Miracle-dz/UniFAR-FTUs huggingface dataset:
PHOTOLYSIS OF PHOSPHODIESTER BONDS IN PLASMID DNA BY HIGH INTENSITY UV LASER IRRADIATION

Abstract— The cleavage of phosphodiester bonds in DNA exposed to high intensity UV laser pulses in aerated aqueous solution has been investigated using a krypton fluoride excimer laser (248 nm) and bacterial plasmid DNA. The dependence of strand breakage on fluence and intensity has been studied in detail and shows that the process is non‐linear with respect to intensity. The relationship between the quantum yield for strand breakage and intensity shows that the strand breakage reaction involves two‐photon excitation of DNA bases. The quantum yield rises with intensity from a lower value of 7 times 10‐5 until a maximum value of 4.5 times 10‐4 is attained at intensities of 1011 W m‐2 and above. This value is approximately fifty‐fold higher than the quantum yield for strand breakage induced by exposure to low density UV irradiation (254 nm, 12 W m‐2). DNA sequencing experiments have shown that strand breakage occurs by the specific cleavage of the phosphodiester bond which lies immediately 3′ to guanine residues in the DNA, leaving some alkali‐labile remnant attached to the terminal phosphate. A mechanism for DNA strand breakage which involves the generation of guanine radical cations is proposed.
Measurement program: Investigation on cache-timing attack

Recent cryptanalysis is able to reduce the strength of a cipher, without breaking the cipher as such, like in traditional cryptographic attacks. This is achieved by obtaining, and subsequently utilizing, some hardware information to recover the secret key or the message, or at least part thereof. This kind of attack is called side channel attack, and has changed the conceptual idea of cryptography from a black box system with a single input and a single output to a complex system, that produces plural, unexpected outputs, the so-called side-channel information in addition to the intended cryptographic output. This additional output can be used to break an implementation of a cipher. Cache-timing is one type of side channel attacks that is mostly done in general purpose computers. In this paper we are investigating cache-timing attacks, and show some experimental results that motivated us to develop a portable measurement program for such attacks.
The Physics of Lyotropic Liquid Crystals: Phase Transitions and Structural Properties

1. Lyotropic systems: main experimental facts and techniques 2. Basic concepts of phase transitions 3. Phase diagrams of lyotropic mixtures 4. Phase transitions between periodically organized lyotropic phases 5. The isotropic micellar and bicontinuous phases 6. The nematic and cholesteric phases 7. The lyotropic one-, two- and three-dimensionally ordered phases 8. Recent developments and related areas
IRGM Is a Common Target of RNA Viruses that Subvert the Autophagy Network

Autophagy is a conserved degradative pathway used as a host defense mechanism against intracellular pathogens. However, several viruses can evade or subvert autophagy to insure their own replication. Nevertheless, the molecular details of viral interaction with autophagy remain largely unknown. We have determined the ability of 83 proteins of several families of RNA viruses (Paramyxoviridae, Flaviviridae, Orthomyxoviridae, Retroviridae and Togaviridae), to interact with 44 human autophagy-associated proteins using yeast two-hybrid and bioinformatic analysis. We found that the autophagy network is highly targeted by RNA viruses. Although central to autophagy, targeted proteins have also a high number of connections with proteins of other cellular functions. Interestingly, immunity-associated GTPase family M (IRGM), the most targeted protein, was found to interact with the autophagy-associated proteins ATG5, ATG10, MAP1CL3C and SH3GLB1. Strikingly, reduction of IRGM expression using small interfering RNA impairs both Measles virus (MeV), Hepatitis C virus (HCV) and human immunodeficiency virus-1 (HIV-1)-induced autophagy and viral particle production. Moreover we found that the expression of IRGM-interacting MeV-C, HCV-NS3 or HIV-NEF proteins per se is sufficient to induce autophagy, through an IRGM dependent pathway. Our work reveals an unexpected role of IRGM in virus-induced autophagy and suggests that several different families of RNA viruses may use common strategies to manipulate autophagy to improve viral infectivity.
Auxin production by the plant trypanosomatid Phytomonas serpens and auxin homoeostasis in infected tomato fruits

SUMMARY Previously we have characterized the complete gene encoding a pyruvate decarboxylase (PDC)/indolepyruvate decarboxylase (IPDC) of Phytomonas serpens, a trypanosomatid highly abundant in tomato fruits. Phylogenetic analyses indicated that the clade that contains the trypanosomatid protein behaves as a sister group of IPDCs of γ-proteobacteria. Since IPDCs are key enzymes in the biosynthesis of the plant hormone indole-3-acetic acid (IAA), the ability for IAA production by P. serpens was investigated. Similar to many microorganisms, the production of IAA and related indolic compounds, quantified by high performance liquid chromatography, increased in P. serpens media in response to amounts of tryptophan. The auxin functionality was confirmed in the hypocotyl elongation assay. In tomato fruits inoculated with P. serpens the concentration of free IAA had no significant variation, whereas increased levels of IAA-amide and IAA-ester conjugates were observed. The data suggest that the auxin produced by the flagellate is converted to IAA conjugates, keeping unaltered the concentration of free IAA. Ethanol also accumulated in P. serpens-conditioned media, as the result of a PDC activity. In the article we discuss the hypothesis of the bifunctionality of P. serpens PDC/IPDC and provide a three-dimensional model of the enzyme.
Topography of projections to posterior cortical areas from the macaque frontal eye fields

Frontal eye field (FEF) projections to posterior cortical areas were mapped by autoradiography of tritiated amino acids (Leu, Pro) in six macaque monkeys. In three monkeys, the large saccade part of the FEF (IFEF) was identified by microstimulation and injected with tracers. In a fourth monkey, the small saccade part of the FEF (sFEF) was identified by microstimulation and injected with tracer. Tracer injections were placed into the sFEF region of two other monkeys using anatomical landmarks. The IFEF and sFEF generally had distinct and largely segregated projections to posterior cortical areas, and the overall pattern of labeling in visual areas with established topology indicates that IFEF neurons preferentially project to areas having large and eccentric receptive fields, whereas sFEF neurons project to areas having smaller, more centrally located fields. The terminal fields from the sFEF were more widespread than those from IFEF. Projections from sFEF terminated in the lateral intraparietal area (LIP), the ventral intraparietal area (VIP), and the parietal part of visual area V3A, in the fundus of the superior temporal visual area (TST), the middle temporal area (MT), the medial superior temporal area (MST), the temporal part of visual area V4, the inferior temporal area (IT), and the temporal‐occipital area (TEO) and in occipital visual areas V2, V3, and V4. Projections from IFEF terminated in parietal areas 7a, LIP, and VIP and the medial part of parietal area PE; in temporal areas MST and the superior temporal polysensory area (STP); and in occipital area V2 and posterior cingulate area 23b. Projections from IFEF and sFEF appeared to terminate in different parts of common target areas in MST, LIP, and V2. The topography of IFEF and sFEF projections to LIP suggests that this posterior eye field may also be organized by saccade amplitude. Most terminal labeling from FEF injections was bilaminar to layers I and V/VI, but labeling in area LIP, area MT, the medial part of area PE, and area 23b was columnar‐form to all layers. © 1995 Wiley‐Liss, Inc.
A BMI approach to the cooperative control of multi-agent systems and optimization

This paper focuses on cooperative controller design and optimization problems of multi-agent systems. Based on the method of bilinear matrix inequalities(BMI), the necessary and sufficient conditions for stabilization of multi-agent systems are presented. Then, the optimization design method for cooperative control is also considered with respect to a quadratic performance index. And problems of designing cooperative controller are formulated into the non-convex optimization problems with BMI constraints. Finally, examples are given to illustrate the better effectiveness than the presented results.
Polycomb group expression signatures in the malignant progression of gliomas

Polycomb group (PcG) proteins form at least two key complexes, namely polycomb repressive complex 1 and polycomb repressive complex 2. These complexes are involved in the progression of various cancers. Systematic research has not been conducted on the aberrant expression of PcG members in gliomas. Using the Chinese Glioma Genome Atlas data set, PcG expression patterns between normal brain tissues and glioma samples were analyzed, and a PcG-based classifier was then developed using BRB Cox regression and risk-score model. These results were validated in an independent GSE16011 set. A total of six PcGs [chromobox protein homolog (CBX) 6, CBX7, PHD finger protein 1, enhancer of zeste homolog 2 (EZH2), DNA (cytosine-5-)-methyltransferase 3β (DNMT3B) and polyhomeotic-like protein 2] were identified to be associated with glioma grade. Survival analysis then revealed a five-PcG gene signature one protective gene (enhancer of zeste homolog 1) and four risky genes (EZH2, PHD finger protein 19, DNMT3A and DNMT3B), which may identify patients with high risk of poor prognosis of glioma. Multivariate Cox analysis indicated that the five-PcG signature was an independent prognostic biomarker. These findings indicated that a novel prognostic classifier, five-PcG signature, served as an independent prognostic marker for patients with glioma.
Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing

The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus.
Aflibercept in the Treatment of Metastatic Colorectal Cancer

Colorectal cancer is the third most common cancer in the US. In recent decades, an improved understanding of the role of the angiogenesis pathway in colorectal cancer has led to advancements in treatment. Bevacizumab has been shown to improve the progression-free survival and overall survival when combined with cytotoxic chemotherapy in patients with metastatic colorectal cancer, and at present is the only antiangiogenesis agent approved for the treatment of this cancer. Aflibercept is a novel angiogenesis-targeting agent, and has demonstrated efficacy in treating metastatic colorectal cancer in a recent randomized Phase III trial. Here we review the role of angiogenesis in the tumorigenesis of colorectal cancer, strategies for targeting angiogenesis, and the clinical development of aflibercept.
SOME EXTENSIONS OF NONPARAMETRIC REGRESSION MODELS

Preface The main topic of this habilitation thesis are nonparametric regression methods, briefly introduced in Chapter 1. The most important author's results related to nonparametric regression may be found in the papers attached in the Appendix. Apart of these attached papers, the same results are summarized in a unified manner in Chapters 2–4 where we also propose some extensions that were necessary in order to unite these papers smoothly into a single publication. The main body of this habilitation thesis is divided into three chapters corresponding, respectively, to the three most important stages of a data-analytical process: 1. design of the experiment (Chapter 2), 2. estimation (Chapter 3), 3. verification of assumptions (Chapter 4). The Appendix contains five papers written by the author and various coauthors during the years 2006–2011. These papers discuss successively the three stages of the data-analytical process and represent most important author's results related to nonparametric regression models during this period: • The first paper, Hlávka (2011): On nonparametric estimators of location of maximum, concerns the planning of a nonparametric regression experiment and it proposes an experimental design that is optimal for the estimation of a location of maximum of an unknown regression function. In Chapter 2, we extend this result also to estimation of zeros under more general assumptions. • The second paper, Härdle and Hlávka (2009): Dynamics of state price densities, concerns a complex application in option pricing, where the nonparametric regression estimator must be adapted in order to account for correlated data and constrained regression function. The third and the fourth paper, Hlávka (2006a): Fast algorithm for nonparametric arbitrage-free SPD estimation and Hlávka and Svojík (2009): Application of extended Kalman filter to SPD estimation, discuss some computational aspects of the proposed estimator. The contents of these three papers is summarized in Chapter 3. • Finally, the fifth paper, Hlávka et al. (2011): Tests for independence in non-parametric heteroscedastic regression models, proposes a new approach to a verification of assumptions of a nonparametric regression model. In Chapter 4, this approach is modified, compared to other tests proposed in the literature, and used to test the validity of assumptions of the constrained nonparametric regression model described in Chapter 3.
Two-stage Approach for Hindi Dependency Parsing Using MaltParser

In this paper, we present our approach towards dependency parsing of Hindi language as a part of Hindi Shared Task on Parsing, COLING 2012. Our approach includes the effect of using different settings available in Malt Parser following the two-step parsing strategy i.e. splitting the data into interChunks and intraChunks to obtain the best possible LAS 1 , UAS 2 and LA 3 accuracy. Our system achieved best LAS of 90.99% for Gold Standard track and second best LAS of 83.91% for Automated data.
Edge-guided resolution enhancement in projectors via optical pixel sharing

Digital projection technology has improved significantly in recent years. But, the relationship of cost with respect to available resolution in projectors is still super-linear. In this paper, we present a method that uses projector light modulator panels (e.g. LCD or DMD panels) of resolution n X n to create a perceptually close match to a target higher resolution cn X cn image, where c is a small integer greater than 1. This is achieved by enhancing the resolution using smaller pixels at specific regions of interest like edges. A target high resolution image (cn X cn) is first decomposed into (a) a high resolution (cn X cn) but sparse edge image, and (b) a complementary lower resolution (n X n) non-edge image. These images are then projected in a time sequential manner at a high frame rate to create an edge-enhanced image -- an image where the pixel density is not uniform but changes spatially. In 3D ready projectors with readily available refresh rate of 120Hz, such a temporal multiplexing is imperceptible to the user and the edge-enhanced image is perceptually almost identical to the target high resolution image. To create the higher resolution edge image, we introduce the concept of optical pixel sharing. This reduces the projected pixel size by a factor of 1/c2 while increasing the pixel density by c2 at the edges enabling true higher resolution edges. Due to the sparsity of the edge pixels in an image we are able to choose a sufficiently large subset of these to be displayed at the higher resolution using perceptual parameters. We present a statistical analysis quantifying the expected number of pixels that will be reproduced at the higher resolution and verify it for different types of images.
Other Folks' Theories of Mind and Behavior

Our everyday, basic understanding of people's mental states and behaviors has recently been a lively topic of debate in the social sciences This article addresses whether some aspects of our European-American theory of mind are universal, by examining ethnographic and experimental reports of cultural variation Implications of that variation for nativist theories of development are discussed and research strategies to augment our understanding are proposed.
A global view of kad

Distributed hash tables (DHTs) have been actively studied in literature and many different proposals have been made on how to organize peers in a DHT. However, very few DHT shave been implemented in real systems and deployed on alarge scale. One exception is <scp>KAD</scp>, a DHT based on Kademlia, which is part of eDonkey2000, a peer-to-peer file sharing system with several million simultaneous users. We have been crawling <scp>KAD</scp> continuously for about six months and obtained information about the total number of peers online and their geographical distribution. Peers are identified by the so called <scp>KAD</scp> ID, which was up to now assumed to remain the same across sessions. However, we observed that this is not the case: There is a large number of peers, in particular in China, that change their <scp>KAD</scp> ID, sometimes as frequently as after each session. This change of <scp>KAD</scp> IDs makes it difficult to characterize end-user availability or membership turnover.
On the O(1/t) Convergence Rate of Alternating Direction Method with Logarithmic-Quadratic Proximal Regularization

It was shown recently that the Douglas--Rachford alternating direction method of multipliers can be combined with the logarithmic-quadratic proximal regularization for solving a class of variational inequalities with separable structures. This paper further shows a worst-case $O(1/t)$ convergence rate for this algorithm where a general Glowinski relaxation factor is used.
Practical timing analysis of asynchronous circuits using time separation of events

We present a unified technique for timing verification and performance analysis of complex asynchronous circuits designed with implicit timing assumptions. We model interacting asynchronous controllers and datapath elements using timing constraint graphs. Performance metrics and circuit timing constraints to be checked are formulated as time separations between appropriate events. Time separations between all pairs of events are then efficiently computed in a single pass. We present results of analyzing a real asynchronous differential equation solver chip using our proposed technique, thereby demonstrating the practicality of our approach.
Voltammetric Detection of S100B Protein Using His-Tagged Receptor Domains for Advanced Glycation End Products (RAGE) Immobilized onto a Gold Electrode Surface

In this work we report on an electrochemical biosensor for the determination of the S100B protein. The His-tagged VC1 domains of Receptors for Advanced Glycation End (RAGE) products used as analytically active molecules were covalently immobilized on a monolayer of a thiol derivative of pentetic acid (DPTA) complex with Cu(II) deposited on a gold electrode surface. The recognition processes between the RAGE VC1 domain and the S100B protein results in changes in the redox activity of the DPTA-Cu(II) centres which were measured by Osteryoung square-wave voltammetry (OSWV). In order to verify whether the observed analytical signal originates from the recognition process between the His6–RAGE VC1 domains and the S100B protein, the electrode modified with the His6–RAGE C2 and His6–RAGE VC1 deleted domains which have no ability to bind S100B peptides were applied. The proposed biosensor was quite sensitive, with a detection limit of 0.52 pM recorded in the buffer solution. The presence of diluted human plasma and 10 nM Aβ1-40 have no influence on the biosensor performance.
miR-34a-5p and miR-34a-3p contribute to the signaling pathway of p53 by targeting overlapping sets of genes

In contrary to the common belief that only one strand of the pre-miRNA is active (usually the 5p one that is the more abundant) while the second one (miRNA*) is discarded, functional 5p and 3p have been observed for many miRNAs. Among those miRNAs is miR-34a which is a target gene of the tumor suppressor p53. In this paper we have re-examined the role of miR-34a-5p and miR-34a-3p in the signaling pathway of p53. We found that they target overlapping sets of genes (MDM2 and THBS1). By a GO enrichment analysis we found that THBS1 is involved in cancer and metastasis relevant processes. We have also deduce that p53, MDM2 and miR-34a are linked by a type 1 incoherent FFL that represent a novel mechanism for accelerating the response of p53 to external stress signals.
A Cascaded NPC/H- Bridge Inverter with Superior Harmonic Content and Improved DC Link Voltage Control for Grid Interface Application

Modeling of Cascaded Multilevel converter has put more emphasize on conventional cascaded H- bridge inverter. First a new phase shifted SPWM control algorithm for cascaded NPC/H-bridge inverter is proposed. Its Superior harmonic suppression is verified by comparing its harmonic spectrum with that of the conventional multicarrier approach. For DC- bus capacitor voltage control, a new, balance circuit is proposed. Because of its modularity, it is simple and can be easily incorporated in cascaded inverter model with any number of levels. Feedback controller design is presented with main focus on grid voltage regulation and overall system capacitor voltage balance. The validity of grid interface model and its control strategies is substantially confirmed by the extensive simulation results.
Technological Innovation Comes to Palliative Care: With a shortage of palliative specialists, telemedicine and remote monitoring offer relief.

Palliative care and technology might seem like strange bedfellows. At its core, palliative care is a very human side of medicine, relying heavily on talking with and listening to people to understand their experiences and goals. Technology, on the other hand, can often feel impersonal, cold, and one-size-fitsall. Despite this apparent disconnect, researchers and clinicians are finding new ways to harness technology to facilitate communication between patients and caregivers.