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At least 1,243 records · Page 69Linked to original sources
PubMed2004

Phase space conduits for reaction in multidimensional systems: HCN isomerization in three dimensions.

The three-dimensional hydrogen cyanide/isocyanide isomerization problem is taken as an example to present a general theory for computing the phase space structures which govern classical reaction dynamics in systems with an arbitrary (finite) number of degrees of freedom. The theory, which is algorithmic in nature, comprises the construction of a dividing surface of minimal flux which is locally a "surface of no return." The theory also allows for the computation of the global phase space transition pathways that trajectories must follow in order to react. The latter are enclosed by the stable and unstable manifolds of a so-called normally hyperbolic invariant manifold (NHIM). A detailed description of the geometrical structures and the resulting constraints on reaction dynamics is given, with particular emphasis on the three degrees of freedom case. A procedure is given which uses these structures to compute orbits homoclinic to, and heteroclinic between, NHIMs. The role of homoclinic and heteroclinic orbits in global recrossings of dividing surfaces and transport in complex systems is explained. The complete description provided here is inherently one within phase space; it cannot be inferred from a configuration space picture. A complexification of the classical phase space structures to incorporate quantum effects is also discussed. The results presented here call into question certain assumptions routinely made on the global dynamics; this paper provides methods that enable one to understand and quantify the phase space dynamics of reactions without making such assumptions.

Journal Article↗
PubMed2005

Phase-space reaction network on a multisaddle energy landscape: HCN isomerization.

By using the HCN/CNH isomerization reaction as an illustrative vehicle of chemical reactions on multisaddle energy landscapes, we give explicit visualizations of molecular motions associated with a straight-through reaction tube in the phase space inside which all reactive trajectories pass from one basin to another, with eliminating recrossing trajectories in the configuration space. This visualization provides us with a chemical intuition of how chemical species "walk along" the reaction-rate slope in the multidimensional phase space compared with the intrinsic reaction path in the configuration space. The distinct nonergodic features in the two different HCN and CNH wells can be easily demonstrated by a section of Poincare surface of section in those potential minima, which predicts in a priori the pattern of trajectories residing in the potential well. We elucidate the global phase-space structure which gives rise to the non-Markovian dynamics or the dynamical correlation of sequential multisaddle chemical reactions. The phase-space structure relevant to the controllability of the product state in chemical reactions is also discussed.

Journal Article↗
PubMed2000

Magnetic resonance imaging-based joint space measurements in temporomandibular joints with disk displacements and in controls.

OBJECTIVE: Previous studies have discussed a posterior displacement of the condyle as a possible risk factor for the development of disk displacements (DDs) of the temporomandibular joint (TMJ). The objective of this study was to compare the posterior and anterior joint spaces in healthy TMJs with those of patients who present different forms of DDs. STUDY DESIGN: The anterior and posterior joint spaces from 58 patients with unilateral or bilateral DD with reduction (DDR) or without reduction (DDNR) and from 30 healthy volunteers were measured with 3 sagittal magnetic resonance images (MRIs) from each TMJ in the maximum intercuspid position. RESULTS: Measurements of anterior and posterior joint spaces showed a good interexaminer reproducibility (rank correlation coefficients ranging from 0.88 to 0.95). Patients with bilateral DDR demonstrated a significantly more posterior position of the condyle, as compared with controls and patients with bilateral DDNR. DDNR presented a significant reduction of the anterior and the posterior joint spaces, leading to a mean concentric position of the condyle. Patients with unilateral DDR or DDNR demonstrated a greater variability of anterior and posterior joint spaces, compared with patients with a bilaterally identical type of DD. CONCLUSIONS: The data of this MRI-based clinical study indicate that different stages of disk displacements are associated with significant changes of condylar position. The variation of anterior and posterior joint spaces was influenced by the diagnosis of the contralateral joint.

Adolescent↗
PubMed2001

Ten-year survival rates of teeth adjacent to treated and untreated posterior bounded edentulous spaces.

STATEMENT OF PROBLEM: Failure to replace a single missing posterior tooth may lead to a variety of dental problems, which may ultimately result in tooth loss. However, little is known about the fate of the adjacent teeth if a missing posterior tooth is not replaced. PURPOSE: This retrospective study evaluated the survival of teeth adjacent to treated and untreated posterior bounded edentulous spaces. MATERIAL AND METHODS: Data were obtained from electronic treatment records from the Kaiser Permanente Dental Care Program, Portland, Ore. A final sample of 317 patients who met the study inclusion criteria was identified. Each bounded edentulous space was placed in 1 of 3 treatment categories: untreated, restored with a fixed partial denture, or restored with a removable partial denture. Subsequent treatment and the status of the teeth adjacent to the bounded edentulous space were followed through December 1999. Ten-year Kaplan-Meier survival estimates were generated for each treatment group, and differences in survival were evaluated with the log-rank chi-square test (alpha=.05). RESULTS: There was a significant difference in survival among the 3 treatment categories (P=.005). Spaces restored with a fixed partial denture had longer 10-year survival estimates (92%) than those that remained untreated (81%). Spaces restored with a removable partial denture had the poorest 10-year survival rate (56%). CONCLUSION: Under the conditions and selection bias associated with this retrospective study, the survival of teeth adjacent to a single posterior edentulous space was negatively associated with removable partial denture placement compared with no treatment or the use of a fixed partial denture.

Adolescent↗
PubMed2002

Protein topology and stability define the space of allowed sequences.

We describe a new approach to explore and quantify the sequence space associated with a given protein structure. A set of sequences are optimized for a given target structure, using all-atom models and a physical energy function. Specificity of the sequence for its target is ensured by using the random energy model, which keeps the amino acid composition of the sequence constant. The designed sequences provide a multiple sequence alignment that describes the sequence space compatible with the structure of interest; here the size of this space is estimated by using an information entropy measure. In parallel, multiple alignments of naturally occurring sequences can be derived by using either sequence or structure alignments. We compared these 3 independent multiple sequence alignments for 10 different proteins, ranging in size from 56 to 310 residues. We observed that the subset of the sequence space derived by using our design procedure is similar in size to the sequence spaces observed in nature. These results suggest that the volume of sequence space compatible with a given protein fold is defined by the length of the protein as well as by the topology (i.e., geometry of the polypeptide chain) and the stability (i.e., free energy of denaturation) of the fold.

Amino Acid Sequence↗
PubMed2006

Self-fulfilling cavitands: packing alkyl chains into small spaces.

The present research was undertaken to determine the conformations of alkyl groups that are forced into small spaces. Unbranched alkyl groups assume fully extended conformations in the free space of solutions, because any bends in the structure create steric clashes between hydrogens along the chain. We synthesized a series of alkyl esters of a carboxylic acid attached to the inner surface of a vase-shaped container structure. The shorter esters (ethyl and propyl) can be accommodated in extended conformations, and even small solvent molecules can share the container's space. Longer (butyl-octyl) esters adopt increasingly coiled conformations that writhe rapidly in the limited space of the cavity. Even longer esters (nonyl and decyl) can be synthesized, but their containers become distorted, and their spectra indicate slowed internal motions of the alkyl groups within the space. In general, alkyl groups are readily contorted when their internal strains are compensated by attraction with the inner surfaces and the proper filling of space.

Journal Article↗
PubMed1995

Spacing of palindromic half sites as a determinant of selective STAT (signal transducers and activators of transcription) DNA binding and transcriptional activity.

Signal transducers and activators of transcription (STAT proteins) bind to palindromic sequence elements related to interferon gamma (IFN-gamma) activation sites, which were first identified in the promoters of IFN-gamma-inducible genes. Although the sequences of the natural palindromic STAT-binding elements vary considerably, they conform to the general structure TT(N)5AA. We have systematically examined the effects of the spacing between the TT and AA core half sites on the binding of the STAT complexes activated by IFN-gamma, interleukin (IL) 6, granulocyte-macrophage colony-stimulating factor, and IL-4. We show that (i) as suggested earlier, a core palindromic TT--AA motif with a 5-bp spacing displays general STAT binding, (ii) a palindromic motif with a spacing of 4 bp selectively binds to complexes containing Stat3, and (iii) a motif with a 6-bp spacing selectively binds the STAT complexes activated by IL-4. We have examined natural elements in the promoters of cytokine-responsive genes that differ in half-site spacing and found that they display binding properties predicted from the synthetic binding sites. Furthermore, the observed differential selective binding characteristics for the most part correlate with the ability to mediate transcriptional activation of transfected test genes in response to the cytokines tested. Our results thus demonstrate that the specificity of STAT-directed transcription in response to particular cytokines or cytokine families depends in part on the spacing of half sites within the conserved response element sequence.

Base Sequence↗
PubMed2003

Spacing of repetitions improves learning and memory after moderate and severe TBI.

Extensive research has determined that new learning in healthy individuals is significantly improved when trials are distributed over time (spaced presentation) compared to consecutive learning trials (massed presentation). This phenomenon known as the "spacing effect" (SE) has been shown to enhance verbal and nonverbal learning in healthy adults of different ages and in different memory paradigms (e.g., recognition, recall, etc.). The purpose of this study was to examine whether learning in adults with moderate and severe traumatic brain injury (TBI) is improved using a spacing-of-repetitions procedure. Using a within-groups design, participants with TBI (n = 20) were presented a list of 115 words that were presented either once (single condition), twice consecutively (massed condition), or twice with 11 words between presentations (spaced condition). Participants were required to rank each word from 1 to 10 according to their familiarity with the word; they were not asked to "memorize" words for a later test. Word list learning was measured with a free recall test immediately following list presentation and with free recall and recognition tests after a 30-min delay. Participants recalled and recognized significantly more spaced words than massed words during this word list learning task. These results strongly indicate that the spacing of repetitions improves learning and memory in individuals who have sustained moderate to severe TBI. Implications for rehabilitation are discussed.

Adolescent↗
PubMed1999

Relationship between severity of middle ear mucosal lesion and middle ear pneumatic space volume in patients with otitis media with effusion.

If we assume that the state of suppression of pneumatic cells is the result of suppression of pneumatic cell growth by inflammatory stimulation in the middle ear pneumatic space, it is possible to improve the state of suppression by performing sufficient treatment during the growth period of the pneumatic cells. We indwelt a tympanic membrane ventilation tube (hereinafter referred to as tube) for treatment of otitis media with effusion (OME) in child patients aged 3-13 years and investigated the following points: i) relationship between the severity of inflammation of the lamina propria of middle ear mucosal specimens (hereinafter referred to as lamina propria) collected at the time of tube indwelling and the degree of growth of the pneumatic space; and ii) changes in the pneumatic space associated with treatment by tube indwelling, which was studied by comparing the above-described mucosal severity with the pneumatic space area of 2 years after tube indwelling, and with increase in the pneumatic space volume measured periodically after tube indwelling. The results indicated that mastoid cell growth suppression is higher in patients with a higher degree of inflammatory changes in the lamina propria. In association with treatment by tube indwelling, effusion accumulated in the pneumatic space and mucosal swelling disappeared early after the treatment, or 2 months of tube indwelling. After that, in patients with severe mucosal lesion, a long time, 1.5-2 years, was found to be required for repneumatization accompanying regrowth of the temporal bone. We confirmed that the severity of inflammation of the lamina propria is deeply involved in the growth and repneumatization of the pneumatic cells.

Adolescent↗
PubMed1995

Dead space in the breathing apparatus; interaction with ventilation.

Dead space in breathing apparatus may cause increased ventilation and/or CO2 retention. Interactions between ventilation and dead space were tested in the breathing apparatus of three divers: a full face mask with an oro-nasal cup (AGA), a full face mask without an oro-nasal cup (EXO-26) but designed to minimize dead space, and one mouthpiece. Experiments were performed at three depths; 0, 30 and 45 m seawater (msw). The breathing gas was air except at 30 msw where it was 36 O2 in N2. Five certified SCUBA divers were exercised at three levels (0, 50 and 100 W). Ventilation and gas exchange were measured. The dead space in the AGA mask was not influenced by either depth or exercise (mean 0.201). The mean dead space of the EXO-26 was 0.341, but it increased with exercise (p < 0.001) and decreased with depth (p < 0.03). Since the dead space can vary with ventilation levels it is not sufficient to test breathing apparatus only at rest as is required by the US National Institute of Occupational Safety and Health. The mean ventilation with the EXO-26 was higher than with the AGA by 10% at 50 W (p < 0.05) and by 12% (p < 0.01) at 100 W. The same comparison for end-tidal CO2 showed mean increase by 0.30 kPa at the 100-W workload (P < 0.05); changes at other workloads were not statistically significant. Comparisons of the mean inspired PCO2 to the maximum values considered acceptable by various organizations showed that the mouthpiece was always acceptable, the AGA mask was marginally acceptable or better, while sometimes the EXO-26 was not acceptable.

Adult↗
PubMed2006

Laboratory-scale analysis of effect of plume spacing of air diffuser system on destratification efficiency.

This paper presents a study conducted to develop guidelines for the design of an air bubble destratification system, with particular concern given to plume spacing. To investigate the effect of plume spacing on the destratification efficiency of the system, we first conducted a dimensional analysis that included major variables in bubble hydrodynamics. Then, we conducted laboratory experiments with various plume spacings and water depths under non-linear stratification conditions, and we evaluated the destratification efficiencies. Our results showed that the highest efficiency was obtained with a plume spacing of 0.75 times the water depth. Our study has shown that the overall efficiency of an air diffuser system can be increased by changing the spacing between diffusers and that plume spacing should be a major design parameter for future air diffuser systems.

Air Movements↗
PubMed1998

The biophysics of the gram-negative periplasmic space.

When subject to an osmotic 'up-shock', water flows outward from bacterial cytoplasm of the bacterium. Lipid bilayers can shrink very little in area and therefore must wrinkle to accommodate the smaller volume. The usual consequence is that all the layers of the cell envelope must become wrinkled together because they adhere to each other and must now cover a smaller surface. Plasmolysis spaces are formed if the cytoplasmic membrane (CM) separates from the other components of the wall. However, because the CM bilayer is essentially an incompressible two-dimensional liquid, this constraint restricts the location and shape of plasmolysis spaces. With mild up-shocks they form at the pole and around constricting regions in the cell. Elsewhere their creation requires the formation of endocytotic or exocytotic vesicles. The formation of endocytotic vesicles occurs in animal and plant cells as well as in bacterial cells. With stronger up-shocks tubular structures (Bayer adhesion sites), or other special geometric shapes (e.g., Scheie structures) allow the bilayer to surround an irregular shaped cytoplast. Periosmotic agents, that is, those that extract water from the periplasm as well as the cytoplasm, are molecules such as poly-vinyl-pyrrolidone and alpha-cyclodextrin that are too large to pass through the porins in the outer membrane. They were found to significantly inhibit the formation of plasmolysis spaces. Presumably, they inhibit the plasmolysis process, which requires that extracellular fluid enter between the CM and the outer membrane (OM). In the extreme case, with the dehydrating action of both osmotic agents and periosmotic agents, periplasmic space formation tends to be prevented and a new kind of space develops within the cytoplasm. We have designated these as 'cytoplasmic voids'. These novel structures are not bounded by lipid bilayers, in contrast to the endocytotic vesicles. These new spaces appear to result from the negative turgor pressure generated by the application of the combination of osmotic and periosmotic agents causing bubble formation. Several ideas in the literature about the wall biology (periseptal annuli, leading edge, osmotic pressure in the periplasm) are presented and critiqued. The basic criticism of these is that much of the phenomena can be explained because of the physics of the phospholipid bilayers and osmotic forces and thus does not imply the existence of a special control mechanism to regulate growth and division.

Biophysical Phenomena↗
PubMed2002

Attachment in infancy and personal space regulation in early adolescence.

This study longitudinally assessed associations between secure and ambivalent attachment with mothers, fathers and professional caregivers in infancy, and personal space regulation and perceived interpersonal competence in 64 early adolescents (31 boys, 33 girls). Children classified as ambivalently attached to their mothers and/or professional caregivers in infancy displayed significantly larger permeability of personal space as compared with children classified as securely attached. Attachment classifications with fathers were not associated with personal space behavior at 12 years of age. Children who had an insecure attachment relationship with both the mother and the professional caregiver in infancy displayed smaller personal space boundaries, and tolerated larger intrusions into their personal space as compared with children who had two secure attachments in infancy. Finally, perceived interpersonal competence was positively correlated with personal space permeability.

Adolescent↗
PubMed1986

Confined spaces--a case for ventilation.

Many exposures, some leading to deaths and injuries, in confined spaces could have been prevented by ventilating the space prior to and during the entry. Current standards and guidelines generally do not require ventilation. Nor do they sufficiently emphasize the need for ventilation or provide guidance on how to ventilate confined spaces. Mechanical ventilation is a positive engineering control action that can usually be taken and that will reduce the hazards of adverse atmospheric conditions inside a confined space. Natural ventilation usually is not sufficiently reliable to serve as a primary means of control. Unfortunately, very little specific information is available for designing and implementing ventilation strategies for confined spaces. More published information is needed, such as examples of effective policy and procedures in use by industry and findings from research on confined space ventilation. Basic and applied research can help to demonstrate effective ventilation actions and develop useful design guidelines. Additional published information should increase hazard awareness and reduce the likelihood of accidents.

Industry↗
PubMed1998

The spacing effect depends on an encoding deficit, retrieval, and time in working memory: evidence from once-presented words.

The spacing effect in list learning occurs because identical massed items suffer encoding deficits and because spaced items benefit from retrieval and increased time in working memory. Requiring the retrieval of identical items produced a spacing effect for recall and recognition, both for intentional and incidental learning. Not requiring retrieval produced spacing only for intentional learning because intentional learning encourages retrieval. Once-presented words provided baselines for these effects. Next, massed and spaced word pairs were judged for matches on their first three letters, forcing retrieval. The words were not identical, so there was no encoding deficit. Retrieval could and did cause spacing only for the first word of each pair; time in working memory, only for the second.

Humans↗
PubMed1991

Ionic strength of the intermembrane space of intact mitochondria as estimated with fluorescein-BSA delivered by low pH fusion.

The electrostatic interactions of cytochrome c with its redox partners and membrane lipids, as well as other protein interactions and biochemical reactions, may be modulated by the ionic strength of the intermembrane space of the mitochondrion. FITC-BSA was used to determine the relative value of the mitochondrial intermembrane ionic strength with respect to bulk medium external to the mitochondrial outer membrane. FITC-BSA exhibited an ionic strength-dependent fluorescence change with an affinity in the mM range as opposed to its pH sensitivity in the microM range. A controlled, low pH-induced membrane fusion procedure was developed to transfer FITC-BSA encapsulated in asolectin liposomes, to the intermembrane space of intact mitochondria. The fusion procedure did not significantly affect mitochondrial ultrastructure, electron transport, or respiratory control ratios. The extent of fusion of liposomes with the mitochondrial outer membrane was monitored by fluorescence dequenching assays using a membrane fluorescent probe (octadecylrhodamine B) and the soluble FITC-BSA fluorescent probe, which report membrane and contents mixing, respectively. Assays were consistent with a rapid, low pH-induced vesicle-outer membrane fusion and delivery of FITC-BSA into the intermembrane space. Similar affinities for the ionic strength-dependent change in fluorescence were found for bulk medium, soluble (9.8 +/- 0.8 mM) and intermembrane space-entrapped FITC-BSA (10.2 +/- 0.6 mM). FITC-BSA consistently reported an ionic strength in the intermembrane space of the functionally and structurally intact mitochondria within +/- 20% of the external bulk solution. These findings reveal that the intermembrane ionic strength changes as does the external ionic strength and suggest that cytochrome c interactions, as well as other protein interactions and biochemical reactions, proceed in the intermembrane space of mitochondria in the intact cell at physiological ionic strength, i.e., 100-150 mM.

Animals↗
PubMed1996

Linear dimension reduction of sequences of medical images: III. Factor analysis in signal space.

A method is presented for improving the precision of factor analysis by utilizing physiological information. The first step is an optimal linear dimension reduction, whereby the data are projected onto a low-dimensional signal space. Then principal component analysis is performed in the signal space rather than in the entire data space. This improves the precision of the principal components. Unlike ordinary principal component analysis, the present method is not degraded when the time intervals are subdivided, provided that the signal space is correct. Alternatively, but with identical results, the covariance matrix can be calculated from the whole data space. The covariance matrix is then transformed and principal component analysis is performed in either a low-rank matrix or a low-dimensional submatrix instead of in the whole covariance matrix. Factor analysis using the intersection method with a theory space may be improved by employing the present method. In simulations based on a [11C]flumazenil study with 27 frames, the proposed method required only 58 per cent of the radioactivity to produce the same precision as the intersection method and only 27 per cent when compared to ordinary principal component analysis.

Biophysical Phenomena↗
PubMed2001

Disembodiment is a cyberspace myth: discourse and the self in real space.

Much social science writing about the Internet is disembodied. This paper will try show how this is rhetorically practiced by the cyberfeminist author Sadie Plant. From the work of Fred Newman, Michael Billig, and also from discourse work, comes the idea that it is not views that should be studied per se, but rather, the giving of views. To understand people, one needs to understand them when they are in dialogue with one another. Not to test them in isolation, but to study their interrelatedness as they perform social life. A social space was constructed through which embodiment could be revealed. This reality is "real space," the space that is on the other side of the screen, so to speak. To understand the psychology of the Internet is to enter into dialogue with people, and real space constitutes the embodied practice of social talk, specifically in the context of the interview. Two semistructured interviews were carried out with a student from the Ukraine. These interviews were transcribed closely. Just as real space constitutes interviews, cyberspace constitutes E-mailing. An international student born in New Zealand was questioned through E-mail. A discourse analysis was performed on selected extracts. The sequences were typified by diversity and multiplicity of theme, which included the drawing upon of embodied resources. The experience of being internationals in a U.K. academic institution were perpetually being negotiated, concomitantly to the giving of views about the Internet. The problematic issues of writing about social life are practically addressed in the discussion. I explore the realities created by real space and cyberspace by deconstructing them. Discourse work allowed for a critical self-reflection concerning the meanings that were given to the performance of the Internet.

Adult↗