Miracle-dz/UniFAR-FTUs huggingface dataset:
E‐cadherin—catenin cell—cell adhesion complex and human cancer

The E‐cadherin–catenin complex plays a crucial role in epithelial cell–cell adhesion and in the maintenance of tissue architecture. Perturbation in the expression or function of this complex results in loss of intercellular adhesion, with possible consequent cell transformation and tumour progression. Recently, much progress has been made in understanding the interaction between the different components of this protein complex and how this cell–cell adhesion complex is modulated in cancer cells.
Enhanced framework for miRNA target prediction

MicroRNAs are small non-coding RNA molecules that play an important role in post-transcriptional gene regulation. They bind with messenger RNAs, affecting the regulation of gene expression causing diseases such as heart diseases and cancer. The two pioneer strategies of miRNA target prediction are either experimentally or computationally. Since experimental techniques are very expensive and slow, several computational tools have been proposed to defeat some of the experimental technical difficulties. In this paper, we propose an enhanced computational framework that predicts miRNA targets depending on structural, positional, and thermodynamic features extracted from the alignment of miRNA and its targets. Then, we select the linearly separable features using the eigenvalue analysis of the covariance matrix of the features. Finally, the selected features are applied to random forest classifier. The obtained results prove that our framework significantly excels other existing tools.
A rigid network of long-range contacts increases thermostability in a mutant endoglucanase

Thermodynamic stability of a protein at elevated temperatures is a key factor for thermostable enzymes to catalyze their specific reactions. Yet our understanding of biological determinants of thermostability is far from complete. Many different atomistic factors have been suggested as possible means for such proteins to preserve their activity at high temperatures. Among these factors are specific local interatomic interactions or enrichment of specific amino acid types. The case of glycosyl hydrolase family endoglucanase of Trichoderma reesei defies current hypotheses for thermostability because a single mutation far from the active site (A35 V) converts this mesostable protein into a thermostable protein without significant change in the protein structure. This substantial change in enzymatic activity cannot be explained on the basis of local intramolecular interactions alone. Here we present a more global view of the induced thermostability and show that the A35 V mutation affects the underlying structural rigidity of the whole protein via a number of long-range, non-local interactions. Our analysis of this structure reveals a precisely tuned, rigid network of atomic interactions. This cooperative, allosteric effect promotes the transformation of this mesostable protein into a thermostable one.
A Novel Role of the Budding Yeast Separin Esp1 in Anaphase Spindle Elongation

In Saccharomyces cerevisiae, the metaphase–anaphase transition is initiated by the anaphase-promoting complex–dependent degradation of Pds1, whereby Esp1 is activated to promote sister chromatid separation. Although this is a fundamental step in the cell cycle, little is known about the regulation of Esp1 and how loss of cohesion is coordinated with movement of the anaphase spindle. Here, we show that Esp1 has a novel role in promoting anaphase spindle elongation. The localization of Esp1 to the spindle apparatus, analyzed by live cell imaging, is regulated in a manner consistent with a function during anaphase B. The protein accumulates in the nucleus in G2 and is mobilized onto the spindle pole bodies and spindle midzone at anaphase onset, where it persists into midanaphase. Association with Pds1 occurs during S phase and is required for efficient nuclear targeting of Esp1. Spindle association is not fully restored in pds1 mutants expressing an Esp1-nuclear localization sequence fusion protein, suggesting that Pds1 is also required to promote Esp1 spindle binding. In agreement, Pds1 interacts with the spindle at the metaphase–anaphase transition and a fraction remains at the spindle pole bodies and the spindle midzone in anaphase cells. Finally, mutational analysis reveals that the conserved COOH-terminal region of Esp1 is important for spindle interaction.
Energy implications of multiprocessor synchronization

Energy consumption is an increasingly important issue in multiprocessor design. The need for energy-aware systems is obvious for mobile systems, where low energy consumption translates to longer battery life, but it is also important for desktop and server systems, where high energy consumption complicates power supply and cooling. While energy consumption in uniprocessors has been the focus of a substantial body of research, energy consumption in multiprocessors has received less attention. This issue is becoming increasingly important as multiprocessor architectures migrate from high-end platforms into everyday platforms such as desktops, laptops, and servers. In this paper we examine the energy implications of how multiprocessors synchronize concurrent access to memory. Whether synchronization is a substantial part of multiprocessor energy consumption is application-dependent. Nevertheless, the trends are clear. The widespread shift to multithreaded and multicore architectures is driven by two trends: Moore’s law continues to provide more and more transistors, hence more and more threads and cores, while clock speed is hardly increasing at all. These trends imply that if applications are going to benefit from advancing technology, then they will have to become more and more parallel, and synchronization costs will become more and more significant. The conventional way for applications to synchronize is by locking. Nevertheless, conventional synchronization techniques based on locks have substantial limitations [2]. Coarse-grained locks simply do not scale. Threads block one another even when they do not really interfere, and the lock itself causes memory contention. Fine-grained locks are more scalable, but they introduce substantial software engineering problems. Locks are also vulnerable to thread failures and delays. Transactional memory [3] is a synchronization architecture that addresses these limitations. A transaction is a finite sequence of memory reads and writes executed by a single thread. Transactions are atomic and serializable. Hardware transactional memory proposals exploit hardware mechanisms such as speculative execution and on-chip caching. As a transaction executes, it caches the memory locations it reads or writes, marking them as transactional. A data conflict occurs if another thread accesses a transactionally cached location, and at least one access is a write. The native hardware cache coherence detects data conflicts. A transaction commits if it completes without encountering a conflict. Here, we evaluate the energy/performance tradeoffs associated with these synchronization architectures. Overall, our tests suggest
Compressive Strength of Concrete Cores with Different Lengths

AbstractCores with diameters of 74 mm and length-to-diameter (l/d) ratios of 0.5, 1.0, 1.5, 2.0, 3.0, and 4.0, were removed from concrete beams. Compressive strength tests were conducted on 300 core specimens. The compressive strengths of concrete cores were fitted to the modified Weibull distribution. This information is useful in the theoretical description of concrete failure. Furthermore, on the basis of the Kolmogorov-Smirnov goodness-of-fit tests, the test data have been verified to follow this modified Weibull distribution. In addition, the modified Weibull model can predict the length effect more accurately than the conventional model.
Short-term Aerobic Exercise Reduces Nitroglycerin-induced Orthostatic Intolerance in Older Adults With Type 2 Diabetes

Aims/Hypothesis: Older adults are at a high risk for syncope due to orthostatic intolerance (OI), and this risk increases with comorbid type 2 diabetes and vasoactive medications. Despite many benefits, previous investigations have shown worsening OI with aerobic training. We examined whether aerobic exercise reduced OI in older adults with type 2 diabetes who were given a short-acting vasoactive agent (nitroglycerin). Methods: Forty older adults (25 males and 15 females, mean age 71.4 ± 0.7 years, ranging in age from 65 to 83 years) with type 2 diabetes were recruited. Subjects were randomized to each of 2 groups: an aerobic group (3 months of vigorous aerobic exercise) and a nonaerobic (no aerobic exercise) group. Exercise sessions were supervised by a certified exercise trainer 3 times per week. After being given 400 μg of sublingual nitroglycerin, each subject was placed in a 70° head-up tilt for 30 minutes. Results: When the 2 groups were compared using a Cox proportional hazards model, tilt table tolerance was significantly better in the aerobic group as compared to in the nonaerobic group (χ2MC = 7.271, P = 0.007). Conclusions: Our findings indicate that a relatively short aerobic exercise intervention can improve postnitroglycerin orthostatic tolerance in older adults with type 2 diabetes.
Chaotic time series : Part 1: estimation of some invariant properties in state space

Certain deterministic non-linear systems may show chaotic behaviour. Time series derived from such systems seem stochastic when analyzed with linear techniques. However, uncovering the deterministic structure is important because it allows constructing more realistic and better models and thus improved predictive capabilities. This paper provides a review of two main key features of chaotic systems, the dimensions of their strange attrac-tors and the Lyapunov exponents. The emphasis is on state space reconstruction techniques that are used to estimate these properties, given scalar observations. Data generated from equations known to display chaotic behaviour are used for illustration. A compilation of applications to real data from widely diierent elds is given. If chaos is found to be present, one may proceed to build non-linear models, which is the topic of the second paper in this series.
Cateslytin, a Chromogranin A Derived Peptide Is Active against Staphylococcus aureus and Resistant to Degradation by Its Proteases

Innate immunity involving antimicrobial peptides represents an integrated and highly effective system of molecular and cellular mechanisms that protects host against infections. One of the most frequent hospital-acquired pathogens, Staphylococcus aureus, capable of producing proteolytic enzymes, which can degrade the host defence agents and tissue components. Numerous antimicrobial peptides derived from chromogranins, are secreted by nervous, endocrine and immune cells during stress conditions. These kill microorganisms by their lytic effect at micromolar range, using a pore-forming mechanism against Gram-positive bacteria, filamentous fungi and yeasts. In this study, we tested antimicrobial activity of chromogranin A-derived peptides (catestatin and cateslytin) against S. aureus and analysed S. aureus-mediated proteolysis of these peptides using HPLC, sequencing and MALDI-TOF mass spectrometry. Interestingly, this study is the first to demonstrate that cateslytin, the active domain of catestatin, is active against S. aureus and is interestingly resistant to degradation by S. aureus proteases.
Permanent-magnet-excited AC servo motors in tooth-coil technology

Permanent-magnet-excited ac servo motors can be produced usefully with tooth-coil windings; they allow an increase of the torque density due to their compact construction. The winding systematics and the winding variants, interesting for ac servo motors, are introduced. The steady-state behavior of the ac servo drive is calculated analytically in dependence of the winding variant. The influence of the winding variant on the M(n)-characteristic is discussed in examples. A comparison between calculations and measurements verifies the represented modeling.
Growth Phase and Metal-Dependent Transcriptional Regulation of the fecA Genes in Helicobacter pylori

ABSTRACT Balancing metal uptake is essential for maintaining a proper intracellular metal concentration. Here, we report the transcriptional control exerted by the two metal-responsive regulators of Helicobacter pylori, Fur (iron-dependent ferric uptake regulator) and NikR (nickel-responsive regulator), on the three copies of the fecA genes present in this species. By monitoring the patterns of transcription throughout growth and in response to nickel, iron, and a metal chelator, we found that the expression of the three fecA genes is temporally regulated, responds to metals in different ways, and is selectively controlled by either one of the two regulators. fecA1 is expressed at a constant level throughout growth, and its expression is iron sensitive; the expression of fecA2 is mainly off, with minor expression coming up in late exponential phase. In contrast, the expression of fecA3 is maximal in early exponential phase, gradually decreases with time, and is repressed by nickel. The direct roles of Fur and NikR were studied both in vitro, by mapping the binding sites of each regulator on the promoter regions via DNase I footprinting analysis, and in vivo, by using primer extension analyses of the fecA transcripts in fur and nikR deletion strains. Overall, the results show that the expression of each fecA gene is finely tuned in response to metal availability, as well as during the bacterial growth phase, suggesting specific and dedicated functions for the three distinct FecA homologues.
Simultaneous camera orientation estimation and road target tracking

Airborne surveillance systems equipped with a vision/infrared camera require good knowledge about the position and orientation of the camera for successful tracking of ground targets. In particular, this is essential when incorporating prior information, like road maps, that is expressed relative a global reference system. Usually, it is possible to obtain good positioning with inertial/satellite navigation systems, but estimating the orientation is generally more difficult. It might be possible to use SLAM (Simultaneous Localization and Mapping) or image registration approaches to support the navigation system, but not always since such approaches require stable features in the images. In this paper the problem of simultaneous orientation error estimation and road target tracking is considered by assuming that the target is constrained to a known road network. A particle filter approach is proposed and it is shown that the result of this filter is close to the performance of the ideal case where the orientation error is perfectly known. However, the performance depends on how informative the road path is and in rare cases the orientation error is unobservable.
Characteristics of a dual-wavelength semiconductor laser near 1550 nm

The implementation of a widely tunable, dual-wavelength semiconductor laser near 1550 nm is reported. The characteristics of its operation under different conditions of injection current and output feedback are discussed. Because the gain spectrum of this laser varied significantly with the injection current level, the signals of the two oscillating wavelengths interplay through the competition for the carriers. Generally, the feedback of the signal of one wavelength enhanced its own output power and suppressed the other unless the gain of the former is significantly lower than the later.
Conduction behaviour of hydrogenated nanocrystalline silicon backward diode

A heavy phosphorus doped hydrogenated nanocrystalline silicon ((n+)nc-Si:H) film was deposited by plasma enhanced chemical vapour deposition technique on a heavy doped p-type crystal silicon substrate to form a heterojunction of (n+)nc-Si:H/(p+)c-Si. From electrical measurements of this prepared structure, both negative resistance in forward current–voltage (I–V) measured plots and large reverse current in reverse I–V experimental curves were observed, which reveal the structure as a semiconductor backward diode. The forward current can be assigned to interband tunnel, excess, hump and thermionic emission component, while the reverse current which shows exponential dependence on applied voltage can be ascribed to an internal field emission (Zener mechanism) term. Also, the crucial role of (n+)nc-Si:H in I–V characteristics was analyzed.
Reactive compatibilization of polypropylene/polyethylene terephthalate blends

The reactive compatibilization of polypropylene/polyethylene terephthalate (PP/PET) blends by addition of glycidyl methacrylate grafted PP (PP-g-GMA) was studied. Two PP-g-GMA copolymers, containing either 0.2 or 1.2 wt% of GMA, were used as interface modifiers. These were incorporated into PP blends (with either 70 or 90 wt% PET). replacing 1/5 of PP in the system. The use of these modifiers changed the blends' tensile mechanical behavior from fragile to ductile. Blend tensile strength was improved by 10% and elongation at break showed 10 to 20-fold increases while stiffness remained constant. Scanning electron micrographs showed the PP average domain size in injection molded specimens to decrease to the micron/sub-micron size upon addition of the GMA modified resins, while the unmodified blends exhibited heterogeneous morphology comprising large lamellae 10-20 μm wide. The low-GMA graft content PP seemed slightly more efficient than the high GMA content PP in emulsifiying PP/PET blends. The GMA grafting level on PP had very limited effects on the blends' mechanical behavior in the range of GMA graft density provided by the two modified resins investigated.
Numerical competence in animals, with an insight from ants

Summary We survey a variety of experimental paradigms for studying animal abilities to count, to understand numerical information and to perform simple arithmetic operations. There is a huge body of evidence that different forms and elements of quantitative judgement and numerical competence are spread across a wide range of species, both vertebrate and invertebrate. Here we pay particular attention to the display of numerical competence in ants. The reason is that most of the existing experimental schemes for studying numerical processing in animals, although often elegant, are restricted by studying subjects at the individual level, or by the use of artificial communicative systems. In contrast, the information-theoretic approach that was elaborated for studying number-related skills in ants employs their own communicative means and, thus, does not require the subjects to solve any artificial learning problems, such as learning intermediary languages, or even learning to solve multiple choice problems. Using this approach, it was discovered that members of highly social ant species possessed numerical competence. They were shown to be able to pass information about numbers and to perform simple arithmetic operations with small numbers. We suggest that applying ideas of information theory and using the natural communication systems of highly social animals can open new horizons in studying numerical cognition.
SoftMoW: Recursive and Reconfigurable Cellular WAN Architecture

The current LTE network architecture is organized into very large regions, each having a core network and a radio access network. The core network contains an Internet edge comprised of packet data network gateways (PGWs). The radio network consists of only base stations. There are minimal interactions among regions other than interference management at the edge. The current architecture has several problems. First, mobile application performance is seriously impacted by the lack of Internet egress points per region. Second, the continued exponential growth of mobile traffic puts tremendous pressure on the scalability of PGWs. Third, the fast growth of signaling traffic known as the signaling storm problem poses a major challenge to the scalability of the control plane. To address these problems, we present SoftMoW, a recursive and reconfigurable cellular WAN architecture that supports seamlessly inter-connected core networks, reconfigurable control plane, and global optimization. To scale the control plane nation-wide, SoftMoW recursively builds up the hierarchical control plane with novel abstractions of both control plane and data plane entities. To enable scalable end-to-end path setup, SoftMoW presents a novel label swapping mechanism such that each controller only operates on its logical topology and each switch along the path only sees at most one label. SoftMoW supports new network-wide optimization functions such as optimal routing and inter-region handover minimization. We demonstrate that SoftMoW improves the performance, flexibility and scalability of cellular WAN using real LTE network traces with thousands of base stations and millions of subscribers. Our evaluation shows that path inflation and inter-region handovers can be reduced by up to 60% and 44% respectively.
Short-term ionic plasticity at GABAergic synapses

Fast synaptic inhibition in the brain is mediated by the pre-synaptic release of the neurotransmitter γ-Aminobutyric acid (GABA)and the post-synaptic activation of GABA-sensitive ionotropic receptors. As with excitatory synapses, it is being increasinly appreciated that a variety of plastic processes occur at inhibitory synapses, which operate over a range of timescales. Here we examine a form of activity-dependent plasticity that is somewhat unique to GABAergic transmission. This involves short-lasting changes to the ionic driving force for the post-synaptic receptors, a process referred to as short-term ionic plasticity. These changes are directly related to the history of activity at inhibitory synapses and are influenced by a variety of factors including the location of the synapse and the post-synaptic cell's ion regulation mechanisms. We explore the processes underlying this form of plasticity, when and where it can occur, and how it is likely to impact network activity.
An Ant Colony Algorithm for Classification Rule Discovery

Real life problems are known to be messy, dynamic and multi-objective, and involve high levels of uncertainty and constraints. Because traditional problem-solving methods are no longer capable of handling this level of complexity, heuristic search methods have attracted increasing attention in recent years for solving such problems. Inspired by nature, biology, statistical mechanics, physics and neuroscience, heuristics techniques are used to solve many problems where traditional methods have failed. Data Mining: A Hueristic Approach will be a repository for the applications of these techniques in the area of data mining.