Miracle-dz/UniFAR-FTUs huggingface dataset:
CRISPR-Cas9-Mediated Silencing of CD44 in Human Highly Metastatic Osteosarcoma Cells

Background/Aims: Metastasis is the major cause of death in patients with osteosarcoma. There is an urgent need to identify molecular markers that promote metastasis. Cluster of differentiation 44 is a receptor for hyaluronic acid (HA) and HA-binding has been proven to participate in various biological tumor activities, including tumor progression and metastasis. Methods: We performed a meta-analysis to investigate the relationship between CD44 expression, survival, and metastasis in patients with osteosarcoma. We then utilized the CRISPR-Cas9 system to specifically silence CD44 in highly metastatic human osteosarcoma cells (MNNG/HOS and 143B) and further determined the functional effects of CD44 knockout in these cells. Results: The meta-analysis demonstrated that a high level of CD44 may predict poor survival and higher potential of metastasis in patients with osteosarcoma. The expression of CD44 in highly metastatic human osteosarcoma cell lines was efficiently blocked by CRISPR-Cas9. When CD44 was silenced, the proliferation and spheroid formation of these osteosarcoma cells was inhibited under 3-D culture conditions. Furthermore, the migratory and invasive functions were also impaired in these highly metastatic osteosarcoma cells. Conclusion: These results suggest that developing new strategies to target CD44 in osteosarcoma may prevent metastasis and improve the clinical outcome of osteosarcoma patients.
Joint probability discrimination between stationary tissue and blood velocity signals

In CFM-mode the blood velocity estimates are overlaid onto the B-mode image. The velocity estimation gives non-zero velocity estimates in both the surrounding tissue and the vessels. A discrimination algorithm is needed to determine, which estimates represent blood flow and should be displayed. This study presents a new statistical discriminator. Investigation of the RF-signals reveals that features can be derived that distinguish the segments of the signal, which do an do not carry information on the blood flow. In this study 4 features, have been determined: (a) the energy content in the segments before and after echo-canceling, and (b) the amplitude variations between samples in consecutive RF-signals before and after echo-canceling. The statistical discriminator was obtained by computing the probability density functions (PDFs) for each feature through histogram analysis of data. The discrimination is performed by determining the joint probability of the features for the segment under investigation and choosing the segment type that is most likely. The method was tested on simulated data resembling RF-signals from the carotid artery.
A wavelet based time frequency analysis of electromyograms to group steps of runners into clusters that contain similar muscle activation patterns

Purpose To wavelet transform the electromyograms of the vastii muscles and generate wavelet intensity patterns (WIP) of runners. Test the hypotheses: 1) The WIP of the vastus medialis (VM) and vastus lateralis (VL) of one step are more similar than the WIPs of these two muscles, offset by one step. 2) The WIPs within one muscle differ by having maximal intensities in specific frequency bands and these intensities are not always occurring at the same time after heel strike. 3) The WIPs that were recorded form one muscle for all steps while running can be grouped into clusters with similar WIPs. It is expected that clusters might have distinctly different, cluster specific mean WIPs. Methods The EMG of the vastii muscles from at least 1000 steps from twelve runners were recorded using a bipolar current amplifier and yielded WIPs. Based on the weights obtained after a principal component analysis the dissimilarities (1-correlation) between the WIPs were computed. The dissimilarities were submitted to a hierarchical cluster analysis to search for groups of steps with similar WIPs. The clusters formed by random surrogate WIPs were used to determine whether the groups were likely to be created in a non-random manner. Results The steps were grouped in clusters showing similar WIPs. The grouping was based on the frequency bands and their timing showing that they represented defining parts of the WIPs. The correlations between the WIPs of the vastii muscles that were recorded during the same step were higher than the correlations of WPIs that were recorded during consecutive steps, indicating the non-randomness of the WIPs. Conclusions The spectral power of EMGs while running varies during the stance phase in time and frequency, therefore a time averaged power spectrum cannot reflect the timing of events that occur while running. It seems likely that there might be a set of predefined patterns that are used upon demand to stabilize the movement.
Static magnetic susceptibility, crystal field and exchange interactions in rare earth titanate pyrochlores

The experimental temperature dependence (T = 2–300 K) of single crystal bulk and site susceptibilities of rare earth titanate pyrochlores R2Ti2O7 (R = Sm, Eu, Gd, Tb, Dy, Ho, Er, Yb) is analyzed in the framework of crystal field theory and a mean field approximation. Analytical expressions for the site and bulk susceptibilities of the pyrochlore lattice are derived taking into account long range dipole–dipole interactions and anisotropic exchange interactions between the nearest neighbor rare earth ions. The sets of crystal field parameters and anisotropic exchange coupling constants have been determined and their variations along the lanthanide series are discussed.
How Traffic Situations and Non-Driving Related Tasks Affect the Take-Over Quality in Highly Automated Driving

Highly automated driving constitutes a temporary transfer of the primary driving task from the driver to the automated vehicle. In case of system limits, drivers take back control of the vehicle. This study investigates the effect of varying traffic situations and non-driving related tasks on the take-over process and quality. The experiment is conducted in a high-fidelity driving simulator. The standardized visual Surrogate Reference Task (SuRT) and the cognitive n-back Task are used to simulate the non-driving related tasks. Participants experience four different traffic situations. Results of this experiment show a strong influence of the traffic situations on the take-over quality in a highway setting, if the traffic density is high. The non-driving related tasks SuRT and the n-back Task show similar effects on the take-over process with a higher total number of collisions by the SuRT in the high density traffic situation.
Technical Note: On maximizing Cherenkov emissions from medical linear accelerators

Purpose Cherenkov light during MV radiotherapy has recently found imaging and therapeutic applications but is challenged by relatively low fluence. Our purpose is to investigate the feasibility of increasing Cherenkov light production during MV radiotherapy by increasing photon energy and applying specialized beam‐hardening filtration. Methods GAMOS 5.0. 0, a GEANT4‐based framework for Monte Carlo simulations, was used to model standard clinical linear accelerator primary photon beams. The photon source was incident upon a 17.8 cm3 cubic water phantom with a 94 cm source to surface distance. Dose and Cherenkov production was determined at depths of 3–9 cm. Filtration was simulated 15 cm below the photon beam source. Filter materials included aluminum, iron, and copper with thicknesses of 2–20 cm. Histories used depended on the level of attenuation from the filter, ranging from 100 million to 2 billion. Comparing average dose per history also allowed for evaluation of dose‐rate reduction for different filters. Results Overall, increasing photon beam energy is more effective at improving Cherenkov production per unit dose than is filtration, with a standard 18 MV beam yielding 3.3–4.0× more photons than 6 MV. Introducing an aluminum filter into an unfiltered 2400 cGy/min 10 MV beam increases the Cherenkov production by 1.6–1.7×, while maintaining a clinical dose rate of 300 cGy/min, compared to increases of ˜1.5× for iron and copper. Aluminum was also more effective than the standard flattening filter, with the increase over the unfiltered beam being 1.4–1.5× (maintaining 600 cGy/min dose rate) vs 1.3–1.4× for the standard flattening filter. Applying a 10 cm aluminum filter to a standard 18 MV, photon beam increased the Cherenkov production per unit dose to 3.9–4.3× beyond that of 6 MV (vs 3.3–4.0× for 18 MV with no aluminum filter). Conclusions Through a combination of increasing photon energy and applying specialized beam‐hardening filtration, the amount of Cherenkov photons per unit radiotherapy dose can be increased substantially.
SWAM: SDN-Based Wi-Fi Small Cells with Joint Access-Backhaul and Multi-Tenant Capabilities

In this paper we present SWAM, a system that builds on commodity Wi-Fi routers with multiple wireless interfaces to provide a wireless access infrastructure supporting multi-tenancy, mobility, and integrated wireless access and backhaul. An infrastructure provider can deploy inexpensive SWAM nodes to cover a given geographical area providing on-demand connectivity for Mobile Network Operators. Our main contribution is the design of the SWAM datapath and control plane, which are inspired by the overlay techniques used to enable multi-tenancy in data-center networks. We prototype SWAM in an office wireless testbed and validate experimentally its functionality.
Traffic control for a swarm of robots: Avoiding group conflicts

A very common problem in the navigation of robotic swarms is when groups of robots move into opposite directions, causing congestion situations that may compromise performance. In this paper, we propose a distributed coordination algorithm to alleviate this type of congestion. By working collaboratively, and warning their teammates about a congestion risk, robots are able to coordinate themselves to avoid these situations. We executed simulations and real experiments to study the performance and effectiveness of the proposed algorithm. Results show that the algorithm allows the swarm to navigate in a smoother and more efficient fashion, and is suitable for large groups of robots.
School-Based Telerehabilitation in Occupational Therapy: Using Telerehabilitation Technologies to Promote Improvements in Student Performance

This article discusses the use of telerehabilitation technologies in occupational therapy for school-based practice. Telerehabilitation, for the purpose of this program, included the implementation of occupational therapy services via two-way interactive videoconferencing technology. The subjects included in this pilot program were children, ages 6 to 11 years, who attended an online charter school and had difficulties in the areas of fine motor and/or visual motor skills which impacted success with handwriting. Each participant completed a virtual evaluation and six 30-minute intervention sessions. The Print Tool™ Assessment was used to determine progress pre- and post-program. A learning coach/student satisfaction survey was given at the end of the program to determine participant satisfaction. Outcomes revealed improvements in handwriting performance for most students who participated in the program and high satisfaction rates reported by all participants.
COMBINING BLIND SOURCE EXTRACTION WITH JOINT APPROXIMATE DIAGONALIZATION: THIN ALGORITHMS FOR ICA

In this paper a multivariate contrast function is proposed for the blind signal extraction of a subset of the independent components from a linear mixture. This contrast combines the robustness of the joint approximate diagonalization techniques with the e xibility of the methods for blind signal extraction. Its maximization leads to hierarchical and simultaneous ICA extraction algorithms which are respectively based on the thin QR and thin SVD factorizations. The interesting similarities and differences with other existing contrasts and algorithms are commented.
Wide temperature range through silicon vias made of Invar and spin-on glass for interposers and MEMS

Through silicon vias (TSVs) are used e.g. to create electrical connections through MEMS wafers or through silicon interposers used in 2.5D packaging. Currently available technologies do not address situations in which TSVs through unthinned wafers have to withstand large temperature variations. We propose using ferromagnetic Invar metal alloy for this purpose due to its low mismatch in heat induced strain in comparison to silicon. We demonstrate the suitability of a magnetic assembly process for Invar TSV fabrication and the use of spin-on glass as a TSV insulator. We demonstrate TSVs, with contact pads, that tolerate temperature cycling between -50 °C and 190 °C and can withstand elevated temperatures of at least up to 365 °C.
A Specially Designed Multi-Gene Panel Facilitates Genetic Diagnosis in Children with Intrahepatic Cholestasis: Simultaneous Test of Known Large Insertions/Deletions

Background and Aims Large indels are commonly identified in patients but are not detectable by routine Sanger sequencing and panel sequencing. We specially designed a multi-gene panel that could simultaneously test known large indels in addition to ordinary variants, and reported the diagnostic yield in patients with intrahepatic cholestasis. Methods The panel contains 61 genes associated with cholestasis and 25 known recurrent large indels. The amplicon library was sequenced on Ion PGM system. Sequencing data were analyzed using a routine data analysis protocol and an internal program encoded for large indels test simultaneously. The validation phase was performed using 54 patients with known genetic diagnosis, including 5 with large insertions. At implement phase, 141 patients with intrahepatic cholestasis were evaluated. Results At validation phase, 99.6% of the variations identified by Sanger sequencing could be detected by panel sequencing. Following the routine protocol, 99.8% of false positives could be filtered and 98.8% of retained variations were true positives. Large insertions in the 5 patients with known genetic diagnosis could be correctly detected using the internal program. At implementation phase, 96.9% of the retained variations, following the routine protocol, were confirmed to be true. Twenty-nine patients received a potential genetic diagnosis when panel sequencing data were analyzed using the routine protocol. Two additional patients, who were found to harbor large insertions in SLC25A13, obtained a potential genetic diagnosis when sequencing data were further analyzed using the internal program. A total of 31 (22.0%) patients obtained a potential genetic diagnosis. Nine different genetic disorders were diagnosed, and citrin deficiency was the commonest. Conclusion Specially designed multi-gene panel can correctly detect large indels simultaneously. By using it, we assigned a potential genetic diagnosis to 22.0% of patients with intrahepatic cholestasis.
Surface Light Field Rendering for Virtual Product Design

Interior and material designers currently refuse to employ Virtual Prototyping software due to potential errors in computer generated images. In this paper we propose real-time rendering of a precomputed global illumination solution including accurate materials, which is stored as an outgoing Surface Light Field (SLF), as a method to improve upon this problem. In addition, suitable SLF compression and computation techniques are presented and the quality of rendered images is demonstrated.
Influence of PbO stoichiometry on the properties of PZT ceramics and multilayer actuators

Lead-oxide stoichiometry of lead-zirconate-titanate (PZT) ceramics and multilayer actuators is a critical issue for fabrication and performance. During sintering, the high vapor pressure and the corresponding volatility of lead oxide (PbO) require a careful design of sintering setup and parameters, as both may significantly impact on the PbO content in ceramics and devices. In order to investigate the effects of PbO stoichiometry, PZT compositions with different PbO contents have been synthesized and were sintered under varying temperature conditions and sintering setups. Structure and microstructure of the material was characterized using X-ray diffraction and scanning electron microscopy (SEM). Dielectric properties and high field strain behavior were analyzed with respect to their relation to PbO content and grain size. Corresponding experiments with multilayer actuators were carried out, whereby the PbO content was varied by controlling the sintering atmosphere. The results indicate that there is a pronounced correlation between PbO content, structure and high field strain in both, PZT ceramics and multilayer actuators.
A Unified Framework of Regularization Methods for Degenerate Non-Linear Optimization Models

In this paper, we study three classes of difficult non-linear optimization, problems with complementarity (MPCC), vanishing (MPVC) and cardinality constraints (OMCC). They all have in common degenerate constraints, which fail to satisfy classical constraint qualifications in a generic way. The feasible sets of these problems are non-convex, possibly non-connected, with an empty relative interior. This causes several difficulties in practice. In a recent work (Dussault et al. 2017), we propose a unified framework of methods that consider a regularization-penalization-active set method to solve the MPCC, which possesses the best-known convergence properties. In this paper, we extend this unified framework to MPVC and OMCC and consider some applications on optimal control problems.
The effect of cryoprotection on the use of PLGA encapsulated iron oxide nanoparticles for magnetic cell labeling

Magnetic PLGA nanoparticles are a significant advancement in the quest to translate MRI-based cell tracking to the clinic. The benefits of these types of particles are that they encapsulate large amounts of iron oxide nanocrystals within an FDA-approved polymer matrix, combining the best aspects of inert micron-sized iron oxide particles, or MPIOs, and biodegradable small particles of iron oxide, or SPIOs. Practically, PLGA nanoparticle fabrication and storage requires some form of cryoprotectant to both protect the particle during freeze drying and to promote resuspension. While this is a commonly employed procedure in the fabrication of drug loaded PLGA nanoparticles, it has yet to be investigated for magnetic particles and what effect this might have on internalization of magnetic particles. As such, in this study, magnetic PLGA nanoparticles were fabricated with various concentrations of two common cryoprotectants, dextrose and sucrose, and analyzed for their ability to magnetically label cells. It was found that cryoprotection with either sugar significantly enhanced the ability to resuspend nanoparticles without aggregation. Magnetic cell labeling was impacted by sugar concentration, with higher sugar concentrations used during freeze drying more significantly reducing magnetic cell labeling than lower concentrations. These studies suggest that cryoprotection with 1% dextrose is an optimal compromise that preserves monodispersity following resuspension and high magnetic cell labeling.
Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade

In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine Roseobacter clade, which, in turn, belongs to the class Alphaproteobacteria. The genus Phaeobacter is well known for members that produce various secondary metabolites. Here we report of putative quorum sensing systems, based on the finding of six N-acyl-homoserine lactone synthetases, and show that the blue color of P. caeruleus is probably due to the production of the secondary metabolite indigoidine. Therefore, P. caeruleus might have inhibitory effects on other bacteria. In this study the genome of the type strain DSM 24564T was sequenced, annotated and characterized. The 5,344,419 bp long genome with its seven plasmids contains 5,227 protein-coding genes (3,904 with a predicted function) and 108 RNA genes.
“Wish You Were Here”: Examining Characteristics, Outcomes, and Statistical Solutions for Missing Cases in Web-Based Psychotherapeutic Trials

Background Missing cases following treatment are common in Web-based psychotherapy trials. Without the ability to directly measure and evaluate the outcomes for missing cases, the ability to measure and evaluate the effects of treatment is challenging. Although common, little is known about the characteristics of Web-based psychotherapy participants who present as missing cases, their likely clinical outcomes, or the suitability of different statistical assumptions that can characterize missing cases. Objective Using a large sample of individuals who underwent Web-based psychotherapy for depressive symptoms (n=820), the aim of this study was to explore the characteristics of cases who present as missing cases at posttreatment (n=138), their likely treatment outcomes, and compare between statistical methods for replacing their missing data. Methods First, common participant and treatment features were tested through binary logistic regression models, evaluating the ability to predict missing cases. Second, the same variables were screened for their ability to increase or impede the rate symptom change that was observed following treatment. Third, using recontacted cases at 3-month follow-up to proximally represent missing cases outcomes following treatment, various simulated replacement scores were compared and evaluated against observed clinical follow-up scores. Results Missing cases were dominantly predicted by lower treatment adherence and increased symptoms at pretreatment. Statistical methods that ignored these characteristics can overlook an important clinical phenomenon and consequently produce inaccurate replacement outcomes, with symptoms estimates that can swing from −32% to 70% from the observed outcomes of recontacted cases. In contrast, longitudinal statistical methods that adjusted their estimates for missing cases outcomes by treatment adherence rates and baseline symptoms scores resulted in minimal measurement bias (<8%). Conclusions Certain variables can characterize and predict missing cases likelihood and jointly predict lesser clinical improvement. Under such circumstances, individuals with potentially worst off treatment outcomes can become concealed, and failure to adjust for this can lead to substantial clinical measurement bias. Together, this preliminary research suggests that missing cases in Web-based psychotherapeutic interventions may not occur as random events and can be systematically predicted. Critically, at the same time, missing cases may experience outcomes that are distinct and important for a complete understanding of the treatment effect.