Miracle-dz/UniFAR-FTUs huggingface dataset:
Upregulation of the tumor suppressor gene menin in hepatocellular carcinomas and its significance in fibrogenesis

The molecular mechanisms underlying the progression of cirrhosis toward hepatocellular carcinoma were investigated by a combination of DNA microarray analysis and literature data mining. By using a microarray screening of suppression subtractive hybridization cDNA libraries, we first analyzed genes differentially expressed in tumor and nontumor livers with cirrhosis from 15 patients with hepatocellular carcinomas. Seventy‐four genes were similarly recovered in tumor (57.8% of differentially expressed genes) and adjacent nontumor tissues (64% of differentially expressed genes) compared with histologically normal livers. Gene ontology analyses revealed that downregulated genes (n = 35) were mostly associated with hepatic functions. Upregulated genes (n = 39) included both known genes associated with extracellular matrix remodeling, cell communication, metabolism, and post‐transcriptional regulation gene (e.g., ZFP36L1), as well as the tumor suppressor gene menin (multiple endocrine neoplasia type 1; MEN1). MEN1 was further identified as an important node of a regulatory network graph that integrated array data with array‐independent literature mining. Upregulation of MEN1 in tumor was confirmed in an independent set of samples and associated with tumor size (P = .016). In the underlying liver with cirrhosis, increased steady‐state MEN1 mRNA levels were correlated with those of collagen α2(I) mRNA (P < .01). In addition, MEN1 expression was associated with hepatic stellate cell activation during fibrogenesis and involved in transforming growth factor beta (TGF‐β)–dependent collagen α2(I) regulation. In conclusion, menin is a key regulator of gene networks that are activated in fibrogenesis associated with hepatocellular carcinoma through the modulation of TGF‐β response. (HEPATOLOGY 2006;44:1296–1307.)
Comparison of the risk of revision in cementless total hip arthroplasty with ceramic-on-ceramic and metal-on-polyethylene bearings

Background and purpose — Ceramic-on-ceramic (CoC) bearings were introduced in total hip arthroplasty (THA) to reduce problems related to polyethylene wear. We compared the 9-year revision risk for cementless CoC THA and for cementless metal-on-polyethylene (MoP) THA. Patients and methods — In this prospective, population-based study from the Danish Hip Arthroplasty Registry, we identified all the primary cementless THAs that had been performed from 2002 through 2009 (n = 25,656). Of these, 1,773 THAs with CoC bearings and 9,323 THAs with MoP bearings were included in the study. To estimate the relative risk (RR) of revision, we used regression with the pseudo-value approach and treated death as a competing risk. Results — 444 revisions were identified: 4.0% for CoC THA (71 of 1,773) and 4.0% for MoP THA (373 of 9,323). No statistically significant difference in the risk of revision for any reason was found for CoC and MoP bearings after 9 years of follow-up (adjusted RR = 1.3, 95% CI: 0.72–2.4). Revision rates due to component failure were 0.5% (n = 8) for CoC bearings and 0.1% (n = 6) for MoP bearings (p < 0.001). 6 patients with CoC bearings (0.34%) underwent revision due to ceramic fracture. Interpretation — When compared to the “standard” MoP bearings, CoC THA had a 33% higher (though not statistically significantly higher) risk of revision for any reason at 9 years.
The BlackWidow High-Radix Clos Network

This paper describes the radix-64 folded-Clos network of the Cray BlackWidow scalable vector multiprocessor. We describe the BlackWidow network which scales to 32Kprocessors with a worst-case diameter of seven hops, and the underlying high-radix router micro architecture and its implementation. By using a high-radix router with many narrow channels we are able to take advantage of the higher pin density and faster signaling rates available in modern ASIC technology. The BlackWidow router is an 800 MHz ASIC with 64 18.75Gb/s bidirectional ports for an aggregate off-chip bandwidth of 2.4Tb/s. Each port consists of three 6.25Gb/s differential signals in each direction. The router supports deterministic and adaptive packet routing with separate buffering for request and reply virtual channels. The router is organized hierarchically (Kim et al., 2005) as an 8times8 array of tiles which simplifies arbitration by avoiding long wires in the arbiters. Each tile of the array contains a router port, its associated buffering, and an 8times8 router subswitch. The router ASIC is implemented in a 90nm CMOS standard cell ASIC technology and went from concept to tapeout in 17 months
The childhood obesity epidemic: lessons for preventing socially determined health conditions.

Between 2000 and 2010, there were almost 3 times as many publications in the Archives about childhood obesity as in the preceding 90 years of the journal’s history. This reflected efforts to understand a child health problem that caught the public’s attention because it was so common, visible, costly, and difficult to treat. Despite all the research on childhood obesity, we have not reversed the epidemic. One explanation may be that obesity, like all health conditions that are primarily socially-determined, resists durable solutions until there is a change in societal norms and the values underlying those norms. The childhood obesity epidemic is just one symptom of our way of living. Reversing the epidemic may require that we apply a new approach to improving child health in the 21st century. One approach is to make societal changes to enhance human well-being rather than to prevent a particular symptom, such as childhood obesity. In the process, we may address obesity and other socially-determined health conditions while preventing new ones from emerging.
Comparison of Decision Learning Models Using the Generalization Criterion Method

It is a hallmark of a good model to make accurate a priori predictions to new conditions (Busemeyer & Wang, 2000). This study compared 8 decision learning models with respect to their generalizability. Participants performed 2 tasks (the Iowa Gambling Task and the Soochow Gambling Task), and each model made a priori predictions by estimating the parameters for each participant from 1 task and using those same parameters to predict on the other task. Three methods were used to evaluate the models at the individual level of analysis. The first method used a post hoc fit criterion, the second method used a generalization criterion for short-term predictions, and the third method again used a generalization criterion for long-term predictions. The results suggest that the models with the prospect utility function can make generalizable predictions to new conditions, and different learning models are needed for making short-versus long-term predictions on simple gambling tasks.
Functional Characterization of Aquaporin-4 Specific T Cells: Towards a Model for Neuromyelitis Optica

Background Antibodies to the water channel protein aquaporin-4 (AQP4), which is expressed in astrocytic endfeet at the blood brain barrier, have been identified in the serum of Neuromyelitis optica (NMO) patients and are believed to induce damage to astrocytes. However, AQP4 specific T helper cell responses that are required for the generation of anti-AQP4 antibodies and most likely also for the formation of intraparenchymal CNS lesions have not been characterized. Methodology/Principal Findings Using overlapping 15-meric peptides of AQP4, we identified the immunogenic T cell epitopes of AQP4 that are restricted to murine major histocompatibility complex (MHC) I-Ab. The N-terminal region of AQP4 was highly immunogenic. More precisely, the intracellular epitope AQP422–36 was detected as major immunogenic determinant. AQP482–108 (located in the second transmembrane domain), AQP4139–153 (located in the second extracellular loop), AQP4211–225 (located in the fifth transmembrane domain), AQP4235–249 (located in the sixth transmembrane domain), as well as AQP4289–306 in the intracellular C-terminal region were also immunogenic epitopes. AQP422–36 and AQP4289–303 specific T cells were present in the natural T cell repertoire of wild type C57BL/6 mice and T cell lines were raised. However, active immunization with these AQP4 peptides did not induce signs of spinal cord disease. Rather, sensitization with AQP4 peptides resulted in production of IFN-γ, but also IL-5 and IL-10 by antigen-specific T cells. Consistent with this cytokine profile, the AQP4 specific antibody response upon immunization with full length AQP4 included IgG1 and IgG2, which are associated with a mixed Th2/Th1 T cell response. Conclusions and Significance AQP4 is able to induce an autoreactive T cell response. The identification of I-Ab restricted AQP4 specific T cell epitopes will allow us to investigate how AQP4 specific autoimmune reactions are regulated and to establish faithful mouse models of NMO that include both cellular and humoral responses against AQP4.
Embryogenesis of the serotonergic system in the earthworm Eisenia fetida (Annelida, Oligochaeta): Immunohistochemical and biochemical studies

Organization of the serotonergic system and changes of the serotonin (5‐HT) content were studied during the embryogenesis of the earthworm Eisenia fetida, using immunocytochemistry and HPLC. A gradual emergence of 5‐HT immunoreactive (IR) cells and their axon projections in the several ganglia of the central (CNS) and peripheral nervous system are described in the context of a staged time‐scale of development. The first 5‐HT‐IR neurons appear in the subesophageal ganglion at an early embryonic stage (E2), followed by neurons in some rostrally located ventral ganglia. In the cerebral ganglion, 5‐HT‐IR cells can be detected only from stage E5. The number of labeled cells in each ganglion of the embryo increases until hatching, when it is still considerably lower than that observed in adults. This shows that the development of the 5‐HTergic system is far from complete by the end of embryogenesis. Organization of 5‐HT‐IR innervation of the body wall starts by stages E3 to E4. In the stomatogastric nervous system the first 5‐HT‐IR fibers can be detected by stage E5. By stage E9 5‐HT immunopositive neurons can be observed in both the stomatogastric ganglia and the enteric plexus. Both 5‐HT levels and the numbers of the labeled cells show a significant increase before hatching, which indicate a functional maturation of the 5‐HTergic system. Based on the early appearance of 5‐HT, we suppose that it may play a regulatory role in both the gangliogenesis and the maturation of peripheral functions necessary during postembryonic life. J. Comp. Neurol. 497:451–467, 2006. © 2006 Wiley‐Liss, Inc.
Interobserver Reproducibility of MIB-1 Labeling Index in Astrocytic Tumors Using Different Counting Methods

MIB-1 labeling index has been used as a complementary method to differentiate better and worse prognostic groups of astrocytic tumors. However, its reproducibility has been doubted because of the interlaboratory and interobserver variability. We studied the interobserver reproducibility of four manual counting methods of MIB-1 labeling index, including direct counting, area fraction, line intersection with a graticule, and line intersection without a graticule to estimate the total number of the cells. Using line intersection estimate, either with or without a graticule, yielded a worse result. Those MIB-1 labeling indices of astrocytomas were overlapping with those of anaplastic astrocytomas and glioblastomas. Besides, the intraclass correlation coefficient was smaller, and the coefficient of variation was greater than that attained when using a graticule and counting the total number of cells either directly or by area-fraction estimate. The level of interobserver agreement using an MIB-1 labeling index cutoff value of 11.0 was moderate to substantial when applying the line-intersection estimate, and it was almost perfect when applying the direct counting or the area-fraction estimate. The interobserver reproducibility and agreement of MIB-1 labeling index in astrocytic tumors were different depending on the counting methods. Direct counting with a graticule yielded the best result. Before establishing reference standards for staining and counting, the reproducibility of MIB-1 labeling index should be verified.
Development of the two-wheeled inverted pendulum type mobile robot WV-2R for educational purposes

The rapidly increase of personal robotic platforms and their applications in Japan represents a great challenge for universities to introduce undergraduate students the basic knowledge required to develop intelligent automated mechanisms. For this purpose; in this paper, we are presenting our approach to introduce first year undergraduate students of the Department of Modern Mechanical Engineering the basics of robotics systems. In order to foster the creativity of undergraduate students of engineering fields, we focused in developing an education tool designed to introduce at different educational levels the principle of developing mechatronic systems. In particular, the development of an inverted pendulum mobile robot Waseda Wheeled Vehicle No. 2 (WV-2R) has been proposed. Different kinds of experiments were proposed to confirm the possibility of implementing controllers as well as changing physical properties of the system to observe differences on the response of the system. From the experimental results, we could confirm the effectiveness of the proposed systems to control the angle of pendulum respect to the body base as well as by changing the radius of the wheel.
Are the Faraday Rotating Magnetic Fields Local to Intracluster Radio Galaxies?

We investigate the origin of the high Faraday rotation measures (RMs) found for polarized radio galaxies in clusters. The two most likely origins are magnetic fields local to the source or magnetic fields located in the foreground intracluster medium. The latter is identified as the null hypothesis. Rudnick & Blundell have recently suggested that the presence of magnetic fields local to the source may be revealed in correlations of the position angles (PAs) of the source-intrinsic linear polarization and the RMs. We investigate the claim of Rudnick & Blundell that they have found a relationship between the intrinsic PA0 of the radio source PKS 1246-410 and its RM by testing the clustering strength of the PA0-RM scatter plot. We show that the claimed relationship is an artifact of an improperly performed null experiment. We describe a gradient alignment statistic aimed at finding correlations between PA0 and RM maps. This statistic does not require any null experiment since it gives a unique (zero) result in the case of uncorrelated maps. We apply it to a number of extended radio sources in galaxy clusters (PKS 1246-410, Cygnus A, Hydra A, and 3C 465). In no case is a significant large-scale alignment of PA0 and RM maps detected. We find significant small-scale co-alignment in all cases, but we are able to fully identify this with map-making artifacts through a suitable statistical test. We conclude that there is presently no existing evidence for Faraday rotation local to radio lobes. Given the existing independent pieces of evidence, we favor the null hypothesis that the observed Faraday screens are produced by intracluster magnetic fields.
GPU Production Rendering

This chapter is not about realtime rendering. It’s about a world in which rendering takes sec-onds, minutes, or hours. It’s about users who require features that are extremely difﬁcult toimplement on modern graphics hardware. But we’d still like to take advantage of the tremen-dous horsepower that GPUs afford us.First, we’ll discuss the arcane world of production rendering for ﬁlm (and other non-gamehigh-end uses) — what people need from a ﬁlm renderer, and how this is different from a gameengine.Next, we’ll dive into the gory details about how GPUs were used for certain features inNVIDIA’s Gelato
QKD in Isabelle - Bayesian Calculation

In this paper, we present a first step towards a formalisation of the Quantum Key Distribution algorithm in Isabelle. We focus on the formalisation of the main probabilistic argument why Bob cannot be certain about the key bit sent by Alice before he does not have the chance to compare the chosen polarization scheme. This means that any adversary Eve is in the same position as Bob and cannot be certain about the transmitted keybits. We introduce the necessary basic probability theory, present a graphical depiction of the protocol steps and their probabilities, and finally how this is translated into a formal proof of the security argument.
Only-Knowing: Taking It Beyond Autoepistemic Reasoning

The idea of only-knowing a collection of sentences has been previously shown to have a close connection with autoepistemic logic. Here we propose a more general account of only-knowing that captures not only autoepistemic logic but default logic as well. This allows us not only to study the properties of default logic in terms of an underlying model of belief, but also the relationship among different forms of nonmonotonic reasoning, all within a classical monotonic logic characterized semantically in terms of possible worlds.
Hierarchical DAG Scheduling for Hybrid Distributed Systems

Accelerator-enhanced computing platforms have drawn a lot of attention due to their massive peak commutational capacity. Despite significant advances in the programming interfaces to such hybrid architectures, traditional programming paradigms struggle with mapping the resulting multi-dimensional heterogeneity and the expression of algorithm parallelism, resulting in sub-optimal effective performance. Task-based programming paradigms have the capability to alleviate some of the programming challenges on distributed hybrid many-core architectures. In this paper we take this concept a step further by showing that the potential of task-based programming paradigms can be greatly increased with minimal modification of the underlying runtime combined with the right algorithmic changes. We propose two novel recursive algorithmic variants for one-sided factorizations and describe the changes to the PaRSEC task-scheduling runtime to build a framework where the task granularity is dynamically adjusted to adapt the degree of available parallelism and kernel efficiency according to runtime conditions. Based on an extensive set of results, we show that, with one-sided factorizations, i.e. Colicky, and QR, a carefully written algorithm, supported by an adaptive tasks-based runtime, is capable of reaching a degree of performance and scalability never achieved before in distributed hybrid environments.
Interpretable Multiclass Models for Corporate Credit Rating Capable of Expressing Doubt

Corporate credit rating is a process to classify commercial enterprises based on their creditworthiness. Machine learning algorithms can construct classification models, but in general they do not tend to be 100% accurate. Since they can be used as decision support for experts, interpretable models are desirable. Unfortunately, interpretable models are provided by only few machine learners. Furthermore, credit rating often is a multiclass problem with more than two rating classes. Due to this fact, multiclass classification is often achieved via meta-algorithms using multiple binary learners. However, most state-of-the-art meta-algorithms destroy the interpretability of binary models. In this study, we present Thresholder, a binary interpretable threshold-based disjunctive normal form (DNF) learning algorithm in addition to modifications of popular multiclass meta-algorithms which maintain the interpretability of our binary classifier. Furthermore, we present an approach to express doubt in the decision of our model. Performance and model size are compared with other interpretable approaches for learning DNFs (RIPPER) and decision trees (C4.5) as well as non-interpretable models like random forests, artificial neural networks, and support vector machines. We evaluate their performances on three real-life data sets divided into three rating classes. In this case study all threshold-based and interpretable models perform equally well and significantly better than other methods. Our new Thresholder algorithm builds the smallest models while its performance is as good as the best methods of our case study. Furthermore, Thresholder marks many potential misclassifications in advance with a doubt label without increasing the classification error.
On Improving the Multicast Performance of Application Layer Multicast

In the group application, poor multicast trees might be built in some join sequences. Additionally, group members are dynamic, which sometimes brings negative influence on the multicast tree. This paper analyzes the poor shapes of multicast trees, and proposes an additional improvement scheme to enhance the multicast performance. The proposed scheme rearranges the locations of members in terms of a distance-heuristics, which makes the improved multicast tree be coincident with the underlying network topology in some degree. The simulation results show that our proposed improvement scheme can effectively enhance the multicast performance.
Securing ad hoc routing protocols

Ad hoc networks are subject of many recent research efforts. Especially in mobile scenarios, self-organizing networks are of high interest. While the routing aspects of mobile ad hoc networks (MANETs) are already well understood, the research activities about security in MANETs are still at their beginning. MANETs pose a number of new security problems in addition to the problems of regular networks. In addition to the classical security threats we identified additional ways how nodes may attack security in an ad hoc network. We explore several aspects of possible (mis)behaviour of MANET participants. We introduce a systematology of attacks on a MANET. Further, we describe the results of simulations that show, how misbehaving nodes affect MANETs based on the DSR routing protocol. Finally we outline a security architecture that provides substantial security services for ad hoc networks.
Rendering and Interaction on Projection-Based Light Field Displays

Current generation glasses-free 3D displays strive to present a 3D scene from multiple viewing positions. Many efforts have been made in recent past to make the discrete viewing positions as continuous as possible as it increases the degree of reality in displaying. Deploying a hologram, projection-based light field displays provide a photorealistic means to display a 3D scene and overcome the shortcomings of other known glasses-free 3D displays. With increased field of view (FOV) and more closer viewing positions/angles, these displays allow multiple users to freely move in front of the display to perceive 3D without any obstacles. Projection-based light field displays, therefore, have a high potential to be the future 3D display solution and novel methods to process the visual data required by such displays are highly needed. The main aim of this work is to explore this visual data to enable deeper understanding and efficient representation. In particular, the work investigates various rendering techniques for light field displays and proposes the requirements for future technologies that deal with light field rendering, distribution and interaction in the context of projection-based light field displays. Using 3D computer graphics, it is possible to acquire and render light rays from any given arbitrary positions to define a light field. However, a stable means to acquire, process and render light field from real-world scenes that meet the requirements of such light field displays in real-time are not fully available yet. The current work outlines the available real-time rendering procedures for light field displays from multiview content and presents the possible directions for improvements. In addition, the work also reports on interaction experiments dealing with interactive visualization in synthetic environment. This work has applications in free view point television, tele-presence, virtual reality and video conferencing systems.