Miracle-dz/UniFAR-FTUs huggingface dataset:
Oncolytic reovirus preferentially induces apoptosis in KRAS mutant colorectal cancer cells, and synergizes with irinotecan

Reovirus is a double stranded RNA virus, with an intrinsic preference for replication in KRAS mutant cells. As 45% of human colorectal cancers (CRC) harbor KRAS mutations, we sought to investigate its efficacy in KRAS mutant CRC cells, and examine its impact in combination with the topoisimerase-1 inhibitor, irinotecan. Reovirus efficacy was examined in the KRAS mutant HCT116, and the isogenic KRAS WT Hke3 cell line, and in the non-malignant rat intestinal epithelial cell line. Apoptosis was determined by flow cytometry and TUNEL staining. Combination treatment with reovirus and irintoecan was investigated in 15 CRC cell lines, including the HCT116 p21 isogenic cell lines. Reovirus preferentially induced apoptosis in KRAS mutant HCT116 cells compared to its isogenic KRAS WT derivative, and in KRAS mutant IEC cells. Reovirus showed a greater degree of caspase 3 activation with PARP 1 cleavage, and preferential inhibition of p21 protein expression in KRAS mutant cells. Reovirus synergistically induced growth inhibition when combined with irinotecan. This synergy was lost upon p21 gene knock out. Reovirus preferentially induces apoptosis in KRAS mutant colon cancer cells. Reovirus and irinotecan combination therapy is synergistic, p21 mediated, and represents a novel potential treatment for patients with CRC.
Detecting Arithmetic Optimization Opportunities for C Compilers by Randomly Generated Equivalent Programs

: This paper presents new methods of detecting missed arithmetic optimization opportunities for C compilers by random testing. For each iteration of random testing, two equivalent programs are generated, where the arithmetic expressions in the second program are more optimized in the C program level. By comparing the two assembly codes compiled from the two C programs, lack of optimization on either of the programs is detected. This method is further extended for detecting erroneous or insu ﬃ cient optimization involving volatile variables. Two random programs differing only on the initial values for volatile variables are generated, and the resulting assembly codes are compared. Random test systems implemented based on the proposed methods have detected missed optimization opportunities on several compilers, including the latest development versions of GCC-5.0. 0 and LLVM / Clang-3.6.
An investigation of erase-mode dependent hole trapping in flash EEPROM memory cell

Hot-hole generation during electrical erase in flash memory cells was investigated and found to be strongly dependent on the lateral electric field of the gated diode junction. It is shown, by erasing the memory cell at a low source voltage in combination with a negative gate voltage, that the operating point can be chosen well away from the onset of avalanche. Using this erasing scheme appreciably reduces the amount of hole trapping in the tunnel oxide. As a result, data retention is significantly improved as compared with conventional erasure. <<ETX>>
An Agent-Based Approach towards Crime Prediction : Evaluating the Potential of Environmental Factors and Human Dynamics to Model Offender Behavior

Crime reduction remains a critical challenge in modern societies. Thus, identifying regions in a city with an elevated risk for future crimes is of high interest to plan prevention strategies. Attempts have been made to apply various statistical and machine learning techniques to predict crime, while computational methods such as agent-based modeling (ABM) can account for the offender and its interactions with the environment in a new manner. In this thesis proposal, I describe an agent-based model to simulate crime, implementing offender mobility and offender decision-making informed by novel data and insights in human dynamics. The result will be a data-driven crime simulation for crime prediction, making it possible to study crime patterns and to reason about likely future high crime areas. This can then flow into a crime prediction tool for the police or into an experimental tool for policy makers and urban planners.
Towards Automatic Error Type Classification of Japanese Language Learners’ Writings

Learner corpora are receiving special attention as an invaluable source of educational feedback and are expected to improve teaching materials and methodology. However, they include various types of incorrect sentences. Error type classification is an important task in learner corpora which enables clarifying for learners why a certain sentence is classified as incorrect in order to help learners not to repeat errors. To address this issue, we defined a set of error type criteria and conducted automatic classification of errors into error types in the sentences from the NAIST Goyo Corpus and achieved an accuracy of 77.6%. We also tried inter-corpus evaluation of our system on the Lang-8 corpus of learner Japanese and achieved an accuracy of 42.3%. To know the accuracy, we also investigated the classification method by human judgement and compared the difference in classification between the machine and the human.
Image Segmentation with Pseudo-marginal MCMC Sampling and Nonparametric Shape Priors

In this paper, we propose an efficient pseudo-marginal Markov chain Monte Carlo (MCMC) sampling approach to draw samples from posterior shape distributions for image segmentation. The computation time of the proposed approach is independent from the size of the training set used to learn the shape prior distribution nonparametrically. Therefore, it scales well for very large data sets. Our approach is able to characterize the posterior probability density in the space of shapes through its samples, and to return multiple solutions, potentially from different modes of a multimodal probability density, which would be encountered, e.g., in segmenting objects from multiple shape classes. Experimental results demonstrate the potential of the proposed approach.
The use of continuous positive airway pressure in preterm babies with respiratory distress syndrome: a report from Baghdad, Iraq

Abstract Objectives: To study maternal and neonatal risk factors related to outcome of preterm babies with respiratory distress syndrome (RDS) on Continuous Positive Airway Pressure (CPAP) in a tertiary Iraqi NICU. Methods: A prospective case study carried out from January 5, 2011 to January 5, 2012, on 70 preterm neonates with RDS who were started on CPAP. Maternal and infant variables of preterm babies with successful or failed CPAP therapy were compared. Results: Seventy neonates, 44 (63%) males and 26 (37%) females were included. Mean (SD) gestation was 32.8 (2.8) weeks and mean (SD) birth weight was 1860 (656) g. Thirty-seven (52.9%) babies failed CPAP, of them 29 (78.3%) were started on mechanical ventilation. The variables associated with failure of CPAP were: Birth weight ≤1500 g, gestational age ≤30 weeks, white out on the chest X-ray, FiO2 ≥50% at 20 min of CPAP, PEEP ≥5.5 cm H2O. Mortality rates were 94.6% in CPAP failures versus 5.4% in CPAP successes (p = 0.001). In infants surviving till discharge, duration of hospital stay was longer in babies who were CPAP successes (9.6 ± 3.7 versus 3.0 ± 2.7 days, p = 0.001). Conclusions: Gestational age, birth weight, whiteout chest X-ray, and FiO2 are important predictive values for success of CPAP therapy. A larger prospective multicenter controlled trial is needed to determine the benefits and risks of CPAP and predictors of its failure in our setting. Our results may be useful for others practicing in similar settings as us.
Intelligent Expression Blending for Performance Driven Facial Animation

Performance-Driven Facial Animation (PDFA) allows an animator to specify the desired facial action in terms of detected face movements of a performer. The animation system works by mimicking the actions of the performer on an animated character. Research efforts in PDFA have mostly concentrated on efficient tracking and re-targeting of facial expressions; very little attention has been paid to the intelligent enhancement of expressions. This paper describes an intelligent system that automatically enhances facial expressions in a PDFA sequence in light of its context. The system models facial expressions as MPEG-4 compliant fuzzy streams. The video context is processed by a fuzzy rule based system (FRBS) in order to find out what expression needs to be added to the detected expression to enhance its naturalness. The FRBS then intelligently blends the detected expression and the expression implied by the context to generate the enhanced expression parameters which are used to animate the target 3D facial model.
Gazetteer of small-scale monuments in prehistoric Hadramawt, Yemen: a radiocarbon chronology from the RASA-AHSD Project research 1996–2008

This paper provides a new, interpretive gazetteer and chronology of Hadramawt’s highland monuments based on results from archaeological survey and test excavations by the RASA-AHSD (Roots of Agriculture in southern Arabia-Arabian Human Social Dynamics) Project. With the exception of a few incidental sightings and an unpublished pipeline survey, the prehistoric record of southern Yemen’s highland plateau has been largely unknown. There are few settlements, so that understanding human landscape history must begin with the numerous small-scale stone monuments left by mobile people. With examples representing monuments from the fifth, fourth, third and first millennia BC, the corpus of small excavations and radiocarbon dates reported here provides the first guide to the monument types of South Arabian highlands. Monument building began under more moist conditions and appears to have commemorated animal sacrifices long before commemorating mortuary rites and interment. There appears to be a temporal break of 1000 years before the widespread and varied practices of Bronze Age tomb construction, which lasted through the third millennium BC. After another break in monument construction, tombs were reused in the first millennium BC, sometimes with successive ritual visits. The data presented offer new material for the interpretation of the lives and activities of prehistoric pastoralists throughout the Holocene.
Decentralized sweep coverage algorithm for uncertain region of multi-agent systems

This paper proposes a new formulation to address sweep coverage problem of multi-agent systems in the uncertain environment. The decentralized sweep coverage algorithm is shown to guarantee the complete coverage of the given region by incorporating two operations: workload partition and sweeping. The theoretical analysis is conducted to focus on the estimation of the upper bound for the error between coverage time and optimal time. Finally, numerical simulations demonstrate the effectiveness of the sweep coverage algorithms.
Hdr Image Rerendering Using GPU-Based Processing

One essential process in image rerendering is to replace existing texture in the region of interest by other user-preferred textures, while preserving the shading and similar texture distortion. In this paper, we propose the graphics processing units (GPU)-accelerated high dynamic range (HDR) image rerendering using revisited NLM processing in parallel on GPU-CUDA platform, to reproduce the realistic rendering of HDR images with retexturing and transparent/translucent effects. Our image-based approach using GPU-based pipeline in gradient domain provides efficient processing with easy-control image retexturing and special shading effects. The experimental results showed the efficiency and high-quality performance of our approach.
IMPACT OF VITREORETINAL INTERFACE ARCHITECTURE ON SUCCESSFUL VITREOMACULAR TRACTION RESOLUTION IN EYES SCHEDULED FOR INTRAVITREAL OCRIPLASMIN THERAPY

Purpose: To evaluate the impact of the vitreoretinal interface architecture, in specific the angle between the posterior vitreous cortex and the internal limiting membrane, on vitreomacular traction (VMT) resolution in eyes treated with intravitreally injected ocriplasmin (Jetrea). Methods: Retrospective, multicenter cohort study and exploratory data analysis. Spectral domain optical coherence tomography assessments were performed before scheduled ocriplasmin injections. General (age and sex) as well as ocular variables (lens status, presence of epiretinal membrane formations, horizontal diameter of VMT, central retinal thickness, and in particular various prespecified angles between the posterior vitreous cortex and internal limiting membrane) were analyzed to evaluate their impact on successful VMT resolution. Results: Fifty-nine eyes of 59 patients were included. Univariate analysis of age (odds ratio [OR]: 0.881; 95% CI: [0.812–0.955]; P = 0.0022) and lens status (OR: 11.03; 95% CI: [2.23–54.57]; P = 0.0033) had a significant impact on successful VMT resolution, whereas sex (OR: 0.668; 95% CI: [0.126–2.065]; P = 0.4906), epiretinal membrane formation (OR: 0.581; 95% CI: [0.168–2.006]; P = 0.3903), horizontal diameter of VMT (OR: 0.99930; 95% CI: [0.99825–1.00035]; P = 0.1886), and central retinal thickness (OR: 0.9985; 95% CI: [0.9934–1.00436]; P = 0.56) failed. The angle at 500 &mgr;m apart from the fovea centralis, irrespective if measured nasally (OR: 1.135; 95% CI: [1.013–1.272]; P = 0.0289) or temporally (OR: 1.099; 95% CI: [1.001–1.208]; P = 0.0485), showed a significant correlation with VMT resolution. Conclusion: The angle between the posterior vitreous cortex and the internal limiting membrane 500 &mgr;m apart from the fovea centralis correlates with VMT resolution and may be a clinically useful marker for selection of patients to be treated with ocriplasmin. This observation needs to be proven in a prospective confirmatory investigation.
13 C values of grasses as a novel indicator of pollution by fossil-fuel-derived greenhouse gas CO 2 in urban areas

A novel fossil-fuel pollution indicator based on the C/C isotopic composition of plants has been designed. This bioindicator is a promising tool for future mapping of the sequestration of fossil-fuel CO2 into urban vegetation. Theoretically, plants growing in fossil-fuel CO2 contaminated areas such as major cities, industrial centers, and highway borders, should assimilate a mixture of global atmospheric CO2 of δC value of 8.02‰ and of fossil-fuel CO2 of average δC value of 27.28‰. This isotopic difference should thus be recorded in plant carbon. Indeed, this study reveals that grasses growing near a major highway in Paris, France, have a strikingly depleted δC values averaging at -35.08‰, versus rural grasses that show an average δC value of 30.59‰. A simple mixing model was used to calculate the contributions of fossil-fuel derived CO2 to the plant tissue. Calculation based on contaminated and non-contaminated isotopic end-members shows that urban grasses assimilate up to 29.1% of fossil-fuel CO2 derived carbon in their tissues. The C isotopic composition of grasses thus represents a promising new tool for the study of the impact of fossil fuel CO2 in major cities.
On the interaction of electromagnetic waves with charged aerosol particles in atmosphere

In this paper we analyze mathematical model of the scattering of electromagnetic wave on the electrical inhomogeneities of clouds and precipitation. This model is based on the well-known Mie's approach together with the fact that a charged aerosol particle has semiconducting properties. The analysis of numerical results (with a size distribution for aerosol particles in the form of gamma-distribution) shows that the resonant phenomena that arise when we irradiate the electrically active areas of clouds and precipitation make it possible to obtain an information both on the magnitude of the charge of aerosol particles and the electric field strength in the clouds and precipitation.
High Affinity Binding of Escherichia coli Cytotoxic Necrotizing Factor 1 (CNF1) to Lu/BCAM Adhesion Glycoprotein

The protein toxin Cytotoxic Necrotizing Factor 1 (CNF1) is a major virulence factor of pathogenic Escherichia coli strains. It belongs to a family of single chain AB-toxins, which enter mammalian cells by receptor-mediated endocytosis. Recently, we identified the Lutheran (Lu) adhesion glycoprotein/basal cell adhesion molecule (BCAM) as a cellular receptor for CNF1. Here, we identified the Ig-like domain 2 of Lu/BCAM as main interaction site of the toxin by direct protein-protein interaction and competition studies. Using surface plasmon resonance, we showed a high affinity CNF-Lu/BCAM interaction with a KD of 2.8 nM. Furthermore, we performed small-angle X-ray scattering to define the molecular envelope of the Lu/BCAM-CNF1 complex, suggesting a 6:1 ratio of Lu/BCAM to CNF1 in the receptor-toxin complex. This study leads to a deeper understanding of the interaction between CNF1 and Lu/BCAM, and presents novel opportunities for the development of future anti-toxin strategies.
Biologia Plantarum Xx (x): Xxx-xxx, 20xx Effect of Salicylic Acid on Freezing Injury in Peach Floral Organs and the Expressions of Cbf Genes

We used flowering branches at the budding stage of two peach cultivars Xiahui 6 and Xiacui with different cold resistance to explore the effect of exogenous salicylic acid (SA) on the freezing injury of peach floral organs and the molecular mechanism. Using water application as the negative control, the effects of spraying with SA at concentrations of 20 or 100 mg dm-3 on stigma receptivity, frost damage characteristics of floral organs, and the expressions of C-repeat-binding factor (PpCBF) gene family members were investigated at 0 °C. No significant frost damage was observed on petals in all treatments. No frost damage was seen in the ovary and style under 20 mg dm-3 SA treatment, but damage was substantial at the other two treatments. Cultivar Xiahui 6 was more susceptible to freezing than cv. Xiacui. The expression peaks of PpCBFs in the SA-pretreated floral organs occurred at 3 or 6 h after low temperature treatment, and peak time was closely related to peach cultivar, organ, and SA concentration. This indicated that appropriate concentration of exogenous SA may alleviate freezing damage to floral organs and enhance cold resistance by the regulated expression pattern of PpCBF.
BluGen: An Analytic Framework for Mission-Cyber Risk Assessment and Mitigation Recommendation

Systems security engineering (SSE) is a complex, manually intensive process, with implications for cost, time required, and repeatability/reproducibility. This paper describes BluGen, an analytic framework that generates risk plots and recommends prioritized mitigations for a target mission/system environment based on a stated level of threat and risk tolerance. The goal is to give working system security engineers a head start in their analysis. We describe BluGen in the context of Design Science Research and evaluate accordingly.
Glucose fluctuations in subjects with normal glucose tolerance, impaired glucose regulation and newly diagnosed type 2 diabetes mellitus

Objective Glycemic variability is poorly studied in the nondiabetic individuals and newly diagnosed patients with type 2 diabetes. The aim of the study is to investigate the characteristics of glucose fluctuations in subjects with normal glucose tolerance (NGT), impaired glucose regulation (IGR) and newly diagnosed, drug‐naïve type 2 diabetes mellitus (DM‐2).
Practical Challenges of Current Video Rate OCT Elastography: Accounting for Dynamic and Static Tissue Properties

Optical coherence tomography (OCT) elastography (OCTE) has the potential to be an important diagnostic tool for pathologies including coronary artery disease, osteoarthritis, malignancies, and even dental caries. Many groups have performed OCTE, including our own, using a wide range of approaches. However, we will demonstrate current OCTE approaches are not scalable to real-time, in vivo imaging. As will be discussed, among the most important reasons is current designs focus on the system and not the target. Specifically, tissue dynamic responses are not accounted, with examples being the tissue strain response time, preload variability, and conditioning variability. Tissue dynamic responses, and to a lesser degree static tissue properties, prevent accurate video rate modulus assessments for current embodiments. Accounting for them is the focus of this paper. A top-down approach will be presented to overcome these challenges to real time in vivo tissue characterization. Discussed first is an example clinical scenario where OTCE would be of substantial relevance, the prevention of acute myocardial infarction or heart attacks. Then the principles behind OCTE are examined. Next, constrains on in vivo application of current OCTE are evaluated, focusing on dynamic tissue responses. An example is the tissue strain response, where it takes about 20 msec after a stress is applied to reach plateau. This response delay is not an issue at slow acquisition rates, as most current OCTE approaches are preformed, but it is for video rate OCTE. Since at video rate each frame is only 30 msec, for essentially all current approaches this means the strain for a given stress is changing constantly during the B-scan. Therefore the modulus can’t be accurately assessed. This serious issue is an even greater problem for pulsed techniques as it means the strain/modulus for a given stress (at a location) is unpredictably changing over a B-scan. The paper concludes by introducing a novel video rate approach to overcome these challenges.
Creatinine measurement: state of the art in accuracy and interlaboratory harmonization.

CONTEXT The National Kidney Disease Education Program recommends calculating glomerular filtration rate from serum creatinine concentration. Accurate creatinine measurements are necessary for this calculation. OBJECTIVE To evaluate the state of the art in measuring serum creatinine, as well as the ability of a proficiency testing program to measure bias for individual laboratories and method peer groups. DESIGN A fresh-frozen, off-the-clot pooled serum specimen plus 4 conventional specimens were sent to participants in the College of American Pathologists Chemistry Survey for assay of creatinine. Creatinine concentrations were assigned by isotope dilution mass spectrometry reference measurement procedures. PARTICIPANTS Clinical laboratories with an acceptable result for all 5 survey specimens (n = 5624). RESULTS The fresh frozen serum (FFS) specimen had a creatinine concentration of 0.902 mg/dL (79.7 micromol/L). Mean bias for 50 instrument-method peer groups varied from -0.06 to 0.31 mg/dL (-5.3 to 27.4 micromol/L), with 30 (60%) of 50 peer groups having significant bias (P < .001). The bias variability was related to instrument manufacturer (P < or = .001) rather than method type (P = .02) with 24 (63%) of 38 alkaline picric acid methods and with 6 (50%) of 12 enzymatic methods having significant biases. Two conventional specimens had creatinine concentrations of 0.795 and 2.205 mg/dL (70.3 and 194.9 micromol/L) and had apparent survey biases significantly different (P < .001) from that of the FFS specimen for 34 (68%) and 35 (70%) of 50 peer groups, respectively. CONCLUSIONS Thirty of 50 peer groups had significant bias for creatinine. Bias was primarily associated with instrument manufacturer, not with type of method used. Proficiency testing using a commutable specimen measured participant bias versus a reference measurement procedure and provided trueness surveillance of instrument-method peer groups.