Evaluating the Quality and Accuracy of TanDEM-X Digital Elevation Models at Archaeological Sites in the Cilician Plain, Turkey

Satellite remote sensing provides a powerful instrument for mapping and monitoring traces of historical settlements and infrastructure, not only in distant areas and crisis regions. It helps archaeologists to embed their findings from field surveys into the broader context of the landscape. With the start of the TanDEM-X mission, spatially explicit 3D-information is available to researchers at an unprecedented resolution worldwide. We examined different experimental TanDEM-X digital elevation models (DEM) that were processed from two different imaging modes (Stripmap/High Resolution Spotlight) using the operational alternating bistatic acquisition mode. The quality and accuracy of the experimental DEM products was compared to other available DEM products and a high precision archaeological field survey. The results indicate the potential of TanDEM-X Stripmap (SM) data for mapping surface elements at regional scale. For the alluvial plain of Cilicia, a suspected palaeochannel could be reconstructed. At the local scale, DEM products from TanDEM-X High Resolution Spotlight (HS) mode were processed at 2 m spatial resolution using a merge of two monostatic/bistatic interferograms. The absolute and relative vertical accuracy of the outcome meet the specification of high resolution elevation data (HRE) standards from the National System for Geospatial Intelligence (NSG) at the HRE20 level.

A novel universal DNA labeling and amplification system for rapid microarray-based detection of 117 antibiotic resistance genes in Gram-positive bacteria.

A rapid and simple DNA labeling system has been developed for disposable microarrays and has been validated for the detection of 117 antibiotic resistance genes abundant in Gram-positive bacteria. The DNA was fragmented and amplified using phi-29 polymerase and random primers with linkers. Labeling and further amplification were then performed by classic PCR amplification using biotinylated primers specific for the linkers. The microarray developed by Perreten et al. (Perreten, V., Vorlet-Fawer, L., Slickers, P., Ehricht, R., Kuhnert, P., Frey, J., 2005. Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria. J.Clin.Microbiol. 43, 2291-2302.) was improved by additional oligonucleotides. A total of 244 oligonucleotides (26 to 37 nucleotide length and with similar melting temperatures) were spotted on the microarray, including genes conferring resistance to clinically important antibiotic classes like β-lactams, macrolides, aminoglycosides, glycopeptides and tetracyclines. Each antibiotic resistance gene is represented by at least 2 oligonucleotides designed from consensus sequences of gene families. The specificity of the oligonucleotides and the quality of the amplification and labeling were verified by analysis of a collection of 65 strains belonging to 24 species. Association between genotype and phenotype was verified for 6 antibiotics using 77 Staphylococcus strains belonging to different species and revealed 95% test specificity and a 93% predictive value of a positive test. The DNA labeling and amplification is independent of the species and of the target genes and could be used for different types of microarrays. This system has also the advantage to detect several genes within one bacterium at once, like in Staphylococcus aureus strain BM3318, in which up to 15 genes were detected. This new microarray-based detection system offers a large potential for applications in clinical diagnostic, basic research, food safety and surveillance programs for antimicrobial resistance.

Evaluation of Swiss slaughterhouse data for integration in a syndromic surveillance system

BACKGROUND: We evaluated Swiss slaughterhouse data for integration in a national syndromic surveillance system for the early detection of emerging diseases in production animals. We analysed meat inspection data for cattle, pigs and small ruminants slaughtered between 2007 and 2012 (including emergency slaughters of sick/injured animals); investigating patterns in the number of animals slaughtered and condemned; the reasons invoked for whole carcass condemnations; reporting biases and regional effects. RESULTS: Whole carcass condemnation rates were fairly uniform (1-2‰) over time and between the different types of production animals. Condemnation rates were much higher and less uniform following emergency slaughters. The number of condemnations peaked in December for both cattle and pigs, a time when individuals of lower quality are sent to slaughter when hay and food are limited and when certain diseases are more prevalent. Each type of production animal was associated with a different profile of condemnation reasons. The most commonly reported one was "severe lesions" for cattle, "abscesses" for pigs and "pronounced weight loss" for small ruminants. These reasons could constitute valuable syndromic indicators as they are unspecific clinical manifestations of a large range of animal diseases (as well as potential indicators of animal welfare). Differences were detected in the rate of carcass condemnation between cantons and between large and small slaughterhouses. A large percentage (>60% for all three animal categories) of slaughterhouses operating never reported a condemnation between 2007 and 2012, a potential indicator of widespread non-reporting bias in our database. CONCLUSIONS: The current system offers simultaneous coverage of cattle, pigs and small ruminants for the whole of Switzerland; and traceability of each condemnation to its farm of origin. The number of condemnations was significantly linked to the number of slaughters, meaning that the former should be always be offset by the later in analyses. Because this denominator is only communicated at the end of the month, condemnations may currently only be monitored on a monthly basis. Coupled with the lack of timeliness (30-60 days delay between condemnation and notification), this limits the use of the data for early-detection.

The energy expenditure of 2 Holstein cow strains in an organic grazing system

Until recently, measurements of energy expenditure (EE; herein defined as heat production) in respiration chambers did not account for the extra energy requirements of grazing dairy cows on pasture. As energy is first limiting in most pasture-based milk production systems, its efficient use is important. Therefore, the aim of the present study was to compare EE, which can be affected by differences in body weight (BW), body composition, grazing behavior, physical activity, and milk production level, in 2 Holstein cow strains. Twelve Swiss Holstein-Friesian (HCH; 616 kg of BW) and 12 New Zealand Holstein-Friesian (HNZ; 570 kg of BW) cows in the third stage of lactation were paired according to their stage of lactation and kept in a rotational, full-time grazing system without concentrate supplementation. After adaption, the daily milk yield, grass intake using the alkane double-indicator technique, nutrient digestibility, physical activity, and grazing behavior recorded by an automatic jaw movement recorder were investigated over 7d. Using the (13)C bicarbonate dilution technique in combination with an automatic blood sampling system, EE based on measured carbon dioxide production was determined in 1 cow pair per day between 0800 to 1400 h. The HCH were heavier and had a lower body condition score compared with HNZ, but the difference in BW was smaller compared with former studies. Milk production, grass intake, and nutrient digestibility did not differ between the 2 cow strains, but HCH grazed for a longer time during the 6-h measurement period and performed more grazing mastication compared with the HNZ. No difference was found between the 2 cow strains with regard to EE (291 ± 15.6 kJ) per kilogram of metabolic BW, mainly due to a high between-animal variation in EE. As efficiency and energy use are important in sustainable, pasture-based, organic milk production systems, the determining factors for EE, such as methodology, genetics, physical activity, grazing behavior, and pasture quality, should be investigated and quantified in more detail in future studies.

How Do Software Architects Specify and Validate Quality Requirements?

Software architecture is the result of a design effort aimed at ensuring a certain set of quality attributes. As we show, quality requirements are commonly specified in practice but are rarely validated using automated techniques. In this paper we analyze and classify commonly specified quality requirements after interviewing professionals and running a survey. We report on tools used to validate those requirements and comment on the obstacles encountered by practitioners when performing such activity (e.g., insufficient tool-support; poor understanding of users needs). Finally we discuss opportunities for increasing the adoption of automated tools based on the information we collected during our study (e.g., using a business-readable notation for expressing quality requirements; increasing awareness by monitoring non-functional aspects of a system).

Selective Transport of Zinc, Manganese, Nickel, Cobalt and Cadmium in the Root System and Transfer to the Leaves in Young Wheat Plants

• Background and Aims The uptake, translocation and redistribution of the heavy metals zinc, manganese, nickel, cobalt and cadmium are relevant for plant nutrition as well as for the quality of harvested plant products. The long-distance transport of these heavy metals within the root system and the release to the shoot in young wheat (Triticum aestivum ‘Arina’) plants were investigated. • Methods After the application of 65Zn, 54Mn, 63Ni, 57Co and 109Cd for 24 h to one seminal root (the other seminal roots being excised) of 54-h-old wheat seedlings, the labelled plants were incubated for several days in hydroponic culture on a medium without radionuclides. • Key Results The content of 65Zn decreased quickly in the labelled part of the root. After the transfer of 65Zn from the roots to the shoot, a further redistribution in the phloem from older to younger leaves was observed. In contrast to 65Zn, 109Cd was released more slowly from the roots to the leaves and was subsequently redistributed in the phloem to the youngest leaves only at trace levels. The content of 63Ni decreased quickly in the labelled part of the root, moving to the newly formed parts of the root system and also accumulating transiently in the expanding leaves. The 54Mn content decreased quickly in the labelled part of the root and increased simultaneously in leaf 1. A strong retention in the labelled part of the root was observed after supplying 57Co. • Conclusions The dynamics of redistribution of 65Zn, 54Mn, 63Ni, 57Co and 109Cd differed considerably. The rapid redistribution of 63Ni from older to younger leaves throughout the experiment indicated a high mobility in the phloem, while 54Mn was mobile only in the xylem and 57Co was retained in the labelled root without being loaded into the xylem.

Taking up national safety alerts to improve patient safety in hospitals: The perspective of healthcare quality and risk managers.

BACKGROUND National safety alert systems publish relevant information to improve patient safety in hospitals. However, the information has to be transformed into local action to have an effect on patient safety. We studied three research questions: How do Swiss healthcare quality and risk managers (qm/rm(1)) see their own role in learning from safety alerts issued by the Swiss national voluntary reporting and analysis system? What are their attitudes towards and evaluations of the alerts, and which types of improvement actions were fostered by the safety alerts? METHODS A survey was developed and applied to Swiss healthcare risk and quality managers, with a response rate of 39 % (n=116). Descriptive statistics are presented. RESULTS The qm/rm disseminate and communicate with a broad variety of professional groups about the alerts. While most respondents felt that they should know the alerts and their contents, only a part of them felt responsible for driving organizational change based on the recommendations. However, most respondents used safety alerts to back up their own patient safety goals. The alerts were evaluated positively on various dimensions such as usefulness and were considered as standards of good practice by the majority of the respondents. A range of organizational responses was applied, with disseminating information being the most common. An active role is related to using safety alerts for backing up own patient safety goals. CONCLUSIONS To support an active role of qm/rm in their hospital's learning from safety alerts, appropriate organizational structures should be developed. Furthermore, they could be given special information or training to act as an information hub on the issues discussed in the alerts.

Scientific assessment of the quality of OSIRIS images

Context. OSIRIS, the scientific imaging system onboard the ESA Rosetta spacecraft, has been imaging the nucleus of comet 67P/Churyumov-Gerasimenko and its dust and gas environment since March 2014. The images serve different scientific goals, from morphology and composition studies of the nucleus surface, to the motion and trajectories of dust grains, the general structure of the dust coma, the morphology and intensity of jets, gas distribution, mass loss, and dust and gas production rates. Aims. We present the calibration of the raw images taken by OSIRIS and address the accuracy that we can expect in our scientific results based on the accuracy of the calibration steps that we have performed. Methods. We describe the pipeline that has been developed to automatically calibrate the OSIRIS images. Through a series of steps, radiometrically calibrated and distortion corrected images are produced and can be used for scientific studies. Calibration campaigns were run on the ground before launch and throughout the years in flight to determine the parameters that are used to calibrate the images and to verify their evolution with time. We describe how these parameters were determined and we address their accuracy. Results. We provide a guideline to the level of trust that can be put into the various studies performed with OSIRIS images, based on the accuracy of the image calibration.

Developing a point-of-care electronic medical record system for TB/HIV co-infected patients: experiences from Lighthouse Trust, Lilongwe, Malawi.

BACKGROUND Implementation of user-friendly, real-time, electronic medical records for patient management may lead to improved adherence to clinical guidelines and improved quality of patient care. We detail the systematic, iterative process that implementation partners, Lighthouse clinic and Baobab Health Trust, employed to develop and implement a point-of-care electronic medical records system in an integrated, public clinic in Malawi that serves HIV-infected and tuberculosis (TB) patients. METHODS Baobab Health Trust, the system developers, conducted a series of technical and clinical meetings with Lighthouse and Ministry of Health to determine specifications. Multiple pre-testing sessions assessed patient flow, question clarity, information sequencing, and verified compliance to national guidelines. Final components of the TB/HIV electronic medical records system include: patient demographics; anthropometric measurements; laboratory samples and results; HIV testing; WHO clinical staging; TB diagnosis; family planning; clinical review; and drug dispensing. RESULTS Our experience suggests that an electronic medical records system can improve patient management, enhance integration of TB/HIV services, and improve provider decision-making. However, despite sufficient funding and motivation, several challenges delayed system launch including: expansion of system components to include of HIV testing and counseling services; changes in the national antiretroviral treatment guidelines that required system revision; and low confidence to use the system among new healthcare workers. To ensure a more robust and agile system that met all stakeholder and user needs, our electronic medical records launch was delayed more than a year. Open communication with stakeholders, careful consideration of ongoing provider input, and a well-functioning, backup, paper-based TB registry helped ensure successful implementation and sustainability of the system. Additional, on-site, technical support provided reassurance and swift problem-solving during the extended launch period. CONCLUSION Even when system users are closely involved in the design and development of an electronic medical record system, it is critical to allow sufficient time for software development, solicitation of detailed feedback from both users and stakeholders, and iterative system revisions to successfully transition from paper to point-of-care electronic medical records. For those in low-resource settings, electronic medical records for integrated care is a possible and positive innovation.

The Chemical Mechanism of a Brown-Rot Decay Mimtic System and its Application in Paper Recycling Processes

This work is aimed at improving our current knowledge of the non-enzymatic inecl~anisins involved in brown-rot decay, as well as the exploration of potential applications of a brown-rot mimetic model system in paper recycling processes. The study was divided into two parts. The first part focussed on the chemical mechanisms involved in chelation and reduction of iron by a low molecular weight chelator (isolated from the brown-rot fungus Gloeophyllz~m tmbeum) and its model compound 2,3- dihydroxybenzoic acid (2,3-DHBA). Chelation as well as free radical generation mediated by this system were studied by ESR measurement. The results indicate that the effects of the chelator/iron ratio, the pH, and other reaction parameters on hydroxyl radical generation by a Fenton type system could be determined using ESR spin-trapping techniques. The results also support the hypothesis that superoxide radicals are involved in the chelator-mediated Fenton process. In the second part of the study, the effect of a chelator-mediated Fenton system for the improvement of deinking efficiency and the n~odification of fiber and paper properties was studied. For the deinking study, copy paper was laser printed with an identical standard pattern. Then repulping and flotation operations were performed to remove ink particles. Under properly controlled deinking conditions, the chelator mediated treatment (CMT) resulted in a reduction in dirt count over that of conventional deinking procedures with no significant loss of pulp strength. To study the effect of the chelator system treatment on the quality of pulp with different fines content, a fully bleached hardwood kraft pulp was beaten to different freeness levels and treated with the chelator-mediated free radical system. The result shows that virgin fiber and heavily beaten fiber respond differently to the free radical treatment. Unbeaten fibers become more flexible and easier to collapse after free radical treatment, while beaten fibers show a reduction in fines and small materials after mild free radical treatment.

Digital Vertical Aerial Camera System for High-resolution Site Inspections in Conservation Easment Monitoring

A three-level satellite to ground monitoring scheme for conservation easement monitoring has been implemented in which high-resolution imagery serves as an intermediate step for inspecting high priority sites. A digital vertical aerial camera system was developed to fulfill the need for an economical source of imagery for this intermediate step. A method for attaching the camera system to small aircraft was designed, and the camera system was calibrated and tested. To ensure that the images obtained were of suitable quality for use in Level 2 inspections, rectified imagery was required to provide positional accuracy of 5 meters or less to be comparable to current commercially available high-resolution satellite imagery. Focal length calibration was performed to discover the infinity focal length at two lens settings (24mm and 35mm) with a precision of O.1mm. Known focal length is required for creation of navigation points representing locations to be photographed (waypoints). Photographing an object of known size at distances on a test range allowed estimates of focal lengths of 25.lmm and 35.4mm for the 24mm and 35mm lens settings, respectively. Constants required for distortion removal procedures were obtained using analytical plumb-line calibration procedures for both lens settings, with mild distortion at the 24mm setting and virtually no distortion found at the 35mm setting. The system was designed to operate in a series of stages: mission planning, mission execution, and post-mission processing. During mission planning, waypoints were created using custom tools in geographic information system (GIs) software. During mission execution, the camera is connected to a laptop computer with a global positioning system (GPS) receiver attached. Customized mobile GIs software accepts position information from the GPS receiver, provides information for navigation, and automatically triggers the camera upon reaching the desired location. Post-mission processing (rectification) of imagery for removal of lens distortion effects, correction of imagery for horizontal displacement due to terrain variations (relief displacement), and relating the images to ground coordinates were performed with no more than a second-order polynomial warping function. Accuracy testing was performed to verify the positional accuracy capabilities of the system in an ideal-case scenario as well as a real-world case. Using many welldistributed and highly accurate control points on flat terrain, the rectified images yielded median positional accuracy of 0.3 meters. Imagery captured over commercial forestland with varying terrain in eastern Maine, rectified to digital orthophoto quadrangles, yielded median positional accuracies of 2.3 meters with accuracies of 3.1 meters or better in 75 percent of measurements made. These accuracies were well within performance requirements. The images from the digital camera system are of high quality, displaying significant detail at common flying heights. At common flying heights the ground resolution of the camera system ranges between 0.07 meters and 0.67 meters per pixel, satisfying the requirement that imagery be of comparable resolution to current highresolution satellite imagery. Due to the high resolution of the imagery, the positional accuracy attainable, and the convenience with which it is operated, the digital aerial camera system developed is a potentially cost-effective solution for use in the intermediate step of a satellite to ground conservation easement monitoring scheme.

Quality of care for uninsured type 2 diabetic patients in a financial assistance medical home model

The medically uninsured population in the United States is 16% or 42 million people and consists of a significant number of Type 2 diabetic patients which is the predominant form of diabetes with 798,000 new cases diagnosed each year. There is limited health services research on uninsured populations concerning health system measures or specific disease conditions. ^ The purpose of this investigation was to determine the impact a newly implemented health care program had on the quality of care provided to patients with Type 2 diabetes. The primary study objective was to compare the quality of care while controlling for utilization, and health status of patients in the new program to their status during the previous financial assistance program. The research design was a retrospective matched-pairs design. The study population consisted of 225 patients who received medical care during 1996 and 1997 at the University Health System in San Antonio, Texas. ^ Six quality of care measures individually failed to demonstrate a statistically significant difference when compared between the two periods. However, an index measure reflecting the number of patients who received all six of the quality of care measures demonstrated a statistically significant increase in 1997 (p-value < 0.05). In 1996, 8 patients (2.6%) received all six medical management components. In 1997, 38 patients (16.8%) received all six medical management components. Four regression models were analyzed; two out of the four models demonstrated inconsistent results based on the program membership variable. ^ It is concluded that there has been a small effect of the Carelink program demonstrated by an increase from 8 to 38 patients receiving all quality of care components for Type 2 diabetics at the UHS. It is recommended that additional research be conducted in order to evaluate the quality of care provided to Type 2 diabetic patients. ^

Evaluating the impact of vertical integration on health system peformance

Vertical integration is grounded in economic theory as a corporate strategy for reducing cost and enhancing efficiency. There were three purposes for this dissertation. The first was to describe and understand vertical integration theory. The review of the economic theory established vertical integration as a corporate cost reduction strategy in response to environmental, structural and performance dimensions of the market. The second purpose was to examine vertical integration in the context of the health care industry, which has greater complexity, higher instability, and more unstable demand than other industries, although many of the same dimensions of the market supported a vertical integration strategy. Evidence on the performance of health systems after integration revealed mixed results. Because the market continues to be turbulent, hybrid non-owned integration in the form of alliances have increased to over 40% of urban hospitals. The third purpose of the study was to examine the application of vertical integration in health care and evaluate the effects. The case studied was an alliance formed between a community hospital and a tertiary medical center to facilitate vertical integration of oncology services while maintaining effectiveness and preserving access. The economic benefits for 1934 patients were evaluated in the delivery system before and after integration with a more detailed economic analysis of breast, lung, colon/rectal, and non-malignant cases. A regression analysis confirmed the relationship between the independent variables of age, sex, location of services, race, stage of disease, and diagnosis, and the dependent variable, cost. The results of the basic regression model, as well as the regression with first-order interaction terms, were statistically significant. The study shows that vertical integration at an intermediate health care system level has economic benefits. If the pre-integration oncology group had been treated in the post-integration model, the expected cost savings from integration would be 31.5%. Quality indicators used were access to health care services and research treatment protocols, and access was preserved in the integrated model. Using survival as a direct quality outcome measure, the survival of lung cancer patients was statistically the same before and after integration. ^

The design and evaluation of a 2D dose verification system for intensity modulated radiotherapy

The usage of intensity modulated radiotherapy (IMRT) treatments necessitates a significant amount of patient-specific quality assurance (QA). This research has investigated the precision and accuracy of Kodak EDR2 film measurements for IMRT verifications, the use of comparisons between 2D dose calculations and measurements to improve treatment plan beam models, and the dosimetric impact of delivery errors. New measurement techniques and software were developed and used clinically at M. D. Anderson Cancer Center. The software implemented two new dose comparison parameters, the 2D normalized agreement test (NAT) and the scalar NAT index. A single-film calibration technique using multileaf collimator (MLC) delivery was developed. EDR2 film's optical density response was found to be sensitive to several factors: radiation time, length of time between exposure and processing, and phantom material. Precision of EDR2 film measurements was found to be better than 1%. For IMRT verification, EDR2 film measurements agreed with ion chamber results to 2%/2mm accuracy for single-beam fluence map verifications and to 5%/2mm for transverse plane measurements of complete plan dose distributions. The same system was used to quantitatively optimize the radiation field offset and MLC transmission beam modeling parameters for Varian MLCs. While scalar dose comparison metrics can work well for optimization purposes, the influence of external parameters on the dose discrepancies must be minimized. The ability of 2D verifications to detect delivery errors was tested with simulated data. The dosimetric characteristics of delivery errors were compared to patient-specific clinical IMRT verifications. For the clinical verifications, the NAT index and percent of pixels failing the gamma index were exponentially distributed and dependent upon the measurement phantom but not the treatment site. Delivery errors affecting all beams in the treatment plan were flagged by the NAT index, although delivery errors impacting only one beam could not be differentiated from routine clinical verification discrepancies. Clinical use of this system will flag outliers, allow physicists to examine their causes, and perhaps improve the level of agreement between radiation dose distribution measurements and calculations. The principles used to design and evaluate this system are extensible to future multidimensional dose measurements and comparisons. ^

Airliner cabin air quality exposure assessment

The airliner cabin environment and its effects on occupant health have not been fully characterized. This dissertation is: (1) A review of airliner environmental control systems (ECSs) that modulate the ventilation, temperature, relative humidity (RH), and barometric pressure (PB) of the cabin environment---variables related to occupant comfort and health. (2) A review and assessment of the methods and findings of key cabin air quality (CAQ) investigations. Several significant deficiencies impede the drawing of inferences about CAQ, e.g., lack of detail about investigative methods, differences in methods between investigations, limited assessment of CAQ variables, small sample sizes, and technological deficiencies of data collection. (3) A comprehensive evaluation of the methods used in the subsequent NIOSH-FAA Airliner CAQ Exposure Assessment Feasibility Study (STUDY) in which this author participated. A number of problems were identified which limit the usefulness of the data. (4) An analysis of the reliable 10-flight STUDY data. Univariate and multivariate methods applied to CO2 (a surrogate for air contaminants), temperature, RH, and PB, in association with percent passenger load, ventilation system, flight duration, airliner body type, and measurement location within the cabin, revealed neither the measured values nor their variability exceeded established health-based exposure limits. Regression analyses suggest CO2, temperature, and RH were affected by percent passenger load. In-flight measurements of CO2 and RH were relatively independent of ventilation system type or flight duration. Cabin temperature was associated with percent passenger load, ventilation system type, and flight duration. (5) A synthesis of the implications of the airliner ECS and cabin O2 environment on occupant health. A model was developed to predict consequences of the airliner cabin pressure altitude 8,000 ft limit and resulting model-estimated PO2 on cardiopulmonary status. Based on the PB, altitude, and environmental data derived from the 10 STUDY flights, the predicted PaO2 of adults with COPD, or elderly adults with or without COPD, breathing ambient cabin air could be < 55 mm Hg (SaO2 < 88%). Reduction in cabin PB found in the STUDY flights could aggravate various medical conditions and require the use of in-flight supplemental O2. ^