Miracle-dz/UniFAR-FTUs huggingface dataset:
The Causal-Compositional Concept of Information Part I. Elementary Theory: From Decompositional Physics to Compositional Information

This first part of the study introduces an elementary concept of information. Our interest for newness, our curiosity in the new, will be considered as a main building block of information, and of reality itself. A typical definition of information (the reduction of uncertainty) needs to be fundamentally inverted: Information is a compositional activity, including the inconsistent, the paradox, the contradiction and the incoherent meaning. This study expands on the analysis of the composition of new structure (new macrophysical laws), and the analysis of the causality and causal state of such structures (“causally active symbols”). The classical, scientific-objective, passive understanding of information gives meaning to the fact that modern information technology does not by itself lead to an increase of human values. However, our social and moral stance is an informational one, and our informational, active conscious process holds the power to mediate and to enforce this process towards an enriched life. The indicator for such enrichment is given to us by information, and the knowledge about this process will feed us with energy to move towards an active spirit of ethics, and towards the information society. Part I of this study expands on the fundament basis and on our intrinsic responsibility to release the forces that are based on the active dimension of information. Those forces are required in order to reveal the so-called information society from its metaphorical character (Part II).
cGraph: A Fast Graph-Based Method for Link Analysis and Queries

Many techniques in the social sciences and graph theory deal with the problem of examining and analyzing patterns found in the underlying structure and associations of a group of entities. However, much of this work assumes that this underlying structure is known or can easily be inferred from data, which may often be an unrealistic assumption for many real-world problems. Below we consider the problem of learning and querying a graph-based model of this underlying structure. The model is learned from noisy observations linking sets of entities. We explicitly allow different types of links (representing different types of relations) and temporal information indicating when a link was observed. We quantitatively compare this representation and learning method against other algorithms on the task of predicting future links and new “friendships” in a variety of real world data sets.
Proprotein convertases: lessons from knockouts

The physiological role of the subtilisin/kexin‐like proprotein convertases (PCs) in rodents has been examined through the use of knockout mice. This review will summarize the major in vivo defects that result from the disruption of the expression of their genes. This includes abnormal embryonic development, hormonal disorder, infertility, and/or modified lipid/sterol metabolism. Members of the PC family play a central role in the processing of various protein precursors ranging from hormones and growth factors to bacterial toxins and viral glycoproteins. Proteolysis occurring at basic residues is mediated by the basic amino acid‐specific proprotein convertases, namely: PC1/3, PC2, furin, PACE4, PC4, PC5/6, and PC7. In contrast, proteolysis at nonbasic residues is performed by the subtilisin/kexin‐like isozyme‐1 (SKI‐1/S1P) and the newly identified neural apoptosis‐regulated convertase‐ 1 (PCSK9/NARC‐1). In addition to their requirement for many physiological processes, these enzymes are also involved in various pathologies such as cancer, obesity, diabetes, lipid disorders, infectious diseases, atherosclerosis and neurodegenerative diseases. —Scamuffa, N. , Calvo, F. , Chrétien, M. , Seidah, N. G. , Khatib, A‐M. Proprotein convertases: lessons from knockouts. FASEB J. 20, 1954–1963 (2006)
A Modified Richardson-Lucy Method for Space-Variant Motion Deblurring

Space-variant motion deblurring is a key component in image processing system. Previous deblurring methods often do not hold in practice due to the space-variant motion blur in the imaging process. In this paper, we presented a modified Richardson-Lucy method for removing space-variant motion blur from a single image, which is also effective for typical space-invariant motion deblurring. Comprehensive compare-sons on a number of synthetic and real-world blurred images show that our method leads to better deblurring performance.
Probabilistic Global Motion Estimation Based on Laplacian Two-Bit Plane Matching for Fast Digital Image Stabilization

Digital image stabilization (DIS) is a technique to prevent images captured by a handheld camera from temporal fluctuation. This paper proposes a new DIS algorithm that reduces the computation time while preserving the accuracy of the algorithm. To reduce the computation time, an image is transformed by a Laplacian operation and then converted into two one-bit spaces, called and spaces. The computation time is reduced because only two-bits-per-pixel are used while the accuracy is maintained because the Laplacian operation preserves the edge information which can be efficiently used for the estimation of camera motion. Either two or four subimages in the corners of an image frame are selected according to the type of the image and five local motion vectors with their probabilities to be a global motion vector are derived for each subimage. The global motion vector is derived from these local motion vectors based on their probabilities. Experimental results show that the proposed algorithm achieves a similar or better accuracy than a conventional DIS algorithm using a local motion estimation based on a full-search scheme and MSE criterion while the complexity of the proposed algorithm is much less than the conventional algorithm.
Investigation of the nonlocal coherent-potential approximation

Recently the nonlocal coherent-potential approximation (NLCPA) has been introduced by Jarrell and Krishnamurthy for describing the electronic structure of substitutionally-disordered systems. The NLCPA provides systematic corrections to the widely used coherent-potential approximation (CPA) whilst preserving the full symmetry of the underlying lattice. Here an analytical and systematic numerical study of the NLCPA is presented for a one-dimensional tight-binding model Hamiltonian, and comparisons with the embedded cluster method (ECM) and molecular coherent potential approximation (MCPA) are made. PACS numbers: 71.23-k, 71.15-m Submitted to: J. Phys.: Condens. Matter
On the Optimal Sample Complexity for Best Arm Identification

We study the best arm identification (BEST-1-ARM) problem, which is defined as follows. We are given $n$ stochastic bandit arms. The $i$th arm has a reward distribution $D_i$ with an unknown mean $\mu_{i}$. Upon each play of the $i$th arm, we can get a reward, sampled i.i. d. from $D_i$. We would like to identify the arm with the largest mean with probability at least $1-\delta$, using as few samples as possible. We provide a nontrivial algorithm for BEST-1-ARM, which improves upon several prior upper bounds on the same problem. We also study an important special case where there are only two arms, which we call the sign problem. We provide a new lower bound of sign, simplifying and significantly extending a classical result by Farrell in 1964, with a completely new proof. Using the new lower bound for sign, we obtain the first lower bound for BEST-1-ARM that goes beyond the classic Mannor-Tsitsiklis lower bound, by an interesting reduction from Sign to BEST-1-ARM. We propose an interesting conjecture concerning the optimal sample complexity of BEST-1-ARM from the perspective of instance-wise optimality.
Comparative study on ChIP-seq data: normalization and binding pattern characterization

MOTIVATION Antibody-based Chromatin Immunoprecipitation assay followed by high-throughput sequencing technology (ChIP-seq) is a relatively new method to study the binding patterns of specific protein molecules over the entire genome. ChIP-seq technology allows scientist to get more comprehensive results in shorter time. Here, we present a non-linear normalization algorithm and a mixture modeling method for comparing ChIP-seq data from multiple samples and characterizing genes based on their RNA polymerase II (Pol II) binding patterns. RESULTS We apply a two-step non-linear normalization method based on locally weighted regression (LOESS) approach to compare ChIP-seq data across multiple samples and model the difference using an Exponential-Normal(K) mixture model. Fitted model is used to identify genes associated with differential binding sites based on local false discovery rate (fdr). These genes are then standardized and hierarchically clustered to characterize their Pol II binding patterns. As a case study, we apply the analysis procedure comparing normal breast cancer (MCF7) to tamoxifen-resistant (OHT) cell line. We find enriched regions that are associated with cancer (P < 0.0001). Our findings also imply that there may be a dysregulation of cell cycle and gene expression control pathways in the tamoxifen-resistant cells. These results show that the non-linear normalization method can be used to analyze ChIP-seq data across multiple samples. AVAILABILITY Data are available at http://www.bmi. osu.edu/~khuang/Data/ChIP/RNAPII/.
On the impact of duty cycle on the estimation of spatial fields with compressed observations in M2M capillary networks

In this paper, we focus on the use capillary M2M (Machine-to-Machine) networks for the estimation of spatial random fields. The observations (samples) collected by the sensors are spatially correlated and, for this reason, we propose a distributed pre-coding scheme based on the Karhunen-Loève (KL) transform. This allows us to obtain an over-the-air compressed representation of such set of observations. We assume that sensors operate with (independent) duty-cycles and we derive a closed-form expression of the optimal power allocation strategy which minimizes the estimation error for a given power constraint. For benchmarking purposes, we also assess the performance of another scheme based on a particularization of the partial KL transform.
Abstract Line Drawings from 2D Images

We present a novel scheme for automatically generating line drawings from 2D images, aiming to facilitate effective visual communication. In contrast to conventional edge detectors, our technique imitates the human line drawing process and consists of two parts: line extraction and line rendering. We propose a novel line extraction method based on likelihood-function estimation, which effectively finds the genuine shape boundaries. We consider the feature scale and the blurriness of lines with which the detail and the focus-level of lines are controlled in the rendering. We also employ stroke textures to provide a variety of illustration styles. Experimental results demonstrate that our technique generates various kinds of line drawings from 2D images enabled by the control over detail, focus, and style.
Increased ω6-Containing Phospholipids and Primary ω6 Oxidation Products in the Brain Tissue of Rats on an ω3-Deficient Diet

Polyunsaturated fatty acyl (PUFA) chains in both the ω3 and ω6 series are essential for normal animal brain development, and cannot be interconverted to compensate for a dietary deficiency of one or the other. Paradoxically, a dietary ω3-PUFA deficiency leads to the accumulation of docosapentaenoate (DPA, 22:5ω6), an ω6-PUFA chain that is normally scarce in the brain. We applied a high-precision LC/MS method to characterize the distribution of DPA chains across phospholipid headgroup classes, the fatty acyl chains with which they were paired, and the extent to which they were oxidatively damaged in the cortical brain of rats on an ω3-deficient diet. Results indicate that dietary ω3-PUFA deficiency markedly increased the concentrations of phospholipids with DPA chains across all headgroup subclasses, including plasmalogen species. The concentrations of phospholipids containing docosahexaenoate chains (22:6ω3) decreased 20–25%, while the concentrations of phospholipids containing arachidonate chains (20:4ω6) did not change significantly. Although DPA chains are more saturated than DHA chains, a larger fraction of DPA chains were monohydroxylated, particularly among diacyl-phosphatidylethanolamines and plasmalogen phosphatidylethanolamines, suggesting that they were disproportionately subjected to oxidative stress. Differences in the pathological significance of ω3 and ω6 oxidation products suggest that greater oxidative damage among the ω6 PUFAs that increase in response to dietary ω3 deficiency may have pathological significance in Alzheimer’s disease.
A file system interface for concurrent access

The paper introduces a transparent service . for synchronized replication across loosely-connected, heterogeneous file systems, and it focuses on the part of the service that supports transactional synchronization. The transaction paradigm is useful for grouping together the file accesses in a program that are logically connected, such that each group of accesses is synchronized as an atomic unit. The service, Parrot, is implemented as a library that an application links and runs in its own address space. The library redefines and extends the file system interface open/close/read/write, while preserving its syntax and semantics. Parrot implements a read-one write-all synchronization protocol that (1) guarantees consistency across all copies of each replicated file at the granularity of individual read and write operations and (2) supports transactional synchronization for sequences of read and write operations on one or more files.
An algorithm for the eigenvalue perturbation problem: reduction of a κ-matrix to a Lidskii matrix

In this article, we present an algorithmic approach to the eigenvalue perturbation problem. We show that any matrix perturbation <italic>A</italic>(<italic>ε</italic>) of an arbitrary nilpotent Jordan canonical form <italic>J</italic> with all eigenvalues having an order of the form O(<italic>ε</italic><supscrpt>1/(a positive integer)</supscrpt>) is similar to a matrix perturbation <italic>Atilde;</italic>(<italic>ε</italic>) in Arnold normal form that can be seen as generic. Calling <italic>A</italic>(<italic>ε</italic>) a <italic>&kgr;</italic>-matrix and <italic>Atilde;</italic>(<italic>ε</italic>) a Lidskii-Arnold matrix, we also provide a reduction algorithm for the computation of the Lidskii-Arnold form of a <italic>&kgr;</italic>-matrix. It is based on the minimization of the leading Jordan structure <italic>J</italic> and on Lidskii's genericity conditions for perturbed eigenvalues.
Understanding Trust and Security

This article is a literature survey on trust theory, the relationship between trust and security and distribution of trust in networks, especially in distributed and open networks. The article is divided into three sections: trust theory, security principles and trust distribution. The trust theory section looks at the theoretical aspects of trust and shows some of the methods researchers use to quantify trust. The security theory section explains the fundamentals of security and tries to establish a relationship between security and trust. This section also attempts to highlight the significance of trust in distributed network security. The final section considers ad hoc networks as one of the latest paradigms in wireless networking and looks at some proposals and initiatives aimed at establishing trust distribution in ad hoc networks.
Mitochondrial membrane lipidome defines yeast longevity

Our studies revealed that lithocholic acid (LCA), a bile acid, is a potent anti-aging natural compound that in yeast cultured under longevity-extending caloric restriction (CR) conditions acts in synergy with CR to enable a significant further increase in chronological lifespan. Here, we investigate a mechanism underlying this robust longevity-extending effect of LCA under CR. We found that exogenously added LCA enters yeast cells, is sorted to mitochondria, resides mainly in the inner mitochondrial membrane, and also associates with the outer mitochondrial membrane. LCA elicits an age-related remodeling of glycerophospholipid synthesis and movement within both mitochondrial membranes, thereby causing substantial changes in mitochondrial membrane lipidome and triggering major changes in mitochondrial size, number and morphology. In synergy, these changes in the membrane lipidome and morphology of mitochondria alter the age-related chronology of mitochondrial respiration, membrane potential, ATP synthesis and reactive oxygen species homeostasis. The LCA-driven alterations in the age-related dynamics of these vital mitochondrial processes extend yeast longevity. In sum, our findings suggest a mechanism underlying the ability of LCA to delay chronological aging in yeast by accumulating in both mitochondrial membranes and altering their glycerophospholipid compositions. We concluded that mitochondrial membrane lipidome plays an essential role in defining yeast longevity.
Study of Multiphase Flow at the Suction of Screw Compressor

Screw compressors are commonly used for industrial and commercial gas processing and refrigeration. These machines are known to be able to admit mixtures of gasses and liquids to a certain concentration. In oil injected compressors, oil is mostly injected in the working domain to seal, cool and lubricate. But would the injection of atomized oil or other liquid in the suction of the compressor be useful for better control of the discharge temperature and reduction in energy consumption, is still to be determined. Similarly, liquid neutral to the process may be injected in an oil free compressor suction to help controlling discharge temperature. It can be erosive and corrosive to the compressor rotors. Therefore mapping a two phase suction flow of a screw compressor may help in understanding the means to improve compressors efficiency and reliability. This paper is the initial phase of PhD program to determine the multiphase flow characteristic at suction of twin screw compressors by means of experimental techniques. Review of most common and up to date measurement techniques in field of multiphase flow was carried out to determine their suitability and feasibility. Also Modelling of single and multiphase flow at the suction domain of a twin screw compressor were performed in order to have a better understanding of flow distribution. The research is performed on an oil free screw compressor with “N” rotor profiles of 128 mm and configuration of 3/5 lobes with L/D of 1.6 and 93 mm centre distance. A simplified CFD model of only suction domain which reduces computational time was compared with the CFD model of the entire compressor and it was found that it predicts most of flow features with same accuracy. The experimental study which will be used to validate the CFD model has been presented.
Sérsic properties of disc galaxy mergers

Sersic parameters characterizing the density profiles of remnants formed in collisionless disc galaxy mergers are obtained; no bulge is included in our simulations. The Sersic index range for the luminous matter, n ∈ (1.7, 5.2), is similar to that found in early-type galaxies, for about the same luminous mass range, while the effective radius tends to be higher, R e ∈ (1.6, 12.3) kpc. A strong correlation of n with the central projected surface density I 0 is found, n ∝ I 0.14 0 , which is consistent with observations. No strong positive linear correlation between the size, R e , and structure, n, of our remnants is found. The derived scaling of the index n with luminous mass, n ∝ M 0.20 L , compares favourably with its observational counterpart, n ∝ L 0.27 . The dependence of the effective radius with luminous mass for our remnants, R e ∝ M 0.48 L , compares well with that determined from early-type galaxies of the Sloan Digital Sky Survey, R e ∝ M 0.56 L . The photometric plane scaling found for the luminous component, n oc R 0.14 e I 0.13 0 , assuming a constant stellar mass-to-light ratio, is consistent with that determined for ellipticals in the B band, n ∝ R 0.09 e I 0.15 0 , and for K-band remnants, n ∝ R 0.11 e I 0.14 0 . We find that the surface defined by Sersic parameters {n, R e , μ 0 } in log space is not a true plane, but a pseudo-plane with a small curvature at low values of n owed to intrinsic properties of the Sersic model. The dark haloes of our remnants have a mean 3D Sersic index of (n) ≈ 4 ± 0.5, that is somewhat smaller than the one obtained for dark haloes in Lambda cold dark matter cosmologies, (n) ≈ 6 ± 1. Also, a tight dark Sersic 'plane' is found to be defined by the parameters of the remnants haloes with n ∝ r 0.10 e ρ 0.09 0 . We conclude that collisionless merger remnants of pure disc galaxies have Sersic properties and correlations consistent with those of observed in early-type galaxies and local remnants.
Effects of mode degeneracy in the LIGO Livingston Observatory recycling cavity

We analyze the electromagnetic fields in a Pound-Drever-Hall locked, marginally unstable, Fabry-Perot cavity as a function of small changes in the cavity length during resonance. More specifically, we compare the results of a detailed numerical model with the behavior of the recycling cavity of the Laser Interferometer Gravitational-wave Observatory (LIGO) detector located in Livingston, Louisiana. In the interferometer's normal mode of operation, the recycling cavity is stabilized by inducing a thermal lens in the cavity mirrors with an external CO2 laser. During our study, this thermal compensation system was not operating, causing the cavity to be marginally optically unstable and cavity modes to become degenerate. In contrast to stable optical cavities, the modal content of the resonating beam in the uncompensated recycling cavity is significantly altered by very small cavity length changes. This modifies the error signals used to control the cavity length in such a way that the zero crossing point is no longer the point of maximum power in the cavity, nor is it the point where the input-beam mode in the cavity is maximized.
Characterization of Binding of Candida albicans to Small Intestinal Mucin and Its Role in Adherence to Mucosal Epithelial Cells

ABSTRACT In order to approximate and adhere to mucosal epithelial cells,Candida must traverse the overlying mucus layer. Interactions of Candida species with mucin and human buccal epithelial cells (BECs) were thus investigated in vitro. Binding of the Candida species to purified small intestinal mucin showed a close correlation with their hierarchy of virulence. Significant differences (P < 0.05) were found among three categories of Candida species adhering highly (C. dubliniensis, C. tropicalis, and C. albicans), moderately (C. parapsilosis and C. lusitaniae) or weakly (C. krusei and C. glabrata) to mucin. Adherence of C. albicans to BECs was quantitatively inhibited by graded concentrations of mucin. However, inhibition of adherence was reversed by pretreatment of mucin with pronase or C. albicans secretory aspartyl proteinase Sap2p but not with sodium periodate. Saturable concentration- and time-dependent binding of mucin to C. albicans was abrogated by pronase or Sap2p treatment of mucin but was unaffected by β-mercaptoethanol, sodium periodate, neuraminidase, lectins, or potentially inhibitory sugars. Probing of membrane blots of the mucin with C. albicans revealed binding of the yeast to the 66-kDa cleavage product of the 118-kDa C-terminal glycopeptide of mucin. Although no evidence was found for the participation of C. albicans cell surface mannoproteins in specific receptor-ligand binding to mucin, inhibition of binding by p-nitrophenol (1 mM) and tetramethylurea (0.36 M) revealed that hydrophobic interactions are involved in adherence of C. albicans to mucin. These results suggest that C. albicans may both adhere to and enzymatically degrade mucins by the action of Saps, and that both properties may act to modulate Candidapopulations in the oral cavity and gastrointestinal tract.