Miracle-dz/UniFAR-FTUs huggingface dataset:
Intracellular single molecule microscopy reveals time and mRNA dependent microRNA assembly

Supplementary Figure 1 Precision and signal intensity of live cell imaging, and cxcr4 control experiments Supplementary Figure 2 Tracking the diffusion of individual PBs in live HeLa cells Supplementary Figure 3 Live cell images after incubation for varying amounts of time after microinjection Supplementary Figure 4 Relative deviation (RD) analysis of diffusion coefficients over time Supplementary Figure 5 Stepwise photobleaching in fixed cells Supplementary Figure 6 Representative images and resulting stepwise photobleaching distributions from fixed cells incubated for various amounts of time after microinjection Supplementary Figure 7 miRNAs assembly is mRNA dependent Supplementary Video legend 1 Videos of both Cy3 and Cy5 labeled miRNAs diffusing in living HeLa cells Supplementary Video legend 2 Different types of motion exhibited by miRNAs in living HeLa cells Supplementary Video legend 3 Live cell imaging control experiments Supplementary Video legend 4 Pseudo-colored video showing photobleaching of let-7-a1-Cy5 miRNAs in fixed cells, imaged 2 hrs after injection Supplementary Table 1 Number of cells and particles used in both live and fixed cell analysis Supplementary Figure S1 │ Precision and signal intensity of live cell imaging, and cxcr4 control experiments. (A) Precision of single particle localization. Histogram depicting the displacement of formaldehyde-fixed let-7-a1-Cy5 particles about their origin (n = 100 randomly selected particles). The location of each particle was tracked over time until it photobleached. The histogram was fit with a Gaussian function, which resulted in a mean of ~30 nm and a standard deviation of ~50 nm. Large jumps (>100 nm) were observed only when there were large fluctuations of intensity. Localization precision of immobilized beads (inset) was ~4 nm, largely owing to their higher signal-to-noise ratio (n = 100 randomly selected particles). (B) Signal intensities of particles undergoing diffusion in living cells. Intensity time trajectories of let-7-a1-Cy3 (green) and let-7-a1-Cy5 (red) particles are shown. Trajectories of both mobile and static particles are shown, as indicated in each trajectory. A significant proportion of particles had a relatively constant intensity during diffusion before disappearing. We infrequently observed large fluctuations in intensity as a particle was diffusing, possibly due to diffusion in the axial dimension (z-axis). We also occasionally observed stepwise changes in intensity of static particles, possibly due to photobleaching (see, for example, second trajectory from the top on the left side). (C-E) Intracellular diffusion of cxcr4 miRNA, with (C) DIC image and (D) the corresponding pseudocolored image of a cell microinjected with cxcr4-Cy3 and imaged …
Identification and Characterization of a Potent Activator of p53-Independent Cellular Senescence via a Small-Molecule Screen for Modifiers of the Integrated Stress Response s

The Integrated Stress Response (ISR) is a signaling program that enables cellular adaptation to stressful conditions like hypoxia and nutrient deprivation in the tumor microenvironment. An important effector of the ISR is activating transcription factor 4 (ATF4), a transcription factor that regulates genes involved in redox homeostasis and amino acid metabolism and transport. Because both inhibition and overactivation of the ISR can induce tumor cell death, modulators of ATF4 expression could prove to be clinically useful. In this study, chemical libraries were screened for modulators of ATF4 expression. We identified one compound, E235 (N-(1-benzyl-piperidin-4-yl)-2-(4-fluoro-phenyl)-benzo[d]imidazo[2,1-b]thiazole-7-carboxamide),thatactivatedtheISRanddose-dependentlyincreasedlevelsofATF4intransformedcells.Adose-dependentdecreaseinviabilitywasobservedinseveralmouseandhumantumorcelllines,andknockdownofATF4 significantly increased the antiproliferative effects of E235. Interestingly, low m M doses of E235 induced senescence in many cell types, including HT1080 human fibrosarcoma and B16F10 mouse melanoma cells. E235-mediated induction of senescence was not dependent on p21 or p53; however, p21 conferred protection against the growth inhibitory effects of E235. Treatment with E235 resulted in an increase in cells arrested at the G2/M phase with a concurrent decrease in S-phase cells. E235 also activated DNA damage response signaling, resulting in increased levels of Ser15-phosphorylated p53, g -H2AX, and phosphorylated checkpoint kinase 2 (Chk2), although E235 does not appear to cause physical DNA damage. Induction of g -H2AX was abrogated in ATF4 knockdown cells. Together, these results suggest that modulation of the ISR pathway with the small molecule E235 could be a promising antitumor strategy.
A Flexible Agent-Oriented Solution to Model Organisational and Normative Requirements in Assistive Technologies

Assistive technologies represent a recent application area of a wide variety of Artificial Intelligence methods and tools to support people in their activities of daily living. But most approaches do only center in the direct interaction between the user and the assistive tool, without taking into consideration the important role that other actors (caregivers, relatives) may have in the user activities, nor they explicitly reflect the norms and regulations that apply in such scenarios. In this paper we present an approach to the development of assistive technologies which uses organisational and normative elements to ease the design of both the social network arround the user and their expected behavioural patterns.
Application of rectangular features for the localization of fertile material in plant images

Analysis of fertile material such as flowers and fruit is a key factor in the proper identification of plant species. Despite object recognition being a mature research area, the use of it in automated plant identification is still relatively new. This paper describes a novel method of detecting fertile material in plant images using rectangular features. Rectangular features are obtained for the grayscale image, the J value image, the magnitude and angle of the gradient of the image. From these, the features with the best performance are selected based on their ability to detect fertile material (flowers) and non-fertile material (leaves). Based on performance, the rectangular features of the grayscale image and J value image are used. Multiple Support Vector Machine (SVM) classifiers with different kernels are tested and the final result is obtained using classifier voting based on the confidence of each classifier. After applying the classifier to the entire image, regions of interest of fertile material are isolated and post processed.
Computerized Provider Order Entry with Pager Notification Improves Efficiency in STAT Radiographic Studies and Respiratory Treatments

Summary Background: The use of computerized provider order entry (CPOE) has been widely linked to improvements in patient safety. We hypothesized that electronic routing of CPOE-generated orders through individual pagers would improve the efficiency of STAT radiographic studies and respiratory treatments. Methods: The study was conducted in two periods before and after implementing pager notification of STAT orders. In the Baseline Period, CPOE-generated STAT orders were communicated to radiology technicians or respiratory therapists through the use of printed orders, manual paging and/or telephone communication. The time to process the order and deliver a radiology result or respiratory treatment was tracked. In the Intervention Period CPOE-generated STAT orders were electronically routed to the radiology technician’s or respiratory therapist’s pager. During both time periods, clinicians completed user satisfaction surveys. Results: Using pager notification, there was a significant reduction in radiology technician arrival time (16.8±2.1 vs 7.9±0.7 mins, p<0.001). Similarly there was a significant reduction in the cumulative time required to capture the radiographic image, image availability in the picture archiving and communication system (PACS) and the verbal report from the radiologist (p<0.05). The time required in obtaining a preliminary or final radiographic written report and the total cycle times were not significantly reduced. For STAT respiratory therapy orders there was a significant reduction in the mean time from ordering to administration of respiratory therapy treatments (124.7±14.1 vs 49.8±11.4 minutes, p<0.01). Radiologists, respiratory therapists and ordering clinicians reported improved satisfaction after implementation of pager notification. Conclusion: Computer-generated orders for STAT radiographic studies and respiratory treatments can be carried out significantly faster through the use of direct pager notification. The implementation of this process has resulted in improved care delivery and widespread clinician satisfaction.
Cytostatic effect of Epstein-Barr virus latent membrane protein-1 analyzed using tetracycline-regulated expression in B cell lines.

Tetracycline-regulated vectors were used to obtain inducible expression in stable transfected B cell lines of two Epstein-Barr virus (EBV) latent genes, LMP1 and EBNA2. The transfected genes were tightly repressed by low, nontoxic concentrations of tetracycline (< or = 1 microgram/ml) and, following removal of tetracycline, were induced to levels comparable to or up to 3x that of EBV-transformed normal lymphoblastoid cell lines. In transfected DG75 cells, induced expression of LMP1, but not of EBNA2, led to the expected upregulation of various cell surface markers, including: CD40, CD54, CD58, and HLA class I.A novel observation was that both LMP1 and EBNA2 independently caused the downregulation of surface IgM, an effect mirrored in EBV-positive Burkitt lymphoma lines undergoing phenotypic drift during the transition from latency I to latency III in which both LMP1 and EBNA2 are upregulated. Most remarkably, induced LMP1 expression almost completely inhibited cell growth for 4 to 5 days, after which the cells recovered a limited proliferative capacity. The cytostatic effect of LMP1 was observed in all three B cell lines studied: DG75, BJAB, and Akata. Further analysis showed that induction of LMP1 coincided with a reduction in the levels of c-myc, and that the cytostatic effect was due to an accumulation of cells at the G2/M phase of the cell cycle. These data suggest a novel function for the LMP1 oncogene in controlling the proliferation of EBV-infected cells by regulating progress through G2/M phase.
Hybrid Cascaded H-Bridge Multilevel-Inverter Induction-Motor-Drive Direct Torque Control for Automotive Applications

This paper presents a hybrid cascaded H-bridge multilevel motor drive direct torque control (DTC) scheme for electric vehicles (EVs) or hybrid EVs. The control method is based on DTC operating principles. The stator voltage vector reference is computed from the stator flux and torque errors imposed by the flux and torque controllers. This voltage reference is then generated using a hybrid cascaded H-bridge multilevel inverter, where each phase of the inverter can be implemented using a dc source, which would be available from fuel cells, batteries, or ultracapacitors. This inverter provides nearly sinusoidal voltages with very low distortion, even without filtering, using fewer switching devices. In addition, the multilevel inverter can generate a high and fixed switching frequency output voltage with fewer switching losses, since only the small power cells of the inverter operate at a high switching rate. Therefore, a high performance and also efficient torque and flux controllers are obtained, enabling a DTC solution for multilevel-inverter-powered motor drives.
An Efficient Context-Free Parsing Algorithm for Natural Languages

This thesis introduces an efficient context-free parsing algorithm and emphasizes its practical value in natural language processing. In the theoretical worst case analysis, the parsing algorithm occasionally takes more than O(n('3)) time with kinds of context-free grammars which are very unlikely to appear in natural languages. As far as practical natural language processing is concerned, on the other hand, the parsing algorithm seems more efficient than any existing algorithms including Earley's algorithm. Experiments with several English grammars and sample sentences show that our algorithm is 5 to 10 times faster than Earley's standard algorithm. The parsing algorithm can be viewed as an extended LR parsing algorithm which embodies the concept of a "graph-structured stack. " Unlike the standard LR, the algorithm is capable of handling arbitrary non-cyclic context-free grammars including ambiguous grammars, with little loss of LR efficiency. In particular, if its grammar is "close" to LR, most of the LR parsing efficiency can be preserved. Natural language grammars are, fortunately, considerably "close" to LR, compared with other general context-free grammars. The algorithm is an all-path parsing algorithm; it produces all possible parse trees (a parse forest) in an efficient representation called a "shared-packed forest. " This thesis also shows that Earley's forest representation has a defect and his representation cannot be used in natural language processing. The last chapters of the thesis suggest practical applications of the algorithm. A concept of left-to-right on-line parsing is introduced, taking advantage of the fact that our algorithm parses a sentence strictly from left to right. Several benefits of on-line parsing are described, and its application to user-friendly natural language interface is discussed. This thesis also proposes a technique to disambiguate a sentence out of the shared-packed forest representation by asking the user questions interactively. Finally, a personal/interactive machine translation system is suggested.
Fall 9-1-2010 Integrating Wikipedia and Facebook Context into Collaborative E-Brainstorming ; CU-CS-1073-10

This paper presents an application for collaborative brainstorming on shared digital displays that integrates online content to help create new ideas during the brainstorming process. The brainstorming application links ideas under discussion to their best matched Wikipedia pages, suggests related ideas for deeper discussion based on items “pinned” on the whiteboard, and recommends a broader scope of new ideas based on users’ experiences and expertise, as derived from their social networking profiles. The software system for this application is described, including its idea recommendation engine and UI component. Experimental tests evaluating the application in the context of real users are presented.
Finding Counterexamples to Inductive Conjectures and Discovering Security Protocol Attacks

We present an implementation of a method for finding counterexamples to universally quantified conjectures in first-order logic. Our method uses the proof by consistency strategy to guide a search for a counterexample and a standard first-order theorem prover to perform a concurrent check for inconsistency. We explain briefly the theory behind the method, describe our implementation, and evaluate results achieved on a variety of incorrect conjectures from various sources. Some work in progress is also presented: we are applying the method to the verification of cryptographic security protocols. In this context, a counterexample to a security property can indicate an attack on the protocol, and our method extracts the trace of messages exchanged in order to effect this attack. This application demonstrates the advantages of the method, in that quite complex side conditions decide whether a particular sequence of messages is possible. Using a theorem prover provides a natural way of dealing with this. Some early results are presented and we discuss future work.
THE CEDUNA SUB-BASIN—A SNAPSHOT OF PROSPECTIVITY

The Ceduna Sub-basin comprises one of the major untested potential petroleum provinces in Australia. It is located in the Great Australian Bight, forming part of the Bight Basin. Water depths range from 100 m in the north to over 4,000 m in the south. Although over 100,000 line km of 2D marine seismic data have been acquired in the Great Australian Bight, only 20,600 line km of 2D marine seismic data of variable vintage and quality have been acquired in the Ceduna Sub-basin. Only one exploration well, Potoroo–1, has been drilled within the Ceduna Sub-basin. The Potoroo–1 well is located on the extreme landward edge of the depocentre which is dominated by the Late Cretaceous Ceduna Delta. Consequently, the hydrocarbon potential of the basin is effectively untested. The most promising play types within the Ceduna Subbasin are dip and fault-dip closures associated with listric faults within the Late Cretaceous (Santonian- Maastrichtian) deltaic sequence and accentuated by slight Late Cretaceous/Tertiary compression. Fault-dip closures are also recognised within the Santonian section. A channel sub-crop play within the Santonian is also potentially viable. Hydrocarbon charge is perceived to be the most significant exploration risk. Although asphaltite strandings have been reported, the hydrocarbon charge system is unproven. Future exploration in the Great Australian Bight will need to address: harsh climatic/meteorological and oceanographic conditions in the Southern Ocean and short seasonal windows; extreme sea floor relief and viability of safe exploration drilling in water depths over 1,500 m; and operating in a responsible and environmentally sensitive way in proximity to the Benthic Protection Zone.
Modulation of cortical activity during different imitative behaviors.

Imitation is a basic form of motor learning during development. We have a preference to imitate the actions of others as if looking in a mirror (specular imitation: i.e., when the actor moves the left hand, the imitator moves the right hand) rather than with the anatomically congruent hand (anatomic imitation: i.e., actor and imitator both moving the right hand). We hypothesized that this preference reflects changes in activity in previously described frontoparietal cortical areas involved in directly matching observed and executed actions (mirror neuron areas). We used functional magnetic resonance imaging to study brain activity in normal volunteers imitating left and right hand movements with their right hand. Bilateral inferior frontal and right posterior parietal cortex were more active during specular imitation compared with anatomic imitation and control motor tasks. Furthermore this same pattern of activity was also observed in the rostral part of the supplementary motor area (SMA-proper) of the right hemisphere. These findings suggest that the degree of involvement of frontoparietal mirror areas in imitation depends on the nature of the imitative behavior, ruling out a linguistic mediation of these areas in imitation. Moreover, activity in the SMA appears to be tightly coupled to frontoparietal mirror areas when subjects copy the actions of others.
Tractable Approach for Hexagonal Cellular Network Model and Its Comparison to Poisson Point Process

Explicit derivation of interferences and SINR distribution in hexagonal wireless networks has been widely considered intractable and generally performed with system level simulations. In this paper, we prove that the hexagonal model is indeed tractable and we provide an explicit formula of downlink interferences and SINR distribution for any arbitrary mobile user locations' distribution reflecting the spatial traffic density in the network. We compare also performances of hexagonal model with those of a Homogeneous Poisson Point Process (HPPP) and we discuss the flexibility of each model in terms of handling the user location variability in the network. We discuss also the importance to have such hexagonal modeling with arbitrary distribution of user locations in the prediction of SINR distribution for each cell in the network.
A Novel Monopulse Technique for Adaptive Phased Array Radar

The monopulse angle measuring technique is widely adopted in radar systems due to its simplicity and speed in accurately acquiring a target’s angle. However, in a spatial adaptive array, beam distortion, due to adaptive beamforming, can result in serious deterioration of monopulse performance. In this paper, a novel constrained monopulse angle measuring algorithm is proposed for spatial adaptive arrays. This algorithm maintains the ability to suppress the unwanted signals without suffering from beam distortion. Compared with conventional adaptive monopulse methods, the proposed algorithm adopts a new form of constraint in forming the difference beam with the merit that it is more robust in most practical situations. At the same time, it also exhibits the simplicity of one-dimension monopulse, helping to make this algorithm even more appealing to use in adaptive planar arrays. The theoretical mean and variance of the proposed monopulse estimator is derived for theoretical analysis. Mathematical simulations are formulated to demonstrate the effectiveness and advantages of the proposed algorithm. Both theoretical analysis and simulation results show that the proposed algorithm can outperform the conventional adaptive monopulse methods in the presence of severe interference near the mainlobe.
The So2 Allowance Trading System: the Ironic History of a Grand Policy Experiment

Two decades have passed since the Clean Air Act Amendments of 1990 launched a grand experiment in market-based environmental policy: the SO2 cap-and-trade system. That system performed well but created four striking ironies. First, by creating this system to reduce SO2 emissions to curb acid rain, the government did the right thing for the wrong reason. Second, a substantial source of this system’s cost-effectiveness was an unanticipated consequence of earlier railroad deregulation. Third, it is ironic that cap-and-trade has come to be demonized by conservative politicians in recent years, since this market-based, cost-effective policy innovation was initially championed and implemented by Republican administrations. Fourth, court decisions and subsequent regulatory responses have led to the collapse of the SO2 market, demonstrating that what the government gives, the government can take away.
Real-time radionuclide cineangiography in the noninvasive evaluation of global and regional left ventricular function at rest and during exercise in patients with coronary-artery disease.

Although coronary angiography defines regions of potential ischemia in patients with coronary-artery disease, accurate assessment of the presence and functional importance of ischemia requires appraisal of regional and global left ventricular function during stress. To perform such assessment, we developed a noninvasive real-time radionuclide cineangiographic procedure permitting continuous monitoring and analysis of left ventricular function during exercise. In 11 patients with coronary disease who had normal regional and global ventricular function at rest, new regions of dysfunction developed during exercise (P less than 0.001), and in 10, global ejection fraction dropped 7 to 47 per cent. Fourteen age-matched normal subjects were studied; during exercise none had regional dysfunction, and each increased global ejection fraction (average increase, 23 +/- 3 per cent [+/-S.E.], P less than 0.001 as compared with patients with coronary disease). Radionuclide cineangiography during exercise permits accurate assessment of the presence and functional severity of ischemic heart disease.