Miracle-dz/UniFAR-FTUs huggingface dataset:
Oncogenic mutations of ALK in neuroblastoma

Neuroblastoma is one of the most common solid cancers among children. Prognosis of advanced neuroblastoma is still poor despite the recent advances in chemo/radiotherapies. In view of improving the clinical outcome of advanced neuroblastoma, it is important to identify the key molecules responsible for the pathogenesis of neuroblastoma and to develop effective drugs that target these molecules. Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase, initially identified through the analysis of a specific translocation associated with a rare subtype of non‐Hodgkin’s lymphoma. Recently it was demonstrated that ALK is frequently mutated in sporadic cases with advanced neuroblastoma. Moreover, germline mutations of ALK were shown to be responsible for the majority of hereditary neuroblastoma. ALK mutants found in neuroblastoma show constitutive active kinase activity and oncogenic potentials. Inhibition of ALK in neuroblastoma cell lines carrying amplified or mutated ALK alleles results in compromised downstream signaling and cell growth, indicating potential roles of small molecule ALK inhibitors in the therapeutics of neuroblastoma carrying mutated ALK kinases. (Cancer Sci 2011; 102: 302–308)
An Evaluation Protocol for Subtype-Specific Breast Cancer Event Prediction

In recent years increasing evidence appeared that breast cancer may not constitute a single disease at the molecular level, but comprises a heterogeneous set of subtypes. This suggests that instead of building a single monolithic predictor, better predictors might be constructed that solely target samples of a designated subtype, which are believed to represent more homogeneous sets of samples. An unavoidable drawback of developing subtype-specific predictors, however, is that a stratification by subtype drastically reduces the number of samples available for their construction. As numerous studies have indicated sample size to be an important factor in predictor construction, it is therefore questionable whether the potential benefit of subtyping can outweigh the drawback of a severe loss in sample size. Factors like unequal class distributions and differences in the number of samples per subtype, further complicate comparisons. We present a novel experimental protocol that facilitates a comprehensive comparison between subtype-specific predictors and predictors that do not take subtype information into account. Emphasis lies on careful control of sample size as well as class and subtype distributions. The methodology is applied to a large breast cancer compendium involving over 1500 arrays, using a state-of-the-art subtyping scheme. We show that the resulting subtype-specific predictors outperform those that do not take subtype information into account, especially when taking sample size considerations into account.
Fabrication of Silicon Nano-wire by Oxidation

In this paper, we report a method of fabricating silicon nano-wire based on thermal oxidation technique. In this method, we first fabricate a wider structure with traditional lithography, and then use a layer of silicon nitride as mask to oxidize silicon. At the same time, due to the lateral diffusion and oxidation of oxidant, silicon is consumed by oxidant and the width of the silicon structure will be reduced to nano range when we remove the silicon dioxide. The factors affecting the ratio of vertical and lateral oxidation, for example, the gentle slope caused by isotropic oxidation and the inhomogeneity of the sidewall of silicon nano-wire, are discussed at last. Our results should be useful in generating silicon–based nanospintronics devices with careful selection of the oxide parameters.
LVS: A WiFi-based system to tackle Location Spoofing in location-based services

The reliability of location-based services (LBS) is strongly dependent on the accuracy of the location of the users. However, existing LBS systems are not able to efficiently validate the position of users in large-scale outdoor environments, leading to possible location spoofing attacks by malicious users. To this end, we present an efficient and scalable Location Validation System (LVS) that secures LBS systems from location spoofing attacks. In particular, the user location is verified with the help of mobile WiFi hotspots (MHSs), who are users activating the WiFi hotspot capability of their smartphones and accept connections from nearby users, thereby validating their position inside the sensing area. The system also comprises a novel verification technique called Chains of Sight, which tackles collusion-based attacks effectively. LVS also includes a reputation-based algorithm that rules out sensing reports of location-spoofing users.
Rapid decline in presentations of genital warts after the implementation of a national quadrivalent human papillomavirus vaccination programme for young women

Objective: This study aimed to determine if the Australian human papillomavirus (HPV) vaccination programme has had a population impact on presentations of genital warts. Methods: Retrospective study comparing the proportion of new clients with genital warts attending Melbourne Sexual Health Centre (MSHC) from January 2004 to December 2008. Australia provided free quadrivalent HPV vaccine to 12–18-year-old girls in a school-based programme from April 2007, and to women 26 years and younger through general practices from July 2007. Results: 36 055 new clients attended MSHC between 2004 and 2008 and genital warts were diagnosed in 3826 (10.6%; 95% CI 10.3 to 10.9). The proportion of women under 28 years with warts diagnosed decreased by 25.1% (95% CI 30.5% to 19.3%) per quarter in 2008. Comparing this to a negligible increase of 1.8% (95% CI 0.2% to 3.4%) per quarter from the start of 2004 to the end of 2007 also in women under 28 years generates strong evidence of a difference in these two trends (p<0.001). There was no evidence of a difference in trend for the quarterly proportions before and after the end of 2007 for any other subgroup, and on only one occasion was there strong evidence of a trend different to zero, for heterosexual men in 2008 in whom the average quarterly change was a decrease of 5% (95% CI 0.5% to 9.4%; p = 0.031). Conclusions: The data suggest that a rapid and marked reduction in the incidence of genital warts among vaccinated women may be achievable through an HPV vaccination programme targeting women, and supports some benefit being conferred to heterosexual men.
POSSIBLE MAGNETIC FIELDS OF SUPER EARTHS GENERATED BY CONVECTING, CONDUCTING OXIDES

Super Earths (SE) are extrasolar planets with masses up to ten times greater than Earth's. Maximum pressure and temperature of oxides in Earth are ~130 GPa and ~3000 K. SEs experience substantially more extreme conditions, which implies dense oxides in SEs could melt, achieve low viscosities, minimum metallic conductivity (MMC), and convect. MMC depends weakly on material, and thus on oxide composition. Shock and static experiments on single-crystal sapphire (Al2O3) and GGG (Gd3Ga5O12) show or suggest these oxides reach MMC at 300-400 GPa under shock and quite possibly under static compression. MMC is a likely upper limit for electrical conductivity of convecting material that can sustain a dynamo (Stevenson, 2010). Metallization is also expected to reduce substantially oxide viscosities in the solid (Karato, 2011). Thus, SEs might produce significant magnetic fields by dynamos in oxides alone, as does Fe in Earth and metallic fluid H in Jupiter.
Experiments on neural networks with different configurations for electroencephalography (EEG) signal pattern classifications in imagination of direction

Here we present experimental results of classification methods for brain activity in the imagination of direction. We used a wireless portable electroencephalography (EEG) headset in our preceding study to collect EEG data from subjects in experiments, during which the subjects imagined arrows indicating one of the four directions: up, down, right, and left. The implemented classification methods consisted of a band-pass filter, fast Fourier transformation, principal component analysis, and neural network. We have applied neural networks with different configurations to the EEG data used in the preceding study in order to improve the classification rate. The experiments conducted in this study demonstrated some improvement results.
Hereditary hypophosphatemias: New genes in the bone–kidney axis (Review Article)

Hypophosphatemia due to isolated renal phosphate wasting is a genetically heterogeneous disease. Two new genes linked to two different forms of hereditary hypophosphatemias have recently been described. Autosomal recessive form of hypophosphatemic rickets was mapped to chromosome 4q21 and identified homozygous mutations in dentin matrix protein 1 (DMP1) gene, which encodes a non‐collagenous bone matrix protein. Intact plasma levels of the phosphaturic protein FGF23 (fibroblast growth factor 23) were clearly elevated in some of the affected individuals, providing a possible explanation for the phosphaturia and inappropriately normal 1,25(OH)2D levels, and suggesting that DMP1 may regulate FGF23 expression. Hereditary hypophosphatemic rickets with hypercalciuria is another rare disorder of autosomal recessive inheritance. Affected individuals present with hypercalciuria due to increased serum 1,25‐dihydroxyvitamin D levels and increased intestinal calcium absorption. The disease was mapped to a 1.6 Mbp region on chromosome 9q34, which contains SLC34A3, the gene encoding the renal sodium‐phosphate cotransporter NaPi‐IIc. This was the first demonstration that NaPi‐IIc has a key role in the regulation of phosphate homeostasis. Thus, DMP1 and NaPi‐IIc add two new members to the bone–kidney axis proposed since it was discovered that the first phosphatonin, FGF23, was of osteoblastic/osteocyte origin. This provides a mechanism for the skeleton to communicate with the kidney to coordinate the mineralization of extracelular matrix and the renal handling of phosphate.
A Mixed Reality Interface for Real Time Tracked Public Transportation

Real time tracking of public transportation with open interfaces unfolds interesting possibilities for potential use cases. We present work towards full mixed reality interfaces, where virtual vehicles are a) embedded in a mobile 3D map, depicting a real city, and b) visualized directly with augmented reality on top of a real world view. Both these graphical application types aim at the same goal, reducing the cognitive distance between representation and the real world in contrast to traditional visualization, i.e. 2D maps. Our main contribution is the technical achievement of combining both representations into one application, with smooth visual transitions between them, together with the capability of representing the dynamically tracked entities in real time.
Kinetic characterization of the chymotryptic activity of the 20S proteasome.

In this paper, we report kinetic studies for the chymotryptic activity of the 20S proteasome. Major observations include the following: (1) Reaction progress curves that are recorded at concentrations of Suc-Leu-Leu-Val-Tyr-AMC greater than about 40 microM are biphasic and characterized by initial velocities that decay by a first-order process to final, steady-state velocities. (2) Also at [Suc-Leu-Leu-Val-Tyr-AMC] > 40 microM, initial and steady-state velocities are smaller than predicted from simple, Michaelis-Menten kinetics. (3) The first-order rate constant for the approach to steady-state has a complex dependence on substrate concentration and decreases sigmoidally as substrate concentration increases. These results indicate that the 20S proteasome is a hysteretic enzyme and is subject to substrate inhibition. To explain these observations we propose a minimal kinetic model with two critical mechanistic features: (1) the 20S proteasome has two cooperative active sites for Suc-Leu-Leu-Val-Tyr-AMC and (2) there are two interconvertible conformers of active 20S proteasome. To probe this mechanism in greater detail, we explored the kinetic mechanism of inhibition of the 20S proteasome-catalyzed hydrolysis of Suc-Leu-Leu-Val-Tyr-AMC by the peptide aldehyde, Ac-Leu-Leu-Nle-H. Our studies reveal a nonlinear dependence of reciprocal steady-state velocity on inhibitor concentration (i.e., parabolic inhibition) as well as a nonlinear dependence of the apparent inhibitor dissociation constant on substrate concentration. Both of these observations are explained by binding of inhibitor at multiple sites on the enzyme. Taken together, the results of this study indicate that the 20S proteasome is a conformationally flexible protein that can adjust to the binding of ligands and that has multiple and cooperative active sites. These results support a view of the proteasome's substrate specificity in which (1) substrates are recognized and hydrolyzed by more than one active site; (2) each active site can bind substrates that possess a variety of P1 residues; and (3) the P1 residue plays a relatively minor role as a specificity determinant. Finally, we interpret the results of this study to suggest that, in vivo, the 20S proteasome requires conformational plasticity for its interactions with regulatory complexes and, after it has combined with appropriate regulatory complexes, to catalyze hydrolysis of proteins.
Using X-parameters to model RFID energy harvesting circuits

In this paper a new behavioral model that describes energy harvester circuits for use in RFID systems will be presented. The use of X parameters, recently proposed for Power Amplifier characterization, will be expanded to RFID circuits. It is expected that this type of model is able to improve the design and optimization of energy harvester circuits, and give a step forward in terms of RFID simulation. Poly-Harmonic Distortion (PHD) and X-parameters models will be presented as a first glance and afterward the theoretical considerations for applying X parameters to RF-DC converters and corresponding simulations will be given.
The Readiness for interprofessional learning scale: A possible more stable sub-scale model for the original version of RIPLS

The original version of the Readiness for Interprofessional Learning Scale (RIPLS) was published by Parsell and Bligh ([8]). Three sub-scales with acceptable or high internal consistencies were suggested, however two publications suggested different sub-scales. An investigation into how to improve the reliability for use of the RIPLS instrument with undergraduate health-care students commenced. Content analysis on the original 19 items involving experienced health-care staff resulted in four sub-scales. These sub-scales were then used to formulate a possible model within a structural equation model. The goodness of fit was assessed using a sample (n = 308) of new first year undergraduate students from 8 different health and social care programmes. The same data was fitted to each of the two original sub-scale models suggested by Parsell and Bligh ([8]) and the results compared. The fit of the new four sub-scale model appears superior to either of the original models. The new four factor model was then tested on subsequent data (n = 247) obtained from the same students at the end of their first year. The fit was seen to be even better at the end of the academic year.
Non-conforming behavior detection for VoIP-based network systems

This work proposes a detection scheme that identifies non-conforming behavior in a VoIP network, based on statistical analysis and hypothesis testing. VoIP networks are a popular, low-cost alternative for telephony that offer lower rates especially for long-distance calls. Other services such as FollowMe, enhance the traditional voice-oriented nature of these networks. Consequently several security concerns such as fraud calls, are related to the high availability required by a VoIP system. Fraud calls account for an average loss of 3% to 5% of the operators' revenue. Thus the detection and prevention of the users from behaving in a non-conforming way, becomes crucial. A trustworthy and secure management and billing scheme is necessary, to guarantee the proper operation. This work proposes a behavioral control scheme for the VoIP clients. An initial training period defines the normal behavior. Then statistical analysis and t-testing is employed to extract results regarding the users' profiles, with pre-defined confidence levels. A Buffer zone creates a more flexible decision-making process. The scheme also offers the ability to configure its parameters, in order to react appropriately under different network conditions and detect possible misuses. It is implemented and its rational operation is verified via several simulation scenarios.
Community of Inquiry Framework: Establishing Community in an Online Course.

Using the Community of Inquiry (CoI) framework, the author conducted a mixed method research study to examine the existence of the three CoI elements in a graduate-level educational technology online course. The author also looked at student perceptions and preference for community in online learning. High mean scores on the CoI showed that all three elements of CoI were more than adequately addressed in the course, particularly teaching presence. Lowest scores indicated that some students were uncomfortable expressing themselves in an online environment and felt a lack of freedom to disagree with class members. Demographic data showed that students preferred a sense of community but were not so fond of collaborative assignments that are essential for building the community they desire. Since collaborative assignments demand a greater degree of communication and ability to bring problems to an adequate resolution, it is plausible that inhibitions in expressing oneself may become more pronounced when more collaboration is required.
Magnetic removal of Entamoeba cysts from water using chitosan oligosaccharide-coated iron oxide nanoparticles

Amebiasis, a major health problem in developing countries, is the second most common cause of death due to parasitic infection. Amebiasis is usually transmitted by the ingestion of Entamoeba histolytica cysts through oral–fecal route. Herein, we report on the use of chitosan oligosaccharide-functionalized iron oxide nanoparticles for efficient capture and removal of pathogenic protozoan cysts under the influence of an external magnetic field. These nanoparticles were synthesized through a chemical synthesis process. The synthesized particles were characterized by transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray diffraction, and zeta potential analysis. The particles were found to be well dispersed and uniform in size. The capture and removal of pathogenic cysts were demonstrated by fluorescent microscopy, transmission electron microscopy, and scanning electron microscopy (SEM). Three-dimensional modeling of various biochemical components of cyst walls, and thereafter, flexible docking studies demonstrate the probable interaction mechanism of nanoparticles with various components of E. histolytica cyst walls. Results of the present study suggest that E. histolytica cysts can be efficiently captured and removed from contaminated aqueous systems through the application of synthesized nanoparticles.
Visual SLAM for autonomous MAVs with dual cameras

This paper extends a monocular visual simultaneous localization and mapping (SLAM) system to utilize two cameras with non-overlap in their respective field of views (FOVs). We achieve using it to enable autonomous navigation of a micro aerial vehicle (MAV) in unknown environments. The methodology behind this system can easily be extended to multi-camera rigs, if the onboard computation capability allows this. We analyze the iterative optimizations for pose tracking and map refinement of the SLAM system in multicamera cases. This ensures the soundness and accuracy of each optimization update. Our method is more resistant to tracking failure than conventional monocular visual SLAM systems, especially when MAVs fly in complex environments. It also brings more flexibility to configurations of multiple cameras used onboard of MAVs. We demonstrate its efficiency with both autonomous flight and manual flight of a MAV. The results are evaluated by comparisons with ground truth data provided by an external tracking system.
Multi-robot distributed visual consensus using epipoles

In this paper we give a distributed solution to the problem of making a team of non-holonomic robots achieve the same heading (attitude consensus problem) using vision sensors with limited field of view. The use of cameras with constrained field of view limits the information the robots perceive compared to other omnidirectional sensors. This makes the consensus problem more complicated, because the robots will not always be able to observe other robots. By using structure from motion computed from images, the robots can estimate the difference in their headings from common observations of the environment without the necessity of directly observe each other. In this way, the robots achieve the consensus in their headings while observing the environment instead of each other. The contribution of the paper is a new controller that uses the epipoles computed from pairs of images to estimate the misalignment between neighbor robots. In addition, the control is robust to changes in the topology of the network and does not require to know the calibration of the cameras in order to achieve the desired configuration. To the best of our knowledge, this is the first time that the epipoles are used in multi-robot consensus, putting their properties in value.
Global profiling of alternative splicing landscape responsive to drought, heat and their combination in wheat (Triticum aestivum L.)

Summary Plant can acquire tolerance to environmental stresses via transcriptome reprogramming at transcriptional and alternative splicing (AS) levels. However, how AS coordinates with transcriptional regulation to contribute to abiotic stresses responses is still ambiguous. In this study, we performed genome‐wide analyses of AS responses to drought stress (DS), heat stress (HS) and their combination (HD) in wheat seedlings, and further compared them with transcriptional responses. In total, we found 200, 3576 and 4056 genes exhibiting significant AS pattern changes in response to DS, HS and HD, respectively, and combined drought and heat stress can induce specific AS compared with individual one. In addition, wheat homeologous genes exhibited differential AS responses under stress conditions that more AS events occurred on B subgenome than on A and D genomes. Comparison of genes regulated at AS and transcriptional levels showed that only 12% of DS‐induced AS genes were subjected to transcriptional regulation, whereas the proportion increased to ~40% under HS and HD. Functional enrichment analysis revealed that abiotic stress‐responsive pathways tended to be highly overrepresented among these overlapped genes under HS and HD. Thus, we proposed that transcriptional regulation may play a major role in response to DS, which coordinates with AS regulation to contribute to HS and HD tolerance in wheat.