Plot2groups: an R package to plot scatter points for two groups of values
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ABSTRACT:
SUBMITTER: Xu Y
PROVIDER: S-EPMC4413984 | biostudies-literature | 2014 Jan
REPOSITORIES: biostudies-literature
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Project description:BackgroundCancer epidemiology studies require sufficient power to assess spatial relationships between exposures and cancer incidence accurately. However, methods for power calculations of spatial statistics are complicated and underdeveloped, and therefore underutilized by investigators. The spatial relative risk function, a cluster detection technique that detects spatial clusters of point-level data for two groups (e.g., cancer cases and controls, two exposure groups), is a commonly used spatial statistic but does not have a readily available power calculation for study design.ResultsWe developed sparrpowR as an open-source R package to estimate the statistical power of the spatial relative risk function. sparrpowR generates simulated data applying user-defined parameters (e.g., sample size, locations) to detect spatial clusters with high statistical power. We present applications of sparrpowR that perform a power calculation for a study designed to detect a spatial cluster of incident cancer in relation to a point source of numerous environmental emissions. The conducted power calculations demonstrate the functionality and utility of sparrpowR to calculate the local power for spatial cluster detection.ConclusionssparrpowR improves the current capacity of investigators to calculate the statistical power of spatial clusters, which assists in designing more efficient studies. This newly developed R package addresses a critically underdeveloped gap in cancer epidemiology by estimating statistical power for a common spatial cluster detection technique.
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Project description:The isoelectric points of erabutoxins a, b and c, neurotoxic proteins of a sea snake, Laticauda semifasciata, were determined by density-gradient isoelectric focusing. The same measurement was also made with monoacyl derivatives of erabutoxin b, in which each one of all amino groups had been either acetylated or propionylated. Erabutoxins a and b showed the same isoelectric point at pH 9.68. The values for ]1-N alpha-acetyl-arginine]-, [15-N6-acetyl-lysine]-, [27-N6-acetyl-lysine]-, [47-N6-propionyl-lysine]- and [51-N6-acetyl-lysine]-erabutoxin b were at pH 9.52, 9.31, 9.45, 9.22 and 9.09 respectively, being definitely different from each other and lower than the value for the unmodified molecule. The isoelectric point of erabutoxin c, which is [51-asparagine]-erabutoxin b, was the same as that of [51-N6-acetyl-lysine]erabutoxin b. Assuming that no change in pK occurs on monoacylation, the pK values of amino groups in erabutoxin b were calculated from the isoelectric-point data. It is indicated that the pK values of zeta-amino groups differ markedly from each other and that the value of alpha-amino group is anomalously high.
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2015-07-21 | GSE71094 | GEO
Project description:Accurate predictions of pKa values of titratable groups require taking into account all relevant processes associated with the ionization/deionization. Frequently, however, the ionization does not involve significant structural changes and the dominating effects are purely electrostatic in origin allowing accurate predictions to be made based on the electrostatic energy difference between ionized and neutral forms alone using a static structure and the subtle structural changes be accounted by using dielectric constant larger than two. On another hand, if the change of the charge state is accompanied by a large structural reorganization of the target protein, then the relevant conformational changes have to be explicitly taken into account in the pKa calculations. Here we report a hybrid approach that first predicts the titratable groups whose ionization is expected to cause large conformational changes, termed "problematic" residues, and then applies a special protocol on them, while the rest of the pK(a)s are predicted with rigid backbone approach as implemented in multi-conformation continuum electrostatics (MCCE) method. The backbone representative conformations for "problematic" groups are generated with either molecular dynamics simulations with charged and uncharged amino acid or with ab-initio local segment modeling. The corresponding ensembles are then used to calculate the titration curves of the "problematic" residues and then the results are averaged to obtain the corresponding pKa.
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Project description:AimTo evaluate the subjective visual functions of early cataracts patients and assess their surgical indications.MethodsEyes were separated into a control group (Group A without cataract) and two early cataracts groups (Group B with 2.0 ≤ OSI < 3.0 and Group C with 3.0 ≤ OSI < 4.0). The objective scatter index (OSI), modulation transfer function cut-off frequency (MTF cut-off), and Strehl ratio (SR) values were applied to measure objective visual functions. The contrast sensitivity (CS) and scores of the questionnaires (QOL and VF-14) characterized subjective visual functions. Above visual functions were compared among three groups. Postoperative visual functions in Group B and C were analyzed to assess the outcome of surgery.ResultsNinety two subjects (126 eyes) were included in the study. All objective visual function in Group B were significantly better than Group C (all P < 0.01), but worse than Group A (all P < 0.01). Except for 1.5 c/d CS, subjective visual function in Group A were significantly better than Group B and C (all P < 0.05), but there was no significant differences between Group B and C. As for eyes that underwent surgery in Group B and C, all visual functions significantly improved after surgery (P < 0.05), except for 1.5 c/d CS in Group C. There were no significant differences among the three groups after surgery.ConclusionThe subjective visual function can be impaired in early cataracts patients with OSI < 3.0, whose objective visual functions were statistically better than patients with OSI ≥ 3.0. These patients can benefit equally from surgery as patients with OSI ≥ 3.0. Subjective visual functions can be used as surgical indications for these patients.
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Project description:Background Understanding the natural history of elevated blood pressure (BP) is important to determine the window for primary prevention of hypertension. The authors aimed to investigate the natural history of elevated BP and examine whether there were inflection points in BP trajectories preceding hypertension onset in Chinese adults. Methods and Results A total of 8688 participants with an average of 5 BP measurements were included from the CHNS (China Health and Nutrition Survey). In each wave, triplicate measurements on the same arm were taken, and the mean systolic BP (SBP) and diastolic BP (DBP) were used in the analysis. Hypertension onset was defined as SBP ≥140 mm Hg or DBP ≥90 mm Hg or diagnosed by physician or currently under antihypertensive treatment. The median follow-up time was 13.0 years. Overall, BP elevation with age prior to the onset of hypertension showed a nonlinear trajectory. The increased rates in both SBP and DBP were obviously faster after the inflection point than before. According to hypertension onset at age 30 to 39, 40 to 49, 50 to 59, 60 to 69, and 70 to 79 years, at the inflection point, patients were ≈29, 38, 48, 57, and 67 years, SBP levels were 112.6, 114.8, 116.8, 117.4, and 118.0 mm Hg, and DBP levels were 73.4, 75.7, 76.9, 76.2, and 73.8 mm Hg, respectively. Conclusions There was a nonlinear trajectory of BP elevation preceding hypertension onset. The inflection points for SBP and DBP were in the range of 112 to 118 mm Hg and 73 to 77 mm Hg, respectively. Once BP levels exceeded the changing points, the level of SBP and DBP increased more rapidly.
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