Phi Values Research Articles

Clinical assessment of transthoracic echocardiography skills: a generalizability study.

BackgroundTransthoracic echocardiography (TTE) is a widely used cardiac imaging technique that all cardiologists should be able to perform competently. Traditionally, TTE competence has been assessed by unstructured observation or in test situations separated from daily clinical practice. An instrument for assessment of clinical TTE technical proficiency including a global rating score and a checklist score has previously shown reliability and validity in a standardised setting. As clinical test situations typically have several sources of error giving rise to variance in scores, a more thorough examination of the generalizability of the assessment instrument is needed.MethodsNine physicians performed a TTE scan on the same three patients. Then, two raters rated all 27 TTE scans using the TTE technical assessment instrument in a fully crossed, all random generalizability study. Estimated variance components were calculated for both the global rating and checklist scores. Finally, dependability (phi) coefficients were also calculated for both outcomes in a decision study.ResultsFor global rating scores, 66.6% of score variance can be ascribed to true differences in performance. For checklist scores this was 88.8%. The difference was primarily due to physician-rater interaction. Four random cases rated by one random rater resulted in a phi value of 0.81 for global ratings and two random cases rated by one random rater showed a phi value of 0.92 for checklist scores.ConclusionsUsing the TTE checklist as opposed to the TTE global rating score had the effect of minimising the largest source of error variance in test scores. Two cases rated by one rater using the TTE checklist are sufficiently reliable for high stakes examinations. As global rating is less time consuming it could be considered performing four global rating assessments in addition to the checklist assessments to account for both reliability and content validity of the assessment.Electronic supplementary materialThe online version of this article (doi:10.1186/s12909-015-0294-5) contains supplementary material, which is available to authorized users.

Multicenter Evaluation of the Prostate Health Index to Detect Aggressive Prostate Cancer in Biopsy Naïve Men

We evaluated the ability of PHI to discriminate aggressive prostate cancer from indolent or no cancer in a biopsy naïve population. Two independent prospective cohorts of 561 and 395 subjects, respectively, with no prior prostate biopsy who were enrolled at different clinical sites were used to validate the results. We compared the diagnostic specificity of PHI to prebiopsy total and percent free prostate specific antigen using prostate biopsy results. We also determined the optimal PHI threshold to discriminate aggressive prostate cancer (Gleason score 7 or greater) from indolent or no prostate cancer (Gleason score 6 or less). In the primary cohort higher PHI values were significantly associated with Gleason score 7 or greater. The AUC to detect aggressive prostate cancer was 0.815. At 95% sensitivity PHI specificity was 36.0% vs 17.2% and 19.4% for total and percent free prostate specific antigen, respectively. At 95% sensitivity for detecting aggressive prostate cancer the optimal PHI cutoff was 24, which would help avoid 41% of unnecessary biopsies. A cutoff of 24 led to 36% biopsies avoided with few aggressive cancers missed. These results were confirmed in the validation cohort. The PHI detected aggressive prostate cancer with better specificity than total and percent free prostate specific antigen in a biopsy naïve population. It could be a useful tool to decrease unnecessary prostate biopsies.

The Role of the M3 Helix in AChR Gating and PAM Action

We are examining the M3 transmembrane helix of mouse muscle AChRs with regard to C↔O gating and the effects of positive allosteric modulators (PAMs). The relative ground and transition state gating energies were estimated from single-channel currents of AChRs having M3 mutations. Diliganded gating rate and equilibrium constants were measured for ∼100 mutations in 5 subunits (α, β, δ, e and γ; 20 mM choline or 500 μM ACh, −100 mV, HEK cells). In general: i) the effects of the mutations were small (≤1 kcal/mol), ii) the effects were similar among subunits, iii) the mutations in different subunits were independent, iv) the mutations have no effect on the energy from the agonist affinity change (≤∼0.3 kcal/mol) and v) most phi values were low (∼0.3). Crystal structures of AChR homologues in detergents suggest that the low phi positions in M3 are interaction sites for PAMs. We investigated the actions of PNU-120596 and IVM (1-1000nM). In WT AChRs (adult and fetal) these ligands increase substantially the frequency and lifetime of constitutive openings in a manner consistent with action at a low-phi position such as in M3. Such potentiation was also apparent at low [agonist] (<1μM ACh or choline), but at higher [agonist] gating kinetics became complex and the potentiation was less clear. The PAMs also increased substantially the frequency and lifetime of constitutive openings in some of the M3 mutants (to W).

Thermodynamics of AChR Activation

Energy changes in muscle acetylcholine receptor (AChR) gating were estimated from single-channel currents by using a cyclic activation scheme. Mutations mainly cause local and independent free energy changes that can be mapped onto structures and used to engineer rate and equilibrium constants. Residue-by-residue maps of reaction progress (phi) show that two separated regions, the agonist binding sites and linkers in the membrane domain, are the first to reach the gating transition state, followed by the extracellular domain, most of the membrane domain and a gate that appears to unlock in three steps. Maps of ground state free energies show big changes at the agonist sites, domain and subunit interfaces, a transmembrane helix and the gate. The local character of side chain energy changes and the similar phi values of the agonist sites and distant linkers suggest that the gating allosteric transition is not a purely mechanical process. Each AChR has 2 agonist sites in the extracellular domain, at αδ and either αe (adult) or αγ (fetal) subunit interfaces. Here, an increase in affinity for the ligand increases Po much as the movement of S4 does in voltage-gated channels. We measured the effects of mutations at each site with regard to their contribution to the binding free energy, active vs. resting (ΔGB). In both adult and fetal AChRs the two agonist sites behave independently. For 4 different agonists ΔGB is more favorable at αγ compared to the others. Only 3 aromatics contribute to ΔGB at the adult sites but 5 do so at αγ. ΔGB values calculated from MD simulations are consistent with the experimental ones and suggest that the αγ site is more compact, better organized and less dynamic than the others.

Characterization and Pervaporation Properties of Modified PU Membranes

Pervaporation will have broad application prospects in the treatment of phenolic wastewater. Polyurethane (PU) membrane is promising but needs to be further modified. In this study, both β-CD and CNT were used to modify the PU membrane. The structure and property of these membranes were characterized by FTIR, DSC and TGA. The pervaporation performances were investigated, and the effects of β-CD and CNT on membrane separation were discussed. TGA shows that three kinds of modified membranes have enough thermal stability to afford pervaporation test and start weight loss at about 200 °C. In pervaporaiton, the total flux, separation factor and PSI value all increase with increased feed temperature. That is anti-trade-off phenomenon. Among these membranes, HTPB+β-CD-PU shows the best comprehensive performance at 80°C and has great potential for further application.

Deconstructing the galaxy stellar mass function with UKIDSS and CANDELS: the impact of colour, structure and environment

We combine photometry from the UDS, and CANDELS UDS and CANDELS GOODS-S surveys to construct the galaxy stellar mass function probing both the low and high mass end accurately in the redshift range 0.3<z<3. The advantages of using a homogeneous concatenation of these datasets include meaningful measures of environment in the UDS, due to its large area (0.88 deg^2), and the high resolution deep imaging in CANDELS (H_160 > 26.0), affording us robust measures of structural parameters. We construct stellar mass functions for the entire sample as parameterised by the Schechter function, and find that there is a decline in the values of phi and of alpha with higher redshifts, and a nearly constant M* up to z~3. We divide the galaxy stellar mass function by colour, structure, and environment and explore the links between environmental over-density, morphology, and the quenching of star formation. We find that a double Schechter function describes galaxies with high Sersic index (n>2.5), similar to galaxies which are red or passive. The low-mass end of the n>2.5 stellar mass function is dominated by blue galaxies, whereas the high-mass end is dominated by red galaxies. This hints that possible links between morphological evolution and star formation quenching are only present in high-mass galaxies. This is turn suggests that there are strong mass dependent quenching mechanisms. In addition, we find that the number density of high mass systems is elevated in dense environments, suggesting that an environmental process is building up massive galaxies quicker in over densities than in lower densities.

Lower-Bound Axisymmetric Formulation for Geomechanics Problems Using Nonlinear Optimization

A lower-bound limit analysis formulation, by using two-dimensional finite elements, the three-dimensional Mohr-Coulomb yield criterion, and nonlinear optimization, has been given to deal with an axisymmetric geomechanics stability problem. The optimization was performed using an interior point method based on the logarithmic barrier function. The yield surface was smoothened (1) by removing the tip singularity at the apex of the pyramid in the meridian plane and (2) by eliminating the stress discontinuities at the corners of the yield hexagon in the pi-plane. The circumferential stress (sigma(theta)) need not be assumed. With the proposed methodology, for a circular footing, the bearing-capacity factors N-c, N-q, and N-gamma for different values of phi have been computed. For phi = 0, the variation of N-c with changes in the factor m, which accounts for a linear increase of cohesion with depth, has been evaluated. Failure patterns for a few cases have also been drawn. The results from the formulation provide a good match with the solutions available from the literature. (C) 2014 American Society of Civil Engineers.

Spatial Variation of Textural Parameters in a Small River: An Example from Khurar River, Khajuraho, Chhaterpur District, Madhya Pradesh, India

Texture (grain size) is one of the many parameters, which is used in determining depositional environments of sediments and sedimentary rocks. In the present investigation, texture was analysed from sixteen stations in the Khurar River, Madhya Pradesh, India. Here, grain size analysis was carried out employing mechanical sieving method using a sonic shaker. Frequency and cumulative frequency curves were prepared from the grain size data on centimetre and arithmetic probability papers, respectively. The phi values were determined and used to calculate the statistical parameters such as mean, standard deviation, skewness and kurtosis. It is found that the mean size value varies from-0.63to 0.80 with a graphic mean distribution ranging from -0.27 to 0.40 ϕ, indicating that the size of the river sand is very coarse to coarse-grained. The standard deviation (sorting) shows a range of 0 .69 to 1.65 ϕ. The skewness values of the sediment samples range from 0.19 to 0.29 ϕ, thus, indicating the presence of fine fraction to near-symmetrical fraction in the population. The kurtosis varies between 1.03 and 1.09 ϕ, indicating that 25% of the samples are leptokurtic, 6.25% are very leptokurtic, 50% are mesokurtic and 12.5% are platykurtic. The platykurtic nature in few cases suggests mixing of sediments from two sources. Bivariate plots prepared combining various textural parameters were used to interpret their behaviour in the river sediments. C-M plot was also prepared to understand the dominant mode of sediments transportation in the Khurar River. In this river, all the sediments are dominantly characterized by the rolling process of transportation. This study reveals that sorting varies from poorly sorted to moderately well sorted in the course of the river may be because of dominance of winnowing and selective sorting in the lower reaches of the river.

Removal of hazardous volatile organic compounds from water by vacuum pervaporation with hydrophobic ceramic membranes

Hydrophobic alumina and titania micro and mesoporous ceramic membranes were prepared by grafting of C6F13C2H4Si(OEt)3 (C6) molecules and subsequently applied in a pervaporation (PV) process to the removal of hazardous organic solvents (MTBE, EtAc and BuOH) from binary aqueous solutions. The transport and separation properties of investigated membranes were discussed. Additionally it was found that membrane material and grafting time have an important impact of the pervaporative properties. All tested membranes were selective toward organics. Titania membrane was the most efficient and was characterized by the highest value of PSI and the highest value of permeate flux of organic compounds in water–EtAc (JEtAc=1.1kgh−1m−2; PSIEtAc=140kgh−1m−2) and water–MTBE (JMTBE=1.0kgh−1m−2; PSIMTBE=194kgh−1m−2) systems. This behavior of titania membrane was also discussed based on the Hansen solubility parameters. In presented work the evaluation of MTBE removal degree with titania modified membrane from water binary mixture in the pervaporation process was discussed.

A Program of Exercise Throughout Pregnancy. Is it Safe to Mother and Newborn?

The aim of the present study was to examine the influence of a program of moderate physical exercise throughout pregnancy on maternal and fetal parameters. The study design was a randomized controlled trial. The study took place at the Hospital of Fuenlabrada in Madrid, Spain. Analyzed were 200 pregnant women (31.54 ± 3.86 years), all of whom had uncomplicated and singleton gestation. Of these subjects, 107 were allocated to the exercise group (EG) and 93 to the control group (CG). Women from EG participated in a physical conditioning program throughout pregnancy, which included a total of 55- to 60-minute weekly sessions, 3 days per week. Pregnancy outcomes. Maternal: gestational age, weight gain, type of delivery, blood pressure during pregnancy, gestational diabetes (n/%). Fetal: birth weight, birth size, head circumference, Apgar score, pH of umbilical cord. Student's unpaired t-test and χ (2) test were used; p values of ≤ .05 indicated statistical significance. Cohen's d was used to determine the effect size. There were significantly more pregnant women in the CG who gained excessive weight during their pregnancies than in the EG group (CG: N = 31, 35.6% versus N = 22, 21.2%; χ(2) = 4.95; p =.02). The effect size was small (Phi value =.16). Other pregnancy outcome showed no differences between groups. A regular and moderate physical exercise program throughout pregnancy is not a risk to maternal and fetal well-being, and it helps to control excessive weight gain.

Conserved nucleation sites reinforce the significance of Phi value analysis in protein-folding studies.

The only experimental strategy to address the structure of folding transition states, the so-called Φ value analysis, relies on the synergy between site directed mutagenesis and the measurement of reaction kinetics. Despite its importance, the Φ value analysis has been often criticized and its power to pinpoint structural information has been questioned. In this hypothesis, we demonstrate that comparing the Φ values between proteins not only allows highlighting the robustness of folding pathways but also provides per se a strong validation of the method.

Pervaporative removal of acetone, butanol and ethanol from binary and multicomponent aqueous mixtures

Results of research on the effectiveness of selected hydrophobic PDMS-based membranes in the pervaporative removal of acetone, butanol and ethanol from binary and quaternary aqueous mixtures are presented. Various investigated PDMS membranes exhibit high selectivity towards butanol. Values of separation factor β in contact with 1wt.% BuOH are in the range from 27 (Pervatech PDMS 2.0) to 40 (Pervap 1070 PDMS 0.2). Pervatech PDMS 2.0 membrane, showing the highest PSI value, was chosen for experiments with binary and quaternary aqueous mixtures.Simulation of batch pervaporation process showed that during 300min of the process it is possible to remove over 95% of organics from the feed mixture, containing initially 3wt.% of ABE mixture and with feed to membrane area ratio of 100kgm−2. It was also found that a longer batch pervaporation process results in a more diluted permeate. Such phenomenon is caused by the fact that organic fluxes decrease with time whereas water flux is constant during batch process.

Factors Related to Practice on DPT Vaccine Distribution and Storage

ABSTRACTThe diptheria outbreak in Surabaya indicated that immunization program failure. Immunization is primary preventif effort to decrease morbidity of disease. An immunization service is very important to protect vaccine quality through cold chain so that vaccine potency be optimal. The purpose of this study was to analysis of factors which are assosiated with midwive’s practice of DPT vaccine distribution and storage to outreach. This study is applying observational approach using cross sectional method. Populations are all village midwives in public health center East Surabaya. The numbers of sample were 38 midwives taken using simple random sampling. The dependent variable was midwive’s practice of DPT vaccine distribution and storage to outreach and the independent variables of this study were work duration, a history of training of cold chain, sosialization, knowledge, attitude. Primary data were obtained through observation and interview. The results showed that 68.4 % midwive’s practice on DPT vaccine distribution and storage at outreach is good. Independent variable which are significant assosiated with midwive’s practice on DPT vaccine distribution and storage at outreach is sosialization about vaccine distribution and storage (p = 0.026) and value of phi and Cramer’s V = 0.431. Enhancement of socialization again be needed to village midwive as efforts for increase knowledge and attitude.Keywords: midwive, cold chain, vaccine distribution, DPT

Factors Related to Practice on DPT Vaccine Distribution and Storage

ABSTRACTThe diptheria outbreak in Surabaya indicated that immunization program failure. Immunization is primary preventif effort to decrease morbidity of disease. An immunization service is very important to protect vaccine quality through cold chain so that vaccine potency be optimal. The purpose of this study was to analysis of factors which are assosiated with midwive’s practice of DPT vaccine distribution and storage to outreach. This study is applying observational approach using cross sectional method. Populations are all village midwives in public health center East Surabaya. The numbers of sample were 38 midwives taken using simple random sampling. The dependent variable was midwive’s practice of DPT vaccine distribution and storage to outreach and the independent variables of this study were work duration, a history of training of cold chain, sosialization, knowledge, attitude. Primary data were obtained through observation and interview. The results showed that 68.4 % midwive’s practice on DPT vaccine distribution and storage at outreach is good. Independent variable which are significant assosiated with midwive’s practice on DPT vaccine distribution and storage at outreach is sosialization about vaccine distribution and storage (p = 0.026) and value of phi and Cramer’s V = 0.431. Enhancement of socialization again be needed to village midwive as efforts for increase knowledge and attitude.Keywords: midwive, cold chain, vaccine distribution, DPT

Effect of the gastrointestinal environment on pH homeostasis of Lactobacillus plantarum and Lactobacillus brevis cells as measured by real-time fluorescence ratio-imaging microscopy

In the present work, an in vitro model of the gastrointestinal tract (GIT) was developed to obtain real-time observations of the pH homeostasis of single cells of probiotic Lactobacillus spp. strains as a measure of their physiological state. Changes in the intracellular pH (pHi) were determined using fluorescence ratio imaging microscopy (FRIM) for potential probiotic strains of Lactobacillus plantarum UFLA CH3 and Lactobacillus brevis UFLA FFC199. Heterogeneous populations were observed, with pHi values ranging from 6.5 to 7.5, 3.5 to 5.6 and 6.5 to 8.0 or higher during passage of saliva (pH 6.4), gastric (pH 3.5) and intestinal juices (pH 6.4), respectively. When nutrients were added to gastric juice, the isolate L. brevis significantly decreased its pHi closer to the extracellular pH (pHex) than in gastric juice without nutrients. This was not the case for L. plantarum.This study is the first to produce an in vitro GIT model enabling real-time monitoring of pH homeostasis of single cells in response to the wide range of pHex of the GIT. Furthermore, it was possible to observe the heterogeneous response of single cells. The technique can be used to determine the survival and physiological conditions of potential probiotics and other microorganisms during passage through the GIT.

PASS-THROUGH FREIGHT MODELING AT THE STATEWIDE AND METROPOLITAN LEVEL

In spite of the important role transport play in any urban area, transport services are frequently insufficient to meet commuters demand with the services provided suffering from low output. This study assesses the quality of intra urban bus services in Kaduna metropolis as perceived by bus commuters. This study relied on systematic sampling of eight major terminals from which 357 bus commuters were purposively interviewed. Descriptive and inferential statistical techniques were used to summarise the data collected. The study revealed that majority of the commuters (70.3%) walk between 1-500 metres to reach bus stops and 66.9% waited between 1-20 minutes before the arrival of bus. A cross tabulation between the age by walking distance of bus passengers shows a clear difference in the walking distance of passengers to bus stops by age distribution. Also the study revealed that there is a strong relationship between the level of education and the problems encountered by commuters (r = 0.70 and Kendall’s Tau = 0.744). Similarly, Phi value = 0.72 and Cramer v = 0.51 indicate a strong relationship between the bus passenger capacity and the problems passengers encountered. Most passengers are not satisfied with the level of bus services provided. The study therefore recommends that certain policy actions such as the use of conventional buses, bus priority measures among others need to be taken in order to improve the quality of intra-urban bus services in Kaduna metropolis.

Energy Maps of Acetylcholine Receptor Gating

Occupancy of an AChR binding site by an agonist (A) shifts a pre-existing equilibrium from the Closed-channel towards the Open-channel conformation. We estimated energy changes in adult mouse A2C↔A2O gating (adult mouse) from single-channels. Mutations mainly cause local energy changes that can be mapped onto structures of related proteins. We made maps showing residue reaction progress (phi values) and approximate extents of energy changes in the channel-opening isomerization. Phi values range from 1 to 0, are approximately constant for each position and have a modal distribution (n=5 populations). Residues having similar phi values are clustered, with phi decreasing approximately longitudinally between the binding site and the gate. Two separated regions in the alpha subunits - the transmitter binding sites and M2-M3 linkers in the membrane domain - have the highest phi values (∼0.95), followed by the rest of the extracellular domain (∼0.8), most of the membrane domain (∼0.6) and the gate region of the pore (0.3). Residues at the extracellular-transmembrane domain interface undergo large energy changes in C→O. Largest energy changes occur at the binding sites, and in the alpha subunit at the M2-M3 linker, M1 and the gate. All of these energy changes, including those associated with the affinity change for the agonist, appear to arise from local ‘resettling’ events that do not transfer significant energy over distance. Expansion and flexure of the M2-M3 linkers in the alpha subunit appears to trigger the global allosteric transition, and the hydrophobic gate appears to unlock in three steps. The local character of side chain energy changes and the similar phi values of the binding sites and distant M2-M3 linkers suggest that the gating transition is not strictly a mechanical process.

Gating Phi Values in the Muscle Acetylcholine Receptor αM2-αM3 Linker with vs. without Agonists

Acetylcholine receptors are ligand gated ion channels that transduce a chemical signal into an electrical signal at the neuromuscular junction (α2βδe subunits arranged around a central pore). A global, reversible allosteric transition between stable closed- and open-channel states ('gating') takes place either in the presence or absence of agonists. Phi (the slope a log-log plot of channel opening rate constant vs. equilibrium constant for a series of mutation of one residue) gives the extent of the perturbed residue's progress in the transition state of the gating reaction, on a scale 1 to 0. Previously-estimated diliganded gating phi values in the α subunit decrease approximately linearly between the transmitter binding site (∼0.95, same as for the agonist), through the extracellular domain (0.8), through M2 (0.6) to the gate region (∼0.3). Some residues away from the binding site have the same phi value without or without agonists (Purohit and Auerbach, PNAS, 2007). However, unliganded phi values for eight binding site residues (αY93, αW149, αY190, αY198, αG147, αG153, eP121, δP123; 0.77±0.023) are lower than the corresponding diliganded values (0.94±0.017). We estimated di- and un-liganded phi gating values for four positions in the αM2-αM3 linker (αI260, αE262, αP265, αS268), another hi-phi domain that is apparently not connected by a high-phi pathway to the binding sites. The unliganded phi values for these four positions (0.88±0.022) were about the same as in diliganded gating (0.90±0.031). So far the mutability in phi appears to pertain only to the binding site, perhaps because the affinity change for the agonist contributes to the gating energy only when ligands are present.

Validation of the Conservation and Robustness of Folding Initiation Sites in Evolutionarily Related Proteins

Despite the recent progress in the protein folding field, how a given amino acid sequence folds into its unique structure is still unclear. According to KA Scott et. al., for Immunoglobulin and Fibronectin-like fold, which are evolutionarily unrelated but have the same topology, share a folding mechanism consisting of 4 key residues and their peripheral residues. However, there are also some cases that two evolutionarily related proteins have different folding mechanisms (for example, PDZ2 and PDZ3 whose sequence identity is nearly 30%). In this study, we aim to investigate whether such folding segments (i.e., folding initiation sites playing important roles for the folding from the denatured state to the transition state) really exist in evolutionarily related proteins by our sequence analysis methods and validate the results with the experimental phi values that provide a degree of the contribution for the structural formation in the transition state for each residue. Our sequence analysis methods are based on the inter-residue average distance statistics and already applied to several proteins, like leghemoglobin, FABP, azurin, and TIM-barrel proteins; they returned reasonable results with HD exchange experiments or phi-value analyses. According to the current study, for the Ferredoxin-like proteins we treat here, the predicted folding initiation sites have good agreements with experimental phi values, and the application to their evolutionarily related proteins returns a suggestion that the location of folding initiation sites are more conservative than sequence. In addition to these analyses, we also investigate the robustness of folding initiation sites by comparing the results of our analyses between naturally evolved proteins, which are under the pressure of nature, and artificially evolved proteins, which are not under the pressure of nature. The details will be reported in the conference.

Exploring multi-dimensional coordinate-dependent diffusion dynamics on the energy landscape of protein conformation change

We explore the multi-dimensional diffusion dynamics of protein conformational change. We found in general that the diffusion is anisotropic and inhomogeneous. The directional and positional dependence of diffusion have significant impacts on the protein conformational kinetics: the dominant kinetic path of conformational change is shifted from the naively expected steepest decent gradient paths. The kinetic transition state is shifted away from the transition state. The effective kinetic free energy barrier height, determining the kinetic rate of the conformational change, is shifted away from the one estimated from the thermodynamic free energy barrier. The shift of the transition state in position and value will modify the phi value analysis for identification of hot residues and interactions responsible for conformational dynamics. Ongoing and future experiments can test the predictions of the model.