Complex Protocols Research Articles

Cross Layer NOMA Interference Mitigation for Femtocell Users in 5G Environment

In this paper, we propose a joint channel allocation and power control algorithm by using cognitive radio non-orthogonal multiple access (CR-NOMA) for femtocell users (FUs). The aim is to maximize the sum rate of the FUs for guaranteed quality of service (QoS). With an aim to have guaranteed QoS for FUs, we use CR-NOMA at the femto base station (FBS). Then, an algorithm for pairing among strong and weak users is proposed by using the channel gain difference. Using pairing, the NOMA interference between them reduces which results in better channel utilization. Moreover, we differentiate the even/odd number of FUs in a femtocell to provide the QoS for weak users also. For this purpose, OMA is used to get a predefined data rate using a greedy channel allocation algorithm. The power of each FBS is controlled by using the successive convex approximation for low complexity (SCALE) protocol with Karush-Kuhn-Tucker (KKT) conditions. Numerical results demonstrate that the proposed scheme enhances the sum rate and provides guaranteed QoS for CR-NOMA based femtocell users in comparison to the existing conventional OMA based-femtocell techniques.

5th Annual Immuno-Oncology 360° Conference: Spanning Science and Business to Bring New Therapies to Patients

5th Annual Immuno-Oncology 360° Conference: Spanning Science and Business to Bring New Therapies to Patients

Tailoring the CRISPR system to transactivate coagulation gene promoters in normal and mutated contexts

Engineered transcription factors (TF) have expanded our ability to modulate gene expression and hold great promise as bio-therapeutics. The first-generation TF, based on Zinc Fingers or Transcription-Activator-like Effectors (TALE), required complex and time-consuming assembly protocols, and were indeed replaced in recent years by the CRISPR activation (CRISPRa) technology. Here, with coagulation F7/F8 gene promoters as models, we exploited a CRISPRa system based on deactivated (d)Cas9, fused with a transcriptional activator (VPR), which is driven to its target by a single guide (sg)RNA.Reporter gene assays in hepatoma cells identified a sgRNA (sgRNAF7.5) triggering a ~35-fold increase in the activity of F7 promoter, either wild-type, or defective due to the c.-61T>G mutation. The effect was higher (~15-fold) than that of an engineered TALE-TF (TF4) targeting the same promoter region. Noticeably, when challenged on the endogenous F7 gene, the dCas9-VPR/sgRNAF7.5 combination was more efficient (~6.5-fold) in promoting factor VII (FVII) protein secretion/activity than TF4 (~3.8-fold). The approach was translated to the promoter of F8, whose reduced expression causes hemophilia A. Reporter gene assays in hepatic and endothelial cells identified sgRNAs that, respectively, appreciably increased F8 promoter activity (sgRNAF8.1, ~8-fold and 3-fold; sgRNAF8.2, ~19-fold and 2-fold) with synergistic effects (~38-fold and 2.7-fold). Since modest increases in F7/F8 expression would ameliorate patients' phenotype, the CRISPRa-mediated transactivation extent might approach the low therapeutic threshold.Through this pioneer study we demonstrated that the CRISPRa system is easily tailorable to increase expression, or rescue disease-causing mutations, of different promoters, with potential intriguing implications for human disease models.

New Platform for the Direct Profiling of microRNAs in Biofluids.

Circulating microRNAs have been identified as potential biomarkers for early detection, prognosis, and prediction of several diseases. Their use in clinical diagnostics has been limited by the lack of suitable detection techniques. Most of the current technologies suffer from requiring complex protocols, not yet able to deliver robust and cost-effective assays in the field of clinical diagnostics. In this work, we report the development of a breakthrough platform for profiling circulating microRNAs. The platform comprises a novel silicon photomultiplier-based reader in conjunction with a chemical-based method for nucleic acid detection. Accurate microRNAs profiling without extraction, pre-amplification, or pre-labeling of the target is now achievable. We designed and synthesized a set of reagents that combined the chemical-based method with a chemiluminescent reaction. The signals generated were read outusing a novel, compact silicon photomultiplier-based reader. The platform sensitivity was determined by measuring known concentrations of hsa-miR-21-5p spike-ins. The limit of detection was calculated as 4.7 pmol/L. The platform was also successfully used to directly detect hsa-miR-21-5p in eight non-small cell lung cancer plasma samples. Levels of plasma hsa-miR-21-5p expression were also measured via TaqMan RT-qPCR. The successful integration of theunique chemical-based method for nucleic acid detection with the novel silicon photomultiplier-based reader created an innovative product (ODG platform) with diagnostic utility, for the direct qualitative and quantitative analysis of microRNA biomarkers in biological fluids.

An easily applicable method to analyse the ankle-foot power absorption and production during walking

BackgroundPower and work at the ankle joint during gait are usually computed considering the foot as a rigid body [1–6] (Ankle Joint method, AJ). The foot is instead a deformable structure and can absorb and produce work by pronation/supination, foot arch deformation and other intrinsic movements. A different approach, named “the Distal Shank method (DS)” [7–12] considers all these aspects without increasing the complexity of the protocol, and thus it seems promising for clinical applications [12].Research questions: a) To characterize the differences in power and work computed using the two mentioned methods for a relatively large number of subjects walking at different velocities, barefoot and with different shoes; b) To assess the practical feasibility of the DS method for clinical applications. Materials and methodsEighteen healthy subjects were evaluated while walking barefoot at slow, natural and fast velocity. Shod walking was analysed at natural velocity. Four subjects were also analysed while walking in high-heel shoes. The power at the ankle joint was computed with both the AJ and the DS methods. We then compared the obtained results. ResultsThe DS method showed a consistent negative peak of power absorption during the load acceptance phase, barely visible with the AJ method. The maximum power production calculated with the DS method was significantly lower. The work at the end of the stride cycle was lower with the DS method, and in most conditions even negative, thus indicating higher energy dissipation. SignificanceWe confirmed on a large cohort of healthy subjects and in different walking conditions that neglecting foot deformations during gait leads to underestimate power absorption and overestimate power production. The DS method does not require a complex gait analysis protocol, nor additional time for the analysis, and can provide information of clinical interest, related to foot mechanical alterations.

Hyperspectral Imaging Based Method for Rapid Detection of Microplastics in the Intestinal Tracts of Fish.

Microplastics (MPs) in aquatic organisms are raising increasing concerns regarding their potential damage to ecosystems. To date, Raman and Fourier transform infrared spectroscopy techniques have been widely used for detection of MPs in aquatic organisms, which requires complex protocols of tissue digestion and MP separation and are time- and reagent-consuming. This novel approach directly separates, identifies, and characterizes MPs from the hyperspectral image (HSI) of the intestinal tract content in combination with a support vector machine classification model, instead of using the real digestion/separation protocols. The procedures of HSI acquisition (1 min) and data analysis (5 min) can be completed within 6 min plus the sample preparation and drying time (30 min) where necessary. This method achieved a promising efficiency (recall >98.80%, precision >96.22%) for identifying five types of MPs (particles >0.2 mm). Moreover, the method was also demonstrated to be effective on field fish from three marine fish species, revealing satisfying detection accuracy (particles >0.2 mm) comparable to Raman analysis. The present technique omits the digestion protocol (reagent free), thereby significantly reducing reagent consumption, saving time, and providing a rapid and efficient method for MP analysis.

Potent stimulation of eosinopoiesis in murine bone-marrow by myriadenolide is mediated by cysteinyl-leukotriene signaling

We describe the potent effect of myriadenolide (Myr), a naturally occurring labdane diterpene, in promoting the production of eosinophils in cultured bone-marrow from several inbred mouse strains. This enhancing effect is lineage-selective and requires the eosinophil growth factors, Interleukin(IL)-5 or GM-CSF. Myr acts over a very low concentration range (10−10–10−14 M), if added at the beginning of the cell cultivation. Its enhancing effect increases between 24 h and 10 days of culture. We used both pharmacological and genetical tools to analyze its mechanism of action. Several lines of evidence show that the enhancing effect of Myr requires functional integrity of the 5-lipoxygenase (5-LO) pathway, and of CysLT1 receptors, which transduce the effects of cysteinyl-leukotrienes generated through this pathway. Myr also protects developing eosinophils from apoptosis induced by exogenous prostaglandin E2 (PGE2), but not by NO, indicating that it acts upstream of NO in the PGE2-initiated proapoptotic pathway which requires iNOS and CD95. Exposure to NO concentrations insufficient to induce apoptosis abolished the ability of eosinophils to respond to Myr, suggesting the involvement of a NO-sensitive cellular target. Myr has potential as a chemically defined research tool, which can be used to generate large numbers of eosinophils, thereby overcoming current limitations in the biochemical and molecular biological study of murine eosinophils, which has so far depended on complex, labor-intensive and long-term culture protocols for in vitro expansion. SummaryPotent enhancing effects of Myr on eosinophil production in bone marrow stimulated by GM-CSF and IL-5 are mediated by the 5-LO pathway.

Assessment of Simplified Methods for Quantification of 18F-FDHT Uptake in Patients with Metastatic Castration-Resistant Prostate Cancer.

18F-fluorodihydrotestosterone (18F-FDHT) PET/CT potentially provides a noninvasive method for assessment of androgen receptor expression in patients with metastatic castration-resistant prostate cancer (mCRPC). The objective of this study was to assess simplified methods for quantifying 18F-FDHT uptake in mCRPC patients and to assess effects of tumor perfusion on these 18F-FDHT uptake metrics. Methods: Seventeen mCRPC patients were included in this prospective observational multicenter study. Test and retest 30-min dynamic 18F-FDHT PET/CT scans with venous blood sampling were performed in 14 patients. In addition, arterial blood sampling and dynamic 15O-H2O scans were obtained in a subset of 6 patients. Several simplified methods were assessed: Patlak plots; SUV normalized to body weight (SUVBW), lean body mass (SUVLBM), whole blood (SUVWB), parent plasma activity concentration (SUVPP), area under the parent plasma curve (SUVAUC,PP), and area under the whole-blood input curve (SUVAUC,WB); and SUVBW corrected for sex hormone-binding globulin levels (SUVSHBG). Results were correlated with parameters derived from full pharmacokinetic 18F-FDHT and 15O-H2O. Finally, the repeatability of individual quantitative uptake metrics was assessed. Results: Eighty-seven 18F-FDHT-avid lesions were evaluated. 18F-FDHT uptake was best described by an irreversible 2-tissue-compartment model. Replacing the continuous metabolite-corrected arterial plasma input function with an image-derived input function in combination with venous sample data provided similar Ki results (R2 = 0.98). Patlak Ki and SUVAUC,PP showed an excellent correlation (R2 > 0.9). SUVBW showed a moderate correlation to Ki (R2 = 0.70, presumably due to fast 18F-FDHT metabolism. When calculating SUVSHBG, correlation to Ki improved (R2 = 0.88). The repeatability of full kinetic modeling parameters was inferior to that of simplified methods (repeatability coefficients > 36% vs. < 28%, respectively). 18F-FDHT uptake showed minimal blood flow dependency. Conclusion:18F-FDHT kinetics in mCRPC patients are best described by an irreversible 2-tissue-compartment model with blood volume parameter. SUVAUC,PP showed a near-perfect correlation with the irreversible 2-tissue-compartment model analysis and can be used for accurate quantification of 18F-FDHT uptake in whole-body PET/CT scans. In addition, SUVSHBG could potentially be used as an even simpler method to quantify 18F-FDHT uptake when less complex scanning protocols and accuracy are required.

A transformative translational change programme to introduce genomics into healthcare: a complexity and implementation science study protocol

IntroductionTranslating scientific advances in genomic medicine into evidence-based clinical practice is challenging. Studying the natural translation of genomics into ‘early-adopting’ health system sectors is essential. We will (a) examine 29...

Automated Chemical Sensing Unit Integration for Parallel Optical Interrogation.

We report the integration of an automated chemical optical sensing unit for the parallel interrogation of 12 BICELLs in a sensing chip. The work was accomplished under the European Project Enviguard (FP7-OCEAN-2013-614057) with the aim of demonstrating an optical nano-biosensing unit for the in-situ detection of various chemical pollutants simultaneously in oceanic waters. In this context, we designed an optical sensing chip based on resonant nanopillars (R-NPs) transducers organized in a layout of twelve biophotonic sensing cells (BICELLs). The sensing chip is interrogated in reflection with a 12-channels optical spectrometer equipped with an embedded computer-on-chip performing image processing for the simultaneous acquisition and analysis (resonant mode fitting) of the 12 spectra. A microfluidic chip and an automated flow control system composed of four pumps and a multi-path micro-valve makes it possible to drive different complex protocols. A rack was designed ad-hoc for the integration of all the modules. As a proof of concept, fluids of different refractive index (RI) were flowed in the system in order to measure the time response (sensogram) of the R-NPs under optical reflectance, and assess the sensors’ bulk sensitivity (285.9 ± 16.4 nm/RIU) and Limit of Detection (LoD) (2.95 × 10−6 RIUS). The real-time response under continuous flow of a sensor chip based on R-NP is showed for the first time, obtaining 12 sensograms simultaneously, featuring the unit as a potential excellent multiplexed detection system. These results indicate the high potential of the developed chemical sensing unit to be used for in-situ, multiplex and automatic optical biosensing.

An efficient scheme for applying software updates in pervasive computing applications

The Internet of Things (IoT) offers a vast infrastructure of numerous interconnected devices capable of communicating and exchanging data. Pervasive computing applications can be formulated on top of the IoT involving nodes that can interact with their environment and perform various processing tasks. Any task is part of intelligent services executed in nodes or the back end infrastructure for supporting end users’ applications. In this setting, one can identify the need for applying updates in the software/firmware of the autonomous nodes. Updates are extensions or patches significant for the efficient functioning of nodes. Legacy methodologies deal with centralized approaches where complex protocols are adopted to support the distribution of the updates in the entire network. In this paper, we depart from the relevant literature and propose a distributed model where each node is responsible to, independently, initiate and conclude the update process. Nodes monitor a set of metrics related to their load and the performance of the network and through a time-optimized scheme identify the appropriate time to conclude the update process. We report on an infinite horizon optimal stopping model on top of the collected performance data. The aim is to make nodes capable of identifying when their performance and the performance of the network are of high quality to efficiently conclude the update process. We provide specific formulations and the analysis of the problem while extensive simulations and a comparison assessment reveal the advantages of the proposed solution.

Rapid and accurate structure-based therapeutic peptide design using GPU accelerated thermodynamic integration.

Peptide-based therapeutics are an alternative to small molecule drugs as they offer superior specificity, lower toxicity, and easy synthesis. Here we present an approach that leverages the dramatic performance increase afforded by the recent arrival of GPU accelerated thermodynamic integration (TI). GPU TI facilitates very fast, highly accurate binding affinity optimization of peptides against therapeutic targets. We benchmarked TI predictions using published peptide binding optimization studies. Prediction of mutations involving charged side-chains was found to be less accurate than for non-charged, and use of a more complex 3-step TI protocol was found to boost accuracy in these cases. Using the 3-step protocol for non-charged side-chains either had no effect or was detrimental. We use the benchmarked pipeline to optimize a peptide binding to our recently discovered cancer target: EME1. TI calculations predict beneficial mutations using both canonical and non-canonical amino acids. We validate these predictions using fluorescence polarization and confirm that binding affinity is increased. We further demonstrate that this increase translates to a significant reduction in pancreatic cancer cell viability.

Optimization of Differentiation of Nonhuman Primate Pluripotent Cells Using a Combinatorial Approach.

The directed differentiation of pluripotent stem cells to a desired lineage often involves complex and lengthy protocols. In order to study the requirements for differentiation in a systematic way, we present here methodology for an iterative approach using combinations of small molecules and biological factors. The factors are used in a cyclical process in which the best combination of factors and concentrations is selected in one round of testing, followed by a modification of the combination and subsequent rounds. While this may produce the desired differentiation in the cell population under study, it is also possible that other strategies may be needed to optimize the differentiation process. These strategies are described in this chapter.

Chromogenic Tissue-Based Methods for Detection of Gene Amplifications (or Rearrangements) Combined with Protein Overexpression in Clinical Samples.

Immunohistochemistry (IHC) is a well-established, tissue-based assay for the visualization of target proteins. For analysis of DNA targets, chromogenic in situ hybridization (CISH) applications have significant advantages over traditional fluorescence in situ hybridization (FISH). CISH slides can be analyzed using a regular light microscope, while FISH slides require the use of a specialized fluorescence microscope in a dark room. CISH slides allow observers to correlate the gene status (gene amplifications, gene rearrangements, and gene deletions) in the context of tissue morphology better than FISH slides. Recently, a combination of IHC and CISH assays (gene-protein assay, GPA) was developed to study the relationship between gene status and protein expression on the same tissue section. CISH and GPA applications can be optimized using an automated tissue slide processing system to generate reproducible results for a long and complex assay protocol. GPA applications are an ideal approach for tumor status and heterogeneity analyses for research and clinical investigations.

Innovative technologies in training and education for maintenance team of NPPs

Many industries, such as nuclear power plants, chemical industry, oil and gas industry have dangerous working environments and hazardous conditions for employees. Maintenance, inspection and decommissioning activities in these safety-critical areas mean a serious risk, downtime is a significant financial loss. The Virtual Reality Training Platform is reflecting on this shortcoming, by providing the possibility for maintenance workers to be trained and prepared for unexpected scenarios, and to learn complex maintenance protocols without being exposed to unnecessary danger, like high temperature, radiation, etc. Employees can have training for equipment maintenance, dismantling of facilities at closed NPP Units. One of the most significant and unique added value of the immersive virtual reality solution is that the operator can experience lifelike emergencies (detonation, shutdown) under psychological pressure, while all of the physiology indicators can be monitored like eye-tracking. Users can work together anywhere in the world. A huge financial outage in industrial production is the preparation and maintenance downtime, which can be significantly reduced by the Virtual Training platform. This method can increase the accuracy, safety, reliability, and accountability of the maintenance and decommissioning procedures, while operational costs can be reduced as well.

Engineering a Multilayered Skin Equivalent: The Importance of Endogenous Extracellular Matrix Maturation to Provide Robustness and Reproducibility.

Human skin equivalents (HSEs) are a valuable tool for both academic and industrial laboratories to further the understanding of skin physiology and associated diseases. Over the last few decades, there have been many advances in the development of HSEs that successfully recapitulate the structure of human skin in vitro; however a main limitation is variability due to the use of complex protocols and exogenous extracellular matrix (ECM) proteins. We have developed a robust and unique full-thickness skin equivalent that is highly reproducible due to the use of a consistent scaffold, commercially available cells, and defined low-serum media. The Alvetex® scaffold technology allows fibroblasts to produce their own endogenous ECM proteins within the scaffold, which alleviates the need for exogenous collagen, and supports the differentiation and stratification of the epidermis. Our full-thickness skin equivalent is generated using a detailed step-by-step protocol, which sequentially forms the multilayered structure of human skin in vitro. This model can be adapted for many downstream applications such as disease modeling and testing of active compounds for cosmetics.

Are only pre-transplant rituximab and plasma exchange sufficient for desensitization protocol of ABO incompatible LDLT?

Introduction: ABO incompatible living donor liver transplantation (ABOi LDLT) has become a feasible option because of improved outcomes by various desensitization strategies. However, the protocol of ABOi LDLT has not been established worldwide. Nevertheless, the results after transplantation are homogenous. The reports for the results of ABOi LDLT using only rituximab and plasma exchange are scarce. We present the outcomes of our desensitization protocol for ABOi LDLT. Method: From January 2015 to August 2018, we performed 117 LDLTs. Of them, 29 patients (25%) received ABOi LDLT. We used only a single dose of rituximab(300 mg/m2) and several plasma exchanges for pre-transplant desensitization in ABOi LDLT and post-transplant immunosuppression consisted of basiliximab, tacrolimus, mycophenolate mofetil and steroid. The target iso-agglutinin IgG titer before transplantation and during post-transplant period were 1:32 and 1:64. Result: The mean initial iso-agglutinin IgG titer was 131 (range, 4∼512) and initial iso-agglutinin IgG titer in recipient blood type O was higher than in another blood types. Pre-transplant plasma exchanges were performed in all recipients with more than target titer (mean number of sessions, 2.32 (range, 1∼5)). Post-transplant plasma exchanges were performed in 3 patients because of higher target isoaaglutinin titer (> 1:64), but none had antibody mediated rejection. Biliary complications were identified in 8 patients, but all was anastomotic site stricture. Acute cellular rejection was confirmed in one patient and resolved by steroid pulse therapy. Conclusion: Both rituximab and plasma exchange along are one of desensitization strategies to eliminate the risk of antibody mediated rejection and our results were also comparable to ABO-identical or compatible LDLT. Hence, we believe that complex protocols including splenectomy, intravenous immunoglobulin, and local infusion therapy are not necessary in most ABOi LDLT.

Three Optimized Methods for In Situ Quantification of Progenitor Cell Proliferation in Embryonic Kidneys Using BrdU, EdU, and PCNA.

Background:Nephron progenitor cells derived from the metanephric mesenchyme undergo a complex balance of self-renewal and differentiation throughout kidney development to give rise to the mature nephron. Cell proliferation is an important index of progenitor population dynamics. However, accurate and reproducible in situ quantification of cell proliferation within progenitor populations can be technically difficult to achieve due to the complexity and harsh tissue treatment required of certain protocols.Objective:To optimize and compare the performance of the 3 most accurate S phase–specific labeling methods used for in situ detection and quantification of nephron progenitor and ureteric bud cell proliferation in the developing kidney, namely, 5-bromo-2’-deoxyuridine (BrdU), 5-ethynyl-2’-deoxyuridine (EdU), and proliferating cell nuclear antigen (PCNA).Methods:Protocols for BrdU, EdU, and PCNA were optimized for fluorescence labeling on paraformaldehyde-fixed, paraffin-embedded mouse kidney tissue sections, with co-labeling of nephron progenitor cells and ureteric bud with Six2 and E-cadherin antibodies, respectively. Image processing and analysis, including quantification of proliferating cells, were carried out using free ImageJ software.Results:All 3 methods detect similar ratios of nephron progenitor and ureteric bud proliferating cells. The BrdU staining protocol is the lengthiest and most complex protocol to perform, requires tissue denaturation, and is most subject to interexperimental signal variability. In contrast, bound PCNA and EdU protocols are relatively more straightforward, consistently yield clear results, and far more easily lend themselves to co-staining; however, the bound PCNA protocol requires substantive additional postexperimental analysis to distinguish the punctate nuclear PCNA staining pattern characteristic of proliferating cells.Conclusions:All 3 markers exhibit distinct advantages and disadvantages in quantifying cell proliferation in kidney progenitor populations, with EdU and PCNA protocols being favored due to greater technical ease and reproducibility of results associated with these methods.

Mild complexation protocol for chiral CpxRh and Ir complexes suitable for in situ catalysis.

A practical complexation method for chiral cyclopentadienyl (Cpx) iridium and rhodium complexes is described. The procedure uses the free CpxH with stable and commercially available rhodium(i) and iridium(i) salts without base or additive. The conditions are mild and do not require the exclusion of air and moisture. A salient feature is the suitability for in situ complexations enhancing the user-friendliness of Cpx ligands in asymmetric catalysis. DFT-calculations confirm an intramolecular proton abstraction pathway by either the bound acetate or methoxide. Furthermore, the superior facial selectivity of the proton abstraction step enabled the development of TMS-containing trisubstituted Cpx ligands which display improved enantioselectivities for the benchmarking dihydroisoquinolone synthesis.

SDN/NFV Based Internet of Things for Multi-Tenant Networks

The Internet of Things (IoT) refers to variety of smart devices such as smartphones, tablets, and sensors that can interact and exchange of data among devices through the Internet. The diversity of IoT devices and their services have posed a larger range requirements of availability, throughput, latency, and performance in heterogeneous connectivity environments. Meanwhile, the existing networks often struggle with such of limitations in complex control protocols and difficulty in internetworking with billions of smart devices with different requirements such as latency and bandwidth allocations. These obstacles become substantial barriers to deploy services, as well as isolate between multiple co-existing tenants on the same physical network, deploy simultaneous protocols in the network, be stable to maintain the bandwidth and latency according to predefined QoS demands. These obstacles have recently been facilitated by Software Defined Network (SDN) and Network Function Virtualization (NFV) technologies that enable the programming and monitoring in data plane. In this study, firstly, the authors investigate and propose a SDN/NFV based architecture for multi-tenant networks with plenty of network slices working in a shared physical infrastructure. Secondly, P4 and ONOS Controller are used to implement a deep programming in BMv2 devices to efficiently maintain the network motoring in order to guarantee the E2E latency of communicating channels. Finally, the VXLAN technologies are exploited to for network slicing with different purposes and applications, and Inband Network Telemetry (INT) is used to monitor network latency.