Miracle-dz/UniFAR-FTUs huggingface dataset:
Complement System in Pathogenesis of AMD: Dual Player in Degeneration and Protection of Retinal Tissue

Age-related macular degeneration (AMD) is the most common cause of blindness among the elderly, especially in Western countries. Although the prevalence, risk factors, and clinical course of the disease are well described, its pathogenesis is not entirely elucidated. AMD is associated with a variety of biochemical abnormalities, including complement components deposition in the retinal pigment epithelium-Bruch's membrane-choriocapillaris complex. Although the complement system (CS) is increasingly recognized as mediating important roles in retinal biology, its particular role in AMD pathogenesis has not been precisely defined. Unrestricted activation of the CS following injury may directly damage retinal tissue and recruit immune cells to the vicinity of active complement cascades, therefore detrimentally causing bystander damage to surrounding cells and tissues. On the other hand, recent evidence supports the notion that an active complement pathway is a necessity for the normal maintenance of the neurosensory retina. In this scenario, complement activation appears to have beneficial effect as it promotes cell survival and tissue remodeling by facilitating the rapid removal of dying cells and resulting cellular debris, thus demonstrating anti-inflammatory and neuroprotective activities. In this review, we discuss both the beneficial and detrimental roles of CS in degenerative retina, focusing on the diverse aspects of CS functions that may promote or inhibit macular disease.
General morphisms of Petri nets

A new notion of a general morphism of Petri nets is introduced. The new morphisms are shown to properly include the morphisms considered so far. The resulting category of general Petri nets is shown to admit products. Here, it is shown that the new notion turns out to be indispensable to facilitate functoriality of synthesis of transition systems by means of (labelled) state machines. In the companion paper this result is used to synthesize concrete asynchronous systems studied by Morin as a mixed products of state machines. Uogolnione Morfizmy Sieci Petriego
Quality estimation of PSK modulated signals

The use of the Ka band (30/20 GHz) for satellite communication systems raises the problem of dealing with rain attenuation. A very important problem in fade countermeasure systems is the need to detect signal quality quickly and accurately. In fact, the countermeasure has to be initiated before the signal degradation effect an the bit error rate is detected by the user. This article presents an overview of different methods to evaluate signal quality, which are based on the availability of soft quantized levels of PSK demodulated signals at the receiver. It is shown that this class of methods has a good theoretical performance. Also, an innovative procedure is presented which adapts one of the methods to some existing hardware, and tunes up a set of parameters in order to compensate for the fact that the hardware is to same extent impaired.
Ataxia with Cerebellar Lesions in Mice Expressing Chimeric PrP-Dpl Protein

Mutations within the central region of prion protein (PrP) have been shown to be associated with severe neurotoxic activity similar to that observed with Dpl, a PrP-like protein. To further investigate this neurotoxic effect, we generated lines of transgenic (Tg) mice expressing three different chimeric PrP-Dpl proteins. Chi1 (amino acids 1–57 of Dpl replaced by amino acids 1–125 of PrP) and Chi2 (amino acids 1–66 of Dpl replaced by amino acids 1–134 of PrP) abrogated the pathogenicity of Dpl indicating that the presence of a N-terminal domain of PrP (23–134) reduced the toxicity of Dpl, as reported. However, when the amino acids 1–24 of Dpl were replaced by amino acids 1–124 of PrP, Chi3 Tg mice, which express the chimeric protein at a very low level, start developing ataxia at the age of 5–7 weeks. This phenotype was not counteracted by a single copy of full-length-PrPc but rather by its overexpression, indicating the strong toxicity of the chimeric protein Chi3. Chi3 Tg mice exhibit severe cerebellar atrophy with a significant loss of granule cells. We concluded that aa25 to aa57 of Dpl, which are not present in Chi1 and Chi2 constructs, confer toxicity to the protein. We tested this possibility by using the 25–57 Dpl peptide in primary culture of mouse embryo cortical neurons and found a significant neurotoxic effect. This finding identifies a protein domain that plays a role in mediating Dpl-related toxicity.
Monitoring and performance measuring distributed systems during operation

This paper describes an integrated tool for monitoring distributed systems continuously during operation. A hybrid monitoring approach is used. As special hardware support a test and measurement processor (TMP) was designed, which is part of each node in an experimental multicomputer system. Each TMP runs local parts of the monitoring software for its node, while all the TMPs are connected to a central test station via a separate TMP interconnection network. The monitoring system is transparent to users. It permanently observes system behavior, measures system performance and records system information. The immense amount of information is graphically displayed in easy-to-read-charts and graphs in an application-oriented manner. The tools promote an improved understanding of run time behavior and performance measurements to derive qualitative and even quantitative assessments about distributed systems. A prototype of the monitoring facility is operational and currently experiments are being conducted in our distributed system consisting of several MC68000 microcomputers.
A capacitive vibration-to-electricity energy converter with integrated mechanical switches

Due to recent advances in low-power VLSI design technology, it has become feasible to power portable or remote electronic devices by scavenging the ambient energy. The design, fabrication and measurement of a capacitive vibration-to-electricity energy converter are presented in this paper. With a device area constraint of 1 cm2 and an auxiliary battery supply of 3.6 V, the device was designed to generate an output power of 31 µW with an output saturation voltage of 40 V. An external mass of 4 g was needed to adjust the device resonance to match the input vibration of 2.25 m s−2 at 120 Hz. Mechanical contact switches were integrated onto the device to provide accurate charge–discharge energy conversion timing. The device was fabricated in SOI (silicon-on-insulator) wafers by deep silicon etching technology. Parasitic capacitance was minimized by partial back side substrate removal. Resonant frequencies of the fabricated device with and without the external mass agreed with the expected values. Without the external mass, the measured ac output power was 1.2 µW with a load of 5 MΩ at 1870 Hz. Detailed circuit modeling and ac output power measurement of the devices with the external mass attached are in progress.
It takes a village: Monitoring the blue waters supercomputer

The performance of science applications on modern HPC equipment depends on many factors. Architectural features, individual hardware characteristics, and scheduler traits all have an impact on how a particular application performs, not only in isolation but when run in concert with other user applications. Being able to correlate system events and conditions at particular times can give insight into causes of good or bad performance. Unfortunately, the information we seek is not necessarily in a readily accessible form. The problem at hand is how to enable efficient query of the raw data and flexible graphical representation of the results. Web applications that access an underlying database serve this sort of functionality for many science applications quite well. Our scenario of data access is not very different. The data collected for a large HPC environment is complex and grows in size with time. This aspect is different from applications that deal with more static data. It is the dynamic nature of the data that make the problem interesting. In this work we present our approach for the analysis and visualization of HPC system performance data based on database access and web based graphical presentation. We discuss the details of how data is collected and processed from raw logs into the database, how queries are formulated, and how the data are graphically displayed. This process includes dynamic formulation of the queries. Finally we discuss how the system is utilized to analyze system performance.
A fast retrieval algorithm for the earth mover’s distance using EMD lower bounds

Earth Mover’s Distance (EMD) is a distance measure between two distributions, and have been widely used in multimedia information retrieval systems, especially content-based image retrieval systems. When the EMD is applied to image problems based on color or texture, the EMD reflects the human perceptual similarities. Its computations, however, is too expensive to use in large-scale databases. In order to achieve the efficient computation of the EMD during query processing, we have developed “fastEMD”, a library for high-speed feature-based similarity retrievals in large databases. This paper introduces techniques that are used in the implementation of the fastEMD and demonstrates the efficiency in extensive experiments.
Cardioprotection in the aging, diabetic heart: the loss of protective Akt signalling.

AIMS Old age and diabetes are risk factors that often coexist increasing the vulnerability of the heart to the lethal effects of ischaemia-reperfusion injury (IRI). However, to our knowledge, no investigations have examined IRI and cardioprotective signalling in animal models bearing these co-morbidities concomitantly. The ability of the heart to recover following IRI is greatly dependent on its innate cardioprotective potential, in which a central role is played by Akt. We aimed to investigate in an aging diabetic rat model, the susceptibility of the heart to IRI, the achievability of ischaemic preconditioning (IPC) against this lethal event, and the changes in Akt signalling, as the main prosurvival intracellular pathway. METHODS AND RESULTS Our data showed that the isolated hearts of aged, diabetic Goto-Kakizaki rats were more susceptible to sub-lethal injury and not amenable to cardioprotection via IPC, compared with younger diabetic rat hearts. Western blot analysis of the heart tissue suggested a chronic up-regulation of Akt phosphorylation, and reduced expression of the mitochondrial regulator PGC-1α and of the anti-oxidant enzyme catalase, potentially due to the Akt up-regulation. Moreover, no further activation of Akt could be achieved following IPC. CONCLUSION An increased susceptibility to IRI in the aged, diabetic heart could be a consequence of impaired Akt signalling due to chronic Akt phosphorylation. Additional Akt phosphorylation required for IPC protection may therefore not be possible in the aged, diabetic rat heart and may explain why this cardioprotective manoeuvre cannot be achieved in these hearts.
Detection of lipid-induced structural changes of the Marburg virus matrix protein VP40 using hydrogen/deuterium exchange-mass spectrometry

Marburg virus (MARV) is a lipid-enveloped virus from the Filoviridae family containing a negative sense RNA genome. One of the seven MARV genes encodes the matrix protein VP40, which forms a matrix layer beneath the plasma membrane inner leaflet to facilitate budding from the host cell. MARV VP40 (mVP40) has been shown to be a dimeric peripheral protein with a broad and flat basic surface that can associate with anionic phospholipids such as phosphatidylserine. Although a number of mVP40 cationic residues have been shown to facilitate binding to membranes containing anionic lipids, much less is known on how mVP40 assembles to form the matrix layer following membrane binding. Here we have used hydrogen/deuterium exchange (HDX) mass spectrometry to determine the solvent accessibility of mVP40 residues in the absence and presence of phosphatidylserine and phosphatidylinositol 4,5-bisphosphate. HDX analysis demonstrates that two basic loops in the mVP40 C-terminal domain make important contributions to anionic membrane binding and also reveals a potential oligomerization interface in the C-terminal domain as well as a conserved oligomerization interface in the mVP40 N-terminal domain. Lipid binding assays confirm the role of the two basic patches elucidated with HD/X measurements, whereas molecular dynamics simulations and membrane insertion measurements complement these studies to demonstrate that mVP40 does not appreciably insert into the hydrocarbon region of anionic membranes in contrast to the matrix protein from Ebola virus. Taken together, we propose a model by which association of the mVP40 dimer with the anionic plasma membrane facilitates assembly of mVP40 oligomers.
Opportunistic sampling-based planning for active visual SLAM

This paper reports on an active visual SLAM path planning algorithm that plans loop-closure paths in order to decrease visual navigation uncertainty. Loop-closing revisit actions bound the robot's uncertainty but also contribute to redundant area coverage and increased path length.We propose an opportunistic path planner that leverages sampling-based techniques and information filtering for planning revisit paths that are coverage efficient. Our algorithm employs Gaussian Process regression for modeling the prediction of camera registrations and uses a two-step optimization for selecting revisit actions. We show that the proposed method outperforms existing solutions for bounding navigation uncertainty with a hybrid simulation experiment using a real-world dataset collected by a ship hull inspection robot.
On the Capacity Achieving Covariance Matrix for Rician MIMO Channels: An Asymptotic Approach

In this paper, the capacity-achieving input covariance matrices for coherent block-fading correlated multiple input multiple output (MIMO) Rician channels are determined. In contrast with the Rayleigh and uncorrelated Rician cases, no closed-form expressions for the eigenvectors of the optimum input covariance matrix are available. Classically, both the eigenvectors and eigenvalues are computed numerically and the corresponding optimization algorithms remain computationally very demanding. In the asymptotic regime where the number of transmit and receive antennas converge to infinity at the same rate, new results related to the accuracy of the approximation of the average mutual information are provided. Based on the accuracy of this approximation, an attractive optimization algorithm is proposed and analyzed. This algorithm is shown to yield an effective way to compute the capacity achieving matrix for the average mutual information and numerical simulation results show that, even for a moderate number of transmit and receive antennas, the new approach provides the same results as direct maximization approaches of the average mutual information.
Frayed at the edges: selective pressure and adaptive response to abiotic stressors are mismatched in low diversity edge populations

1 Theory predicts that population structure and dynamics affect a population's capacity for adaptation to environmental change. For isolated, small and fragmented populations at the trailing edge of species distributions, loss of genetic diversity through random genetic drift may reduce adaptive potential and fitness levels for complex traits. This has important consequences for understanding population responses to, for example changing climate, but has rarely been tested in natural populations. 2 We measured the intertidal thermal environment and tidal exposure (emersion) times for natural populations of the intertidal seaweed Fucus serratus at the centre (southwest UK) and southern edge (northern Portugal) of its range in the Eastern Atlantic, and for a congener, F. vesiculosus, whose range extends further south to Morocco. Fitness‐related traits of individuals at each location were measured in common garden experiments: physiological resilience to desiccation and heat shock (PSII quantum yield), and the molecular phenotype of the heat shock response (quantitative PCR of heat shock protein gene transcripts). 3 The realized thermal environment experienced by F. serratus was similar at the centre and southern edge of its distribution because the maximum shore height (and emersion period) was reduced in southern populations. For F. vesiculosus, thermal maxima were higher and occurred more frequently in the south, although maximum vertical height (emersion time) remained similar to central populations. 4 Edge populations of F. serratus were less resilient to desiccation and heat shock than central populations, and expression of heat shock genes was higher at the same temperature, suggesting greater cellular stress. In contrast, there was no evidence for physiological divergence in heat shock response in F. vesiculosus, and little variation in gene expression. 5 Synthesis. We provide evidence that compared with range‐centre populations upper intertidal limits of F. serratus at the southern edge are ‘pruned back’ by abiotic stressors. Rather than being locally adapted, these small populations are less resilient to abiotic stresses and experience greater cellular stress during heat shock. These results suggest that ongoing climate forcing factors may threaten small, fragmented rear edge populations because of inherently reduced fitness and lower adaptive capacity relative to larger central populations.
A Novel (DDCC-SFG)-Based Systematic Design Technique of Active Filters

This paper proposes a novel idea for the synthe- sis of active filters that is based on the use of signal-flow graph (SFG) stamps of differential difference current con- veyors (DDCCs). On the basis of an RLC passive network or a filter symbolic transfer function, an equivalent SFG is constructed. DDCCs' SFGs are identified inside the con- structed 'active' graph, and thus the equivalent circuit can be easily synthesized. We show that the DDCC and its 'derivatives', i.e. differential voltage current conveyors and the conventional current conveyors, are the main basic building blocks in such design. The practicability of the proposed technique is showcased via three application examples. Spice simulations are given to show the viability of the proposed technique.
Stream fusion using reactive programming, LINQ and magic updates

The paradigm of reactive programming has attained more and more interest in recent time. In this paper, we show why reactive programming is a well-suited paradigm for sensor fusion algorithms. As a new contribution, we show how the efficiency of stream-oriented reactive programs can be enhanced by applying the magic update method that originally stems from the field of update propagation in deductive databases.
Head pose estimation using random forest and texture analysis

In this paper, we propose a new head pose estimation technique based on Random Forest (RF) and Multi-scale Block Local Block Pattern (MB-LBP) features. In the proposed technique we aim to learn a randomized tree with useful attributes to improve the estimation accuracy and tolerance of occlusions and illumination. Precisely, a number of MB-LBP feature spaces are generated from a face image, and random inputs and random features such as the MB-LBP scale parameter and the block coordinate in the pool are used for building the tree. Furthermore we develop a split function considering the properties of the uniform LBP, applied to each internal node of the tree to maximize the information gain at that node. The randomized trees put together in RF are used for the final decision in a Maximum-A-Posteriori criterion. Experimental results demonstrate that the proposed technique provides impressive performance in the head pose estimation in various conditions of illumination, poses, expressions, and facial occlusions.
Speech enhancement method with geometric phase estimation by incorporating MIXMAX model

In this paper, we propose a frequency-domain speech enhancement algorithm with phase estimation, in which the speech model is modeled by a Gaussian mixture model (GMM) in the log-spectral domain and two closed-form log-spectral amplitude estimators for speech and noise are derived directly by using a Mixture-Maximum (MIXMAX) model. Because the accurate estimation of speech phase could help to reduce the undesired noise residues in the enhanced signal, our two log-spectral estimators are also used to construct a geometric approach for phase estimation in each frequency bin. In order to solve the ambiguity problem in phase estimation, we utilize the complex linear predictive analysis (CLPA) and inconsistency constraint to find an appropriate phase. Experimental results show that, in comparison with the reference methods, the proposed method achieves an efficient improvement in speech quality.
Mammary gland-derived nestin + cell populations can be isolated from human male and female donors

Mammary gland-derived nestin+ cell populations can be isolated from human male and female donors Stem Cell Research & Therapy 2013, 4:78 doi:10.1186/scrt229 Anja Richter (anjarichter3011@gmail.com) Nicole Nissen (nicole.nissen@emb.fraunhofer.de) Peter Mailänder (peter.mailaender@uni-luebeck.de) Felix Stang (felix.stang@gmx.de) Frank Siemers (f.siemers@gmx.de) Charli Kruse (charli.kruse@emb.fraunhofer.de) Sandra Danner (sandra.danner@emb.fraunhofer.de)
Meta-analyses comparing theory of mind abilities of individuals with autism, individuals with mental retardation, and normally developing individuals.

A deficit in theory of mind (ToM) abilities has been described as the core deficit in autism. The authors performed 3 meta-analyses, comparing ToM abilities of individuals with autism, individuals with mental retardation (MR), and normally developing individuals. Results indicated that individuals with autism and MR have impaired ToM abilities. The etiology associated with MR (i.e., Down syndrome, undifferentiated etiology) was found to be an important moderator variable. Chronological age (CA) and verbal mental age (VMA) of the normally developing children and CA, VMA, and performance mental age of individuals with MR, and type of matching between the groups were also found to be moderator variables. Discussion focuses on the implication of the findings and emphasizes the need to consider the specific etiology of comparison groups when studying abilities and impairments of individuals with autism and MR.