A neuron membrane mesh representation for visualization of electrophysiological simulations

We present a process to automatically generate three-dimensional mesh representations of the complex, arborized cell membrane surface of cortical neurons (the principal information processing cells of the brain) from nonuniform morphological measurements. Starting from manually sampled morphological points (3D points and diameters) from neurons in a brain slice preparation, we construct a polygonal mesh representation that realistically represents the continuous membrane surface, closely matching the original experimental data. A mapping between the original morphological points and the newly generated mesh enables simulations of electrophysiolgical activity to be visualized on this new membrane representation. We compare the new mesh representation with the state of the art and present a series of use cases and applications of this technique to visualize simulations of single neurons and networks of multiple neurons.     

Retraction of “Using ergonomic digital human modeling in evaluation of workplace design and prevention of workrelated musculoskeletal disorders onboard small fishing vessel”

The following article from Human Factors and Ergonomics in Manufacturing & Service Industries, “Using ergonomic digital human modeling in evaluation of workplace design and prevention of workrelated musculoskeletal disorders onboard small fishing vessel,” by Enrique Álvarez‐Casado, Bing Zhang, Sonia Tello Sandoval and Mondelo Pedro, published online on October 11, 2011 in Wiley Online Library ( www.onlinelibrary.wiley.com ), has been retracted by agreement between the authors, the journal Editors‐in‐Chief, Waldemar Karwowski and Gavriel Salvendy, and Publisher Wiley Periodicals, Inc. The retraction has been agreed as these articles were mistakenly published after being rejected.     

Delay-bounded data gathering in urban vehicular sensor networks

Vehicular sensor networks are an emerging network paradigm, suitable for various applications in vehicular environment making use of vehicles’ sensors as data sources and Inter-Vehicle Communication systems for the transmissions. We present a solution, based on vehicular sensor networks, for gathering data from a certain geographic area while satisfying with a specific delay bound. The method leverages the time interval during which the query is active in order to make the gathering process efficient, properly alternating data muling and multi-hop forwarding strategies like in delay-bounded routing protocols. Simulations show that our proposed solution succeeds in performing efficient data gathering outperforming other solutions.     

Intracellular Ca2+ Signaling in Protozoan Parasites: An Overview with a Focus on Mitochondria

Ca²⁺ signaling has been involved in controling critical cellular functions such as activation of proteases, cell death, and cell cycle control. The endoplasmatic reticulum plays a significant role in Ca²⁺ storage inside the cell, but mitochondria have long been recognized as a fundamental Ca²⁺ pool. Protozoan parasites such as Plasmodium falciparum, Toxoplasma gondii, and Trypanosoma cruzi display a Ca²⁺ signaling toolkit with similarities to higher eukaryotes, including the participation of mitochondria in Ca²⁺-dependent signaling events. This review summarizes the most recent knowledge in mitochondrial Ca²⁺ signaling in protozoan parasites, focusing on the mechanism involved in mitochondrial Ca²⁺ uptake by pathogenic protists.     

Visceral Adipose Tissue Displays Unique Metabolomic Fingerprints in Obesity,Pre-Diabetes and Type 2 Diabetes

Visceral adipose tissue (VAT) metabolic profiling harbors the potential to disentangle molecular changes underlying obesity-related dysglycemia. In this study, the VAT exometabolome of subjects with obesity and different glycemic statuses are analyzed. The subjects (n = 19) are divided into groups according to body mass index and glycemic status: subjects with obesity and euglycemia (Ob+NGT, n = 5), subjects with obesity and pre-diabetes (Ob+Pre-T2D, n = 5), subjects with obesity and type 2 diabetes under metformin treatment (Ob+T2D, n = 5) and subjects without obesity and with euglycemia (Non-Ob, n = 4), used as controls. VATs are incubated in culture media and extracellular metabolite content is determined by proton nuclear magnetic resonance (¹H-NMR). Glucose consumption is not different between the groups. Pyruvate and pyroglutamate consumption are significantly lower in all groups of subjects with obesity compared to Non-Ob, and significantly lower in Ob+Pre-T2D as compared to Ob+NGT. In contrast, isoleucine consumption is significantly higher in all groups of subjects with obesity, particularly in Ob+Pre-T2D, compared to Non-Ob. Acetate production is also significantly lower in Ob+Pre-T2D compared to Non-Ob. In sum, the VAT metabolic fingerprint is associated with pre-diabetes and characterized by higher isoleucine consumption, accompanied by lower acetate production and pyruvate and pyroglutamate consumption. We propose that glucose metabolism follows different fates within the VAT, depending on the individuals’ health status.     

Isobaric vapor—liquid equilibria for binary systems composed of methyl butanoate with ethanol and with propan-1-ol at 114.66 and 127.99 kpa

Vapor-liquid equilibrium data for the binary systems methyl butanoate/ethanol and methyl butanoate/propan-l-ol at pressures of 114.66 and 127.99 kPa are presented. Both mixtures yield an azeotrope, the compositions (ester) of which decrease quasi-linearly as the pressure increases. The experimental data for all the binary mixtures were fitted to a suitable equation and then used for comparison with predictions by ASOG and UNIFAC methods. These group contribution models give a good estimation of activity coefficients with an overall mean error less than 5% for all cases.     

Fast finite difference Poisson solvers on heterogeneous architectures

In this paper we propose and evaluate a set of new strategies for the solution of three dimensional separable elliptic problems on CPU–GPU platforms. The numerical solution of the system of linear equations arising when discretizing those operators often represents the most time consuming part of larger simulation codes tackling a variety of physical situations. Incompressible fluid flows, electromagnetic problems, heat transfer and solid mechanic simulations are just a few examples of application areas that require efficient solution strategies for this class of problems. GPU computing has emerged as an attractive alternative to conventional CPUs for many scientific applications. High speedups over CPU implementations have been reported and this trend is expected to continue in the future with improved programming support and tighter CPU–GPU integration. These speedups by no means imply that CPU performance is no longer critical. The conventional CPU-control–GPU-compute pattern used in many applications wastes much of CPU’s computational power. Our proposed parallel implementation of a classical cyclic reduction algorithm to tackle the large linear systems arising from the discretized form of the elliptic problem at hand, schedules computing on both the GPU and the CPUs in a cooperative way. The experimental result demonstrates the effectiveness of this approach.     

Improving the performance of Invertible Bloom Lookup Tables

Invertible Bloom Lookup Tables (IBLTs) have been recently introduced as an extension of traditional Bloom filters. IBLTs store key-value pairs. Unlike traditional Bloom filters, IBLTs support both a lookup operation (given a key, return a value) and an operation that lists out all the key-value pairs stored. One issue with IBLTs is that there is a probability that a lookup operation will return “not found” for a key. In this paper, a technique to reduce this probability without affecting the storage requirement and only moderately increasing the search time is presented and evaluated. The results show that it can significantly reduce the probability of not returning a value that is actually stored in the IBLT. The overhead of the modified search procedure, compared to the standard IBLT search procedure, is small and has little impact on the average search time.