Miracle-dz/UniFAR-FTUs huggingface dataset:
SR and SR-related proteins redistribute to segregated fibrillar components of nucleoli in a response to DNA damage

Pre-mRNA splicing factors are often redistributed to nucleoli in response to physiological conditions and cell stimuli. In telophase nuclei, serine-arginine rich (SR) proteins, which usually reside in nuclear speckles, localize transiently to active ribosomal DNA (rDNA) transcription sites called nucleolar organizing region-associated patches (NAPs). Here, we show that ultraviolet light and DNA damaging chemicals induce the redistribution of SR and SR-related proteins to areas around nucleolar fibrillar components in interphase nuclei that are similar to, but distinct from, NAPs, and these areas have been termed DNA damage-induced NAPs (d-NAPs). In vivo labeling of nascent RNA distinguished d-NAPs from NAPs in that d-NAPs were observed even after full rDNA transcriptional arrest as a result of DNA damage. Studies under a variety of conditions revealed that d-NAP formation requires both RNA polymerase II-dependent transcriptional arrest and nucleolar segregation, in particular, the disorganization of the granular nucleolar components. Despite the redistribution of SR proteins, splicing factor-enriched nuclear speckles were not disrupted because other nuclear speckle components, such as nuclear poly(A) RNA and the U5-116K protein, remained in DNA-damaged cells. These data suggest that the selective redistribution of splicing factors contributes to the regulation of specific genes via RNA metabolism. Finally, we demonstrate that a change in alternative splicing of apoptosis-related genes is coordinated with the occurrence of d-NAPs. Our results reveal a novel response to DNA damage that involves the dynamic redistribution of splicing factors to nucleoli.
Novel conditions for the synchronization of linear systems

This article presents the derivation of novel necessary and sufficient conditions for the synchronization of a network of arbitrary but homogeneous linear dynamic systems. We solely focus on the case of full-state coupling. Consequently, it is assumed that the agents can measure and exchange their complete state. The result is given for static but directed communication networks. It requires the agent dynamics to be stabilizable and the underlying digraph of the network to be connected. The novel conditions are fully characterized by solving a decentralized control problem. Based on this, it is possible to recast the design of the full-state coupling controller to linear matrix inequalities (LMIs). Finally, the efficacy of the approach is shown in computer simulations involving the synchronization of three aircraft with unstable dynamics.
On Visual Real Time Mapping for Unmanned Aerial Vehicles

: This paper addresses the challenge of a real-time capable vision system in the task of trajectory and surface reconstruction by aerial image sequences. The goal is to present the design, methods and strategies of a real-time capable vision system solving the mapping task for secure navigation of small UAVs with a single camera. This includes the estimation process, map representation, initialization processes, loop closing detection and exploration strategies. The estimation process is based on the Kalman-Filter and a landmark based map representation. We introduce a new initialization method for new observed landmarks. We will show that the initialization process and the exploration strategy has a signiﬁcant effect on the accuracy of the estimated camera trajectory and of the map
The HCI bibliography project

The HCI Bibliography project has just released its first collections of a free-access online extended bibliography on Human-Computer Interaction. The basic goal of the project is to put an online bibliography for most of HCI on the screens of all researchers and developers in the field through anonymous ftp access, mail servers, and Mac and DOS floppy disks. Through the efforts of volunteers, the bibliography is approaching 1000 entries, with abstracts and/or tables of contents; eventually, citation information and hypertext access will be added. The first release contains the complete contents of all the ACM CHI conference, the complete journal Human-Computer Interaction, and several other important sources. Eventually, all of HCI will be online and freely accessible around the world.
High-throughput single-base resolution mapping of RNA 2΄-O-methylated residues

Abstract Functional characterization of the transcriptome requires tools for the systematic investigation of RNA post-transcriptional modifications. 2΄-O-methylation (2΄-OMe) of the ribose moiety is one of the most abundant post-transcriptional modifications of RNA, although its systematic analysis is difficult due to the lack of reliable high-throughput mapping methods. We describe here a novel high-throughput approach, named 2OMe-seq, that enables fast and accurate mapping at single-base resolution, and relative quantitation, of 2΄-OMe modified residues. We compare our method to other state-of-art approaches, and show that it achieves higher sensitivity and specificity. By applying 2OMe-seq to HeLa cells, we show that it is able to recover the majority of the annotated 2΄-OMe sites on ribosomal RNA. By performing knockdown of the Fibrillarin methyltransferase in mouse embryonic stem cells (ESCs) we show the ability of 2OMe-seq to capture 2΄-O-Methylation level variations. Moreover, using 2OMe-seq data we here report the discovery of 12 previously unannotated 2΄-OMe sites across 18S and 28S rRNAs, 11 of which are conserved in both human and mouse cells, and assigned the respective snoRNAs for all sites. Our approach expands the repertoire of methods for transcriptome-wide mapping of RNA post-transcriptional modifications, and promises to provide novel insights into the role of this modification.
Trust (and mistrust) in secure applications

Trust and trustworthiness are the foundations of security. Homeowners trust lock manufacturers to create quality locks to protect their homes. Some locks are trustworthy; others are not. Businesses trust security guards to admit only authorized personnel into sensitive areas. Some security guards should be trusted; some should not. CGI programmers trust users to provide valid inputs to the data fields on Web pages. Although most users can be trusted, some cannot. The basis for these trust relationships and how they are formed can dramatically affect the underlying security of any system—be it home protection or online privacy. Because these trust assumptions are often illusive, software development efforts seldom handle these assumptions correctly. Several common ways in which erroneous trust assumptions in software applications can wreak havoc on the security of those applications are explored here. We consider the common trust assumptions and why they are often wrong, how these trust assumptions can arise during an application’s development process, and how to minimize the number of problematic trust assumptions in an application. A trust relationship is a relationship involving multiple entities (such as companies, people, or software components). Entities in a relationship trust each other to have or not have certain properties (the so-called trust assumptions). If the trusted entities satisfy these properties, then they are trustworthy. Unfortunately, because these properties are seldom explicitly defined, misguided trust relationships in software applications are not uncommon. Software developers have trust relationships during every stage of software development. Before a software project is conceived, there are business and personal trust relationships that developers generally assume will not be abused. For example, many corporations trust that their employees will not attack the information systems of the company. Because of this trust, a company might have a software application talking to a database over the company’s network without the aid of encryption and authentication. Employees could easily abuse the lack of security to convince database applications to run phony updates. Companies usually trust their software developers and assume their developers will not leave back doors or other artifacts in their code that could potentially compromise the security of the system. System architects must constantly deal with trust issues during an application’s design cycle. Proprietary design documents and other data are often communicated over channels that should not be trusted (such as the Internet); the developer must weigh his or her trust in the people who might have access to this data, John Viega,
Generating Novel Waveguides for Stimulated Brillouin Scattering with Genetic Algorithms

Over the last few years a rapid development has been going on in demonstrating stimulated Brillouin scattering (SBS) in chip-integrated optical waveguides. Most of the work has focused on finding good materials for achieving net gain however[1], rather than on exploring novel waveguide designs. To design a waveguide for high SBS gain is difficult because one needs to compromise between having a good optical waveguide, a good mechanical resonator, and a strong coupling between the two, all in the same physical structure. To approach this problem we used genetic algorithms (GA) and explored a wide range of possible waveguide shapes to achieve high gain in silicon and silicon oxide based integrated platforms. GAs have been shown to often provide counter intuitive but educational answers in domains ranging from the growth of plants and website design to Othello strategies[2,3].
Chromosomal abnormalities in cancer.

This review gives an account of chromosomal aberrations in cancer cells. Such abnormalities have typically been associated with hematologic cancers, but recent work has shown a variety of chromosomal changes in solid tumors, including prostate cancer and non–small-cell lung cancer. The authors point out that some of the chromosomal abnormalities have revealed targets for cancer treatment, and others have clinical application in the diagnosis of certain types of neoplasms and in the formulation of a prognosis.
First observation of the thermal Sunyaev-Zel’dovich effect with kinetic inductance detectors

Clusters of galaxies provide precious informations on the evolution of the Universe and large scale structures. Recent cluster observations via the thermal Sunyaev-Zel'dovich (tSZ) effect have proven to be a powerful tool to detect and study them. In this context, high resolution tSZ observations (about tens of arcsec) are of particular interest to probe intermediate and high redshift clusters. Such observations will be carried out with the millimeter dual-band NIKA2 camera, based on Kinetic Inductance Detectors (KIDs) and to be installed at the IRAM 30-meter telescope in 2015. To demonstrate the potential of such an instrument, we present tSZ observations with the NIKA camera prototype, consisting of two arrays of 132 and 224 detectors observing at 140 and 240 GHz with a 18.5 and 12.5 arcsec angular resolution, respectively. The cluster RX J1347.5-1145 was observed simultaneously at 140 and 240 GHz. We used a spectral decorrelation technique to remove the atmospheric noise and obtain a map of the cluster at 140 GHz. The efficiency of this procedure has been characterized through realistic simulations of the observations. The obtained 140 GHz map presents a decrement at the cluster position consistent with the tSZ nature of the signal. We used this map to study the pressure distribution of the cluster by fitting a gNFW model to the data. Subtracting this model from the map, we confirm that RX J1347.5-1145 is an ongoing merger, in agreement with and complementary to previous tSZ and X-ray observations. For the first time, we demonstrate the tSZ capability of KIDs based instruments. The NIKA2 camera, with about 5000 detectors and a 6.5 arcmin field of view, will be a well-suited instrument for in-depth studies of the Intra Cluster Medium from intermediate to distant clusters and so for the follow-up of recently detected clusters by the Planck satellite.
Moisture diffusion coefficient estimation in peas drying by means of a modified Hawlader and Uddin method

The aim of the present work is to determine the moisture diffusion coefficient in peas applying, in a first step, a methodology previously published in the literature by Uddin et al.[1] for determining constant diffusion coefficients taking in account the volume reduction associated to the drying process. Then, in a second step, refine it by means of an optimization step. The optimization step is justified because the methodology of Uddin et al. is based in a solution of the diffusion equation that is not mathematically valid for the drying-shrinking problem. Keywords: : moisture diffusivity; drying-shrinking; peas drying
Conspiracy theory and cognitive style: a worldview

This paper assessed whether belief in conspiracy theories was associated with a particularly cognitive style (worldview). The sample comprised 223 volunteers recruited via convenience sampling and included undergraduates, postgraduates, university employees, and alumni. Respondents completed measures assessing a range of cognitive-perceptual factors (schizotypy, delusional ideation, and hallucination proneness) and conspiratorial beliefs (general attitudes toward conspiracist thinking and endorsement of individual conspiracies). Positive symptoms of schizotypy, particularly the cognitive-perceptual factor, correlated positively with conspiracist beliefs. The best predictor of belief in conspiracies was delusional ideation. Consistent with the notion of a coherent conspiratorial mindset, scores across conspiracy measures correlated strongly. Whilst findings supported the view that belief in conspiracies, within the sub-clinical population, was associated with a delusional thinking style, cognitive-perceptual factors in combination accounted for only 32% of the variance.
The epidermal growth factor receptor family in breast cancer

The human epidermal growth factor receptor (HER) family comprises four homologous members: EGFR, HER-2, HER-3, and HER-4. The activation of these receptors triggers a complex series of signal transduction pathways which affect pivotal tumorigenic processes. The deregulation of HER signaling is seen in several human malignancies. HER-2 is now recognized as a key oncogene in breast cancer pathogenesis. Assessment of HER-2 status is of central importance in the prognosis of breast cancer patients. In the light of clinical data suggesting that HER-2 can also be useful as a predictive marker both for trastuzumab and chemotherapy, standardized determination of the HER-2 status in tumors has become more important. Moreover, current data provide evidence for the significance of HER-3 and HER-4 alterations in breast carcinogenesis. Because of the complex interactions among the HER receptors, it is likely that the effect on cell proliferation and tumor growth depends on receptor trans-signaling and thus, the evaluation of the combined expression pattern of all family members is of particular interest. This review presents the current evidence highlighting the role of the family as a whole panel and an update on the role of HER-3 and HER-4 receptors in breast cancer. Moreover, we provide updated data regarding the prognostic value of HER family members giving emphasis to novel methods for the determination of their status, such as real-time polymerase chain reaction. In addition, we review recent therapeutic approaches aimed at targeting the HER family in breast cancer patients.
Behaviour of hydrogels swollen in polymer solutions under mechanical action

The behaviour of highly swollen polyelectrolyte gels containing linear polymer solutions submitted to mechanical stresses (shear, compression) was studied using rheo-optical tools in order to gain understanding in gel behaviour and to open the way towards the application of hydrogels in cosmetic applications. Shear stresses were imposed on isolated gel particles suspended in a silicone oil matrix. Different regimes were identified: at the lowest stresses, the particle only deforms, but less than a droplet of its solvent would do. Above a first threshold stress, release of some solvent is observed in the flow direction. The solvent tips stay attached to the particle. The solvent can be detached and dispersed into the matrix at stresses above a second critical stress. Release and ejection were also observed in the vorticity direction. Important volumes of solvent can be set free. The effects of particle size, degree of swelling, polymer solution concentration and interfacial tension were evaluated. The compression tests were executed with gel disks swollen at equilibrium in water or in a polymer solution and surrounded by air. The gel deforms and releases some solvent as soon as it undergoes some stress. The thermodynamical analysis of such system predicts that release is more important for weakly charged gels than for neutral-ones.
DC therapy induces long‐term NK reactivity to tumors via host DC

We vaccinated mice with DC loaded with or without invariant NKT‐cell ligand α‐galactosylceramide and evaluated long‐term resistance against tumor challenge. When mice had been given either DC or DC/galactosylceramide and were challenged with tumor cells even 6–12 months later, both NK and NKT cells were quickly activated to express CD69 and produce IFN‐γ. The NK cells could resist a challenge with several different tumors in vivo. The activated NK and NKT cells could be depleted with anti‐NK1.1 treatment. In spite of this, the activated cells recovered, indicating that tumor‐responsive NK and NKT cells were being generated continuously as a result of vaccination with DC and were not true memory cells. The NK and NKT antitumor response in DC‐vaccinated mice depended on CD4+ T cells, but neither CD8+T cells nor CD4+CD25+ regulatory T cells. However, both vaccine DC and host DC were required for the development of long‐term, tumor reactive innate immunity. These results indicate that DC therapy in mice induces long‐lasting innate NK‐ and NKT‐cell activation through a pathway that requires host DC and CD4+ T cells and that the continued generation of active NK cells resists the establishment of metastases in vivo.
Total knee surgery: our experience

Introduction: Revision knee arthroplasty is not a routine procedure and almost always it is a technically demanding operation. The paradigm in revision total knee arthroplasty is to achieve correct alignment of the components, maintenance of the joint space and ligament balance by providing a stable bone – implant fusion. Metaphyseal bone loss is a crucial problem in revision total knee arthroplasty. The bone loss is due to primary arthroplasty technical errors and design, or problematic removal of the implants. Aim: The aim of this article is to present our experience on total knee revision surgery using tantalum metal cones as a structural bone graft substitute in total arthroplasty failure with gross metaphyseal bone loss categorized by the AORI classification, performed by a specific surgical technique and evaluated by the Knee Society Score (KSS). Material and methods: From 2013 to 2016 at the University Clinic for Orthopedic Surgery in Skopje 21 patient has been treated with revision total knee arthroplasty. Twelve patients had type 1/type 2 bone defects according to AORI, and nine had type 3 bone defect. We used trabecular metal bone graft in type 3 bone defects. A special emphasis is placed on preoperative planning according to the classification system for ligament and soft tissue damage as well as the AORI classification in order to determine the quantity, location and extent of the bone loss. In our series in patients with type 3 deformities, trabecular metal augments were used. This material resembles the human trabecular bone by its cellular structure and elastic characteristics. Results: Preoperatively, all the patients had Knee Society Score below 60, most of them were housebound, experiencing great pain and disability. After six months 95% were rated excellent, and on one year follow up, 89% were rated good or excellent (KSS score above 82, mean score 81.5), 1 patient was marked as poor with a complication – dislocation of the prosthesis. In the follow up period there was no infection. Conclusion: Our results of revision knee arthroplasty by using the trabecular metal augments with at least a year of follow up are excellent according to the KSS compared to the other studies. The disadvantages of the study are mentioned and the need for further investigation is stressed.
Dynamical scaling exponents for polymer translocation through a nanopore.

We determine the scaling exponents of polymer translocation (PT) through a nanopore by extensive computer simulations of various microscopic models for chain lengths extending up to N=800 in some cases. We focus on the scaling of the average PT time tau approximately Nalpha and the mean-square change of the PT coordinate, approximately tbeta. We find alpha=1+2nu and beta=2/alpha for unbiased PT in two dimensions (2D) and three dimensions (3D). The relation alphabeta=2 holds for driven PT in 2D, with a crossover from alpha approximately 2nu for short chains to alpha approximately 1+nu for long chains. This crossover is, however, absent in 3D where alpha=1.42+/-0.01 and alphabeta approximately 2.2 for N approximately 40-800.
New insights into neuropeptide modulation of aggression: field studies of arginine vasotocin in a territorial tropical damselfish

The neuropeptides arginine vasotocin (AVT) and arginine vasopressin are key modulators of affiliation and aggression among non-mammalian and mammalian vertebrates, respectively. Here, we explored AVT's effect on aggression in a wild population of beaugregory damselfish, Stegastes leucostictus, a highly territorial species. Aggression by territorial males towards ‘intruders’ (bottled fishes) was assessed before and after each male received intramuscular injections of either AVT, Manning compound (an AVT V1a receptor antagonist), isotocin (the teleost homologue of mammalian oxytocin differing from AVT by two amino acids) or saline (vehicle control). Compared to saline controls, AVT and Manning increased and decreased aggression, respectively, while isotocin had no effect. Response selectivity was further established in a dose–response study that revealed an inverted U-shaped function. Compared to saline controls, aggression levels for low and high AVT doses were similar, while medium dose treatments were significantly greater. This type of behavioural response, the first that we know of for a vertebrate neuropeptide, could depend on the binding of AVT to both V1-type and other AVT or non-AVT receptors. The pattern revealed here for damselfish may be symptomatic of species- and context-dependent specificity of AVT's modulation of aggression across teleosts, as is currently proposed for tetrapods.
Interval extreme learning machine for big data based on uncertainty reduction

Choosing representative samples and removing data redundancy are two key issues in large-scale data classification. This paper proposes a new model, named interval extreme learning machine (ELM), for big data classification with continuous- valued attributes. The interval ELM model is built up based on two techniques, i.e., discretization of conditional attributes and fuzzification of class labels. First, inspired by the traditional decision tree (DT) induction algorithm, each conditional attribute is discretized into a number of intervals based on uncertainty reduction scheme. Then, the center and range of each interval are calculated as the mean and standard deviation of the values in it. Afterwards, the samples in the same intervals with regard to all the conditional attributes are merged as one record, and a fuzzification process is performed on the class labels. As a result, the original data set is transferred into a smaller one with fuzzy classes, and the interval ELM model is developed. Experimental comparisons demonstrate the feasibility and effectiveness of the proposed approach.