Miracle-dz/UniFAR-FTUs huggingface dataset:
RPS3a Over-Expressed in HBV-Associated Hepatocellular Carcinoma Enhances the HBx-Induced NF-κB Signaling via Its Novel Chaperoning Function

Hepatitis B virus (HBV) infection is one of the major causes of hepatocellular carcinoma (HCC) development. Hepatitis B virus X protein (HBx) is known to play a key role in the development of hepatocellular carcinoma (HCC). Several cellular proteins have been reported to be over-expressed in HBV-associated HCC tissues, but their role in the HBV-mediated oncogenesis remains largely unknown. Here, we explored the effect of the over-expressed cellular protein, a ribosomal protein S3a (RPS3a), on the HBx-induced NF-κB signaling as a critical step for HCC development. The enhancement of HBx-induced NF-κB signaling by RPS3a was investigated by its ability to translocate NF-κB (p65) into the nucleus and the knock-down analysis of RPS3a. Notably, further study revealed that the enhancement of NF-κB by RPS3a is mediated by its novel chaperoning activity toward physiological HBx. The over-expression of RPS3a significantly increased the solubility of highly aggregation-prone HBx. This chaperoning function of RPS3a for HBx is closely correlated with the enhanced NF-κB activity by RPS3a. In addition, the mutational study of RPS3a showed that its N-terminal domain (1–50 amino acids) is important for the chaperoning function and interaction with HBx. The results suggest that RPS3a, via extra-ribosomal chaperoning function for HBx, contributes to virally induced oncogenesis by enhancing HBx-induced NF-κB signaling pathway.
Detecting of Driver's Drowsiness Using Multiwavelet Packet Energy Spectrum

Driver drowsiness/fatigue is an important cause of combination-unit truck crashes. The purpose of this study is to detect drowsiness in drivers unobtrusively to prevent accidents and to improve safety on the highways. This paper is the culmination of previous work to determine if steering behavior could be used to unobtrusively detect driver fatigue. In order to investigate the relationship of driver fatigue with steering wheel motion, a fatigue driving model was established. The results of computer simulation demonstrate that the information of driver fatigue hide in steering wheel motion. In order to extract state information contained in it, a multiple scaling functions based multi-wavelet algorithm was proposed which can represent the fatigues characteristic signal and the fatigue characteristic library was be built by using multi wavelet frequency band energy which can represent the fatigue feature of a driver. Finally the paper propose a method of detecting the fatigue driving state by using Support Vector Machines (SVM) which provide the theoretical basis of the development of simple practical driving fatigue monitoring devices. Keywords-component; formatting; style; styling; insert (key words)
Bladder explosion during transurethral resection of prostate: Bladder diverticula as an additional risk factor

Vesical explosion during transurethral resection of the prostate (TURP) is a very rare occurrence. Very few cases have been reported in the literature. The literature was reviewed pertaining to the etiology of bladder explosion during transurethral resection. The underlying mechanism for intravesical explosion is the generation and trapping of explosive gasses under the dome of the bladder which eventually detonates when it comes into contact with the cautery electrode during TURP. Various techniques have been suggested to prevent this dreaded complication. A 75-year-old male with chronic retention of urine underwent TURP. There was Grade 2 trilobar enlargement of the prostate. There were multiple diverticula with one large diverticulum in the dome of the bladder. During hemostasis, there was a loud pop sound and the bladder exploded. Lower midline laparotomy was performed and the intraperitoneal bladder rupture was repaired. He had an uneventful postoperative recovery, and he is asymptomatic at 6 months of follow-up. Even though all the precautions were taken to avoid this complication, bladder rupture was encountered. The presence of multiple diverticula is being suggested as an additional risk factor for this complication as the bladder is thinned out and also possibly due to trapping of air bubble within the diverticulum. In such cases where there are multiple bladder diverticula, the employment of a suprapubic trocar for continuous drainage of the air bubble, could well be a practical consideration.
A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations

Complex phenotypes such as the transformation of a normal population of cells into cancerous tissue result from a series of molecular triggers gone awry. We describe a method that searches for a genetic network consistent with expression changes observed under the knock-down of a set of genes that share a common role in the cell, such as a disease phenotype. The method extends the Nested Effects Model of Markowetz et al. (2005) by using a probabilistic factor graph to search for a network representing interactions among these silenced genes. The method also expands the network by attaching new genes at specific downstream points, providing candidates for subsequent perturbations to further characterize the pathway. We investigated an extension provided by the factor graph approach in which the model distinguishes between inhibitory and stimulatory interactions. We found that the extension yielded significant improvements in recovering the structure of simulated and Saccharomyces cerevisae networks. We applied the approach to discover a signaling network among genes involved in a human colon cancer cell invasiveness pathway. The method predicts several genes with new roles in the invasiveness process. We knocked down two genes identified by our approach and found that both knock-downs produce loss of invasive potential in a colon cancer cell line. Nested effects models may be a powerful tool for inferring regulatory connections and genes that operate in normal and disease-related processes.
Improved Mapping of RFID Tags by Fusion with Spatial Structure

This paper shows how to exploit knowledge about the spatial structure of an environment in order to obtain more accurate position estimates of passive RFID tags. Such labels are increasingly used as electronic product codes and are originally aimed at identifying goods. Estimating the positions of labeled products, however, is difficult because passive tags only reveal their presence and neither bearings nor distances to them. Previous related work showed that tag detection rates yield decent tag position estimates. Our method combines these solely RFIDbased methods with structural information. Indoor experiments with a mobile robot show increased accuracy as compared to mapping purely based on RFID measurements.
Market Channel Analysis of Ornamental Plants using Clustering Procedures

Market channel alternatives that include garden centers, landscapers, mass merchandisers and re-wholesalers have contributed to the growth of ornamental crops sales in the United States (U. S.). The homogenous subpopulation of the U.S. nursery producer was clustered using mixture of export method and found that there exist four homogenous group of Nursery Producer. The impact of growers’ business characteristics on shares of sales to these channels by firm size was estimated using multivariate fractional regression and nonparametric model. Important explanatory variables were regions of the U.S., sales of plant groups, kinds of contract sales, and promotional expenses, and their effect varies by cluster. We also found that in some cases nonparametric estimation procedure is better than parametric estimates.
Analysis of Real-World Driver's Frustration

This paper investigates a method for estimating a driver's spontaneous frustration in the real world. In line with a specific definition of emotion, the proposed method integrates information about the environment, the driver's emotional state, and the driver's responses in a single model. Driving data are recorded using an instrumented vehicle on which multiple sensors are mounted. While driving, drivers also interact with an automatic speech recognition (ASR) system to retrieve and play music. Using a Bayesian network, we combine knowledge on the driving environment assessed through data annotation, speech recognition errors, the driver's emotional state (frustration), and the driver's responses measured through facial expressions, physiological condition, and gas- and brake-pedal actuation. Experiments are performed with data from 20 drivers. We discuss the relevance of the proposed model and features of frustration estimation. When all of the available information is used, the overall estimation achieves a true positive rate of 80% and a false positive rate of 9% (i.e., the system correctly estimates 80% of the frustration and, when drivers are not frustrated, makes mistakes 9% of the time).
Practical Human Resource Allocation in Software Projects Using Genetic Algorithm

Software planning is becoming more complicated as the size of software project grows, making the planning process more important. Many approaches have been proposed to help software project managers by providing optimal human resource allocations in terms of minimizing the cost. Since previous approaches only concentrated on minimizing the cost, there has not been a study that considers the practical issues affecting project schedule in practice. We elicited the practical considerations on the human resource allocation problem by communicating with a group of software project experts. In this paper, we propose an approach for solving the human resource allocation problem using a genetic algorithm (GA) reflecting the practical considerations. Our experiment shows that our algorithm considers the practical considerations well, in terms of continuous allocation on relevant tasks, minimization of developer multitasking time, and balance of allocation.
Generation of humanoid robot motions with physical constraints using hierarchical B-spline

From recorded human motion, trajectory optimization of a humanoid robot with physical limits being the key constraint is presented. The optimization's objective function preserves the salient characteristics of the original motion, while constraints are used to transform the motion to the limit of the capabilities of the humanoid robot. It is shown that using constraints to limit generated trajectories to physically realizable motion ensures that limits are being met more precisely than by reducing them using a standard objective function. The use of wavelets vs. B-spline is compared, and it is shown that B-spline data representation has pronounced advantages. Furthermore, in regions of high-frequency motion not adequately modeled by an initial splining, B-spline is extensible into a hierarchy so that optimizations can be performed locally which still meet global criteria. It is shown how to use B-spline coefficients in angle-, velocity-, acceleration-, and dynamic force-constraints. To detect trajectory subsections with excessive error in need of control point adjustment and local re-optimization, not only is a traditional error detector used, but also a B-spline density detector is also presented. Generated motions were tested using our simulation program and the robot HRP-2.
Freeze-fracture identification of sterol-digitonin complexes in cell and liposome membranes

To advance our understanding of the organization of cholesterol within cell membranes, we used digitonin in freeze-fracture investigations of model lipid vesicles and tissues. Cholesterol suspensions or multilamellar liposomes composed of phosphatidylcholine with and without cholesterol were exposed to digitonin. Freeze-fracture replicas of those multilamellar liposomes containing cholesterol displayed either 50--60-nm wide intramembrane corrugations or extramembrane tubular complexes. Comparable intramembrane hemitubular scallops and extra-cellular free tubular complexes were observed in thin sections. Exposure of sperm, erythrocytes (whole and ghosts), and intact tissues (skin, liver, adrenal gland, epididymis) to digitonin produced the same types of intra- and extramembrane complexes or furrows as were formed in liposomes. The plasma membrane of guinea pig serum tail had two unfurrowed regions: the annulus and the zipper. Incubating erythrocyte membranes with digitonin resulted in rapid displacement of cholesterol, accompanied by intramembrane particle clustering and membrane faceting, a feature which we did not see in the intact epithelia studied. In freeze-fractured epithelia, we found that plasma membranes, lysosomes, and some vesicular organelles commonly furrowed, but that mitochondrial membranes and nuclear envelopes were generally spared, correlating well with their known cholesterol content. Finally, plasma membrane corrugations approached but did not impinge on either gap or tight junctions, or on coated vesicles. We conclude that freeze-fracture of membranes exposed to digitonin: (a) reveals distinctive cholesterol- digitonin structural complexes; (b) distinguishes cholesterol-rich and - poor organelle membranes; and (c) demonstrates membrane domains rich or poor in cholesterol.
Exemplar-based Texture Synthesis: the Efros-Leung Algorithm

Exemplar-based texture synthesis aims at creating, from an input sample, new texture images that are visually similar to the input, but are not plain copy of it. The Efros–Leung algorithm is one of the most celebrated approaches to this problem. It relies on a Markov assumption and generates new textures in a non-parametric way, directly sampling new values from the input sample. In this paper, we provide a detailed analysis and implementation of this algorithm. The code closely follows the algorithm description from the original paper. It also includes a PCA-based acceleration of the method, yielding results that are generally visually indistinguishable from the original results. To the best of our knowledge, this is the first publicly available implementation of this algorithm running in acceptable time. Even though numerous improvements have been proposed since this seminal work, we believe it is of interest to provide an easy way to test the initial approach from Efros and Leung. In particular, we provide the user with a graphical illustration of the innovation capacity of the algorithm. Experimentation often shows that the path between verbatim copy of the exemplar and garbage growing is somewhat narrow, and that in most favorable cases the algorithm produces new texture images by stitching together entire regions from the exemplar.
Distinct sites in E-cadherin regulate different steps in Drosophila tracheal tube fusion

We have investigated how E-cadherin controls the elaboration of adherens junction associated cytoskeletal structures crucial for assembling tubular networks. During Drosophila development, tracheal branches are joined at branch tips through lumens that traverse doughnut-shaped fusion cells. Fusion cells form E-cadherin contacts associated with a track that contains F-actin, microtubules, and Shot, a plakin that binds F-actin and microtubules. Live imaging reveals that fusion occurs as the fusion cell apical surfaces meet after invaginating along the track. Initial track assembly requires E-cadherin binding to β-catenin. Surprisingly, E-cadherin also controls track maturation via a juxtamembrane site in the cytoplasmic domain. Fusion cells expressing an E-cadherin mutant in this site form incomplete tracks that contain F-actin and Shot, but lack microtubules. These results indicate that E-cadherin controls track initiation and maturation using distinct, evolutionarily conserved signals to F-actin and microtubules, and employs Shot to promote adherens junction-associated cytoskeletal assembly.
Ternary WD40 Repeat-Containing Protein Complexes: Evolution, Composition and Roles in Plant Immunity

Plants, like mammals, rely on their innate immune system to perceive and discriminate among the majority of their microbial pathogens. Unlike mammals, plants respond to this molecular dialog by unleashing a complex chemical arsenal of defense metabolites to resist or evade pathogen infection. In basal or non-host resistance, plants utilize signal transduction pathways to detect “non-self,” “damaged-self,” and “altered-self”- associated molecular patterns and translate these “danger” signals into largely inducible chemical defenses. The WD40 repeat (WDR)-containing proteins Gβ and TTG1 are constituents of two independent ternary protein complexes functioning at opposite ends of a plant immune signaling pathway. They are also encoded by single-copy genes that are ubiquitous in higher plants, implying the limited diversity and functional conservation of their respective complexes. In this review, we summarize what is currently known about the evolutionary history of these WDR-containing ternary complexes, their repertoire and combinatorial interactions, and their downstream effectors and pathways in plant defense.
Detecting constituent sequences by means of HP pattern-based grammars to synthesize proteins: Inferring sequence-structure-function relationship

The detection of protein characters that could reveal how protein chains are constituted, is an important step to understand the main functions of specific classes of proteins. We made use of the concept of "HP pattern-based" grammars to study the connection between protein chains and protein functions. In order to consider the structure of the proteins the HP models were used. Amino acid sequences were treated as a formal language, and it was built a set of HP pattern-based grammars to describe this language by means the Teiresiaspattern discovery tool. First, this methodology was tested on the class of antimicrobial peptides (AmPs). The deduced derivation rules of HP pattern-based grammars were validated by the regular grammar designed by [Loose, C. , et al., 2006] which was used to create new, unnatural, AmPs sequences. Then, our approach was applied to characterize a function of the Pleckstrin homology domain (PH Domain) which represents an important three dimensional domain which bind to phosphoinositides. Nowadays, interactions among PH domain amino acids and inositol phosphate are not well characterized. For the first time, by means of an HP pattern-based grammar, we highlight that this binding function can be described in terms of hydrophocity patterns. Our approach points out some fundamental aspects regarding the relationship between sequence, structure and function of proteins.
Mutagenic Effects of Iron Oxide Nanoparticles on Biological Cells

In recent years, there has been an increased interest in the design and use of iron oxide materials with nanoscale dimensions for magnetic, catalytic, biomedical, and electronic applications. The increased manufacture and use of iron oxide nanoparticles (IONPs) in consumer products as well as industrial processes is expected to lead to the unintentional release of IONPs into the environment. The impact of IONPs on the environment and on biological species is not well understood but remains a concern due to the increased chemical reactivity of nanoparticles relative to their bulk counterparts. This review article describes the impact of IONPs on cellular genetic components. The mutagenic impact of IONPs may damage an organism’s ability to develop or reproduce. To date, there has been experimental evidence of IONPs having mutagenic interactions on human cell lines including lymphoblastoids, fibroblasts, microvascular endothelial cells, bone marrow cells, lung epithelial cells, alveolar type II like epithelial cells, bronchial fibroblasts, skin epithelial cells, hepatocytes, cerebral endothelial cells, fibrosarcoma cells, breast carcinoma cells, lung carcinoma cells, and cervix carcinoma cells. Other cell lines including the Chinese hamster ovary cells, mouse fibroblast cells, murine fibroblast cells, Mytilus galloprovincialis sperm cells, mice lung cells, murine alveolar macrophages, mice hepatic and renal tissue cells, and vero cells have also shown mutagenic effects upon exposure to IONPs. We further show the influence of IONPs on microorganisms in the presence and absence of dissolved organic carbon. The results shed light on the transformations IONPs undergo in the environment and the nature of the potential mutagenic impact on biological cells.
VLC-Based Positioning System for an Indoor Environment Using an Image Sensor and an Accelerometer Sensor

Recently, it is believed that lighting and communication technologies are being replaced by high power LEDs, which are core parts of the visible light communication (VLC) system. In this paper, by taking advantages of VLC, we propose a novel design for an indoor positioning system using LEDs, an image sensor (IS) and an accelerometer sensor (AS) from mobile devices. The proposed algorithm, which provides a high precision indoor position, consists of four LEDs mounted on the ceiling transmitting their own three-dimensional (3D) world coordinates and an IS at an unknown position receiving and demodulating the signals. Based on the 3D world coordinates and the 2D image coordinate of LEDs, the position of the mobile device is determined. Compared to existing algorithms, the proposed algorithm only requires one IS. In addition, by using an AS, the mobile device is allowed to have arbitrary orientation. Last but not least, a mechanism for reducing the image sensor noise is proposed to further improve the accuracy of the positioning algorithm. A simulation is conducted to verify the performance of the proposed algorithm.
Toward achieving the unthinkable: transforming conversations about criminalized others through service-learning in correctional facilities

ABSTRACT Building supportive communities and improving programming for incarcerated persons can be difficult due to stereotypes derived from culture, media, and personal upbringing. Such stereotypes, like the narratives from which they are derived, are socially constructed. To develop an understanding of how those narratives construct “others” and to transform stereotypes of incarcerated “others,” we adopted a communication perspective on the problem of overcoming stigma, designed a course to promote transformative learning, and employed service-learning as a way to bring students into contact with incarcerated men in a regional prison facility. Students’ reflections over two semesters in the service-learning course revealed that interaction with people who were incarcerated transformed their beliefs and values about those with whom they worked, resulting in an attitude of “just mercy” toward people who were incarcerated and making possible a more humane understanding of themselves and those members of our communities who are incarcerated.