Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct Targeting of MEK1/2 and RSK2 by Silybin Induces Cell-Cycle Arrest and Inhibits Melanoma Cell Growth

Abnormal functioning of multiple gene products underlies the neoplastic transformation of cells. Thus, chemopreventive and/or chemotherapeutic agents with multigene targets hold promise in the development of effective anticancer drugs. Silybin, a component of milk thistle, is a natural anticancer agent. In the present study, we investigated the effect of silybin on melanoma cell growth and elucidated its molecular targets. Our study revealed that silybin attenuated the growth of melanoma xenograft tumors in nude mice. Silybin inhibited the kinase activity of mitogen-activated protein kinase (MEK)-1/2 and ribosomal S6 kinase (RSK)-2 in melanoma cells. The direct binding of silybin with MEK1/2 and RSK2 was explored using a computational docking model. Treatment of melanoma cells with silybin attenuated the phosphorylation of extracellular signal-regulated kinase (ERK)-1/2 and RSK2, which are regulated by the upstream kinases MEK1/2. The blockade of MEK1/2-ERK1/2-RSK2 signaling by silybin resulted in a reduced activation of NF-κB, activator protein-1, and STAT3, which are transcriptional regulators of a variety of proliferative genes in melanomas. Silybin, by blocking the activation of these transcription factors, induced cell-cycle arrest at the G1 phase and inhibited melanoma cell growth in vitro and in vivo. Taken together, silybin suppresses melanoma growth by directly targeting MEK- and RSK-mediated signaling pathways. Cancer Prev Res; 6(5); 455–65. ©2013 AACR.
Tool usage within a globally distributed software development course and implications for teaching

There have been many case studies looking at the work processes and use of tools within globally distributed software engineering teams. These studies usually use interviews, or other qualitative methods to ascertain their results. Additionally they may use data mining on particular modes of communication. In this paper, we report from observations in a Global Software Development class where students were free to choose the tools that best suited their needs, with minimal constraints. We discuss tool usage in three student teams and show how communication can be visually compared and correlated with implementation effort. We provide GSD teaching implications for tool selection and for monitoring progress of student teams. Finally, we suggest as a point of discussion that lightweight tools are not only preferred by students, but provide the same learning effect as more feature-complex collaboration infrastructures.
A Multiscale Community Blockmodel for Network Exploration

Real-world networks exhibit a complex set of phenomena such as underlying hierarchical organization, multiscale interaction, and varying topologies of communities. Most existing methods do not adequately capture the intrinsic interplay among such phenomena. We propose a nonparametric multiscale community blockmodel (MSCB) to model the generation of hierarchies in social communities, selective membership of actors to subsets of these communities, and the resultant networks due to within- and cross-community interactions. By using the nested Chinese restaurant process, our model automatically infers the hierarchy structure from the data. We develop a collapsed Gibbs sampling algorithm for posterior inference, conduct extensive validation using synthetic networks, and demonstrate the utility of our model in real-world datasets, such as predator–prey networks and citation networks.
Learning to Avoid Collisions

Members of a multi-robot team, operating within close quarters, need to avoid crashing into each other. Simple collision avoidance methods can be used to prevent such collisions, typically by computing the distance to other robots and stopping, perhaps moving away, when this distance falls below a fixed threshold. While a simple method like this may skirt disaster, the results may be inefficient in terms of the amount of time that robots are halted, waiting for others to pass by, or in terms of the path traversed, moving around other robots. The experiments reported here describe a method in which a human operator, through a graphical user interface, watches robots performing an exploration task and can manually interrupt robots’ movements before they crash into each other, and then resume their movements when their paths are clear. Experiment logs record the robots’ state when they are halted and resumed, and a behavior pattern for collision avoidance is learned, by classifying the states in which “halt” and “resume” commands are issued. Preliminary work is reported here.
Cell-free DNA for diagnosing myocardial infarction: not ready for prime time

Abstract A modest amount of cell-free DNA is constantly present in human blood, originating from programmed cell death, apoptosis and rupture of blood cells or pathogens. Acute or chronic cell injury contributes to enhance the pool of circulating nucleic acids, so that their assessment may be regarded as an appealing perspective for diagnosing myocardial ischemia. We performed a search in Medline, Web of Science and Scopus to identify clinical studies that investigated the concentration of cell-free DNA in patients with myocardial ischemia. Overall, eight case-control studies could be detected and reviewed. Although the concentration of cell-free DNA was found to be higher in the diseased than in the healthy population, the scenario was inconclusive due to the fact that the overall number of subjects studied was modest, the populations were unclearly defined, cases and controls were not adequately matched, the methodology for measuring the reference cardiac biomarkers was inadequately described, and the diagnostic performance of cell-free DNA was not benchmarked against highly sensitive troponin immunoassays. Several biological and technical hurdles were also identified in cell-free DNA testing, including the lack of specificity and unsuitable kinetics for early diagnosis of myocardial ischemia, the long turnaround time and low throughput, the need for specialized instrumentation and dedicated personnel, the lack of standardization or harmonization of analytical techniques, the incremental costs and the high vulnerability to preanalytical variables. Hence it seems reasonable to conclude that the analysis of cell-free DNA is not ready for prime time in diagnostics of myocardial ischemia.
Making more out of pixel-level change information: using a neighbourhood approach to improve land change characterization across large and heterogeneous areas

Abstract The paper demonstrates two issues; (i) how a ‘moving window approach’, that translates pixel level detected changes to landscape level, can be implemented; (ii) how the approach can overcome the limitations of pixel level change information to characterize change over large areas. First we detected changes from two periods (1986 and 2010) of LULC maps. On the pixel-based changes, we ran focal statistics summation operator separately for selected window sizes (1–10 km). Further, we assessed effect of scale in depicting the pattern and amount of change. The approach is found useful to overcome major shortfalls of pixel-based change characterization. However, varying scale of analysis provide varying amount of change and differently represent change patterns. Thus, implementing the approach over complex and large areas requires multi-scale approach. Subdividing complex and large areas into homogeneous zones can help to implement the multi-scale approach and facilitate the selection of appropriate scale of analysis.
A programmable pre-cursor ISI equalization circuit for high-speed serial link over highly lossy backplane channel

This paper presents a programmable pre-cursor ISI equalization circuit for high-speed serial data transmission over highly lossy electrical backplane channels. Although decision-feedback-equalizer (DFE) provides an effective way to compensate various channel impairments, such as frequency dependent loss, dispersion and reflections in the legacy backplane environment, for high-speed, highly lossy band-limited channel, the pre-cursor inter-symbol interference (ISI) is still a significant problem for channel equalization. A programmable pre-cursor ISI equalizer combined with a 3-tap DFE is implemented to work at 10-Gb/s and compensate the channel loss of −20 dB. The results show it outperform a traditional 5-tap DFE.
Discrete binary muscle-inspired actuation with motor unit overpowering and binary control strategy

On novel actuator research in the field of cellular muscle-inspired actuators, skeletal muscles are often used as inspiration due to their modular and compact design and seemingly effortless control. Amongst others, the remaining challenges to tackle are robust designs, energy consumption minimization and control strategies. We have developed a discrete muscle-inspired actuator, in which solenoids can be overpowered and locked to recruit springs in series. This paper describes the spring and electronics design and proposes a binary actuator segmentation for increased resolution. Next, we propose and simulate a control strategy based on a lookup table, to cope with multiple discrete inputs, uni-directional force inputs and solenoid cooling time. Currently, the actuation units and springs are modular and can be tailored easily for specific applications. The resolution is maximized without under utilization of the actuator's capabilities, and our control strategy can currently control 12 motor units in real-time, which can be increased to 30. The experiments confirm the working of the control strategy.
[Sensitivity of MRI in detecting alveolar Infiltrates: Experimental studies].

PURPOSE An experimental study using porcine lung explants and a dedicated chest phantom to evaluate the signal intensity of artificial alveolar infiltrates with T 1 - and T 2 -weighted MRI sequences. MATERIAL AND METHODS 10 porcine lung explants were intubated, transferred into the cavity of a MRI-compatible chest phantom and inflated by continuous evacuation of the artificial pleural space. All lungs were examined with MRI at 1.5 T before and after intra-tracheal instillation of either 100 or 200 ml gelatine-stabilised liquid to simulate alveolar infiltrates. MR-examination comprised gradient echo (2D- and 3D-GRE) and fast spin echo sequences (T 2 -TSE and T 2 -HASTE). The signal intensity of lung parenchyma was evaluated at representative cross sections using a standardised scheme. Control studies were acquired with helical CT. RESULTS The instilled liquid caused patchy confluent alveolar infiltrates resembling the findings in patients with pneumonia or ARDS. CT revealed typical ground-glass opacities. Before the application of the liquid, only T 2 -HASTE and T 2 -TSE displayed lung parenchyma signals with a signal/noise ratio of 3.62 and 1.39, respectively. After application of the liquid, both T 2 -weighted sequences showed clearly visible infiltrates with an increase in signal intensity of approx. 30 % at 100 ml (p < 0.01) and 60 % at 200 ml (p < 0.01). With 2D- and 3D-GRE the infiltrates were not visible, although the lung parenchyma signal increase was statistically significant. On 2D-GRE the increase in signal intensity reached 0.74 % (p = 0.32) after 100 ml and 5.6 % (p < 0.01) after 200 ml (for 3D-GRE: 2.2 % [p = 0.02] at 100 ml and 4.4 % at 200 ml [p < 0.01]). The CT controls revealed a significant increase of lung density of 17 H.E. at 100 ml (p = 0.02) and 75 H.E. at 200 ml (p < 0.01). CONCLUSIONS MRI with T 2 -weighted sequences detects artificial alveolar infiltrates with high signal intensity and may be a highly sensitive tool to detect pneumonia in patients.
3D Modeling and Refinement of Residential Maps Using Range Scanners

This paper introduces a method of making 3D models of buildings in a 2D residential digital map, and refining the building data in the digital map. The range image of the streets acquired by line scan laser scanners that moves in the streets is used. The pattern lines of the range image are determined using edge detection or depth analysis. Then these pattern lines are matched with pattern lines of the digital map using a pattern matching algorithm based on dynamic programming. Thus the buildings in digital map and their range images are linked together. The 3D model of the buildings can be constructed from their corresponding range images.
Using Linguistic Tools and Resources in Cross-Language Retrieval

A system to process bilingual/multilingual text corpora is described. Thesystem includes components for crosslanguage querying’on parallel (ietranslation equivalent) and comparable (ie domain-specific) collections oRexts in more than one language. Both sets of procedures are dependent on lexical resources (bilingual lexicaldatabases) and linguistic tools (morphological. procedures). The system was originally designed to meet the requirements ofvarious types of contrastive language studies. However, we are now studyingapplications to cross-language retrieval.
Data Mining to Support Engineering Design Decision

The design and maintenance of an aero-engine generates a significant amount of documentation. When designing new engines, engineers must obtain knowledge gained from maintenance of existing engines to identify possible areas of concern. Firstly, this paper investigate the use of advanced business intelligence tenchniques to solve the problem of knowledge transfer from maintenance to design of aeroengines. Based on data availability and quality, various models were deployed. An association model was used to uncover hidden trends among parts involved in maintenance events. Classification techniques comprising of various algorithms was employed to determine severity of events. Causes of high severity events that lead to major financial loss was traced with the help of summarization techniques. Secondly this paper compares and evaluates the business intelligence approach to solve the problem of knowledge transfer with solutions available from the Semantic Web. The results obtained provide a compelling need to have data mining support on RDF/OWL-based warehoused data.
Mediator-Based Immediate Attribute Revocation Mechanism for CP-ABE in Multicast Group Communications

Attribute Based Encryption (ABE) scheme is a mechanism that allows implementing cryptographic fine grained access control to shared information. It achieves information sharing of type one-to-many users, without considering the number of users and their identities. However, original ABE systems presents some drawbacks, especially the non-efficiency of their attribute/key revocation mechanisms.Based on Ciphertext-Policy ABE (CP-ABE) scheme, we propose an efficient proxy-based immediate private key update for multicast group communications. Our solution does require neither re-encrypting cipher-texts, nor affecting other users (Updating secret keys). The proxy that has been introduced plays the role of a necessary semi-trusted assistant during the decryption process without taking decisions about who is eligible or not to decrypt data.Finally, we demonstrate that our scheme guarantees security requirements that we target and we also show through analysis that our scheme achieves effectively its goals.
GHOTI : capacitive touch interaction prototyping for non-programmers

Copyright is held by the author/owner(s). CS260 Final Presentations, December 6, 2011, Berkeley, CA, USA. Abstract In this paper we introduce a system which allows non-programmers to prototype touch interactions on arbitrary objects using cheaply-available and hobbyist-friendly plug-and-play tools. The system includes a vinyl cutter, sheets of copper foil, a microcontroller, and a computer interface. Copper touch sensors which serve as input devices are printed using the vinyl cutter and are hooked up to the microcontroller, which reports via a serial connection when one of the sensors has been touched. The touch interactions are tied to Sikuli scripts in the computer interface, which relies on programming by demonstration. Subjects in our study were able to successfully prototype media navigation on an arbitrary object: an ordinary coffee mug.
Deep tremor in New Zealand triggered by the 2010 Mw8.8 Chile earthquake

Deep non‐volcanic tremor (NVT) is usually associated with episodic slow‐slip events. New Zealand is one notable exception where numerous slow slip events have been identified, yet NVT has remained undetected. Here we present the first known case of triggered NVT at New Zealand's Hikurangi subduction margin. Following the Mw8.8 Chilean earthquake of February 27, 2010, we identify coherent high‐frequency tremor signals that are in phase with, and modulated by, the passing Rayleigh waves. This is consistent with the surface wave triggering potential for strike‐normal incidence on a low‐angle thrust fault. After constraining the tremor depth on the plate interface, we locate the tremor source within 20 km of the source area of episodic slow slip. The tremor location is also near the edge of a region with high seismic attenuation that marks the boundary between dehydrated subducted slab and inferred hydrated, underplated sediment. We speculate that reduced interface friction and high fluid pressures provided by fluid‐rich underplated sediment facilitates the tremor generation.
Gene transfer of glial cell‐derived neurotrophic factor and cardiotrophin‐1 protects PC12 cells from injury: Involvement of the phosphatidylinositol 3‐kinase and mitogen‐activated protein kinase kinase pathways

Gene therapy for neurodegenerative diseases may utilize the expression of neurotrophic factors because of their potential to promote survival and regeneration of injured neuronal cells. Increasing numbers of these factors are being considered for gene transfer, but their specificity and efficacy in neuroprotection are greatly variable. The major aims of this study were to carry out gene transfer of various neurotrophic factors and investigate their mechanisms of action as well as their protective effects on the viability of rat pheochromocytoma (PC12) cells. We used glutamate, S‐nitroso‐N‐acetyl‐DL‐penicillamine (SNAP), and staurosporine to induce excitatory damage, oxidative stress, and apoptosis, respectively, because these mechanisms are thought to participate in various disease processes leading to degeneration of cells. We utilized adenovirus vectors for efficient gene transfer of trophic factors (glial‐cell derived neurotrophic factor [GDNF] and cardiotrophin‐1 [CT‐1]) or calbindin‐D28k. We found that GDNF and CT‐1 gene transfers were equally effective in saving PC12 cells from injury, but calbindin expression did not show any beneficial effects. GDNF gene transfer was much more efficient in protecting PC12 cells from damage than direct GDNF administration. The protection by GDNF expression against staurosporine was mediated through both phosphatidylinositol 3‐kinase (PI3K) and mitogen‐activated protein kinase kinase (MAPK kinase; MEK) pathways, but only the MEK pathway was involved in the protection against SNAP. In contrast, the protective effect of GDNF against glutamate toxicity was independent of these RET‐dependent signal transduction pathways. © 2002 Wiley‐Liss, Inc.
Kolmogorov Random Graphs and the Incompressibility Method

We investigate topological, combinatorial, statistical, and enumeration properties of finite graphs with high Kolmogorov complexity (almost all graphs) using the novel incompressibility method. Example results are (i) the mean and variance of the number of (possibly overlapping) ordered labeled subgraphs of a labeled graph as a function of its randomness deficiency (how far it falls short of the maximum possible Kolmogorov complexity) and (ii) a new elementary proof for the number of unlabeled graphs.
On Accurate and Robust Estimation of Fundamental Matrix

This paper is concerned with accurate and robust estimation of the fundamental matrix. We show that, given certain conditions, a basic linear algorithm can yield excellent accuracy, in some cases two orders of magnitude better than sophisticated algorithms. The key element of the success is the relative accuracy of displacement estimates used as input and the use of statistical distribution of the errors. We propose a low-level, gradient-based (as opposed to feature-based) algorithm based on the Hough Transform to extract the low-level measurements. We show that it is much more efficient, both in terms of computational expense and accuracy of the final estimate, to remove the errors in the intermediate representation (optic-flow) than to attempt to improve the final estimate by complicated nonlinear algorithms. Experimental results are also included.
Extremum seeking control with data-based disturbance feedforward

This paper presents a practical extension to the classical gradient-based extremum seeking control for the case when the disturbances responsible for the changes in the extremum of a related performance function can be measured. The additional information is used to improve accuracy, convergence speed and robustness of the underlying ESC scheme. Based on the disturbance measurements a map between them and the optimal inputs is iteratively constructed and used as an extremum seeking feedforward. A supervising state-machine is designed to regulate feedforward and search processes ensuring the latter is conducted in the close vicinity of an extremum. The search is based on the sinusoidal input perturbation introduced each time the disturbance is detected and removed once the optimal set-point is identified. Simulation results for the cases of photovoltaic and turbine driven electrical generator systems demonstrate the benefits of the presented design.