XML for Model Specification in Neuroscience

One of the main roles of the Neural Open Markup Language, NeuroML, is to facilitate cooperation in building, simulating, testing and publishing models of channels, neurons and networks of neurons. MorphML, which was developed as a common format for exchange of neural morphology data, is distributed as part of NeuroML but can be used as a stand-alone application. In this collection of tutorials and workshop summary, we provide an overview of these XML schemas and provide examples of their use in down-stream applications. We also summarize plans for the further development of XML specifications for modeling channels, channel distributions, and network connectivity.

Narrated PowerPoints and Audio Podcasts in Clinical Teaching: One Clerkship's Experience

Introduction: Clinical medical education is increasingly utilizing novel technological approaches in order to supplement traditional lecture-based didactics. The Neurology Core Clerkship at Baylor College of Medicine is a four week required course taken by clinical medical students. Given the large amount of information to be disseminated in a short period of time, part of the didactic material has been provided online in the form of narrated PowerPoint files or lecture audio tracks along with stand-alone PowerPoint files. The narrated files are generated using the native PowerPoint narration function while the stand-alone audio files are created as MP3 format files using an inexpensive digital recording device. [See PDF for complete abstract]

Visible and Infrared Spectroscopical Applications

Spectra in the visible (VIS) and infrared (IR) region contain a wide variety of information about inorganic and organic substances in sediments. The information from the spectra enables a wide array of applications that allow quantitative, semiquantitative, and qualitative characterization of sediment. Due to the fact that instrument/experimental setups are simple, rapid, and cost-saving and that only small sample quantities are required, the technique has become valuable in paleolimnological and Quaternary science. This article summarizes the theoretical background of VIS and IR spectroscopy, explains the analytical process, introduces statistical tools used for interpretation of spectra, and provides examples of applications in Quaternary science.

Combination of Psychological Intervention and Phosphodiesterase-5 Inhibitors for Erectile Dysfunction: A Narrative Review and Meta-Analysis

INTRODUCTION Erectile dysfunction (ED) is an increasing health problem that demands effective treatment. There is evidence that phosphodiesterase-5 inhibitors (PDE5-Is) and psychological intervention (PI) are effective treatment options; however, little is known about their comparative efficacy and the efficacy of combined treatments. AIM The aim of this systematic review and meta-analysis is to evaluate the comparative efficacy of PI, PDE5-Is, and their combination in the treatment of ED. MAIN OUTCOME MEASURES Primary outcome was ED symptoms, and secondary outcome was sexual satisfaction of the patient. METHODS A systematic literature search was conducted in order to identify relevant articles published between 1998 and 2012. We included randomized controlled trials and controlled trials comparing PI with PDE5-I treatment or one of them against a combination of both. RESULTS Eight studies with a total number of 562 patients were included in the meta-analysis. The results of the included studies are inconclusive, though they show a trend towards a larger effect of combined treatment compared with PI or PDE5-I treatment alone. The meta-analysis found that, overall, combined treatment was more efficacious for ED symptoms than PDE5-I treatment or PI alone. Combined treatment was more efficacious than PDE5-I use alone on sexual satisfaction. No differences were found between PDE5-Is and PI as stand-alone treatments. None of the moderators (treatment duration, methodological quality, or researcher allegiance) altered the effects. CONCLUSIONS The combination of PI and PDE5-Is is a promising strategy for a favorable outcome in ED and can be considered as a first-choice option for ED patients. Stronger RCTs are required to confirm this initial finding. Schmidt HM, Munder T, Gerger H, Frühauf S, and Barth J. Combination of psychological intervention and phosphodiesterase-5 inhibitors for erectile dysfunction: A narrative review and meta-analysis. J Sex Med **;**:**-**.

Household Hardships, Public Programs, and Their Associations with the Health and Development of Very Young Children: Insights from Children’s HealthWatch

America’s low-income families struggle to protect their children from multiple threats to their health and growth. Many research and advocacy groups explore the health and educational effects of food insecurity, but less is known about these effects on very young children. Children’s HealthWatch, a group of pediatric clinicians and public health researchers, has continuously collected data on the effects of food insecurity alone and in conjunction with other household hardships since 1998. The group’s peer reviewed research has shown that a number of economic risks at the household level, including food, housing and energy insecurity, tend to be correlated. These insecurities alone or in conjunction increase the risk that a young child will suffer various negative health consequences, including increases in lifetime hospitalizations, parental report of fair or poor health,1 or risk for developmental delays.2 Child food insecurity is an incremental risk indicator above and beyond the risk imposed by household-level food insecurity. The Children’sHealthwatch research also suggests public benefits programs modify some of these effects for families experiencing hardships. This empirical evidence is presented in a variety of public venues outside the usual scientific settings, such as congressional hearings, to support the needs of America’s most vulnerable population through policy change. Children’s HealthWatch research supports legislative solutions to food insecurity, including sustained funding for public programs and re-evaluation of the use of the Thrifty Food Plan as the basis of SNAP benefits calculations. Children’s HealthWatch is one of many models to support the American Academy of Pediatrics’ call to “stand up, speak up, and step up for children.”3 No isolated group or single intervention will solve child poverty or multiple hardships. However, working collaboratively each group has a role to play in supporting the health and well-being of young children and their families. 1. Cook JT, Frank DA, Berkowitz C, et al. Food insecurity is associated with adverse health outcomes among human infants and toddlers. J Nutr. 2004;134:1432-1438. 2. Rose-Jacobs R, Black MM, Casey PH, et al. Household food insecurity: associations with at-risk infant and toddler development. Pediatrics. 2008;121:65-72. 3. AAP leader says to stand up, speak up, and step up for child health [news release]. Boston, MA: American Academy of Pediatrics; October 11, 2008. http://www2.aap.org/pressroom/nce/nce08childhealth.htm. Accessed January 1, 2012.

Digital Data Collection and Processing in Field and Lab: The Approach of Kinneret Regional Project

The paper showcases the field- and lab-documentation system developed for Kinneret Regional Project, an international archaeological expedition to the Northwestern shore of the Sea of Galilee (Israel) under the auspices of the University of Bern, the University of Helsinki, Leiden University and Wofford College. The core of the data management system is a fully relational, server-based database framework, which also includes time-based and static GIS services, stratigraphic analysis tools and fully indexed document/digital image archives. Data collection in the field is based on mobile, hand-held devices equipped with a custom-tailored stand-alone application. Comprehensive three-dimensional documentation of all finds and findings is achieved by means of total stations and/or high-precision GPS devices. All archaeological information retrieved in the field – including tachymetric data – is synched with the core system on the fly and thus immediately available for further processing in the field lab (within the local network) or for post-excavation analysis at remote institutions (via the WWW). Besides a short demonstration of the main functionalities, the paper also presents some of the key technologies used and illustrates usability aspects of the system’s individual components.

Highlights in Analytical Chemistry in Switzerland: OMA & OPA - A Software Tool for Mass Spectrometric Sequencing of Nucleic Acids

Oligonucleotides comprising unnatural building blocks, which interfere with the translation machinery, have gained increased attention for the treatment of gene-related diseases (e.g. antisense, RNAi). Due to structural modifications, synthetic oligonucleotides exhibit increased biostability and bioavailability upon administration. Consequently, classical enzyme-based sequencing methods are not applicable to their sequence elucidation and verification. Tandem mass spectrometry is the method of choice for performing such tasks, since gas-phase dissociation is not restricted to natural nucleic acids. However, tandem mass spectrometric analysis can generate product ion spectra of tremendous complexity, as the number of possible fragments grows rapidly with increasing sequence length. The fact that structural modifications affect the dissociation pathways greatly increases the variety of analytically valuable fragment ions. The gas-phase dissociation of oligonucleotides is characterized by the cleavage of one of the four bonds along the phosphodiester chain, by the accompanying loss of nucleases, and by the generation of internal fragments due to secondary backbone cleavage. For example, an 18-mer oligonucleotide yields a total number of 272’920 theoretical fragment ions. In contrast to the processing of peptide product ion spectra, which nowadays is highly automated, there is a lack of tools assisting the interpretation of oligonucleotide data. The existing web-based and stand-alone software applications are primarily designed for the sequence analysis of natural nucleic acids, but do not account for chemical modifications and adducts. Consequently, we developed a software to support the interpretation of mass spectrometric data of natural and modified nucleic acids and their adducts with chemotherapeutic agents.

Space-based space surveillance and tracking demonstrator: mission and system design

This paper presents the capabilities of a Space-Based Space Surveillance (SBSS) demonstration mission for Space Surveillance and Tracking (SST) based on a micro-satellite platform. The results have been produced in the frame of ESA’s "Assessment Study for Space Based Space Surveillance Demonstration Mission" performed by the Airbus Defence and Space consortium. The assessment of SBSS in an SST system architecture has shown that both an operational SBSS and also already a well- designed space-based demonstrator can provide substantial performance in terms of surveillance and tracking of beyond-LEO objects. Especially the early deployment of a demonstrator, possible by using standard equipment, could boost initial operating capability and create a self-maintained object catalogue. Furthermore, unique statistical information about small-size LEO debris (mm size) can be collected in-situ. Unlike classical technology demonstration missions, the primary goal is the demonstration and optimisation of the functional elements in a complex end-to-end chain (mission planning, observation strategies, data acquisition, processing, etc.) until the final products can be offered to the users and with low technological effort and risk. The SBSS system concept takes the ESA SST System Requirements into account and aims at fulfilling SST core requirements in a stand-alone manner. Additionally, requirements for detection and characterisation of small-sizedLEO debris are considered. The paper presents details of the system concept, candidate micro-satellite platforms, the instrument design and the operational modes. Note that the detailed results of performance simulations for space debris coverage and cataloguing accuracy are presented in a separate paper “Capability of a Space-based Space Surveillance System to Detect and Track Objects in GEO, MEO and LEO Orbits” by J. Silha (AIUB) et al., IAC-14, A6, 1.1x25640.

Service level agreements-driven management of distributed applications in cloud computing environments

Advancements in cloud computing have enabled the proliferation of distributed applications, which require management and control of multiple services. However, without an efficient mechanism for scaling services in response to changing workload conditions, such as number of connected users, application performance might suffer, leading to violations of Service Level Agreements (SLA) and possible inefficient use of hardware resources. Combining dynamic application requirements with the increased use of virtualised computing resources creates a challenging resource Management context for application and cloud-infrastructure owners. In such complex environments, business entities use SLAs as a means for specifying quantitative and qualitative requirements of services. There are several challenges in running distributed enterprise applications in cloud environments, ranging from the instantiation of service VMs in the correct order using an adequate quantity of computing resources, to adapting the number of running services in response to varying external loads, such as number of users. The application owner is interested in finding the optimum amount of computing and network resources to use for ensuring that the performance requirements of all her/his applications are met. She/he is also interested in appropriately scaling the distributed services so that application performance guarantees are maintained even under dynamic workload conditions. Similarly, the infrastructure Providers are interested in optimally provisioning the virtual resources onto the available physical infrastructure so that her/his operational costs are minimized, while maximizing the performance of tenants’ applications. Motivated by the complexities associated with the management and scaling of distributed applications, while satisfying multiple objectives (related to both consumers and providers of cloud resources), this thesis proposes a cloud resource management platform able to dynamically provision and coordinate the various lifecycle actions on both virtual and physical cloud resources using semantically enriched SLAs. The system focuses on dynamic sizing (scaling) of virtual infrastructures composed of virtual machines (VM) bounded application services. We describe several algorithms for adapting the number of VMs allocated to the distributed application in response to changing workload conditions, based on SLA-defined performance guarantees. We also present a framework for dynamic composition of scaling rules for distributed service, which used benchmark-generated application Monitoring traces. We show how these scaling rules can be combined and included into semantic SLAs for controlling allocation of services. We also provide a detailed description of the multi-objective infrastructure resource allocation problem and various approaches to satisfying this problem. We present a resource management system based on a genetic algorithm, which performs allocation of virtual resources, while considering the optimization of multiple criteria. We prove that our approach significantly outperforms reactive VM-scaling algorithms as well as heuristic-based VM-allocation approaches.

Multiple gradient echo propeller (MGREP) MRI: Technical development and potential applications

The PROPELLER (Periodically Rotated Overlapping Parallel Lines with Enhanced Reconstruction) magnetic resonance imaging (MRI) technique has inherent advantages over other fast imaging methods, including robust motion correction, reduced image distortion, and resistance to off-resonance effects. These features make PROPELLER highly desirable for T2*-sensitive imaging, high-resolution diffusion imaging, and many other applications. However, PROPELLER has been predominantly implemented as a fast spin-echo (FSE) technique, which is insensitive to T2* contrast, and requires time-inefficient signal averaging to achieve adequate signal-to-noise ratio (SNR) for many applications. These issues presently constrain the potential clinical utility of FSE-based PROPELLER. ^ In this research, our aim was to extend and enhance the potential applications of PROPELLER MRI by developing a novel multiple gradient echo PROPELLER (MGREP) technique that can overcome the aforementioned limitations. The MGREP pulse sequence was designed to acquire multiple gradient-echo images simultaneously, without any increase in total scan time or RF energy deposition relative to FSE-based PROPELLER. A new parameter was also introduced for direct user-control over gradient echo spacing, to allow variable sensitivity to T2* contrast. In parallel to pulse sequence development, an improved algorithm for motion correction was also developed and evaluated against the established method through extensive simulations. The potential advantages of MGREP over FSE-based PROPELLER were illustrated via three specific applications: (1) quantitative T2* measurement, (2) time-efficient signal averaging, and (3) high-resolution diffusion imaging. Relative to the FSE-PROPELLER method, the MGREP sequence was found to yield quantitative T2* values, increase SNR by ∼40% without any increase in acquisition time or RF energy deposition, and noticeably improve image quality in high-resolution diffusion maps. In addition, the new motion algorithm was found to improve the performance considerably in motion-artifact reduction. ^ Overall, this work demonstrated a number of enhancements and extensions to existing PROPELLER techniques. The new technical capabilities of PROPELLER imaging, developed in this thesis research, are expected to serve as the foundation for further expanding the scope of PROPELLER applications. ^

An assessment of post-disaster psychological stress in hazardous waste operations and emergency response (HAZWOPER) workers

Personnel involved in natural or man-made disaster response and recovery efforts may be exposed to a wide variety of physical and mental stressors that can exhibit long-lasting and detrimental psychopathological outcomes. In a disaster situation, huge numbers of "secondary" responders can be involved in contaminant clean-up and debris removal and can be at risk of developing stress-related mental health outcomes. The Occupational Safety and Health Administration (OSHA) worker training hierarchy typically required for response workers, known as "Hazardous Waste Operations and Emergency Response" (HAZWOPER), does not address the mental health and safety concerns of workers. This study focused on the prevalence of traumatic stress experienced by secondary responders that had received or expressed interest in receiving HAZWOPER training through the National Institute of Environmental Health Sciences Worker Education and Training Program (NIEHS WETP). ^ The study involved the modification of two preexisting and validated survey tools to assess secondary responder awareness of physical, mental, and traumatic stressors on mental health and sought to determine if a need existed to include traumatic stress-related mental health education in the current HAZWOPER training regimen. The study evaluated post-traumatic stress disorder (PTSD), resiliency, mental distress, and negative effects within a secondary responder population of 176 respondents. Elevated PTSD levels were seen in the study population as compared to a general responder population (32.9% positive vs. 8%-22.5% positive). Results indicated that HAZWOPER-trained disaster responders were likely to test positive for PTSD, whereas, untrained responders with no disaster experience and responders who possessed either training or disaster experience only were likely to test PTSD negative. A majority (68.75%) of the population tested below the mean resiliency to cope score (80.4) of the average worker population. Results indicated that those who were trained only or who possessed both training and disaster work experience were more likely to have lower resiliency scores than those with no training or experience. There were direct correlations between being PTSD positive and having worked at a disaster site and experiencing mental distress and negative effects. However, HAZWOPER training status does not significantly correlate with mental distress or negative effect. ^ The survey indicated clear support (91% of respondents) for mental health education. The development of a pre- and post-deployment training module is recommended. Such training could provide responders with the necessary knowledge and skills to recognize the symptomology of PTSD, mental stressors, and physical and traumatic stressors, thus empowering them to employ protective strategies or seek professional help if needed. It is further recommended that pre-deployment mental health education be included in the current HAZWOPER 24- and 40-hour course curriculums, as well as, consideration be given towards integrating a stand-alone post-deployment mental health education training course into the current HAZWOPER hierarchy.^