bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interfacial studies of incompressible binary blends
Authors: Tang Hai , Freed Karl F. 
Published: July 2002

Density functional theory is used to investigate two of the possible reasons for the discrepancy between theory and experiment for the interfacial width and tension of phase separated binary blends. The two reasons are the inadequacy of the density functionals used previously and the neglect of the composition dependence of the Flory interaction parameter χ. For the sake of algebraic simplicity, our computations are restricted to symmetric, incompressible binary blends with correlation functions taken in the random phase approximation. We extend the analysis in Paper I [Tang and Freed, J. Chem. Phys. 94, 1572 (1991)] on the validy of density functionals for binary blends to the strong segregation limit with narrow interfaces by studying the conditions under which the Roe free energy functional is appropriate. Our derivation in this limit resums a rigorous Landau expansion to show that the Roe functional is appropriate only for infinite molecular weights. Nevertheless, even in the strong segregation limit this functional becomes incorrect in the wings of the concentration profile where a Landau expansion is valid despite the current unavailability of a local density functional.
Interfacial properties in the theoretically simplest weak segregation limit are in accord with those of previous workers, but we are able to suggest an interpolation form for the interfacial width and tension of symmetric blends that crosses over between the weak and strong segregation limits. The composition dependence of the Flory interaction parameter χ poses several problems when experimental χeff are substituted into theories that ignore this composition dependence. We therefore investigate the errors incurred by the use of different experimental measures of χ and by the use of χ measured at different compositions for two simple models in which χ varies linearly or quadratically with blend composition. Situations arise where there exists an experimental χeff that yields the correct interfacial width in the composition independent theory, but other examples produce substantial errors. Dimensionless combinations of the interfacial width and tension are constructed that should be weakly dependent on molecular weight and temperature unless ignored factors, such as blend compressibility, have a significant influence on interfacial properties. The relevance of the composition dependece of χ to interfacial profiles suggests a similar relevance of blend compressibility because compressibility influences χ and its composition dependence.
O2(X,v=8–22) 300 K quenching rate coefficients for O2 and N2, and O2(x) vibrational distribution from 248 nm O3 photodissociation
Authors: Park H. , Slanger T. G. 
Published: July 2002

Vibrationally excited oxygen (O‡2) is produced in the atmosphere by ozone photodissociation in the 200–300 nm Hartley band. It has been suggested that photoexcitation of O‡2 in the O2 Schumann–Runge bands will lead to predissociation, and autocatalytic production of O3. The resultant new source of atmospheric O3 could help alleviate current discrepancies between observed and modeled O3 profiles. To evaluate this possibility, we have examined two critical factors—the nascent distribution of O‡2 levels for 248 nm photodissociation, near the peak of the Hartley band, and the rate coefficients for their relaxation by O2 and N2. We find that the distribution extends to v=22, close to the thermodynamic limit, with a peak near v=8. The 300 K quenching rate coefficients have been evaluated using a cascade model, in which it is assumed that relaxation by O2 occurs through single-quantum vibration–vibration (V–V) and vibration–translation (V–T) steps. By modeling the relaxation from the top of the distribution downwards, we simultaneously obtain both the quenching rate coefficients and the nascent vibrational distribution. Agreement with new rate coefficient measurements carried out in a state-specific manner is good, as is also true for the comparison with new V–V and V–T calculations. Data from experiments on O‡2 quenching by N2 show that in the v=16–22 range, potentially important in the atmosphere, quenching proceeds up to five times faster than for the case of O2.
The hypothesized explanation is that two-quantum V–V transfer, peaking at the resonant condition of O2(v=18–19), is the dominant process. As a consequence, atmospheric quenching of O‡2 for levels above v=14 is basically controlled by N2, and at low stratospheric temperatures, the effect of N2 quenching near v=18 is likely to be 2 orders of magnitude greater than quenching by O2. This unexpected effect probably precludes a significant role for O‡2 photodissociation as a new source of stratospheric O3, but the existence of these high-energy entities can have other consequences, among them being enhanced activity with minor species, and the possibility that energy may flow from the relatively stable O2(v=1) and N2(v=1) levels into infrared-active H2O and CO2, respectively. Measurements have also been made for O‡2 quenching by O3, CO2, and He, particularly to establish whether O3 and CO2 can play a competitive quenching role in the atmosphere. Although O3 is a fast quencher, with CO2 being 2 orders of magnitude slower, they are unlikely to compete with O2 and N2. The data on He is particularly interesting, suggesting that considerably more O‡2 is present in the nascent O3 photodissociation products than subsequently appears from O(1D)+O3 interaction. The implications of this finding are discussed.
Kaposi's Sarcoma‐Associated Herpesvirus: From Cell Biology to Pathogenesis
Authors: Sharp Tyson V. , Boshoff Chris 
Published: July 2002

AbstractKaposi's sarcoma‐associated herpesvirus (KSHV or HHV‐8) is linked to the etiopathogenesis of Kaposi's sarcoma, a plasmablastic variant of Castleman's disease and primary effusion lymphoma. KSHV is related to a number of non‐human primate viruses. Only a limited number of KSHV proteins are expressed in tumor cells. Here we discuss the putative role of these proteins in KSHV pathogenesis.
Calcium and Protein Kinase C Regulate the Actin Cytoskeleton in the Synaptic Terminal of Retinal Bipolar Cells
Authors: Job Christy , Lagnado Leon 
Published: July 2002

The organization of filamentous actin (F-actin) in the synaptic pedicle of depolarizing bipolar cells from the goldfish retina was studied using fluorescently labeled phalloidin. The amount of F-actin in the synaptic pedicle relative to the cell body increased from a ratio of 1.6 ± 0.1 in the dark to 2.1 ± 0.1 after exposure to light. Light also caused the retraction of spinules and processes elaborated by the synaptic pedicle in the dark.
Isolated bipolar cells were used to characterize the factors affecting the actin cytoskeleton. When the electrical effect of light was mimicked by depolarization in 50 mM K+, the actin network in the synaptic pedicle extended up to 2.5 μm from the plasma membrane. Formation of F-actin occurred on the time scale of minutes and required Ca2+ influx through L-type Ca2+ channels. Phorbol esters that activate protein kinase C (PKC) accelerated growth of F-actin. Agents that inhibit PKC hindered F-actin growth in response to Ca2+ influx and accelerated F-actin breakdown on removal of Ca2+.
To test whether activity-dependent changes in the organization of F-actin might regulate exocytosis or endocytosis, vesicles were labeled with the fluorescent membrane marker FM1-43. Disruption of F-actin with cytochalasin D did not affect the continuous cycle of exocytosis and endocytosis that was stimulated by maintained depolarization, nor the spatial distribution of recycled vesicles within the synaptic terminal. We suggest that the actions of Ca2+ and PKC on the organization of F-actin regulate the morphology of the synaptic pedicle under varying light conditions.
Thurston boundary of Teichmüller spaces and the commensurability modular group
Authors: Biswas Indranil , Mitra Mahan , Nag Subhashis 
Published: July 2002

If

p
:
Y
→
X

p : Y \rightarrow X

is an unramified covering map between two compact oriented surfaces of genus at least two, then it is proved that the embedding map, corresponding to

p
p

, from the Teichmüller space

T

(
X
)

\mathcal {T}(X)

, for

X
X

, to

T

(
Y
)

\mathcal {T}(Y)

actually extends to an embedding between the Thurston compactification of the two Teichmüller spaces. Using this result, an inductive limit of Thurston compactified Teichmüller spaces has been constructed, where the index for the inductive limit runs over all possible finite unramified coverings of a fixed compact oriented surface of genus at least two. This inductive limit contains the inductive limit of Teichmüller spaces, constructed by I. Biswas, S. Nag and D. Sullivan, Determinant bundles, Quillen metrics and Mumford isomorphisms over the Universal Commensurability Teichmüller Space, Acta Mathematica, 176 (1996), 145–169, as a subset. The universal commensurability modular group, which was constructed in the above mentioned article, has a natural action on the inductive limit of Teichmüller spaces. It is proved here that this action of the universal commensurability modular group extends continuously to the inductive limit of Thurston compactified Teichmüller spaces.
SWAN: sliding window analysis of nucleotide sequence variability.
Authors: Proutski V , Holmes E 
Published: July 2002

Abstract
RESULTS: This paper describes a new program which reveals, analyses and graphically represents patterns of variability along nucleotide sequences. AVAILABILITY: The program, 'SWAN', is available from the WWW at http://evolve.zoo.ox.ac.uk/ or from the authors upon request. CONTACT: Vitali.Proutski@zoology.oxford.ac.uk
Zomit: biological data visualization and browsing.
Authors: Pook S , Vaysseix G , Barillot E 
Published: July 2002

Abstract
MOTIVATION: The problems caused by the difficulty in visualizing and browsing biological databases have become crucial. Scientists can no longer interact directly with the huge amount of available data. However, future breakthroughs in biology depend on this interaction. We propose a new metaphor for biological data visualization and browsing that allows navigation in very large databases in an intuitive way. The concepts underlying our approach are based on navigation and visualization with zooming, semantic zooming and portals; and on data transformation via magic lenses. We think that these new visualization and navigation techniques should be applied globally to a federation of biological databases. RESULTS: We have implemented a generic tool, called Zomit, that provides an application programming interface for developing servers for such navigation and visualization, and a generic architecture-independent client (Javatrade mark applet) that queries such servers. As an illustration of the capabilities of our approach, we have developed ZoomMap, a prototype browser for the HuGeMap human genome map database. AVAILABILITY: Zomit and ZoomMap are available at the URL http://www.infobiogen.fr/services/zomit.
Browsing protein families via the ‘Rich Family
Description’ format
Authors: Corpet Florence , Gouzy Jérôme , Kahn Daniel 
Published: July 2002

Abstract
Motivation: Multiple alignments of protein sequences are the basis of structural and functional analysis of protein families. It is however difficult even for an expert biologist to comprehend an alignment of more than 50 to 100 homologous sequences.
Results: This paper presents a browser for the analysis of multiple alignments of large numbers of protein sequences. Phylogenetic trees and consensus sequences are computed and used to summarise the alignments; these data are stored in a structure called Rich Family Description. Summary alignments and trees are displayed in HTML pages and can be developed or reduced by the user. This browser is used to display the ProDom domain families on the Web. Its zooming facilities allow extracting information from alignments of more than 1000 homologous sequences.
Availability: Programs are available free of charge on request from the authors. The ProDom database can be consulted at http://www.toulouse.inra.fr/prodom.html
Contact: fcorpet@toulouse.inra.fr
Transformation distances: a family of dissimilarity measures based on movements of segments.
Authors: Varr√© J S , Delahaye J P , Rivals E 
Published: July 2002

Abstract
MOTIVATION: Evolution acts in several ways on DNA: either by mutating a base, or by inserting, deleting or copying a segment of the sequence (Ruddle, 1997; Russell, 1994; Li and Grauer, 1991). Classical alignment methods deal with point mutations (Waterman, 1995), genome-level mutations are studied using genome rearrangement distances (Bafna and Pevzner, 1993, 1995; Kececioglu and Sankoff, 1994; Kececioglu and Ravi, 1995). The latter distances generally operate, not on the sequences, but on an ordered list of genes. To our knowledge, no measure of distance attempts to compare sequences using a general set of segment-based operations. RESULTS: Here we define a new family of distances, called transformation distances, which quantify the dissimilarity between two sequences in terms of segment-based events. We focus on the case where segment-copy, -reverse-copy and -insertion are allowed in our set of operations. Those events are weighted by their description length, but other sets of weights are possible when biological information is available. The transformation distance from sequence S to sequence T is then the Minimum Description Length among all possible scripts that build T knowing S with segment-based operations. The underlying idea is related to Kolmogorov complexity theory. We present an algorithm which, given two sequences S and T, computes exactly and efficiently the transformation distance from S to T. Unlike alignment methods, the method we propose does not necessarily respect the order of the residues within the compared sequences and is therefore able to account for duplications and translocations that cannot be properly described by sequence alignment. A biological application on Tnt1 tobacco retrotransposon is presented. AVAILABILITY: The algorithm and the graphical interface can be downloaded at http://www.lifl.fr/ approximately varre/TD
Complex SNP-Based Haplotypes in Three Human Helicases: Implications for Cancer Association Studies
Authors: Trikka Dimitra , Fang Zhe , Renwick Alex , Jones Sally H. , Chakraborty Ranajit , Kimmel Marek , Nelson David L. 
Published: July 2002

We have initiated a candidate gene approach to study variation and predisposition to cancer in the four major ethnic groups that constitute the U.S. population (African Americans, Caucasians, Hispanics, and Asians). We resequenced portions of three helicase genes (BLM, WRN, and RECQL) identifying a total of 37 noncoding single nucleotide polymorphisms (SNPs). Haplotype inference predicted 50 haplotypes in BLM, 56 in WRN, and 47 in RECQL in a sample of 600 chromosomes. Approximately 10% of the predicted haplotypes were shared among all ethnic groups. Linkage disequilibrium and recombination effects showed that each locus has taken a diverse evolutionary path. Primate DNA analysis of the same loci revealed one human haplotype per gene shared with the great apes, indicating that the observed diversity occurred since the divergence of humans from the last common ancestor. In BLM, we confirmed the presence of a founder haplotype among Ashkenazi Jews homozygous for theblmAsh mutation. The cosegregating haplotype was seen in all (6/6) samples of Ashkenazi descent, whereas in the general population it has a low frequency (0.02) and was not found in African Americans. In WRN, ethnic samples were studied for their haplotype content and the presence or absence of six previously described coding SNPs (cSNPs). Hispanic individuals carrying two of these cSNPs showed a 60% increase in the frequency of a common haplotype (haplotype No. 28). In the pooled sample, no association was found. Because (1) the majority of the haplotypes are population specific and (2) the patterns of linkage disequilibrium, recombination, and haplotype diversity are markedly different between gene regions, these data show the importance of either ethnically matched controls or within-family-based disease-gene association studies.[The sequence data described in this paper have been submitted to the GenBank data library under accession no. AC006559. Online supplemental material available at http://www.genome.org]
Participatory design of a sleep intervention with correctional supervisors using a root causes approach
Authors: Namazi Sara , Dugan Alicia G. , Cavallari Jennifer M. , Rinker Robert D. , Preston Julius C. , Steele Vincent L. , El Ghaziri Mazen , Cherniack Martin G. 
Published: December 2022

AbstractBackgroundAfter a Design Team (DT) conducted a workforce health assessment of correctional supervisors, they selected sleep as an intervention priority, given its numerous health and work consequences. Existing workplace sleep interventions are designed with little worker input, but participatory solutions that incorporate workers' lived experiences and root causes of poor sleep may be more relevant, appropriate, and acceptable to end‐users, resulting in better uptake.MethodsThe DT met bi‐monthly to complete the Intervention Design and Analysis Scorecard (IDEAS) tool to brainstorm interventions that address root causes of poor sleep, and evaluate, rank, and select interventions for implementation. We conducted a qualitative review of meeting notes and worksheets from each IDEAS step, and present our findings on root causes and prioritized solutions.ResultsThe DT consisted of two university researchers and seven members of a correctional supervisors' union, with 5–9 participants attending each meeting. IDEAS Steps 1–5 were completed in eight meetings over six months. Root causes of poor sleep included mind/body and environmental disruptions, and insufficient time. Three solutions were proposed: training on sleep hygiene, meditation, and sleep debt management; a sleep‐tracking smartphone app; and a shared overtime policy based on splitting one 8‐hour shift between two supervisors.ConclusionsThis is the first known application of IDEAS to address sleep, and targeting root causes may result in more efficacious interventions for sleep improvement. Moreover, because IDEAS guides DTs in selecting solutions with the greatest perceived health benefits, reach, cost‐effectiveness, and feasibility, it may result in more successful implementation.
Cardiometabolic profiles in children and adults with overweight and obesity and down syndrome
Authors: Oreskovic Nicolas M. , Baumer Nicole T. , Di Camillo Chiara , Cornachia Michelle , Franklin Catherine , Hart Sarah J. , Kishnani Priya S. , McCormick Andrew , Milliken Anna L. , Patsiogiannis Vasiliki , Pawlowski Katherine G. , Santoro Stephanie L. , Sargado Sabrina , Scoppola Vittorio , Torres Amy , Valentini Diletta , Vellody Kishore , Villani Alberto , Skotko Brian G. 
Published: December 2022

AbstractIndividuals with Down syndrome (DS) are at increased risk for being overweight/obese, but the associated cardiometabolic risk (CR) is not clear. Cross‐sectional anthropometric and clinical laboratory data from a multi‐site, international cohort of individuals with DS were analyzed to determine cardiometabolic risk by reporting observed distributions of cardiometabolic biomarkers in overweight/obese individuals with DS throughout the lifespan. Descriptive statistics and regression analyses by age categories determined the distributive percentiles for cardiometabolic biomarkers and tested for adiposity as a predictor of CR. Across seven DS clinics, data were collected on 240 patients between the ages of 3 and 63 years, with one quarter overweight and three quarters obese among children and nearly all adults being obese. In children and adults, most cardiometabolic biomarker profiles showed distributive values within normal ranges. Blood lipids were positively associated with body mass index (BMI) in children (high density lipid‐cholesterol, p = 0.01; low density lipid‐cholesterol, p = 0.02). Levels of hs‐CRP were elevated in both children and adults, with BMI positively associated with hs‐CRP in adults with DS (p = 0.04). Liver enzyme values were positively associated with BMI in children and adults. The data suggest that in contrast to the general population, in individuals with Down syndrome, being overweight and obese does not appear to confer a significantly increased risk for cardiometabolic disease by biomarker profile. Individuals with DS who are overweight/obese appear to have unique cardiometabolic profiles unrelated to adiposity, notable for increased hs‐CRP and normal HA1c levels.
Head‐to‐Head Comparison of Four Plasma Phospho‐Tau Immunoassays in the Neuropathological Diagnosis of Alzheimer’s Disease
Authors: Malek‐Ahmadi Michael H. , Ashton Nicholas J. , Karikari Thomas K , Beach Thomas G , Serrano Geidy E , Chen Yinghua , Chen Kewei , Ghisays Valentina , Hansson Oskar , Palmqvist Sebastian , Janelidze Shorena , Su Yi , Zetterberg Henrik , Dage Jeffrey L. , Blennow Kaj , Reiman Eric M. 
Published: December 2022

AbstractBackgroundPlasma ptau is a promising indicator of amyloid‐β (Aβ) mediated tau pathophysiology. We previously characterized the ability of Lilly’s MesoScale Discovery (MSD)‐based plasma ptau217 and ptau181 assays to discriminate between those with and without the neuropathological diagnosis of Alzheimer’s disease (AD) in Banner research participants with near‐end‐of‐life blood samples and extensive postmortem neuropathological assessments. We now extend this work in a head‐to‐head comparison of those assays to the University of Gothenburg’s Single molecule array (Simoa)‐based plasma ptau181 and 231 assays.MethodAssays were performed blindly in plasma samples acquired 1.0±0.7 years before death from up to 106 Banner research participants with and without cognitive impairment and different neuropathological diagnoses. ROC analyses were used to discriminate between those with and without the neuropathological diagnosis of AD and presence or absence of neuritic Aβ plaques. Spearman correlations were used to characterize their associations with mean cortical neuritic plaque counts and with mean cortical tau tangle counts in those with and without the diagnosis of AD or neuritic plaques.ResultLilly’s ptau217 assay was better than Lilly’s ptau181 and Gothenburg’s ptau231 and ptau181 assays in discriminating between the neuropathological diagnosis of Intermediate/High Likelihood versus Low Likelihood/No AD (respective AUCs=0.86, 0.67, 0.62 and 0.61), the diagnosis of High Likelihood versus Low Likelihood/No AD (AUCs=0.95, 0.83, 0.67 and 0.67), and presence or absence of neuritic Aβ plaques (AUCs=0.86, 0.70, 0.61 and 0.62). It also provided better indicators of mean cortical neuritic plaque (r’s=0.69, 0.35, 0.26 and 0.29) and tangle counts (r’s=0.73, 0.60, 0.19, ‐0.04) in those with the neuropathological diagnosis of AD or at least moderately frequent neuritic plaques (r’s=0.71, 0.59, 0.22, 0.01). The assays were not correlated with tangle counts in those without AD or neuritic plaques.ConclusionLilly’s MSD‐based plasma ptau217 assay performed better than the other three ptau assays in the neuropathological diagnosis of AD, discriminating between those with and without neuritic Aβ plaques, and providing an indicator of Aβ‐related tau tangle burden. Banner Sun Health Research Institute's growing brain donation program resources could help characterize and compare blood‐based biomarkers in the neuropathological diagnosis of AD, Parkinson’s disease and related diseases.