Miracle-dz/UniFAR-FTUs huggingface dataset:
Micron-scale coherence in interphase chromatin dynamics

Significance Chromatin, the functional form of DNA inside the cell nucleus, has been heavily studied using biochemical and genetic methods, but we still know little about its large-scale organization and even less about its dynamics. We present a unique method, displacement correlation spectroscopy (DCS), which allows us to map interphase chromatin dynamics simultaneously across the entire nucleus and follow the temporal evolution of the global chromatin dynamics in vivo. Using DCS we discovered that chromatin moves coherently across micron-scale regions for a few seconds, which implies a transient mechanical coupling between chromatin on different chromosomes. This coupling might allow different regions of the nucleus to communicate by a unique, mechanochemical mechanism, e.g., to coordinate responses to DNA damage. Chromatin structure and dynamics control all aspects of DNA biology yet are poorly understood, especially at large length scales. We developed an approach, displacement correlation spectroscopy based on time-resolved image correlation analysis, to map chromatin dynamics simultaneously across the whole nucleus in cultured human cells. This method revealed that chromatin movement was coherent across large regions (4–5 µm) for several seconds. Regions of coherent motion extended beyond the boundaries of single-chromosome territories, suggesting elastic coupling of motion over length scales much larger than those of genes. These large-scale, coupled motions were ATP dependent and unidirectional for several seconds, perhaps accounting for ATP-dependent directed movement of single genes. Perturbation of major nuclear ATPases such as DNA polymerase, RNA polymerase II, and topoisomerase II eliminated micron-scale coherence, while causing rapid, local movement to increase; i.e., local motions accelerated but became uncoupled from their neighbors. We observe similar trends in chromatin dynamics upon inducing a direct DNA damage; thus we hypothesize that this may be due to DNA damage responses that physically relax chromatin and block long-distance communication of forces.
International Conference on Communication Networks ( ICCN ) Design of Novel Low Power Dynamic Latch Comparator Using Multi-Fin Technology

The designing of high speed (ADC) analog to digital converter in low power for improving the performance like speed and power efficiency in dynamic latch comparator. This paper deals in reduction of leakage power and propagation delay of this dynamic latch comparator. Using various techniques designers can simulate and observe the different factors for enhancing the performance of the circuit. The conventional circuit is modified by using FinFET technique and with the help of proposed circuit the performance of the comparator circuit is enhanced. Performance parameters of the comparator like average power dissipation, energy efficiency, delay are being improved by using FinFET technique as compared to that of the conventional comparator circuit. Leakage power obtained using FinFET is 56.84 pW which is very less than that of conventional comparator. Simulation is done in 45-nm CMOS technology which confirms the analysis results.
Maturation Stages of Mouse Dendritic Cells in Growth Factor–dependent Long-Term Cultures

The signals controlling the checkpoints of dendritic cells (DC) maturation and the correlation between phenotypical and functional maturational stages were investigated in a defined model system of growth factor–dependent immature mouse DC. Three sequential stages of DC maturation (immature, mature, and apoptotic) were defined and characterized. Immature DC (stage 1) had low expression of costimulatory molecules, highly organized cytoskeleton, focal adhesion plaques, and slow motility; accordingly, they were very efficient in antigen uptake and processing of soluble proteins. Further, at this stage most of major histocompatibility complex class II molecules were within cytoplasmic compartments consistent with a poor allostimulatory capacity. Bacteria or cytokines were very efficient in inducing progression from stage 1 towards stage 2 (mature). Morphological changes were observed by confocal analysis including depolymerization of F-actin and loss of vinculin containing adhesive structures which correlates with acquisition of high motility. Antigen uptake and presentation of native protein antigen was reduced. In contrast, presentation of immunogenic peptides and allostimulatory activity became very efficient and secretion of IL-12 p75 was detectable after antigen presentation. This functional DC maturation ended by apoptotic cell death, and no reversion to the immature phenotype was observed.
Feature-Based Similarity Retrieval in Content-Based Image Retrieval

Content-based image retrieval (CBIR), providing query by image examples other than key words, is a hot topic in recent years. Querying by words mainly depends on the performance of crawler, whereas query by example is more unpredictable, since feature extraction is still challenging due to the rich content of the image. This paper focuses on the issue of similarity retrieval in high-dimensional space, a problem of performing nearest neighbor queries efficiently and effectively over large high-dimensional databases. Although some arguments have advocated that nearest-neighbor queries do not even make sense for high-dimensional data, we review the existing techniques of working in vector space of high dimension, and provide our unique view towards the issue of time complexity and precision during similarity retrieval in CBIR.
Coxiella burnetii lipopolysaccharide blocks p38α-MAPK activation through the disruption of TLR-2 and TLR-4 association

To survive in macrophages, Coxiella burnetii hijacks the activation pathway of macrophages. Recently, we have demonstrated that C. burnetii, via its lipopolysaccharide (LPS), avoids the activation of p38α-MAPK through an antagonistic engagement of Toll-like receptor (TLR)-4. We investigated the fine-tuned mechanism leading to the absence of activation of the p38α-MAPK despite TLR-4 engagement. In macrophages challenged with LPS from the avirulent variants of C. burnetii, TLR-4 and TLR-2 co-immunoprecipitated. This association was absent in cells challenged by the LPS of pathogenic C. burnetii. The disruption makes TLRs unable to signal during the recognition of the LPS of pathogenic C. burnetii. The disruption of TLR-2 and TLR-4 was induced by the re-organization of the macrophage cytoskeleton by C. burnetii LPS. Interestingly, blocking the actin cytoskeleton re-organization relieved the disruption of the association TLR-2/TLR-4 by pathogenic C. burnetii and rescued the p38α-MAPK activation by C. burnetii. We elucidated an unexpected mechanism allowing pathogenic C. burnetii to avoid macrophage activation by the disruption of the TLR-2 and TLR-4 association.
Using a typed mind map as data model in a TDD DICE system

This paper introduces a new typed mind map extension for a data model in parse-tree-based online referee system with a TDD (test-driven development) model and DALM (DICE adaptive learning model) model named DICE. Typed mind maps and a semantic node are defined by OWL-DL. Typed mind maps are now widely used in the DICE system as a uniform data model for the system, instructors, learners and materials. The mind maps are used for system configuration, system deployment, learnerpsilas information, organization of training materials, answer parsing and some widgets. An implementation based on this data model has been working for years in a real teaching and learning environment.
Corrosion in Reinforced Concrete Panels: Wireless Monitoring and Wavelet-Based Analysis

To realize the efficient data capture and accurate analysis of pitting corrosion of the reinforced concrete (RC) structures, we first design and implement a wireless sensor and network (WSN) to monitor the pitting corrosion of RC panels, and then, we propose a wavelet-based algorithm to analyze the corrosion state with the corrosion data collected by the wireless platform. We design a novel pitting corrosion-detecting mote and a communication protocol such that the monitoring platform can sample the electrochemical emission signals of corrosion process with a configured period, and send these signals to a central computer for the analysis. The proposed algorithm, based on the wavelet domain analysis, returns the energy distribution of the electrochemical emission data, from which close observation and understanding can be further achieved. We also conducted test-bed experiments based on RC panels. The results verify the feasibility and efficiency of the proposed WSN system and algorithms.
Performance analysis of AODV with multi-radio in hybrid wireless mesh network

Wireless Mesh Network (WMN) is a promising wireless technology for several emerging and commercially interesting applications. It is a multi-hop wireless access network where nodes can act both as a host as well as a router. The proposed work focuses on architecture of hybrid mesh network such that gateway routers are used for accessing the internal or external network. The mesh router has been divided into two parts that is, backbone mesh router and border mesh router (BMR). With the recent 802.11e quality-of-service (QOS) extension realtime applications such as voice over IP and video streaming are finding their way to be running over WLANs. This paper proposes twin adaptation of hybrid mesh network architecture at physical layer and 802.11e MAC layer considering a network model, which is an enhancement of AODV-MR routing protocol. Based on simulation results, we show that there is a significant improvement on standard AODV in terms of key performance metrics such as Throughput, delay, packet delivery ratio and normalized routing overhead.
Annotating Opinions in German Political News

This paper presents an approach to construction of an annotated corpus for German political news for the opinion mining task. The annotated corpus has been applied to learn relation extraction rules for extraction of opinion holders, opinion content and classification of polarities. An adapted annotated schema has been developed on top of the state-of-the-art research. Furthermore, a general tool for annotating relations has been utilized for the annotation task. An evaluation of the inter-annotator agreement has been conducted. The rule learning is realized with the help of a minimally supervised machine learning framework DARE.
Harmine and Imipramine Promote Antioxidant Activities in Prefrontal Cortex and Hippocampus

A growing body of evidence has suggested that reactive oxygen species (ROS) may play an important role in the physiopathology of depression. Evidence has pointed to the β-carboline harmine as a potential therapeutic target for the treatment of depression. The present study we evaluated the effects of acute and chronic administration of harmine (5, 10 and 15 mg/kg) and imipramine (10, 20 and 30 mg/kg) or saline in lipid and protein oxidation levels and superoxide dismutase (SOD) and catalase (CAT) activities in rat prefrontal cortex and hippocampus. Acute and chronic treatments with imipramine and harmine reduced lipid and protein oxidation, compared to control group in prefrontal cortex and hippocampus. The SOD and CAT activities increased with acute and chronic treatments with imipramine and harmine, compared to control group in prefrontal cortex and hippocampus. In conclusion, our results indicate positive effects of imipramine antidepressant and β-carboline harmine of oxidative stress parameters, increasing SOD and CAT activities and decreasing lipid and protein oxidation.
Multi-Agent Learning in Conflicting Multi-Level Games with Incomplete Information

Coordination to some equilibrium point is an interesting problem in multi-agent reinforcement learning. In common interest single stage settings this problem has been studied profoundly and efficient solution techniques have been found. Also for particular multi-stage games some experiments show good results. However, for a large scale of problems the agents do not share a common pay-off function. Again, for single stage problems, a solution technique exists that finds a fair solution for all agents. In this paper we report on a technique that is based on learning automata theory and periodical policies. Letting pseudo-independent agents play periodical policies enables them to behave socially in pure conflicting multi-stage games as defined by E. Billard (Billard & Lakshmivarahan 1999; Zhou, Billard, & Lakshmivarahan 1999). We experimented with this technique on games where simple learning automata have the tendency not to cooperate or to show oscillating behavior resulting in a suboptimal pay-off. Simulation results illustrate that our technique overcomes these problems and our agents find a fair solution for both agents.
What are the characteristics of patients with severe, symptomatic, mitral regurgitation who are denied surgery?

AIM To identify the proportion and characteristics of patients with severe symptomatic mitral regurgitation (MR) who are denied surgery. METHODS AND RESULTS In the Euro Heart Survey on valvular heart disease, 396 patients had severe symptomatic MR as assessed by Doppler-echocardiography (grade > or =3/4) and New York Heart Association class II or greater. Patient characteristics were analysed according to the decision to operate or not. A decision not to operate was taken in 193 patients (49%). In multivariable analysis, decreased left ventricular ejection fraction (LVEF) [OR = 1.39 per 10% decrease, 95% CI (1.17-1.66), P = 0.0002], non-ischaemic aetiology [OR = 4.44, 95% CI (1.96-10.76), P = 0.0006], older age [OR = 1.40 per 10-year increase, 95% CI (1.15-1.72), P = 0.001], increased Charlson comorbidity index [OR = 1.38 per 1 point increase, 95% CI (1.12-1.72), P = 0.004], and grade 3 MR [OR = 2.23, 95% CI (1.28-3.29), P = 0.005] were associated with the decision not to operate. One-year survival was 96.0 +/- 1.4% in patients with a positive decision for intervention vs. 89.5 +/- 2.3% in those with a negative decision (P = 0.02). CONCLUSION Surgery was denied in 49% of patients with severe symptomatic MR. Impaired LVEF, older age, and comorbidity were the most striking characteristics of patients who were denied surgery. The weight of age and LVEF in the decision do not seem justified according to current knowledge.
Bindungsstile und Kommunikation

Beziehungsqualität Vor mehr als 25 Jahren untersuchten Batholomev et al. das Bindungsverhalten von 635 Personen in Bezug auf 15 Beziehungsqualitäten. Sie berücksichtigten dabei auch die Einschätzung von Familienangehörigen und Freunden [2]. Demgemäß unterscheidet man noch heute im Allgemeinen folgende vier Bindungsstile: sicher, unsicher-vermeidend, unsicher-ambivalent sowie desorganisiert-desorientiert.
Planck intermediate results: VI. The dynamical structure of PLCKG214.6+37.0, a Planck discovered triple system of galaxy clusters

The survey of galaxy clusters performed by Planck through the Sunyaev-Zeldovich e ect has already discovered many interesting objects, thanks to the whole coverage of the sky. One of the SZ candidates detected in the early months of the mission near to the signal to noise threshold, PLCKG214.6+37.0, was later revealed by XMM-Newton to be a triple system of galaxy clusters. We have further investigated this puzzling system with a multi-wavelength approach and we present here the results from a deep XMM-Newton re-observation. The characterisation of the physical properties of the three components has allowed us to build a template model to extract the total SZ signal of this system with Planck data. We partly reconciled the discrepancy between the expected SZ signal from X-rays and the observed one, which are now consistent at less than 1:2 . We measured the redshift of the three components with the iron lines in the X-ray spectrum, and confirmed that the three clumps are likely part of the same supercluster structure. The analysis of the dynamical state of the three components, as well as the absence of detectable excess X-ray emission, suggest that we are witnessing the formation of a massive cluster at an early phase of interaction.
Spatio-temporal analysis of constitutive exocytosis in epithelial cells

Exocytosis is an essential cellular trafficking process integral to the proper distribution and function of a plethora of molecules, including transporters, receptors, and enzymes. Moreover, incorrect protein targeting can lead to pathological conditions. Recently, the application of evanescent wave microscopy has allowed us to image the final steps of exocytosis. However, spatio-temporal analysis of fusion of constitutive vesicular traffic with the plasma membrane has not been systematically performed. Also, the spatial sites and times of vesicle fusion have not yet been analyzed together. In addition, more formal tests are required in testing biological hypotheses, rather than visual inspection combined with statistical descriptives. Ripley K-functions are used to examine the joint and marginal behavior of locations and fusion times. Semiautomatic detection and mapping of constitutive fusion sites reveals spatial and temporal clustering, but no dependency between the locations and times of fusion events. Our novel approach could be translated to other studies of membrane trafficking in health and diseases such as diabetes
Bulletin a Publication to Promote Communication among Stata Users Editor Associate Editors Stata54 Multiple Curves Plotted with Stcurv Command New Options

Editor Associate Editors H. Joseph Newton Nicholas J. Cox, University of Durham Department of Statistics Francis X. Diebold, University of Pennsylvania Texas A & M University Joanne M. Garrett, University of North Carolina College Station, Texas 77843 Marcello Pagano, Harvard School of Public Health 979-845-3142 J. Patrick Royston, Imperial College School of Medicine 979-845-3144 FAX stb@stata.com EMAIL
Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering

The nonrandom gene organization in eukaryotes plays a significant role in genome evolution and function. Chromosomal structural changes impact meiotic fitness and, in several organisms, are associated with speciation and rapid adaptation to different environments. Small sized chromosomal inversions, encompassing few genes, are pervasive in Saccharomyces “sensu stricto” species, while larger inversions are less common in yeasts compared with higher eukaryotes. To explore the effect of gene order on phenotype, reproductive isolation, and gene expression, we engineered 16 Saccharomyces cerevisiae strains carrying all possible paracentric and pericentric inversions between Ty1 elements, a natural substrate for rearrangements. We found that 4 inversions were lethal, while the other 12 did not show any fitness advantage or disadvantage in rich and minimal media. At meiosis, only a weak negative correlation with fitness was seen with the size of the inverted region. However, significantly lower fertility was seen in heterozygote invertant strains carrying recombination hotspots within the breakpoints. Altered transcription was observed throughout the genome rather than being overrepresented within the inversions. In spite of the large difference in gene expression in the inverted strains, mitotic fitness was not impaired in the majority of the 94 conditions tested, indicating that the robustness of the expression network buffers the deleterious effects of structural changes in several environments. Overall, our results support the notion that transcriptional changes may compensate for Ty-mediated rearrangements resulting in the maintenance of a constant phenotype, and suggest that large inversions in yeast are unlikely to be a selectable trait during vegetative growth.
Glioblastoma specific antigens, GD2 and CD90, are not involved in cancer stemness

Glioblastoma multiforme (GBM) is the most malignant World Health Organization grade IV brain tumor. GBM patients have a poor prognosis because of its resistance to standard therapies, such as chemotherapy and radiation. Since stem-like cells have been associated with the treatment resistance of GBM, novel therapies targeting the cancer stem cell (CSC) population is critically required. However, GBM CSCs share molecular and functional characteristics with normal neural stem cells (NSCs). To elucidate differential therapeutic targets of GBM CSCs, we compared surface markers of GBM CSCs with adult human NSCs and found that GD2 and CD90 were specifically overexpressed in GBM CSCs. We further tested whether the GBM CSC specific markers are associated with the cancer stemness using primarily cultured patient-derived GBM cells. However, results consistently indicated that GBM cells with or without GD2 and CD90 had similar in vitro sphere formation capacity, a functional characteristics of CSCs. Therefore, GD2 and CD90, GBM specific surface markers, might not be used as specific therapeutic targets for GBM CSCs, although they could have other clinical utilities.
A comparison of neutral landscapes - NK, NKp and NKq

Recent research in molecular evolution has raised awareness of the importance of selective neutrality. Several different models of neutrality have been proposed based on Kauffman's well-known NK landscape model. Two of these models, NKp and NKq, are investigated and found to display significantly different structural properties. The fitness distributions of these neutral landscapes reveal that their levels of correlation with non-neutral landscapes are significantly different, as are the distributions of neutral mutations. In this paper we describe a series of simulations of a hill climbing search algorithm on NK, NKp and NKq landscapes with varying levels of epistatic interaction. These simulations demonstrate differences in the way that epistatic interaction affects the 'searchability' of neutral landscapes. We conclude that the method used to implement neutrality has an impact on both the structure of the resulting landscapes and on the performance of evolutionary search algorithms on these landscapes. These model-dependent effects must be taken into consideration when modelling biological phenomena.
On the Complexity of Link Scheduling in Multi-hop Radio Networks

The problem of efficiently scheduling the links of a multi-hop radio network is studied using a graph theoretic representation. It is shown that link scheduling is NP-complete even when restricted to planar graphs. In contrast to the general case for which no good approximation algorithms are known, we describe a constant times optimal algorithm for the case of planar graphs. For the general case, this algorithm is shown to produce a schedule which is bounded by a length proportional to the graph thickness times optimal. The behaviour of the algorithm is experimentally studied in comparison with existing methods. These results show that the algorithm presented here improves (in terms of worst-case performance and average performance) upon previous methods.
Throughput Analysis of Cognitive MIMO System

In this paper, we consider a simple cognitive MIMO system, in which the cognitive link communicates using two transmission antennas and one receiving antenna. In order to ensure the primary link's transmission unaffected, the cognitive user has to detect the activity of the primary link, and transmit when it senses an idle slot. The maximum stable throughput of the cognitive link in this scenario is derived for a fixed throughput selected by the primary link. In particular, we consider two different scenarios: 1) the ideal system, which assumes that the detection is always correct; 2) the real system, in which detection error occurs due to channel fading. This analysis sheds some light on the research and application of cognitive MIMO technique.