Comparison of three methods for driven pile capacity

A significant cost for foundations is the design and installation of piles when they are required due to poor ground conditions. Not only is it important that piles be designed properly, but also that the installation equipment and total cost be evaluated. To assist in the evaluation of piles a number of methods have been developed. In this research three of these methods were investigated, which were developed by the Federal Highway Administration, the US Corps of Engineers and the American Petroleum Institute (API). The results from these methods were entered into the program GRLWEAPTM to assess the pile drivability and to provide a standard base for comparing the three methods. An additional element of this research was to develop EXCEL spreadsheets to implement these three methods. Currently the Army Corps and API methods do not have publicly available software and must be performed manually, which requires that data is taken off of figures and tables, which can introduce error in the prediction of pile capacities. Following development of the EXCEL spreadsheet, they were validated with both manual calculations and existing data sets to ensure that the data output is correct. To evaluate the three pile capacity methods data was utilized from four project sites from North America. The data included site geotechnical data along with field determined pile capacities. In order to achieve a standard comparison of the data, the pile capacities and geotechnical data from the three methods were entered into GRLWEAPTM. The sites consisted of both cohesive and cohesionless soils; where one site was primarily cohesive, one was primarily cohesionless, and the other two consisted of inter-bedded cohesive and cohesionless soils. Based on this limited set of data the results indicated that the US Corps of Engineers method more closely compared with the field test data, followed by the API method to a lesser degree. The DRIVEN program compared favorably in cohesive soils, but over predicted in cohesionless material.

Age modeling of young non-varved lake sediments: methods and limits. Examples from two lakes in Central Chile

High-resolution and highly precise age models for recent lake sediments (last 100–150 years) are essential for quantitative paleoclimate research. These are particularly important for sedimentological and geochemical proxies, where transfer functions cannot be established and calibration must be based upon the relation of sedimentary records to instrumental data. High-precision dating for the calibration period is most critical as it determines directly the quality of the calibration statistics. Here, as an example, we compare radionuclide age models obtained on two high-elevation glacial lakes in the Central Chilean Andes (Laguna Negra: 33°38′S/70°08′W, 2,680 m a.s.l. and Laguna El Ocho: 34°02′S/70°19′W, 3,250 m a.s.l.). We show the different numerical models that produce accurate age-depth chronologies based on 210Pb profiles, and we explain how to obtain reduced age-error bars at the bottom part of the profiles, i.e., typically around the end of the 19th century. In order to constrain the age models, we propose a method with five steps: (i) sampling at irregularly-spaced intervals for 226Ra, 210Pb and 137Cs depending on the stratigraphy and microfacies, (ii) a systematic comparison of numerical models for the calculation of 210Pb-based age models: constant flux constant sedimentation (CFCS), constant initial concentration (CIC), constant rate of supply (CRS) and sediment isotope tomography (SIT), (iii) numerical constraining of the CRS and SIT models with the 137Cs chronomarker of AD 1964 and, (iv) step-wise cross-validation with independent diagnostic environmental stratigraphic markers of known age (e.g., volcanic ash layer, historical flood and earthquakes). In both examples, we also use airborne pollutants such as spheroidal carbonaceous particles (reflecting the history of fossil fuel emissions), excess atmospheric Cu deposition (reflecting the production history of a large local Cu mine), and turbidites related to historical earthquakes. Our results show that the SIT model constrained with the 137Cs AD 1964 peak performs best over the entire chronological profile (last 100–150 years) and yields the smallest standard deviations for the sediment ages. Such precision is critical for the calibration statistics, and ultimately, for the quality of the quantitative paleoclimate reconstruction. The systematic comparison of CRS and SIT models also helps to validate the robustness of the chronologies in different sections of the profile. Although surprisingly poorly known and under-explored in paleolimnological research, the SIT model has a great potential in paleoclimatological reconstructions based on lake sediments

Implementation status of error disclosure standards reported by Swiss hospitals

QUESTION UNDER STUDY To establish at what stage Swiss hospitals are in implementing an internal standard concerning communication with patients and families after an error that resulted in harm. METHODS Hospitals were identified via the Swiss Hospital Association's website. An anonymous questionnaire was sent during September and October 2011 to 379 hospitals in German, French or Italian. Hospitals were asked to specify their hospital type and the implementation status of an internal hospital standard that decrees that patients or their relatives are to be promptly informed about medical errors that result in harm. RESULTS Responses from a total of 205 hospitals were received, a response rate of 54%. Most responding hospitals (62%) had an error disclosure standard or planned to implement one within 12 months. The majority of responding university and acute care (75%) hospitals had introduced a disclosure standard or were planning to do so. In contrast, the majority of responding psychiatric, rehabilitation and specialty (53%) clinics had not introduced a standard. CONCLUSION It appears that Swiss hospitals are in a promising state in providing institutional support for practitioners disclosing medical errors to patients. This has been shown internationally to be one important factor in encouraging the disclosure of medical errors. However, many hospitals, in particular psychiatric, rehabilitation and specialty clinics, have not implemented an error disclosure policy. Further research is needed to explore the underlying reasons.

Multiscale methods for shape constraints in deconvolution: Confidence statements for qualitative features

We derive multiscale statistics for deconvolution in order to detect qualitative features of the unknown density. An important example covered within this framework is to test for local monotonicity on all scales simultaneously. We investigate the moderately ill-posed setting, where the Fourier transform of the error density in the deconvolution model is of polynomial decay. For multiscale testing, we consider a calibration, motivated by the modulus of continuity of Brownian motion. We investigate the performance of our results from both the theoretical and simulation based point of view. A major consequence of our work is that the detection of qualitative features of a density in a deconvolution problem is a doable task, although the minimax rates for pointwise estimation are very slow.

Evaluating statistical methods used to estimate the number of postsynaptic receptors.

Calcium levels in spines play a significant role in determining the sign and magnitude of synaptic plasticity. The magnitude of calcium influx into spines is highly dependent on influx through N-methyl D-aspartate (NMDA) receptors, and therefore depends on the number of postsynaptic NMDA receptors in each spine. We have calculated previously how the number of postsynaptic NMDA receptors determines the mean and variance of calcium transients in the postsynaptic density, and how this alters the shape of plasticity curves. However, the number of postsynaptic NMDA receptors in the postsynaptic density is not well known. Anatomical methods for estimating the number of NMDA receptors produce estimates that are very different than those produced by physiological techniques. The physiological techniques are based on the statistics of synaptic transmission and it is difficult to experimentally estimate their precision. In this paper we use stochastic simulations in order to test the validity of a physiological estimation technique based on failure analysis. We find that the method is likely to underestimate the number of postsynaptic NMDA receptors, explain the source of the error, and re-derive a more precise estimation technique. We also show that the original failure analysis as well as our improved formulas are not robust to small estimation errors in key parameters.

Cost and power analysis of linkage disequilibrium methods for locating genes influencing quantitative traits in humans

Linkage disequilibrium methods can be used to find genes influencing quantitative trait variation in humans. Linkage disequilibrium methods can require smaller sample sizes than linkage equilibrium methods, such as the variance component approach to find loci with a specific effect size. The increase in power is at the expense of requiring more markers to be typed to scan the entire genome. This thesis compares different linkage disequilibrium methods to determine which factors influence the power to detect disequilibrium. The costs of disequilibrium and equilibrium tests were compared to determine whether the savings in phenotyping costs when using disequilibrium methods outweigh the additional genotyping costs.^ Nine linkage disequilibrium tests were examined by simulation. Five tests involve selecting isolated unrelated individuals while four involved the selection of parent child trios (TDT). All nine tests were found to be able to identify disequilibrium with the correct significance level in Hardy-Weinberg populations. Increasing linked genetic variance and trait allele frequency were found to increase the power to detect disequilibrium, while increasing the number of generations and distance between marker and trait loci decreased the power to detect disequilibrium. Discordant sampling was used for several of the tests. It was found that the more stringent the sampling, the greater the power to detect disequilibrium in a sample of given size. The power to detect disequilibrium was not affected by the presence of polygenic effects.^ When the trait locus had more than two trait alleles, the power of the tests maximized to less than one. For the simulation methods used here, when there were more than two-trait alleles there was a probability equal to 1-heterozygosity of the marker locus that both trait alleles were in disequilibrium with the same marker allele, resulting in the marker being uninformative for disequilibrium.^ The five tests using isolated unrelated individuals were found to have excess error rates when there was disequilibrium due to population admixture. Increased error rates also resulted from increased unlinked major gene effects, discordant trait allele frequency, and increased disequilibrium. Polygenic effects did not affect the error rates. The TDT, Transmission Disequilibrium Test, based tests were not liable to any increase in error rates.^ For all sample ascertainment costs, for recent mutations ($<$100 generations) linkage disequilibrium tests were less expensive than the variance component test to carry out. Candidate gene scans saved even more money. The use of recently admixed populations also decreased the cost of performing a linkage disequilibrium test. ^

High Incorrect Use of the Standard Error of the Mean (SEM) in Original Articles in Three Cardiovascular Journals Evaluated for 2012.

RATIONALE In biomedical journals authors sometimes use the standard error of the mean (SEM) for data description, which has been called inappropriate or incorrect. OBJECTIVE To assess the frequency of incorrect use of SEM in articles in three selected cardiovascular journals. METHODS AND RESULTS All original journal articles published in 2012 in Cardiovascular Research, Circulation: Heart Failure and Circulation Research were assessed by two assessors for inappropriate use of SEM when providing descriptive information of empirical data. We also assessed whether the authors state in the methods section that the SEM will be used for data description. Of 441 articles included in this survey, 64% (282 articles) contained at least one instance of incorrect use of the SEM, with two journals having a prevalence above 70% and "Circulation: Heart Failure" having the lowest value (27%). In 81% of articles with incorrect use of SEM, the authors had explicitly stated that they use the SEM for data description and in 89% SEM bars were also used instead of 95% confidence intervals. Basic science studies had a 7.4-fold higher level of inappropriate SEM use (74%) than clinical studies (10%). LIMITATIONS The selection of the three cardiovascular journals was based on a subjective initial impression of observing inappropriate SEM use. The observed results are not representative for all cardiovascular journals. CONCLUSION In three selected cardiovascular journals we found a high level of inappropriate SEM use and explicit methods statements to use it for data description, especially in basic science studies. To improve on this situation, these and other journals should provide clear instructions to authors on how to report descriptive information of empirical data.

Fully Adaptive Newton--Galerkin Methods for Semilinear Elliptic Partial Differential Equations

In this paper we develop an adaptive procedure for the numerical solution of general, semilinear elliptic problems with possible singular perturbations. Our approach combines both prediction-type adaptive Newton methods and a linear adaptive finite element discretization (based on a robust a posteriori error analysis), thereby leading to a fully adaptive Newton–Galerkin scheme. Numerical experiments underline the robustness and reliability of the proposed approach for various examples

Second, do less harm: The state of states' medical error reporting programs

Statement of the problem and public health significance. Hospitals were designed to be a safe haven and respite from disease and illness. However, a large body of evidence points to preventable errors in hospitals as the eighth leading cause of death among Americans. Twelve percent of Americans, or over 33.8 million people, are hospitalized each year. This population represents a significant portion of at risk citizens exposed to hospital medical errors. Since the number of annual deaths due to hospital medical errors is estimated to exceed 44,000, the magnitude of this tragedy makes it a significant public health problem. ^ Specific aims. The specific aims of this study were threefold. First, this study aimed to analyze the state of the states' mandatory hospital medical error reporting six years after the release of the influential IOM report, "To Err is Human." The second aim was to identify barriers to reporting of medical errors by hospital personnel. The third aim was to identify hospital safety measures implemented to reduce medical errors and enhance patient safety. ^ Methods. A descriptive, longitudinal, retrospective design was used to address the first stated objective. The study data came from the twenty-one states with mandatory hospital reporting programs which report aggregate hospital error data that is accessible to the public by way of states' websites. The data analysis included calculations of expected number of medical errors for each state according to IOM rates. Where possible, a comparison was made between state reported data and the calculated IOM expected number of errors. A literature review was performed to achieve the second study aim, identifying barriers to reporting medical errors. The final aim was accomplished by telephone interviews of principal patient safety/quality officers from five Texas hospitals with more than 700 beds. ^ Results. The state medical error data suggests vast underreporting of hospital medical errors to the states. The telephone interviews suggest that hospitals are working at reducing medical errors and creating safer environments for patients. The literature review suggests the underreporting of medical errors at the state level stems from underreporting of errors at the delivery level. ^

Comparison of multiple comparison methods for identifying differential gene expression in simulated and real papillary thyroid cancer microarray data

The difficulty of detecting differential gene expression in microarray data has existed for many years. Several correction procedures try to avoid the family-wise error rate in multiple comparison process, including the Bonferroni and Sidak single-step p-value adjustments, Holm's step-down correction method, and Benjamini and Hochberg's false discovery rate (FDR) correction procedure. Each multiple comparison technique has its advantages and weaknesses. We studied each multiple comparison method through numerical studies (simulations) and applied the methods to the real exploratory DNA microarray data, which detect of molecular signatures in papillary thyroid cancer (PTC) patients. According to our results of simulation studies, Benjamini and Hochberg step-up FDR controlling procedure is the best process among these multiple comparison methods and we discovered 1277 potential biomarkers among 54675 probe sets after applying the Benjamini and Hochberg's method to PTC microarray data.^

Nursing-related medication errors: A review of factors that facilitate and hinder error reporting, and recommendations for improvement

Medication errors, one of the most frequent types of medical errors, are a common cause of patient harm in hospital systems today. Nurses at the bedside are in a position to encounter many of these errors since they are there at the start of the process (ordering/prescribing) and the end of the process (administration). One of the recommendations from the IOM (Institute of Medicine) report, "To Err is Human," was for organizations to identify and learn from medical errors through event reporting systems. While many organizations have reporting systems in place, research studies report a significant amount of underreporting by nurses. A systematic review of the literature was performed to identify contributing factors related to the reporting and not reporting of medication errors by nurses at the bedside.^ Articles included in the literature review were primary or secondary studies, dated January 1, 2000 – July 2009, related to nursing medication error reporting. All 634 articles were reviewed with an algorithm developed to standardize the review process and help filter out those that did not meet the study criteria. In addition, 142 article bibliographies were reviewed to find additional studies that were not found in the original literature search.^ After reviewing the 634 articles and the additional 108 articles discovered in the bibliography review, 41 articles met the study criteria and were used in the systematic literature review results.^ Fear of punitive reactions to medication errors was a frequent barrier to error reporting. Nurses fear reactions from their leadership, peers, patients and their families, nursing boards, and the media. Anonymous reporting systems and departments/organizations with a strong safety culture in place helped to encourage the reporting of medication errors by nursing staff.^ Many of the studies included in this literature review do not allow results that can be generalized. The majority of them took place in single institutions/organizations with limited sample sizes. Stronger studies with larger sample sizes need to be performed, utilizing data collection methods that have been validated, to determine stronger correlations between safety cultures and nurse error reporting.^

Evaluation of risk factors for long term changes in refractive error among adult patients at a Dallas Texas private setting A retrospective chart-review study

Background. Over 39.9% of the adult population forty or older in the United States has refractive error, little is known about the etiology of this condition and associated risk factors and their entailed mechanism due to the paucity of data regarding the changes of refractive error for the adult population over time.^ Aim. To evaluate risk factors over a long term, 5-year period, in refractive error changes among persons 43 or older by testing the hypothesis that age, gender, systemic diseases, nuclear sclerosis and baseline refractive errors are all significantly associated with refractive errors changes in patients at a Dallas, Texas private optometric office.^ Methods. A retrospective chart review of subjective refraction, eye health, and self-report health history was done on patients at a private optometric office who were 43 or older in 2000 who had eye examinations both in 2000 and 2005. Aphakic and pseudophakic eyes were excluded as well as eyes with best corrected Snellen visual acuity of 20/40 and worse. After exclusions, refraction was obtained on 114 right eyes and 114 left eyes. Spherical equivalent (sum of sphere + ½ cylinder) was used as the measure of refractive error.^ Results. Similar changes in refractive error were observed for the two eyes. The 5-year change in spherical power was in a hyperopic direction for younger age groups and in a myopic direction for older subjects, P<0.0001. The gender-adjusted mean change in refractive error in right eyes of persons aged 43 to 54, 55 to 64, 65 to 74, and 75 or older at baseline was +0.43D, +0.46 D, -0.09 D, and -0.23D, respectively. Refractive change was strongly related to baseline nuclear cataract severity; grades 4 to 5 were associated with a myopic shift (-0.38 D, P< 0.0001). The mean age-adjusted change in refraction was +0.27 D for hyperopic eyes, +0.56 D for emmetropic eyes, and +0.26 D for myopic eyes.^ Conclusions. This report has documented refractive error changes in an older population and confirmed reported trends of a hyperopic shift before age 65 and a myopic shift thereafter associated with the development of nuclear cataract.^

DEVELOPMENT OF NOVEL METHODS TO MINIMIZE THE IMPACT OF SEQUENCING ERRORS IN THE NEXT-GENERATION SEQUENCING DATA ANALYSIS

Next-generation sequencing (NGS) technology has become a prominent tool in biological and biomedical research. However, NGS data analysis, such as de novo assembly, mapping and variants detection is far from maturity, and the high sequencing error-rate is one of the major problems. . To minimize the impact of sequencing errors, we developed a highly robust and efficient method, MTM, to correct the errors in NGS reads. We demonstrated the effectiveness of MTM on both single-cell data with highly non-uniform coverage and normal data with uniformly high coverage, reflecting that MTM’s performance does not rely on the coverage of the sequencing reads. MTM was also compared with Hammer and Quake, the best methods for correcting non-uniform and uniform data respectively. For non-uniform data, MTM outperformed both Hammer and Quake. For uniform data, MTM showed better performance than Quake and comparable results to Hammer. By making better error correction with MTM, the quality of downstream analysis, such as mapping and SNP detection, was improved. SNP calling is a major application of NGS technologies. However, the existence of sequencing errors complicates this process, especially for the low coverage (

New methods for quantification and analysis of quantitative real-time polymerase chain reaction data

Quantitative real-time polymerase chain reaction (qPCR) is a sensitive gene quantitation method that has been widely used in the biological and biomedical fields. The currently used methods for PCR data analysis, including the threshold cycle (CT) method, linear and non-linear model fitting methods, all require subtracting background fluorescence. However, the removal of background fluorescence is usually inaccurate, and therefore can distort results. Here, we propose a new method, the taking-difference linear regression method, to overcome this limitation. Briefly, for each two consecutive PCR cycles, we subtracted the fluorescence in the former cycle from that in the later cycle, transforming the n cycle raw data into n-1 cycle data. Then linear regression was applied to the natural logarithm of the transformed data. Finally, amplification efficiencies and the initial DNA molecular numbers were calculated for each PCR run. To evaluate this new method, we compared it in terms of accuracy and precision with the original linear regression method with three background corrections, being the mean of cycles 1-3, the mean of cycles 3-7, and the minimum. Three criteria, including threshold identification, max R2, and max slope, were employed to search for target data points. Considering that PCR data are time series data, we also applied linear mixed models. Collectively, when the threshold identification criterion was applied and when the linear mixed model was adopted, the taking-difference linear regression method was superior as it gave an accurate estimation of initial DNA amount and a reasonable estimation of PCR amplification efficiencies. When the criteria of max R2 and max slope were used, the original linear regression method gave an accurate estimation of initial DNA amount. Overall, the taking-difference linear regression method avoids the error in subtracting an unknown background and thus it is theoretically more accurate and reliable. This method is easy to perform and the taking-difference strategy can be extended to all current methods for qPCR data analysis.^

(Appendix 1-4) Geochemistry, desorption methods, TOC, TC, and mineral content of different settings

Sorption of volatile hydrocarbon gases (VHCs) to marine sediments is a recognized phenomenon that has been investigated in the context of petroleum exploration. However, little is known about the biogeochemistry of sorbed methane and higher VHCs in environments that are not influenced by thermogenic processes. This study evaluated two different extraction protocols for sorbed VHCs, used high pressure equipment to investigate the sorption of methane to pure clay mineral phases, and conducted a geochemical and mineralogical survey of sediment samples from different oceanographic settings and geochemical regimes that are not significantly influenced by thermogenic gas. Extraction of sediments under alkaline conditions yielded higher concentrations of sorbed methane than the established protocol for acidic extraction. Application of alkaline extraction in the environmental survey revealed the presence of substantial amounts of sorbed methane in 374 out of 411 samples (91%). Particularly high amounts, up to 2.1 mmol kg**-1 dry sediment, were recovered from methanogenic sediments. Carbon isotopic compositions of sorbed methane suggested substantial contributions from biogenic sources, both in sulfate-depleted and sulfate-reducing sediments. Carbon isotopic relationships between sorbed and dissolved methane indicate a coupling of the two pools. While our sorption experiments and extraction conditions point to an important role for clay minerals as sorbents, mineralogical analyses of marine sediments suggest that variations in mineral composition are not controlling variations in quantities of sorbed methane. We conclude that the distribution of sorbed methane in sediments is strongly influenced by in situ production.