Miracle-dz/UniFAR-FTUs huggingface dataset:
Ion RNA-Seq Methods , tools , and pipelines for analysis of Ion PGM

High-resolution measurements of transcriptional activity and organization have been made possible in recent years through massively parallel RNA sequencing (RNA-Seq) technologies. The level of precision enabled by this technology has been demonstrated to be superior to traditional platforms for measuring gene expression in a cell type or tissue [1,2]. Furthermore, with increased sequencing depth, other more specialized analyses such as identification of novel splice variants [3], transcript fusions in cancer [4], and microRNAs [5] (miRNA) are possible. The depth needed for a given experiment is informed by the biological question at hand and complexity of the transcriptome being measured.
Frame-guided exploration of WordNet

In this paper we claim that an integration of FrameNet and WordNet will improve interoperability, user-friendliness and usability of both lexical resources. If the former provides a sophisticated representational structure compared to a narrow lexical coverage, the latter - on the other side - supplies a dense network of word senses and semantic relations although not supporting advanced accessibility (i
] 3 0 Ju l 2 00 4 How to simulate the quasi-stationary state

For a large class of processes with an absorbing state, statistical properties of the surviving sample attain time-independent values in the quasi-stationary (QS) regime. We propose a practical simulation method for studying quasi-stationary properties, based on the equation of motion governing the QS distribution. The method is tested in applications to the contact process. At the critical point, our method is about an order of magnitude more efficient than conventional simulation. PACS: 05.10. -a, 02.50. Ga, 05.40. -a, 05.70. Ln ∗electronic address: mancebo@fisica.ufmg. br †electronic address: dickman@fisica.ufmg. br
Multi-criteria distribution network selection

Balancing high levels of performance and reduced costs has become a crucial goal for organizations. Managers nowadays thrive to achieve a competitive advantage through the optimization of the supply chain distribution network (DN). This work proposes a decision making approach for choosing the right DN. Based on prioritized criteria such as SC responsiveness and costs, it allows comparing different distribution networks and selecting the most appropriate one; in two cases of prioritization of the decision maker. The ranking of these alternatives is done through the application of the multi-criteria decision analysis (MCDA) method AHP (Analytic Hierarchy Process).
Computerized paleography: Tools for historical manuscripts

The Digital Age has brought with it large-scale digitization of historical records. The modern scholar of history or of other disciplines is often faced today with hundreds of thousands of readily-available and potentially-relevant full or fragmentary documents, but without computer aids that would make it possible to find the sought-after needles in the proverbial haystack of online images. The problems are even more acute when documents are handwritten, since optical character recognition does not provide quality results. We consider two tools: (1) a handwriting matching tool that is used to join together fragments of the same scribe, and (2) a paleographic classification tool that matches a given document to a large set of paleographic samples. Both tools are carefully designed not only to provide a high level of accuracy, but also to provide a clean and concise justification of the inferred results. This last requirement engenders challenges, such as sparsity of the representation, for which existing solutions are inappropriate for document analysis.
Fast feature selection using hybrid ranking and wrapper approach for automatic fault diagnosis of motorpumps based on vibration signals

This work presents a novel hybrid approach for feature selection using a combination of ranking and wrapper methods. Its main goal is to select features quickly, without significant loss of classification performance. Experiments comparing this approach with Sequential Forward Feature (SFS) selection showed its viability using Support Vector Machine and K-Nearest Neighbor classifiers in specific scenarios. As a test bed, vibrational signals were employed which need a previous feature extraction stage to create a classification system. In two experiments, 74 and 130 features were extracted from these databases. The proposed approach performed at least ten times faster than SFS, with 0.32% loss of accuracy in the worst case, requiring 26% to 57.5% less features to achieve its highest accuracy.
Gastrointestinal effects of resistant starch, soluble maize fibre and pullulan in healthy adults

Fibre has been shown to exert a number of benefits on gastrointestinal (GI) health, yet its intake is low. Addition of novel fibres to food products may increase fibre intake and improve gut health. The objective of the present study was to evaluate the influence of three novel fibres on GI outcomes in healthy human subjects. A total of twenty healthy participants (ten men and ten women) with normal BMI (23 (sem 2) kg/m2) participated in the present randomised, double-blind, cross-over study with five treatment periods. Participants consumed a maltodextrin control or 20–25 g/d fibre from soluble maize fibre (SCF) or resistant starch (RS), alone or in combination with pullulan (SCF+P and RS+P). The treatment periods were 7 d with a 3-week washout between the periods. Stool samples were collected on day 7 of each period, and GI tolerance was assessed via a questionnaire on days 1 and 6. There were no treatment differences in stool weight or consistency. SCF significantly reduced stool pH and increased total SCFA production compared with RS and control. RS+P significantly increased the percentage of butyrate compared with all the other treatments. Overall, GI symptoms were minimal. SCF+P led to the highest GI score on day 1, while RS+P had the highest score on day 6. Both SCF treatments caused a significant shift in the gut microbial community. These functional fibres are generally well tolerated, have minimal effects on laxation and may lead to beneficial changes in SCFA production in healthy adults.
Software Power as Soft Power. A Literature Review on Computational Propaganda Effects in Public Opinion and Political Process

This article draws on a systematic literature review of recently-published material to investigate the state of the art of research into how social network profiles are being used to manipulate public opinion on political issues. The aim of this review is to discuss how the use of these profiles impacts on constructing consensus, authority, legitimacy and representativeness of politicians, parties, hegemonic and minority groups. In total, 369 articles were obtained following a bibliographic search on four different scientific citation indexing databases. Of those, 16 were considered relevant to the research question. In order to identify general trends and specific results, the pertinent papers were subjected to descriptive and critical analysis. Five main approaches were observed: A) Usage policies and platform neutrality; B) Definition, detection and description of the manipulation agents; C) Political role of agents on social networks; D) Attempted electoral predictions via social networks; and E) Network dynamics and strategies for disseminating information. In the conclusion, the results of the literature review are discussed.
European Union Data Protection Policy ’Location privacy in the next generation mobile Internet’

The global telecommunication infrastructure will slowly converge toward an integrated packet switched network using the Internet Protocol as the common communication technology. First evidence of this convergence is the deployment of the third generation wireless infrastructure that brings together the radio access network and core network by using the next generation Internet Protocol IPv6. The paper presents how ’mobility’ is supported in IPv6. Mobility is the capability of mobile terminal to be reachable by its home network IP address with independence of the point of attachment to the Internet. We show the kind of information items that are required to be in transit in the network to allow a mobile node to seamlessly communicate on the move. The European Commission proposal for a Directive (COM(2000)385) on ’processing of personal data and protection of privacy in the electronic communication sector’ is kept in a technological neutral manner which means that no standards are imposed. It includes de(cid:28)nitions inter alia on ’location data’ and ’tra(cid:30)c data’ and foresees privacy safeguards and different levels of protection for distinct kind of data. After the technical and legal overview we discuss the di(cid:30)culties to apply the de(cid:28)nitions provided by the Directive to certain technology as mobility in IPv6. Based on the reasoning included in the paper we argue that classifying and de(cid:28)ning data by traditional means and ways without taking into account Inter-net’s multi-layered architecture might lead to an in-su(cid:30)cient level of privacy protection for certain sensitive data and might not be the most appropriate way to adapt and update the existing provisions to new and foreseeable developments in electronic communications services and technologies.
Botnet Detection with DNS Monitoring

Botnets are today the universal tool for malicious activities in the Internet. They can send out spam messages, host fairly redundant malicious webpages, perform DDoS attacks and do much more. Of course, researchers have therefore been trying to eectively find and shut down botnets as quickly as possible. The Domain Name System has become an important part of such botnets, for both the botmaster and the defender. It enables botmasters to either hide their content servers via fast-flux, but also oers a good possibility to communicate with the Command and Control server in the background with the help of Domain Generation Algorithms. This paper gives an overview on recent developments in the field of detecting botnets with the help of the Domain Name System and evaluates the dierent solutions in terms of required input, practicability, eciency and privacy.
Draft Contractual Savings and Capital Markets Development : An Analysis of OECD Countries ’ Evidence *

This paper analyzes the mechanics of the relationship between the development of contractual savings (pension funds and life insurance) and capital markets. The focus is on macroeconomics and financial effects of contractual savings development. It is mainly an empirical study. The evidence on the relation between contractual savings and capital markets development is presented for OECD countries. At the theoretical level, we explain how the growth of the contractual savings sector promotes financial development and economic growth. We find that among institutional investors, contractual savings institutions are the most effective to develop capital markets. This is because their liabilities are illiquid assets in asset holders’ portfolio.
Specificities of killing by T lymphocytes generated against syngeneic SV40 transformants: studies employing recombinants within the H-2 complex.

T lymphocyte effectors to syngeneic SV40-transformed cells, generated by secondary in vitro sensitization of immune spleen cells, lyse SV40 transformed targets that are syngeneic at the H-2 locus. In this study we have employed recombinants within the H-2 region to examine in detail this H-2 specificity. H-2b effectors were found to lyse SV40-transformed targets from recombinants bearing either H-2Kb or H-2Db.H-2k effectors recognized only SV40-transformed H-2Kk, and not H-2Dk target cells. By using the same protocol for sensitization, no effector cells could be detected in H-2d mice. Effectors generated in H-2 recombinant mice showed that the response capacity resides with K and D. For example, HTG, which is H-2d except at the D locus (H-2Db), produced effector cells specific for SV40-transformed H-2Db targets. Thus, the secondary in vitro response to SV40 transformants was found to depend only on the K and D alleles and not to be modified by the I region to any measurable extent.
Unified Boundary-Aware Texturing for Interactive Volume Rendering

In this paper, we describe a novel approach for applying texture mapping to volumetric data sets. In contrast to previous approaches, the presented technique enables a unified integration of 2D and 3D textures and thus allows to emphasize material boundaries as well as volumetric regions within a volumetric data set at the same time. One key contribution of this paper is a parametrization technique for volumetric data sets, which takes into account material boundaries and volumetric regions. Using this technique, the resulting parametrizations of volumetric data sets enable texturing effects which create a higher degree of realism in volume rendered images. We evaluate the quality of the parametrization and demonstrate the usefulness of the proposed concepts by combining volumetric texturing with volumetric lighting models to generate photorealistic volume renderings. Furthermore, we show the applicability in the area of illustrative visualization.
Understanding and Augmenting Ideation Processes

To effectively support individual contributors in large scale ideation settings, we need a computational understanding of their cognitive processes. Although related work exists that references models from psychology, there are two shortcomings in existing approaches: First, they only analyse ideas on a statistical level. Second, they lack a notion of individual ideator differences. This work proposes a new user model for ideation, based on process-models from psychology and knowledge-graph based information extraction from submitted idea-texts. By building a computational model of ideation, this work aims to enable new graph-based analysis methods of cognitive ideation processes and new approaches to adaptive ideation support systems. These systems could be used to detect and counter fixation in individuals and to guide group efforts based on categories that should be explored.
Decision-Making in Recommender Systems: The Role of User's Goals and Bounded Resources

factors that influence users' decision making processes in Recommender Systems (RSs) have been investigated by a relatively vast research of empirical and theoretical nature, mostly in the field of e - commerce . In this paper, we discuss some aspects of the user experience with RSs that may affect the decision making process and outcome, and have been marginally addressed by prior research. These include the nature of users' goals and the dynamic characteristics of the resources space (e.g., availability during the search process) . We arg ue that these subjective and objective factors of the user experience with a RS call for a rethinking of the decision making process as it is normally assumed in traditional RSs, and raise a number or research challenges. These concepts are exemplified in the application domain of on - line services , specifically, hotel booking - a field where w e are carrying on a number of activities in cooperation with a large stakeholder ( Venere.com - a company of Expedia Inc.). Still, most of the arguments discussed in the paper can be extended to other domains, and have general implications for RS design and evaluation.
SHAPIRO STEPS IN A SUPERCONDUCTING FILM WITH AN ANTIDOT LATTICE

Shapiro voltage steps at voltages V_n=nV_0 (n integer) have been observed in the voltage-current characteristics of a superconducting film with a square lattice of perforating microholes (antidots)in the presence of radiofrequent radiation. These equidistant steps appear at the second matching field H_2 when the flow of the interstitial vortex lattice in the periodic potential created by the antidots and the vortices trapped by them, is in phase with the applied rf frequency. Therefore, the observation of Shapiro steps clearly reveals the presence of mobile intersitial vortices in superconducting films with regular pinning arrays. The interstitial vortices, moved by the driving current, coexist with immobile vortices strongly pinned at the antidots.
Comet 67P/Churyumov-Gerasimenko preserved the pebbles that formed planetesimals

Solar System formation models predict that the building-blocks of planetesimals were mm- to cm-sized pebbles, aggregates of ices and non-volatile materials, consistent with the compact particles ejected by comet 67P/Churyumov-Gerasimenko (67P hereafter) and detected by GIADA (Grain Impact Analyzer and Dust Accumulator) on-board the Rosetta spacecraft. Planetesimals were formed by the gentle gravitational accretion of pebbles, so that they have an internal macroporosity of 40%. We measure the average dust bulk density ${\rho}D = 795 _{-65}^{+840} kg m^{-3}$ that, coupled to the 67P nucleus bulk density, provides the average dust-to-ices mass ratio δ = 8.5. We find that the measured densities of the 67P pebbles are consistent with a mixture of (15 ± 6)% of ices, (5 ± 2)% of Fe-sulfides, (28 ± 5)% of silicates, and (52 ± 12)% of hydrocarbons, in average volume abundances. This composition matches both the solar and CI-chondritic chemical abundances, thus showing that GIADA has sampled the typical non-volatile composition of the pebbles that formed all planetesimals. The GIADA data do not constrain the abundance of amorphous silicates vs. crystalline Mg,Fe- olivines and pyroxenes. We find that the pebbles have a microporosity of (52 ± 8)% (internal volume filling factor φP = 0.48±0.08), implying an average porosity for the 67P nucleus of (71 ± 8)%, lower than previously estimated.
Prevention of Fault Propagation in Web Service: a Complex Network Approach

How to prevent the fault propagation problems in Web Service has become an important issue. The recent research works mostly take some fault tolerance method in service based system. These methods detect or diagnose faults in the composition process, find the failure service, take tolerance action and recover the system. However, in the service oriented architecture, one service is shared by different service based systems. The fault tolerance method only considers from the view of one service user, and tolerance action not considering the whole network would change its load and even the global redistribution of loads over all of the services, trigger a cascade of overload, and result in service network paralysis. The research of cascading failure in Complex Network provides a set of models to help study the above problems. Consequently, this paper proposes a new approach to deal with the fault propagation for Web Service from the view point of the whole service network, which could analyze its resistance influenced by the size of network, different types of attacks and load allocation strategies and prevent the disasters from happening. Firstly, it constructs a Web Service Complex Network (WSCN) composed of single service and their functional similarity. Then it models fault propagation based on WSCN, and simulates the propagation process by analyzing WSCN performance under small attack, large attack, random attack and calculated attack. When fault happens in WSCN, our method uses weight-based and spare-load-based load allocation methods of failed service to compare their influences on the whole network. The experimental results show that when fault happens in WSCN, the network has better resistance for small scale failure than big scale one, and resists stronger for random attack than deliberate one; when the service failure happens, the remaining space based load allocation strategy on it has higher robustness than weight based one. The simulation of fault propagation for Web Service could set example for preventing and reducing probabilities of collapse in the service network.
A new criterion to compare different LDPC codes for hardware implementation

In this paper we propose a new combinational criterion as a mean for comparison between different LDPC codes in terms of complexity and efficiency. The main idea behind the proposed criterion is to merge different aspects of a code to a unique number. We will show that the new criterion, named ldquoGoodness Numberrdquo or GN, is applicable, and in some circumstances it is preferred to other criteria such as complexity and error probability criteria and at the same time it maintains computational simplicity.
Neuronal Nicotinic Receptors in Sleep-Related Epilepsy: Studies in Integrative Biology

Although Mendelian diseases are rare, when considered one by one, overall they constitute a significant social burden. Besides the medical aspects, they propose us one of the most general biological problems. Given the simplest physiological perturbation of an organism, that is, a single gene mutation, how do its effects percolate through the hierarchical biological levels to determine the pathogenesis? And how robust is the physiological system to this perturbation? To solve these problems, the study of genetic epilepsies caused by mutant ion channels presents special advantages, as it can exploit the full range of modern experimental methods. These allow to extend the functional analysis from single channels to whole brains. An instructive example is autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE), which can be caused by mutations in neuronal nicotinic acetylcholine receptors. In vitro, such mutations often produce hyperfunctional receptors, at least in heterozygous condition. However, understanding how this leads to sleep-related frontal epilepsy is all but straightforward. Several available animal models are helping us to determine the effects of ADNFLE mutations on the mammalian brain. Because of the complexity of the cholinergic regulation in both developing and mature brains, several pathogenic mechanisms are possible, which also present different therapeutic implications.
Interactive Image Segmentation Using Graph Cuts

This paper presents an accurate interactive image segmentation tool using graph cuts and image properties. Graph cuts is a fast algorithm for performing binary segmentation, used to find the global optimum of a cost function based on the region and boundary properties of the image. The user marks certain pixels as background and foreground, and Gaussian mixture models (GMMs) for these classes are built using the colour and texture features of corresponding pixels. A likelihood ratio is used to calculate the relative probability of each pixel being foreground or background, based on the GMMs. Many features and their combinations are analyzed on images from the Berkeley Seg-mentation Dataset. Results of different segmentations are compared using precision-recall curves, F-score and accuracy. The average accuracy of the algorithm was 92% over a set of 20 images and the best accuracy was 99.5%.
Translation Quality and Effort: Options versus Post-editing

Past research has shown that various types of computer assistance can reduce translation effort and improve translation quality over manual translation. This paper directly compares two common assistance types – selection from lists of translation options, and post-editing of machine translation (MT) output produced by Google Translate – across two significantly different subject domains for Chinese-to-English translation. In terms of translation effort, we found that the use of options can require less technical effort than MT post-editing for a domain that yields lower-quality MT output. In terms of translation quality, our analysis suggests that individual preferences play a more decisive role than assistance type: a translator tends to consistently work better either with options or with MT post-editing, regardless of domain and of their translation ability.