the first crystal structure of the surface protein Cwp84 is described at 1.4 Å resolution and the key structural components are identified. The truncated Cwp84 active-site mutant (amino-acid residues 33–497; C116A) exhibits three regions: a cleavable propeptide and a cysteine protease domain which exhibits a cathepsin L-like fold followed by a newly identified putative carbohydrate-binding domain with a bound calcium ion, which is referred to here as a lectin-like domain. This study thus provides the first structural insights into Cwp84 and a strong base to elucidate its role in the C. difficile S-layer maturation mechanism.« less

Semi-Supervised Clustering for High-Dimensional and Sparse Features

ERIC Educational Resources Information Center

Yan, Su

2010-01-01

Clustering is one of the most common data mining tasks, used frequently for data organization and analysis in various application domains. Traditional machine learning approaches to clustering are fully automated and unsupervised where class labels are unknown a priori. In real application domains, however, some "weak" form of side…

Attenuated Auditory Event-Related Potentials and Associations with Atypical Sensory Response Patterns in Children with Autism

ERIC Educational Resources Information Center

Donkers, Franc C. L.; Schipul, Sarah E.; Baranek, Grace T.; Cleary, Katherine M.; Willoughby, Michael T.; Evans, Anna M.; Bulluck, John C.; Lovmo, Jeanne E.; Belger, Aysenil

2015-01-01

Neurobiological underpinnings of unusual sensory features in individuals with autism are unknown. Event-related potentials elicited by task-irrelevant sounds were used to elucidate neural correlates of auditory processing and associations with three common sensory response patterns (hyperresponsiveness; hyporesponsiveness; sensory seeking).…

Socioeconomic Status and Executive Function: Developmental Trajectories and Mediation

ERIC Educational Resources Information Center

Hackman, Daniel A.; Gallop, Robert; Evans, Gary W.; Farah, Martha J.

2015-01-01

Childhood socioeconomic status (SES) predicts executive function (EF), but fundamental aspects of this relation remain unknown: the developmental course of the SES disparity, its continued sensitivity to SES changes during that course, and the features of childhood experience responsible for the SES-EF relation. Regarding course, early disparities…

Identification and characterization of neutrophil extracellular trap shapes in flow cytometry

NASA Astrophysics Data System (ADS)

Ginley, Brandon; Emmons, Tiffany; Sasankan, Prabhu; Urban, Constantin; Segal, Brahm H.; Sarder, Pinaki

2017-03-01

Neutrophil extracellular trap (NET) formation is an alternate immunologic weapon used mainly by neutrophils. Chromatin backbones fused with proteins derived from granules are shot like projectiles onto foreign invaders. It is thought that this mechanism is highly anti-microbial, aids in preventing bacterial dissemination, is used to break down structures several sizes larger than neutrophils themselves, and may have several more uses yet unknown. NETs have been implied to be involved in a wide array of systemic host immune defenses, including sepsis, autoimmune diseases, and cancer. Existing methods used to visually quantify NETotic versus non-NETotic shapes are extremely time-consuming and subject to user bias. These limitations are obstacles to developing NETs as prognostic biomarkers and therapeutic targets. We propose an automated pipeline for quantitatively detecting neutrophil and NET shapes captured using a flow cytometry-imaging system. Our method uses contrast limited adaptive histogram equalization to improve signal intensity in dimly illuminated NETs. From the contrast improved image, fixed value thresholding is applied to convert the image to binary. Feature extraction is performed on the resulting binary image, by calculating region properties of the resulting foreground structures. Classification of the resulting features is performed using Support Vector Machine. Our method classifies NETs from neutrophils without traps at 0.97/0.96 sensitivity/specificity on n = 387 images, and is 1500X faster than manual classification, per sample. Our method can be extended to rapidly analyze whole-slide immunofluorescence tissue images for NET classification, and has potential to streamline the quantification of NETs for patients with diseases associated with cancer and autoimmunity.

Testing the role of bedforms as controls on the morphodynamics of sandy braided rivers with CFD

NASA Astrophysics Data System (ADS)

Unsworth, C. A.; Nicholas, A. P.; Ashworth, P. J.; Best, J.; Lane, S. N.; Parsons, D. R.; Sambrook Smith, G.; Simpson, C.; Strick, R. J. P.

2017-12-01

Sand-bed rivers are characterised by multiple scales of topography (e.g., channels, bars and bedforms). Small scale topographic features (e.g., dunes) exert a significant influence on coherent flow structures and sediment transport processes, over distances that scale with channel depth. However, the extent to which such dune-scale effects control larger, channel and bar-scale morphology and morphodynamics remains unknown. Moreover, such bedform effects are typically neglected in two-dimensional (depth-averaged) morphodynamic models that are used to simulate river evolution. To evaluate the significance of these issues, we report results from a combined numerical modelling and field monitoring study, undertaken in the South Saskatchewan River, Canada. Numerical simulations were carried out, using the OpenFOAM CFD code, to quantify the mean three-dimensional flow structure within a 90 x 350 m section of channel. To isolate the role of bedforms as a control on flow and sediment transport, two simulations were undertaken. The first used a high-resolution ( 3 cm) bedform-resolving DEM. The second used a filtered DEM in which dunes were removed and only large scale topographic features (e.g., bars, scour pools etc) were resolved. The results of these simulations are compared here, in order to quantify the degree to which topographic steering by bedforms influences flow and sediment transport directions at bar and channel scales. Analysis of the CFD simulation results within a 2D morphodynamic modelling framework demonstrates that dunes exert a significant influence on sediment transport, and hence morphodynamics, and highlights important shortcomings in existing 2D model parameterisations of topographic steering.

Moving force identification based on redundant concatenated dictionary and weighted l1-norm regularization

NASA Astrophysics Data System (ADS)

Pan, Chu-Dong; Yu, Ling; Liu, Huan-Lin; Chen, Ze-Peng; Luo, Wen-Feng

2018-01-01

Moving force identification (MFI) is an important inverse problem in the field of bridge structural health monitoring (SHM). Reasonable signal structures of moving forces are rarely considered in the existing MFI methods. Interaction forces are complex because they contain both slowly-varying harmonic and impact signals due to bridge vibration and bumps on a bridge deck, respectively. Therefore, the interaction forces are usually hard to be expressed completely and sparsely by using a single basis function set. Based on the redundant concatenated dictionary and weighted l1-norm regularization method, a hybrid method is proposed for MFI in this study. The redundant dictionary consists of both trigonometric functions and rectangular functions used for matching the harmonic and impact signal features of unknown moving forces. The weighted l1-norm regularization method is introduced for formulation of MFI equation, so that the signal features of moving forces can be accurately extracted. The fast iterative shrinkage-thresholding algorithm (FISTA) is used for solving the MFI problem. The optimal regularization parameter is appropriately chosen by the Bayesian information criterion (BIC) method. In order to assess the accuracy and the feasibility of the proposed method, a simply-supported beam bridge subjected to a moving force is taken as an example for numerical simulations. Finally, a series of experimental studies on MFI of a steel beam are performed in laboratory. Both numerical and experimental results show that the proposed method can accurately identify the moving forces with a strong robustness, and it has a better performance than the Tikhonov regularization method. Some related issues are discussed as well.

Structural features based genome-wide characterization and prediction of nucleosome organization

PubMed Central

2012-01-01

Background Nucleosome distribution along chromatin dictates genomic DNA accessibility and thus profoundly influences gene expression. However, the underlying mechanism of nucleosome formation remains elusive. Here, taking a structural perspective, we systematically explored nucleosome formation potential of genomic sequences and the effect on chromatin organization and gene expression in S. cerevisiae. Results We analyzed twelve structural features related to flexibility, curvature and energy of DNA sequences. The results showed that some structural features such as DNA denaturation, DNA-bending stiffness, Stacking energy, Z-DNA, Propeller twist and free energy, were highly correlated with in vitro and in vivo nucleosome occupancy. Specifically, they can be classified into two classes, one positively and the other negatively correlated with nucleosome occupancy. These two kinds of structural features facilitated nucleosome binding in centromere regions and repressed nucleosome formation in the promoter regions of protein-coding genes to mediate transcriptional regulation. Based on these analyses, we integrated all twelve structural features in a model to predict more accurately nucleosome occupancy in vivo than the existing methods that mainly depend on sequence compositional features. Furthermore, we developed a novel approach, named DLaNe, that located nucleosomes by detecting peaks of structural profiles, and built a meta predictor to integrate information from different structural features. As a comparison, we also constructed a hidden Markov model (HMM) to locate nucleosomes based on the profiles of these structural features. The result showed that the meta DLaNe and HMM-based method performed better than the existing methods, demonstrating the power of these structural features in predicting nucleosome positions. Conclusions Our analysis revealed that DNA structures significantly contribute to nucleosome organization and influence chromatin structure and gene expression regulation. The results indicated that our proposed methods are effective in predicting nucleosome occupancy and positions and that these structural features are highly predictive of nucleosome organization. The implementation of our DLaNe method based on structural features is available online. PMID:22449207

Location-Unbound Color-Shape Binding Representations in Visual Working Memory.

PubMed

Saiki, Jun

2016-02-01

The mechanism by which nonspatial features, such as color and shape, are bound in visual working memory, and the role of those features' location in their binding, remains unknown. In the current study, I modified a redundancy-gain paradigm to investigate these issues. A set of features was presented in a two-object memory display, followed by a single object probe. Participants judged whether the probe contained any features of the memory display, regardless of its location. Response time distributions revealed feature coactivation only when both features of a single object in the memory display appeared together in the probe, regardless of the response time benefit from the probe and memory objects sharing the same location. This finding suggests that a shared location is necessary in the formation of bound representations but unnecessary in their maintenance. Electroencephalography data showed that amplitude modulations reflecting location-unbound feature coactivation were different from those reflecting the location-sharing benefit, consistent with the behavioral finding that feature-location binding is unnecessary in the maintenance of color-shape binding. © The Author(s) 2015.

Feature-to-Feature Inference Under Conditions of Cue Restriction and Dimensional Correlation.

PubMed

Lancaster, Matthew E; Homa, Donald

2017-01-01

The present study explored feature-to-feature and label-to-feature inference in a category task for different category structures. In the correlated condition, each of the 4 dimensions comprising the category was positively correlated to each other and to the category label. In the uncorrelated condition, no correlation existed between the 4 dimensions comprising the category, although the dimension to category label correlation matched that of the correlated condition. After learning, participants made inference judgments of a missing feature, given 1, 2, or 3 feature cues; on half the trials, the category label was also included as a cue. The results showed superior inference of features following training on the correlated structure, with accurate inference when only a single feature was presented. In contrast, a single-feature cue resulted in chance levels of inference for the uncorrelated structure. Feature inference systematically improved with number of cues after training on the correlated structure. Surprisingly, a similar outcome was obtained for the uncorrelated structure, an outcome that must have reflected mediation via the category label. A descriptive model is briefly introduced to explain the results, with a suggestion that this paradigm might be profitably extended to hierarchical structures where the levels of feature-to-feature inference might vary with the depth of the hierarchy.

Novel chromatin texture features for the classification of pap smears

NASA Astrophysics Data System (ADS)

Bejnordi, Babak E.; Moshavegh, Ramin; Sujathan, K.; Malm, Patrik; Bengtsson, Ewert; Mehnert, Andrew

2013-03-01

This paper presents a set of novel structural texture features for quantifying nuclear chromatin patterns in cells on a conventional Pap smear. The features are derived from an initial segmentation of the chromatin into bloblike texture primitives. The results of a comprehensive feature selection experiment, including the set of proposed structural texture features and a range of different cytology features drawn from the literature, show that two of the four top ranking features are structural texture features. They also show that a combination of structural and conventional features yields a classification performance of 0.954±0.019 (AUC±SE) for the discrimination of normal (NILM) and abnormal (LSIL and HSIL) slides. The results of a second classification experiment, using only normal-appearing cells from both normal and abnormal slides, demonstrates that a single structural texture feature measuring chromatin margination yields a classification performance of 0.815±0.019. Overall the results demonstrate the efficacy of the proposed structural approach and that it is possible to detect malignancy associated changes (MACs) in Papanicoloau stain.

Geological and hydrogeological investigations in west Malaysia

NASA Technical Reports Server (NTRS)

Ahmad, J. B. (Principal Investigator); Khoon, S. Y.

1977-01-01

The author has identified the following significant results. Large structures along the east coast of the peninsula were discovered. Of particular significance were the circular structures which were believed to be associated with mineralization and whose existence was unknown. The distribution of the younger sediments along the east coast appeared to be more widespread than previously indicated. Along the Pahang coast on the southern end, small traces of raised beach lines were noted up to six miles inland. The existence of these beach lines was unknown due to their isolation in large coastal swamps.

HyMoTrack: A Mobile AR Navigation System for Complex Indoor Environments.

PubMed

Gerstweiler, Georg; Vonach, Emanuel; Kaufmann, Hannes

2015-12-24

Navigating in unknown big indoor environments with static 2D maps is a challenge, especially when time is a critical factor. In order to provide a mobile assistant, capable of supporting people while navigating in indoor locations, an accurate and reliable localization system is required in almost every corner of the building. We present a solution to this problem through a hybrid tracking system specifically designed for complex indoor spaces, which runs on mobile devices like smartphones or tablets. The developed algorithm only uses the available sensors built into standard mobile devices, especially the inertial sensors and the RGB camera. The combination of multiple optical tracking technologies, such as 2D natural features and features of more complex three-dimensional structures guarantees the robustness of the system. All processing is done locally and no network connection is needed. State-of-the-art indoor tracking approaches use mainly radio-frequency signals like Wi-Fi or Bluetooth for localizing a user. In contrast to these approaches, the main advantage of the developed system is the capability of delivering a continuous 3D position and orientation of the mobile device with centimeter accuracy. This makes it usable for localization and 3D augmentation purposes, e.g. navigation tasks or location-based information visualization.

Congenital capillary proliferation of the kidney: a distinctive renal vascular lesion of childhood.

PubMed

Cajaiba, Mariana M; North, Paula E; Gong, Shunyou; Dickman, Paul S; Mroczek-Musulman, Elizabeth; Sauer, David A; Perlman, Elizabeth J

2017-08-01

Renal vascular lesions (RVL) are rare, and their morphological spectrum remains largely unknown, particularly in children. In this study, we characterize the clinicopathological features of RVL in a cohort of 12 children. Seven lesions were classified as previously recognized entities: vascular malformations (4), papillary endothelial hyperplasia (2), and pyogenic granuloma (lobular capillary hemangioma; 1). An eighth lesion showed nonspecific findings, which were interpreted as reactive during our review. The remaining 4 cases presented either prenatally, at birth, or shortly after birth and were morphologically similar. These were characterized by a peculiar pattern of capillary proliferation with entrapment of native renal structures, variable amounts of extramedullary hematopoiesis and reactive lymphocytes, foci of infarction and hemorrhage, and the presence of feeding and draining vessels at their periphery. To our knowledge, this represents a previously undescribed congenital vascular lesion involving the kidney, which we have descriptively and provisionally termed congenital capillary proliferation of the kidney (CCPK). While it is unclear whether CCPK represents a malformation or neoplastic proliferation, it shows overlapping features with congenital hemangioma of the liver (solitary congenital hepatic hemangioma) and congenital nonprogressive hemangioma (CNH) of the skin and soft tissue, suggesting a possible common pathogenesis among these 3 entities. Copyright © 2017 Elsevier Inc. All rights reserved.

Python and computer vision

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

Doak, J. E.; Prasad, Lakshman

2002-01-01

This paper discusses the use of Python in a computer vision (CV) project. We begin by providing background information on the specific approach to CV employed by the project. This includes a brief discussion of Constrained Delaunay Triangulation (CDT), the Chordal Axis Transform (CAT), shape feature extraction and syntactic characterization, and normalization of strings representing objects. (The terms 'object' and 'blob' are used interchangeably, both referring to an entity extracted from an image.) The rest of the paper focuses on the use of Python in three critical areas: (1) interactions with a MySQL database, (2) rapid prototyping of algorithms, andmore » (3) gluing together all components of the project including existing C and C++ modules. For (l), we provide a schema definition and discuss how the various tables interact to represent objects in the database as tree structures. (2) focuses on an algorithm to create a hierarchical representation of an object, given its string representation, and an algorithm to match unknown objects against objects in a database. And finally, (3) discusses the use of Boost Python to interact with the pre-existing C and C++ code that creates the CDTs and CATS, performs shape feature extraction and syntactic characterization, and normalizes object strings. The paper concludes with a vision of the future use of Python for the CV project.« less

HyMoTrack: A Mobile AR Navigation System for Complex Indoor Environments

PubMed Central

Gerstweiler, Georg; Vonach, Emanuel; Kaufmann, Hannes

2015-01-01

Navigating in unknown big indoor environments with static 2D maps is a challenge, especially when time is a critical factor. In order to provide a mobile assistant, capable of supporting people while navigating in indoor locations, an accurate and reliable localization system is required in almost every corner of the building. We present a solution to this problem through a hybrid tracking system specifically designed for complex indoor spaces, which runs on mobile devices like smartphones or tablets. The developed algorithm only uses the available sensors built into standard mobile devices, especially the inertial sensors and the RGB camera. The combination of multiple optical tracking technologies, such as 2D natural features and features of more complex three-dimensional structures guarantees the robustness of the system. All processing is done locally and no network connection is needed. State-of-the-art indoor tracking approaches use mainly radio-frequency signals like Wi-Fi or Bluetooth for localizing a user. In contrast to these approaches, the main advantage of the developed system is the capability of delivering a continuous 3D position and orientation of the mobile device with centimeter accuracy. This makes it usable for localization and 3D augmentation purposes, e.g. navigation tasks or location-based information visualization. PMID:26712755

PDZ Ligand Binding-Induced Conformational Coupling of the PDZ-SH3-GK Tandems in PSD-95 Family MAGUKs.

PubMed

Zeng, Menglong; Ye, Fei; Xu, Jia; Zhang, Mingjie

2018-01-05

Discs large (DLG) MAGUKs are abundantly expressed in glutamatergic synapses, crucial for synaptic transmission, and plasticity by anchoring various postsynaptic components including glutamate receptors, downstream scaffold proteins and signaling enzymes. Different DLG members have shared structures and functions, but also contain unique features. How DLG family proteins function individually and cooperatively is largely unknown. Here, we report that PSD-95 PDZ3 directly couples with SH3-GK tandem in a PDZ ligand binding-dependent manner, and the coupling can promote PSD-95 dimerization and multimerization. Aided by sortase-mediated protein ligation and selectively labeling, we elucidated the PDZ3/SH3-GK conformational coupling mechanism using NMR spectroscopy. We further demonstrated that PSD-93, but not SAP102, can also undergo PDZ3 ligand binding-induced conformational coupling with SH3-GK and form homo-oligomers. Interestingly, PSD-95 and PSD-93 can also form ligand binding-induced hetero-oligomers, suggesting a cooperative assembly mechanism for the mega-N-methyl-d-aspartate receptor synaptic signaling complex. Finally, we provide evidence showing that ligand binding-induced conformational coupling between PDZ and SH3-GK is a common feature for other MAGUKs including CASK and PALS1. Copyright © 2017 Elsevier Ltd. All rights reserved.

Morphological differences in the mirror neuron system in Williams syndrome.

PubMed

Ng, Rowena; Brown, Timothy T; Erhart, Matthew; Järvinen, Anna M; Korenberg, Julie R; Bellugi, Ursula; Halgren, Eric

2016-01-01

Williams syndrome (WS) is a genetic condition characterized by an overly gregarious personality, including high empathetic concern for others. Although seemingly disparate from the profile of autism spectrum disorder (ASD), both are associated with deficits in social communication/cognition. Notably, the mirror neuron system (MNS) has been implicated in social dysfunction for ASD; yet, the integrity of this network and its association with social functioning in WS remains unknown. Magnetic resonance imaging (MRI) methods were used to examine the structural integrity of the MNS of adults with WS versus typically developing (TD) individuals. The Social Responsiveness Scale (SRS), a tool typically used to screen for social features of ASD, was also employed to assess the relationships between social functioning with the MNS morphology in WS participants. WS individuals showed reduced cortical surface area of MNS substrates yet relatively preserved cortical thickness as compared to TD adults. Increased cortical thickness of the inferior parietal lobule (IPL) was associated with increased deficits in social communication, social awareness, social cognition, and autistic mannerisms. However, social motivation was not related to anatomical features of the MNS. Our findings indicate that social deficits typical to both ASD and WS may be attributed to an aberrant MNS, whereas the unusual social drive marked in WS is subserved by substrates distinct from this network.

A Hydrological Tomography Collocated with Time-varying Gravimetry for Hydrogeology -An Example in Yun-Lin Alluvial Plain and Ming-Ju Basin in Taiwan

NASA Astrophysics Data System (ADS)

Chen, K. H.; Cheng, C. C.; Hwang, C.

2016-12-01

A new inversion technique featured by the collocation of hydrological modeling and gravimetry observation is presented in this report. Initially this study started from a project attempting to build a sequence of hydrodynamic models of ground water system, which was applied to identify the supplement areas of alluvial plains and basins along the west coast of Taiwan. To calibrate the decent hydro-geological parameters for the modeling, geological evolution were carefully investigated and absolute gravity observations, along with other on-site hydrological monitoring data were specially introduced. It was discovered in the data processing that the time-varying gravimetrical data are highly sensitive to certain boundary conditions in the hydrodynamic model, which are correspondent with respective geological features. A new inversion technique coined by the term "hydrological tomography" is therefore developed by reversing the boundary condition into the unknowns to be solved. An example of accurate estimate for water storage and precipitation infiltration of a costal alluvial plain Yun-Lin is presented. In the mean time, the study of an anticline structure of the upstream basin Ming-Ju is also presented to demonstrate how a geological formation is outlined when the gravimetrical data and hydrodynamic model are re-directed into an inversion.

Morphological differences in the mirror neuron system in Williams Syndrome

PubMed Central

Ng, Rowena; Brown, Timothy T.; Erhart, Matthew; Järvinen, Anna M.; Korenberg, Julie R.; Bellugi, Ursula; Halgren, Eric

2015-01-01

Williams syndrome (WS) is a genetic condition characterized by an overly gregarious personality, including high empathetic concern for others. Although seemingly disparate from the profile of autism spectrum disorder (ASD), both are associated with deficits in social communication/cognition. Notably, the mirror neuron system (MNS) has been implicated in social dysfunction for ASD; yet, the integrity of this network and its association with social functioning in WS remains unknown. Magnetic resonance imaging methods were used to examine the structural integrity of the MNS of adults with WS versus typically developing (TD) individuals. The Social Responsiveness Scale (SRS), a tool typically used to screen for social features of ASD, was also employed to assess the relationships between social functioning with the MNS morphology in WS participants. WS individuals showed reduced cortical surface area of MNS substrates yet relatively preserved cortical thickness as compared to TD adults. Increased cortical thickness of the inferior parietal lobule was associated with increased deficits in social communication, social awareness, social cognition, and autistic mannerisms. However, social motivation was not related to anatomical features of the MNS. Our findings indicate that social deficits typical to both ASD and WS may be attributed to an aberrant MNS, whereas the unusual social drive marked in WS is subserved by substrates distinct from this network. PMID:26230578

Strategic Functionalization of Single Walled Carbon Nanotubes to Manipulate Their Electronic and Optical Properties

NASA Astrophysics Data System (ADS)

Gifford, Brendan Joel

Single-walled carbon nanotubes (SWCNTs) are unique materials that exhibit chirality-specific properties due to their one-dimensional confinement. As a result, they are explored for a wide range of applications including single-photon sources in communications devices. Despite progress in this area, SWCNTs still suffer from a relatively narrow range of energies of emission features that fall short of the 1500 nm desired for long-distance lossless data transfer. One approach that is frequently used to resolve this involves chemical functionalization with aryl groups. However, this approach is met with a number of fundamental issues. First, chirality-specific SWCNTs must be acquired for subsequent functionalization. Synthesis of such samples has thus far eluded experimental efforts. As such, post-synthetic non-covalent functionalization is required to break bundles and create disperse SWCNTs that can undergo further separation, processing, and functionalization. Second, a number of low-energy emission features are introduced upon functionalization across a 200 nm range. The origin of such diverse emission features remains unknown. The research presented here focuses on computationally addressing these issues. A series of polyfluorene polymers possessing sidechains of varying length are explored using molecular mechanics to determine the impact of alkyl sidechains on SWCNT-conjugated polymer interaction strength and morphology. Additionally, density functional theory (DFT) and linear-response time-dependent DFT (TDDFT) are used to explore the effect of functionalization on emission features. A prerequisite to these calculations involves constructing finite-length SWCNT systems with similar electronic structure to their infinite counterparts: a methodological approach for the formation of such systems is presented. The optical features for aryl-functionalized SWCNTs are then explored. It is shown that the predominant effect on the energies of emission features involves the configuration of functionalization, with the identity of the functional group only playing a minor role. While the qualitative effect of such functionalization is determined, a quantitative comparison to experiment requires correction for several sources of computational error. A model to correct for such effects is also developed. This research not only explains the origin of the multiple emission features in functionalized SWCNTs for the first time but also lays the groundwork for their further computational exploration.

Cloud structure of the nearest brown dwarfs. II: High-amplitude variability for Luhman 16 A and B in and out of the 0.99 μm FeH feature

DOE PAGES

Buenzli, Esther; Marley, Mark S.; Apai, Daniel; ...

2015-10-20

The re-emergence of the 0.99 μm FeH feature in brown dwarfs of early- to mid-T spectral type has been suggested as evidence for cloud disruption where flux from deep, hot regions below the Fe cloud deck can emerge. The same mechanism could account for color changes at the L/T transition and photometric variability. We present the first observations of spectroscopic variability of brown dwarfs covering the 0.99 μm FeH feature. We observed the spatially resolved very nearby brown dwarf binary WISE J104915.57–531906.1 (Luhman 16AB), a late-L and early-T dwarf, with Hubble Space Telescope/WFC3 in the G102 grism at 0.8–1.15 μm.more » We find significant variability at all wavelengths for both brown dwarfs, with peak-to-valley amplitudes of 9.3% for Luhman 16B and 4.5% for Luhman 16A. This represents the first unambiguous detection of variability in Luhman 16A. We estimate a rotational period between 4.5 and 5.5 hr, very similar to Luhman 16B. Variability in both components complicates the interpretation of spatially unresolved observations. The probability for finding large amplitude variability in any two brown dwarfs is less than 10%. Our finding may suggest that a common but yet unknown feature of the binary is important for the occurrence of variability. For both objects, the amplitude is nearly constant at all wavelengths except in the deep K i feature below 0.84 μm. No variations are seen across the 0.99 μm FeH feature. The observations lend strong further support to cloud height variations rather than holes in the silicate clouds, but cannot fully rule out holes in the iron clouds. Here, we re-evaluate the diagnostic potential of the FeH feature as a tracer of cloud patchiness.« less

A Set of Handwriting Features for Use in Automated Writer Identification.

PubMed

Miller, John J; Patterson, Robert Bradley; Gantz, Donald T; Saunders, Christopher P; Walch, Mark A; Buscaglia, JoAnn

2017-05-01

A writer's biometric identity can be characterized through the distribution of physical feature measurements ("writer's profile"); a graph-based system that facilitates the quantification of these features is described. To accomplish this quantification, handwriting is segmented into basic graphical forms ("graphemes"), which are "skeletonized" to yield the graphical topology of the handwritten segment. The graph-based matching algorithm compares the graphemes first by their graphical topology and then by their geometric features. Graphs derived from known writers can be compared against graphs extracted from unknown writings. The process is computationally intensive and relies heavily upon statistical pattern recognition algorithms. This article focuses on the quantification of these physical features and the construction of the associated pattern recognition methods for using the features to discriminate among writers. The graph-based system described in this article has been implemented in a highly accurate and approximately language-independent biometric recognition system of writers of cursive documents. © 2017 American Academy of Forensic Sciences.

Integrative and distinctive coding of visual and conceptual object features in the ventral visual stream

PubMed Central

Douglas, Danielle; Newsome, Rachel N; Man, Louisa LY

2018-01-01

A significant body of research in cognitive neuroscience is aimed at understanding how object concepts are represented in the human brain. However, it remains unknown whether and where the visual and abstract conceptual features that define an object concept are integrated. We addressed this issue by comparing the neural pattern similarities among object-evoked fMRI responses with behavior-based models that independently captured the visual and conceptual similarities among these stimuli. Our results revealed evidence for distinctive coding of visual features in lateral occipital cortex, and conceptual features in the temporal pole and parahippocampal cortex. By contrast, we found evidence for integrative coding of visual and conceptual object features in perirhinal cortex. The neuroanatomical specificity of this effect was highlighted by results from a searchlight analysis. Taken together, our findings suggest that perirhinal cortex uniquely supports the representation of fully specified object concepts through the integration of their visual and conceptual features. PMID:29393853

Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae.

PubMed

Shahbaaz, Mohd; Ahmad, Faizan; Imtaiyaz Hassan, Md

2015-06-01

Haemophilus influenzae is a small pleomorphic Gram-negative bacteria which causes several chronic diseases, including bacteremia, meningitis, cellulitis, epiglottitis, septic arthritis, pneumonia, and empyema. Here we extensively analyzed the sequenced genome of H. influenzae strain Rd KW20 using protein family databases, protein structure prediction, pathways and genome context methods to assign a precise function to proteins whose functions are unknown. These proteins are termed as hypothetical proteins (HPs), for which no experimental information is available. Function prediction of these proteins would surely be supportive to precisely understand the biochemical pathways and mechanism of pathogenesis of Haemophilus influenzae. During the extensive analysis of H. influenzae genome, we found the presence of eight HPs showing lyase activity. Subsequently, we modeled and analyzed three-dimensional structure of all these HPs to determine their functions more precisely. We found these HPs possess cystathionine-β-synthase, cyclase, carboxymuconolactone decarboxylase, pseudouridine synthase A and C, D-tagatose-1,6-bisphosphate aldolase and aminodeoxychorismate lyase-like features, indicating their corresponding functions in the H. influenzae. Lyases are actively involved in the regulation of biosynthesis of various hormones, metabolic pathways, signal transduction, and DNA repair. Lyases are also considered as a key player for various biological processes. These enzymes are critically essential for the survival and pathogenesis of H. influenzae and, therefore, these enzymes may be considered as a potential target for structure-based rational drug design. Our structure-function relationship analysis will be useful to search and design potential lead molecules based on the structure of these lyases, for drug design and discovery.

Structure-based function prediction of the expanding mollusk tyrosinase family

NASA Astrophysics Data System (ADS)

Huang, Ronglian; Li, Li; Zhang, Guofan

2017-11-01

Tyrosinase (Ty) is a common enzyme found in many different animal groups. In our previous study, genome sequencing revealed that the Ty family is expanded in the Pacific oyster ( Crassostrea gigas). Here, we examine the larger number of Ty family members in the Pacific oyster by high-level structure prediction to obtain more information about their function and evolution, especially the unknown role in biomineralization. We verified 12 Ty gene sequences from Crassostrea gigas genome and Pinctada fucata martensii transcriptome. By using phylogenetic analysis of these Tys with functionally known Tys from other molluscan species, eight subgroups were identified (CgTy_s1, CgTy_s2, MolTy_s1, MolTy-s2, MolTy-s3, PinTy-s1, PinTy-s2 and PviTy). Structural data and surface pockets of the dinuclear copper center in the eight subgroups of molluscan Ty were obtained using the latest versions of prediction online servers. Structural comparison with other Ty proteins from the protein databank revealed functionally important residues (HA1, HA2, HA3, HB1, HB2, HB3, Z1-Z9) and their location within these protein structures. The structural and chemical features of these pockets which may related to the substrate binding showed considerable variability among mollusks, which undoubtedly defines Ty substrate binding. Finally, we discuss the potential driving forces of Ty family evolution in mollusks. Based on these observations, we conclude that the Ty family has rapidly evolved as a consequence of substrate adaptation in mollusks.

Characterizing unknown systematics in large scale structure surveys

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

Agarwal, Nishant; Ho, Shirley; Myers, Adam D.

Photometric large scale structure (LSS) surveys probe the largest volumes in the Universe, but are inevitably limited by systematic uncertainties. Imperfect photometric calibration leads to biases in our measurements of the density fields of LSS tracers such as galaxies and quasars, and as a result in cosmological parameter estimation. Earlier studies have proposed using cross-correlations between different redshift slices or cross-correlations between different surveys to reduce the effects of such systematics. In this paper we develop a method to characterize unknown systematics. We demonstrate that while we do not have sufficient information to correct for unknown systematics in the data,more » we can obtain an estimate of their magnitude. We define a parameter to estimate contamination from unknown systematics using cross-correlations between different redshift slices and propose discarding bins in the angular power spectrum that lie outside a certain contamination tolerance level. We show that this method improves estimates of the bias using simulated data and further apply it to photometric luminous red galaxies in the Sloan Digital Sky Survey as a case study.« less

CHIMERA: Top-down model for hierarchical, overlapping and directed cluster structures in directed and weighted complex networks

NASA Astrophysics Data System (ADS)

Franke, R.

2016-11-01

In many networks discovered in biology, medicine, neuroscience and other disciplines special properties like a certain degree distribution and hierarchical cluster structure (also called communities) can be observed as general organizing principles. Detecting the cluster structure of an unknown network promises to identify functional subdivisions, hierarchy and interactions on a mesoscale. It is not trivial choosing an appropriate detection algorithm because there are multiple network, cluster and algorithmic properties to be considered. Edges can be weighted and/or directed, clusters overlap or build a hierarchy in several ways. Algorithms differ not only in runtime, memory requirements but also in allowed network and cluster properties. They are based on a specific definition of what a cluster is, too. On the one hand, a comprehensive network creation model is needed to build a large variety of benchmark networks with different reasonable structures to compare algorithms. On the other hand, if a cluster structure is already known, it is desirable to separate effects of this structure from other network properties. This can be done with null model networks that mimic an observed cluster structure to improve statistics on other network features. A third important application is the general study of properties in networks with different cluster structures, possibly evolving over time. Currently there are good benchmark and creation models available. But what is left is a precise sandbox model to build hierarchical, overlapping and directed clusters for undirected or directed, binary or weighted complex random networks on basis of a sophisticated blueprint. This gap shall be closed by the model CHIMERA (Cluster Hierarchy Interconnection Model for Evaluation, Research and Analysis) which will be introduced and described here for the first time.

The structure of the exopolyphsophatase (PPX) from Escherchia coli O157:H7 suggests a binding mode for long polyphosphate chains

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

Rangarajan,E.; Nadeau, G.; Li, Y.

2006-01-01

Polyphosphate (polyP) is a linear polymer consisting of tens to hundreds of phosphate molecules joined together by high-energy anhydride bonds. These polymers are found in virtually all prokaryotic and eukaryotic cells and perform many functions; prominent among them are the responses to many stresses. Polyphosphate is synthesized by polyP kinase (PPK), using the terminal phosphate of ATP as the substrate, and degraded to inorganic phosphate by both endo- and exopolyphosphatases. Here we report the crystal structure and analysis of the polyphosphate phosphatase PPX from Escherichia coli O157:H7 refined at 2.2 Angstroms resolution. PPX is made of four domains. Domains Imore » and II display structural similarity with one another and share the ribonuclease-H-like fold. Domain III bears structural similarity to the N-terminal, HD domain of SpoT. Domain IV, the smallest domain, has structural counterparts in cold-shock associated RNA-binding proteins but is of unknown function in PPX. The putative PPX active site is located at the interface between domains I and II. In the crystal structure of PPX these two domains are close together and represent the 'closed' state. Comparison with the crystal structure of PPX/GPPA from Aquifex aeolicus reveals close structural similarity between domains I and II of the two enzymes, with the PPX/GPPA representing an 'open' state. A striking feature of the dimer is a deep S-shaped canyon extending along the dimer interface and lined with positively charged residues. The active site region opens to this canyon. We postulate that this is a likely site of polyP binding.« less

THE RADIO CONTINUUM STRUCTURE OF CENTAURUS A AT 1.4 GHz

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

Feain, I. J.; Cornwell, T. J.; Ekers, R. D.

2011-10-10

A 45 deg{sup 2} radio continuum imaging campaign of the nearest radio galaxy, Centaurus A, is reported. Using the Australia Telescope Compact Array and the Parkes 64 m radio telescope at 1.4 GHz, the spatial resolution of the resultant image is {approx}600 pc ({approx}50''), resolving the {approx}>500 kpc giant radio lobes with approximately five times better physical resolution compared to any previous image, and making this the most detailed radio continuum image of any radio galaxy to date. In this paper, we present these new data and discuss briefly some of the most interesting morphological features that we have discoveredmore » in the images. The two giant outer lobes are highly structured and considerably distinct. The southern part of the giant northern lobe naturally extends out from the northern middle lobe with uniformly north-streaming emission. The well known northern loop is resolved into a series of semi-regular shells with a spacing of approximately 25 kpc. The northern part of the giant northern lobe also contains identifiable filaments and partial ring structures. As seen in previous single-dish images at lower angular resolution, the giant southern lobe is not physically connected to the core at radio wavelengths. Almost the entirety of the giant southern lobe is resolved into a largely chaotic and mottled structure which appears considerably different (morphologically) to the diffuse regularity of the northern lobe. We report the discovery of a vertex and a vortex near the western boundary of the southern lobe, two striking, high surface brightness features that are named based on their morphology and not their dynamics (which are presently unknown). The vortex and vertex are modeled as reaccelerated lobe emission due to shocks from the active galactic nucleus itself or from the passage of a dwarf elliptical galaxy through the lobe. Preliminary polarimetric and spectral index studies support a plasma reacceleration model and could explain the origin of the Faraday rotation structure detected in the southern lobe. In addition, there are a series of low surface brightness wisps detected around the edges of both the giant lobes.« less

Capability assessment and challenges for quantum technology gravity sensors for near surface terrestrial geophysical surveying

NASA Astrophysics Data System (ADS)

Boddice, Daniel; Metje, Nicole; Tuckwell, George

2017-11-01

Geophysical surveying is widely used for the location of subsurface features. Current technology is limited in terms of its resolution (thus size of features it can detect) and penetration depth and a suitable technique is needed to bridge the gap between shallow near surface investigation using techniques such as EM conductivity mapping and GPR commonly used to map the upper 5 m below ground surface, and large features at greater depths detectable using conventional microgravity (> 5 m below ground surface). This will minimise the risks from unknown features buried in and conditions of the ground during civil engineering work. Quantum technology (QT) gravity sensors potentially offer a step-change in technology for locating features which lie outside of the currently detectable range in terms of size and depth, but that potential is currently unknown as field instruments have not been developed. To overcome this, a novel computer simulation was developed for a large range of different targets of interest. The simulation included realistic noise modelling of instrumental, environmental and location sources of noise which limit the accuracy of current microgravity measurements, in order to assess the potential capability of the new QT instruments in realistic situations and determine some of the likely limitations on their implementation. The results of the simulations for near surface features showed that the new technology is best employed in a gradiometer configuration as opposed to the traditional single sensor gravimeter used by current instruments due to the ability to suppress vibrational environmental noise effects due to common mode rejection between the sensors. A significant improvement in detection capability of 1.5-2 times was observed, putting targets such as mineshafts into the detectability zone which would be a major advantage for subsurface surveying. Thus this research, for the first time, has demonstrated clearly the benefits of QT gravity gradiometer sensors thereby increasing industry's confidence in this new technology.

In vivo engineering of bone tissues with hematopoietic functions and mixed chimerism

PubMed Central

Shih, Yu-Ru; Kang, Heemin; Rao, Vikram; Chiu, Yu-Jui; Kwon, Seong Keun; Varghese, Shyni

2017-01-01

Synthetic biomimetic matrices with osteoconductivity and osteoinductivity have been developed to regenerate bone tissues. However, whether such systems harbor donor marrow in vivo and support mixed chimerism remains unknown. We devised a strategy to engineer bone tissues with a functional bone marrow (BM) compartment in vivo by using a synthetic biomaterial with spatially differing cues. Specifically, we have developed a synthetic matrix recapitulating the dual-compartment structures by modular assembly of mineralized and nonmineralized macroporous structures. Our results show that these matrices incorporated with BM cells or BM flush transplanted into recipient mice matured into functional bone displaying the cardinal features of both skeletal and hematopoietic compartments similar to native bone tissue. The hematopoietic function of bone tissues was demonstrated by its support for a higher percentage of mixed chimerism compared with i.v. injection and donor hematopoietic cell mobilization in the circulation of nonirradiated recipients. Furthermore, hematopoietic cells sorted from the engineered bone tissues reconstituted the hematopoietic system when transplanted into lethally irradiated secondary recipients. Such engineered bone tissues could potentially be used as ectopic BM surrogates for treatment of nonmalignant BM diseases and as a tool to study hematopoiesis, donor–host cell dynamics, tumor tropism, and hematopoietic cell transplantation. PMID:28484009

Scene Segmentation For Autonomous Robotic Navigation Using Sequential Laser Projected Structured Light

NASA Astrophysics Data System (ADS)

Brown, C. David; Ih, Charles S.; Arce, Gonzalo R.; Fertell, David A.

1987-01-01

Vision systems for mobile robots or autonomous vehicles navigating in an unknown terrain environment must provide a rapid and accurate method of segmenting the scene ahead into regions of pathway and background. A major distinguishing feature between the pathway and background is the three dimensional texture of these two regions. Typical methods of textural image segmentation are very computationally intensive, often lack the required robustness, and are incapable of sensing the three dimensional texture of various regions of the scene. A method is presented where scanned laser projected lines of structured light, viewed by a stereoscopically located single video camera, resulted in an image in which the three dimensional characteristics of the scene were represented by the discontinuity of the projected lines. This image was conducive to processing with simple regional operators to classify regions as pathway or background. Design of some operators and application methods, and demonstration on sample images are presented. This method provides rapid and robust scene segmentation capability that has been implemented on a microcomputer in near real time, and should result in higher speed and more reliable robotic or autonomous navigation in unstructured environments.

Computational design and experimental verification of a symmetric protein homodimer.

PubMed

Mou, Yun; Huang, Po-Ssu; Hsu, Fang-Ciao; Huang, Shing-Jong; Mayo, Stephen L

2015-08-25

Homodimers are the most common type of protein assembly in nature and have distinct features compared with heterodimers and higher order oligomers. Understanding homodimer interactions at the atomic level is critical both for elucidating their biological mechanisms of action and for accurate modeling of complexes of unknown structure. Computation-based design of novel protein-protein interfaces can serve as a bottom-up method to further our understanding of protein interactions. Previous studies have demonstrated that the de novo design of homodimers can be achieved to atomic-level accuracy by β-strand assembly or through metal-mediated interactions. Here, we report the design and experimental characterization of a α-helix-mediated homodimer with C2 symmetry based on a monomeric Drosophila engrailed homeodomain scaffold. A solution NMR structure shows that the homodimer exhibits parallel helical packing similar to the design model. Because the mutations leading to dimer formation resulted in poor thermostability of the system, design success was facilitated by the introduction of independent thermostabilizing mutations into the scaffold. This two-step design approach, function and stabilization, is likely to be generally applicable, especially if the desired scaffold is of low thermostability.

Distribution network design under demand uncertainty using genetic algorithm and Monte Carlo simulation approach: a case study in pharmaceutical industry

NASA Astrophysics Data System (ADS)

Izadi, Arman; Kimiagari, Ali mohammad

2014-01-01

Distribution network design as a strategic decision has long-term effect on tactical and operational supply chain management. In this research, the location-allocation problem is studied under demand uncertainty. The purposes of this study were to specify the optimal number and location of distribution centers and to determine the allocation of customer demands to distribution centers. The main feature of this research is solving the model with unknown demand function which is suitable with the real-world problems. To consider the uncertainty, a set of possible scenarios for customer demands is created based on the Monte Carlo simulation. The coefficient of variation of costs is mentioned as a measure of risk and the most stable structure for firm's distribution network is defined based on the concept of robust optimization. The best structure is identified using genetic algorithms and 14% reduction in total supply chain costs is the outcome. Moreover, it imposes the least cost variation created by fluctuation in customer demands (such as epidemic diseases outbreak in some areas of the country) to the logistical system. It is noteworthy that this research is done in one of the largest pharmaceutical distribution firms in Iran.

Distribution network design under demand uncertainty using genetic algorithm and Monte Carlo simulation approach: a case study in pharmaceutical industry

NASA Astrophysics Data System (ADS)

Izadi, Arman; Kimiagari, Ali Mohammad

2014-05-01

Distribution network design as a strategic decision has long-term effect on tactical and operational supply chain management. In this research, the location-allocation problem is studied under demand uncertainty. The purposes of this study were to specify the optimal number and location of distribution centers and to determine the allocation of customer demands to distribution centers. The main feature of this research is solving the model with unknown demand function which is suitable with the real-world problems. To consider the uncertainty, a set of possible scenarios for customer demands is created based on the Monte Carlo simulation. The coefficient of variation of costs is mentioned as a measure of risk and the most stable structure for firm's distribution network is defined based on the concept of robust optimization. The best structure is identified using genetic algorithms and 14 % reduction in total supply chain costs is the outcome. Moreover, it imposes the least cost variation created by fluctuation in customer demands (such as epidemic diseases outbreak in some areas of the country) to the logistical system. It is noteworthy that this research is done in one of the largest pharmaceutical distribution firms in Iran.

In vivo engineering of bone tissues with hematopoietic functions and mixed chimerism.

PubMed

Shih, Yu-Ru; Kang, Heemin; Rao, Vikram; Chiu, Yu-Jui; Kwon, Seong Keun; Varghese, Shyni

2017-05-23

Synthetic biomimetic matrices with osteoconductivity and osteoinductivity have been developed to regenerate bone tissues. However, whether such systems harbor donor marrow in vivo and support mixed chimerism remains unknown. We devised a strategy to engineer bone tissues with a functional bone marrow (BM) compartment in vivo by using a synthetic biomaterial with spatially differing cues. Specifically, we have developed a synthetic matrix recapitulating the dual-compartment structures by modular assembly of mineralized and nonmineralized macroporous structures. Our results show that these matrices incorporated with BM cells or BM flush transplanted into recipient mice matured into functional bone displaying the cardinal features of both skeletal and hematopoietic compartments similar to native bone tissue. The hematopoietic function of bone tissues was demonstrated by its support for a higher percentage of mixed chimerism compared with i.v. injection and donor hematopoietic cell mobilization in the circulation of nonirradiated recipients. Furthermore, hematopoietic cells sorted from the engineered bone tissues reconstituted the hematopoietic system when transplanted into lethally irradiated secondary recipients. Such engineered bone tissues could potentially be used as ectopic BM surrogates for treatment of nonmalignant BM diseases and as a tool to study hematopoiesis, donor-host cell dynamics, tumor tropism, and hematopoietic cell transplantation.

iDBPs: a web server for the identification of DNA binding proteins.

PubMed

Nimrod, Guy; Schushan, Maya; Szilágyi, András; Leslie, Christina; Ben-Tal, Nir

2010-03-01

The iDBPs server uses the three-dimensional (3D) structure of a query protein to predict whether it binds DNA. First, the algorithm predicts the functional region of the protein based on its evolutionary profile; the assumption is that large clusters of conserved residues are good markers of functional regions. Next, various characteristics of the predicted functional region as well as global features of the protein are calculated, such as the average surface electrostatic potential, the dipole moment and cluster-based amino acid conservation patterns. Finally, a random forests classifier is used to predict whether the query protein is likely to bind DNA and to estimate the prediction confidence. We have trained and tested the classifier on various datasets and shown that it outperformed related methods. On a dataset that reflects the fraction of DNA binding proteins (DBPs) in a proteome, the area under the ROC curve was 0.90. The application of the server to an updated version of the N-Func database, which contains proteins of unknown function with solved 3D-structure, suggested new putative DBPs for experimental studies. http://idbps.tau.ac.il/

Caregiver Strain and Sensory Features in Children with Autism Spectrum Disorder and other Developmental Disabilities

PubMed Central

Kirby, Anne V.; White, Tamira J.; Baranek, Grace T.

2015-01-01

Caring for children with disabilities contributes to increased levels of parent stress, or caregiver strain. However, the potential relationship of sensory features to strain among caregivers of children with autism spectrum disorder (ASD) and other developmental disabilities (DD) is unknown. Sensory features include over-reactions, under-reactions, and unusual interests in sensations, which may negatively impact family functioning. This descriptive study confirmed three caregiver strain types (i.e., objective, subjective internalized, subjective externalized) and explored differences among ASD (n=71) and DD (n=36) groups, with the ASD group reporting higher levels. Furthermore, this study explored the contribution of sensory features to caregiver strain, finding differential contributions to strain in the ASD group and covariate contributions (i.e., child cognition, mother’s education) in the DD group. PMID:25551265

Conjunction search revisited.

PubMed

Treisman, A; Sato, S

1990-08-01

Search for conjunctions of highly discriminable features can be rapid or even parallel. This article explores three possible accounts based on (a) perceptual segregation, (b) conjunction detectors, and (c) inhibition controlled separately by two or more distractor features. Search rates for conjunctions of color, size, orientation, and direction of motion correlated closely with an independent measure of perceptual segregation. However, they appeared unrelated to the physiology of single-unit responses. Each dimension contributed additively to conjunction search rates, suggesting that each was checked independently of the others. Unknown targets appear to be found only by serial search for each in turn. Searching through 4 sets of distractors was slower than searching through 2. The results suggest a modification of feature integration theory, in which attention is controlled not only by a unitary "window" but also by a form of feature-based inhibition.

Palaeohydrology of a 3D-maze cave (Hermannshöhle, Lower Austria)

NASA Astrophysics Data System (ADS)

Schober, Andrea; Plan, Lukas

2013-04-01

The 4.4 km-long Hermannshöhle (located in Kirchberg/Wechsel, Lower Austria) is one of the largest caves in the Lower Austroalpine Unit. It is developed in an isolated block of carbonate marble, taking up only 140 x 160 m of ground area and 73 m of elevation difference. The cave is unusual in two respects: (a) its dense network of corridors is arranged in a three-dimensional maze and (b) the most outstanding macro- and micromorphologic features were caused by paragenesis. Speleothems are abundant throughout the cave comprising flowstones, dripstones, helictites, popcorn, calcite rafts, a shield, and moonmilk. Even though most passages are canyon-shaped, the cave shows exclusively phreatic features. Sediment fills are abundant as well, mostly covering the floor of passages to an unknown depth, containing mainly allochthonous material, i.e. schists and gneisses. Besides some vadose dripwater the cave is dry today. A conspicuous feature is the lack of a single water path and instead a maze with multiple flow paths formed. Another interesting feature is that one part of the cave developed below the nearby Ramsbach brook but is still dry. There are small ponors reported from the Ramsbach brook (which were observed during river regulation) indicating an actively draining karst system, which is not yet explored. The aim of this study was to enlighten the palaeohydrology of this cave using morphological and sedimentological observations as well as U/Th dating of speleothems. First results show that the palaeo-environment and the hydrologic setting of the Hermannshöhle were drastically different from today. Undersaturated water sourced from nearby non-karstic gneisses and schists gave rise to well-developed contact karst features. Surprisingly the palaeo flow direction deduced from indicators like scallops and sediment structures was opposite to the flow direction of the present nearby brooks (Rams- and Feistrizbach). Following pulses of clastic sediment input a distinct system of paragenetic canyons developed creating the unique maze character of the cave.

Exploration of the canyon-incised continental margin of the northeastern United States reveals dynamic habitats and diverse communities

USGS Publications Warehouse

Quattrini, Andrea; Nizinski, Martha S.; Chaytor, Jason; Demopoulos, Amanda W.J.; Roark, E. Brendan; France, Scott; Moore, Jon A.; Heyl, Taylor P.; Auster, Peter J.; Ruppel, Carolyn D.; Elliott, Kelley P.; Kennedy, Brian R.C.; Lobecker, Elizabeth A.; Skarke, Adam; Shank, Timothy M.

2015-01-01

The continental margin off the northeastern United States (NEUS) contains numerous, topographically complex features that increase habitat heterogeneity across the region. However, the majority of these rugged features have never been surveyed, particularly using direct observations. During summer 2013, 31 Remotely-Operated Vehicle (ROV) dives were conducted from 494 to 3271 m depth across a variety of seafloor features to document communities and to infer geological processes that produced such features. The ROV surveyed six broad-scale habitat features, consisting of shelf-breaching canyons, slope-sourced canyons, inter-canyon areas, open-slope/landslide-scar areas, hydrocarbon seeps, and Mytilus Seamount. Four previously unknown chemosynthetic communities dominated by Bathymodiolus mussels were documented. Seafloor methane hydrate was observed at two seep sites. Multivariate analyses indicated that depth and broad-scale habitat significantly influenced megafaunal coral (58 taxa), demersal fish (69 taxa), and decapod crustacean (34 taxa) assemblages. Species richness of fishes and crustaceans significantly declined with depth, while there was no relationship between coral richness and depth. Turnover in assemblage structure occurred on the middle to lower slope at the approximate boundaries of water masses found previously in the region. Coral species richness was also an important variable explaining variation in fish and crustacean assemblages. Coral diversity may serve as an indicator of habitat suitability and variation in available niche diversity for these taxonomic groups. Our surveys added 24 putative coral species and three fishes to the known regional fauna, including the black coral Telopathes magna, the octocoral Metallogorgia melanotrichosand the fishes Gaidropsarus argentatus, Guttigadus latifrons, and Lepidion guentheri. Marine litter was observed on 81% of the dives, with at least 12 coral colonies entangled in debris. While initial exploration revealed the NEUS region to be both geologically dynamic and biologically diverse, further research into the abiotic conditions and the biotic interactions that influence species abundance and distribution is needed.

Exploration of the Canyon-Incised Continental Margin of the Northeastern United States Reveals Dynamic Habitats and Diverse Communities.

PubMed

Quattrini, Andrea M; Nizinski, Martha S; Chaytor, Jason D; Demopoulos, Amanda W J; Roark, E Brendan; France, Scott C; Moore, Jon A; Heyl, Taylor; Auster, Peter J; Kinlan, Brian; Ruppel, Carolyn; Elliott, Kelley P; Kennedy, Brian R C; Lobecker, Elizabeth; Skarke, Adam; Shank, Timothy M

2015-01-01

The continental margin off the northeastern United States (NEUS) contains numerous, topographically complex features that increase habitat heterogeneity across the region. However, the majority of these rugged features have never been surveyed, particularly using direct observations. During summer 2013, 31 Remotely-Operated Vehicle (ROV) dives were conducted from 494 to 3271 m depth across a variety of seafloor features to document communities and to infer geological processes that produced such features. The ROV surveyed six broad-scale habitat features, consisting of shelf-breaching canyons, slope-sourced canyons, inter-canyon areas, open-slope/landslide-scar areas, hydrocarbon seeps, and Mytilus Seamount. Four previously unknown chemosynthetic communities dominated by Bathymodiolus mussels were documented. Seafloor methane hydrate was observed at two seep sites. Multivariate analyses indicated that depth and broad-scale habitat significantly influenced megafaunal coral (58 taxa), demersal fish (69 taxa), and decapod crustacean (34 taxa) assemblages. Species richness of fishes and crustaceans significantly declined with depth, while there was no relationship between coral richness and depth. Turnover in assemblage structure occurred on the middle to lower slope at the approximate boundaries of water masses found previously in the region. Coral species richness was also an important variable explaining variation in fish and crustacean assemblages. Coral diversity may serve as an indicator of habitat suitability and variation in available niche diversity for these taxonomic groups. Our surveys added 24 putative coral species and three fishes to the known regional fauna, including the black coral Telopathes magna, the octocoral Metallogorgia melanotrichos and the fishes Gaidropsarus argentatus, Guttigadus latifrons, and Lepidion guentheri. Marine litter was observed on 81% of the dives, with at least 12 coral colonies entangled in debris. While initial exploration revealed the NEUS region to be both geologically dynamic and biologically diverse, further research into the abiotic conditions and the biotic interactions that influence species abundance and distribution is needed.

MO-DE-207A-02: A Feature-Preserving Image Reconstruction Method for Improved Pancreaticlesion Classification in Diagnostic CT Imaging

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

Xu, J; Tsui, B; Noo, F

Purpose: To develop a feature-preserving model based image reconstruction (MBIR) method that improves performance in pancreatic lesion classification at equal or reduced radiation dose. Methods: A set of pancreatic lesion models was created with both benign and premalignant lesion types. These two classes of lesions are distinguished by their fine internal structures; their delineation is therefore crucial to the task of pancreatic lesion classification. To reduce image noise while preserving the features of the lesions, we developed a MBIR method with curvature-based regularization. The novel regularization encourages formation of smooth surfaces that model both the exterior shape and the internalmore » features of pancreatic lesions. Given that the curvature depends on the unknown image, image reconstruction or denoising becomes a non-convex optimization problem; to address this issue an iterative-reweighting scheme was used to calculate and update the curvature using the image from the previous iteration. Evaluation was carried out with insertion of the lesion models into the pancreas of a patient CT image. Results: Visual inspection was used to compare conventional TV regularization with our curvature-based regularization. Several penalty-strengths were considered for TV regularization, all of which resulted in erasing portions of the septation (thin partition) in a premalignant lesion. At matched noise variance (50% noise reduction in the patient stomach region), the connectivity of the septation was well preserved using the proposed curvature-based method. Conclusion: The curvature-based regularization is able to reduce image noise while simultaneously preserving the lesion features. This method could potentially improve task performance for pancreatic lesion classification at equal or reduced radiation dose. The result is of high significance for longitudinal surveillance studies of patients with pancreatic cysts, which may develop into pancreatic cancer. The Senior Author receives financial support from Siemens GmbH Healthcare.« less

Exploration of the Canyon-Incised Continental Margin of the Northeastern United States Reveals Dynamic Habitats and Diverse Communities

PubMed Central

Quattrini, Andrea M.; Nizinski, Martha S.; Chaytor, Jason D.; Demopoulos, Amanda W. J.; Roark, E. Brendan; France, Scott C.; Moore, Jon A.; Heyl, Taylor; Auster, Peter J.; Kinlan, Brian; Ruppel, Carolyn; Elliott, Kelley P.; Kennedy, Brian R.C.; Lobecker, Elizabeth; Skarke, Adam; Shank, Timothy M.

2015-01-01

The continental margin off the northeastern United States (NEUS) contains numerous, topographically complex features that increase habitat heterogeneity across the region. However, the majority of these rugged features have never been surveyed, particularly using direct observations. During summer 2013, 31 Remotely-Operated Vehicle (ROV) dives were conducted from 494 to 3271 m depth across a variety of seafloor features to document communities and to infer geological processes that produced such features. The ROV surveyed six broad-scale habitat features, consisting of shelf-breaching canyons, slope-sourced canyons, inter-canyon areas, open-slope/landslide-scar areas, hydrocarbon seeps, and Mytilus Seamount. Four previously unknown chemosynthetic communities dominated by Bathymodiolus mussels were documented. Seafloor methane hydrate was observed at two seep sites. Multivariate analyses indicated that depth and broad-scale habitat significantly influenced megafaunal coral (58 taxa), demersal fish (69 taxa), and decapod crustacean (34 taxa) assemblages. Species richness of fishes and crustaceans significantly declined with depth, while there was no relationship between coral richness and depth. Turnover in assemblage structure occurred on the middle to lower slope at the approximate boundaries of water masses found previously in the region. Coral species richness was also an important variable explaining variation in fish and crustacean assemblages. Coral diversity may serve as an indicator of habitat suitability and variation in available niche diversity for these taxonomic groups. Our surveys added 24 putative coral species and three fishes to the known regional fauna, including the black coral Telopathes magna, the octocoral Metallogorgia melanotrichos and the fishes Gaidropsarus argentatus, Guttigadus latifrons, and Lepidion guentheri. Marine litter was observed on 81% of the dives, with at least 12 coral colonies entangled in debris. While initial exploration revealed the NEUS region to be both geologically dynamic and biologically diverse, further research into the abiotic conditions and the biotic interactions that influence species abundance and distribution is needed. PMID:26509818

A semi-supervised learning approach for RNA secondary structure prediction.

PubMed

Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki

2015-08-01

RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited. Copyright © 2015 Elsevier Ltd. All rights reserved.

Introducing Graduate Students to High-Resolution Mass Spectrometry (HRMS) Using a Hands-On Approach

ERIC Educational Resources Information Center

Stock, Naomi L.

2017-01-01

High-resolution mass spectrometry (HRMS) features both high resolution and high mass accuracy and is a powerful tool for the analysis and quantitation of compounds, determination of elemental compositions, and identification of unknowns. A hands-on laboratory experiment for upper-level undergraduate and graduate students to investigate HRMS is…

The Beaks of Finches & the Tool Analogy: Use with Care

ERIC Educational Resources Information Center

Milne, Catherine

2008-01-01

Analogies are an integral feature of scientific theories, like evolution. They are developed to support explanations, proposed on the basis of evidence collected from experimental studies, field studies, and other observational studies. They map a known source or process to an unknown or target with the goal of helping educators understand the…

Neurocognitive Features of Attention Deficit Hyperactivity Disorder in a Non-Clinical Adult Sample

DTIC Science & Technology

2004-01-01

samples. Whether these cognitive weaknesses are associated with ADHD symptoms in non-clinical samples is unknown. The current study examined the...relationship between ADHD symptoms and cognitive performance in a non-clinical adult sample of 75 men and women (ages 20 to 49). Self-report measures of ADHD

Observations of neutral iron emission in twilight spectra

NASA Technical Reports Server (NTRS)

Tepley, C. A.; Meriwether, J. W., Jr.; Walker, J. C. G.; Mathews, J. D.

1981-01-01

A method is presented for the analysis of twilight airglow spectra that may be contaminated by atmospheric continuum emission of unknown brightness. The necessity of correcting for this continuum emission when measuring weak airglow features in twilight is illustrated by application of the method to the neutral iron line at 3860 A.

Campylobacter fetus subspecies contain conserved type IV secretion systems on multiple genomic islands and plasmids

USDA-ARS?s Scientific Manuscript database

The features contributing to the differences in pathogenicity of the C. fetus subspecies are unknown. Putative factors involved in pathogenesis are located in genomic islands that encode type IV secretion system (T4SS) and fic-domain (filamentation induced by cyclic AMP) proteins. In the genomes of ...

Understanding Clicker Discussions: Student Reasoning and the Impact of Instructional Cues

ERIC Educational Resources Information Center

Knight, Jennifer K.; Wise, Sarah B.; Southard, Katelyn M.

2013-01-01

Previous research has shown that undergraduate science students learn from peer discussions of in-class clicker questions. However, the features that characterize such discussions are largely unknown, as are the instructional factors that may lead students into productive discussions. To explore these questions, we recorded and transcribed 83…

Early Adolescent Outcomes of Institutionally Deprived and Non-Deprived Adoptees. III. Quasi-Autism

ERIC Educational Resources Information Center

Rutter, Michael; Kreppner, Jana; Croft, Carla; Murin, Marianna; Colvert, Emma; Beckett, Celia; Castle, Jenny; Sonuga-Barke, Edmund

2007-01-01

Background: Some young children reared in profoundly depriving institutions have been found to show autistic-like patterns, but the developmental significance of these features is unknown. Methods: A randomly selected, age-stratified, sample of 144 children who had experienced an institutional upbringing in Romania and who were adopted by UK…

Spike Timing Matters in Novel Neuronal Code Involved in Vibrotactile Frequency Perception.

PubMed

Birznieks, Ingvars; Vickery, Richard M

2017-05-22

Skin vibrations sensed by tactile receptors contribute significantly to the perception of object properties during tactile exploration [1-4] and to sensorimotor control during object manipulation [5]. Sustained low-frequency skin vibration (<60 Hz) evokes a distinct tactile sensation referred to as flutter whose frequency can be clearly perceived [6]. How afferent spiking activity translates into the perception of frequency is still unknown. Measures based on mean spike rates of neurons in the primary somatosensory cortex are sufficient to explain performance in some frequency discrimination tasks [7-11]; however, there is emerging evidence that stimuli can be distinguished based also on temporal features of neural activity [12, 13]. Our study's advance is to demonstrate that temporal features are fundamental for vibrotactile frequency perception. Pulsatile mechanical stimuli were used to elicit specified temporal spike train patterns in tactile afferents, and subsequently psychophysical methods were employed to characterize human frequency perception. Remarkably, the most salient temporal feature determining vibrotactile frequency was not the underlying periodicity but, rather, the duration of the silent gap between successive bursts of neural activity. This burst gap code for frequency represents a previously unknown form of neural coding in the tactile sensory system, which parallels auditory pitch perception mechanisms based on purely temporal information where longer inter-pulse intervals receive higher perceptual weights than short intervals [14]. Our study also demonstrates that human perception of stimuli can be determined exclusively by temporal features of spike trains independent of the mean spike rate and without contribution from population response factors. Copyright © 2017 Elsevier Ltd. All rights reserved.

A spectral reflectance estimation technique using multispectral data from the Viking lander camera

NASA Technical Reports Server (NTRS)

Park, S. K.; Huck, F. O.

1976-01-01

A technique is formulated for constructing spectral reflectance curve estimates from multispectral data obtained with the Viking lander camera. The multispectral data are limited to six spectral channels in the wavelength range from 0.4 to 1.1 micrometers and most of these channels exhibit appreciable out-of-band response. The output of each channel is expressed as a linear (integral) function of the (known) solar irradiance, atmospheric transmittance, and camera spectral responsivity and the (unknown) spectral responsivity and the (unknown) spectral reflectance. This produces six equations which are used to determine the coefficients in a representation of the spectral reflectance as a linear combination of known basis functions. Natural cubic spline reflectance estimates are produced for a variety of materials that can be reasonably expected to occur on Mars. In each case the dominant reflectance features are accurately reproduced, but small period features are lost due to the limited number of channels. This technique may be a valuable aid in selecting the number of spectral channels and their responsivity shapes when designing a multispectral imaging system.

Cross Flow Parameter Calculation for Aerodynamic Analysis

NASA Technical Reports Server (NTRS)

Norman, David, Jr. (Inventor)

2014-01-01

A system and method for determining a cross flow angle for a feature on a structure. A processor unit receives location information identifying a location of the feature on the structure, determines an angle of the feature, identifies flow information for the location, determines a flow angle using the flow information, and determines the cross flow angle for the feature using the flow angle and the angle of the feature. The flow information describes a flow of fluid across the structure. The flow angle comprises an angle of the flow of fluid across the structure for the location of the feature.

Fuzzy similarity measures for ultrasound tissue characterization

NASA Astrophysics Data System (ADS)

Emara, Salem M.; Badawi, Ahmed M.; Youssef, Abou-Bakr M.

1995-03-01

Computerized ultrasound tissue characterization has become an objective means for diagnosis of diseases. It is difficult to differentiate diffuse liver diseases, namely cirrhotic and fatty liver from a normal one, by visual inspection from the ultrasound images. The visual criteria for differentiating diffused diseases is rather confusing and highly dependent upon the sonographer's experience. The need for computerized tissue characterization is thus justified to quantitatively assist the sonographer for accurate differentiation and to minimize the degree of risk from erroneous interpretation. In this paper we used the fuzzy similarity measure as an approximate reasoning technique to find the maximum degree of matching between an unknown case defined by a feature vector and a family of prototypes (knowledge base). The feature vector used for the matching process contains 8 quantitative parameters (textural, acoustical, and speckle parameters) extracted from the ultrasound image. The steps done to match an unknown case with the family of prototypes (cirr, fatty, normal) are: Choosing the membership functions for each parameter, then obtaining the fuzzification matrix for the unknown case and the family of prototypes, then by the linguistic evaluation of two fuzzy quantities we obtain the similarity matrix, then by a simple aggregation method and the fuzzy integrals we obtain the degree of similarity. Finally, we find that the similarity measure results are comparable to the neural network classification techniques and it can be used in medical diagnosis to determine the pathology of the liver and to monitor the extent of the disease.

Spirosoma aerolatum sp. nov., isolated from a motor car air conditioning system.

PubMed

Kim, Dong-Uk; Lee, Hyosun; Kim, Song-Gun; Ahn, Jae-Hyung; Yoon Park, So; Ka, Jong-Ok

2015-11-01

A Gram-stain-negative, yellow-pigmented bacterial strain, designated PR1012KT, was isolated from a motor car evaporator core collected in Korea. Cells of the strain were facultatively anaerobic, non-spore-forming and rod-shaped. The strain grew at 10-40 °C (optimum, 25 °C), at pH 6.5-8.0 (optimum, pH 7.0-8.0) and in the presence of 0-1% (w/v) NaCl. Phylogenetically, the strain was closely related to members of the genus Spirosoma (97.50-90.74% 16S rRNA gene sequence similarities) and showed highest sequence similarity to Spirosoma panaciterrae DSM 21099T (97.50%). Its predominant fatty acids included summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16:1ω5c, iso-C15:0 and summed feature 4 (iso-C17:1 I and/or anteiso B) and it had MK-7 as the major menaquinone. The polar lipids present included phosphatidylethanolamine, one unknown aminophospholipid, two unknown aminolipids and five unknown polar lipids. The DNA G+C content of this strain was 54 mol%. Based on phenotypic, genotypic and chemotaxonomic data, strain PR1012KT represents a novel species in the genus Spirosoma, for which the name Spirosoma aerolatum sp. nov. is proposed. The type strain is PR1012KT ( = KACC 17939T = NBRC 110794T).

MUSIC-type imaging of small perfectly conducting cracks with an unknown frequency

NASA Astrophysics Data System (ADS)

Park, Won-Kwang

2015-09-01

MUltiple SIgnal Classification (MUSIC) is a famous non-iterative detection algorithm in inverse scattering problems. However, when the applied frequency is unknown, inaccurate locations are identified via MUSIC. This fact has been confirmed through numerical simulations. However, the reason behind this phenomenon has not been investigated theoretically. Motivated by this fact, we identify the structure of MUSIC-type imaging functionals with unknown frequency, by establishing a relationship with Bessel functions of order zero of the first kind. Through this, we can explain why inaccurate results appear.

Lidar-enhanced geologic mapping, examples from the Medford and Hood River areas, Oregon

NASA Astrophysics Data System (ADS)

Wiley, T. J.; McClaughry, J. D.

2012-12-01

Lidar-based 3-foot digital elevation models (DEMs) and derivatives (slopeshade, hillshade, contours) were used to help map geology across 1700 km2 (650 mi2) near Hood River and Medford, Oregon. Techniques classically applied to interpret coarse DEMs and small-scale topographic maps were adapted to take advantage of lidar's high resolution. Penetration and discrimination of plant cover by the laser system allowed recognition of fine patterns and textures related to underlying geologic units and associated soils. Surficial geologic maps were improved by the ability to examine tiny variations in elevation and slope. Recognition of low-relief features of all sizes was enhanced where pixel elevation ranges of centimeters to meters, established by knowledge of the site or by trial, were displayed using thousands of sequential colors. Features can also be depicted relative to stream level by preparing a DEM that compensates for gradient. Near Medford, lidar-derived contour maps with 1- to 3-foot intervals revealed incised bajada with young, distal lobes defined by concentric contour lines. Bedrock geologic maps were improved by recognizing geologic features associated with surface textures and patterns or topographic anomalies. In sedimentary and volcanic terrain, structure was revealed by outcrops or horizons lying at one stratigraphic level. Creating a triangulated irregular network (TIN) facet from positions of three or more such points gives strike and dip. Each map area benefited from hundreds of these measurements. A more extensive DEM in the plane of the TIN facet can be subtracted from surface elevation (lidar DEM) to make a DEM with elevation zero where the stratigraphic horizon lies at the surface. The distribution of higher and lower stratigraphic horizons can be shown by highlighting areas similarly higher or lower on the same DEM. Poor fit of contacts or faults projected between field traverses suggest the nature and amount of intervening geologic structure. Intrusive bodies were locally delimited by linear mounds where contact metamorphism hardened soft, fractured country rock. Bedrock faults were revealed where fault traces formed topographic anomalies or where topography associated with stratigraphic horizons or bedding-parallel textural fabrics was offset. This was important for identification of young faults and associated earthquake hazards. Previously unknown Holocene faults southwest of Hood River appear as subtle lineaments redirecting modern drainages or offsetting glacial moraines or glaciated bedrock. West of Medford, the presence young faulting was confirmed by elevation data that showed bedrock in the channel of the Rogue River at higher elevations below Gold Ray dam than in boreholes upstream. Such obscure structural features would have gone unrecognized using traditional topographic analysis or field reconnaissance. Fieldwork verified that lidar techniques improved our early geologic models, resolution of geologic features, and mapping of surficial and bedrock geology between traverses.

Learning about the internal structure of categories through classification and feature inference.

PubMed

Jee, Benjamin D; Wiley, Jennifer

2014-01-01

Previous research on category learning has found that classification tasks produce representations that are skewed toward diagnostic feature dimensions, whereas feature inference tasks lead to richer representations of within-category structure. Yet, prior studies often measure category knowledge through tasks that involve identifying only the typical features of a category. This neglects an important aspect of a category's internal structure: how typical and atypical features are distributed within a category. The present experiments tested the hypothesis that inference learning results in richer knowledge of internal category structure than classification learning. We introduced several new measures to probe learners' representations of within-category structure. Experiment 1 found that participants in the inference condition learned and used a wider range of feature dimensions than classification learners. Classification learners, however, were more sensitive to the presence of atypical features within categories. Experiment 2 provided converging evidence that classification learners were more likely to incorporate atypical features into their representations. Inference learners were less likely to encode atypical category features, even in a "partial inference" condition that focused learners' attention on the feature dimensions relevant to classification. Overall, these results are contrary to the hypothesis that inference learning produces superior knowledge of within-category structure. Although inference learning promoted representations that included a broad range of category-typical features, classification learning promoted greater sensitivity to the distribution of typical and atypical features within categories.

29. Photocopy of photograph. VIEW, LOOKING NORTHEAST, OF NORTHEAST SECTION ...

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

29. Photocopy of photograph. VIEW, LOOKING NORTHEAST, OF NORTHEAST SECTION OF THE STRUCTURE, SHOWING ORIGINAL WOOD DECK, RAILING AND EARLY 1930'S PACKARD AUTOMOBILE IN BACKGROUND. Photographer unknown, date unknown. (Print in possession of the Washington County Highway Department). - Hegeman-Hill Street Bridge, Spanning Batten Kill, .65 mile West of Greenwich, Easton, Washington County, NY

Endemic chronic kidney disease of unknown etiology in Sri Lanka: Correlation of pathology with clinical stages.

PubMed

Wijetunge, S; Ratnatunga, N V I; Abeysekera, T D J; Wazil, A W M; Selvarajah, M

2015-01-01

Chronic kidney disease of unknown etiology (CKDU) is endemic among the rural farming communities in several localities in and around the North Central region of Sri Lanka. This is an interstitial type renal disease and typically has an insidious onset and slow progression. This study was conducted to identify the pathological features in the different clinical stages of CKDU. This is a retrospective study of 251 renal biopsies identified to have a primary interstitial disease from regions endemic for CKDU. Pathological features were assessed and graded in relation to the clinical stage. The mean age of those affected by endemic CKDU was 37.3 ± 12.5 years and the male to female ratio was 3.3:1. The predominant feature of stage I disease was mild and moderate interstitial fibrosis; most did not have interstitial inflammation. The typical stage II disease had moderate interstitial fibrosis with or without mild interstitial inflammation. Stage III disease had moderate and severe interstitial fibrosis, moderate interstitial inflammation, tubular atrophy and some glomerulosclerosis. Stage IV disease typically had severe interstitial fibrosis and inflammation, tubular atrophy and glomerulosclerosis. The mean age of patients with stage I disease (27 ± 10.8 years) was significantly lower than those of the other stages. About 79.2%, 55%, 49.1% and 50% in stage I, II, III and IV disease respectively were asymptomatic at the time of biopsy.

Risk factors for early death in transient myeloproliferative disorder without phenotypic features of Down syndrome: a case report and literature review.

PubMed

Kawase, Koya; Azuma, Eiichi; Ohshita, Hironori; Tanaka, Tatsushi; Hanada, Yu; Sasaki, Tomoaki; Sugimoto, Mari; Togawa, Takao; Kouwaki, Masanori; Ito, Tsuyoshi; Hirayama, Masahiro; Koyama, Norihisa

2012-08-01

Not only in newborns with Down syndrome, but newborns without phenotypic features of Down syndrome also develop transient myeloproliferative disorder (TMD). In these cases, trisomy 21 and related chromosomal abnormalities are either constitutionally mosaic or limited to blood cells. Risk factors for early death of these patients are unknown so far. We here report a fatal case of TMD without phenotypic features of Down syndrome and review literature to identify risk factors associated with early death. Not only are gestational age and white blood cell count risk factors for early death in TMD with Down syndrome, but they also appear to be risk factors in TMD without Down syndrome.

New structures and composition of cell wall teichoic acids from Nocardiopsis synnemataformans, Nocardiopsis halotolerans, Nocardiopsis composta and Nocardiopsis metallicus: a chemotaxonomic value.

PubMed

Tul'skaya, Elena M; Shashkov, Alexander S; Streshinskaya, Galina M; Potekhina, Natalia V; Evtushenko, Ludmila I

2014-12-01

The structures of the cell wall teichoic acids (TA) from some species of the genus Nocardiopsis were established by chemical and NMR spectroscopic methods. The cell walls of Nocardiopsis synnemataformans VKM Ac-2518(T) and Nocardiopsis halotolerans VKM Ac-2519(T) both contain two TA with unique structures-poly(polyol phosphate-glycosylpolyol phosphate)-belonging to the type IV TA. In both organisms, the minor TA have identical structures: poly(glycerol phosphate-N-acetyl-β-galactosaminylglycerol phosphate) with the phosphodiester bond between C-3 of glycerol and C-4 of the amino sugar. This structure is found for the first time. The major TA of N. halotolerans has a hitherto unknown structure: poly(glycerol phosphate-N-acetyl-β-galactosaminylglycerol phosphate), the N-acetyl-β-galactosamine being acetalated with pyruvic acid at positions 4 and 6. The major TA of N. synnemataformans is a poly(glycerol phosphate-N-acetyl-β-galactosaminylglycerol phosphate) with the phosphodiester bond between C-3 of glycerol and C-3 of the amino sugar. The cell walls of Nocardiopsis composta VKM Ac-2520 and N. composta VKM Ac-2521(T) contain only one TA, namely 1,3-poly(glycerol phosphate) partially substituted with N-acetyl-α-glucosamine. The cell wall of Nocardiopsis metallicus VKM Ac-2522(T) contains two TA. The major TA is 1,5-poly(ribitol phosphate), each ribitol unit carrying a pyruvate ketal group at positions 2 and 4. The structure of the minor TA is the same as that of N. composta. The results presented correlate well with the phylogenetic grouping of strains and confirm the species and strain specific features of cell wall TA in members of the genus Nocardiopsis.

Optimal multi-type sensor placement for response and excitation reconstruction

NASA Astrophysics Data System (ADS)

Zhang, C. D.; Xu, Y. L.

2016-01-01

The need to perform dynamic response reconstruction always arises as the measurement of structural response is often limited to a few locations, especially for a large civil structure. Besides, it is usually very difficult, if not impossible, to measure external excitations under the operation condition of a structure. This study presents an algorithm for optimal placement of multi-type sensors, including strain gauges, displacement transducers and accelerometers, for the best reconstruction of responses of key structural components where there are no sensors installed and the best estimation of external excitations acting on the structure at the same time. The algorithm is developed in the framework of Kalman filter with unknown excitation, in which minimum-variance unbiased estimates of the generalized state of the structure and the external excitations are obtained by virtue of limited sensor measurements. The structural responses of key locations without sensors can then be reconstructed with the estimated generalized state and excitation. The asymptotic stability feature of the filter is utilized for optimal sensor placement. The number and spatial location of the multi-type sensors are determined by adding the optimal sensor which gains the maximal reduction of the estimation error of reconstructed responses. For the given mode number in response reconstruction and the given locations of external excitations, the optimal multi-sensor placement achieved by the proposed method is independent of the type and time evolution of external excitation. A simply-supported overhanging steel beam under multiple types of excitation is numerically studied to demonstrate the feasibility and superiority of the proposed method, and the experimental work is then carried out to testify the effectiveness of the proposed method.

Structural Analysis of PTM Hotspots (SAPH-ire) – A Quantitative Informatics Method Enabling the Discovery of Novel Regulatory Elements in Protein Families*

PubMed Central

Dewhurst, Henry M.; Choudhury, Shilpa; Torres, Matthew P.

2015-01-01

Predicting the biological function potential of post-translational modifications (PTMs) is becoming increasingly important in light of the exponential increase in available PTM data from high-throughput proteomics. We developed structural analysis of PTM hotspots (SAPH-ire)—a quantitative PTM ranking method that integrates experimental PTM observations, sequence conservation, protein structure, and interaction data to allow rank order comparisons within or between protein families. Here, we applied SAPH-ire to the study of PTMs in diverse G protein families, a conserved and ubiquitous class of proteins essential for maintenance of intracellular structure (tubulins) and signal transduction (large and small Ras-like G proteins). A total of 1728 experimentally verified PTMs from eight unique G protein families were clustered into 451 unique hotspots, 51 of which have a known and cited biological function or response. Using customized software, the hotspots were analyzed in the context of 598 unique protein structures. By comparing distributions of hotspots with known versus unknown function, we show that SAPH-ire analysis is predictive for PTM biological function. Notably, SAPH-ire revealed high-ranking hotspots for which a functional impact has not yet been determined, including phosphorylation hotspots in the N-terminal tails of G protein gamma subunits—conserved protein structures never before reported as regulators of G protein coupled receptor signaling. To validate this prediction we used the yeast model system for G protein coupled receptor signaling, revealing that gamma subunit–N-terminal tail phosphorylation is activated in response to G protein coupled receptor stimulation and regulates protein stability in vivo. These results demonstrate the utility of integrating protein structural and sequence features into PTM prioritization schemes that can improve the analysis and functional power of modification-specific proteomics data. PMID:26070665

Layered classification techniques for remote sensing applications

NASA Technical Reports Server (NTRS)

Swain, P. H.; Wu, C. L.; Landgrebe, D. A.; Hauska, H.

1975-01-01

The single-stage method of pattern classification utilizes all available features in a single test which assigns the unknown to a category according to a specific decision strategy (such as the maximum likelihood strategy). The layered classifier classifies the unknown through a sequence of tests, each of which may be dependent on the outcome of previous tests. Although the layered classifier was originally investigated as a means of improving classification accuracy and efficiency, it was found that in the context of remote sensing data analysis, other advantages also accrue due to many of the special characteristics of both the data and the applications pursued. The layered classifier method and several of the diverse applications of this approach are discussed.

Crystal Structure of VC0702 at 2.0 angstrom: A Conserved Hypothetical Protein from Vibrio Cholerae

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

Ni, Shuisong; Forouhar, Farhad; Bussiere, Dirksen E.

2006-06-01

VC0702, a conserved hypothetical protein of unknown function from Vibrio cholerae, resides in a putative three-gene operon containing the MbaA gene, which is involved in regulating formation of the extracellular matrix of biofilms in Vibrio cholerae. The VC0702 crystal structure has been determined at 2.0? and refined to Rwork=22.8% and Rfree=26.3%. VC0702 crystallized in an orthorhombic crystal lattice in the C2221 space group with dimensions of a=66.61 ?, b=88.118 ?, and c=118.35 ? with a homodimer in the asymmetric unit. VC0702 belongs to the Pfam DUF84 and COG1986 family of proteins. Sequence conservation within the DUF84 and COG1986 families wasmore » used to identify a conserved patch of surface residues that define a cleft and potential substrate-binding site in VC0702. The three-dimensional structure of VC0702 is similar to that of Mj0226 from Methanococcus janeshii, which has been identified as a novel NTPase. The NTP-binding site in Mj0226 is similarly located in comparison to the conserved patch of surface residues in VC0702. Furthermore, the NTP binds to MJ0226 in a cleft and deep cavity, features that are present in the VC0702 structure as well, suggesting that VC0702 may have a biochemical function involving NTP binding that is associated with a cellular function of regulating biofilm formation in Vibrio cholerae.« less

An Evaluation of Subsurface Plumbing of a Hydrothermal Seep Field and Possible Influence from Local Seismicity from New Time-Series Data Collected at the Davis-Schrimpf Seep Field, Salton Trough, California

NASA Astrophysics Data System (ADS)

Rao, A.; Onderdonk, N.

2016-12-01

The Davis­-Schrimpf Seep Field (DSSF) is a group of approximately 50 geothermal mud seeps (gryphons) in the Salton Trough of southeastern California. Its location puts it in line with the mapped San Andreas Fault, if extended further south, as well as within the poorly-understood Brawley Seismic Zone. Much of the geomorphology, geochemistry, and other characteristics of the DSSF have been analyzed, but its subsurface structure remains unknown. Here we present data and interpretations from five new temperature time­series from four separate gryphons at the DSSF, and compare them both amongst themselves, and within the context of all previously collected data to identify possible patterns constraining the subsurface dynamics. Simultaneously collected time-series from different seeps were cross-correlated to quantify similarity. All years' time-series were checked against the record of local seismicity to identify any seismic influence on temperature excursions. Time-series captured from the same feature in different years were statistically summarized and the results plotted to examine their evolution over time. We found that adjacent vents often alternate in temperature, suggesting a switching of flow path of the erupted mud at the scale of a few meters or less. Noticeable warming over time was observed in most of the features with time-series covering multiple years. No synchronicity was observed between DSSF features' temperature excursions, and seismic events within a 24 kilometer radius covering most of the width of the surrounding Salton Trough.

Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons

PubMed Central

Gelfman, Sahar; Burstein, David; Penn, Osnat; Savchenko, Anna; Amit, Maayan; Schwartz, Schraga; Pupko, Tal; Ast, Gil

2012-01-01

Exon–intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon–intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3′ and 5′ splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long introns. Reconstruction of the ancestral state suggests these phenomena were not prevalent in the vertebrate ancestor, but appeared during vertebrate evolution. By calculating evolutionary rate shifts in exons, we identified cis-acting regulatory sequences that became fixed during the transition from early vertebrates to mammals. Experimental validations performed on a selection of these hexamers confirmed their regulatory function. We additionally revealed many features of exons that can discriminate alternative from constitutive exons. These features were integrated into a machine-learning approach to predict whether an exon is alternative. Our algorithm obtains very high predictive power (AUC of 0.91), and using these predictions we have identified and successfully validated novel alternatively spliced exons. Overall, we provide novel insights regarding the evolutionary constraints acting upon exons and their recognition by the splicing machinery. PMID:21974994

Characterization of unknown brominated disinfection byproducts during chlorination using ultrahigh resolution mass spectrometry.

PubMed

Zhang, Haifeng; Zhang, Yahe; Shi, Quan; Zheng, Hongdie; Yang, Min

2014-03-18

Brominated disinfection byproducts (Br-DBPs), formed from the reaction of disinfectant(s) with natural organic matter in the presence of bromide in raw water, are generally more cytotoxic and genotoxic than their chlorinated analogues. To date, only a few Br-DBPs in drinking water have been identified, while a significant portion of Br-DBPs in drinking water is still unknown. In this study, negative ion electrospray ionization ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) was used to characterize unknown Br-DBPs in artificial drinking water. In total, 441 formulas for one-bromine-containing products and 37 formulas for two-bromine-containing products, most of which had not been previously reported, were detected in the chlorinated sample. Most Br-DBPs have corresponding chlorine-containing analogues with identical CHO composition. In addition, on-resonance collision-induced dissociation (CID) of single ultrahigh resolved bromine containing mass peaks was performed in the ICR cell to isolate single bromine-containing components in a very complex natural organic matter spectrum and provide structure information. Relatively abundant neutral loss of CO2 was observed in MS-MS spectra, indicating that the unknown Br-DBPs are rich in carboxyl groups. The results demonstrate that the ESI FT-ICR MS method could provide valuable molecular composition and structure information on unknown Br-DBPs.

Intermediate phases in some rare earth-ruthenium systems

NASA Technical Reports Server (NTRS)

Sharifrazi, P.; Raman, A.; Mohanty, R. C.

1984-01-01

The phase equilibria and crystal structures of intermediate phases were investigated in eight representative RE-Ru systems using powder X-ray diffraction and metallographic techniques. The Fe3C, Mn5C2 and Er5Ru3 structures occur in all but the Ce-Ru systems. Phases analogous to Er5Ru3 possess an unknown crystal structure similar to Er5Rh3(I). MgCu2 and MgZn2 type Laves phases are encountered in the light rare earth and heavy rare earth systems, respectively, and RERu2 phases, where RE = Nd and Sm, possess both the Laves phase structures. An intermediate phase, NdRu, with an unknown structure, occurs only in the Nd-Ru system. A bcc structure with 40 atoms per unit cell is encountered in the phases Er3Ru2 and Y3Ru2. The behavior of cerium in Ce-Ru alloys is unique in that four unidentified structures, not encountered in other RE-Ru systems, have been encountered. Also a phase designated as Ce3Ru is found with the Th7Fe3 type structure.

Usher syndrome with psychotic symptoms: two cases in the same family.

PubMed

Wu, Chen-Ying; Chiu, Chih-Chiang

2006-10-01

Usher syndrome is a heterogeneous autosomal recessive disorder characterized by hearing and visual sensory impairment. Retinitis pigmentosa is essential for its diagnosis. There are only a few reports describing patients with Usher syndrome presenting with psychotic features and the etiology of its psychiatric manifestation is still unknown. Herein, the authors report variable congenital hearing impairment and progressive visual loss occurring in five of seven family members and two of them meeting the diagnostic criteria of Usher syndrome with psychotic features. Furthermore, the authors compare their psychiatric symptoms with other reports and the possible etiologies of psychotic symptoms are discussed.

Growth hormone deficiency: an unusual presentation of floating harbor syndrome.

PubMed

Galli-Tsinopoulou, Assimina; Kyrgios, Ioannis; Emmanouilidou, Eleftheria; Maggana, Ioanna; Kotanidou, Eleni; Kokka, Paraskevi; Stylianou, Charilaos

2011-01-01

Floating-Harbor Syndrome (FHS) is a very rare condition of unknown etiology characterized by short stature, delayed bone age, characteristic facial features, delayed language skills and usually normal motor development. This syndrome has only once been associated with growth hormone deficiency and precocious puberty in the same patient. We describe a 5 4/12 year-old girl with the typical features of FHS in whom growth hormone deficiency was diagnosed and two years later central precocious puberty was noted. The patient showed a good response to human recombinant growth hormone as well as gonadotropin releasing hormone analogue treatment.

Chronic systemic pesticide exposure reproduces features of Parkinson's disease.

PubMed

Betarbet, R; Sherer, T B; MacKenzie, G; Garcia-Osuna, M; Panov, A V; Greenamyre, J T

2000-12-01

The cause of Parkinson's disease (PD) is unknown, but epidemiological studies suggest an association with pesticides and other environmental toxins, and biochemical studies implicate a systemic defect in mitochondrial complex I. We report that chronic, systemic inhibition of complex I by the lipophilic pesticide, rotenone, causes highly selective nigrostriatal dopaminergic degeneration that is associated behaviorally with hypokinesia and rigidity. Nigral neurons in rotenone-treated rats accumulate fibrillar cytoplasmic inclusions that contain ubiquitin and alpha-synuclein. These results indicate that chronic exposure to a common pesticide can reproduce the anatomical, neurochemical, behavioral and neuropathological features of PD.

Metamorphic Testing for Cybersecurity.

PubMed

Chen, Tsong Yueh; Kuo, Fei-Ching; Ma, Wenjuan; Susilo, Willy; Towey, Dave; Voas, Jeffrey; Zhou, Zhi Quan

2016-06-01

Testing is a major approach for the detection of software defects, including vulnerabilities in security features. This article introduces metamorphic testing (MT), a relatively new testing method, and discusses how the new perspective of MT can help to conduct negative testing as well as to alleviate the oracle problem in the testing of security-related functionality and behavior. As demonstrated by the effectiveness of MT in detecting previously unknown bugs in real-world critical applications such as compilers and code obfuscators, we conclude that software testing of security-related features should be conducted from diverse perspectives in order to achieve greater cybersecurity.

Metamorphic Testing for Cybersecurity

PubMed Central

Chen, Tsong Yueh; Kuo, Fei-Ching; Ma, Wenjuan; Susilo, Willy; Towey, Dave; Voas, Jeffrey

2016-01-01

Testing is a major approach for the detection of software defects, including vulnerabilities in security features. This article introduces metamorphic testing (MT), a relatively new testing method, and discusses how the new perspective of MT can help to conduct negative testing as well as to alleviate the oracle problem in the testing of security-related functionality and behavior. As demonstrated by the effectiveness of MT in detecting previously unknown bugs in real-world critical applications such as compilers and code obfuscators, we conclude that software testing of security-related features should be conducted from diverse perspectives in order to achieve greater cybersecurity. PMID:27559196

Matrix- and tensor-based recommender systems for the discovery of currently unknown inorganic compounds

NASA Astrophysics Data System (ADS)

Seko, Atsuto; Hayashi, Hiroyuki; Kashima, Hisashi; Tanaka, Isao

2018-01-01

Chemically relevant compositions (CRCs) and atomic arrangements of inorganic compounds have been collected as inorganic crystal structure databases. Machine learning is a unique approach to search for currently unknown CRCs from vast candidates. Herein we propose matrix- and tensor-based recommender system approaches to predict currently unknown CRCs from database entries of CRCs. Firstly, the performance of the recommender system approaches to discover currently unknown CRCs is examined. A Tucker decomposition recommender system shows the best discovery rate of CRCs as the majority of the top 100 recommended ternary and quaternary compositions correspond to CRCs. Secondly, systematic density functional theory (DFT) calculations are performed to investigate the phase stability of the recommended compositions. The phase stability of the 27 compositions reveals that 23 currently unknown compounds are newly found to be stable. These results indicate that the recommender system has great potential to accelerate the discovery of new compounds.

Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics

PubMed Central

Shevchuk, Roman; Hub, Jochen S.

2017-01-01

Small-angle X-ray scattering is an increasingly popular technique used to detect protein structures and ensembles in solution. However, the refinement of structures and ensembles against SAXS data is often ambiguous due to the low information content of SAXS data, unknown systematic errors, and unknown scattering contributions from the solvent. We offer a solution to such problems by combining Bayesian inference with all-atom molecular dynamics simulations and explicit-solvent SAXS calculations. The Bayesian formulation correctly weights the SAXS data versus prior physical knowledge, it quantifies the precision or ambiguity of fitted structures and ensembles, and it accounts for unknown systematic errors due to poor buffer matching. The method further provides a probabilistic criterion for identifying the number of states required to explain the SAXS data. The method is validated by refining ensembles of a periplasmic binding protein against calculated SAXS curves. Subsequently, we derive the solution ensembles of the eukaryotic chaperone heat shock protein 90 (Hsp90) against experimental SAXS data. We find that the SAXS data of the apo state of Hsp90 is compatible with a single wide-open conformation, whereas the SAXS data of Hsp90 bound to ATP or to an ATP-analogue strongly suggest heterogenous ensembles of a closed and a wide-open state. PMID:29045407

Spontaneously amplified homochiral organic-inorganic nano-helix complexes via self-proliferation.

PubMed

Zhai, Halei; Quan, Yan; Li, Li; Liu, Xiang-Yang; Xu, Xurong; Tang, Ruikang

2013-04-07

Most spiral coiled biomaterials in nature, such as gastropod shells, are homochiral, and the favoured chiral feature can be precisely inherited. This inspired us that selected material structures, including chirality, could be specifically replicated into the self-similar populations; however, a physicochemical understanding of the material-based heritage is unknown. We study the homochirality by using calcium phosphate mineralization in the presence of racemic amphiphilic molecules and biological protein. The organic-inorganic hybrid materials with spiral coiling characteristics are produced at the nanoscale. The resulted helixes are chiral with the left- and right-handed characteristics, which are agglomerated hierarchically to from clusters and networks. It is interesting that each cluster or network is homochiral so that the enantiomorphs can be separated readily. Actually, each homochiral architecture is evolved from an original chiral helix, demonstrating the heritage of the matrix chirality during the material proliferation under a racemic condition. By using the Ginzburg-Landaue expression we find that the chiral recognition in the organic-inorganic hybrid formation may be determined by a spontaneous chiral separation and immobilization of asymmetric amphiphilic molecules on the mineral surface, which transferred the structural information from the mother matrix to the descendants by an energetic control. This study shows how biomolecules guide the selective amplification of chiral materials via spontaneous self-replication. Such a strategy can be applied generally in the design and production of artificial materials with self-similar structure characteristics.

Visual object agnosia is associated with a breakdown of object-selective responses in the lateral occipital cortex.

PubMed

Ptak, Radek; Lazeyras, François; Di Pietro, Marie; Schnider, Armin; Simon, Stéphane R

2014-07-01

Patients with visual object agnosia fail to recognize the identity of visually presented objects despite preserved semantic knowledge. Object agnosia may result from damage to visual cortex lying close to or overlapping with the lateral occipital complex (LOC), a brain region that exhibits selectivity to the shape of visually presented objects. Despite this anatomical overlap the relationship between shape processing in the LOC and shape representations in object agnosia is unknown. We studied a patient with object agnosia following isolated damage to the left occipito-temporal cortex overlapping with the LOC. The patient showed intact processing of object structure, yet often made identification errors that were mainly based on the global visual similarity between objects. Using functional Magnetic Resonance Imaging (fMRI) we found that the damaged as well as the contralateral, structurally intact right LOC failed to show any object-selective fMRI activity, though the latter retained selectivity for faces. Thus, unilateral damage to the left LOC led to a bilateral breakdown of neural responses to a specific stimulus class (objects and artefacts) while preserving the response to a different stimulus class (faces). These findings indicate that representations of structure necessary for the identification of objects crucially rely on bilateral, distributed coding of shape features. Copyright © 2014 Elsevier Ltd. All rights reserved.

3D bioprinting matrices with controlled pore structure and release function guide in vitro self-organization of sweat gland.

PubMed

Liu, Nanbo; Huang, Sha; Yao, Bin; Xie, Jiangfan; Wu, Xu; Fu, Xiaobing

2016-10-03

3D bioprinting matrices are novel platforms for tissue regeneration. Tissue self-organization is a critical process during regeneration that implies the features of organogenesis. However, it is not clear from the current evidences whether 3D printed construct plays a role in guiding tissue self-organization in vitro. Based on our previous study, we bioprinted a 3D matrix as the restrictive niche for direct sweat gland differentiation of epidermal progenitors by different pore structure (300-μm or 400-μm nozzle diameters printed) and reported a long-term gradual transition of differentiated cells into glandular morphogenesis occurs within the 3D construct in vitro. At the initial 14-day culture, an accelerated cell differentiation was achieved with inductive cues released along with gelatin reduction. After protein release completed, the 3D construct guide the self-organized formation of sweat gland tissues, which is similar to that of the natural developmental process. However, glandular morphogenesis was only observed in 300-μm-printed constructs. In the absence of 3D architectural support, glandular morphogenesis was not occurred. This striking finding made us to identify a previously unknown role of the 3D-printed structure in glandular tissue regeneration, and this self-organizing strategy can be applied to forming other tissues in vitro.

Prediction of the characteristics of two types of pressure waves in the cochlea: Theoretical considerations

NASA Astrophysics Data System (ADS)

Andoh, Masayoshi; Wada, Hiroshi

2004-07-01

The aim of this study was to predict the characteristics of two types of cochlear pressure waves, so-called fast and slow waves. A two-dimensional finite-element model of the organ of Corti (OC), including fluid-structure interaction with the surrounding lymph fluid, was constructed. The geometry of the OC at the basal turn was determined from morphological measurements of others in the gerbil hemicochlea. As far as mechanical properties of the materials within the OC are concerned, previously determined mechanical properties of portions within the OC were adopted, and unknown mechanical features were determined from the published measurements of static stiffness. Time advance of the fluid-structure scheme was achieved by a staggered approach. Using the model, the magnitude and phase of the fast and slow waves were predicted so as to fit the numerically obtained pressure distribution in the scala tympani with what is known about intracochlear pressure measurement. When the predicted pressure waves were applied to the model, the numerical result of the velocity of the basilar membrane showed good agreement with the experimentally obtained velocity of the basilar membrane documented by others. Thus, the predicted pressure waves appeared to be reliable. Moreover, it was found that the fluid-structure interaction considerably influences the dynamic behavior of the OC at frequencies near the characteristic frequency.

Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.

PubMed

Jelínek, Jan; Škoda, Petr; Hoksza, David

2017-12-06

Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has been an active field of research for some time, the quality of in-silico methods is still far from perfect. We have developed a novel prediction method called INSPiRE which benefits from a knowledge base built from data available in Protein Data Bank. All proteins involved in PPIs were converted into labeled graphs with nodes corresponding to amino acids and edges to pairs of neighboring amino acids. A structural neighborhood of each node was then encoded into a bit string and stored in the knowledge base. When predicting PPIs, INSPiRE labels amino acids of unknown proteins as interface or non-interface based on how often their structural neighborhood appears as interface or non-interface in the knowledge base. We evaluated INSPiRE's behavior with respect to different types and sizes of the structural neighborhood. Furthermore, we examined the suitability of several different features for labeling the nodes. Our evaluations showed that INSPiRE clearly outperforms existing methods with respect to Matthews correlation coefficient. In this paper we introduce a new knowledge-based method for identification of protein-protein interaction sites called INSPiRE. Its knowledge base utilizes structural patterns of known interaction sites in the Protein Data Bank which are then used for PPI prediction. Extensive experiments on several well-established datasets show that INSPiRE significantly surpasses existing PPI approaches.

Structure Identification Using the US EPA's CompTox Chemistry Dashboard (CompTox CoP)

EPA Science Inventory

Community of practice webinar presentation on the Identification of unknowns in non-targeted analyses (NTA) requires the integration of complementary data types to generate a confident consensus structure.

Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C).

PubMed

McErlean, Peter; Shackelton, Laura A; Andrews, Emily; Webster, Dale R; Lambert, Stephen B; Nissen, Michael D; Sloots, Theo P; Mackay, Ian M

2008-04-02

Human rhinoviruses (HRVs) are the most frequently detected pathogens in acute respiratory tract infections (ARTIs) and yet little is known about the prevalence, recurrence, structure and clinical impact of individual members. During 2007, the complete coding sequences of six previously unknown and highly divergent HRV strains were reported. To catalogue the molecular and clinical features distinguishing the divergent HRV strains, we undertook, for the first time, in silico analyses of all available polyprotein sequences and performed retrospective reviews of the medical records of cases in which variants of the prototype strain, HRV-QPM, had been detected. Genomic analyses revealed that the six divergent strains, residing within a clade we previously called HRV A2, had the shortest polyprotein of all picornaviruses investigated. Structure-based amino acid alignments identified conserved motifs shared among members of the genus Rhinovirus as well as substantive deletions and insertions unique to the divergent strains. Deletions mostly affected regions encoding proteins traditionally involved in antigenicity and serving as HRV and HEV receptor footprints. Because the HRV A2 strains cannot yet be cultured, we created homology models of predicted HRV-QPM structural proteins. In silico comparisons confirmed that HRV-QPM was most closely related to the major group HRVs. HRV-QPM was most frequently detected in infants with expiratory wheezing or persistent cough who had been admitted to hospital and required supplemental oxygen. It was the only virus detected in 65% of positive individuals. These observations contributed to an objective clinical impact ranging from mild to severe. The divergent strains did not meet classification requirements for any existing species of the genus Rhinovirus or Enterovirus. HRV A2 strains should be partitioned into at least one new species, putatively called Human rhinovirus C, populated by members detected with high frequency, from individuals with respiratory symptoms requiring hospital admission.

Radio-nuclide mixture identification using medium energy resolution detectors

DOEpatents

Nelson, Karl Einar

2013-09-17

According to one embodiment, a method for identifying radio-nuclides includes receiving spectral data, extracting a feature set from the spectral data comparable to a plurality of templates in a template library, and using a branch and bound method to determine a probable template match based on the feature set and templates in the template library. In another embodiment, a device for identifying unknown radio-nuclides includes a processor, a multi-channel analyzer, and a memory operatively coupled to the processor, the memory having computer readable code stored thereon. The computer readable code is configured, when executed by the processor, to receive spectral data, to extract a feature set from the spectral data comparable to a plurality of templates in a template library, and to use a branch and bound method to determine a probable template match based on the feature set and templates in the template library.

Oral lichenoid lesions: distinguishing the benign from the deadly.

PubMed

Müller, Susan

2017-01-01

Oral lichen planus is a chronic inflammatory disease of unknown etiology or pathogenesis with varied disease severity that waxes and wanes over a long period of time. Although a common oral mucosal disease, accurate diagnosis is often challenging due to the overlapping clinical and histopathological features of oral lichen planus and other mucosal diseases. Other immune-mediated mucocutaneous diseases can exhibit lichenoid features including mucous membrane pemphigoid, chronic graft-versus-host disease, and discoid lupus erythematosus. Reactive changes to dental materials or to systemic medications can mimic oral lichen planus both clinically and histologically. In these situations the clinical presentation can be useful, as oral lichen planus presents as a multifocal process and is usually symmetrical and bilateral. Dysplasia of the oral cavity can exhibit a lichenoid histology, which may mask the potentially premalignant features. Proliferative verrucous leukoplakia, an unusual clinical disease, can often mimic oral lichen planus clinically, requiring careful correlation of the clinical and pathologic features.

In vacuo dispersion features for gamma-ray-burst neutrinos and photons

NASA Astrophysics Data System (ADS)

Amelino-Camelia, Giovanni; D'Amico, Giacomo; Rosati, Giacomo; Loret, Niccoló

2017-07-01

Over the past 15 years there has been considerable interest in the possibility of quantum-gravity-induced in vacuo dispersion, the possibility that spacetime itself might behave essentially like a dispersive medium for particle propagation. Two recent studies have exposed what might be in vacuo dispersion features for gamma-ray-burst (GRB) neutrinos of energy in the range of 100 TeV and for GRB photons with energy in the range of 10 GeV. We here show that these two features are roughly compatible with a description such that the same effects apply over four orders of magnitude in energy. We also show that it should not happen so frequently that such pronounced features arise accidentally, as a result of (still unknown) aspects of the mechanisms producing photons at GRBs or as a result of background neutrinos accidentally fitting the profile of a GRB neutrino affected by in vacuo dispersion.

Cracking the Neural Code for Sensory Perception by Combining Statistics, Intervention, and Behavior.

PubMed

Panzeri, Stefano; Harvey, Christopher D; Piasini, Eugenio; Latham, Peter E; Fellin, Tommaso

2017-02-08

The two basic processes underlying perceptual decisions-how neural responses encode stimuli, and how they inform behavioral choices-have mainly been studied separately. Thus, although many spatiotemporal features of neural population activity, or "neural codes," have been shown to carry sensory information, it is often unknown whether the brain uses these features for perception. To address this issue, we propose a new framework centered on redefining the neural code as the neural features that carry sensory information used by the animal to drive appropriate behavior; that is, the features that have an intersection between sensory and choice information. We show how this framework leads to a new statistical analysis of neural activity recorded during behavior that can identify such neural codes, and we discuss how to combine intersection-based analysis of neural recordings with intervention on neural activity to determine definitively whether specific neural activity features are involved in a task. Copyright © 2017 Elsevier Inc. All rights reserved.

Bayesian Semiparametric Structural Equation Models with Latent Variables

ERIC Educational Resources Information Center

Yang, Mingan; Dunson, David B.

2010-01-01

Structural equation models (SEMs) with latent variables are widely useful for sparse covariance structure modeling and for inferring relationships among latent variables. Bayesian SEMs are appealing in allowing for the incorporation of prior information and in providing exact posterior distributions of unknowns, including the latent variables. In…

A multiple-dimension liquid chromatography coupled with mass spectrometry data strategy for the rapid discovery and identification of unknown compounds from a Chinese herbal formula (Er-xian decoction).

PubMed

Wang, Caihong; Zhang, Jinlan; Wu, Caisheng; Wang, Zhe

2017-10-06

It is very important to rapidly discover and identify the multiple components of traditional Chinese medicine (TCM) formula. High performance liquid chromatography with high resolution tandem mass spectrometry (HPLC-HRMS/MS) has been widely used to analyze TCM formula and contains multiple-dimension data including retention time (RT), high resolution mass (HRMS), multiple-stage mass spectrometric (MS n ), and isotope intensity distribution (IID) data. So it is very necessary to exploit a useful strategy to utilize multiple-dimension data to rapidly probe structural information and identify chemical compounds. In this study, a new strategy to initiatively use the multiple-dimension LC-MS data has been developed to discover and identify unknown compounds of TCM in many styles. The strategy guarantees the fast discovery of candidate structural information and provides efficient structure clues for identification. The strategy contains four steps in sequence: (1) to discover potential compounds and obtain sub-structure information by the mass spectral tree similarity filter (MTSF) technique, based on HRMS and MS n data; (2) to classify potential compounds into known chemical classes by discriminant analysis (DA) on the basis of RT and HRMS data; (3) to hit the candidate structural information of compounds by intersection sub-structure between MTSF and DA (M,D-INSS); (4) to annotate and confirm candidate structures by IID data. This strategy allowed for the high exclusion efficiency (greater than 41%) of irrelevant ions in er-xian decoction (EXD) while providing accurate structural information of 553 potential compounds and identifying 66 candidates, therefore accelerating and simplifying the discovery and identification of unknown compounds in TCM formula. Copyright © 2017 Elsevier B.V. All rights reserved.

Serologic Evidence of Powassan Virus Infection in Patients with Suspected Lyme Disease1.

PubMed

Frost, Holly M; Schotthoefer, Anna M; Thomm, Angela M; Dupuis, Alan P; Kehl, Sue C; Kramer, Laura D; Fritsche, Thomas R; Harrington, Yvette A; Knox, Konstance K

2017-08-01

Powassan virus (POWV) lineage II is an emerging tickborne flavivirus with an unknown seroprevalence in humans. In a Lyme disease-endemic area, we examined the seroreactivity to POWV in 2 patient cohorts and described the clinical features of the POWV-seroreactive patients. POWV disease might be less neuroinvasive than previously thought.

Serologic Evidence of Powassan Virus Infection in Patients with Suspected Lyme Disease1

PubMed Central

Schotthoefer, Anna M.; Thomm, Angela M.; Dupuis, Alan P.; Kehl, Sue C.; Kramer, Laura D.; Fritsche, Thomas R.; Harrington, Yvette A.; Knox, Konstance K.

2017-01-01

Powassan virus (POWV) lineage II is an emerging tickborne flavivirus with an unknown seroprevalence in humans. In a Lyme disease–endemic area, we examined the seroreactivity to POWV in 2 patient cohorts and described the clinical features of the POWV-seroreactive patients. POWV disease might be less neuroinvasive than previously thought. PMID:28726610

Prevalence of Clinically and Empirically Defined Talents and Strengths in Autism

ERIC Educational Resources Information Center

Meilleur, Andrée-Anne S.; Jelenic, Patricia; Mottron, Laurent

2015-01-01

Outstanding skills, including special isolated skills (SIS) and perceptual peaks (PP) are frequent features of autism. However, their reported prevalence varies between studies and their co-occurrence is unknown. We determined the prevalence of SIS in a large group of 254 autistic individuals and searched for PP in 46 of these autistic individuals…

Category vs. Object Knowledge in Category-Based Induction

ERIC Educational Resources Information Center

Murphy, Gregory L.; Ross, Brian H.

2010-01-01

In one form of category-based induction, people make predictions about unknown properties of objects. There is a tension between predictions made based on the object's specific features (e.g., objects above a certain size tend not to fly) and those made by reference to category-level knowledge (e.g., birds fly). Seven experiments with artificial…

41. Photocopy of progress photograph ca. 1974, photographer unknown. Original ...

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

41. Photocopy of progress photograph ca. 1974, photographer unknown. Original photograph Property of United States Air Force, 21" Space Command. This is the source for views 41 to 47. CAPE COD AIR STATION PAVE PAWS FACILITY - SHOWING BUILDING "RED IRON" STEEL STRUCTURE NEARING COMPLETION. - Cape Cod Air Station, Technical Facility-Scanner Building & Power Plant, Massachusetts Military Reservation, Sandwich, Barnstable County, MA

Map generation in unknown environments by AUKF-SLAM using line segment-type and point-type landmarks

NASA Astrophysics Data System (ADS)

Nishihta, Sho; Maeyama, Shoichi; Watanebe, Keigo

2018-02-01

Recently, autonomous mobile robots that collect information at disaster sites are being developed. Since it is difficult to obtain maps in advance in disaster sites, the robots being capable of autonomous movement under unknown environments are required. For this objective, the robots have to build maps, as well as the estimation of self-location. This is called a SLAM problem. In particular, AUKF-SLAM which uses corners in the environment as point-type landmarks has been developed as a solution method so far. However, when the robots move in an environment like a corridor consisting of few point-type features, the accuracy of self-location estimated by the landmark is decreased and it causes some distortions in the map. In this research, we propose AUKF-SLAM which uses walls in the environment as a line segment-type landmark. We demonstrate that the robot can generate maps in unknown environment by AUKF-SLAM, using line segment-type and point-type landmarks.

shiftNMFk 1.1: Robust Nonnegative matrix factorization with kmeans clustering and signal shift, for allocation of unknown physical sources, toy version for open sourcing with publications

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

Alexandrov, Boian S.; Lliev, Filip L.; Stanev, Valentin G.

This code is a toy (short) version of CODE-2016-83. From a general perspective, the code represents an unsupervised adaptive machine learning algorithm that allows efficient and high performance de-mixing and feature extraction of a multitude of non-negative signals mixed and recorded by a network of uncorrelated sensor arrays. The code identifies the number of the mixed original signals and their locations. Further, the code also allows deciphering of signals that have been delayed in regards to the mixing process in each sensor. This code is high customizable and it can be efficiently used for a fast macro-analyses of data. Themore » code is applicable to a plethora of distinct problems: chemical decomposition, pressure transient decomposition, unknown sources/signal allocation, EM signal decomposition. An additional procedure for allocation of the unknown sources is incorporated in the code.« less

Near-island biological hotspots in barren ocean basins

PubMed Central

Gove, Jamison M.; McManus, Margaret A.; Neuheimer, Anna B.; Polovina, Jeffrey J.; Drazen, Jeffrey C.; Smith, Craig R.; Merrifield, Mark A.; Friedlander, Alan M.; Ehses, Julia S.; Young, Charles W.; Dillon, Amanda K.; Williams, Gareth J.

2016-01-01

Phytoplankton production drives marine ecosystem trophic-structure and global fisheries yields. Phytoplankton biomass is particularly influential near coral reef islands and atolls that span the oligotrophic tropical oceans. The paradoxical enhancement in phytoplankton near an island-reef ecosystem—Island Mass Effect (IME)—was first documented 60 years ago, yet much remains unknown about the prevalence and drivers of this ecologically important phenomenon. Here we provide the first basin-scale investigation of IME. We show that IME is a near-ubiquitous feature among a majority (91%) of coral reef ecosystems surveyed, creating near-island ‘hotspots' of phytoplankton biomass throughout the upper water column. Variations in IME strength are governed by geomorphic type (atoll vs island), bathymetric slope, reef area and local human impacts (for example, human-derived nutrient input). These ocean oases increase nearshore phytoplankton biomass by up to 86% over oceanic conditions, providing basal energetic resources to higher trophic levels that support subsistence-based human populations. PMID:26881874

Nanomorphology Effects in Semiconductors with Native Ferromagnetism: Hierarchical Europium (II) Oxide Tubes Prepared via a Topotactic Nanostructure Transition.

PubMed

Trepka, Bastian; Erler, Philipp; Selzer, Severin; Kollek, Tom; Boldt, Klaus; Fonin, Mikhail; Nowak, Ulrich; Wolf, Daniel; Lubk, Axel; Polarz, Sebastian

2018-01-01

Semiconductors with native ferromagnetism barely exist and defined nanostructures are almost unknown. This lack impedes the exploration of a new class of materials characterized by a direct combination of effects on the electronic system caused by quantum confinement effects with magnetism. A good example is EuO for which currently no reliable routes for nanoparticle synthesis can be established. Bottom-up approaches applicable to other oxides fail because of the labile oxidation state +II. Instead of targeting a direct synthesis, the two steps-"structure control" and "chemical transformation"-are separated. The generation of a transitional, hybrid nanophase is followed by its conversion into EuO under full conservation of all morphological features. Hierarchical EuO materials are now accessible in the shape of oriented nanodisks stacked to tubular particles. Magnetically, the coupling of either vortex or onion states has been found. An unexpected temperature dependence is governed by thermally activated transitions between these states. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The impact of large-scale, long-term optical surveys on pulsating star research

NASA Astrophysics Data System (ADS)

Soszyński, Igor

2017-09-01

The era of large-scale photometric variability surveys began a quarter of a century ago, when three microlensing projects - EROS, MACHO, and OGLE - started their operation. These surveys initiated a revolution in the field of variable stars and in the next years they inspired many new observational projects. Large-scale optical surveys multiplied the number of variable stars known in the Universe. The huge, homogeneous and complete catalogs of pulsating stars, such as Cepheids, RR Lyrae stars, or long-period variables, offer an unprecedented opportunity to calibrate and test the accuracy of various distance indicators, to trace the three-dimensional structure of the Milky Way and other galaxies, to discover exotic types of intrinsically variable stars, or to study previously unknown features and behaviors of pulsators. We present historical and recent findings on various types of pulsating stars obtained from the optical large-scale surveys, with particular emphasis on the OGLE project which currently offers the largest photometric database among surveys for stellar variability.

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

DOE PAGES

Nik-Zainal, Serena; Davies, Helen; Staaf, Johan; ...

2016-05-02

Here, we analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, anothermore » with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.« less

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

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

Nik-Zainal, Serena; Davies, Helen; Staaf, Johan

Here, we analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, anothermore » with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.« less

Advances in computational metabolomics and databases deepen the understanding of metabolisms.

PubMed

Tsugawa, Hiroshi

2018-01-29

Mass spectrometry (MS)-based metabolomics is the popular platform for metabolome analyses. Computational techniques for the processing of MS raw data, for example, feature detection, peak alignment, and the exclusion of false-positive peaks, have been established. The next stage of untargeted metabolomics would be to decipher the mass fragmentation of small molecules for the global identification of human-, animal-, plant-, and microbiota metabolomes, resulting in a deeper understanding of metabolisms. This review is an update on the latest computational metabolomics including known/expected structure databases, chemical ontology classifications, and mass spectrometry cheminformatics for the interpretation of mass fragmentations and for the elucidation of unknown metabolites. The importance of metabolome 'databases' and 'repositories' is also discussed because novel biological discoveries are often attributable to the accumulation of data, to relational databases, and to their statistics. Lastly, a practical guide for metabolite annotations is presented as the summary of this review. Copyright © 2018 Elsevier Ltd. All rights reserved.

Post-transcriptional trafficking and regulation of neuronal gene expression.

PubMed

Goldie, Belinda J; Cairns, Murray J

2012-02-01

Intracellular messenger RNA (mRNA) traffic and translation must be highly regulated, both temporally and spatially, within eukaryotic cells to support the complex functional partitioning. This capacity is essential in neurons because it provides a mechanism for rapid input-restricted activity-dependent protein synthesis in individual dendritic spines. While this feature is thought to be important for synaptic plasticity, the structures and mechanisms that support this capability are largely unknown. Certainly specialized RNA binding proteins and binding elements in the 3' untranslated region (UTR) of translationally regulated mRNA are important, but the subtlety and complexity of this system suggests that an intermediate "specificity" component is also involved. Small non-coding microRNA (miRNA) are essential for CNS development and may fulfill this role by acting as the guide strand for mediating complex patterns of post-transcriptional regulation. In this review we examine post-synaptic gene regulation, mRNA trafficking and the emerging role of post-transcriptional gene silencing in synaptic plasticity.

Bulk measurements of messy chemistries are needed for a theory of the origins of life

NASA Astrophysics Data System (ADS)

Guttenberg, Nicholas; Virgo, Nathaniel; Chandru, Kuhan; Scharf, Caleb; Mamajanov, Irena

2017-11-01

A feature of many of the chemical systems plausibly involved in the origins of terrestrial life is that they are complex and messy-producing a wide range of compounds via a wide range of mechanisms. However, the fundamental behaviour of such systems is currently not well understood; we do not have the tools to make statistical predictions about such complex chemical networks. This is, in part, due to a lack of quantitative data from which such a theory could be built; specifically, functional measurements of messy chemical systems. Here, we propose that the pantheon of experimental approaches to the origins of life should be expanded to include the study of `functional measurements'-the direct study of bulk properties of chemical systems and their interactions with other compounds, the formation of structures and other behaviours, even in cases where the precise composition and mechanisms are unknown. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Cygnus A super-resolved via convex optimization from VLA data

NASA Astrophysics Data System (ADS)

Dabbech, A.; Onose, A.; Abdulaziz, A.; Perley, R. A.; Smirnov, O. M.; Wiaux, Y.

2018-05-01

We leverage the Sparsity Averaging Re-weighted Analysis approach for interferometric imaging, that is based on convex optimization, for the super-resolution of Cyg A from observations at the frequencies 8.422 and 6.678 GHz with the Karl G. Jansky Very Large Array (VLA). The associated average sparsity and positivity priors enable image reconstruction beyond instrumental resolution. An adaptive Preconditioned primal-dual algorithmic structure is developed for imaging in the presence of unknown noise levels and calibration errors. We demonstrate the superior performance of the algorithm with respect to the conventional CLEAN-based methods, reflected in super-resolved images with high fidelity. The high-resolution features of the recovered images are validated by referring to maps of Cyg A at higher frequencies, more precisely 17.324 and 14.252 GHz. We also confirm the recent discovery of a radio transient in Cyg A, revealed in the recovered images of the investigated data sets. Our MATLAB code is available online on GitHub.

The topography of mutational processes in breast cancer genomes

DOE PAGES

Morganella, Sandro; Alexandrov, Ludmil B.; Glodzik, Dominik; ...

2016-01-01

Somatic mutations in human cancers show unevenness in genomic distribution that correlate with aspects of genome structure and function. These mutations are, however, generated by multiple mutational processes operating through the cellular lineage between the fertilized egg and the cancer cell, each composed of specific DNA damage and repair components and leaving its own characteristic mutational signature on the genome. Using somatic mutation catalogues from 560 breast cancer whole-genome sequences, here we show that each of 12 base substitution, 2 insertion/deletion (indel) and 6 rearrangement mutational signatures present in breast tissue, exhibit distinct relationships with genomic features relating to transcription,more » DNA replication and chromatin organization. This signature-based approach permits visualization of the genomic distribution of mutational processes associated with APOBEC enzymes, mismatch repair deficiency and homologous recombinational repair deficiency, as well as mutational processes of unknown aetiology. Lastly, it highlights mechanistic insights including a putative replication-dependent mechanism of APOBEC-related mutagenesis.« less

Energy based simulation of a Timoshenko beam in non-forced rotation. Influence of the piano hammer shank flexibility on the sound

NASA Astrophysics Data System (ADS)

Chabassier, Juliette; Duruflé, Marc

2014-12-01

A nonlinear model for a vibrating Timoshenko beam in non-forced unknown rotation is derived from the virtual work principle applied to a system of beam with mass at the end. The system represents a piano hammer shank coupled to a hammer head. An energy-based numerical scheme is then provided, obtained by non-classical approaches. A major difficulty for time discretization comes from the nonlinear behavior of the kinetic energy of the system. This new numerical scheme is then coupled to a global energy-preserving numerical solution for the whole piano. The obtained numerical simulations show that the pianistic touch clearly influences the spectrum of the piano sound of equally loud isolated notes. These differences do not come from a possible shock excitation on the structure, or from a changing impact point, or a “longitudinal rubbing motion” on the string, since neither of these features is modeled in our study.

Parametric Transformation Analysis

NASA Technical Reports Server (NTRS)

Gary, G. Allan

2003-01-01

Because twisted coronal features are important proxies for predicting solar eruptive events, and, yet not clearly understood, we present new results to resolve the complex, non-potential magnetic field configurations of active regions. This research uses free-form deformation mathematics to generate the associated coronal magnetic field. We use a parametric representation of the magnetic field lines such that the field lines can be manipulated to match the structure of EUV and SXR coronal loops. The objective is to derive sigmoidal magnetic field solutions which allows the beta greater than 1 regions to be included, aligned and non-aligned electric currents to be calculated, and the Lorentz force to be determined. The advantage of our technique is that the solution is independent of the unknown upper and side boundary conditions, allows non-vanishing magnetic forces, and provides a global magnetic field solution, which contains high- and low-beta regimes and is consistent with all the coronal images of the region. We show that the mathematical description is unique and physical.

Gauged multisoliton baby Skyrme model

NASA Astrophysics Data System (ADS)

Samoilenka, A.; Shnir, Ya.

2016-03-01

We present a study of U (1 ) gauged modification of the 2 +1 -dimensional planar Skyrme model with a particular choice of the symmetry breaking potential term which combines a short-range repulsion and a long-range attraction. In the absence of the gauge interaction, the multisolitons of the model are aloof, as they consist of the individual constituents which are well separated. A peculiar feature of the model is that there are usually several different stable static multisoliton solutions of rather similar energy in a topological sector of given degree. We investigate the pattern of the solutions and find new previously unknown local minima. It is shown that coupling of the aloof planar multi-Skyrmions to the magnetic field strongly affects the pattern of interaction between the constituents. We analyze the dependency of the structure of the solutions, their energies, and magnetic fluxes on the strength of the gauge coupling. It is found that, generically, in the strong coupling limit, the coupling to the gauge field results in effective recovery of the rotational invariance of the configuration.

Thermodynamic assessments and inter-relationships between systems involving Al, Am, Ga, Pu, and U

NASA Astrophysics Data System (ADS)

Perron, A.; Turchi, P. E. A.; Landa, A.; Oudot, B.; Ravat, B.; Delaunay, F.

2016-12-01

A newly developed self-consistent CALPHAD thermodynamic database involving Al, Am, Ga, Pu, and U is presented. A first optimization of the slightly characterized Am-Al and completely unknown Am-Ga phase diagrams is proposed. To this end, phase diagram features as crystal structures, stoichiometric compounds, solubility limits, and melting temperatures have been studied along the U-Al → Pu-Al → Am-Al, and U-Ga → Pu-Ga → Am-Ga series, and the thermodynamic assessments involving Al and Ga alloying are compared. In addition, two distinct optimizations of the Pu-Al phase diagram are proposed to account for the low temperature and Pu-rich region controversy. The previously assessed thermodynamics of the other binary systems (Am-Pu, Am-U, Pu-U, and Al-Ga) is also included in the database and is briefly described in the present work. Finally, predictions on phase stability of ternary and quaternary systems of interest are reported to check the consistency of the database.

Architectural transitions in Vibrio cholerae biofilms at single-cell resolution

PubMed Central

Drescher, Knut; Dunkel, Jörn; Nadell, Carey D.; van Teeffelen, Sven; Grnja, Ivan; Wingreen, Ned S.; Stone, Howard A.; Bassler, Bonnie L.

2016-01-01

Many bacterial species colonize surfaces and form dense 3D structures, known as biofilms, which are highly tolerant to antibiotics and constitute one of the major forms of bacterial biomass on Earth. Bacterial biofilms display remarkable changes during their development from initial attachment to maturity, yet the cellular architecture that gives rise to collective biofilm morphology during growth is largely unknown. Here, we use high-resolution optical microscopy to image all individual cells in Vibrio cholerae biofilms at different stages of development, including colonies that range in size from 2 to 4,500 cells. From these data, we extracted the precise 3D cellular arrangements, cell shapes, sizes, and global morphological features during biofilm growth on submerged glass substrates under flow. We discovered several critical transitions of the internal and external biofilm architectures that separate the major phases of V. cholerae biofilm growth. Optical imaging of biofilms with single-cell resolution provides a new window into biofilm formation that will prove invaluable to understanding the mechanics underlying biofilm development. PMID:26933214

Quantification of coffee blends for authentication of Asian palm civet coffee (Kopi Luwak) via metabolomics: A proof of concept.

PubMed

Jumhawan, Udi; Putri, Sastia Prama; Yusianto; Bamba, Takeshi; Fukusaki, Eiichiro

2016-07-01

Asian palm civet coffee (Kopi Luwak), an animal-digested coffee with an exotic feature, carries a notorious reputation of being the rarest and most expensive coffee beverage in the world. Considering that illegal mixture of cheap coffee into civet coffee is a growing concern among consumers, we evaluated the use of metabolomics approach and orthogonal projection to latent structures (OPLS) prediction technique to quantify the degree of coffee adulteration. Two prediction sets, consisting of certified and commercial coffee, were made from a blend of civet and regular coffee with eleven mixing percentages. The prediction model exhibited accurate estimation of coffee blend percentage thus, successfully validating the prediction and quantification of the mixing composition of known-unknown samples. This work highlighted proof of concept of metabolomics application to predict degree of coffee adulteration by determining the civet coffee fraction in blends. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Thermodynamic assessments and inter-relationships between systems involving Al, Am, Ga, Pu, and U

DOE PAGES

Perron, A.; Turchi, P. E. A.; Landa, A.; ...

2016-12-01

We present a newly developed self-consistent CALPHAD thermodynamic database involving Al, Am, Ga, Pu, and U. A first optimization of the slightly characterized Am-Al and completely unknown Am-Ga phase diagrams is proposed. To this end, phase diagram features as crystal structures, stoichiometric compounds, solubility limits, and melting temperatures have been studied along the U-Al → Pu-Al → Am-Al, and U-Ga → Pu-Ga → Am-Ga series, and the thermodynamic assessments involving Al and Ga alloying are compared. In addition, two distinct optimizations of the Pu-Al phase diagram are proposed to account for the low temperature and Pu-rich region controversy. We includedmore » the previously assessed thermodynamics of the other binary systems (Am-Pu, Am-U, Pu-U, and Al-Ga) in the database and is briefly described in the present work. In conclusion, predictions on phase stability of ternary and quaternary systems of interest are reported to check the consistency of the database.« less

Landscape of somatic mutations in 560 breast cancer whole genome sequences

PubMed Central

Nik-Zainal, Serena; Davies, Helen; Staaf, Johan; Ramakrishna, Manasa; Glodzik, Dominik; Zou, Xueqing; Martincorena, Inigo; Alexandrov, Ludmil B.; Martin, Sancha; Wedge, David C.; Van Loo, Peter; Ju, Young Seok; Smid, Marcel; Brinkman, Arie B; Morganella, Sandro; Aure, Miriam R.; Lingjærde, Ole Christian; Langerød, Anita; Ringnér, Markus; Ahn, Sung-Min; Boyault, Sandrine; Brock, Jane E.; Broeks, Annegien; Butler, Adam; Desmedt, Christine; Dirix, Luc; Dronov, Serge; Fatima, Aquila; Foekens, John A.; Gerstung, Moritz; Hooijer, Gerrit KJ; Jang, Se Jin; Jones, David R.; Kim, Hyung-Yong; King, Tari A.; Krishnamurthy, Savitri; Lee, Hee Jin; Lee, Jeong-Yeon; Li, Yilong; McLaren, Stuart; Menzies, Andrew; Mustonen, Ville; O’Meara, Sarah; Pauporté, Iris; Pivot, Xavier; Purdie, Colin A.; Raine, Keiran; Ramakrishnan, Kamna; Rodríguez-González, F. Germán; Romieu, Gilles; Sieuwerts, Anieta M.; Simpson, Peter T; Shepherd, Rebecca; Stebbings, Lucy; Stefansson, Olafur A; Teague, Jon; Tommasi, Stefania; Treilleux, Isabelle; Van den Eynden, Gert G.; Vermeulen, Peter; Vincent-Salomon, Anne; Yates, Lucy; Caldas, Carlos; van’t Veer, Laura; Tutt, Andrew; Knappskog, Stian; Tan, Benita Kiat Tee; Jonkers, Jos; Borg, Åke; Ueno, Naoto T; Sotiriou, Christos; Viari, Alain; Futreal, P. Andrew; Campbell, Peter J; Span, Paul N.; Van Laere, Steven; Lakhani, Sunil R; Eyfjord, Jorunn E.; Thompson, Alastair M.; Birney, Ewan; Stunnenberg, Hendrik G; van de Vijver, Marc J; Martens, John W.M.; Børresen-Dale, Anne-Lise; Richardson, Andrea L.; Kong, Gu; Thomas, Gilles; Stratton, Michael R.

2016-01-01

We analysed whole genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. 93 protein-coding cancer genes carried likely driver mutations. Some non-coding regions exhibited high mutation frequencies but most have distinctive structural features probably causing elevated mutation rates and do not harbour driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed 12 base substitution and six rearrangement signatures. Three rearrangement signatures, characterised by tandem duplications or deletions, appear associated with defective homologous recombination based DNA repair: one with deficient BRCA1 function; another with deficient BRCA1 or BRCA2 function; the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operative, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer. PMID:27135926

Towards physics of neural processes and behavior

PubMed Central

Latash, Mark L.

2016-01-01

Behavior of biological systems is based on basic physical laws, common across inanimate and living systems, and currently unknown physical laws that are specific for living systems. Living systems are able to unite basic laws of physics into chains and clusters leading to new stable and pervasive relations among variables (new physical laws) involving new parameters and to modify these parameters in a purposeful way. Examples of such laws are presented starting from the tonic stretch reflex. Further, the idea of control with referent coordinates is formulated and merged with the idea of hierarchical control and the principle of abundance. The notion of controlled stability of behaviors is linked to the idea of structured variability, which is a common feature across living systems and actions. The explanatory and predictive power of this approach is illustrated with respect to the control of both intentional and unintentional movements, the phenomena of equifinality and its violations, preparation to quick actions, development of motor skills, changes with aging and neurological disorders, and perception. PMID:27497717

Circular RNA biogenesis can proceed through an exon-containing lariat precursor

PubMed Central

Barrett, Steven P; Wang, Peter L; Salzman, Julia

2015-01-01

Pervasive expression of circular RNA is a recently discovered feature of eukaryotic gene expression programs, yet its function remains largely unknown. The presumed biogenesis of these RNAs involves a non-canonical ‘backsplicing’ event. Recent studies in mammalian cell culture posit that backsplicing is facilitated by inverted repeats flanking the circularized exon(s). Although such sequence elements are common in mammals, they are rare in lower eukaryotes, making current models insufficient to describe circularization. Through systematic splice site mutagenesis and the identification of splicing intermediates, we show that circular RNA in Schizosaccharomyces pombe is generated through an exon-containing lariat precursor. Furthermore, we have performed high-throughput and comprehensive mutagenesis of a circle-forming exon, which enabled us to discover a systematic effect of exon length on RNA circularization. Our results uncover a mechanism for circular RNA biogenesis that may account for circularization in genes that lack noticeable flanking intronic secondary structure. DOI: http://dx.doi.org/10.7554/eLife.07540.001 PMID:26057830