Miracle-dz/UniFAR-FTUs huggingface dataset:
Oxidative stress during mitochondrial biogenesis compromises mtDNA integrity in growing hearts and induces a global DNA repair response

Cardiomyocyte development in mammals is characterized by a transition from hyperplastic to hypertrophic growth soon after birth. The rise of cardiomyocyte cell mass in postnatal life goes along with a proportionally bigger increase in the mitochondrial mass in response to growing energy requirements. Relatively little is known about the molecular processes regulating mitochondrial biogenesis and mitochondrial DNA (mtDNA) maintenance during developmental cardiac hypertrophy. Genome-wide transcriptional profiling revealed the activation of transcriptional regulatory circuits controlling mitochondrial biogenesis in growing rat hearts. In particular, we detected a specific upregulation of factors involved in mtDNA expression and translation. More surprisingly, we found a specific upregulation of DNA repair proteins directly linked to increased oxidative damage during heart mitochondrial biogenesis, but only relatively minor changes in the mtDNA replication machinery. Our study paves the way for improved understanding of mitochondrial biogenesis, mtDNA maintenance and physiological adaptation processes in the heart and provides the first evidence for the recruitment of nucleotide excision repair proteins to mtDNA in cardiomyocytes upon DNA damage.
EXIT Chart Aided Design of Near-Capacity Self-Concatenated Trellis Coded Modulation Using Iterative Decoding

In this contribution we design the Iteratively Decoded Self-Concatenated Convolutional Codes (SECCC-ID) using extrinsic information transfer (EXIT) charts. Good constituent Trellis Coded Modulation (TCM) codes are selected for communicating over both uncorrelated Rayleigh fading and Additive White Gaussian Noise (AWGN) channels. At the receiver iterative decoding is invoked for exchanging extrinsic information between the hypothetical decoder components. The convergence behaviour of the decoder is analysed with the aid of symbol-based EXIT charts. Similarly, the search for the best TCM constituent codes is also based on EXIT chart analysis. Finally, we demonstrate that the selected codes are capable of operating within 1 dB from the maximum achievable rate.
A Quantum Algorithm of Constructing Image Histogram I World

Histogram plays an important statistical role in digital image processing. However, the existing quantum image models are deficient to do this kind of image statistical processing because different gray scales are not distinguishable. In this paper, a novel quantum image representation model is proposed firstly in which the pixels with different gray scales can be distinguished and operated simultaneously. Based on the new model, a fast quantum algorithm of constructing histogram for quantum image is designed. Performance comparison reveals that the new quantum algorithm could achieve an approximately quadratic speedup than the classical counterpart. The proposed quantum model and algorithm have significant meanings for the future researches of quantum image processing. Keywords—Quantum Image Representation, Quantum Algorithm, Image Histogram.
Hyperactive TORC1 sensitizes yeast cells to endoplasmic reticulum stress by compromising cell wall integrity

The disruption of protein folding homeostasis in the endoplasmic reticulum (ER) results in an accumulation of toxic misfolded proteins and activates a network of signaling events collectively known as the unfolded protein response (UPR). While UPR activation upon ER stress is well characterized, how other signaling pathways integrate into the ER proteostasis network is unclear. Here, we sought to investigate how the target of rapamycin complex 1 (TORC1) signaling cascade acts in parallel with the UPR to regulate ER stress sensitivity. Using S. cerevisiae, we found that TORC1 signaling is attenuated during ER stress and constitutive activation of TORC1 increases sensitivity to ER stressors such as tunicamycin and inositol deprivation. This phenotype is independent of the UPR. Transcriptome analysis revealed that TORC1 hyperactivation results in cell wall remodelling. Conversely, hyperactive TORC1 sensitizes cells to cell wall stressors, including the antifungal caspofungin. Elucidating the crosstalk between the UPR, cell wall integrity, and TORC1 signaling may uncover new paradigms through which the response to protein misfolding is regulated, and thus have crucial implications for the development of novel therapeutics against pathogenic fungal infections. IMPORTANCE The prevalence of pathogenic fungal infections, coupled with the emergence of new fungal pathogens, has brought these diseases to the forefront of global health problems. While antifungal treatments have advanced over the last decade, patient outcomes have not substantially improved. These shortcomings are largely attributed to the evolutionary similarity between fungi and humans, which limits the scope of drug development. As such, there is a pressing need to understand the unique cellular mechanisms that govern fungal viability. Given that Saccharomyces cerevisiae is evolutionarily related to a number of pathogenic fungi, and in particular to the Candida species, most genes from S. cerevisiae are highly conserved in pathogenic fungal strains. Here we show that hyperactivation of TORC1 signaling sensitizes S. cerevisiae cells to both endoplasmic reticulum stress and cell wall stressors by compromising cell wall integrity. Therefore, targeting TORC1 signaling and endoplasmic reticulum stress pathways may be useful in developing novel targets for antifungal drugs.
Successful discrimination of protein interactions

We present results from the prediction of protein complexes associated with the first Critical Assessment of PRediction of Interactions (CAPRI) experiment. Our algorithm, SmoothDock, comprises four steps: (1) we perform rigid body docking using the program DOT, keeping the top 20,000 structures as ranked by surface complementarity; (2) we rerank these structures according to a free energy estimate that includes both desolvation and electrostatics and retain the top 2000 complexes; (3) we cluster the filtered complexes using a pairwise root‐mean‐square deviation (RMSD) criterion; (4) the 25 largest clusters are subject to a smooth docking discrimination algorithm where van der Waals forces are taken into account. We predicted targets 1, 6, and 7 with RMSDs of 9.5, 2.4, and 2.6 Å, respectively. More importantly, from the perspective of biological applications, our approach consistently ranked the correct model first (i.e., with highest confidence). For target 5 we identified the binding region but not the correct orientation. Although we were able to find reasonable clusters for all targets, low‐affinity complexes (Kd < nM) were harder to discriminate. For four of seven targets, the top models predicted by our automated procedure were among the best communitywide predictions. Proteins 2003;52:92–97. © 2003 Wiley‐Liss, Inc.
A multi-winding transformer model for predictive SMPS design and analysis

This paper outlines the applicability of a multi-winding transformer model for the predictive analysis and design of switched-mode power supplies (SMPSs). The transformer model is PSPICE-compatible and its parameters are obtained from the physical dimensions and material properties of the transformer. Skin and proximity effects in the conducting layers, as well as transformer parasitic capacitances and non-linear core properties, are considered. The model has proven very useful for the predictive design and analysis of SMPS transformers, especially those of forward-converters and enables the prediction of conducted EMI in SMPSs at an early design stage, even before the construction of the first proto-types.
Fabrication of a nanostructure thermal property measurement platform

Measurements of the electrical and thermal transport properties of one-dimensional nanostructures (e.g. nanotubes and nanowires) are typically obtained without detailed knowledge of the specimen’s atomic-scale structure or defects. To address this deficiency, we have developed a microfabricated, chip-based characterization platform that enables both transmission electron microscopy (TEM) of the atomic structure and defects as well as measurement of the thermal transport properties of individual nanostructures. The platform features a suspended heater line that physically contacts the center of a suspended nanostructure/nanowire that was placed using in situ scanning electron microscope nanomanipulators. Suspension of the nanostructure across a through-hole enables TEM characterization of the atomic and defect structure (dislocations, stacking faults, etc) of the test sample. This paper explains, in detail, the processing steps involved in creating this thermal property measurement platform. As a model study, we report the use of this platform to measure the thermal conductivity and defect structure of a GaN nanowire.
On Efficient External-Memory Triangle Listing

Discovering triangles in large graphs is a well-studied area, however, both external-memory performance of existing methods and our understanding of the complexity involved leave much room for improvement. To shed light on this problem, we first generalize the existing in-memory algorithms into a single framework of 18 triangle-search techniques. We then develop a novel external-memory approach, which we call Pruned Companion Files (PCF), that supports operation of all 18 algorithms, while significantly reducing I/O compared to the common methods in this area. After finding the best node-traversal order, we build an implementation around it using SIMD instructions for list intersection and PCF for I/O. This method runs 5-10 times faster than the best available implementation and exhibits orders of magnitude less I/O. In one of our graphs, the program finds 1 trillion triangles in 237 seconds using a desktop CPU.
Family studies in an extremely large mild haemophilia A pedigree which includes 10% of Greek haemophiliacs

Summary. We illustrate the usefulness of direct mutation detection for genetic counselling by showing its application to an extremely large mild haemophilia A pedigree (91 haemophiliacs) originating from the village of Aiani in Macedonia, northern Greece. The causative mutation has already been shown to be an A to T transversion in codon 280 of the FVIII gene which replaces Asn 280 (AAC) by He (ATC) and which creates a new Bam HI restriction site in exon 7. The latter permitted direct, rapid and reliable detection of the mutation in relevant family members. All major branches of the family were shown to share the mutation, and carrier status was diagnosed or excluded for 23 possible carriers. Other interesting characteristics of the Aiani haemophilic population are a slightly higher longevity and fecundity than that observed in the general population and a wide range of FVIILC levels (5–25%) associated with the mutation.
A study of modified mesoporous silica for the adsorption of selected organic pollutants.

ix ACKNOWLEDGMENTS . xi TABLE OF CONTENTS . xiii LIST OF TABLES . xxiv LIST OF FIGURES . xxvi 1.0 CHAPTER 1: INTRODUCTION . 1 1.1 Background to Study . 1 1.2 Adsorption of Organic Pollutants . 2 1.3 Modification of Silica Surface . 3 1.4 Statement of Problem . 3 1.5 Justification . 4 1.6 Hypothesis . 4 1.7 Aim and Objectives . 5 References . 6 2.0 CHAPTER 2: LITERATURE REVIEW . 8 2.
Distances in inhomogeneous quintessence cosmology

We investigate the properties of cosmological distances in locally inhomogeneous universes with pressureless matter and dark energy (quintessence), with constant equation of state, , . We give exact solutions for angular diameter distances in the empty beam approximation. In this hypothesis, the distance–redshift equation is derived from the multiple-lens-plane theory. The case of a flat universe is considered with particular attention. We show how this general scheme makes distances degenerate with respect to wX and the smoothness parameters αi, accounting for the homogeneously distributed fraction of energy of the i-components. We analyse how this degeneracy influences the critical redshift where the angular diameter distance takes its maximum, and discuss future prospects for measuring the smoothness parameter of the pressureless matter, αM.
Blossom

Blossom is an open-source social robotics platform responding to three challenges in human-robot interaction (HRI) research: (1) Designing, manufacturing, and programming social robots requires a high level of technical knowledge; (2) social robot designs are fixed in appearance and movement capabilities, making them hard to adapt to a specific application; and (3) the use of rigid mechanisms and hard outer shells limits the robots’ expressive capabilities. Addressing these challenges, Blossom aims at three design objectives: accessibility, flexibility, and expressiveness. The robot’s mechanism can be quickly assembled and partially extended by end-users. Blossom’s appearance is open-ended through handcrafted fabric exteriors created and customized by users. Smooth organic movements are achieved with tensile mechanisms, elastic components, and a soft exterior cover attached loosely to the body. Blossom’s smartphone-based gesture generation requires neither programming nor character animation experience, allowing lay users to create their own behaviors. All elements in the design were conceived with a low barrier-of-entry in mind. The result is an accessible and customizable social robot for researchers. This article details the implementation of Blossom’s design and demonstrates the platform’s potential through four field deployment case studies.
Scaling POMDPs for dialog management with composite summary point-based value iteration (CSPBVI)

Although partially observable Markov decision processes (POMDPs) have shown great promise as a framework for dialog management in spoken dialog systems, important scalability issues remain. This paper tackles the problem of scaling slot-filling POMDP-based dialog managers to many slots with a novel technique called composite point-based value iteration (CSPBVI). CSPBVI creates a "local" POMDP policy for each slot; at runtime, each slot nominates an action and a heuristic chooses which action to take. Experiments in dialog simulation show that CSPBVI successfully scales POMDP-based dialog managers without compromising performance gains over baseline techniques and preserving robustness to errors in user model estimation. Copyright © 2006, American Association for Artificial Intelligence (www.aaai.org). All rights reserved.
Expression of human beta-defensins-1-4 in thyroid cancer cells and new insight on biologic activity of hBD-2 in vitro.

UNLABELLED The study was aimed on analysis of human beta-defensin-1-4 (hBDs) mRNA expression in cultured thyroid cancer cells and evaluation of effects of recombinant hBD-2 (rec-hBD-2) on growth patterns, migration properties and expression of E-cadherin and vimentin in these cells. METHODS The study was performed on cultured follicular thyroid cancer WRO cells, papillary thyroid cancer TPC1 cells, and anaplastic thyroid cancer KTC-2 cells. For analysis of hBD-1-4 mRNA expression in thyroid cancer cells, semiquantitative RT-PCR was used. Effects of rec-hBD-2 on cell proliferation, viability, and migration were analyzed using direct cell counting, MTT test, and scratch assay respectively. Expression of vimentin and E-cadherin was evaluated by quantitative PCR (qPCR). RESULTS By the data of RT-PCR, all three studied thyroid cancer cell lines express hBD-1 and -4 mRNA, but not hBD-2 mRNA, while hBD-3 expression was detected in WRO and KTC-2 cells. The treatment of TPC-1, WRO, and KTC-2 cells with 100-1000 nM rec-hBD-2 resulted in significant concentration-dependent suppression of cell proliferation, viability, and migratory property. By the data of qPCR, significant up-regulation of vimentin expression was registered in KTC-2 and WRO cells treated with 500 nM rec-hBD-2. Significant down-regulation of E-cadherin expression (p < 0.05) was detected only in KTC-2 cells treated with the defensin. Also, it has been shown that TPC-1 cells treated with 500 nM rec-hBD-2 acquired more elongated morphology. CONCLUSION The data demonstrate that hBD-2 in concentrations higher than 100 nM exerts significant concentration-dependent suppression of thyroid cancer cell growth and migration, and affects vimentin and E-cadherin expression dependent on histologic type of thyroid cancer cells.
Multi-modal Tracking for Object based SLAM

We present an on-line 3D visual object tracking framework for monocular cameras by incorporating spatial knowledge and uncertainty from semantic mapping along with high frequency measurements from visual odometry. Using a combination of vision and odometry that are tightly integrated we can increase the overall performance of object based tracking for semantic mapping. We present a framework for integration of the two data-sources into a coherent framework through information based fusion/arbitration. We demonstrate the framework in the context of OmniMapper[1] and present results on 6 challenging sequences over multiple objects compared to data obtained from a motion capture systems. We are able to achieve a mean error of 0.23m for per frame tracking showing 9% relative error less than state of the art tracker.
Dissociable Representations of Environmental Size and Complexity in the Human Hippocampus

The hippocampus is widely assumed to play a central role in representing spatial layouts in the form of “cognitive maps. ” It remains unclear, however, which properties of the world are explicitly encoded in the hippocampus, and how these properties might contribute to the formation of cognitive maps. Here we investigated how physical size and complexity, two key properties of any environment, affect memory-related neural activity in the human hippocampus. We used functional magnetic resonance imaging and a virtual maze-learning task to examine retrieval-related activity for three previously learned virtual mazes that differed systematically in their physical size and complexity (here defined as the number of distinct paths within the maze). Before scanning, participants learned to navigate each of the three mazes; hippocampal activity was then measured during brief presentations of static images from within each maze. Activity within the posterior hippocampus scaled with maze size but not complexity, whereas activity in the anterior hippocampus scaled with maze complexity but not size. This double dissociation demonstrates that environmental size and complexity are explicitly represented in the human hippocampus, and reveals a functional specialization for these properties along its anterior–posterior axis.
β1 Integrin Is Essential for Teratoma Growth and Angiogenesis

Teratomas are benign tumors that form after ectopic injection of embryonic stem (ES) cells into mice and contain derivatives of all primitive germ layers. To study the role of β1 integrin during teratoma formation, we compared teratomas induced by normal and β1-null ES cells. Injection of normal ES cells gave rise to large teratomas. In contrast, β1-null ES cells either did not grow or formed small teratomas with an average weight of <5% of that of normal teratomas. Histological analysis of β1-null teratomas revealed the presence of various differentiated cells, however, a much lower number of host-derived stromal cells than in normal teratomas. Fibronectin, collagen I, and nidogen were expressed but, in contrast to normal teratomas, diffusely deposited in β1-null teratomas. Basement membranes were present but with irregular shape and detached from the cell surface. Normal teratomas had large blood vessels with a smooth inner surface, containing both host- and ES cell–derived endothelial cells. In contrast, β1-null teratomas had small vessels that were loosely embedded into the connective tissue. Furthermore, endothelial cells were always of host-derived origin and formed blood vessels with an irregular inner surface. Although β1- deficient endothelial cells were absent in teratomas, β1-null ES cells could differentiate in vitro into endothelial cells. The formation of a complex vasculature, however, was significantly delayed and of poor quality in β1-null embryoid bodies. Moreover, while vascular endothelial growth factor induced proliferation of endothelial cells as well as an extensive branching of blood vessels in normal embryoid bodies, it had no effect in β1-null embryoid bodies.
CSMA/SF: Carrier Sense Multiple Access with Shortest First

Energy efficiency is the main concern in wireless sensor networks (WSNs) due to devices' limited battery power. Because the heavy burden of nodes that near the sink, this "energy hole problem" makes nodes near the sink have faster energy depletion than others. Because of this, the lifetime of WSNs, to some extent, is determined by the power consumption of communication between sink and sensing nodes that near the sink. To address this issue, we propose CSMA/SF (Shortest First) protocol to reduce power consumption of sink-node communication by minimizing energy cost in carrier sense during nodes' channel contention. CSMA/SF modifies existed CSMA/CA MAC protocol. Instead of complete contention-based, CSMA/SF ensures nodes remaining shorter message has higher priority in contention by implementing a distributed scheduling algorithm and incorporating Length Detection scheme. Further, CSMA/SF employs an Anti-Starvation mechanism to solve the starvation problem of shortest-first protocol. CSMA/SF also optimizes channel utilization by reducing the probability of collisions. We have implemented CSMA/SF into USRP2 platform and also conducted comprehensive simulations. The experimental results show that CSMA/SF can reduce overall energy consumption by around 20%. CSMA/SF can improve channel utilization up to 40%.
Effect of 1,2-dimethylhydrazine and diethylnitrosamine on cell replication and unscheduled DNA synthesis in target and nontarget cell populations in rat liver following chronic administration.

Marked differences in the rates of de novo DNA synthesis and unscheduled DNA synthesis were observed in hepatocytes and nonparenchymal cells (NPC) isolated from Fischer 344 rats following in vivo exposure to 1,2-dimethylhydrazine (SDMH) or diethylnitrosamine (DEN) for 1.5, 4, 8, 16, and 28 days. Liver cells were labeled in vivo with bromodeoxyuridine and [3H]thymidine, following which, hepatocytes and NPC were separated by elutriation centrifugation. Purified DNA was then separated into fully replicated and nonreplicated DNA by ultracentrifugation in CsCl gradients. Following exposure to SDMH, the rate of de novo DNA replication in NPC was greatly increased over both control NPC and the corresponding hepatocytes for the entire time course. Unscheduled DNA synthesis was only observed in hepatocytes after exposure to SDMH. Following exposure to DEN, both cell populations exhibited changes in de novo DNA synthesis that were directly proportional to one antoher except at 1.5 days. Increases occurred first in hepatocytes at 1.5 days but were delayed in NPC until 4 days. Hepatocyte replication returned to control values by 28 days. Unscheduled DNA synthesis was much lower following exposure to DEN than SDMH. Therefore, SDMH, which induces hemangioendotheliomas of the liver at the dose given, induces a marked increase in cell replication in the target cell population and unscheduled DNA synthesis in the resistant cell population. DEN, which induces hepatocellular carcinoma, moderately stimulates cell replication in both liver cell populations and induces little unscheduled DNA synthesis in either population.