Probabilistic Graphical Models on Multi-Core CPUs using Java 8

In this paper, we discuss software design issues related to the development of parallel computational intelligence algorithms on multi-core CPUs, using the new Java 8 functional programming features. In particular, we focus on probabilistic graphical models (PGMs) and present the parallelisation of a collection of algorithms that deal with inference and learning of PGMs from data. Namely, maximum likelihood estimation, importance sampling, and greedy search for solving combinatorial optimisation problems. Through these concrete examples, we tackle the problem of defining efficient data structures for PGMs and parallel processing of same-size batches of data sets using Java 8 features. We also provide straightforward techniques to code parallel algorithms that seamlessly exploit multi-core processors. The experimental analysis, carried out using our open source AMIDST (Analysis of MassIve Data STreams) Java toolbox, shows the merits of the proposed solutions.Comment: Pre-print version of the paper presented in the special issue on Computational Intelligence Software at IEEE Computational Intelligence Magazine journa

Evaluating a gas-permeable culture surface for the generation of megakaryocytes for in-vitro platelet production

The ability to generate large numbers of platelets for transfusions is limited by the challenges of (1) efficiently generating platelet-like-particles (PLPs) from megakaryocytes (Mks) and (2) producing many Mks from each input CD34+ cell. Clinical-scale cell culture technologies for expanding CD34+ cells and differentiating them into Mks must be able to handle large media volumes and cell numbers. Recently, the G-Rex membrane system has been used to expand large numbers of T-cells within a scalable closed system. The gas-permeable membrane provides efficient gas transfer from the incubator atmosphere to the cells. CO2/O2 diffusion is no longer dictated by the media height, which restricts media usage in standard tissue culture flasks and wells. Additionally, the system allows the use of various of cell densities and larger volumes of media without the need for numerous media exchanges. Although the G-Rex membrane system has shown extensive benefits for expansion of different T-cell populations and cell lines, it has not been evaluated for its impact on the expansion and differentiation of CD34+ cells into Mks. In the bone marrow, megakaryopoiesis occurs over a gradient of oxygen tension – with hypoxic conditions near the bone and higher O2 concentrations at the vasculature. Our lab has previously published a three-phase Mk expansion protocol that mimics the O2 transition, as shown in Figure 1A. In this study we investigated the use of G-Rex membrane systems for Mk production from mobilized peripheral blood (mPB) CD34+ cells. High initial cell surface densities (0.1 x 106 cells/cm2 or greater) stunted the expansion and differentiation of cells through the first two phases of the process, whereas low surface densities (0.011 x 106 cells/cm2) led to expansion comparable to the standard protocol. However, a starting surface density of 0.04 x 106 cells/cm2 in the first phase of the culture resulted in a 2.3-fold increase in the number of Mks per input CD34+ cell compared to the standard process (Figure 1B). A media dilution scheme on Day 5 promoted not only expansion in the G-Rex system, but also for the control protocol. The G-Rex system with a media dilution scheme led to 3.6-fold increase in the number of Mks produced per mL of media used, thus potentially reducing the cost of a scaled-up process (Figure 1C). Finally, Mks produced using the G-Rex system demonstrated normal maturation aspects such as polyploidization, proplatelet formation, and PLP generation ex vivo. While this study primarily focused on the starting cell surface densities and a dilution scheme, other variables that could be optimized include starting media volumes, cytokine concentrations, transferring cells to larger G-Rex systems at later phases, and even potentially lowering the oxygen levels in phase one

Enabling large-scale ex vivo production of megakaryocytes and platelets from CD34+ cells using gas-permeable surfaces and microfluidic bioreactors

Patients suffering from acute or sustained thrombocytopenia require platelet transfusions, which are entirely donor-based and limited by challenges related to storage and fluctuating supply. Developing cell-culture technologies enables ex vivo and donor-independent platelet production. However, the ability to generate large numbers of platelets is limited by the challenges of (1) producing many megakaryocytes (Mks) from each input CD34+ cell and (2) efficiently generating platelet-like-particles (PLPs) from Mks. To address the first challenge, we evaluated Mk production from mobilized peripheral blood CD34+ cells cultured on a commercially available gas-permeable silicone membrane, which provides efficient gas exchange, and investigated the use of fed-batch media dilution schemes. Starting with a cell surface density of 4 x 104 CD34+ cells/cm2 (G4), culturing cells on the membrane for the first 5 days and employing media dilutions yielded 38 ± 25 Mks per input CD34+ cell by day 11 – a 2.2-fold increase compared to using standard tissue culture surfaces with full media exchanges. By day 7, G4 conditions generated 1.5-fold more CD34+ cells due to greater CD34 retention. Media dilution schemes for G4 and standard tissue culture surfaces improved culture viability, leading to a 3.6-fold increase in Mks produced per mL of media for G4 and 2.8-fold for tissue culture compared to controls. G4-Mks exhibited lower mean ploidy yet the number of high-ploidy Mks was equal to or greater than controls. Finally, G4-Mks produced proplatelets and PLPs that activated and aggregated upon stimulation. Further optimization is required to take full advantage of the gas-permeable system for Mk production. Additional studies would include refining surface densities, adjusting cytokine concentrations and initial media volumes and evaluating cord blood CD34+ cells. To address the second challenge, we applied computational fluid dynamics (CFD) modeling to assess published microfluidic platelet bioreactors and used those results to develop an improved 7-μm slit bioreactor with well-defined flow patterns and uniform shear profiles (USRB-7µm). The slits mimic fenestrations in endothelial cells lining sinuses in the bone marrow through which Mks extend cytoplasmic projections, called proplatelets (proPLTs), that are sheared off (50-200 s-1) into platelets. In the USRB-7µm, a center channel flow pushes Mks into 7-μm slits, with shear rates of 5000 s-1. Two outside flows converge at the slits exerting near uniform shear rates (250-350 s-1) to fragment extending proPLTs, similar to the in vivo process. The USRB-7µm permits real-time visualization of proPLT formation and the rapid-release of individual platelet-like-particles (PLPs), which has been observed in vivo, but not previously reported for bioreactors. Collected PLPs exhibited characteristics similar to fresh blood platelets. Surprisingly, using only the center flow without the outside flows led to a 6-fold increase in PLP production. Based on this, we scaled-up the USRB-7µm using only a single flow to carry Mks into high-shear slit regions, mimicking in vivo observations of Mks being processed directly into platelets within the lung capillary bed (\u3e2600 s-1). The new lung-USRB retained uniform shear rates with a 93-fold capture area increase to allow more Mks to be processed into PLPs. The USRB-7µm and lung-USRB will be useful tools for the analysis of proPLT/PLP formation to further understanding of how to increase ex vivo platelet production. These results highlight distinct improvements in Mk cell-culture and demonstrate how new technologies and techniques are needed to enable clinically-relevant production of Mks for platelet generation and cell-based therapies

Paper and toner three-dimensional fluidic devices: Programming fluid flow to improve point-of-care diagnostics

We present a new method for fabricating three-dimensional paper-based fluidic devices that uses toner as a thermal adhesive to bond multiple layers of patterned paper together. The fabrication process is rapid, involves minimal equipment (a laser printer and a laminator) and produces complex channel networks with dimensions down to 1 mm. The devices can run multiple diagnostic assays on one or more samples simultaneously, can incorporate positive and negative controls and can be programmed to display the results of the assays in a variety of patterns. The patterns of the results can encode information, which could be used to identify counterfeit devices, identify samples, encrypt the results for patient privacy or monitor patient compliance

Correction to Fully Enclosed Microfluidic Paper-Based Analytical Devices

There is an error in the units of the concentrations of potassium iodide and trehalose described in the experimental details on page 1581. The correct concentrations are 0.6 M potassium iodide and 0.3 M trehalose

Fully Enclosed Microfluidic Paper-Based Analytical Devices

This article introduces fully enclosed microfluidic paper-based analytical devices (microPADs) fabricated by printing toner on the top and bottom of the devices using a laser printer. Enclosing paper-based microfluidic channels protects the channels from contamination, contains and protects reagents stored on the device, contains fluids within the channels so that microPADs can be handled and operated more easily, and reduces evaporation of solutions from the channels. These benefits extend the capabilities of microPADs for applications as low-cost point-of-care diagnostic devices

Two-ply channels for faster wicking in paper-based microfluidic devices

This article describes the development of porous two-ply channels for paper-based microfluidic devices that wick fluids significantly faster than conventional, porous, single-ply channels. The two-ply channels were made by stacking two single-ply channels on top of each other and were fabricated entirely out of paper, wax and toner using two commercially available printers, a convection oven and a thermal laminator. The wicking in paper-based channels was studied and modeled using a modified Lucas–Washburn equation to account for the effect of evaporation, and a paper-based titration device incorporating two-ply channels was demonstrated

Adaptation and Validation of the MapMe Body Image Scales in Spanish Parents of Schoolchildren

\ua9 2024 by the authors.Childhood overweight and obesity is a worldwide problem and to treat it parents’ detection has to be improved. The MapMe Body Image Scales (BIS) are a visual tool developed to improve parental perception of child weight in the United Kingdon (UK) based on British growth reference criteria. The aim of this study was to make a transcultural adaptation and validation of the MapMe BIS in Spain based on International Obesity Task Force (IOTF) cut offs A descriptive cross-sectional study was done. First, a translation and cultural adaptation was carried out. A total of 155 10–11-year-old children and their parents participated in this study. Children were measured to calculate their weight status, Body Mass Index (BMI), Body Fat Percentage (BFP) and Waist Circumference (WC), and their parents completed a purpose designed questionnaire about their perception and satisfaction of child’s body weight status using the adapted BIS. Test-retest reliability, criterion validity and concurrent validity of the adapted BIS were analyzed. This study shows that the adapted MapMe BIS has good psychometric properties and is a suitable visual scale to assess parental perception of weight status in 10 and 11-year-old children in Spain

MAP inference in dynamic hybrid Bayesian networks

In this paper, we study the maximum a posteriori (MAP) problem in dynamic hybrid Bayesian networks. We are interested in finding the sequence of values of a class variable that maximizes the posterior probability given evidence. We propose an approximate solution based on transforming the MAP problem into a simpler belief update problem. The proposed solution constructs a set of auxiliary networks by grouping consecutive instantiations of the variable of interest, thus capturing some of the potential temporal dependences between these variables while ignoring others. Belief update is carried out independently in the auxiliary models, after which the results are combined, producing a configuration of values for the class variable along the entire time sequence. Experiments have been carried out to analyze the behavior of the approach. The algorithm has been implemented using Java 8 streams, and its scalability has been evaluated