An integrated system for building and running reproducible research

Our generation of computational scientists is living in an exciting time: not only do we get to pioneer important algorithms and computations, we also get to set standards on how computational research should be conducted and published. From Euclid’s reasoning and Galileo’s experiments, it took hundreds of years for the theoretical and experimental branches of science to develop standards for publication and peer review. Computational science, rightly regarded as the third branch, can walk the same road much faster. The success and credibility of science are anchored in the willingness of scientists to expose their ideas and results to independent testing and replication by other scientists. This requires the complete and open exchange of data, procedures and materials. The idea of a “replication by other scientists” in reference to computations is more commonly known as “reproducible research”. In this context the journal “EAI Endorsed Transactions on Performance & Modeling, Simulation, Experimentation and Complex Systems” had the exciting and original idea to make the scientist able to submit simultaneously the article and the computation materials (software, data, etc..) which has been used to produce the contents of the article. The goal of this procedure is to allow the scientific community to verify the content of the paper, reproducing it in the platform independently from the OS chosen, confirm or invalidate it and especially allow its reuse to reproduce new results. This procedure is therefore not helpful if there is no minimum methodological support. In fact, the raw data sets and the software are difficult to exploit without the logic that guided their use or their production. This led us to think that in addition to the data sets and the software, an additional element must be provided: the workflow that relies all of them.

Intraneuronal angiotensinergic system in rat and human dorsal root ganglia

To elucidate the local formation of angiotensin II (Ang II) in the neurons of sensory dorsal root ganglia (DRG), we studied the expression of angiotensinogen (Ang-N)-, renin-, angiotensin converting enzyme (ACE)- and cathepsin D-mRNA, and the presence of protein renin, Ang II, Substance P and calcitonin gene-related peptide (CGRP) in the rat and human thoracic DRG. Quantitative real time PCR (qRT-PCR) studies revealed that rat DRG expressed substantial amounts of Ang-N- and ACE mRNA, while renin mRNA as well as the protein renin were untraceable. Cathepsin D-mRNA and cathepsin D-protein were detected in the rat DRG indicating the possibility of existence of pathways alternative to renin for Ang I formation. Angiotensin peptides were successfully detected with high performance liquid chromatography and radioimmunoassay in human DRG extracts. In situ hybridization in rat DRG confirmed additionally expression of Ang-N mRNA in the cytoplasm of numerous neurons. Intracellular Ang II staining could be shown in number of neurons and their processes in both the rat and human DRG. Interestingly we observed neuronal processes with angiotensinergic synapses en passant, colocalized with synaptophysin, within the DRG. In the DRG, we also identified by qRT-PCR, expression of Ang II receptor AT(1A) and AT(2)-mRNA while AT(1B)-mRNA was not traceable. In some neurons Substance P and CGRP were found colocalized with Ang II. The intracellular localization and colocalization of Ang II with Substance P and CGRP in the DRG neurons may indicate a participation and function of Ang II in the regulation of nociception. In conclusion, these results suggest that Ang II may be produced locally in the neurons of rat and human DRG and act as a neurotransmitter.

Organ transplantation in Switzerland: impact of the new transplant law on cold ischaemia time and organ transports

On 1 July 2007 a new transplant law came into force in Switzerland. The principal item of this new law is the change from centre-oriented allocation to patient-oriented national allocation of organs. The aim of the present study is to assess the impact on cold ischaemia time (CIT) and transport requirements.

Central venous pulse pressure analysis using an R-synchronized pressure measurement system

Objective. The information derived from central venous catheters is underused. We developed an EKG-R synchronization and averaging system to obtained distinct CVP waveforms and analyzed components of these. Methods. Twenty-five paralyzed surgical patients undergoing CVP monitoring under mechanical ventilation were studied. CVP and EKG signals were analyzed employing our system, the mean CVP and CVP at end-diastole during expiration were compared, and CVP waveform components were measured using this system. Results. CVP waveforms were clearly visualized in all patients. They showed the a peak to be 1.8+/- 0.7 mmHg, which was the highest of three peaks, and the x trough to be lower than the y trough (-1.6+/- 0.7mmHgand-0.9+/- 0.5mmHg, respectively), withameanpulsepressureof3.4mmHg.ThedifferencebetweenthemeanCVPandCVPatend-diastoleduringexpirationwas0.58+/- 0.81 mmHg. Conclusions. The mean CVP can be used as an index of right ventricular preload in patients under mechanical ventilation with regular sinus rhythm. Our newly developed system is useful for clinical monitoring and for education in circulatory physiology.

[The SPI implant system: clinical experience and one-year results]

The new Swiss implant system SPI became available three years ago and is used in combination with fixed and removable prosthetic reconstructions. In a pilot study the clinical procedures were evaluated and data of prosthetic complications of maintenance service were collected. 25 patients participated in the study with a total of 79 SPI implants during the time period from 2003-2004. 37 implants were located in the maxilla and 42 implants in the mandible. Two implants failed during the healing period, but no loaded implant was lost. Thus, the survival rate was 97.5% (77/79). 44 implants supported a fixed prosthesis, including nine single crowns and 33 implants were used in combination with removable partial denture. Four implants were used with ball anchor retention, 29 with bar support. The ELEMENT implant with the low implant shoulder allows very good esthetics. Prosthetic complications and maintenance service during the first year of function was comparable with other implant systems. Since the design of the abutment screws, healing caps and screwdriver was changed, the system has become easier in its application.

An implantable carotid sinus baroreflex activating system: surgical technique and short-term outcome from a multi-center feasibility trial for the treatment of resistant hypertension

OBJECTIVES: To assess perioperative outcomes and blood pressure (BP) responses to an implantable carotid sinus baroreflex activating system being investigated for the treatment of resistant hypertension. METHODS: We report on the first seventeen patients enrolled in a multicenter study. Bilateral perivascular carotid sinus electrodes (CSL) and a pulse generator (IPG) are permanently implanted. Optimal placement of the CSL is determined by intraoperative BP responses to test activations. Acute BP responses were tested postoperatively and during the first four months of follow-up. RESULTS: Prior to implant, BP was 189.6+/-27.5/110.7+/-15.3 mmHg despite stable therapy (5.2+/-1.8 antihypertensive drugs). The mean procedure time was 202+/-43 minutes. No perioperative strokes or deaths occurred. System tests performed 1 or up to 3 days postoperatively resulted in significant (all p < or = 0.0001) mean maximum reduction, with standard deviations and 95% confidence limits for systolic BP, diastolic BP and heart rate of 28+/-22 (17, 39) mmHg, 16+/-11 (10, 22) mmHg and 8+/-4 (6, 11) BPM, respectively. Repeated testing during 3 months of therapeutic electrical activation demonstrated a durable response. CONCLUSIONS: These preliminary data suggest an acceptable safety of the procedure with a low rate of adverse events and support further clinical development of baroreflex activation as a new concept to treat resistant hypertension.

Basic Erosive Wear Examination (BEWE): a new scoring system for scientific and clinical needs

A new scoring system, the Basic Erosive Wear Examination (BEWE), has been designed to provide a simple tool for use in general practice and to allow comparison to other more discriminative indices. The most severely affected surface in each sextant is recorded with a four level score and the cumulative score classified and matched to risk levels which guide the management of the condition. The BEWE allows re-analysis and integration of results from existing studies and, in time, should initiate a consensus within the scientific community and so avoid continued proliferation of indices. Finally, this process should lead to the development of an internationally accepted, standardised and validated index. The BEWE further aims to increase the awareness of tooth erosion amongst clinicians and general dental practitioners and to provide a guide as to its management.

Measurement of nitric oxide and brain tissue oxygen tension in patients after severe subarachnoid hemorrhage

OBJECTIVE: Nitric oxide (NO), one of the most powerful endogenous vasodilators, is thought to play a major role in the development of delayed vasospasm in patients with subarachnoid hemorrhage (SAH). However, the role of the production of cerebral NO in patients with SAH is not known. In other SAH studies, NO metabolites such as nitrite and nitrate have been demonstrated to be decreased in cerebrospinal fluid and in plasma. METHODS: In this study, a microdialysis probe was used, along with a multiparameter sensor, to measure NO metabolites, brain tissue oxygen tension, brain tissue carbon dioxide tension, and pH in the cortex of patients with severe SAH who were at risk for developing secondary brain damage and vasospasm. NO metabolites, glucose, and lactate were analyzed in the dialysates to determine the time course of NO metabolite changes and to test the interrelationship between the analytes and clinical variables. RESULTS: Brain tissue oxygen tension was strongly correlated to dialysate nitrate and nitrite (r2 = 0.326; P < 0.001); however, no correlation was noted between brain tissue oxygen tension and NO metabolites in cerebrospinal fluid (r2 = 0.018; P = 0.734). No significant correlation between NO production, brain tissue carbon dioxide tension, and dialysate glucose and lactate was observed. CONCLUSION: Cerebral ischemia and compromised substrate delivery are often responsible for high morbidity rates and poor outcomes after SAH. The relationship between brain tissue oxygen and cerebral NO metabolites that we demonstrate suggests that substrate delivery and NO are linked in the pathophysiology of vasospasm after SAH.

A comparison of ground cover and frequency estimation methods for post-harvest soil monitoring

The amount and type of ground cover is an important characteristic to measure when collecting soil disturbance monitoring data after a timber harvest. Estimates of ground cover and bare soil can be used for tracking changes in invasive species, plant growth and regeneration, woody debris loadings, and the risk of surface water runoff and soil erosion. A new method of assessing ground cover and soil disturbance was recently published by the U.S. Forest Service, the Forest Soil Disturbance Monitoring Protocol (FSDMP). This protocol uses the frequency of cover types in small circular (15cm) plots to compare ground surface in pre- and post-harvest condition. While both frequency and percent cover are common methods of describing vegetation, frequency has rarely been used to measure ground surface cover. In this study, three methods for assessing ground cover percent (step-point, 15cm dia. circular and 1x5m visual plot estimates) were compared to the FSDMP frequency method. Results show that the FSDMP method provides significantly higher estimates of ground surface condition for most soil cover types, except coarse wood. The three cover methods had similar estimates for most cover values. The FSDMP method also produced the highest value when bare soil estimates were used to model erosion risk. In a person-hour analysis, estimating ground cover percent in 15cm dia. plots required the least sampling time, and provided standard errors similar to the other cover estimates even at low sampling intensities (n=18). If ground cover estimates are desired in soil monitoring, then a small plot size (15cm dia. circle), or a step-point method can provide a more accurate estimate in less time than the current FSDMP method.

Community managed rural water supply systems in the Dominican Republic : assessment of sustainability of systems built by the National Institute of Potable Water and Peace Corps, Dominican Republic

In the Dominican Republic economic growth in the past twenty years has not yielded sufficient improvement in access to drinking water services, especially in rural areas where 1.5 million people do not have access to an improved water source (WHO, 2006). Worldwide, strategic development planning in the rural water sector has focused on participatory processes and the use of demand filters to ensure that service levels match community commitment to post-project operation and maintenance. However studies have concluded that an alarmingly high percentage of drinking water systems (20-50%) do not provide service at the design levels and/or fail altogether (up to 90%): BNWP (2009), Annis (2006), and Reents (2003). World Bank, USAID, NGOs, and private consultants have invested significant resources in an effort to determine what components make up an “enabling environment” for sustainable community management of rural water systems (RWS). Research has identified an array of critical factors, internal and external to the community, which affect long term sustainability of water services. Different frameworks have been proposed in order to better understand the linkages between individual factors and sustainability of service. This research proposes a Sustainability Analysis Tool to evaluate the sustainability of RWS, adapted from previous relevant work in the field to reflect the realities in the Dominican Republic. It can be used as a diagnostic tool for government entities and development organizations to characterize the needs of specific communities and identify weaknesses in existing training regimes or support mechanisms. The framework utilizes eight indicators in three categories (Organization/Management, Financial Administration, and Technical Service). Nineteen independent variables are measured resulting in a score of sustainability likely (SL), possible (SP), or unlikely (SU) for each of the eight indicators. Thresholds are based upon benchmarks from the DR and around the world, primary data collected during the research, and the author’s 32 months of field experience. A final sustainability score is calculated using weighting factors for each indicator, derived from Lockwood (2003). The framework was tested using a statistically representative geographically stratified random sample of 61 water systems built in the DR by initiatives of the National Institute of Potable Water (INAPA) and Peace Corps. The results concluded that 23% of sample systems are likely to be sustainable in the long term, 59% are possibly sustainable, and for 18% it is unlikely that the community will be able to overcome any significant challenge. Communities that were scored as unlikely sustainable perform poorly in participation, financial durability, and governance while the highest scores were for system function and repair service. The Sustainability Analysis Tool results are verified by INAPA and PC reports, evaluations, and database information, as well as, field observations and primary data collected during the surveys. Future research will analyze the nature and magnitude of relationships between key factors and the sustainability score defined by the tool. Factors include: gender participation, legal status of water committees, plumber/operator remuneration, demand responsiveness, post construction support methodologies, and project design criteria.

Four-window technique for measuring optical-phase-space-time-frequency tomography

A new approach, the four-window technique, was developed to measure optical phase-space-time-frequency tomography (OPSTFT). The four-window technique is based on balanced heterodyne detection with two local oscillator (LO) fields. This technique can provide independent control of position, momentum, time and frequency resolution. The OPSTFT is a Wigner distribution function of two independent Fourier transform pairs, phase-space and time-frequency. The OPSTFT can be applied for early disease detection.

A Discussion of the Geology and an Isopach Map of the Pennsylvanian System in Wyoming and Adjacent Areas

Pennsylvanian strata in Wyoming and adjacent areas have been the subject of much work and discussion. Most of the work has been due to the economic importance of the system as an oil producer in this region. Oil production from strata of Pennsylvanian age is rather recent history; and therefore, much of the available information is local­ized and incomplete.

A Measurement System Experiment to Evaluate the Nosing-to-nosing Method for Measuring Dimensions of Steps

Non-uniformity of steps within a flight is a major risk factor for falls. Guidelines and requirements for uniformity of step risers and tread depths assume the measurement system provides precise dimensional values. The state-of-the-art measurement system is a relatively new method, known as the nosing-to-nosing method. It involves measuring the distance between the noses of adjacent steps and the angle formed with the horizontal. From these measurements, the effective riser height and tread depth are calculated. This study was undertaken for the purpose of evaluating the measurement system to determine how much of total measurement variability comes from the step variations versus that due to repeatability and reproducibility (R&R) associated with the measurers. Using an experimental design quality control professionals call a measurement system experiment, two measurers measured all steps in six randomly selected flights, and repeated the process on a subsequent day. After marking each step in a flight in three lateral places (left, center, and right), the measurers took their measurement. This process yielded 774 values of riser height and 672 values of tread depth. Results of applying the Gage R&R ANOVA procedure in Minitab software indicated that the R&R contribution to riser height variability was 1.42%; and to tread depth was 0.50%. All remaining variability was attributed to actual step-to-step differences. These results may be compared with guidelines used in the automobile industry for measurement systems that consider R&R less than 1% as an acceptable measurement system; and R&R between 1% and 9% as acceptable depending on the application, the cost of the measuring device, cost of repair, or other factors.

Prediction of PA12 melt viscosity in Laser Sintering by a Time and Temperature dependent rheological model

Ein auf Basis von Prozessdaten kalibriertes Viskositätsmodell wird vorgeschlagen und zur Vorhersage der Viskosität einer Polyamid 12 (PA12) Kunststoffschmelze als Funktion von Zeit, Temperatur und Schergeschwindigkeit angewandt. Im ersten Schritt wurde das Viskositätsmodell aus experimentellen Daten abgeleitet. Es beruht hauptsächlich auf dem drei-parametrigen Ansatz von Carreau, wobei zwei zusätzliche Verschiebungsfaktoren eingesetzt werden. Die Temperaturabhängigkeit der Viskosität wird mithilfe des Verschiebungsfaktors aT von Arrhenius berücksichtigt. Ein weiterer Verschiebungsfaktor aSC (Structural Change) wird eingeführt, der die Strukturänderung von PA12 als Folge der Prozessbedingungen beim Lasersintern beschreibt. Beobachtet wurde die Strukturänderung in Form einer signifikanten Viskositätserhöhung. Es wurde geschlussfolgert, dass diese Viskositätserhöhung auf einen Molmassenaufbau zurückzuführen ist und als Nachkondensation verstanden werden kann. Abhängig von den Zeit- und Temperaturbedingungen wurde festgestellt, dass die Viskosität als Folge des Molmassenaufbaus exponentiell gegen eine irreversible Grenze strebt. Die Geschwindigkeit dieser Nachkondensation ist zeit- und temperaturabhängig. Es wird angenommen, dass die Pulverbetttemperatur einen Molmassenaufbau verursacht und es damit zur Kettenverlängerung kommt. Dieser fortschreitende Prozess der zunehmenden Kettenlängen setzt molekulare Beweglichkeit herab und unterbindet die weitere Nachkondensation. Der Verschiebungsfaktor aSC drückt diese physikalisch-chemische Modellvorstellung aus und beinhaltet zwei zusätzliche Parameter. Der Parameter aSC,UL entspricht der oberen Viskositätsgrenze, wohingegen k0 die Strukturänderungsrate angibt. Es wurde weiterhin festgestellt, dass es folglich nützlich ist zwischen einer Fließaktivierungsenergie und einer Strukturänderungsaktivierungsenergie für die Berechnung von aT und aSC zu unterscheiden. Die Optimierung der Modellparameter erfolgte mithilfe eines genetischen Algorithmus. Zwischen berechneten und gemessenen Viskositäten wurde eine gute Übereinstimmung gefunden, so dass das Viskositätsmodell in der Lage ist die Viskosität einer PA12 Kunststoffschmelze als Folge eines kombinierten Lasersinter Zeit- und Temperatureinflusses vorherzusagen. Das Modell wurde im zweiten Schritt angewandt, um die Viskosität während des Lasersinter-Prozesses in Abhängigkeit von der Energiedichte zu berechnen. Hierzu wurden Prozessdaten, wie Schmelzetemperatur und Belichtungszeit benutzt, die mithilfe einer High-Speed Thermografiekamera on-line gemessen wurden. Abschließend wurde der Einfluss der Strukturänderung auf das Viskositätsniveau im Prozess aufgezeigt.

Topographic time-frequency decomposition of the EEG

Frequency-transformed EEG resting data has been widely used to describe normal and abnormal brain functional states as function of the spectral power in different frequency bands. This has yielded a series of clinically relevant findings. However, by transforming the EEG into the frequency domain, the initially excellent time resolution of time-domain EEG is lost. The topographic time-frequency decomposition is a novel computerized EEG analysis method that combines previously available techniques from time-domain spatial EEG analysis and time-frequency decomposition of single-channel time series. It yields a new, physiologically and statistically plausible topographic time-frequency representation of human multichannel EEG. The original EEG is accounted by the coefficients of a large set of user defined EEG like time-series, which are optimized for maximal spatial smoothness and minimal norm. These coefficients are then reduced to a small number of model scalp field configurations, which vary in intensity as a function of time and frequency. The result is thus a small number of EEG field configurations, each with a corresponding time-frequency (Wigner) plot. The method has several advantages: It does not assume that the data is composed of orthogonal elements, it does not assume stationarity, it produces topographical maps and it allows to include user-defined, specific EEG elements, such as spike and wave patterns. After a formal introduction of the method, several examples are given, which include artificial data and multichannel EEG during different physiological and pathological conditions.