Miracle-dz/UniFAR-FTUs huggingface dataset:
Toward angiogenesis of implanted bio-artificial liver using scaffolds with type I collagen and adipose tissue-derived stem cells

Backgrounds/Aims Stem cell therapies for liver disease are being studied by many researchers worldwide, but scientific evidence to demonstrate the endocrinologic effects of implanted cells is insufficient, and it is unknown whether implanted cells can function as liver cells. Achieving angiogenesis, arguably the most important characteristic of the liver, is known to be quite difficult, and no practical attempts have been made to achieve this outcome. We carried out this study to observe the possibility of angiogenesis of implanted bio-artificial liver using scaffolds. Methods This study used adipose tissue-derived stem cells that were collected from adult patients with liver diseases with conditions similar to the liver parenchyma. Specifically, microfilaments were used to create an artificial membrane and maintain the structure of an artificial organ. After scratching the stomach surface of severe combined immunocompromised (SCID) mice (n=4), artificial scaffolds with adipose tissue-derived stem cells and type I collagen were implanted. Expression levels of angiogenesis markers including vascular endothelial growth factor (VEGF), CD34, and CD105 were immunohistochemically assessed after 30 days. Results Grossly, the artificial scaffolds showed adhesion to the stomach and surrounding organs; however, there was no evidence of angiogenesis within the scaffolds; and VEGF, CD34, and CD105 expressions were not detected after 30 days. Conclusions Although implantation of cells into artificial scaffolds did not facilitate angiogenesis, the artificial scaffolds made with type I collagen helped maintain implanted cells, and surrounding tissue reactions were rare. Our findings indicate that type I collagen artificial scaffolds can be considered as a possible implantable biomaterial.
Lossy kernelization

In this paper we propose a new framework for analyzing the performance of preprocessing algorithms. Our framework builds on the notion of kernelization from parameterized complexity. However, as opposed to the original notion of kernelization, our definitions com- bine well with approximation algorithms and heuristics. The key new definition is that of a polynomial size α-approximate kernel. Loosely speaking, a polynomial size α-approximate kernel is a polynomial time pre-processing algorithm that takes as input an instance (I, k) to a parameterized problem, and outputs another instance (I′,k′) to the same problem, such that |I′| + k′ ≤ kO(1). Additionally, for every c ≥ 1, a c-approximate solution s′ to the pre-processed instance (I′, k′) can be turned in polynomial time into a (c · α)-approximate solution s to the original instance (I,k). Amongst our main technical contributions are α-approximate kernels of polynomial size for three problems, namely Connected Vertex Cover, Disjoint Cycle Packing and Disjoint Factors. These problems are known not to admit any polynomial size kernels unless NP ⊆ coNP/Poly. Our approximate kernels simultaneously beat both the lower bounds on the (normal) kernel size, and the hardness of approximation lower bounds for all three problems. On the negative side we prove that Longest Path parameterized by the length of the path and Set Cover parameterized by the universe size do not admit even an α-approximate kernel of polynomial size, for any α≥1, unless NP ⊆ coNP/Poly. In order to prove this lower bound we need to combine in a non-trivial way the techniques used for showing kernelization lower bounds with the methods for showing hardness of approximation.
Nucleosome positioning and composition modulate in silico chromatin flexibility

The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes—the familiar assemblies of ∼150 DNA base pairs and eight histone proteins—found on chromatin fibers. Here we introduce a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs. We explore the effects of nucleosome positioning and the presence or absence of cationic N-terminal histone tails on the ‘local’ inter-nucleosomal interactions and the global deformations of the simulated chains. The correspondence between the predicted and observed effects of nucleosome composition and numbers on the long-range communication between the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We also extract effective nucleosome-nucleosome potentials from the simulations and implement the potentials in a larger-scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable effect of nucleosome spacing on chromatin flexibility, with small changes in DNA linker length significantly altering the interactions of nucleosomes and the dimensions of the fiber as a whole. In addition, we find that these changes in nucleosome positioning influence the statistical properties of long chromatin constructs. That is, simulated chromatin fibers with the same number of nucleosomes exhibit polymeric behaviors ranging from Gaussian to worm-like, depending upon nucleosome spacing. These findings suggest that the physical and mechanical properties of chromatin can span a wide range of behaviors, depending on nucleosome positioning, and that care must be taken in the choice of models used to interpret the experimental properties of long chromatin fibers.
Recursion patterns and time-analysis

This paper explores some ideas concerning the time-analysis of functional programs defined by instantiating typical recursion patterns such as folds, unfolds, and hylomorphisms. The concepts in this paper are illustrated through a rich set of examples in the Haskell programming language. We concentrate on unfolds and folds (also known as anamorphisms and catamorphisms respectively) of recursively defined types, as well as the more general hylomorphism pattern. For the latter, we use as case-studies two famous sorting algorithms, mergesort and quicksort. Even though time analysis is not compositional, we argue that splitting functions to expose the explicit construction of the recursion tree and its later consumption helps with this analysis.
Understanding others: empathy and cognitive perspective taking in the human brain

After defining “cognitive perspective taking” and “empathy” we will review the main results of neuroscientific studies of the human ability to understand other people's intentions, beliefs, and experiences. We will then present several fMRI studies investigating empathic brain responses elicited by the observation of others in pain and show how these empathic brain responses are modulated by several contextual and stimulus factors. We will integrate these results with findings on patients with Alexithymia (inability to understand and label distinct emotions and emotional experiences) and Autistic Spectrum Disorder (ASD; a neurological condition associated with a variety of social and linguistic deficits) to create a deeper understanding of the relations between interoceptive awareness, empathy, and cognitive perspective taking.
Deep brain stimulation of the subcallosal cingulate gyrus for depression: anatomical location of active contacts in clinical responders and a suggested guideline for targeting.

OBJECT Deep brain stimulation (DBS) of the subcallosal cingulate gyrus (SCG), including Brodmann area 25, is currently being investigated for the treatment of major depressive disorder (MDD). As a potential emerging therapy, optimal target selection within the SCG has still to be determined. The authors compared the location of the electrode contacts in responders and nonresponders to DBS of the SCG and correlated the results with clinical outcome to help in identifying the optimal target within the region. Based on the location of the active contacts used for long-term stimulation in responders, the authors suggest a standardized method of targeting the SCG in patients with MDD. METHODS Postoperative MR imaging studies of 20 patients with MDD treated with DBS of the SCG were analyzed. The authors assessed the location of the active contacts relative to the midcommissural point and in relation to anatomical landmarks within the medial aspect of the frontal lobe. For this, a grid with 2 main lines was designed, with 1 line in the anterior-posterior and 1 line in the dorsal-ventral axis. Each of these lines was divided into 100 units, and data were converted into percentages. The anterior-posterior line extended from the anterior commissure (AC) to the projection of the anterior aspect of the corpus callosum (CCa). The dorsal-ventral line extended from the inferior portion of the CC (CCi) to the most ventral aspect of the frontal lobe (abbreviated "Fr" for the formula). RESULTS Because the surgical technique did not vary across patients, differences in stereotactic coordinates between responders and nonresponders did not exceed 1.5 mm in any axis (x, y, or z). In patients who responded to the procedure, contacts used for long-term stimulation were in close approximation within the SCG. In the anterior-posterior line, these contacts were located within a 73.2 +/- 7.7 percentile distance from the AC (with the AC center being 0% and the line crossing the CCa being 100%). In the dorsal-ventral line, active contacts in responders were located within a 26.2 +/- 13.8 percentile distance from the CCi (with the CCi edge being 0% and the Fr inferior limit being 100%). In the medial-lateral plane, most electrode tips were in the transition between the gray and white matter of SCG. CONCLUSIONS Active contacts in patients who responded to DBS were relatively clustered within the SCG. Because of the anatomical variability in the size and shape of the SCG, the authors developed a method to standardize the targeting of this region.
The Role of Internet Service Providers in Botnet Mitigation

We studied how Internet Service Providers (ISPs) are involved in botnet mitigation in the Netherlands. Although Dutch ISPs on average perform very well with respect to botnet mitigation, botnets still are a significant threat and many end-user systems are infected by bot-malware. We created a reference model which summarizes measures for botnet mitigation from scientific literature that ISPs can take. Our model is structured according to the five stages in the anti-botnet lifecycle: prevention, detection, notification, remediation, and recovery. We validated our reference model in an empirical study by means of semi-structured interviews with a representative sample of Dutch ISPs. Our study identified which measures actually have been taken by ISPs, and why other measures have not been taken (yet). It became clear that ISPs spend most effort on prevention and notification towards customers, thereby focusing on individual bots. ISPs currently have little incentive to implement further measures for detection, remediation, and recovery. Although ISPs are well capable of applying advanced detection and follow up actions, they do not apply such measures mainly due to privacy concerns of customer data. Furthermore, although ISPs do cooperate in various ways, there still is room for improvement, particularly in the sharing of information on botnet infections and mitigation practices with stakeholders and peer ISPs.
Digital Landform Mapping 6.1 Motivation 6.2 Related Work 6.2.1 Image Segmentation 6.2.2 Intelligent Scissors Based Methods 6.2.3 Graph Cut Based Methods

Geomorphological maps are the standard means in geomorphology to perceive and investigate an area at focus in a complex and holistic way. Such maps compile knowledge on landforms, surface processes and surface materials, and have widespread applications in land management practices, natural hazard assessments or landform evolution studies [Cooke & Doornkamp 1974][Otto & Dikau 2004][Seijmonsbergen & de Graaff 2006]. Geomorphological mapping or landform mapping is the process of decomposing the land surface into structural patterns, landforms and landform elements. Traditionally, landform mapping is based on field work supplemented by the interpretation of aerial photographs and literature research. However, due to the increasing availability and quality of digital elevation models, satellite and aerial images , landform mapping is nowadays mainly performed digitally on screen. Legends and guidelines for geomorphological maps differ from country to country. A review of different geomorphological mapping systems can be found in [Rothenbühler 2003], whereas a presentation of recent mapping concepts is given in [Gustavsson et al. 2006][Seijmonsbergen & de Graaff 2006]. In Germany guidelines for geomorphological mapping at large scales (1:25,000 and 1:100,000) have been developed by [Kugler 1964] and within a national geomorphological mapping research program [Stäblein 1980]. At large scales information is often generalized for cartographic reasons, which restricts resolution and therefore the ability to discriminate between individ-91 CHAPTER 6. DIGITAL LANDFORM MAPPING ual landforms. The classification of individual landforms implies different attributes that do not only describe the individual characteristics, but also reveal information about patterns of distribution and relationships between the landforms. Dikau [Dikau 1989] divided these attributes into primary and secondary attributes. Primary attributes include only geomorphometric parameters , such as slope, aspect and curvature, that represent derivates of the elevation data. Secondary attributes refer to the position of the landform relative to the surrounding environment, shape, material, and the geomor-phodynamic and geomorphogenetic processes responsible for the landform evolution. Some recent approaches in remote sensing and GIS aim at an automatic recognition of geomorphological objects based on digital terrain data. Automatic landform recognition can be performed using elevation data only [Schmidt & Hewitt 2004][van Asselen & Seijmonsbergen 2006], or by combining elevation data and imagery information [Schneevoigt & Schrott 2006]. However, so far automatic recognition suffers from land surface complexity and its continuous character, represented by diffuse landform boundaries, overlapping landforms and a great variety of structural properties. Consequently , fully automatic landform recognition is (at least at the moment) restricted …
Performance Comparison of Entropy-Based Multipath Routing Protocol

A Mobile Ad Hoc Network (MANET) is a dynamic wireless network that can be formed without the need for any pre-existing infrastructure in which each node can act as a router. One of the main challenges MANET is the design of robust routing algorithms that adapt to the frequent and randomly changing network topology. In this paper, we compare the performance of different protocols for ad hoc networks - Ad Hoc On-Demand Distance Vector Routing (AODV), Ad Hoc On-Demand Multipath Distant Vector (AOMDV) routing. Therefore, we propose an Entropy-based multipath routing protocol in AOMDV (EAOMDV). The performance differentials are analyzed using varying node mobility. Simulations demonstrate the performance benefits of our proposal EAOMDV over AOMDV in most movement scenarios.
Fuzzy decision forest

We investigate the extension of fuzzy decision trees into fuzzy forests. Decision forests attempt to alleviate some problems often associated with decision trees: decision trees are minimalistic in their contained information, and they often degrade in complex domains, when multidimensional relationships are needed, or when there is no preference over similar actions. Moreover, the minimalistic approach often degrades the performance when some necessary features are either missing, noisy, or simply unreliable. These problems have been addressed in the last few years in hybrid systems, in which a number of distinct trees were extracted and used with some voting rules. Fuzzy decision forests follow the same ideas, except that they use more elaborate alternatives specific to local partitioning of the space. Therefore, it is an extension of those hybrid methods. In other words, while in those hybrid systems multiple choices are allowed at the level of the global search space, a fuzzy decision forest allows alternatives at every subspace level. Moreover the choice of available alternatives is data and domain-driven.
Connecting research and practice: Perspectives on the role of manualized programs in youth work

ABSTRACT While there is a strong movement in favor of the use of manual-based programs in the arena of social care, there is a view that such programs are not applicable in the more fluid setting of youth work, which operates informally, using dynamic and organic methods. A critical pedagogical approach to youth work engages young people by encouraging them to become inquisitive, to question why things are the way they are and to pose problems through which they can learn. For some, manualized or evidence-based programs are not seen as having a role in such contexts. However, to date, the international debate in relation to this issue has been limited by an absence of published studies focusing specifically on strategies to implement evidence-informed practice in youth work contexts. This article aims to address this gap in the literature. The Irish national youth organization Foróige, which works with more than 56,000 young people in Ireland on an annual basis, has developed a range of manualized evidence-informed resources to support its youth work over recent years. Drawing on research findings from a range of studies conducted with youth workers focusing on implementation of these resources, the article explores the benefits and tensions associated with the use of program manuals in a youth work context. The findings suggest that such resources have a valuable role to play in youth work if designed in collaboration with youth workers, showing respect for core youth work values and allowing for flexibility and adaptability in implementation.
A network-layer proxy for bandwidth aggregation and reduction of IP packet reordering

With today's widespread deployment of wireless technologies, it is often the case that a single communication device can select from a variety of access networks. At the same time, there is an ongoing trend towards integration of multiple network interfaces into end-hosts, such as cell phones with HSDPA, Bluetooth and WLAN. By using multiple Internet connections concurrently, network applications can benefit from aggregated bandwidth and increased fault tolerance. However, the heterogeneity of wireless environments introduce challenges with respect to implementation, deployment, and protocol compatibility. Variable link characteristics cause reordering when sending IP packets of the same flow over multiple paths. This paper introduces a multilink proxy that is able to transparently stripe traffic destined for multihomed clients. Operating on the network layer, the proxy uses path monitoring statistics to adapt to changes in throughput and latency. Experimental results obtained from a proof-of-concept implementation verify that our approach is able to fully aggregate the throughput of heterogeneous downlink streams, even if the path characteristics change over time. In addition, our novel method of equalizing delays by buffering packets on the proxy significantly reduces IP packet reordering and the buffer requirements of clients.
Irreducible form for AP algorithm for detecting the number of coherent signals based on the MDL principle

This paper presents an improvement of the alternating projection (AP) algorithm for detecting the number of coherent signals based on the minimum description length (MDL) principle using a uniform linear array of sensors. The criterion of the AP algorithm for the detection becomes indefinite, when estimated bearings more than one approach to the identical value. This paper derives an irreducible form of the AP criterion for the detection, which never get indefinite. The irreducible form is represented as a rational function and real-valued version of the FFT can be exploited efficiently. The proposed algorithm reduces the order of the amount of arithmetic operations. Finally, simulation results are shown to demonstrate the validity of the proposed algorithm.
Research Note - Quality Uncertainty and the Performance of Online Sponsored Search Markets: An Empirical Investigation

Online sponsored search advertising has emerged as the dominant online advertising format largely because of their pay-for-performance nature, wherein advertising expenditures are closely tied to outcomes. While the pay-for-performance format substantially reduces the wastage incurred by advertisers compared to traditional pay-per-exposure advertising formats, the reduction of such wastage also carries the risk of reducing the signaling properties of advertising. Lacking a separating equilibrium, low-quality firms in these markets may be able to mimic the advertising strategies of high-quality firms. This study examines this issue in the context of online sponsored search markets. Using data gathered from sponsored search auctions for keywords in a market without intervention by the intermediary, we find evidence of adverse selection for products/services characterized by high uncertainty. On the other hand, there is no evidence of adverse selection for similar products in a regulated sponsored search market, suggesting that intervention by the search intermediary can have a significant impact on market outcomes and consumer welfare.
Shape-based Transfer Function Using Laplace-Beltrami Operator

We exploit the Laplace-Beltrami operator to represent shapes which in turn is used for designing a shape based transfer function for volume rendering. Laplace-Beltrami spectral measures are isometry invariant and are one of the most powerful ways to represent shape, also called “Shape-DNA”. Isosurfaces are extracted from the volume data and the Laplace-Beltrami operator is applied on these extracted isosurfaces. We use the Laplace-Beltrami spectrum of the extracted isosurfaces and the corresponding eigenvalues and eigenvectors for representing shape. These eigenvalues and eigenvectors are used to design the transfer function based on shape. We call these eigenvectors shape eigenvectors as they successfully define various shapes in a model. These shape eigenvectors are represented as parallel lines and the color and opacity values are varied using an interface which is a modified form of parallel coordinates, termed as parallel segmentation. We demonstrate the results of our method on several standard datasets. As we are using the shape eigenvectors to design the transfer function, we call this transfer function as shape-frequency based transfer function.