Kronos: a workflow assembler for genome analytics and informatics.

BackgroundThe field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into "best practices" for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise.ResultsWe present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows.ConclusionsThe Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos

The effects of combined low level laser therapy and mesenchymal stem cells on bone regeneration in rabbit calvarial defects

Abstract: This study evaluated the effect of Low Level Laser Therapy (LLLT) and Mesenchymal Stem Cells (MSCs) on bone regeneration. Background data: Although several studies evaluated the effects of MSCs and LLLT, there is little information available regarding in vivo application of LLLT in conjunction with MSCs. Methods: Forty-eight circular bone defects (6 mm in diameter) were prepared in the calvaria of 12 New- Zealand white rabbits. The defects of each animal were randomly assigned to 4 groups: (C) no treatment; (L) applying LLLT; (SC) filled with MSCs; (SCL) application of both MSCs and LLLT. LLL was applied on alternate days at wavelength of 810 nm, power density of 0.2 W/cm2 and a fluency of 4 J/cm2 using a Gallium–Aluminum–Arsenide (GaAlAs) diode laser. The animals were sacrificed after 3 weeks and then histological samples were evaluated to determine the amount of new bone formation and the remaining scaffold and inflammation. Results: The histological evaluation showed a statistically significant increase in new bone formation of LLLT group relative to the control and the other two experimental groups (p < 0.05). There was no significant difference in bone formation of the control group compared to experimental groups filled with MSCs. Laser irradiation had no significant effect on resorption of the scaffold material. In addition, inflammation was significantly reduced in LLLT group compared to the control defects and the other two experimental groups. Conclusion: Low level laser therapy could be effective in bone regeneration but there is no evidence of a synergistic effect when applied in conjunction with MSCs

A Roadmap for the Production of a GMP-Compatible Cell Bank of Allogeneic Bone Marrow-Derived Clonal Mesenchymal Stromal Cells for Cell Therapy Applications

Background: Allogeneic mesenchymal stromal cells (MSCs) have been used extensively in various clinical trials. Nevertheless, there are concerns about their efficacy, attributed mainly to the heterogeneity of the applied populations. Therefore, producing a consistent population of MSCs is crucial to improve their therapeutic efficacy. This study presents a good manufacturing practice (GMP)-compatible and cost-effective protocol for manufacturing, banking, and lot-release of a homogeneous population of human bone marrow-derived clonal MSCs (cMSCs). Methods: Here, cMSCs were isolated based on the subfractionation culturing method. Afterward, isolated clones that could reproduce up to passage three were stored as the seed stock. To select proliferative clones, we used an innovative, cost-effective screening strategy based on lengthy serial passaging. Finally, the selected clones re-cultured from the seed stock to establish the following four-tired cell banking system: initial, master, working, and end of product cell banks (ICB, MCB, WCB, and EoPCB). Results: Through a rigorous screening strategy, three clones were selected from a total of 21 clones that were stored during the clonal isolation process. The selected clones met the identity, quality, and safety assessments criteria. The validated clones were stored in the four-tiered cell bank system under GMP conditions, and certificates of analysis were provided for the three-individual ready-to-release batches. Finally, a stability study validated the EoPCB, release, and transport process of the frozen final products. Conclusion: Collectively, this study presents a technical and translational overview of a GMP-compatible cMSCs manufacturing technology that could lead to the development of similar products for potential therapeutic applications. Graphical Abstract: [Figure not available: see fulltext.

Evaluating the Efficiency of Jackson Model in the Learning of the Learners in an Adaptive Learning System

One of the most important parameters in personalization of adaptive learning web-based educational systems is learning style. Up to now, various  learning styles proposed and this paper tries to evaluate the efficiency of using one of them, Jackson model. In this study, we  categorized students as model says and delivered learning content matched to each group learning style.  Findings of the study indicate differences in performance between matched and non-matched students in one case of the study and in the other case, demonstrate no significant difference. Although these results pertain to an undergraduate educational session, however our proposed framework is general enough to be applied to effective and efficient pedagogy in any area at any level

Relay selection with imperfect CSI in bidirectional cooperative networks

We study the performance of bidirectional multi-relay cooperative networks in the presence of imperfect channel state information by means of the correlation coefficient of the estimated channel gains and their actual values, where the max-min relay selection is used. We show that the performance is determined by the average performance of the two links and neither of them dominates it individually. We also present a power allocation scheme that minimizes the outage probability

Effects of Photobiomodulation and Mesenchymal Stem Cells on Articular Cartilage Defects in a Rabbit Model

Objective: The aim of this study was to evaluate the effectiveness of the application of cultured autologous bone marrow mesenchymal stem cells (BMSCs) with scaffold and low-level laser therapy (LLLT) on the repair of articular cartilage defects in rabbits. Background data: For healing of the articular cartilage defects, although positive effects of BMSCs and LLLT have been demonstrated, their combination effect is still unknown; therefore, we investigated combining these two techniques has a synergistic effect. Materials and methods: After bone marrow aspiration from 10 rabbits, BMSCs were isolated, cultured in monolayer, suspended on a type I collagen scaffold and then implanted onto a full-thickness osteochondral defect (4 mm in diameter), artificially made on the patellar groove of both knees in the same rabbits. Then a knee was selected randomly in each rabbit as the experimental group, and subjected to Ga-Al-As (810 nm) laser irradiation with energy density of 4 J/cm2 every other day for 3 weeks. As the control group, the other knee did not receive LLLT. After this period, animals were euthanized and osteochondral defects were evaluated by histomorphometric methods. Results: No significant difference in new cartilage formation and inflammation was found between the groups (p > 0.05). However, there was significantly more new bone formation in the experimental group (p < 0.05). Conclusions: In terms of our research, although better healing in osteochondral defects was seen when combining BMSCs and LLLT compared with the use of BMSCs alone, this improvement was predominantly caused by new bone formation rather than new cartilage formation. © 2016, Mary Ann Liebert, Inc