Miracle-dz/UniFAR-FTUs huggingface dataset:
Studying the epigenome using next generation sequencing

The advances in next generation sequencing (NGS) technologies have had a significant impact on epigenomic research. The arrival of NGS technologies has enabled a more powerful sequencing based method—that is, ChIP-Seq—to interrogate whole genome histone modifications, improving on the conventional microarray based method (ChIP-chip). Similarly, the first human DNA methylome was mapped using NGS technologies. More importantly, studies of DNA methylation and histone modification using NGS technologies have yielded new discoveries and improved our knowledge of human biology and diseases. The concept that cytosine methylation was restricted to CpG dinucleotides has only been recently challenged by new data generated from sequencing the DNA methylome. Approximately 25% of all cytosine methylation identified in stem cells was in a non-CG context. The non-CG methylation was more enriched in gene bodies and depleted in protein binding sites and enhancers. The recent developments of third generation sequencing technologies have shown promising results of directly sequencing methylated nucleotides and having the ability to differentiate between 5-methylcytosine and 5-hydroxymethylcytosine. The importance of 5-hydroxymethylcytosine remains largely unknown, but it has been found in various tissues. 5-hydroxymethylcytosine was particularly enriched at promoters and in intragenic regions (gene bodies) but was largely absent from non-gene regions in DNA from human brain frontal lobe tissue. The presence of 5-hydroxymethylcytosine in gene bodies was more positively correlated with gene expression levels. The importance of studying 5-methylcytosine and 5-hydroxymethylcytosine separately for their biological roles will become clearer when more efficient methods to distinguish them are available.
Interaction between a history of depression and rumination on neural response to emotional faces

Background Both past depressive episodes and the personality trait of depressive rumination are strong risk factors for future depression. Depression is associated with abnormal emotional processing, which may be a neurobiological marker for vulnerability to depression. A consistent picture has yet to emerge as to how a history of depression and the tendency to ruminate influence emotional processing. The aim of this study was to investigate the relationship between rumination, past depression and neural responses when processing face emotions. Method The Ruminative Responses Scale (RRS) was completed by 30 remitted depressives and 37 controls who underwent functional magnetic resonance imaging (fMRI) scanning while viewing happy, sad, fearful and neutral faces. Results The remitted depressives showed overall reductions in neural responses to negative emotions relative to the controls. However, in the remitted depressives, but not the controls, RRS scores were correlated with increased neural responses to negative emotions and decreased responses to happiness in limbic regions. Conclusions Automatic emotion processing biases and rumination seem to be correlated to aspects of vulnerability to depression. However, remission from depression may be maintained by a general suppression of limbic responsiveness to negative emotion.
Structural changes in myosin motors and filaments during relaxation of skeletal muscle

Structural changes in myosin motors and filaments during relaxation from short tetanic contractions of intact single fibres of frog tibialis anterior muscles at sarcomere length 2.14 μm, 4°C were investigated by X‐ray diffraction. Force declined at a steady rate for several hundred milliseconds after the last stimulus, while sarcomere lengths remained almost constant. During this isometric phase of relaxation the intensities of the equatorial and meridional M3 X‐ray reflections associated with the radial and axial distributions of myosin motors also recovered at a steady rate towards their resting values, consistent with progressive net detachment of myosin motors from actin filaments. Stiffness measurements confirmed that the fraction of motors attached to actin declined at a constant rate, but also revealed a progressive increase in force per motor. The interference fine structure of the M3 reflection suggested that actin‐attached myosin motors are displaced towards the start of their working stroke during isometric relaxation. There was negligible recovery of the intensities of the meridional and layer‐line reflections associated with the quasi‐helical distribution of myosin motors in resting muscle during isometric relaxation, and the 1.5% increase in the axial periodicity of the myosin filament associated with muscle activation was not reversed. When force had decreased to roughly half its tetanus plateau value, the isometric phase of relaxation abruptly ended, and the ensuing chaotic relaxation had an exponential half‐time of ca 60 ms. Recovery of the equatorial X‐ray intensities was largely complete during chaotic relaxation, but the other X‐ray signals recovered more slowly than force.
Base Transformation With Injective Residue Mapping for Dynamic Range Reduction in RNS

Many RNS-based implementations of digital signal processing algorithms have experienced the overkill of arithmetic operator sizes due to the choice of moduli set to accommodate for the occasional high precision operations. As the sizes of modulo arithmetic operators are fixed by the choice of their moduli, they are not scalable even if there is a subsequent reduction in the dynamic range. This paper introduces the notion of base transformation to complement residue scaling in reducing the overall arithmetic processing costs of multi-base RNS. A new algorithm is proposed to directly map the residues of signed integers from one modulo-arithmetic friendly base S1 ≡ {2n-1, 2n+k, 2n+1} to another S2 ≡ {2n-α-1, 2n+k-α, 2n-α+1}, to reduce the word lengths of residue arithmetic operators by α bits along with the reduction of dynamic range. It infers the quantized segment in S2 directly from the quantized segment of the input residues in S1 to avoid the complex reverse conversion and sign detection operations. Our synthesis results show that its VLSI implementation efficiency, in terms of area-delay product and energy consumption, outperforms the best possible improvised solution and the approach of removing one modulus channel. Noticeably, the improvements enhance with increasing α.
Adaptive feedforward cancellation for nonlinear systems using RLLM networks

An algorithm for adaptive feedforward cancellation (AFC) of high frequency measurable disturbances for a class of nonlinear dynamical systems is developed. A rectangular local linear model (RLLM) network is used to model nonlinear dynamical behaviour of the system and to predict the effect of the disturbances. Another network of the same kind containing local linear compensation units is used as a feedforward controller based on the prediction mentioned above. This scheme is appended with a feedback controller for the sake of better tracking performance.
Subcell Modeling of Frequency-Dependent Thin Layers in the FDTD Method

A subcell modeling technique for frequency-dependent thin layers in finite-difference time-domain method is introduced. The proposed method is based on the application of the integral form of the Maxwell-Ampere equation and the solution of a set of auxiliary equations to advance the field components. It has the ability to handle one or several frequency-dependent thin layers embedded in a frequency-dependent medium without solving high-order differential equations. To validate our proposed method, we compare the obtained results with analytical solutions and with numerical references in both time domain and frequency domain.
Synergistic effects of tacrolimus and human interferon-alpha A/D in murine viral myocarditis.

The effects of interferon-alpha A/D (IFN) therapy in combination with various immunosuppressants were investigated in a murine model of viral myocarditis. Viral infection is an important cause of morbidity in immunocompromised hosts and transplant recipients. Human IFN therapy reduces viral replication, reducing the virus-induced myocardial destruction. Groups consisting of 25 C3H/He mice received i.p. injections of prednisolone, azathioprine, 15-deoxyspergualin, cyclosporine or tacrolimus (FK506), for 16 days beginning 2 days before inoculation with 500 plaque-forming units of encephalomyocarditis virus (EMCV). IFN, 10(4) U/g daily, was administered i.p. alone or in combination with immunosuppressants to separate groups of mice beginning on the day of viral inoculation. Animals were sacrificed at random at 4 or 10 days after inoculation with EMCV. The survival rate was significantly higher in mice treated with azathioprine, 15-deoxyspergualin, cyclosporine or FK506 in combination with IFN than in infected controls (P < .01) and was similar to the rate in the IFN monotherapy group. Survival in mice treated with prednisolone resembled that in infected controls and was significantly lower than in mice treated with IFN (P < .01). Heart weight was lower and cellular infiltration in the myocardium was reduced in mice treated with both FK506 and IFN compared with mice given IFN monotherapy. The results suggest that the effect of IFN therapy in viral myocarditis differs depending on which immunosuppressants is used. The findings suggest that the combination of FK506 and IFN may have beneficial effects in hosts with viral myocarditis by reducing cellular infiltration of heart.
Genetics of intracisternal-A-particle-related envelope-encoding proviral elements in mice

Intracisternal-A-particle-related envelope-encoding (IAPE) proviral elements in the mouse genome encode and express an envelope-like protein that may allow transmission of IAPEs as infectious agents. To test IAPE mobility and potential transmission in mice, we have analyzed the distribution of IAPE elements in the genomes of Mus spretus and Mus musculus inbred strains and wild-caught animals. Potential full-length (IAPE-A) proviral elements are present as repetitive copies in DNA from male but not female animals of M. musculus inbred strains and Mus musculus castaneus. Analysis of IAPE-cellular junction fragments indicates that fixation of most IAPEs in the germ line occurred in M. musculus and M. spretus after speciation but before M. musculus inbred strains were derived.
How does insertion in global value chains affect upgrading in industrial clusters?

Humphrey J. and Schmitz H. (2002) How does insertion in global value chains affect upgrading in industrial clusters? , Reg. Studies 36, 1017–1027. What is the scope for local upgrading strategies where producers operate in global value chains? The literature on industrial clusters emphasizes the role of inter-firm co-operation and local institutions in enabling upgrading. The value chain literature focuses on the role of global buyers and chain governance in defining upgrading opportunities. This paper argues that clusters are inserted into global value chains in different ways, and that this has consequences for enabling or disabling local-level upgrading efforts. It pays particular attention to the position of developing country firms selling to large, global buyers.
Institutional Innovation in Central Europe

analyze the following successful institutional innovations: Building entirely new institutions: the case of a new Slovakian institute, the Academia Istropolitana, represents one of the most ambitious undertakings. There, the leaders’ main goal has been to challenge traditional higher educational institutions by responding more flexibly to the demands of the labor market and offering training in previously “obscure” programs like public administration, applied economics or environmental policy. Peter Darvar Peter Dorror, Visiting Fellow, at the Institute for Human Sciences, Spittelauer lande 3, A-I090 Vienna, Aurfria, fel: (43 I J 3 13 58-0, fax: (43 I j 3 I3 58-30, m o i l : pda~as@iiwm.univie. acot].
Characterization of horse plasma gelsolin.

Gelsolin can be purified from horse blood plasma by treating the plasma sequentially with an anion-exchange medium in the presence and then the absence of free Ca2+. The purified gelsolin migrates as a 90-kilodalton protein on electrophoresis in polyacrylamide gels in the presence of sodium dodecyl sulfate. It has an absorption coefficient of 1.4 mL/(mg.cm) and is similar in amino acid composition to other plasma gelsolins. Horse plasma gelsolin has an intrinsic sedimentation coefficient of 4.8S and a Stokes' radius of 3.8 nm. Hydrodynamic calculations suggest it to be a rather globular protein of 75,000 relative mass, a value similar to those calculated for human and pig plasma gelsolins from their amino acid sequences. Horse plasma gelsolin is able to nucleate actin polymerization, i.e., to abolish the lag observed between the initiation of polymerization of monomeric actin by the addition of salts and the rapid elongation phase of actin filament growth. This nucleation activity also results in lower final viscosities of F-actin solutions, as the existence of a larger number of filaments in samples that contain gelsolin requires that their average length be shorter.
Quality and Property Performance

Quality and profit are often considered to be connected. The property market is one in which the concept often arises. For example, the definition of prime property is a quality judgement. In property development, the production of high‐quality property may be thought to improve returns, or to reduce risk. Considers the question whether (and if so, how) quality in property development (excluding site factors) is likely to lead to high returns. Recently published work defines quality as resistance to depreciation, where depreciation is defined in purely financial (return) terms. Fully considers this work, which concentrates on offices and industrials. Extends this work, describing new research which considers the application of the relevant concepts and quality definitions to shopping centres. Quality and cost are also considered to be connected. In property development, high construction costs may be expected to produce quality. This produces a complex subsidiary question concerning this relationship, whi.
Higher-order Beliefs in Simple Trading Models

We examine the role of higher order beliefs in asset markets where coordination between a buyer and seller can lead to gains to trade. The scenarios are modeled such that trader’s strategies do not only depend upon their beliefs of underlying economic phenomena, but also upon the others’ beliefs regarding the beliefs of themselves. Under certain parameters the breakdown of coordination is predicted–even when both traders are certain the underlying phenomena dictates trade is advantageous. We demonstrate the equilibrium predictions can be constructed via a small number of iterated thought exercises. The experimental design allows us to control for various behavioral phenomena and examine subjects’ decisions across different accounting regimes as to tease out strategic uncertainty due solely to information asymmetry. In this setting we find evidence supporting higher order beliefs. An implication is that the lack of uniformity leads to lack of common knowledge of the beliefs of others, which in turn leads to the spreading of inefficient outcomes.
Epidermal Growth Factor Receptor Mutations and Their Correlation with Gefitinib Therapy in Patients with Non-small Cell Lung Cancer: A Meta-Analysis Based on Updated Individual Patient Data from Six Medical Centers in Mainland China

Background: Convincing data on epidermal growth factor receptor (EGFR) mutations in Chinese patients with non-small-cell lung cancer (NSCLC) remain limited. We investigated the relevance of demographic characteristics and EGFR mutations, correlations between the efficacy of gefitinib and EGFR mutations in NSCLC, and to identify individuals who would likely benefit from gefitinib. Methods: We conducted a meta-analysis based on updated individual patient data from six medical centers in mainland China. Outcome measures included the EGFR mutation status, demographic characteristics, response, and survival. Results: Among 506 patients with NSCLC who received EGFR mutation analysis, the EGFR mutation rate was 30.04%. Patients with adenocarcinoma had a higher mutation rate than those with non-adenocarcinoma (44.1% vs 9.2%; p < 0.00001). The EGFR mutation rate for smokers was 15.1%, lower than that for non-smokers (45.5%) (p < 0.00001). Male patients had a lower mutation rate than female patients (23.1% vs 42.9%; p < 0.0001). Multivariate analysis showed that “adenocarcinoma” and “non-smoker” were independent predictors of EGFR mutations. In a subgroup of 57 patients with complete treatment data, the response rate to gefitinib in the EGFR mutant group was 60.7%, significantly higher than that in the wild-type EGFR group (17.2%) (odds ratio, 5.78; 95% CI, 1.95–17.13; p = 0.002). “EGFR mutation”, “adenocarcinoma,” and “non-smoker” were independent predictors of response. Overall survival in the EGFR mutant group and the wild-type group did not differ significantly (hazard ratio, 0.60; 95% CI, 0.32–1.12; p = 0.110). “Adenocarcinoma status” was an independent prognostic factor for survival. Conclusions: In mainland China, “adenocarcinoma” and “non-smoker” are independent predictors for EGFR mutations. Response to gefitinib favors patients with EGFR mutations. The clinical selected populations for gefitinib are non-smokers with adenocarcinoma.
Finite-time analysis of the multi-armed bandit problem with known trend

We study here an a problem called “the multi-armed bandit problem with known trend”, where an agent knows the shape of the reward function of each arm but not its distribution. This problem is motivated by different real world tasks, where when an arm is sampled by the model the received reward change according to a known trend. By adapting the standard multi-armed bandit algorithms, we propose to study the regret upper bounds of three algorithms: the two first one assumes a stochastic model; and the last one is based on a Bayesian approach.
Forensic Tracking and Surveillance: Algorithms for Homogeneous and Heterogeneous Settings

Digital forensics is an emerging field that has uniquely brought together academics, practitioners and law enforcement. Research in this area was inspired by the numerous challenges posed by the increased sophistication of criminal tools. Traditionally, digital forensics has been confined to the extraction of digital evidence from electronic devices. This direct extraction of digital evidence, however, no longer suffices. Indeed, extracting completely raw data without further processing and/or filtering is, in some cases, useless. These problems can be tackled by the so-called “computational forensics” where the reconstructs evidence are undertaken further processing. One important application of computational forensics is criminal tracking, which we collectively call “forensic tracking” and is the main subject of this thesis. This thesis adopts an algorithmic approach to investigate the feasibility of conducting forensic tracking in various environments and settings. Unlike conventional tracking, forensic tracking has to be passive such that the target (who is usually a suspect) should not be aware of the tracking process. We begin by adopting pedestrian setting and propose several online (real-time) forensic tracking algorithms to track a single or multiple targets passively. Beside the core tracking algorithms, we also propose other auxiliary algorithms to improve the robustness and resilience of tracking. We then extend the scope and consider vehicular forensic tracking, where we investigate both online and offline tracking. In online vehicular tracking, we also propose algorithms for motion prediction to estimate the near future movement of target vehicles. Offline vehicular tracking, on the other hand, entails the post-hoc extraction and probabilistic reconstruction of vehicular traces, which we adopt Bayesian approach for. Finally, the contributions of the thesis concludes with building an algorithmic solution for multi-modal tracking, which is a mixed environment combining both pedestrian and vehicular settings.
How Knowledge, Policy Planning, and Implementation Succeed or Fail: The Jatropha Projects in Tanzania

Promoting successful biofuel production in developing economies requires an appreciation of local culture. In Tanzania, where soaring economic expectations have accompanied disappointing commercial outcomes, contemporary project managers would do well to adopt inclusive agricultural planning strategies. Overlooked in the past, Tanzania's farmers now demand a place at the project planning table. Meanwhile, the Tanzanian government has called on the Japan International Cooperation Agency to assess local obstacles to economic development. Strongly influenced by Professor Ikujiro Nonaka, the Japan International Cooperation Agency's methodology suggests community participation and local management are central to project success, and both are vital to assessing success and failure in Tanzania's Jatropha biofuel industry.
Evolutionary mechanisms shaping the genetic population structure of marine fishes; lessons from the European flounder (Platichthys flesus L.)

A number of evolutionary mechanisms have been suggested for generating low but significant genetic structuring among marine fish populations. We used nine microsatellite loci and recently developed methods in landscape genetics and coalescence‐based estimation of historical gene flow and effective population sizes to assess temporal and spatial dynamics of the population structure in European flounder (Platichthys flesus L.). We collected 1062 flounders from 13 localities in the northeast Atlantic and Baltic Seas and found temporally stable and highly significant genetic differentiation among samples covering a large part of the species’ range (global FST = 0.024, P < 0.0001). In addition to historical processes, a number of contemporary acting evolutionary mechanisms were associated with genetic structuring. Physical forces, such as oceanographic and bathymetric barriers, were most likely related with the extreme isolation of the island population at the Faroe Islands. A sharp genetic break was associated with a change in life history from pelagic to benthic spawners in the Baltic Sea. Partial Mantel tests showed that geographical distance per se was not related with genetic structuring among Atlantic and western Baltic Sea samples. Alternative factors, such as dispersal potential and/or environmental gradients, could be important for generating genetic divergence in this region. The results show that the magnitude and scale of structuring generated by a specific mechanism depend critically on its interplay with other evolutionary mechanisms, highlighting the importance of investigating species with wide geographical and ecological distributions to increase our understanding of evolution in the marine environment.