Miracle-dz/UniFAR-FTUs huggingface dataset:
HGF Rescues Colorectal Cancer Cells from EGFR Inhibition via MET Activation

Purpose: Cetuximab, an antibody targeting the epidermal growth factor receptor (EGFR), is active in colorectal cancer (CRC). However, response rates range from only 10% to 20%. Here, we investigate hepatocyte growth factor (HGF)-dependent mesenchymal-epithelial transition factor (MET) activation as a mediator of cetuximab resistance through signal diversification in CRC cell lines. Experimental Design: DiFi, GEO, and LIM1215 cells were treated with varying concentrations and combinations of EGF, HGF, cetuximab, and PHA-665752 (a highly specific MET kinase inhibitor). Biological end points included proliferation, cell cycle arrest, and apoptosis. Proliferation was measured using WST-1 assays and synergy investigated via isobolograms. Expression and signaling were examined using immunoblotting. Results: EGFR and MET are coexpressed in these CRC cell lines, and dual receptor activation synergistically increased proliferation. Cetuximab inhibited cell growth by 60%–80% with an associated dephosphorylation of EGFR, MAPK, and/or AKT. Addition of HGF to cetuximab-treated cells phosphorylated MET, but not EGFR or ErbB3, restimulated the MAPK and AKT pathways, restored cell proliferation, and rescued cells from G1 arrest and apoptosis. Importantly, this effect could be abrogated by inhibiting MET activation with PHA-665752 or by downregulating MET expression with RNAi. Conclusions: HGF-induced MET activation is a novel mechanism of cetuximab resistance in CRC. Inhibition of the HGF-MET pathway may improve response to EGFR inhibitors in CRC, and combination therapy should be further investigated. Clin Cancer Res; 17(3); 472–82. ©2010 AACR.
Recent Development of Augmented Reality in Surgery: A Review

Introduction The development augmented reality devices allow physicians to incorporate data visualization into diagnostic and treatment procedures to improve work efficiency, safety, and cost and to enhance surgical training. However, the awareness of possibilities of augmented reality is generally low. This review evaluates whether augmented reality can presently improve the results of surgical procedures. Methods We performed a review of available literature dating from 2010 to November 2016 by searching PubMed and Scopus using the terms “augmented reality” and “surgery. ” Results. The initial search yielded 808 studies. After removing duplicates and including only journal articles, a total of 417 studies were identified. By reading of abstracts, 91 relevant studies were chosen to be included. 11 references were gathered by cross-referencing. A total of 102 studies were included in this review. Conclusions The present literature suggest an increasing interest of surgeons regarding employing augmented reality into surgery leading to improved safety and efficacy of surgical procedures. Many studies showed that the performance of newly devised augmented reality systems is comparable to traditional techniques. However, several problems need to be addressed before augmented reality is implemented into the routine practice.
Object-Based Shadow Extraction and Correction of High-Resolution Optical Satellite Images

Shadows in remote sensing images often cause problems, especially in land-cover classification and change detection. Hence, it is very useful if the radiance of shadow areas is corrected to the same level as that of shadow-free areas. In this study, a radiance measurement was carried out to investigate the spectral characteristics of sunlight. Then a method is proposed for shadow detection and correction of optical imagery. First, building shadow areas are detected using an object-based classification method that employs brightness values and their relationship with the neighboring area. Next, the detected shadow areas are corrected using a linear function to produce a shadow-free image. The shadow pixels with different darkness levels are corrected by using different ratios to obtain a smoothly restored image. The proposed semi-automated method was applied to a QuickBird and a WorldView-2 images of Tokyo, Japan, to demonstrate the effectiveness of the method.
Programming with tiles

The importance of tiles or blocks in scientific computing cannot be overstated. Many algorithms, both iterative and recursive, can be expressed naturally if tiles are represented explicitly. From the point of view of performance, tiling, either as a code or a data layout transformation, is one of the most effective ways to exploit locality, which is a must to achieve good performance in current computers because of the significant difference in speed between processor and memory. Furthermore, tiles are also useful to express data distribution in parallel computations. However, despite the importance of tiles, most languages do not support them directly. This gives place to bloated programs populated with numerous subscript expressions which make the code difficult to read and coding mistakes more likely. This paper discusses Hierarchically Tiled Arrays (HTAs), a data type which facilitates the easy manipulation of tiles in object-oriented languages with emphasis on two new features, dynamic partitioning and overlapped tiling. These features facilitate the expression of locality and communication while maintaining the same performance of algorithms written using conventional languages.
The effectiveness of a motivational-targeted feedback message intervention on increasing physical activity in long-term maintenance cardiac rehabilitation patients

Purpose: The aim of the study was to determine the relative effectiveness of a motivational-targeted (MT) message intervention designed to increase physical activity (PA) in cardiac patients beginning a long-term maintenance cardiac rehabilitation (CR) program to enable them to meet recommended PA levels. Methods: Fifty two individuals (34 males, 18 females) volunteered for the study and were randomly assigned to either the Usual Care Group (UC), or the Motivational Message Group (MM). Participants in the MM group received, in addition to the usual long-term maintenance CR program, 12 –standard, MT newsletters at the beginning of each week during the intervention period. Thirtythree individuals (mean age: 61.4 ± 11.4 years) completed the study with viable data. PA was assessed for 12 weeks with the use of a Lifecorder PLUS accelerometer. Baseline and post measures of weight, body mass index (BMI), body fat percentage, resting heart rate and blood pressure measures, and fasting blood measures were completed on all subjects. Subjects also completed an exercise self-efficacy questionnaire and a stage of change of physical activity readiness questionnaire at these timeframes. Results: Independent sample ttests indicated there were no significant differences between baseline characteristics between the UC group and MM group. Results indicated slight
Diagnostic Value of Presepsin ( Scd 14-St Subtype ) Evaluation in the Detection of Severe Neonatal Infections

The clinical usefulness of assesment of presepsin concentration in peripheral vein blood in male and female severe infected newborns, including their birth weight, fetal maturity, gender, birth asphyxia, mode of mother’s delivery was studies and compared with C-reactive protein, procalcitonin, hemoglobine, hematocrit and platelet count in a multicenter prospective study. The study population comprised 124 newborns (41 septic, 37 with severe local infections without bacteriemia, 16 without infections, but with clinical symptoms suggesting infection and perinatal risk factors and 30 healthy as control), in which by rapid chemiluminescent enzyme immunoassay, using fully automated PATHFAST TM analyser from Mitsubishi Kagaku Iatron Inc, presepsin concentration in whole blood was measured. The mean presepsin concentration in septic newborns, independently of their gender, fetal maturity, birth asphyxia (1389±861 pg/ml) was significantly (p<0,001) higher than in others newborns. In severe local infected newborns (mainly pneumonic, with negative blood cultures) independently of their fetal maturity, birth asphyxia and mode of delivery, significant presepsin increase than in noninfected newborns was stated. Positive correlation between presepsin and CRP concentrations, negative correlation between presepsin and hemoglobin, hematocrit value and platelet count in septic newborns were noted. Positive correlation between presepsin and procalcitonin in local infected newborns was observed. The cutoff value of presepsin for discrimination of neonatal sepsis was determined to be 1066 pg/ml, of which the clinical specyfity and sensivity were 89,2% and 63,4%, respectively. Presepsin determination might be used as a high specyfity biomarker for the early diagnosis of neonatal sepsis and severe local infections, both early and late-onset.
JFlow: Practical refactorings for flow-based parallelism

Emerging applications in the domains of recognition, mining and synthesis (RMS); image and video processing; data warehousing; and automatic financial trading admit a particular style of parallelism termed flow-based parallelism. To help developers exploit flow-based parallelism, popular parallel libraries such as Groovy's GPars, Intel's TBB Flow Graph and Microsoft's TPL Dataflow have begun introducing many new and useful constructs. However, to reap the benefits of such constructs, developers must first use them. This involves refactoring their existing sequential code to incorporate these constructs - a manual process that overwhelms even experts. To alleviate this burden, we introduce a set of novel analyses and transformations targeting flow-based parallelism. We implemented these ideas in JFlow, an interactive refactoring tool integrated into the Eclipse IDE. We used JFlow to parallelize seven applications: four from a previously known benchmark and three from a suite of large open source projects. JFlow, with minimal interaction from the developer, can successfully parallelize applications from the aforementioned domains with good performance (offering up to 3.45x speedup on a 4-core machine) and is fast enough to be used interactively as part of a developer's workflow.
Induction of growth arrest and apoptosis in human breast cancer cells by 3,3-diindolylmethane is associated with induction and nuclear localization of p27kip

3,3′-Diindolylmethane (DIM) is a stable condensation product of indole-3-carbanol, a potential breast cancer chemoprevention agent. Human breast cancer cell lines were studied to better understand its mechanisms. In vitro experiments were done in MCF-7, T47D, BT-20 and BT-474 cells using MTT, ELISA, immunoblotting assays, reverse transcription-PCR, protein half-life, confocal microscopy, cell fractionation, and immunoprecipitation assays. We found that DIM inhibited the growth of all four breast cancer cell lines (IC50s, 25-56 μmol/L). Because BT-20 and BT-474 overexpressed Her-2 and activated Akt, and BT-20 lacks estrogen receptor, these were studied further. In both cell lines, DIM appeared to induce expression of p27kip protein before the loss of cell viability and apoptosis. In BT-20 cells, DIM also inhibited expression of activated Akt, but this appeared after p27kip induction. In both cell lines, DIM induced p27kip transcript expression within 6 h. DIM prolonged the p27kip protein half-life in BT-20 but not BT-474 cells. We also showed, for the first time, that DIM induced nuclear localization of p27kip in both cell lines. Moreover, in BT-20 cells, DIM induced a decrease in p27kip phosphorylation at Thr187, and its association with the 14-3-3 protein, which helped to explain the protein half-life increase and nuclear localization, respectively. DIM modulates p27kip through transcription, prolongation of protein half-life, and nuclear localization. These effects appear to be independent of Her-2, Akt, or estrogen receptor status and should support further study for its chemoprevention potential in breast cancer. [Mol Cancer Ther 2008;7(2):341–9]
Binding of berberine to human telomeric quadruplex – spectroscopic, calorimetric and molecular modeling studies

This study examines the characteristics of binding of berberine to the human telomeric d[AG3(T2AG3)3] quadruplex. By employing UV‐visible spectroscopy, fluorescence spectroscopy and isothermal titration calorimetry, we found that the binding affinity of berberine to the human telomeric quadruplex is 106. The complete thermodynamic profile for berberine binding to the quadruplex, at 25 °C, shows a small negative enthalpy (ΔH) of −1.7 kcal·mol−1, an entropy change with TΔS of +6.5 kcal·mol−1, and an overall favorable free energy (ΔG) of −8.2 kcal·mol−1 . Through the temperature dependence of ΔH, we obtained a heat capacity (ΔCp) of −94 (± 5) cal·mol−1·K−1. The osmotic stress method revealed that there is an uptake of 13 water molecules in the complex relative to the free reactants. Furthermore, the molecular modeling studies on different quadruplex–berberine complexes show that berberine stacking at the external G‐quartet is mainly aided by the π–π interaction and the stabilization of the high negative charge density of O6 of guanines by the positively charged N7 of berberine. The theoretical heat capacity (ΔCp) values for quadruplex–berberine models are −89 and −156 cal·mol−1·K−1.
Structural properties of post-dominator trees

The concepts of post dominators and post dominator trees are extensively used in code optimisation (J. Ferrante et al., 1987), program slicing (H. Agrawal and J.R. Horgan, 1990) and test suite reduction (R. Gupta and M.L. Soffa, 1093). The paper studies some characteristics of post dominator trees. These results can form the basis for the development of a more efficient construction algorithm of post dominator tree.
Evaluation of a generalized dynamic cepstrum in distant speech recognition

This paper examines the effectiveness of a generalized dynamic cepstrum in distant speech recognition. The generalized dynamic cepstrum (DyMFGC) is based upon the forward masking on the generalized logarithmic spectrum instead of the log-spectrum, which intends to make it robust to additive noise as well as convolutional noise. Digit recognition tests were carried out in a relatively quiet and small sized office environment. Under white noise environments, the DyMFGC outperforms the dynamic cepstrum on the logarithmic spectrum and the MFCC with cepstral mean normalization. It also maintains the word accuracy of 90% to 95% within a 1m distance from a source. In speech babble noise environments, the performance of the DyMFGC is approximately the same as that of the dynamic cepstrum on the logarithmic amplitude scale.
News shocks, expectation driven business cycles and financial market frictions

This paper explores the booms and busts induced by news shocks in a model economy with financial market frictions. Firms can accumulate capital through either purchase of the existing capital or producing new capital by themselves. Firms need to borrow from financial intermediaries to finance their purchases of capital. With the presence of financial market frictions, firms have to pay an external finance premium which depends inversely on their net values. This provides firms with an incentive to build up capital stocks now to lower the external finance premium in the future. When firms receive news indicating a future technology improvement, they anticipate the need for more capital and so more external finance in the future; they could lower their future external finance costs by building up their capital and net values now. By adding financial market frictions into an otherwise standard RBC model, this paper succeeds in generating a boom when a news shock hits the economy.
Robustness and Safe Sampling of Distributed-Delay Control Laws for Unstable Delayed Systems

In the control of delayed systems by a finite spectrum assignment (FSA) , in the control law, the integral over the time delay of a function of past control appears. This assignment is in fact available for continuous delayed process independently of the stability of the latter, which is very interesting since Smith predictor is usually only used with stable processes. Nevertheless, in case of FSA control implementation, this integral control should be sampled so that spectrum assignment is not necessarily preserved and an unstable discrete closed loop can be obtained , . In this technical note, FSA integral control robustness with respect to prediction time uncertainty is analyzed for an unstable continuous linear system. A transformation approach is also proposed to understand the effects of different ways of sampling control laws. In a last part, a case study shows how Simpson approximation of integral control law leads to an unstable digital closed loop.
A Nested Marker for Augmented Reality

A Nested Marker, a novel visual marker for camera calibration in augmented reality (AR), enables accurate calibration even when the observer is moving very close to or far away from the marker. Our proposed Nested Marker has a recursive layered structure. One marker at an upper layer contains four smaller markers at the lower layer. Smaller markers can also have lower-layer markers nesting inside them. Each marker can be identified by its inside pattern, so the system can select a proper calibration parameter set for the marker. When the observer views the marker close-up, the lowest layer marker will work. When the observer views the marker from a distance, the top-layer marker will work. It is also possible to simultaneously utilize all visible markers in different layers for more stable calibration. Note that Nested Marker can be used in a standard ARToolkit framework. We have also developed an AR system to demonstrate the ability of Nested Marker
A Differential Evolution Framework with Two Subpopulations for Handling Multi-objective Optimization Problems

A differential evolution framework with two subpopulations for multi-objective optimization is presented. Based on the strength values of the individuals, the current population is divided into two subpopulations to search the space of solutions effectively. One subpopulation consists of the top individuals of the current population and employs scheme DE/best/1/bin to improve the convergence speed by learning the non-dominated individuals; the other is composed of the rest individuals of the current population and uses scheme DE/rand/2/bin to improve and guarantee the convergence rate. Through validating the two performance metrics on three benchmark multi-objective optimization test problems, the presented algorithm is compared with three state-of-the-art algorithms. Simulation results show that the presented algorithm can obtain better performance. Thereafter, three scalable test problems for evolutionary multi-objective optimization are tested to further demonstrate that the algorithm is feasible and effective.
Current and future policies regarding laboratory animal welfare.

Laboratory animal welfare has made tremendous strides in recent years. The first laboratory animal welfare law was not enacted until 1966, and laboratory animal medicine as a specialty did not even exist until the 1960s. The AAALAC accreditation program has stimulated improvements in accredited institutions, and the FDA and EPA Good Laboratory Practices Acts had a major impact on industry in the 1970s, but the most visible impact upon academic institutions was made by NIH enforcing their Policy in the 1980s by suspending funding to several programs and institutions. The Association of American Medical Colleges and the Association of American Universities jointly published Recommendations for Governance and Management of Institutional Animal Resources in October 1985, following very closely the provisions of NIH and the Guide. Animal rights groups have even contributed toward the improvement of animal welfare policies by their recent flurry of demonstrations, thefts, and vandalism. The end result has been an impressively rapid upgrading and standardization of animal care and use policies and programs at all types of institutions that use animals in their work. Most major institutions now have qualified and credentialed laboratory animal medicine specialists directing their programs, conscientious and responsive animal care and use committees overseeing and evaluating animal welfare, and qualified, well-trained animal care staff and investigators. Institutions that do not meet these standards undergo great pressure from the USDA, NIH, their peers, and the public to bring their programs into compliance quickly and appropriately. (ABSTRACT TRUNCATED AT 250 WORDS)
Mapping EU fishing activities using ship tracking data

ABSTRACT Information and understanding of fishing activities at sea are fundamental components of marine knowledge and maritime situational awareness. Such information is important to fisheries science, public authorities and policy-makers. In this paper we introduce a first map at European scale of EU fishing activities extracted using Automatic Identification System ship tracking data. The resulting map is a density of points that identify fishing activities. A measure of the reliability of such information is also presented as a map of coverage reception capabilities.
Survival in Patients With Severe Ischemic Cardiomyopathy Undergoing Revascularization Versus Medical Therapy: Association With End-Systolic Volume and Viability

Background— The value of assessment of viability as a predictor of surgical revascularization benefit in ischemic cardiomyopathy has recently been questioned in a large trial. We sought to determine whether the contribution of viability as myocardial scar burden (SB) to predict revascularization outcomes could be modulated by end-systolic volume index (ESVi). Methods and Results— Delayed hyperenhancement–MRI was obtained in 450 patients with ≥70% stenosis in ≥1 epicardial coronary artery (75% men; median age, 62.8±10.7 years; mean left ventricular ejection fraction, 23±9%; mean ESVi, 115±50 mL) from 2002 to 2006. SB was quantified as scar percentage (infarcted mass/total left ventricular mass). Subsequent surgical revascularization was performed in 245 (54%) patients and subsequent percutaneous coronary interventions were performed in 28 (6%) patients. A propensity score was developed for revascularization. Cox proportional hazards models of all-cause mortality were used for risk adjustment. Over a mean follow-up of 5.8±2.7 years, 186 (41%) deaths occurred. After adjusting for prior revascularization, sex, diabetes, age, use of cardiac resynchronization therapy, implantable cardioverter defibrillator, mitral regurgitation, and mitral valve procedures; an interaction between scar percentage and ESVi (P=0.016) and an interaction between post-MRI revascularization and ESVi (P=0.0017) were independently associated with mortality. ESVi demonstrated a significant interaction with revascularization and female sex, such that enhanced survival was associated with ESVi. ESVi also showed an interaction with SB; better survival was associated with lower volumes and less scar. Conclusions— ESVi and SB provide independent, incremental prognostic value in patients with severe ischemic cardiomyopathy. The risk associated with SB should not be assessed in isolation.
OPTIMALITY OF COMBINED SOURCE-CHANNEL CODING SYSTEMS WITH MULTIPLE SOURCES AND PARALLEL CHANNELS

Source-channel coding in multichannel systems may be a good candidate for making robust and efficient transmission systems. In this paper, the theoretical limit (OPTA) for such systems is found for Gaussian sources and AWGN channels. In general, the number of sources and channels is different and their individual bandwidths are arbitrary. Such systems can implement any bandwidth change, in practical systems the bandwidth change can be performed using only a small set of nonlinear mappings. The paper also describes the loss in performance due to a finite number of theoretical mappings between signal and channel spaces.