Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a Colon Cancer GEMM-Derived Orthotopic Transplant Model for Drug Discovery and Validation

Purpose: Effective therapies for KRAS-mutant colorectal cancer (CRC) are a critical unmet clinical need. Previously, we described genetically engineered mouse models (GEMM) for sporadic Kras-mutant and non-mutant CRC suitable for preclinical evaluation of experimental therapeutics. To accelerate drug discovery and validation, we sought to derive low-passage cell lines from GEMM Kras-mutant and wild-type tumors for in vitro screening and transplantation into the native colonic environment of immunocompetent mice for in vivo validation. Experimental Design: Cell lines were derived from Kras-mutant and non-mutant GEMM tumors under defined media conditions. Growth kinetics, phosphoproteomes, transcriptomes, drug sensitivity, and metabolism were examined. Cell lines were implanted in mice and monitored for in vivo tumor analysis. Results: Kras-mutant cell lines displayed increased proliferation, mitogen-activated protein kinase signaling, and phosphoinositide-3 kinase signaling. Microarray analysis identified significant overlap with human CRC-related gene signatures, including KRAS-mutant and metastatic CRC. Further analyses revealed enrichment for numerous disease-relevant biologic pathways, including glucose metabolism. Functional assessment in vitro and in vivo validated this finding and highlighted the dependence of Kras-mutant CRC on oncogenic signaling and on aerobic glycolysis. Conclusions: We have successfully characterized a novel GEMM-derived orthotopic transplant model of human KRAS-mutant CRC. This approach combines in vitro screening capability using low-passage cell lines that recapitulate human CRC and potential for rapid in vivo validation using cell line-derived tumors that develop in the colonic microenvironment of immunocompetent animals. Taken together, this platform is a clear advancement in preclinical CRC models for comprehensive drug discovery and validation efforts. Clin Cancer Res; 19(11); 2929–40. ©2013 AACR.
Ieee Transactions on Intelligent Transportation Systems 1 Online Travel Mode Identification Using Smartphones with Battery Saving Considerations

—Personal trips in modern urban society usually involve multiple travel modes. Recognizing a traveler's transportation mode is not only critical to personal context-awareness in related applications, but also essential to urban traffic operations , transportation planning and facility design. While most of current practice often leverages infrastructure based fixed sensors or GPS for traffic mode recognition, the emergence of the smartphone provides an alternative promising way with its ever-growing computing, networking and sensing powers. In this paper, we propose a GPS-and-network-free method to detect a traveler's travel mode using mobile phone sensors. Our application is built on the latest Android platform with multimodality sensors. By developing a hierarchical classification method with an online learning model, we achieve almost 100% accuracy in a binary classification of wheeled/unwheeled travel modes, and an average of 97.1% accuracy with all six travel modes (buses, subways, cars, bicycling, walking, and jogging). Our system (a) could adapt to each traveler's pattern by using the online learning model and it performs significantly faster in computation than the offline model (b) works with a low sampling frequency for sensing so that it saves the smartphone battery.
CNN model of the feature-linked synchronized activities in the visual thalamo-cortical system

In order to investigate whether thalamic synchronization may contribute to the binding of different cortical representations in visual information processing, we made a neuromorphic model of the thalamo-cortical loop, using the cellular neural network (CNN) model and simulator. It is demonstrated with the aid of this model that the cortico-thalamic feedback by synchronizing dLGN relay cell responses, provides a temporal code and this may induce correlated activities in the target cortical neuron population. Our results support the notion that using synchronization of temporally structured activities as general integration mechanism, the processing of visual information occurs simultaneously in the highly interconnected thalamo-cortical system.
Characterizing the Global Impact of the P 2 P Overlay on the AS-level Underlay

This paper examines the problem of characterizing and assessing the global impact of the load imposed by a Peer-toPeer (P2P) overlay on the AS-level underlay. Toward this end, we make three contributions: (i) We describe the major challenges in addressing this problem (e.g., capturing overlay snapshots, determining the load generated by of individual connections, and identifying the AS-level paths taken by individual overlay connections) and present existing techniques for addressing the s issues along with their limitations. (ii) We present a methodology that combines a collection of best practices for tackling the above challenges. (iii) We apply the proposed methodology to characterize several aspects of the load imposed by a real-world P2P overlay (e.g., Gnutella) on the AS-level underlay. This study represents an initial attempt at deepening our understanding of how overlays get mapped into the AS underlay.
A New Trigger Criterion for Improved Real-Time Performance of Onsite Earthquake Early Warning in Southern California

We have implemented and tested an algorithm for onsite earthquake early warning (EEW) in California using the infrastructure of the Southern California Seismic Network (SCSN). The algorithm relies on two parameters derived from the initial 3 sec of P waveform data at a single seismic sensor: period parameter τ_c and high-pass filtered displacement amplitude P_d. Previous studies have determined empirical relationships between c and the moment magnitude M_w of an earthquake, and between P_d and the peak ground velocity (PGV) at the site of observation. In 2007, seven local earthquakes in southern California with 4.0≤M_L≤4.7 have triggered the calculation of M_w and PGV by the EEW algorithm. While the mean values of estimated parameters were in the expected range, the scatter was large, in particular for the smallest events. During the same time period the EEW algorithm produced a large number of false triggers due to low trigger thresholds. To improve the real-time performance of the onsite approach, we have developed a new trigger criterion that is based on combinations of observed τ _c and P_d values. This new criterion removes 97% of previous false triggers and leads to a significant reduction of the scatter in magnitude estimates for small earthquakes.
Realtime Generation of Harmonic Progressions Using Constrained Markov Selection

In this paper, we describe a method of generating harmonic progressions using case-based analysis of existing material that employs a variable-order Markov model. Using a unique method for quantifying harmonic complexity and tension between chord transitions, as well as specifying a desired bass-line, the user specifies a 3 dimensional vector, which the realtime generative algorithm attempts to match during chord sequence generation. The proposed system thus offers a balance between user-requested material and coherence within the database.
Stability and Secretion of Acetylcholinesterase Forms in Skeletal Muscle Cells

Muscle cells express a distinct splice variant of acetylcholinesterase (AChET), but the specific mechanisms governing this restricted expression remain unclear. In these cells, a fraction of AChE subunits is associated with a triple helical collagen, ColQ, each strand of which can recruit a tetramer of AChET. In the present study, we examined the expression of the various splice variants of AChE by transfection in the mouse C2C12 myogenic cells in vitro, as well as in vivo by injecting plasmid DNA directly into tibialis anterior muscles of mice and rats. Surprisingly, we found that transfection with an ACHEH cDNA, generating a glycophosphatidylinositol-anchored enzyme species, produced much more activity than transfection with AChET cDNA in both C2C12 cells and in vivo. This indicates that the exclusive expression of AChET in mature muscle is governed by specific splicing. Interaction of AChET subunits with the complete collagen tail ColQ increased enzyme activity in cultured cells, as well as in muscle fibers in vivo. Truncated ColQ subunits, presenting more or less extensive C-terminal deletions, also increased AChE activity and secretion in C2C12 cells, although the triple helix could not form in the case of the larger deletion. This suggests that heteromeric associations are stabilized compared with isolated AChET subunits. Coinjections of AChETand ColQ resulted in the production and secretion of asymmetric forms, indicating that assembly, processing, and externalization of these molecules can occur outside the junctional region of muscle fibers and hence does not require the specialized junctional Golgi apparatus.
Lack of polymorphism of the agouti signaling protein (ASIP) gene among four different brown hare (Lepus europaeus Pallas 1778) populations

SUMMARY The brown hare ( Lepus europaeus Pallas 1778) is a common palearctic and a popular game species therefore it has been an obvious subject for population genetic studies since the second part of the 20 th century. Among the several mitochondrial DNA studies some have been carried out concerning nuclear genes as well. The agouti signaling protein gene (ASIP) is involved in regulating the synthesis of eumelanin and pheomelanin in melanocytes of mammals. Though many studies focused on it in relation with several mammalian species, minimal information is available on this topic concerning the brown hare. Here we present a short communication concerning the agouti signaling protein (ASIP) gene in four different country’s L. europaeus populations, namely Lithuania, Hungary, Serbia and Georgia. N=45 tissue samples have been investigated from overall 17 sampling sites of the different countries. There has not been found any polymorphism among the sequences. In an alignment with other Leporid species’ partial ASIP sequences downloaded from ENA we have found that based on a 178 base pairs long DNA sequence the haplotype of our samples contains three other Lepus species as well. This is concordant with the findings of a previous study focusing predominantly on the European rabbit ( Oryc-to lagus cuniculus Linnaeus 1758) and the several mutations of its ASIP gene.
Generalized monotonicity and strategy-proofness for non-resolute social choice correspondences

Recently there are several works which analyzed the strategy-proofness of non-resolute social choice rules such as Duggan and Schwartz (2000) and Ching and Zhou (2001). In these analyses it was assumed that individual preferences are linear, that is, they excluded indifference from individual preferences. We present an analysis of the strategy-proofness of non-resolute social choice rules when indifference in individual preferences is allowed. Following to the definition of the strategy-proofness by Ching and Zhou (2001) we shall show that a generalized version of monotonicity and the strategy-proofness are equivalent. It is an extension of the equivalence of monotonicity and the strategy-proofness for resolute social choice rules with linear individual preferences proved by Muller and Satterthwate (1980) to the case of non-resolute social choice rules with general individual preferences.
El Niño and La Niña influence on mean river flows of southern South America in the 20th century

ABSTRACT The influence of the El Niño Southern Oscillation (ENSO) phenomenon on monthly mean river flows of 12 rivers in the extreme south of South America in the 20th century is analysed. The original dataset of each river is divided into two subsets, i.e. warm ENSO events or El Niño, and cold ENSO events or La Niña. The elements of the subsets are composites of 24 consecutive months, from January of the year when the ENSO event begins to December of the following year. The ENSO signal is analysed by comparing the monthly mean value of each subset to the long-term monthly mean. The results reveal that, in general, monthly mean El Niño (La Niña) river flows are predominantly larger (smaller) than the long-term monthly mean in the rivers studied. The anomalies are more evident during the second half of the year in which the event starts and the first months of the following year.
Planning for Loosely Coupled Agents Using Partial Order Forward-Chaining

We investigate a hybrid between temporal partial-order and forward-chaining planning where each action in a partially ordered plan is associated with a partially defined state. The focus is on centralized planning for multi-agent domains and on loose commitment to the precedence between actions belonging to distinct agents, leading to execution schedules that are flexible where it matters the most. Each agent, on the other hand, has a sequential thread of execution reminiscent of forward-chaining. This results in strong and informative agent-specific partial states that can be used for partial evaluation of preconditions as well as precondition control formulas used as guidance. Empirical evaluation shows the resulting planner to be competitive with TLplan and TALplanner, two other planners based on control formulas, while using a considerably more expressive and flexible plan structure.
Retinal safety of intravitreal rtPA in healthy rats and under excitotoxic conditions

Purpose Intravitreal recombinant tissue plasminogen activator (rtPA) is used off-label for the surgical management of submacular hemorrhage, a severe complication of neovascular age-related macular degeneration. rtPA is approved for coronary and cerebral thrombolysis. However, in ischemic stroke rtPA is known to increase excitotoxic neural cell death by interacting with the N-methyl-D-aspartate (NMDA) receptor. We therefore investigated the retinal toxicity of rtPA in healthy rats and in a model of NMDA-induced retinal excitotoxicity. Methods First, rtPA at three different doses (2.16 µg/5 µl, 0.54 µg/5 µl, and 0.27 µg/5 µl) or vehicle (NaCl 0.9%) was injected intravitreally in healthy rat eyes. Electroretinograms (ERGs) were performed at 24 h or 7 days. Annexin V-fluorescein isothiocyanate (FITC)-labeled apoptotic retinal ganglion cells (RGCs) were counted on flatmounted retinas at 24 h or 7 days. Next, NMDA + vehicle or NMDA + rtPA (0.27 µg/5 µl) was injected intravitreally to generate excitotoxic conditions. Apoptotic annexin V-FITC-labeled RGCs and surviving Brn3a-labeled RGCs were quantified on flatmounted retinas and radial sections, 18 h after treatment. Results In healthy rat eyes, the number of apoptotic RGCs was statistically significantly increased 24 h after the administration of rtPA at the highest dose (2.16 µg/5 µl; p = 0.0250) but not at the lower doses of 0.54 and 0.27 µg/5 µl (p = 0.36 and p = 0.20), compared to vehicle. At day 7, there was no difference in the apoptotic RGC count between the rtPA- and vehicle-injected eyes (p = 0.70, p = 0.52, p = 0.11). ERG amplitudes and implicit times were not modified at 24 h or 7 days after injection of any tested rtPA doses, compared to the baseline. Intravitreal administration of NMDA induced RGC death, but under these excitotoxic conditions, coadministration of rtPA did not increase the number of dead RGCs (p = 0.70). Similarly, the number of surviving RGCs on the flatmounted retinas and retinal sections did not differ between the eyes injected with NMDA + vehicle and NMDA + rtPA (p = 0.59 and p = 0.67). Conclusions At low clinical equivalent doses corresponding to 25 µg/0.1 ml in humans, intravitreal rtPA is not toxic for healthy rat retinas and does not enhance NMDA-induced excitotoxicity. Vitreal equivalent doses ≥200 µg/0.1 ml should be avoided in patients, due to potential RGC toxicity.
More Bang for the Buck: Media Freedom and Organizational Strategies in the Agenda-Setting of Human Rights Groups

Studies investigating the agenda-setting of human rights groups disagree on both their prospects of garnering political attention, and the factors that help them in that quest. This study makes the argument that we need to take account of both macro-institutional opportunity structures and actor-level strategies in order to gain a more complete understanding of the group-media interface. Specifically, it posits that the urgency of social problems only drives media attention toward groups if a country’s media landscape is sufficiently free, and that within these institutional constraints, groups themselves can enhance their media access by providing newsmakers with information subsidies. These claims are substantiated by way of a novel cross-nationally comparative data set of more than 1,000 domestic election monitoring and advocacy organizations. Findings show that media attention is structurally limited by the degree to which the news media serve as an open arena, and that even in countries with a free press, few groups achieve media access. At the same time, the most successful groups are not necessarily the most resourceful ones. Rather, strategic choices to invest in media effort, narrow policy engagement, and professionalization substitute for scarce resources, thereby giving groups “more bang for their buck. ” The results clarify the causal mechanisms behind the dominance of resource-rich groups on the media agenda and reinforce calls for more globally comparative research into media agenda-setting.
Putting theory-oriented evaluation into practice : A logic model approach for evaluating SIMGAME

Evaluations of gaming simulations and business games as teaching devices are typically end-state driven. This emphasis fails to detect how the simulation being evaluated does or does not bring about its desired consequences. This paper advances the use of a logic model approach, which possesses a holistic perspective that aims at including all elements associated with the situation created by a game. The use of the logic model approach is illustrated as applied to SIMGAME, a board game created for secondary school level business education in six European Union countries.
Testing the AGN-Starburst Connection in Seyfert Galaxies

We use the CO band at 2.3 μm to constrain the populations of young stars in the central regions of Seyfert galaxies. We report new CO band spectroscopy of 46 Seyfert galaxies. In most cases, the observed CO indices appear diluted by the presence of a nonstellar component (most likely, warm dust surrounding the active nucleus). We used JHKL aperture photometry to estimate the nonstellar contribution at 2.3 μm. We successfully corrected the CO band for the dilution for 16 galaxies which were not dominated by the nonstellar component. Comparing with CO indices measured in elliptical and purely starbursting galaxies, we find no evidence for strong starbursts in the majority of these galaxies.
Journal of Internet Banking and Commerce Quality of Web-based Information Systems

His areas of interest are software engineering and software reliability modeling. His research interests include information systems used in management and analytical methods used in the management. Abstract The scope and complexity of current World Wide Web applications vary widely: from smallscale, short-lived services to large-scale enterprise applications distributed across the Internet and corporate intranets and extranets. As Web applications have evolved, the demands placed on Web-based systems and the complexity of designing, developing, maintaining, and managing these systems have also increased significantly. They provided vast, dynamic information in-2-multiple media formats (graphics, images, and video). Web site design for these and many other applications demand balance among information content, aesthetics, and performance. In accordance with the growth of the Internet and World Wide Web, there has been some research on quality issues of Web-based software systems. The differences between the Web-based information systems and conventional information systems are discussed in a paper from the perspective of software quality.
Near-Wall Flow Visualization in Flattened Surface Neighborhoods

We present a method that flattens a curved surface and its neighborhood to create effective, uncluttered visualizations by applying standard flow visualization techniques in the deformed space. Level sets of the distance from the curved surface are mapped to parallel planes. Data fields are mapped accordingly. Our method eases the visual inspection and analysis of a curved surface’s vicinity by providing a flat space that supports the creation of standardized views. This is particularly useful for visualizing flow fields in the boundary layer.
Reconfigurable Multiparameter Biosignal Acquisition SoC for Low Power Wearable Platform

A low power and low noise reconfigurable analog front-end (AFE) system on a chip (SoC) for biosignal acquisition is presented. The presented AFE can be reconfigured for use in electropotential, bioimpedance, electrochemical, and photoelectrical modes. The advanced healthcare services based on multiparameter physiological biosignals can be easily implemented with these multimodal and highly reconfigurable features of the proposed system. The reconfigurable gain and input referred noise of the core instrumentation amplifier block are 25 dB to 52 dB, and 1 μVRMS, respectively. The power consumption of the analog blocks in one readout channel is less than 52 μW. The reconfigurable capability among various modes of applications including electrocardiogram, blood glucose concentration, respiration, and photoplethysmography are shown experimentally.
Cystatin C and Contrast-Induced Acute Kidney Injury

Background— Cystatin C (CyC) is more sensitive than serum creatinine (sCr) to rapidly detect acute changes in renal function. Methods and Results— We measured CyC together with sCr in 410 consecutive patients with chronic kidney disease undergoing either coronary and/or peripheral angiography and/or angioplasty. sCr was assessed at baseline and 24 and 48 hours after contrast media exposure. CyC was assessed at baseline and at 24 hours. Major adverse events (including death of any cause and dialysis) at 12 months were assessed. At 48 hours after contrast media exposure, contrast-induced acute kidney injury (defined as a sCr increase ≥0.3 mg/dL) occurred in 34 patients (8.2%). A CyC increase concentration ≥10% at 24 hours after contrast media exposure was detected in 87 patients (21.2%). This was the best CyC cutoff for the early identification of patients at risk for contrast-induced acute kidney injury (negative predictive value=100%; positive predictive value=39.1%). According to the defined cutoffs (that is, increase in CyC ≥10% and sCr ≥0.3 mg/dL), major adverse events occurred in 16 of 297 patients (5.4%) without any cutoffs satisfied (group 1), in 9 of 49 patients (18.4%) with only a CyC increase ≥10% (group 2), and in 9 of 31 patients (29%) with both cutoffs satisfied (group 3). By logistic regression analysis, the independent predictors of major adverse events at 1 year were group 2 (odds ratio=2.52; 95% confidence interval, 1.17 to 5.41; P=0.02), group 3 (odds ratio=4.45; 95% confidence interval, 1.72 to 11.54; P=0.002), and baseline glomerular filtration rate (odds ratio=0.91; 95% confidence interval, 0.88 to 0.95; P<0.001). Conclusions— In patients with chronic kidney disease, CyC seems to be a reliable marker for the early diagnosis and prognosis of contrast-induced acute kidney injury.