aggregating partially resolved: Topics by Science.gov

Sample records for aggregating partially resolved

Properties of concrete containing ground palm oil fuel ash as fine aggregate replacement

NASA Astrophysics Data System (ADS)

Saffuan, W. A.; Muthusamy, K.; Salleh, N. A. Mohd; Nordin, N.

2017-11-01

Environmental degradation resulting from increasing sand mining activities and disposal of palm oil fuel ash (POFA), a solid waste generated from palm oil mill needs to be resolved. Thus, the present research investigates the effect of ground palm oil fuel ash as partial fine aggregate replacement on workability, compressive and flexural strength of concrete. Five mixtures of concrete containing POFA as partial sand replacement designed with 0%, 10%, 20%, 30% and 40% of POFA by the weight of sand were used in this experimental work. The cube and beam specimens were casted and water cured up to 28 days before subjected to compressive strength and flexural strength testing respectively. Finding shows that concrete workability reduces as the amount of POFA added become larger. It is worth to note that 10% of POFA is the best amount to be used as partial fine aggregate replacement to produce concrete with enhanced strength.
Aggregation Trade Offs in Family Based Recommendations

NASA Astrophysics Data System (ADS)

Berkovsky, Shlomo; Freyne, Jill; Coombe, Mac

Personalized information access tools are frequently based on collaborative filtering recommendation algorithms. Collaborative filtering recommender systems typically suffer from a data sparsity problem, where systems do not have sufficient user data to generate accurate and reliable predictions. Prior research suggested using group-based user data in the collaborative filtering recommendation process to generate group-based predictions and partially resolve the sparsity problem. Although group recommendations are less accurate than personalized recommendations, they are more accurate than general non-personalized recommendations, which are the natural fall back when personalized recommendations cannot be generated. In this work we present initial results of a study that exploits the browsing logs of real families of users gathered in an eHealth portal. The browsing logs allowed us to experimentally compare the accuracy of two group-based recommendation strategies: aggregated group models and aggregated predictions. Our results showed that aggregating individual models into group models resulted in more accurate predictions than aggregating individual predictions into group predictions.
Spatially aggregated multiclass pattern classification in functional MRI using optimally selected functional brain areas.

PubMed

Zheng, Weili; Ackley, Elena S; Martínez-Ramón, Manel; Posse, Stefan

2013-02-01

In previous works, boosting aggregation of classifier outputs from discrete brain areas has been demonstrated to reduce dimensionality and improve the robustness and accuracy of functional magnetic resonance imaging (fMRI) classification. However, dimensionality reduction and classification of mixed activation patterns of multiple classes remain challenging. In the present study, the goals were (a) to reduce dimensionality by combining feature reduction at the voxel level and backward elimination of optimally aggregated classifiers at the region level, (b) to compare region selection for spatially aggregated classification using boosting and partial least squares regression methods and (c) to resolve mixed activation patterns using probabilistic prediction of individual tasks. Brain activation maps from interleaved visual, motor, auditory and cognitive tasks were segmented into 144 functional regions. Feature selection reduced the number of feature voxels by more than 50%, leaving 95 regions. The two aggregation approaches further reduced the number of regions to 30, resulting in more than 75% reduction of classification time and misclassification rates of less than 3%. Boosting and partial least squares (PLS) were compared to select the most discriminative and the most task correlated regions, respectively. Successful task prediction in mixed activation patterns was feasible within the first block of task activation in real-time fMRI experiments. This methodology is suitable for sparsifying activation patterns in real-time fMRI and for neurofeedback from distributed networks of brain activation. Copyright © 2013 Elsevier Inc. All rights reserved.
Characterization of network structure in stereoEEG data using consensus-based partial coherence.

PubMed

Ter Wal, Marije; Cardellicchio, Pasquale; LoRusso, Giorgio; Pelliccia, Veronica; Avanzini, Pietro; Orban, Guy A; Tiesinga, Paul He

2018-06-06

Coherence is a widely used measure to determine the frequency-resolved functional connectivity between pairs of recording sites, but this measure is confounded by shared inputs to the pair. To remove shared inputs, the 'partial coherence' can be computed by conditioning the spectral matrices of the pair on all other recorded channels, which involves the calculation of a matrix (pseudo-) inverse. It has so far remained a challenge to use the time-resolved partial coherence to analyze intracranial recordings with a large number of recording sites. For instance, calculating the partial coherence using a pseudoinverse method produces a high number of false positives when it is applied to a large number of channels. To address this challenge, we developed a new method that randomly aggregated channels into a smaller number of effective channels on which the calculation of partial coherence was based. We obtained a 'consensus' partial coherence (cPCOH) by repeating this approach for several random aggregations of channels (permutations) and only accepting those activations in time and frequency with a high enough consensus. Using model data we show that the cPCOH method effectively filters out the effect of shared inputs and performs substantially better than the pseudo-inverse. We successfully applied the cPCOH procedure to human stereotactic EEG data and demonstrated three key advantages of this method relative to alternative procedures. First, it reduces the number of false positives relative to the pseudo-inverse method. Second, it allows for titration of the amount of false positives relative to the false negatives by adjusting the consensus threshold, thus allowing the data-analyst to prioritize one over the other to meet specific analysis demands. Third, it substantially reduced the number of identified interactions compared to coherence, providing a sparser network of connections from which clear spatial patterns emerged. These patterns can serve as a starting point of further analyses that provide insight into network dynamics during cognitive processes. These advantages likely generalize to other modalities in which shared inputs introduce confounds, such as electroencephalography (EEG) and magneto-encephalography (MEG). Copyright © 2018. Published by Elsevier Inc.
Using partial site aggregation to reduce bias in random utility travel cost models

NASA Astrophysics Data System (ADS)

Lupi, Frank; Feather, Peter M.

1998-12-01

We propose a "partial aggregation" strategy for defining the recreation sites that enter choice sets in random utility models. Under the proposal, the most popular sites and sites that will be the subject of policy analysis enter choice sets as individual sites while remaining sites are aggregated into groups of similar sites. The scheme balances the desire to include all potential substitute sites in the choice sets with practical data and modeling constraints. Unlike fully aggregate models, our analysis and empirical applications suggest that the partial aggregation approach reasonably approximates the results of a disaggregate model. The partial aggregation approach offers all of the data and computational advantages of models with aggregate sites but does not suffer from the same degree of bias as fully aggregate models.
Conformational transition of κ-casein in micellar environment: Insight from the tryptophan fluorescence

NASA Astrophysics Data System (ADS)

Mishra, Smruti; Meher, Geetanjali; Chakraborty, Hirak

2017-11-01

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

PubMed Central

Hutchings, Regina L.; Singh, Surinder M.; Cabello-Villegas, Javier; Mallela, Krishna M. G.

2014-01-01

One-third of protein formulations are multi-dose. These require antimicrobial preservatives (APs); however, some APs have been shown to cause protein aggregation. Our previous work on a model protein cytochrome c indicated that partial protein unfolding, rather than complete unfolding, triggers aggregation. Here, we examined the relative strength of five commonly used APs on such unfolding and aggregation, and explored whether stabilizing the aggregation “hot-spot” reduces such aggregation. All APs induced protein aggregation in the order m-cresol > phenol > benzyl alcohol > phenoxyethanol > chlorobutanol. All these enhanced the partial protein unfolding that includes a local region which was predicted to be the aggregation “hot-spot”. The extent of destabilization correlated with the extent of aggregation. Further, we show that stabilizing the “hot-spot” reduces aggregation induced by all five APs. These results indicate that m-cresol causes the most protein aggregation, whereas chlorobutanol causes the least protein aggregation. The same protein region acts as the “hot-spot” for aggregation induced by different APs, implying that developing strategies to prevent protein aggregation induced by one AP will also work for others. PMID:23169345
Pressure effects on the structure, kinetic, and thermodynamic properties of heat-induced aggregation of protein studied by FT-IR spectroscopy

NASA Astrophysics Data System (ADS)

Taniguchi, Y.; Okuno, A.; Kato, M.

2010-03-01

Pressure can retrain the heat-induced aggregation and dissociate the heat-induced aggregates. We observed the aggregation-preventing pressure effect and the aggregates-dissociating pressure effect to characterize the heat-induced aggregation of equine serum albumin (ESA) by FT-IR spectroscopy. The results suggest the α-helical structure collapses at the beginning of heat-induced aggregation through the swollen structure, and then the rearrangement of structure to the intermolecular β-sheet takes place through partially unfolded structure. We determined the activation volume for the heat-induced aggregation (ΔV# = +93 ml/mol) and the partial molar volume difference between native state and heat-induced aggregates (ΔV=+32 ml/mol). This positive partial molar volume difference suggests that the heat-induced aggregates have larger internal voids than the native structure. Moreover, the positive volume change implies that the formation of the intermolecular β-sheet is unfavorable under high pressure.
The roles of prostaglandin endoperoxides, thromboxane A2 and adenosine diphosphate in collagen-induced aggregation in man and the rat.

PubMed Central

Emms, H.; Lewis, G. P.

1986-01-01

The effects of aspirin, carboxyheptylimidazole (CHI) and creatine phosphate/creatine phosphokinase (CP/CPK) on platelet aggregation and thromboxane B2 (TxB2) formation induced by collagen have been examined in vitro. Platelets from two species, man and the rat, have been used. In man, aspirin and CHI abolished TxB2 production but only partially inhibited aggregation. CP/CPK partially inhibited aggregation and TxB2 formation. In the rat, aspirin and CHI abolished TxB2 formation but had no effect on aggregation. CP/CPK completely inhibited aggregation and partially inhibited TxB2 generation. In man, collagen-induced aggregation is largely dependent on ADP and to a lesser extent on arachidonate metabolites whereas, in the rat, ADP alone mediates aggregation induced by this agonist. The results with CP/CPK suggest that TxB2 formation is dependent either on the prior release of platelet ADP or on aggregation itself rather than being responsible for the aggregation response. PMID:3082399
Mechanisms of m-cresol induced protein aggregation studied using a model protein cytochrome c†

PubMed Central

Singh, Surinder M.; Hutchings, Regina L.; Mallela, Krishna M.G.

2014-01-01

Multi-dose protein formulations require an effective antimicrobial preservative (AP) to inhibit microbial growth during long-term storage of unused formulations. m-cresol is one such AP, but has been shown to cause protein aggregation. However, the fundamental physical mechanisms underlying such AP-induced protein aggregation are not understood. In this study, we used a model protein cytochrome c to identify the protein unfolding that triggers protein aggregation. m-cresol induced cytochrome c aggregation at preservative concentrations that are commonly used to inhibit microbial growth. Addition of m-cresol decreased the temperature at which the protein aggregated and increased the aggregation rate. However, m-cresol did not perturb the tertiary or secondary structure of cytochrome c. Instead, it populated an “invisible” partially unfolded intermediate where a local protein region around the methionine residue at position 80 was unfolded. Stabilizing the Met80 region drastically decreased the protein aggregation, which conclusively shows that this local protein region acts as an aggregation “hot-spot”. Based on these results, we propose that APs induce protein aggregation by partial rather than global unfolding. Because of the availability of site-specific probes to monitor different levels of protein unfolding, cytochrome c provided a unique advantage in characterizing the partial protein unfolding that triggers protein aggregation. PMID:21229618
Properties of concrete containing foamed concrete block waste as fine aggregate replacement

NASA Astrophysics Data System (ADS)

Muthusamy, K.; Budiea, A. M. A.; Zaidan, A. L. F.; Rasid, M. H.; Hazimmah, D. S.

2017-11-01

Environmental degradation due to excessive sand mining dumping at certain places and disposal of foamed concrete block waste from lightweight concrete producing industry are issues that should be resolved for a better and cleaner environment of the community. Thus, the main intention of this study is to investigate the potential of foamed concrete block waste as partial sand replacement in concrete production. The foamed concrete waste (FCW) used in this research that were supplied by a local lightweight concrete producing industry. The workability and compressive strength of concrete containing various percentage of foamed concrete waste as partial sand replacement has been investigated. Prior to the use, the foamed concrete waste were crushed to produce finer particles. Six concrete mixes containing various content of crushed foamed concrete waste that are 0%, 10%, 20%, 30%, 40% and 50% were used in this experimental work. Then the prepared specimens were placed in water curing until the testing age. Compressive strength test and flexural strength tests were conducted at 7, 14 and 28 days. The result shows that integration of crushed foamed concrete waste as partial sand replacement in concrete reduces the mix workability. It is interesting to note that both compressive strength and flexural strength of concrete improves when 30% crushed foamed concrete waste is added as partial sand replacement.
Compressive strength performance of OPS lightweight aggregate concrete containing coal bottom ash as partial fine aggregate replacement

NASA Astrophysics Data System (ADS)

Muthusamy, K.; Mohamad Hafizuddin, R.; Mat Yahaya, F.; Sulaiman, M. A.; Syed Mohsin, S. M.; Tukimat, N. N.; Omar, R.; Chin, S. C.

2018-04-01

Concerns regarding the negative impact towards environment due to the increasing use of natural sand in construction industry and dumping of industrial solid wastes namely coal bottom ash (CBA) and oil palm shell (OPS) has resulted in the development of environmental friendly lightweight concrete. The present study investigates the effect of coal bottom ash as partial fine aggregate replacement towards workability and compressive strength of oil palm shell lightweight aggregate concrete (OPS LWAC). The fresh and mechanical properties of this concrete containing various percentage of coal bottom ash as partial fine aggregate replacement were investigated. The result was compared to OPS LWAC with 100 % sand as a control specimen. The concrete workability investigated by conducting slump test. All specimens were cast in form of cubes and water cured until the testing age. The compressive strength test was carried out at 7 and 28 days. The finding shows that integration of coal bottom ash at suitable proportion enhances the strength of oil palm shell lightweight aggregate concrete.
Detecting beta-amyloid aggregation from time-resolved emission spectra

NASA Astrophysics Data System (ADS)

Alghamdi, A.; Vyshemirsky, V.; Birch, D. J. S.; Rolinski, O. J.

2018-04-01

The aggregation of beta-amyloids is one of the key processes responsible for the development of Alzheimer’s disease. Early molecular-level detection of beta-amyloid oligomers may help in early diagnosis and in the development of new intervention therapies. Our previous studies on the changes in beta-amyloid’s single tyrosine intrinsic fluorescence response during aggregation demonstrated a four-exponential fluorescence intensity decay, and the ratio of the pre-exponential factors indicated the extent of the aggregation in the early stages of the process before the beta-sheets were formed. Here we present a complementary approach based on the time-resolved emission spectra (TRES) of amyloid’s tyrosine excited at 279 nm and fluorescence in the window 240-450 nm. TRES have been used to demonstrate sturctural changes occuring on the nanosecond time scale after excitation which has significant advantages over using steady-state spectra. We demonstrate this by resolving the fluorescent species and revealing that beta-amyloid’s monomers show very fast dielectric relaxation, and its oligomers display a substantial spectral shift due to dielectric relaxation, which gradually decreases when the oligomers become larger.
Effects of humic and fulvic acids on aggregation of aqu/nC60 nanoparticles

EPA Science Inventory

Aggregation of fullerene nanoparticles (nC60) is a fundamental process influencing its environmental fate and transport, and toxicity. Using time-resolved dynamic light scattering we systematically investigated aggregation kinetics of nC60 generated from extended mixing in water ...
Pre-attentive mental processing of music expectation: event-related potentials of a partially violating and resolving paradigm.

PubMed

Pei, Yu-Cheng; Chen, Chia-Ling; Chung, Chia-Ying; Chou, Shi-Wei; Wong, Alice M K; Tang, Simon F T

2004-02-01

Auditory event-related potentials (ERPs) were investigated in an oddball paradigm to verify electrophysiological evidence of music expectation, which is a key component of artistic presentation. The non-target condition consisted of four-chord harmonic chord sequences, while the target condition was manifested by a partially violating third chord and a resolving fourth chord. The results showed that the specific mismatch negativity (MMN) elicited in the resolving chord is as robust as that elicited in the partially violating chord. Moreover, the P3b (P300) elicited in the resolving chord was smaller than the one in the violating chord. Taken together these data indicates that the human brain pre-attentatively may be able to anticipate a subsequent resolving chord when music expectation is generated by a partially violating chord.
Misfolded rhodopsin mutants display variable aggregation properties.

PubMed

Gragg, Megan; Park, Paul S-H

2018-06-08

The largest class of rhodopsin mutations causing autosomal dominant retinitis pigmentosa (adRP) is mutations that lead to misfolding and aggregation of the receptor. The misfolding mutants have been characterized biochemically, and categorized as either partial or complete misfolding mutants. This classification is incomplete and does not provide sufficient information to fully understand the disease pathogenesis and evaluate therapeutic strategies. A Förster resonance energy transfer (FRET) method was utilized to directly assess the aggregation properties of misfolding rhodopsin mutants within the cell. Partial (P23H and P267L) and complete (G188R, H211P, and P267R) misfolding mutants were characterized to reveal variability in aggregation properties. The complete misfolding mutants all behaved similarly, forming aggregates when expressed alone, minimally interacting with the wild-type receptor when coexpressed, and were unresponsive to treatment with the pharmacological chaperone 9-cis retinal. In contrast, variability was observed between the partial misfolding mutants. In the opsin form, the P23H mutant behaved similarly as the complete misfolding mutants. In contrast, the opsin form of the P267L mutant existed as both aggregates and oligomers when expressed alone and formed mostly oligomers with the wild-type receptor when coexpressed. The partial misfolding mutants both reacted similarly to the pharmacological chaperone 9-cis retinal, displaying improved folding and oligomerization when expressed alone but aggregating with wild-type receptor when coexpressed. The observed differences in aggregation properties and effect of 9-cis retinal predict different outcomes in disease pathophysiology and suggest that retinoid-based chaperones will be ineffective or even detrimental. Copyright © 2018 Elsevier B.V. All rights reserved.
Interaction of tau protein with model lipid membranes induces tau structural compaction and membrane disruption

PubMed Central

Jones, Emmalee M.; Dubey, Manish; Camp, Phillip J.; Vernon, Briana C.; Biernat, Jacek; Mandelkow, Eckhard; Majewski, Jaroslaw; Chi, Eva Y.

2012-01-01

The misfolding and aggregation of the intrinsically disordered, microtubule-associated tau protein into neurofibrillary tangles is implicated in the pathogenesis of Alzheimer's disease. However, the mechanisms of tau aggregation and toxicity remain unknown. Recent work has shown that lipid membrane can induce tau aggregation and that membrane permeabilization may serve as a pathway by which protein aggregates exert toxicity, suggesting that the plasma membrane may play dual roles in tau pathology. This prompted our investigation to assess tau's propensity to interact with membranes and to elucidate the mutually disruptive structural perturbations the interactions induce in both tau and the membrane. We show that although highly charged and soluble, the full-length tau (hTau40) is also highly surface active, selectively inserts into anionic DMPG lipid monolayers and induces membrane morphological changes. To resolve molecular-scale structural details of hTau40 associated with lipid membranes, X-ray and neutron scattering techniques are utilized. X-ray reflectivity indicates hTau40's presence underneath a DMPG monolayer and penetration into the lipid headgroups and tailgroups, whereas grazing incidence X-ray diffraction shows that hTau40 insertion disrupts lipid packing. Moreover, both air/water and DMPG lipid membrane interfaces induce the disordered hTau40 to partially adopt a more compact conformation with density similar to that of a folded protein. Neutron reflectivity shows that tau completely disrupts supported DMPG bilayers while leaving the neutral DPPC bilayer intact. Our results show that hTau40's strong interaction with anionic lipids induces tau structural compaction and membrane disruption, suggesting possible membrane-based mechanisms of tau aggregation and toxicity in neurodegenerative diseases. PMID:22401494
Structural elucidation of the interaction between neurodegenerative disease-related tau protein with model lipid membranes

NASA Astrophysics Data System (ADS)

Jones, Emmalee M.

A protein's sequence of amino acids determines how it folds. That folded structure is linked to protein function, and misfolding to dysfunction. Protein misfolding and aggregation into beta-sheet rich fibrillar aggregates is connected with over 20 neurodegenerative diseases, including Alzheimer's disease (AD). AD is characterized in part by misfolding, aggregation and deposition of the microtubule associated tau protein into neurofibrillary tangles (NFTs). However, two questions remain: What is tau's fibrillization mechanism, and what is tau's cytotoxicity mechanism? Tau is prone to heterogeneous interactions, including with lipid membranes. Lipids have been found in NFTs, anionic lipid vesicles induced aggregation of the microtubule binding domain of tau, and other protein aggregates induced ion permeability in cells. This evidence prompted our investigation of tau's interaction with model lipid membranes to elucidate the structural perturbations those interactions induced in tau protein and in the membrane. We show that although tau is highly charged and soluble, it is highly surface active and preferentially interacts with anionic membranes. To resolve molecular-scale structural details of tau and model membranes, we utilized X-ray and neutron scattering techniques. X-ray reflectivity indicated tau aggregated at air/water and anionic lipid membrane interfaces and penetrated into membranes. More significantly, membrane interfaces induced tau protein to partially adopt a more compact conformation with density similar to folded protein and ordered structure characteristic of beta-sheet formation. This suggests possible membrane-based mechanisms of tau aggregation. Membrane morphological changes were seen using fluorescence microscopy, and X-ray scattering techniques showed tau completely disrupts anionic membranes, suggesting an aggregate-based cytotoxicity mechanism. Further investigation of protein constructs and a "hyperphosphorylation" disease mimic helped clarify the role of the microtubule binding domain in anionic lipid affinity and demonstrated even "hyperphosphorylation" did not prevent interaction with anionic membranes. Additional studies investigated more complex membrane models to increase physiological relevance. These insights revealed structural changes in tau protein and lipid membranes after interaction. We observed tau's affinity for interfaces, and aggregation and compaction once tau partitions to interfaces. We observed the beginnings of beta-sheet formation in tau at anionic lipid membranes. We also examined disruption to the membrane on a molecular scale.
Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae.

PubMed

Straub, Shannon C K; Moore, Michael J; Soltis, Pamela S; Soltis, Douglas E; Liston, Aaron; Livshultz, Tatyana

2014-11-01

Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way polytomy, leaving ambiguous the homology of aggregated pollen in two major lineages, the Periplocoideae, which possess pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae), which possess pollinia. To assess whether greatly increased character sampling would resolve these relationships, a plastome sequence data matrix was assembled for 13 taxa of Apocynaceae, including nine newly generated complete plastomes, one partial new plastome, and three previously reported plastomes, collectively representing all primary crown clade lineages and outgroups. The effects of phylogenetic noise, long-branch attraction, and model selection (linked versus unlinked branch lengths among data partitions) were evaluated in a hypothesis-testing framework based on Shimodaira-Hasegawa tests. Discrimination among alternative crown clade resolutions was affected by all three factors. Exclusion of the noisiest alignment positions and topologies influenced by long-branch attraction resulted in a trichotomy along the spine of the crown clade consisting of Rhabdadenia+the Asian clade, Baisseeae+milkweeds, and Periplocoideae+the New World clade. Parsimony reconstruction on all optimal topologies after noise exclusion unambiguously supports parallel evolution of aggregated pollen in Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic approach has greatly advanced the resolution of one of the most perplexing radiations in Apocynaceae, providing the basis for study of convergent floral morphologies and their adaptive value. Copyright © 2014 Elsevier Inc. All rights reserved.
Cold rescue of the thermolabile tailspike intermediate at the junction between productive folding and off-pathway aggregation.

PubMed Central

Betts, S. D.; King, J.

1998-01-01

Off-pathway intermolecular interactions between partially folded polypeptide chains often compete with correct intramolecular interactions, resulting in self-association of folding intermediates into the inclusion body state. Intermediates for both productive folding and off-pathway aggregation of the parallel beta-coil tailspike trimer of phage P22 have been identified in vivo and in vitro using native gel electrophoresis in the cold. Aggregation of folding intermediates was suppressed when refolding was initiated and allowed to proceed for a short period at 0 degrees C prior to warming to 20 degrees C. Yields of refolded tailspike trimers exceeding 80% were obtained using this temperature-shift procedure, first described by Xie and Wetlaufer (1996, Protein Sci 5:517-523). We interpret this as due to stabilization of the thermolabile monomeric intermediate at the junction between productive folding and off-pathway aggregation. Partially folded monomers, a newly identified dimer, and the protrimer folding intermediates were populated in the cold. These species were electrophoretically distinguished from the multimeric intermediates populated on the aggregation pathway. The productive protrimer intermediate is disulfide bonded (Robinson AS, King J, 1997, Nat Struct Biol 4:450-455), while the multimeric aggregation intermediates are not disulfide bonded. The partially folded dimer appears to be a precursor to the disulfide-bonded protrimer. The results support a model in which the junctional partially folded monomeric intermediate acquires resistance to aggregation in the cold by folding further to a conformation that is activated for correct recognition and subunit assembly. PMID:9684883

Synchronization of coupled large-scale Boolean networks

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

Li, Fangfei, E-mail: li-fangfei@163.com

2014-03-15

This paper investigates the complete synchronization and partial synchronization of two large-scale Boolean networks. First, the aggregation algorithm towards large-scale Boolean network is reviewed. Second, the aggregation algorithm is applied to study the complete synchronization and partial synchronization of large-scale Boolean networks. Finally, an illustrative example is presented to show the efficiency of the proposed results.
State National Pollutant Discharge Elimination System (NPDES) Program Withdrawal Petitions

EPA Pesticide Factsheets

Search for pending and resolved NPDES withdrawal petitions by state, region, date, or keyword. Pending means EPA has received the petition and is working with the state and petitioner to resolve it. Withdrew petition means that the petitioner has withdrawn the petition they submitted. Resolved means that EPA has resolved the issues raised in the petition and has denied the petition. Partially resolved means that EPA has partially denied the petition by resolving some of the issues, while continuing to work with the state and petitioner on other pending issues. Program withdrawn would apply if, after conducting investigations, EPA withdrew a state's NPDES authority.
Site-specific structural dynamics of α-Synuclein revealed by time-resolved fluorescence spectroscopy: a review

NASA Astrophysics Data System (ADS)

Sahay, Shruti; Krishnamoorthy, G.; Maji, Samir K.

2016-12-01

Aggregation of α-Synuclein (α-Syn) into amyloid fibrils is known to be associated with the pathogenesis of Parkinson’s disease (PD). Several missense mutations of the α-Syn gene have been associated with rare, early onset familial forms of PD. Despite several studies done so far, the local/residue-level structure and dynamics of α-Syn in its soluble and aggregated fibril form and how these are affected by the familial PD associated mutations are still not clearly understood. Here, we review studies performed by our group as well as other research groups, where time-resolved fluorescence spectroscopy has been used to understand the site-specific structure and dynamics of α-Syn under physiological conditions as well as under conditions that alter the aggregation properties of the protein such as low pH, high temperature, presence of membrane mimics and familial PD associated mutations. These studies have provided important insights into the critical structural properties of α-Syn that may govern its aggregation. The review also highlights time-resolved fluorescence as a promising tool to study the critical conformational transitions associated with early oligomerization of α-Syn, which are otherwise not accessible using other commonly used techniques such as thioflavin T (ThT) binding assay.
The durability of concrete containing recycled tyres as a partial replacement of fine aggregate

NASA Astrophysics Data System (ADS)

Syamir Senin, Mohamad; Shahidan, Shahiron; Syazani Leman, Alif; Othman, Nurulain; Shamsuddin, Shamrul-mar; Ibrahim, M. H. W.; Zuki, S. S. Mohd

2017-11-01

Nowadays, uncontrolled disposal of waste materials such as tyres can affect the environment. Therefore, careful management of waste disposal must be done in order to conserve the environment. Waste tyres can be use as a replacement for both fine aggregate and coarse aggregate in the production of concrete. This research was conducted to assess the durability of concrete containing recycled tyres which have been crushed into fine fragments to replace fine aggregate in the concrete mix. This study presents an overview of the use of waste rubber as a partial replacement of natural fine aggregate in a concrete mix. 36 concrete cubes measuring 100mm × 100mm × 100mm and 12 concrete cubes measuring 150mm × 150mm × 150mm were prepared and added with different percentages of rubber from recycled tyres (0%, 3%, 5% and 7%) as fine aggregate replacement. The results obtained show that the replacement of fine aggregate with 7% of rubber recorded a compressive strength of 43.7MPa while the addition of 3% of rubber in the concrete sample recorded a high compressive strength of 50.8MPa. This shows that there is a decrease in the strength and workability of concrete as the amount of rubber used a replacement for fine aggregate in concrete increases. On the other hand, the water absorption test indicated that concrete which contains rubber has better water absorption ability. In this study, 3% of rubber was found to be the optimal percentage as a partial replacement for fine aggregate in the production of concrete.
Differences in the Pathways of Proteins Unfolding Induced by Urea and Guanidine Hydrochloride: Molten Globule State and Aggregates

PubMed Central

Povarova, Olga I.; Kuznetsova, Irina M.; Turoverov, Konstantin K.

2010-01-01

It was shown that at low concentrations guanidine hydrochloride (GdnHCl) can cause aggregation of proteins in partially folded state and that fluorescent dye 1-anilinonaphthalene-8-sulfonic acid (ANS) binds with these aggregates rather than with hydrophobic clusters on the surface of protein in molten globule state. That is why the increase in ANS fluorescence intensity is often recorded in the pathway of protein denaturation by GdnHCl, but not by urea. So what was previously believed to be the molten globule state in the pathway of protein denaturation by GdnHCl, in reality, for some proteins represents the aggregates of partially folded molecules. PMID:21152408
Polarization resolved angular optical scattering of aerosol particles

NASA Astrophysics Data System (ADS)

Redding, B.; Pan, Y.; Wang, C.; Videen, G.; Cao, Hui

2014-05-01

Real-time detection and identification of bio-aerosol particles are crucial for the protection against chemical and biological agents. The strong elastic light scattering properties of airborne particles provides a natural means for rapid, non-invasive aerosol characterization. Recent theoretical predictions suggested that variations in the polarization dependent angular scattering cross section could provide an efficient means of classifying different airborne particles. In particular, the polarization dependent scattering cross section of aggregate particles is expected to depend on the shape of the primary particles. In order to experimentally validate this prediction, we built a high throughput, sampling system, capable of measuring the polarization resolved angular scattering cross section of individual aerosol particles flowing through an interrogating volume with a single shot of laser pulse. We calibrated the system by comparing the polarization dependent scattering cross section of individual polystyrene spheres with that predicted by Mie theory. We then used the system to study different particles types: Polystyrene aggregates composed 500 nm spheres and Bacillus subtilis (BG, Anthrax simulant) spores composed of elongated 500 nm × 1000 nm cylinder-line particles. We found that the polarization resolved scattering cross section depends on the shape of the constituent elements of the aggregates. This work indicates that the polarization resolved scattering cross section could be used for rapid discrimination between different bio-aerosol particles.
Time-resolved forward-light-scattering monitoring of protein–lysozyme aggregation in precrystalline solutions

NASA Astrophysics Data System (ADS)

Wakamatsu, Takashi; Onoda, Takashi; Ogata, Makoto

2018-05-01

An in situ measurement method of monitoring protein aggregation in precrystalline solutions is presented. The method is based on a small-angle forward static light scattering (F-SLS) technique. This technique uses an accurate optical arrangement of a combination of a collimating lens and a CCD to obtain an F-SLS pattern from an aggregate-containing protein solution in one shot. The real-time observation of a crystallizing lysozyme captured the formation of fractal aggregates in the initial formation stage.
Real-time measurement of size-resolved elemental composition ratio for flame synthesized composite nanoparticle aggregates using a tandem SMPS-ICP-OES

PubMed Central

Reed, Nathan; Fang, Jiaxi; Chavalmane, Sanmathi; Biswas, Pratim

2017-01-01

Composite nanoparticles find application in catalysis, drug delivery, and energy storage and require increasingly fine control of their physical properties and composition. While composite nanoparticles have been widely synthesized and characterized, little work has systematically correlated the initial concentration of precursors and the final composition of flame synthesized composite nanoparticles. This relationship is explored in a diffusion flame aerosol reactor by coupling a scanning mobility particle sizer (SMPS) with an inductively coupled plasma optical emission spectrometer (ICP-OES). A framework for studying the relationship between the initial precursor concentrations of different elements and the final nanoparticle composition is explored. The size-resolved elemental composition was measured by directly injecting size-selected fractions of aggregated magnetite and silicon dioxide composite nanoparticles into the ICP-OES plasma. This work showed a correlation between precursor molar ratio and the measured elemental ratio in the mobility size range of 50 to 140 nm. Building on previous work studying size resolved elemental composition of engineered nanoparticles, the analysis is extended to flame synthesized composite nanoparticle aggregates in this work. PMID:28435179
Real-time measurement of size-resolved elemental composition ratio for flame synthesized composite nanoparticle aggregates using a tandem SMPS-ICP-OES.

PubMed

Reed, Nathan; Fang, Jiaxi; Chavalmane, Sanmathi; Biswas, Pratim

2017-01-01

Composite nanoparticles find application in catalysis, drug delivery, and energy storage and require increasingly fine control of their physical properties and composition. While composite nanoparticles have been widely synthesized and characterized, little work has systematically correlated the initial concentration of precursors and the final composition of flame synthesized composite nanoparticles. This relationship is explored in a diffusion flame aerosol reactor by coupling a scanning mobility particle sizer (SMPS) with an inductively coupled plasma optical emission spectrometer (ICP-OES). A framework for studying the relationship between the initial precursor concentrations of different elements and the final nanoparticle composition is explored. The size-resolved elemental composition was measured by directly injecting size-selected fractions of aggregated magnetite and silicon dioxide composite nanoparticles into the ICP-OES plasma. This work showed a correlation between precursor molar ratio and the measured elemental ratio in the mobility size range of 50 to 140 nm. Building on previous work studying size resolved elemental composition of engineered nanoparticles, the analysis is extended to flame synthesized composite nanoparticle aggregates in this work.
Fluorescence of acridinic dyes in anionic surfactant solution

NASA Astrophysics Data System (ADS)

Pereira, Robson Valentim; Gehlen, Marcelo Henrique

2005-10-01

The interaction of the cationic dyes acridine, 9-aminoacridine (9AA), and proflavine, with sodium dodecyl sulfate (SDS) was studied by electronic absorption, steady-state and time-resolved fluorescence spectroscopies. The dyes interact with SDS in the pre-micellar region leading in two cases to dimerization in dye-surfactant aggregates, but with distinct molecular arrangements. For proflavine, the observed red shift of the electronic absorption band indicates the presence of J-aggregate, which are nonfluorescent. In the case of 9AA, the aggregates were characterized as nonspecific (neither J- nor H-type is spectroscopically observed). The time-resolved emission spectra gives evidences of the presence of weakly bound dimers by the recovery of three defined decay times by global analysis: dye monomer ( τ1 = 16.4 ns), dimer ( τ2 = 7.1 ns), and a faster component ( τ3 = 2.1 ns) ascribed to intracluster energy migration between monomer and dimer. Acridine has a weak interaction with SDS forming only an ion pair without further self-aggregation of the dye.
Fluorescence of acridinic dyes in anionic surfactant solution.

PubMed

Pereira, Robson Valentim; Gehlen, Marcelo Henrique

2005-10-01

The interaction of the cationic dyes acridine, 9-aminoacridine (9AA), and proflavine, with sodium dodecyl sulfate (SDS) was studied by electronic absorption, steady-state and time-resolved fluorescence spectroscopies. The dyes interact with SDS in the pre-micellar region leading in two cases to dimerization in dye-surfactant aggregates, but with distinct molecular arrangements. For proflavine, the observed red shift of the electronic absorption band indicates the presence of J-aggregate, which are nonfluorescent. In the case of 9AA, the aggregates were characterized as nonspecific (neither J- nor H-type is spectroscopically observed). The time-resolved emission spectra gives evidences of the presence of weakly bound dimers by the recovery of three defined decay times by global analysis: dye monomer (tau1 = 16.4 ns), dimer (tau2 = 7.1 ns), and a faster component (tau3 = 2.1 ns) ascribed to intracluster energy migration between monomer and dimer. Acridine has a weak interaction with SDS forming only an ion pair without further self-aggregation of the dye.
Predicting the mineral composition of dust aerosols: Insights from elemental composition measured at the Izaña Observatory

NASA Astrophysics Data System (ADS)

Pérez García-Pando, Carlos; Miller, Ron L.; Perlwitz, Jan P.; Rodríguez, Sergio; Prospero, Joseph M.

2016-10-01

Regional variations of dust mineral composition are fundamental to climate impacts but generally neglected in climate models. A challenge for models is that atlases of soil composition are derived from measurements following wet sieving, which destroys the aggregates potentially emitted from the soil. Aggregates are crucial to simulating the observed size distribution of emitted soil particles. We use an extension of brittle fragmentation theory in a global dust model to account for these aggregates. Our method reproduces the size-resolved dust concentration along with the approximately size-invariant fractional abundance of elements like Fe and Al in the decade-long aerosol record from the Izaña Observatory, off the coast of West Africa. By distinguishing between Fe in structural and free forms, we can attribute improved model behavior to aggregation of Fe and Al-rich clay particles. We also demonstrate the importance of size-resolved measurements along with elemental composition analysis to constrain models.
Top-d Rank Aggregation in Web Meta-search Engine

NASA Astrophysics Data System (ADS)

Fang, Qizhi; Xiao, Han; Zhu, Shanfeng

In this paper, we consider the rank aggregation problem for information retrieval over Web making use of a kind of metric, the coherence, which considers both the normalized Kendall-τ distance and the size of overlap between two partial rankings. In general, the top-d coherence aggregation problem is defined as: given collection of partial rankings Π = {τ 1,τ 2, ⋯ , τ K }, how to find a final ranking π with specific length d, which maximizes the total coherence Φ(π,Pi)=sum_{i=1}^K Φ(π,tau_i). The corresponding complexity and algorithmic issues are discussed in this paper. Our main technical contribution is a polynomial time approximation scheme (PTAS) for a restricted top-d coherence aggregation problem.
A Free Energy Barrier Caused by the Refolding of an Oligomeric Intermediate Controls the Lag Time of Amyloid Formation by hIAPP.

PubMed

Serrano, Arnaldo L; Lomont, Justin P; Tu, Ling-Hsien; Raleigh, Daniel P; Zanni, Martin T

2017-11-22

Transiently populated oligomers formed en route to amyloid fibrils may constitute the most toxic aggregates associated with many amyloid-associated diseases. Most nucleation theories used to describe amyloid aggregation predict low oligomer concentrations and do not take into account free energy costs that may be associated with structural rearrangements between the oligomer and fiber states. We have used isotope labeling and two-dimensional infrared spectroscopy to spectrally resolve an oligomeric intermediate during the aggregation of the human islet amyloid protein (hIAPP or amylin), the protein associated with type II diabetes. A structural rearrangement includes the F 23 G 24 A 25 I 26 L 27 region of hIAPP, which starts from a random coil structure, evolves into ordered β-sheet oligomers containing at least 5 strands, and then partially disorders in the fibril structure. The supercritical concentration is measured to be between 150 and 250 μM, which is the thermodynamic parameter that sets the free energy of the oligomers. A 3-state kinetic model fits the experimental data, but only if it includes a concentration independent free energy barrier >3 kcal/mol that represents the free energy cost of refolding the oligomeric intermediate into the structure of the amyloid fibril; i.e., "oligomer activation" is required. The barrier creates a transition state in the free energy landscape that slows fibril formation and creates a stable population of oligomers during the lag phase, even at concentrations below the supercritical concentration. Largely missing in current kinetic models is a link between structure and kinetics. Our experiments and modeling provide evidence that protein structural rearrangements during aggregation impact the populations and kinetics of toxic oligomeric species.
Internalization of aggregated photosensitizers by tumor cells: subcellular time-resolved fluorescence spectroscopy on derivatives of pyropheophorbide-a ethers and chlorin e6 under femtosecond one- and two-photon excitations.

PubMed

Kelbauskas, L; Dietel, W

2002-12-01

Amphiphilic sensitizers self-associate in aqueous environments and form aggregated species that exhibit no or only negligible photodynamic activity. However, amphiphilic photosensitizers number among the most potent agents of photodynamic therapy. The processes by which these sensitizers are internalized into tumor cells have yet to be fully elucidated and thus remain the subject of debate. In this study the uptake of photosensitizer aggregates into tumor cells was examined directly using subcellular time-resolved fluorescence spectroscopy with a high temporal resolution (20-30 ps) and high sensitivity (time-correlated single-photon counting). The investigations were performed on selected sensitizers that exhibit short fluorescence decay times (< 50 ps) in aggregated form. Derivatives of pyropheophorbide-a ether and chlorin e6 with varying lipophilicity were used for the study. The characteristic fluorescence decay times and spectroscopic features of the sensitizer aggregates measured in aqueous solution also could be observed in A431 human endothelial carcinoma cells administered with these photosensitizers. This shows that tumor cells can internalize sensitizers in aggregated form. Uptake of aggregates and their monomerization inside cells were demonstrated directly for the first time by means of fluorescence lifetime imaging with a high temporal resolution. Internalization of the aggregates seems to be endocytosis mediated. The degree of their monomerization in tumor cells is strongly influenced by the lipophilicity of the compounds.
Insulin aggregation tracked by its intrinsic TRES

NASA Astrophysics Data System (ADS)

Chung, Li Hung C.; Birch, David J. S.; Vyshemirsky, Vladislav; Ryadnov, Maxim G.; Rolinski, Olaf J.

2017-12-01

Time-resolved emission spectra (TRES) have been used to detect conformational changes of intrinsic tyrosines within bovine insulin at a physiological pH. The approach offers the ability to detect the initial stages of insulin aggregation at the molecular level. The data analysis has revealed the existence of at least three fluorescent species undergoing dielectric relaxation and significant spectral changes due to insulin aggregation. The results indicate the suitability of the intrinsic TRES approach for insulin studies and for monitoring its stability during storage and aggregation in insulin delivery devices.
Spatial capture–recapture with partial identity: An application to camera traps

USGS Publications Warehouse

Augustine, Ben C.; Royle, J. Andrew; Kelly, Marcella J.; Satter, Christopher B.; Alonso, Robert S.; Boydston, Erin E.; Crooks, Kevin R.

2018-01-01

Camera trapping surveys frequently capture individuals whose identity is only known from a single flank. The most widely used methods for incorporating these partial identity individuals into density analyses discard some of the partial identity capture histories, reducing precision, and, while not previously recognized, introducing bias. Here, we present the spatial partial identity model (SPIM), which uses the spatial location where partial identity samples are captured to probabilistically resolve their complete identities, allowing all partial identity samples to be used in the analysis. We show that the SPIM outperforms other analytical alternatives. We then apply the SPIM to an ocelot data set collected on a trapping array with double-camera stations and a bobcat data set collected on a trapping array with single-camera stations. The SPIM improves inference in both cases and, in the ocelot example, individual sex is determined from photographs used to further resolve partial identities—one of which is resolved to near certainty. The SPIM opens the door for the investigation of trapping designs that deviate from the standard two camera design, the combination of other data types between which identities cannot be deterministically linked, and can be extended to the problem of partial genotypes.
Physical and mechanical properties of mortars containing PET and PC waste aggregates.

PubMed

Hannawi, Kinda; Kamali-Bernard, Siham; Prince, William

2010-11-01

Non-biodegradable plastic aggregates made of polycarbonate (PC) and polyethylene terephthalate (PET) waste are used as partial replacement of natural aggregates in mortar. Various volume fractions of sand 3%, 10%, 20% and 50% are replaced by the same volume of plastic. This paper investigates the physical and mechanical properties of the obtained composites. The main results of this study show the feasibility of the reuse of PC and PET waste aggregates materials as partial volume substitutes for natural aggregates in cementitious materials. Despite of some drawbacks like a decrease in compressive strength, the use of PC and PET waste aggregates presents various advantages. A reduction of the specific weight of the cementitious materials and a significant improvement of their post-peak flexural behaviour are observed. The calculated flexural toughness factors increase significantly with increasing volume fraction of PET and PC-aggregates. Thus, addition of PC and PET plastic aggregates in cementitious materials seems to give good energy absorbing materials which is very interesting for several civil engineering applications like structures subjected to dynamic or impact efforts. The present study has shown quite encouraging results and opened new way for the recycling of PC waste aggregate in cement and concrete composites. Copyright © 2010 Elsevier Ltd. All rights reserved.
Confinement of Aggregation-Induced Emission Molecular Rotors in Ultrathin Two-Dimensional Porous Organic Nanosheets for Enhanced Molecular Recognition.

PubMed

Dong, Jinqiao; Li, Xu; Zhang, Kang; Di Yuan, Yi; Wang, Yuxiang; Zhai, Linzhi; Liu, Guoliang; Yuan, Daqiang; Jiang, Jianwen; Zhao, Dan

2018-03-21

Despite the rapid development of molecular rotors over the past decade, it still remains a huge challenge to understand their confined behavior in ultrathin two-dimensional (2D) nanomaterials for molecular recognition. Here, we report an all-carbon, 2D π-conjugated aromatic polymer, named NUS-25, containing flexible tetraphenylethylene (TPE) units as aggregation-induced emission (AIE) molecular rotors. NUS-25 bulk powder can be easily exfoliated into micrometer-sized lamellar freestanding nanosheets with a thickness of 2-5 nm. The dynamic behavior of the TPE rotors is partially restricted through noncovalent interactions in the ultrathin 2D nanosheets, which is proved by comparative experimental studies including AIE characteristics, size-selective molecular recognition, and theoretical calculations of rotary energy barrier. Because of the partially restricted TPE rotors, NUS-25 nanosheets are highly fluorescent. This property allows NUS-25 nanosheets to be used as a chemical sensor for the specific detection of acenaphthylene among a series of polycyclic aromatic hydrocarbons (PAHs) via fluorescent quenching mechanism. Further investigations show that NUS-25 nanosheets have much higher sensitivity and selectivity than their stacked bulk powder and other similar polymers containing dynamic TPE rotors. The highly efficient molecular recognition can be attributed to the photoinduced electron transfer (PET) from NUS-25 nanosheets to acenaphthylene, which is investigated by time-resolved photoluminescence measurements (TRPL), excitation and emission spectra, and density functional theory (DFT) calculations. Our findings demonstrate that confinement of AIE molecular rotors in 2D nanomaterials can enhance the molecular recognition. We anticipate that the material design strategy demonstrated in this study will inspire the development of other ultrathin 2D nanomaterials equipped with smart molecular machines for various applications.
Novel magnetic cross-linked lipase aggregates for improving the resolution of (R, S)-2-octanol.

PubMed

Liu, Ying; Guo, Chen; Liu, Chun-Zhao

2015-03-01

Novel magnetic cross-linked lipase aggregates were fabricated by immobilizing the cross-linked lipase aggregates onto magnetic particles with a high number of -NH2 terminal groups using p-benzoquinone as the cross-linking agent. At the optimal fabrication conditions, 100% of immobilization efficiency and 139% of activity recovery of the magnetic cross-linked lipase aggregates were achieved. The magnetic cross-linked lipase aggregates were able to efficiently resolve (R, S)-2-octanol, and retained 100% activity and 100% enantioselectivity after 10 cycles of reuse, whereas the cross-linked lipase aggregates only retained about 50% activity and 70% enantioselectivity due to insufficient cross-linking. These results provide a great potential for industrial applications of the magnetic cross-linked lipase aggregates. © 2014 Wiley Periodicals, Inc.

COMPUTER SIMULATION STUDY OF AMYLOID FIBRIL FORMATION BY PALINDROMIC SEQUENCES IN PRION PEPTIDES

PubMed Central

Wagoner, Victoria; Cheon, Mookyung; Chang, Iksoo; Hall, Carol

2011-01-01

We simulate the aggregation of large systems containing palindromic peptides from the Syrian hamster prion protein SHaPrP 113–120 (AGAAAAGA) and the mouse prion protein MoPrP 111–120 (VAGAAAAGAV) and eight sequence variations: GAAAAAAG, (AG)4, A8, GAAAGAAA, A10, V10, GAVAAAAVAG, and VAVAAAAVAV The first two peptides are thought to act as the Velcro that holds the parent prion proteins together in amyloid structures and can form fibrils themselves. Kinetic events along the fibrillization pathway influence the types of structures that occur and variations in the sequence affect aggregation kinetics and fibrillar structure. Discontinuous molecular dynamics simulations using the PRIME20 force field are performed on systems containing 48 peptides starting from a random coil configuration. Depending on the sequence, fibrillar structures form spontaneously over a range of temperatures, below which amorphous aggregates form and above which no aggregation occurs. AGAAAAGA forms well organized fibrillar structures whereas VAGAAAAGAV forms less well organized structures that are partially fibrillar and partially amorphous. The degree of order in the fibrillar structure stems in part from the types of kinetic events leading up to its formation, with AGAAAAGA forming less amorphous structures early in the simulation than VAGAAAAGAV. The ability to form fibrils increases as the chain length and the length of the stretch of hydrophobic residues increase. However as the hydrophobicity of the sequence increases, the ability to form well-ordered structures decreases. Thus, longer hydrophobic sequences form slightly disordered aggregates that are partially fibrillar and partially amorphous. Subtle changes in sequence result in slightly different fibril structures. PMID:21557317
Familial aggregation of focal seizure semiology in the Epilepsy Phenome/Genome Project.

PubMed

Tobochnik, Steven; Fahlstrom, Robyn; Shain, Catherine; Winawer, Melodie R

2017-07-04

To improve phenotype definition in genetic studies of epilepsy, we assessed the familial aggregation of focal seizure types and of specific seizure symptoms within the focal epilepsies in families from the Epilepsy Phenome/Genome Project. We studied 302 individuals with nonacquired focal epilepsy from 149 families. Familial aggregation was assessed by logistic regression analysis of relatives' traits (dependent variable) by probands' traits (independent variable), estimating the odds ratio for each symptom in a relative given presence vs absence of the symptom in the proband. In families containing multiple individuals with nonacquired focal epilepsy, we found significant evidence for familial aggregation of ictal motor, autonomic, psychic, and aphasic symptoms. Within these categories, ictal whole body posturing, diaphoresis, dyspnea, fear/anxiety, and déjà vu/jamais vu showed significant familial aggregation. Focal seizure type aggregated as well, including complex partial, simple partial, and secondarily generalized tonic-clonic seizures. Our results provide insight into genotype-phenotype correlation in the nonacquired focal epilepsies and a framework for identifying subgroups of patients likely to share susceptibility genes. © 2017 American Academy of Neurology.
Boundary Layer Height and Buoyancy Determine the Horizontal Scale of Convective Self-Aggregation

DOE PAGES

Yang, Da

2018-01-24

Organized rainstorms and their associated overturning circulations can self-emerge over an ocean surface with uniform temperature in cloud-resolving simulations. This phenomenon is referred to as convective self-aggregation. Convective self-aggregation is argued to be an important building block for tropical weather systems and may help regulate tropical atmospheric humidity and thereby tropical climate stability. Here the author presents a boundary layer theory for the horizontal scale λ of 2D (x, z) convective self-aggregation by considering both the momentum and energy constraints for steady circulations. This theory suggests that λ scales with the product of the boundary layer height h and themore » square root of the amplitude of density variation between aggregated moist and dry regions in the boundary layer, and that this density variation mainly arises from the moisture variation due to the virtual effect of water vapor. Furthermore, this theory predicts the following: 1) the order of magnitude of λ is ~2000 km, 2) the aspect ratio of the boundary layer λ/h increases with surface warming, and 3) λ decreases when the virtual effect of water vapor is disabled. These predictions are confirmed using a sui te of cloud-resolving simulations spanning a wide range of climates.« less
Boundary Layer Height and Buoyancy Determine the Horizontal Scale of Convective Self-Aggregation

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

Yang, Da

Organized rainstorms and their associated overturning circulations can self-emerge over an ocean surface with uniform temperature in cloud-resolving simulations. This phenomenon is referred to as convective self-aggregation. Convective self-aggregation is argued to be an important building block for tropical weather systems and may help regulate tropical atmospheric humidity and thereby tropical climate stability. Here the author presents a boundary layer theory for the horizontal scale λ of 2D (x, z) convective self-aggregation by considering both the momentum and energy constraints for steady circulations. This theory suggests that λ scales with the product of the boundary layer height h and themore » square root of the amplitude of density variation between aggregated moist and dry regions in the boundary layer, and that this density variation mainly arises from the moisture variation due to the virtual effect of water vapor. Furthermore, this theory predicts the following: 1) the order of magnitude of λ is ~2000 km, 2) the aspect ratio of the boundary layer λ/h increases with surface warming, and 3) λ decreases when the virtual effect of water vapor is disabled. These predictions are confirmed using a sui te of cloud-resolving simulations spanning a wide range of climates.« less
Influence of the valine zipper region on the structure and aggregation of the basic leucine zipper (bZIP) domain of activating transcription factor 5 (ATF5).

PubMed

Ciaccio, Natalie A; Reynolds, T Steele; Middaugh, C Russell; Laurence, Jennifer S

2012-11-05

Protein aggregation is a major problem for biopharmaceuticals. While the control of aggregation is critically important for the future of protein pharmaceuticals, mechanisms of aggregate assembly, particularly the role that structure plays, are still poorly understood. Increasing evidence indicates that partially folded intermediates critically influence the aggregation pathway. We have previously reported the use of the basic leucine zipper (bZIP) domain of activating transcription factor 5 (ATF5) as a partially folded model system to investigate protein aggregation. This domain contains three regions with differing structural propensity: a N-terminal polybasic region, a central helical leucine zipper region, and a C-terminal extended valine zipper region. Additionally, a centrally positioned cysteine residue readily forms an intermolecular disulfide bond that reduces aggregation. Computational analysis of ATF5 predicts that the valine zipper region facilitates self-association. Here we test this hypothesis using a truncated mutant lacking the C-terminal valine zipper region. We compare the structure and aggregation of this mutant to the wild-type (WT) form under both reducing and nonreducing conditions. Our data indicate that removal of this region results in a loss of α-helical structure in the leucine zipper and a change in the mechanism of self-association. The mutant form displays increased association at low temperature but improved resistance to thermally induced aggregation.
Multivariate Analysis of Mixed Lipid Aggregate Phase Transitions Monitored Using Raman Spectroscopy.

PubMed

Neal, Sharon L

2018-01-01

The phase behavior of aqueous 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC)/1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) mixtures between 8.0 ℃ and 41.0 ℃ were monitored using Raman spectroscopy. Temperature-dependent Raman matrices were assembled from series of spectra and subjected to multivariate analysis. The consensus of pseudo-rank estimation results is that seven to eight components account for the temperature-dependent changes observed in the spectra. The spectra and temperature response profiles of the mixture components were resolved by applying a variant of the non-negative matrix factorization (NMF) algorithm described by Lee and Seung (1999). The rotational ambiguity of the data matrix was reduced by augmenting the original temperature-dependent spectral matrix with its cumulative counterpart, i.e., the matrix formed by successive integration of the spectra across the temperature index (columns). Successive rounds of constrained NMF were used to isolate component spectra from a significant fluorescence background. Five major components exhibiting varying degrees of gel and liquid crystalline lipid character were resolved. Hydrogen-bonded water networks exhibiting varying degrees of organization are associated with the lipid components. Spectral parameters were computed to compare the chain conformation, packing, and hydration indicated by the resolved spectra. Based on spectral features and relative amounts of the components observed, four components reflect long chain lipid response. The fifth component could reflect the response of the short chain lipid, DHPC, but there were no definitive spectral features confirming this assignment. A minor component of uncertain assignment that exhibits a striking response to the DMPC pre-transition and chain melting transition also was recovered. While none of the spectra resolved exhibit features unequivocally attributable to a specific aggregate morphology or step in the gelation process, the results are consistent with the evolution of mixed phase bicelles (nanodisks) and small amounts of worm-like DMPC/DHPC aggregates, and perhaps DHPC micelles, at low temperature to suspensions of branched and entangled worm-like aggregates above the DMPC gel phase transition and perforated multi-lamellar aggregates at high temperature.
p-( sup 125 I)iodoclonidine is a partial agonist at the alpha 2-adrenergic receptor

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

Gerhardt, M.A.; Wade, S.M.; Neubig, R.R.

1990-08-01

The binding properties of p-(125I)iodoclonidine (( 125I)PIC) to human platelet membranes and the functional characteristics of PIC are reported. (125I)PIC bound rapidly and reversibly to platelet membranes, with a first-order association rate constant (kon) at room temperature of 8.0 +/- 2.7 x 10(6) M-1 sec-1 and a dissociation rate constant (koff) of 2.0 +/- 0.8 x 10(-3) sec-1. Scatchard plots of specific (125I)PIC binding (0.1-5 nM) were linear, with a Kd of 1.2 +/- 0.1 nM. (125I)PIC bound to the same number of high affinity sites as the alpha 2-adrenergic receptor (alpha 2-AR) full agonist (3H) bromoxidine (UK14,304), which representedmore » approximately 40% of the sites bound by the antagonist (3H)yohimbine. Guanosine 5'-(beta, gamma-imido)triphosphate greatly reduced the amount of (125I)PIC bound (greater than 80%), without changing the Kd of the residual binding. In competition experiments, the alpha 2-AR-selective ligands yohimbine, bromoxidine, oxymetazoline, clonidine, p-aminoclonidine, (-)-epinephrine, and idazoxan all had Ki values in the low nanomolar range, whereas prazosin, propranolol, and serotonin yielded Ki values in the micromolar range. Epinephrine competition for (125I)PIC binding was stereoselective. Competition for (3H)bromoxidine binding by PIC gave a Ki of 1.0 nM (nH = 1.0), whereas competition for (3H)yohimbine could be resolved into high and low affinity components, with Ki values of 3.7 and 84 nM, respectively. PIC had minimal agonist activity in inhibiting adenylate cyclase in platelet membranes, but it potentiated platelet aggregation induced by ADP with an EC50 of 1.5 microM. PIC also inhibited epinephrine-induced aggregation, with an IC50 of 5.1 microM. Thus, PIC behaves as a partial agonist in a human platelet aggregation assay. (125I)PIC binds to the alpha 2B-AR in NG-10815 cell membranes with a Kd of 0.5 +/- 0.1 nM.« less
Sedimentation, viscosity and partial specific volumes of membrane proteins and lipoproteins

PubMed Central

Brown, A. D.; Netschey, A.

1967-01-01

1. Lipoproteins or defatted proteins from the membrane of Halobacterium halobium were dissolved in 0·02m-phosphate buffer, pH7·4, with or without urea (8m). Physicochemical measurements were made on these solutions with and without addition of sodium chloride. 2. In the presence of 8m-urea the lipoproteins could be resolved into two sedimenting groups. The faster group had an average apparent molecular weight of 390 000; sedimentation coefficients of the slower group could not be determined. 3. Proteins that had been defatted by extraction with a chloroform–methanol mixture could also be resolved into two groups distinguished by their sedimentation velocities. Sedimentation coefficients of both groups were readily determined. The average apparent molecular weight of the faster group of defatted proteins in 8m-urea was 340 000 and that of the slower group was 97 000. It is concluded that attachment of lipid does not affect the state of aggregation of the proteins in 8m-urea. 4. Intrinsic viscosities of lipoproteins and defatted proteins were higher than is customary for globular proteins and suggest expanded highly-solvated molecules, consistent with the `denaturing' action on the proteins of solutions of low ionic strength. ImagesFig. 1. PMID:6033765
A method to solubilise protein aggregates for immunoassay quantification which overcomes the neurofilament "hook" effect.

PubMed

Lu, Ching-Hua; Kalmar, Bernadett; Malaspina, Andrea; Greensmith, Linda; Petzold, Axel

2011-02-15

Neurofilament (Nf) aggregates are a common pathological feature of neurodegenerative disorders. Although Nf levels have been investigated as a potential disease biomarker, Nf aggregates may mask Nf epitopes, preventing accurate quantification by immunoassay. Using the SOD1(G93A) mouse model of amyotrophic lateral sclerosis, we developed a method to disrupt Nf aggregates, allowing optimal immunoassay performance. Phosphorylated (NfH(SMI35)) and hyperphosphorylated (NfH(SMI34)) Nf levels in plasma from 120-day SOD1(G93A) mice were quantified using an in-house ELISA modified for use with small volumes. Different pre-analytical methods were tested for their ability to solubilize Nf aggregates and immunoblotting was used for qualitative analysis. A 'hook effect' was observed for serially diluted plasma samples quantified using an ELISA originally developed for CSF samples. Immunoblotting confirmed the existence of high molecular-weight NfH aggregates in plasma and the resolving effect of timed urea on these aggregates. Thermostatic (pre-thawing) and chemical (calcium chelators, urea) pre-analytical processing of samples had variable success in disrupting NfH aggregates. Timed urea-calcium chelator incubation yielded the most consistent plasma NfH levels. A one hour sample pre-incubation with 0.5M urea in Barbitone-EDTA buffer at room temperature resolved the "hook effect" without compromising the ELISA. In SOD1(G93A) mice, median levels of NfH(SMI34) were over 10-fold and NfH(SMI35) levels 5-fold greater than controls. NfH aggregates can be solubilised and the "hook effect" abolished by a one-hour sample pre-incubation in a urea-calcium chelator-enriched buffer. This method is applicable for quantification of NfH phosphoforms in experimental and disease settings where Nf aggregate formation occurs. © 2010 Elsevier B.V. All rights reserved.
Resolving individual Shockley partials of a dissociated dislocation by STEM

NASA Astrophysics Data System (ADS)

Iwata, Hiroyuki; Saka, Hiroyasu

2017-02-01

A practical method was developed to image detailed features of defects in a crystal using STEM. This method is essentially a STEM version of the conventional CTEM g/3g weak beam dark field (WBDF) method. The method was successfully applied to resolving individual Shockley partials of a dissociated dislocation in a Cu-6.44at.%Al alloy.
Bottom ash as aggregate replacement in concrete.

DOT National Transportation Integrated Search

2013-06-01

The objective of the proposed study is to evaluate bottom ash as a partial or total replacement of the fine and coarse aggregate in : concrete. This program will characterize and evaluate available bottom ash sources as potential replacement of both ...
Exploring Partial Order of European Countries

ERIC Educational Resources Information Center

Annoni, Paola; Bruggemann, Rainer

2009-01-01

Partial Order Theory has been recently more and more employed in applied science to overcome the intrinsic disadvantage hidden in aggregation, if a multiple attribute system is available. Despite its numerous positive features, there are many practical cases where the interpretation of the partial order can be rather troublesome. In these cases…
Quality Assessment of Mixed and Ceramic Recycled Aggregates from Construction and Demolition Wastes in the Concrete Manufacture According to the Spanish Standard.

PubMed

Rodríguez-Robles, Desirée; García-González, Julia; Juan-Valdés, Andrés; Morán-Del Pozo, Julia Mª; Guerra-Romero, Manuel I

2014-08-13

Construction and demolition waste (CDW) constitutes an increasingly significant problem in society due to the volume generated, rendering sustainable management and disposal problematic. The aim of this study is to identify a possible reuse option in the concrete manufacturing for recycled aggregates with a significant ceramic content: mixed recycled aggregates (MixRA) and ceramic recycled aggregates (CerRA). In order to do so, several tests are conducted in accordance with the Spanish Code on Structural Concrete (EHE-08) to determine the composition in weight and physic-mechanical characteristics (particle size distributions, fine content, sand equivalent, density, water absorption, flakiness index, and resistance to fragmentation) of the samples for the partial inclusion of the recycled aggregates in concrete mixes. The results of these tests clearly support the hypothesis that this type of material may be suitable for such partial replacements if simple pretreatment is carried out. Furthermore, this measure of reuse is in line with European, national, and regional policies on sustainable development, and presents a solution to the environmental problem caused by the generation of CDW.
Binding and relaxation behavior of Coumarin-153 in lecithin-taurocholate mixed micelles: A time resolved fluorescence spectroscopic study

NASA Astrophysics Data System (ADS)

Chakrabarty, Debdeep; Chakraborty, Anjan; Seth, Debabrata; Hazra, Partha; Sarkar, Nilmoni

2005-09-01

The microenvironment of the bile salt-lecithin mixed aggregates has been investigated using steady state and picosecond time resolved fluorescence spectroscopy. The steady state spectra show that the polarity of the bile salt is higher compared to lecithin vesicles or the mixed aggregates. We have observed slow solvent relaxation in bile salt micelles and lecithin vesicles. The solvation time is gradually slowed down due to gradual addition of the bile salt in lecithin vesicles. Addition of bile salt leads to the tighter head group packing in lecithin. Thus, mobility of the water molecules becomes slower and consequently the solvation time is also retarded. We have observed bimodal slow rotational relaxation time in all these systems.
Design and evaluation of high strength concrete for girders : final report.

DOT National Transportation Integrated Search

1980-05-01

The scope of the study was to make concrete mixes in the laboratory using a partial factorial, with three cement contents, two coarse aggregates and three fine-to-coarse aggregate ratios. The mixes showing the best properties and highest compressive ...
Linker histone partial phosphorylation: effects on secondary structure and chromatin condensation

PubMed Central

Lopez, Rita; Sarg, Bettina; Lindner, Herbert; Bartolomé, Salvador; Ponte, Inma; Suau, Pedro; Roque, Alicia

2015-01-01

Linker histones are involved in chromatin higher-order structure and gene regulation. We have successfully achieved partial phosphorylation of linker histones in chicken erythrocyte soluble chromatin with CDK2, as indicated by HPCE, MALDI-TOF and Tandem MS. We have studied the effects of linker histone partial phosphorylation on secondary structure and chromatin condensation. Infrared spectroscopy analysis showed a gradual increase of β-structure in the phosphorylated samples, concomitant to a decrease in α-helix/turns, with increasing linker histone phosphorylation. This conformational change could act as the first step in the phosphorylation-induced effects on chromatin condensation. A decrease of the sedimentation rate through sucrose gradients of the phosphorylated samples was observed, indicating a global relaxation of the 30-nm fiber following linker histone phosphorylation. Analysis of specific genes, combining nuclease digestion and qPCR, showed that phosphorylated samples were more accessible than unphosphorylated samples, suggesting local chromatin relaxation. Chromatin aggregation was induced by MgCl2 and analyzed by dynamic light scattering (DLS). Phosphorylated chromatin had lower percentages in volume of aggregated molecules and the aggregates had smaller hydrodynamic diameter than unphosphorylated chromatin, indicating that linker histone phosphorylation impaired chromatin aggregation. These findings provide new insights into the effects of linker histone phosphorylation in chromatin condensation. PMID:25870416
Local Intermolecular Order Controls Photoinduced Charge Separation at Donor/Acceptor Interfaces in Organic Semiconductors

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

Feier, Hilary M.; Reid, Obadiah G.; Pace, Natalie A.

2016-03-23

How free charge is generated at organic donor-acceptor interfaces is an important question, as the binding energy of the lowest energy (localized) charge transfer states should be too high for the electron and hole to escape each other. Recently, it has been proposed that delocalization of the electronic states participating in charge transfer is crucial, and aggregated or otherwise locally ordered structures of the donor or the acceptor are the precondition for this electronic characteristic. The effect of intermolecular aggregation of both the polymer donor and fullerene acceptor on charge separation is studied. In the first case, the dilute electronmore » acceptor triethylsilylhydroxy-1,4,8,11,15,18,22,25-octabutoxyphthalocyaninatosilicon(IV) (SiPc) is used to eliminate the influence of acceptor aggregation, and control polymer order through side-chain regioregularity, comparing charge generation in 96% regioregular (RR-) poly(3-hexylthiophene) (P3HT) with its regiorandom (RRa-) counterpart. In the second case, ordered phases in the polymer are eliminated by using RRa-P3HT, and phenyl-C61-butyric acid methyl ester (PC61BM) is used as the acceptor, varying its concentration to control aggregation. Time-resolved microwave conductivity, time-resolved photoluminescence, and transient absorption spectroscopy measurements show that while ultrafast charge transfer occurs in all samples, long-lived charge carriers are only produced in films with intermolecular aggregates of either RR-P3HT or PC61BM, and that polymer aggregates are just as effective in this regard as those of fullerenes.« less
Scanning electron microscopy study of adhesion in sea urchin blastulae. M.S. Thesis

NASA Technical Reports Server (NTRS)

Crowther, Susan D.

1988-01-01

The dissociation supernatant (DS) isolated by disaggregating Strongylocentrotus purpuratus blastulae in calcium- and magnesium-free seawater specifically promotes reaggregation of S. purpuratus blastula cells. The purpose of this study was to use scanning electron microscopy to examine the gross morphology of aggregates formed in the presence of DS to see if it resembles adhesion in partially dissociated blastulae. A new reaggregation procedure developed here, using large volumes of cell suspension and a large diameter of rotation, was utilized to obtain sufficient quantities of aggregates for scanning electron microscopy. The results indicate that aggregates formed in the presence of DS resemble partially dissociated intact embryos in terms of the direct cell-cell adhesion observed. DS did not cause aggregation to form as a result of the entrapment of cells in masses of extracellular material. These studies provide the groundwork for further studies using transmission electron microscopy to more precisely define the adhesive contacts made by cells in the presence of the putative adhesion molecules present in DS.
Oriented nanometric aggregates of partially inverted zinc ferrite: One-step processing and tunable high-frequency magnetic properties

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

Sai, Ranajit, E-mail: ranajit@ecei.tohoku.ac.jp; Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore; Endo, Yasushi

2015-05-07

In this work, it is demonstrated that the in situ growth of oriented nanometric aggregates of partially inverted zinc ferrite can potentially pave a way to alter and tune magnetocrystalline anisotropy that, in turn, dictates ferromagnetic resonance frequency (f{sub FMR}) by inducing strain due to aggregation. Furthermore, the influence of interparticle interaction on magnetic properties of the aggregates is investigated. Mono-dispersed zinc ferrite nanoparticles (<5 nm) with various degrees of aggregation were prepared through decomposition of metal-organic compounds of zinc (II) and iron (III) in an alcoholic solution under controlled microwave irradiation, below 200 °C. The nanocrystallites were found to possess highmore » degree of inversion (>0.5). With increasing order of aggregation in the samples, saturation magnetization (at 5 K) is found to decrease from 38 emu/g to 24 emu/g, while coercivity is found to increase gradually by up to 100% (525 Oe to 1040 Oe). Anisotropy-mediated shift of f{sub FMR} has also been measured and discussed. In essence, the result exhibits an easy way to control the magnetic characteristics of nanocrystalline zinc ferrite, boosted with significant degree of inversion, at GHz frequencies.« less
[Krigle estimation and its simulated sampling of Chilo suppressalis population density].

PubMed

Yuan, Zheming; Bai, Lianyang; Wang, Kuiwu; Hu, Xiangyue

2004-07-01

In order to draw up a rational sampling plan for the larvae population of Chilo suppressalis, an original population and its two derivative populations, random population and sequence population, were sampled and compared with random sampling, gap-range-random sampling, and a new systematic sampling integrated Krigle interpolation and random original position. As for the original population whose distribution was up to aggregative and dependence range in line direction was 115 cm (6.9 units), gap-range-random sampling in line direction was more precise than random sampling. Distinguishing the population pattern correctly is the key to get a better precision. Gap-range-random sampling and random sampling are fit for aggregated population and random population, respectively, but both of them are difficult to apply in practice. Therefore, a new systematic sampling named as Krigle sample (n = 441) was developed to estimate the density of partial sample (partial estimation, n = 441) and population (overall estimation, N = 1500). As for original population, the estimated precision of Krigle sample to partial sample and population was better than that of investigation sample. With the increase of the aggregation intensity of population, Krigel sample was more effective than investigation sample in both partial estimation and overall estimation in the appropriate sampling gap according to the dependence range.

Effectiveness of partially soluble photosensitizer in photodynamic microbiological inactivation: a curcumin example

NASA Astrophysics Data System (ADS)

Pratavieira, Sebastião.; Matroodi, Fatima; Pinto-Júnior, Fabio Francisco; Rastelli, Alessandra Nara Souza; Bagnato, Vanderlei S.; Guimarães, Francisco E. G.

2017-07-01

We show that partial solubility of a photosensitizer is not necessarily a bad property when dealing with microbiological control. The presence of curcumin aggregates in solution may present advantages with respect the photoand chemical stability.
Boundary-layer diabatic processes, the virtual effect, and convective self-aggregation

NASA Astrophysics Data System (ADS)

Yang, D.

2017-12-01

The atmosphere can self-organize into long-lasting large-scale overturning circulations over an ocean surface with uniform temperature. This phenomenon is referred to as convective self-aggregation and has been argued to be important for tropical weather and climate systems. Here we use a 1D shallow water model and a 2D cloud-resolving model (CRM) to show that boundary-layer diabatic processes are essential for convective self-aggregation. We will show that boundary-layer radiative cooling, convective heating, and surface buoyancy flux help convection self-aggregate because they generate available potential energy (APE), which sustains the overturning circulation. We will also show that evaporative cooling in the boundary layer (cold pool) inhibits convective self-aggregation by reducing APE. Both the shallow water model and CRM results suggest that the enhanced virtual effect of water vapor can lead to convective self-aggregation, and this effect is mainly in the boundary layer. This study proposes new dynamical feedbacks for convective self-aggregation and complements current studies that focus on thermodynamic feedbacks.
Quality Assessment of Mixed and Ceramic Recycled Aggregates from Construction and Demolition Wastes in the Concrete Manufacture According to the Spanish Standard †

PubMed Central

Rodríguez-Robles, Desirée; García-González, Julia; Juan-Valdés, Andrés; Pozo, Julia Mª Morán-del; Guerra-Romero, Manuel I

2014-01-01

Construction and demolition waste (CDW) constitutes an increasingly significant problem in society due to the volume generated, rendering sustainable management and disposal problematic. The aim of this study is to identify a possible reuse option in the concrete manufacturing for recycled aggregates with a significant ceramic content: mixed recycled aggregates (MixRA) and ceramic recycled aggregates (CerRA). In order to do so, several tests are conducted in accordance with the Spanish Code on Structural Concrete (EHE-08) to determine the composition in weight and physic-mechanical characteristics (particle size distributions, fine content, sand equivalent, density, water absorption, flakiness index, and resistance to fragmentation) of the samples for the partial inclusion of the recycled aggregates in concrete mixes. The results of these tests clearly support the hypothesis that this type of material may be suitable for such partial replacements if simple pretreatment is carried out. Furthermore, this measure of reuse is in line with European, national, and regional policies on sustainable development, and presents a solution to the environmental problem caused by the generation of CDW. PMID:28788164
Radiative-convective equilibrium model intercomparison project

NASA Astrophysics Data System (ADS)

Wing, Allison A.; Reed, Kevin A.; Satoh, Masaki; Stevens, Bjorn; Bony, Sandrine; Ohno, Tomoki

2018-03-01

RCEMIP, an intercomparison of multiple types of models configured in radiative-convective equilibrium (RCE), is proposed. RCE is an idealization of the climate system in which there is a balance between radiative cooling of the atmosphere and heating by convection. The scientific objectives of RCEMIP are three-fold. First, clouds and climate sensitivity will be investigated in the RCE setting. This includes determining how cloud fraction changes with warming and the role of self-aggregation of convection in climate sensitivity. Second, RCEMIP will quantify the dependence of the degree of convective aggregation and tropical circulation regimes on temperature. Finally, by providing a common baseline, RCEMIP will allow the robustness of the RCE state across the spectrum of models to be assessed, which is essential for interpreting the results found regarding clouds, climate sensitivity, and aggregation, and more generally, determining which features of tropical climate a RCE framework is useful for. A novel aspect and major advantage of RCEMIP is the accessibility of the RCE framework to a variety of models, including cloud-resolving models, general circulation models, global cloud-resolving models, single-column models, and large-eddy simulation models.
Third Partial and 3.0L Second Partial and 2.0L Partial and Amended Consent Decree

EPA Pesticide Factsheets

The settlement partially resolves allegations that Volkswagen violated the Clean Air Act (“CAA”) by the sale of approximately 500,000 model year 2009 to 2015 motor vehicles containing 2.0 liter diesel engines equipped with “defeat devices” (“CAA 2.0 liter.
Effect of fly ash on the strength of porous concrete using recycled coarse aggregate to replace low-quality natural coarse aggregate

NASA Astrophysics Data System (ADS)

Arifi, Eva; Cahya, Evi Nur; Christin Remayanti, N.

2017-09-01

The performance of porous concrete made of recycled coarse aggregate was investigated. Fly ash was used as cement partial replacement. In this study, the strength of recycled aggregate was coMPared to low quality natural coarse aggregate which has high water absorption. Compression strength and tensile splitting strength test were conducted to evaluate the performance of porous concrete using fly ash as cement replacement. Results have shown that the utilization of recycled coarse aggregate up to 75% to replace low quality natural coarse aggregate with high water absorption increases compressive strength and splitting tensile strength of porous concrete. Using fly ash up to 25% as cement replacement improves compressive strength and splitting tensile strength of porous concrete.
A chemometric approach for characterization of serum transthyretin in familial amyloidotic polyneuropathy type I (FAP-I) by electrospray ionization-ion mobility mass spectrometry.

PubMed

Pont, Laura; Sanz-Nebot, Victoria; Vilaseca, Marta; Jaumot, Joaquim; Tauler, Roma; Benavente, Fernando

2018-05-01

In this study, we describe a chemometric data analysis approach to assist in the interpretation of the complex datasets from the analysis of high-molecular mass oligomeric proteins by ion mobility mass spectrometry (IM-MS). The homotetrameric protein transthyretin (TTR) is involved in familial amyloidotic polyneuropathy type I (FAP-I). FAP-I is associated with a specific TTR mutant variant (TTR(Met30)) that can be easily detected analyzing the monomeric forms of the mutant protein. However, the mechanism of protein misfolding and aggregation onset, which could be triggered by structural changes in the native tetrameric protein, remains under investigation. Serum TTR from healthy controls and FAP-I patients was purified under non-denaturing conditions by conventional immunoprecipitation in solution and analyzed by IM-MS. IM-MS allowed separation and characterization of several tetrameric, trimeric and dimeric TTR gas ions due to their differential drift time. After an appropriate data pre-processing, multivariate curve resolution alternating least squares (MCR-ALS) was applied to the complex datasets. A group of seven independent components being characterized by their ion mobility profiles and mass spectra were resolved to explain the observed data variance in control and patient samples. Then, principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were considered for exploration and classification. Only four out of the seven resolved components were enough for an accurate differentiation. Furthermore, the specific TTR ions identified in the mass spectra of these components and the resolved ion mobility profiles provided a straightforward insight into the most relevant oligomeric TTR proteoforms for the disease. Copyright © 2018 Elsevier B.V. All rights reserved.
Platelet aggregation caused by a partially purified jellyfish toxin from Carybdea rastonii.

PubMed

Azuma, H; Sekizaki, S; Satoh, A; Nakajima, T; Ishikawa, M

1986-01-01

A partially purified toxin (pCrTX) was obtained from the tentacles of the jellyfish, Carybdea rastonii. When pCrTX (3 X 10(-8) - 3 X 10(-7) g/ml) was added to citrated platelet-rich plasma, aggregation was produced in a concentration-dependent manner. Scanning electron microscopic examination revealed that both pCrTX and collagen produced aggregates of platelets possessing many pseudopods. The concentration which produced 50% aggregation for pCrTX was 1.8 X 10(-7) g/ml, as compared to 2.3 X 10(-6) g/ml for collagen. The pCrTX-induced aggregation was only slightly inhibited by indomethacin and quinacrine in concentrations sufficient to inhibit arachidonic acid- and collagen-induced aggregation. pCrTX was less active in washed platelets suspended in Ca2+ free medium, whereas the pCrTX-induced aggregation was significantly augmented in the presence of Ca2+. The augmentation of aggregation by Ca2+ was only slightly attenuated by pretreatment with 100 microM verapamil. pCrTX significantly increased the concentration of cytoplasmic free Ca2+ ([Ca2+]i) and depolarized the platelet membrane in concentrations that produced aggregation. The increase in [Ca2+]i caused by pCrTX was little affected by verapamil. The depolarization by pCrTX was unchanged in the presence or absence of Ca2+, or by sodium or potassium transport inhibitors. The movement of 22Na+ into platelets was significantly increased by pCrTX. This increase in the movement of 22N+ into platelets was unaffected by tetrodotoxin. On the other hand, pCrTX-induced aggregation, depolarization and the increase in [Ca2+]i were all significantly attenuated in low Na+ medium. These results suggest that pCrTX causes a massive depolarization by increasing cation permeability indiscriminately and this generalized depolarization permits an inward movement of calcium down an electrochemical gradient which, in turn triggers platelet aggregation.
TFE-induced local unfolding and fibrillation of SOD1: bridging the experiment and simulation studies.

PubMed

Kumar, Vijay; Prakash, Amresh; Pandey, Preeti; Lynn, Andrew M; Hassan, Md Imtaiyaz

2018-05-18

Misfolding and aggregation of Cu, Zn Superoxide dismutase (SOD1) is involved in the neurodegenerative disease, amyotrophic lateral sclerosis. Many studies have shown that metal-depleted, monomeric form of SOD1 displays substantial local unfolding dynamics and is the precursor for aggregation. Here, we have studied the structure and dynamics of different apo monomeric SOD1 variants associated with unfolding and aggregation in aqueous trifluoroethanol (TFE) through experiments and simulation. TFE induces partially unfolded β-sheet-rich extended conformations in these SOD1 variants, which subsequently develops aggregates with fibril-like characteristics. Fibrillation was achieved more easily in disulfide-reduced monomeric SOD1 when compared with wild-type and mutant monomeric SOD1. At higher concentrations of TFE, a native-like structure with the increase in α-helical content was observed. The molecular dynamics simulation results illustrate distinct structural dynamics for different regions of SOD1 variants and show uniform local unfolding of β-strands. The strands protected by the zinc-binding and electrostatic loops were found to unfold first in 20% (v/v) TFE, leading to a partial unfolding of β-strands 4, 5, and 6 which are prone to aggregation. Our results thus shed light on the role of local unfolding and conformational dynamics in SOD1 misfolding and aggregation. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.
Observing the atmosphere in moisture space

NASA Astrophysics Data System (ADS)

Schulz, Hauke; Stevens, Bjorn

2017-04-01

Processes behind convective aggregation have mostly been analysed and identified on the basis of relatively idealized cloud resolving model studies. Relatively little effort has been spent on using observations to test or quantify the findings coming from the models. In 2010 the Barbados Cloud Observatory (BCO) was established on Barbados, which is on the edge of the ITCZ, in part to test hypotheses such as those emerging form the analysis of cloud resolving models. To better test ideas related to the driving forces of convective aggregation, we analyse BCO measurements to identify the processes changing the moist static energy flux, in moisture space, i.e., as a function of rank column water vapour. Similar approaches are used to analyse cloud resolving models. We composite five years of cloud- and water-vapor profiles, from a cloud radar, and Raman water vapour lidar to construct the structure of the observed atmosphere in moisture space. The data show both agreement and disagreement with the models: radiative transfer calculations of the cross-section reveal a strong anomalous radiative cooling in the boundary layer at the dry end of the moisture space. We show that the radiation, mainly in the long-wave, implies a shallow circulation. This circulation agrees generally with supplementary used reanalysis datasets, but the strength and extent vary more markedly across the analyses. Consistent with the modelling, the implied radiative driven circulation supports the aggregation process by importing net moist static energy into the moist regimes.
37 CFR 262.3 - Royalty fees for public performances of sound recordings and for ephemeral recordings.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Option—(A) Non-Music Programming. $0.000762 (0.0762¢) per Aggregate Tuning Hour for programming... experience in respect of partial performances. (ii) Aggregate Tuning Hour Option—(A) Non-Music Programming... on its statements of account the pertinent music use information upon which such reduction has been...
Decay Estimates in Chemotaxis:. Aggregation of Glia and a Possible Application to ALZHEIMER'S Disease Senile Plaques

NASA Astrophysics Data System (ADS)

Webber, M.; Straughan, B.

2006-03-01

Some models of chemotaxis are reviewed, particularly those involving three coupled nonlinear partial differential equations. It is shown how decay bounds may be formulated in these cases. Applications are considered, in particular to a model for glia aggregation, and the possible connection with Alzheimer's disease.
Application of Glass Fiber Waste Polypropylene Aggregate in Lightweight Concrete – thermal properties

NASA Astrophysics Data System (ADS)

Citek, D.; Rehacek, S.; Pavlik, Z.; Kolisko, J.; Dobias, D.; Pavlikova, M.

2018-03-01

Actual paper focus on thermal properties of a sustainable lightweight concrete incorporating high volume of waste polypropylene aggregate as partial substitution of natural aggregate. In presented experiments a glass fiber reinforced polypropylene (GFPP) which is a by-product of PP tubes production, partially substituted fine natural silica aggregate in 10, 20, 30, 40 and 50 mass %. Results were compared with a reference concrete mix without plastic waste in order to quantify the effect of GFPP use on concrete properties. Main material physical parameters were studied (bulk density, matrix density without air content, and particle size distribution). Especially a thermal transport and storage properties of GFPP were examined in dependence on compaction time. For the developed lightweight concrete, thermal properties were accessed using transient impulse technique, where the measurement was done in dependence on moisture content (from the fully water saturated state to dry state). It was found that the tested lightweight concrete should be prospective construction material possessing improved thermal insulation function and the reuse of waste plastics in concrete composition was beneficial both from the environmental and financial point of view.
Properties of lightweight aggregate concrete prepared with PVC granules derived from scraped PVC pipes.

PubMed

Kou, S C; Lee, G; Poon, C S; Lai, W L

2009-02-01

This paper aims to investigate the fresh and hardened properties of lightweight aggregate concretes that are prepared with the use of recycled plastic waste sourced from scraped PVC pipes to replace river sand as fine aggregates. A number of laboratory prepared concrete mixes were tested, in which river sand was partially replaced by PVC plastic waste granules in percentages of 0%, 5%, 15%, 30% and 45% by volume. Two major findings are identified. The positive side shows that the concrete prepared with a partial replacement by PVC was lighter (lower density), was more ductile (greater Poisson's ratios and reduced modulus of elasticity), and had lower drying shrinkage and higher resistance to chloride ion penetration. The negative side reveals that the workability, compressive strength and tensile splitting strength of the concretes were reduced. The results gathered would form a part of useful information for recycling PVC plastic waste in lightweight concrete mixes.
Monomeric and fibrillar α-synuclein exert opposite effects on the catalytic cycle that promotes the proliferation of Aβ42 aggregates

PubMed Central

Chia, Sean; Habchi, Johnny; Lattanzi, Veronica; Dobson, Christopher M.; Knowles, Tuomas P. J.; Vendruscolo, Michele

2017-01-01

The coaggregation of the amyloid-β peptide (Aβ) and α-synuclein is commonly observed in a range of neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases. The complex interplay between Aβ and α-synuclein has led to seemingly contradictory results on whether α-synuclein promotes or inhibits Aβ aggregation. Here, we show how these conflicts can be rationalized and resolved by demonstrating that different structural forms of α-synuclein exert different effects on Aβ aggregation. Our results demonstrate that whereas monomeric α-synuclein blocks the autocatalytic proliferation of Aβ42 (the 42-residue form of Aβ) fibrils, fibrillar α-synuclein catalyses the heterogeneous nucleation of Aβ42 aggregates. It is thus the specific balance between the concentrations of monomeric and fibrillar α-synuclein that determines the outcome of the Aβ42 aggregation reaction. PMID:28698377
Aggregation behaviour and electron injection/recombination dynamics of symmetrical and unsymmetrical Zn-phthalocyanines on TiO2 film.

PubMed

Ashokkumar, R; Kathiravan, A; Ramamurthy, P

2014-01-21

We have synthesized symmetrical and unsymmetrical Zn-phthalocyanine derivatives (PZnPc, MPZnPc and TPZnPc) for dye sensitized solar cells (DSSCs). Steady state and time-resolved absorption and fluorescence studies were performed in DMF solvent and on a TiO2 surface. The mode and extent of aggregation (H- and J-aggregates) of ZnPc adsorbed on a TiO2 surface were demonstrated. MPZnPc shows both H- and J-aggregation, while TPZnPc shows only H-aggregation. Moreover, the fluorescence of ZnP/TiO2 was completely quenched and this was assigned to electron injection from excited ZnPc to TiO2. Energy level calculations show both ZnPc deriviatives have enough driving force to inject electrons into the conduction band of TiO2. Furthermore, the radical cation of ZnPc was observed in nanosecond transient absorption measurements.
Energy transfer in aggregated CuInS2/ZnS core-shell quantum dots deposited as solid films

NASA Astrophysics Data System (ADS)

Gardelis, S.; Fakis, M.; Droseros, N.; Georgiadou, D.; Travlos, A.; Nassiopoulou, A. G.

2017-01-01

We report on the morphology and optical properties of CuInS2/ZnS core-shell quantum dots in solid films by means of AFM, SEM, HRTEM, steady state and time-resolved photoluminescence (PL) spectroscopy. The amount of aggregation of the CuInS2/ZnS QDs was controlled by changing the preparation conditions of the films. A red-shift of the PL spectrum of CuInS2/ZnS core-shell quantum dots, deposited as solid films on silicon substrates, is observed upon increasing the amount of aggregation. The presence of larger aggregates was found to lead to a larger PL red-shift. Besides, as the degree of aggregation increased, the PL decay became slower. We attribute the observed PL red-shift to energy transfer from the smaller to the larger dots within the aggregates, with the emission being realized via a long decay recombination mechanism (100-200 ns), the origin of which is discussed.
Hemin as a generic and potent protein misfolding inhibitor

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

Liu, Yanqin; Carver, John A.; Ho, Lam H.

2014-11-14

Highlights: • Hemin prevents Aβ42, α-synuclein and RCM-κ-casein forming amyloid fibrils. • Hemin inhibits the β-sheet structure formation of Aβ42. • Hemin reduces the cell toxicity caused by fibrillar Aβ42. • Hemin dissociates partially formed Aβ42 fibrils. • Hemin prevents amorphous aggregation by ADH, catalase and γs-crystallin. - Abstract: Protein misfolding causes serious biological malfunction, resulting in diseases including Alzheimer’s disease, Parkinson’s disease and cataract. Molecules which inhibit protein misfolding are a promising avenue to explore as therapeutics for the treatment of these diseases. In the present study, thioflavin T fluorescence and transmission electron microscopy experiments demonstrated that hemin preventsmore » amyloid fibril formation of kappa-casein, amyloid beta peptide and α-synuclein by blocking β-sheet structure assembly which is essential in fibril aggregation. Further, inhibition of fibril formation by hemin significantly reduces the cytotoxicity caused by fibrillar amyloid beta peptide in vitro. Interestingly, hemin degrades partially formed amyloid fibrils and prevents further aggregation to mature fibrils. Light scattering assay results revealed that hemin also prevents protein amorphous aggregation of alcohol dehydrogenase, catalase and γs-crystallin. In summary, hemin is a potent agent which generically stabilises proteins against aggregation, and has potential as a key molecule for the development of therapeutics for protein misfolding diseases.« less
Scaling symmetry, renormalization, and time series modeling: the case of financial assets dynamics.

PubMed

Zamparo, Marco; Baldovin, Fulvio; Caraglio, Michele; Stella, Attilio L

2013-12-01

We present and discuss a stochastic model of financial assets dynamics based on the idea of an inverse renormalization group strategy. With this strategy we construct the multivariate distributions of elementary returns based on the scaling with time of the probability density of their aggregates. In its simplest version the model is the product of an endogenous autoregressive component and a random rescaling factor designed to embody also exogenous influences. Mathematical properties like increments' stationarity and ergodicity can be proven. Thanks to the relatively low number of parameters, model calibration can be conveniently based on a method of moments, as exemplified in the case of historical data of the S&P500 index. The calibrated model accounts very well for many stylized facts, like volatility clustering, power-law decay of the volatility autocorrelation function, and multiscaling with time of the aggregated return distribution. In agreement with empirical evidence in finance, the dynamics is not invariant under time reversal, and, with suitable generalizations, skewness of the return distribution and leverage effects can be included. The analytical tractability of the model opens interesting perspectives for applications, for instance, in terms of obtaining closed formulas for derivative pricing. Further important features are the possibility of making contact, in certain limits, with autoregressive models widely used in finance and the possibility of partially resolving the long- and short-memory components of the volatility, with consistent results when applied to historical series.
Scaling symmetry, renormalization, and time series modeling: The case of financial assets dynamics

NASA Astrophysics Data System (ADS)

Zamparo, Marco; Baldovin, Fulvio; Caraglio, Michele; Stella, Attilio L.

2013-12-01

We present and discuss a stochastic model of financial assets dynamics based on the idea of an inverse renormalization group strategy. With this strategy we construct the multivariate distributions of elementary returns based on the scaling with time of the probability density of their aggregates. In its simplest version the model is the product of an endogenous autoregressive component and a random rescaling factor designed to embody also exogenous influences. Mathematical properties like increments’ stationarity and ergodicity can be proven. Thanks to the relatively low number of parameters, model calibration can be conveniently based on a method of moments, as exemplified in the case of historical data of the S&P500 index. The calibrated model accounts very well for many stylized facts, like volatility clustering, power-law decay of the volatility autocorrelation function, and multiscaling with time of the aggregated return distribution. In agreement with empirical evidence in finance, the dynamics is not invariant under time reversal, and, with suitable generalizations, skewness of the return distribution and leverage effects can be included. The analytical tractability of the model opens interesting perspectives for applications, for instance, in terms of obtaining closed formulas for derivative pricing. Further important features are the possibility of making contact, in certain limits, with autoregressive models widely used in finance and the possibility of partially resolving the long- and short-memory components of the volatility, with consistent results when applied to historical series.

Local atomic structure of Fe/Cr multilayers: Depth-resolved method

NASA Astrophysics Data System (ADS)

Babanov, Yu. A.; Ponomarev, D. A.; Devyaterikov, D. I.; Salamatov, Yu. A.; Romashev, L. N.; Ustinov, V. V.; Vasin, V. V.; Ageev, A. L.

2017-10-01

A depth-resolved method for the investigation of the local atomic structure by combining data of X-ray reflectivity and angle-resolved EXAFS is proposed. The solution of the problem can be divided into three stages: 1) determination of the element concentration profile with the depth z from X-ray reflectivity data, 2) determination of the X-ray fluorescence emission spectrum of the element i absorption coefficient μia (z,E) as a function of depth and photon energy E using the angle-resolved EXAFS data Iif (E , ϑl) , 3) determination of partial correlation functions gij (z , r) as a function of depth from μi (z , E) . All stages of the proposed method are demonstrated on a model example of a multilayer nanoheterostructure Cr/Fe/Cr/Al2O3. Three partial pair correlation functions are obtained. A modified Levenberg-Marquardt algorithm and a regularization method are applied.
Aggregate Size and Architecture Determine Microbial Activity Balance for One-Stage Partial Nitritation and Anammox ▿

PubMed Central

Vlaeminck, Siegfried E.; Terada, Akihiko; Smets, Barth F.; De Clippeleir, Haydée; Schaubroeck, Thomas; Bolca, Selin; Demeestere, Lien; Mast, Jan; Boon, Nico; Carballa, Marta; Verstraete, Willy

2010-01-01

Aerobic ammonium-oxidizing bacteria (AerAOB) and anoxic ammonium-oxidizing bacteria (AnAOB) cooperate in partial nitritation/anammox systems to remove ammonium from wastewater. In this process, large granular microbial aggregates enhance the performance, but little is known about granulation so far. In this study, three suspended-growth oxygen-limited autotrophic nitrification-denitrification (OLAND) reactors with different inoculation and operation (mixing and aeration) conditions, designated reactors A, B, and C, were used. The test objectives were (i) to quantify the AerAOB and AnAOB abundance and the activity balance for the different aggregate sizes and (ii) to relate aggregate morphology, size distribution, and architecture putatively to the inoculation and operation of the three reactors. A nitrite accumulation rate ratio (NARR) was defined as the net aerobic nitrite production rate divided by the anoxic nitrite consumption rate. The smallest reactor A, B, and C aggregates were nitrite sources (NARR, >1.7). Large reactor A and C aggregates were granules capable of autonomous nitrogen removal (NARR, 0.6 to 1.1) with internal AnAOB zones surrounded by an AerAOB rim. Around 50% of the autotrophic space in these granules consisted of AerAOB- and AnAOB-specific extracellular polymeric substances. Large reactor B aggregates were thin film-like nitrite sinks (NARR, <0.5) in which AnAOB were not shielded by an AerAOB layer. Voids and channels occupied 13 to 17% of the anoxic zone of AnAOB-rich aggregates (reactors B and C). The hypothesized granulation pathways include granule replication by division and budding and are driven by growth and/or decay based on species-specific physiology and by hydrodynamic shear and mixing. PMID:19948857
DOE Office of Scientific and Technical Information (OSTI.GOV)

Lopez-Buendia, A.M.; Climent, V.; Verdu, P.

The reactivity of carbonate rock with the alkali content of cement, commonly called alkali-carbonate reaction (ACR), has been investigated. Alkali-silica reaction (ASR) can also contribute in the alkali-aggregate reaction (AAR) in carbonate rock, mainly due to micro- and crypto-crystalline quartz or clay content in carbonate aggregate. Both ACR and ASR can occur in the same system, as has been also evidenced on this paper. Carbonate aggregate samples were selected using lithological reactivity criteria, taking into account the presence of dedolomitization, partial dolomitization, micro- and crypto-crystalline quartz. Selected rocks include calcitic dolostone with chert (CDX), calcitic dolostone with dedolomitization (CDD), limestonemore » with chert (LX), marly calcitic dolostone with partial dolomitization (CD), high-porosity ferric dolostone with clays (FD). To evaluate the reactivity, aggregates were studied using expansion tests following RILEM AAR-2, AAR-5, a modification using LiOH AAR-5Li was also tested. A complementary study was done using petrographic monitoring with polarised light microscopy on aggregates immersed in NaOH and LiOH solutions after different ages. SEM-EDAX has been used to identify the presence of brucite as a product of dedolomitization. An ACR reaction showed shrinkage of the mortar bars in alkaline solutions explained by induced dedolomitization, while an ASR process typically displayed expansion. Neither shrinkage nor expansion was observed when mortar bars were immersed in solutions of lithium hydroxide. Carbonate aggregate classification with AAR pathology risk has been elaborated based on mechanical behaviours by expansion and shrinkage. It is proposed to be used as a petrographic method for AAR diagnosis to complement the RILEM AAR1 specifically for carbonate aggregate. Aggregate materials can be classified as I (non-reactive), II (potentially reactive), and III (probably reactive), considering induced dedolomitization ACR (dedolomitization degree) and ASR.« less
Aggregation of Trp > Glu point mutants of human gamma-D crystallin provides a model for hereditary or UV-induced cataract.

PubMed

Serebryany, Eugene; Takata, Takumi; Erickson, Erika; Schafheimer, Nathaniel; Wang, Yongting; King, Jonathan A

2016-06-01

Numerous mutations and covalent modifications of the highly abundant, long-lived crystallins of the eye lens cause their aggregation leading to progressive opacification of the lens, cataract. The nature and biochemical mechanisms of the aggregation process are poorly understood, as neither amyloid nor native-state polymers are commonly found in opaque lenses. The βγ-crystallin fold contains four highly conserved buried tryptophans, which can be oxidized to more hydrophilic products, such as kynurenine, upon UV-B irradiation. We mimicked this class of oxidative damage using Trp→Glu point mutants of human γD-crystallin. Such substitutions may represent a model of UV-induced photodamage-introduction of a charged group into the hydrophobic core generating "denaturation from within." The effects of Trp→Glu substitutions were highly position dependent. While each was destabilizing, only the two located in the bottom of the double Greek key fold-W42E and W130E-yielded robust aggregation of partially unfolded intermediates at 37°C and pH 7. The αB-crystallin chaperone suppressed aggregation of W130E, but not W42E, indicating distinct aggregation pathways from damage in the N-terminal vs C-terminal domain. The W130E aggregates had loosely fibrillar morphology, yet were nonamyloid, noncovalent, showed little surface hydrophobicity, and formed at least 20°C below the melting temperature of the native β-sheets. These features are most consistent with domain-swapped polymerization. Aggregation of partially destabilized crystallins under physiological conditions, as occurs in this class of point mutants, could provide a simple in vitro model system for drug discovery and optimization. © 2016 The Protein Society.
Effect of Gravity Waves from Small Islands in the Southern Ocean on the Southern Hemisphere Atmospheric Circulation

NASA Technical Reports Server (NTRS)

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

2018-01-01

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

PubMed

Sutter, Marc; Oliveira, Sabrina; Sanders, Niek N; Lucas, Bart; van Hoek, Arie; Hink, Mark A; Visser, Antonie J W G; De Smedt, Stefaan C; Hennink, Wim E; Jiskoot, Wim

2007-03-01

The fluorescent dye Nile red was used as a probe for the sensitive detection of large, denatured aggregates of the model protein beta-galactosidase (E. coli) in solution. Aggregates were formed by irreversible heat denaturation of beta-galactosidase below and above the protein's unfolding temperature of 57.4 degrees C, and the presence of aggregates in heated solutions was confirmed by static light scattering. Interaction of Nile red with beta-galactosidase aggregates led to a shift of the emission maximum (lambda (max)) from 660 to 611 nm, and to an increase of fluorescence intensity. Time-resolved fluorescence and fluorescence correlation spectroscopy (FCS) measurements showed that Nile red detected large aggregates with hydrodynamic radii around 130 nm. By steady-state fluorescence measurements, it was possible to detect 1 nM of denatured and aggregated beta-galactosidase in solution. The comparison with size exclusion chromatography (SEC) showed that native beta-galactosidase and small aggregates thereof had no substantial effect on the fluorescence of Nile red. Large aggregates were not detected by SEC, because they were excluded from the column. The results with beta-galactosidase demonstrate the potential of Nile red for developing complementary analytical methods that overcome the size limitations of SEC, and can detect the formation of large protein aggregates at early stages.
Structure-based inhibitors of tau aggregation

NASA Astrophysics Data System (ADS)

Seidler, P. M.; Boyer, D. R.; Rodriguez, J. A.; Sawaya, M. R.; Cascio, D.; Murray, K.; Gonen, T.; Eisenberg, D. S.

2018-02-01

Aggregated tau protein is associated with over 20 neurological disorders, which include Alzheimer's disease. Previous work has shown that tau's sequence segments VQIINK and VQIVYK drive its aggregation, but inhibitors based on the structure of the VQIVYK segment only partially inhibit full-length tau aggregation and are ineffective at inhibiting seeding by full-length fibrils. Here we show that the VQIINK segment is the more powerful driver of tau aggregation. Two structures of this segment determined by the cryo-electron microscopy method micro-electron diffraction explain its dominant influence on tau aggregation. Of practical significance, the structures lead to the design of inhibitors that not only inhibit tau aggregation but also inhibit the ability of exogenous full-length tau fibrils to seed intracellular tau in HEK293 biosensor cells into amyloid. We also raise the possibility that the two VQIINK structures represent amyloid polymorphs of tau that may account for a subset of prion-like strains of tau.
Assessing the role of aromatic residues in the amyloid aggregation of human muscle acylphosphatase

PubMed Central

Bemporad, Francesco; Taddei, Niccolò; Stefani, Massimo; Chiti, Fabrizio

2006-01-01

Among the many parameters that have been proposed to promote amyloid fibril formation is the π-stacking of aromatic residues. We have studied the amyloid aggregation of several mutants of human muscle acylphosphatase in which an aromatic residue was substituted with a non-aromatic one. The aggregation rate was determined using the Thioflavin T test under conditions in which the variants populated initially an ensemble of partially unfolded conformations. Substitutions in aggregation-promoting fragments of the sequence result in a dramatically decreased aggregation rate of the protein, confirming the propensity of aromatic residues to promote this process. Nevertheless, a statistical analysis shows that the measured decrease of aggregation rate following mutation arises predominantly from a reduction of hydrophobicity and intrinsic β-sheet propensity. This suggests that aromatic residues favor aggregation because of these factors rather than for their aromaticity. PMID:16600970
MBAR-enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation

NASA Astrophysics Data System (ADS)

Xu, Yuanwei; Rodger, P. Mark

2017-03-01

We study the effect of helical structure on the aggregation of proteins using a simplified lattice protein model with an implicit membrane environment. A recently proposed Monte Carlo approach, which exploits the proven statistical optimality of the MBAR estimator in order to improve simulation efficiency, was used. The results show that with both two and four proteins present, the tendency to aggregate is strongly expedited by the presence of amphipathic helix (APH), whereas a transmembrane helix (TMH) slightly disfavours aggregation. When four protein molecules are present, partially aggregated states (dimers and trimers) were more common when the APH was present, compared with the cases where no helices or only the TMH is present.
Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

PubMed

Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

2016-02-01

Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation. © 2015 Wiley Periodicals, Inc.
Study on performance of concrete with over-burnt bricks aggregates and micro-silica admixture

NASA Astrophysics Data System (ADS)

Praveen, K.; Sathyan, Dhanya; Mini, K. M.

2016-09-01

Concrete is made by mixing cement, sand, aggregates and water in required proportion, where aggregates occupy the major volume. Addition of aggregates in concrete improves properties of concrete. With the natural resources depleting rapidly, limiting the use of natural resources and enhancing the use of waste materials is very important for sustainable development. Over-burnt bricks are a waste material which cannot be used in construction directly because of their irregular shape and dark colour. Use of over-burnt bricks helps to preserve natural aggregate source. The present study focuses on the effects of microsilica at various percentages as a partial cement replacement in concrete with over-burnt bricks as coarse aggregates. The mechanical properties of hardened concrete such as splitting tensile strength, flexural strength and compressive strength are studied and analyzed.
Understanding curcumin-induced modulation of protein aggregation.

PubMed

Ahmad, Basir; Borana, Mohanish S; Chaudhary, Ankur P

2017-07-01

Curcumin, a diarylheptanoid compound, found in spice turmeric is known to alter the aggregation of proteins and reduce the toxicity of the aggregates. This review looks at the molecular basis of modulating protein aggregation and toxicity of the aggregates. Foremost, we identify the interaction of curcumin and its derivatives with proteins/peptides and the effect of their interaction on the conformational stability and unfolding/folding pathway(s). The unfolding/folding processes generate partially folded/unfolded intermediate, which serve as aggregation precursor state. Secondly, we discuss the effect of curcumin binding on the kinetics parameters of the aggregation process, which give information about the mechanism of the aggregation inhibition. We describe, in addition, that curcumin can accelerate/promote fibril formation by binding to oligomeric intermediate(s) accumulated in the aggregation pathway. Finally, we discuss the correlation of curcumin-induced monomeric and/or oligomeric precursor states with aggregate structure and toxicity. On the basis of these discussions, we propose a model describing curcumin-induced inhibition/promotion of formation of amyloid-like fibrils. Copyright © 2016 Elsevier B.V. All rights reserved.
Properties of cold-bonded lightweight artificial aggregate containing bottom ash with different curing regime

NASA Astrophysics Data System (ADS)

Mohamad Ibrahim, Norlia; Nizar Ismail, Khairul; Che Amat, Roshazita; Mohamad Ghazali, Mohamad Iqbal

2018-03-01

Cold-bonded pelletizing technique is frequently used in aggregate manufacturing process as it can minimise the energy consumption. It has contributed to both economical and environmental advantages because it helps to reduce the gas emissions problems. Bottom ash collected from municipal solid waste incineration (MSWI) plant was selected as raw material in this study and was utilised as a partial replacement for cement for artificial aggregate production. Several percentage of ash replacement was selected ranged from 10 to 50%. Aggregate pellets were subjected to different types of curing condition which is room-water (RW), room-room (RR), oven-room (OR) and oven-water (OW) condition. Properties of aggregate pellets were examined to obtain its density, water absorption, aggregate impact value (AIV) and specific gravity (SG). The results indicated that the most efficient curing regime is by exposing the aggregate in RW condition. The optimum aggregate was selected at 20% where it has satisfied the required density of 739.5kg/m3, and classified as strong aggregate with AIV 14. However, the water absorption of aggregate increased proportionately with the increment of ash content.
A synergistic aggregation pheromone component in the banana weevil Cosmopolites sordidus Germar 1824 (Coleoptera: Curculionidae).

PubMed

Cerda, H; Mori, K; Nakayama, T; Jaffe, K

1998-01-01

Cosmopolites sordidus is an important pest on banana plantations worldwide. The chemistry of the aggregation pheromone of this insect has been recently resolved and here we present the first evidence from field trails that sordidin, a compound from the male released aggregation pheromone, attracts significant number of weevils only if host plant odors are also present. Sordidin attracts few insects when it is presented without the host plant tissue. However, the attractiveness of host plant tissue increases more than tenfold when it is presented simultaneously with sordidin in field traps. We confirm experimentally that sordidin may be used as part of a system for mass trapping and monitoring this insect.
Low temperature time resolved photoluminescence in ordered and disordered Cu2ZnSnS4 single crystals

NASA Astrophysics Data System (ADS)

Raadik, Taavi; Krustok, Jüri; Kauk-Kuusik, M.; Timmo, K.; Grossberg, M.; Ernits, K.; Bleuse, J.

2017-03-01

In this work we performed time-resolved micro-photoluminescence (TRPL) studies of Cu2ZnSnS4 (CZTS) single crystals grown in molten KI salt. The order/disorder degree of CZTS was varied by the thermal post treatment temperature. Photoluminescence spectra measured at T=8 K showed an asymmetric band with a peak position of 1.33 eV and 1.27 eV for partially ordered and disordered structures, respectively. Thermal activation energies were found to be ET (PO) =65±9 meV for partially ordered and ET (PD) =27±4 meV for partially disordered. These low activation energy values indicating to the defect cluster recombination model for both partially ordered and disordered structures. TRPL was measured for both crystals and their decay curves were fitted with a stretched exponential function, in order to describe the charge carriers' recombination dynamics at low temperature.
Calcium oxalate monohydrate aggregation induced by aggregation of desialylated Tamm-Horsfall protein

PubMed Central

Viswanathan, Pragasam; Rimer, Jeffrey D.; Kolbach, Ann M.; Kleinman, Jack G.

2011-01-01

Tamm-Horsfall protein (THP) is thought to protect against calcium oxalate monohydrate (COM) stone formation by inhibiting COM aggregation. Several studies reported that stone formers produce THP with reduced levels of glycosylation, particularly sialic acid levels, which leads to reduced negative charge. In this study, normal THP was treated with neuraminidase to remove sialic acid residues, confirmed by an isoelectric point shift to higher pH. COM aggregation assays revealed that desialylated THP (ds-THP) promoted COM aggregation, while normal THP inhibited aggregation. The appearance of protein aggregates in solutions at ds-THP concentrations ≥1 µg/mL in 150 mM NaCl correlated with COM aggregation promotion, implying that ds-THP aggregation induced COM aggregation. The aggregation-promoting effect of the ds-THP was independent of pH above its isoelectric point, but was substantially reduced at low ionic strength, where protein aggregation was much reduced. COM aggregation promotion was maximized at a ds-THP to COM mass ratio of ~0.025, which can be explained by a model wherein partial COM surface coverage by ds-THP aggregates promotes crystal aggregation by bridging opposing COM surfaces, whereas higher surface coverage leads to repulsion between adsorbed ds-THP aggregates. Thus, desialylation of THP apparently abrogates a normal defensive action of THP by inducing protein aggregation, and subsequently COM aggregation, a condition that favors kidney stone formation. PMID:21229239
Numerical Investigation on Absorption Enhancement of Black Carbon Aerosols Partially Coated With Nonabsorbing Organics

NASA Astrophysics Data System (ADS)

Zhang, Xiaolin; Mao, Mao; Yin, Yan; Wang, Bin

2018-01-01

This study numerically evaluates the effects of aerosol microphysics, including coated volume fraction of black carbon (BC), shell/core ratio, and size distribution, on the absorption enhancement (Eab) of polydisperse BC aggregates partially coated by organics, which is calculated by the exact multiple-sphere T-matrix method. The coated volume fraction of BC plays a substantial role in determining the absorption enhancement of partially coated BC aggregates, which typically have an Eab in the range of 1.0-2.0 with a larger value for larger coated volume fraction of BC as the shell/core ratio, BC geometry, and size distribution are fixed. The shell/core ratio, BC geometry, and size distribution have little impact on the Eab of coated BC with small coated volume fraction of BC, while they become significant for large coated volume fraction of BC. The Eab of partially coated BC particles can be slightly less than 1.0 for the large BC in the accumulation mode exhibiting large shell/core ratio and small coated volume fraction of BC, indicating that the absorption shows even slight decrease relative to uncoated BC particles. For partially coated BC aggregates in the accumulation and coarse modes, the refractive index uncertainties of BC result in the Eab differences of less than 9% and 2%, respectively, while those of organics can induce larger variations with the maximum differences up to 22% and 18%, respectively. Our study indicates that accounting for particle coating microphysics, particularly the coated volume fraction of BC, can potentially help to understand the differences in observations of largely variable absorption enhancements over various regions.
Aggregation and Stability of Reduced Graphene Oxide: Complex Roles of Divalent Cations, pH, and Natural Organic Matter

EPA Science Inventory

The aggregation and stability of graphene oxide (GO) and three successively reduced GO (rGO) nanomaterials were investigated. Reduced GO species were partially reduced GO (rGO-1h), intermediately reduced GO (rGO-2h), and fully reduced GO (rGO-5h). Specifically, influence of pH, i...
Combining analytical hierarchy process and agglomerative hierarchical clustering in search of expert consensus in green corridors development management.

PubMed

Shapira, Aviad; Shoshany, Maxim; Nir-Goldenberg, Sigal

2013-07-01

Environmental management and planning are instrumental in resolving conflicts arising between societal needs for economic development on the one hand and for open green landscapes on the other hand. Allocating green corridors between fragmented core green areas may provide a partial solution to these conflicts. Decisions regarding green corridor development require the assessment of alternative allocations based on multiple criteria evaluations. Analytical Hierarchy Process provides a methodology for both a structured and consistent extraction of such evaluations and for the search for consensus among experts regarding weights assigned to the different criteria. Implementing this methodology using 15 Israeli experts-landscape architects, regional planners, and geographers-revealed inherent differences in expert opinions in this field beyond professional divisions. The use of Agglomerative Hierarchical Clustering allowed to identify clusters representing common decisions regarding criterion weights. Aggregating the evaluations of these clusters revealed an important dichotomy between a pragmatist approach that emphasizes the weight of statutory criteria and an ecological approach that emphasizes the role of the natural conditions in allocating green landscape corridors.
Combining Analytical Hierarchy Process and Agglomerative Hierarchical Clustering in Search of Expert Consensus in Green Corridors Development Management

NASA Astrophysics Data System (ADS)

Shapira, Aviad; Shoshany, Maxim; Nir-Goldenberg, Sigal

2013-07-01

Environmental management and planning are instrumental in resolving conflicts arising between societal needs for economic development on the one hand and for open green landscapes on the other hand. Allocating green corridors between fragmented core green areas may provide a partial solution to these conflicts. Decisions regarding green corridor development require the assessment of alternative allocations based on multiple criteria evaluations. Analytical Hierarchy Process provides a methodology for both a structured and consistent extraction of such evaluations and for the search for consensus among experts regarding weights assigned to the different criteria. Implementing this methodology using 15 Israeli experts—landscape architects, regional planners, and geographers—revealed inherent differences in expert opinions in this field beyond professional divisions. The use of Agglomerative Hierarchical Clustering allowed to identify clusters representing common decisions regarding criterion weights. Aggregating the evaluations of these clusters revealed an important dichotomy between a pragmatist approach that emphasizes the weight of statutory criteria and an ecological approach that emphasizes the role of the natural conditions in allocating green landscape corridors.

Environmental Impact Of The Use Of Contaminated Sediments As Partial Replacement Of The Aggregate Used In Road Construction

EPA Science Inventory

The Indiana Harbor Canal (IHC) is a waterway extensively polluted with heavy metals and petroleum. Since there are limited disposal options for the petroleum-contaminated sediments (PCSs) of the canal, the environmental impact of IHC dewatered sediment when used as partial repla...
Value-added utilisation of recycled concrete in hot-mix asphalt.

PubMed

Wong, Yiik Diew; Sun, Darren Delai; Lai, Dickson

2007-01-01

The feasibility of partial substitution of granite aggregate in hot-mix asphalt (HMA) with waste concrete aggregate was investigated. Three hybrid HMA mixes incorporating substitutions of granite fillers/fines with 6%, 45% untreated, and 45% heat-treated concrete were evaluated by the Marshall mix design method; the optimum binder contents were found to be 5.3%, 6.5% and 7.0% of grade Pen 60/70 bitumen, respectively. All three hybrid mixes satisfied the Marshall criteria of the Singapore Land Transport Authority (LTA) W3B wearing course specification. The hybrid mix with 6% concrete fillers gave comparable resilient modulus and creep resistance as the conventional W3B mix, while hybrid mixes with higher concrete substitutions achieved better performance. X-ray diffraction (XRD) showed the distinct presence of free lime in the heat-treated concrete, while the scanning electron microscope (SEM) provided an in-depth perspective of the concrete grains in the HMA matrix. The results suggest feasible use of waste concrete as partial aggregate substitution in HMA.
Crystal induced phosphorescence from Benz(a)anthracene microcrystals at room temperature

NASA Astrophysics Data System (ADS)

Maity, Samir; Mazumdar, Prativa; Shyamal, Milan; Sahoo, Gobinda Prasad; Misra, Ajay

2016-03-01

Pure organic compounds that are also phosphorescent at room temperature are very rare in literature. Here, we report efficient phosphorescence emission from aggregated hydrosol of Benz(a)anthracene (BaA) at room temperature. Aggregated hydrosol of BaA has been synthesized by re-precipitation method and SDS is used as morphology directing agent. Morphology of the particles is characterized using optical and scanning electronic microcopy (SEM). Photophysical properties of the aggregated hydrosol are carried out using UV-vis, steady state and time resolved fluorescence study. The large stoke shifted structured emission from aggregated hydrosol of BaA has been explained due to phosphorescence emission of BaA at room temperature. In the crystalline state, the restricted intermolecular motions (RIM) such as rotations and vibrations are activated by crystal lattice. This rigidification effect makes the chromophore phosphorescent at room temperature. The possible stacking arrangement of the neighboring BaA within the aggregates has been substantiated by computing second order Fukui parameter as local reactivity descriptors. Computational study also reveals that the neighboring BaA molecules are present in parallel slipped conformation in its aggregated crystalline form.
Reversible Aggregation Plays a Crucial Role on the Folding Landscape of p53 Core Domain

PubMed Central

Ishimaru, Daniella; Lima, Luis M. T. R.; Maia, Lenize F.; Lopez, Priscila M.; Ano Bom, Ana P.; Valente, Ana P.; Silva, Jerson L.

2004-01-01

The role of tumor suppressor protein p53 in cell cycle control depends on its flexible and partially unstructured conformation, which makes it crucial to understand its folding landscape. Here we report an intermediate structure of the core domain of the tumor suppressor protein p53 (p53C) during equilibrium and kinetic folding/unfolding transitions induced by guanidinium chloride. This partially folded structure was undetectable when investigated by intrinsic fluorescence. Indeed, the fluorescence data showed a simple two-state transition. On the other hand, analysis of far ultraviolet circular dichroism in 1.0 M guanidinium chloride demonstrated a high content of secondary structure, and the use of an extrinsic fluorescent probe, 4,4′-dianilino-1,1′ binaphthyl-5,5′-disulfonic acid, indicated an increase in exposure of the hydrophobic core at 1 M guanidinium chloride. This partially folded conformation of p53C was plagued by aggregation, as suggested by one-dimensional NMR and demonstrated by light-scattering and gel-filtration chromatography. Dissociation by high pressure of these aggregates reveals the reversibility of the process and that the aggregates have water-excluded cavities. Kinetic measurements show that the intermediate formed in a parallel reaction between unfolded and folded structures and that it is under fine energetic control. They are not only crucial to the folding pathway of p53C but may explain as well the vulnerability of p53C to undergo departure of the native to an inactive state, which makes the cell susceptible to malignant transformation. PMID:15298872
Stepwise Nucleation of Aniline: Emergence of Spectroscopic Fingerprints of the Liquid Phase.

PubMed

Leon, Iker; Usabiaga, Imanol; Arnaiz, Pedro Felipe; Lesarri, Alberto; Fernández, Jose Andres

2018-06-11

We deal here with the controlled nucleation of aniline from the isolated molecule until formation of a moderately large aggregate: aniline nonamer. The structure of the cluster at each step of the nucleation was unravelled combining mass-resolved IR spectroscopy and computational chemistry, demonstrating that aggregation is primarily guided by formation of extensive N-H···N hydrogen bond networks that give the aggregates a sort of branched backbone, in clear competition with multiple N-H/C-H···pi and pi···pi interactions. The result is the co-existence of close nucleation paths connecting relational aggregates. The delicate balance of molecular forces makes the aniline clusters a challenge for molecular orbital calculations and an ideal system to refine the present nucleation models. Noticeably, spectroscopic signatures characteristic of the condensed phase are apparent in the nanometer-size aggregates formed in this work. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Acceleration of tropical cyclogenesis by self-aggregation feedbacks

NASA Astrophysics Data System (ADS)

Muller, Caroline J.; Romps, David M.

2018-03-01

Idealized simulations of tropical moist convection have revealed that clouds can spontaneously clump together in a process called self-aggregation. This results in a state where a moist cloudy region with intense deep convection is surrounded by extremely dry subsiding air devoid of deep convection. Because of the idealized settings of the simulations where it was discovered, the relevance of self-aggregation to the real world is still debated. Here, we show that self-aggregation feedbacks play a leading-order role in the spontaneous genesis of tropical cyclones in cloud-resolving simulations. Those feedbacks accelerate the cyclogenesis process by a factor of 2, and the feedbacks contributing to the cyclone formation show qualitative and quantitative agreement with the self-aggregation process. Once the cyclone is formed, wind-induced surface heat exchange (WISHE) effects dominate, although we find that self-aggregation feedbacks have a small but nonnegligible contribution to the maintenance of the mature cyclone. Our results suggest that self-aggregation, and the framework developed for its study, can help shed more light into the physical processes leading to cyclogenesis and cyclone intensification. In particular, our results point out the importance of the longwave radiative cooling outside the cyclone.
Properties of Concrete with Tire Derived Aggregate Partially Replacing Coarse Aggregates.

PubMed

Siringi, Gideon; Abolmaali, Ali; Aswath, Pranesh B

2015-01-01

Tire derived aggregate (TDA) has been proposed as a possible lightweight replacement for mineral aggregate in concrete. The role played by the amount of TDA replacing coarse aggregate as well as different treatment and additives in concrete on its properties is examined. Conventional concrete (without TDA) and concrete containing TDA are compared by examining their compressive strength based on ASTM C39, workability based on ASTM C143, splitting tensile strength based on ASTM C496, modulus of rupture (flexural strength) based on ASTM C78, and bond stress based on ASTM C234. Results indicate that while replacement of coarse aggregates with TDA results in reduction in strength, it may be mitigated with addition of silica fume to obtain the desired strength. The greatest benefit of using TDA is in the development of a higher ductile product while utilizing recycled TDA.
Properties of Concrete with Tire Derived Aggregate Partially Replacing Coarse Aggregates

PubMed Central

Siringi, Gideon; Abolmaali, Ali; Aswath, Pranesh B.

2015-01-01

Tire derived aggregate (TDA) has been proposed as a possible lightweight replacement for mineral aggregate in concrete. The role played by the amount of TDA replacing coarse aggregate as well as different treatment and additives in concrete on its properties is examined. Conventional concrete (without TDA) and concrete containing TDA are compared by examining their compressive strength based on ASTM C39, workability based on ASTM C143, splitting tensile strength based on ASTM C496, modulus of rupture (flexural strength) based on ASTM C78, and bond stress based on ASTM C234. Results indicate that while replacement of coarse aggregates with TDA results in reduction in strength, it may be mitigated with addition of silica fume to obtain the desired strength. The greatest benefit of using TDA is in the development of a higher ductile product while utilizing recycled TDA. PMID:26161440
Archean Earth Atmosphere Fractal Haze Aggregates: Light Scattering Calculations and the Faint Young Sun Paradox

NASA Astrophysics Data System (ADS)

Boness, D. A.; Terrell-Martinez, B.

2010-12-01

As part of an ongoing undergraduate research project of light scattering calculations involving fractal carbonaceous soot aggregates relevant to current anthropogenic and natural sources in Earth's atmosphere, we have read with interest a recent paper [E.T. Wolf and O.B Toon,Science 328, 1266 (2010)] claiming that the Faint Young Sun paradox discussed four decades ago by Carl Sagan and others can be resolved without invoking heavy CO2 concentrations as a greenhouse gas warming the early Earth enough to sustain liquid water and hence allow the origin of life. Wolf and Toon report that a Titan-like Archean Earth haze, with a fractal haze aggregate nature due to nitrogen-methane photochemistry at high altitudes, should block enough UV light to protect the warming greenhouse gas NH3 while allowing enough visible light to reach the surface of the Earth. To test this hypothesis, we have employed a rigorous T-Matrix arbitrary-particle light scattering technique, to avoid the simplifications inherent in Mie-sphere scattering, on haze fractal aggregates at UV and visible wavelenths of incident light. We generate these model aggregates using diffusion-limited cluster aggregation (DLCA) algorithms, which much more closely fit actual haze fractal aggregates than do diffusion-limited aggregation (DLA) algorithms.
Early Amyloidogenic Oligomerization Studied through Fluorescence Lifetime Correlation Spectroscopy

PubMed Central

Paredes, Jose M.; Casares, Salvador; Ruedas-Rama, Maria J.; Fernandez, Elena; Castello, Fabio; Varela, Lorena; Orte, Angel

2012-01-01

Amyloidogenic protein aggregation is a persistent biomedical problem. Despite active research in disease-related aggregation, the need for multidisciplinary approaches to the problem is evident. Recent advances in single-molecule fluorescence spectroscopy are valuable for examining heterogenic biomolecular systems. In this work, we have explored the initial stages of amyloidogenic aggregation by employing fluorescence lifetime correlation spectroscopy (FLCS), an advanced modification of conventional fluorescence correlation spectroscopy (FCS) that utilizes time-resolved information. FLCS provides size distributions and kinetics for the oligomer growth of the SH3 domain of α-spectrin, whose N47A mutant forms amyloid fibrils at pH 3.2 and 37 °C in the presence of salt. The combination of FCS with additional fluorescence lifetime information provides an exciting approach to focus on the initial aggregation stages, allowing a better understanding of the fibrillization process, by providing multidimensional information, valuable in combination with other conventional methodologies. PMID:22949804
Determination of Patterson group symmetry from sparse multi-crystal data sets in the presence of an indexing ambiguity.

PubMed

Gildea, Richard J; Winter, Graeme

2018-05-01

Combining X-ray diffraction data from multiple samples requires determination of the symmetry and resolution of any indexing ambiguity. For the partial data sets typical of in situ room-temperature experiments, determination of the correct symmetry is often not straightforward. The potential for indexing ambiguity in polar space groups is also an issue, although methods to resolve this are available if the true symmetry is known. Here, a method is presented to simultaneously resolve the determination of the Patterson symmetry and the indexing ambiguity for partial data sets. open access.
Slow Auger Relaxation in HgTe Colloidal Quantum Dots.

PubMed

Melnychuk, Christopher; Guyot-Sionnest, Philippe

2018-05-03

The biexciton lifetimes in HgTe colloidal quantum dots are measured as a function of particle size. Samples produced by two synthetic methods, leading to partially aggregated or well-dispersed particles, exhibit markedly different dynamics. The relaxation characteristics of partially aggregated HgTe inhibit reliable determinations of the Auger lifetime. In well-dispersed HgTe quantum dots, the biexciton lifetime increases approximately linearly with particle volume, confirming trends observed in other systems. The extracted Auger coefficient is three orders of magnitude smaller than that for bulk HgCdTe materials with similar energy gaps. We discuss these findings in the context of understanding Auger relaxation in quantum-confined systems and their relevance to mid-infrared optoelectronic devices based on HgTe colloidal quantum dots.
EFFECTS OF CORRELATED PROBABILISTIC EXPOSURE MODEL INPUTS ON SIMULATED RESULTS

EPA Science Inventory

In recent years, more probabilistic models have been developed to quantify aggregate human exposures to environmental pollutants. The impact of correlation among inputs in these models is an important issue, which has not been resolved. Obtaining correlated data and implementi...
High-pressure studies of aggregation of recombinant human interleukin-1 receptor antagonist: Thermodynamics, kinetics, and application to accelerated formulation studies

PubMed Central

Seefeldt, Matthew B.; Kim, Yong-Sung; Tolley, Kevin P.; Seely, Jim; Carpenter, John F.; Randolph, Theodore W.

2005-01-01

Recombinant human interleukin-1 receptor antagonist (IL-1ra) in aqueous solutions unfolds and aggregates when subjected to hydrostatic pressures greater than about 180 MPa. This study examined the mechanism and thermodynamics of pressure-induced unfolding and aggregation of IL-1ra. The activation free energy for growth of aggregates (ΔG∓aggregation) was found to be 37 ± 3 kJ/mol, whereas the activation volume (ΔV∓aggregation) was −120 ± 20 mL/mol. These values compare closely with equilibrium values for denaturation: The free energy for denaturation, ΔGdenaturation, was 20 ± 5 kJ/mol, whereas the partial specific volume change for denaturation, ΔVdenaturation, was −110 ± 30 mL/mol. When IL-1ra begins to denature at pressures near 140 MPa, cysteines that are normally buried in the native state become exposed. Under oxidizing conditions, this results in the formation of covalently cross-linked aggregates containing nonnative, intermolecular disulfide bonds. The apparent activation free energy for nucleation of aggregates, ΔG∓nuc, was 42 ± 4 kJ/mol, and the activation volume for nucleation, ΔV∓nuc,was −175 ± 37 mL/mol, suggesting that a highly solvent-exposed conformation is needed for nucleation. We hypothesize that the large specific volume of IL-1ra, 0.752 ± 0.004 mL/g, coupled with its relatively low conformational stability, leads to its susceptibility to denaturation at relatively low pressures. The positive partial specific adiabatic compressibility of IL-1ra, 4.5 ± 0.7 ± 10−12 cm2/dyn, suggests that a significant component of the ΔVdenaturation is attributable to the elimination of solvent-free cavities. Lastly, we propose that hydrostatic pressure is a useful variable to conduct accelerated formulation studies of therapeutic proteins. PMID:16081653
Partially-Averaged Navier Stokes Model for Turbulence: Implementation and Validation

NASA Technical Reports Server (NTRS)

Girimaji, Sharath S.; Abdol-Hamid, Khaled S.

2005-01-01

Partially-averaged Navier Stokes (PANS) is a suite of turbulence closure models of various modeled-to-resolved scale ratios ranging from Reynolds-averaged Navier Stokes (RANS) to Navier-Stokes (direct numerical simulations). The objective of PANS, like hybrid models, is to resolve large scale structures at reasonable computational expense. The modeled-to-resolved scale ratio or the level of physical resolution in PANS is quantified by two parameters: the unresolved-to-total ratios of kinetic energy (f(sub k)) and dissipation (f(sub epsilon)). The unresolved-scale stress is modeled with the Boussinesq approximation and modeled transport equations are solved for the unresolved kinetic energy and dissipation. In this paper, we first present a brief discussion of the PANS philosophy followed by a description of the implementation procedure and finally perform preliminary evaluation in benchmark problems.
Ultrafast exciton migration in an HJ-aggregate: Potential surfaces and quantum dynamics

NASA Astrophysics Data System (ADS)

Binder, Robert; Polkehn, Matthias; Ma, Tianji; Burghardt, Irene

2017-01-01

Quantum dynamical and electronic structure calculations are combined to investigate the mechanism of exciton migration in an oligothiophene HJ aggregate, i.e., a combination of oligomer chains (J-type aggregates) and stacked aggregates of such chains (H-type aggregates). To this end, a Frenkel exciton model is parametrized by a recently introduced procedure [Binder et al., J. Chem. Phys. 141, 014101 (2014)] which uses oligomer excited-state calculations to perform an exact, point-wise mapping of coupled potential energy surfaces to an effective Frenkel model. Based upon this parametrization, the Multi-Layer Multi-Configuration Time-Dependent Hartree (ML-MCTDH) method is employed to investigate ultrafast dynamics of exciton transfer in a small, asymmetric HJ aggregate model composed of 30 sites and 30 active modes. For a partially delocalized initial condition, it is shown that a torsional defect confines the trapped initial exciton, and planarization induces an ultrafast resonant transition between an HJ-aggregated segment and a covalently bound "dangling chain" end. This model is a minimal realization of experimentally investigated mixed systems exhibiting ultrafast exciton transfer between aggregated, highly planarized chains and neighboring disordered segments.
Thermal aggregation of glycated bovine serum albumin.

PubMed

Rondeau, Philippe; Navarra, Giovanna; Cacciabaudo, Francesco; Leone, Maurizio; Bourdon, Emmanuel; Militello, Valeria

2010-04-01

Aggregation and glycation processes in proteins have a particular interest in medicine fields and in food technology. Serum albumins are model proteins which are able to self-assembly in aggregates and also sensitive to a non-enzymatic glycation in cases of diabetes. In this work, we firstly reported a study on the glycation and oxidation effects on the structure of bovine serum albumin (BSA). The experimental approach is based on the study of conformational changes of BSA at secondary and tertiary structures by FTIR absorption and fluorescence spectroscopy, respectively. Secondly, we analysed the thermal aggregation process on BSA glycated with different glucose concentrations. Additional information on the aggregation kinetics are obtained by light scattering measurements. The results show that glycation process affects the native structure of BSA. Then, the partial unfolding of the tertiary structure which accompanies the aggregation process is similar both in native and glycated BSA. In particular, the formation of aggregates is progressively inhibited with growing concentration of glucose incubated with BSA. These results bring new insights on how aggregation process is affected by modification of BSA induced by glycation. Copyright 2009 Elsevier B.V. All rights reserved.
Recycling of rubble from building demolition for low-shrinkage concretes.

PubMed

Corinaldesi, Valeria; Moriconi, Giacomo

2010-04-01

In this project concrete mixtures were prepared that were characterized by low ductility due to desiccation by using debris from building demolition, which after a suitable treatment was used as aggregate for partial replacement of natural aggregates. The recycled aggregate used came from a recycling plant, in which rubble from building demolition was selected, crushed, cleaned, sieved, and graded. Such aggregates are known to be more porous as indicated by the Saturated Surface Dry (SSD) moisture content. The recycled concrete used as aggregates were added to the concrete mixture in order to study their influence on the fresh and hardened concrete properties. They were added either after water pre-soaking or in dry condition, in order to evaluate the influence of moisture in aggregates on the performance of concrete containing recycled aggregate. In particular, the effect of internal curing, due to the use of such aggregates, was studied. Concrete behavior due to desiccation under dehydration was studied by means of both drying shrinkage test and German angle test, through which shrinkage under the restrained condition of early age concrete can be evaluated. Copyright 2009 Elsevier Ltd. All rights reserved.
Phosphodiesterase from Daboia russelli russelli venom: purification, partial characterization and inhibition of platelet aggregation.

PubMed

Mitra, Jyotirmoy; Bhattacharyya, Debasish

2014-09-01

Phosphodiesterases (PDEs) belong to a super-family of enzymes that have multiple roles in the metabolism of extracellular nucleotides and regulation of nucleotide-based intercellular signalling. A PDE from Russell's viper (Daboia russelli russelli) venom (DR-PDE) was purified by gel filtration, ion exchange and affinity chromatographies. Homogeneity of the preparation was verified by SDS-PAGE, SE-HPLC and mass spectrometry. It was free from 5'-nucleotidase, alkaline phosphatase and protease activities. Identity of the enzyme was ensured from partial sequence homology with other PDEs. DR-PDE was inactivated by polyvalent anti-venom serum and metal chelators. The enzyme was partially inhibited by the root extracts of four medicinal plants but remained unaffected by inhibitors of intracellular PDEs. DR-PDE hydrolyses ADP and thus, strongly inhibits ADP-induced platelet aggregation in human platelet rich plasma. This study leads to better understanding of a component of Russell's viper venom that affects homoeostatic system of the victim. Copyright © 2014 Elsevier Ltd. All rights reserved.
76 FR 16607 - Carbon and Certain Alloy Steel Wire Rod From Mexico: Notice of Partial Rescission of Antidumping...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-24

... phosphorus, more than 0.05 percent of selenium, or more than 0.01 percent of tellurium). Also excluded from....01 percent of aluminum, (3) 0.040 percent or less, in the aggregate, of phosphorus and sulfur, (4) 0... aggregate, of phosphorus and sulfur, (4) 0.008 percent or less of nitrogen, and (5) either not more than 0...

Recycling ground granulated blast furnace slag as cold bonded artificial aggregate partially used in self-compacting concrete.

PubMed

Gesoğlu, Mehmet; Güneyisi, Erhan; Mahmood, Swara Fuad; Öz, Hatice Öznur; Mermerdaş, Kasım

2012-10-15

Ground granulated blast furnace slag (GGBFS), a by-product from iron industry, was recycled as artificial coarse aggregate through cold bonding pelletization process. The artificial slag aggregates (ASA) replaced partially the natural coarse aggregates in production of self-compacting concrete (SCC). Moreover, as being one of the most widely used mineral admixtures in concrete industry, fly ash (FA) was incorporated as a part of total binder content to impart desired fluidity to SCCs. A total of six concrete mixtures having various ASA replacement levels (0%, 20%, 40%, 60%, and 100%) were designed with a water-to-binder (w/b) ratio of 0.32. Fresh properties of self-compacting concretes (SCC) were observed through slump flow time, flow diameter, V-funnel flow time, and L-box filling height ratio. Compressive strength of hardened SCCs was also determined at 28 days of curing. It was observed that increasing the replacement level of ASA resulted in decrease in the amount of superplasticizer to achieve a constant slump flow diameter. Moreover, passing ability and viscosity of SCC's enhanced with increasing the amount of ASA in the concrete. The maximum compressive strength was achieved for the SCC having 60% ASA replacement. Copyright © 2012 Elsevier B.V. All rights reserved.
Ash aggregation during the 11 February 2010 partial dome collapse of the Soufrière Hills Volcano, Montserrat

NASA Astrophysics Data System (ADS)

Burns, F. A.; Bonadonna, C.; Pioli, L.; Cole, P. D.; Stinton, A.

2017-04-01

On 11 February 2010, Soufrière Hills Volcano, Montserrat, underwent a partial dome collapse ( 50 × 106 m3) and a short-lived Vulcanian explosion towards the end. Three main pyroclastic units were identified N and NE of the volcano: dome-collapse pyroclastic density current (PDC) deposits, fountain-collapse PDC deposits formed by the Vulcanian explosion, and tephra-fallout deposits associated with elutriation from the dome-collapse and fountain-collapse PDCs (i.e. co-PDC fallout deposit). The fallout associated with the Vulcanian explosion was mostly dispersed E and SE by high altitude winds. All units N and NE of the volcano contain variable amounts and types of particle aggregates, although the co-PDC fallout deposit is associated with the largest abundance (i.e. up to 24 wt%). The size of aggregates found in the co-PDC fallout deposit increases with distance from the volcano and proximity to the sea, reaching a maximum diameter of 12 mm about 500 m from the coast. The internal grain size of all aggregates have nearly identical distributions (with Mdϕ ≈ 4-5), with particles in the size categories > 3 ϕ (i.e. < 250 μm) being distributed in similar proportions within the aggregates but in different proportions within distinct internal layers. In fact, most aggregates are characterized by a coarse grained central core occupying the main part of the aggregate, coated by a thin layer of finer ash (single-layer aggregates), while others have one or two additional layers accreted over the core (multiple-layer aggregates). Calculated aggregate porosity and settling velocity vary between 0.3 and 0.5 and 11-21 m s- 1, respectively. The aggregate size shows a clear correlation with both the core size and the size of the largest particles found in the core. The large abundance of aggregates in the co-PDC fallout deposits suggests that the buoyant plumes elutriated above PDCs represent an optimal environment for the formation (particle collision) and development (aggregate layering) of particle aggregates. However, specific conditions are required, including i) a large availability of water (in this case provided by the steam plumes associated with the entrance of PDCs into the ocean), ii) presence of plume regions with different grain-size features (i.e. both median size and sorting) that allows for the development of multiple layers, iii) strong turbulence that permits both particle collision and the transition of the aggregates through different plume regions, iv) presence of hot regions (e.g. PDCs) that promote aggregate preservation (in this case also facilitated by the presence of sea salt).
Membrane-micelle model for humus in soils and sediments and its relation to humification

USGS Publications Warehouse

Wershaw, Robert L.

1994-01-01

Humification, the process whereby biomass consisting of dead plant and animal remains is converted into soil organic matter (humus), is one of the basic processes of the carbon cycle. The organic compounds that make up plant and animal tissue are thermodynamically unstable in the oxidizing atmosphere at the surface of the Earth. After the organisms in which they are incorporated die, the compounds are converted back to carbon dioxide and water by degradation reactions catalyzed by enzymes secreted by micro-organisms. However, not all the organic compounds in the dead biomass are immediately converted; some of the material is only partially oxidized. The residue left after partial oxidative degradation of the dead biomass is the source of the organic compounds that accumulate in soils and sediments as humus. Previously, humification was thought to involve a conversion of degradation products by a series of polymerization reactions into new types of polymeric species that are different from the precursor molecular species in the original biomass. However, it is proposed here that the depolymerization and oxidation reactions that take place during the enzymatic degradation of biopolymers produce amphiphiles--molecules that have a polar (hydrophilic) part and a nonpolar (hydrophobic) part. These amphiphiles that result from the partial oxidative degradation of dead biomass assemble spontaneously into ordered aggregates in which the hydrophobic parts of the molecules form the interiors and the hydrophilic parts of the molecules make up the exterior surfaces of the aggregates. These ordered aggregates constitute the humus in soils and sediments. Humus ordered aggregates most likely exist as bilayer membranes coating mineral grains and as micelles in solution.
The intrinsically disordered protein LEA7 from Arabidopsis thaliana protects the isolated enzyme lactate dehydrogenase and enzymes in a soluble leaf proteome during freezing and drying.

PubMed

Popova, Antoaneta V; Rausch, Saskia; Hundertmark, Michaela; Gibon, Yves; Hincha, Dirk K

2015-10-01

The accumulation of Late Embryogenesis Abundant (LEA) proteins in plants is associated with tolerance against stresses such as freezing and desiccation. Two main functions have been attributed to LEA proteins: membrane stabilization and enzyme protection. We have hypothesized previously that LEA7 from Arabidopsis thaliana may stabilize membranes because it interacts with liposomes in the dry state. Here we show that LEA7, contrary to this expectation, did not stabilize liposomes during drying and rehydration. Instead, it partially preserved the activity of the enzyme lactate dehydrogenase (LDH) during drying and freezing. Fourier-transform infrared (FTIR) spectroscopy showed no evidence of aggregation of LDH in the dry or rehydrated state under conditions that lead to complete loss of activity. To approximate the complex influence of intracellular conditions on the protective effects of a LEA protein in a convenient in-vitro assay, we measured the activity of two Arabidopsis enzymes (glucose-6-P dehydrogenase and ADP-glucose pyrophosphorylase) in total soluble leaf protein extract (Arabidopsis soluble proteome, ASP) after drying and rehydration or freezing and thawing. LEA7 partially preserved the activity of both enzymes under these conditions, suggesting its role as an enzyme protectant in vivo. Further FTIR analyses indicated the partial reversibility of protein aggregation in the dry ASP during rehydration. Similarly, aggregation in the dry ASP was strongly reduced by LEA7. In addition, mixtures of LEA7 with sucrose or verbascose reduced aggregation more than the single additives, presumably through the effects of the protein on the H-bonding network of the sugar glasses. Copyright © 2015 Elsevier B.V. All rights reserved.
Molecular dynamics studies of protein folding and aggregation

NASA Astrophysics Data System (ADS)

Ding, Feng

This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism that globular proteins under a denaturing environment partially unfold and aggregate by forming stabilizing hydrogen bonds between the backbones of the partial folded substructures. Proteins or peptides rich in alpha-helices also aggregate into beta-rich amyloid fibrils. Upon aggregation, the protein or peptide undergoes a conformational transition from alpha-helices to beta-sheets. The transition of alpha-helix to beta-hairpin (two-stranded beta-sheet) is studied in an all-heavy-atom discrete molecular dynamics model of a polyalanine chain. An entropical driving scenario for the alpha-helix to beta-hairpin transition is discovered.
Spatially: resolved heterogeneous dynamics in a strong colloidal gel

NASA Astrophysics Data System (ADS)

Buzzaccaro, Stefano; Alaimo, Matteo David; Secchi, Eleonora; Piazza, Roberto

2015-05-01

We re-examine the classical problem of irreversible colloid aggregation, showing that the application of Digital Fourier Imaging (DFI), a class of optical correlation methods that combine the power of light scattering and imaging, allows one to pick out novel useful evidence concerning the restructuring processes taking place in a strong colloidal gel. In particular, the spatially-resolved displacement fields provided by DFI strongly suggest that the temporally-intermittent local rearrangements taking place in the course of gel ageing are characterized by very long-ranged spatial correlations.
Human-murine transthyretin heterotetramers are kinetically stable and non-amyloidogenic. A lesson in the generation of transgenic models of diseases involving oligomeric proteins.

PubMed

Reixach, Natàlia; Foss, Ted R; Santelli, Eugenio; Pascual, Jaime; Kelly, Jeffery W; Buxbaum, Joel N

2008-01-25

The transthyretin amyloidoses appear to be caused by rate-limiting tetramer dissociation and partial monomer unfolding of the human serum protein transthyretin, resulting in aggregation and extracellular deposition of amorphous aggregates and amyloid fibrils. Mice transgenic for few copies of amyloid-prone human transthyretin variants, including the aggressive L55P mutant, failed to develop deposits. Silencing the murine transthyretin gene in the presence of the L55P human gene resulted in enhanced tissue deposition. To test the hypothesis that the murine protein interacted with human transthyretin, preventing the dissociation and partial unfolding required for amyloidogenesis, we produced recombinant murine transthyretin and human/murine transthyretin heterotetramers and compared their structures and biophysical properties to recombinant human transthyretin. We found no significant differences between the crystal structures of murine and human homotetramers. Murine transthyretin is not amyloidogenic because the native homotetramer is kinetically stable under physiologic conditions and cannot dissociate into partially unfolded monomers, the misfolding and aggregation precursor. Heterotetramers composed of murine and human subunits are also kinetically stable. These observations explain the lack of transthyretin deposition in transgenics carrying a low copy number of human transthyretin genes. The incorporation of mouse subunits into tetramers otherwise composed of human amyloid-prone transthyretin subunits imposes kinetic stability, preventing dissociation and subsequent amyloidogenesis.
Electrostatic Unfolding and Interactions of Albumin Driven by pH Changes: A Molecular Dynamics Study

PubMed Central

2015-01-01

A better understanding of protein aggregation is bound to translate into critical advances in several areas, including the treatment of misfolded protein disorders and the development of self-assembling biomaterials for novel commercial applications. Because of its ubiquity and clinical potential, albumin is one of the best-characterized models in protein aggregation research; but its properties in different conditions are not completely understood. Here, we carried out all-atom molecular dynamics simulations of albumin to understand how electrostatics can affect the conformation of a single albumin molecule just prior to self-assembly. We then analyzed the tertiary structure and solvent accessible surface area of albumin after electrostatically triggered partial denaturation. The data obtained from these single protein simulations allowed us to investigate the effect of electrostatic interactions between two proteins. The results of these simulations suggested that hydrophobic attractions and counterion binding may be strong enough to effectively overcome the electrostatic repulsions between the highly charged monomers. This work contributes to our general understanding of protein aggregation mechanisms, the importance of explicit consideration of free ions in protein solutions, provides critical new insights about the equilibrium conformation of albumin in its partially denatured state at low pH, and may spur significant progress in our efforts to develop biocompatible protein hydrogels driven by electrostatic partial denaturation. PMID:24393011
Plasma Cell Cheilitis: A Clinicopathological and Immunohistochemical Study of 13 Cases

PubMed Central

Lee, Jin Yong; Kim, Kwang Ho; Hahm, Ji Eun; Ha, Jae Won; Kwon, Won Joo; Kim, Chul Woo

2017-01-01

Background Plasma cell cheilitis is an unusual benign plasma cell proliferative disease of an unknown etiology that typically presents on the lip. Objective The aim of this study was to investigate the clinicopathological characteristics of 13 cases of plasma cell cheilitis. Methods The present study investigated the clinical manifestations, treatment modalities, and outcome of 13 patients diagnosed with plasma cell cheilitis from 2011 to 2016 at Kangdong Sacred Heart Hospital and Hallym University Sacred Heart Hospital. Biopsy specimens of the all cases were evaluated using conventional hematoxylin and eosin staining with kappa and lambda immunoglobulin light chain immunohistochemistry. Results The age of the patients ranged from 39 to 86 years (mean, 64.7 years), with male predominance. Histopathologically, 61.5% and 38.5% of patients showed band-like and pan dermal plasmacytic infiltrates, respectively. Eosinophilic infiltration was noted in 69.2% of patients. All cases showed both kappa and lambda immunoglobulin light chain reactivities, and kappa predominance was confirmed in 9 patients (69.2%). A majority of the patients was treated with local therapy, such as intralesional steroid injection with topical tacrolimus. Among the 13 patients, plasma cell cheilitis completely resolved, partially resolved, and recurred in 3 (23.1%), 5 (38.5%), and 5 patients (38.5%), respectively. Conclusion Plasma cell cheilitis presented as erosive edematous circumscribed patches or plaques affecting mainly the lower lip of elderly male patients. The majority of histopathology cases showed characteristic plasma cell aggregation on the upper dermis that was immunopositive for immunoglobulin light chain, with kappa predominance. PMID:28966508
Value-added utilisation of recycled concrete in hot-mix asphalt

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

Wong, Yiik Diew; Sun, Darren Delai; Lai, Dickson

2007-07-01

The feasibility of partial substitution of granite aggregate in hot-mix asphalt (HMA) with waste concrete aggregate was investigated. Three hybrid HMA mixes incorporating substitutions of granite fillers/fines with 6%, 45% untreated, and 45% heat-treated concrete were evaluated by the Marshall mix design method; the optimum binder contents were found to be 5.3%, 6.5% and 7.0% of grade Pen 60/70 bitumen, respectively. All three hybrid mixes satisfied the Marshall criteria of the Singapore Land Transport Authority (LTA) W3B wearing course specification. The hybrid mix with 6% concrete fillers gave comparable resilient modulus and creep resistance as the conventional W3B mix, whilemore » hybrid mixes with higher concrete substitutions achieved better performance. X-ray diffraction (XRD) showed the distinct presence of free lime in the heat-treated concrete, while the scanning electron microscope (SEM) provided an in-depth perspective of the concrete grains in the HMA matrix. The results suggest feasible use of waste concrete as partial aggregate substitution in HMA.« less
Antiplatelet effects of protopine isolated from Corydalis tubers.

PubMed

Ko, F N; Wu, T S; Lu, S T; Wu, Y C; Huang, T F; Teng, C M

1989-10-15

Protopine inhibited the aggregation and ATP release of rabbit platelets induced by ADP, arachidonic acid, PAF, collagen and ionophore A23187. Although the platelet aggregation caused by thrombin was not inhibited by protopine (100 micrograms/ml), the release reaction was partially suppressed. In rabbit platelet-rich plasma, protopine also inhibited the platelet aggregation caused by ADP, arachidonic acid, PAF and collagen. The thromboxane B2 formation of washed platelets caused by arachidonic acid, collagen, ionophore A23187 and thrombin was suppressed by protopine. Protopine inhibited the intracellular calcium increase caused by arachidonic acid in quin-2/AM loaded rabbit platelets. In the presence of indomethacin, the intracellular calcium increase caused by collagen and PAF was completely suppressed by protopine, and the intracellular calcium increase caused by thrombin was partially inhibited. The phosphoinositides breakdown caused by collagen and PAF was inhibited by protopine, but that by thrombin was not affected significantly. Protopine did not cause the elevation of cyclic AMP level of platelets. It is concluded that the antiplatelet effects of protopine is due to inhibition on thromboxane formation and phosphoinositides breakdown and then lead to the decrease of intracellular calcium concentration.
A passive physical model for DnaK chaperoning

NASA Astrophysics Data System (ADS)

Uhl, Lionel; Dumont, Audrey; Dukan, Sam

2018-03-01

Almost all living organisms use protein chaperones with a view to preventing proteins from misfolding or aggregation either spontaneously or during cellular stress. This work uses a reaction-diffusion stochastic model to describe the dynamic localization of the Hsp70 chaperone DnaK in Escherichia coli cells during transient proteotoxic collapse characterized by the accumulation of insoluble proteins. In the model, misfolded (‘abnormal’) proteins are produced during alcoholic stress and have the propensity to aggregate with a polymerization-like kinetics. When aggregates diffuse more slowly they grow larger. According to Michaelis-Menten-type kinetics, DnaK has the propensity to bind with misfolded proteins or aggregates in order to catalyse refolding. To match experimental fluorescence microscopy data showing clusters of DnaK-GFP localized in multiple foci, the model includes spatial zones with local reduced diffusion rates to generate spontaneous assemblies of DnaK called ‘foci’. Numerical simulations of our model succeed in reproducing the kinetics of DnaK localization experimentally observed. DnaK starts from foci, moves to large aggregates during acute stress, resolves those aggregates during recovery and finally returns to its initial punctate localization pattern. Finally, we compare real biological events with hypothetical repartitions of the protein aggregates or DnaK. We then notice that DnaK action is more efficient on protein aggregates than on protein homogeneously distributed.
Operational Plasticity Enables Hsp104 to Disaggregate Diverse Amyloid and Non-Amyloid Clients

PubMed Central

DeSantis, Morgan E.; Leung, Eunice H.; Sweeny, Elizabeth A.; Jackrel, Meredith E.; Cushman-Nick, Mimi; Neuhaus-Follini, Alexandra; Vashist, Shilpa; Sochor, Matthew A.; Knight, M. Noelle; Shorter, James

2012-01-01

Summary It is not understood how Hsp104, a hexameric AAA+ ATPase from yeast, disaggregates diverse structures including stress-induced aggregates, prions, and α-synuclein conformers connected to Parkinson disease. Here, we establish that Hsp104 hexamers adapt different mechanisms of intersubunit collaboration to disaggregate stress-induced aggregates versus amyloid. To resolve disordered aggregates, Hsp104 subunits collaborate non-co-operatively via probabilistic substrate binding and ATP hydrolysis. To disaggregate amyloid, several subunits co-operatively engage substrate and hydrolyze ATP. Importantly, Hsp104 variants with impaired intersubunit communication dissolve disordered aggregates but not amyloid. Unexpectedly, prokaryotic ClpB subunits collaborate differently than Hsp104 and couple probabilistic substrate binding to cooperative ATP hydrolysis, which enhances disordered aggregate dissolution but sensitizes ClpB to inhibition and diminishes amyloid disaggregation. Finally, we establish that Hsp104 hexamers deploy more subunits to disaggregate Sup35 prion strains with more stable ‘cross-β’ cores. Thus, operational plasticity enables Hsp104 to robustly dissolve amyloid and non-amyloid clients, which impose distinct mechanical demands. PMID:23141537
Development of lightweight concrete mixes for construction industry at the state of Arkansas

NASA Astrophysics Data System (ADS)

Almansouri, Mohammed Abdulwahab

As the construction industry evolved, the need for more durable, long lasting infrastructure increased. Therefore, more efforts have been put to find new methods to improve the properties of the concrete to prolong the service life of the structural elements. One of these methods is the use of lightweight aggregate as an internal curing agent to help reducing self-desiccation and shrinkage. This research studied the effects of using locally available lightweight aggregate (expanded clay), as a partial replacement of normal weight aggregate in the concrete matrix. The concrete mixtures contained lightweight aggregate with a replacement percentage of 12.5, 25, 37.5, and 50 percent by volume. Fresh properties as well as compressive strength, modulus of rupture, and drying shrinkage were measured. While was effective in reducing drying shrinkage, the use of lightweight aggregate resulted in slightly reducing both the compressive strength and modulus of rupture.
Conformational stability as a design target to control protein aggregation.

PubMed

Costanzo, Joseph A; O'Brien, Christopher J; Tiller, Kathryn; Tamargo, Erin; Robinson, Anne Skaja; Roberts, Christopher J; Fernandez, Erik J

2014-05-01

Non-native protein aggregation is a prevalent problem occurring in many biotechnological manufacturing processes and can compromise the biological activity of the target molecule or induce an undesired immune response. Additionally, some non-native aggregation mechanisms lead to amyloid fibril formation, which can be associated with debilitating diseases. For natively folded proteins, partial or complete unfolding is often required to populate aggregation-prone conformational states, and therefore one proposed strategy to mitigate aggregation is to increase the free energy for unfolding (ΔGunf) prior to aggregation. A computational design approach was tested using human γD crystallin (γD-crys) as a model multi-domain protein. Two mutational strategies were tested for their ability to reduce/increase aggregation rates by increasing/decreasing ΔGunf: stabilizing the less stable domain and stabilizing the domain-domain interface. The computational protein design algorithm, RosettaDesign, was implemented to identify point variants. The results showed that although the predicted free energies were only weakly correlated with the experimental ΔGunf values, increased/decreased aggregation rates for γD-crys correlated reasonably well with decreases/increases in experimental ΔGunf, illustrating improved conformational stability as a possible design target to mitigate aggregation. However, the results also illustrate that conformational stability is not the sole design factor controlling aggregation rates of natively folded proteins.
Accelerated simulation of stochastic particle removal processes in particle-resolved aerosol models

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

Curtis, J.H.; Michelotti, M.D.; Riemer, N.

2016-10-01

Stochastic particle-resolved methods have proven useful for simulating multi-dimensional systems such as composition-resolved aerosol size distributions. While particle-resolved methods have substantial benefits for highly detailed simulations, these techniques suffer from high computational cost, motivating efforts to improve their algorithmic efficiency. Here we formulate an algorithm for accelerating particle removal processes by aggregating particles of similar size into bins. We present the Binned Algorithm for particle removal processes and analyze its performance with application to the atmospherically relevant process of aerosol dry deposition. We show that the Binned Algorithm can dramatically improve the efficiency of particle removals, particularly for low removalmore » rates, and that computational cost is reduced without introducing additional error. In simulations of aerosol particle removal by dry deposition in atmospherically relevant conditions, we demonstrate about 50-times increase in algorithm efficiency.« less
Kinetics of temperature response of PEO-b-PNIPAM-b-PAA triblock terpolymer aggregates and of their complexes with lysozyme

DOE PAGES

Papagiannopoulos, Aristeidis; Meristoudi, Anastasia; Hong, Kunlun; ...

2015-12-18

We present the kinetics of temperature response of a PEO-b-PNIPAM-b-PAA triblock terpolymer and of its complexes with lysozyme in aqueous solution. It is found that during the coil-to-globule transition of PNIPAM new bonds within the polymer aggregates are created, making the transition of the aggregates partially irreversible. This effect is also found for the protein loaded PEO-b-PNIPAM-b-PAA aggregates whereas in this case protein globules appear to enhance the formation of bonds, making the transition totally irreversible. The internal dynamics of both aggregates and complexes are “frozen” once the temperature is increased upon PINIPAM's LCST in water and remain so evenmore » when the temperature drops below LCST. As a result, we investigate the complexation kinetics of lysozyme and PEO-b-PNIPAM-b-PAA and observe that it occurs in two stages, one where protein globules adsorb on single pre-formed aggregates and one where protein globules cause inter-aggregate clustering.« less
Computational study of aggregation mechanism in human lysozyme[D67H

PubMed Central

Patel, Dharmeshkumar

2017-01-01

Aggregation of proteins is an undesired phenomena that affects both human health and bioengineered products such as therapeutic proteins. Finding preventative measures could be facilitated by a molecular-level understanding of dimer formation, which is the first step in aggregation. Here we present a molecular dynamics (MD) study of dimer formation propensity in human lysozyme and its D67H variant. Because the latter protein aggregates while the former does not, they offer an ideal system for testing the feasibility of the proposed MD approach which comprises three stages: i) partially unfolded conformers involved in dimer formation are generated via high-temperature MD simulations, ii) potential dimer structures are searched using docking and refined with MD, iii) free energy calculations are performed to find the most stable dimer structure. Our results provide a detailed explanation for how a single mutation (D67H) turns human lysozyme from non-aggregating to an aggregating protein. Conversely, the proposed method can be used to identify the residues causing aggregation in a protein, which can be mutated to prevent it. PMID:28467454
Kinetics of temperature response of PEO-b-PNIPAM-b-PAA triblock terpolymer aggregates and of their complexes with lysozyme

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

Papagiannopoulos, Aristeidis; Meristoudi, Anastasia; Hong, Kunlun

We present the kinetics of temperature response of a PEO-b-PNIPAM-b-PAA triblock terpolymer and of its complexes with lysozyme in aqueous solution. It is found that during the coil-to-globule transition of PNIPAM new bonds within the polymer aggregates are created, making the transition of the aggregates partially irreversible. This effect is also found for the protein loaded PEO-b-PNIPAM-b-PAA aggregates whereas in this case protein globules appear to enhance the formation of bonds, making the transition totally irreversible. The internal dynamics of both aggregates and complexes are “frozen” once the temperature is increased upon PINIPAM's LCST in water and remain so evenmore » when the temperature drops below LCST. As a result, we investigate the complexation kinetics of lysozyme and PEO-b-PNIPAM-b-PAA and observe that it occurs in two stages, one where protein globules adsorb on single pre-formed aggregates and one where protein globules cause inter-aggregate clustering.« less
Emergence of cooperativity in a model biofilm

NASA Astrophysics Data System (ADS)

Rotrattanadumrong, Rachapun; Endres, Robert G.

2017-06-01

Evolution to multicellularity from an aggregate of cells involves altruistic cooperation between individual cells, which is in conflict with Darwinian evolution. How cooperation arises and how a cell community resolves such conflicts remains unclear. In this study, we investigated the spontaneous emergence of cell differentiation and the subsequent division of labour in evolving cellular metabolic networks. In spatially extended cell aggregates, our findings reveal that resource limitation can lead to the formation of subpopulations and cooperation of cells, and hence multicellular communities. A specific example of our model can explain the recently observed oscillatory growth in Bacillus subtilis biofilms.

Effects of ionic strength and temperature on the aggregation and deposition of multi-walled carbon nanotubes.

PubMed

Wang, Lixin; Yang, Xuezhi; Wang, Qi; Zeng, Yuxuan; Ding, Lei; Jiang, Wei

2017-01-01

The aggregation and deposition of carbon nanotubes (CNTs) determines their transport and fate in natural waters. Therefore, the aggregation kinetics of humic-acid treated multi-walled carbon nanotubes (HA-MWCNTs) was investigated by time-resolved dynamic light scattering in NaCl and CaCl 2 electrolyte solutions. Increased ionic strength induced HA-MWCNT aggregation due to the less negative zeta potential and the reduced electrostatic repulsion. The critical coagulation concentration (CCC) values of HA-MWCNTs were 80mmol/L in NaCl and 1.3mmol/L in CaCl 2 electrolyte, showing that Ca 2+ causes more serious aggregation than Na + . The aggregation behavior of HA-MWCNTs was consistent with Derjaguin-Landau-Verwey-Overbeek theory. The deposition kinetics of HA-MWCNTs was measured by the optical absorbance at 800nm. The critical deposition concentrations for HA-MWCNT in NaCl and CaCl 2 solutions were close to the CCC values, therefore the rate of deposition cannot be increased by changing the ionic strength in the diffusion-limited aggregation regime. The deposition process was correlated to the aggregation since larger aggregates increased gravitational deposition and decreased random Brownian diffusion. HA-MWCNTs hydrodynamic diameters were evaluated at 5, 15 and 25°C. Higher temperature caused faster aggregation due to the reduced electrostatic repulsion and increased random Brownian motion and collision frequency. HA-MWCNTs aggregate faster at higher temperature in either NaCl or CaCl 2 electrolyte due to the decreased electrostatic repulsion and increased random Brownian motion. Our results suggest that CNT aggregation and deposition are two correlated processes governed by the electrolyte, and CNT transport is favored at low ionic strength and low temperature. Copyright © 2016. Published by Elsevier B.V.
Effects of partial harvest on the carbon stores in Douglas-fir/western hemlock forests: a simulation study

Treesearch

Mark E. Harmon; Adam Moreno; James B. Domingo

2009-01-01

The STANDCARB 2.0 model was used to examine the effects of partial harvest of trees within stands on forest-related carbon (C) stores in a typical Pacific Northwest Pseudotsuga/Tsuga forest. For harvest rotation intervals of 20 to 250 years the effect of completely dispersed (that is, a checkerboard) versus completely aggregated cutting patterns (...
The Multivariate Regression Statistics Strategy to Investigate Content-Effect Correlation of Multiple Components in Traditional Chinese Medicine Based on a Partial Least Squares Method.

PubMed

Peng, Ying; Li, Su-Ning; Pei, Xuexue; Hao, Kun

2018-03-01

Amultivariate regression statisticstrategy was developed to clarify multi-components content-effect correlation ofpanaxginseng saponins extract and predict the pharmacological effect by components content. In example 1, firstly, we compared pharmacological effects between panax ginseng saponins extract and individual saponin combinations. Secondly, we examined the anti-platelet aggregation effect in seven different saponin combinations of ginsenoside Rb1, Rg1, Rh, Rd, Ra3 and notoginsenoside R1. Finally, the correlation between anti-platelet aggregation and the content of multiple components was analyzed by a partial least squares algorithm. In example 2, firstly, 18 common peaks were identified in ten different batches of panax ginseng saponins extracts from different origins. Then, we investigated the anti-myocardial ischemia reperfusion injury effects of the ten different panax ginseng saponins extracts. Finally, the correlation between the fingerprints and the cardioprotective effects was analyzed by a partial least squares algorithm. Both in example 1 and 2, the relationship between the components content and pharmacological effect was modeled well by the partial least squares regression equations. Importantly, the predicted effect curve was close to the observed data of dot marked on the partial least squares regression model. This study has given evidences that themulti-component content is a promising information for predicting the pharmacological effects of traditional Chinese medicine.
Colloidal Properties and Stability of Graphene Oxide Nanomaterials in the Aquatic Environment

EPA Science Inventory

While graphene oxide (GO) has been found to be the most toxic graphene-based nanomaterial, its environmental fate is still unexplored. In this study, the aggregation kinetics and stability of GO were investigated using time-resolved dynamic light scattering over a wide range of a...
Sequestration of synaptic proteins by alpha-synuclein aggregates leading to neurotoxicity is inhibited by small peptide

PubMed Central

Choi, Mal-Gi; Kim, Mi Jin; Kim, Do-Geun; Yu, Ri; Jang, You-Na

2018-01-01

α-Synuclein (α-syn) is a major component of Lewy bodies found in synucleinopathies including Parkinson’s disease (PD) and Dementia with Lewy Bodies (DLB). Under the pathological conditions, α-syn tends to generate a diverse form of aggregates showing toxicity to neuronal cells and able to transmit across cells. However, mechanisms by which α-syn aggregates affect cytotoxicity in neurons have not been fully elucidated. Here we report that α-syn aggregates preferentially sequester specific synaptic proteins such as vesicle-associated membrane protein 2 (VAMP2) and synaptosomal-associated protein 25 (SNAP25) through direct binding which is resistant to SDS. The sequestration effect of α-syn aggregates was shown in a cell-free system, cultured primary neurons, and PD mouse model. Furthermore, we identified a specific blocking peptide derived from VAMP2 which partially inhibited the sequestration by α-syn aggregates and contributed to reduced neurotoxicity. These results provide a mechanism of neurotoxicity mediated by α-syn aggregates and suggest that the blocking peptide interfering with the pathological role of α-syn aggregates could be useful for designing a potential therapeutic drug for the treatment of PD. PMID:29608598
Changes in precipitation isotope-climate relationships from temporal grouping and aggregation of weekly-resolved USNIP data: impacts on paleoclimate and environmental applications

NASA Astrophysics Data System (ADS)

Akers, P. D.; Welker, J. M.

2015-12-01

Spatial variations in precipitation isotopes have been the focus of much recent research, but relatively less work has explored changes at various temporal scales. This is partly because most spatially-diverse and long-term isotope databases are offered at a monthly resolution, while daily or event-level records are spatially and temporally limited by cost and logistics. A subset of 25 United States Network for Isotopes in Precipitation (USNIP) sites with weekly-resolution in the east-central United States was analyzed for site-specific relationships between δ18O and δD (the local meteoric water line/LMWL), δ18O and surface temperature, and δ18O and precipitation amount. Weekly data were then aggregated into monthly and seasonal data to examine the effect of aggregation on correlation and slope values for each of the relationships. Generally, increasing aggregation improved correlations (>25% for some sites) due to a reduced effect of extreme values, but estimates on regression variable error increased (>100%) because of reduced sample sizes. Aggregation resulted in small, but significant drops (5-25%) in relationship slope values for some sites. Weekly data were also grouped by month and season to explore changes in relationships throughout the year. Significant subannual variability exists in slope values and correlations even for sites with very strong overall correlations. LMWL slopes are highest in winter and lowest in summer, while the δ18O-surface temperature relationship is strongest in spring. Despite these overall trends, a high level of month-to-month and season-to-season variability is the norm for these sites. Researchers blindly applying overall relationships drawn from monthly-resolved databases to paleoclimate or environmental research risk assuming these relationships apply at all temporal resolutions. When possible, researchers should match the temporal resolution used to calculate an isotopic relationship with the temporal resolution of their applied proxy.
Optical spectroscopy and system-bath interactions in molecular aggregates with full configuration interaction Frenkel exciton model

NASA Astrophysics Data System (ADS)

Seibt, Joachim; Sláma, Vladislav; Mančal, Tomáš

2016-12-01

Standard application of the Frenkel exciton model neglects resonance coupling between collective molecular aggregate states with different number of excitations. These inter-band coupling terms are, however, of the same magnitude as the intra-band coupling between singly excited states. We systematically derive the Frenkel exciton model from quantum chemical considerations, and identify it as a variant of the configuration interaction method. We discuss all non-negligible couplings between collective aggregate states, and provide compact formulae for their calculation. We calculate absorption spectra of molecular aggregate of carotenoids and identify significant band shifts as a result of inter-band coupling. The presence of inter-band coupling terms requires renormalization of the system-bath coupling with respect to standard formulation, but renormalization effects are found to be weak. We present detailed discussion of molecular dimer and calculate its time-resolved two-dimensional Fourier transformed spectra to find weak but noticeable effects of peak amplitude redistribution due to inter-band coupling.
The effects of side-chain-induced disorder on the emission spectra and quantum yields of oligothiophene nano-aggregates. A combined experimental and MD-TDDFT study

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

Hong, Jiyun; Jeon, SuKyung; Kim, Janice J.

2014-07-24

Oligomeric thiophenes are commonly-used components in organic electronics and solar cells. These molecules stack and/or aggregate readily under the processing conditions used to form thin films for these applications, significantly altering their optical and charge-transport properties. To determine how these effects depend on the substitution pattern of the thiophene main chains, nano-aggregates of three sexi-thiophene (6T) oligomers having different alkyl substitution patterns were formed using solvent poisoning techniques and studied using steady-state and time-resolved emission spectroscopy. The results indicate the substantial role played by the side-chain substituents in determining the emissive properties of these species. Both the measured spectral changesmore » and their dependence on substitution are well modeled by combined quantum chemistry and molecular dynamics simulations. The simulations connect the side-chain-induced disorder, which determines the favorable chain packing configurations within the aggregates, with their measured electronic spectra.« less
Surface properties and aggregate morphology of partially fluorinated carboxylate-type anionic gemini surfactants.

PubMed

Yoshimura, Tomokazu; Bong, Miri; Matsuoka, Keisuke; Honda, Chikako; Endo, Kazutoyo

2009-11-01

Three anionic homologues of a novel partially fluorinated carboxylate-type anionic gemini surfactant, N,N'-di(3-perfluoroalkyl-2-hydroxypropyl)-N,N'-diacetic acid ethylenediamine (2C(n)(F) edda, where n represents the number of carbon atoms in the fluorocarbon chain (4, 6, and 8)) were synthesized. In these present gemini surfactants, the relatively small carboxylic acid moieties form hydrophilic head groups. The surface properties or structures of the aggregates of these surfactants are strongly influenced by the nonflexible fluorocarbons and small head groups; this is because these surfactants have a closely packed molecular structure. The equilibrium surface tension properties of these surfactants were measured at 298.2K for various fluorocarbon chain lengths. The plot of the logarithm of the critical micelle concentration (cmc) against the fluorocarbon chain lengths for 2C(n)(F) edda (n=4, 6, and 8) showed a minimum for n=6. Furthermore, the lowest surface tension of 2C(6)(F) edda at the cmc was 16.4mNm(-1). Such unique behavior has not been observed even in the other fluorinated surfactants. Changes in the shapes and sizes of these surfactant aggregate with concentration were investigated by dynamic light scattering and transmission electron microscopy (TEM). The TEM micrographs showed that in an aqueous alkali solution, 2C(n)(F) edda mainly formed aggregates with stringlike (n=4), cagelike (n=6), and distorted bilayer structures (n=8). The morphological changes in the aggregates were affected by the molecular structure composed of nonflexible fluorocarbon chains and flexible hydrocarbon chains.
Facilitation in Caribbean coral reefs: high densities of staghorn coral foster greater coral condition and reef fish composition.

PubMed

Huntington, Brittany E; Miller, Margaret W; Pausch, Rachel; Richter, Lee

2017-05-01

Recovery of the threatened staghorn coral (Acropora cervicornis) is posited to play a key role in Caribbean reef resilience. At four Caribbean locations (including one restored and three extant populations), we quantified characteristics of contemporary staghorn coral across increasing conspecific densities, and investigated a hypothesis of facilitation between staghorn coral and reef fishes. High staghorn densities in the Dry Tortugas exhibited significantly less partial mortality, higher branch growth, and supported greater fish abundances compared to lower densities within the same population. In contrast, partial mortality, branch growth, and fish community composition did not vary with staghorn density at the three other study locations where staghorn densities were lower overall. This suggests that density-dependent effects between the coral and fish community may only manifest at high staghorn densities. We then evaluated one facilitative mechanism for such density-dependence, whereby abundant fishes sheltering in dense staghorn aggregations deliver nutrients back to the coral, fueling faster coral growth, thereby creating more fish habitat. Indeed, dense staghorn aggregations within the Dry Tortugas exhibited significantly higher growth rates, tissue nitrogen, and zooxanthellae densities than sparse aggregations. Similarly, higher tissue nitrogen was induced in a macroalgae bioassay outplanted into the same dense and sparse aggregations, confirming greater bioavailability of nutrients at high staghorn densities. Our findings inform staghorn restoration efforts, suggesting that the most effective targets may be higher coral densities than previously thought. These coral-dense aggregations may reap the benefits of positive facilitation between the staghorn and fish community, favoring the growth and survivorship of this threatened species.
Detection and Characterization of Aggregates, Prefibrillar Amyloidogenic Oligomers, and Protofibrils Using Fluorescence Spectroscopy

PubMed Central

Lindgren, Mikael; Sörgjerd, Karin; Hammarström, Per

2005-01-01

Transthyretin (TTR) is a protein linked to a number of different amyloid diseases including senile systemic amyloidosis and familial amyloidotic polyneuropathy. The transient nature of oligomeric intermediates of misfolded TTR that later mature into fibrillar aggregates makes them hard to study, and methods to study these species are sparse. In this work we explore a novel pathway for generation of prefibrillar aggregates of TTR, which provides important insight into TTR misfolding. Prefibrillar amyloidogenic oligomers and protofibrils of misfolded TTR were generated in vitro through induction of the molten globule type A-state from acid unfolded TTR through the addition of NaCl. The aggregation process produced fairly monodisperse oligomers (300–500 kD) within 2 h that matured after 20 h into larger spherical clusters (30–50 nm in diameter) and protofibrils as shown by transmission electron microscopy. Further maturation of the aggregates showed shrinkage of the spheres as the fibrils grew in length, suggesting a conformational change of the spheres into more rigid structures. The structural and physicochemical characteristics of the aggregates were investigated using fluorescence, circular dichroism, chemical cross-linking, and transmission electron microscopy. The fluorescent dyes 1-anilinonaphthalene-8-sulfonate (ANS), 4-4-bis-1-phenylamino-8-naphthalene sulfonate (Bis-ANS), 4-(dicyanovinyl)-julolidine (DCVJ), and thioflavin T (ThT) were employed in both static and kinetic assays to characterize these oligomeric and protofibrillar states using both steady-state and time-resolved fluorescence techniques. DCVJ, a molecular rotor, was employed for the first time for studies of an amyloidogenic process and is shown useful for detection of the early steps of the oligomerization process. DCVJ bound to the early prefibrillar oligomers (300–500 kD) with an apparent dissociation constant of 1.6 μM, which was slightly better than for ThT (6.8 μM). Time-resolved fluorescence anisotropy decay of ANS was shown to be a useful tool for giving further structural and kinetic information of the oligomeric aggregates. ThT dramatically increases its fluorescence quantum yield when bound to amyloid fibrils; however, the mechanism behind this property is unknown. Data from this work suggest that unbound ThT is also intrinsically quenched and functions similarly to a molecular rotor, which in combination with its environmental dependence provides a blue shift to the characteristic 482 nm wavelength when bound to amyloid fibrils. PMID:15764666
When Anaphor Resolution Fails: Partial Encoding of Anaphoric Inferences

ERIC Educational Resources Information Center

Klin, Celia M.; Guzman, Alexandria E.; Weingartner, Kristin M.; Ralano, Angela S.

2006-01-01

Klin et al., 2004 and Levine et al., 2000 concluded that readers fail to resolve noun phrase anaphors when the antecedent is difficult to retrieve from memory and the inference is not necessary for comprehension. In four experiments we investigated the hypothesis that these inferences were actually partially encoded. Although the results of a…
Double silicone tube intubation for the management of partial lacrimal system obstruction.

PubMed

Demirci, Hakan; Elner, Victor M

2008-02-01

To evaluate the effectiveness of double silicone intubation for the management of partial lacrimal drainage system obstruction in adults. Observational retrospective case series. Twenty-four eyes of 18 consecutive adult patients with partial lacrimal system obstruction managed at the University of Michigan. Retrospective review of symptoms and signs, duration of silicone intubation, and complications. Resolution of tearing. Preoperative tearing, negative Jones I testing, positive Jones II testing, and resistance to positive-pressure irrigation were present in all eyes (100%). The first silicone tube was removed after a mean of 11+/-7 months, and the second tube after 16+/-6 months. Postoperatively, at a mean of 21+/-9 months after removal of both tubes, tearing remained resolved in 19 eyes (79%) and remained improved in 2 eyes (8%). In eyes with resolved tearing, Jones I testing became positive, and there was no resistance to positive-pressure irrigation. Persistent tearing in 3 eyes (13%) required treatment with external dacryocystorhinostomy. The only complication was peripunctal pyogenic granulomas in 2 eyes. Double silicone intubation is an effective minimally invasive technique for treatment of partial lacrimal system obstruction in adults.
Strength and durability studies on concrete with partial replacement over burnt brick bat waste

NASA Astrophysics Data System (ADS)

Kanchidurai, S.; Bharani, G.; Saravana Raja Mohan, K.

2017-07-01

This paper presents the partial and complete replacement of over burnt brick bat (OBB) 20-30mm as coarse aggregate in the concrete. OBB are formed at extreme heating to a temperature not less than 1600 degree Celsius. The burnt bricks change from red to blue-black ceramics color. The series of tests are conducted to study the effect of 0%, 25%, 50%, 75% and 100% replacement of coarse aggregate with over burnt bricks. Totally 36numbers of 150mm concrete cube with 5 different percentage replacement mix are cast and tested and three numbers of the flexural beam. In durability aspects, water absorption and sorptivity were tested. Experimental results found 25-50% of overburnt brick bat wastes can be replaced with the normal and mass concrete without quality compromisation.
AGGREGATION PATHWAYS OF THE AMYLOID β(1–42) PEPTIDE DEPEND ON ITS COLLOIDAL STABILITY AND ORDERED β-SHEET STACKING

PubMed Central

Jiang, Dianlu; Rauda, Iris; Han, Shubo; Chen, Shu; Zhou, Feimeng

2012-01-01

Amyloid β (Aβ) fibrils are present as a major component in senile plaques, the hallmark of Alzheimer’s disease (AD). Diffuse plaques (non-fibrous, loosely packed Aβ aggregates) containing amorphous Aβ aggregates are also formed in brain. This work examines the influence of Cu2+ complexation by Aβ on the aggregation process in the context of charge and structural variations. Changes in the surface charges of Aβ molecules due to Cu2+ binding, measured with a zeta potential measurement device, were correlated with the aggregate morphologies examined by atomic force microscopy. As a result of the charge variation, the “colloid-like” stability of the aggregation intermediates, which is essential to the fibrillation process, is affected. Consequently Cu2+ enhances the amorphous aggregate formation. By monitoring variations in the secondary structures with circular dichroism spectroscopy, a direct transformation from the unstructured conformation to the β-sheet structure was observed for all types of aggregates observed (oligomers, fibrils, and/or amorphous aggregates). Compared to the Aβ aggregation pathway in the absence of Cu2+ and taking other factors affecting Aβ aggregation (i.e., pH and temperature) into account, our investigation indicates that formations of amorphous and fibrous aggregates diverge from the same β-sheet-containing partially folded intermediate. This study suggests that the hydrophilic domain of Aβ also plays a role in the Aβ aggregation process. A kinetic model was proposed to account for the effects of the Cu2+ binding on these two aggregation pathways in terms of charge and structural variations. PMID:22870885
Vapor-pressure osmometric study of the molecular weight and aggregation tendency of a reference-soil fulvic acid

USGS Publications Warehouse

Marinsky, J.A.; Reddy, M.M.

1990-01-01

The molecular weight and aggregation tendency of a reference-soil fulvic acid in Armadale horizon Bh were determined by vapor-pressure osmometry using tetrahydrofuran and water as solvents. With tetrahydrofuran, number-average molecular weight values of 767 ?? 34 and 699 ?? 8 daltons were obtained from two separate sets of measurements. Two sets of measurements with water also yielded values within this range (754 ?? 70 daltons) provided that the fulvic acid concentration in water did not exceed 7 mg ml-1; at higher concentrations (9.1-13.7 mg ml-1) a number-average molecular weight of 956 ?? 25 daltons was resolved, providing evidence of molecular aggregation. Extension of these studies to 80% neutralized fulvic acid showed that a sizeable fraction of the sodium counter ion is not osmotically active.
Assessment of the Partially Resolved Numerical Simulation (PRNS) Approach in the National Combustion Code (NCC) for Turbulent Nonreacting and Reacting Flows

NASA Technical Reports Server (NTRS)

Shih, Tsan-Hsing; Liu, Nan-Suey

2008-01-01

This paper describes an approach which aims at bridging the gap between the traditional Reynolds-averaged Navier-Stokes (RANS) approach and the traditional large eddy simulation (LES) approach. It has the characteristics of the very large eddy simulation (VLES) and we call this approach the partially-resolved numerical simulation (PRNS). Systematic simulations using the National Combustion Code (NCC) have been carried out for fully developed turbulent pipe flows at different Reynolds numbers to evaluate the PRNS approach. Also presented are the sample results of two demonstration cases: nonreacting flow in a single injector flame tube and reacting flow in a Lean Direct Injection (LDI) hydrogen combustor.
Marine Boundary Layer Cloud Property Retrievals from High-Resolution ASTER Observations: Case Studies and Comparison with Terra MODIS

NASA Technical Reports Server (NTRS)

Werner, Frank; Wind, Galina; Zhang, Zhibo; Platnick, Steven; Di Girolamo, Larry; Zhao, Guangyu; Amarasinghe, Nandana; Meyer, Kerry

2016-01-01

A research-level retrieval algorithm for cloud optical and microphysical properties is developed for the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) aboard the Terra satellite. It is based on the operational MODIS algorithm. This paper documents the technical details of this algorithm and evaluates the retrievals for selected marine boundary layer cloud scenes through comparisons with the operational MODIS Data Collection 6 (C6) cloud product. The newly developed, ASTERspecific cloud masking algorithm is evaluated through comparison with an independent algorithm reported in Zhao and Di Girolamo (2006). To validate and evaluate the cloud optical thickness (tau) and cloud effective radius (r(sub eff)) from ASTER, the high-spatial-resolution ASTER observations are first aggregated to the same 1000m resolution as MODIS. Subsequently, tau(sub aA) and r(sub eff, aA) retrieved from the aggregated ASTER radiances are compared with the collocated MODIS retrievals. For overcast pixels, the two data sets agree very well with Pearson's product-moment correlation coefficients of R greater than 0.970. However, for partially cloudy pixels there are significant differences between r(sub eff, aA) and the MODIS results which can exceed 10 micrometers. Moreover, it is shown that the numerous delicate cloud structures in the example marine boundary layer scenes, resolved by the high-resolution ASTER retrievals, are smoothed by the MODIS observations. The overall good agreement between the research-level ASTER results and the operational MODIS C6 products proves the feasibility of MODIS-like retrievals from ASTER reflectance measurements and provides the basis for future studies concerning the scale dependency of satellite observations and three-dimensional radiative effects.
Marine boundary layer cloud property retrievals from high-resolution ASTER observations: case studies and comparison with Terra MODIS

NASA Astrophysics Data System (ADS)

Werner, Frank; Wind, Galina; Zhang, Zhibo; Platnick, Steven; Di Girolamo, Larry; Zhao, Guangyu; Amarasinghe, Nandana; Meyer, Kerry

2016-12-01

A research-level retrieval algorithm for cloud optical and microphysical properties is developed for the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) aboard the Terra satellite. It is based on the operational MODIS algorithm. This paper documents the technical details of this algorithm and evaluates the retrievals for selected marine boundary layer cloud scenes through comparisons with the operational MODIS Data Collection 6 (C6) cloud product. The newly developed, ASTER-specific cloud masking algorithm is evaluated through comparison with an independent algorithm reported in [Zhao and Di Girolamo(2006)]. To validate and evaluate the cloud optical thickness (τ) and cloud effective radius (reff) from ASTER, the high-spatial-resolution ASTER observations are first aggregated to the same 1000 m resolution as MODIS. Subsequently, τaA and reff, aA retrieved from the aggregated ASTER radiances are compared with the collocated MODIS retrievals. For overcast pixels, the two data sets agree very well with Pearson's product-moment correlation coefficients of R > 0.970. However, for partially cloudy pixels there are significant differences between reff, aA and the MODIS results which can exceed 10 µm. Moreover, it is shown that the numerous delicate cloud structures in the example marine boundary layer scenes, resolved by the high-resolution ASTER retrievals, are smoothed by the MODIS observations. The overall good agreement between the research-level ASTER results and the operational MODIS C6 products proves the feasibility of MODIS-like retrievals from ASTER reflectance measurements and provides the basis for future studies concerning the scale dependency of satellite observations and three-dimensional radiative effects.
Methane Emissions from Natural Gas Vehicles in Beijing, Baoding, and Shijiazhuang, China during CAREBEIJING Field Campaign

NASA Astrophysics Data System (ADS)

Pérez García-Pando, C.; Miller, R. L.; Perlwitz, J. P.; Kok, J. F.; Scanza, R.; Mahowald, N. M.

2014-12-01

Mineral dust created by wind erosion of soil particles is the dominant aerosol by mass in the atmosphere. It exerts significant effects on radiative fluxes, clouds, ocean biogeochemistry, and human health. Models that predict the lifecycle of mineral dust aerosols generally assume a globally uniform mineral composition. However, this simplification limits our understanding of the role of dust in the Earth system, since the effects of dust strongly depend on the particles' physical and chemical properties, which vary with their mineral composition. Hence, not only a detailed understanding of the processes determining the dust emission flux is needed, but also information about its size dependent mineral composition. Determining the mineral composition of dust aerosols is complicated. The largest uncertainty derives from the current atlases of soil mineral composition. These atlases provide global estimates of soil mineral fractions, but they are based upon massive extrapolation of a limited number of soil samples assuming that mineral composition is related to soil type. This disregards the potentially large variability of soil properties within each defined soil type. In addition, the analysis of these soil samples is based on wet sieving, a technique that breaks the aggregates found in the undisturbed parent soil. During wind erosion, these aggregates are subject to partial fragmentation, which generates differences on the size distribution and composition between the undisturbed parent soil and the emitted dust aerosols. We review recent progress on the representation of the mineral and chemical composition of dust in climate models. We discuss extensions of brittle fragmentation theory to prescribe the emitted size-resolved dust composition, and we identify key processes and uncertainties based upon model simulations and an unprecedented compilation of observations.

Dust Composition in Climate Models: Current Status and Prospects

NASA Astrophysics Data System (ADS)

Pérez García-Pando, C.; Miller, R. L.; Perlwitz, J. P.; Kok, J. F.; Scanza, R.; Mahowald, N. M.

2015-12-01

Mineral dust created by wind erosion of soil particles is the dominant aerosol by mass in the atmosphere. It exerts significant effects on radiative fluxes, clouds, ocean biogeochemistry, and human health. Models that predict the lifecycle of mineral dust aerosols generally assume a globally uniform mineral composition. However, this simplification limits our understanding of the role of dust in the Earth system, since the effects of dust strongly depend on the particles' physical and chemical properties, which vary with their mineral composition. Hence, not only a detailed understanding of the processes determining the dust emission flux is needed, but also information about its size dependent mineral composition. Determining the mineral composition of dust aerosols is complicated. The largest uncertainty derives from the current atlases of soil mineral composition. These atlases provide global estimates of soil mineral fractions, but they are based upon massive extrapolation of a limited number of soil samples assuming that mineral composition is related to soil type. This disregards the potentially large variability of soil properties within each defined soil type. In addition, the analysis of these soil samples is based on wet sieving, a technique that breaks the aggregates found in the undisturbed parent soil. During wind erosion, these aggregates are subject to partial fragmentation, which generates differences on the size distribution and composition between the undisturbed parent soil and the emitted dust aerosols. We review recent progress on the representation of the mineral and chemical composition of dust in climate models. We discuss extensions of brittle fragmentation theory to prescribe the emitted size-resolved dust composition, and we identify key processes and uncertainties based upon model simulations and an unprecedented compilation of observations.
Comparing the energy landscapes for native folding and aggregation of PrP

PubMed Central

Dee, Derek R.; Woodside, Michael T.

2016-01-01

ABSTRACT Protein sequences are evolved to encode generally one folded structure, out of a nearly infinite array of possible folds. Underlying this code is a funneled free energy landscape that guides folding to the native conformation. Protein misfolding and aggregation are also a manifestation of free-energy landscapes. The detailed mechanisms of these processes are poorly understood, but often involve rare, transient species and a variety of different pathways. The inherent complexity of misfolding has hampered efforts to measure aggregation pathways and the underlying energy landscape, especially using traditional methods where ensemble averaging obscures important rare and transient events. We recently studied the misfolding and aggregation of prion protein by examining 2 monomers tethered in close proximity as a dimer, showing how the steps leading to the formation of a stable aggregated state can be resolved in the single-molecule limit and the underlying energy landscape thereby reconstructed. This approach allows a more quantitative comparison of native folding versus misfolding, including fundamental differences in the dynamics for misfolding. By identifying key steps and interactions leading to misfolding, it should help to identify potential drug targets. Here we describe the importance of characterizing free-energy landscapes for aggregation and the challenges involved in doing so, and we discuss how single-molecule studies can help test proposed structural models for PrP aggregates. PMID:27191683
Contrasting self-aggregation over land and ocean surfaces

NASA Astrophysics Data System (ADS)

Inda Diaz, H. A.; O'Brien, T. A.

2017-12-01

The spontaneous organization of convection into clusters, or self-aggregation, demonstrably changes the nature and statistics of precipitation. While there has been much recent progress in this area, the processes that control self-aggregation are still poorly understood. Most of the work to date has focused on self-aggregation over ocean-like surfaces, but it is particularly pressing to understand what controls convective aggregation over land, since the associated change in precipitation statistics—between non-aggregated and aggregated convection—could have huge impacts on society and infrastructure. Radiative-convective equilibrium (RCE), has been extensively used as an idealized framework to study the tropical atmosphere. Self-aggregation manifests in numerous numerical models of RCE, nevertheless, there is still a lack of understanding in how it relates to convective organization in the observed world. Numerous studies have examined self-aggregation using idealized Cloud Resolving Models (CRMs) and General Circulation Models over the ocean, however very little work has been done on RCE and self-aggregation over land. Idealized models of RCE over ocean have shown that aggregation is sensitive to sea surface temperature (SST), more intense precipitation occurs in aggregated systems, and a variety of feedbacks—such as surface flux, cloud radiative, and upgradient moisture transport— contribute to the maintenance of aggregation, however it is not clear if these results apply over land. Progress in this area could help relate understanding of self-aggregation in idealized simulations to observations. In order to explore the behavior of self-aggregation over land, we use a CRM to simulate idealized RCE over land. In particular, we examine the aggregation of convection and how it compares with aggregation over ocean. Based on previous studies, where a variety of different CRMs exhibit a SST threshold below which self-aggregation does not occur, we hypothesize that idealized land simulations will exhibit similar threshold behavior when there is an adequate surface moisture supply. We systematically explore this by varying parameters that exert strong control on the surface enthalpy and moisture budget, such as type of land, surface albedo, and greenhouse gas concentration.
Light Scattering by Fractal Dust Aggregates. II. Opacity and Asymmetry Parameter

NASA Astrophysics Data System (ADS)

Tazaki, Ryo; Tanaka, Hidekazu

2018-06-01

Optical properties of dust aggregates are important at various astrophysical environments. To find a reliable approximation method for optical properties of dust aggregates, we calculate the opacity and the asymmetry parameter of dust aggregates by using a rigorous numerical method, the T-Matrix Method, and then the results are compared to those obtained by approximate methods: the Rayleigh–Gans–Debye (RGD) theory, the effective medium theory (EMT), and the distribution of hollow spheres method (DHS). First of all, we confirm that the RGD theory breaks down when multiple scattering is important. In addition, we find that both EMT and DHS fail to reproduce the optical properties of dust aggregates with fractal dimensions of 2 when the incident wavelength is shorter than the aggregate radius. In order to solve these problems, we test the mean field theory (MFT), where multiple scattering can be taken into account. We show that the extinction opacity of dust aggregates can be well reproduced by MFT. However, it is also shown that MFT is not able to reproduce the scattering and absorption opacities when multiple scattering is important. We successfully resolve this weak point of MFT, by newly developing a modified mean field theory (MMF). Hence, we conclude that MMF can be a useful tool to investigate radiative transfer properties of various astrophysical environments. We also point out an enhancement of the absorption opacity of dust aggregates in the Rayleigh domain, which would be important to explain the large millimeter-wave opacity inferred from observations of protoplanetary disks.
Formation and decay of charge carriers in aggregate nanofibers consisting of poly(3-hexylthiophene)-coated gold nanoparticles.

PubMed

Lee, Dongki; Lee, Jaewon; Song, Ki-Hee; Rhee, Hanju; Jang, Du-Jeon

2016-01-21

Thin nanofibers (NFs) of J-dominant aggregates with a thickness of 15 nm and thick NFs of H-dominant aggregates with a thickness of 25 nm were fabricated by the self-assembly of poly(3-hexylthiophene)-coated gold nanoparticles. The formation and decay dynamics of the charge carriers, which are dependent on the aggregate types of NFs, was investigated by time-resolved emission and transient-absorption spectroscopy. With increasing excitation energy, the fraction of the fast emission decay component decreased, suggesting that the fast formation of polaron pairs (PP), localized (LP), and delocalized polarons (DP) results from higher singlet exciton states produced by the singlet fusion. The faster decay dynamics of DP and LP in the thick NFs than in thin NFs is due to the increased delocalization of DP and LP. As the interchain aggregation is weaker than intrachain aggregation, PP decays faster in thin NFs than in thick NFs. In both thin and thick NFs, although triplet (T1) excitons were barely observed with excitation at 532 nm on a nanosecond time scale, they were observed with excitation at 355 nm, showing that T1 excitons within NFs are generated mainly through the singlet fission from a higher singlet exciton state rather than through intersystem crossing.
Insights into the Aggregation Mechanism of PolyQ Proteins with Different Glutamine Repeat Lengths.

PubMed

Yushchenko, Tetyana; Deuerling, Elke; Hauser, Karin

2018-04-24

Polyglutamine (polyQ) diseases, including Huntington's disease, result from the aggregation of an abnormally expanded polyQ repeat in the affected protein. The length of the polyQ repeat is essential for the disease's onset; however, the molecular mechanism of polyQ aggregation is still poorly understood. Controlled conditions and initiation of the aggregation process are prerequisites for the detection of transient intermediate states. We present an attenuated total reflection Fourier-transform infrared spectroscopic approach combined with protein immobilization to study polyQ aggregation dependent on the polyQ length. PolyQ proteins were engineered mimicking the mammalian N-terminus fragment of the Huntingtin protein and containing a polyQ sequence with the number of glutamines below (Q11), close to (Q38), and above (Q56) the disease threshold. A monolayer of the polyQ construct was chemically immobilized on the internal reflection element of the attenuated total reflection cell, and the aggregation was initiated via enzymatic cleavage. Structural changes of the polyQ sequence were monitored by time-resolved infrared difference spectroscopy. We observed faster aggregation kinetics for the longer sequences, and furthermore, we could distinguish β-structured intermediates for the different constructs, allowing us to propose aggregation mechanisms dependent on the repeat length. Q11 forms a β-structured aggregate by intermolecular interaction of stretched monomers, whereas Q38 and Q56 undergo conformational changes to various β-structured intermediates, including intramolecular β-sheets. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.
AGGREGATING FOOD SOURCES IN STABLE ISOTOPE DIETARY STUDIES: LUMP IT OR LEAVE IT?

EPA Science Inventory

A common situation when stable isotope mixing models are used to estimate food source dietary contributions is that there are too many sources to allow a unique solution. To resolve this problem one option is to combine sources with similar signatures such that the number of sou...
SOURCE AGGREGATION IN STABLE ISOTOPE MIXING MODELS: LUMP IT OR LEAVE IT?

EPA Science Inventory

A common situation when stable isotope mixing models are used to estimate source contributions to a mixture is that there are too many sources to allow a unique solution. To resolve this problem one option is to combine sources with similar signatures such that the number of sou...
Chaperone-client complexes: A dynamic liaison

NASA Astrophysics Data System (ADS)

Hiller, Sebastian; Burmann, Björn M.

2018-04-01

Living cells contain molecular chaperones that are organized in intricate networks to surveil protein homeostasis by avoiding polypeptide misfolding, aggregation, and the generation of toxic species. In addition, cellular chaperones also fulfill a multitude of alternative functionalities: transport of clients towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver clients towards proteolysis machineries. Until recently, the only available source of atomic resolution information for virtually all chaperones were crystal structures of their client-free, apo-forms. These structures were unable to explain details of the functional mechanisms underlying chaperone-client interactions. The difficulties to crystallize chaperones in complexes with clients arise from their highly dynamic nature, making solution NMR spectroscopy the method of choice for their study. With the advent of advanced solution NMR techniques, in the past few years a substantial number of structural and functional studies on chaperone-client complexes have been resolved, allowing unique insight into the chaperone-client interaction. This review summarizes the recent insights provided by advanced high-resolution NMR-spectroscopy to understand chaperone-client interaction mechanisms at the atomic scale.
Nanowires formed by the co-assembly of a negatively charged low-molecular weight gelator and a zwitterionic polythiophene.

PubMed

Li, Feng; Palaniswamy, Ganesan; de Jong, Menno R; Aslund, Andreas; Konradsson, Peter; Marcelis, Antonius T M; Sudhölter, Ernst J R; Stuart, Martien A Cohen; Leermakers, Frans A M

2010-06-21

Conjugated organic nanowires have been prepared by co-assembling a carboxylate containing low-molecular weight gelator (LMWG) and an amino acid substituted polythiophene derivative (PTT). Upon introducing the zwitterionic polyelectrolyte PTT to a basic molecular solution of the organogelator, the negative charges on the LMWG are compensated by the positive charges of the PTT. As a result, nanowires form through co-assembly. These nanowires are visualized by both transmission electron microscopy (TEM) and atomic force microscopy (AFM). Depending on the concentration and ratio of the components these nanowires can be micrometers long. These measurements further suggest that the aggregates adopt a helical conformation. The morphology of these nanowires are studied with fluorescent confocal laser scanning microscopy (CLSM). The interactions between LMWG and PTT are characterized by steady-state and time-resolved fluorescence spectroscopy studies. The steady-state spectra indicate that the backbone of the PTT adopts a more planar and more aggregated conformation when interacting with LMWG. The time- resolved fluorescence decay studies confirm this interpretation.
Spatial heterodyne interferometry of VY Canis Major's, alpha Orionis, alpha Scorpii, and R leonis at 11 microns

NASA Technical Reports Server (NTRS)

Sutton, E. C.; Storey, J. W. V.; Betz, A. L.; Townes, C. H.; Spears, D. L.

1977-01-01

Using the technique of heterodyne interferometry, measurements were made of the spatial distribution of 11 micron radiation from four late type stars. The circumstellar shells surrounding VY Canis Majoris, alpha Orionis, and alpha Scorpii were resolved, whereas that of R Leonis was only partially resolved at a fringe spacing of 0.4 sec.
Aloe emodin, an anthroquinone from Aloe vera acts as an anti aggregatory agent to the thermally aggregated hemoglobin

NASA Astrophysics Data System (ADS)

Furkan, Mohammad; Alam, Md Tauqir; Rizvi, Asim; Khan, Kashan; Ali, Abad; Shamsuzzaman; Naeem, Aabgeena

2017-05-01

Aggregation of proteins is a physiological process which contributes to the pathophysiology of several maladies including diabetes mellitus, Huntington's and Alzheimer's disease. In this study we have reported that aloe emodin (AE), an anthroquinone, which is one of the active components of the Aloe vera plant, acts as an inhibitor of hemoglobin (Hb) aggregation. Hb was thermally aggregated at 60 °C for four days as evident by increased thioflavin T and ANS fluorescence, shifted congo red absorbance, appearance of β sheet structure, increase in turbidity and presence of oligomeric aggregates. Increasing concentration of AE partially reverses the aggregation of the model heme protein (hemoglobin). The maximum effect of AE was observed at 100 μM followed by saturation at 125 μM. The results were confirmed by UV-visible spectrometry, intrinsic fluorescence, ThT, ANS, congo red assay as well as transmission electron microscopy (TEM). These results were also supported by fourier transform infrared spectroscopy (FTIR) and circular dichroism (CD) which shows the disappearance of β sheet structure and appearance of α helices. This study will serve as baseline for translatory research and the development of AE based therapeutics for diseases attributed to protein aggregation.
ppcor: An R Package for a Fast Calculation to Semi-partial Correlation Coefficients.

PubMed

Kim, Seongho

2015-11-01

Lack of a general matrix formula hampers implementation of the semi-partial correlation, also known as part correlation, to the higher-order coefficient. This is because the higher-order semi-partial correlation calculation using a recursive formula requires an enormous number of recursive calculations to obtain the correlation coefficients. To resolve this difficulty, we derive a general matrix formula of the semi-partial correlation for fast computation. The semi-partial correlations are then implemented on an R package ppcor along with the partial correlation. Owing to the general matrix formulas, users can readily calculate the coefficients of both partial and semi-partial correlations without computational burden. The package ppcor further provides users with the level of the statistical significance with its test statistic.
Fluorescence dye-based detection of mAb aggregates in CHO culture supernatants.

PubMed

Paul, Albert Jesuran; Schwab, Karen; Prokoph, Nina; Haas, Elena; Handrick, René; Hesse, Friedemann

2015-06-01

Product yields, efficacy, and safety of monoclonal antibodies (mAbs) are reduced by the formation of higher molecular weight aggregates during upstream processing. In-process characterization of mAb aggregate formation is a challenge since there is a lack of a fast detection method to identify mAb aggregates in cell culture. In this work, we present a rapid method to characterize mAb aggregate-containing Chinese hamster ovary (CHO) cell culture supernatants. The fluorescence dyes thioflavin T (ThT) and 4-4-bis-1-phenylamino-8-naphthalene sulfonate (Bis-ANS) enabled the detection of soluble as well as large mAb aggregates. Partial least square (PLS) regression models were used to evaluate the linearity of the dye-based mAb aggregate detection in buffer down to a mAb aggregate concentration of 2.4 μg mL(-1). Furthermore, mAb aggregates were detected in bioprocess medium using Bis-ANS and ThT. Dye binding to aggregates was stable for 60 min, making the method robust and reliable. Finally, the developed method using 10 μmol L(-1) Bis-ANS enabled discrimination between CHO cell culture supernatants containing different levels of mAb aggregates. The method can be adapted for high-throughput screening, e.g., to screen for cell culture conditions influencing mAb product quality, and hence can contribute to the improvement of production processes of biopharmaceuticals in mammalian cell culture.
The effect of sulfated polysaccharides on the crystallization of calcite superstructures

NASA Astrophysics Data System (ADS)

Fried, Ruth; Mastai, Yitzhak

2012-01-01

Calcite with unique morphology and uniform size has been successfully synthesized in the presence of classes of polysaccharides based on carrageenans. In the crystallization of calcite, the choice of different carrageenans, (iota, lambda and kappa), as additives concedes systematic study of the influence of different chemical structures and particularly molecular charge on the formation of CaCO 3 crystals. The uniform calcite superstructures are formed by assemblies and aggregation of calcite crystals. The mechanism for the formation of calcite superstructures was studied by a variety of techniques, SEM, TEM, XRD, time-resolved conductivity and light scattering measurements, focusing on the early stages of crystals' nucleation and aggregation.
Observation of sub-100-fs optical response from spin-coated films of squarylium dye J aggregates

NASA Astrophysics Data System (ADS)

Furuki, Makoto; Tian, Minquan; Sato, Yasuhiro; Pu, Lyong Sun; Kawashima, Hitoshi; Tatsuura, Satoshi; Wada, Osamu

2001-04-01

For spin-coated films of squarylium dye J aggregates, ultrafast nonlinear optical responses were investigated by pump-probe measurements. By using a broadband mode-locked titanium:sapphire laser, we succeeded in observing the optical response with a time resolution of better than 60 fs. Time-resolved transmission data are shown for different excitation wavelengths, resonant to the excitonic absorption band and off-resonant. Relaxation times of the absorption saturation were evaluated to be 140 fs (fast component) and 950 fs (slow component) in the case of resonant excitation and 98 fs in the case of off-resonant excitation.
Aggregation-Induced Emission Luminogen-Based Direct Visualization of Concentration Gradient Inside an Evaporating Binary Sessile Droplet.

PubMed

Cai, Xin; Xie, Ni; Qiu, Zijie; Yang, Junxian; He, Minghao; Wong, Kam Sing; Tang, Ben Zhong; Qiu, Huihe

2017-08-30

In this study, the concentration gradient inside evaporating binary sessile droplets of 30, 50, and 60 vol % tetrahydrofuran (THF)/water mixtures was investigated. The 5 μL THF/water droplets were evaporated on a transparent hydrophobic substrate. This is the first demonstration of local concentration mapping within an evaporating binary droplet utilizing the aggregation-induced emission material. During the first two evaporation stages of the binary droplet, the local concentration can be directly visualized by the change of fluorescence emission intensity. Time-resolved average and local concentrations can be estimated by using the pre-established function of fluorescence intensity versus water volume fraction.
Utilization of fly ash as partial sand replacement in oil palm shell lightweight aggregate concrete

NASA Astrophysics Data System (ADS)

Nazrin Akmal, A. Z. Muhammad; Muthusamy, K.; Mat Yahaya, F.; Hanafi, H. Mohd; Nur Azzimah, Z.

2017-11-01

Realization on the increasing demand for river sand supply in construction sector has inspired the current research to find alternative material to reduce the use of natural sand in oil palm shell lightweight aggregate concrete (OPS LWAC) production. The existence of fly ash, a by-product generated from coal power plant, which pose negative impact to the environment when it is disposed as waste, were used in this research. The effect of fly ash content as partial sand replacement towards workability and compressive strength of OPS lightweight aggregate concrete were investigated. Four concrete mixes containing various percentage of fly ash that are 0%, 10%, 20% and 30% by weight of sand were used in the experimental work. All mixes were cast in form of cubes before subjected to water curing until the testing age. Compressive strength test were conducted at 1, 3, 7 and 28 days. The finding shows that the workability of the OPS LWAC decreases when more fly ash are used as sand replacement. It was found that adding of 10% fly ash as sand replacement content resulted in better compressive strength of OPS LWAC, which is higher than the control mix.
Progranulin inhibits platelet aggregation and prolongs bleeding time in rats.

PubMed

Al-Yahya, A M; Al-Masri, A A; El Eter, E A; Hersi, A; Lateef, R; Mawlana, O

2018-05-01

Several adipokines secreted by adipose tissue have an anti-thrombotic and anti-atherosclerotic function. Recently identified adipokine progranulin was found to play a protective role in atherosclerosis. Bearing in mind the central role of platelets in inflammation and atherosclerosis, we aimed, in this study, to examine the effect of progranulin on platelet function and coagulation profile in rats. Healthy male albino Wistar rats weighing (250-300 g) were divided into 4 groups. Three groups were given increasing doses of progranulin (0.001 µg, 0.01 µg, and 0.1 µg) intraperitoneally, while the control group received phosphate-buffered saline (PBS). Bleeding time, prothrombin time, activated partial thromboplastin time and platelet aggregation responses to adenosine diphosphate and arachidonic acid were assessed. Administration of progranulin resulted in a significant inhibition of platelet aggregation in response to both adenosine diphosphate, and arachidonic acid. Bleeding time, prothrombin time and activated partial thromboplastin time were significantly prolonged in all groups that received progranulin, in particular, the 0.1 µg dose, in comparison to the control group. This preliminary data is first suggesting that the antiplatelet and anticoagulant action of progranulin could have a physiological protective function against thrombotic disorders associated with obesity and atherosclerosis. However, these results merit further exploration.
Thermal properties of light-weight concrete with waste polypropylene aggregate

NASA Astrophysics Data System (ADS)

Záleská, Martina; Pokorný, Jaroslav; Pavlíková, Milena; Pavlík, Zbyšek

2017-07-01

Thermal properties of a sustainable light-weight concrete incorporating high volume of waste polypropylene as partial substitution of natural aggregate were studied in the paper. Glass fiber reinforced polypropylene (GFPP), a by-product of PP tubes production, partially substituted fine natural silica aggregate in 10, 20, 30, 40, and 50 mass%. In order to quantify the effect of GFPP use on concrete properties, a reference concrete mix without plastic waste was studied as well. For the applied GFPP, bulk density, matrix density, and particle size distribution were measured. Specific attention was paid to thermal transport and storage properties of GFPP that were examined in dependence on compaction time. For the developed light-weight concrete, thermal properties were accessed using transient impulse technique, whereas the measurement was done in dependence on moisture content, from the dry state to fully water saturated state. Additionally, the investigated thermal properties were plotted as function of porosity. The tested light-weight concrete was found to be prospective construction material possessing improved thermal insulation function. Moreover, the reuse of waste plastics in concrete composition was beneficial both from the environmental and financial point of view considering plastics low biodegradability and safe disposal.

Sub-Micellar Concentration of Sodium Dodecyl Sulphate Prevents Thermal Denaturation Induced Aggregation of Plant Lectin, Jacalin.

PubMed

Lavanya, V; Anil Kumar, B; Jamal, Shazia; Khan, Md Khurshid Alam; Ahmed, Neesar

2017-02-01

The irreversible thermal unfolding of jacalin, the lectin purified from jackfruit seeds was accompanied by aggregation, where intermolecular interactions among the subunits are favoured over intramolecular interactions. The extent of aggregation increased as a function of temperature, time and protein concentration. The anionic surfactant, sodium dodecyl sulphate (SDS) significantly suppressed the formation of aggregates as observed by turbidity measurements and Rayleigh scattering assay. Moreover, far UV-CD spectra indicate that the protein β sheet transforms into α helical structure, when denatured in the presence of 3 mM SDS. Further, jacalin when heated in the presence of SDS partially retained the hemagglutination activity when jacalin-SDS mixture was diluted to 1:8 factor since 3 mM SDS was found to lyse the red blood cells. Thus, SDS only altered the aggregation behaviour of jacalin by preventing intermolecular hydrogen bonding among the exposed residues but did not completely stabilize the native conformation.
Distal Renal Tubules Are Deficient in Aggresome Formation and Autophagy upon Aldosterone Administration

PubMed Central

Cheema, Muhammad Umar; Damkier, Helle Hasager; Nielsen, Jakob; Poulsen, Ebbe Toftgaard; Enghild, Jan J.; Fenton, Robert A.; Praetorius, Jeppe

2014-01-01

Prolonged elevations of plasma aldosterone levels are associated with renal pathogenesis. We hypothesized that renal distress could be imposed by an augmented aldosterone-induced protein turnover challenging cellular protein degradation systems of the renal tubular cells. Cellular accumulation of specific protein aggregates in rat kidneys was assessed after 7 days of aldosterone administration. Aldosterone induced intracellular accumulation of 60 s ribosomal protein L22 in protein aggregates, specifically in the distal convoluted tubules. The mineralocorticoid receptor inhibitor spironolactone abolished aldosterone-induced accumulation of these aggregates. The aldosterone-induced protein aggregates also contained proteasome 20 s subunits. The partial de-ubiquitinase ataxin-3 was not localized to the distal renal tubule protein aggregates, and the aggregates only modestly colocalized with aggresome transfer proteins dynactin p62 and histone deacetylase 6. Intracellular protein aggregation in distal renal tubules did not lead to development of classical juxta-nuclear aggresomes or to autophagosome formation. Finally, aldosterone treatment induced foci in renal cortex of epithelial vimentin expression and a loss of E-cadherin expression, as signs of cellular stress. The cellular changes occurred within high, but physiological aldosterone concentrations. We conclude that aldosterone induces protein accumulation in distal renal tubules; these aggregates are not cleared by autophagy that may lead to early renal tubular damage. PMID:25000288
Chaperonin-based biolayer interferometry to assess the kinetic stability of metastable, aggregation-prone proteins

PubMed Central

Lea, Wendy A.; Naik, Subhashchandra; Chaudhri, Tapan; Machen, Alexandra J.; O’Neil, Pierce T.; McGinn-Straub, Wesley; Tischer, Alexander; Auton, Matthew T.; Burns, Joshua R.; Baldwin, Michael R.; Khar, Karen R.; Karanicolas, John; Fisher, Mark T.

2017-01-01

Stabilizing the folded state of metastable and/or aggregation-prone proteins through exogenous ligand binding is an appealing strategy to decrease disease pathologies brought on by protein folding defects or deleterious kinetic transitions. Current methods of examining ligand binding to these marginally stable native states are limited, because protein aggregation typically interferes with analysis. Here, we describe a rapid method for assessing the kinetic stability of folded proteins and monitoring the effects of ligand stabilization for both intrinsically stable proteins (monomers, oligomers, multi-domain) and metastable proteins (e.g. low Tm) that uses a new GroEL chaperonin-based biolayer interferometry (BLI) denaturant-pulse platform. A kinetically controlled denaturation isotherm is generated by exposing a target protein immobilized on a BLI biosensor to increasing denaturant concentrations (urea or GnHCl) in a pulsatile manner to induce partial or complete unfolding of the attached protein population. Following the rapid removal of the denaturant, the extent of hydrophobic unfolded/partially folded species that remain is detected by increased GroEL binding. Since this kinetic denaturant pulse is brief, the amplitude of the GroEL binding to the immobilized protein depends on the duration of exposure to denaturant, the concentration of denaturant, wash times, and the underlying protein unfolding/refolding kinetics; fixing all other parameters and plotting GroEL binding amplitude versus denaturant pulse concentration results in a kinetically controlled denaturation isotherm. When folding osmolytes or stabilizing ligands are added to the immobilized target proteins before and during the denaturant pulse, the diminished population of unfolded/partially folded protein is manifested by a decreased GroEL binding and/or a marked shift in these kinetically controlled denaturation profiles to higher denaturant concentrations. This particular platform approach can be used to identify small molecules/solution conditions that can stabilize or destabilize thermally stable proteins, multi-domain proteins, oligomeric proteins, and most importantly, aggregation prone metastable proteins. PMID:27505032
Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity

NASA Astrophysics Data System (ADS)

Frigori, Rafael B.; Rizzi, Leandro G.; Alves, Nelson A.

2013-01-01

The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid β-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid β isoforms and Src SH3 domain indicated that the folding process described by this CG model is related to a negative specific heat, a phenomenon that can only be verified in the microcanonical ensemble in first-order phase transitions. The CG simulation of the hPrP heteropolymer yielded a continuous folding transition. The absence of a free-energy barrier and latent heat favors the presence of partially unfolded conformations, and in this context, this thermodynamic aspect could explain the reason why the hPrP heteropolymer is more aggregation-prone than the other heteropolymers considered in this study. We introduced the hydrophobic radius of gyration as an order parameter and found that it can be used to obtain reliable information about the hydrophobic packing and the transition temperatures in the folding process.
The effect of charge mutations on the stability and aggregation of a human single chain Fv fragment.

PubMed

Austerberry, James I; Dajani, Rana; Panova, Stanislava; Roberts, Dorota; Golovanov, Alexander P; Pluen, Alain; van der Walle, Christopher F; Uddin, Shahid; Warwicker, Jim; Derrick, Jeremy P; Curtis, Robin

2017-06-01

The aggregation propensities for a series of single-chain variable fragment (scFv) mutant proteins containing supercharged sequences, salt bridges and lysine/arginine-enriched motifs were characterised as a function of pH and ionic strength to isolate the electrostatic contributions. Recent improvements in aggregation predictors rely on using knowledge of native-state protein-protein interactions. Consistent with previous findings, electrostatic contributions to native protein-protein interactions correlate with aggregate growth pathway and rates. However, strong reversible self-association observed for selected mutants under native conditions did not correlate with aggregate growth, indicating 'sticky' surfaces that are exposed in the native monomeric state are inaccessible when aggregates grow. We find that even though similar native-state protein-protein interactions occur for the arginine and lysine-enriched mutants, aggregation propensity is increased for the former and decreased for the latter, providing evidence that lysine suppresses interactions between partially folded states under these conditions. The supercharged mutants follow the behaviour observed for basic proteins under acidic conditions; where excess net charge decreases conformational stability and increases nucleation rates, but conversely reduces aggregate growth rates due to increased intermolecular electrostatic repulsion. The results highlight the limitations of using conformational stability and native-state protein-protein interactions as predictors for aggregation propensity and provide guidance on how to engineer stabilizing charged mutations. Copyright © 2017. Published by Elsevier B.V.
Intra-aggregate CO2 enrichment: a modelling approach for aerobic soils

NASA Astrophysics Data System (ADS)

Schlotter, D.; Schack-Kirchner, H.

2013-02-01

CO2 concentration gradients inside soil aggregates, caused by the respiration of soil microorganisms and fungal hyphae, might lead to variations in the soil solution chemistry on a mm-scale, and to an underestimation of the CO2 storage. But, up to now, there seems to be no feasible method for measuring CO2 inside natural aggregates with sufficient spatial resolution. We combined a one-dimensional model for gas diffusion in the inter-aggregate pore space with a cylinder diffusion model, simulating the consumption/production and diffusion of O2 and CO2 inside soil aggregates with air- and water-filled pores. Our model predicts that for aerobic respiration (respiratory quotient = 1) the intra-aggregate increase in the CO2 partial pressure can never be higher than 0.9 kPa for siliceous, and 0.1 kPa for calcaric aggregates, independent of the level of water-saturation. This suggests that only for siliceous aggregates CO2 produced by aerobic respiration might cause a high small-scale spatial variability in the soil solution chemistry. In calcaric aggregates, however, the contribution of carbonate species to the CO2 transport should lead to secondary carbonates on the aggregate surfaces. As regards the total CO2 storage in aerobic soils, both siliceous and calcaric, the effect of intra-aggregate CO2 gradients seems to be negligible. To assess the effect of anaerobic respiration on the intra-aggregate CO2 gradients, the development of a device for measuring CO2 on a mm-scale in soils is indispensable.
Design and evaluation of foamed asphalt base materials.

DOT National Transportation Integrated Search

2013-05-01

Foamed asphalt stabilized base (FASB) combines reclaimed asphalt pavement (RAP), recycled : concrete (RC), and/or graded aggregate base (GAB) with a foamed asphalt binder to produce a : partially stabilized base material. The objectives of this study...
Design and evaluation of foamed asphalt base materials : [research summary].

DOT National Transportation Integrated Search

2013-05-01

Foamed asphalt stabilized base (FASB) combines reclaimed asphalt pavement (RAP), : recycled concrete (RC), and/or graded aggregate base (GAB) with a foamed asphalt : binder to produce a partially stabilized base material. Although widely used, most :...
EBV+ HHV-8+ Multicentric Castleman Disease With Plasmablastic Aggregates in an HIV+ Man: An Evolving Clinicopathologic Entity.

PubMed

Shivane, Aditya; Pearce, Amy; Khatib, Nadia; Smith, Mark E F

2018-06-01

We report a case of EBV+ and HHV-8+ multicentric Castleman disease with plasmablastic aggregates in an HIV-positive individual. A 41-year-old man presented in early 2015 with fevers, sweats, weight loss, intractable itching, and on subsequent testing was found to be HIV positive. Investigations showed cervical lymphadenopathy and splenomegaly. He was treated for HIV and his symptoms resolved. His symptoms recurred in January 2016, and a provisional diagnosis of multicentric Castleman disease was entertained. The HHV-8 (human herpesvirus-8) and EBV (Epstein-Barr virus) viral load was elevated. A left supraclavicular lymph node core biopsy was performed, which showed features of multicentric Castleman disease with plasmablastic aggregates that are EBV (EBER) and HHV-8 positive. He responded well to rituximab treatment and remains well with no symptoms at recent follow-up.
Facilitated aggregation of FG nucleoporins under molecular crowding conditions.

PubMed

Milles, Sigrid; Huy Bui, Khanh; Koehler, Christine; Eltsov, Mikhail; Beck, Martin; Lemke, Edward A

2013-02-01

Intrinsically disordered and phenylalanine-glycine-rich nucleoporins (FG Nups) form a crowded and selective transport conduit inside the NPC that can only be transited with the help of nuclear transport receptors (NTRs). It has been shown in vitro that FG Nups can assemble into two distinct appearances, amyloids and hydrogels. If and how these phenomena are linked and if they have a physiological role still remains unclear. Using a variety of high-resolution fluorescence and electron microscopic (EM) tools, we reveal that crowding conditions mimicking the NPC environment can accelerate the aggregation and amyloid formation speed of yeast and human FG Nups by orders of magnitude. Aggregation can be inhibited by NTRs, providing a rationale on how the cell might control amyloid formation of FG Nups. The superb spatial resolving power of EM also reveals that hydrogels are enlaced amyloid fibres, and these findings have implications for existing transport models and for NPC assembly.
Facilitated aggregation of FG nucleoporins under molecular crowding conditions

PubMed Central

Milles, Sigrid; Huy Bui, Khanh; Koehler, Christine; Eltsov, Mikhail; Beck, Martin; Lemke, Edward A

2013-01-01

Intrinsically disordered and phenylalanine–glycine-rich nucleoporins (FG Nups) form a crowded and selective transport conduit inside the NPC that can only be transited with the help of nuclear transport receptors (NTRs). It has been shown in vitro that FG Nups can assemble into two distinct appearances, amyloids and hydrogels. If and how these phenomena are linked and if they have a physiological role still remains unclear. Using a variety of high-resolution fluorescence and electron microscopic (EM) tools, we reveal that crowding conditions mimicking the NPC environment can accelerate the aggregation and amyloid formation speed of yeast and human FG Nups by orders of magnitude. Aggregation can be inhibited by NTRs, providing a rationale on how the cell might control amyloid formation of FG Nups. The superb spatial resolving power of EM also reveals that hydrogels are enlaced amyloid fibres, and these findings have implications for existing transport models and for NPC assembly. PMID:23238392
Effect of carprofen on hemostatic variables in dogs.

PubMed

Hickford, F H; Barr, S C; Erb, H N

2001-10-01

To evaluate the effect of carprofen on hemostatic variables in clinically normal dogs. 12 clinically normal Labrador Retrievers. 10 dogs (6 females, 4 males) received carprofen (2.2 mg/kg of body weight, PO, q 12 h) for 5 days. Two dogs (untreated control group; 1 female, 1 male) did not receive carprofen. Hemostatic variables (platelet count, activated partial thromboplastin time, prothrombin time, fibrinogen, platelet aggregation, and bleeding time) were assessed for all dogs prior to treatment, on day 5 of treatment, and 2 and 7 days after discontinuation of the drug (days 7 and 12). Serum biochemical variables and Hct were assessed prior to treatment and on days 5 and 12. In dogs receiving carprofen, platelet aggregation was significantly decreased, and onset of aggregation was significantly delayed on days 5, 7, and 12, compared with pretreatment values. Activated partial thromboplastin time was significantly increased on days 5, 7, and 12 over pretreatment values in treated dogs, but values remained within reference ranges. Significant differences were not detected in buccal mucosal bleeding time, other serum biochemical and hemostatic variables, or Hct, compared with pretreatment values and the internal control group. Administration of carprofen for 5 days causes minor but not clinically important alterations in hemostatic and serum biochemical variables in clinically normal Labrador Retrievers. Carprofen is commonly used to treat osteoarthritis and chronic pain in dogs, but prior to this study, its effect on platelet aggregation and hemostatic variables was unknown.
Kin discrimination increases with genetic distance in a social amoeba.

PubMed

Ostrowski, Elizabeth A; Katoh, Mariko; Shaulsky, Gad; Queller, David C; Strassmann, Joan E

2008-11-25

In the social amoeba Dictyostelium discoideum, thousands of cells aggregate upon starvation to form a multicellular fruiting body, and approximately 20% of them die to form a stalk that benefits the others. The aggregative nature of multicellular development makes the cells vulnerable to exploitation by cheaters, and the potential for cheating is indeed high. Cells might avoid being victimized if they can discriminate among individuals and avoid those that are genetically different. We tested how widely social amoebae cooperate by mixing isolates from different localities that cover most of their natural range. We show here that different isolates partially exclude one another during aggregation, and there is a positive relationship between the extent of this exclusion and the genetic distance between strains. Our findings demonstrate that D. discoideum cells co-aggregate more with genetically similar than dissimilar individuals, suggesting the existence of a mechanism that discerns the degree of genetic similarity between individuals in this social microorganism.
A small molecule chemical chaperone optimizes its unfolded state contraction and denaturant like properties

NASA Astrophysics Data System (ADS)

Sharma, Sunny; Sarkar, Suparna; Paul, Simanta Sarani; Roy, Syamal; Chattopadhyay, Krishnananda

2013-12-01

Protein aggregation is believed to occur through the formation of misfolded conformations. It is expected that, in order to minimize aggregation, an effective small molecule chaperone would destabilize these intermediates. To study the mechanism of a chemical chaperone, we have designed a series of mutant proteins in which a tryptophan residue experiences different local environments and solvent exposures. We show that these mutants correspond to a series of conformationally altered proteins with varying degree of misfolding stress and aggregation propensities. Using arginine as a model small molecule, we show that a combination of unfolded state contraction and denaturant like properties results in selective targeting and destabilization of the partially folded proteins. In comparison, the effect of arginine towards the folded like control mutant, which is not aggregation prone, is significantly less. Other small molecules, lacking either of the above two properties, do not offer any specificity towards the misfolded proteins.
Protein kinase C involvement in the acetylcholine release reduction induced by amyloid-beta(25-35) aggregates on neuromuscular synapses.

PubMed

Tomàs, Marta; Garcia, Neus; Santafé, Manuel M; Lanuza, Maria; Tomàs, Josep

2009-01-01

Using intracellular recording of the diaphragm muscle of adult rats, we have investigated the short-term functional effects of amyloid-beta (Abeta(25-35) peptide aggregates on the modulation of acetylcholine (ACh) release and the involvement of protein kinase C (PKC). The non-aggregated form of this peptide does not change the evoked and spontaneous transmitter release parameters on the neuromuscular synapse. However, the aggregated form of Abeta(25-35) acutely interferes with evoked quantal ACh release (approximately 40% reduction) when synaptic activity in the ex vivo neuromuscular preparation is maintained by low frequency (1 Hz) electrical stimulation. This effect is partially dependent on the activity of PKC that may have a permissive action. The end result of Abeta(25-35) is in opposition to the PKC-dependent maintenance effect on ACh release manifested in active synapses.
The effects of 7.5% NaCl/6% dextran 70 on coagulation and platelet aggregation in humans

NASA Technical Reports Server (NTRS)

Hess, J. R.; Dubick, M. A.; Summary, J. J.; Bangal, N. R.; Wade, C. E.

1992-01-01

The combination solution of 7.5% NaCl/6% dextran 70 (HSD) administered IV gives hemodynamic improvement in the treatment of hemorrhagic hypotension. Since earlier dextran solutions were reported to interfere with blood coagulation, the effects of HSD on the prothrombin time (PT), the activated partial thromboplastin time (APTT), platelet aggregation, and platelet concentration were studied. The HSD mixed with human plasma (1:5 and 1:10) slightly prolonged PT, but had no effect on the APTT, compared with saline controls. The HSD also decreased human platelet aggregation at the 1:5 dilution. In separate mixing studies, the hypertonic saline component of HSD was associated with the prolongation of PT and decreased platelet aggregation. The data from these studies indicate that at its proposed therapeutic dose, HSD is expected to have minimal effect on blood coagulation.
Analyzing Multilevel Data: An Empirical Comparison of Parameter Estimates of Hierarchical Linear Modeling and Ordinary Least Squares Regression

ERIC Educational Resources Information Center

Rocconi, Louis M.

2011-01-01

Hierarchical linear models (HLM) solve the problems associated with the unit of analysis problem such as misestimated standard errors, heterogeneity of regression and aggregation bias by modeling all levels of interest simultaneously. Hierarchical linear modeling resolves the problem of misestimated standard errors by incorporating a unique random…
Visualizing the quality of partially accruing data for use in decision making

PubMed Central

Eaton, Julia; Painter, Ian; Olson, Don; Lober, William B

2015-01-01

Secondary use of clinical health data for near real-time public health surveillance presents challenges surrounding its utility due to data quality issues. Data used for real-time surveillance must be timely, accurate and complete if it is to be useful; if incomplete data are used for surveillance, understanding the structure of the incompleteness is necessary. Such data are commonly aggregated due to privacy concerns. The Distribute project was a near real-time influenza-like-illness (ILI) surveillance system that relied on aggregated secondary clinical health data. The goal of this work is to disseminate the data quality tools developed to gain insight into the data quality problems associated with these data. These tools apply in general to any system where aggregate data are accrued over time and were created through the end-user-as-developer paradigm. Each tool was developed during the exploratory analysis to gain insight into structural aspects of data quality. Our key finding is that data quality of partially accruing data must be studied in the context of accrual lag—the difference between the time an event occurs and the time data for that event are received, i.e. the time at which data become available to the surveillance system. Our visualization methods therefore revolve around visualizing dimensions of data quality affected by accrual lag, in particular the tradeoff between timeliness and completion, and the effects of accrual lag on accuracy. Accounting for accrual lag in partially accruing data is necessary to avoid misleading or biased conclusions about trends in indicator values and data quality. PMID:27252794
Visualizing the quality of partially accruing data for use in decision making.

PubMed

Eaton, Julia; Painter, Ian; Olson, Don; Lober, William B

2015-01-01

Secondary use of clinical health data for near real-time public health surveillance presents challenges surrounding its utility due to data quality issues. Data used for real-time surveillance must be timely, accurate and complete if it is to be useful; if incomplete data are used for surveillance, understanding the structure of the incompleteness is necessary. Such data are commonly aggregated due to privacy concerns. The Distribute project was a near real-time influenza-like-illness (ILI) surveillance system that relied on aggregated secondary clinical health data. The goal of this work is to disseminate the data quality tools developed to gain insight into the data quality problems associated with these data. These tools apply in general to any system where aggregate data are accrued over time and were created through the end-user-as-developer paradigm. Each tool was developed during the exploratory analysis to gain insight into structural aspects of data quality. Our key finding is that data quality of partially accruing data must be studied in the context of accrual lag-the difference between the time an event occurs and the time data for that event are received, i.e. the time at which data become available to the surveillance system. Our visualization methods therefore revolve around visualizing dimensions of data quality affected by accrual lag, in particular the tradeoff between timeliness and completion, and the effects of accrual lag on accuracy. Accounting for accrual lag in partially accruing data is necessary to avoid misleading or biased conclusions about trends in indicator values and data quality.
Effects of Convective Aggregation on Radiative Cooling and Precipitation in a CRM

NASA Astrophysics Data System (ADS)

Naegele, A. C.; Randall, D. A.

2017-12-01

In the global energy budget, the atmospheric radiative cooling (ARC) is approximately balanced by latent heating, but on regional scales, the ARC and precipitation rates are inversely related. We use a cloud-resolving model to explore how the relationship between precipitation and the ARC is affected by convective aggregation, in which the convective activity is confined to a small portion of the domain that is surrounded by a much larger region of dry, subsiding air. Sensitivity tests show that the precipitation rate and ARC are highly sensitive to both SST and microphysics; a higher SST and 1-moment microphysics both act to increase the domain-averaged ARC and precipitation rates. In all simulations, both the domain-averaged ARC and precipitation rates increased due to convective aggregation, resulting in a positive temporal correlation. Furthermore, the radiative effect of clouds in these simulations is to decrease the ARC. This finding is consistent with our observational results of the cloud effect on the ARC, and has implications for convective aggregation and the geographic extent in which it can occur.

Simulation study of 2D spectrum of molecular aggregates coupled to correlated vibrations

NASA Astrophysics Data System (ADS)

Abramavicius, Darius; Butkus, Vytautas; Valkunas, Leonas; Mukamel, Shaul

2011-03-01

Oscillatory dynamics of two-dimensional (2D) spectra of photosynthetic pigment-protein complexes raise the questions of how to disentangle various origins of these oscillations, which may include quantum beats, quantum transport, or molecular vibrations. We study the effects of correlated overdamped fluctuations and under-damped vibrations on the 2D spectra of Fenna-Matthews-Olson (FMO) aggregate, which has well-resolved exciton resonances, and a circular porphyrin aggregate (P6), whose absorption shows vibrational progression. We use a generic exciton Hamiltonian coupled to a bath, characterized by a spectral density. Fluctuations have smooth, while vibtations have δ -type spectral densities. We show how various scenarios of correlated molecular fluctuations lead to some highly oscillatory crosspeaks. Molecular vibrations cause progression of diagonal peaks in the 2D spectrum and make their corresponding cross-peaks highly oscillatory. We, thus, demonstrate that bath fluctuations and molecular vibrations of realistic molecular aggregates are highly entangled in 2D spectroscopy. DA acknowledges grant VP1-3.1-SMM-07-V, SM - the grants CHE0745892 (NSF), DRPA BAA-10-40 QUBE.
1,2,4-trihydroxynaphthalene-2-O-β-D-glucopyranoside: A new powerful antioxidant and inhibitor of Aβ42 aggregation isolated from the leaves of Lawsonia inermis.

PubMed

Dhouafli, Zohra; Ben Jannet, Hichem; Mahjoub, Borhane; Leri, Manuela; Guillard, Jérôme; Saidani Tounsi, Moufida; Stefani, Massimo; Hayouni, El Akrem

2017-12-29

Mounting evidence indicates free radicals as toxic species causing damage to human cells leading to the pathogenesis of many diseases such as neurodegenerative disease. Plant derived antioxidants are considered as promising strategy to prevent free radical toxicity. In this study, the crude extract (CE), 50%MeOH, Petroleum Ether (PE) and Ethyl acetate (EA) fractions of Lawsonia inermis leaves were investigated for their antioxidant activity and their ability to counteract amyloid-β 42 (Aβ 42 ) aggregation. Elution of the most bioactive fraction (EA) on silica gel column chromatography led to six sub-fractions. The most active sub-fraction (1) was further resolved on silica gel column chromatography. A new compound with powerful antioxidant and anti-Aβ 42 aggregation properties was purified and characterised by spectroscopic methods as 1,2,4-trihydroxynaphthalene-2-O-β-D-glucopyranoside (THNG). This finding suggests that the antioxidant and anti-Aβ 42 aggregation activities of L. inermis leaves are strongly correlated to this compound.
Parameterizing Aggregation Rates: Results of cold temperature ice-ash hydrometeor experiments

NASA Astrophysics Data System (ADS)

Courtland, L. M.; Dufek, J.; Mendez, J. S.; McAdams, J.

2014-12-01

Recent advances in the study of tephra aggregation have indicated that (i) far-field effects of tephra sedimentation are not adequately resolved without accounting for aggregation processes that preferentially remove the fine ash fraction of volcanic ejecta from the atmosphere as constituent pieces of larger particles, and (ii) the environmental conditions (e.g. humidity, temperature) prevalent in volcanic plumes may significantly alter the types of aggregation processes at work in different regions of the volcanic plume. The current research extends these findings to explore the role of ice-ash hydrometeor aggregation in various plume environments. Laboratory experiments utilizing an ice nucleation chamber allow us to parameterize tephra aggregation rates under the cold (0 to -50 C) conditions prevalent in the upper regions of volcanic plumes. We consider the interaction of ice-coated tephra of variable thickness grown in a controlled environment. The ice-ash hydrometers interact collisionally and the interaction is recorded by a number of instruments, including high speed video to determine if aggregation occurs. The electric charge on individual particles is examined before and after collision to examine the role of electrostatics in the aggregation process and to examine the charge exchange process. We are able to examine how sticking efficiency is related to both the relative abundance of ice on a particle as well as to the magnitude of the charge carried by the hydrometeor. We here present preliminary results of these experiments, the first to constrain aggregation efficiency of ice-ash hydrometeors, a parameter that will allow tephra dispersion models to use near-real-time meteorological data to better forecast particle residence time in the atmosphere.
Random Fields and Collective Effects in Molecular Magnets

DTIC Science & Technology

2018-01-29

longitudinal fields the final state consists of only partially reversed spins. Further, we measured the front speed as a function of applied magnetic...field. The theory of magnetic deflagration, together with a modification that takes into account the partial spin reversal, fits the transverse field...Conference Paper or Presentation Conference Name: APS March Meeting 2016 Conference Location: Baltimore, Paper Title: Time-resolved Measurements
Effects of recycled shingles and increased RAP percentages : [research brief].

DOT National Transportation Integrated Search

2012-01-01

As asphalt binder becomes more expensive, the use of recycled asphalt materials becomes : more attractive. Recycled asphalt pavement (RAP) and recycled asphalt shingles (RAS) offer a partial substitute for virgin aggregate and binder in asphalt pavem...
Classification and Characterization of Therapeutic Antibody Aggregates

PubMed Central

Joubert, Marisa K.; Luo, Quanzhou; Nashed-Samuel, Yasser; Wypych, Jette; Narhi, Linda O.

2011-01-01

A host of diverse stress techniques was applied to a monoclonal antibody (IgG2) to yield protein particles with varying attributes and morphologies. Aggregated solutions were evaluated for percent aggregation, particle counts, size distribution, morphology, changes in secondary and tertiary structure, surface hydrophobicity, metal content, and reversibility. Chemical modifications were also identified in a separate report (Luo, Q., Joubert, M. K., Stevenson, R., Narhi, L. O., and Wypych, J. (2011) J. Biol. Chem. 286, 25134–25144). Aggregates were categorized into seven discrete classes, based on the traits described. Several additional molecules (from the IgG1 and IgG2 subtypes as well as intravenous IgG) were stressed and found to be defined with the same classification system. The mechanism of protein aggregation and the type of aggregate formed depends on the nature of the stress applied. Different IgG molecules appear to aggregate by a similar mechanism under the same applied stress. Aggregates created by harsh mechanical stress showed the largest number of subvisible particles, and the class generated by thermal stress displayed the largest number of visible particles. Most classes showed a disruption of the higher order structure, with the degree of disorder depending on the stress process. Particles in all classes (except thermal stress) were at least partially reversible upon dilution in pH 5 buffer. High copper content was detected in isolated metal-catalyzed aggregates, a stress previously shown to produce immunogenic aggregates. In conclusion, protein aggregates can be a very heterogeneous population, whose qualities are the result of the type of stress that was experienced. PMID:21454532
Disaggregation of adenylate cyclase during polyacrylamide-gel electrophoresis in mixtures of ionic and non-ionic detergents.

PubMed

Newby, A C; Chrambach, A

1979-02-01

1. Adenylate cyclase [ATP pyrophosphate-lyase (cyclizing), EC 4.6.1.1] solubilized from the rat liver plasma membrane with 1% Lubrol PX and partially purified by gel filtration in buffer containing 0.01% Lubrol PX was physically characterized by polyacrylamide-gel electrophoresis. 2. The molecular radius determined for the partially purified enzyme was 4.9nm, compared with the value of 3.9nm obtained for the enzyme before gel filtration. 3. This difference, representing an approximate doubling of the molecular volume of the enzyme, implied that aggregation with itself or other proteins had occurred during partial purification. 4. Aggregation was not reversed by electrophoresis in the presence of high Lubrol concentrations. 5. Substitution of deoxycholate or N-dodecylsarcosinate for Lubrol PX either for solubilization or during electrophoresis led to poorer resolution of membrane proteins at concentrations giving greater than 70% loss of enzyme activity. 6. Partially purified adenylate cyclase was electrophoresed in the presence of mixed micelles of Lubrol PX and deoxycholate or Lubrol PX and N-dodecylsarcosinate. Different mixtures were examined simultaneously in a suitable apparatus. 7. Electrophoresis in the presence of 0.1% Lubrol plus 0.03% deoxycholate decreased the molecular radius of the cyclase to 4.0nm, with greater than 90% recovery of enzymic activity. The net charge of the enzyme was also increased, indicating ionic detergent binding. 8. With 0.1% Lubrol plus 0.03% N-dodecylsarcosinate the molecular radius was 4.3nm, recovery approx. 50% and net charge similar to that seen in Lubrol plus deoxycholate. 9. The resolution of cyclase from bulk protein, on an analytical scale, was improved in the presence of detergent mixtures, as compared with resolution in Lubrol alone. 10. The results demonstrate the usefulness of polyacrylamide-gel electrophoresis to detect and overcome aggregation problems with membrane proteins and suggest that detergent mixtures in specific ratios may be useful in the purification of adenylate cyclase and other intrinsic membrane proteins.
Preventing α-synuclein aggregation: the role of the small heat-shock molecular chaperone proteins.

PubMed

Cox, Dezerae; Carver, John A; Ecroyd, Heath

2014-09-01

Protein homeostasis, or proteostasis, is the process of maintaining the conformational and functional integrity of the proteome. The failure of proteostasis can result in the accumulation of non-native proteins leading to their aggregation and deposition in cells and in tissues. The amyloid fibrillar aggregation of the protein α-synuclein into Lewy bodies and Lewy neuritis is associated with neurodegenerative diseases classified as α-synucleinopathies, which include Parkinson's disease and dementia with Lewy bodies. The small heat-shock proteins (sHsps) are molecular chaperones that are one of the cell's first lines of defence against protein aggregation. They act to stabilise partially folded protein intermediates, in an ATP-independent manner, to maintain cellular proteostasis under stress conditions. Thus, the sHsps appear ideally suited to protect against α-synuclein aggregation, yet these fail to do so in the context of the α-synucleinopathies. This review discusses how sHsps interact with α-synuclein to prevent its aggregation and, in doing so, highlights the multi-faceted nature of the mechanisms used by sHsps to prevent the fibrillar aggregation of proteins. It also examines what factors may contribute to α-synuclein escaping the sHsp chaperones in the context of the α-synucleinopathies. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.
Investigation of aggregation in solvent extraction of lanthanides by acidic extractants (organophosphorus and naphthenic acid)

USGS Publications Warehouse

Zhou, N.; Wu, J.; Yu, Z.; Neuman, R.D.; Wang, D.; Xu, G.

1997-01-01

Three acidic extractants (I) di(2-ethylhexyl) phosphoric acid (HDEHP), (II) 2-ethylhexyl phosphonic acid mono-2-ethylhexyl ester (HEHPEHE) and (III) naphthenic acid were employed in preparing the samples for the characterization of the coordination structure of lanthanide-extractant complexes and the physicochemical nature of aggregates formed in the organic diluent of the solvent extraction systems. Photo correlation spectroscopy (PCS) results on the aggregates formed by the partially saponified HDEHP in n-heptane showed that the hydrodynamic radius of the aggregates was comparable to the molecular dimensions of HDEHP. The addition of 2-octanol into the diluent, by which the mixed solvent was formed, increased the dimensions of the corresponding aggregates. Aggregates formed from the lanthanide ions and HDEHP in the organic phase of the extraction systems were found very unstable. In the case of naphthenic acid, PCS data showed the formation of w/o microemulsion from the saponified naphthenic acid in the mixed solvent. The extraction of lanthanides by the saponified naphthenic acid in the mixed solvent under the given experimental conditions was a process of destruction of the w/o microemulsion. A possible mechanism of the breakdown of the w/o microemulsion droplets is discussed.
Linking Microbial Community Structure to β-Glucosidic Function in Soil Aggregates

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

Bailey, Vanessa L.; Fansler, Sarah J.; Stegen, James C.

2013-10-01

To link microbial community 16S structure to a measured function in a natural soil we have scaled both DNA and β-glucosidase assays down to a volume of soil that may approach a unique microbial community. β-glucosidase activity was assayed in 450 individual aggregates which were then sorted into classes of high or low activities, from which groups of 10 or 11 aggregates were identified and grouped for DNA extraction and pyrosequencing. Tandem assays of ATP were conducted for each aggregate in order to normalize these small groups of aggregates for biomass size. In spite of there being no significant differencesmore » in the richness or diversity of the microbial communities associated with high β-glucosidase activities compared with the communities associated with low β-glucosidase communities, several analyses of variance clearly show that the communities of these two groups differ. The separation of these groups is partially driven by the differential abundances of members of the Chitinophagaceae family. It may be that observed functional differences in otherwise similar soil aggregates can be largely attributed to differences in resource availability, rather than to presence or absence of particular taxonomic groups.« less
Inhibitory effects of Atractylodis lanceae rhizoma and Poria on collagen- or thromboxane A2-induced aggregation in rabbit platelets.

PubMed

Nasu, Yuiko; Iwashita, Masaya; Saito, Masaki; Fushiya, Shinji; Nakahata, Norimichi

2009-05-01

Kami-shoyo-san (Jia-Wei-Xiao-Yao-San), Toki-shakuyaku-san (Dang-Gui-Shao-Yao-San) and Toki-shigyaku-ka-goshuyu-shokyo-to (Dang-Gui-Si-Ni-Jia-Wu-Zhu-Yu-Sheng-Jiang-Tang) are Kampo (traditional Chinese) medicines which are traditionally and effectively used for the treatment of chilly sensation (Hiesho) in Japan, but the active components and their detailed mechanisms have not yet been clarified. Etiologies of Hiesho include poor peripheral blood circulation and platelet aggregability contributes to peripheral blood circulation; therefore, we investigated the effect of Kampo medicines on platelet aggregation using rabbit platelets in vitro. Collagen and U46619, a thromboxane A(2) receptor agonist, caused rabbit platelet aggregation, which was potently inhibited by pretreatment of platelets with Kami-shoyo-san and Toki-shakuyaku-san in vitro. Toki-shigyaku-ka-goshuyu-shokyo-to, however, did not significantly inhibit collagen- or U46619-induced platelet aggregation. Therefore, we examined the effect on platelet aggregation of two herbal medicines, Atractylodis Lanceae Rhizoma and Poria, both of which are contained in Kami-shoyo-san and Toki-shakuyaku-san but not in Toki-shigyaku-ka-goshuyu-shokyo-to. As the results indicate, Atractylodis Lanceae Rhizoma inhibited platelet aggregation induced by collagen but not by U46619. Poria effectively inhibited U46619-induced platelet aggregation and it partially inhibited collagen-induced platelet aggregation. On the other hand, Atractylodis Lanceae Rhizoma and Poria did not inhibit adrenaline/adenosine diphosphate- or adrenaline/serotonin-induced platelet aggregation. These results suggest the possibility that the inhibition of platelet aggregation by two Kampo medicines, Kami-shoyo-san and Toki-shakuyaku-san, is one of the mechanisms underlying the improvement of Hiesho. Furthermore, Atractylodis Lanceae Rhizoma and Poria are possible herbal medicines for the inhibition of platelet aggregation.
Structural formation of huntingtin-like aggregates probed by small-angle neutron scattering

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

Stanley, Christopher B; Perevozchikova, Tatiana; Berthelier-Jung, Valerie M

2011-01-01

In several neurodegenerative disorders, including Huntington s disease (HD), aspects concerning the earliest of protein structures that form along the aggregation pathway have increasingly gained attention since these particular species are likely to be neurotoxic. We used time-resolved small-angle neutron scattering (SANS) to probe in solution these transient structures formed by peptides having the N-terminal sequence context of mutant huntingtin (Htt) exon 1. We obtained snapshots of the formed aggregates as the kinetic reaction ensued to yield quantitative information on their size and mass. At the early stage, small precursor species with an initial radius of gyration (Rg) of 16.1more » 5.9 and average mass of a dimer to trimer were monitored. Structural growth was treated as two modes with a transition from three-dimensional early aggregate formation to two-dimensional fibril growth and association. Our SANS results on the internal structure of the mature fibrils demonstrate loose packing with about 1 peptide per 4.75 -sheet repeat distance, which is shown to be quantitatively consistent with a -helix model. This research provides new insights into the structures forming along the pathway of Htt exon 1 aggregation and should assist in determining the role that precursors play in neuronal toxicity.« less
Effects of surfaces and leachables on the stability of biopharmaceuticals.

PubMed

Bee, Jared S; Randolph, Theodore W; Carpenter, John F; Bishop, Steven M; Dimitrova, Mariana N

2011-10-01

Therapeutic proteins are exposed to various potential contact surfaces, particles, and leachables during manufacturing, shipping, storage, and delivery. In this review, we present published examples of interfacial- or leachable-induced aggregation or particle formation, and discuss the mitigation strategies that were successfully utilized. Adsorption to interfaces or interactions with leachables and/or particles in some cases has been reported to cause protein aggregation or particle formation. Identification of the cause(s) of particle formation involving minute amounts of protein over extended periods of time can be challenging. Various formulation strategies such as addition of a nonionic surfactant (e.g., polysorbate) have been demonstrated to effectively mitigate adsorption-induced protein aggregation. However, not all stability problems associated with interfaces or leachables are best resolved by formulation optimization. Detectable leachables do not necessarily have any adverse impact on the protein but control of the leachable source is preferred when there is a concern. In other cases, preventing protein aggregation and particle formation may require manufacturing process and/or equipment changes, use of compatible materials at contact interfaces, and so on. This review summarizes approaches that have been used to minimize protein aggregation and particle formation during manufacturing and fill-finish operations, product storage and transportation, and delivery of protein therapeutics. Copyright © 2011 Wiley-Liss, Inc.
Application of Recycled Ceramic Aggregates for the Production of Mineral-Asphalt Mixtures.

PubMed

Andrzejuk, Wojciech; Barnat-Hunek, Danuta; Siddique, Rafat; Zegardło, Bartosz; Łagód, Grzegorz

2018-04-24

This paper describes a method of designing and producing innovative mineral⁻asphalt mixtures, which utilize waste aggregate from the recycling of sanitary ceramics. The work presents the basic properties of the ceramic material, the investigation concerning the microstructure of the aggregate obtained from the grinding of waste, and a comparison with the images obtained for the aggregates usually employed in mineral⁻asphalt mixtures. The mixtures were designed for the application in the wearing course. Four series of mixtures were prepared. In the first and second, the ceramic aggregate constituted a partial substitute for dolomite, whereas in the third, we substituted granodiorite, and the fourth series contained only dolomite. The mixtures were examined for the content of soluble binder, the bulk density of samples, the presence of voids, the space filled with binder, and the susceptibility to water and frost corrosion. The obtained results were compared with the standard requirements. The microstructure as well as the contact zone in the considered mineral⁻asphalt mixtures are presented based on research conducted by means of a scanning electron microscope (SEM).
Application of Recycled Ceramic Aggregates for the Production of Mineral-Asphalt Mixtures

PubMed Central

Andrzejuk, Wojciech; Barnat-Hunek, Danuta; Siddique, Rafat; Zegardło, Bartosz; Łagód, Grzegorz

2018-01-01

This paper describes a method of designing and producing innovative mineral–asphalt mixtures, which utilize waste aggregate from the recycling of sanitary ceramics. The work presents the basic properties of the ceramic material, the investigation concerning the microstructure of the aggregate obtained from the grinding of waste, and a comparison with the images obtained for the aggregates usually employed in mineral–asphalt mixtures. The mixtures were designed for the application in the wearing course. Four series of mixtures were prepared. In the first and second, the ceramic aggregate constituted a partial substitute for dolomite, whereas in the third, we substituted granodiorite, and the fourth series contained only dolomite. The mixtures were examined for the content of soluble binder, the bulk density of samples, the presence of voids, the space filled with binder, and the susceptibility to water and frost corrosion. The obtained results were compared with the standard requirements. The microstructure as well as the contact zone in the considered mineral–asphalt mixtures are presented based on research conducted by means of a scanning electron microscope (SEM). PMID:29695115
Controlling ion aggregation and conduction in PEO-based ionomers.

NASA Astrophysics Data System (ADS)

Caldwell, David, II; Maranas, Janna

2015-03-01

PEO-based ionomers are ideal for reducing concentration polarization found in typical solid polymer electrolytes. This is achieved by binding the anion to the polymer backbone, significantly reducing the anions mobility. Ion aggregation is prevalent in these systems, but their influence on SPE performance is difficult to study experimentally. We present results of molecular dynamics simulations that explore the relationship between ion content and temperature on ion aggregation, polymer motion, and ion conduction. An unforeseen result of ionomers is the creation of string like aggregates that form conduction pathways in the amorphous region. These conduction pathways allow for a partial decoupling of ion conduction with polymer dynamics. The improvement in conductivity through the use of ion aggregates can be quantified by calculating the inverse of the Haven Ratio, dubbed f-value. Typical SPEs have an f-value less than 0.2, while the ionomers of study exhibit f-values near unity or higher. Understanding what properties influence the development and use of these conduction pathways will provide insight for further development of solid polymer electrolytes.
Pendulum Swings in Educational Policymaking: The Effects of Organizational, School, Financial and Social Characteristics on Student Performance Outcomes in Michigan School Districts

ERIC Educational Resources Information Center

Dyson, Dana D.

2009-01-01

Reforms in American public education have not resolved the wide academic performance gap between students attending schools in poor, large, urban centers versus schools in wealthier areas. Aggregate performance outcomes on state achievement tests reveal that some school districts consistently outperform others, a few fluctuate over time but are…
Strategy for the elucidation of elemental compositions of trace analytes based on a mass resolution of 100,000 full width at half maximum.

PubMed

Kaufmann, Anton

2010-07-30

Elemental compositions (ECs) can be elucidated by evaluating the high-resolution mass spectra of unknown or suspected unfragmented analyte ions. Classical approaches utilize the exact mass of the monoisotopic peak (M + 0) and the relative abundance of isotope peaks (M + 1 and M + 2). The availability of high-resolution instruments like the Orbitrap currently permits mass resolutions up to 100,000 full width at half maximum. This not only allows the determination of relative isotopic abundances (RIAs), but also the extraction of other diagnostic information from the spectra, such as fully resolved signals originating from (34)S isotopes and fully or partially resolved signals related to (15)N isotopes (isotopic fine structure). Fully and partially resolved peaks can be evaluated by visual inspection of the measured peak profiles. This approach is shown to be capable of correctly discarding many of the EC candidates which were proposed by commercial EC calculating algorithms. Using this intuitive strategy significantly extends the upper mass range for the successful elucidation of ECs. Copyright 2010 John Wiley & Sons, Ltd.
Interaction of Aluminum with PHFτ in Alzheimer’s Disease Neurofibrillary Degeneration Evidenced by Desferrioxamine-Assisted Chelating Autoclave Method

PubMed Central

Murayama, Harunobu; Shin, Ryong-Woon; Higuchi, Jun; Shibuya, Satoshi; Muramoto, Tamaki; Kitamoto, Tetsuyuki

1999-01-01

To demonstrate that aluminum III (Al) interacts with PHFτ in neurofibrillary degeneration (NFD) of Alzheimer’s disease (AD) brain, we developed a “chelating autoclave method” that allows Al chelation by using trivalent-cationic chelator desferrioxamine. Its application to AD brain sections before Morin histochemistry for Al attenuated the positive fluorescence of neurofibrillary tangles, indicating Al removal from them. This method, applied for immunostaining with phosphorylation-dependent anti-τ antibodies, significantly enhanced the PHFτ immunoreactivity of the NFD. These results suggest that each of the phosphorylated epitopes in PHFτ are partially masked by Al binding. Incubation of AD sections with AlCl3 before Morin staining revealed Al accumulation with association to neurofibrillary tangles. Such incubation before immunostaining with the phosphorylation-dependent anti-τ antibodies abolished the immunolabeling of the NFD and this abolition was reversed by the Al chelation. These findings indicate cumulative Al binding to and thereby antigenic masking of the phosphorylated epitopes of PHFτ. Al binding was further documented for electrophoretically-resolved PHFτ on immunoblots, indicating direct Al binding to PHFτ. In vitro aggregation by AlCl3 was observed for PHFτ but was lost on dephosphorylation of PHFτ. Taken together, phosphorylation-dependent and direct PHFτ-Al interaction occurs in the NFD of the AD brain. PMID:10487845
Flow Partitioning in Fully Saturated Soil Aggregates

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

Yang, Xiaofan; Richmond, Marshall C.; Scheibe, Timothy D.

2014-03-30

Microbes play an important role in facilitating organic matter decomposition in soils, which is a major component of the global carbon cycle. Microbial dynamics are intimately coupled to environmental transport processes, which control access to labile organic matter and other nutrients that are needed for the growth and maintenance of microorganisms. Transport of soluble nutrients in the soil system is arguably most strongly impacted by preferential flow pathways in the soil. Since the physical structure of soils can be characterized as being formed from constituent micro aggregates which contain internal porosity, one pressing question is the partitioning of the flowmore » among the “inter-aggregate” and “intra-aggregate” pores and how this may impact overall solute transport within heterogeneous soil structures. The answer to this question is particularly important in evaluating assumptions to be used in developing upscaled simulations based on highly-resolved mechanistic models. We constructed a number of diverse multi-aggregate structures with different packing ratios by stacking micro-aggregates containing internal pores and varying the size and shape of inter-aggregate pore spacing between them. We then performed pore-scale flow simulations using computational fluid dynamics methods to determine the flow patterns in these aggregate-of-aggregates structures and computed the partitioning of the flow through intra- and inter-aggregate pores as a function of the spacing between the aggregates. The results of these numerical experiments demonstrate that soluble nutrients are largely transported via flows through inter-aggregate pores. Although this result is consistent with intuition, we have also been able to quantify the relative flow capacity of the two domains under various conditions. For example, in our simulations, the flow capacity through the aggregates (intra-aggregate flow) was less than 2% of the total flow when the spacing between the aggregates was larger than 18 micron. Inter-aggregate pores continued to be the dominant flow pathways even at much smaller spacing; intra-aggregate flow was less than 10% of the total flow when the inter- and intra-aggregate pore sizes were comparable. Such studies are making it possible to identify which model upscaling assumptions are realistic and what computational methods are required for detailed numerical investigation of microbial carbon cycling dynamics in soil systems.« less

Detection of Sources of Harmful Radiation using Portable Sensors

DTIC Science & Technology

2016-05-01

Department Carnegie Mellon University Pittsburgh, PA Thesis Committee Artur Dubrawski, Chair Srinivas Narasimhan Submitted in partial fulfillment of the...Aggregation of Evidence for Detection and Characterization of Patterns in Multiple Noisy Observations”. PhD thesis. Carnegie Mellon, 2015. [15] Prateek Tandon
Mechanical Properties of Portland Cement Concrete With Recycled Asphalt Pavement as Partial Replacement for Coarse Aggregate

DOT National Transportation Integrated Search

2016-06-01

Finding constructive uses for construction waste byproducts contributes to green engineering principles. One such plentiful material is recycled asphalt pavement (RAP). This report looks at the mechanical viability of including RAP in a high strength...
DOE Office of Scientific and Technical Information (OSTI.GOV)

Prof. P. Somasundaran

The aim of the project is to develop and evaluate efficient novel surfactant mixtures for enhanced oil recovery. Preliminary ultra-filtration tests suggest that two kinds of micelles may exist in binary surfactant mixtures at different concentrations. Due to the important role played in interfacial processes by micelles as determined by their structures, focus of the current work is on the delineation of the relationship between such aggregate structures and chemical compositions of the surfactants. A novel analytical centrifuge application is explored to generate information on structures of different surfactants aggregates. In this report, optical systems, typical output of the analyticalmore » ultracentrifuge results and four basic experiments are discussed. Initial sedimentation velocity investigations were conducted using nonyl phenol ethoxylated decyl ether (NP-10) to choose the best analytical protocol, calculate the partial specific volume and obtain information on sedimentation coefficient, aggregation mass of micelles. The partial specific volume was calculated to be 0.920. Four softwares: Optima{trademark} XL-A/XL-I data analysis software, DCDT+, Svedberg and SEDFIT, were compared for the analysis of sedimentation velocity experimental data. The sedimentation coefficient and aggregation number of NP-10 micelles obtained using the first three softwares at 25 C are 209, 127, and 111, respectively. The last one is closest to the result from Light Scattering. The reason for the differences in numbers obtained using the three softwares is discussed. Based on these tests, Svedberg and SEDFIT analysis are chosen for further studies. This approach using the analytical ultracentrifugation offers an unprecedented opportunity now to obtain important information on mixed micelles and their role in interfacial processes.« less
The Regulatory Subunit of PKA-I Remains Partially Structured and Undergoes β-Aggregation upon Thermal Denaturation

PubMed Central

Dao, Khanh K.; Pey, Angel L.; Gjerde, Anja Underhaug; Teigen, Knut; Byeon, In-Ja L.; Døskeland, Stein O.; Gronenborn, Angela M.; Martinez, Aurora

2011-01-01

Background The regulatory subunit (R) of cAMP-dependent protein kinase (PKA) is a modular flexible protein that responds with large conformational changes to the binding of the effector cAMP. Considering its highly dynamic nature, the protein is rather stable. We studied the thermal denaturation of full-length RIα and a truncated RIα(92-381) that contains the tandem cyclic nucleotide binding (CNB) domains A and B. Methodology/Principal Findings As revealed by circular dichroism (CD) and differential scanning calorimetry, both RIα proteins contain significant residual structure in the heat-denatured state. As evidenced by CD, the predominantly α-helical spectrum at 25°C with double negative peaks at 209 and 222 nm changes to a spectrum with a single negative peak at 212–216 nm, characteristic of β-structure. A similar α→β transition occurs at higher temperature in the presence of cAMP. Thioflavin T fluorescence and atomic force microscopy studies support the notion that the structural transition is associated with cross-β-intermolecular aggregation and formation of non-fibrillar oligomers. Conclusions/Significance Thermal denaturation of RIα leads to partial loss of native packing with exposure of aggregation-prone motifs, such as the B' helices in the phosphate-binding cassettes of both CNB domains. The topology of the β-sandwiches in these domains favors inter-molecular β-aggregation, which is suppressed in the ligand-bound states of RIα under physiological conditions. Moreover, our results reveal that the CNB domains persist as structural cores through heat-denaturation. PMID:21394209
Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions.

PubMed

Choi, Jun-Ho; Lee, Hochan; Choi, Hyung Ran; Cho, Minhaeng

2018-04-20

In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute molecules and the structure and dynamics of water.
Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions

NASA Astrophysics Data System (ADS)

Choi, Jun-Ho; Lee, Hochan; Choi, Hyung Ran; Cho, Minhaeng

2018-04-01

In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute molecules and the structure and dynamics of water.
Dynamics and mechanisms of asbestos-fiber aggregate growth in water

NASA Astrophysics Data System (ADS)

Wu, L.; Ortiz, C. P.; Jerolmack, D. J.

2015-12-01

Most colloidal particles including asbestos fibers form aggregates in water, when solution chemistry provides favorable conditions. To date, the growth of colloidal aggregates has been observed in many model systems under optical and scanning electron microscopy; however, all of these studies have used near-spherical particles. The highly elongated nature of asbestos fibers may cause anomalous aggregate growth and morphology, but this has never been examined. Although the exposure pathway of concern for asbestos is through the air, asbestos particles typically reside in soil that is at least partially saturated, and aggregates formed in the aqueous phase may influence the mobility of particles in the environment. Here we study solution-phase aggregation kinetics of asbestos fibers using a liquid-cell by in situ microscopy, over micron to centimeter length scales and from a tenth of a second to hours. We employ an elliptical particle tracking technique to determine particle trajectories and to quantify diffusivity. Experiments reveal that diffusing fibers join by cross linking, but that such linking is sometimes reversible. The resulting aggregates are very sparse and non-compact, with a fractal dimension that is lower than any previously reported value. Their morphology, growth rate and particle size distribution exhibit non-classical behavior that deviates significantly from observations of aggregates composed of near-spherical particles. We also perform experiments using synthetic colloidal particles, and compare these to asbestos in order to separate the controls of particle shape vs. material properties. This direct method for quantitatively observing aggregate growth is a first step toward predicting asbestos fiber aggregate size distributions in the environment. Moreover, many emerging environmental contaminants - such as carbon nanotubes - are elongated colloids, and our work suggests that theories for aggregate growth may need to be modified in order to model these particles.
Platelet aggregation caused by Carybdea rastonii toxins (CrTX-I, II and III) obtained from a jellyfish, Carybdea rastonii.

PubMed

Azuma, H; Sekizaki, S; Satoh, A; Nakajima, T

1986-05-01

The pharmacological mechanisms of platelet aggregation induced by highly toxic proteins (CrTX-I, CrTX-II, and CrTX-III) obtained from tentacles of a jellyfish, Carybdea rastonii, were investigated. When the partially purified toxin (pCrTX) and CrTXs were added to the citrated platelet-rich plasma (PRP), aggregation was produced in a concentration-dependent manner. The activity of CrTXs was approximately 100 times more potent than pCrTX. The CrTXs-induced aggregation was little affected by indomethacin and quinacrine at concentrations sufficient to inhibit arachidonic acid- and collagen-induced aggregation. The CrTXs-induced aggregation in washed platelets was significantly augmented in the presence of Ca2+. The pretreatment with verapamil failed to modify this augmentation of aggregation. The concentration of cytoplasmic-free calcium ([Ca2+]i) of platelets was increased by CrTXs at the same concentrations that produced aggregation. This effect of CrTXs was again little affected by verapamil. CrTXs at the same concentrations as those that produced aggregation and increased [Ca2+]i caused depolarization of platelets, which was unchanged after pretreatment with sodium or potassium transport inhibitors. CrTX-I significantly increased the 22Na flux into platelets and this effect of CrTX-I was unaffected by tetrodotoxin. The CrTX-I-induced aggregation, depolarization, and increase in [Ca2+]i were all significantly attenuated in the low Na+ medium. These results suggest that CrTXs cause a massive depolarization by increasing cation permeability and this generalized depolarization permits an inward movement of Ca2+ down its electrochemical gradient which, in turn, triggers platelet aggregation.
Mechanistic modeling of microbial interactions at pore to profile scale resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-05-01

The sensitivity of polar regions to raising global temperatures is reflected in rapidly changing hydrological processes associated with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and stimulation of other soil-borne greenhouse gas emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and other environmental factors. Soil structural elements such as aggregates and layering affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hot spots). We developed a mechanistic individual-based model to quantify microbial activity dynamics in soil pore networks considering transport processes and enzymatic activity associated with methane production in soil. The model was upscaled from single aggregates to the soil profile where freezing/thawing provides macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged profile) for resolving methane production and oxidation rates. Methane transport pathways by diffusion and ebullition of bubbles vary with hydration dynamics. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability and enzyme activity) on long-term methane emissions and carbon decomposition rates in the rapidly changing polar regions.
Opal photonic crystals infiltrated with chalcogenide glasses

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

Astratov, V. N.; Adawi, A. M.; Skolnick, M. S.

Composite opal structures for nonlinear applications are obtained by infiltration with chalcogenide glasses As{sub 2}S{sub 3} and AsSe by precipitation from solution. Analysis of spatially resolved optical spectra reveals that the glass aggregates into submillimeter areas inside the opal. These areas exhibit large shifts in the optical stop bands by up to 80 nm, and by comparison with modelling are shown to have uniform glass filling factors of opal pores up to 40%. Characterization of the domain structure of the opals prior to infiltration by large area angle-resolved spectroscopy is an important step in the analysis of the properties ofmore » the infiltrated regions. {copyright} 2001 American Institute of Physics.« less
nDEP-driven cell patterning and bottom-up construction of cell aggregates using a new bioelectronic chip.

PubMed

Menad, S; Franqueville, L; Haddour, N; Buret, F; Frenea-Robin, M

2015-04-01

Creating cell aggregates of controlled size and shape and patterning cells on substrates using a bottom-up approach constitutes important challenges for tissue-engineering applications and studies of cell-cell interactions. In this paper, we report nDEP (negative dielectrophoresis) driven assembly of cells as compact aggregates or onto defined areas using a new bioelectronic chip. This chip is composed of a quadripolar electrode array obtained using coplanar electrodes partially covered with a thin, micropatterned PDMS membrane. This thin PDMS layer was coated with poly-L-lysine and played the role of adhesive substrate for cell patterning. For the formation of detachable cell aggregates, the PDMS was not pretreated and cells were simply immobilized into assemblies maintained by cell-cell adhesion after the electric field removal. Cell viability after exposition to DEP buffer was also assessed, as well as cell spreading activity following DEP-driven assembly. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
First Global Analysis of Saturation Artifacts in the VIIRS Infrared Channels and the Effects of Detector Aggregation

NASA Astrophysics Data System (ADS)

Wang, J.; Polivka, T. N.; Hyer, E. J.; Peterson, D. A.

2014-12-01

Unlike previous space-borne Earth-observing sensors, the Visible Infrared Imaging Radiometer Suite (VIIRS) employs aggregation to reduce downlink bandwidth requirements and preserve spatial resolution across the swath. To examine the potentially deleterious impacts of aggregation when encountering detector saturation, nearly four months of NOAA's Nightfire product were analyzed, which contains a subset of the hottest observed nighttime pixels. An empirical method for identifying saturation was devised. The 3.69 µm band (M12) was the most frequently-saturating band with 0.15% of the Nightfire pixels at or near the ~359 K hard saturation limit, with possible saturation also occurring in M14, M15, and M16. Artifacts consistent with detector saturation were seen with M12 temperatures as low as 330 K in the scene center. This partial saturation and aggregation influence must be considered when using VIIRS radiances for quantitative characterization of hot emission sources such as fires and gas flaring.
Computational design and biophysical characterization of aggregation-resistant point mutations for γD crystallin illustrate a balance of conformational stability and intrinsic aggregation propensity.

PubMed

Sahin, Erinc; Jordan, Jacob L; Spatara, Michelle L; Naranjo, Andrea; Costanzo, Joseph A; Weiss, William F; Robinson, Anne Skaja; Fernandez, Erik J; Roberts, Christopher J

2011-02-08

γD crystallin is a natively monomeric eye-lens protein that is associated with hereditary juvenile cataract formation. It is an attractive model system as a multidomain Greek-key protein that aggregates through partially folded intermediates. Point mutations M69Q and S130P were used to test (1) whether the protein-design algorithm RosettaDesign would successfully predict mutants that are resistant to aggregation when combined with informatic sequence-based predictors of peptide aggregation propensity and (2) how the mutations affected relative unfolding free energies (ΔΔG(un)) and intrinsic aggregation propensity (IAP). M69Q was predicted to have ΔΔG(un) ≫ 0, without significantly affecting IAP. S130P was predicted to have ΔΔG(un) ∼ 0 but with reduced IAP. The stability, conformation, and aggregation kinetics in acidic solution were experimentally characterized and compared for the variants and wild-type (WT) protein using circular dichroism and intrinsic fluorescence spectroscopy, calorimetric and chemical unfolding, thioflavin-T binding, chromatography, static laser light scattering, and kinetic modeling. Monomer secondary and tertiary structures of both variants were indistinguishable from WT, while ΔΔG(un) > 0 for M69Q and ΔΔG(un) < 0 for S130P. Surprisingly, despite being the least conformationally stable, S130P was the most resistant to aggregation, indicating a significant decrease of its IAP compared to WT and M69Q.
Effects of aggregate morphology and size on laser-induced incandescence and scattering from black carbon (mature soot)

DOE PAGES

Bambha, Ray P.; Michelsen, Hope A.

2015-07-03

We have used a Single-Particle Soot Photometer (SP2) to measure time-resolved laser-induced incandescence (LII) and laser scatter from combustion-generated mature soot with a fractal dimension of 1.88 extracted from a burner. We have also made measurements on restructured mature-soot particles with a fractal dimension of 2.3–2.4. We reproduced the LII and laser-scatter temporal profiles with an energy- and mass-balance model, which accounted for heating of particles passed through a CW-laser beam over laser–particle interaction times of ~10 μs. Furthermore, the results demonstrate a strong influence of aggregate size and morphology on LII and scattering signals. Conductive cooling competes with absorptivemore » heating on these time scales; the effects are reduced with increasing aggregate size and fractal dimension. These effects can lead to a significant delay in the onset of the LII signal and may explain an apparent low bias in the SP2 measurements for small particle sizes, particularly for fresh, mature soot. The results also reveal significant perturbations to the measured scattering signal from LII interference and suggest rapid expansion of the aggregates during sublimation.« less
Sub-nanometer surface chemistry and orbital hybridization in lanthanum-doped ceria nano-catalysts revealed by 3D electron microscopy.

PubMed

Collins, Sean M; Fernandez-Garcia, Susana; Calvino, José J; Midgley, Paul A

2017-07-14

Surface chemical composition, electronic structure, and bonding characteristics determine catalytic activity but are not resolved for individual catalyst particles by conventional spectroscopy. In particular, the nano-scale three-dimensional distribution of aliovalent lanthanide dopants in ceria catalysts and their effect on the surface electronic structure remains unclear. Here, we reveal the surface segregation of dopant cations and oxygen vacancies and observe bonding changes in lanthanum-doped ceria catalyst particle aggregates with sub-nanometer precision using a new model-based spectroscopic tomography approach. These findings refine our understanding of the spatially varying electronic structure and bonding in ceria-based nanoparticle aggregates with aliovalent cation concentrations and identify new strategies for advancing high efficiency doped ceria nano-catalysts.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Gupta, Preeti; Deep, Shashank, E-mail: sdeep@chemistry.iitd.ac.in

Highlights: • HCAII forms amyloid-like aggregates at moderate concentration of trifluoroethanol. • Protein adopts a state between β-sheet and α-helix at moderate % of TFE. • Hydrophobic surface(s) of partially structured conformation forms amyloid. • High % of TFE induces stable α-helical state preventing aggregation. - Abstract: In the present work, we examined the correlation between 2,2,2-trifluoroethanol (TFE)-induced conformational transitions of human carbonic anhydrase II (HCAII) and its aggregation propensity. Circular dichroism data indicates that protein undergoes a transition from β-sheet to α-helix on addition of TFE. The protein was found to aggregate maximally at moderate concentration of TFE atmore » which it exists somewhere between β-sheet and α-helix, probably in extended non-native β-sheet conformation. Thioflavin-T (ThT) and Congo-Red (CR) assays along with fluorescence microscopy and transmission electron microscopy (TEM) data suggest that the protein aggregates induced by TFE possess amyloid-like features. Anilino-8-naphthalene sulfonate (ANS) binding studies reveal that the exposure of hydrophobic surface(s) was maximum in intermediate conformation. Our study suggests that the exposed hydrophobic surface and/or the disruption of the structural features protecting a β-sheet protein might be the major reason(s) for the high aggregation propensity of non-native intermediate conformation of HCAII.« less
Protein aggregation induced during glass bead lysis of yeast

PubMed Central

Papanayotou, Irene; Sun, Beimeng; Roth, Amy F.; Davis, Nicholas G.

2013-01-01

Yeast cell lysates produced by mechanical glass bead disruption are widely used in a variety of applications, including for the analysis of native function, e.g. protein–protein interaction, enzyme assays and membrane fractionations. Below, we report a striking case of protein denaturation and aggregation that is induced by this lysis protocol. Most of this analysis focuses on the type 1 casein kinase Yck2, which normally tethers to the plasma membrane through C-terminal palmitoylation. Surprisingly, when cells are subjected to glass bead disruption, non-palmitoylated, cytosolic forms of the kinase denature and aggregate, while membrane-associated forms, whether attached through their native palmitoyl tethers or through a variety of artificial membrane-tethering sequences, are wholly protected from denaturation and aggregation. A wider look at the yeast proteome finds that, while the majority of proteins resist glass bead-induced aggregation, a significant subset does, in fact, succumb to such denaturation. Thus, yeast researchers should be aware of this potential artifact when embarking on biochemical analyses that employ glass bead lysates to look at native protein function. Finally, we demonstrate an experimental utility for glass bead-induced aggregation, using its fine discrimination of membrane-associated from non-associated Yck2 forms to discern fractional palmitoylation states of Yck2 mutants that are partially defective for palmitoylation. PMID:20641011
DISTRIBUTIONS, ASSOCIATIONS, AND PARTIAL AGGREGATE EXPOSURE OF PESTICIDES AND POLYNUCLEAR AROMATIC HYDROCARBONS IN THE MINNESOTA CHILDREN'S PESTICIDE EXPOSURE STUDY (MNCPES)

EPA Science Inventory

The Minnesota Children's Pesticide Exposure Study (MNCPES) provides exposure, environmental, and biologic data relating to multi-pathway exposures of children for four primary pesticides (chlorpyrifos, malathion, diazinon, and atrazine), 14 secondary pesticides, and 13 polynucl...
Resveratrol Interferes with an Early Step in the Fibrillization Pathway of Human Lysozyme and Modulates it towards Less-Toxic, Off-Pathway Aggregates.

PubMed

Kamal Zaidi, Fatima; Bhat, Rajiv

2018-01-18

The effect of resveratrol, a polyphenol in red wine, on the amyloid fibril formation of human lysozyme (HuL) was investigated, towards elucidating the mechanism of resveratrol action and probing its role as a possible modulator of lysozyme aggregation and toxicity. By using a number of biophysical tools, resveratrol was observed to alter the fibrillization kinetics of HuL and inhibit its fibrillization by binding with weak to moderate affinity to the conformations populated at the early stages of the pathway with concomitant stabilization of these initial conformations. The marginal decrease in the lifetime of HuL in the presence of resveratrol by time-resolved fluorescence measurements indicated the involvement of a static quenching mechanism in the interaction between HuL and resveratrol. Docking studies predicted the binding of resveratrol to aggregation-prone regions in HuL, and structure and activity analyses demonstrated the retention of much of the α-helical structure and activity of HuL in the presence of resveratrol. Resveratrol modulated the fibrillization pathway towards less-hydrophobic, less-toxic, off-pathway aggregates. These results demonstrate that binding of resveratrol to HuL could protect against the formation of pathogenic, cytotoxic aggregates formed in amyloidogenic disorders, such as systemic amyloidosis; thus suggesting its potential as a plausible therapeutic agent against lysozyme amyloidosis. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Structural stability of E. coli transketolase to temperature and pH denaturation.

PubMed

Jahromi, Raha R F; Morris, Phattaraporn; Martinez-Torres, Ruben J; Dalby, Paul A

2011-09-10

We have previously shown that the denaturation of TK with urea follows a non-aggregating though irreversible denaturation pathway in which the cofactor binding appears to become altered but without dissociating, then followed at higher urea by partial denaturation of the homodimer prior to any further unfolding or dissociation of the two monomers. Urea is not typically present during biocatalysis, whereas access to TK enzymes that retain activity at increased temperature and extreme pH would be useful for operation under conditions that increase substrate and product stability or solubility. To provide further insight into the underlying causes of its deactivation in process conditions, we have characterised the effects of temperature and pH on the structure, stability, aggregation and activity of Escherichia coli transketolase. The activity of TK was initially found to progressively improve after pre-incubation at increasing temperatures. Loss of activity at higher temperature and low pH resulted primarily from protein denaturation and subsequent irreversible aggregation. By contrast, high pH resulted in the formation of a native-like state that was only partially inactive. The apo-TK enzyme structure content also increased at pH 9 to converge on that of the holo-TK. While cofactor dissociation was previously proposed for high pH deactivation, the observed structural changes in apo-TK but not holo-TK indicate a more complex mechanism. Copyright © 2011 Elsevier B.V. All rights reserved.

Environmental impact of the use of contaminated sediments as partial replacement of the aggregate used in road construction.

PubMed

Pinto, Patricio X; Al-Abed, Souhail R; Barth, Edwin; Loftspring, Catherine; Voit, James; Clark, Patrick; Ioannides, Anastasios M

2011-05-15

The Indiana Harbor Canal (IHC) is a waterway extensively polluted with heavy metals and petroleum. Since there are limited disposal options for the petroleum-contaminated sediments (PCSs) of the canal, the environmental impact of IHC dewatered sediment when used as partial replacement of the aggregate used in hot mix asphalt (HMA) for road construction was investigated. In order to assess the long term migration of the target contaminants into the environment, the TCLP, SPLP, and a Constant pH leaching test were applied to a HMA mixture containing 10% of dewatered PCS, a conventional HMA, and the dewatered PCS. None of the heavy metals significantly leached from any of the tested materials in any of the conducted tests. Despite the presence of PAHs in the PCS, these were not found in any of the leachate samples. Finally, among the measured VOCs, only acetone and 2-butanone were found to leach from the asphalt mixtures and the sediment in the Constant pH experiment. It was concluded that it may be environmentally safe to replace the aggregates of the HMA used in road construction in the studied proportions with dewatered PCS based upon leaching levels as compared to TCLP regulated levels. This could be a viable, beneficial use option for the PCS, and therefore, for the canal remediation. Published by Elsevier B.V.
Recovery of MSWI and soil washing residues as concrete aggregates.

PubMed

Sorlini, Sabrina; Abbà, Alessandro; Collivignarelli, Carlo

2011-02-01

The aim of the present work was to study if municipal solid waste incinerator (MSWI) residues and aggregates derived from contaminated soil washing could be used as alternative aggregates for concrete production. Initially, chemical, physical and geometric characteristics (according to UNI EN 12620) of municipal solid waste incineration bottom ashes and some contaminated soils were evaluated; moreover, the pollutants release was evaluated by means of leaching tests. The results showed that the reuse of pre-treated MSWI bottom ash and washed soil is possible, either from technical or environmental point of view, while it is not possible for the raw wastes. Then, the natural aggregate was partially and totally replaced with these recycled aggregates for the production of concrete mixtures that were characterized by conventional mechanical and leaching tests. Good results were obtained using the same dosage of a high resistance cement (42.5R calcareous Portland cement instead of 32.5R); the concrete mixture containing 400 kg/m(3) of washed bottom ash and high resistance cement was classified as structural concrete (C25/30 class). Regarding the pollutants leaching, all concrete mixtures respected the limit values according to the Italian regulation. Copyright © 2010 Elsevier Ltd. All rights reserved.
Disaggregation of adenylate cyclase during polyacrylamide-gel electrophoresis in mixtures of ionic and non-ionic detergents

PubMed Central

Newby, Andrew C.; Chrambach, Andreas

1979-01-01

1. Adenylate cyclase [ATP pyrophosphate-lyase (cyclizing), EC 4.6.1.1] solubilized from the rat liver plasma membrane with 1% Lubrol PX and partially purified by gel filtration in buffer containing 0.01% Lubrol PX was physically characterized by polyacrylamide-gel electrophoresis. 2. The molecular radius determined for the partially purified enzyme was 4.9nm, compared with the value of 3.9nm obtained for the enzyme before gel filtration. 3. This difference, representing an approximate doubling of the molecular volume of the enzyme, implied that aggregation with itself or other proteins had occurred during partial purification. 4. Aggregation was not reversed by electrophoresis in the presence of high Lubrol concentrations. 5. Substitution of deoxycholate or N-dodecylsarcosinate for Lubrol PX either for solubilization or during electrophoresis led to poorer resolution of membrane proteins at concentrations giving greater than 70% loss of enzyme activity. 6. Partially purified adenylate cyclase was electrophoresed in the presence of mixed micelles of Lubrol PX and deoxycholate or Lubrol PX and N-dodecylsarcosinate. Different mixtures were examined simultaneously in a suitable apparatus. 7. Electrophoresis in the presence of 0.1% Lubrol plus 0.03% deoxycholate decreased the molecular radius of the cyclase to 4.0nm, with greater than 90% recovery of enzymic activity. The net charge of the enzyme was also increased, indicating ionic detergent binding. 8. With 0.1% Lubrol plus 0.03% N-dodecylsarcosinate the molecular radius was 4.3nm, recovery approx. 50% and net charge similar to that seen in Lubrol plus deoxycholate. 9. The resolution of cyclase from bulk protein, on an analytical scale, was improved in the presence of detergent mixtures, as compared with resolution in Lubrol alone. 10. The results demonstrate the usefulness of polyacrylamide-gel electrophoresis to detect and overcome aggregation problems with membrane proteins and suggest that detergent mixtures in specific ratios may be useful in the purification of adenylate cyclase and other intrinsic membrane proteins. ImagesFig. 3. PMID:435255
The Spatial Distribution of Resolved Young Stars in Blue Compact Dwarf Galaxies

NASA Astrophysics Data System (ADS)

Murphy, K.; Crone, M. M.

2002-12-01

We present the first results from a survey of the distribution of resolved young stars in Blue Compact Dwarf Galaxies. In order to identify the dominant physical processes driving star formation in these puzzling galaxies, we use a multi-scale cluster-finding algorithm to quantify the characteristic scales and properties of star-forming regions, from sizes smaller than 10 pc up to the size of each entire galaxy. This project was partially funded by the Lubin Chair at Skidmore College.
Experimental and Theoretical Aspects of Excited State Electron Transfer and Related Phenomena: Conference Held in Honour of Zbigniew R. Grabowski in Pultusk, Poland on September 27-October 2, 1992

DTIC Science & Technology

1992-10-01

DBMBF2 ) undergoes photoreaction with olefins through a partial electron transfer that leads to cycloaddition or sensitized Diels - Alder reactions. We...8217 Fluorescence. 10:00 J.M. WARMAN: Photon-induced Intramolecular Charge Sepaiation Studied byTime-Resolved Microwave Conductivity. 10:30 Coffee 11:)) W...26 Photon-Induced Intramolecular Charge Separation Studied by Time-Resolved Microwave Conductivity John M. Warman IRI, Delft University of Technology
Robustness of the Process of Nucleoid Exclusion of Protein Aggregates in Escherichia coli

PubMed Central

Neeli-Venkata, Ramakanth; Martikainen, Antti; Gupta, Abhishekh; Gonçalves, Nadia; Fonseca, Jose

2016-01-01

ABSTRACT Escherichia coli segregates protein aggregates to the poles by nucleoid exclusion. Combined with cell divisions, this generates heterogeneous aggregate distributions in subsequent cell generations. We studied the robustness of this process with differing medium richness and antibiotics stress, which affect nucleoid size, using multimodal, time-lapse microscopy of live cells expressing both a fluorescently tagged chaperone (IbpA), which identifies in vivo the location of aggregates, and HupA-mCherry, a fluorescent variant of a nucleoid-associated protein. We find that the relative sizes of the nucleoid's major and minor axes change widely, in a positively correlated fashion, with medium richness and antibiotic stress. The aggregate's distribution along the major cell axis also changes between conditions and in agreement with the nucleoid exclusion phenomenon. Consequently, the fraction of aggregates at the midcell region prior to cell division differs between conditions, which will affect the degree of asymmetries in the partitioning of aggregates between cells of future generations. Finally, from the location of the peak of anisotropy in the aggregate displacement distribution, the nucleoid relative size, and the spatiotemporal aggregate distribution, we find that the exclusion of detectable aggregates from midcell is most pronounced in cells with mid-sized nucleoids, which are most common under optimal conditions. We conclude that the aggregate management mechanisms of E. coli are significantly robust but are not immune to stresses due to the tangible effect that these have on nucleoid size. IMPORTANCE Escherichia coli segregates protein aggregates to the poles by nucleoid exclusion. From live single-cell microscopy studies of the robustness of this process to various stresses known to affect nucleoid size, we find that nucleoid size and aggregate preferential locations change concordantly between conditions. Also, the degree of influence of the nucleoid on aggregate positioning differs between conditions, causing aggregate numbers at midcell to differ in cell division events, which will affect the degree of asymmetries in the partitioning of aggregates between cells of future generations. Finally, we find that aggregate segregation to the cell poles is most pronounced in cells with mid-sized nucleoids. We conclude that the energy-free process of the midcell exclusion of aggregates partially loses effectiveness under stressful conditions. PMID:26728194
Next Step Toward Widespread Residential Deep Energy Retrofits

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

McIlvaine, J.; Saunders, S.; Bordelon, E.

The complexity of deep energy retrofits warrants additional training to successfully manage multiple improvements that will change whole house air, heat, and moisture flow dynamics. The home performance contracting industry has responded to these challenges by aggregating skilled labor for assessment of and implementation under one umbrella. Two emerging business models are profiled that seek to resolve many of the challenges, weaknesses, opportunities, and threats described for the conventional business models.
Approaches to Aggregation and Decision Making-A Health Economics Approach: An ISPOR Special Task Force Report [5].

PubMed

Phelps, Charles E; Lakdawalla, Darius N; Basu, Anirban; Drummond, Michael F; Towse, Adrian; Danzon, Patricia M

2018-02-01

The fifth section of our Special Task Force report identifies and discusses two aggregation issues: 1) aggregation of cost and benefit information across individuals to a population level for benefit plan decision making and 2) combining multiple elements of value into a single value metric for individuals. First, we argue that additional elements could be included in measures of value, but such elements have not generally been included in measures of quality-adjusted life-years. For example, we describe a recently developed extended cost-effectiveness analysis (ECEA) that provides a good example of how to use a broader concept of utility. ECEA adds two features-measures of financial risk protection and income distributional consequences. We then discuss a further option for expanding this approach-augmented CEA, which can introduce many value measures. Neither of these approaches, however, provide a comprehensive measure of value. To resolve this issue, we review a technique called multicriteria decision analysis that can provide a comprehensive measure of value. We then discuss budget-setting and prioritization using multicriteria decision analysis, issues not yet fully resolved. Next, we discuss deliberative processes, which represent another important approach for population- or plan-level decisions used by many health technology assessment bodies. These use quantitative information on CEA and other elements, but the group decisions are reached by a deliberative voting process. Finally, we briefly discuss the use of stated preference methods for developing "hedonic" value frameworks, and conclude with some recommendations in this area. Copyright © 2018 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.
Mechanistic modeling of thermo-hydrological processes and microbial interactions at pore to profile scales resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-04-01

The sensitivity of the Earth's polar regions to raising global temperatures is reflected in rapidly changing hydrological processes with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and the stimulation of other soil-borne GHG emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and a host of other environmental factors. Soil structural elements such as aggregates and layering and hydration status affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hotspots or hot-layers). We developed a mechanistic individual based model to quantify microbial activity dynamics within soil pore networks considering, hydration, temperature, transport processes and enzymatic activity associated with methane production in soil. The model was the upscaled from single aggregates (or hotspots) to quantifying emissions from soil profiles in which freezing/thawing processes provide macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged parts of the profile) for resolving methane production and oxidation rates. Methane transport pathways through soil by diffusion and ebullition of bubbles vary with hydration dynamics and affect emission patterns. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability, enzyme activity, PH) on long term methane emissions and carbon decomposition rates in the rapidly changing polar regions.
Hugoniot measurements of double-shocked precompressed dense xenon plasmas

NASA Astrophysics Data System (ADS)

Zheng, J.; Chen, Q. F.; Gu, Y. J.; Chen, Z. Y.

2012-12-01

The current partially ionized plasmas models for xenon show substantial differences since the description of pressure and thermal ionization region becomes a formidable task, prompting the need for an improved understanding of dense xenon plasmas behavior at above 100 GPa. We performed double-shock compression experiments on dense xenon to determine accurately the Hugoniot up to 172 GPa using a time-resolved optical radiation method. The planar strong shock wave was produced using a flyer plate impactor accelerated up to ˜6 km/s with a two-stage light-gas gun. The time-resolved optical radiation histories were acquired by using a multiwavelength channel optical transience radiance pyrometer. Shock velocity was measured and mass velocity was determined by the impedance-matching methods. The experimental equation of state of dense xenon plasmas are compared with the self-consistent fluid variational calculations of dense xenon in the region of partial ionization over a wide range of pressures and temperatures.
Application of mid-infrared free-electron laser tuned to amide bands for dissociation of aggregate structure of protein.

PubMed

Kawasaki, Takayasu; Yaji, Toyonari; Ohta, Toshiaki; Tsukiyama, Koichi

2016-01-01

A mid-infrared free-electron laser (FEL) is a linearly polarized, high-peak powered pulse laser with tunable wavelength within the mid-infrared absorption region. It was recently found that pathogenic amyloid fibrils could be partially dissociated to the monomer form by the irradiation of the FEL targeting the amide I band (C=O stretching vibration), amide II band (N-H bending vibration) and amide III band (C-N stretching vibration). In this study, the irradiation effect of the FEL on keratin aggregate was tested as another model to demonstrate an applicability of the FEL for dissociation of protein aggregates. Synchrotron radiation infrared microscopy analysis showed that the α-helix content in the aggregate structure decreased to almost the same level as that in the monomer state after FEL irradiation tuned to 6.06 µm (amide I band). Both irradiations at 6.51 µm (amide II band) and 8.06 µm (amide III band) also decreased the content of the aggregate but to a lesser extent than for the irradiation at the amide I band. On the contrary, the irradiation tuned to 5.6 µm (non-absorbance region) changed little the secondary structure of the aggregate. Scanning-electron microscopy observation at the submicrometer order showed that the angular solid of the aggregate was converted to non-ordered fragments by the irradiation at each amide band, while the aggregate was hardly deformed by the irradiation at 5.6 µm. These results demonstrate that the amide-specific irradiation by the FEL was effective for dissociation of the protein aggregate to the monomer form.
Role of radiative-convective feedbacks in tropical cyclogenesis in rotating radiative-convective equilibrium simulations

NASA Astrophysics Data System (ADS)

Wing, A. A.; Camargo, S. J.; Sobel, A. H.

2015-12-01

"Self-aggregation" is a mode of convective organization found in idealized numerical simulations, in which there is a spontaneous transition from randomly distributed to organized convection despite homogeneous boundary conditions. Self-aggregation has primarily been studied in a non-rotating framework, but it has been hypothesized to be important to tropical cyclogenesis. In numerical simulations of tropical cyclones, a broad vortex or saturated column is often used to initialize the circulation. Here, we instead allow a circulation to develop spontaneously from a homogeneous environment in 3-d cloud-resolving simulations of radiative-convective equilibrium in a rotating framework, with interactive radiation and surface fluxes and fixed sea surface temperature. The goals of this study are two-fold: to study tropical cyclogenesis in an unperturbed environment free from the influence of a prescribed initial vortex or external disturbances, and to compare cyclogenesis to non-rotating self-aggregation. We quantify the feedbacks leading to tropical cyclogenesis using a variance budget equation for the vertically integrated frozen moist static energy. In the initial development of a broad circulation, the feedback processes are similar to the initial phase of non-rotating aggregation. Sensitivity tests in which the degree of interactive radiation is modified are also performed to determine the extent to which the radiative feedbacks that are essential to non-rotating self-aggregation are important for tropical cyclogenesis. Finally, we examine the evolution of the rotational and divergent flow, to determine the point at which rotation becomes important and the cyclogenesis process begins to differ from non-rotating aggregation.
Partial Measurements and the Realization of Quantum-Mechanical Counterfactuals

NASA Astrophysics Data System (ADS)

Paraoanu, G. S.

2011-07-01

We propose partial measurements as a conceptual tool to understand how to operate with counterfactual claims in quantum physics. Indeed, unlike standard von Neumann measurements, partial measurements can be reversed probabilistically. We first analyze the consequences of this rather unusual feature for the principle of superposition, for the complementarity principle, and for the issue of hidden variables. Then we move on to exploring non-local contexts, by reformulating the EPR paradox, the quantum teleportation experiment, and the entanglement-swapping protocol for the situation in which one uses partial measurements followed by their stochastic reversal. This leads to a number of counter-intuitive results, which are shown to be resolved if we give up the idea of attributing reality to the wavefunction of a single quantum system.
Effects of clopidogrel therapy on whole blood platelet aggregation, the Plateletworks® assay and coagulation parameters in cats with asymptomatic hypertrophic cardiomyopathy: a pilot study.

PubMed

den Toom, M L; van Leeuwen, M W; Szatmári, V; Teske, E

2017-12-01

Although scientific evidence is limited, clopidogrel is frequently used as prophylaxis for arterial thromboembolism in cats with hypertrophic cardiomyopathy (HCM). Evaluating effects of clopidogrel therapy in asymptomatic cats with HCM on (1) conventional whole blood aggregation (WBA), (2) alternative platelet aggregation assessed with tubes of the Plateletworks® assay and (3) standard coagulation parameters. Prospective, randomized, double-blind, placebo-controlled pilot study. Fourteen asymptomatic HCM cats were randomly allocated to receive placebo (n = 5) or clopidogrel (18.75 mg/cat q24h, n = 9) as part of a larger study. Aggregation responses (to 20 µM adenosine diphosphate (ADP) and 10 µg/ml collagen) in WBA and the Plateletworks® assay and standard coagulation parameters were evaluated at baseline and after seven days of therapy. Clopidogrel therapy significantly reduced aggregation responses to ADP and collagen in the Plateletworks® agonists tubes (ADP and collagen: P < 0.001), but did not significantly reduce aggregation responses to ADP and collagen in the WBA technique (ADP: P = 0.07, collagen: P = 0.30). Clopidogrel therapy did not show a significant effect on prothrombin time, activated partial thromboplastin time, antithrombin, D-dimers and fibrinogen concentrations. Clopidogrel therapy at a dose of 18.75 mg/cat q24h for seven days causes a significant decrease in in vitro platelet aggregation evaluated with the Plateletworks® assay, without affecting standard coagulation parameters in cats with asymptomatic HCM.
Impact of asymmetrical flow field-flow fractionation on protein aggregates stability.

PubMed

Bria, Carmen R M; Williams, S Kim Ratanathanawongs

2016-09-23

The impact of asymmetrical flow field-flow fractionation (AF4) on protein aggregate species is investigated with the aid of multiangle light scattering (MALS) and dynamic light scattering (DLS). The experimental parameters probed in this study include aggregate stability in different carrier liquids, shear stress (related to sample injection), sample concentration (during AF4 focusing), and sample dilution (during separation). Two anti-streptavidin (anti-SA) IgG1 samples composed of low and high molar mass (M) aggregates are subjected to different AF4 conditions. Aggregates suspended and separated in phosphate buffer are observed to dissociate almost entirely to monomer. However, aggregates in citric acid buffer are partially stable with dissociation to 25% and 5% monomer for the low and high M samples, respectively. These results demonstrate that different carrier liquids change the aggregate stability and low M aggregates can behave differently than their larger counterparts. Increasing the duration of the AF4 focusing step showed no significant changes in the percent monomer, percent aggregates, or the average Ms in either sample. Syringe-induced shear related to sample injection resulted in an increase in hydrodynamic diameter (dh) as measured by batch mode DLS. Finally, calculations showed that dilution during AF4 separation is significantly lower than in size exclusion chromatography with dilution occurring mainly at the AF4 channel outlet and not during the separation. This has important ramifications when analyzing aggregates that rapidly dissociate (<∼2s) upon dilution as the size calculated by AF4 theory may be more accurate than that measured by online DLS. Experimentally, the dhs determined by online DLS generally agreed with AF4 theory except for the more well retained larger aggregates for which DLS showed smaller sizes. These results highlight the importance of using AF4 retention theory to understand the impacts of dilution on analytes. Copyright © 2016 Elsevier B.V. All rights reserved.
Ion conduction in high ion content PEO-based ionomers

NASA Astrophysics Data System (ADS)

Caldwell, David, II; Maranas, Janna

Solid Polymer Electrolytes (SPEs) can enable the design of batteries that are safer and have higher capacity than batteries with traditional volatile organic electrolytes. The current limitation for SPEs is their low conductivity, resulting from a conduction mechanism strongly coupled to the dynamics of the polymer host matrix. Our previous work indicated the possibility of a conduction mechanism through the use of ion aggregates. In order to investigate this mechanism, we performed a series of molecular dynamics simulations of PEO-based ionomers at high ion content. Our results indicate that conduction through ion aggregates are partially decoupled from polymer dynamics and could enable the development of higher conductive SPEs.
The Antithrombotic and Fibrinolytic Effect of Natto in Hypercholesterolemia Rats

PubMed Central

Park, Kum-Ju; Kang, Jung Il; Kim, Tae-Seok; Yeo, Ik-Hyun

2012-01-01

Antithrombotic and fibrinolytic activity of natto was evaluated on platelet aggregation in vitro and in vivo. Natto showed inhibitory effects on platelet aggregation induced by adenosine 5′diphosphate (ADP) and collagen. Orally administered natto also showed fibrinolytic activity in hypercholesterolemia rats. Normal levels of natto, when administered for four weeks, shortened euglobulin clot lysis time (ECLT) and prolonged partial thromboplastin time (PATT) significantly compared to non-treated group. In addition, the natto treatment decreased total cholesterol in serum. These results showed that intake of normal levels of natto can elicit antithrombotic and fibrinolytic effects, suggesting its consumption may improve blood circulation. PMID:24471066
Erosion and the limits to planetesimal growth

NASA Astrophysics Data System (ADS)

Krijt, S.; Ormel, C. W.; Dominik, C.; Tielens, A. G. G. M.

2015-02-01

Context. The coagulation of microscopic dust into planetesimals is the first step towards the formation of planets. The composition, size, and shape of the growing aggregates determine the efficiency of this early growth. In particular, it has been proposed that fluffy ice aggregates can grow very efficiently in protoplanetary disks, suffering less from the bouncing and radial drift barriers. Aims: While the collision velocity between icy aggregates of similar size is thought to stay below the fragmentation threshold, they may nonetheless lose mass from collisions with much smaller projectiles. As a result, erosive collisions have the potential to terminate the growth of pre-planetesimal bodies. We investigate the effect of these erosive collisions on the ability of porous ice aggregates to cross the radial drift barrier. Methods: We develop a Monte Carlo code that calculates the evolution of the masses and porosities of growing aggregates, while resolving the entire mass distribution at all times. The aggregate's porosity is treated independently of its mass, and is determined by collisional compaction, gas compaction, and eventually self-gravity compaction. We include erosive collisions and study the effect of the erosion threshold velocity on aggregate growth. Results: For erosion threshold velocities of 20-40 m s-1, high-velocity collisions with small projectiles prevent the largest aggregates from growing when they start to drift. In these cases, our local simulations result in a steady-state distribution, with most of the dust mass in particles with Stokes numbers close to unity. Only for the highest erosion threshold considered (60 m s-1) do porous aggregates manage to cross the radial drift barrier in the inner 10 AU of MMSN-like disks. Conclusions: Erosive collisions are more effective in limiting the growth than fragmentary collisions between similar-size particles. Conceivably, erosion limits the growth before the radial drift barrier, although the robustness of this statement depends on uncertain material properties of icy aggregates. If erosion inhibits planetesimal formation through direct sticking, the sea of ~109 g, highly porous particles appears suitable for triggering streaming instability.
Measures of health sciences journal use: a comparison of vendor, link-resolver, and local citation statistics.

PubMed

De Groote, Sandra L; Blecic, Deborah D; Martin, Kristin

2013-04-01

Libraries require efficient and reliable methods to assess journal use. Vendors provide complete counts of articles retrieved from their platforms. However, if a journal is available on multiple platforms, several sets of statistics must be merged. Link-resolver reports merge data from all platforms into one report but only record partial use because users can access library subscriptions from other paths. Citation data are limited to publication use. Vendor, link-resolver, and local citation data were examined to determine correlation. Because link-resolver statistics are easy to obtain, the study library especially wanted to know if they correlate highly with the other measures. Vendor, link-resolver, and local citation statistics for the study institution were gathered for health sciences journals. Spearman rank-order correlation coefficients were calculated. There was a high positive correlation between all three data sets, with vendor data commonly showing the highest use. However, a small percentage of titles showed anomalous results. Link-resolver data correlate well with vendor and citation data, but due to anomalies, low link-resolver data would best be used to suggest titles for further evaluation using vendor data. Citation data may not be needed as it correlates highly with other measures.
On low temperature glide of dissociated <1 1 0> dislocations in strontium titanate

NASA Astrophysics Data System (ADS)

Ritterbex, Sebastian; Hirel, Pierre; Carrez, Philippe

2018-05-01

An elastic interaction model is presented to quantify low temperature plasticity of SrTiO3 via glide of dissociated <1 1 0>{1 1 0} screw dislocations. Because <1 1 0> dislocations are dissociated, their glide, controlled by the kink-pair mechanism at T < 1050 K, involves the formation of kink-pairs on partial dislocations, either simultaneously or sequentially. Our model yields results in good quantitative agreement with the observed non-monotonic mechanical behaviour of SrTiO3. This agreement allows to explain the experimental results in terms of a (progressive) change in <1 1 0>{1 1 0} glide mechanism, from simultaneous nucleation of two kink-pairs along both partials at low stress, towards nucleation of single kink-pairs on individual partials if resolved shear stress exceeds a critical value of 95 MPa. High resolved shear stress allows thus for the activation of extra nucleation mechanisms on dissociated dislocations impossible to occur under the sole action of thermal activation. We suggest that stress condition in conjunction with core dissociation is key to the origin of non-monotonic plastic behaviour of SrTiO3 at low temperatures.

Model Uncertainty Quantification Methods For Data Assimilation In Partially Observed Multi-Scale Systems

NASA Astrophysics Data System (ADS)

Pathiraja, S. D.; van Leeuwen, P. J.

2017-12-01

Model Uncertainty Quantification remains one of the central challenges of effective Data Assimilation (DA) in complex partially observed non-linear systems. Stochastic parameterization methods have been proposed in recent years as a means of capturing the uncertainty associated with unresolved sub-grid scale processes. Such approaches generally require some knowledge of the true sub-grid scale process or rely on full observations of the larger scale resolved process. We present a methodology for estimating the statistics of sub-grid scale processes using only partial observations of the resolved process. It finds model error realisations over a training period by minimizing their conditional variance, constrained by available observations. Special is that these realisations are binned conditioned on the previous model state during the minimization process, allowing for the recovery of complex error structures. The efficacy of the approach is demonstrated through numerical experiments on the multi-scale Lorenz 96' model. We consider different parameterizations of the model with both small and large time scale separations between slow and fast variables. Results are compared to two existing methods for accounting for model uncertainty in DA and shown to provide improved analyses and forecasts.
McSnow: A Monte-Carlo Particle Model for Riming and Aggregation of Ice Particles in a Multidimensional Microphysical Phase Space

NASA Astrophysics Data System (ADS)

Brdar, S.; Seifert, A.

2018-01-01

We present a novel Monte-Carlo ice microphysics model, McSnow, to simulate the evolution of ice particles due to deposition, aggregation, riming, and sedimentation. The model is an application and extension of the super-droplet method of Shima et al. (2009) to the more complex problem of rimed ice particles and aggregates. For each individual super-particle, the ice mass, rime mass, rime volume, and the number of monomers are predicted establishing a four-dimensional particle-size distribution. The sensitivity of the model to various assumptions is discussed based on box model and one-dimensional simulations. We show that the Monte-Carlo method provides a feasible approach to tackle this high-dimensional problem. The largest uncertainty seems to be related to the treatment of the riming processes. This calls for additional field and laboratory measurements of partially rimed snowflakes.
Modulation of the aggregation properties of sodium deoxycholate in presence of hydrophilic imidazolium based ionic liquid: water dynamics study to probe the structural alteration of the aggregates.

PubMed

Kundu, Niloy; Banik, Debasis; Roy, Arpita; Kuchlyan, Jagannath; Sarkar, Nilmoni

2015-10-14

In this article, we have investigated the effect of a hydrophilic ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]-BF4), on the aggregation properties of a biological surfactant, sodium deoxycholate (NaDC), in water. In solution, unlike conventional surfactants it shows stepwise aggregation and the effect of the conventional ionic liquid on the aggregation properties is rather interesting. We have observed concentration dependent dual role of the ionic liquid; at their low concentration, the aggregated structure of NaDC reorganizes itself into an elongated rod like structure. However, the aggregated network is disintegrated into small aggregates upon further addition of ionic liquid. TEM (Transmission Electron Microscopy), SEM (Scanning Electron Microscopy) and FLIM (Fluorescence Lifetime Imaging Microscopy) images also confirmed the structural alteration of NaDC upon varying the concentration of the ionic liquid. The proton NMR data indicate that hydrophobic as well as electrostatic interaction is solely responsible for such structural adaptation of NaDC in the presence of an ionic liquid. The host-guest interaction inside the aggregates is monitored using Coumarin-153 (C-153) and the location of C-153 is probed by varying the excitation wavelength from 375 nm to 440 nm and the two binding sites of the aggregates are affected in a different fashion in the presence of ionic liquid. Excitation in the blue region selects the fluorophores which preferably bind to the buried region of the aggregates, whereas 440 nm excitation corresponds to the guest molecules which are exposed to the solvent molecules. The average solvation time of C-153 is increased in the presence of 1.68 wt% [bmim]-BF4 at λexc = 440 nm i.e. the probe molecules relocate themselves to a more restricted region. However, the average solvation time became 2.6 times faster in the presence of 11.2 wt% [bmim]-BF4, which corresponds to a more polar and exposed region. The time resolved anisotropy measurements and polarity determined by pyrene also supported our results in addition to solvation dynamics measurements. In summary, ionic liquids can modulate the host-guest interaction of bile salt aggregates, which can be used as nanocarriers for drug delivery.
Spatial Modeling of Iron Transformations Within Artificial Soil Aggregates

NASA Astrophysics Data System (ADS)

Kausch, M.; Meile, C.; Pallud, C.

2008-12-01

Structured soils exhibit significant variations in transport characteristics at the aggregate scale. Preferential flow occurs through macropores while predominantly diffusive exchange takes place in intra-aggregate micropores. Such environments characterized by mass transfer limitations are conducive to the formation of small-scale chemical gradients and promote strong spatial variation in processes controlling the fate of redox-sensitive elements such as Fe. In this study, we present a reactive transport model used to spatially resolve iron bioreductive processes occurring within a spherical aggregate at the interface between advective and diffusive domains. The model is derived from current conceptual models of iron(hydr)oxide (HFO) transformations and constrained by literature and experimental data. Data were obtained from flow-through experiments on artificial soil aggregates inoculated with Shewanella putrefaciens strain CN32, and include the temporal evolution of the bulk solution composition, as well as spatial information on the final solid phase distribution within aggregates. With all iron initially in the form of ferrihydrite, spatially heterogeneous formation of goethite/lepidocrocite, magnetite and siderite was observed during the course of the experiments. These transformations were reproduced by the model, which ascribes a central role to divalent iron as a driver of HFO transformations and master variable in the rate laws of the considered reaction network. The predicted dissolved iron breakthrough curves also match the experimental ones closely. Thus, the computed chemical concentration fields help identify factors governing the observed trends in the solid phase distribution patterns inside the aggregate. Building on a mechanistic description of transformation reactions, fluid flow and solute transport, the model was able to describe the observations and hence illustrates the importance of small-scale gradients and dynamics of bioreductive processes for assessing bulk iron cycling. As HFOs are ubiquitous in soils, such process-level understanding of aggregate-scale iron dynamics has broad implications for the prediction of the subsurface fate of nutrients and contaminants that interact strongly with HFO surfaces.
Evolution and Impartiality*

PubMed Central

Kahane, Guy

2014-01-01

Lazari-Radek and Singer argue that evolutionary considerations can resolve Sidgwick’s dualism of practical reason, because such considerations debunk moral views that give weight to self-interested or partial considerations, but cannot threaten the principle Universal Benevolence. I argue that even if we grant these claims, this appeal to evolution is ultimately self-defeating. Lazari-Radek and Singer face a dilemma. Either their evolutionary argument against partial morality succeeds, but then we need to also give up our conviction that suffering is bad; or there is a way to defend this conviction, but then their argument against partiality fails. Utilitarians, I suggest, should resist the temptation to appeal to evolutionary debunking arguments. PMID:24711673
Aggregation Kinetics of Hematite Particles in the Presence of Outer Membrane Cytochrome OmcA of Shewanella oneidenesis MR-1

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

Sheng, Anxu; Liu, Feng; Shi, Liang

2016-09-20

The aggregation behavior of 9, 36, and 112 nm hematite particles was studied in the presence of OmcA, a bacterial extracellular protein, in aqueous dispersions at pH 5.7 through time-resolved dynamic light scattering, electrophoretic mobility, and circular dichroism spectra, respectively. At low salt concentration, the attachment efficiencies of hematite particles in all sizes first increased, then decreased, and finally remained stable with the increase of OmcA concentration, indicating the dominant interparticle interaction changed along with the increase in the protein-to-particle ratio. Nevertheless, at high salt concentration, the attachment efficiencies of all hematite samples gradually decreased with increasing OmcA concentration, whichmore » can be attributed to increasing steric force. Additionally, the aggregation behavior of OmcA-hematite conjugates was more correlated to total particle-surface area than primary particle size. It was further established that OmcA could stabilize hematite nanoparticles more efficiently than bovine serum albumin (BSA), a model plasma protein, due to the higher affinity of OmcA to hematite surface. This study highlighted the effects of particle properties, solution conditions, and protein properties on the complicated aggregation behavior of protein-nanoparticle conjugates in aqueous environments.« less
Quality assurance and quality control for autonomously collected geoscience data

NASA Astrophysics Data System (ADS)

Versteeg, R. J.; Richardson, A.; Labrecque, D.

2006-12-01

The growing interest in processes, coupled with the reduction in cost and complexity of sensors which allow for continuous data collection and transmission is giving rise to vast amounts of semi autonomously collected data. Such data is typically collected from a range of physical and chemical sensors and transmitted - either at the time of collection, or periodically as a collection of measurements - to a central server. Such setups can collect vast amounts of data. In cases where power is not an issue one datapoint can be collected every minute, resulting in tens of thousands of data points per month per sensor. Especially in cases in which multiple sensors are deployed it is infeasible to examine each individual datapoint for each individual sensor, and users typically will look at aggregates of such data on a periodic (once a week to once every few months) basis. Such aggregates (and the timelag between data collection and data evaluation) will impact the ability to rapidly identify and resolve data issues. Thus, there is a need to integrate data qa/qc rules and procedures in the data collection process. These should be implemented such that data is analyzed for compliance the moment it arrives at the server, and that any issues with this data result in notification of cognizant personnel. Typical issues (encountered in the field) include complete system failure (resulting in no data arriving at all), to complete sensor failure (data is collected, but is meaningless), to partial sensor failure (sensor gives erratic readings, or starts to exhibit a bias) to partial powerloss (system collects and transmits data only intermittently). We have implemented a suite of such rules and tests as part of the INL developed performance monitoring system. These rules are invoked as part of a data qa/qc workflow, and result in quality indicators for each datapoint as well as user alerts in case of issues. Tests which are applied to the data include tests on individual datapoints, tests on suites of datapoints, and tests applied over the whole dataset. Example of tests include: Did data arrive on time, is received data in a valid format, are all measurements present, is data within valid range, is data collected at appropriate time intervals, are the statistics of the data changing over time and is the data collected within an appropriate instrument calibration window? This approach, which is executed automatically on all data provides data end users with confidence and auditability regarding the quality and useability of autonomously collected data.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.

Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. Inmore » these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the average distance between branches of type 2 or 3 aggregates. Furthermore, this direct comparison of X-ray scattering data to the atomistic MD simulations is a substantive step toward providing a comprehensive, predictive model for ionomer morphology, gives substantial support for this atomistic MD model, and provides new credibility to the presence of stringy, branched, and percolated ionic aggregates in precise ionomer melts.« less
Pseudolatex preparation using a novel emulsion-diffusion process involving direct displacement of partially water-miscible solvents by distillation.

PubMed

Quintanar-Guerrero, D; Allémann, E; Fessi, H; Doelker, E

1999-10-25

Pseudolatexes were obtained by a new process based on an emulsification-diffusion technique involving partially water-miscible solvents. The preparation method consisted of emulsifying an organic solution of polymer (saturated with water) in an aqueous solution of a stabilizing agent (saturated with solvent) using conventional stirrers, followed by direct solvent distillation. The technique relies on the rapid displacement of the solvent from the internal into the external phase which thereby provokes polymer aggregation. Nanoparticle formation is believed to occur because rapid solvent diffusion produces regions of local supersaturation near the interface, and nanoparticles are formed due to the ensuing interfacial phase transformations and polymer aggregation that occur in these interfacial domains. Using this method, it was possible to prepare pseudolatexes of biodegradable and non-biodegradable polymers such as poly(D,L-lactic acid) and poly(epsilon-caprolactone), Eudragit E, cellulose acetate phthalate, cellulose acetate trimellitate using ethyl acetate or 2-butanone as partially water-miscible solvents and poly(vinyl alcohol) or poloxamer 407 as stabilizing agent. A transition from nano- to microparticles was observed at high polymer concentrations. At concentrations above 30% w/v of Eudragit E in ethyl acetate or cellulose acetate phthalate in 2-butanone only microparticles were obtained. This behaviour was attributed to decreased transport of polymer molecules into the aqueous phase.
Case study #3 -- severe scaling of an interstate bridge deck, and Potentially reactive carbonate aggregates, progress report #6 (partial): an example of bridge deterioration promoted by alkali-carbonate reaction.

DOT National Transportation Integrated Search

1971-01-01

The project designated "Concrete Durability Studies" comprises case studies of unusual durability, either in kind or extent. These case studies are directed toward situations in which appearances suggest materials or construction rather than structur...
The Next Step Toward Widespread Residential Deep Energy Retrofits

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

McIlvaine, J.; Martin, E.; Saunders, S.

The complexity of deep energy retrofits warrants additional training to successfully manage multiple improvements that will change whole house air, heat, and moisture flow dynamics. The home performance contracting industry has responded to these challenges by aggregating skilled labor for assessment of and implementation under one umbrella. Two emerging business models are profiled that seek to resolve many of the challenges, weaknesses, opportunities, and threats described for the conventional business models.
Recognition-Mediated Assembly of Quantum Dot Polymer Conjugates with Controlled Morphology

PubMed Central

Nandwana, Vikas; Subramani, Chandramouleeswaran; Eymur, Serkan; Yeh, Yi-Cheun; Tonga, Gulen Yesilbag; Tonga, Murat; Jeong, Youngdo; Yang, Boqian; Barnes, Michael D.; Cooke, Graeme; Rotello, Vincent M.

2011-01-01

We have demonstrated a polymer mediated “bricks and mortar” method for the self-assembly of quantum dots (QDs). This strategy allows QDs to self-assemble into structured aggregates using complementary three-point hydrogen bonding. The resulting nanocomposites have distinct morphologies and inter-particle distances based on the ratio between QDs and polymer. Time resolved photoluminescence measurements showed that the optical properties of the QDs were retained after self-assembly. PMID:22016664
Use of ion-mobility mass spectrometry (IMS-MS) to map polyoxometalate Keplerate clusters and their supramolecular assemblies.

PubMed

Robbins, Philip J; Surman, Andrew J; Thiel, Johannes; Long, De-Liang; Cronin, Leroy

2013-03-07

We present the high-resolution (HRES-MS) and ion-mobility (IMS-MS) mass spectrometry studies of icosahedral nanoscale polyoxometalate-based {L(30)}{(Mo)Mo(5)} Keplerate clusters, and demonstrate the use of IMS-MS to resolve and map intact nanoclusters, and its potential for the discovery of new structures, in this case the first gas phase observation of 'proto-clustering' of higher order Keplerate supramolecular aggregates.
Time-resolved SAXS study of the effect of a double hydrophilic block-copolymer on the formation of CaCO3 from a supersaturated salt solution.

PubMed

Bolze, J; Pontoni, D; Ballauff, M; Narayanan, T; Cölfen, H

2004-09-01

The effect of a double hydrophilic block-copolymer additive (made of polyaspartic acid and polyethyleneglycol, pAsp(10)-b-PEG(110)) on the initial formation of calcium carbonate from a supersaturated salt solution has been studied in situ by means of time-resolved synchrotron small-angle X-ray scattering (SAXS). A stopped-flow cell was used for rapidly mixing the 20 mM aqueous reactant solutions of calcium chloride and sodium carbonate. In reference measurements without polymer additive the very rapid formation of primary, overall spherical CaCO(3) particles with a radius of ca. 19 nm and a size polydispersity of ca. 26% was observed within the first 10 ms after mixing. A subsequent, very rapid aggregation of these primary particles was evidenced by a distinct upturn of the SAXS intensity at smallest angles. During the aggregation process the size of the primary particles remained unchanged. From an analysis of the absolute scattering intensity the mass density of these particles was determined to 1.9 g/cm(3). From this rather low density it is concluded that those precursor particles are amorphous, which has been confirmed by simultaneous wide-angle X-ray diffraction measurements. Upon adding 200 pm of the block-copolymer no influence on the size, the size polydispersity and morphology of the primary particles, nor on the kinetics of their formation and growth, was found. On the other hand, the subsequent aggregation and precipitation process is considerably slowed down by the additive and smaller aggregates result. The crystalline morphology of the sediment was studied in situ by WAXS ca. 50 min after mixing the reactants. Several diffraction rings could be detected, which indicate that a transformation of the metastable, amorphous precursor particles to randomly oriented vaterite nanocrystallites has taken place. In addition, a few isolated Bragg spots of high intensity were detected, which are attributed to individual, oriented calcite microcrystals that nucleated at the wall of the capillary.
A mobile system for a comprehensive online-characterization of nanoparticle aggregates based on wide-angle light scattering and laser-induced incandescence

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

Huber, Franz J. T.; Will, Stefan, E-mail: stefan.will@fau.de; Erlangen Graduate School in Advanced Optical Technologies

A mobile demonstrator for the comprehensive online-characterization of gas-borne nanoparticle aggregates is presented. Two optical measurement techniques are combined, both utilizing a pulsed Nd:YAG laser as light source. Aggregate size and fractal dimension are measured by Wide-Angle Light Scattering (WALS). An ellipsoidal mirror images elastically scattered light from scattering angles between 10° and 165° onto a CCD-camera chip resulting in an almost complete scattering diagram with high angular resolution. Primary particle size and volume fraction are measured by time-resolved Laser-Induced Incandescence (TiRe-LII). Here, particles are heated up to about 3000 K by the short laser pulse, the enhanced thermal radiationmore » signal is detected with gated photomultiplier tubes. Analysis of the signal decay time and maximum LII-signal allows for the determination of primary particle diameter and volume fraction. The performance of the system is demonstrated by combined measurements on soot nanoparticle aggregates from a soot aerosol generator. Particle and aggregate sizes are varied by using different equivalence ratios of the combustion in the generator. Soot volume fraction can be adjusted by different levels of dilution with air. Online-measurements were carried out demonstrating the favorable performance of the system and the potential for industrial applications such as process control and product development. The particle properties obtained are confirmed through transmission electron microscopy analysis on representative samples.« less
Demography and movement patterns of leopard sharks (Triakis semifasciata) aggregating near the head of a submarine canyon along the open coast of southern California, USA

USGS Publications Warehouse

Nosal, D.C.; Cartamil, D.C.; Long, J.W.; Luhrmann, M.; Wegner, N.C.; Graham, J.B.

2013-01-01

The demography, spatial distribution, and movement patterns of leopard sharks (Triakis semifasciata) aggregating near the head of a submarine canyon in La Jolla, California, USA, were investigated to resolve the causal explanations for this and similar shark aggregations. All sharks sampled from the aggregation site (n=140) were sexually mature and 97.1 % were female. Aerial photographs taken during tethered balloon surveys revealed high densities of milling sharks of up to 5470 sharks ha-1. Eight sharks were each tagged with a continuous acoustic transmitter and manually tracked without interruption for up to 48 h. Sharks exhibited strong site-fidelity and were generally confined to a divergence (shadow) zone of low wave energy, which results from wave refraction over the steep bathymetric contours of the submarine canyon. Within this divergence zone, the movements of sharks were strongly localized over the seismically active Rose Canyon Fault. Tracked sharks spent most of their time in shallow water (≤2 m for 71.0 % and ≤10 m for 95.9 % of time), with some dispersing to deeper (max: 53.9 m) and cooler (min: 12.7 °C) water after sunset, subsequently returning by sunrise. These findings suggest multiple functions of this aggregation and that the mechanism controlling its formation, maintenance, and dissolution is complex and rooted in the sharks' variable response to numerous confounding environmental factors.
A mobile system for a comprehensive online-characterization of nanoparticle aggregates based on wide-angle light scattering and laser-induced incandescence.

PubMed

Huber, Franz J T; Altenhoff, Michael; Will, Stefan

2016-05-01

A mobile demonstrator for the comprehensive online-characterization of gas-borne nanoparticle aggregates is presented. Two optical measurement techniques are combined, both utilizing a pulsed Nd:YAG laser as light source. Aggregate size and fractal dimension are measured by Wide-Angle Light Scattering (WALS). An ellipsoidal mirror images elastically scattered light from scattering angles between 10° and 165° onto a CCD-camera chip resulting in an almost complete scattering diagram with high angular resolution. Primary particle size and volume fraction are measured by time-resolved Laser-Induced Incandescence (TiRe-LII). Here, particles are heated up to about 3000 K by the short laser pulse, the enhanced thermal radiation signal is detected with gated photomultiplier tubes. Analysis of the signal decay time and maximum LII-signal allows for the determination of primary particle diameter and volume fraction. The performance of the system is demonstrated by combined measurements on soot nanoparticle aggregates from a soot aerosol generator. Particle and aggregate sizes are varied by using different equivalence ratios of the combustion in the generator. Soot volume fraction can be adjusted by different levels of dilution with air. Online-measurements were carried out demonstrating the favorable performance of the system and the potential for industrial applications such as process control and product development. The particle properties obtained are confirmed through transmission electron microscopy analysis on representative samples.
A mobile system for a comprehensive online-characterization of nanoparticle aggregates based on wide-angle light scattering and laser-induced incandescence

NASA Astrophysics Data System (ADS)

Huber, Franz J. T.; Altenhoff, Michael; Will, Stefan

2016-05-01

A mobile demonstrator for the comprehensive online-characterization of gas-borne nanoparticle aggregates is presented. Two optical measurement techniques are combined, both utilizing a pulsed Nd:YAG laser as light source. Aggregate size and fractal dimension are measured by Wide-Angle Light Scattering (WALS). An ellipsoidal mirror images elastically scattered light from scattering angles between 10° and 165° onto a CCD-camera chip resulting in an almost complete scattering diagram with high angular resolution. Primary particle size and volume fraction are measured by time-resolved Laser-Induced Incandescence (TiRe-LII). Here, particles are heated up to about 3000 K by the short laser pulse, the enhanced thermal radiation signal is detected with gated photomultiplier tubes. Analysis of the signal decay time and maximum LII-signal allows for the determination of primary particle diameter and volume fraction. The performance of the system is demonstrated by combined measurements on soot nanoparticle aggregates from a soot aerosol generator. Particle and aggregate sizes are varied by using different equivalence ratios of the combustion in the generator. Soot volume fraction can be adjusted by different levels of dilution with air. Online-measurements were carried out demonstrating the favorable performance of the system and the potential for industrial applications such as process control and product development. The particle properties obtained are confirmed through transmission electron microscopy analysis on representative samples.
A spectroscopic and thermodynamic study of porphyrin/DNA supramolecular assemblies.

PubMed Central

Pasternack, R F; Goldsmith, J I; Szép, S; Gibbs, E J

1998-01-01

Assemblies of trans-bis(N-methylpyridinium-4-yl)diphenylporphine ions on the surface of calf thymus DNA have been studied using several spectroscopic techniques: absorbance, circular dichroism, and resonance light scattering. The aggregation equilibrium can be treated as a two-state system-monomer and assembly-each bound to the nucleic acid template. The aggregate absorption spectrum in the Soret region is resolved into two bands of Lorentzian line shape, while the DNA-bound monomer spectrum in this region is composed of two Gaussian bands. The Beer-Lambert law is obeyed by both porphyrin forms. The assembly is also characterized by an extremely large, bisignate induced circular dichroism (CD) profile and by enhanced resonance light scattering (RLS). Both the CD and RLS intensities depend linearly on aggregate concentration. The RLS result is consistent with a model for the aggregates as being either of a characteristic size or of a fixed distribution of sizes, independent of total porphyrin concentration or ionic strength. Above threshold values of concentration and ionic strength, the mass action expression for the equilibrium has a particularly simple form: K' = cac-1; where cac is defined as the "critical assembly concentration."offe dependence of the cac upon temperature and ionic strength (NaCl) has been investigated at a fixed DNA concentration. The value of the cac scales as the inverse square of the sodium chloride concentration and, from temperature dependence studies, the aggregation process is shown to be exothermic. PMID:9675203
Interaction Forces and Aggregation Rates of Colloidal Latex Particles in the Presence of Monovalent Counterions.

PubMed

Montes Ruiz-Cabello, F Javier; Trefalt, Gregor; Oncsik, Tamas; Szilagyi, Istvan; Maroni, Plinio; Borkovec, Michal

2015-06-25

Force profiles and aggregation rates involving positively and negatively charged polystyrene latex particles are investigated in monovalent electrolyte solutions, whereby the counterions are varied within the Hofmeister series. The force measurements are carried out with the colloidal probe technique, which is based on the atomic force microscope (AFM), while the aggregation rates are measured with time-resolved multiangle light scattering. The interaction force profiles cannot be described by classical DLVO theory, but an additional attractive short-ranged force must be included. An exponential force profile with a decay length of about 0.5 nm is consistent with the measured forces. Furthermore, the Hamaker constants extracted from the measured force profiles are substantially smaller than the theoretical values calculated from dielectric spectra. The small surface roughness of the latex particles (below 1 nm) is probably responsible for this deviation. Based on the measured force profiles, the aggregation rates can be predicted without adjustable parameters. The measured absolute aggregation rates in the fast regime are somewhat lower than the calculated ones. The critical coagulation concentration (CCC) agrees well with the experiment, including the respective shifts of the CCC within the Hofmeister series. These shifts are particularly pronounced for the positively charged particles. However, the consideration of the additional attractive short-ranged force is essential to quantify these shifts correctly. In the slow regime, the calculated rates are substantially smaller than the experimental ones. This disagreement is probably related to surface charge heterogeneities.

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

Bambha, Ray P.; Michelsen, Hope A.

We have used a Single-Particle Soot Photometer (SP2) to measure time-resolved laser-induced incandescence (LII) and laser scatter from combustion-generated mature soot with a fractal dimension of 1.88 extracted from a burner. We have also made measurements on restructured mature-soot particles with a fractal dimension of 2.3–2.4. We reproduced the LII and laser-scatter temporal profiles with an energy- and mass-balance model, which accounted for heating of particles passed through a CW-laser beam over laser–particle interaction times of ~10 μs. Furthermore, the results demonstrate a strong influence of aggregate size and morphology on LII and scattering signals. Conductive cooling competes with absorptivemore » heating on these time scales; the effects are reduced with increasing aggregate size and fractal dimension. These effects can lead to a significant delay in the onset of the LII signal and may explain an apparent low bias in the SP2 measurements for small particle sizes, particularly for fresh, mature soot. The results also reveal significant perturbations to the measured scattering signal from LII interference and suggest rapid expansion of the aggregates during sublimation.« less
Three-Dimensional Orientation of Anisotropic Plasmonic Aggregates at Intracellular Nuclear Indentation Sites by Integrated Light Sheet Super-Resolution Microscopy.

PubMed

Chakkarapani, Suresh Kumar; Sun, Yucheng; Lee, Seungah; Fang, Ning; Kang, Seong Ho

2018-05-22

Three-dimensional (3D) orientations of individual anisotropic plasmonic nanoparticles in aggregates were observed in real time by integrated light sheet super-resolution microscopy ( iLSRM). Asymmetric light scattering of a gold nanorod (AuNR) was used to trigger signals based on the polarizer angle. Controlled photoswitching was achieved by turning the polarizer and obtaining a series of images at different polarization directions. 3D subdiffraction-limited super-resolution images were obtained by superlocalization of scattering signals as a function of the anisotropic optical properties of AuNRs. Varying the polarizer angle allowed resolution of the orientation of individual AuNRs. 3D images of individual nanoparticles were resolved in aggregated regions, resulting in as low as 64 nm axial resolution and 28 nm spatial resolution. The proposed imaging setup and localization approach demonstrates a convenient method for imaging under a noisy environment where the majority of scattering noise comes from cellular components. This integrated 3D iLSRM and localization technique was shown to be reliable and useful in the field of 3D nonfluorescence super-resolution imaging.
Localization length and intraband scattering of excitons in linear aggregates

NASA Astrophysics Data System (ADS)

Lemaistre, J. P.

1999-07-01

A theoretical model to describe the intraband scattering of excitons in linear aggregates of finite size which exhibit strong intermolecular interactions is presented. From the calculation of the aggregate eigenstates, the localization length of excitons is evaluated for various configurations featuring physical situations like trapping, edge effects, inclusion of diagonal and/or orientational disorders. The intraband scattering is studied by considering the exciton-phonon stochastic coupling induced by the thermal bath. This coupling creates local dynamical fluctuations in the site energies which are characterized by their amplitude ( Δ) and their correlation time ( τc). Expressions of scattering rates are provided and used in a Pauli master equation to calculate the time dependence of the eigenstates populations after initial excitation of the quasi exciton-band. It is shown that the time evolution of the lowest state population as well as the Stokes shift strongly depend on τc. Comparison of the theoretical results to time-resolved experiments performed on triaryl pyrylium salts allows us to interpret the observed Stokes shift and to derive an average value of the exciton-phonon correlation time.
Amended Complaint for Volkswagen

EPA Pesticide Factsheets

The settlement partially resolves allegations that Volkswagen violated the Clean Air Act (“CAA”) by the sale of approximately 500,000 model year 2009 to 2015 motor vehicles containing 2.0 liter diesel engines equipped with “defeat devices” (“CAA 2.0 liter.
Electrical conductivity of partially-molten olivine aggregate and melt interconnectivity in the oceanic upper mantle

NASA Astrophysics Data System (ADS)

Laumonier, Mickael; Frost, Dan; Farla, Robert; Katsura, Tomoo; Marquardt, Katharina

2016-04-01

A consistent explanation for mantle geophysical anomalies such as the Lithosphere-Astenosphere Boundary (LAB) relies on the existence of little amount of melt trapped in the solid peridotite. Mathematical models have been used to assess the melt fraction possibly lying at mantle depths, but they have not been experimentally checked at low melt fraction (< 2 vol. %). To fill this gap, we performed in situ electrical conductivity (EC) measurement on a partially-molten olivine aggregate (Fo92-olivine from a natural peridotite of Lanzarote, Canary Islands, Spain) containing various amount of basaltic (MORB-like composition) melt (0 to 100%) at upper mantle conditions. We used the MAVO 6-ram press (BGI) combined with a Solartron gain phase analyser to acquire the electrical resistance of the sample at pressure of 1.5 GPa and temperature up to 1400°C. The results show the increase of the electrical conductivity with the temperature following an Arrhenius law, and with the melt fraction, but the effect of pressure between 1.5 and 3.0 GPa was found negligible at a melt fraction of 0.5 vol.%. The conductivity of a partially molten aggregate fits the modified Archie's law from 0.5 to 100 vol.%. At melt fractions of 0.25, 0.15 and 0.0 vol.%, the EC value deviates from the trend previously defined, suggesting that the melt is no longer fully interconnected through the sample, also supported by chemical mapping. Our results extend the previous results obtained on mixed system between 1 and 10% of melt. Since the melt appears fully interconnected down to very low melt fraction (0.5 vol.%), we conclude that (i) only 0.5 to 1 vol.% of melt is enough to explain the LAB EC anomaly, lower than previously determined; and (ii) deformation is not mandatory to enhance electrical conductivity of melt-bearing mantle rocks.
Waste tyre rubberized concrete: properties at fresh and hardened state.

PubMed

Aiello, M A; Leuzzi, F

2010-01-01

The main objective of this paper is to investigate the properties of various concrete mixtures at fresh and hardened state, obtained by a partial substitution of coarse and fine aggregate with different volume percentages of waste tyres rubber particles, having the same dimensions of the replaced aggregate. Workability, unit weight, compressive and flexural strength and post-cracking behaviour were evaluated and a comparison of the results for the different rubcrete mixtures were proposed in order to define the better mix proportions in terms of mechanical properties of the rubberized concrete. Results showed in this paper were also compared to data reported in literature. Moreover, a preliminary geometrical, physical and mechanical characterization on scrap tyre rubber shreds was made. The rubberized concrete mixtures showed lower unit weight compared to plain concrete and good workability. The results of compressive and flexural tests indicated a larger reduction of mechanical properties of rubcrete when replacing coarse aggregate rather than fine aggregate. On the other hand, the post-cracking behaviour of rubberized concrete was positively affected by the substitution of coarse aggregate with rubber shreds, showing a good energy absorption and ductility indexes in the range observed for fibrous concrete, as suggested by standard (ASTM C1018-97, 1997). 2010 Elsevier Ltd. All rights reserved.
Crystallography and Molecular Arrangement of Polymorphic Monolayer J-Aggregates of a Cyanine Dye: Multiangle Polarized Light Fluorescence Optical Microscopy Study.

PubMed

Prokhorov, Valery V; Pozin, Sergey I; Perelygina, Olga M; Mal'tsev, Eugene I

2018-04-24

The molecular orientation in monolayer J-aggregates of 3,3-di(γ-sulfopropyl)-5,5-dichlorotiamonomethinecyanine dye has been precisely estimated using improved linear polarization measurements in the fluorescence microscope in which a multiangle set of polarization data is obtained using sample rotation. The estimated molecular orientation supplemented with the previously established crystallographic constraints based on the analysis of the well-developed two-dimensional J-aggregate shapes unambiguously indicate the staircase type of molecular arrangement for striplike J-aggregates with the staircases oriented along strips. The molecular transition dipoles are inclined at an angle of ∼25° to the strip direction, whereas the characteristic strip vertex angle ∼45° is formed by the [100] and [1-10] directions of the monoclinic unit cell. Measurements of the geometry of partially unwound tubes and their polarization properties support the model of tube formation by close-packed helical winding of flexible monolayer strips. In the tubes, the long molecular axes are oriented at a small angle in the range of 5-15° to the normal to the tube axis providing low bending energy. At a nanoscale, high-resolution atomic force microscopy imaging of J-aggregate monolayers reveals a complex quasi-one-dimensional organization.
Three cyanobacteriochromes work together to form a light color-sensitive input system for c-di-GMP signaling of cell aggregation.

PubMed

Enomoto, Gen; Ni-Ni-Win; Narikawa, Rei; Ikeuchi, Masahiko

2015-06-30

Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors that have diverse spectral properties and domain compositions. Although large numbers of CBCR genes exist in cyanobacterial genomes, no studies have assessed whether multiple CBCRs work together. We recently showed that the diguanylate cyclase (DGC) activity of the CBCR SesA from Thermosynechococcus elongatus is activated by blue-light irradiation and that, when irradiated, SesA, via its product cyclic dimeric GMP (c-di-GMP), induces aggregation of Thermosynechococcus vulcanus cells at a temperature that is suboptimum for single-cell viability. For this report, we first characterize the photobiochemical properties of two additional CBCRs, SesB and SesC. Blue/teal light-responsive SesB has only c-di-GMP phosphodiesterase (PDE) activity, which is up-regulated by teal light and GTP. Blue/green light-responsive SesC has DGC and PDE activities. Its DGC activity is enhanced by blue light, whereas its PDE activity is enhanced by green light. A ΔsesB mutant cannot suppress cell aggregation under teal-green light. A ΔsesC mutant shows a less sensitive cell-aggregation response to ambient light. ΔsesA/ΔsesB/ΔsesC shows partial cell aggregation, which is accompanied by the loss of color dependency, implying that a nonphotoresponsive DGC(s) producing c-di-GMP can also induce the aggregation. The results suggest that SesB enhances the light color dependency of cell aggregation by degrading c-di-GMP, is particularly effective under teal light, and, therefore, seems to counteract the induction of cell aggregation by SesA. In addition, SesC seems to improve signaling specificity as an auxiliary backup to SesA/SesB activities. The coordinated action of these three CBCRs highlights why so many different CBCRs exist.
Effects of Combined Application of Biogas Slurry and Chemical Fertilizer on Soil Aggregation and C/N Distribution in an Ultisol.

PubMed

Zheng, Xuebo; Fan, Jianbo; Xu, Lei; Zhou, Jing

2017-01-01

Unreasonable use of chemical fertilizer (CF) on agricultural soil leads to massive losses of soil organic carbon (SOC) and total nitrogen (TN) in tropical and subtropical areas, where soil conditions are unfavorable for aggregate formation. This study evaluated the effects of combined application of biogas slurry (BS) plus CF on soil aggregation and aggregate-associated C/N concentration and storage in an Ultisol. Six treatments included: no fertilizer (T1), CF only (T2), partial (15% (T3), 30% (T4) and 45% (T5)) substitution of TN with BS and BS only (T6). Soil mechanical-stable aggregates (MSAs) formation and stability as well as MSAs-associated C/N concentration and storage were observed in different aggregate sizes (>5, 5-2, 2-1, 1.0-0.5, 0.50-0.25 and <0.25 mm). The proportion of MSAs >5 mm significantly increased with BS substitution (T5), while the proportions of MSAs 1.0-0.5 mm, MSAs 0.50-0.25 mm and MSAs <0.25 mm significantly decreased. Both mean weight diameter and geometric mean diameter were highest in T5, which improved soil aggregation stability as well as resulted in significantly higher SOC and TN concentrations and storage in MSAs >0.5 mm that constituted 72-82% of MSAs. Stepwise regression analysis showed that MSAs >5 mm, SOC in MSAs >5 mm and TN in MSAs >5 mm were the dominant variables affecting aggregate stability. Meanwhile SOC in MSAs <0.25 mm and TN in MSAs 2-1 mm were independent variables affecting SOC and TN concentrations in bulk soils. Therefore, certain rate of combined application of BS plus CF is an effective, eco-friendly way to improve soil quality in an Ultisol.
Pigment Translocation in Caridean Shrimp Chromatophores: Receptor Type, Signal Transduction, Second Messengers, and Cross Talk Among Multiple Signaling Cascades.

PubMed

Milograna, Sarah Ribeiro; Ribeiro, Márcia Regina; Bell, Fernanda Tinti; McNamara, John Campbell

2016-11-01

Pigment aggregation in shrimp chromatophores is triggered by red pigment concentrating hormone (RPCH), a neurosecretory peptide whose plasma membrane receptor may be a G-protein coupled receptor (GPCR). While RPCH binding activates the Ca 2+ /cGMP signaling cascades, a role for cyclic AMP (cAMP) in pigment aggregation is obscure, as are the steps governing Ca 2+ release from the smooth endoplasmic reticulum (SER). A role for the antagonistic neuropeptide, pigment dispersing homone (α-PDH) is also unclear. In red, ovarian chromatophores from the freshwater shrimp Macrobrachium olfersi, we show that a G-protein antagonist (AntPG) strongly inhibits RPCH-triggered pigment aggregation, suggesting that RPCH binds to a GPCR, activating an inhibitory G-protein. Decreasing cAMP levels may cue pigment aggregation, since cytosolic cAMP titers, when augmented by cholera toxin, forskolin or vinpocentine, completely or partially impair pigment aggregation. Triggering opposing Ca 2+ /cGMP and cAMP cascades by simultaneous perfusion with lipid-soluble cyclic nucleotide analogs induces a "tug-of-war" response, pigments aggregating in some chromatosomes with unpredictable, oscillatory movements in others. Inhibition of cAMP-dependent protein kinase accelerates aggregation and reduces dispersion velocities, suggesting a role in phosphorylation events, possibly regulating SER Ca 2+ release and pigment aggregation. The second messengers IP 3 and cADPR do not stimulate SER Ca 2+ release. α-PDH does not sustain pigment dispersion, suggesting that pigment translocation in caridean chromatophores may be regulated solely by RPCH, since PDH is not required. We propose a working hypothesis to further unravel key steps in the mechanisms of pigment translocation within crustacean chromatophores that have remained obscure for nearly a century. © 2016 Wiley Periodicals, Inc.
Embryo aggregation does not improve the development of interspecies somatic cell nuclear transfer embryos in the horse.

PubMed

Gambini, Andrés; De Stéfano, Adrián; Jarazo, Javier; Buemo, Carla; Karlanian, Florencia; Salamone, Daniel Felipe

2016-09-01

The low efficiency of interspecies somatic cell nuclear transfer (iSCNT) makes it necessary to investigate new strategies to improve embryonic developmental competence. Embryo aggregation has been successfully applied to improve cloning efficiency in mammals, but it remains unclear whether it could also be beneficial for iSCNT. In this study, we first compared the effect of embryo aggregation over in vitro development and blastocyst quality of porcine, bovine, and feline zona-free (ZF) parthenogenetic (PA) embryos to test the effects of embryo aggregation on species that were later used as enucleated oocytes donors in our iSCNT study. We then assessed whether embryo aggregation could improve the in vitro development of ZF equine iSCNT embryos after reconstruction with porcine, bovine, and feline ooplasm. Bovine- and porcine-aggregated PA blastocysts had significantly larger diameters compared with nonaggregated embryos. On the other hand, feline- and bovine-aggregated PA embryos had higher blastocyst cell number. Embryo aggregation of equine-equine SCNT was found to be beneficial for embryo development as we have previously reported, but the aggregation of three ZF reconstructed embryos did not improve embryo developmental rates on iSCNT. In vitro embryo development of nonaggregated iSCNT was predominantly arrested around the stage when transcriptional activation of the embryonic genome is reported to start on the embryo of the donor species. Nevertheless, independent of embryo aggregation, equine blastocyst-like structures could be obtained in our study using domestic feline-enucleated oocytes. Taken together, these results reported that embryo aggregation enhance in vitro PA embryo development and embryo quality but effects vary depending on the species. Embryo aggregation also improves, as expected, the in vitro embryo development of equine-equine SCNT embryos; however, we did not observe positive effects on equine iSCNT embryo development. Among oocytes from domestic animals tested in our study, the feline ooplasm might be the most appropriate recipient to partially allow preimplantation embryo development of iSCNT equine embryos. Copyright © 2016 Elsevier Inc. All rights reserved.
Molecular Mechanism of Mutant p53 Stabilization: The Role of HSP70 and MDM2

PubMed Central

Wiech, Milena; Olszewski, Maciej B.; Tracz-Gaszewska, Zuzanna; Wawrzynow, Bartosz; Zylicz, Maciej; Zylicz, Alicja

2012-01-01

Numerous p53 missense mutations possess gain-of-function activities. Studies in mouse models have demonstrated that the stabilization of p53 R172H (R175H in human) mutant protein, by currently unknown factors, is a prerequisite for its oncogenic gain-of-function phenotype such as tumour progression and metastasis. Here we show that MDM2-dependent ubiquitination and degradation of p53 R175H mutant protein in mouse embryonic fibroblasts is partially inhibited by increasing concentration of heat shock protein 70 (HSP70/HSPA1-A). These phenomena correlate well with the appearance of HSP70-dependent folding intermediates in the form of dynamic cytoplasmic spots containing aggregate-prone p53 R175H and several molecular chaperones. We propose that a transient but recurrent interaction with HSP70 may lead to an increase in mutant p53 protein half-life. In the presence of MDM2 these pseudoaggregates can form stable amyloid-like structures, which occasionally merge into an aggresome. Interestingly, formation of folding intermediates is not observed in the presence of HSC70/HSPA8, the dominant-negative K71S variant of HSP70 or HSP70 inhibitor. In cancer cells, where endogenous HSP70 levels are already elevated, mutant p53 protein forms nuclear aggregates without the addition of exogenous HSP70. Aggregates containing p53 are also visible under conditions where p53 is partially unfolded: 37°C for temperature-sensitive variant p53 V143A and 42°C for wild-type p53. Refolding kinetics of p53 indicate that HSP70 causes transient exposure of p53 aggregate-prone domain(s). We propose that formation of HSP70- and MDM2-dependent protein coaggregates in tumours with high levels of these two proteins could be one of the mechanisms by which mutant p53 is stabilized. Moreover, sequestration of p73 tumour suppressor protein by these nuclear aggregates may lead to gain-of-function phenotypes. PMID:23251530
Interface-Resolving Simulation of Collision Efficiency of Cloud Droplets

NASA Astrophysics Data System (ADS)

Wang, Lian-Ping; Peng, Cheng; Rosa, Bodgan; Onishi, Ryo

2017-11-01

Small-scale air turbulence could enhance the geometric collision rate of cloud droplets while large-scale air turbulence could augment the diffusional growth of cloud droplets. Air turbulence could also enhance the collision efficiency of cloud droplets. Accurate simulation of collision efficiency, however, requires capture of the multi-scale droplet-turbulence and droplet-droplet interactions, which has only been partially achieved in the recent past using the hybrid direct numerical simulation (HDNS) approach. % where Stokes disturbance flow is assumed. The HDNS approach has two major drawbacks: (1) the short-range droplet-droplet interaction is not treated rigorously; (2) the finite-Reynolds number correction to the collision efficiency is not included. In this talk, using two independent numerical methods, we will develop an interface-resolved simulation approach in which the disturbance flows are directly resolved numerically, combined with a rigorous lubrication correction model for near-field droplet-droplet interaction. This multi-scale approach is first used to study the effect of finite flow Reynolds numbers on the droplet collision efficiency in still air. Our simulation results show a significant finite-Re effect on collision efficiency when the droplets are of similar sizes. Preliminary results on integrating this approach in a turbulent flow laden with droplets will also be presented. This work is partially supported by the National Science Foundation.
Estimates of olivine-basaltic melt electrical conductivity using a digital rock physics approach

NASA Astrophysics Data System (ADS)

Miller, Kevin J.; Montési, Laurent G. J.; Zhu, Wen-lu

2015-12-01

Estimates of melt content beneath fast-spreading mid-ocean ridges inferred from magnetotelluric tomography (MT) vary between 0.01 and 0.10. Much of this variation may stem from a lack of understanding of how the grain-scale melt geometry influences the bulk electrical conductivity of a partially molten rock, especially at low melt fraction. We compute bulk electrical conductivity of olivine-basalt aggregates over 0.02 to 0.20 melt fraction by simulating electric current in experimentally obtained partially molten geometries. Olivine-basalt aggregates were synthesized by hot-pressing San Carlos olivine and high-alumina basalt in a solid-medium piston-cylinder apparatus. Run conditions for experimental charges were 1.5 GPa and 1350 °C. Upon completion, charges were quenched and cored. Samples were imaged using synchrotron X-ray micro-computed tomography (μ-CT). The resulting high-resolution, 3-dimensional (3-D) image of the melt distribution constitutes a digital rock sample, on which numerical simulations were conducted to estimate material properties. To compute bulk electrical conductivity, we simulated a direct current measurement by solving the current continuity equation, assuming electrical conductivities for olivine and melt. An application of Ohm's Law yields the bulk electrical conductivity of the partially molten region. The bulk electrical conductivity values for nominally dry materials follow a power-law relationship σbulk = Cσmeltϕm with fit parameters m = 1.3 ± 0.3 and C = 0.66 ± 0.06. Laminar fluid flow simulations were conducted on the same partially molten geometries to obtain permeability, and the respective pathways for electrical current and fluid flow over the same melt geometry were compared. Our results indicate that the pathways for flow fluid are different from those for electric current. Electrical tortuosity is lower than fluid flow tortuosity. The simulation results are compared to existing experimental data, and the potential influence of volatiles and melt films on electrical conductivity of partially molten rocks is discussed.
Effect of supplementary implantation of a sulcus-fixated intraocular lens in patients with negative dysphotopsia.

PubMed

Makhotkina, Natalia Y; Dugrain, Vincent; Purchase, Daniel; Berendschot, Tos T J M; Nuijts, Rudy M M A

2018-02-01

To evaluate whether the outcome of negative dysphotopsia treatment by implantation of a Sulcoflex intraocular lens (IOL) can be understood using individual biometry and optical modeling data. University Eye Clinic, Maastricht University Medical Centre, Maastricht, the Netherlands. Retrospective case series. Patients with negative dysphotopsia were treated with supplementary implantation of a sulcus-fixated IOL. Preoperative and postoperative ray-tracing optical models of eyes with negative dysphotopsia were constructed in the Zemax Optic Studio program using individual biometric data. The relationship between biometric parameters, ray-tracing data, and the course of negative dysphotopsia was evaluated. The study comprised 8 patients (10 eyes). After surgery, negative dysphotopsia resolved completely in 6 eyes, partially in 2 eyes, and persisted in 2 eyes. There was no relationship between the course of negative dysphotopsia and age, IOL power, or individual biometry results other than a larger angle κ that was observed in 2 patients with persistent negative dysphotopsia after surgery. Preoperative ray-tracing models showed a decrease in light irradiance at the periphery relative to the center of visual field. After sulcus-fixated IOL implantation, this decrease partially resolved, in particular, for a small pupil aperture (P < .05), and it was more prominent in patients in whom negative dysphotopsia resolved completely than in those with partial or persistent negative dysphotopsia (P = .065 at 1.5 mm aperture). Of all individual biometry results, only angle κ showed a relationship with the course of negative dysphotopsia. In patient-specific optical modeling of sulcus-fixated IOL implantation, the increase in simulated light irradiance at the periphery was related to the course of negative dysphotopsia. Copyright © 2018 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.
Measures of health sciences journal use: a comparison of vendor, link-resolver, and local citation statistics*

PubMed Central

De Groote, Sandra L.; Blecic, Deborah D.; Martin, Kristin

2013-01-01

Objective: Libraries require efficient and reliable methods to assess journal use. Vendors provide complete counts of articles retrieved from their platforms. However, if a journal is available on multiple platforms, several sets of statistics must be merged. Link-resolver reports merge data from all platforms into one report but only record partial use because users can access library subscriptions from other paths. Citation data are limited to publication use. Vendor, link-resolver, and local citation data were examined to determine correlation. Because link-resolver statistics are easy to obtain, the study library especially wanted to know if they correlate highly with the other measures. Methods: Vendor, link-resolver, and local citation statistics for the study institution were gathered for health sciences journals. Spearman rank-order correlation coefficients were calculated. Results: There was a high positive correlation between all three data sets, with vendor data commonly showing the highest use. However, a small percentage of titles showed anomalous results. Discussion and Conclusions: Link-resolver data correlate well with vendor and citation data, but due to anomalies, low link-resolver data would best be used to suggest titles for further evaluation using vendor data. Citation data may not be needed as it correlates highly with other measures. PMID:23646026
Space and Time Resolved Detection of Platelet Activation and von Willebrand Factor Conformational Changes in Deep Suspensions.

PubMed

Biasetti, Jacopo; Sampath, Kaushik; Cortez, Angel; Azhir, Alaleh; Gilad, Assaf A; Kickler, Thomas S; Obser, Tobias; Ruggeri, Zaverio M; Katz, Joseph

2017-01-01

Tracking cells and proteins' phenotypic changes in deep suspensions is critical for the direct imaging of blood-related phenomena in in vitro replica of cardiovascular systems and blood-handling devices. This paper introduces fluorescence imaging techniques for space and time resolved detection of platelet activation, von Willebrand factor (VWF) conformational changes, and VWF-platelet interaction in deep suspensions. Labeled VWF, platelets, and VWF-platelet strands are suspended in deep cuvettes, illuminated, and imaged with a high-sensitivity EM-CCD camera, allowing detection using an exposure time of 1 ms. In-house postprocessing algorithms identify and track the moving signals. Recombinant VWF-eGFP (rVWF-eGFP) and VWF labeled with an FITC-conjugated polyclonal antibody are employed. Anti-P-Selectin FITC-conjugated antibodies and the calcium-sensitive probe Indo-1 are used to detect activated platelets. A positive correlation between the mean number of platelets detected per image and the percentage of activated platelets determined through flow cytometry is obtained, validating the technique. An increase in the number of rVWF-eGFP signals upon exposure to shear stress demonstrates the technique's ability to detect breakup of self-aggregates. VWF globular and unfolded conformations and self-aggregation are also observed. The ability to track the size and shape of VWF-platelet strands in space and time provides means to detect pro- and antithrombotic processes.
Discrimination, Crypticity and Incipient Taxa in Entamoeba1

PubMed Central

Espinosa, Avelina; Paz-y-Miño-C, Guillermo

2011-01-01

Persistent difficulties in resolving clear lineages in diverging populations of prokaryotes or unicellular eukaryotes (protistan polyphyletic groups) are challenging the classical species concept. Although multiple integrated approaches would render holistic taxonomies, most phylogenetic studies are still based on single-gene or morphological traits. Such methodologies conceal natural lineages, which are considered ‘cryptic’. The concept of species is considered artificial and inadequate to define natural populations. Social organisms display differential behaviors toward kin than to non-related individuals. In ‘social’ microbes, kin discrimination has been used to help resolve crypticity. Aggregative behavior could be explored in a non-social protist to define phylogenetic varieties that are considered ‘cryptic’. Two Entamoeba invadens strains, VK-1:NS and IP-1 are considered close populations of the same ‘species’. This study demonstrates that VK-1:NS and IP-1 trophozoites aggregate only with alike members and discriminate individuals from different strains based on behavioral and chemical signals. Combined morphological, behavioral/chemical and ecological studies could improve Archamoebae phylogenies and define cryptic varieties. Evolutionary processes in which selection acted continuously and cumulatively on ancestors of Entamoeba populations gave rise to behavioral and chemical signals that allowed individuals to discriminate non-population members and gradually, to new lineages; alternative views that claim a ‘Designer’ or ‘Creator’ as responsible for protistan diversity are unfounded. PMID:22299709
Conspecific aggregations mitigate the effects of ocean acidification on calcification of the coral Pocillopora verrucosa.

PubMed

Evensen, Nicolas R; Edmunds, Peter J

2017-03-15

In densely populated communities, such as coral reefs, organisms can modify the physical and chemical environment for neighbouring individuals. We tested the hypothesis that colony density (12 colonies each placed ∼0.5 cm apart versus ∼8 cm apart) can modulate the physiological response (measured through rates of calcification, photosynthesis and respiration in the light and dark) of the coral Pocillopora verrucosa to partial pressure of CO 2 ( P CO 2 ) treatments (∼400 μatm and ∼1200 μatm) by altering the seawater flow regimes experienced by colonies placed in aggregations within a flume at a single flow speed. While light calcification decreased 20% under elevated versus ambient P CO 2 for colonies in low-density aggregations, light calcification of high-density aggregations increased 23% at elevated versus ambient P CO 2 As a result, densely aggregated corals maintained calcification rates over 24 h that were comparable to those maintained under ambient P CO 2 , despite a 45% decrease in dark calcification at elevated versus ambient P CO 2 Additionally, densely aggregated corals experienced reduced flow speeds and higher seawater retention times between colonies owing to the formation of eddies. These results support recent indications that neighbouring organisms, such as the conspecific coral colonies in the present example, can create small-scale refugia from the negative effects of ocean acidification. © 2017. Published by The Company of Biologists Ltd.
Kinetic Studies of Inhibition of the Aβ(1–42) Aggregation Using a Ferrocene-tagged β-Sheet Breaker Peptide

PubMed Central

Zhang, Lin; Yagnik, Gargey; Peng, Yong; Wang, Jianxiu; Xu, H. Howard; Hao, Yuanqiang; Liu, You-Nian; Zhou, Feimeng

2013-01-01

The aggregation of amyloidogenic proteins/peptides has been closely linked to the neuropathology of several important neurological disorders. In Alzheimer's disease (AD), amyloid beta (Aβ) peptides and their aggregation are believed to be at least partially responsible for the etiology of AD. The aggregate-inflicted cellular toxicity can be inhibited by short peptides whose sequence are homologous to segments of the Aβ(1–42) peptide responsible for β-sheet stacking (referred to as the β-sheet breaker peptides). Herein a water-soluble ferrocene (Fc)-tagged β-sheet breaker peptide (Fc-KLVFFK6) is used as an electrochemical probe for kinetic studies of the inhibition of the Aβ(1–42) fibrillation process and for determination of the optimal concentration of β-sheet breaker peptide for efficient inhibition. Our results demonstrated that Fc-KLVFFK6 interacts with the Aβ aggregates instantaneously in solution, and sub-stoichiometric amount of Fc-KLVFFK6 is sufficient to inhibit the formation of the Aβ oligomers and fibrils and to reduce the toxicity of Aβ(1–42). The interaction between Fc-KLVFFK6 and Aβ(1–42) follows a pseudo-first-order reaction, with a rate constant of 1.89 ± 0.05 × 10−4 s−1. Tagging β-sheet breaker peptides with a redox label facilitates design, screening, and rational use of peptidic inhibitors for impeding/altering Aβ aggregation. PMID:23232068

Solvent and solute ingress into hydrogels resolved by a combination of imaging techniques

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

Wagner, D.; Burbach, J.; Egelhaaf, S. U.

2016-05-28

Using simultaneous neutron, fluorescence, and optical brightfield transmission imaging, the diffusion of solvent, fluorescent dyes, and macromolecules into a crosslinked polyacrylamide hydrogel was investigated. This novel combination of different imaging techniques enables us to distinguish the movements of the solvent and fluorescent molecules. Additionally, the swelling or deswelling of the hydrogels can be monitored. From the sequence of images, dye and solvent concentrations were extracted spatially and temporally resolved. Diffusion equations and different boundary conditions, represented by different models, were used to quantitatively analyze the temporal evolution of these concentration profiles and to determine the diffusion coefficients of solvent andmore » solutes. Solute size and network properties were varied and their effect was investigated. Increasing the crosslinking ratio or partially drying the hydrogel was found to hinder solute diffusion due to the reduced pore size. By contrast, solvent diffusion seemed to be slightly faster if the hydrogel was only partially swollen and hence solvent uptake enhanced.« less
Influence of hydrostatic pressure on dynamics and spatial distribution of protein partial molar volume: time-resolved surficial Kirkwood-Buff approach.

PubMed

Yu, Isseki; Tasaki, Tomohiro; Nakada, Kyoko; Nagaoka, Masataka

2010-09-30

The influence of hydrostatic pressure on the partial molar volume (PMV) of the protein apomyoglobin (AMb) was investigated by all-atom molecular dynamics (MD) simulations. Using the time-resolved Kirkwood-Buff (KB) approach, the dynamic behavior of the PMV was identified. The simulated time average value of the PMV and its reduction by 3000 bar pressurization correlated with experimental data. In addition, with the aid of the surficial KB integral method, we obtained the spatial distributions of the components of PMV to elucidate the detailed mechanism of the PMV reduction. New R-dependent PMV profiles identified the regions that increase or decrease the PMV under the high pressure condition. The results indicate that besides the hydration in the vicinity of the protein surface, the outer space of the first hydration layer also significantly influences the total PMV change. These results provide a direct and detailed picture of pressure induced PMV reduction.
Dynamic Computation of Change Operations in Version Management of Business Process Models

NASA Astrophysics Data System (ADS)

Küster, Jochen Malte; Gerth, Christian; Engels, Gregor

Version management of business process models requires that changes can be resolved by applying change operations. In order to give a user maximal freedom concerning the application order of change operations, position parameters of change operations must be computed dynamically during change resolution. In such an approach, change operations with computed position parameters must be applicable on the model and dependencies and conflicts of change operations must be taken into account because otherwise invalid models can be constructed. In this paper, we study the concept of partially specified change operations where parameters are computed dynamically. We provide a formalization for partially specified change operations using graph transformation and provide a concept for their applicability. Based on this, we study potential dependencies and conflicts of change operations and show how these can be taken into account within change resolution. Using our approach, a user can resolve changes of business process models without being unnecessarily restricted to a certain order.
Assessing coral reef health across onshore to offshore stress gradients in the US Virgin Islands.

PubMed

Smith, T B; Nemeth, R S; Blondeau, J; Calnan, J M; Kadison, E; Herzlieb, S

2008-12-01

Managing the effects of anthropogenic disturbance on coral reefs is highly dependant on effective strategies to assess degradation and recovery. We used five years of field data in the US Virgin Islands to investigate coral reef response to a potential gradient of stress. We found that the prevalence of old partial mortality, bleaching, and all forms of coral health impairment (a novel category) increased with nearshore anthropogenic processes, such as a five-fold higher rate of clay and silt sedimentation. Other patterns of coral health, such as recent partial mortality, other diseases, and benthic cover, did not respond to this potential gradient of stress or their response could not be resolved at the frequency or scale of monitoring. We suggest that persistent signs of disturbance are more useful to short-term, non-intensive (annual) coral reef assessments, but more intensive (semi-annual) assessments are necessary to resolve patterns of transient signs of coral health impairment.
Velocity-Resolved LES (VR-LES) technique for simulating turbulent transport of high Schmidt number passive scalars

NASA Astrophysics Data System (ADS)

Verma, Siddhartha; Blanquart, Guillaume; P. K. Yeung Collaboration

2011-11-01

Accurate simulation of high Schmidt number scalar transport in turbulent flows is essential to studying pollutant dispersion, weather, and several oceanic phenomena. Batchelor's theory governs scalar transport in such flows, but requires further validation at high Schmidt and high Reynolds numbers. To this end, we use a new approach with the velocity field fully resolved, but the scalar field only partially resolved. The grid used is fine enough to resolve scales up to the viscous-convective subrange where the decaying slope of the scalar spectrum becomes constant. This places the cutoff wavenumber between the Kolmogorov scale and the Batchelor scale. The subgrid scale terms, which affect transport at the supergrid scales, are modeled under the assumption that velocity fluctuations are negligible beyond this cutoff wavenumber. To ascertain the validity of this technique, we performed a-priori testing on existing DNS data. This Velocity-Resolved LES (VR-LES) technique significantly reduces the computational cost of turbulent simulations of high Schmidt number scalars, and yet provides valuable information of the scalar spectrum in the viscous-convective subrange.
Changes on aggregation in mine waste amended with biochar and marble mud

NASA Astrophysics Data System (ADS)

Ángeles Muñoz, María; Guzmán, Jose; Zornoza, Raúl; Moreno-Barriga, Fabián; Faz, Ángel; Lal, Rattan

2016-04-01

Mining activities have produced large amounts of wastes over centuries accumulated in tailing ponds in Southeast Spain. Applications of biochar may have a high potential for reclamation of degraded soils. Distribution, size and stability of aggregates are important indices of soil physical quality. However, research data on aggregation processes at amended mining tailings with biochar are scanty. Therefore, the aim of this study was to determine the effects of seven different treatments involving biochar and marble mud (MM) on the aggregation in mine waste (MW). Seven different treatments were tested after 90 days of incubation in the laboratory. These treatments were the mix of MW and: biochar from solid pig manure (PM), biochar from cotton crop residues (CR), biochar from municipal solid waste (MSW), marble mud (MM), PM+MM, CR+MM, MSW+MM and control without amendment. High sand percentages were identified in the MW. The biochars made from wastes (PM, CR, MSW) were obtained through pyrolysis of feedstocks. The water stability of soil aggregates was studied. The data on total aggregation were corrected for the primary particles considering the sandy texture of the MW. Moreover, partial aggregation was determined for each fraction and the mean weight diameter (MWD) of aggregates was computed. Soil bulk density and total porosity were also determined. No significant differences were observed in total aggregation and MWD among treatments including the control. For the size range of >4.75 mm, there were significant differences in aggregates > 4.75 mm between CR+MM in comparison with that for CT. There were also significant differences between MSW and PM+MM for the 1-0.425 mm fraction, and between CT and MM and CR for 0.425-0.162 mm aggregate size fractions. Therefore, CR-derived biochar applied with MM enhanced stability of macro-aggregates. Furthermore, soil bulk density was also the lowest bulk density and total porosity the highest for the CR-derived biochar treatment because macro aggregate stability is largely responsible for macro-porosity. The decrease in bulk density may be an indication of a positive effect for mine waste reclamation. Conversely, no differences were observed among treatments in micro-aggregate stability. Apparently, low organic matter contents in MW needed to be co-amended with labile organic amendments to effectively increase soil aggregation. Furthermore, the presence of Fe hydroxides could also increase the micro-aggregation. Additional research is needed to understand the mechanisms of mine soil reclamation. Acknowledgement : This work has been funded by Fundación Séneca (Agency of Science and Technology of the Region of Murcia, Spain
Von Willebrand's disease with spontaneous platelet aggregation induced by an abnormal plasma von Willebrand factor.

PubMed Central

Grainick, H R; Williams, S B; McKeown, L P; Rick, M E; Maisonneuve, P; Jenneau, C; Sultan, Y

1985-01-01

We have investigated and characterized the abnormalities in four unrelated patients with von Willebrand's disease (vWd) who have (a) enhanced ristocetin-induced platelet aggregation (RIPA) at low ristocetin concentrations, (b) absence of the largest plasma von Willebrand factor (vWf) multimers, and (c) thrombocytopenia. The platelet-rich plasma of these patients aggregates spontaneously without the addition of any agonists. When isolated normal platelets are resuspended in patient plasma spontaneous aggregation occurs; however, the patients' plasmas did not induce platelet aggregation of normal washed formalinized platelets. When the patients' platelets are suspended in normal plasma, spontaneous aggregation is not observed. The spontaneous platelet aggregation (SPA) is associated with dense granule secretion as measured by ATP release and alpha granule release as measured by beta-thromboglobulin and platelet factor 4 release. The SPA is totally inhibited by 5 mM EDTA, prostaglandin I2, and dibutryl cyclic AMP, while it is only partially inhibited by 1 mM EDTA, acetylsalicylic acid, or apyrase. A monoclonal antibody directed against glycoprotein Ib (GPIb) and/or a monoclonal antibody against the glycoprotein IIb/IIIa (GPIIb/IIIa) complex totally inhibits the SPA. The vWf was isolated from the plasma of one of these patients. The purified vWf induced platelet aggregation of normal platelets resuspended in either normal or severe vWd plasma, but the vWf did not induce platelet aggregation of normal platelets resuspended in afibrinognemic plasma. Sialic acid and galactose quantification of the patient's vWf revealed approximately a 50% reduction compared with normal vWf. These studies indicate that a form of vWd exists, which is characterized by SPA that is induced by the abnormal plasma vWf. The SPA is dependent on the presence of plasma fibrinogen, and the availability of the GPIb and the GPIIb/IIIa complex. In this variant form of vWd the abnormal vWf causes enhanced RIPA, SPA, and thrombocytopenia. Images PMID:2932469
Intrinsic Lens Forming Potential of Mouse Lens Epithelial versus Newt Iris Pigment Epithelial Cells in Three-Dimensional Culture

PubMed Central

Nakamura, Kenta; Tsonis, Panagiotis A.

2014-01-01

Adult newts (Notophthalmus viridescens) are capable of complete lens regeneration that is mediated through dorsal iris pigment epithelial (IPE) cells transdifferentiation. In contrast, higher vertebrates such as mice demonstrate only limited lens regeneration in the presence of an intact lens capsule with remaining lens epithelial cells. To compare the intrinsic lens regeneration potential of newt IPE versus mouse lens epithelial cells (MLE), we have established a novel culture method that uses cell aggregation before culture in growth factor-reduced Matrigel™. Dorsal newt IPE aggregates demonstrated complete lens formation within 1 to 2 weeks of Matrigel culture without basic fibroblast growth factor (bFGF) supplementation, including the establishment of a peripheral cuboidal epithelial cell layer, and the appearance of central lens fibers that were positive for αA-crystallin. In contrast, the lens-forming potential of MLE cell aggregates cultured in Matrigel was incomplete and resulted in the formation of defined-size lentoids with partial optical transparency. While the peripheral cell layers of MLE aggregates were nucleated, cells in the center of aggregates demonstrated a nonapoptotic nuclear loss over a time period of 3 weeks that was representative of lens fiber formation. Matrigel culture supplementation with bFGF resulted in higher transparent bigger-size MLE aggregates that demonstrated increased appearance of βB1-crystallin expression. Our study demonstrates that bFGF is not required for induction of newt IPE aggregate-dependent lens formation in Matrigel, while the addition of bFGF seems to be beneficial for the formation of MLE aggregate-derived lens-like structures. In conclusion, the three-dimensional aggregate culture of IPE and MLE in Matrigel allows to a higher extent than older models the indepth study of the intrinsic lens-forming potential and the corresponding identification of lentogenic factors. PMID:23672748
Periorbital hemangiomas.

PubMed

Goldberg, N S; Rosanova, M A

1992-10-01

1. Any hemangioma that involves the upper or lower lid and leads to partial closure in infancy may interfere with or prevent development of normal binocular vision in a matter of days to weeks. 2. Hemangiomas least likely to interfere with vision are lower lid lesions occupying one third of the lid margin or less, not extending beyond the eyelid region, and resolving early. 3. Hemangiomas associated with deprivation amblyopia (with or without anisometropia) are lesions occupying more than one half of the lid margin, extending beyond the eyelid region, resolving late, and obstructing the visual axis. 4. Hemangiomas associated with isolated anisometropic amblyopia are local but bulky lesions that are usually but not always restricted to the upper lid, closing the eye partly and resolving late. 5. The treatment of choice for periorbital hemangiomas is corticosteroids, either systemic or intralesional.
Communication: Electron ionization of DNA bases.

PubMed

Rahman, M A; Krishnakumar, E

2016-04-28

No reliable experimental data exist for the partial and total electron ionization cross sections for DNA bases, which are very crucial for modeling radiation damage in genetic material of living cell. We have measured a complete set of absolute partial electron ionization cross sections up to 500 eV for DNA bases for the first time by using the relative flow technique. These partial cross sections are summed to obtain total ion cross sections for all the four bases and are compared with the existing theoretical calculations and the only set of measured absolute cross sections. Our measurements clearly resolve the existing discrepancy between the theoretical and experimental results, thereby providing for the first time reliable numbers for partial and total ion cross sections for these molecules. The results on fragmentation analysis of adenine supports the theory of its formation in space.
Grain-resolving simulations of settling cohesive sediment

NASA Astrophysics Data System (ADS)

Vowinckel, Bernhard; Whithers, Jade; Meiburg, Eckart; Luzzatto-Fegiz, Paolo

2017-11-01

Cohesive sediment is ubiquitous in natural environments such as rivers, lakes and coastal ecosystems. For this type of sediment, we can no longer ignore the short-range attractive forces that result in flocculation of aggregates much larger than the individual grain size. Hence, understanding the complex dynamics of the interplay between flocculated sediment and the ambient fluid is of prime interest for managing aquatic environments, although a comprehensive understanding of these phenomena is still lacking. In the present study, we address this issue by carrying out grain-resolved simulations of cohesive particles settling under gravity using the Immersed Boundary Method. We present a computational model formulation to accurately resolve the process of flocculation. The cohesive model is then applied to a complex test case. A randomly distributed ensemble of 1261 polydisperse particles is released in a tank of quiescent fluid. Subsequently, particles start to settle, thereby replacing fluid at the bottom of the tank, which induces a counter flow opposing the settling direction. This mechanism will be compared to experimental studies from the literature, as well as to the non-cohesive counterpart to assessthe impact of flocculation on sedimentation.
Direct comparisons of X-ray scattering and atomistic molecular dynamics simulations for precise acid copolymers and ionomers

DOE PAGES

Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.; ...

2015-02-09

Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. Inmore » these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the average distance between branches of type 2 or 3 aggregates. Furthermore, this direct comparison of X-ray scattering data to the atomistic MD simulations is a substantive step toward providing a comprehensive, predictive model for ionomer morphology, gives substantial support for this atomistic MD model, and provides new credibility to the presence of stringy, branched, and percolated ionic aggregates in precise ionomer melts.« less
Protein Oxidation in Aging: Does It Play a Role in Aging Progression?

PubMed Central

Reeg, Sandra

2015-01-01

Abstract Significance: A constant accumulation of oxidized proteins takes place during aging. Oxidation of proteins leads to a partial unfolding and, therefore, to aggregation. Protein aggregates impair the activity of cellular proteolytic systems (proteasomes, lysosomes), resulting in further accumulation of oxidized proteins. In addition, the accumulation of highly crosslinked protein aggregates leads to further oxidant formation, damage to macromolecules, and, finally, to apoptotic cell death. Furthermore, protein oxidation seems to play a role in the development of various age-related diseases, for example, neurodegenerative diseases. Recent Advances: The highly oxidized lipofuscin accumulates during aging. Lipofuscin formation might cause impaired lysosomal and proteasomal degradation, metal ion accumulation, increased reactive oxygen species formation, and apoptosis. Critical Issues: It is still unclear to which extent protein oxidation is involved in the progression of aging and in the development of some age-related diseases. Future Directions: An extensive knowledge of the effects of protein oxidation on the aging process and its contribution to the development of age-related diseases could enable further strategies to reduce age-related impairments. Strategies aimed at lowering aggregate formation might be a straightforward intervention to reduce age-related malfunctions of organs. Antioxid. Redox Signal. 23, 239–255. PMID:25178482
Loss of keratin K2 expression causes aberrant aggregation of K10, hyperkeratosis, and inflammation.

PubMed

Fischer, Heinz; Langbein, Lutz; Reichelt, Julia; Praetzel-Wunder, Silke; Buchberger, Maria; Ghannadan, Minoo; Tschachler, Erwin; Eckhart, Leopold

2014-10-01

Keratin K2 is one of the most abundant structural proteins of the epidermis; however, its biological significance has remained elusive. Here we show that suprabasal type II keratins, K1 and K2, are expressed in a mutually exclusive manner at different body sites of the mouse, with K2 being confined to the ear, sole, and tail skin. Deletion of K2 caused acanthosis and hyperkeratosis of the ear and the tail epidermis, corneocyte fragility, increased transepidermal water loss, and local inflammation in the ear skin. The loss of K2 was partially compensated by upregulation of K1 expression. However, a significant portion of K2-deficient suprabasal keratinocytes lacked a regular cytoskeleton and developed massive aggregates of the type I keratin, K10. Aggregate formation, but not hyperkeratosis, was suppressed by the deletion of both K2 and K10, whereas deletion of K10 alone caused clumping of K2 in ear skin. Taken together, this study demonstrates that K2 is a necessary and sufficient binding partner of K10 at distinct body sites of the mouse and that unbalanced expression of these keratins results in aggregate formation.
Interaction between Paracoccidioides brasiliensis conidia and the coagulation system: involvement of fibrinogen

PubMed Central

Tamayo, Diana; Hernández, Orville; Muñoz-Cadavid, Cesar; Cano, Luz Elena; González, Angel

2013-01-01

The infectious process starts with an initial contact between pathogen and host. We have previously demonstrated that Paracoccidioides brasiliensis conidia interact with plasma proteins including fibrinogen, which is considered the major component of the coagulation system. In this study, we evaluated the in vitro capacity of P. brasiliensis conidia to aggregate with plasma proteins and compounds involved in the coagulation system. We assessed the aggregation of P. brasiliensis conidia after incubation with human serum or plasma in the presence or absence of anticoagulants, extracellular matrix (ECM) proteins, metabolic and protein inhibitors, monosaccharides and other compounds. Additionally, prothrombin and partial thromboplastin times were determined after the interaction of P. brasiliensis conidia with human plasma. ECM proteins, monosaccharides and human plasma significantly induced P. brasiliensis conidial aggregation; however, anticoagulants and metabolic and protein inhibitors diminished the aggregation process. The extrinsic coagulation pathway was not affected by the interaction between P. brasiliensis conidia and plasma proteins, while the intrinsic pathway was markedly altered. These results indicate that P. brasiliensis conidia interact with proteins involved in the coagulation system. This interaction may play an important role in the initial inflammatory response, as well as fungal disease progression caused by P. brasiliensis dissemination. PMID:23827999
Tensile strength and fracture of cemented granular aggregates.

PubMed

Affes, R; Delenne, J-Y; Monerie, Y; Radjaï, F; Topin, V

2012-11-01

Cemented granular aggregates include a broad class of geomaterials such as sedimentary rocks and some biomaterials such as the wheat endosperm. We present a 3D lattice element method for the simulation of such materials, modeled as a jammed assembly of particles bound together by a matrix partially filling the interstitial space. From extensive simulation data, we analyze the mechanical properties of aggregates subjected to tensile loading as a function of matrix volume fraction and particle-matrix adhesion. We observe a linear elastic behavior followed by a brutal failure along a fracture surface. The effective stiffness before failure increases almost linearly with the matrix volume fraction. We show that the tensile strength of the aggregates increases with both the increasing tensile strength at the particle-matrix interface and decreasing stress concentration as a function of matrix volume fraction. The proportion of broken bonds in the particle phase reveals a range of values of the particle-matrix adhesion and matrix volume fraction for which the cracks bypass the particles and hence no particle damage occurs. This limit is shown to depend on the relative toughness of the particle-matrix interface with respect to the particles.
Characterization of a protein conjugate using an asymmetrical-flow field-flow fractionation and a size-exclusion chromatography with multi-detection system.

PubMed

Rebolj, Katja; Pahovnik, David; Zagar, Ema

2012-09-04

In this study we present detailed characterization of a protein-PEG conjugate using two separation techniques, that is, asymmetrical-flow field-flow fractionation (AF4) and size-exclusion chromatography (SEC), which were online coupled to a series of successively connected detectors: an ultraviolet, a multiangle light-scattering, a quasi-elastic light-scattering, and a refractive-index detector (UV-MALS(QELS)-RI). Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used as a complementary characterization technique. The results of AF4 as well as SEC on two columns connected in series, with both separation techniques coupled to a multidetection system, indicate the uniform molar mass and chemical composition of the conjugate, that is, the molar ratio of protein to PEG is 1/1, the presence of minute amounts of residual unreacted protein and the aggregates with the same chemical composition as that of the conjugate. Since the portion of aggregated species is smaller in the acetate buffer solution containing 5% sorbitol than in the acetate buffer solution with 200-mM sodium chloride, the former buffer solution is more suitable for conjugate storage. The separation using only one SEC column results in poorly resolved peaks of the PEGylated protein conjugate and the aggregates, whereas MALDI-TOF MS analysis reveal the presence of the residual protein, but not the aggregates.
In situ imaging of ultra-fast loss of nanostructure in nanoparticle aggregates

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

Egan, Garth C.; Sullivan, Kyle T.; LaGrange, Thomas

2014-02-28

The word “nanoparticle” nominally elicits a vision of an isolated sphere; however, the vast bulk of nanoparticulate material exists in an aggregated state. This can have significant implications for applications such as combustion, catalysis, and optical excitation, where particles are exposed to high temperature and rapid heating conditions. In such environments, particles become susceptible to morphological changes which can reduce surface area, often to the detriment of functionality. Here, we report on thermally-induced coalescence which can occur in aluminum nanoparticle aggregates subjected to rapid heating (10{sup 6}–10{sup 11} K/s). Using dynamic transmission electron microscopy, we observed morphological changes in nanoparticle aggregatesmore » occurring in as little as a few nanoseconds after the onset of heating. The time-resolved probes reveal that the morphological changes initiate within 15 ns and are completed in less than 50 ns. The morphological changes were found to have a threshold temperature of about 1300 ± 50 K, as determined by millisecond-scale experiments with a calibrated heating stage. The temperature distribution of aggregates during laser heating was modeled with various simulation approaches. The results indicate that, under rapid heating conditions, coalescence occurs at an intermediate temperature between the melting points of aluminum and the aluminum oxide shell, and proceeds rapidly once this threshold temperature is reached.« less
Aggregation Rates of Sediments (Montmorillonite, Kaolinite, Illite and Goethite) with the Enveloped Φ6 Bacteriophage

NASA Astrophysics Data System (ADS)

Katz, A.; Block, K. A.; Peña, S.; Alimova, A.; Gottlieb, P.

2015-12-01

The interaction between sediments and viruses has been studied extensively from the prospective of virus survivability and infectivity. However, the role of soil organisms, including viruses in C and N sequestration in soil has not been studied as extensively. Φ6, a member of the cystoviridae family, is a bacteriophage that infects Pseudomonas syringae, a common plant pathogen known to readily form biofilms.The small mineral fraction (< 0.2 μm) of soil and Φ6 are colloidal particles, therefore aggregation can be explained by DLVO (Derjaguin & Landau, Verwey & Overbeek) theory. Time-resolved visible-light turbidity measurements were used to calculate the heteroaggregation rates of Φ6 with the sediments. Samples were suspended in a low-concentration cation buffer so that the kinetics were in the reaction limited cluster aggregation (RLCA) regime in where the probability of two particles adhering after collision is determined by the interaction forces between the particles.At neutral pH to slightly acidic pH, Φ6 is slightly negatively charged; montmorillonite and illite are negatively charged; and kaolinite and goethite are positively charged. In isolation, neither Φ6 nor the sediments aggregated in the modified buffer. However, in mixtures, Φ6 and montmorillonite, and Φ6 and illite, exhibited increases in turbidity, indicating heteroaggregation. Neither Φ6 and kaolinite, nor Φ6 and goethite, exhibited increased turbidity upon mixing indicating little or no aggregation. These results suggest that the interaction of the virus with the sediments is governed by hydrophobic rather than electrostatic forces. Heteroaggregation rates were calculated from the time rate of change of the turbidity.
Aggregation of gluten proteins in model dough after fibre polysaccharide addition.

PubMed

Nawrocka, Agnieszka; Szymańska-Chargot, Monika; Miś, Antoni; Wilczewska, Agnieszka Z; Markiewicz, Karolina H

2017-09-15

FT-Raman spectroscopy, thermogravimetry and differential scanning calorimetry were used to study changes in structure of gluten proteins and their thermal properties influenced by four dietary fibre polysaccharides (microcrystalline cellulose, inulin, apple pectin and citrus pectin) during development of a model dough. The flour reconstituted from wheat starch and wheat gluten was mixed with the polysaccharides in five concentrations: 3%, 6%, 9%, 12% and 18%. The obtained results showed that all polysaccharides induced similar changes in secondary structure of gluten proteins concerning formation of aggregates (1604cm -1 ), H-bonded parallel- and antiparallel-β-sheets (1690cm -1 ) and H-bonded β-turns (1664cm -1 ). These changes concerned mainly glutenins since β-structures are characteristic for them. The observed structural changes confirmed hypothesis about partial dehydration of gluten network after polysaccharides addition. The gluten aggregation and dehydration processes were also reflected in the DSC results, while the TGA ones showed that gluten network remained thermally stable after polysaccharides addition. Copyright © 2017 Elsevier Ltd. All rights reserved.

Amyloidogenesis abolished by proline substitutions but enhanced by lipid binding.

PubMed

Jiang, Ping; Xu, Weixin; Mu, Yuguang

2009-04-01

The influence of lipid molecules on the aggregation of a highly amyloidogenic segment of human islet amyloid polypeptide, hIAPP20-29, and the corresponding sequence from rat has been studied by all-atom replica exchange molecular dynamics (REMD) simulations with explicit solvent model. hIAPP20-29 fragments aggregate into partially ordered beta-sheet oligomers and then undergo large conformational reorganization and convert into parallel/antiparallel beta-sheet oligomers in mixed in-register and out-of-register patterns. The hydrophobic interaction between lipid tails and residues at positions 23-25 is found to stabilize the ordered beta-sheet structure, indicating a catalysis role of lipid molecules in hIAPP20-29 self-assembly. The rat IAPP variants with three proline residues maintain unstructured micelle-like oligomers, which is consistent with non-amyloidogenic behavior observed in experimental studies. Our study provides the atomic resolution descriptions of the catalytic function of lipid molecules on the aggregation of IAPP peptides.
High pCO2-induced exopolysaccharide-rich ballasted aggregates of planktonic cyanobacteria could explain Paleoproterozoic carbon burial.

PubMed

Kamennaya, Nina A; Zemla, Marcin; Mahoney, Laura; Chen, Liang; Holman, Elizabeth; Holman, Hoi-Ying; Auer, Manfred; Ajo-Franklin, Caroline M; Jansson, Christer

2018-05-29

The contribution of planktonic cyanobacteria to burial of organic carbon in deep-sea sediments before the emergence of eukaryotic predators ~1.5 Ga has been considered negligible owing to the slow sinking speed of their small cells. However, global, highly positive excursion in carbon isotope values of inorganic carbonates ~2.22-2.06 Ga implies massive organic matter burial that had to be linked to oceanic cyanobacteria. Here to elucidate that link, we experiment with unicellular planktonic cyanobacteria acclimated to high partial CO 2 pressure (pCO 2 ) representative of the early Paleoproterozoic. We find that high pCO 2 boosts generation of acidic extracellular polysaccharides (EPS) that adsorb Ca and Mg cations, support mineralization, and aggregate cells to form ballasted particles. The down flux of such self-assembled cyanobacterial aggregates would decouple the oxygenic photosynthesis from oxidative respiration at the ocean scale, drive export of organic matter from surface to deep ocean and sustain oxygenation of the planetary surface.
Amyloidogenesis Abolished by Proline Substitutions but Enhanced by Lipid Binding

PubMed Central

Jiang, Ping; Xu, Weixin; Mu, Yuguang

2009-01-01

The influence of lipid molecules on the aggregation of a highly amyloidogenic segment of human islet amyloid polypeptide, hIAPP20–29, and the corresponding sequence from rat has been studied by all-atom replica exchange molecular dynamics (REMD) simulations with explicit solvent model. hIAPP20–29 fragments aggregate into partially ordered β-sheet oligomers and then undergo large conformational reorganization and convert into parallel/antiparallel β-sheet oligomers in mixed in-register and out-of-register patterns. The hydrophobic interaction between lipid tails and residues at positions 23–25 is found to stabilize the ordered β-sheet structure, indicating a catalysis role of lipid molecules in hIAPP20–29 self-assembly. The rat IAPP variants with three proline residues maintain unstructured micelle-like oligomers, which is consistent with non-amyloidogenic behavior observed in experimental studies. Our study provides the atomic resolution descriptions of the catalytic function of lipid molecules on the aggregation of IAPP peptides. PMID:19360098
Preparation of gold nanoparticle aggregates and their photothermal heating property.

PubMed

Kim, Jun-Hyun; Lavin, Brian W

2011-01-01

This report describes simple synthetic strategies to prepare partially aggregated gold nanoparticles (GNPs) and their ability to produce photothermally-induced heating of an aqueous medium upon exposure to broadband light. The formation of various GNPs and their aggregates were accomplished in the absence of surfactants at room temperature. The morphologies, structures, and absorption properties of these GNPs were carefully characterized. Given that the resulting GNPs possessing strong and wide absorption bands fall in the most intense solar radiation spectrum, the photothermally-induced heating of water was examined in the presence of the GNPs via irradiation with a solar simulator (i.e., 100 mW/cm2; 1-sun condition). Our GNPs exhibited a slightly greater increase in the water temperature (3-4 degrees C) than that of conventional citrate-stabilized GNPs. This superior photothermal heating property of our GNPs directly indicated that the intense and broad absorption band effectively improved the conversion of highly absorbed photon energy into heat.
Aggregation of γ-crystallins associated with human cataracts via domain swapping at the C-terminal β-strands

PubMed Central

Das, Payel; King, Jonathan A.; Zhou, Ruhong

2011-01-01

The prevalent eye disease age-onset cataract is associated with aggregation of human γD-crystallins, one of the longest-lived proteins. Identification of the γ-crystallin precursors to aggregates is crucial for developing strategies to prevent and reverse cataract. Our microseconds of atomistic molecular dynamics simulations uncover the molecular structure of the experimentally detected aggregation-prone folding intermediate species of monomeric native γD-crystallin with a largely folded C-terminal domain and a mostly unfolded N-terminal domain. About 30 residues including a, b, and c strands from the Greek Key motif 4 of the C-terminal domain experience strong solvent exposure of hydrophobic residues as well as partial unstructuring upon N-terminal domain unfolding. Those strands comprise the domain–domain interface crucial for unusually high stability of γD-crystallin. We further simulate the intermolecular linkage of these monomeric aggregation precursors, which reveals domain-swapped dimeric structures. In the simulated dimeric structures, the N-terminal domain of one monomer is frequently found in contact with residues 135–164 encompassing the a, b, and c strands of the Greek Key motif 4 of the second molecule. The present results suggest that γD-crystallin may polymerize through successive domain swapping of those three C-terminal β-strands leading to age-onset cataract, as an evolutionary cost of its very high stability. Alanine substitutions of the hydrophobic residues in those aggregation-prone β-strands, such as L145 and M147, hinder domain swapping as a pathway toward dimerization. These findings thus provide critical molecular insights onto the initial stages of age-onset cataract, which is important for understanding protein aggregation diseases. PMID:21670251
Adsorption Properties of p -Methyl Red Monomeric-to-Pentameric Dye Aggregates on Anatase (101) Titania Surfaces: First-Principles Calculations of Dye/TiO 2 Photoanode Interfaces for Dye-Sensitized Solar Cells

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

Zhang, Lei; Cole, Jacqueline M.

2014-08-29

The optical and electronic properties of dye aggregates of p-methyl red on a TiO2 anatase (101) surface were modeled as a function of aggregation order (monomer to pentameric dye) via first principles calculations. A progressive red-shifting and intensity increase toward the visible region in UV/vis absorption spectra is observed from monomeric-to-tetrameric dyes, with each molecule in a given aggregate binding to one of the four possible TiO2 (101) adsorption sites. The pentamer exhibits a blue-shifted peak wave- length in the UV/vis absorption spectra and less absorption intensity in the visible region in comparison; a corresponding manifestation of H-aggregation occurs sincemore » one of these five molecules cannot occupy an adsorption site. This finding is consistent with experiment. Calculated density of states (DOS) and partial DOS spectra reveal similar dye…TiO2 nanocomposite conduction band characteristics but different valence band features. Associated molecular orbital distributions reveal dye-to-TiO2 interfacial charge transfer in all five differing aggregate orders; meanwhile, the level of intramolecular charge transfer in the dye becomes progressively localized around its azo- and electron-donating groups, up to the tetrameric dye/TiO2 species. Dye adsorption energies and dye coverage levels are calculated and compared with experiment. Overall, the findings of this case study serve to aid the molecular design of azo dyes towards better performing DSSC devices wherein they are incorporated. In addition, they provide a helpful example reference for understanding the effects of dye aggregation on the adsorbate…TiO2 interfacial optical and electronic properties.« less
Signal transduction, plasma membrane calcium movements, and pigment translocation in freshwater shrimp chromatophores.

PubMed

Milograna, Sarah Ribeiro; Bell, Fernanda Tinti; McNamara, John Campbell

2010-11-01

Crustacean color change results from the differential translocation of chromatophore pigments, regulated by neurosecretory peptides like red pigment concentrating hormone (RPCH) that, in the red ovarian chromatophores of the freshwater shrimp Macrobrachium olfersi, triggers pigment aggregation via increased cytosolic cGMP and Ca(2+) of both smooth endoplasmatic reticulum (SER) and extracellular origin. However, Ca(2+) movements during RPCH signaling and the mechanisms that regulate intracellular [Ca(2+)] are enigmatic. We investigate Ca(2+) transporters in the chromatophore plasma membrane and Ca(2+) movements that occur during RPCH signal transduction. Inhibition of the plasma membrane Ca(2+)-ATPase by La(3+) and indirect inhibition of the Na(+)/Ca(2+) exchanger by ouabain induce pigment aggregation, revealing a role for both in Ca(2+) extrusion. Ca(2+) channel blockade by La(3+) or Cd(2+) strongly inhibits slow-phase RPCH-triggered aggregation during which pigments disperse spontaneously. L-type Ca(2+) channel blockade by gabapentin markedly reduces rapid-phase translocation velocity; N- or P/Q-type blockade by ω-conotoxin MVIIC strongly inhibits RPCH-triggered aggregation and reduces velocity, effects revealing RPCH-signaled influx of extracellular Ca(2+). Plasma membrane depolarization, induced by increasing external K(+) from 5 to 50 mM, produces Ca(2+)-dependent pigment aggregation, whereas removal of K(+) from the perfusate causes pigment hyperdispersion, disclosing a clear correlation between membrane depolarization and pigment aggregation; K(+) channel blockade by Ba(2+) also partially inhibits RPCH action. We suggest that, during RPCH signal transduction, Ca(2+) released from the SER, together with K(+) channel closure, causes chromatophore membrane depolarization, leading to the opening of predominantly N- and/or P/Q-type voltage-gated Ca(2+) channels, and a Ca(2+)/cGMP cascade, resulting in pigment aggregation.
Evaluation of conceptual models of natural organic matter (humus) from a consideration of the chemical and biochemical processes of humification

USGS Publications Warehouse

Wershaw, Robert L.

2004-01-01

Natural organic matter (NOM) has been studied for more than 200 years because of its importance in enhancing soil fertility, soil structure, and water-holding capacity and as a carbon sink in the global carbon cycle. Two different types of models have been proposed for NOM: (1) the humic polymer models and (2) the molecular aggregate models. In the humic polymer models, NOM molecules are depicted as large (humic) polymers that have unique chemical structures that are different from those of the precursor plant degradation products. In the molecular aggregate models, NOM is depicted as being composed of molecular aggregates (supramolecular aggregates) of plant degradation products held together by non-covalent bonds. The preponderance of evidence favors the supramolecular aggregate models. These models were developed by studying the properties of NOM extracted from soils and natural waters, and as such, they provide only a very generalized picture of the structure of NOM aggregates in soils and natural waters prior to extraction. A compartmental model, in which the structure of the NOM in each of the compartments is treated separately, should provide a more accurate representation of NOM in soil and sediment systems. The proposed NOM compartments are: (1) partially degraded plant tissue, (2) biomass from microorganisms, (3) organic coatings on mineral grains, (4) pyrolytic carbon, (5) organic precipitates, and (6) dissolved organic matter (DOM) in interstitial water. Within each of these compartments there are NOM supramolecular aggregates that will be dissolved by the solvent systems that are used by researchers for extraction of NOM from soils and sediments. In natural water systems DOM may be considered as existing in two subcompartments: (1) truly dissolved DOM and (2) colloidal DOM.
The second Cu(II)-binding site in a proton-rich environment interferes with the aggregation of amyloid-beta(1-40) into amyloid fibrils.

PubMed

Jun, Sangmi; Gillespie, Joel R; Shin, Byong-kyu; Saxena, Sunil

2009-11-17

The overall morphology and Cu(II) ion coordination for the aggregated amyloid-beta(1-40) [Abeta(1-40)] in N-ethylmorpholine (NEM) buffer are affected by Cu(II) ion concentration. This effect is investigated by transmission electron microscopy (TEM), atomic force microscopy (AFM), and electron spin echo envelope modulation (ESEEM) spectroscopy. At lower than equimolar concentrations of Cu(II) ions, fibrillar aggregates of Abeta(1-40) are observed. At these concentrations of Cu(II), the monomeric and fibrillar Abeta(1-40) ESEEM data indicate that the Cu(II) ion is coordinated by histidine residues. For aggregated Abeta(1-40) at a Cu(II):Abeta molar ratio of 2:1, TEM and AFM images show both linear fibrils and granular amorphous aggregates. The ESEEM spectra show that the multi-histidine coordination for Cu(II) ion partially breaks up and becomes exposed to water or exchangeable protons of the peptide at a higher Cu(II) concentration. Since the continuous-wave electron spin resonance results also suggest two copper-binding sites in Abeta(1-40), the proton ESEEM peak may arise from the second copper-binding site, which may be significantly involved in the formation of granular amorphous aggregates. Thioflavin T fluorescence and circular dichroism experiments also show that Cu(II) inhibits the formation of fibrils and induces a nonfibrillar beta-sheet conformation. Therefore, we propose that Abeta(1-40) has a second copper-binding site in a proton-rich environment and the second binding Cu(II) ion interferes with a conformational transition into amyloid fibrils, inducing the formation of granular amorphous aggregates.
The Dictyostelium MAP kinase kinase DdMEK1 regulates chemotaxis and is essential for chemoattractant-mediated activation of guanylyl cyclase.

PubMed Central

Ma, H; Gamper, M; Parent, C; Firtel, R A

1997-01-01

We have identified a MAP kinase kinase (DdMEK1) that is required for proper aggregation in Dictyostelium. Null mutations produce extremely small aggregate sizes, resulting in the formation of slugs and terminal fruiting bodies that are significantly smaller than those of wild-type cells. Time-lapse video microscopy and in vitro assays indicate that the cells are able to produce cAMP waves that move through the aggregation domains. However, these cells are unable to undergo chemotaxis properly during aggregation in response to the chemoattractant cAMP or activate guanylyl cyclase, a known regulator of chemotaxis in Dictyostelium. The activation of guanylyl cyclase in response to osmotic stress is, however, normal. Expression of putative constitutively active forms of DdMEK1 in a ddmek1 null background is capable, at least partially, of complementing the small aggregate size defect and the ability to activate guanylyl cyclase. However, this does not result in constitutive activation of guanylyl cyclase, suggesting that DdMEK1 activity is necessary, but not sufficient, for cAMP activation of guanylyl cyclase. Analysis of a temperature-sensitive DdMEK1 mutant suggests that DdMEK1 activity is required throughout aggregation at the time of guanylyl cyclase activation, but is not essential for proper morphogenesis during the later multicellular stages. The activation of the MAP kinase ERK2, which is essential for chemoattractant activation of adenylyl cyclase, is not affected in ddmek1 null strains, indicating that DdMEK1 does not regulate ERK2 and suggesting that at least two independent MAP kinase cascades control aggregation in Dictyostelium. PMID:9250676
Mathematical model of macrophage-facilitated breast cancer cells invasion.

PubMed

Knútsdóttir, Hildur; Pálsson, Eirikur; Edelstein-Keshet, Leah

2014-09-21

Mortality from breast cancer stems from its tendency to invade into surrounding tissues and organs. Experiments have shown that this metastatic process is facilitated by macrophages in a short-ranged chemical signalling loop. Macrophages secrete epidermal growth factor, EGF, and respond to the colony stimulating factor 1, CSF-1. Tumor cells secrete CSF-1 and respond to EGF. In this way, the cells coordinate aggregation and cooperative migration. Here we investigate this process in a model for in vitro interactions using two distinct but related mathematical approaches. In the first, we analyze and simulate a set of partial differential equations to determine conditions for aggregation. In the second, we use a cell-based discrete 3D simulation to follow the fates and motion of individual cells during aggregation. Linear stability analysis of the PDE model reveals that decreasing the chemical secretion, chemotaxis coefficients or density of cells or increasing the chemical degradation in the model could eliminate the spontaneous aggregation of cells. Simulations with the discrete model show that the ratio between tumor cells and macrophages in aggregates increases when the EGF secretion parameter is increased. The results also show how CSF-1/CSF-1R autocrine signalling in tumor cells affects the ratio between the two cell types. Comparing the continuum results with simulations of a discrete cell-based model, we find good qualitative agreement. Copyright © 2014 Elsevier Ltd. All rights reserved.
Steel slag: a waste industrial by-product as an alternative sustainable green building material in construction applications--an attempt for solid waste management.

PubMed

Pofale, Arun D; Nadeem, Mohammed

2012-01-01

This investigation explores the possibility of utilizing granular slag as an alternative to fine aggregate (natural sand) in construction applications like masonry and plastering. Construction industry utilizes large volume of fine aggregate in all the applications which has resulted into shortage of good quality naturally available fine aggregate. Use of granular slag serves two fold purposes, i.e. waste utilisation as well as alternative eco-friendly green building material for construction. The investigation highlights comparative study of properties with partial and full replacement of fine aggregate (natural sand) by granular slag in cement mortar applications (masonry and plastering). For this purpose, cement mortar mix proportions from 1:3, 1:4, 1:5 & 1:6 by volume were selected for 0, 25, 50, 75 & 100% replacement levels with w/c ratios of 0.60, 0.65, 0.70 & 0.72 respectively. Based on the study results, it could be inferred that replacement of natural sand with granular slag from 25 to 75% increased the packing density of mortar which resulted into reduced w/c ratio, increased strength properties of all mortar mixes. Hence, it could be recommended that the granular slag could be effectively utilized as fine aggregate in masonry and plastering applications in place of conventional cement mortar mixes using natural sand.
Aggregation-induced chemical reactions: acid dissociation in growing water clusters.

PubMed

Forbert, Harald; Masia, Marco; Kaczmarek-Kedziera, Anna; Nair, Nisanth N; Marx, Dominik

2011-03-23

Understanding chemical reactivity at ultracold conditions, thus enabling molecular syntheses via interstellar and atmospheric processes, is a key issue in cryochemistry. In particular, acid dissociation and proton transfer reactions are ubiquitous in aqueous microsolvation environments. Here, the full dissociation of a HCl molecule upon stepwise solvation by a small number of water molecules at low temperatures, as relevant to helium nanodroplet isolation (HENDI) spectroscopy, is analyzed in mechanistic detail. It is found that upon successive aggregation of HCl with H(2)O molecules, a series of cyclic heteromolecular structures, up to and including HCl(H(2)O)(3), are initially obtained before a precursor state for dissociation, HCl(H(2)O)(3)···H(2)O, is observed upon addition of a fourth water molecule. The latter partially aggregated structure can be viewed as an "activated species", which readily leads to dissociation of HCl and to the formation of a solvent-shared ion pair, H(3)O(+)(H(2)O)(3)Cl(-). Overall, the process is mostly downhill in potential energy, and, in addition, small remaining barriers are overcome by using kinetic energy released as a result of forming hydrogen bonds due to aggregation. The associated barrier is not ruled by thermal equilibrium but is generated by athermal non-equilibrium dynamics. These "aggregation-induced chemical reactions" are expected to be of broad relevance to chemistry at ultralow temperature much beyond HENDI spectroscopy.
Photoinduced Disaggregation of TiO2 Nanoparticles Enables Transdermal Penetration

PubMed Central

Bennett, Samuel W.; Zhou, Dongxu; Mielke, Randall; Keller, Arturo A.

2012-01-01

Under many aqueous conditions, metal oxide nanoparticles attract other nanoparticles and grow into fractal aggregates as the result of a balance between electrostatic and Van Der Waals interactions. Although particle coagulation has been studied for over a century, the effect of light on the state of aggregation is not well understood. Since nanoparticle mobility and toxicity have been shown to be a function of aggregate size, and generally increase as size decreases, photo-induced disaggregation may have significant effects. We show that ambient light and other light sources can partially disaggregate nanoparticles from the aggregates and increase the dermal transport of nanoparticles, such that small nanoparticle clusters can readily diffuse into and through the dermal profile, likely via the interstitial spaces. The discovery of photoinduced disaggregation presents a new phenomenon that has not been previously reported or considered in coagulation theory or transdermal toxicological paradigms. Our results show that after just a few minutes of light, the hydrodynamic diameter of TiO2 aggregates is reduced from ∼280 nm to ∼230 nm. We exposed pigskin to the nanoparticle suspension and found 200 mg kg−1 of TiO2 for skin that was exposed to nanoparticles in the presence of natural sunlight and only 75 mg kg−1 for skin exposed to dark conditions, indicating the influence of light on NP penetration. These results suggest that photoinduced disaggregation may have important health implications. PMID:23155401
Canopy arthropod response to density and distribution of green trees retained after partial harvest.

Treesearch

Timothy D. Schowalter; Yanli Zhang; Robert A. Progar

2005-01-01

We measured canopy arthropod responses to six contrasting green-tree retention treatments at six locations (blocks) in western Oregon and Washington as part of the Demonstration of Ecosystem Management Options (DEMO) study. Treatments were 100% retention (uncut), 75% retention with three 1-ha harvested gaps, 40% dispersed retention, 40% aggregated retention with five 1...
Amyloidogenesis of Natively Unfolded Proteins

PubMed Central

Uversky, Vladimir N.

2009-01-01

Aggregation and subsequent development of protein deposition diseases originate from conformational changes in corresponding amyloidogenic proteins. The accumulated data support the model where protein fibrillogenesis proceeds via the formation of a relatively unfolded amyloidogenic conformation, which shares many structural properties with the pre-molten globule state, a partially folded intermediate first found during the equilibrium and kinetic (un)folding studies of several globular proteins and later described as one of the structural forms of natively unfolded proteins. The flexibility of this structural form is essential for the conformational rearrangements driving the formation of the core cross-beta structure of the amyloid fibril. Obviously, molecular mechanisms describing amyloidogenesis of ordered and natively unfolded proteins are different. For ordered protein to fibrillate, its unique and rigid structure has to be destabilized and partially unfolded. On the other hand, fibrillogenesis of a natively unfolded protein involves the formation of partially folded conformation; i.e., partial folding rather than unfolding. In this review recent findings are surveyed to illustrate some unique features of the natively unfolded proteins amyloidogenesis. PMID:18537543
Properties of palm oil fuel ash cement sand brick containing pulverized cockle shell as partial sand replacement

NASA Astrophysics Data System (ADS)

Mat Aris, S.; Muthusamy, K.; Uzer, A.; Ahmad, S. Wan

2018-04-01

Environmental pollution caused by the disposal of solid wastes generated from both palm oil industry and cockle shell trade has motivated researches to explore the potential of these wastes. Integrating these wastes in production of construction material is one of the ways to reduce amount of waste thrown at dumping area. Thus, the present investigation investigates the performance of palm oil fuel ash (POFA) cement sand brick containing pulverized cockle shell as partial fine aggregate replacement. All mixes used contain 20% of POFA as partial cement replacement. Total of six mixes were prepared by adding a range of pulverized cockle shell that is 0%, 10%, 20%, 30%, 40% and 50% as partial sand replacement. The mixes were prepared in form of brick. All the water cured samples were tested for compressive strength and flexural strength until 28 days. Findings show that brick produced using 20% pulverized cockle shell exhibit the highest compressive strength and flexural strength also the lowest water absorption value.
Preliminary results of sulfide melt/silicate wetting experiments in a partially melted ordinary chondrite

NASA Technical Reports Server (NTRS)

Jurewicz, Stephen R.; Jones, John H.

1994-01-01

Recently, mechanisms for core formation in planetary bodies have received considerable attention. Most current theories emphasize the need for large degrees of silicate partial melting to facilitate the coalescence and sinking of sulfide-metal liquid blebs through a low strength semi-crystalline silicate mush. This scenario is based upon observations that sulfide-metal liquid tends to form circular blebs in partially molten meteorites during laboratory experiments. However, recent experimental work by Herpfer and Larimer indicates that some sulfide-Fe liquids have wetting angles at and slightly below 60 deg in an olivine aggregate, implying an interconnected melt structure at any melt fraction. Such melt interconnectivity provides a means for gravitational compaction and extraction of the majority of a sulfide liquid phase in small planetary bodies without invoking large degrees of silicate partial melting. Because of the important ramifications of these results, we conducted a series of experiments using H-chondrite starting material in order to evaluate sulfide-liquid/silicate wetting behavior in a more complex natural system.
Mechanisms of protein misfolding: Novel therapeutic approaches to protein-misfolding diseases

NASA Astrophysics Data System (ADS)

Salahuddin, Parveen; Siddiqi, Mohammad Khursheed; Khan, Sanaullah; Abdelhameed, Ali Saber; Khan, Rizwan Hasan

2016-11-01

In protein misfolding, protein molecule acquires wrong tertiary structure, thereby induces protein misfolding diseases. Protein misfolding can occur through various mechanisms. For instance, changes in environmental conditions, oxidative stress, dominant negative mutations, error in post-translational modifications, increase in degradation rate and trafficking error. All of these factors cause protein misfolding thereby leading to diseases conditions. Both in vitro and in vivo observations suggest that partially unfolded or misfolded intermediates are particularly prone to aggregation. These partially misfolded intermediates aggregate via the interaction with the complementary intermediates and consequently enhance oligomers formation that grows into fibrils and proto-fibrils. The amyloid fibrils for example, accumulate in the brain and central nervous system (CNS) as amyloid deposits in the Parkinson's disease (PD), Alzheimer's disease (AD), Prion disease and Amylo lateral Sclerosis (ALS). Furthermore, tau protein shows intrinsically disorder conformation; therefore its interaction with microtubule is impaired and this protein undergoes aggregation. This is also underlying cause of Alzheimers and other neurodegenerative diseases. Treatment of such misfolding maladies is considered as one of the most important challenges of the 21st century. Currently, several treatments strategies have been and are being discovered. These therapeutic interventions partly reversed or prevented the pathological state. More recently, a new approach was discovered, which employs nanobodies that targets multisteps in fibril formation pathway that may possibly completely cure these misfolding diseases. Keeping the above views in mind in the current review, we have comprehensively discussed the different mechanisms underlying protein misfolding thereby leading to diseases conditions and their therapeutic interventions.
Assessing the Potential Consequences of Subsurface Bioremediation: Fe-oxide Bioreductive Processes and the Propensity for Contaminant-colloid Co-transport and Media Structural Breakdown

DTIC Science & Technology

2017-05-12

were resolved by a technical approach that included three well-integrated experimental tasks follows: Task A: Quantify the impact of time- dependent ...aggregate breakdown and colloid dispersion depending on the extent of Fe(III) reduction and altered the pore structure and chemical reactivity of the porous...have significant effect on the transport of molecular and colloidal tracers (but not on the ionic tracer Br-) and colloid generation depending on

Stability region maximization by decomposition-aggregation method. [Skylab stability

NASA Technical Reports Server (NTRS)

Siljak, D. D.; Cuk, S. M.

1974-01-01

This work is to improve the estimates of the stability regions by formulating and resolving a proper maximization problem. The solution of the problem provides the best estimate of the maximal value of the structural parameter and at the same time yields the optimum comparison system, which can be used to determine the degree of stability of the Skylab. The analysis procedure is completely computerized, resulting in a flexible and powerful tool for stability considerations of large-scale linear as well as nonlinear systems.
Femtosecond timing measurement and control using ultrafast organic thin films

NASA Astrophysics Data System (ADS)

Naruse, Makoto; Mitsu, Hiroyuki; Furuki, Makoto; Iwasa, Izumi; Sato, Yasuhiro; Tatsuura, Satoshi; Tian, Minquan

2003-12-01

We show a femtosecond timing measurement and control technique using a squarylium dye J-aggregate film, which is an organic thin film that acts as an ultrafast two-dimensional optical switch. Optical pulse timing is directly mapped to space-domain position on the film, and the large area and ultrafast response offer a femtosecond-resolved, large dynamic range, real-time, multichannel timing measurement capability. A timing fluctuation (jitter, wander, and skew) reduction architecture is presented and experimentally demonstrated.
Women with Red Hair Report A Slightly Increased Rate of Bruising, but Have Normal Coagulation Tests

PubMed Central

Liem, Edwin B.; Hollensead, Sandra C.; Joiner, Teresa V.

2005-01-01

There is an anecdotal impression that redheads experience more perioperative bleeding complications than those with other hair colors. We, therefore, tested the hypothesis that perceived problems with hemostasis could be detected with commonly used coagulation tests. Se studied healthy female Caucasian volunteers, 18 to 40 years, comparable in terms of height, weight, and age, with natural bright red (n = 25) or black or dark brown (n = 26) hair. Volunteers were questioned about their bleeding history and the following tests were performed: complete blood count, prothrombin time/international normalized ratio, activated partial thromboplastin time, platelet function analysis (PFA-100), and platelet aggregation using standard turbidimetric methodology. Agonists for aggregation were adenosine diphosphate, arachidonic acid, collagen, epinephrine, and two concentrations of ristocetin. The red-haired volunteers reported significantly more bruising, but there were no significant differences between the red- and dark-haired groups in hemoglobin concentration, platelet numbers, prothrombin time/international normalized ratio, or activated partial thromboplastin time. Furthermore, no significant differences in platelet function, as measured with the PFA-100 or with platelet aggregometry, were observed. We conclude that if redheads have hemostasis abnormalities, they are subtle. PMID:16368849
Modeling thermionic emission from laser-heated nanoparticles

DOE PAGES

Mitrani, J. M.; Shneider, M. N.; Stratton, B. C.; ...

2016-02-01

An adjusted form of thermionic emission is applied to calculate emitted current from laser-heated nanoparticles and to interpret time-resolved laser-induced incandescence (TR-LII) signals. This adjusted form of thermionic emission predicts significantly lower values of emitted current compared to the commonly used Richardson-Dushman equation, since the buildup of positive charge in a laser-heated nanoparticle increases the energy barrier for further emission of electrons. Thermionic emission influences the particle's energy balance equation, which can influence TR-LII signals. Additionally, reports suggest that thermionic emission can induce disintegration of nanoparticle aggregates when the electrostatic Coulomb repulsion energy between two positively charged primary particles ismore » greater than the van der Waals bond energy. Furthermore, since the presence and size of aggregates strongly influences the particle's energy balance equation, using an appropriate form of thermionic emission to calculate emitted current may improve interpretation of TR-LII signals.« less
In Vitro Self-Assembly of the Light Harvesting Pigment-Protein LH2 Revealed by Ultrafast Spectroscopy and Electron Microscopy

PubMed Central

Schubert, Axel; Stenstam, Anna; Beenken, Wichard J. D.; Herek, Jennifer L.; Cogdell, Richard; Pullerits, Tõnu; Sundström, Villy

2004-01-01

Controlled ensemble formation of protein-surfactant systems provides a fundamental concept for the realization of nanoscale devices with self-organizing capability. In this context, spectroscopic monitoring of pigment-containing proteins yields detailed structural information. Here we have studied the association behavior of the bacterial light-harvesting protein LH2 from Rhodobacter spheroides in an n,n-dimethyldodecylamine-n-oxide/water environment. Time-resolved studies of the excitation annihilation yielded information about aggregate sizes and packing of the protein complexes therein. The results are compared to transmission electron microscopy images of instantaneously frozen samples. Our data indicate the manifestation of different phases, which are discussed with respect to the thermodynamic equilibrium in ternary protein-surfactant-water systems. Accordingly, by varying the concentration the formation of different types of aggregates can be controlled. Conditions for the appearance of isolated LH2 complexes are defined. PMID:15041674
Structural and electronic properties of extremely long perylene bisimide nanofibers formed through a stoichiometrically mismatched, hydrogen-bonded complexation.

PubMed

Yagai, Shiki; Seki, Tomohiro; Murayama, Haruno; Wakikawa, Yusuke; Ikoma, Tadaaki; Kikkawa, Yoshihiro; Karatsu, Takashi; Kitamura, Akihide; Honsho, Yoshihito; Seki, Shu

2010-12-06

Extremely long nanofibers, whose lengths reach the millimeter regime, are generated via co-aggregation of a melamine-appended perylene bisimide semiconductor and a substituted cyanurate, both of which are ditopic triple-hydrogen-bonding building blocks; they co-aggregate in an unexpected stoichiometrically mismatched 1:2 ratio. Various microscopic and X-ray diffraction studies suggest that hydrogen-bonded polymeric chains are formed along the long axis of the nanofibers by the 1:2 complexation of the two components, which further stack along the short axis of the nanofibers. The photocarrier generation mechanism in the nanofibers is investigated by time-of-flight (TOF) experiments under electric and magnetic fields, revealing the birth and efficient recombination of singlet geminate electron-hole pairs. Flash-photolysis time-resolved microwave conductivity (FP-TRMC) measurements revealed intrinsic 1D electron mobilities up to 0.6 cm(2) V(-1) s(-1) within nanofibers.
Anthropogenic iron oxide aerosols enhance atmospheric heating

NASA Astrophysics Data System (ADS)

Moteki, Nobuhiro; Adachi, Kouji; Ohata, Sho; Yoshida, Atsushi; Harigaya, Tomoo; Koike, Makoto; Kondo, Yutaka

2017-05-01

Combustion-induced carbonaceous aerosols, particularly black carbon (BC) and brown carbon (BrC), have been largely considered as the only significant anthropogenic contributors to shortwave atmospheric heating. Natural iron oxide (FeOx) has been recognized as an important contributor, but the potential contribution of anthropogenic FeOx is unknown. In this study, we quantify the abundance of FeOx over East Asia through aircraft measurements using a modified single-particle soot photometer. The majority of airborne FeOx particles in the continental outflows are of anthropogenic origin in the form of aggregated magnetite nanoparticles. The shortwave absorbing powers (Pabs) attributable to FeOx and to BC are calculated on the basis of their size-resolved mass concentrations and the mean Pabs(FeOx)/Pabs(BC) ratio in the continental outflows is estimated to be at least 4-7%. We demonstrate that in addition to carbonaceous aerosols the aggregate of magnetite nanoparticles is a significant anthropogenic contributor to shortwave atmospheric heating.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Seiple, Timothy E.; Coleman, André M.; Skaggs, Richard L.

Within the United States and Puerto Rico, publicly owned treatment works (POTWs) process 130.5 Gl/d (34.5 Bgal/d) of wastewater, producing sludge as a waste product. Emerging technologies offer novel waste-to-energy pathways through whole sludge conversion into biofuels. Assessing the feasibility, scalability and tradeoffs of various energy conversion pathways is difficult in the absence of highly spatially resolved estimates of sludge production. In this study, average wastewater solids concentrations and removal rates, and site specific daily average influent flow are used to estimate site specific annual sludge production on a dry weight basis for >15,000 POTWs. Current beneficial uses, regional productionmore » hotspots and feedstock aggregation potential are also assessed. Analyses indicate 1) POTWs capture 12.56 Tg/y (13.84 MT/y) of dry solids; 2) 50% are not beneficially utilized, and 3) POTWs can support seven regions that aggregate >910 Mg/d (1000 T/d) of sludge within a travel distance of 100 km.« less
Surface Pb nanoparticle aggregation, coalescence and differential capacitance in a deep eutectic solvent using a simultaneous sample-rotated small angle x-ray scattering and electrochemical methods approach [Surface Pb nanoparticle aggregation, coalescence and differential capacitance in a deep eutectic solvent using a simultaneous grazing transmission small angle x-ray scattering and electrochemical methods approach

DOE PAGES

Hammons, Joshua A.; Ilavsky, Jan

2017-01-18

Nanoparticle electrodeposition is a simple and scalable approach to synthesizing supported nanoparticles. Used with a deep eutectic solvent (DES), surface nanoparticles can be assembled and exhibit unique surface charge separation when the DES is adsorbed on the nanoparticle surface. Key to understanding and controlling the assembly and the capacitance is a thorough understanding of surface particle mobility and charge screening, which requires an in-situ approach. In this study, Pb particle formation, size, shape and capacitance are resolved in a 1:2 choline Cl –: urea deep eutectic solvent whilst sweeping the cell potential in the range: 0.2 V to –1.2 Vmore » (vs. Ag/AgCl). These system parameters were resolved using a complementary suite of sample-rotated small angle X-ray scattering (SR-SAXS) and electrochemical impedance spectroscopy (EIS), which are presented and discussed in detail. This approach is able to show that both particle and ion transport are impeded in the DES, as aggregation occurs over the course of 6 minutes, and dissolved Pb ions accumulate and remain near the surface after a nucleation pulse is applied. The DES-Pb interactions strongly depend on the cell potential as evidenced by the specific differential capacitance of the Pb deposit, which has a maximum value of 2.5 +/– 0.5 F g –1 at –1.0 V vs. Ag/AgCl. Together, the SR-SAXS-EIS approach is able to characterize the unique nanoparticle capacitance, mobility and ion mobility in a DES and can be used to study a wide range of nanoparticle deposition systems in-situ.« less
Surface Pb nanoparticle aggregation, coalescence and differential capacitance in a deep eutectic solvent using a simultaneous sample-rotated small angle x-ray scattering and electrochemical methods approach [Surface Pb nanoparticle aggregation, coalescence and differential capacitance in a deep eutectic solvent using a simultaneous grazing transmission small angle x-ray scattering and electrochemical methods approach

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

Hammons, Joshua A.; Ilavsky, Jan

Nanoparticle electrodeposition is a simple and scalable approach to synthesizing supported nanoparticles. Used with a deep eutectic solvent (DES), surface nanoparticles can be assembled and exhibit unique surface charge separation when the DES is adsorbed on the nanoparticle surface. Key to understanding and controlling the assembly and the capacitance is a thorough understanding of surface particle mobility and charge screening, which requires an in-situ approach. In this study, Pb particle formation, size, shape and capacitance are resolved in a 1:2 choline Cl –: urea deep eutectic solvent whilst sweeping the cell potential in the range: 0.2 V to –1.2 Vmore » (vs. Ag/AgCl). These system parameters were resolved using a complementary suite of sample-rotated small angle X-ray scattering (SR-SAXS) and electrochemical impedance spectroscopy (EIS), which are presented and discussed in detail. This approach is able to show that both particle and ion transport are impeded in the DES, as aggregation occurs over the course of 6 minutes, and dissolved Pb ions accumulate and remain near the surface after a nucleation pulse is applied. The DES-Pb interactions strongly depend on the cell potential as evidenced by the specific differential capacitance of the Pb deposit, which has a maximum value of 2.5 +/– 0.5 F g –1 at –1.0 V vs. Ag/AgCl. Together, the SR-SAXS-EIS approach is able to characterize the unique nanoparticle capacitance, mobility and ion mobility in a DES and can be used to study a wide range of nanoparticle deposition systems in-situ.« less
Interaction of partially denatured insulin with a DSPC floating lipid bilayer.

PubMed

Dennison, A J C; Jones, R A L; Staniforth, R A; Parnell, A J

2016-01-21

The carefully controlled permeability of cellular membranes to biological molecules is key to life. In degenerative diseases associated with protein misfolding and aggregation, protein molecules or their aggregates are believed to permeate these barriers and threaten membrane integrity. We used neutron reflectivity to study the interaction of insulin, a model amyloidogenic protein, with a DSPC floating lipid bilayer. Structural changes consistent with protein partitioning to the membrane interior and adsorption to a gel phase model lipid bilayer were observed under conditions where the native fold of the protein is significantly destabilised. We propose that the perturbation of the membrane by misfolded proteins involves long term occupation of the membrane by these proteins, rather than transient perforation events.
Crime, shame, reintegration, and cross-national homicide: a partial test of reintegrative shaming theory.

PubMed

Schaible, Lonnie M; Hughes, Lorine A

2011-01-01

Reintegrative shaming theory (RST) argues that social aggregates characterized by high levels of communitarianism and nonstigmatizing shaming practices benefit from relatively low levels of crime. We combine aggregate measures from the World Values Survey with available macro-level data to test this hypothesis. Additionally, we examine the extent to which communitarianism and shaming mediate the effects of cultural and structural factors featured prominently in other macro-level theoretical frameworks (e.g., inequality, modernity, sex ratio, etc.). Findings provide some support for RST, showing homicide to vary with societal levels of communitarianism and informal stigmatization. However, while the effects of modernity and sex ratio were mediated by RST processes, suppression was indicated for economic inequality. Implications for theory and research are discussed.
Genetic structure of lake whitefish (Coregonus clupeaformis) in Lake Michigan

USGS Publications Warehouse

VanDeHey, J.A.; Sloss, Brian L.; Peeters, Paul J.; Sutton, T.M.

2009-01-01

Genetic relationships among lake whitefish (Coregonus clupeaformis) spawning aggregates in Lake Michigan were assessed and used to predict a stock or management unit (MU) model for the resource. We hypothesized that distinct spawning aggregates represented potential MUs and that differences at molecular markers underlie population differentiation. Genetic stock identification using 11 microsatellite loci indicated the presence of six genetic MUs. Resolved MUs corresponded to geographically proximate spawning aggregates clustering into genetic groups. Within MUs, analyses suggested that all but one delineated MU was a stable grouping (i.e., no between-population differences), with the exception being the Hog Island - Traverse Bay grouping. Elk Rapids was the most genetically divergent population within Lake Michigan. However, low F st values suggested that moderate to high levels of gene flow occur or have occurred in the past between MUs. Significant tests of isolation by distance and low pairwise Fst values potentially led to conflicting results between traditional analyses and a Bayesian approach. This data set could provide baseline data from which a comprehensive mixed-stock analysis could be performed, allowing for more efficient and effective management of this economically and socially important resource.
Microstructure of β-Sitosterol:γ-Oryzanol Edible Organogels.

PubMed

Matheson, Andrew B; Koutsos, Vasileios; Dalkas, Georgios; Euston, Stephen; Clegg, Paul

2017-05-09

Rheology and atomic force microscopy (AFM) were employed to examine the microstructure of β-sitosterol:γ-oryzanol organogels in sunflower oil. Using time-resolved rheology, we followed gel formation, paying specific attention to the fibril aggregation process, which had not been studied in detail previously for this system. Using AFM, we observed gel structures directly and obtained detailed information on the gel structure, far exceeding previous studies. Our analysis suggests that though gels are formed by the self-assembly and aggregation of one-dimensional fibrils, the manner in which these fibrils aggregate into ribbons results in complex structures of higher dimensionality. We emphasize that it is a surprise to find ribbons and not twisted strands. Comparing AFM images of 10% w/w and 20% w/w gelator systems, we observed differences in the degree of branching which are consistent with the rheology. We also observed the individual self-assembled fibrils which make up these gels with much greater clarity than in previous microscopy studies, and the fibril diameters of ∼9.8 nm we measured agree excellently with those obtained from existing small-angle neutron scattering data. These results provide new insight into the structure and formation kinetics of this important organogel system.
A method of transition conflict resolving in hierarchical control

NASA Astrophysics Data System (ADS)

Łabiak, Grzegorz

2016-09-01

The paper concerns the problem of automatic solving of transition conflicts in hierarchical concurrent state machines (also known as UML state machine). Preparing by the designer a formal specification of a behaviour free from conflicts can be very complex. In this paper, it is proposed a method for solving conflicts through transition predicates modification. Partially specified predicates in the nondeterministic diagram are transformed into a symbolic Boolean space, whose points of the space code all possible valuations of transition predicates. Next, all valuations under partial specifications are logically multiplied by a function which represents all possible orthogonal predicate valuations. The result of this operation contains all possible collections of predicates, which under given partial specification make that the original diagram is conflict free and deterministic.
Possible induction of West syndrome by oxcarbazepine therapy in a patient with complex partial seizures.

PubMed

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

2012-03-01

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

PubMed Central

Upadhyay, Arun K.; Murmu, Aruna; Singh, Anupam; Panda, Amulya K.

2012-01-01

The objective of the research was to understand the structural determinants governing protein aggregation into inclusion bodies during expression of recombinant proteins in Escherichia coli. Recombinant human growth hormone (hGH) and asparaginase were expressed as inclusion bodies in E.coli and the kinetics of aggregate formation was analyzed in details. Asparaginase inclusion bodies were of smaller size (200 nm) and the size of the aggregates did not increase with induction time. In contrast, the seeding and growth behavior of hGH inclusion bodies were found to be sequential, kinetically stable and the aggregate size increased from 200 to 800 nm with induction time. Human growth hormone inclusion bodies showed higher resistance to denaturants and proteinase K degradation in comparison to those of asparaginase inclusion bodies. Asparaginase inclusion bodies were completely solubilized at 2–3 M urea concentration and could be refolded into active protein, whereas 7 M urea was required for complete solubilization of hGH inclusion bodies. Both hGH and asparaginase inclusion bodies showed binding with amyloid specific dyes. In spite of its low β-sheet content, binding with dyes was more prominent in case of hGH inclusion bodies than that of asparaginase. Arrangements of protein molecules present in the surface as well as in the core of inclusion bodies were similar. Hydrophobic interactions between partially folded amphiphillic and hydrophobic alpha-helices were found to be one of the main determinants of hGH inclusion body formation. Aggregation behavior of the protein molecules decides the nature and properties of inclusion bodies. PMID:22479486
Soil compaction: Evaluation of stress transmission and resulting soil structure

NASA Astrophysics Data System (ADS)

Naveed, Muhammad; Schjønning, Per; Keller, Thomas; Lamande, Mathieu

2016-04-01

Accurate estimation of stress transmission and resultant deformation in soil profiles is a prerequisite for the development of predictive models and decision support tools for preventing soil compaction. Numerous studies have been carried out on the effects of soil compaction, whilst relatively few studies have focused on the cause (mode of stress transmission in the soil). We have coupled both cause and effects together in the present study by carrying out partially confined compression tests on (1) wet aggregates, (2) air dry aggregates, and (3) intact soils to quantify stress transmission and compaction-resulted soil structure at the same time. Stress transmission was quantified using both X-ray CT and Tactilus sensor mat, and soil-pore structure was quantified using X-ray CT. Our results imply that stress transmission through soil highly depends on the magnitude of applied load and aggregate strength. As soon as the applied load is lower than the aggregate strength, the mode of stress transmission is discrete as stresses were mainly transmitted through chain of aggregates. With increasing applied load soil aggregates start deforming that transformed heterogeneous soil into homogenous, as a result stress transmission mode was shifted from discrete towards more like a continuum. Continuum-like stress transmission mode was better simulated with Boussinesq (1885) model based on theory of elasticity compared to discrete. The soil-pore structure was greatly affected by increasing applied stresses. Total porosity was reduced 5-16% and macroporosity 50-85% at 620 kPa applied stress for the intact soils. Similarly, significant changes in the morphological indices of the macropore space were also observed with increasing applied stresses.
Soil aggregation, erodibility, and erosion rates in mountain soils (NW Alps, Italy)

NASA Astrophysics Data System (ADS)

Stanchi, S.; Falsone, G.; Bonifacio, E.

2015-04-01

Erosion is a relevant soil degradation factor in mountain agrosilvopastoral ecosystems that can be enhanced by the abandonment of agricultural land and pastures left to natural evolution. The on-site and off-site consequences of soil erosion at the catchment and landscape scale are particularly relevant and may affect settlements at the interface with mountain ecosystems. RUSLE (Revised Universal Soil Loss Equation) estimates of soil erosion consider, among others, the soil erodibility factor (K), which depends on properties involved in structure and aggregation. A relationship between soil erodibility and aggregation should therefore be expected. However, erosion may limit the development of soil structure; hence aggregates should not only be related to erodibility but also partially mirror soil erosion rates. The aim of the research was to evaluate the agreement between aggregate stability and erosion-related variables and to discuss the possible reasons for discrepancies in the two kinds of land use considered (forest and pasture). Topsoil horizons were sampled in a mountain catchment under two vegetation covers (pasture vs. forest) and analyzed for total organic carbon, total extractable carbon, pH, and texture. Soil erodibility was computed, RUSLE erosion rate was estimated, and aggregate stability was determined by wet sieving. Aggregation and RUSLE-related parameters for the two vegetation covers were investigated through statistical tests such as ANOVA, correlation, and regression. Soil erodibility was in agreement with the aggregate stability parameters; i.e., the most erodible soils in terms of K values also displayed weaker aggregation. Despite this general observation, when estimating K from aggregate losses the ANOVA conducted on the regression residuals showed land-use-dependent trends (negative average residuals for forest soils, positive for pastures). Therefore, soil aggregation seemed to mirror the actual topsoil conditions better than soil erodibility. Several hypotheses for this behavior were discussed. A relevant effect of the physical protection of the organic matter by the aggregates that cannot be considered in K computation was finally hypothesized in the case of pastures, while in forests soil erodibility seemed to keep trace of past erosion and depletion of finer particles. A good relationship between RUSLE soil erosion rates and aggregate stability occurred in pastures, while no relationship was visible in forests. Therefore, soil aggregation seemed to capture aspects of actual vulnerability that are not visible through the erodibility estimate. Considering the relevance and extension of agrosilvopastoral ecosystems partly left to natural colonization, further studies on litter and humus protective action might improve the understanding of the relationship among erosion, erodibility, and structure.
The yeast Holliday junction resolvase, CCE1, can restore wild-type mitochondrial DNA to human cells carrying rearranged mitochondrial DNA.

PubMed

Sembongi, Hiroshi; Di Re, Miriam; Bokori-Brown, Monika; Holt, Ian J

2007-10-01

Rearrangements of mitochondrial DNA (mtDNA) are a well-recognized cause of human disease; deletions are more frequent, but duplications are more readily transmitted to offspring. In theory, partial duplications of mtDNA can be resolved to partially deleted and wild-type (WT) molecules, via homologous recombination. Therefore, the yeast CCE1 gene, encoding a Holliday junction resolvase, was introduced into cells carrying partially duplicated or partially triplicated mtDNA. Some cell lines carrying the CCE1 gene had substantial amounts of WT mtDNA suggesting that the enzyme can mediate intramolecular recombination in human mitochondria. However, high levels of expression of CCE1 frequently led to mtDNA loss, and so it is necessary to strictly regulate the expression of CCE1 in human cells to ensure the selection and maintenance of WT mtDNA.

Communication: Electron ionization of DNA bases

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

Rahman, M. A.; Krishnakumar, E., E-mail: ekkumar@tifr.res.in

2016-04-28

No reliable experimental data exist for the partial and total electron ionization cross sections for DNA bases, which are very crucial for modeling radiation damage in genetic material of living cell. We have measured a complete set of absolute partial electron ionization cross sections up to 500 eV for DNA bases for the first time by using the relative flow technique. These partial cross sections are summed to obtain total ion cross sections for all the four bases and are compared with the existing theoretical calculations and the only set of measured absolute cross sections. Our measurements clearly resolve themore » existing discrepancy between the theoretical and experimental results, thereby providing for the first time reliable numbers for partial and total ion cross sections for these molecules. The results on fragmentation analysis of adenine supports the theory of its formation in space.« less
Resolved magnetic-field structure and variability near the event horizon of Sagittarius A.

PubMed

Johnson, Michael D; Fish, Vincent L; Doeleman, Sheperd S; Marrone, Daniel P; Plambeck, Richard L; Wardle, John F C; Akiyama, Kazunori; Asada, Keiichi; Beaudoin, Christopher; Blackburn, Lindy; Blundell, Ray; Bower, Geoffrey C; Brinkerink, Christiaan; Broderick, Avery E; Cappallo, Roger; Chael, Andrew A; Crew, Geoffrey B; Dexter, Jason; Dexter, Matt; Freund, Robert; Friberg, Per; Gold, Roman; Gurwell, Mark A; Ho, Paul T P; Honma, Mareki; Inoue, Makoto; Kosowsky, Michael; Krichbaum, Thomas P; Lamb, James; Loeb, Abraham; Lu, Ru-Sen; MacMahon, David; McKinney, Jonathan C; Moran, James M; Narayan, Ramesh; Primiani, Rurik A; Psaltis, Dimitrios; Rogers, Alan E E; Rosenfeld, Katherine; SooHoo, Jason; Tilanus, Remo P J; Titus, Michael; Vertatschitsch, Laura; Weintroub, Jonathan; Wright, Melvyn; Young, Ken H; Zensus, J Anton; Ziurys, Lucy M

2015-12-04

Near a black hole, differential rotation of a magnetized accretion disk is thought to produce an instability that amplifies weak magnetic fields, driving accretion and outflow. These magnetic fields would naturally give rise to the observed synchrotron emission in galaxy cores and to the formation of relativistic jets, but no observations to date have been able to resolve the expected horizon-scale magnetic-field structure. We report interferometric observations at 1.3-millimeter wavelength that spatially resolve the linearly polarized emission from the Galactic Center supermassive black hole, Sagittarius A*. We have found evidence for partially ordered magnetic fields near the event horizon, on scales of ~6 Schwarzschild radii, and we have detected and localized the intrahour variability associated with these fields. Copyright © 2015, American Association for the Advancement of Science.
Continuum modeling of twinning, amorphization, and fracture: theory and numerical simulations

NASA Astrophysics Data System (ADS)

Clayton, J. D.; Knap, J.

2018-03-01

A continuum mechanical theory is used to model physical mechanisms of twinning, solid-solid phase transformations, and failure by cavitation and shear fracture. Such a sequence of mechanisms has been observed in atomic simulations and/or experiments on the ceramic boron carbide. In the present modeling approach, geometric quantities such as the metric tensor and connection coefficients can depend on one or more director vectors, also called internal state vectors. After development of the general nonlinear theory, a first problem class considers simple shear deformation of a single crystal of this material. For homogeneous fields or stress-free states, algebraic systems or ordinary differential equations are obtained that can be solved by numerical iteration. Results are in general agreement with atomic simulation, without introduction of fitted parameters. The second class of problems addresses the more complex mechanics of heterogeneous deformation and stress states involved in deformation and failure of polycrystals. Finite element calculations, in which individual grains in a three-dimensional polycrystal are fully resolved, invoke a partially linearized version of the theory. Results provide new insight into effects of crystal morphology, activity or inactivity of different inelasticity mechanisms, and imposed deformation histories on strength and failure of the aggregate under compression and shear. The importance of incorporation of inelastic shear deformation in realistic models of amorphization of boron carbide is noted, as is a greater reduction in overall strength of polycrystals containing one or a few dominant flaws rather than many diffusely distributed microcracks.
Illuminating the early signaling pathway of a fungal light-oxygen-voltage photoreceptor.

PubMed

Peter, Emanuel; Dick, Bernhard; Baeurle, Stephan A

2012-02-01

Circadian clocks are molecular timekeepers encountered in a wide variety of organisms, which allow to adapt the cell's metabolism and behavior to the daily and seasonal periods. Their function is regulated by light-sensing proteins, among which Vivid, a light-oxygen-voltage (LOV) sensitive domain of the fungus Neurospora crassa, constitutes one of the most prominent examples. Although the major photochemical and structural changes during the photocycle of this photosensor have been elucidated through experimental means, its signal transduction pathway is still poorly resolved at the molecular level. In this article, we show through molecular dynamics simulation that the primary steps after adduct formation involve a switch of Gln182 in vicinity of the chromophore FAD (flavin-adenine-dinucleotide), followed by a coupling between the Iβ- and Hβ-strands through H-bond formation between Gln182 and Asn161 as well as subsequent weakening of the H-bonding interaction between the Iβ- and Aβ-strands. These processes then induce a reorientation of the Aβ-Bβ-loop with respect to the protein core as well as a simultaneous contraction of the partially unfolded α-helix onto the α-Aβ-linker at the Ncap. Finally, we demonstrate through additional dimer simulations that the light-induced conformational changes, observed in the monomeric case, play a decisive role in controlling the dimerization tendency of Vivid with its partner domains and that the light-state homodimer shows a much larger affinity for aggregation than the dark state. Copyright © 2011 Wiley Periodicals, Inc.
Reaction Mechanism for Direct Propylene Epoxidation by Alumina-Supported Silver Aggregates. The Role of the Particle / Support Interface

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

Cheng, Lei; Yin, Chunrong; Mehmood, Faisal

2013-11-21

Sub-nanometer Ag aggregates on alumina supports have been found to be active toward direct propylene epoxidation to propylene oxide by molecular oxygen at low temperatures, with a negligible amount of carbon dioxide formation (Science 328, p. 224, 2010). In this work, we computationally and experimentally investigate the origin of the high reactivity of the sub-nanometer Ag aggregates. Computationally, we study O 2 dissociation and propylene epoxidation on unsupported Ag 19 and Ag 20 clusters, as well as alumina-supported Ag 19. The O 2 dissociation and propylene epoxidation apparent barriers at the interface between the Ag aggregate and the alumina supportmore » are calculated to be 0.2 and 0.2~0.4 eV, respectively. These barriers are somewhat lower than those on sites away from the interface. The mechanism at the interface is similar to what was previously found for the silver trimer on alumina and can account for the high activity observed for the direct oxidation of propylene on the Ag aggregates. The barriers for oxygen dissociation on these model systems both at the interface and on the surfaces are small compared to crystalline surfaces, indicating that availability of oxygen will not be a rate limiting step for the aggregates, as in the case of the crystalline surfaces. Experimentally, we investigate Ultrananocrystalline Diamond (UNCD)-supported silver aggregates under reactive conditions of propylene partial oxidation. The UNCD-supported Ag clusters are found to be not measurably active toward propylene oxidation, in contrast to the alumina supported Ag clusters. This suggests that the lack of metal-oxide interfacial sites of the Ag-UNCD catalyst, limits the epoxidation catalytic activity. This combined computational and experimental study shows the importance of the metal-oxide interface as well as the non-crystalline nature of the alumina-supported sub-nanometer Ag aggregate catalysts for propylene epoxidation.« less
Chalcogenide nanocrystal assembly: Controlling heterogeneity and modulating heterointerfaces

NASA Astrophysics Data System (ADS)

Davis, Jessica

This dissertation work is focused on developing methods to facilitate charge transport in heterostructured materials that comprise a nanoscale component. Multicomponent semiconductor materials were prepared by (1) spin coating of discrete nanomaterials onto porous silicon (pSi) or (2) self-assembly. Spin-coating of colloidal quantum dot (QD) PbS solutions was employed to create prototype PbS QD based radiation detection devices using porous silicon (pSi) as an n-type support and charge transport material. These devices were initially tested as a photodetector to ascertain the possibility of their use in high energy radiation detection. Short chain thiolate ligands (4-fluorothiophenolate) and anion passivation at the particle interface were evaluated to augment interparticle transport. However, the samples showed minimum interaction with the light source possibly due to poor infiltration into the pSi. The second project was also driven by the potential synergistic properties that can be achieved in multicomponent metal chalcogenide nanostructures, potentially useful in optoelectronic devices. Working with well-established methods for single component metal chalcogenide (MQ) particle gels this dissertation research sought to develop practical methods for co-gelation of different component particles with complimentary functionalities. By monitoring the kinetics of aggregation using time resolved dynamic light scattering and NMR spectroscopy the kinetics of aggregation of the two most common crystal structures for CdQ nanocrystals was studied and it was determined that the hexagonal (wurtzite) crystal structure aggregated faster than the cubic (zinc blende) crystal structure. For gel coupling of nanoparticles with differing Q (Q=S, Se and Te), once we accounted for the crystal structure effects, it was determined that the relative redox characteristics of Q govern the reaction rate. The oxidative sol-gel assembly routes were also employed to fabricate metal chalcogenide NC gels with different NC components with control over the degree of mixing. In order to control the degree of mixing, the factors that underscore sol-gel oxidative assembly were elucidated and the aggregation and gelation kinetics of metal chalcogenide QDs were monitored through time-resolved dynamic light scattering (TR-DLS), and nuclear magnetic resonance spectroscopy (NMR). Through these kinetic studies of the surface speciation of metal chalcogenides, control over heterogeneity in dual component CdSe-ZnS system, was achieved through adjustment of the capping ligand, the native crystal structure and the chalcogenide, thereby changing the relative rates of assembly for each component independently.
Non-invasive localization of organic matter in soil aggregates using SR-μCT

NASA Astrophysics Data System (ADS)

Peth, Stephan; Mordhorst, Anneka; Chenu, Claire; Uteau Puschmann, Daniel; Garnier, Patricia; Nunan, Naoise; Pot, Valerie; Beckmann, Felix; Ogurreck, Malte

2014-05-01

Knowledge of the location of soil organic matter (SOM) and its spatial association to soil structure is an important step in improving modeling approaches for simulating organic matter turnover processes. Advanced models for carbon mineralization are able to account for the 3D distribution of SOM which is assumed to influence mineralisation. However, their application is still limited by the fact that no method exists to non-invasively determine the 3D spatial distribution of SOM in structured soils. SR-based X-ray microtomography (SR-µCT) is an advanced and promising tool in gaining knowledge on the 3-dimensional organization of soil phases (minerals, organic matter, water, air) which on a voxel level could be implemented into spatially explicit models. However, since the contrast of linear attenuation coefficients of soil organic matter on the one hand and mineral components and water on the other hand are relatively low, especially when materials are finely dispersed, organic matter within the soil pore space is often not resolved in ordinary X-ray absorption contrast imaging. To circumvent this problem we have developed a staining procedure for organic matter using Osmium-tetroxide since Osmium is an element with an absorption edge at a higher X-ray energy level. Osmium is known from transmission electron microscopy analysis (TEM) to stain organic matter specifically and irreversibly while having an absorption edge at approximately 74 keV. We report on the application of a novel Osmium vapor staining method to analyze differences in organic matter content and identify small scale spatial distribution of SOM in soil aggregates. To achieve this we have taken soil aggregate samples (6-8 mm across) obtained from arable soils differing in soil management. Aggregate samples were investigated by synchrotron-based X-ray microtomography (SR-µCT) after staining the sample with Osmium-tetroxide (OsO4) vapor. We utilized the monochromatic X-ray beam to locate osmium bound to SOM in the stained soil aggregate samples by scanning the aggregates at different photon energies: 30 keV at which the attenuation contrast is optimal for distinguishing other soil constituents, 70 keV (below the absorption of osmium) and 78 keV (above the absorption edge of osmium). The results suggest that particulate organic matter, which was not visibly by scanning samples at energy levels optimal for resolving soil structure (30 keV), was identified after osmium staining and scanning the samples at energy levels just below (70 keV) and above (78 keV) the absorption edge of Osmium. Subtracting the images below from the images above the osmium edged we were able to isolate stained particulate organic matter which otherwise would have been wrongly interpreted as pore space without staining. Combining both pore space and organic matter distribution we are able to investigate the association of SOM with soil structure.
Analysis of partial discharge activity by a conducting particle in liquid nitrogen under AC voltages adopting UHF technique

NASA Astrophysics Data System (ADS)

Sarathi, R.; Giridhar, A. V.; Sethupathi, K.

2010-01-01

Liquid nitrogen (LN 2) is used as an insulant as well as coolant in high temperature superconducting power equipments. Particle contamination in liquid nitrogen is one of the major cause for formation of partial discharges during operation. An attempt has been made in the present study to understand the feasibility of using Ultra High Frequency (UHF) sensors for identification of partial discharge (PD) formed due to particle movement in liquid nitrogen under AC voltages. It is observed that the partial discharge formed in LN 2 radiates UHF signal. The results of the study indicate that the conventional partial discharge measurement and UHF peak amplitude measurement have direct correlation. The Phase Resolved Partial Discharge (PRPD) analysis indicates that the partial discharge formed due to particle movement occurs in the entire phase windows of the AC voltage. The PD magnitude increases with increase in applied voltage. The frequency content of UHF signal generated due to particle movement in liquid nitrogen under AC voltages lies in the range of 0.5-1.5 GHz. The UHF sensor output signal analyzed using spectrum analyzer by operating it in zero-span mode, indicates that burst type PD occurs due to particle movement.
East Europe Report

DTIC Science & Technology

1987-02-25

definite solution from among those admissible, specified in the from of a vector of criteria and weights. The set of criteria can be different depending on...was developed in stages, by aggregating an increasing number of submodels (i.e. partial models) prepared by different teams. Nor can its present...entities operating under different constraints and towards different objectives. These models and various combinations thereof can also be useful to
Quantitative mass imaging of single biological macromolecules.

PubMed

Young, Gavin; Hundt, Nikolas; Cole, Daniel; Fineberg, Adam; Andrecka, Joanna; Tyler, Andrew; Olerinyova, Anna; Ansari, Ayla; Marklund, Erik G; Collier, Miranda P; Chandler, Shane A; Tkachenko, Olga; Allen, Joel; Crispin, Max; Billington, Neil; Takagi, Yasuharu; Sellers, James R; Eichmann, Cédric; Selenko, Philipp; Frey, Lukas; Riek, Roland; Galpin, Martin R; Struwe, Weston B; Benesch, Justin L P; Kukura, Philipp

2018-04-27

The cellular processes underpinning life are orchestrated by proteins and their interactions. The associated structural and dynamic heterogeneity, despite being key to function, poses a fundamental challenge to existing analytical and structural methodologies. We used interferometric scattering microscopy to quantify the mass of single biomolecules in solution with 2% sequence mass accuracy, up to 19-kilodalton resolution, and 1-kilodalton precision. We resolved oligomeric distributions at high dynamic range, detected small-molecule binding, and mass-imaged proteins with associated lipids and sugars. These capabilities enabled us to characterize the molecular dynamics of processes as diverse as glycoprotein cross-linking, amyloidogenic protein aggregation, and actin polymerization. Interferometric scattering mass spectrometry allows spatiotemporally resolved measurement of a broad range of biomolecular interactions, one molecule at a time. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
Identification of effective exciton-exciton annihilation in squaraine-squaraine copolymers.

PubMed

Hader, Kilian; May, Volkhard; Lambert, Christoph; Engel, Volker

2016-05-11

Ultrafast time-resolved transient absorption spectroscopy is able to monitor the fate of the excited state population in molecular aggregates or polymers. Due to many competing decay processes, the identification of exciton-exciton annihilation (EEA) is difficult. Here, we use a microscopic model to describe exciton annihilation processes in squaraine-squaraine copolymers. Transient absorption time traces measured at different laser powers exhibit an unusual time-dependence. The analysis points towards dynamics taking place on three time-scales. Immediately after laser-excitation a localization of excitons takes place within the femtosecond time-regime. This is followed by exciton-exciton annihilation which is responsible for a fast decay of the exciton population. At later times, excitations being localized on units which are not directly connected remain so that diffusion dominates the dynamics and leads to a slower decay. We thus provide evidence for EEA tracked by time-resolved spectroscopy which has not been reported that clearly before.
Microstructural constraints on complex thermal histories of refractory CAI-like objects in an amoeboid olivine aggregate from the ALHA77307 CO3.0 chondrite

NASA Astrophysics Data System (ADS)

Han, Jangmi; Brearley, Adrian J.

2016-06-01

We have carried out a FIB/TEM study of refractory CAI-like objects in one AOA from the ALHA77307 CO3.0 chondrite. The CAI-like objects in the AOA consist of a zoned sequence with a spinel-rich core through an intergrowth layer of spinel and Al-Ti-rich diopside to a diopside rim. The spinel-rich core consists of polycrystalline aggregates of spinel and ±minor melilite showing equilibrated grain boundary textures. The intergrowth layer contains fine-grained diopside and spinel with minor anorthite with highly curved and embayed grain boundaries. The diopside rim consists of polycrystalline aggregates of diopside. The compositions of pyroxene change significantly outward from Al-Ti-rich diopside in contact with the spinel-rich core to Al-Ti-poor diopside next to the surrounding olivine of the AOA. Overall microstructural and chemical characteristics suggest that the spinel-rich core formed under equilibrium conditions whereas the intergrowth layer is the result of reactions that occurred under conditions that departed significantly from equilibrium. The remarkable changes in formation conditions of the CAI-like objects may have been achieved by transport and injection of refractory objects into a region of a partially-condensed, Ca,Ti-saturated gas which reacted with spinel and melilite to form Al-Ti-rich diopside. Crystallographically-oriented TiO2 nanoparticles decorate the grain boundaries between spinel grains and between spinel and Al-Ti-rich diopside grains. During the disequilibrium back-reaction of spinel with a partially-condensed, Ca,Ti-saturated gas, metastable TiO2 nanoparticles may have condensed by an epitaxial nucleation mechanism and grown on the surface of spinel. These TiO2 nanoparticles are disordered intergrowths of the two TiO2 polymorphs, anatase and rutile. These nanoparticles are inferred to have nucleated as anatase that underwent partial transformation into rutile. The local presence of the TiO2 nanoparticles and intergrowth of anatase and rutile imply that the disequilibrium back-reaction of spinel with the gas occurred on a short timescale, i.e., minutes to hours at maximum.
Scope of partial least-squares regression applied to the enantiomeric composition determination of ketoprofen from strongly overlapped chromatographic profiles.

PubMed

Padró, Juan M; Osorio-Grisales, Jaiver; Arancibia, Juan A; Olivieri, Alejandro C; Castells, Cecilia B

2015-07-01

Valuable quantitative information could be obtained from strongly overlapped chromatographic profiles of two enantiomers by using proper chemometric methods. Complete separation profiles where the peaks are fully resolved are difficult to achieve in chiral separation methods, and this becomes a particularly severe problem in case that the analyst needs to measure the chiral purity, i.e., when one of the enantiomers is present in the sample in very low concentrations. In this report, we explore the scope of a multivariate chemometric technique based on unfolded partial least-squares regression, as a mathematical tool to solve this quite frequent difficulty. This technique was applied to obtain quantitative results from partially overlapped chromatographic profiles of R- and S-ketoprofen, with different values of enantioresolution factors (from 0.81 down to less than 0.2 resolution units), and also at several different S:R enantiomeric ratios. Enantiomeric purity below 1% was determined with excellent precision even from almost completely overlapped signals. All these assays were tested on the most demanding condition, i.e., when the minor peak elutes immediately after the main peak. The results were validated using univariate calibration of completely resolved profiles and the method applied to the determination of enantiomeric purity of commercial pharmaceuticals. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Insights in understanding aggregate formation and dissociation in cation exchange chromatography for a structurally unstable Fc-fusion protein.

PubMed

Chen, Zhiqiang; Huang, Chao; Chennamsetty, Naresh; Xu, Xuankuo; Li, Zheng Jian

2016-08-19

Cation-exchange chromatography (CEX) of a structurally unstable Fc-fusion protein exhibited multi-peak elution profile upon a salt-step elution due to protein aggregation during intra-column buffer transition where low pH and high salt coexisted. The protein exhibited a single-peak elution behavior during a pH-step elution; nevertheless, the levels of soluble aggregates (i.e. high molecular weight species, HMW) in the CEX eluate were still found up to 12-fold higher than that for the load material. The amount of the aggregates formed upon the pH-step elution was dependent on column loading with maximum HMW achieved at intermediate loading levels, supporting the hypothesis that the aggregation was the result of both the conformational changes of the bound protein and the solution concentration of the aggregation-susceptible proteins during elution. Factors such as high load pH, short protein/resin contact time, hydrophilic resin surface, and weak ionizable ligand were effective, to some extent, to reduce aggregate formation by improving the structural integrity of the bound protein. An orthogonal technique, differential scanning fluorimetry (DSF) using Sypro Orange dye confirmed that the bound protein exposed more hydrophobic area than the native molecule in free solution, especially in the pH 4-5 range. The Sypro Orange dye study of resin surface property also demonstrated that the poly[styrene-divinylbenzene]-based Poros XS with polyhydroxyl surface coating is more hydrophobic compared to the agarose-based CM Sepharose FF and SP Sepharose FF. The hydrophobic property of Poros XS contributed to stronger interactions with the partially unfolded bound protein and consequently to the higher aggregate levels seen in Poros XS eluate. This work also investigates the aggregation reversibility in CEX eluate where up to 66% of the aggregates were observed to dissociate into native monomers over a period of 120h, and links the aggregate stability to such conditions as resin surface properties and charged ligand type. Experimental data was correlated semi-quantitatively with theoretical protein charge and hydrophobicity calculations using homology modeling within the BIOVIA Discovery Studio software. Finally, an arginine-sulphopropyl (Arg-SP) agarose resin immobilized with multi-functional ligands was prepared to verify the proposed hypothesis and to eliminate the aggregate formation. The findings of this work provide general insights in understanding aggregate formation and dissociation for structurally unstable proteins in the CEX step. Copyright © 2016 Elsevier B.V. All rights reserved.
Hemostatic abnormalities in Noonan syndrome.

PubMed

Artoni, Andrea; Selicorni, Angelo; Passamonti, Serena M; Lecchi, Anna; Bucciarelli, Paolo; Cerutti, Marta; Cianci, Paola; Gianniello, Francesca; Martinelli, Ida

2014-05-01

A bleeding diathesis is a common feature of Noonan syndrome, and various coagulation abnormalities have been reported. Platelet function has never been carefully investigated. The degree of bleeding diathesis in a cohort of patients with Noonan syndrome was evaluated by a validated bleeding score and investigated with coagulation and platelet function tests. If ratios of prothrombin time and/or activated partial thromboplastin time were prolonged, the activity of clotting factors was measured. Individuals with no history of bleeding formed the control group. The study population included 39 patients and 28 controls. Bleeding score was ≥2 (ie, suggestive of a moderate bleeding diathesis) in 15 patients (38.5%) and ≥4 (ie, suggestive of a severe bleeding diathesis) in 7 (17.9%). Abnormal coagulation and/or platelet function tests were found in 14 patients with bleeding score ≥2 (93.3%) but also in 21 (87.5%) of those with bleeding score <2. The prothrombin time and activated partial thromboplastin time were prolonged in 18 patients (46%) and partial deficiency of factor VII, alone or in combination with the deficiency of other vitamin K-dependent factors, was the most frequent coagulation abnormality. Moreover, platelet aggregation and secretion were reduced in 29 of 35 patients (82.9%, P < .01 for all aggregating agents). Nearly 40% of patients with the Noonan syndrome had a bleeding diathesis and >90% of them had platelet function and/or coagulation abnormalities. Results of these tests should be taken into account in the management of bleeding or invasive procedures in these patients. Copyright © 2014 by the American Academy of Pediatrics.
RNA-binding proteins with basic-acidic dipeptide (BAD) domains self-assemble and aggregate in Alzheimer's disease.

PubMed

Bishof, Isaac; Dammer, Eric B; Duong, Duc M; Kundinger, Sean; Gearing, Marla; Lah, James J; Levey, Allan I; Seyfried, Nicholas T

2018-05-25

U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and other RNA-binding proteins (RBPs) are mislocalized to cytoplasmic neurofibrillary tau aggregates in Alzheimer's disease (AD), yet the co-aggregation mechanisms are incompletely understood. U1-70K harbors two disordered low-complexity domains (LC1 and LC2) that are necessary for aggregation in AD brain extracts. The LC1 domain contains highly repetitive basic (R/K) and acidic (D/E) residues, referred to as a basic-acidic dipeptide (BAD) domain. We report here that this domain shares many of the properties of the Q/N-rich LC domains in RBPs that also aggregate in neurodegenerative disease. These properties included self-assembly into oligomers and localization to nuclear granules. Co-immunoprecipitations of recombinant U1-70K and deletions lacking the LC domain(s) followed by quantitative proteomic analyses were used to resolve functional classes of U1-70K-interacting proteins that depend on the BAD domain for their interaction. Within this interaction network, we identified a class of RBPs with BAD domains nearly identical to that found in U1-70K. Two members of this class, LUC7L3 and RBM25, required their respective BAD domains for reciprocal interactions with U1-70K and nuclear granule localization. Strikingly, a significant proportion of RBPs with BAD domains had elevated insolubility in the AD brain proteome. Furthermore, we show that the BAD domain of U1-70K can interact with tau from AD brains, but not from other tauopathies. These findings highlight a mechanistic role for BAD domains in stabilizing RBP interactions and in potentially mediating co-aggregation with pathological, AD-specific tau isoforms. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.
Polymorphism of Lysozyme Condensates.

PubMed

Safari, Mohammad S; Byington, Michael C; Conrad, Jacinta C; Vekilov, Peter G

2017-10-05

Protein condensates play essential roles in physiological processes and pathological conditions. Recently discovered mesoscopic protein-rich clusters may act as crucial precursors for the nucleation of ordered protein solids, such as crystals, sickle hemoglobin polymers, and amyloid fibrils. These clusters challenge settled paradigms of protein condensation as the constituent protein molecules present features characteristic of both partially misfolded and native proteins. Here we employ the antimicrobial enzyme lysozyme and examine the similarities between mesoscopic clusters, amyloid structures, and disordered aggregates consisting of chemically modified protein. We show that the mesoscopic clusters are distinct from the other two classes of aggregates. Whereas cluster formation and amyloid oligomerization are both reversible, aggregation triggered by reduction of the intramolecular S-S bonds is permanent. In contrast to the amyloid structures, protein molecules in the clusters retain their enzymatic activity. Furthermore, an essential feature of the mesoscopic clusters is their constant radius of less than 50 nm. The amyloid and disordered aggregates are significantly larger and rapidly grow. These findings demonstrate that the clusters are a product of limited protein structural flexibility. In view of the role of the clusters in the nucleation of ordered protein solids, our results suggest that fine-tuning the degree of protein conformational stability is a powerful tool to control and direct the pathways of protein condensation.
Multi-step process for concentrating magnetic particles in waste sludges

DOEpatents

Watson, John L.

1990-01-01

This invention involves a multi-step, multi-force process for dewatering sludges which have high concentrations of magnetic particles, such as waste sludges generated during steelmaking. This series of processing steps involves (1) mixing a chemical flocculating agent with the sludge; (2) allowing the particles to aggregate under non-turbulent conditions; (3) subjecting the mixture to a magnetic field which will pull the magnetic aggregates in a selected direction, causing them to form a compacted sludge; (4) preferably, decanting the clarified liquid from the compacted sludge; and (5) using filtration to convert the compacted sludge into a cake having a very high solids content. Steps 2 and 3 should be performed simultaneously. This reduces the treatment time and increases the extent of flocculation and the effectiveness of the process. As partially formed aggregates with active flocculating groups are pulled through the mixture by the magnetic field, they will contact other particles and form larger aggregates. This process can increase the solids concentration of steelmaking sludges in an efficient and economic manner, thereby accomplishing either of two goals: (a) it can convert hazardous wastes into economic resources for recycling as furnace feed material, or (b) it can dramatically reduce the volume of waste material which must be disposed.
Multi-step process for concentrating magnetic particles in waste sludges

DOEpatents

Watson, J.L.

1990-07-10

This invention involves a multi-step, multi-force process for dewatering sludges which have high concentrations of magnetic particles, such as waste sludges generated during steelmaking. This series of processing steps involves (1) mixing a chemical flocculating agent with the sludge; (2) allowing the particles to aggregate under non-turbulent conditions; (3) subjecting the mixture to a magnetic field which will pull the magnetic aggregates in a selected direction, causing them to form a compacted sludge; (4) preferably, decanting the clarified liquid from the compacted sludge; and (5) using filtration to convert the compacted sludge into a cake having a very high solids content. Steps 2 and 3 should be performed simultaneously. This reduces the treatment time and increases the extent of flocculation and the effectiveness of the process. As partially formed aggregates with active flocculating groups are pulled through the mixture by the magnetic field, they will contact other particles and form larger aggregates. This process can increase the solids concentration of steelmaking sludges in an efficient and economic manner, thereby accomplishing either of two goals: (a) it can convert hazardous wastes into economic resources for recycling as furnace feed material, or (b) it can dramatically reduce the volume of waste material which must be disposed. 7 figs.
Collective Intelligence: Aggregation of Information from Neighbors in a Guessing Game.

PubMed

Pérez, Toni; Zamora, Jordi; Eguíluz, Víctor M

2016-01-01

Complex systems show the capacity to aggregate information and to display coordinated activity. In the case of social systems the interaction of different individuals leads to the emergence of norms, trends in political positions, opinions, cultural traits, and even scientific progress. Examples of collective behavior can be observed in activities like the Wikipedia and Linux, where individuals aggregate their knowledge for the benefit of the community, and citizen science, where the potential of collectives to solve complex problems is exploited. Here, we conducted an online experiment to investigate the performance of a collective when solving a guessing problem in which each actor is endowed with partial information and placed as the nodes of an interaction network. We measure the performance of the collective in terms of the temporal evolution of the accuracy, finding no statistical difference in the performance for two classes of networks, regular lattices and random networks. We also determine that a Bayesian description captures the behavior pattern the individuals follow in aggregating information from neighbors to make decisions. In comparison with other simple decision models, the strategy followed by the players reveals a suboptimal performance of the collective. Our contribution provides the basis for the micro-macro connection between individual based descriptions and collective phenomena.

Collective Intelligence: Aggregation of Information from Neighbors in a Guessing Game

PubMed Central

Pérez, Toni; Zamora, Jordi; Eguíluz, Víctor M.

2016-01-01

Complex systems show the capacity to aggregate information and to display coordinated activity. In the case of social systems the interaction of different individuals leads to the emergence of norms, trends in political positions, opinions, cultural traits, and even scientific progress. Examples of collective behavior can be observed in activities like the Wikipedia and Linux, where individuals aggregate their knowledge for the benefit of the community, and citizen science, where the potential of collectives to solve complex problems is exploited. Here, we conducted an online experiment to investigate the performance of a collective when solving a guessing problem in which each actor is endowed with partial information and placed as the nodes of an interaction network. We measure the performance of the collective in terms of the temporal evolution of the accuracy, finding no statistical difference in the performance for two classes of networks, regular lattices and random networks. We also determine that a Bayesian description captures the behavior pattern the individuals follow in aggregating information from neighbors to make decisions. In comparison with other simple decision models, the strategy followed by the players reveals a suboptimal performance of the collective. Our contribution provides the basis for the micro-macro connection between individual based descriptions and collective phenomena. PMID:27093274
Anticoagulant and Antiplatelet Activities of Artemisia princeps Pampanini and Its Bioactive Components.

PubMed

Ryu, Ri; Jung, Un Ju; Kim, Hye-Jin; Lee, Wonhwa; Bae, Jong-Sup; Park, Yong Bok; Choi, Myung-Sook

2013-09-01

Artemisia princeps Pampanini (AP) has been used as a traditional medicine in Korea, China and Japan and reported to exhibit various beneficial biological effects including anti-inflammatory, antioxidant, anti-atherogenic and lipid lowering activities; however, its antiplatelet and anticoagulant properties have not been studied. In the present study, we evaluated the effects of an ethanol extract of Artemisia princeps Pampanini (EAP) and its major flavonoids, eupatilin and jaceosidin, on platelet aggregation and coagulation. To determine the antiplatelet activity, arachidonic acid (AA)-, collagen- and ADP (adenosine diphosphate)-induced platelet aggregation were examined along with serotonin and thromboxane A2 (TXA2) generation in vitro. The anticoagulant activity was determined by monitoring the activated partial thromboplastin time (aPTT) and prothrombin time (PT) in vitro. The data showed that EAP and its major flavonoids, eupatilin and jaceosidin, significantly reduced AA-induced platelet aggregation and the generation of serotonin and TXA2, although no significant change in platelet aggregation induced by collagen and ADP was observed. Moreover, EAP significantly prolonged the PT and aPTT. The PT and/or aPTT were significantly increased in the presence of eupatilin and jaceosidin. Thus, these results suggest that EAP may have the potential to prevent or improve thrombosis by inhibiting platelet activation and blood coagulation.
Anticoagulant and Antiplatelet Activities of Artemisia princeps Pampanini and Its Bioactive Components

PubMed Central

Ryu, Ri; Jung, Un Ju; Kim, Hye-jin; Lee, Wonhwa; Bae, Jong-Sup; Park, Yong Bok; Choi, Myung-Sook

2013-01-01

Artemisia princeps Pampanini (AP) has been used as a traditional medicine in Korea, China and Japan and reported to exhibit various beneficial biological effects including anti-inflammatory, antioxidant, anti-atherogenic and lipid lowering activities; however, its antiplatelet and anticoagulant properties have not been studied. In the present study, we evaluated the effects of an ethanol extract of Artemisia princeps Pampanini (EAP) and its major flavonoids, eupatilin and jaceosidin, on platelet aggregation and coagulation. To determine the antiplatelet activity, arachidonic acid (AA)-, collagen- and ADP (adenosine diphosphate)-induced platelet aggregation were examined along with serotonin and thromboxane A2 (TXA2) generation in vitro. The anticoagulant activity was determined by monitoring the activated partial thromboplastin time (aPTT) and prothrombin time (PT) in vitro. The data showed that EAP and its major flavonoids, eupatilin and jaceosidin, significantly reduced AA-induced platelet aggregation and the generation of serotonin and TXA2, although no significant change in platelet aggregation induced by collagen and ADP was observed. Moreover, EAP significantly prolonged the PT and aPTT. The PT and/or aPTT were significantly increased in the presence of eupatilin and jaceosidin. Thus, these results suggest that EAP may have the potential to prevent or improve thrombosis by inhibiting platelet activation and blood coagulation. PMID:24471130
Disruption and reassociation of casein micelles under high pressure: influence of milk serum composition and casein micelle concentration.

PubMed

Huppertz, Thom; de Kruif, Cornelis G

2006-08-09

In this study, factors influencing the disruption and aggregation of casein micelles during high-pressure (HP) treatment at 250 MPa for 40 min were studied in situ in serum protein-free casein micelle suspensions. In control milk, light transmission increased with treatment time for approximately 15 min, after which a progressive partial reversal of the HP-induced increase in light transmission occurred, indicating initial HP-induced disruption of casein micelles, followed by reformation of casein aggregates from micellar fragments. The extent of HP-induced micellar disruption was negatively correlated with the concentration of casein micelles, milk pH, and levels of added ethanol, calcium chloride, or sodium chloride and positively correlated with the level of added sodium phosphate. The reformation of casein aggregates during prolonged HP treatment did not occur when HP-induced disruption of casein micelles was limited (<60%) or very extensive (>95%) and was promoted by a low initial milk pH or added sodium phosphate, sodium chloride, or ethanol. On the basis of these findings, a mechanism for HP-induced disruption of casein micelles and subsequent aggregation of micellar fragments is proposed, in which the main element appears to be HP-induced solubilization of micellar calcium phosphate.
The Utilisation of Shredded PET as Aggregate Replacement for Interlocking Concrete Block

NASA Astrophysics Data System (ADS)

Mokhtar, M.; Kaamin, M.; Sahat, S.; Hamid, N. B.

2018-03-01

The consumption of plastic has grown substantially all over the world in recent years and this has created huge quantities of plastic-based waste. Plastic waste is now a serious environmental threat to the modern way of living, although steps were taken to reduce its consumption. This creates substantial garbage every day, which is much unhealthy. Plastic bottles such as Polyethylene terephthalate (PET) was use as the partially component in this making of interlocking blocks concrete. This project investigates the strength and workability of the interlocking block concrete by replacing course aggregate with % PET. The suitability of recycled plastics (PET) as course aggregate in interlocking block concrete and its advantages are discussed here. Moreover, there were more benefits when using interlocking block than using conventional block such as it easy for construction because they are aligning, easy to place, high speed stacking and they offer more resistance to shear and buildings would be even stronger. Based on the test perform, the failure parameter were discussed .From the compressive strength test result, it shows that the strength of concrete block decreased with increased of PET used. From the results, it shows that higher compressive strength was found with 5% natural course aggregate replaced with PET compared to other percentages.
Resolving Partial Name Mentions Using String Metrics

DTIC Science & Technology

2007-12-01

Ladin) Pair 5: ( Franz Liszt , Franz Listz) These examples typically require one or two string edits to revert from the source to the target name...0.9556 Franz Listz Franz Liszt 2 0.1818 9 franz listz|fran z lisz 0.8182 0.9697 0.9818 The Levenshtein distance metric gives some indication of
A unified understanding of (γ, n) and (n, γ) reactions and direct neutron-multiplicity sorting

NASA Astrophysics Data System (ADS)

Utsunomiya, Hiroaki; Goriely, Stephane; m, Therese Renstrø; Katayama, Seitaro; Gheorghe, Ioana; Filipescu, Dan; Belyshev, Sergey; Varlamov, Vladimir

2017-09-01

We discuss the γ-ray strength function toward a unified understanding of (γ,n) and (n,γ) reactions and propose a novel technique of direct neutron-multiplicity sorting to resolve the long-standing discrepancy between the Livermore and Scalya data of partial photoneutron cross sections.
Infrared Photodissociation Spectroscopy of Metal Ion -WATER Complexes

NASA Astrophysics Data System (ADS)

Bandyopadhyay, B.; Carnegie, P. D.; Duncan, M. A.

2011-06-01

Metal ion-water complexes are produced in a supersonic expansion cluster source via laser vaporization technique. Infrared photodissociation spectroscopy has been performed in the O-H stretch region. DFT calculations have also been carried out to obtain the structures and vibrational frequencies. Infrared spectra show partially resolved rotational structures which will be analyzed.
A Nonlinear Dynamic Subscale Model for Partially Resolved Numerical Simulation (PRNS)/Very Large Eddy Simulation (VLES) of Internal Non-Reacting Flows

NASA Technical Reports Server (NTRS)

Shih, Tsan-Hsing; Liu, nan-Suey

2010-01-01

A brief introduction of the temporal filter based partially resolved numerical simulation/very large eddy simulation approach (PRNS/VLES) and its distinct features are presented. A nonlinear dynamic subscale model and its advantages over the linear subscale eddy viscosity model are described. In addition, a guideline for conducting a PRNS/VLES simulation is provided. Results are presented for three turbulent internal flows. The first one is the turbulent pipe flow at low and high Reynolds numbers to illustrate the basic features of PRNS/VLES; the second one is the swirling turbulent flow in a LM6000 single injector to further demonstrate the differences in the calculated flow fields resulting from the nonlinear model versus the pure eddy viscosity model; the third one is a more complex turbulent flow generated in a single-element lean direct injection (LDI) combustor, the calculated result has demonstrated that the current PRNS/VLES approach is capable of capturing the dynamically important, unsteady turbulent structures while using a relatively coarse grid.
Resolving intramolecular-distortion changes induced by the partial fluorination of pentacene adsorbed on Cu(111)

NASA Astrophysics Data System (ADS)

Franco-Cañellas, Antoni; Wang, Qi; Broch, Katharina; Shen, Bin; Gerlach, Alexander; Bettinger, Holger F.; Duhm, Steffen; Schreiber, Frank

2018-04-01

We experimentally quantify the molecular bending of a partially fluorinated pentacene (PEN) compound, namely 2,3,9,10-tetrafluoropentacene (F4PEN), adsorbed on Cu(111). By means of the x-ray standing wave (XSW) technique, we directly measure the adsorption distance of three inequivalent carbon sites, the fluorine atoms as well as the total and backbone carbon average adsorption distances. The precise positioning of different sites within the carbon core allows us to resolve two adsorption behaviors, namely a PEN-like strong coupling between the backbone and the substrate, and a repulsive interaction involving the fluorinated short molecular edges, which are 0.91 ±0.09 Å above the central benzene ring. This finding is further supported by additional electronic and in-plane-structure measurements, thus showing that the selective fluorination of a PEN molecule has only a local conformational effect and it is not sufficient to modify its interface properties. Yet, in the multilayer regime, the electronic and growth properties of the film differ completely from those of PEN and its perfluorinated derivative.
Comparison of causality analysis on simultaneously measured fMRI and NIRS signals during motor tasks.

PubMed

Anwar, Abdul Rauf; Muthalib, Makii; Perrey, Stephane; Galka, Andreas; Granert, Oliver; Wolff, Stephan; Deuschl, Guenther; Raethjen, Jan; Heute, Ulrich; Muthuraman, Muthuraman

2013-01-01

Brain activity can be measured using different modalities. Since most of the modalities tend to complement each other, it seems promising to measure them simultaneously. In to be presented research, the data recorded from Functional Magnetic Resonance Imaging (fMRI) and Near Infrared Spectroscopy (NIRS), simultaneously, are subjected to causality analysis using time-resolved partial directed coherence (tPDC). Time-resolved partial directed coherence uses the principle of state space modelling to estimate Multivariate Autoregressive (MVAR) coefficients. This method is useful to visualize both frequency and time dynamics of causality between the time series. Afterwards, causality results from different modalities are compared by estimating the Spearman correlation. In to be presented study, we used directionality vectors to analyze correlation, rather than actual signal vectors. Results show that causality analysis of the fMRI correlates more closely to causality results of oxy-NIRS as compared to deoxy-NIRS in case of a finger sequencing task. However, in case of simple finger tapping, no clear difference between oxy-fMRI and deoxy-fMRI correlation is identified.
Impairment of autophagy by TTR V30M aggregates: in vivo reversal by TUDCA and curcumin.

PubMed

Teixeira, Cristina A; Almeida, Maria do Rosário; Saraiva, Maria João

2016-09-01

Transthyretin (TTR)-related amyloidoses are diseases characterized by extracellular deposition of amyloid fibrils and aggregates in tissues composed of insoluble misfolded TTR that becomes toxic. Previous studies have demonstrated the ability of small compounds in preventing and reversing TTR V30M deposition in transgenic mice gastrointestinal (GI) tract as well as lowering biomarkers associated with cellular stress and apoptotic mechanisms. In the present study we aimed to study TTR V30M aggregates effect in autophagy, a cellular mechanism crucial for cell survival that has been implicated in the development of several neurodegenerative diseases. We were able to demonstrate in cell culture that TTR V30M aggregates cause a partial impairment of the autophagic machinery as shown by p62 accumulation, whereas early steps of the autophagic flux remain unaffected as shown by autophagosome number evaluation and LC3 turnover assay. Our studies performed in TTR V30M transgenic animals demonstrated that tauroursodeoxycholic acid (TUDCA) and curcumin effectively reverse p62 accumulation in the GI tract pointing to the ability of both compounds to modulate autophagy additionally to mitigate apoptosis. Overall, our in vitro and in vivo studies establish an association between TTR V30M aggregates and autophagy impairment and suggest the use of autophagy modulators as an additional and alternative therapeutic approach for the treatment of TTR V30M-related amyloidosis. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.
Quantitative characterization of 3-dimensional melt distribution in partially molten olivine-basalt aggregates using X-ray synchrotron microtomography

NASA Astrophysics Data System (ADS)

Zhu, W.; Gaetani, G. A.; Fusseis, F.

2009-12-01

Quantitative knowledge of the distribution of small amounts of silicate melt in peridotite and of its influence on permeability are critical to our understanding of melt migration and segregation processes in the upper mantle. Estimates for the permeability of partially molten rock require 3D melt distribution at the grain-scale. Existing studies of melt distribution, carried out on 2D slices through experimental charges, have produced divergent models for melt distribution at small melt fractions. While some studies conclude that small amounts of melt are distributed primarily along triple junctions [e.g., Wark et al., 2003], others predict an important role for melt distribution along grain boundaries at low melt fractions [e.g., Faul 1997]. Using X-ray synchrotron microtomography, we have obtained the first high quality non-destructive imaging of 3D melt distribution in olivine-basalt aggregates. Textually equilibrated partially molten samples consisting of magnesian olivine plus 2, 5, 10, or 20% primitive basalt were synthesized at 1.5 GPa and 1350°C in experiments lasting 264-336 hours. Microtomographic images of melt distribution were obtained on cylindrical cores, 1 mm in diameter, at a spatial resolution of 1 micron. Textual information such as melt channel size, dihedral angle and channel connectivity was then quantified using AVIZO and MATLAB. Our results indicate that as melt fraction decreases, melt becomes increasingly distributed along 3 grain junctions, in agreement with theoretical predictions. We do not find significant amounts of melt along grain boundaries at low melt fractions. We found that the true dihedral angle ranges from 50 to 70°, in agreements with results using 2D microcopy. Comparison between the samples provides a quantitative characterization of how melt fraction affects melt distribution including connectivity. The geometrical data have been incorporated into our network model to obtain macroscale transport properties for partially molten dunite. Results from this tomographic study thus provide constraints on rates of melt migration and melt extraction within the partially molten regions beneath ocean ridges. Fig 1. Melt channels in an olivine-basalt sample with 10 vol% melt.
X-ray absorption and Mössbauer spectroscopies characterization of iron nanoclusters prepared by the gas aggregation technique.

PubMed

Sánchez-Marcos, J; Laguna-Marco, M A; Martínez-Morillas, R; Céspedes, E; Menéndez, N; Jiménez-Villacorta, F; Prieto, C

2012-11-01

Partially oxidized iron nanoclusters have been prepared by the gas-phase aggregation technique with typical sizes of 2-3 nm. This preparation technique has been reported to obtain clusters with interesting magnetic properties such as very large exchange bias. In this paper, a sample composition study carried out by Mössbauer and X-ray absorption spectroscopies is reported. The information reached by these techniques, which is based on the iron short range order, results to be an ideal way to have a characterization of the whole sample since the obtained data are an average over a very large amount of the clusters. In addition, our results indicate the presence of ferrihydrite, which is a compound typically ignored when studying this type of systems.
High-resolution 3D simulations of NIF ignition targets performed on Sequoia with HYDRA

NASA Astrophysics Data System (ADS)

Marinak, M. M.; Clark, D. S.; Jones, O. S.; Kerbel, G. D.; Sepke, S.; Patel, M. V.; Koning, J. M.; Schroeder, C. R.

2015-11-01

Developments in the multiphysics ICF code HYDRA enable it to perform large-scale simulations on the Sequoia machine at LLNL. With an aggregate computing power of 20 Petaflops, Sequoia offers an unprecedented capability to resolve the physical processes in NIF ignition targets for a more complete, consistent treatment of the sources of asymmetry. We describe modifications to HYDRA that enable it to scale to over one million processes on Sequoia. These include new options for replicating parts of the mesh over a subset of the processes, to avoid strong scaling limits. We consider results from a 3D full ignition capsule-only simulation performed using over one billion zones run on 262,000 processors which resolves surface perturbations through modes l = 200. We also report progress towards a high-resolution 3D integrated hohlraum simulation performed using 262,000 processors which resolves surface perturbations on the ignition capsule through modes l = 70. These aim for the most complete calculations yet of the interactions and overall impact of the various sources of asymmetry for NIF ignition targets. This work was performed under the auspices of the Lawrence Livermore National Security, LLC, (LLNS) under Contract No. DE-AC52-07NA27344.
A Fictitious Domain Method for Resolving the Interaction of Blood Flow with Clot Growth

NASA Astrophysics Data System (ADS)

Mukherjee, Debanjan; Shadden, Shawn

2016-11-01

Thrombosis and thrombo-embolism cause a range of diseases including heart attack and stroke. Closer understanding of clot and blood flow mechanics provides valuable insights on the etiology, diagnosis, and treatment of thrombotic diseases. Such mechanics are complicated, however, by the discrete and multi-scale phenomena underlying thrombosis, and the complex interactions of unsteady, pulsatile hemodynamics with a clot of arbitrary shape and microstructure. We have developed a computational technique, based on a fictitious domain based finite element method, to study these interactions. The method can resolve arbitrary clot geometries, and dynamically couple fluid flow with static or growing clot boundaries. Macroscopic thrombus-hemodynamics interactions were investigated within idealized vessel geometries representative of the common carotid artery, with realistic unsteady flow profiles as inputs. The method was also employed successfully to resolve micro-scale interactions using a model driven by in-vivo morphology data. The results provide insights into the flow structures and hemodynamic loading around an arbitrarily grown clot at arterial length-scales, as well as flow and transport within the interstices of platelet aggregates composing the clot. The work was supported by AHA Award No: 16POST27500023.
GEN1 from a thermophilic fungus is functionally closely similar to non-eukaryotic junction-resolving enzymes.

PubMed

Freeman, Alasdair D J; Liu, Yijin; Déclais, Anne-Cécile; Gartner, Anton; Lilley, David M J

2014-12-12

Processing of Holliday junctions is essential in recombination. We have identified the gene for the junction-resolving enzyme GEN1 from the thermophilic fungus Chaetomium thermophilum and expressed the N-terminal 487-amino-acid section. The protein is a nuclease that is highly selective for four-way DNA junctions, cleaving 1nt 3' to the point of strand exchange on two strands symmetrically disposed about a diagonal axis. CtGEN1 binds to DNA junctions as a discrete homodimer with nanomolar affinity. Analysis of the kinetics of cruciform cleavage shows that cleavage of the second strand occurs an order of magnitude faster than the first cleavage so as to generate a productive resolution event. All these properties are closely similar to those described for bacterial, phage and mitochondrial junction-resolving enzymes. CtGEN1 is also similar in properties to the human enzyme but lacks the problems with aggregation that currently prevent detailed analysis of the latter protein. CtGEN1 is thus an excellent enzyme with which to engage in biophysical and structural analysis of eukaryotic GEN1. Copyright © 2014. Published by Elsevier Ltd.
A Methodology for Robust Comparative Life Cycle Assessments Incorporating Uncertainty.

PubMed

Gregory, Jeremy R; Noshadravan, Arash; Olivetti, Elsa A; Kirchain, Randolph E

2016-06-21

We propose a methodology for conducting robust comparative life cycle assessments (LCA) by leveraging uncertainty. The method evaluates a broad range of the possible scenario space in a probabilistic fashion while simultaneously considering uncertainty in input data. The method is intended to ascertain which scenarios have a definitive environmentally preferable choice among the alternatives being compared and the significance of the differences given uncertainty in the parameters, which parameters have the most influence on this difference, and how we can identify the resolvable scenarios (where one alternative in the comparison has a clearly lower environmental impact). This is accomplished via an aggregated probabilistic scenario-aware analysis, followed by an assessment of which scenarios have resolvable alternatives. Decision-tree partitioning algorithms are used to isolate meaningful scenario groups. In instances where the alternatives cannot be resolved for scenarios of interest, influential parameters are identified using sensitivity analysis. If those parameters can be refined, the process can be iterated using the refined parameters. We also present definitions of uncertainty quantities that have not been applied in the field of LCA and approaches for characterizing uncertainty in those quantities. We then demonstrate the methodology through a case study of pavements.
Crystal Structure of a Four-Layer Aggregate of Engineered TMV CP Implies the Importance of Terminal Residues for Oligomer Assembly

PubMed Central

Li, Xiangyang; Song, Baoan; Chen, Xi; Wang, Zhenchao; Zeng, Mengjiao; Yu, Dandan; Hu, Deyu; Chen, Zhuo; Jin, Linhong; Yang, Song; Yang, Caiguang; Chen, Baoen

2013-01-01

Background Crystal structures of the tobacco mosaic virus (TMV) coat protein (CP) in its helical and disk conformations have previously been determined at the atomic level. For the helical structure, interactions of proteins and nucleic acids in the main chains were clearly observed; however, the conformation of residues at the C-terminus was flexible and disordered. For the four-layer aggregate disk structure, interactions of the main chain residues could only be observed through water–mediated hydrogen bonding with protein residues. In this study, the effects of the C-terminal peptides on the interactions of TMV CP were investigated by crystal structure determination. Methodology/Principal Findings The crystal structure of a genetically engineered TMV CP was resolved at 3.06 Å. For the genetically engineered TMV CP, a six-histidine (His) tag was introduced at the N-terminus, and the C-terminal residues 155 to 158 were truncated (N-His-TMV CP19). Overall, N-His-TMV CP19 protein self-assembled into the four-layer aggregate form. The conformations of residues Gln36, Thr59, Asp115 and Arg134 were carefully analyzed in the high radius and low radius regions of N-His-TMV CP19, which were found to be significantly different from those observed previously for the helical and four-layer aggregate forms. In addition, the aggregation of the N-His-TMV CP19 layers was found to primarily be mediated through direct hydrogen-bonding. Notably, this engineered protein also can package RNA effectively and assemble into an infectious virus particle. Conclusion The terminal sequence of amino acids influences the conformation and interactions of the four-layer aggregate. Direct protein–protein interactions are observed in the major overlap region when residues Gly155 to Thr158 at the C-terminus are truncated. This engineered TMV CP is reassembled by direct protein–protein interaction and maintains the normal function of the four-layer aggregate of TMV CP in the presence of RNA. PMID:24223721
Leaching assessment of concrete made of recycled coarse aggregate: physical and environmental characterisation of aggregates and hardened concrete.

PubMed

Galvín, A P; Agrela, F; Ayuso, J; Beltrán, M G; Barbudo, A

2014-09-01

Each year, millions of tonnes of waste are generated worldwide, partially through the construction and demolition of buildings. Recycling the resulting waste could reduce the amount of materials that need to be manufactured. Accordingly, the present work has analysed the potential reuse of construction waste in concrete manufacturing by replacing the natural aggregate with recycled concrete coarse aggregate. However, incorporating alternative materials in concrete manufacturing may increase the pollutant potential of the product, presenting an environmental risk via ground water contamination. The present work has tested two types of concrete batches that were manufactured with different replacement percentages. The experimental procedure analyses not only the effect of the portion of recycled aggregate on the physical properties of concrete but also on the leaching behaviour as indicative of the contamination degree. Thus, parameters such as slump, density, porosity and absorption of hardened concrete, were studied. Leaching behaviour was evaluated based on the availability test performed to three aggregates (raw materials of the concrete batches) and on the diffusion test performed to all concrete. From an environmental point of view, the question of whether the cumulative amount of heavy metals that are released by diffusion reaches the availability threshold was answered. The analysis of concentration levels allowed the establishment of different groups of metals according to the observed behaviour, the analysis of the role of pH and the identification of the main release mechanisms. Finally, through a statistical analysis, physical parameters and diffusion data were interrelated. It allowed estimating the relevance of porosity, density and absorption of hardened concrete on diffusion release of the metals in study. Copyright © 2014 Elsevier Ltd. All rights reserved.

Rapid flow cytometric measurement of protein inclusions and nuclear trafficking

PubMed Central

Whiten, D. R.; San Gil, R.; McAlary, L.; Yerbury, J. J.; Ecroyd, H.; Wilson, M. R.

2016-01-01

Proteinaceous cytoplasmic inclusions are an indicator of dysfunction in normal cellular proteostasis and a hallmark of many neurodegenerative diseases. We describe a simple and rapid new flow cytometry-based method to enumerate, characterise and, if desired, physically recover protein inclusions from cells. This technique can analyse and resolve a broad variety of inclusions differing in both size and protein composition, making it applicable to essentially any model of intracellular protein aggregation. The method also allows rapid quantification of the nuclear trafficking of fluorescently labelled molecules. PMID:27516358
Influence of the individual or combined application of biochar and slurry on soil macro-aggregate formation under varying moisture conditions

NASA Astrophysics Data System (ADS)

Kaiser, Michael; Grunwald, Dennis; Koch, Heinz-Josef; Rauber, Rolf; Ludwig, Bernard

2017-04-01

The formation of aggregates is of large importance for the structure and the storage of organic matter (OM) in soil. Although positive effects of organic soil additives on the formation of macro-aggregates (> 250 µm) have been reported, the influence of biochar especially applied in combination with other organic amendments remains unclear. Furthermore, studies on the effect of varying soil moisture conditions in form of drying-rewetting cycles on soil aggregate dynamics in the presence of biochar are almost missing. The objectives of this study were to analyze the effects of biochar and slurry applied to the soil individually or in combination on the formation of macro-aggregates under constant and under varying moisture conditions. We sampled four silty loam soils, carefully crushed the soil macro-aggregates, and incubated the soil at 15 °C for 60 days with the following additions: (i) none (control), (ii) biochar (12 % of dry soil mass), (iii) slurry (150 kg N ha-1), (iv) biochar (6 %) + slurry (75 kg N ha-1), (v) biochar (12 %) + slurry (75 kg N ha-1), (vi) biochar (6 %) + slurry (150 kg N ha-1) and (vii) biochar (12 %) + slurry (150 kg N ha-1). The samples were further subdivided into two groups that were incubated under conditions of constant soil moisture and of three drying-rewetting cycles. The CO2 fluxes were continuously measured during the incubation period and the samples were analyzed for microbial biomass C, macro-aggregate yields and macro-aggregate-associated C after finishing the experiment. We found the application of biochar to result in lower macro-aggregate yields with or without slurry compared to the control or the individual slurry application. In contrast, similar or higher C contents in the macro-aggregate fraction of the biochar treatments as compared to the control or slurry treatments were found indicating an occlusion of biochar in macro-aggregates. Due to the sorption characteristics of biochar, we assume the aggregate formation to be partially abiotic with direct interactions between biochar, (adsorbed) slurry, and the mineral phase of the soil. Therefore, in the presence of slurry, a prolonged period of microbial processing does not seem to be necessary to render the biochar suitable to form aggregates. Drying and rewetting of the samples resulted in significantly lower aggregate yields especially for the biochar/slurry mixtures. The drying of slurry as thought to be the most important macro-aggregate binding agent in these treatments might irreversibly disrupt large amounts of the macro-aggregates formed. Additionally, the general lower microbial biomass C and CO2 emissions for the samples experiencing drying-rewetting cycles compared to the constantly moist soils point toward less microbial activity under varying moisture conditions. This might have led to less microbial derived aggregate binding agents contributing to the lower aggregate yields found for the samples from the drying-rewetting treatments. Beside the amount and type of binding agents derived from organic soil additives, the formation and stability of soil macro-aggregate seem also to be controlled by climatically controlled soil moisture conditions.
Triflavin, an Arg‐Gly‐Asp‐containing Antiplatelet Peptide Inhibits Cell‐substratum Adhesion and Melanoma Cell‐induced Lung Colonization

PubMed Central

Sheu, Joen R.; Lin, Chao H.; Chung, Jih L.; Teng, Che M.

1992-01-01

Triflavin, an Arg‐Gly‐Asp (RGD) containing peptide purified from Trimeresurus flavoviridis snake venom, inhibits human platelet aggregation by blocking fibrinogen binding to fibrinogen receptors associated with glycoprotein Ilb/IIIa complex. In this study, we show that triflavin (1‐30 μg/mouse) inhibits B16‐F10 melanoma cell‐induced lung colonization in C57BL/6 mice in a dose‐dependent manner. In vitro, triflavin dose‐dependently inhibits adhesion of B16‐F10 melanoma cells to extracellular matrices (ECMs; i.e., fibronectin, fibrinogen, vitronectin, and collagen type I). Triflavin is approximately 600‐800 times more potent than GRGDS at inhibiting cell adhesion. In addition, triflavin dose‐dependently inhibits B16‐F10 cell‐induced platelet aggregation. These results imply that the inhibitory effect of triflavin on the adhesion of tumor cells to ECMs (e.g., fibronectin, vitronectin and collagen type I) and/or tumor cell‐induced platelet aggregation may be partially responsible for its antimetastatic activity in C57BL/6 mice. PMID:1399825
Review on Current Research Status on Bottom Ash: An Indian Prospective

NASA Astrophysics Data System (ADS)

Mandal, A. K.; Sinha, O. P.

2014-12-01

India focuses on attention towards "greener and cleaner" environment surrounding us. For that, the engineers and scientists have joined hands together to accept the challenges for recycling wastes from industries. The generation of Bottom Ash (BA) from thermal power plants which are being increased day by day and facing disposal and environmental problems. In spite of that, it is being used as landfills which has no commercial value, but now needs to think on its utilization as useable supplementary materials. But from the literature survey, it was found that a little amount of research have been carried out on BA in the area based on its adsorption capability of dyes; pelletization efficiency of cold bonded aggregate; compressive strength, durability, water absorption characteristics and density variation in concrete and mortar; in order to ensure its usage as adsorption as well as construction material. The present paper deals with a critical review on BA as an adsorbent, light weight aggregate as well as partial replacement of fine aggregate in concrete. In addition, physical and chemical properties, transportation and disposal mechanism and environmental effects are also discussed.
Studies on use of Copper Slag as Replacement Material for River Sand in Building Constructions

NASA Astrophysics Data System (ADS)

Madheswaran, C. K.; Ambily, P. S.; Dattatreya, J. K.; Rajamane, N. P.

2014-09-01

This work focuses on the use of copper slag, as a partial replacement of sand for use in cement concrete and building construction. Cement mortar mixtures prepared with fine aggregate made up of different proportions of copper slag and sand were tested for use as masonry mortars and plastering. Three masonry wall panels of dimensions 1 × 1 m were plastered. The studies showed that although copper slag based mortar is suitable for plastering, with the increase in copper slag content, the wastage due to material rebounding from the plastered surfaces increases. It is therefore suggested that the copper slag can be used for plastering of floorings and horizontal up to 50 % by mass of the fine aggregate, and for vertical surfaces, such as, brick/block walls it can be used up to 25 %. In this study on concrete mixtures were prepared with two water cement ratios and different proportions of copper slag ranging from 0 % (for the control mix) to 100 % of fine aggregate. The Concrete mixes were evaluated for workability, density, and compressive strength.
High pCO 2-induced exopolysaccharide-rich ballasted aggregates of planktonic cyanobacteria could explain Paleoproterozoic carbon burial

DOE PAGES

Kamennaya, Nina A.; Zemla, Marcin; Mahoney, Laura; ...

2018-05-29

Here, the contribution of planktonic cyanobacteria to burial of organic carbon in deep-sea sediments before the emergence of eukaryotic predators ~1.5 Ga has been considered negligible owing to the slow sinking speed of their small cells. However, global, highly positive excursion in carbon isotope values of inorganic carbonates ~2.22–2.06 Ga implies massive organic matter burial that had to be linked to oceanic cyanobacteria. Here to elucidate that link, we experiment with unicellular planktonic cyanobacteria acclimated to high partial CO 2 pressure ( pCO 2) representative of the early Paleoproterozoic. We find that high pCO 2 boosts generation of acidic extracellularmore » polysaccharides (EPS) that adsorb Ca and Mg cations, support mineralization, and aggregate cells to form ballasted particles. The down flux of such self-assembled cyanobacterial aggregates would decouple the oxygenic photosynthesis from oxidative respiration at the ocean scale, drive export of organic matter from surface to deep ocean and sustain oxygenation of the planetary surface.« less
Advertising bans as a means of tobacco control policy: a systematic literature review of time-series analyses.

PubMed

Quentin, Wilm; Neubauer, Simone; Leidl, Reiner; König, Hans-Helmut

2007-01-01

This paper reviews the international literature that employed time-series analysis to evaluate the effects of advertising bans on aggregate consumption of cigarettes or tobacco. A systematic search of the literature was conducted. Three groups of studies representing analyses of advertising bans in the U.S.A., in other countries and in 22 OECD countries were defined. The estimated effects of advertising bans and their significance were analysed. 24 studies were identified. They used a wide array of explanatory variables, models, estimating methods and data sources. 18 studies found a negative effect of an advertising ban on aggregate consumption, but only ten of these studies found a significant effect. Two studies using data from 22 OECD countries suggested that partial bans would have little or no influence on aggregate consumption, whereas complete bans would significantly reduce consumption. The results imply that advertising bans have a negative but sometimes only narrow impact on consumption. Complete bans let expect a higher effectiveness. Because of methodological restrictions of analysing advertising bans' effects by time series approaches, also different approaches should be used in the future.
High pCO 2-induced exopolysaccharide-rich ballasted aggregates of planktonic cyanobacteria could explain Paleoproterozoic carbon burial

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

Kamennaya, Nina A.; Zemla, Marcin; Mahoney, Laura

Here, the contribution of planktonic cyanobacteria to burial of organic carbon in deep-sea sediments before the emergence of eukaryotic predators ~1.5 Ga has been considered negligible owing to the slow sinking speed of their small cells. However, global, highly positive excursion in carbon isotope values of inorganic carbonates ~2.22–2.06 Ga implies massive organic matter burial that had to be linked to oceanic cyanobacteria. Here to elucidate that link, we experiment with unicellular planktonic cyanobacteria acclimated to high partial CO 2 pressure ( pCO 2) representative of the early Paleoproterozoic. We find that high pCO 2 boosts generation of acidic extracellularmore » polysaccharides (EPS) that adsorb Ca and Mg cations, support mineralization, and aggregate cells to form ballasted particles. The down flux of such self-assembled cyanobacterial aggregates would decouple the oxygenic photosynthesis from oxidative respiration at the ocean scale, drive export of organic matter from surface to deep ocean and sustain oxygenation of the planetary surface.« less
Reassociation of dissociated caseins upon acidification of heated pH-adjusted skim milk.

PubMed

Anema, Skelte G; Li, Yuming

2015-05-01

Milk was heated at different pH (pH 6.5-7.1) and temperatures (20-120 °C/10 min). This resulted in different levels of casein and denatured whey proteins to be distributed between the colloidal and serum phases. The milks were subsequently acidified and the distribution of protein between colloidal and serum was monitored at different pH. On acidification to pH 5.4, the serum phase caseins and denatured whey proteins partially reassociated with the caseins, although a complex behaviour was observed at ∼ pH 5.4 where additional casein dissociation occurred in some samples. At pH below 5.4 the caseins and denatured whey proteins rapidly aggregated. No separate aggregation of κ-casein/denatured whey protein complexes or κ-casein depleted micelles was observed. The earlier gelation of milks heated at higher pH was likely to be due to the destabilisation of the entire milk protein system rather than a preferential aggregation of the serum phase proteins. Copyright © 2014 Elsevier Ltd. All rights reserved.
Sustainable materials used as stone column filler: A short review

NASA Astrophysics Data System (ADS)

Zukri, Azhani; Nazir, Ramli

2018-04-01

Stone columns (also known as granular piles) are one of the methods for soft soil stabilization and typically used to increase bearing capacity and stability of slope.; Apart from decreasing the compressibility of loose and fine graded soils, it also accelerates the consolidation effect by improving the drainage path for pore water pressure dissipation and reduces the liquefaction potential of soils during earthquake event. Stone columns are probably the most “natural” ground treatment method or foundation system in existence to date. The benefit of stone columns is owing to the partial replacement of compressible soil by more competent materials such as stone aggregate, sand and other granular materials. These substitutes also act as reinforcement material, hence increasing overall strength and stiffness of the soft soil. Nowadays, a number of research has been conducted on the behaviour and performance of stone columns with various materials utilized as column filler replacing the normal aggregate. This paper will review extensively on previously conducted research on some of the materials used as stone column backfill materials, its suitability and the effectiveness as a substitute for regular aggregates in soft soil improvement works.
Nanoscopic insights into seeding mechanisms and toxicity of α-synuclein species in neurons

PubMed Central

Pinotsi, Dorothea; Michel, Claire H.; Buell, Alexander K.; Laine, Romain F.; Mahou, Pierre; Dobson, Christopher M.; Kaminski, Clemens F.; Kaminski Schierle, Gabriele S.

2016-01-01

New strategies for visualizing self-assembly processes at the nanoscale give deep insights into the molecular origins of disease. An example is the self-assembly of misfolded proteins into amyloid fibrils, which is related to a range of neurodegenerative disorders, such as Parkinson's and Alzheimer's diseases. Here, we probe the links between the mechanism of α-synuclein (AS) aggregation and its associated toxicity by using optical nanoscopy directly in a neuronal cell culture model of Parkinson’s disease. Using superresolution microscopy, we show that protein fibrils are taken up by neuronal cells and act as prion-like seeds for elongation reactions that both consume endogenous AS and suppress its de novo aggregation. When AS is internalized in its monomeric form, however, it nucleates and triggers the aggregation of endogenous AS, leading to apoptosis, although there are no detectable cross-reactions between externally added and endogenous protein species. Monomer-induced apoptosis can be reduced by pretreatment with seed fibrils, suggesting that partial consumption of the externally added or excess soluble AS can be significantly neuroprotective. PMID:26993805
Heated probe diagnostic inside of the gas aggregation nanocluster source

NASA Astrophysics Data System (ADS)

Kolpakova, Anna; Shelemin, Artem; Kousal, Jaroslav; Kudrna, Pavel; Tichy, Milan; Biederman, Hynek; Surface; Plasma Science Team

2016-09-01

Gas aggregation cluster sources (GAS) usually operate outside common working conditions of most magnetrons and the size of nanoparticles created in GAS is below that commonly studied in dusty plasmas. Therefore, experimental data obtained inside the GAS are important for better understanding of process of nanoparticles formation. In order to study the conditions inside the gas aggregation chamber, special ``diagnostic GAS'' has been constructed. It allows simultaneous monitoring (or spatial profiling) by means of optical emission spectroscopy, mass spectrometry and probe diagnostic. Data obtained from Langmuir and heated probes map the plasma parameters in two dimensions - radial and axial. Titanium has been studied as an example of metal for which the reactive gas in the chamber starts nanoparticles production. Three basic situations were investigated: sputtering from clean titanium target in argon, sputtering from partially pre-oxidized target and sputtering with oxygen introduced into the discharge. It was found that during formation of nanoparticles the plasma parameters differ strongly from the situation without nanoparticles. These experimental data will support the efforts of more realistic modeling of the process. Czech Science Foundation 15-00863S.
A 2 x 2 Taxonomy of Multilevel Latent Contextual Models: Accuracy-Bias Trade-Offs in Full and Partial Error Correction Models

ERIC Educational Resources Information Center

Ludtke, Oliver; Marsh, Herbert W.; Robitzsch, Alexander; Trautwein, Ulrich

2011-01-01

In multilevel modeling, group-level variables (L2) for assessing contextual effects are frequently generated by aggregating variables from a lower level (L1). A major problem of contextual analyses in the social sciences is that there is no error-free measurement of constructs. In the present article, 2 types of error occurring in multilevel data…
Modelling the aggregation process of cellular slime mold by the chemical attraction.

PubMed

Atangana, Abdon; Vermeulen, P D

2014-01-01

We put into exercise a comparatively innovative analytical modus operandi, the homotopy decomposition method (HDM), for solving a system of nonlinear partial differential equations arising in an attractor one-dimensional Keller-Segel dynamics system. Numerical solutions are given and some properties show evidence of biologically practical reliance on the parameter values. The reliability of HDM and the reduction in computations give HDM a wider applicability.
Symplectic potentials and resolved Ricci-flat ACG metrics

NASA Astrophysics Data System (ADS)

Balasubramanian, Aswin K.; Govindarajan, Suresh; Gowdigere, Chethan N.

2007-12-01

We pursue the symplectic description of toric Kähler manifolds. There exists a general local classification of metrics on toric Kähler manifolds equipped with Hamiltonian 2-forms due to Apostolov, Calderbank and Gauduchon (ACG). We derive the symplectic potential for these metrics. Using a method due to Abreu, we relate the symplectic potential to the canonical potential written by Guillemin. This enables us to recover the moment polytope associated with metrics and we thus obtain global information about the metric. We illustrate these general considerations by focusing on six-dimensional Ricci-flat metrics and obtain Ricci-flat metrics associated with real cones over Lpqr and Ypq manifolds. The metrics associated with cones over Ypq manifolds turn out to be partially resolved with two blow-up parameters taking special (non-zero) values. For a fixed Ypq manifold, we find explicit metrics for several inequivalent blow-ups parametrized by a natural number k in the range 0 < k < p. We also show that all known examples of resolved metrics such as the resolved conifold and the resolution of {\\bb C}^3/{\\bb Z}_3 also fit the ACG classification.
The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm.

PubMed

Liu, Haiguang; Spence, John C H

2014-11-01

Crystallographic auto-indexing algorithms provide crystal orientations and unit-cell parameters and assign Miller indices based on the geometric relations between the Bragg peaks observed in diffraction patterns. However, if the Bravais symmetry is higher than the space-group symmetry, there will be multiple indexing options that are geometrically equivalent, and hence many ways to merge diffraction intensities from protein nanocrystals. Structure factor magnitudes from full reflections are required to resolve this ambiguity but only partial reflections are available from each XFEL shot, which must be merged to obtain full reflections from these 'stills'. To resolve this chicken-and-egg problem, an expectation maximization algorithm is described that iteratively constructs a model from the intensities recorded in the diffraction patterns as the indexing ambiguity is being resolved. The reconstructed model is then used to guide the resolution of the indexing ambiguity as feedback for the next iteration. Using both simulated and experimental data collected at an X-ray laser for photosystem I in the P63 space group (which supports a merohedral twinning indexing ambiguity), the method is validated.
Localization of serotoni (5-hydroxytryptamine, 5-HT) with partial purification and characterization of a serotonin binding protein in the intestinal tissue of the nematode Ascaris suum

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

Martin, R.E.

1989-01-01

An intracellular 5-HT binding protein (SBP) from intestinal tissue was partially purified and characterized. Binding of ({sup 3}H) 5-HT to the protein appeared to be Fe{sup +2}-sensitive and maximal (20.8pmol/mg protein) at 5 {times} 10{sup {minus}4}M Fe{sup +2} and 10{sup {minus}7}M ({sup 3}H) 5-HT. There were two 5-HT binding sites present at optimum Fe{sup +2} concentrations. The Bmax values of these sites were more sensitive to Fe{sup +2} than Kd values. Sulfhydryl reducing agents, cation chelators, Fe{sup +3}, Ca{sup +2} and antagonists of 5-HT uptake and storage inhibited binding of 5-HT to SBP. Gel exclusion chromatography indicated the presence ofmore » a 45Kda SBP that in 5 {times} 10{sup {minus}5}M Fe{sup +2} may form aggregates ranging in size from approximately 80 to >1000Kda. The data indicate these in vitro aggregates may correspond to the electron-opaque patches observed in situ. Ascaris suum may provide a model system to further elucidate the physiological role of analogous serotonin binding proteins that have been identified in mammalian systems.« less
Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding.

PubMed

Nagpal, Suhani; Tiwari, Satyam; Mapa, Koyeli; Thukral, Lipi

2015-01-01

Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central "hubs". Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates.
Misfit dislocation patterns of Mg-Nb interfaces

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

Chen, Youxing; Shao, Shuai; Liu, Xiang-Yang

The role of heterogeneous interfaces in improving mechanical properties of polycrystalline aggregates and laminated composites has been well recognized with interface structure being of fundamental importance in designing composites containing multiple interfaces. In this paper, taking the Mg (hexagonal close-packed (hcp))/Nb (body-centered cubic (bcc)) interface as an example, we develop Mg-Nb interatomic potentials for predicting atomic configurations of Mg/Nb interfaces. We systematically characterize interface dislocations of Mg/Nb interfaces with Nishiyama-Wassermann (NW) and Kurdjumov-Sachs (KS) orientation relationships and propose a generalized procedure of characterizing interface structure by combining atomistic simulation and interface dislocation theory, which is applicable for not only hcp/bccmore » interfaces, but also other systems with complicated interface dislocation configurations.Here, in Mg/Nb, interface dislocation networks of two types of interfaces are significantly different although they originate from partial dislocations of similar character: the NW interface is composed of three sets of partial dislocations, while the KS interface is composed of four sets of interface dislocations - three sets of partial dislocations and one set of full dislocations that forms from the reaction of two close partial dislocations.« less
The Spatial Scale of Convective Aggregation in Cloud Resolving Simulations of Radiative Convective Equilibrium

NASA Astrophysics Data System (ADS)

Patrizio, Casey

A three-dimensional cloud-resolving model (CRM) was used to investigate the preferred separation distance between humid, rainy regions formed by convective aggregation in radiative-convective equilibrium without rotation. We performed the simulations with doubly-periodic square domains of widths 768 km, 1536 km and 3072 km over a time period of about 200 days. The simulations in the larger domains were initialized using multiple copies of the results in the small domain at day 90, plus a small perturbation. With all three domain sizes, the simulations evolved to a single statistically steady convective cluster surrounded by a broader region of dry, subsiding air by about day 150. In the largest domain case, however, we found that an additional convective cluster formed when we the simulation was run for an extended period of time. Specifically, a smaller convective cluster formed at around day 185 at a maximum radial distance from the larger cluster and then re-merged with the larger cluster after about 10 days. We explored how the aggregated state was different in each domain case, before the smaller cluster formed in the large domain. In particular, we investigated changes in the radial structure of the aggregated state by calculating profiles for the water, dynamics and radiation as a function of distance from the center of the convective region. Changes in the vertical structure were also investigated by compositing on the convective region and dry, subsiding region at each height. We found that, with increasing domain size, the convective region boundary layer became more buoyant, the convective cores reached deeper into the troposphere, the mesoscale convective updraft became weaker, and the mesoscale convective region spread out. Additionally, as the domain size was increased, conditions in the remote environment became favorable for convection. We describe a physical mechanism for the weakening of the mesoscale convective updraft and associated broadening of the convective region with increasing domain size, which involves mid-level stable layer enhancement as a result of the deeper convection. Finally, a simple analytical model of the aggregated state was used to explore the dependency of the convective fractional area on the domain size. The simple model solutions that had net radiative cooling and surface evaporation in the convective region were consistent with the simulation results. In particular, the solutions captured the broadening of the convective region, the weakening of the convective region updraft, as well as the positive and declining gross moist stability (GMS) that occurred with increasing domain size in the simulations. Furthermore, the simple model transitioned from positive to negative GMS at a domain length of about 7000 km because the convective region boundary layer became progressively more humid with increasing domain size. This suggests that the spatial scale of the aggregated RCE state in the simulations would be limited to a length scale of about 7000 km, as convectively-active areas are commonly observed to have positive GMS. This work additionally suggests that the processes that influence the water vapor content in the convective region boundary layer, such as convectively-driven turbulent water vapor fluxes, are important for determining the spatial scale of the aggregated RCE state.

Aggregation and charging of sulfate and amidine latex particles in the presence of oxyanions.

PubMed

Sugimoto, Takuya; Cao, Tianchi; Szilagyi, Istvan; Borkovec, Michal; Trefalt, Gregor

2018-08-15

Electrophoretic mobility and time resolved light scattering are used to measure the effect on charging and aggregation of amidine and sulfate latex particles of different oxyanions namely, phosphate, arsenate, sulfate, and selenate. In the case of negatively charged sulfate latex particles oxyanions represent the coions, while they represent counterions in the case of the positively charged amidine latex. Repulsive interaction between the sulfate latex surface and the coions results in weak ion specific effects on the charging and aggregation. On the other hand the interaction of oxyanions with the amidine latex surface is highly specific. The monovalent dihydrogen phosphate ion strongly adsorbs to the positively charged surface and reverses the charge of the particle. This charge reversal leads also to the restabilization of the amidine latex suspension at the intermediate phosphate concentrations. In the case of dihydrogen arsenate the adsorption to amidine latex surface is weaker and no charge reversal and restabilization occurs. Similar differences are seen between the sulfate and selenate analogues, where selenate adsorbs more strongly to the surface as compared to the sulfate ion and invokes charge reversal. The present results indicate that ion specificity is much more pronounced in the case of counterions. Copyright © 2018 Elsevier Inc. All rights reserved.
Identification of Structural Features of Condensed Tannins That Affect Protein Aggregation

PubMed Central

Ropiak, Honorata M.; Lachmann, Peter; Ramsay, Aina; Green, Rebecca J.; Mueller-Harvey, Irene

2017-01-01

A diverse panel of condensed tannins was used to resolve the confounding effects of size and subunit composition seen previously in tannin-protein interactions. Turbidimetry revealed that size in terms of mean degree of polymerisation (mDP) or average molecular weight (amw) was the most important tannin parameter. The smallest tannin with the relatively largest effect on protein aggregation had an mDP of ~7. The average size was significantly correlated with aggregation of bovine serum albumin, BSA (mDP: r = -0.916; amw: r = -0.925; p<0.01; df = 27), and gelatin (mDP: r = -0.961; amw: r = -0.981; p<0.01; df = 12). The procyanidin/prodelphinidin and cis-/trans-flavan-3-ol ratios gave no significant correlations. Tryptophan fluorescence quenching indicated that procyanidins and cis-flavan-3-ol units contributed most to the tannin interactions on the BSA surface and in the hydrophobic binding pocket (r = 0.677; p<0.05; df = 9 and r = 0.887; p<0.01; df = 9, respectively). Circular dichroism revealed that higher proportions of prodelphinidins decreased the apparent α-helix content (r = -0.941; p<0.01; df = 5) and increased the apparent β-sheet content (r = 0.916; p<0.05; df = 5) of BSA. PMID:28125657
Identification of Structural Features of Condensed Tannins That Affect Protein Aggregation.

PubMed

Ropiak, Honorata M; Lachmann, Peter; Ramsay, Aina; Green, Rebecca J; Mueller-Harvey, Irene

2017-01-01

A diverse panel of condensed tannins was used to resolve the confounding effects of size and subunit composition seen previously in tannin-protein interactions. Turbidimetry revealed that size in terms of mean degree of polymerisation (mDP) or average molecular weight (amw) was the most important tannin parameter. The smallest tannin with the relatively largest effect on protein aggregation had an mDP of ~7. The average size was significantly correlated with aggregation of bovine serum albumin, BSA (mDP: r = -0.916; amw: r = -0.925; p<0.01; df = 27), and gelatin (mDP: r = -0.961; amw: r = -0.981; p<0.01; df = 12). The procyanidin/prodelphinidin and cis-/trans-flavan-3-ol ratios gave no significant correlations. Tryptophan fluorescence quenching indicated that procyanidins and cis-flavan-3-ol units contributed most to the tannin interactions on the BSA surface and in the hydrophobic binding pocket (r = 0.677; p<0.05; df = 9 and r = 0.887; p<0.01; df = 9, respectively). Circular dichroism revealed that higher proportions of prodelphinidins decreased the apparent α-helix content (r = -0.941; p<0.01; df = 5) and increased the apparent β-sheet content (r = 0.916; p<0.05; df = 5) of BSA.
Pan-Antarctic analysis aggregating spatial estimates of Adélie penguin abundance reveals robust dynamics despite stochastic noise.

PubMed

Che-Castaldo, Christian; Jenouvrier, Stephanie; Youngflesh, Casey; Shoemaker, Kevin T; Humphries, Grant; McDowall, Philip; Landrum, Laura; Holland, Marika M; Li, Yun; Ji, Rubao; Lynch, Heather J

2017-10-10

Colonially-breeding seabirds have long served as indicator species for the health of the oceans on which they depend. Abundance and breeding data are repeatedly collected at fixed study sites in the hopes that changes in abundance and productivity may be useful for adaptive management of marine resources, but their suitability for this purpose is often unknown. To address this, we fit a Bayesian population dynamics model that includes process and observation error to all known Adélie penguin abundance data (1982-2015) in the Antarctic, covering >95% of their population globally. We find that process error exceeds observation error in this system, and that continent-wide "year effects" strongly influence population growth rates. Our findings have important implications for the use of Adélie penguins in Southern Ocean feedback management, and suggest that aggregating abundance across space provides the fastest reliable signal of true population change for species whose dynamics are driven by stochastic processes.Adélie penguins are a key Antarctic indicator species, but data patchiness has challenged efforts to link population dynamics to key drivers. Che-Castaldo et al. resolve this issue using a pan-Antarctic Bayesian model to infer missing data, and show that spatial aggregation leads to more robust inference regarding dynamics.
Applying chaperones to protein-misfolding disorders: molecular chaperones against α-synuclein in Parkinson's disease.

PubMed

Chaari, Ali; Hoarau-Véchot, Jessica; Ladjimi, Moncef

2013-09-01

Parkinson's disease (PD) is a neurodegenerative disorder characterized by the accumulation of a protein called α-synuclein (α-syn) into inclusions known as lewy bodies (LB) within neurons. This accumulation is also due to insufficient formation and activity of dopamine produced in certain neurons within the substantia nigra. Lewy bodies are the pathological hallmark of the idiopathic disorder and the cascade that allows α-synuclein to misfold, aggregate and form these inclusions has been the subject of intensive research. Targeting these early steps of oligomerization is one of the main therapeutic approaches in order to develop neurodegenerative-modifying agents. Because the folding and refolding of alpha synuclein is the key point of this cascade, we are interested in this review to summarize the role of some molecular chaperones proteins such as Hsp70, Hsp90 and small heat shock proteins (sHsp) and Hsp 104. Hsp70 and its co-chaperone, Hsp70 and small heat shock proteins can prevent neurodegeneration by preventing α-syn misfolding, oligomerization and aggregation in vitro and in Parkinson disease animal models. Hsp104 is able to resolve disordered protein aggregates and cross beta amyloid conformers. Together, these chaperones have a complementary effect and can be a target for therapeutic intervention in PD. Published by Elsevier B.V.
Investigating the Structural Impact of the Glutamine Repeat in Huntingtin Assembly

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

Perevozchikova, Tatiana; Stanley, Christopher B; McWilliams-Koeppen, Helen P

2014-01-01

Acquiring detailed structural information about the various aggregation states of the huntingtin-exon1 protein (Htt-exon1) is crucial not only for identifying the true nature of the neurotoxic species responsible for Huntington s disease (HD) but also for designing effective therapeutics. Using time-resolved small-angle neutron scattering (TR-SANS), we followed the conformational changes that occurred during fibrillization of the pathologic form of Htt-exon1 (NtQ42P10) and compared the results with those obtained for the wild-type (NtQ22P10). Our results show that the aggregation pathway of NtQ22P10 is very different from that of NtQ42P10, as the initial steps require a monomer to 7-mer transition stage. Inmore » contrast, the earliest species identified for NtQ42P10 are monomer and dimer. The divergent pathways ultimately result in NtQ22P10 fibrils that possess a pack- ing arrangement consistent with the common amyloid sterical zipper model, whereas NtQ42P10 fibrils present a better fit to the Perutz b-helix structural model. The structural details obtained by TR-SANS should help to delineate the key mechanisms that underpin Htt-exon1 aggregation leading to HD.« less
Effects of Combined Application of Biogas Slurry and Chemical Fertilizer on Soil Aggregation and C/N Distribution in an Ultisol

PubMed Central

Zheng, Xuebo; Fan, Jianbo; Xu, Lei; Zhou, Jing

2017-01-01

Unreasonable use of chemical fertilizer (CF) on agricultural soil leads to massive losses of soil organic carbon (SOC) and total nitrogen (TN) in tropical and subtropical areas, where soil conditions are unfavorable for aggregate formation. This study evaluated the effects of combined application of biogas slurry (BS) plus CF on soil aggregation and aggregate—associated C/N concentration and storage in an Ultisol. Six treatments included: no fertilizer (T1), CF only (T2), partial (15% (T3), 30% (T4) and 45% (T5)) substitution of TN with BS and BS only (T6). Soil mechanical—stable aggregates (MSAs) formation and stability as well as MSAs—associated C/N concentration and storage were observed in different aggregate sizes (>5, 5–2, 2–1, 1.0–0.5, 0.50–0.25 and <0.25 mm). The proportion of MSAs >5 mm significantly increased with BS substitution (T5), while the proportions of MSAs 1.0–0.5 mm, MSAs 0.50–0.25 mm and MSAs <0.25 mm significantly decreased. Both mean weight diameter and geometric mean diameter were highest in T5, which improved soil aggregation stability as well as resulted in significantly higher SOC and TN concentrations and storage in MSAs >0.5 mm that constituted 72–82% of MSAs. Stepwise regression analysis showed that MSAs >5 mm, SOC in MSAs >5 mm and TN in MSAs >5 mm were the dominant variables affecting aggregate stability. Meanwhile SOC in MSAs <0.25 mm and TN in MSAs 2–1 mm were independent variables affecting SOC and TN concentrations in bulk soils. Therefore, certain rate of combined application of BS plus CF is an effective, eco—friendly way to improve soil quality in an Ultisol. PMID:28125647
TiO2 nanoparticles aggregation and disaggregation in presence of alginate and Suwannee River humic acids. pH and concentration effects on nanoparticle stability.

PubMed

Loosli, Frédéric; Le Coustumer, Philippe; Stoll, Serge

2013-10-15

The behavior of manufactured TiO2 nanoparticles is studied in a systematic way in presence of alginate and Suwannee River humic acids at variable concentrations. TiO2 nanoparticles aggregation, disaggregation and stabilization are investigated using dynamic light scattering and electrophoretic experiments allowing the measurement of z-average hydrodynamic diameters and zeta potential values. Stability of the TiO2 nanoparticles is discussed by considering three pH-dependent electrostatic scenarios. In the first scenario, when pH is below the TiO2 nanoparticle point of zero charge, nanoparticles exhibit a positively charged surface whereas alginate and Suwannee River humic acids are negatively charged. Fast adsorption at the TiO2 nanoparticles occurs, promotes surface charge neutralization and aggregation. By increasing further alginate and Suwannee River humic acids concentrations charge inversion and stabilization of TiO2 nanoparticles are obtained. In the second electrostatic scenario, at the surface charge neutralization pH, TiO2 nanoparticles are rapidly forming aggregates. Adsorption of alginate and Suwannee River humic acids on aggregates leads to their partial fragmentation. In the third electrostatic scenario, when nanoparticles, alginate and Suwannee River humic acids are negatively charged, only a small amount of Suwannee River humic acids is adsorbed on TiO2 nanoparticles surface. It is found that the fate and behavior of individual and aggregated TiO2 nanoparticles in presence of environmental compounds are mainly driven by the complex interplay between electrostatic attractive and repulsive interactions, steric and van der Waals interactions, as well as concentration ratio. Results also suggest that environmental aquatic concentration ranges of humic acids and biopolymers largely modify the stability of aggregated or dispersed TiO2 nanoparticles. Copyright © 2013 Elsevier Ltd. All rights reserved.
In Their Own Words: Reasons Underlying the Achievement Striving of Students in Schools

ERIC Educational Resources Information Center

Lee, Minhye; Bong, Mimi

2016-01-01

By analyzing the open-ended reasons for studying generated by 3 different groups of Korean middle school students, we aimed to provide partial answers to current issues in achievement goal research that are difficult to resolve solely with the use of survey ratings. We categorized student responses using the achievement goal frameworks of Midgley…
Column-by-column observation of dislocation motion in CdTe: Dynamic scanning transmission electron microscopy

NASA Astrophysics Data System (ADS)

Li, Chen; Zhang, Yu-Yang; Pennycook, Timothy J.; Wu, Yelong; Lupini, Andrew R.; Paudel, Naba; Pantelides, Sokrates T.; Yan, Yanfa; Pennycook, Stephen J.

2016-10-01

The dynamics of partial dislocations in CdTe have been observed at the atomic scale using aberration-corrected scanning transmission electron microscopy (STEM), allowing the mobility of different dislocations to be directly compared: Cd-core Shockley partial dislocations are more mobile than Te-core partials, and dislocation cores with unpaired columns have higher mobility than those without unpaired columns. The dynamic imaging also provides insight into the process by which the dislocations glide. Dislocations with dangling bonds on unpaired columns are found to be more mobile because the dangling bonds mediate the bond exchanges required for the dislocations to move. Furthermore, a screw dislocation has been resolved to dissociate into a Shockley partial-dislocation pair along two different directions, revealing a way for the screw dislocation to glide in the material. The results show that dynamic STEM imaging has the potential to uncover the details of dislocation motion not easily accessible by other means.
Heterogeneous database integration in biomedicine.

PubMed

Sujansky, W

2001-08-01

The rapid expansion of biomedical knowledge, reduction in computing costs, and spread of internet access have created an ocean of electronic data. The decentralized nature of our scientific community and healthcare system, however, has resulted in a patchwork of diverse, or heterogeneous, database implementations, making access to and aggregation of data across databases very difficult. The database heterogeneity problem applies equally to clinical data describing individual patients and biological data characterizing our genome. Specifically, databases are highly heterogeneous with respect to the data models they employ, the data schemas they specify, the query languages they support, and the terminologies they recognize. Heterogeneous database systems attempt to unify disparate databases by providing uniform conceptual schemas that resolve representational heterogeneities, and by providing querying capabilities that aggregate and integrate distributed data. Research in this area has applied a variety of database and knowledge-based techniques, including semantic data modeling, ontology definition, query translation, query optimization, and terminology mapping. Existing systems have addressed heterogeneous database integration in the realms of molecular biology, hospital information systems, and application portability.
Förster Resonance Energy Transfer Evidence for Lysozyme Oligomerization in Lipid Environment

PubMed Central

Trusova, Valeriya M.; Gorbenko, Galyna P.; Sarkar, Pabak; Luchowski, Rafal; Akopova, Irina; Patsenker, Leonid D.; Klochko, Oleksii; Tatarets, Anatoliy L.; Kudriavtseva, Yuliia O.; Terpetschnig, Ewald A.; Gryczynski, Ignacy; Gryczynski, Zygmunt

2012-01-01

Intermolecular time-resolved and single-molecule Förster resonance energy transfer (FRET) have been applied to detect quantitatively the aggregation of polycationic protein lysozyme (Lz) in the presence of lipid vesicles composed of phosphatidylcholine (PC) and its mixture with 5, 10, 20, or 40 mol % of phosphatidylglycerol (PG) (PG5, PG10, PG20, or PG40, respectively). Upon binding to PC, PG5, or PG10 model membranes, Lz was found to retain its native monomeric conformation, while increasing content of anionic lipid up to 20 or 40 mol % resulted in the formation of Lz aggregates. The structural parameters of protein self-association (the degree of oligomerization, the distance between the monomers in protein assembly, and the fraction of donors present in oligomers) have been derived. The crucial role of the factors such as lateral density of the adsorbed protein and electrostatic and hydrophobic Lz–lipid interactions in controlling the protein self-association behavior has been proposed. PMID:21126034
Super-resolved FT-IR spectroscopy: Strategies, challenges, and opportunities for membrane biophysics.

PubMed

Li, Jessica J; Yip, Christopher M

2013-10-01

Direct correlation of molecular conformation with local structure is critical to studies of protein- and peptide-membrane interactions, particularly in the context of membrane-facilitated aggregation, and disruption or disordering. Infrared spectroscopy has long been a mainstay for determining molecular conformation, following folding dynamics, and characterizing reactions. While tremendous advances have been made in improving the spectral and temporal resolution of infrared spectroscopy, it has only been with the introduction of scanned-probe techniques that exploit the raster-scanning tip as either a source, scattering tool, or measurement probe that researchers have been able to obtain sub-diffraction limit IR spectra. This review will examine the history of correlated scanned-probe IR spectroscopies, from their inception to their use in studies of molecular aggregates, membrane domains, and cellular structures. The challenges and opportunities that these platforms present for examining dynamic phenomena will be discussed. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies. Copyright © 2013 Elsevier B.V. All rights reserved.
Impact of Uncoordinated Plug-in Electric Vehicle Charging on Residential Power Demand

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

Muratori, Matteo

Electrification of transport offers opportunities to increase energy security, reduce carbon emissions, and improve local air quality. Plug-in electric vehicles (PEVs) are creating new connections between the transportation and electric sectors, and PEV charging will create opportunities and challenges in a system of growing complexity. Here, I use highly resolved models of residential power demand and PEV use to assess the impact of uncoordinated in-home PEV charging on residential power demand. While the increase in aggregate demand might be minimal even for high levels of PEV adoption, uncoordinated PEV charging could significantly change the shape of the aggregate residential demand,more » with impacts for electricity infrastructure, even at low adoption levels. Clustering effects in vehicle adoption at the local level might lead to high PEV concentrations even if overall adoption remains low, significantly increasing peak demand and requiring upgrades to the electricity distribution infrastructure. This effect is exacerbated when adopting higher in-home power charging.« less
Impact of uncoordinated plug-in electric vehicle charging on residential power demand

NASA Astrophysics Data System (ADS)

Muratori, Matteo

2018-03-01

Electrification of transport offers opportunities to increase energy security, reduce carbon emissions, and improve local air quality. Plug-in electric vehicles (PEVs) are creating new connections between the transportation and electric sectors, and PEV charging will create opportunities and challenges in a system of growing complexity. Here, I use highly resolved models of residential power demand and PEV use to assess the impact of uncoordinated in-home PEV charging on residential power demand. While the increase in aggregate demand might be minimal even for high levels of PEV adoption, uncoordinated PEV charging could significantly change the shape of the aggregate residential demand, with impacts for electricity infrastructure, even at low adoption levels. Clustering effects in vehicle adoption at the local level might lead to high PEV concentrations even if overall adoption remains low, significantly increasing peak demand and requiring upgrades to the electricity distribution infrastructure. This effect is exacerbated when adopting higher in-home power charging.
Municipal wastewater sludge as a sustainable bioresource in the United States

DOE PAGES

Seiple, Timothy E.; Coleman, André M.; Skaggs, Richard L.

2017-04-20

Within the United States and Puerto Rico, publicly owned treatment works (POTWs) process 130.5 Gl/d (34.5 Bgal/d) of wastewater, producing sludge as a waste product. Emerging technologies offer novel waste-to-energy pathways through whole sludge conversion into biofuels. Assessing the feasibility, scalability and tradeoffs of various energy conversion pathways is difficult in the absence of highly spatially resolved estimates of sludge production. In this study, average wastewater solids concentrations and removal rates, and site specific daily average influent flow are used to estimate site specific annual sludge production on a dry weight basis for >15,000 POTWs. Current beneficial uses, regional productionmore » hotspots and feedstock aggregation potential are also assessed. Analyses indicate 1) POTWs capture 12.56 Tg/y (13.84 MT/y) of dry solids; 2) 50% are not beneficially utilized, and 3) POTWs can support seven regions that aggregate >910 Mg/d (1000 T/d) of sludge within a travel distance of 100 km.« less
Morphological changes in the cellulose and lignin components of biomass occur at different stages of steam pretreatment

DOE PAGES

Pingali, Sai Venkatesh; O'Neill, Hugh Michael; Nishiyama, Yoshiharu; ...

2014-01-09

Morphological changes to the different components of lignocellulosic biomass were observed as they occurred during steam pretreatment by placing a pressure reaction cell in a neutron beam and collecting time-resolved neutron scattering data. Changes to cellulose morphology occurred mainly in the heating phase, whereas changes in lignin morphology occurred mainly in the holding and cooling phases. During the heating stage, water is irreversibly expelled from cellulose microfibrils as the elementary fibrils coalesce. During the holding phase lignin aggregates begin to appear and they increase in size most noticeably during the cooling phase. This experiment demonstrates the unique information that inmore » situ small angle neutron scattering studies of pretreatment can provide. This approach is potentially useful in optimizing the heating, holding and cooling stages of pretreatments to allow the exact size and nature of lignin aggregates to be controlled in order to enhance enzyme accessibility to cellulose and therefore the efficiency of biomass conversion.« less
Processing and representation of meta-data for sleep apnea diagnosis with an artificial intelligence approach.

PubMed

Nettleton, D; Muñiz, J

2001-09-01

In this article, we revise and try to resolve some of the problems inherent in questionnaire screening of sleep apnea cases and apnea diagnosis based on attributes which are relevant and reliable. We present a way of learning information about the relevance of the data, comparing this with the definition of the information by the medical expert. We generate a predictive data model using a data aggregation operator which takes relevance and reliability information about the data into account to produce a diagnosis for each case. We also introduce a grade of membership for each question response which allows the patient to indicate a level of confidence or doubt in their own judgement. The method is tested with data collected from patients in a Sleep Clinic using questionnaires specially designed for the study. Other artificial intelligence predictive modeling algorithms are also tested on the same data and their predictive accuracy compared to that of the aggregation operator.
On the predictive ability of mechanistic models for the Haitian cholera epidemic.

PubMed

Mari, Lorenzo; Bertuzzo, Enrico; Finger, Flavio; Casagrandi, Renato; Gatto, Marino; Rinaldo, Andrea

2015-03-06

Predictive models of epidemic cholera need to resolve at suitable aggregation levels spatial data pertaining to local communities, epidemiological records, hydrologic drivers, waterways, patterns of human mobility and proxies of exposure rates. We address the above issue in a formal model comparison framework and provide a quantitative assessment of the explanatory and predictive abilities of various model settings with different spatial aggregation levels and coupling mechanisms. Reference is made to records of the recent Haiti cholera epidemics. Our intensive computations and objective model comparisons show that spatially explicit models accounting for spatial connections have better explanatory power than spatially disconnected ones for short-to-intermediate calibration windows, while parsimonious, spatially disconnected models perform better with long training sets. On average, spatially connected models show better predictive ability than disconnected ones. We suggest limits and validity of the various approaches and discuss the pathway towards the development of case-specific predictive tools in the context of emergency management. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
Anthropogenic iron oxide aerosols enhance atmospheric heating

PubMed Central

Moteki, Nobuhiro; Adachi, Kouji; Ohata, Sho; Yoshida, Atsushi; Harigaya, Tomoo; Koike, Makoto; Kondo, Yutaka

2017-01-01

Combustion-induced carbonaceous aerosols, particularly black carbon (BC) and brown carbon (BrC), have been largely considered as the only significant anthropogenic contributors to shortwave atmospheric heating. Natural iron oxide (FeOx) has been recognized as an important contributor, but the potential contribution of anthropogenic FeOx is unknown. In this study, we quantify the abundance of FeOx over East Asia through aircraft measurements using a modified single-particle soot photometer. The majority of airborne FeOx particles in the continental outflows are of anthropogenic origin in the form of aggregated magnetite nanoparticles. The shortwave absorbing powers (Pabs) attributable to FeOx and to BC are calculated on the basis of their size-resolved mass concentrations and the mean Pabs(FeOx)/Pabs(BC) ratio in the continental outflows is estimated to be at least 4–7%. We demonstrate that in addition to carbonaceous aerosols the aggregate of magnetite nanoparticles is a significant anthropogenic contributor to shortwave atmospheric heating. PMID:28508863

Influence of reactive gas admixture on transition metal cluster nucleation in a gas aggregation cluster source

NASA Astrophysics Data System (ADS)

Peter, Tilo; Polonskyi, Oleksandr; Gojdka, Björn; Mohammad Ahadi, Amir; Strunskus, Thomas; Zaporojtchenko, Vladimir; Biederman, Hynek; Faupel, Franz

2012-12-01

We quantitatively assessed the influence of reactive gases on the formation processes of transition metal clusters in a gas aggregation cluster source. A cluster source based on a 2 in. magnetron is used to study the production rate of titanium and cobalt clusters. Argon served as working gas for the DC magnetron discharge, and a small amount of reactive gas (oxygen and nitrogen) is added to promote reactive cluster formation. We found that the cluster production rate depends strongly on the reactive gas concentration for very small amounts of reactive gas (less than 0.1% of total working gas), and no cluster formation takes place in the absence of reactive species. The influence of discharge power, reactive gas concentration, and working gas pressure are investigated using a quartz micro balance in a time resolved manner. The strong influence of reactive gas is explained by a more efficient formation of nucleation seeds for metal-oxide or nitride than for pure metal.
[Evaluation of Image Quality of Readout Segmented EPI with Readout Partial Fourier Technique].

PubMed

Yoshimura, Yuuki; Suzuki, Daisuke; Miyahara, Kanae

Readout segmented EPI (readout segmentation of long variable echo-trains: RESOLVE) segmented k-space in the readout direction. By using the partial Fourier method in the readout direction, the imaging time was shortened. However, the influence on image quality due to insufficient data sampling is concerned. The setting of the partial Fourier method in the readout direction in each segment was changed. Then, we examined signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and distortion ratio for changes in image quality due to differences in data sampling. As the number of sampling segments decreased, SNR and CNR showed a low value. In addition, the distortion ratio did not change. The image quality of minimum sampling segments is greatly different from full data sampling, and caution is required when using it.
Pulse shape measurements using single shot-frequency resolved optical gating for high energy (80 J) short pulse (600 fs) laser

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

Palaniyappan, S.; Johnson, R.; Shimada, T.

2010-10-15

Relevant to laser based electron/ion accelerations, a single shot second harmonic generation frequency resolved optical gating (FROG) system has been developed to characterize laser pulses (80 J, {approx}600 fs) incident on and transmitted through nanofoil targets, employing relay imaging, spatial filter, and partially coated glass substrates to reduce spatial nonuniformity and B-integral. The device can be completely aligned without using a pulsed laser source. Variations of incident pulse shape were measured from durations of 613 fs (nearly symmetric shape) to 571 fs (asymmetric shape with pre- or postpulse). The FROG measurements are consistent with independent spectral and autocorrelation measurements.
Energy-dispersive neutron imaging and diffraction of magnetically driven twins in a Ni2MnGa single crystal magnetic shape memory alloy

NASA Astrophysics Data System (ADS)

Kabra, Saurabh; Kelleher, Joe; Kockelmann, Winfried; Gutmann, Matthias; Tremsin, Anton

2016-09-01

Single crystals of a partially twinned magnetic shape memory alloy, Ni2MnGa, were imaged using neutron diffraction and energy-resolved imaging techniques at the ISIS spallation neutron source. Single crystal neutron diffraction showed that the crystal produces two twin variants with a specific crystallographic relationship. Transmission images were captured using a time of flight MCP/Timepix neutron counting detector. The twinned and untwinned regions were clearly distinguishable in images corresponding to narrow-energy transmission images. Further, the spatially-resolved transmission spectra were used to elucidate the orientations of the crystallites in the different volumes of the crystal.
State-resolved differential and integral cross sections for the Ne + H{sub 2}{sup +} (v = 0–2, j = 0) → NeH{sup +} + H reaction

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

Wu, Hui; Yao, Cui-Xia; He, Xiao-Hu

State-to-state quantum dynamic calculations for the proton transfer reaction Ne + H{sub 2}{sup +} (v = 0–2, j = 0) are performed on the most accurate LZHH potential energy surface, with the product Jacobi coordinate based time-dependent wave packet method including the Coriolis coupling. The J = 0 reaction probabilities for the title reaction agree well with previous results in a wide range of collision energy of 0.2-1.2 eV. Total integral cross sections are in reasonable agreement with the available experiment data. Vibrational excitation of the reactant is much more efficient in enhancing the reaction cross sections than translational andmore » rotational excitation. Total differential cross sections are found to be forward-backward peaked with strong oscillations, which is the indication of the complex-forming mechanism. As the collision energy increases, state-resolved differential cross section changes from forward-backward symmetric peaked to forward scattering biased. This forward bias can be attributed to the larger J partial waves, which makes the reaction like an abstraction process. Differential cross sections summed over two different sets of J partial waves for the v = 0 reaction at the collision energy of 1.2 eV are plotted to illustrate the importance of large J partial waves in the forward bias of the differential cross sections.« less
Light-induced nonadiabatic dynamics in molecular assemblies and nanostructures

NASA Astrophysics Data System (ADS)

Mitric, Roland

The combination of mixed quantum-classical dynamics with efficient electronic structure methods was developed in order to simulate the light-induced processes in complex molecules, multichromophoric aggregates and metallic nanostructures. We will demonstrate how the combination of nonadiabatic dynamics with experimental pump-probe techniques such as time-resolved photoelectron imaging (TRPEI) allows to fully resolve the mechanism of excited state relaxation through conical intersections in several prototype organic- and biomolecules. Specifically, the role of the solvent in the excited state relaxation in microsolvated and fully solvated systems will be addressed. Currently there is growing evidence that nonadiabatic relaxation processes also play a fundamental role in determining the efficiency of excitonic transfer or charge injection in multichromophoric assemblies. Since such systems are currently out of the reach of the state-of-the-art quantum chemistry a development of even more efficient quantum chemical approaches is necessary in order to describe the excited state dynamics in such assemblies. For this purpose we have recently developed long-range corrected time-dependent density functional tight binding (LC-TDDFTB) nonadiabatic dynamics and combined it with the QM/MM approach in order to simulate exciton relaxation in complex systems. The applications of the method to the investigation of the optical properties and dynamics in multichromophoric assemblies including stacked pi-conjugated organic chromophores, model molecular crystals as well as self-organized dye aggregates will be presented. Finally, we will address exciton transport dynamics coupled with the light propagation in hybrid exciton-plasmon nanostructures, which represent promising materials fort the development of novel light-harvesting systems.
Protein-silver nanoparticle interactions to colloidal stability in acidic environments.

PubMed

Tai, Jui-Ting; Lai, Chao-Shun; Ho, Hsin-Chia; Yeh, Yu-Shan; Wang, Hsiao-Fang; Ho, Rong-Ming; Tsai, De-Hao

2014-11-04

We report a kinetic study of Ag nanoparticles (AgNPs) under acidic environments (i.e., pH 2.3 to pH ≈7) and systematically investigate the impact of protein interactions [i.e., bovine serum albumin (BSA) as representative] to the colloidal stability of AgNPs. Electrospray-differential mobility analysis (ES-DMA) was used to characterize the particle size distributions and the number concentrations of AgNPs. Transmission electron microscopy was employed orthogonally to provide visualization of AgNPs. For unconjugated AgNPs, the extent of aggregation, or the average particle size, was shown to be increased significantly with an increase of acidity, where a partial coalescence was found between the primary particles of unconjugated AgNP clusters. Aggregation rate constant, kD, was also shown to be proportional to acidity, following a correlation of log(kD) = -1.627(pH)-9.3715. Using ES-DMA, we observe BSA had a strong binding affinity (equilibrium binding constant, ≈ 1.1 × 10(6) L/mol) to the surface of AgNPs, with an estimated maximum molecular surface density of ≈0.012 nm(-2). BSA-functionalized AgNPs exhibited highly-improved colloidal stability compared to the unconjugated AgNPs under acidic environments, where both the acid-induced interfacial dissolution and the particle aggregation became negligible. Results confirm a complex mechanism of colloidal stability of AgNPs: the aggregation process was shown to be dominant, and the formation of BSA corona on AgNPs suppressed both particle aggregation and interfacial dissolution of AgNP samples under acidic environments.
Modifying the Cold Gelation Properties of Quinoa Protein Isolate: Influence of Heat-Denaturation pH in the Alkaline Range.

PubMed

Mäkinen, Outi E; Zannini, Emanuele; Arendt, Elke K

2015-09-01

Heat-denaturation of quinoa protein isolate (QPI) at alkali pH and its influence on the physicochemical and cold gelation properties was investigated. Heating QPI at pH 8.5 led to increased surface hydrophobicity and decreases in free and bound sulfhydryl group contents. Heating at pH 10.5 caused a lesser degree of changes in sulfhydryl groups and surface hydrophobicity, and the resulting solutions showed drastically increased solubility. SDS PAGE revealed the presence of large aggregates only in the sample heated at pH 8.5, suggesting that any aggregates present in the sample heated at pH 10.5 were non-covalently bound and disintegrated in the presence of SDS. Reducing conditions partially dissolved the aggregates in the pH 8.5 heated sample indicating the occurrence of disulphide bonding, but caused no major alterations in the separation pattern of the pH 10.5 heated sample. Denaturation pH influenced the cold gelation properties greatly. Solutions heated at pH 8.5 formed a coarse coagulum with maximum G' of 5 Pa. Heat-denaturation at 10.5 enabled the proteins to form a finer and regularly structured gel with a maximum G' of 1140 Pa. Particle size analysis showed that the pH 10.5 heated sample contained a higher level of very small particles (0.1-2 μm), and these readily aggregated into large particles (30-200 μm) when pH was lowered to 5.5. Differences in the nature of aggregates formed during heating may explain the large variation in gelation properties.
Individual aerosol particles in ambient and updraft conditions below convective cloud bases in the Oman mountain region

NASA Astrophysics Data System (ADS)

Semeniuk, T. A.; Bruintjes, R. T.; Salazar, V.; Breed, D. W.; Jensen, T. L.; Buseck, P. R.

2014-03-01

An airborne study of cloud microphysics provided an opportunity to collect aerosol particles in ambient and updraft conditions of natural convection systems for transmission electron microscopy (TEM). Particles were collected simultaneously on lacey carbon and calcium-coated carbon (Ca-C) TEM grids, providing information on particle morphology and chemistry and a unique record of the particle's physical state on impact. In total, 22 particle categories were identified, including single, coated, aggregate, and droplet types. The fine fraction comprised up to 90% mixed cation sulfate (MCS) droplets, while the coarse fraction comprised up to 80% mineral-containing aggregates. Insoluble (dry), partially soluble (wet), and fully soluble particles (droplets) were recorded on Ca-C grids. Dry particles were typically silicate grains; wet particles were mineral aggregates with chloride, nitrate, or sulfate components; and droplets were mainly aqueous NaCl and MCS. Higher numbers of droplets were present in updrafts (80% relative humidity (RH)) compared with ambient conditions (60% RH), and almost all particles activated at cloud base (100% RH). Greatest changes in size and shape were observed in NaCl-containing aggregates (>0.3 µm diameter) along updraft trajectories. Their abundance was associated with high numbers of cloud condensation nuclei (CCN) and cloud droplets, as well as large droplet sizes in updrafts. Thus, compositional dependence was observed in activation behavior recorded for coarse and fine fractions. Soluble salts from local pollution and natural sources clearly affected aerosol-cloud interactions, enhancing the spectrum of particles forming CCN and by forming giant CCN from aggregates, thus, making cloud seeding with hygroscopic flares ineffective in this region.
Co-production of GroELS discriminates between intrinsic and thermally-induced recombinant protein aggregation during substrate quality control

PubMed Central

2011-01-01

Background The effects and effectiveness of the chaperone pair GroELS on the yield and quality of recombinant polypeptides produced in Escherichia coli are matter of controversy, as the reported activities of this complex are not always consistent and eventually indicate undesired side effects. The divergence in the reported data could be due, at least partially, to different experimental conditions in independent research approaches. Results We have then selected two structurally different model proteins (namely GFP and E. coli β-galactosidase) and two derived aggregation-prone fusions to explore, in a systematic way, the eventual effects of GroELS co-production on yield, solubility and conformational quality. Host cells were cultured at two alternative temperatures below the threshold at which thermal stress is expected to be triggered, to minimize the involvement of independent stress factors. Conclusions From the analysis of protein yield, solubility and biological activity of the four model proteins produced alone or along the chaperones, we conclude that GroELS impacts on yield and quality of aggregation-prone proteins with intrinsic determinants but not on thermally induced protein aggregation. No effective modifications of protein solubility have been observed, but significant stabilization of small (encapsulable) substrates and moderate chaperone-induced degradation of larger (excluded) polypeptides. These findings indicate that the activities of this chaperone pair in the context of actively producing recombinant bacteria discriminate between intrinsic and thermally-induced protein aggregation, and that the side effects of GroELS overproduction might be determined by substrate size. PMID:21992454
Summarizing an Ontology: A "Big Knowledge" Coverage Approach.

PubMed

Zheng, Ling; Perl, Yehoshua; Elhanan, Gai; Ochs, Christopher; Geller, James; Halper, Michael

2017-01-01

Maintenance and use of a large ontology, consisting of thousands of knowledge assertions, are hampered by its scope and complexity. It is important to provide tools for summarization of ontology content in order to facilitate user "big picture" comprehension. We present a parameterized methodology for the semi-automatic summarization of major topics in an ontology, based on a compact summary of the ontology, called an "aggregate partial-area taxonomy", followed by manual enhancement. An experiment is presented to test the effectiveness of such summarization measured by coverage of a given list of major topics of the corresponding application domain. SNOMED CT's Specimen hierarchy is the test-bed. A domain-expert provided a list of topics that serves as a gold standard. The enhanced results show that the aggregate taxonomy covers most of the domain's main topics.
Review of coal bottom ash and coconut shell in the production of concrete

NASA Astrophysics Data System (ADS)

Faisal, S. K.; Mazenan, P. N.; Shahidan, S.; Irwan, J. M.

2018-04-01

Concrete is the main construction material in the worldwide construction industry. High demand of sand in the concrete production have been increased which become the problems in industry. Natural sand is the most common material used in the construction industry as natural fine aggregate and it caused the availability of good quality of natural sand keep decreasing. The need for a sustainable and green construction building material is required in the construction industry. Hence, this paper presents utilization of coal bottom ash and coconut shell as partial sand replacement in production of concrete. It is able to save cost and energy other than protecting the environment. In summary, 30% usage of coal bottom ash and 25% replacement of coconut shell as aggregate replacement show the acceptable and satisfactory strength of concrete.
Use of partial order in environmental pollution studies demonstrated by urban BTEX air pollution in 20 major cities worldwide.

PubMed

Carlsen, Lars; Bruggemann, Rainer; Kenessov, Bulat

2018-01-01

Urban air pollution with benzene, toluene, ethyl benzene and xylenes (BTEX) is a common phenomenon in major cities where the pollution mainly originates from traffic as well as from residential heating. An attempt to rank cities according to their BTEX air pollution is not necessarily straight forward as we are faced with several individual pollutants simultaneously. A typical procedure is based on aggregation of data for the single compounds, a process that not only hides important information but is also subject to compensation effects. The present study applies a series of partial ordering tools to circumvent the aggregation. Based on partial ordering, most important indicators are disclosed, and an average ranking of the cities included in the study is derived. Since air pollution measurements are often subject to significant uncertainties, special attention has been given to the possible effect of uncertainty and/or data noise. Finally, the effect of introducing weight regimes is studied. In a concluding section the gross national income per person (GNI) is brought into play, demonstrating a positive correlation between BTEX air pollution and GNI. The results are discussed in terms of the ability/willingness to combat air pollution in the cities studied. The present study focuses on Almaty, the largest city in Kazakhstan and compares the data from Almaty to another 19 major cities around the world. It is found that the benzene for Almaty appears peculiar high. Overall Almaty appears ranked as the 8th most BTEX polluted city among the 20 cities included in the study. Copyright © 2017 Elsevier B.V. All rights reserved.
Preparation of Composite Fluoropolymers with Enhanced Dewetting Using Fluorinated Silsesquioxanes as Drop-In Modifiers (Preprint)

DTIC Science & Technology

2010-02-17

Dewetting Using Fluorinated Silsesquioxanes as Drop-In Modifiers (Preprint) 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Scott T... Dewetting Using Fluorinated Silsesquioxanes as Drop-In Modifiers (Preprint) Scott T. Iacono, a,b Stephen M. Budy, a,c Dennis W. Smith, a and...nanometer-sized surface roughness due to POSS aggregation. 23 Likewise, similar dewetting behavior, 90 albeit modest, was observed utilizing partially
Zinc-Amyloid Interactions on a Millisecond Time-Scale Stabilize Non-Fibrillar Alzheimer Related Species

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

Noy,D.; Solomonov, I.; Sinkevich, O.

2008-01-01

The role of zinc, an essential element for normal brain function, in the pathology of Alzheimer's disease (AD) is poorly understood. On one hand, physiological and genetic evidence from transgenic mouse models supports its pathogenic role in promoting the deposition of the amyloid {beta}-protein (A{beta}) in senile plaques. On the other hand, levels of extracellular ('free') zinc in the brain, as inferred by the levels of zinc in cerebrospinal fluid, were found to be too low for inducing A{beta} aggregation. Remarkably, the release of transient high local concentrations of zinc during rapid synaptic events was reported. The role of suchmore » free zinc pulses in promoting A{beta} aggregation has never been established. Using a range of time-resolved structural and spectroscopic techniques, we found that zinc, when introduced in millisecond pulses of micromolar concentrations, immediately interacts with A{beta} 1-40 and promotes its aggregation. These interactions specifically stabilize non-fibrillar pathogenic related aggregate forms and prevent the formation of A{beta} fibrils (more benign species) presumably by interfering with the self-assembly process of A{beta}. These in vitro results strongly suggest a significant role for zinc pulses in A{beta} pathology. We further propose that by interfering with A{beta} self-assembly, which leads to insoluble, non-pathological fibrillar forms, zinc stabilizes transient, harmful amyloid forms. This report argues that zinc represents a class of molecular pathogens that effectively perturb the self-assembly of benign A{beta} fibrils, and stabilize harmful non-fibrillar forms.« less
Liquid Crystal Based Sensor to Detect Beta-Sheet Formation of Peptides

NASA Astrophysics Data System (ADS)

Sadati, Monirosadat; Izmitli Apik, Aslin; Abbott, Nicholas L.; de Pablo, Juan J.

2015-03-01

Protein aggregation into amyloid fibrils is involved in the progression of Alzheimer's, typeII diabetes and Huntington's diseases. Although larger aggregates remain important for clinical determination, small oligomers are of great interest due to their potentially toxic nature. It is therefore crucial to develop methods that probe the aggregation process at early stages and in the vicinity of biological membranes. Here, we present a simple method that relies on liquid crystalline materials and a Langmuir monolayer at the aqueous-liquid crystal (LC) interface. The approach is based on the LC's specific response to β-sheet structures, which abound in amyloid fibrils. When the system is observed under polarized light, the fibrils formed by amyloidogenic peptides give rise to the formation of elongated and branched structures in the LCs. Moreover, the PolScope measurements prove that the LCs are predominantly aligned along the fibrils when exposed to a β-sheet forming peptide. In contrast, non-amyloidogenic peptides form ellipsoidal domains of irregularly tilted LCs. This method is capable of reporting aggregation at lipid-aqueous interfaces at nanomolar concentrations of the peptide, and much earlier than commonly used fluorescence-based techniques. We thank Prof. Oleg D. Levrentovich and Young-Ki Kim from the Liquid Crystal Institute of Kent State University for the use of their PolScope instrument. This work was partially supported by the Swiss National Science Foundation (P300P2_151342).
Structure based aggregation studies reveal the presence of helix-rich intermediate during α-Synuclein aggregation

PubMed Central

Ghosh, Dhiman; Singh, Pradeep K.; Sahay, Shruti; Jha, Narendra Nath; Jacob, Reeba S.; Sen, Shamik; Kumar, Ashutosh; Riek, Roland; Maji, Samir K.

2015-01-01

Mechanistic understanding of nucleation dependent polymerization by α-synuclein (α-Syn) into toxic oligomers and amyloids is important for the drug development against Parkinson's disease. However the structural and morphological characterization during nucleation and subsequent fibrillation process of α-Syn is not clearly understood. Using a variety of complementary biophysical techniques monitoring entire pathway of nine different synucleins, we found that transition of unstructured conformation into β-sheet rich fibril formation involves helix-rich intermediates. These intermediates are common for all aggregating synucleins, contain high solvent-exposed hydrophobic surfaces, are cytotoxic to SHSY-5Y cells and accelerate α-Syn aggregation efficiently. A multidimensional NMR study characterizing the intermediate accompanied with site-specific fluorescence study suggests that the N-terminal and central portions mainly participate in the helix-rich intermediate formation while the C-terminus remained in an extended conformation. However, significant conformational transitions occur at the middle and at the C-terminus during helix to β-sheet transition as evident from Trp fluorescence study. Since partial helix-rich intermediates were also observed for other amyloidogenic proteins such as Aβ and IAPP, we hypothesize that this class of intermediates may be one of the important intermediates for amyloid formation pathway by many natively unstructured protein/peptides and represent a potential target for drug development against amyloid diseases. PMID:25784353
Does whole blood coagulation analysis reflect developmental haemostasis?

PubMed

Ravn, Hanne Berg; Andreasen, Jo Bønding; Hvas, Anne-Mette

2017-04-01

: Developmental haemostasis has been well documented over the last 3 decades and age-dependent reference ranges have been reported for a number of plasmatic coagulation parameters. With the increasing use of whole blood point-of-care tests like rotational thromboelastometry (ROTEM) and platelet function tests, an evaluation of age-dependent changes is warranted for these tests as well. We obtained blood samples from 149 children, aged 1 day to 5.9 years, and analysed conventional plasmatic coagulation tests, including activated partial prothrombin time, prothrombin time, and fibrinogen (functional). Whole blood samples were analysed using ROTEM to assess overall coagulation capacity and Multiplate analyzer to evaluate platelet aggregation. Age-dependent changes were analysed for all variables. We found age-dependent differences in all conventional coagulation tests (all P values < 0.05), but there was no sign of developmental changes in whole blood coagulation assessment when applying ROTEM, apart from clotting time in the EXTEM assay (P < 0.03). Despite marked differences in mean platelet aggregation between age groups, data did not reach statistical significance. Citrate-anticoagulated blood showed significantly reduced platelet aggregation compared with blood anticoagulated with heparin or hirudin (all P values < 0.003). We confirmed previous developmental changes in conventional plasmatic coagulation test. However, these age-dependent changes were not displayed in whole blood monitoring using ROTEM or Multiplate analyzer. Type of anticoagulant had a significant influence on platelet aggregation across all age groups.
Polypeptide Grafted Hyaluronan: Synthesis and Characterization

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

Wang, Xiaojun; Messman, Jamie M; Mays, Jimmy

2010-01-01

Poly(L-leucine) grafted hyaluronan (HA-g-PLeu) has been synthesized via a Michael addition reaction between primary amine terminated poly(L-leucine) and acrylate-functionalized HA (TBAHA-acrylate). The precursor hyaluronan was first functionalized with acrylate groups by reaction with acryloyl chloride in the presence of triethylamine in N,N-dimethylformamide. 1H NMR analysis of the resulting product indicated that an increase in the concentration of acryloylchoride with respect to hydroxyl groups on HA has only a moderate effect on functionalization efficiency, f. A precise control of stoichiometry was not achieved, which could be attributed to partial solubility of intermolecular aggregates and the hygroscopic nature of HA. Michael additionmore » at high [PLeu- NH2]/[acrylate]TBAHA ratios gave a molar grafting ratio of only 0.20 with respect to the repeat unit of HA, indicating grafting limitation due to insolubility of the grafted HA-g-PLeu. Soluble HA-g-PLeu graft copolymers were obtained for low grafting ratios (<0.039) with <8.6% by mass of PLeu and were characterized thoroughly using light scattering, 1H NMR, FT-IR, and AFM techniques. Light scattering experiments showed a strong hydrophobic interaction between PLeu chains, resulting in aggregates with segregated nongrafted HA segments. This yields local networks of aggregates, as demonstrated by atomic force microscopy. Circular dichroism spectroscopy showed a -sheet conformation for aggregates of poly(L-leucine).« less
Geopolymerisation of silt generated from construction and demolition waste washing plants.

PubMed

Lampris, C; Lupo, R; Cheeseman, C R

2009-01-01

Recycling plants that size, sort and wash construction and demolition waste can produce high quality aggregate. However, they also produce up to 80ton per hour of filter cake waste containing fine (<63mum) silt particles that is classified as inert waste and normally landfilled. This research investigated the potential to form geopolymers containing silt, which would allow this problematic waste to be beneficially reused as aggregate. This would significantly improve the economic viability of recycling plants that wash wastes. Silt filter cakes have been collected from a number of aggregate washing plants operating in the UK. These were found to contain similar aluminosilicate crystalline phases. Geopolymer samples were produced using silt and silt mixed with either metakaolin or pulverised fuel ash (PFA). Silt geopolymers cured at room temperature had average 7-day compressive strengths of 18.7MPa, while partial substitution of silt by metakaolin or PFA increased average compressive strengths to 30.5 and 21.9MPa, respectively. Curing specimens for 24h at 105 degrees C resulted in a compressive strength of 39.7MPa and microstructural analysis confirmed the formation of dense materials. These strengths are in excess of those required for materials to be used as aggregate, particularly in unbound applications. The implications of this research for the management of waste silt at construction and demolition waste washing plants are discussed.

Does aggregate school-wide achievement mediate fifth grade outcomes for former early childhood education participants?

PubMed

Curenton, Stephanie M; Dong, Nianbo; Shen, Xiangjin

2015-07-01

This study used a multilevel mediation model to test the theory that former early childhood education (ECE) attendees' 5th grade achievement is mediated by the aggregate school-wide achievement of their elementary school. Aggregate school-wide achievement was defined as the percentage of 5th graders in a school who were at/above academic proficiency in reading or math. Research questions were: (a) Do ECE program participants have better achievement at 5th grade compared with their matched peers who did not participate in an ECE program?; and (b) Is the association between ECE attendance and 5th grade academic performance mediated by school-wide achievement? Results indicated that children who attended prekindergarten (pre-K) and child care outperformed their matched peers who had not attended ECE programs; conversely, those children who did not attend ECE actually outperformed their Head Start counterparts. Mediation analyses indicated that aggregate school-wide achievement at 5th grade partially mediated the association between former ECE attendance and 5th grade performance; however, these mediated effects were small. Overall, the size of the total effects of ECE and the 5th grade academic outcomes were consistent with prior studies. This research confirms the long-term effects of pre-K and child care until 5th grade. (c) 2015 APA, all rights reserved).
New theory for crack-tip twinning in fcc metals

NASA Astrophysics Data System (ADS)

Andric, Predrag; Curtin, W. A.

2018-04-01

Dislocation emission from a crack tip is a necessary mechanism for crack tip blunting and toughening. In fcc metals under Mode I loading, a first partial dislocation is emitted, followed either by a trailing partial dislocation ("ductile" behaviour) or a twinning partial dislocation ("quasi-brittle"). The twinning tendency is usually estimated using the Tadmor and Hai extension of the Rice theory. Extensive molecular statics simulations reveal that the predictions of the critical stress intensity factor for crack tip twinning are always systematically lower (20-35%) than observed. Analyses of the energy change during nucleation reveal that twin partial emission is not accompanied by creation of a surface step while emission of the trailing partial creates a step. The absence of the step during twinning motivates a modified model for twinning nucleation that accounts for the fact that nucleation does not occur directly at the crack tip. Predictions of the modified theory are in excellent agreement with all simulations that show twinning. Emission of the trailing partial dislocation, including the step creation, is predicted using a model recently introduced to accurately predict the first partial emission and shows why twinning is preferred. A second mode of twinning is found wherein the crack first advances by cleavage and then emits the twinning partial at the new crack tip; this mode dominates for emission beyond the first twinning partial. These new theories resolve all the discrepancies between the Tadmor twinning analysis and simulations, and have various implications for fracture behaviour and transitions.
Doubly robust estimation of generalized partial linear models for longitudinal data with dropouts.

PubMed

Lin, Huiming; Fu, Bo; Qin, Guoyou; Zhu, Zhongyi

2017-12-01

We develop a doubly robust estimation of generalized partial linear models for longitudinal data with dropouts. Our method extends the highly efficient aggregate unbiased estimating function approach proposed in Qu et al. (2010) to a doubly robust one in the sense that under missing at random (MAR), our estimator is consistent when either the linear conditional mean condition is satisfied or a model for the dropout process is correctly specified. We begin with a generalized linear model for the marginal mean, and then move forward to a generalized partial linear model, allowing for nonparametric covariate effect by using the regression spline smoothing approximation. We establish the asymptotic theory for the proposed method and use simulation studies to compare its finite sample performance with that of Qu's method, the complete-case generalized estimating equation (GEE) and the inverse-probability weighted GEE. The proposed method is finally illustrated using data from a longitudinal cohort study. © 2017, The International Biometric Society.
A model reduction approach to numerical inversion for a parabolic partial differential equation

NASA Astrophysics Data System (ADS)

Borcea, Liliana; Druskin, Vladimir; Mamonov, Alexander V.; Zaslavsky, Mikhail

2014-12-01

We propose a novel numerical inversion algorithm for the coefficients of parabolic partial differential equations, based on model reduction. The study is motivated by the application of controlled source electromagnetic exploration, where the unknown is the subsurface electrical resistivity and the data are time resolved surface measurements of the magnetic field. The algorithm presented in this paper considers inversion in one and two dimensions. The reduced model is obtained with rational interpolation in the frequency (Laplace) domain and a rational Krylov subspace projection method. It amounts to a nonlinear mapping from the function space of the unknown resistivity to the small dimensional space of the parameters of the reduced model. We use this mapping as a nonlinear preconditioner for the Gauss-Newton iterative solution of the inverse problem. The advantage of the inversion algorithm is twofold. First, the nonlinear preconditioner resolves most of the nonlinearity of the problem. Thus the iterations are less likely to get stuck in local minima and the convergence is fast. Second, the inversion is computationally efficient because it avoids repeated accurate simulations of the time-domain response. We study the stability of the inversion algorithm for various rational Krylov subspaces, and assess its performance with numerical experiments.
Advantages of soft versus hard constraints in self-modeling curve resolution problems. Alternating least squares with penalty functions.

PubMed

Gemperline, Paul J; Cash, Eric

2003-08-15

A new algorithm for self-modeling curve resolution (SMCR) that yields improved results by incorporating soft constraints is described. The method uses least squares penalty functions to implement constraints in an alternating least squares algorithm, including nonnegativity, unimodality, equality, and closure constraints. By using least squares penalty functions, soft constraints are formulated rather than hard constraints. Significant benefits are (obtained using soft constraints, especially in the form of fewer distortions due to noise in resolved profiles. Soft equality constraints can also be used to introduce incomplete or partial reference information into SMCR solutions. Four different examples demonstrating application of the new method are presented, including resolution of overlapped HPLC-DAD peaks, flow injection analysis data, and batch reaction data measured by UV/visible and near-infrared spectroscopy (NIR). Each example was selected to show one aspect of the significant advantages of soft constraints over traditionally used hard constraints. Incomplete or partial reference information into self-modeling curve resolution models is described. The method offers a substantial improvement in the ability to resolve time-dependent concentration profiles from mixture spectra recorded as a function of time.
Multiple, simultaneous, independent gradients for a versatile multidimensional liquid chromatography. Part II: Application 1 - Large increases in isoform resolution of human transferrin by use of dual simultaneous independent gradients of pH & acetonitrile on a mixed bed (anion exchange plus reversed phase) stationary phase.

PubMed

Tsonev, Latchezar I; Hirsh, Allen G

2016-10-14

We have previously described a liquid chromatographic (LC) method for uncoupling controlled, wide range pH gradients and simultaneous controlled gradients of a non-buffering solute on ion exchange resins (Hirsh and Tsonev, 2012) [1]. Here we report the application of this two dimensional LC technique to the problem of resolving Human Transferrin (HT) isoforms. This important iron transporting protein should theoretically occur in several thousand glycoforms, but only about a dozen have been reported. Using dual simultaneous independent gradients (DSIGs) of acetonitrile (ACN) and pH on a mixed bed stationary phase (SP) consisting of a mixture of an anion exchange resin and a reversed phase (RP) resin we partially resolve about 60 isoforms. These are likely to be partially refolded glycoforms generated by interaction of HT with the highly hydrophobic RP SP, as well as distinct folded glycoforms. Thus this study should have interesting implications for both glycoform separation and the study of protein folding. Copyright © 2016 Elsevier B.V. All rights reserved.
A project based on multi-configuration Dirac-Fock calculations for plasma spectroscopy

NASA Astrophysics Data System (ADS)

Comet, M.; Pain, J.-C.; Gilleron, F.; Piron, R.

2017-09-01

We present a project dedicated to hot plasma spectroscopy based on a Multi-Configuration Dirac-Fock (MCDF) code, initially developed by J. Bruneau. The code is briefly described and the use of the transition state method for plasma spectroscopy is detailed. Then an opacity code for local-thermodynamic-equilibrium plasmas using MCDF data, named OPAMCDF, is presented. Transition arrays for which the number of lines is too large to be handled in a Detailed Line Accounting (DLA) calculation can be modeled within the Partially Resolved Transition Array method or using the Unresolved Transition Arrays formalism in jj-coupling. An improvement of the original Partially Resolved Transition Array method is presented which gives a better agreement with DLA computations. Comparisons with some absorption and emission experimental spectra are shown. Finally, the capability of the MCDF code to compute atomic data required for collisional-radiative modeling of plasma at non local thermodynamic equilibrium is illustrated. In addition to photoexcitation, this code can be used to calculate photoionization, electron impact excitation and ionization cross-sections as well as autoionization rates in the Distorted-Wave or Close Coupling approximations. Comparisons with cross-sections and rates available in the literature are discussed.
High sensitivity detection and sorting of infectious human immunodeficiency virus (HIV-1) particles by flow virometry

PubMed Central

Bonar, Micha M.; Tilton, John C.

2017-01-01

Detection of viruses by flow cytometry is complicated by their small size. Here, we characterized the ability of a standard (FACSAria II) and a sub-micron flow cytometer (A50 Micro) to resolve HIV-1 viruses. The A50 was superior at resolving small particles but did not reliably distinguish HIV-1, extracellular vesicles, and laser noise by light scatter properties alone. However, single fluorescent HIV-1 particles could readily be detected by both cytometers. Fluorescent particles were sorted and retained infectivity, permitting further exploration of the functional consequences of HIV-1 heterogeneity. Finally, flow cytometry had a limit of detection of 80 viruses/ml, nearly equal to PCR assays. These studies demonstrate the power of flow cytometry to detect and sort viral particles and provide a critical toolkit to validate methods to label wild-type HIV-1; quantitatively assess integrity and aggregation of viruses and virus-based therapeutics; and efficiently screen drugs inhibiting viral assembly and release. PMID:28235684
High sensitivity detection and sorting of infectious human immunodeficiency virus (HIV-1) particles by flow virometry.

PubMed

Bonar, Michał M; Tilton, John C

2017-05-01

Detection of viruses by flow cytometry is complicated by their small size. Here, we characterized the ability of a standard (FACSAria II) and a sub-micron flow cytometer (A50 Micro) to resolve HIV-1 viruses. The A50 was superior at resolving small particles but did not reliably distinguish HIV-1, extracellular vesicles, and laser noise by light scatter properties alone. However, single fluorescent HIV-1 particles could readily be detected by both cytometers. Fluorescent particles were sorted and retained infectivity, permitting further exploration of the functional consequences of HIV-1 heterogeneity. Finally, flow cytometry had a limit of detection of 80 viruses/ml, nearly equal to PCR assays. These studies demonstrate the power of flow cytometry to detect and sort viral particles and provide a critical toolkit to validate methods to label wild-type HIV-1; quantitatively assess integrity and aggregation of viruses and virus-based therapeutics; and efficiently screen drugs inhibiting viral assembly and release. Copyright © 2017 Elsevier Inc. All rights reserved.
Determination of Spatially Resolved Tablet Density and Hardness Using Near-Infrared Chemical Imaging (NIR-CI).

PubMed

Talwar, Sameer; Roopwani, Rahul; Anderson, Carl A; Buckner, Ira S; Drennen, James K

2017-08-01

Near-infrared chemical imaging (NIR-CI) combines spectroscopy with digital imaging, enabling spatially resolved analysis and characterization of pharmaceutical samples. Hardness and relative density are critical quality attributes (CQA) that affect tablet performance. Intra-sample density or hardness variability can reveal deficiencies in formulation design or the tableting process. This study was designed to develop NIR-CI methods to predict spatially resolved tablet density and hardness. The method was implemented using a two-step procedure. First, NIR-CI was used to develop a relative density/solid fraction (SF) prediction method for pure microcrystalline cellulose (MCC) compacts only. A partial least squares (PLS) model for predicting SF was generated by regressing the spectra of certain representative pixels selected from each image against the compact SF. Pixel selection was accomplished with a threshold based on the Euclidean distance from the median tablet spectrum. Second, micro-indentation was performed on the calibration compacts to obtain hardness values. A univariate model was developed by relating the empirical hardness values to the NIR-CI predicted SF at the micro-indented pixel locations: this model generated spatially resolved hardness predictions for the entire tablet surface.
O 1s core levels in Bi2Sr2CaCu2O8+δ single crystals

NASA Astrophysics Data System (ADS)

Parmigiani, F.; Shen, Z. X.; Mitzi, D. B.; Lindau, I.; Spicer, W. E.; Kapitulnik, A.

1991-02-01

High-quality Bi2Sr2CaCu2O8+δ superconducting single crystals, annealed at different oxygen partial pressures, have been studied using angular-resolved x-ray photoelectron spectroscopy with a resolution higher than that used in any previous study. Two states of the oxygen, separated by ~=0.7 eV, are unambiguously observed. Examining these components at different angles makes it possible to distinguish bulk from surface components. Using this capability we discover that annealing under lower oxygen partial pressure (1 atm) results in oxygen intercalation beneath the Bi-O surface layer of the crystal, whereas for higher-pressure anneals (12 atm) additional oxygen is found on the Bi-O surfaces. This steplike intercalation mechanism is also confirmed by the changes observed in the Cu and Bi core lines as a function of the annealing oxygen partial pressure.
A Comparison of Inductive Sensors in the Characterization of Partial Discharges and Electrical Noise Using the Chromatic Technique.

PubMed

Ardila-Rey, Jorge Alfredo; Montaña, Johny; de Castro, Bruno Albuquerque; Schurch, Roger; Covolan Ulson, José Alfredo; Muhammad-Sukki, Firdaus; Bani, Nurul Aini

2018-03-29

Partial discharges (PDs) are one of the most important classes of ageing processes that occur within electrical insulation. PD detection is a standardized technique to qualify the state of the insulation in electric assets such as machines and power cables. Generally, the classical phase-resolved partial discharge (PRPD) patterns are used to perform the identification of the type of PD source when they are related to a specific degradation process and when the electrical noise level is low compared to the magnitudes of the PD signals. However, in practical applications such as measurements carried out in the field or in industrial environments, several PD sources and large noise signals are usually present simultaneously. In this study, three different inductive sensors have been used to evaluate and compare their performance in the detection and separation of multiple PD sources by applying the chromatic technique to each of the measured signals.
Consistent transport coefficients in astrophysics

NASA Technical Reports Server (NTRS)

Fontenla, Juan M.; Rovira, M.; Ferrofontan, C.

1986-01-01

A consistent theory for dealing with transport phenomena in stellar atmospheres starting with the kinetic equations and introducing three cases (LTE, partial LTE, and non-LTE) was developed. The consistent hydrodynamical equations were presented for partial-LTE, the transport coefficients defined, and a method shown to calculate them. The method is based on the numerical solution of kinetic equations considering Landau, Boltzmann, and Focker-Planck collision terms. Finally a set of results for the transport coefficients derived for a partially ionized hydrogen gas with radiation was shown, considering ionization and recombination as well as elastic collisions. The results obtained imply major changes is some types of theoretical model calculations and can resolve some important current problems concerning energy and mass balance in the solar atmosphere. It is shown that energy balance in the lower solar transition region can be fully explained by means of radiation losses and conductive flux.
Solvability of some partial functional integrodifferential equations with finite delay and optimal controls in Banach spaces.

PubMed

Ezzinbi, Khalil; Ndambomve, Patrice

2016-01-01

In this work, we consider the control system governed by some partial functional integrodifferential equations with finite delay in Banach spaces. We assume that the undelayed part admits a resolvent operator in the sense of Grimmer. Firstly, some suitable conditions are established to guarantee the existence and uniqueness of mild solutions for a broad class of partial functional integrodifferential infinite dimensional control systems. Secondly, it is proved that, under generally mild conditions of cost functional, the associated Lagrange problem has an optimal solution, and that for each optimal solution there is a minimizing sequence of the problem that converges to the optimal solution with respect to the trajectory, the control, and the functional in appropriate topologies. Our results extend and complement many other important results in the literature. Finally, a concrete example of application is given to illustrate the effectiveness of our main results.
Specification aggregate quarry expansion: a case study demonstrating sustainable management of natural aggregate resources

USGS Publications Warehouse

Langer, William H.; Tucker, M.L.

2003-01-01

Many countries, provinces, territories, or states in the European Union, Australia, Canada, the United States, and elsewhere have begun implementing sustainability programs, but most of those programs stop short of sustainable management of aggregate resources. Sustainable practices do not always have to be conducted under the title of sustainability. This case study describes how Lafarge, a large multinational construction materials supplier, implemented the principles of sustainability even though there was an absence of existing local government policies or procedures addressing sustainable resource management. Jefferson County, Colorado, USA, is one of three counties in the six-county Denver, Colorado, region that has potentially available sources of crushed stone. Crushed stone comprises 30 percent of the aggregate produced in the area and plays a major role in regional aggregate resource needs. Jefferson County is home to four of the five crushed stone operations in the Denver region. Lafarge operates one of those four quarries. Lafarge recently proposed to expand its reserves by exchanging company-owned land for existing dedicated open space land adjacent to their quarry but owned by Jefferson County. A similar proposal submitted about 10 years earlier had been denied. Contrary to the earlier proposal, which was predicated on public relations, the new proposal was predicated on public trust. Although not explicitly managed under the moniker of sustainability, Lafarge used basic management principles that embody the tenets of sustainability. To achieve the goals of sustainable aggregate management where no governmental policies existed, Lafarge not only assumed their role of being a responsible corporate and environmental member of the community, but also assumed the role of facilitator to encourage and enable other stakeholders to responsibly resolve legitimate concerns regarding the Lafarge quarry proposal. Lafarge successfully presented an enlightened proposal where the county will gain 745 acres of new open space land in exchange for 60 acres of current open space land adjacent to the quarry. The process involved collaborative efforts by all stakeholders and resulted in an outcome that balances the needs of society, the environment, and business.
A partially folded structure of amyloid-beta(1-40) in an aqueous environment.

PubMed

Vivekanandan, Subramanian; Brender, Jeffrey R; Lee, Shirley Y; Ramamoorthy, Ayyalusamy

2011-07-29

Aggregation of the Aβ(1-40) peptide is linked to the development of extracellular plaques characteristic of Alzheimer's disease. While previous studies commonly show the Aβ(1-40) is largely unstructured in solution, we show that Aβ(1-40) can adopt a compact, partially folded structure. In this structure (PDB ID: 2LFM), the central hydrophobic region of the peptide forms a 3(10) helix from H13 to D23 and the N- and C-termini collapse against the helix due to the clustering of hydrophobic residues. Helical intermediates have been predicted to be crucial on-pathway intermediates in amyloid fibrillogenesis, and the structure presented here presents a new target for investigation of early events in Aβ(1-40) fibrillogenesis. Copyright © 2011 Elsevier Inc. All rights reserved.
Spatially resolved x-ray fluorescence spectroscopy of beryllium capsule implosions at the NIF

NASA Astrophysics Data System (ADS)

MacDonald, M. J.; Bishel, D. T.; Saunders, A. M.; Scott, H. A.; Kyrala, G.; Kline, J.; MacLaren, S.; Thorn, D. B.; Yi, S. A.; Zylstra, A. B.; Falcone, R. W.; Doeppner, T.

2017-10-01

Beryllium ablators used in indirectly driven inertial confinement fusion implosions are doped with copper to prevent preheat of the cryogenic hydrogen fuel. Here, we present analysis of spatially resolved copper K- α fluorescence spectra from the beryllium ablator layer. It has been shown that K- α fluorescence spectroscopy can be used to measure plasma conditions of partially ionized dopants in high energy density systems. In these experiments, K-shell vacancies in the copper dopant are created by the hotspot emission at stagnation, resulting in K-shell fluorescence at bang time. Spatially resolved copper K- α emission spectra are compared to atomic kinetics and radiation code simulations to infer density and temperature profiles. This work was supported by the US DOE under Grant No. DE-NA0001859, under the auspices of the US DOE by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and by Los Alamos National Laboratory under contract DE-AC52-06NA52396.
Abrasion Resistance of Nano Silica Modified Roller Compacted Rubbercrete: Cantabro Loss Method and Response Surface Methodology Approach

NASA Astrophysics Data System (ADS)

Adamu, Musa; Mohammed, Bashar S.; Shafiq, Nasir

2018-04-01

Roller compacted concrete (RCC) when used for pavement is subjected to skidding/rubbing by wheels of moving vehicles, this causes pavement surface to wear out and abrade. Therefore, abrasion resistance is one of the most important properties of concern for RCC pavement. In this study, response surface methodology was used to design, evaluate and analyze the effect of partial replacement of fine aggregate with crumb rubber, and addition of nano silica on the abrasion resistance of roller compacted rubbercrete (RCR). RCR is the terminology used for RCC pavement where crumb rubber was used as partial replacement to fine aggregate. The Box-Behnken design method was used to develop the mixtures combinations using 10%, 20%, and 30% crumb rubber with 0%, 1%, and 2% nano silica. The Cantabro loss method was used to measure the abrasion resistance. The results showed that the abrasion resistance of RCR decreases with increase in crumb rubber content, and increases with increase in addition of nano silica. The analysis of variance shows that the model developed using response surface methodology (RSM) has a very good degree of correlation, and can be used to predict the abrasion resistance of RCR with a percentage error of 5.44%. The combination of 10.76% crumb rubber and 1.59% nano silica yielded the best combinations of RCR in terms of abrasion resistance of RCR.
Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding

PubMed Central

Nagpal, Suhani; Tiwari, Satyam; Mapa, Koyeli; Thukral, Lipi

2015-01-01

Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central “hubs”. Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates. PMID:26394388
Effect of film multi-scale structure on the water vapor permeability in hydroxypropyl starch (HPS)/Na-MMT nanocomposites.

PubMed

Liu, Siyuan; Cai, Panfu; Li, Xiaoxi; Chen, Ling; Li, Lin; Li, Bing

2016-12-10

To improve the water vapor resistance of starch-based films, Na-MMT (Na-montmorillonite) as nanofillers were fabricated into hydroxypropyl starch and the multi-scale structural changes (including intermolecular interaction, short-range conformation, long-range ordered structure and the aggregated structure of the film) were revealed. The elongation of the water vapor molecule pathway by tortuous path is generally recognized as the main reason for the improvement of water resistance. However this study observed the lowest water vapor permeability (WVP) was at the 3% Na-MMT/hydroxypropyl starch (HPS) ratio instead of 5% even nanofillers were partially exfoliated at both ratio. Except for the "tortuous path" caused by nanofillers, this observation proposed that the short-range conformation of HPS chains, long-range ordered structure and the aggregated structure likely influenced the water barrier property. The relationship between WVP and multi-scale structure of the film was investigated. The results suggested that a good balance of short-range conformationin the amorphous region, long-range ordered structure and the aggregated structure of the film was required for the improvement of water vapor barrier property. Copyright © 2016 Elsevier Ltd. All rights reserved.

Competitive displacement of sodium caseinate by low-molecular-weight emulsifiers and the effects on emulsion texture and rheology.

PubMed

Munk, M B; Larsen, F H; van den Berg, F W J; Knudsen, J C; Andersen, M L

2014-07-29

Low-molecular-weight (LMW) emulsifiers are used to promote controlled destabilization in many dairy-type emulsions in order to obtain stable foams in whippable products. The relation between fat globule aggregation induced by three LMW emulsifiers, lactic acid ester of monoglyceride (LACTEM), saturated monoglyceride (GMS), and unsaturated monoglyceride (GMU) and their effect on interfacial protein displacement was investigated. It was found that protein displacement by LMW emulsifiers was not necessary for fat globule aggregation in emulsions, and conversely fat globule aggregation was not necessarily accompanied by protein displacement. The three LMW emulsifiers had very different effects on emulsions. LACTEM induced shear instability of emulsions, which was accompanied by protein displacement. High stability was characteristic for emulsions with GMS where protein was displaced from the interface. Emulsions containing GMU were semisolid, but only low concentrations of protein were detected in the separated serum phase. The effects of LACTEM, GMS, and GMU may be explained by three different mechanisms involving formation of interfacial α-gel, pickering stabilization and increased exposure of bound casein to the water phase. The latter may facilitate partial coalescence. Stabilizing hydrocolloids did not have any effect on the LMW emulsifiers' ability to induce protein displacement.
A suite of global, cross-scale topographic variables for environmental and biodiversity modeling

NASA Astrophysics Data System (ADS)

Amatulli, Giuseppe; Domisch, Sami; Tuanmu, Mao-Ning; Parmentier, Benoit; Ranipeta, Ajay; Malczyk, Jeremy; Jetz, Walter

2018-03-01

Topographic variation underpins a myriad of patterns and processes in hydrology, climatology, geography and ecology and is key to understanding the variation of life on the planet. A fully standardized and global multivariate product of different terrain features has the potential to support many large-scale research applications, however to date, such datasets are unavailable. Here we used the digital elevation model products of global 250 m GMTED2010 and near-global 90 m SRTM4.1dev to derive a suite of topographic variables: elevation, slope, aspect, eastness, northness, roughness, terrain roughness index, topographic position index, vector ruggedness measure, profile/tangential curvature, first/second order partial derivative, and 10 geomorphological landform classes. We aggregated each variable to 1, 5, 10, 50 and 100 km spatial grains using several aggregation approaches. While a cross-correlation underlines the high similarity of many variables, a more detailed view in four mountain regions reveals local differences, as well as scale variations in the aggregated variables at different spatial grains. All newly-developed variables are available for download at Data Citation 1 and for download and visualization at http://www.earthenv.org/topography.
Exploring how organic matter controls structural transformations in natural aquatic nanocolloidal dispersions.

PubMed

King, Stephen M; Jarvie, Helen P

2012-07-03

The response of the dispersion nanostructure of surface river bed sediment to the controlled removal and readdition of natural organic matter (NOM), in the absence and presence of background electrolyte, was examined using the technique of small-angle neutron scattering (SANS). Partial NOM removal induced aggregation of the mineral particles, but more extensive NOM removal restored colloidal stability. When peat humic acid (PHA) was added to a NOM-deficient sediment concentration-related structural transformations were observed: at 255 mg/L PHA aggregation of the nanocolloid was actually enhanced, but at 380 mg/L PHA disaggregation and colloidal stability were promoted. The addition of 2 mM CaCl(2) induced mild aggregation in the native sediment but not in sediments with added PHA, suggesting that the native NOM and the PHA respond differently to changes in ionic strength. A first attempt at using SANS to directly characterize the thickness and coverage of an adsorbed PHA layer in a natural nanocolloid is also presented. The results are discussed in the context of a hierarchical aquatic colloidal nanostructure, and the implications for contemporary studies of the role of dissolved organic carbon (DOC) in sustaining the transport of colloidal iron in upland catchments.
Replacement of Fine Aggregate by using Recyclable Materials in Paving Blocks

NASA Astrophysics Data System (ADS)

Koganti, Shyam Prakash; Hemanthraja, Kommineni; Sajja, Satish

2017-08-01

Cement concrete paving blocks are precast hard products complete out of cement concrete. The product is made in various sizes and shapes like square, round and rectangular blocks of different dimensions with designs for interlocking of adjacent tiles blocks. Several Research Works have been carried out in the past to study the possibility of utilizing waste materials and industrial byproducts in the manufacturing of paver blocks. Various industrial waste materials like quarry dust, glass powder, ceramic dust and coal dust are used as partial replacement of fine aggregate and assessed the strength parameters and compared the profit percentages after replacement with waste materials. Quarry dust can be replaced by 20% and beyond that the difference in strength is not much higher but considering cost we can replace upto 40% so that we can get a profit of almost 10%. Similarly we can replace glass powder and ceramic dust by 20% only beyond that there is decrement in strength and even with 20% replacement we can get 1.34 % and 2.42% of profit. Coal dust is not suitable for alternative material as fine aggregate as it reduces the strength.
Impact of grain sizes on the quantitative concrete analysis using laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Gottlieb, C.; Günther, T.; Wilsch, G.

2018-04-01

In civil engineering concrete is the most used building material for making infrastructures like bridges and parking decks worldwide. It is as a porous and multiphase material made of aggregates with a defined grain size distribution, cement and water as well as different additives and admixtures depending on the application. Different grain sizes are important to ensure the needed density and compressive strength. The resulting porous cement matrix contains a mixture of flour grains (aggregates with a grain size below 125 μm) and cement particles (particle size ≈ 50μm). Harmful species like chlorides may penetrate together with water through the capillary pore space and may trigger different damage processes. The damage assessment of concrete structures in Germany is estimated due to the quantification of harmful elements regarding to the cement content only. In the evaluation of concrete using LIBS a two-dimensional scanning is necessary to consider the heterogeneity caused by the aggregates. Therefore, a LIBS system operating with a low energy NdCr:YAG laser, a pulse energy of 3 mJ, a wavelength of 1064 nm, a pulse width of 1.5 ns and a repetition rate of 100 Hz has been used. Different Czerny-Turner spectrometers with CCD detectors in the UV and NIR range have been used for the detection. Large aggregates (macro-heterogeneity) can be excluded from the evaluation, whereas small aggregates in the range of the laser spot size (flour grains) cannot be spatially resolved. In this work the micro heterogeneity caused by flour grains and their impact on the quantification with LIBS will be discussed. To analyze the effect of changing grain sizes and ratios, the ablation behavior has been determined and compared. Samples with defined grain sizes were made and analyzed using LIBS. The grain size distributions were analyzed with laser diffraction (LDA).
Unusual Nonemissive Behavior of Rubrene J-Aggregates: A Rare Violation.

PubMed

Aggarwal, Nikhil; Patnaik, Archita

2017-04-13

Structure-property correlations in rubrene (RB) colloidal J-aggregates were unravelled by steady state and time-resolved spectroscopy in conjunction with excited state density functional calculations. The RB J-aggregate with a slippage angle θ = 30.4°, estimated from the monomeric transition dipole moment directions, exhibited a broad fwhm of 1073 cm -1 and a 5 nm red-shifted absorption band carrying a transition dipole moment (M⃗ λ agg = 1.80 D) almost equivalent to the monomeric dye (M⃗ λ mon = 1.89 D). A significantly low magnitude of exciton coupling energy, ΔE exc = -358 cm -1 for the rhombic-RB colloidal J-aggregates resulted owing to the weaker electronic communication between the largely separated RB subunits (r = 7.2 Å) and a restricted exciton delocalization over the RB J-dimer (N = 2). The RB J-dimer exhibited a perfect balance between the computed singlet (2.53 eV) and the triplet (1.29 eV) exciton energies for singlet fission (SF). Supporting this, the PL decay profile of the J-aggregates revealed a delayed fluorescence, substantiating triplet pair formation via SF. The experimental evidence for the long-lived triplet formation was furthermore confirmed by its transient absorption (T 1 → T N ) at 530 nm. Consequently, a high probability for SF and a low probability for triplet-triplet recombination, leading to a dramatic lowering in photoluminescence quantum yield from 0.172 down to 0.035 was noted. The electronic structure calculations for the RB J-dimer followed TD-DFT-M062X/6-31G+(d,p) level of theory following integral equation formalism polarizable continuum model (IEFPCM) in water. S 1 excited state for RB J-dimer was carefully analyzed using integral overlap of electron and hole density distribution (ϕ) and the defined t-indexes along all three spatial directions, and was found to be of locally excited in character.
Comparison of increased aspirin dose versus combined aspirin plus clopidogrel therapy in patients with diabetes mellitus and coronary heart disease and impaired antiplatelet response to low-dose aspirin.

PubMed

Duzenli, Mehmet Akif; Ozdemir, Kurtulus; Aygul, Nazif; Soylu, Ahmet; Tokac, Mehmet

2008-08-15

The effects of therapy with aspirin 300 mg/day and with combined aspirin 100 mg/day plus clopidogrel 75 mg/day on platelet function were compared in patients with diabetes mellitus and coronary artery disease and impaired antiplatelet responses to aspirin 100 mg/day. The study population consisted of 151 outpatients with type II diabetes mellitus and coronary artery disease who were taking aspirin 100 mg/day. Of the 151 patients, a subgroup of subjects with impaired aspirin response were selected on the basis of the results of platelet aggregometry. Nonresponsiveness to aspirin was defined as mean aggregation > or =69% with 3 micromol/L adenosine diphosphate and mean aggregation > or =70% with 2 micromol/L collagen. Aspirin semiresponders were defined as meeting 1 but not both of these criteria. Nonresponders and semiresponders were randomized equally to aspirin 300 mg/day and aspirin 100 mg/day plus clopidogrel 75 mg/day, and aggregation tests were repeated after 2 weeks. Sixty of the 151 patients with diabetes (40%) were found to respond to aspirin inadequately. Platelet aggregation induced by adenosine diphosphate and collagen decreased significantly after aspirin 300 mg/day or combined therapy. Combined treatment was found to have a stronger inhibitory effect on platelet aggregation induced by adenosine diphosphate than aspirin 300 mg/day (p = 0.002). Impaired aspirin response was resolved by increasing the aspirin dose or adding clopidogrel to aspirin (p <0.0001 for each). However, desired platelet inhibition was achieved in significantly more patients by combined treatment than by aspirin 300 mg/day (p <0.05). In conclusion, aspirin 100 mg/day does not inhibit platelet function adequately in a significant number of patients with diabetes mellitus and coronary artery disease. Increasing the aspirin dose to 300 mg/day or adding clopidogrel to aspirin can provide adequate platelet inhibition in a significant number of those patients with impaired responses to low-dose aspirin.
Effects of Southern Hemisphere Wind Changes on the Meridional Overturning Circulation in Ocean Models.

PubMed

Gent, Peter R

2016-01-01

Observations show that the Southern Hemisphere zonal wind stress maximum has increased significantly over the past 30 years. Eddy-resolving ocean models show that the resulting increase in the Southern Ocean mean flow meridional overturning circulation (MOC) is partially compensated by an increase in the eddy MOC. This effect can be reproduced in the non-eddy-resolving ocean component of a climate model, providing the eddy parameterization coefficient is variable and not a constant. If the coefficient is a constant, then the Southern Ocean mean MOC change is balanced by an unrealistically large change in the Atlantic Ocean MOC. Southern Ocean eddy compensation means that Southern Hemisphere winds cannot be the dominant mechanism driving midlatitude North Atlantic MOC variability.
Continuum-level modelling of cellular adhesion and matrix production in aggregates.

PubMed

Geris, Liesbet; Ashbourn, Joanna M A; Clarke, Tim

2011-05-01

Key regulators in tissue-engineering processes such as cell culture and cellular organisation are the cell-cell and cell-matrix interactions. As mathematical models are increasingly applied to investigate biological phenomena in the biomedical field, it is important, for some applications, that these models incorporate an adequate description of cell adhesion. This study describes the development of a continuum model that represents a cell-in-gel culture system used in bone-tissue engineering, namely that of a cell aggregate embedded in a hydrogel. Cell adhesion is modelled through the use of non-local (integral) terms in the partial differential equations. The simulation results demonstrate that the effects of cell-cell and cell-matrix adhesion are particularly important for the survival and growth of the cell population and the production of extracellular matrix by the cells, concurring with experimental observations in the literature.
Reversible Age-Related Phenotypes Induced during Larval Quiescence in C. elegans

PubMed Central

Roux, Antoine E.; Langhans, Kelley; Huynh, Walter; Kenyon, Cynthia

2017-01-01

Summary Cells can enter quiescent states in which cell cycling and growth are suspended. We find that during a long developmental arrest (quiescence) induced by starvation, newly-hatched C. elegans acquire features associated with impaired proteostasis and aging: mitochondrial fission, ROS production, protein aggregation, decreased proteotoxic-stress resistance, and at the organismal level, decline of mobility and high mortality. All signs of aging but one, the presence of protein aggregates, were reversed upon return to development induced by feeding. The endoplasmic reticulum receptor IRE-1 is completely required for recovery, and the downstream transcription factor XBP-1, as well as a protein kinase, KGB-1, are partially required. Interestingly, kgb-1(−) mutants that do recover fail to reverse aging-like mitochondrial phenotypes and have a short adult lifespan. Our study describes the first pathway that reverses phenotypes of aging at the exit of prolonged quiescence. PMID:27304510
Origin of spinel-rich chondrules and inclusions in carbonaceous and ordinary chondrites

NASA Technical Reports Server (NTRS)

Kornacki, A. S.; Fegley, B., Jr.

1984-01-01

The evaluation of three models of the origin of spinel-rich chondrules and inclusions presented here includes new calculations of the major-element refractory mineral condensation sequence from a gas of solar composition over a wide pressure interval. Condensation calculations show that spinel-rich chondrules did not crystallize from metastable liquid condensates, and that spinel-rich inclusions are not aggregates of refractory nebular condensates. It is proposed that spinel-rich objects are fractionated distillation residues of small aggregates of primitive dust that lost Ca, Si-rich partial melts by evaporation, ablation, or splashing during collisions. This model also explains why spinel-rich chondrules and inclusions (1) are usually smaller than melilite-rich chondrules and inclusions; (2) often have highly fractionated trace-element compositions; and (3) usually do not contain Pt-metal nuggets even when they are more enriched in the Pt-group metals than nugget-bearing melilite-rich objects.
Second harmonic generation from small particle aggregates

NASA Astrophysics Data System (ADS)

Mochan, W. Luis; Ortiz, Guillermo P.; Mendoza, Bernardo S.; Brudny, Vera L.

2001-03-01

Novel nanofabrication techniques are capable of producing nanoparticles with controled structures which include small clusters, self-assembled particles, quantum dots, vesicles, etc. The non-linear optical scattering of these structures are important for applications, and can be used for their physical characterization. The second harmonic (SH) field radiated by a single small spherical particle has surface and bulk, dipolar and quadrupolar contributions of similar intensities and is strongly dependent of the local environment of the particle [1], in contrast to the linear case. In this work we calculate the nonlinear scattering by particle aggregates and we investigate the effects on the SH generation of the disorder induced field fluctuations and of the localization of light. We acknowledge the partial support from DGAPA-UNAM (grant IN110999), Conacyt (31120-E and 26651-E), CIP and UBACyT. [1] Vera L. Brudny, Bernardo S. Mendoza, and W. Luis Mochán, Phys. Rev. B 62, 11152 (2000).
Properties of lightweight cement-based composites containing waste polypropylene

NASA Astrophysics Data System (ADS)

Záleská, Martina; Pavlíková, Milena; Pavlík, Zbyšek

2016-07-01

Improvement of buildings thermal stability represents an increasingly important trend of the construction industry. This work aims to study the possible use of two types of waste polypropylene (PP) for the development of lightweight cement-based composites with enhanced thermal insulation function. Crushed PP waste originating from the PP tubes production is used for the partial replacement of silica sand by 10, 20, 30, 40 and 50 mass%, whereas a reference mixture without plastic waste is studied as well. First, basic physical and thermal properties of granular PP random copolymer (PPR) and glass fiber reinforced PP (PPGF) aggregate are studied. For the developed composite mixtures, basic physical, mechanical, heat transport and storage properties are accessed. The obtained results show that the composites with incorporated PP aggregate exhibit an improved thermal insulation properties and acceptable mechanical resistivity. This new composite materials with enhanced thermal insulation function are found to be promising materials for buildings subsoil or floor structures.
Lumpy investment, sectoral propagation, and business cycles (Invited Paper)

NASA Astrophysics Data System (ADS)

Nirei, Makoto

2005-05-01

This paper proposes a model of endogenous fluctuations in investment. A monopolistic producer has an incentive to invest when the aggregate demand is high. The investment at the firm level is also known to exhibit a threshold behavior called an (S,s) policy. These two facts lead us to consider that the fluctuation in aggregate investment is generated by the global coupling of the non-linear oscillators. From this perspective, we characterize the probability distribution of the investment clustering in a partial equilibrium of product markets, and show that its variance can be large enough to match the observed investment fluctuations. We then implement this mechanism in a dynamic general equilibrium model to explore an investment-driven business cycle. By calibrating the model with the SIC 4-digit level industry data, we numerically show that the model replicates the basic structure of the business cycles.
Structural-functional integrated concrete with macro-encapsulated inorganic PCM

NASA Astrophysics Data System (ADS)

Mohseni, Ehsan; Tang, Waiching; Wang, Zhiyu

2017-09-01

Over the last few years the application of thermal energy storage system incorporating phase change materials (PCMs) to foster productivity and efficiency of buildings energy has grown rapidly. In this study, a structural-functional integrated concrete was developed using macro-encapsulated PCM-lightweight aggregate (LWA) as partial replacement (25 and 50% by volume) of coarse aggregate in control concrete. The PCM-LWA was prepared by incorporation of an inorganic PCM into porous LWAs through vacuum impregnation. The mechanical and thermal performance of PCM-LWA concrete were studied. The test results revealed that though the compressive strength of concrete with PCM-LWA was lower than the control concrete, but ranged from 22.02 MPa to 42.88 MPa which above the minimum strength requirement for structural application. The thermal performance test indicated that macro-encapsulated PCM-LWA has underwent the phase change transition reducing the indoor temperature.
Sensitivity of geographic information system outputs to errors in remotely sensed data

NASA Technical Reports Server (NTRS)

Ramapriyan, H. K.; Boyd, R. K.; Gunther, F. J.; Lu, Y. C.

1981-01-01

The sensitivity of the outputs of a geographic information system (GIS) to errors in inputs derived from remotely sensed data (RSD) is investigated using a suitability model with per-cell decisions and a gridded geographic data base whose cells are larger than the RSD pixels. The process of preparing RSD as input to a GIS is analyzed, and the errors associated with classification and registration are examined. In the case of the model considered, it is found that the errors caused during classification and registration are partially compensated by the aggregation of pixels. The compensation is quantified by means of an analytical model, a Monte Carlo simulation, and experiments with Landsat data. The results show that error reductions of the order of 50% occur because of aggregation when 25 pixels of RSD are used per cell in the geographic data base.
Resolving the multifaceted mechanisms of the ferric chloride thrombosis model using an interdisciplinary microfluidic approach

PubMed Central

Ciciliano, Jordan C.; Sakurai, Yumiko; Myers, David R.; Fay, Meredith E.; Hechler, Beatrice; Meeks, Shannon; Li, Renhao; Dixon, J. Brandon; Lyon, L. Andrew; Gachet, Christian

2015-01-01

The mechanism of action of the widely used in vivo ferric chloride (FeCl3) thrombosis model remains poorly understood; although endothelial cell denudation is historically cited, a recent study refutes this and implicates a role for erythrocytes. Given the complexity of the in vivo environment, an in vitro reductionist approach is required to systematically isolate and analyze the biochemical, mass transfer, and biological phenomena that govern the system. To this end, we designed an “endothelial-ized” microfluidic device to introduce controlled FeCl3 concentrations to the molecular and cellular components of blood and vasculature. FeCl3 induces aggregation of all plasma proteins and blood cells, independent of endothelial cells, by colloidal chemistry principles: initial aggregation is due to binding of negatively charged blood components to positively charged iron, independent of biological receptor/ligand interactions. Full occlusion of the microchannel proceeds by conventional pathways, and can be attenuated by antithrombotic agents and loss-of-function proteins (as in IL4-R/Iba mice). As elevated FeCl3 concentrations overcome protective effects, the overlap between charge-based aggregation and clotting is a function of mass transfer. Our physiologically relevant in vitro system allows us to discern the multifaceted mechanism of FeCl3-induced thrombosis, thereby reconciling literature findings and cautioning researchers in using the FeCl3 model. PMID:25931587
The metazoan protein disaggregase and amyloid depolymerase system: Hsp110, Hsp70, Hsp40, and small heat shock proteins.

PubMed

Torrente, Mariana P; Shorter, James

2013-01-01

A baffling aspect of metazoan proteostasis is the lack of an Hsp104 ortholog that rapidly disaggregates and reactivates misfolded polypeptides trapped in stress induced disordered aggregates, preamyloid oligomers, or amyloid fibrils. By contrast, in bacteria, protozoa, chromista, fungi, and plants, Hsp104 orthologs are highly conserved and confer huge selective advantages in stress tolerance. Moreover, in fungi, the amyloid remodeling activity of Hsp104 has enabled deployment of prions for various beneficial modalities. Thus, a longstanding conundrum has remained unanswered: how do metazoan cells renature aggregated proteins or resolve amyloid fibrils without Hsp104? Here, we highlight recent advances that unveil the metazoan protein-disaggregase machinery, comprising Hsp110, Hsp70, and Hsp40, which synergize to dissolve disordered aggregates, but are unable to rapidly solubilize stable amyloid fibrils. However, Hsp110, Hsp70, and Hsp40 exploit the slow monomer exchange dynamics of amyloid, and can slowly depolymerize amyloid fibrils from their ends in a manner that is stimulated by small heat shock proteins. Upregulation of this system could have key therapeutic applications in various protein-misfolding disorders. Intriguingly, yeast Hsp104 can interface with metazoan Hsp110, Hsp70, and Hsp40 to rapidly eliminate disease associated amyloid. Thus, metazoan proteostasis is receptive to augmentation with exogenous disaggregases, which opens a number of therapeutic opportunities.
Time-resolved Sensing of Meso-scale Shock Compression with Multilayer Photonic Crystal Structures

NASA Astrophysics Data System (ADS)

Scripka, David; Lee, Gyuhyon; Summers, Christopher J.; Thadhani, Naresh

2017-06-01

Multilayer Photonic Crystal structures can provide spatially and temporally resolved data needed to validate theoretical and computational models relevant for understanding shock compression in heterogeneous materials. Two classes of 1-D photonic crystal multilayer structures were studied: optical microcavities (OMC) and distributed Bragg reflectors (DBR). These 0.5 to 5 micron thick structures were composed of SiO2, Al2O3, Ag, and PMMA layers fabricated primarily via e-beam evaporation. The multilayers have unique spectral signatures inherently linked to their time-resolved physical states. By observing shock-induced changes in these signatures, an optically-based pressure sensor was developed. Results to date indicate that both OMCs and DBRs exhibit nanosecond-resolved spectral shifts of several to 10s of nanometers under laser-driven shock compression loads of 0-10 GPa, with the magnitude of the shift strongly correlating to the shock load magnitude. Additionally, spatially and temporally resolved spectral shifts under heterogeneous laser-driven shock compression created by partial beam blocking have been successfully demonstrated. These results illustrate the potential for multilayer structures to serve as meso-scale sensors, capturing temporal and spatial pressure profile evolutions in shock-compressed heterogeneous materials, and revealing meso-scale pressure distributions across a shocked surface. Supported by DTRA Grant HDTRA1-12-1-005 and DoD, AFOSR, National Defense Science and Eng. Graduate Fellowship, 32 CFR 168a.
DOE Office of Scientific and Technical Information (OSTI.GOV)

P. Somasundaran

The aim of the project is to develop a knowledge base to help the design of enhanced processes for mobilizing and extracting untrapped oil. We emphasize evaluation of novel surfactant mixtures and obtaining optimum combinations of the surfactants for efficient chemical flooding EOR processes. In this regard, an understanding of the aggregate shape, size and structure is crucial since these properties govern the crude oil removal efficiency. During the three-year period, the adsorption and aggregation behavior of sugar-based surfactants and their mixtures with other types of surfactants have been studied. Sugar-based surfactants are made from renewable resources, nontoxic and biodegradable.more » They are miscible with water and oil. These environmentally benign surfactants feature high surface activity, good salinity, calcium and temperature tolerance, and unique adsorption behavior. They possess the characteristics required for oil flooding surfactants and have the potential for replacing currently used surfactants in oil recovery. A novel analytical ultracentrifugation technique has been successfully employed for the first time, to characterize the aggregate species present in mixed micellar solution due to its powerful ability to separate particles based on their size and shape and monitor them simultaneously. Analytical ultracentrifugation offers an unprecedented opportunity to obtain important information on mixed micelles, structure-performance relationship for different surfactant aggregates in solution and their role in interfacial processes. Initial sedimentation velocity investigations were conducted using nonyl phenol ethoxylated decyl ether (NP-10) to choose the best analytical protocol, calculate the partial specific volume and obtain information on sedimentation coefficient, aggregation mass of micelles. Four softwares: OptimaTM XL-A/XL-I data analysis software, DCDT+, Svedberg and SEDFIT, were compared for the analysis of sedimentation velocity experimental data. The results have been compared to that from Light Scattering. Based on the tests, Svedberg and SEDFIT analysis were chosen for further studies.« less

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