Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemical mapping of cytosines enzymatically flipped out of the DNA helix

Haloacetaldehydes can be employed for probing unpaired DNA structures involving cytosine and adenine residues. Using an enzyme that was structurally proven to flip its target cytosine out of the DNA helix, the HhaI DNA methyltransferase (M.HhaI), we demonstrate the suitability of the chloroacetaldehyde modification for mapping extrahelical (flipped-out) cytosine bases in protein–DNA complexes. The generality of this method was verified with two other DNA cytosine-5 methyltransferases, M.AluI and M.SssI, as well as with two restriction endonucleases, R.Ecl18kI and R.PspGI, which represent a novel class of base-flipping enzymes. Our results thus offer a simple and convenient laboratory tool for detection and mapping of flipped-out cytosines in protein–DNA complexes.
Testing 3D chips containing through-silicon vias

Today's miniaturization and performance requirements result in the usage of high-density integration and packaging technologies, such as 3D Stacked ICs (3D-SICs) based on Through-Silicon Vias (TSVs). Due to their advanced manufacturing processes and physical access limitations, the complexity and cost associated with testing this type of 3D-SICs are considered major challenges. This Embedded Tutorial provides an overview of the manufacturing steps of TSV-based 3D chips and their associated test challenges. It discusses the necessary flows for wafer-level and package-level tests, the challenges with respect to test contents and wafer-level probe access, and the on-chip DfT infrastructure required for 3D-SICs.
Reversible, Fast, and High-Quality Grid Conversions

A new grid conversion method is proposed to resample between two 2-D periodic lattices with the same sampling density. The main feature of our approach is the symmetric reversibility, which means that when using the same algorithm for the converse operation, then the initial data is recovered exactly. To that purpose, we decompose the lattice conversion process into (at most) three successive shear operations. The translations along the shear directions are implemented by 1-D fractional delay operators, which revert to simple 1-D convolutions, with appropriate filters that yield the property of symmetric reversibility. We show that the method is fast and provides high-quality resampled images. Applications of our approach can be found in various settings, such as grid conversion between the hexagonal and the Cartesian lattice, or fast implementation of affine transformations such as rotations.
Calibration of the chaotic interest rate model

In this thesis we establish a relationship between the Potential Approach to interest rates and the Market Models. This relationship allows us to derive the dynamics of forward LIBOR rates and forward swap rates by modelling the state price density. It means that we are able to secure the arbitrage-free condition and positive interest rate feature when we model the volatility drifts of those dynamics. On the other hand, we develop the Potential Approach, particularly the Hughston-Rafailidis Chaotic Interest Rate Model. The early argument enables us to infer that the Chaos Models belong to the Stochastic Volatility Market Models. In particular, we propose One-variable Chaos Models with the application of exponential polynomials. This maintains the generality of the Chaos Models and performs well for yield curves comparing with the NelsonSiegel Form and the Svensson Form. Moreover, we calibrate the One-variable Chaos Model to European Caplets and European Swaptions. We show that the One-variable Chaos Models can reproduce the humped shape of the term structure of caplet volatility and also the volatility smile/skew curve. The calibration errors are small compared with the Lognormal Forward LIBOR Model, the SABR Model, traditional Short Rate Models, and other models under the Potential Approach. After the calibration, we introduce some new interest rate models under the Potential Approach. In particular, we suggest a new framework where the volatility drifts can be indirectly modelled from the short rate via the state price density.
Targeting CD146 in combination with vorinostat for the treatment of ovarian cancer cells

Drug resistance is the predominant cause of mortality in late-stage patients with ovarian cancer. Histone deacetylase inhibitors (HDACis) have emerged as a novel type of second line drug with high specificity for tumor cells, including ovarian cancer cells. However, HDACis usually exhibit relatively low potencies when used as a single agent. The majority of current clinical trials are combination strategies. These strategies are more empirical than mechanism-based applications. Previously, it was reported that the adhesion molecule cluster of differentiation 146 (CD146) is significantly induced in HDACi-treated tumor cells. The present study additionally confirmed that the induction of CD146 is a common phenomenon in vorinostat-treated ovarian cancer cells. AA98, an anti-CD146 monoclonal antibody (mAb), was used to target CD146 function. Synergistic antitumoral effects between AA98 and vorinostat were examined in vitro and in vivo. The potential effect of combined AA98 and vorinostat treatment on the protein kinase B (Akt) pathway was determined by western blotting. The present study found that targeting of CD146 substantially enhanced vorinostat-induced killing via the suppression of activation of Akt pathways in ovarian cancer cells. AA98 in combination with vorinostat significantly inhibited cell proliferation and increased apoptosis. In vivo, AA98 synergized with vorinostat to inhibit tumor growth and prolong survival in ovarian cancer. These data suggest that an undesired induction of CD146 may serve as a protective response to offset the antitumor efficacy of vorinostat. By contrast, targeting CD146 in combination with vorinostat may be exploited as a novel strategy to more effectively kill ovarian cancer cells.
Bimodal brush functionalized TiO2/silicone nanocomposites with improved dielectric properties

Bimodal ligand engineering was applied in TiO2/silicone nanocomposites to independently control the nanoparticle dispersion and interface properties. The introduction of well-dispersed anthracene grafted TiO2 nanoparticles improved the AC breakdown strength and retarded the space charge accumulation in silicone rubber. A candidate mechanism of charge trapping and impact ionization of TiO2 and anthracene is proposed to explain the improvements.
Volatility of agrarian markets aimed at the price development.

Significant price volatility has been observed at the world agri-food markets in these latter years. it has been caused by the triggers of the so-called market shocks that negatively influenced the stability of supply and demand of agri-food commodities. The contribution analyzes the causes of the price volatility incidence, it calls attention to the potential jeopardy of the price volatility transmission on the territory of Slovakia and it finds appropriate measures for its elimination. The price volatility of the Slovak agri-food commodities was reviewed pursuant to the variation coefficient calculation in three consecutive five-year intervals.
Using random shape theory to model blockage in random cellular networks

Shadow fading is severe in downtown areas where buildings are densely located. This paper proposes a stochastic model to quantify blockages due to shadowing, using methods from random shape theory. Buildings inside a cell are modeled as line segments with random sizes and orientations, with locations from a spatial Poisson point process. Dense urban areas can be modeled by the parameters of the line process. Based on this construction, the distribution of the power loss caused by shadowing in a particular path is expressed in closed form. The distribution can be used to compute several performance metrics of interest in random systems. Simulations illustrate coverage and connectivity as a function of the metrics of blockages, such as the density and the average size of buildings.
A Second-Order Markov Random Walk Approach for Collaborative Filtering

Collaborative filtering is the most widely used technique to generate recommendations for an active user by the opinions of the others. However, the challenge is that sometimes the data set is too sparse to identify the similarities of user interests. Random walk on bipartite graphs has been proposed to solve this problem. By exploring transitive association through the first-order Markov process, it is able to find a group of like-minded users for an active user, even if they have no co-rated items. It works for the ratings in binary, but quite often people rate items with numerical scale (e.g. 1-5), which makes it hard to be applied. In this paper, we propose a second-order Markov process to overcome the limitation. Experimental results demonstrate that this approach outperforms the classic collaborative filtering methods with substantial improvements in prediction accuracy and coverage on sparse data set.
BDNF increases release probability and the size of a rapidly recycling vesicle pool within rat hippocampal excitatory synapses

Exerting its actions pre‐, post‐ and peri‐synaptically, brain‐derived neurotrophic factor (BDNF) is one of the most potent modulators of hippocampal synaptic function. Here, we examined the effects of BDNF on a rapidly recycling pool (RRP) of vesicles within excitatory synapses. First, we estimated vesicular release in hippocampal cultures by performing FM4‐64 imaging in terminals impinging on enhanced green fluorescent protein (eGFP)‐labelled dendritic spines – a hallmark of excitatory synapses. Consistent with a modulation of the RRP, BDNF increased the evoked destaining rate of FM4‐64 only during the initial phase of field stimulation. Multiphoton microscopy in acute hippocampal slices confirmed these observations by selectively imaging the RRP, which was loaded with FM1‐43 by hyperosmotic shock. Slices exposed to BDNF showed an increase in the evoked and spontaneous rates of FM1‐43 destaining from terminals in CA1 stratum radiatum, mostly representing excitatory terminals of Schaffer collaterals. Variance‐mean analysis of evoked EPSCs in CA1 pyramidal neurons further confirmed that release probability is increased in BDNF‐treated slices, without changes in the number of independent release sites or average postsynaptic quantal amplitude. Because BDNF was absent during dye loading, imaging, destaining and whole‐cell recordings, these results demonstrate that BDNF induces a long‐lasting enhancement in the probability of transmitter release at hippocampal excitatory synapses by modulating the RRP. Since the endogenous BDNF scavenger TrkB‐IgG prevented the enhancement of FM1‐43 destaining rate caused by induction of long‐term potentiation in acute hippocampal slices, the modulation of a rapidly recycling vesicle pool may underlie the role of BDNF in hippocampal long‐term synaptic plasticity.
Performance Analysis of a Grid-connected High Concentrating Photovoltaic System under Practical Operation Conditions

High concentrating photovoltaic (HCPV) is a promising technique for the practical commercial utilization of solar energy. However, the performance of a HCPV system is significantly influenced by environmental parameters such as solar direct normal irradiance (DNI) level and environmental temperature. This paper analyzes the performance of a 9 kW p grid-connected HCPV system in Kunming (Yunnan, China), during practical field operations over an entire year, and discusses how the environmental parameters influence the performance from both the energy conversion and power inversion perspective. Large variations in the performance of the HCPV system have been observed for different months, due to the respective changes in the environmental parameters. The DNI level has been found to be a dominant parameter that mainly determines the amount of energy production as well as the performance ratio of the HCPV system. The environmental temperature and wind velocity have less influence on the system performance ratio than expected. Based on the performance of the present HCPV system, a quantified correlation between the output power and the direct normal irradiance has been derived, which provides guidelines for both the cogent application and the modeling of HCPV techniques for grid-connected power generation.
The effect of playful experiences on the plasticity and metaplasticity of the brain

The influence of play behavior on the brain was investigated through plasticity and metaplasticity methodology. Regions in both cortical and sub-cortical areas were investigated. Animals in both studies either experienced play with juvenile partners or did not experience play by being paired with an adult. Play experience alone was shown to affect the plasticity in the prefrontal cortex, although it did not show structural changes to sub-cortical regions. If animals were given nicotine after play experiences, the affects of play in the prefrontal cortex were abolished. In addition, playful behaviors appear to prime some sub-cortical regions of the brain for expression of later plasticity. Thus, play appears to alter the structure of multiple brain areas, but do so in different ways.
Efficiency and Stability of Large Agricultural Enterprises

The problem of efficiency and stability of large agricultural enterprises is examined. Despite widespread opinion, based on average data and a priori conclusions, that large enterprises are inefficient, the study of agricultural enterprises in the St. Petersburg Region1 demonstrates that a considerable number of large enterprises are effective, meaning that they have a potential for further growth, which is being put into practice. Moreover, current data show that the efficiency of an enterprise depends pro rata on the number of workers. On the whole, by approximately 50 percent, the efficiency of enterprises is defined by the quality of management. The study also investigates the economic ways in which unprofitable agricultural enterprises survive. The major factors of success of the most effective enterprises include monthly planning of an enterprise's manufacturing and its basic divisions, regular control of expenses, regular monitoring of receipts and expenditures, a system of motivation that depends on specific results on the part of top managers and specialists, and the disposition of profits mainly for investment. Top management's attention to concentration of land and property shares in the hands of enterprise management was unexpectedly low.
The ruddy duck Oxyura jamaicensis in Europe: natural colonization or human introduction?

Native to North America, ruddy ducks Oxyura jamaicensis now occur in 21 countries in the western Palaearctic (including Iceland) and their expanding population threatens the native white‐headed duck, Oxyura leucocephala, through hybridization and possibly competition for food and nest sites. We used mitochondrial DNA sequences and nuclear microsatellites to test whether the European ruddy duck population is descended solely from the captive population in the UK, which traces to seven individuals imported from the USA in 1948, or, alternatively, has been augmented by natural dispersal of birds from North America. Limited genetic diversity in the European population is consistent with a founder population as small as seven birds. In addition, shifts in allele frequencies at several loci, presumably due to genetic drift in the founding population, result in significant differentiation between the European and North American populations. Despite the recent separation of these populations, almost all individuals could be unambiguously assigned based on their composite genotypes, to one of two distinct populations, one comprising all of the European ruddy ducks we sampled (including those from Iceland and captive birds in the UK) and the other comprising all North American samples. Our results confirm that the European ruddy duck population is likely to derive solely from the captive population in the UK and we find no evidence of recent arrivals from North America or of admixture between ruddy ducks from Europe and North America.
On the Iron content in rich nearby Clusters of Galaxies

In this paper we study the iron content of a sample of 22 nearby hot clusters observed with BeppoSAX . W e fi nd that the global iron mass of clusters is tightly related to the cluster luminosity and that the relatively loose correlation between the iron mass and the cluster temperature follows from the combination of the iron mass vs. luminosity and luminosity vs. temperature correlations. The iron mass is found to scale linearly with the intracluster gas mass, implying that the global iron abundance in clusters is roughly constant. This result suggests that enrichment mechanisms operate at a similar rate in all clusters. By employing population synthesis and chemical enrichment models, we show that the iron mass associated with the abundance excess which is always found in the centre of cool core clusters can be entirely produced by the brightest cluster galaxy (BCG), which is always found at the centre of cool core clusters. The iron mass associated with the excess, the optical magnitude of the BCG and the temperature of the cluster are found to correlate with one another suggesting a link between the properties of the BCG and the hosting cluster. These observational facts lends strength to current formation theories which envisage a strong connection between the formation of the giant BCG and its hosting cluster.
Global Capitalism and Sustainable Development

This paper was prepared as a background paper for the panel on "Global Capitalism and Sustainable Development"; in the International Conference on Global Ethos to be held at the United Nations University in Tokyo, Japan, in October 2000. It surveys the major issues involved in defining sustainability, and the relationship thereof to development and the behaviour of capitalist economies. A particular focus throughout, in line with the aims of the conference, is the importance of the fundamental changes in values that are required if sustainability to be achieved and maintained.
Application of a modified real-time PCR technique for relative gene copy number quantification to the determination of the relationship between NKX3.1 loss and MYC gain in prostate cancer.

Gene amplifications and deletions play an important role in the pathogenesis of solid tumors, including prostate cancer. Real-time PCR is a powerful tool for quantitative DNA analysis, particularly when starting quantities of tumor tissue are minimal (1)(2)(3)(4)(5). In the present study, we describe a modification of the 2−ΔΔCT method, which recently was shown to be suitable for relative gene expression analyses (6). We used our technique to analyze prostate cancer cell lines and tissue samples to determine the relationship between homeodomain-containing transcription factor 3.1 (NKX3.1) and MYC gene copy number alterations in this tumor type. The specimens analyzed included (a) blood samples from healthy donors; (b) the prostate cancer cell lines DU145 (ATCC no. HTB-81) and PC3 (ATCC no. CRL-1435) and their derived sublines DU145MN1, PC3-N, and PC3-125-1L (7); (c) the colorectal cell line COLO320DM (ATCC no. CCL-220), which harbors a high-level MYC amplification; and (d) primary prostate adenocarcinoma samples obtained after radical prostatectomy from previously untreated patients. The specimens were histologically verified, and samples were taken as described previously (8). We extracted DNA from the snap-frozen prostate carcinoma samples, blood samples, and cell lines, using the Blood and Cell Culture DNA Midi Kit (Qiagen). We performed quantitative real-time PCR using the LightCycler™ system (Roche Diagnostics) with the FastStart DNA Master SYBR Green I LightCycler Kit (Roche Diagnostics). PCRs were run in duplicate with 20-μL reaction volumes containing 1× SYBR Green I PCR Buffer Mix, 5 mM MgCl2, 0.5 μM each primer, 1× FastStart Taq DNA Polymerase (Roche Diagnostics), and 50 ng of genomic DNA. The cycling conditions are given in Table 1⇓ . The hot start PCR method was applied to prevent incomplete DNA denaturation as discussed by Wilhelm et al. (9). Melting curve analysis was performed …
Chinese-Language Montreal Cognitive Assessment for Cantonese or Mandarin Speakers: Age, Education, and Gender Effects

The Montreal Cognitive Assessment Chinese-Language Los Angeles version (MoCA-ChLA) was developed and administered during an in-home interview to 1,192 participants (mean age 62.5 years, mean education 11.6 years) in a population-based Chinese American Eye Study (CHES) in Los Angeles. The MoCA-ChLA score (mean ± SD) was 23.8 ± 4.2 with little ceiling and no floor effects. The score increased with higher education, decreased with advancing age, and was not related to gender. Compared to the education 1–6 years group, the mean MoCA-ChLA score was 2.6 and 4.6 higher in the education 7–11 and 12–20 years groups, respectively. The Mandarin- (n = 612) and Cantonese- (n = 612) speaking subgroups performed comparably; Cronbach's alpha of the MoCA-ChLA score was 0.78 and 0.79 for these two groups, respectively. Item response theory analysis showed good discriminating power for executive function and memory. These properties support the MoCA-ChLA as a useful screening tool for aging and dementia studies for Mandarin or Cantonese speakers.
Robust state feedback control of LTV systems: Nonlinear is better than linear

Examples of linear control systems with fast time-varying uncertain coefficients arc given, which can be stabilized by a nonlinear memoryless state feedback, but cannot be stabilized by a linear time invariant dynamic state feedback. By means of one of these examples we show that the closed-loop quadratic stability margin may be infinitely smaller than the actual stability margin.
Mental Health and Working Conditions in Europe

The authors investigate recent patterns in mental health at the workplace across 15 European countries using three waves of the European Working Conditions Survey. Their study shows that adverse working conditions, defined in terms of job demands and job hazards, are strongly associated with workers' mental health problems, and it also finds a causal effect of job quality on workers' mental health. Their analysis detects heterogeneous effects across countries and demographic groups and shows that labor market regulations and health care systems explain some of these crosscountry differences.
Matrix Lyapunov inequalities for ordinary and elliptic partial differential equations

This paper is devoted to the study of $L_p$ Lyapunov-type inequalities for linear systems of equations with Neumann boundary conditions and for any constant $p \geq 1$. We consider ordinary and elliptic problems. The results obtained in the linear case are combined with Schauder fixed point theorem to provide new results about the existence and uniqueness of solutions for resonant nonlinear problems. The proof uses in a fundamental way the nontrivial relation between the best Lyapunov constants and the minimum value of some especial minimization problems.
An overview of process query systems

Process Query Systems (PQS) are a new kind of information retrieval technology in which user queries are expressed as process descriptions. The goal of a PQS is to detect the processes using a datastream or database of events that are correlated with the processes' states. This is in contrast with most traditional database query processing, information retrieval systems and web search engines in which user queries are typically formulated as Boolean expressions. In this paper, we outline the main features of Process Query Systems and the technical challenges that process detection entails. Furthermore, we describe several importance application areas that can benefit from PQS technology. Our working prototype of a PQS, called TRAFEN (for TRAcking and Fusion ENgine) is described as well.