Miracle-dz/UniFAR-FTUs huggingface dataset:
Title Determination of particle number and brightness using a laser scanning confocal microscope operating in the analog mode Permalink

We describe a method to obtain the brightness and number of molecules at each pixel of an image stack obtained with a laser scanning microscope. The method is based on intensity fluctuations due to the diffusion of molecules in a pixel. For a detector operating in the analog mode, the variance must be proportional to the intensity. Once this constant has been calibrated, we use the ratio between the variance and the intensity to derive the particle brightness. Then, from the ratio of the intensity to the brightness we obtain the average number of particles in the pixel. We show that the method works with molecules in solution and that the results are comparable to those obtained with fluctuation correlation spectroscopy. We compare the results obtained with the detector operating in the analog and photon counting mode. Although the dynamic range of the detector operating in the photon counting mode is superior, the performance of the analog detector is acceptable under common experimental conditions. Since most commercial laser scanning microscopes operate in the analog mode, the calculation of brightness and number of particles can be applied to data obtained with these instruments, provided that the variance is proportional to the intensity. We demonstrate that the recovered brightness of mEGFP, independent of concentration, is similar whether measured in solution or in two different cell types. Furthermore, we distinguish between mobile and immobile components, and introduce a method to correct for slow variations in intensity. Microsc. Res. Tech. 71:69–81, 2008. VC 2007 Wiley-Liss, Inc.
Relationship between Profitability and Efficiency in the Czech Banking Sector

The aim of the paper is to estimate the relationship between profitability and efficiency in the Czech banking sector during the period 2004 – 2014. First, the profitability and efficiency of the Czech banks were estimated. We used two ratios for banking profitability, namely Return on Assets and Return on Equity. For estimation of banking efficiency we used the non-parametric approach, the Data Envelopment Analysis, slack-based model with variable return to scale. We calculated relationship between profitability and efficiency using Granger causality and correlation coefficient. The models did not confirm the relationship between profitability and efficiency.
The Effect of Radiation Emitted by Cell Phone on The Gelatinolytic Activity of Matrix Metalloproteinase-2 and -9 of Mouse Pre-Antral Follicles during In Vitro Culture

Objective The unfavorable effects of electromagnetic radiation (EMR) emitted by the cell phone on reproduction health are controversial. Metalloproteinases play a vital role in ovarian follicle development. This study was designed to investigate the effects of exposure to the cell phone on the gelatinolytic activity of in vitro cultured mouse pre-antral follicle. Materials and Methods In this experimental study, pre-antral follicles were isolated from ovaries of immature mice (n=16) and cultured with or without exposure to the cell phone in talking mode for 60 minutes. The gelatinolytic activity was evaluated through the zymography method, as well as the gene expression of matrix metalloproteinases (MMPs) namely MMP-2 and -9 and tissue inhibitors of metalloproteinases (TIMPs) namely, TIMP-1 and -2 by the real-time polymerase chain reaction (PCR) method. Also, in parallel, the development of pre-antral follicles was assessed. Results The maturation parameters of the cell phone-exposed pre-antral follicles were significantly lower compared with the control group (P<0.05). The gelatinolytic activity was significantly decreased in the cell phone-exposed pre- antral follicles compared with the control group (P<0.05). The relative mRNA expression of the MMP-2 gene was significantly (P<0.05) increased in the cell phone-exposed pre-antral follicles whereas the expression rate of the MMP-9 gene was considerably (P<0.05) reduced when compared with the control group. Conversely, the relative expression of the TIMP-1 was markedly (P<0.05) increased in the cell phone-exposed pre-antral follicles while the expression of the TIMP-2 was (P<0.05) significantly diminished in comparison with the control group. Conclusion Exposure to the cell phone alters the growth and maturation rate of murine ovarian follicle through the changing in the expression of the MMP-2 and -9 genes, as well as the gelatinolytic activity.
Optimization of Meniscus Cell Transduction Using Lentivirus and Adeno-Associated Virus for Gene Editing and Tissue Engineering Applications

Objectives The utilization of viral vectors to deliver genes of interest directly to meniscus cells and promote long-term modulation of gene expression may prove useful to enhance meniscus repair and regeneration. The objective of this study was to optimize and compare the potential of lentivirus (LV) and adeno-associated virus (AAV) to deliver transgenes to meniscus cells in both intact meniscus tissue and isolated primary cells in monolayer. Design Porcine meniscus tissue explants and primary meniscus cells in monolayer were transduced with LV or self-complementary AAV2 (scAAV2) encoding green fluorescent protein (GFP). Following transduction, explants were enzymatically digested to isolate meniscus cells, and monolayer cells were trypsinized. Isolated cells were analyzed by flow cytometry to determine percent transduction. Results LV and scAAV2 showed a high transduction efficiency in monolayer meniscus cells. scAAV2 was most effective at transducing cells within intact meniscus tissue but the efficiency was less than 20%. Outer zone meniscus cells were more readily transduced by both LV and scAAV2 than the inner zone cells. Higher virus titers and higher cell density resulted in improved transduction efficiency. Polybrene was necessary for the highest transduction efficiency with LV, but it reduced scAAV2 transduction. Conclusions Both LV and scAAV2 efficiently transduce primary meniscus cells but only scAAV2 can modestly transduce cells embedded in meniscus tissue. This work lays the foundation for viral gene transfer to be utilized to deliver bioactive transgenes or gene editing machinery, which can induce long-term and tunable expression of therapeutic proteins from tissue-engineered constructs for meniscus repair and regeneration.
An Efficient Way to Convert 1 D Signal to 2 D Digital Image Using Energy Values Group members

1 CHAPTER 1: INTRODUCTION 1.1 Motivations. 2 1.2 Description of feature extraction. 3 1.3 Contribution of summary. 3 1.4 Thesis orientation. 4 CHAPTER 2: BACKGROUND STUDY 2.1 The time domain features. 5 2.2 The frequency domain features. 5 2.3 Energy of a signal. 5 2.4 Empirical Mode Decomposition (EMD). 6 2.5 Segmentation based Fractal Texture Analysis (SFTA). 9 2.6 Support Vector Machine (SVM). 11 2.7 Multi-class Support Vector Machine.12
Comparison of The Expression of miR-326 between Interferon beta Responders and Non-Responders in Relapsing-Remitting Multiple Sclerosis

Objective Multiple sclerosis (MS) is an inflammatory disease resulting in demyelination of the central nervous system (CNS). T helper 17 (Th17) subset protects the human body against pathogens and induces neuroinflammation, which leads to neurodegeneration. MicroRNAs (miRNAs) are a specific class of small (~22 nt) non-coding RNAs that act as post-transcriptional regulators. The expression of the miR-326 is highly associated with the pathogenesis of MS disease in patients through the promotion of Th17 development. Recently, studies showed that disease-modifying therapies (DMTs) could balance the dysregulation of miRNAs in the immune cells of patients with relapsing-remitting MS (RRMS). Interferon-beta (IFN-β) has emerged as one of the most common drugs for the treatment of RR-MS patients. The purpose of this study was to evaluate the expression of the miR-326 in RRMS patients who were responders and non- responders to IFN-β treatment. Materials and Methods In this cross-sectional study, a total of 70 patients (35 responders and 35 non-responders) were enrolled. We analyzed the expression of the miR-326 in peripheral blood mononuclear cells (PBMCs) of RRMS patients at least one year after the initiation of IFN-β therapy. Real-time polymerase chain reaction (RT-PCR) was applied to measure the expression of the miR-326. Results The results showed no substantial change in the expression of the miR-326 between responders and non- responders concerning the treatment with IFN-β. Although the expression of the miR-326 was slightly reduced in IFN-β-responders compared with IFN-β-non-responders; however, the reduction of the miR-326 was not statistically significant. Conclusion Overall, since IFN-β doesn’t normalize abnormal expression of miR-326, this might suggest that IFN-β affects Th17 development through epigenetic mechanisms other than miR-326 regulation.
The effect of surgical margin on cancer-specific survival in patients treated with nephron-sparing surgery

Background: Nephron-sparing surgery (NSS) is currently the recommended treatment modality for selected renal tumors. The prognostic significance of positive surgical margin (PSM) and surgical margin width (SMW) after NSS is controversial. Aim: To evaluate the effect of PSM and SMW on cancer-specific survival (CSS) in patients who underwent NSS. Materials and Methods: The pathological samples of 142 patients who underwent NSS were reviewed. Patients were divided into two groups with PSM and negative surgical margin (NSM), and after that those with PSM were divided into two groups according to SMW as those with 0.1–2 mm and those >2 mm. CSS was calculated using Kaplan–Meier method. Cox regression analysis was used to adjust the clinicopathologic variables. A P value < 0.05 was considered statistically significant. Results: Local recurrence rate and distant metastasis rate were higher in patients with PSMs than those with NSMs (P = 0.018 and P = 0.039, respectively). However, there was no significant difference between the two groups in terms of CSS. In the group with SMW 0.1–2 mm, the tumor diameter was longer (P = 0.018), enucleation number was higher (P = 0.026), and local recurrence was higher (P = 0.034) than the group with SMW > 2 mm. There was no significant difference between the two groups in terms of CSS. Conclusion: In patients who underwent NSS, PSMs and SMWs have a negative effect on local recurrence but have no significant effect on CSS.
Augmentation of morphine-conditioned place preference by food restriction is associated with alterations in the oxytocin/oxytocin receptor in rat models

ABSTRACT Background Studies indicate that food restriction (FR) reinforces the effects of morphine. The exact mechanisms by which FR influences the reward circuitry of morphine have not yet been determined. Objectives We hypothesized that the effects of FR on the oxytocin (OXT) system and HPA axis can be associated with substance abuse disorders. In this study, the serum levels of OXT and corticosterone, and the expression of OXT/OXT receptor (OXTR), glucocorticoid receptor (GR), and brain-derived neurotrophic factor (BDNF) in the hippocampus, prefrontal cortex, and nucleus accumbens were investigated in an FR model. Methods First, the male rats (n = 8 per group) were subjected to FR for 3 weeks. Then, morphine-induced conditioned place preference (CPP) was observed using two doses of morphine (3 and 5 mg/kg). The serum concentrations of corticosterone and OXT were determined by ELISA and the expression of genes was examined by qPCR. Results FR induced an enhanced preference in the animals for the 5 mg/kg dose of morphine compared to the controls. Serum corticosterone levels increased after FR but OXT levels decreased. Meanwhile, FR actuated downregulation of GR, BDNF, and OXT genes, while inducing the overexpression of OXTR. Conclusion We propose the inclusion of OXT and OXTR alterations in the enhancement of morphine-induced CPP and addiction vulnerability following FR. Moreover, we conclude that altered BDNF levels and HPA axis activity may be the mechanisms involved in the effects of FR on morphine-induced behavior.
Prognostic significance of Epstein‐Barr virus viral load in patients with T1‐T2 nasopharyngeal cancer

Nasopharyngeal cancer (NPC) is highly prevalent in southern Chinese populations but it is rare in most parts of the world. A few studies were performed in nonendemic regions of the world, and suggested the prognostic value of Epstein‐Barr virus (EBV) DNA load in blood. In this study, EBV DNA presence and viral load (VL) level in the blood of patients with NPC in Polish population were presented. In addition, its prognostic value for locoregional control among other clinicopathological features was evaluated. Patients with carcinoma of the nasopharynx treated definitively with radiotherapy or radiochemotherapy were included in the study. Real‐time polymerase chain reaction was performed for quantitating of EBV DNA in plasma. Among patients with NPC, 51% (22 of 43) were classified as EBV‐positive with the mean of the VL of 4934 ± 8693 copies/mL. Multiple regression analysis between log EBV DNA VL and clinical parameters revealed that the most important factors increasing the VLs were advanced N disease together with no‐smoking status and advanced T tumors. Multivariate Cox regression analysis revealed that T3‐T4 tumors were an independent prognostic factor for poor locoregional control. Analysis for the subgroup of patients with T1‐T2 tumors showed that T1‐T2 EBV‐negative patients had better locoregional control compared with T1‐T2 EBV‐positive, though without statistical significance. In conclusion, it seems that EBV DNA determination may have an important role in diagnostics of patients with NPC with T1‐T2 tumors indicating a subgroup with poorer prognosis, though it needs to be proven on a larger cohort.
Artificial Visual Attention Autonomous real-time search & track by saliency computation for a humanoid robotic head

Visual attention is currently actively researched across many different fields. In the domain of computer vision and artificial intelligence, it is both studied and applied, often inspired by observing nature’s solutions. The object of this research, the Binnobot, is a robotic head in which the two camera sensors have embedded perceptual systems, capable of real-time feature tracking. As the hardware takes care of tracking features, the functionality can be extended by adding visual attention. This study investigates if this can be achieved through saliency computation. However, this must not compromise the real-time performance of the feature tracking, merely complement it. Using parallel processing, a measure of saliency for a frame is computed, after which the algorithm decides whether and what to track. Due to a multithreaded approach, the robot is still capable of searching for new or different regions of interest whilst tracking. By selecting the appropriate parameters for the salient region, the Binnobot (re-)configures the relevant features to track. Master of Science Thesis J.C. B. Donker
Applying ACO To Large Scale TSP Instances 3 3 Addressing the Scalability of ACO

Ant Colony Optimisation (ACO) is a well known metaheuristic that has proven successful at solving Travelling Salesman Problems (TSP). However, ACO suffers from two issues; the first is that the technique has significant memory requirements for storing pheromone levels on edges between cities and second, the iterative probabilistic nature of choosing which city to visit next at every step is computationally expensive. This restricts ACO from solving larger TSP instances. This paper will present a methodology for deploying ACO on larger TSP instances by removing the high memory requirements, exploiting parallel CPU hardware and introducing a significant efficiency saving measure. The approach results in greater accuracy and speed. This enables the proposed ACO approach to tackle TSP instances of up to 200K cities within reasonable timescales using a single CPU. Speedups of as much as 1200 fold are achieved by the technique.
Machine Learning-Based Antenna Selection in Untrusted Relay Networks

This paper studies the transmit antenna selection based on machine learning (ML) schemes in untrusted relay networks. First, the exhaustive search antenna selection scheme is stated. Then, we implement three ML schemes, namely, the support vector machine-based scheme, the naïve-Bayes-based scheme, and the k-nearest neighbors-based scheme, which are applied to select the best antenna with the highest secrecy rate. The simulation results are presented in terms of system secrecy rate and secrecy outage probability. From the simulation, it can be concluded that the proposed ML-based antenna selection schemes can achieve the same performance without amplification at the relay, or small performance degradation with transmitted power constraint at the relay, comparing with exhaustive search scheme. However, when the training is completed, the proposed schemes can perform the antenna selection with a small computational complexity.
Merced Proceedings of the Annual Meeting of the Cognitive Science Society Title

We introduce a connectionist version of the Syntagmatic Paradigmatic model (Dennis, 2005) and train it on subcorpora drawn from the gigaword corpus. Decaying syntagmatic representations of the words to the left and right are used to estimate the paradigmatic associates of a word. The pattern of paradigmatic associates is then combined with an order independent associative representation of the surrounding words to predict the word that will appear in a given slot. The best performing version of the model produced a perplexity of 28.3 on a vocabulary of 5006 words, significantly lower than Good Turing and Kneser Ney ngram models trained under the same conditions. Furthermore, we changed parameters and lesioned components to isolate which properties of the model are critical to its performance. Online update of the weights a kind of priming allows the model to track short term contingencies and significantly improves performance. When we removed the paradigmatic and associative layers performance dropped, when we removed just the associative layer performance dropped and when we removed the right context from the syntagmatic and associative layers performance also dropped suggesting that all of the hypothesized components of the model are crucial to its performance.
Estimation of Lateral Forces on Retaining Walls Adjacent to Layered Embankments in Saturated and non-Saturated Conditions

Investigation of development behavior and the dimensions of the embankments behind retaining walls explains the effect of the movement of the wall and its destructing effect. Majority of the natural embankments are layered and are usually in saturated condition. Hence, this research investigates the failure wedge caused by the wall’s rotation around the heel. Physical measurements were performed in order to provide data to use the graphical approach of calculation of lateral pressure of layered embankments in both saturated and non-saturated conditions. Thus, 4 layering models were tested including: 1) two layered (upper layer: clay, bottom layer: sand), 2) two layered (upper layer: sand, bottom layer: clay), 3) three layered (upper layer: sand, middle layer: clay, bottom layer: sand) and 4) a for layered model (upper layer: clay, first middle layer: sand, second middle layer: clay, bottom layer: sand). Elevation of layers in each layering model were determined to be equal. Results indicated that using common theoretical methods will result in a conservative design for walls which increases the construction costs. Absence of the failure wedge at wall toe as well as the 32.75% and 29.25% difference between experimental results to theoretical results of Rankin and Sirnivasa methods are other evidence for the conservative design of walls using common methods. Review History: Received: 8 August 2016 Revised: 25 February 2017 Accepted: 12 March 2017 Available Online: 7 May 2017
heory and numerical simulation of fluid-pressure iffusion in anisotropic porous media

The physics of fluid diffusion in anisotropic media was studied, based on Biot’s theory of poroelasticity and using wave propagation concepts. Diffusion and elastic strain can be uncoupled fully, being a good approximation in many situations. We have used a correction to the stiffness of the rock under conditions of transverse isotropy and uniaxial strain to model borehole conditions. The concepts of phase, group, and energy velocities were analyzed to describe the location of the diffusion front, and the attenuation and quality factors were obtained to quantify the amplitude decay. We have found that the location of the front is described correctly by the energy velocity. The Green’s function in anisotropic media can be obtained by applying a change of coordinates to the isotropic solution. We have simulated the diffusion in inhomogeneous media using a time-domain spectral explicit scheme and the staggered Fourier pseudospectral method to compute the spatial derivatives. The method is based on a spectral Chebychev expansion of the evolution operator of the system. The scheme allows the solution of linear periodic parabolic equations, having accuracy within the machine precision, in time and in space. The results match the analytic solution obtained from the Green’s function. The performance of the algorithm is confirmed in the case of a pressure field generated by a fluid-injection source in a hydrocarbon reservoir where the properties vary fractally.
Accuracy Investigations of Multifunctional Two-coordinate Drive System

Every specific task for two-coordinate drive system such as positioning or scanning requires specific control algorithm. The multifunctional control system proposed in [7, 9] enables to control several problems leaving the hardware of two-coordinate drive system unmodified. These control methods are represented in detail in [6,8,10]. In this article there is analyzed one of the most important characteristics of this kind of systems – position absolute and repetition accuracy. The influence of control methods that ensure optimum rapidity and increase long life of the system and power efficiency on position repetition accuracy is evaluated. The main purpose of this article is to show the investigation technique and results on position accuracy of multifunctional two-coordinate drive system. The reminder of this article has been organized in such order. In section 2, there is given the discussion on different positioning and scanning modes in twodimensional space. The main notice is pointed to the mode, which is optimal in respect to cycle time and optimization of mechanical actions to the mechanical part of the system and power consumption. The investigation technique of position absolute and repetition accuracy of two-coordinate drive system is shown in section 3. Section 4 illustrates the framework for experiments with industrial drives. The experimental and estimation results on absolute and repetition accuracy of multifunctional two-coordinate drive system are given in section 5. Finally, conclusions are presented in section 6.