Analysis of complex molecular systems: The impact of multivariate analysis for resolving the interactions of small molecules with biopolymers - a review

This review is focused on the impact of chemometrics for resolving data sets collected from investigations of the interactions of small molecules with biopolymers. These samples have been analyzed with various instrumental techniques, such as fluorescence, ultraviolet–visible spectroscopy, and voltammetry. The impact of two powerful and demonstrably useful multivariate methods for resolution of complex data—multivariate curve resolution–alternating least squares (MCR–ALS) and parallel factor analysis (PARAFAC)—is highlighted through analysis of applications involving the interactions of small molecules with the biopolymers, serum albumin, and deoxyribonucleic acid. The outcomes illustrated that significant information extracted by the chemometric methods was unattainable by simple, univariate data analysis. In addition, although the techniques used to collect data were confined to ultraviolet–visible spectroscopy, fluorescence spectroscopy, circular dichroism, and voltammetry, data profiles produced by other techniques may also be processed. Topics considered including binding sites and modes, cooperative and competitive small molecule binding, kinetics, and thermodynamics of ligand binding, and the folding and unfolding of biopolymers. Applications of the MCR–ALS and PARAFAC methods reviewed were primarily published between 2008 and 2013.

The role of environmental factors in the spatial distribution of Japanese encephalitis in mainland China

Japanese encephalitis (JE) is the most common cause of viral encephalitis and an important public health concern in the Asia-Pacific region, particularly in China where 50% of global cases are notified. To explore the association between environmental factors and human JE cases and identify the high risk areas for JE transmission in China, we used annual notified data on JE cases at the center of administrative township and environmental variables with a pixel resolution of 1 km×1 km from 2005 to 2011 to construct models using ecological niche modeling (ENM) approaches based on maximum entropy. These models were then validated by overlaying reported human JE case localities from 2006 to 2012 onto each prediction map. ENMs had good discriminatory ability with the area under the curve (AUC) of the receiver operating curve (ROC) of 0.82-0.91, and low extrinsic omission rate of 5.44-7.42%. Resulting maps showed JE being presented extensively throughout southwestern and central China, with local spatial variations in probability influenced by minimum temperatures, human population density, mean temperatures, and elevation, with contribution of 17.94%-38.37%, 15.47%-21.82%, 3.86%-21.22%, and 12.05%-16.02%, respectively. Approximately 60% of JE cases occurred in predicted high risk areas, which covered less than 6% of areas in mainland China. Our findings will help inform optimal geographical allocation of the limited resources available for JE prevention and control in China, find hidden high-risk areas, and increase the effectiveness of public health interventions against JE transmission.

Reproducibility of fatmax and fat oxidation rates during exercise in recreationally trained males

Aerobic exercise training performed at the intensity eliciting maximal fat oxidation (Fatmax) has been shown to improve the metabolic profile of obese patients. However, limited information is available on the reproducibility of Fatmax and related physiological measures. The aim of this study was to assess the intra-individual variability of: a) Fatmax measurements determined using three different data analysis approaches and b) fat and carbohydrate oxidation rates at rest and at each stage of an individualized graded test. Fifteen healthy males [body mass index 23.1±0.6 kg/m2, maximal oxygen consumption () 52.0±2.0 ml/kg/min] completed a maximal test and two identical submaximal incremental tests on ergocycle (30-min rest followed by 5-min stages with increments of 7.5% of the maximal power output). Fat and carbohydrate oxidation rates were determined using indirect calorimetry. Fatmax was determined with three approaches: the sine model (SIN), measured values (MV) and 3rd polynomial curve (P3). Intra-individual coefficients of variation (CVs) and limits of agreement were calculated. CV for Fatmax determined with SIN was 16.4% and tended to be lower than with P3 and MV (18.6% and 20.8%, respectively). Limits of agreement for Fatmax were −2±27% of with SIN, −4±32 with P3 and −4±28 with MV. CVs of oxygen uptake, carbon dioxide production and respiratory exchange rate were <10% at rest and <5% during exercise. Conversely, CVs of fat oxidation rates (20% at rest and 24–49% during exercise) and carbohydrate oxidation rates (33.5% at rest, 8.5–12.9% during exercise) were higher. The intra-individual variability of Fatmax and fat oxidation rates was high (CV>15%), regardless of the data analysis approach employed. Further research on the determinants of the variability of Fatmax and fat oxidation rates is required.

Inertial sensor real-time feedback enhances the learning of cervical spine manipulation: A prospective study

Background Cervical Spinal Manipulation (CSM) is considered a high-level skill of the central nervous system because it requires bimanual coordinated rhythmical movements therefore necessitating training to achieve proficiency. The objective of the present study was to investigate the effect of real-time feedback on the performance of CSM. Methods Six postgraduate physiotherapy students attending a training workshop on Cervical Spine Manipulation Technique (CSMT) using inertial sensor derived real-time feedback participated in this study. The key variables were pre-manipulative position, angular displacement of the thrust and angular velocity of the thrust. Differences between variables before and after training were investigated using t-tests. Results There were no significant differences after training for the pre-manipulative position (rotation p = 0.549; side bending p = 0.312) or for thrust displacement (rotation p = 0.247; side bending p = 0.314). Thrust angular velocity demonstrated a significant difference following training for rotation (pre-training mean (sd) 48.9°/s (35.1); post-training mean (sd) 96.9°/s (53.9); p = 0.027) but not for side bending (p = 0.521). Conclusion Real-time feedback using an inertial sensor may be valuable in the development of specific manipulative skill. Future studies investigating manipulation could consider a randomized controlled trial using inertial sensor real time feedback compared to traditional training.

The dependence of computed tomography number to relative electron density conversion on phantom geometry and its impact on planned dose

A computed tomography number to relative electron density (CT-RED) calibration is performed when commissioning a radiotherapy CT scanner by imaging a calibration phantom with inserts of specified RED and recording the CT number displayed. In this work, CT-RED calibrations were generated using several commercially available phantoms to observe the effect of phantom geometry on conversion to electron density and, ultimately, the dose calculation in a treatment planning system. Using an anthropomorphic phantom as a gold standard, the CT number of a material was found to depend strongly on the amount and type of scattering material surrounding the volume of interest, with the largest variation observed for the highest density material tested, cortical bone. Cortical bone gave a maximum CT number difference of 1,110 when a cylindrical insert of diameter 28 mm scanned free in air was compared to that in the form of a 30 × 30 cm2 slab. The effect of using each CT-RED calibration on planned dose to a patient was quantified using a commercially available treatment planning system. When all calibrations were compared to the anthropomorphic calibration, the largest percentage dose difference was 4.2 % which occurred when the CT-RED calibration curve was acquired with heterogeneity inserts removed from the phantom and scanned free in air. The maximum dose difference observed between two dedicated CT-RED phantoms was ±2.1 %. A phantom that is to be used for CT-RED calibrations must have sufficient water equivalent scattering material surrounding the heterogeneous objects that are to be used for calibration.

Analysis of focal adhesion turnover: A quantitative live-cell imaging example

Recent advances in optical and fluorescent protein technology have rapidly raised expectations in cell biology, allowing quantitative insights into dynamic intracellular processes like never before. However, quantitative live-cell imaging comes with many challenges including how best to translate dynamic microscopy data into numerical outputs that can be used to make meaningful comparisons rather than relying on representative data sets. Here, we use analysis of focal adhesion turnover dynamics as a straightforward specific example on how to image, measure, and analyze intracellular protein dynamics, but we believe this outlines a thought process and can provide guidance on how to understand dynamic microcopy data of other intracellular structures.

Threat of resource loss: The role of self-regulation in adaptive task performance

Changes at work are often accompanied with the threat of, or actual, resource loss. Through an experiment, we investigated the detrimental effect of the threat of resource loss on adaptive task performance. Self-regulation (i.e., task focus and emotion control) was hypothesized to buffer the negative relationship between the threat of resource loss and adaptive task performance. Adaptation was conceptualized as relearning after a change in task execution rules. Threat of resource loss was manipulated for 100 participants undertaking an air traffic control task. Using discontinuous growth curve modeling, 2 kinds of adaptation—transition adaptation and reacquisition adaptation—were differentiated. The results showed that individuals who experienced the threat of resource loss had a stronger drop in performance (less transition adaptation) and a subsequent slower recovery (less reacquisition adaptation) compared with the control group who experienced no threat. Emotion control (but not task focus) moderated the relationship between the threat of resource loss and transition adaptation. In this respect, individuals who felt threatened but regulated their emotions performed better immediately after the task change (but not later on) compared with those individuals who felt threatened and did not regulate their emotions as well. However, later on, relearning (reacquisition adaptation) under the threat of resource loss was facilitated when individuals concentrated on the task at hand.

Patient reported adherence to hypertension treatment: A revalidation study

Background Adherence to hypertension management in patients with hypertension is known to influence their blood pressure control. It is important to measure patients’ adherence behaviours to assist with designing appropriate interventions to improve blood pressure control. Aims The purposes of this study were to use confirmatory factor analysis to revalidate the Therapeutic Adherence Scale for Hypertensive Patients (TASHP), and to calculate the cut-off score for classifying adherence behaviours into two groups: satisfactory and low adherence behaviours. Methods Systematic random sampling was used to recruit patients with hypertension in China. Demographic characteristics, the TASHP and blood pressure were collected. The psychometric tests of the TASHP included: construct validity, criteria-related validity, internal reliability, and split-half reliability. The area under the receiver operating characteristics curve and Youden index were used to identify the cut-off score of the TASHP for blood pressure control. Results This study involved 366 patients. Confirmatory factor analysis supported the four-component structure of the TASHP proposed in the original scale development study. The TASHP has a satisfactory internal reliability (Cronbach’s α > 0.7) and a satisfactory split-half reliability (Spearman–Brown coefficients > 0.7). The patients with overall scores of the TASHP ⩾ 109 points were considered to have satisfactory adherence behaviours. Conclusion The TASHP is a validated and reliable instrument to measure the adherence to hypertension management in Chinese patients with hypertension. The cut-off score of 109 points can be considered as an effective measure to classify the level of adherence into satisfactory and low adherence behaviours.

Simulating the dissipation of two herbicides using micro paddy lysimeters

A set of packed micro paddy lysimeters, placed in a greenhouse, was used to simulate the dissipation of two herbicides, simetryn and thiobencarb, in a controlled environment. Data from a field monitoring study in 2003, including the soil condition and water balances, were used in the simulation. The herbicides were applied and monitored over a period of 21 d. The water balances under two water management scenarios, intermittent irrigation management (AI) and continuous irrigation management (CI), were simulated. In the AI scenario, the pattern of herbicide dissipation in the surface water of the field were simulated, following the first-order kinetics. In the CI scenario, similarity was observed in most lysimeter and field concentrations, but there were differences in some data points. Dissipation curves of both herbicides in the surface water of the two simulated scenarios were not significantly different (P > 0.05) from the field data except for intercept of the thiobencarb curve in the CI scenario. The distribution of simetryn and thiobencarb in the soil profile after simulation were also similar to the field data. The highest concentrations of both herbicides were found on the topsoil layer at 0-2.5 cm depth. Only a small amount of herbicides moved down to the deeper soil layers. Micro paddy lysimeters are thus a good alternative for the dissipation study of pesticides in the paddy environment.

The effects of high temperature on cardiovascular admissions in the most populous tropical city in Vietnam

This study examined the short-term effects of temperature on cardiovascular hospital admissions (CHA) in the largest tropical city in Southern Vietnam. We applied Poisson time-series regression models with Distributed Lag Non-Linear Model (DLNM) to examine the temperature-CHA association while adjusting for seasonal and long-term trends, day of the week, holidays, and humidity. The threshold temperature and added effects of heat waves were also evaluated. The exposure-response curve of temperature-CHA reveals a J-shape relationship with a threshold temperature of 29.6 °C. The delayed effects temperature-CHA lasted for a week (0–5 days). The overall risk of CHA increased 12.9% (RR, 1.129; 95%CI, 0.972–1.311) during heatwave events, which were defined as temperature ≥ the 99th percentile for ≥2 consecutive days. The modification roles of gender and age were inconsistent and non-significant in this study. An additional prevention program that reduces the risk of cardiovascular disease in relation to high temperatures should be developed.

Growth patterns in preterm infants born appropriate for gestational age

Aim: This study aimed to document the growth patterns of a contemporary cohort of preterm infants born appropriate for gestational age (AGA). It was hypothesised that preterm AGA (PT-AGA) infants would display poorer growth than full-term AGA (FT-AGA) infants. Methods: Sixty-four PT-AGA infants and 64 FT-AGA infants were assessed at 0, 4, 8 and 12 months of corrected age (CA). Measurements of weight and length were recorded at each of the specified ages. Centers for Disease Control and Prevention growth data were used to calculate Z-scores for weight and length based on CA. Results: The mean length and weight Z-scores of PT-AGA infants were found to be significantly less than those of FT-AGA infants at term, 4, 8 and 12 months of CA (P < 0.001). The mean weight Z-score of PT-AGA infants was found to be less than their mean length Z-score at each time point, though the differences were not significant. Conclusions: The results of this study suggest that PT-AGA infants are likely to display poorer growth than FT-AGA infants until at least 1 year of CA. Long-term growth monitoring in this population is recommended. © 2008 The Authors.

Finite element analysis investigation of response of pumpkin tissue under uniaxial loading

Finite element analysis (FEA) models of uniaxial loading of pumpkin peel and flesh tissues were developed and validated using experimental results. The tensile model was developed for both linear elastic and plastic material models, the compression model was develop d only with the plastic material model. The outcomes of force versus time curves obtained from FEA models followed similar pattern to the experimental curves however the curve resulted with linear elastic material properties had a higher difference with the experimental curves. The values of predicted forces were determined and compared with the experimental curve. An error indicator was introduced and computed for each case and compared. Additionally Root Mean Square Error (RMSE) values were also calculated for each model and compared. The results of modelling were used to develop material model for peel and flesh tissues in FEA modelling of mechanical peeling of tough skinned vegetables.

Discovery of candidate serum proteomic and metabolomic biomarkers in ankylosing spondylitis

Ankylosing Spondylitis (AS) is a common inflammatory rheumatic disease with a predilection for the axial skeleton, affecting 0.2% of the population. Current diagnostic criteria rely on a composite of clinical and radiological changes, with a mean time to diagnosis of 5 to 10 years. In this study we employed nano liquid-chromatography mass spectrometry analysis to detect and quantify proteins and small compounds including endogenous peptides and metabolites in serum from 18 AS patients and nine healthy individuals. We identified a total of 316 proteins in serum, of which 22 showed significant up- or down-regulation (p < 0.05) in AS patients. Receiver operating characteristic analysis of combined levels of serum amyloid P component and inter-α-trypsin inhibitor heavy chain 1 revealed high diagnostic value for Ankylosing Spondylitis (area under the curve = 0.98). We also depleted individual sera of proteins to analyze endogenous peptides and metabolic compounds. We detected more than 7000 molecular features in patients and healthy individuals. Quantitative MS analysis revealed compound profiles that correlate with the clinical assessment of disease activity. One molecular feature identified as a Vitamin D3 metabolite-(23S,25R)-25-hydroxyvitamin D3 26,23-peroxylactone-was down-regulated in AS. The ratio of this vitamin D metabolite versus vitamin D binding protein serum levels was also altered in AS as compared with controls. These changes may contribute to pathological skeletal changes in AS. Our study is the first example of an integration of proteomic and metabolomic techniques to find new biomarker candidates for the diagnosis of Ankylosing Spondylitis

Probabilistic seismic hazard analysis for Bangalore

This article presents the results of probabilistic seismic hazard analysis (PSHA) for Bangalore, South India. Analyses have been carried out considering the seismotectonic parameters of the region covering a radius of 350 km keeping Bangalore as the center. Seismic hazard parameter `b' has been evaluated considering the available earthquake data using (1) Gutenberg-Richter (G-R) relationship and (2) Kijko and Sellevoll (1989, 1992) method utilizing extreme and complete catalogs. The `b' parameter was estimated to be 0.62 to 0.98 from G-R relation and 0.87 +/- A 0.03 from Kijko and Sellevoll method. The results obtained are a little higher than the `b' values published earlier for southern India. Further, probabilistic seismic hazard analysis for Bangalore region has been carried out considering six seismogenic sources. From the analysis, mean annual rate of exceedance and cumulative probability hazard curve for peak ground acceleration (PGA) and spectral acceleration (Sa) have been generated. The quantified hazard values in terms of the rock level peak ground acceleration (PGA) are mapped for 10% probability of exceedance in 50 years on a grid size of 0.5 km x 0.5 km. In addition, Uniform Hazard Response Spectrum (UHRS) at rock level is also developed for the 5% damping corresponding to 10% probability of exceedance in 50 years. The peak ground acceleration (PGA) value of 0.121 g obtained from the present investigation is slightly lower (but comparable) than the PGA values obtained from the deterministic seismic hazard analysis (DSHA) for the same area. However, the PGA value obtained in the current investigation is higher than PGA values reported in the global seismic hazard assessment program (GSHAP) maps of Bhatia et al. (1999) for the shield area.

High-Pressure Kinetics of Vinyl Polyperoxides

This is the first report on studies carried out in detail on high-pressure oxygen copolymerization (> 50 psi) of the vinyl monomers styrene and alpha-methylstyrene (AMS). The saturation pressure of oxygen for AMS oxidation, hitherto obscure, is found to be 300 psi. Whereas the ease of oxidation is more favorable for styrene, the rate and yield of polyperoxide formation are higher for AMS. This is explained on the basis of the reactivity of the corresponding alkyl and peroxy radicals. Below 50 degrees C, degradation of the poly(styrene peroxide) formed is about 2.5 times less than that observed above 50 degrees C, so much so that it gives a break in the rate curve, and thereafter the rate is lowered. Normal free radical kinetics is followed before the break point, after which the monomer and initiator exponents become unusually high. This is interpreted on the basis of chain transfer to the degradation products. The low molecular weight of polyperoxides has been attributed to the (i) low reactivity of RO(2)(.) toward the monomer, (ii) chain transfer to degradation products, (iii) facile cleavage of O-O bond, followed by unzipping to nonradical products, and (iv) higher stability of the reinitiating radicals. At lower temperatures, (i) predominates, whereas at higher temperatures, chiefly (ii)-(iv) are the case.