Miracle-dz/UniFAR-FTUs huggingface dataset:
Document Visualization Overview and Detail by Selectively Varying Density

The challenges of network data display are among the most longstanding in visualization. Current approaches typically rely on some form of network abstraction to reduce network density, or “clutter”, to reveal structural elements salient for the task at hand. Any reduction of complexity must consider the competing goals of providing visual representations that reveal overall, global relations, as well as detailed, local relations. The present work addresses this issue by utilizing the Pathfinder network representation, which allows systematic variation in density, to provide differing, but formally complementary, visual representations. These representations can provide both global context and local detail by selectively increasing structural complexity in a way that overcomes some of the limitations of other techniques. The paper’s examples are drawn from the domain of document relations, though the techniques are broadly applicable.
Simulating Secondary Inorganic Aerosols using the chemistry transport model MOCAGE version R2.15.0

The study presents the development and evaluation of a Secondary Inorganic Aerosol (SIA) scheme within the chemical transport model (CTM) MOCAGE. Global and regional evaluation is performed to asses the performance of the CTM with and without the SIA scheme. Overall results are consistent with other studies and indicate a better performance of the CTM with the SIA scheme, in most cases. A variety of validation datasets at the global and European scales are used in the assessment of the performance as well as established statistical measures. Overall the model version with the SIA scheme performs better in terms of modeled Aerosol Optical Depth (AOD) against satellite data. It also has better agreement with in situ measurements of secondary inorganic aerosols precursos showing a reduction in Modified Normalized Mean Bias (MNMB). Overall the paper is well written and easy to read. It presents new model developments and it is definitely appropriate for GMD. I have a few comments below, but otherwise I can recommend it for publication.
Finite element modeling of a vibrating beam with a breathing crack: observations on crack detection

This article develops a finite element model in order to study the vibrational behavior of a beam with a nonpropagating edge crack. According to this model, the beam is discretized into finite elements while the breathing crack behavior is treated as a full frictional contact problem between the crack surfaces. The nonlinear dynamic equations of this model are solved using an incremental iterative procedure. The derived response is analyzed using either Fourier or wavelet transforms in order to determine the breathing crack effects. This study is applied to a cantilever beam subjected to dynamic loadings. Parametric studies are conducted to investigate the sensitivity of vibrational behavior to the crack angle, depth, and position. The accuracy of the results is validated through comparisons with results available from the literature.
Establishing Logical Rules from Empirical Data

We review a method of generating logical rules, or axioms, from empirical data. This method, using closed set properties of formal concept analysis, has been previously described and tested on rather large sets of deterministic data. The contribution of this paper is a completely new extension of this method to create implications involving numeric inequalities.
ETH-CVL @ MediaEval 2015: Learning Objective Functions for Improved Image Retrieval

In this paper, we present a method to select a rened subset of images, given an initial list of retrieved images. The goal of any image retrieval system is to present results that are maximally relevant as well as diverse. We formulate this as a subset selection problem and we address it using submodularity. In order to select the best subset, we learn an objective function as a linear combination of submodular functions. This objective quanties how relevant and representative a selected subset it. Using this method we obtain promising results at MediaEval 2015.
Multiuser Random Coding Techniques for Mismatched Decoding

This paper studies multiuser random coding techniques for channel coding with a given (possibly suboptimal) decoding rule. For the mismatched discrete memoryless multiple-access channel, an error exponent is obtained that is tight with respect to the ensemble average, and positive within the interior of Lapidoth's achievable rate region. This exponent proves the ensemble tightness of the exponent of Liu and Hughes in the case of maximum-likelihood decoding. An equivalent dual form of Lapidoth's achievable rate region is given, and the latter is shown to immediately extend to channels with infinite and continuous alphabets. In the setting of single-user mismatched decoding, similar analysis techniques are applied to a refined version of superposition coding, which is shown to achieve rates at least as high as standard superposition coding for any set of random-coding parameters.
Arabidopsis Type III Gγ Protein AGG3 Is a Positive Regulator of Yield and Stress Responses in the Model Monocot Setaria viridis

Heterotrimeric G-proteins are key regulators of a multitude of growth and development pathways in eukaryotes. Along with the conserved G-protein components found in all organisms, plants have certain novel variants with unique architecture, which may be involved in the regulation of plant-specific traits. The higher plant-specific type III (or Class C) Gγ protein, which possesses a large C terminal extension, represented by AGG3 in Arabidopsis, is one such variant of canonical Gγ proteins. The type III Gγ proteins are involved in regulation of many agronomically important traits in plants, including seed yield, organ size regulation, abscisic acid (ABA)-dependent signaling and stress responses, and nitrogen use efficiency. However, the extant data, especially in the monocots, present a relatively complex and sometimes contradictory picture of the regulatory role of these proteins. It remains unclear if the positive traits observed in certain naturally occurring populations are due to the presence of specific allelic variants of the proteins or due to the altered expression of the gene itself. To address these possibilities, we have overexpressed the Arabidopsis AGG3 gene in the model monocot Setaria viridis and systematically evaluated its role in conferring agriculturally relevant phenotypes. Our data show that AtAGG3 is indeed functional in Setaria and suggest that a subset of the traits affected by the type III Gγ proteins are indeed positively correlated with the gene expression level, while others might have more complex, allele specific regulation.
A low complexity Reed-Solomon architecture using the Euclid's algorithm

This paper describes an efficient pipelined Reed-Solomon (RS) decoder. The proposed RS decoder architecture is based on the Euclid's algorithm, which can reduce the hardware complexity by more than 16% of existing RS architecture. The proposed RS decoder can be programmed to decode four RS codes defined in Galois field 2/sup 8/, i.e. (200, 188), (120, 108), (60, 48), and (40, 28) and can correct up to six errors. We have developed VHDL models and performed logic synthesis using the SYNOPSYS CAD tool. We have used the SAMSUNG 0.6 /spl mu/m SOG (Sea-of-Gates) cell library (KG75000). The total number of gates is about 31,000 and the proposed RS decoder operates at 40 MHz for the worst case simulations.
The ECCO Tool: Extraction and Composition for Clone-and-Own

Software reuse has become mandatory for companies to compete and a wide range of reuse techniques are available today. However, ad hoc practices such as copying existing systems and customizing them to meet customer-specific needs are still pervasive, and are generically called clone-and-own. We have developed a conceptual framework to support this practice named ECCO that stands for Extraction and Composition for Clone-and-Own. In this paper we present our Eclipse-based tool to support this approach. Our tool can automatically locate reusable parts from previously developed products and subsequently compose a new product from a selection of desired features. The tools demonstration video can be found here: http://youtu.be/N6gPekuxU6o.
A Convex Approach to Validation-Based Learning of the Regularization Constant

This letter investigates a tight convex relaxation to the problem of tuning the regularization constant with respect to a validation based criterion. A number of algorithms is covered including ridge regression, regularization networks, smoothing splines, and least squares support vector machines (LS-SVMs) for regression. This convex approach allows the application of reliable and efficient tools, thereby improving computational cost and automatization of the learning method. It is shown that all solutions of the relaxation allow an interpretation in terms of a solution to a weighted LS-SVM
Compliance measurements of chevron notched four point bend specimen

The experimental stress intensity factors for various chevron notched four point bend specimens are presented. The experimental compliance is verified using the analytical solution for a straight through crack four point bend specimen and the boundary integral equation method for one chevron geometry. Excellent agreement is obtained between the experimental and analytical results. In this report, stress intensity factors, loading displacements and crack mouth opening displacements are reported for different crack lengths and different chevron geometries, under four point bend loading condition.
Shape from Video : Dense Shape , Texture , Motion and Lighting from Monocular Image Streams

This paper presents a probabilistic framework for robust recovery of dense 3D shape, motion, texture and lighting from monocular image streams. We assume that the object is smooth, Lambertian, illuminated by one distant light source, and subject to smoothly-varying rigid motion. The problem is formulated as a MAP estimation problem in which all shape, motion, noise variances and outlier probabilities are estimated simultaneously. Estimation is performed using a multi-stage initialization process followed by a large-scale quasi-Newtonian optimization technique.
Three-Dimensional Statistical Analysis of Sulcal Variability in the Human Brain

Morphometric variance of the human brain is qualitatively observable in surface features of the cortex. Statistical analysis of sulcal geometry will facilitate multisubject atlasing, neurosurgical studies, and multimodality brain mapping applications. This investigation describes the variability in location and geometry of five sulci surveyed in each hemisphere of six postmortem human brains placed within the Talairach stereotaxic grid. The sulci were modeled as complex internal surfaces in the brain. Heterogeneous profiles of three-dimensional (3D) variation were quantified locally within individual sulci. Whole human heads, sectioned at 50 μm, were digitally photographed and high-resolution 3D data volumes were reconstructed. The parieto-occipital sulcus, the anterior and posterior rami of the calcarine sulcus, the cingulate and marginal sulci, and the supracallosal sulcus were delineated manually on sagittally resampled sections. Sulcal outlines were reparameterized for surface comparisons. Statistics of 3D variation for arbitrary points on each surface were calculated locally from the standardized individual data. Additional measures of surface area, extent in three dimensions, surface curvature, and fractal dimension were used to characterize variations in sulcal geometry. Paralimbic sulci exhibited a greater degree of anterior– posterior variability than vertical variability. Occipital sulci displayed the reverse trend. Both trends were consistent with developmental growth patterns. Points on the occipital sulci displayed a profile of variability highly correlated with their 3D distance from the posterior commissure. Surface curvature was greater for the arched paralimbic sulci than for those bounding occipital gyri in each hemisphere. On the other hand, fractal dimension measures were remarkably similar for all sulci examined, and no significant hemispheric asymmetries were found for any of the selected spatial and geometric parameters. Implications of cortical morphometric variability for multisubject comparisons and brain mapping applications are discussed.
The Impact of Local Search on Protein-Ligand Docking Optimization

Common evolutionary approaches to protein-ligand docking optimization use mutation operators based on Gaussian and Cauchy distributions, with local search hybrids. The choice of a local search method is important for an efficient algorithm. We investigate the impact of local search with mutation operators by performing a locality analysis. High locality means that small variations in the genotype imply small variations in the phenotype. Results show that local search hybrids reduce locality and act as local optimizers with the solution as a starting point.
A New Road Map for Neuroprotection

Background and Purpose— There have now been numerous phase III trials of neuroprotection that have failed to live up to the expectations created by preclinical testing in animal models, the most recent of which was the second pivotal trial of the spin trap agent NXY-059. We have reached a stage at which research in this area should stop altogether or radical new approaches adopted. The purpose of this article is to review how we reached this stage and make recommendations for a new approach to neuroprotection research. Methods— The background to neuroprotection research is reviewed and its problems are highlighted based on the research of others and of our own research group. From this, a series of questions are posed that require answers if the field is to progress. A road map for future research is then proposed. Results— The road map involves the following steps for putative neuroprotectants: (1) better proof of efficacy in animal models; (2) in vivo evidence of efficacy in human tissue using cell cultures or brain slices; (3) in vivo studies of their distribution in the normal and ischemic human brain, particularly focusing on the ischemic penumbra; (4) demonstration of efficacy in novel human models of cerebral ischemia; and (5) phase II and III clinical trails with penumbral selection using imaging techniques. Conclusions— The accumulated evidence suggests that neuroprotection failure in clinical trial is due to identifiable preclinical and clinical factors. Neuroprotection research should be pursued but with a very different and more rigorous approach.
Paging with multiple caches

Modern content delivery networks consist of one or more "back-end" servers which store the entire content catalog, assisted by multiple "front-end" servers with limited storage and service capacities located near the end-users. Appropriate replication of content on the front-end servers is key to maximize the fraction of requests served by the front-end servers. Motivated by this, a multiple cache variant of the classical single cache paging problem is studied, which is referred to as the Multiple Cache Paging (MCP) problem. In each time-slot, a batch of content requests arrive that have to be served by a bank of caches, and each cache can serve exactly one request. If a content is not found in the bank, it is fetched from the back-end server, and one currently stored content is ejected, and counted as `fault'. As in the classical paging problem, the goal is to minimize the total number of faults. The competitive ratio of any online algorithm for the MCP problem is shown to be unbounded for arbitrary input, thus concluding that the MCP problem is fundamentally different from the classical paging problem. Consequently, stochastic arrivals setting is considered, where requests arrive according to a known/unknown stochastic process. It is shown that near optimal performance can be achieved with simple policies that require no co-ordination across the caches.
Diagnosis of non-overt disseminated intravascular coagulation made according to the International Society on Thrombosis and Hemostasis criteria with some modifications

Background An early diagnosis of disseminated intravascular coagulation (DIC) before its progression to an overt stage is necessary for early treatment and positive outcomes. In 2001, the Scientific and Standardization Committee (SCC) of the International Society on Thrombosis and Hemostasis (ISTH) proposed new criteria for the preclinical diagnosis of overt and non-overt DICs. We investigated the clinical usefulness of the modified ISTH criteria for non-overt DIC diagnosis. Methods We enrolled 296 DIC patients (170 males and 126 females) admitted and evaluated at the Gangnam Severance Hospital, Seoul, Korea, between March 2006 and April 2007. Hemostatic tests, including platelet counts, prothrombin time (PT), D-dimer levels with antithrombin, and protein-C levels, were evaluated by excluding negative scores with clinical signs, in which more than 5 points of interest denoted non-overt DIC. Mortality rates were also evaluated. Results There were 289 patients with increased D-dimer levels and significant parametric changes suggesting DIC progression. Protein C and antithrombin levels were lower (99.2% each) and appeared earlier in patients with non-overt DIC than in patients with overt DIC. In all, 125 (43.3%) patients had non-overt DIC and, of which 27 died (mortality rate, 21.6%). The sensitivity and specificity for mortality were 73.0% and 55.9%, respectively, which were same as those for the original ISTH criteria. Conclusion The modified ISTH criteria can be used for the early detection of non-overt DIC, and may be useful for the improvement of outcomes of non-overt DIC patients.
Practical application of probabilistic reliability analyses

Liberalization of the energy markets has increased the cost pressure on network operators significantly. Corresponding cost saving measures in general will have negative effects on quality of supply, especially on supply reliability. On the other hand, a decrease of supply reliability is not acceptable for customers and politicians - and the public awareness was focused by several blackouts in the European and American transmission systems. In order to handle this delicate question of balancing network costs and supply reliability, detailed and above all quantitative information is required in the network planning process. A suitable tool for this task is probabilistic reliability analysis, which has already been in use for several years successfully. The method and possible applications are briefly described here and application is demonstrated with various examples from practical studies focusing on distribution systems. The results prove that reliability analyses are becoming an indispensable component of customer-oriented network planning
Biomedical Applications of Graphene

Graphene exhibits unique 2-D structure and exceptional phyiscal and chemical properties that lead to many potential applications. Among various applications, biomedical applications of graphene have attracted ever-increasing interests over the last three years. In this review, we present an overview of current advances in applications of graphene in biomedicine with focus on drug delivery, cancer therapy and biological imaging, together with a brief discussion on the challenges and perspectives for future research in this field.
A novel operating scheme of five-level hybrid inverters for medium voltage applications

In this paper, a new operating scheme for five-level hybrid flying-capacitor (5L-HFC) inverters is proposed, of which structure is derived from the conventional five-level active neutral-point-clamped (5L-ANPC) topology by splitting the DC-link into three capacitors in series. In this inverter, the lower number of switching devices is required, thus its cost is reduced considerably compared with the existing five-level inverter topologies. In addition, a balancing scheme of the DC-link and flying capacitor voltages is developed. Simulation and experiment results have verified the validity of the proposed topology.
Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events

Lung cancer is a highly heterogeneous disease in terms of both underlying genetic lesions and response to therapeutic treatments. We performed deep whole-genome sequencing and transcriptome sequencing on 19 lung cancer cell lines and three lung tumor/normal pairs. Overall, our data show that cell line models exhibit similar mutation spectra to human tumor samples. Smoker and never-smoker cancer samples exhibit distinguishable patterns of mutations. A number of epigenetic regulators, including KDM6A, ASH1L, SMARCA4, and ATAD2, are frequently altered by mutations or copy number changes. A systematic survey of splice-site mutations identified 106 splice site mutations associated with cancer specific aberrant splicing, including mutations in several known cancer-related genes. RAC1b, an isoform of the RAC1 GTPase that includes one additional exon, was found to be preferentially up-regulated in lung cancer. We further show that its expression is significantly associated with sensitivity to a MAP2K (MEK) inhibitor PD-0325901. Taken together, these data present a comprehensive genomic landscape of a large number of lung cancer samples and further demonstrate that cancer-specific alternative splicing is a widespread phenomenon that has potential utility as therapeutic biomarkers. The detailed characterizations of the lung cancer cell lines also provide genomic context to the vast amount of experimental data gathered for these lines over the decades, and represent highly valuable resources for cancer biology.
Mild cognitive impairment: conceptual issues and structural and functional brain correlates.

Mild cognitive impairment (MCI) is a prevalent condition among older adults that carries a high risk of progression to Alzheimer's disease or other dementias. Given the potential for delaying or preventing the onset of dementia, efforts aimed at early detection and early intervention are important. The current paper reviews the conceptualization and diagnosis of MCI, assessment of memory complaints and deficits in the elderly, as well as recent research on the neurobiological basis of the disorder, including neurochemical, structural, and functional neuroimaging findings.
Restoring Phineas Gage: A 150th Retrospective

September 13 1998 marked the 150th anniversary of the accident to Phineas Gage, one of the most famous cases of survival after massive injury to the brain, and certainly the most famous case of personality change after brain damage. For this article a sample of the current literature about Gage was examined. It was found that although his case is mentioned in about 60% of introductory textbooks in psychology, there is a good deal of inaccuracy in what has been written about him. Similar inaccuracy was found in a smaller sampling of the psychiatric, medical, physiological, linguistic, and general neuroscientific literature. The main basis of the inaccuracies is an ignorance or disregard of what is contained in the primary sources about Gage, coupled with a tendency to attribute to him characteristics that belong to other cases of frontal damage. The errors and their bases are discussed in an endeavour to restore the picture of Gage to its original state. The paper includes an Appendix of verbatim quotations from the primary sources that can be compared with the later, inaccurate renditions.