Selection of optimal reference genes for normalization in quantitative RT-PCR

Background  

Normalization in real-time qRT-PCR is necessary to compensate for experimental variation. A popular normalization strategy employs reference gene(s), which may introduce additional variability into normalized expression levels due to innate variation (between tissues, individuals, etc). To minimize this innate variability, multiple reference genes are used. Current methods of selecting reference genes make an assumption of independence in their innate variation. This assumption is not always justified, which may lead to selecting a suboptimal set of reference genes.     

Identifying diabetic patients with cardiac autonomic neuropathy by heart rate complexity analysis

Background  

Cardiac autonomic neuropathy (CAN) in diabetes has been called a "silent killer", because so few patients realize that they suffer from it, and yet its effect can be lethal. Early sub clinical detection of CAN and intervention are of prime importance for risk stratification in preventing sudden death due to silent myocardial infarction. This study presents the usefulness of heart rate variability (HRV) and complexity analyses from short term ECG recordings as a screening tool for CAN.     

Life cycle assessment of Australian sugarcane production with a focus on sugarcane growing

Purpose  

Past life cycle assessments (LCA) of sugarcane (Saccharum officinarum) production have commonly been based on limited datasets, and variability has not been well described. In this work, Australian sugarcane production was assessed more comprehensively in order to generate a robust set of LCA results for use in subsequent assessments of sugarcane products and also to investigate: (1) variability due to regional differences, (2) factors influencing variability, and (3) significance of the impacts.     

A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips

Background  

In gene expression studies a key role is played by the so called "pre-processing", a series of steps designed to extract the signal and account for the sources of variability due to the technology used rather than to biological differences between the RNA samples. At the moment there is no commonly agreed gold standard pre-processing method and each researcher has the responsibility to choose one method, incurring the risk of false positive and false negative features arising from the particular method chosen.     

Geographic variability of agriculture requires sector-specific uncertainty characterization

Purpose

Regionalization in life cycle assessment (LCA) has focused on spatially differentiated environmental variables for regional impact assessment models. Relatively less attention has been paid to spatial disparities in intermediate flows for life cycle inventory (LCI).

Methods

First, we compiled state-specific LCIs for four major crops in the USA and evaluated their geographic variability in the characterized results due to the differences in intermediate inputs. Second, we evaluated the consequence of choosing average or region-specific LCIs in understanding the life cycle environmental implications of land use change from cotton to corn or soybean. Finally, we analyzed the implications of our findings in characterizing the uncertainties associated with geographic variability under the conventional pedigree approach.

Results and discussion

Our results show that spatial disparities in LCI alone lead to two to fourfold differences in characterized results for most impact categories. The differences, however, increase to over an order of magnitude for freshwater ecotoxicity and human health non-cancer. Among the crops analyzed, winter wheat shows higher variability partly due to a larger difference in yield. As a result, the use of national average data derived from top corn and soybean producing states significantly underestimates the characterized impacts of corn and soybean in the states where land conversion from cotton to corn or soybean actually took place. The results also show that the conventional pedigree approach to uncertainty characterization in LCA substantially underestimates uncertainties arising from geographic variability of agriculture. Compared to the highest geometric standard deviation (GSD) value of 1.11 under the pedigree approach, the GSDs that we derived are as high as 7.1, with the median around 1.9.

Conclusions

The results highlight the importance of building regional life cycle inventory for understanding the environmental impacts of crops at the regional level. The high geographic variability of crops also indicates the need for sector-specific approaches to uncertainty characterization. Our results also suggest that the uncertainty values in the existing LCI databases might have been signficantly underestimated especially for those products with high geographic variability, demanding a cautious interpretation of the results derived from them. 

     

Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences

Background  

The secondary structure of an RNA must be known before the relationship between its structure and function can be determined. One way to predict the secondary structure of an RNA is to identify covarying residues that maintain the pairings (Watson-Crick, Wobble and non-canonical pairings). This "comparative approach" consists of identifying mutations from homologous sequence alignments. The sequences must covary enough for compensatory mutations to be revealed, but comparison is difficult if they are too different. Thus the choice of homologous sequences is critical. While many possible combinations of homologous sequences may be used for prediction, only a few will give good structure predictions. This can be due to poor quality alignment in stems or to the variability of certain sequences. This problem of sequence selection is currently unsolved.     

Sparse estimation for structural variability

Background  

Proteins are dynamic molecules that exhibit a wide range of motions; often these conformational changes are important for protein function. Determining biologically relevant conformational changes, or true variability, efficiently is challenging due to the noise present in structure data.     

Inducible indoleamine 2,3-dioxygenase 1 and programmed death ligand 1 expression as the potency marker for mesenchymal stromal cells

Aim

Establishment of a potency assay in the manufacturing of clinical-grade mesenchymal stromal cells (MSCs) has been a challenge due to issues of relevance to function, timeline and variability of responder cells. In this study, we attempted to develop a potency assay for MSCs.

Intralimb Coordination Patterns in Absent,Mild, and Severe Stages of Diabetic Neuropathy: Looking Beyond Kinematic Analysis of Gait Cycle

Aim

Diabetes Mellitus progressively leads to impairments in stability and joint motion and might affect coordination patterns, mainly due to neuropathy. This study aims to describe changes in intralimb joint coordination in healthy individuals and patients with absent, mild and, severe stages of neuropathy.

Methods

Forty-seven diabetic patients were classified into three groups of neuropathic severity by a fuzzy model: 18 without neuropathy (DIAB), 7 with mild neuropathy (MILD), and 22 with moderate to severe neuropathy (SVRE). Thirteen healthy subjects were included as controls (CTRL). Continuous relative phase (CRP) was calculated at each instant of the gait cycle for each pair of lower limb joints. Analysis of Variance compared each frame of the CRP time series and its standard deviation among groups (α = 5%).

Results

For the ankle-hip CRP, the SVRE group presented increased variability at the propulsion phase and a distinct pattern at the propulsion and initial swing phases compared to the DIAB and CTRL groups. For the ankle-knee CRP, the 3 diabetic groups presented more anti-phase ratios than the CTRL group at the midstance, propulsion, and terminal swing phases, with decreased variability at the early stance phase. For the knee-hip CRP, the MILD group showed more in-phase ratio at the early stance and terminal swing phases and lower variability compared to all other groups. All diabetic groups were more in-phase at early the midstance phase (with lower variability) than the control group.

Conclusion

The low variability and coordination differences of the MILD group showed that gait coordination might be altered not only when frank evidence of neuropathy is present, but also when neuropathy is still incipient. The ankle-knee CRP at the initial swing phase showed distinct patterns for groups from all degrees of neuropathic severity and CTRLs. The ankle-hip CRP pattern distinguished the SVRE patients from other diabetic groups, particularly in the transitional phase from stance to swing.     

A methodology for separating uncertainty and variability in the life cycle greenhouse gas emissions of coal-fueled power generation in the USA

Purpose

Results of life cycle assessments (LCAs) of power generation technologies are increasingly reported in terms of typical values and possible ranges. Extents of these ranges result from both variability and uncertainty. Uncertainty may be reduced via additional research. However, variability is a characteristic of supply chains as they exist; as such, it cannot be reduced without modifying existing systems. The goal of this study is to separately quantify uncertainty and variability in LCA.

Methods

In this paper, we present a novel method for differentiating uncertainty from variability in life cycle assessments of coal-fueled power generation, with a specific focus on greenhouse gas emissions. Individual coal supply chains were analyzed for 364 US coal power plants. Uncertainty in CO₂ and CH₄ emissions throughout these supply chains was quantified via Monte Carlo simulation. The method may be used to identify key factors that drive the range of life cycle emissions as well as the limits of precision of an LCA.

Results and discussion

Using this method, we statistically characterized the carbon footprint of coal power in the USA in 2009. Our method reveals that the average carbon footprint of coal power (100 year time horizon) ranges from 0.97 to 1.69 kg CO₂eq/kWh of generated electricity (95 % confidence interval), primarily due to variability in plant efficiency. Uncertainty in the carbon footprints of individual plants spans a factor of 1.04 for the least uncertain plant footprint to a factor of 1.2 for the most uncertain plant footprint (95 % uncertainty intervals). The uncertainty in the total carbon footprint of all US coal power plants spans a factor of 1.05.

Conclusions

We have developed and successfully implemented a framework for separating uncertainty and variability in the carbon footprint of coal-fired power plants. Reduction of uncertainty will not substantially reduce the range of predicted emissions. The range can only be reduced via substantial changes to the US coal power infrastructure. The finding that variability is larger than uncertainty can obviously not be generalized to other product systems and impact categories. Our framework can, however, be used to assess the relative influence of uncertainty and variability for a whole range of product systems and environmental impacts.     

Intraindividual Variability in Inhibitory Function in Adults with ADHD – An Ex-Gaussian Approach

Objective

Attention deficit disorder (ADHD) is commonly associated with inhibitory dysfunction contributing to typical behavioral symptoms like impulsivity or hyperactivity. However, some studies analyzing intraindividual variability (IIV) of reaction times in children with ADHD (cADHD) question a predominance of inhibitory deficits. IIV is a measure of the stability of information processing and provides evidence that longer reaction times (RT) in inhibitory tasks in cADHD are due to only a few prolonged responses which may indicate deficits in sustained attention rather than inhibitory dysfunction. We wanted to find out, whether a slowing in inhibitory functioning in adults with ADHD (aADHD) is due to isolated slow responses.

Methods

Computing classical RT measures (mean RT, SD), ex-Gaussian parameters of IIV (which allow a better separation of reaction time (mu), variability (sigma) and abnormally slow responses (tau) than classical measures) as well as errors of omission and commission, we examined response inhibition in a well-established GoNogo task in a sample of aADHD subjects without medication and healthy controls matched for age, gender and education.

Results

We did not find higher numbers of commission errors in aADHD, while the number of omissions was significantly increased compared with controls. In contrast to increased mean RT, the distributional parameter mu did not document a significant slowing in aADHD. However, subjects with aADHD were characterized by increased IIV throughout the entire RT distribution as indicated by the parameters sigma and tau as well as the SD of reaction time. Moreover, we found a significant correlation between tau and the number of omission errors.

Conclusions

Our findings question a primacy of inhibitory deficits in aADHD and provide evidence for attentional dysfunction. The present findings may have theoretical implications for etiological models of ADHD as well as more practical implications for neuropsychological testing in aADHD.     

Estimating the global warming emissions of the LCAXVII conference: connecting flights matter

Purpose

Conferences are an important element of scientific activity but can also be a major cause of environmental burden. With this in mind, we analysed the global warming emissions of the 2017 annual conference of the American Center for Life Cycle Assessment (ACLCA), in order to estimate the carbon footprint and identify potential ways to reduce it.

Methods

We used survey data from participants as well as literature sources to complete an attributional assessment of the greenhouse gas emissions per participant. A method to calculate the ‘ideal’ location is proposed, which can be used to identify ‘unreasonably’ distant conference locations.

Results and discussion

The average emissions per participant were found to be 952 kg CO_2eq, but with a large variability due to differences in travelled distance. Connecting flights were found to increase emissions up to 32% compared to direct flights, due to the increased number of take-offs and landings.

Conclusions

Results indicate that future studies should use distance-dependent flight emissions to increase the accuracy of the assessment. Some measures, such as meat-free menus, had a relatively minor contribution to emission reductions, but could be important as scientists advocating for the reduction of environmental burden should lead by example.

     

Development of a Screening Tool for Sleep Disordered Breathing in Children Using the Phone Oximeter?

Background

Sleep disordered breathing (SDB) can lead to daytime sleepiness, growth failure and developmental delay in children. Polysomnography (PSG), the gold standard to diagnose SDB, is a highly resource-intensive test, confined to the sleep laboratory.

Aim

To combine the blood oxygen saturation (SpO₂) characterization and cardiac modulation, quantified by pulse rate variability (PRV), to identify children with SDB using the Phone Oximeter, a device integrating a pulse oximeter with a smartphone.

Methods

Following ethics approval and informed consent, 160 children referred to British Columbia Children''s Hospital for overnight PSG were recruited. A second pulse oximeter sensor applied to the finger adjacent to the one used for standard PSG was attached to the Phone Oximeter to record overnight pulse oximetry (SpO₂ and photoplethysmogram (PPG)) alongside the PSG.

Results

We studied 146 children through the analysis of the SpO₂ pattern, and PRV as an estimate of heart rate variability calculated from the PPG. SpO₂ variability and SpO₂ spectral power at low frequency, was significantly higher in children with SDB due to the modulation provoked by airway obstruction during sleep (p-value ). PRV analysis reflected a significant augmentation of sympathetic activity provoked by intermittent hypoxia in SDB children. A linear classifier was trained with the most discriminating features to identify children with SDB. The classifier was validated with internal and external cross-validation, providing a high negative predictive value (92.6%) and a good balance between sensitivity (88.4%) and specificity (83.6%). Combining SpO₂ and PRV analysis improved the classification performance, providing an area under the receiver operating characteristic curve of 88%, beyond the 82% achieved using SpO₂ analysis alone.

Conclusions

These results demonstrate that the implementation of this algorithm in the Phone Oximeter will provide an improved portable, at-home screening tool, with the capability of monitoring patients over multiple nights.     

New Insights into Measurement Variability in Glaucomatous Visual Fields from Computer Modelling

Objective

To develop a model to simulate visual fields (VFs) in glaucoma patients, and to characterize variability of the Mean Deviation (MD) VF summary measurement using real VFs and simulations.

Methods

Pointwise VF variability was previously approximated using longitudinal VF data (24–2 SITA Standard, Humphrey Field Analyzer) from 2,736 patients; these data were used to build a non-parametric model to simulate VFs. One million VF simulations were generated from 1,000 VFs (1,000 simulations per ‘ground-truth’ VF), and the variability of simulated MDs was characterized as a function of ground-truth MD and Pattern Standard Deviation (PSD).

Results

The median (interquartile range, IQR) patient age and MD was 66 (56 to 75) years and −3.5 (−8.3 to −1.1) decibels, respectively. The inferred variability as a function of ground-truth MD and PSD indicated that variability, on average, increased rapidly as glaucoma worsened. However, the pattern of VF damage significantly affects the level of MD variability, with more than three-fold differences between patients with approximately the same levels of MD but different patterns of loss.

Conclusions

A novel approach for simulating VFs is introduced. A better understanding of VF variability will help clinicians to differentiate real VF progression from measurement variability. This study highlights that, overall, MD variability increases as the level of damage increases, but variability is highly dependent on the pattern of VF damage. Future research, using VF simulations, could be employed to provide benchmarks for measuring the performance of VF progression detection algorithms and developing new strategies for measuring VF progression.     

The relationship of creatine kinase variability with body composition and muscle damage markers following eccentric muscle contractions

[Purpose]

The purpose of the study was to investigate the relationship between CK variability and body composition and muscle damage markers following eccentric exercise.

[Methods]

Total 119 healthy male subjects were recruited to perform 50 eccentric contractions consisted of 2 sets of 25 contractions. Then, blood creatine kinase (CK) activity was analyzed to divide into three groups based on their CK activity levels. Maximum isometric strength (MIS), muscle soreness (SOR) and body composition data were obtained before and after exercise.

[Results]

The results showed that high CK responders had a significant decrease in MIS (p<0.001) and greater SOR (p<0.01) following eccentric exercise compared to low CK responders. Percent body fat was also higher in high responders compared to low responders (p=0.014). Peak CK activity was significantly correlated with MIS and SOR but no correlation with % body fat, muscle mass, and body mass index.

[Conclusion]

CK variability following eccentric exercise is closely related to MIS and SOR and % body fat may be a potent factor for CK variability.     

The Gait Disorder in Downbeat Nystagmus Syndrome

Background

Downbeat nystagmus (DBN) is a common form of acquired fixation nystagmus with key symptoms of oscillopsia and gait disturbance. Gait disturbance could be a result of impaired visual feedback due to the involuntary ocular oscillations. Alternatively, a malfunction of cerebellar locomotor control might be involved, since DBN is considered a vestibulocerebellar disorder.

Methods

Investigation of walking in 50 DBN patients (age 72±11 years, 23 females) and 50 healthy controls (HS) (age 70±11 years, 23 females) using a pressure sensitive carpet (GAITRite). The patient cohort comprised subjects with only ocular motor signs (DBN) and subjects with an additional limb ataxia (DBNCA). Gait investigation comprised different walking speeds and walking with eyes closed.

Results

In DBN, gait velocity was reduced (p<0.001) with a reduced stride length (p<0.001), increased base of support (p<0.050), and increased double support (p<0.001). Walking with eyes closed led to significant gait changes in both HS and DBN. These changes were more pronounced in DBN patients (p<0.001). Speed-dependency of gait variability revealed significant differences between the subgroups of DBN and DBNCA (p<0.050).

Conclusions

(I) Impaired visual control caused by involuntary ocular oscillations cannot sufficiently explain the gait disorder. (II) The gait of patients with DBN is impaired in a speed dependent manner. (III) Analysis of gait variability allows distinguishing DBN from DBNCA: Patients with pure DBN show a speed dependency of gait variability similar to that of patients with afferent vestibular deficits. In DBNCA, gait variability resembles the pattern found in cerebellar ataxia.     

Variability in adherence to clinical practice guidelines and recommendations in COPD outpatients: a multi-level,cross-sectional analysis of the EPOCONSUL study

Background

Clinical audits have reported considerable variability in COPD medical care and frequent inconsistencies with recommendations. The objectives of this study were to identify factors associated with a better adherence to clinical practice guidelines and to explore determinants of this variability at the the hospital level.

Methods

EPOCONSUL is a Spanish nationwide clinical audit that evaluates the outpatient management of COPD. Multilevel logistic regression with two levels was performed to assess the relationships between individual and disease-related factors, as well as hospital characteristics.

Results

A total of 4508 clinical records of COPD patients from 59 Spanish hospitals were evaluated. High variability was observed among hospitals in terms of medical care. Some of the patient’s characteristics (airflow obstruction, degree of dyspnea, exacerbation risk, presence of comorbidities), the hospital factors (size and respiratory nurses available) and treatment at a specialized COPD outpatient clinic were identified as factors associated with a better adherence to recommendations, although this only explains a small proportion of the total variance.

Conclusion

To be treated at a specialized COPD outpatient clinic and some intrinsic patient characteristics were factors associated with a better adherence to guideline recommendations, although these variables were only explaining part of the high variability observed among hospitals in terms of COPD medical care.

     

“How Much Will I Get Charged for This?” Patient Charges for Top Ten Diagnoses in the Emergency Department

Objectives

We examined the charges, their variability, and respective payer group for diagnosis and treatment of the ten most common outpatient conditions presenting to the Emergency department (ED).

Methods

We conducted a cross-sectional study of the 2006–2008 Medical Expenditure Panel Survey. Analysis was limited to outpatient visits with non-elderly, adult (years 18–64) patients with a single discharge diagnosis.

Results

We studied 8,303 ED encounters, representing 76.6 million visits. Median charges ranged from $740 (95% CI $651–$817) for an upper respiratory infection to $3437 (95% CI $2917–$3877) for a kidney stone. The median charge for all ten outpatient conditions in the ED was $1233 (95% CI $1199– $1268), with a high degree of charge variability. All diagnoses had an interquartile range (IQR) greater than $800 with 60% of IQRs greater than $1550.

Conclusion

Emergency department charges for common conditions are expensive with high charge variability. Greater acute care charge transparency will at least allow patients and providers to be aware of the emergency department charges patients may face in the current health care system.