Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrating multiple resources to identify specific transcriptional cooperativity with a Bayesian approach

MOTIVATION Limited cohort of transcription factors is capable to structure various gene-expression patterns. Transcriptional cooperativity (TC) is deemed to be the main mechanism of complexity and precision in regulatory programs. Although many data types generated from numerous experimental technologies are utilized in an attempt to understand combinational transcriptional regulation, complementary computational approach that can integrate diverse data resources and assimilate them into biological model is still under development. RESULTS We developed a novel Bayesian approach for integrative analysis of proteomic, transcriptomic and genomic data to identify specific TC. The model evaluation demonstrated distinguishable power of features derived from distinct data sources and their essentiality to model performance. Our model outperformed other classifiers and alternative methods. The application that contextualized TC within hepatocarcinogenesis revealed carcinoma associated alterations. Derived TC networks were highly significant in capturing validated cooperativity as well as revealing novel ones. Our methodology is the first multiple data integration approach to predict dynamic nature of TC. It is promising in identifying tissue- or disease-specific TC and can further facilitate the interpretation of underlying mechanisms for various physiological conditions. CONTACT tieliushi01@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Outer Membrane Proteins A (OmpA) and X (OmpX) Are Essential for Basolateral Invasion of Cronobacter sakazakii

ABSTRACT Cronobacter sakazakii is an opportunistic pathogen that actively invades host eukaryotic cells. To identify invasion factors responsible for the intestinal translocation of C. sakazakii, we constructed for the first time outer membrane protein X (OmpX) and A (OmpA) deletion mutants using the lambda Red recombination system. The ompX and ompA deletion mutants showed significantly reduced invasion of human enterocyte-like epithelial Caco-2 and human intestinal epithelial INT-407 cells, and significantly fewer mutant cells were recovered from the livers and spleens of rat pups. Furthermore, compared with intact target cells, the invasion and initial association potentials of the mutants increased at a rate similar to that of the wild type in tight-junction-disrupted target cells, suggesting that OmpX and OmpA are involved in basolateral invasion by C. sakazakii. This is the first report of C. sakazakii virulence determinants that are essential for basolateral invasion and that may be critical for the virulence of C. sakazakii.
Principal Component Analysis and Higher Correlations for Distributed Data

We consider algorithmic problems in the setting in which the input data has been partitioned arbitrarily on many servers. The goal is to compute a function of all the data, and the bottleneck is the communication used by the algorithm. We present algorithms for two illustrative problems on massive data sets: (1) computing a low-rank approximation of a matrix $A=A^1 + A^2 + \ldots + A^s$, with matrix $A^t$ stored on server $t$ and (2) computing a function of a vector $a_1 + a_2 + \ldots + a_s$, where server $t$ has the vector $a_t$; this includes the well-studied special case of computing frequency moments and separable functions, as well as higher-order correlations such as the number of subgraphs of a specified type occurring in a graph. For both problems we give algorithms with nearly optimal communication, and in particular the only dependence on $n$, the size of the data, is in the number of bits needed to represent indices and words ($O(\log n)$).
Therapeutic Potential of Epigallocatechin Gallate Nanodelivery Systems

Nowadays, the society is facing a large health problem with the rising of new diseases, including cancer, heart diseases, diabetes, neurodegenerative diseases, and obesity. Thus, it is important to invest in substances that enhance the health of the population. In this context, epigallocatechin gallate (EGCG) is a flavonoid found in many plants, especially in tea. Several studies support the notion that EGCG has several benefits in fighting cancer, heart diseases, diabetes, and obesity, among others. Nevertheless, the poor intestinal absorbance and instability of EGCG constitute the main drawback to use this molecule in prevention and therapy. The encapsulation of EGCG in nanocarriers leads to its enhanced stability and higher therapeutic effects. A comprehensive review of studies currently available on the encapsulation of EGCG by means of nanocarriers will be addressed.
Production , Manufacturing and Logistics A rewarding-punishing coordination mechanism based on Trust in a divergent supply chain

Coordination of decentralized supply chains using contract design is a problem that has been widely addressed in the literature. We consider a divergent supply chain including a supplier and several retailers producing fashion products with short sale seasons. The retailers cooperate with the supplier as sales agents; i.e., they work in the framework of revenue sharing contracts. Because of their proximity to the market, retailers can provide more accurate demand forecasts to the supplier that is used to decide on issues such as capacity building and market prices with regard to retailers stiff due dates, different lead times and different price-dependent demand functions. To ensure abundant supply and cope with the demand variability, the retailers have an incentive to exaggerate their private forecast information. In this study, we propose a new rewarding-punishing coordination mechanism based on trust between supply chain tiers, considered as a differentiation factor between honest and deceptive partners. An optimization model is developed as a building block of this mechanism. An approximation method is used to simplify and solve the problem. The model is then implemented using Monte-Carlo simulation in four different situations, according to 10 different strategies for forecast information sharing. The findings from the tests show that the mechanism including trust as a decisional factor performs better than ‘No Trust’ mechanism in all situations. These results suggest that taking into account Trust in designing coordination mechanism may have significant influence on the financial performance of the supply chain. 2013 Elsevier B.V. All rights reserved.
VISIBLE PATTERNS OF SOUND.

Visible Patterns of Sound: RALPH K. PoTTER . i. 463 M. SELLE. Concerning the Term "Race Differences " and the Concept " Culture ": DR. C. W. Obituary: WEIANT . 484 Walter Bradford Cannon: DL CEcm K. DRINKER. Deaths and Memorials . 470 Scientific Books: Mainsprings of Civillation: Dli. WARRAIN S. Scientific Events: THOMPSON. Physical Geology: DR. HARRY S. Nuclear Physics and Chemistry at Harvard UniLADD. General Chetmistry: DR HUBERT N. ALYA. versity; The Research Corporation of New York; Books Received . 486 Freedom for Scientific Work; News from Abroad. 472 ~~~~~~~~~~~~~~~~~~~~~~~~~~Science News . -. 12 Scientific Notes and News . 475
Cortical pathology in multiple sclerosis: experimental approaches to studies on the mechanisms of demyelination and remyelination

Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of unknown etiology that can involve all parts of the central nervous system and is unique to humans. Therefore, analysis of human tissue is critical for generating hypotheses for testing in animal or in vitro models and for validating research findings from these experimental models. This article reviews data on demyelination and remyelination in the cerebral cortex. We show that research on cerebral cortical demyelination and remyelination in appropriately processed postmortem MS tissues provides innovative approaches for developing hypotheses for studies on the pathogenesis MS lesions including identification of targets for therapy at early stages of the disease.
Automatic mesh animation preview

With growing number of high quality 3D models published online, the technique of generating efficient and economical 3D model previews has raised increasing concerns. Although several previous work has been done on the preview of static mesh, that of animated mesh is different and more complex due to the difficulty in describing the animation. In this paper, we present a novel method of automatic preview generation for 3D mesh animation. A new measure named inter-frame surface saliency, which evaluates both inter-frame motions and surface saliency in each frame, is introduced. Given an animated mesh, an energy function combining this measure and camera smoothness is constructed for the representative viewpoints selection in key frames, and then an optimal camera path is generated. Finally, a brief but informative preview could be created by moving the camera along this path with frame rate control.
The Effects of Product Attribute's New Information on Consumer Elaboration and Brand Attitude

This article examines the effects of inconsistent product attribute information on consumer elaboration and brand attitude. That is, when product attribute goals are inconsistent with more product attribute goals (new information), whether consumer can create elaboration, as well as strengthen brand attitude. The empirical results show that new information extent has the main effect, need for cognitive has main effect, interaction effect of new information degree and need for cognitive. Implicitly it provided more attribute information which help to stimulate the elaboration of the consumer on the product. In addition, consumer’s prior knowledge has main effect on elaboration extent, and new information and prior knowledge has interaction effect. It showed not only the level of new information would lead to elaboration, prior knowledge will adjust the level of new information can lead to the elaboration. As to high prior knowledge, new information would more likely cause elaboration. As to low prior knowledge, new information is less likely to cause elaboration.
Design, synthesis, and evaluation of pyrazolo-pyrazole derivatives on Methylisocitratelyase of Pseudomonas aeruginosa: in silico and in vitro study

Pseudomonas aeruginosa is an opportunistic micro-organism causing diseases both in animals and humans. In case of human pathology, the role of P. aeruginosa is one of the major concerns in intensive care septicemia. Presently, the drug resistance strains of P. aeruginosa are arising mainly by developing multiple mechanisms due to its natural and acquired resistance to many of the antimicrobial agents commonly used in clinical practice. As a result, there is a direct need to invent new drugs so that they may restrict the outbreak of multidrug resistant strains. Virtual high-throughput insilico screening, which helps to identify the chemical ligands that bind to the enzymes, is an important tool in drug discovery and the drugs discovered in this way are clinically tested. In this study, Methylisocitratelyase (MICL), which is essential for the survival of the bacterium and which doesn’t show any similarity with the humans, was selected to evaluate the functions of high-afﬁnity inhibitors (PPI-analogs) that are identified using the virtual screening approach. By adopting the computational analysis tools, structural, functional, and inhibitor interactions of MICL against P. aeruginosa were identified. The PPIA-32 is found to be the best binding interactions with MICL. PPIA-32 reduces the binding afﬁnity for substrate to residues required for MICL enzyme activity and also Root Mean Square Deviation simulations show the most stable nature of PPA32-MICL(complex) than that of MICL alone, thereby effectively inhibiting the growth of virulent P. aeruginosa. To our surprise, the same phenomenon is also identified with other gram-negative bacteria like Escherichia coli, Klebsiella pneumoniae, and Salmonella typhi.
Third Generation Teleassistance: Intelligent Monitoring Makes the Difference

Elderly people aim to preserve their independence and autonomy at their own home as long as possible. However, as they get old the risks of disease and injuries increase making critical to assist and provide them the right care whenever needed. Unfortunately, neither relatives, private institutions nor public care services are viable long-term solutions due to the large amount of required time and cost. Thus, smart teleassistance solutions must be investigated. In particular, IoT paradigm helps in designing third generation teleassistance systems by relying on sensors to gather the more data as possible. Moreover, we claim that providing IoT solutions of intelligent monitoring improves the overall efficacy. In this paper, we presents an intelligent monitoring solution, fully integrated in a IoTbased teleassistance system, showing how it helps in giving better support to both end-users and carers. Thanks to intelligent monitoring, carers can instantly access to the relevant information regarding the status of the end-user, also receiving alarms in case of any anomaly or emergency situations have been detected.
Manure – an agronomic and environmental challenge 5-6 September 2005

So called ‘dry fermentation’ prototype plants for anaerobic digestion of organic material containing 15-50 % total solids show added advantages compared to slurry digestion plants (Hoffman 2001): Less reactor volume, less process energy, less transport capacity, less odour emissions. However on-farm dry fermentation plants are not common and rarely commercially available. Recent on-farm research (Kusch & Oechsner 2004) and prototype research (Linke 2004) show promising technical solutions for dry fermentation batch reactors on-farm. The Biodynamic Research Institute in Järna developed a two-phase on-farm biogas plant. The plant digests manure of dairy cattle and organic residues originating from the farm and the surrounding food processing units containing 17.7-19.6 % total solids. A new technology for continuously filling and discharging the hydrolysis reactor was developed and implemented. The output of the hydrolysis reactor is separated into a solid and liquid fraction. The solid fraction is composted. The liquid fraction is further digested in a methane reactor and the effluent used as liquid fertiliser. Initial results show that anaerobic digestion followed by aerobic composting of the solid fraction improves the nutrient balance of the farm compared to mere aerobic composting. Composted solid fraction and effluent together contain about 70 % of total input nitrogen and 94 % of input NH4. The manure that was merely aerobic digested contained about 51 % of total input nitrogen and 3.9 % of input NH4. Additionally anaerobic digestion improves the energy balance of the farm producing up to 269 l biogas kg volatile solids or 1,7 kWh heat kg volatile solids. References Hoffmann, M. 2001. Trockenfermentation. Entwicklungsstand und Perspektiven. Landtechnik 56, 410-411. Kusch, S. , Oechsner, H. 2004. Feststoffvergärung in Batchreaktoren – erste Veruchsergebnisse. In Tagungsband zur 13. Jahrestagung „Biogas und Bioenergie in der Landwirtschaft“. 2. -4. Dezember 2004 in Wolpertshausen. (Ed. Internationales Biogas und Bioenergie Kompetenzzentrum, Fachgruppe Biogas), pp. 115-124. Linke, B. 2004. Substrateinsatz bei der Trockenfermentation – Einschätzung des F+EBedarfs. In Gülzower Fachgespräche 23 (Ed. Fachagentur Nachwachsende Rohstoffe), pp. 35-48. Möller, K. 2003. Systemwirkungen einer "Biogaswirtschaft" im ökologischen Landbau: Pflanzenbauliche Aspekte, Auswirkungen auf den N-Haushalt und auf die Spurengasemissionen. Biogas Journal 1, 20-29. Møller, H. , Sommer, S. , Ahring, B. 2004. Methane productivity of manure, straw and solid fractions of manure. Biomass & Bioenergy 26, 485-495.
2 . Federated database system ’ s architecture based on DOK

This paper defines architecture and frame work of Distributed Object Kernel (DOK) that federated systems may be built. Distributing control and decision making allows the user to exploit most of the available parallelism within this type of system in order to provide scalability. Concurrency control is provided by time stamping and transaction classes in autonomous, distributed and heterogeneous databases.
The ultrasound elastography inverse problem and the effective criteria

The elastography (elasticity imaging) is one of the recent state-of-the-art methods for diagnosis of abnormalities in soft tissue. The idea is based on the computation of the tissue elasticity distribution. This leads to the inverse elasticity problem; in that, displacement field and boundary conditions are known, and elasticity distribution of the tissue is aimed for computation. We treat this problem by the Gauss–Newton method. This iterative method results in an ill-posed problem, and therefore, regularization schemes are required to deal with this issue. The impacts of the initial guess for tissue elasticity distribution, contrast ratio between elastic modulus of tumor and normal tissue, and noise level of the input data on the estimated solutions are investigated via two different regularization methods. The numerical results show that the accuracy and speed of convergence vary when different regularization methods are applied. Also, the semi-convergence behavior has been observed and discussed. At the end, we signify the necessity of a clever initial guess and intelligent stopping criteria for the iterations. The main purpose here is to highlight some technical factors that have an influence on elasticity image quality and diagnostic accuracy, and we have tried our best to make this article accessible for a broad audience.
Mobility management techniques for the next-generation wireless networks

The tremendous demands from social market are pushing the booming development of mobile communications faster than ever before, leading to plenty of new advanced techniques emerging. With the converging of mobile and wireless communications with Internet services, the boundary between mobile personal telecommunications and wireless computer networks is disappearing. Wireless networks of the next generation need the support of all the advances on new architectures, standards, and protocols. Mobility management is an important issue in the area of mobile communications, which can be best solved at the network layer. One of the key features of the next generation wireless networks is all-IP infrastructure. This paper discusses the mobility management schemes for the next generation mobile networks through extending IP's functions with mobility support. A global hierarchical framework model for the mobility management of wireless networks is presented, in which the mobility management is divided into two complementary tasks: macro mobility and micro mobility. As the macro mobility solution, a basic principle of Mobile IP is introduced, together with the optimal schemes and the advances in IPv6. The disadvantages of the Mobile IP on solving the micro mobility problem are analyzed, on the basis of which three main proposals are discussed as the micro mobility solutions for mobile communications, including Hierarchical Mobile IP (HMIP), Cellular IP, and Handoff-Aware Wireless Access Internet Infrastructure (HAWAII). A unified model is also described in which the different micro mobility solutions can coexist simultaneously in mobile networks.
Large‐scale expansion of rat CD4+ CD25+ Treg cells in the absence of T‐cell receptor stimulation

T‐cell receptor (TCR) stimulation is both central to homeostatic maintenance of CD4+ CD25+ regulatory T cells (Treg cells) in vivo and a prerequisite for the initiation of suppression by Treg cells, both in vivo and in vitro. However, TCR‐independent stimulation of Treg cells, e.g. with superagonistic CD28‐specific monoclonal antibodies (CD28‐SA), not only expands these cells in vivo but, as we show here, also mediates large‐scale expansion of rat Treg cells in vitro. Interestingly, CD28‐SA stimulation plus interleukin (IL)‐2 was even superior to conventional costimulation plus IL‐2 in promoting Treg cell growth in vitro. Despite their highly activated phenotype suppression by Treg cells expanded in the absence of TCR stimulation remained fully dependent on TCR‐triggering for initiation and cell contact was required to exert suppression. With regard to the regulation of suppression by CD28 stimulation we observed that neither the presence of a conventional anti‐CD28 monoclonal antibody nor a CD28‐SA generally rendered conventional T cells resistant to suppression by preactivated Treg cells. Taken together, we provide a novel protocol for long‐term propagation of Treg cells in vitro and our data are the first to reveal a difference in the signals required for activation and expansion of Treg cells and those, involving the TCR, necessary for the initiation of suppression.
On the Cascaded Decomposition of Automata, its Complexity and its Application to Logic

The primary decomposition theorem due to Krohn and Rhodes KR which has been considered as one of the fundamental results in the theory of automata and semigroups states that every automaton is homomorphic to a cascaded de composition wreath product of simpler automata of two kinds reset automata and permutation automata If the automaton is non counting and correspond ingly its transformation semigroup is group free then it can be decomposed using only reset components There exist various proofs and partial proofs for the primary decomposition theorem e g HS Ze a Ze b Gi MT La We Ei None of them give explicit bounds on the size of the decomposition In this paper we give tight exponential bounds on the size of the decomposition as a function of the size of the original automaton For the upper bound we give an exponential algorithm by modifying the implicit construction appearing in Ei Our algorithm is con structive enough to allow implementation We apply the algorithm to give an exponential upper bound on transforming star free regular resp regular sets expressed by counter free automata resp automata into past resp future temporal logic formulae These upper bounds improve upon previously known non elementary translations MNP LPZ Zu Some of the results in this paper has been presented in O Maler A Pnueli Tight Bounds on the Complexity of Cascaded Decomposition of Automata Proc st Annual Symposium on Foundations of Computer Science St Louis Missouri IEEE Press To quote the last paragraph in Ginzburg s book Gi Finally notice that the above theory does not indicate how many particular basic building blocks are needed to construct a cascade product covering of a given semiautomaton Our decomposition construction is proved to be optimal by showing the exis tence of a family of automata such that the size of their minimal permutation free decomposition is exponential in the size of the automaton by size we refer to the total number of de ned transitions
A coupled estimation and control analysis for attitude stabilisation of mini aerial vehicles

Commercially viable aerial robotic vehicles require robust and efficient, but low-cost attitude (vehicle orientation) stabilisation systems. A typical attitude stabilisation system employs a low-cost IMU and consists of an attitude estimator as well as an attitude controller. This paper proposes a coupled non-linear attitude estimation and control design for the attitude stabilisation of low-cost aerial robotic vehicles. Attitude estimation is based on a non-linear complementary filter expressed on the rotation group. The attitude control algorithm is based on a non-linear control Lyapunov function analysis derived directly in terms of the rigid-body attitude dynamics. The interaction terms are bounded in terms of estimation and control errors and the full coupled system is shown to be (almost) globally stable.