Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell Type Influences Local Delivery of Biomolecules from a Bioinspired Apatite Drug Delivery System

Recently, the benefit of step-wise sequential delivery of fibroblast growth factor-2 (FGF-2) and bone morphogenetic protein-2 from a bioinspired apatite drug delivery system on mouse calvarial bone repair was demonstrated. The thicknesses of the nanostructured poly-l-Lysine/poly-l-Glutamic acid polyelectrolyte multilayer (PEM) and the bone-like apatite barrier layer that make up the delivery system, were varied. The effects of the structural variations of the coating on the kinetics of cell access to a cytotoxic factor delivered by the layered structure were evaluated. FGF-2 was adsorbed into the outer PEM, and cytotoxic antimycin-A (AntiA) was adsorbed to the substrate below the barrier layer to detect the timing of the cell access. While MC3T3-E1 osteoprogenitor cells accessed AntiA after three days, the RAW 264.7 macrophage access occurred within 4 h, unless the PEM layer was removed, in which case the results were reversed. Pits were created in the coating by the RAW 264.7 macrophages and initiated delivery, while the osteoprogenitor cell access to drugs occurred through a solution-mediated coating dissolution, at junctions between the islands of crystals. Macrophage-mediated degradation is therefore a mechanism that controls drug release from coatings containing bioinspired apatite.
Long Non-Coding RNAs in Gliomas: From Molecular Pathology to Diagnostic Biomarkers and Therapeutic Targets

Gliomas are the most common malignancies of the central nervous system. Because of tumor localization and the biological behavior of tumor cells, gliomas are characterized by very poor prognosis. Despite significant efforts that have gone into glioma research in recent years, the therapeutic efficacy of available treatment options is still limited, and only a few clinically usable diagnostic biomarkers are available. More and more studies suggest non-coding RNAs to be promising diagnostic biomarkers and therapeutic targets in many cancers, including gliomas. One of the largest groups of these molecules is long non-coding RNAs (lncRNAs). LncRNAs show promising potential because of their unique tissue expression patterns and regulatory functions in cancer cells. Understanding the role of lncRNAs in gliomas may lead to discovery of the novel molecular mechanisms behind glioma biological features. It may also enable development of new solutions to overcome the greatest obstacles in therapy of glioma patients. In this review, we summarize the current knowledge about lncRNAs and their involvement in the molecular pathology of gliomas. A conclusion follows that these RNAs show great potential to serve as powerful diagnostic, prognostic, and predictive biomarkers as well as therapeutic targets.
An algorithm for trajectory prediction of flight plan based on relative motion between positions

Traditional methods for plan path prediction have low accuracy and stability. In this paper, we propose a novel approach for plan path prediction based on relative motion between positions (RMBP) by mining historical flight trajectories. A probability statistical model is introduced to model the stochastic factors during the whole flight process. The model object is the sequence of velocity vectors in the three-dimensional Earth space. First, we model the moving trend of aircraft including the speed (constant, acceleration, or deceleration), yaw (left, right, or straight), and pitch (climb, descent, or cruise) using a hidden Markov model (HMM) under the restrictions of aircraft performance parameters. Then, several Gaussian mixture models (GMMs) are used to describe the conditional distribution of each moving trend. Once the models are built, machine learning algorithms are applied to obtain the optimal parameters of the model from the historical training data. After completing the learning process, the velocity vector sequence of the flight is predicted by the proposed model under the Bayesian framework, so that we can use kinematic equations, depending on the moving patterns, to calculate the flight position at every radar acquisition cycle. To obtain higher prediction accuracy, a uniform interpolation method is used to correct the predicted position each second. Finally, a plan trajectory is concatenated by the predicted discrete points. Results of simulations with collected data demonstrate that this approach not only fulfils the goals of traditional methods, such as the prediction of fly-over time and altitude of waypoints along the planned route, but also can be used to plan a complete path for an aircraft with high accuracy. Experiments are conducted to demonstrate the superiority of this approach to some existing methods.
Using Satellite-Derived Vegetation Products to Evaluate LDAS-Monde over the Euro-Mediterranean Area

Within a global Land Data Assimilation System (LDAS-Monde), satellite-derived Surface Soil Moisture (SSM) and Leaf Area Index (LAI) products are jointly assimilated with a focus on the Euro-Mediterranean region at 0.5∘ resolution between 2007 and 2015 to improve the monitoring quality of land surface variables. These products are assimilated in the CO2 responsive version of ISBA (Interactions between Soil, Biosphere and Atmosphere) land surface model, which is able to represent the vegetation processes including the functional relationship between stomatal aperture and photosynthesis, plant growth and mortality (ISBA-A-gs). This study shows the positive impact on SSM and LAI simulations through assimilating their satellite-derived counterparts into the model. Using independent flux estimates related to vegetation dynamics (evapotranspiration, Sun-Induced Fluorescence (SIF) and Gross Primary Productivity (GPP)), it is also shown that simulated water and CO2 fluxes are improved with the assimilation. These vegetation products tend to have higher root-mean-square deviations in summer when their values are also at their highest, representing 20–35% of their absolute values. Moreover, the connection between SIF and GPP is investigated, showing a linear relationship depending on the vegetation type with correlation coefficient values larger than 0.8, which is further improved by the assimilation.
Phosphoinositide‐dependent kinase 1–associated glycolysis is regulated by miR‐409‐3p in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most popular kidney cancer in adults. Metabolic shift toward aerobic glycolysis is a fundamental factor for ccRCC therapy. MicroRNAs (miRNAs) are thought to be important regulators in ccRCC development and progression. Phosphoinositide‐dependent kinase 1 (PDK1) is required for metabolic activation; however, the role of PDK1‐induced glycolytic metabolism regulated by miRNAs is unclear in ccRCC. So, the purpose of the current study is to elucidate the underlying mechanism in ccRCC cell metabolism mediated by PDK1. Our results revealed that miR‐409‐3p inhibited glycolysis by regulating PDK1 expression in ccRCC cells. We also found that miR‐409‐3p was regulated by hypoxia. Our results indicated that PDK1 facilitated ccRCC cell glycolysis, regulated by miR‐409‐3p in hypoxia.
Mapping Damage-Affected Areas after Natural Hazard Events Using Sentinel-1 Coherence Time Series

The emergence of the Sentinel-1A and 1B satellites now offers freely available and widely accessible Synthetic Aperture Radar (SAR) data. Near-global coverage and rapid repeat time (6–12 days) gives Sentinel-1 data the potential to be widely used for monitoring the Earth’s surface. Subtle land-cover and land surface changes can affect the phase and amplitude of the C-band SAR signal, and thus the coherence between two images collected before and after such changes. Analysis of SAR coherence therefore serves as a rapidly deployable and powerful tool to track both seasonal changes and rapid surface disturbances following natural disasters. An advantage of using Sentinel-1 C-band radar data is the ability to easily construct time series of coherence for a region of interest at low cost. In this paper, we propose a new method for Potentially Affected Area (PAA) detection following a natural hazard event. Based on the coherence time series, the proposed method (1) determines the natural variability of coherence within each pixel in the region of interest, accounting for factors such as seasonality and the inherent noise of variable surfaces; and (2) compares pixel-by-pixel syn-event coherence to temporal coherence distributions to determine where statistically significant coherence loss has occurred. The user can determine to what degree the syn-event coherence value (e.g., 1st, 5th percentile of pre-event distribution) constitutes a PAA, and integrate pertinent regional data, such as population density, to rank and prioritise PAAs. We apply the method to two case studies, Sarpol-e, Iran following the 2017 Iran-Iraq earthquake, and a landslide-prone region of NW Argentina, to demonstrate how rapid identification and interpretation of potentially affected areas can be performed shortly following a natural hazard event.
A Case for Granularity Aware Page Migration

Memory is becoming increasingly heterogeneous with the emergence of disparate memory technologies ranging from non-volatile memories like PCM, STT-RAM, and memristors to 3D-stacked memories like HBM. In such systems, data is of ten migrated across memory regions backed by different technologies for better overall performance. An effective migration mechanism is a prerequisite in such systems. Prior works on OS-directed page migration have focused on what data to migrate and/or on when to migrate. In this work, we demonstrate the need to investigate another dimension -- how much to migrate. Specifically, we show that the amount of data migrated in a single migration operation (called "migration granularity") is vital to the overall performance. Through analysis on real hardware, we further show that different applications benefit from different migration granularities, owing to their distinct memory access characteristics. Since this preferred migration granularity may not be known a priori, we propose a novel scheme to infer this for any given application at runtime. When implemented in the Linux OS, running on a current hardware, the performance improved by up to 36% over a baseline with a fixed migration granularity.
Reducing the Attentional Demands of In-Vehicle Touchscreens with Stencil Overlays

Vehicle manufacturers are increasingly using touchscreens to support driver access to controls. However, input mechanisms displayed on touchscreens lack the tactile sensations of physical controls, creating risks of greater demand for visual attention. These risks can potentially be mitigated by restoring some degree of tactile feedback to touchscreen interaction. This paper describes a study that examines whether touchscreen target selection during simulated driving is improved by overlaying the touchscreen with a see-through 3D printed stencil that allows underlying touchscreen controls to be located or guided by feel. Results showed that touchscreen targets were selected more quickly and with shorter periods of visual attention towards the touchscreen when the stencil was present than when it was absent. Subjective preferences also favoured the stencil condition. The work demonstrates the value of adding tactile feedback to touchscreen interaction, and shows that stencils are a simple and effective way to reduce attentional demands.
Oxidative Damage and Nrf2 Translocation Induced by Toxicities of Deoxynivalenol on the Placental and Embryo on Gestation Day 12.5 d and 18.5 d

Deoxynivalenol (DON) is a kind of natural pollutant belonging to the trichothecenes family. The aim of this study is to use diverse assays to evaluate oxidative damage as well as translocation of nuclear factor erythroid 2-related factor 2 (Nrf2), and to investigate their mechanisms in DON-induced toxicities on a placenta and embryo. Pregnant C57BL/6 mice were randomly assigned to three groups with different doses of DON: 0, 1.0, 2.5 mg/(kg·day). In gestation day (GD) 12.5 d and 18.5 d, DON induced an elevated resorption rate of the embryos as well as structural and functional damage of the placenta. In the placenta, altered levels of the antioxidant enzymes malondialdehyde, superoxide dismutase and glutathione indicated remarkable oxidative stress. Furthermore, an elevated level of heme oxygenase-1 (HO-1) and the translocation of Nrf2 from nucleus to cytoplasm indicated Nrf2/HO-1 pathway activation in DON-L group (1.0 mg/(kg·day)). It is noteworthy that the results in this experiment in GD 12.5 d were similar to those in GD 18.5 d. In conclusion, DON-induced placental oxidative damage and Nrf2 translocation were similar in GD 12.5 d and GD 18.5 d. Oxidative stress is one of the most important molecular mechanisms for embryotoxicity induced by DON, and Nrf2 translocation may play a substantial role against it.
Partitioned security processor architecture on FPGA platform

Internet protocol security (IPSec), secure sockets layer (SSL)/transport layer security (TLS) and other security protocols necessitate high throughput hardware implementation of cryptographic functions. In recent literature, cryptographic functions implemented in software, application specific integrated circuit (ASIC) and field programmable gate array (FPGA). They are not necessarily optimized for throughput. Due to the various side-channel based attacks on cache and memory, and various malware based exfiltration of security keys and other sensitive information, cryptographic enclave processors are implemented which isolates the cryptographically sensitive information like keys. We propose a partitioned enclave architecture targeting IPSec, TLS and SSL where the partitioned area ensures that the processor data-path is completely isolated from the secret-key memory. The security processor consists of a Trivium random number generator, Rivest–Shamir–Adleman (RSA), advanced encryption standard (AES) and KECCAK cryptos. We implement three different optimized KECCAK architectures. The processing element (PE) handles all communication interfaces, data paths, and control hazards of network security processor. The memory of KECCAK and AES communication is done via a direct memory access controller to reduce the PE overhead. The whole system is demonstrated by FPGA implementation using Vivado 2015.2 on Artix-7 (XC7A100T, CSG324). The performances of the implemented KECCAKs are better in terms of security, throughput and resource than the existing literature.
ComPEND: Computation Pruning through Early Negative Detection for ReLU in a Deep Neural Network Accelerator

While negative inputs for ReLU are useless, it consumes a lot of computing power to calculate them for deep neural networks. We propose a computation pruning technique that detects at an early stage that the result of a sum of products will be negative by adopting an inverted two's complement expression for weights and a bit-serial sum of products. Therefore, it can skip a large amount of computations for negative results and simply set the ReLU outputs to zero. Moreover, we devise a DNN accelerator architecture that can efficiently apply the proposed technique. The evaluation shows that the accelerator using the computation pruning through early negative detection technique significantly improves the energy efficiency and the performance.
Complement C3-targeted gene therapy restricts onset and progression of neurodegeneration in chronic mouse glaucoma

Dysregulation of the complement system is implicated in neurodegeneration, including human and animal glaucoma. Optic nerve and retinal damage in glaucoma is preceded by local complement upregulation and activation, but whether targeting this early innate immune response could have therapeutic benefit remains undefined. Because complement signals through three pathways that intersect at complement C3 activation, here we targeted this step to restore complement balance in the glaucomatous retina, and to determine its contribution to degeneration onset and/or progression. To achieve this, we combined adeno-associated viral retinal gene therapy with the targeted C3 inhibitor CR2-Crry. We show that intravitreal injection of AAV2.CR2-Crry produced sustained Crry overexpression in the retina, and reduced deposition of the activation product complement C3d on retinal ganglion cells and the inner retina of DBA/2J mice. This resulted in neuroprotection of retinal ganglion cell axons and somata despite continued intraocular pressure elevation, suggesting a direct restriction of neurodegeneration onset and progression, and significant delay to terminal disease stages. Our study uncovers a damaging effect of complement C3 or downstream complement activation in glaucoma and establishes AAV2.CR2-Crry as a viable therapeutic strategy to target pathogenic C3-mediated complement activation in the glaucomatous retina.
Parallelisation of equation-based simulation programs on heterogeneous computing systems

Numerical solutions of equation-based simulations require computationally intensive tasks such as evaluation of model equations, linear algebra operations and solution of systems of linear equations. The focus in this work is on parallel evaluation of model equations on shared memory systems such as general purpose processors (multi-core CPUs and manycore devices), streaming processors (Graphics Processing Units and Field Programmable Gate Arrays) and heterogeneous systems. The current approaches for evaluation of model equations are reviewed and their capabilities and shortcomings analysed. Since stream computing differs from traditional computing in that the system processes a sequential stream of elements, equations must be transformed into a data structure suitable for both types. The postfix notation expression stacks are recognised as a platform and programming language independent method to describe, store in computer memory and evaluate general systems of differential and algebraic equations of any size. Each mathematical operation and its operands are described by a specially designed data structure, and every equation is transformed into an array of these structures (a Compute Stack). Compute Stacks are evaluated by a stack machine using a Last In First Out queue. The stack machine is implemented in the DAE Tools modelling software in the C99 language using two Application Programming Interface (APIs)/frameworks for parallelism. The Open Multi-Processing (OpenMP) API is used for parallelisation on general purpose processors, and the Open Computing Language (OpenCL) framework is used for parallelisation on streaming processors and heterogeneous systems. The performance of the sequential Compute Stack approach is compared to the direct C++ implementation and to the previous approach that uses evaluation trees. The new approach is 45% slower than the C++ implementation and more than five times faster than the previous one. The OpenMP and OpenCL implementations are tested on three medium-scale models using a multi-core CPU, a discrete GPU, an integrated GPU and heterogeneous computing setups. Execution times are compared and analysed and the advantages of the OpenCL implementation running on a discrete GPU and heterogeneous systems are discussed. It is found that the evaluation of model equations using the parallel OpenCL implementation running on a discrete GPU is up to twelve times faster than the sequential version while the overall simulation speed-up gained is more than three times.
Early Declines in Vaccine Type Pneumococcal Carriage in Children Less Than 5 Years Old After Introduction of 10-valent Pneumococcal Conjugate Vaccine in Mozambique

Background: Pneumococcal carriage is a precursor of invasive pneumococcal disease. Mozambique introduced 10-valent pneumococcal conjugate vaccine (PCV10) in April 2013, using a 3-dose schedule without a booster. We evaluated PCV10 impact on pneumococcal carriage and colonization density by HIV status. Methods: We conducted 2 cross-sectional surveys (pre and post PCV10 introduction) among children 6 weeks to 59 months old. Participants included HIV-infected children presenting for routine care at outpatient clinics and a random sample of HIV-uninfected children from the community. We collected demographic data, vaccination history and nasopharyngeal swabs. Swabs were cultured and isolates serotyped by Quellung. We selected serotypes 11A, 19A and 19F for bacterial density analyses. We compared vaccine-type (VT) carriage prevalence from the pre-PCV10 with the post-PCV10 period by HIV status. Findings: Prevalence of VT carriage declined from 35.9% (110/306) pre already defined in the background. It should be pre-PCV (PCV) to 20.7% (36/174 fully vaccinated) post PCV (P < 0.001) in HIV-uninfected and from 34.8% (144/414) to 19.7% (27/137 fully vaccinated) (P = 0.002) in HIV-infected children. Colonization prevalence for the 3 serotypes (3, 6A, 19A) included in the 13-valent PCV but not in PCV10 increased from 12.4% (38/306) to 20.7% (36/174 fully vaccinated) (P = 0.009) among HIV- uninfected children, mainly driven by 19A; no significant increase was observed in HIV-infected children. VT carriage among unvaccinated children decreased by 30% (P = 0.005) in HIV-infected children, with no significant declines observed in HIV-uninfected children. Conclusion: Declines in VT carriage were observed in both HIV-uninfected and HIV-infected children after PCV10 introduction with an early signal of herd effect especially in HIV-infected children. Ongoing monitoring of increases in 19A carriage and disease is necessary.
Patterns of Screen Time Among Rural Mexican-American Children on the New Mexico-Mexico Border

Introduction The prevalence of obesity is 26% among Hispanic children and teenagers and 47% among Hispanic adults. One contributor to obesity is sedentary behavior, such as using electronic screen devices (ie, screens). Low-income and Hispanic youths spend more time using such devices than other youths. Methods We interviewed 202 parents of Mexican-origin children aged 6 to 10 years in 2 rural communities near the US–Mexico border to determine screen use among children. We tested for associations between covariates and heavy screen use (≥4 hours/day) and calculated adjusted odds ratios (AORs) to identify independent, modifiable risk factors for such use. Results More than two-thirds (68.3%) of households had an annual income of less than $24,000, 89.1% spoke primarily Spanish, and 92.1% had internet access. The percentage of children with heavy screen use was 14.9% on weekdays and 25.2% on weekends. Smartphones were used by 62.4% of children, desktops or laptops by 60.9%; homework was the most common reason for use of these devices. One in 3 children used them for social media. Increased odds of heavy screen use were associated with having a television on while the child ate (weekday AOR = 3.02; 95% confidence interval [CI], 1.08–8.45 and weekend AOR = 2.38; 95% CI, 1.04–5.40) and using electronics to entertain (weekend AOR = 2.94; 95% CI, 1.15–7.51). More than 3 family meals per week (AOR = 0.40; 95% CI, 0.17–0.94 compared with ≤3 meals) and 2 or 3 family activities per week (AOR = 0.33; 95% CI, 0.12–0.87 compared with ≤1 activity) were associated with decreased odds of heavy weekend use. Conclusion Even in low-income, Spanish-speaking communities, children have access to electronic devices, social media, and the internet, and a substantial fraction of them are heavy users. Efforts to reduce screen time might focus on understanding and changing the social norms that promote it.