Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational reconstruction of fMRI-BOLD from neural activity

In this paper, we model function magnetic resonance imaging signals generated by neural activity (fMRI). fMRI measures changes in metabolic oxygen in blood in brain circuits based on changes in biophysical factors like concentration of total cerebral blood flow, oxy-hemoglobin and deoxy-hemoglobin content. A modified version of the Windkessel model by incorporating compliance has been used with a balloon model to generate cerebellar granular layer and visual cortex blood oxygen-level dependent (BOLD) responses. Spike raster patterns were adapted from a biophysical granular layer model as input. The model fits volume changes in blood flow to predict the BOLD responses in the cerebellum granular layer and in visual cortex. As a comparison, we tested the balloon model and the modified Windkessel model with the mathematically reconstructed BOLD response under the same input condition. Delayed compliance contributed to BOLD signal and reconstructed signals were compared to experimental measurements indicating the usability of the approach. The current study allows to correlate dynamic changes of flow and oxygenation during brain activation which connects single neuron and network activity to clinical measurements.
Efficient Collaborative Filtering in Content-Addressable Spaces

Collaborative Filtering (CF) is currently one of the most popular and most widely used personalization techniques. It generates personalized predictions based on the assumption that users with similar tastes prefer similar items. One of the major drawbacks of the CF from the computational point of view is its limited scalability since the computational effort required by the CF grows linearly both with the number of available users and items. This work proposes a novel efficient variant of the CF employed over a multidimensional content-addressable space. The proposed approach heuristically decreases the computational effort required by the CF algorithm by limiting the search process only to potentially similar users. Experimental results demonstrate that the proposed heuristic approach is capable of generating predictions with high levels of accuracy, while significantly improving the performance in comparison with the traditional implementations of the CF.
Higher-Degree Stochastic Integration Filtering

We obtain a class of higher-degree stochastic integration filters (SIF) for nonlinear filtering applications. SIF are based on stochastic spherical-radial integration rules that achieve asymptotically exact evaluations of Gaussian weighted multivariate integrals found in nonlinear Bayesian filtering. The superiority of the proposed scheme is demonstrated by comparing the performance of the proposed fifth-degree SIF against a number of existing stochastic, quasi-stochastic and cubature (Kalman) filters. The proposed filter is demonstrated to outperform existing filters in all cases.
A New Linear-Time Dynamic Dictionary Matching Algorithm

This research presents inverted lists as a new data structure for the dynamic dictionary matching algorithm. The inverted lists structure, which derives from the inverted index, is implemented by the perfect hashing table. The dictionary is constructed in optimal time and the individual patterns can be updated in minimal time. The searching phase scans the given text in a single pass, even in a worst case scenario. In experimental results, the inverted lists used less time and space than the traditional structures; the searches were processed and showed an efficient linear time.
An improved multilevel green's function interpolation scheme for 3D full-wave problems

A series of oscillatory radial basis functions (RBFs) with Bessel functions of different orders are compared at different cube lengths. An adaptive choice of the interpolation functions with the best orders is then adopted to enhance the interpolation accuracy when implementing the multilevel Green's function interpolation method (MLGFIM). In order to further improve the interpolation accuracy, a new type of boundary clustering procedure is proposed to reduce the error near the cube boundary which dominates the total error. Numerical results reveal that the interpolation accuracy is significantly improved using the adaptive oscillatory RBFs with non-uniform new staggered Tartan grid which is generated by the boundary clustering procedure.
ACUTE MYELOID LEUKAEMIA OF MIXED MEGAKARYOCYTIC AND ERYTHROID ORIGIN: A CASE REPORT AND REVIEW OF THE LITERATURE

Abstract We report the case of a 78-year-old man who presented with acute myeloid leukaemia showing subpopulations of cells expressing platelet-associated markers and the presence of a pan-myeloid component, besides glycophorin A-positive cells. Most of the immature cells had a proerythroblastlike morphology and we classified this case as an FAB-M6 variant, as suggested by Bain (1). According to the WHO classification, this leukaemia fulfilled the criteria of ‘AML with multilineage dysplasia’ (2). Immunophenotyping characteristics showed two distinct aberrant subpopulations, a young panmyeloid (CD45+ with low density, CD34+, CD117+, CD13+, CD33+, partial cytoplasmic myeloperoxidase (MPO)+) population with platelet-associated markers (CD41+, CD42+, CD61+) and a CD45+, CD117+, CD34- population with partial CD235a positivity indicative for erythroid maturation. This case belongs to the group of ‘early’ erythroblastic leukaemias where a subset of progenitor cells present with erythroid-megakaryocyte bipotentiality or are blocked at an early BFU-E (burst-forming unit erythrocyte)-like stage of erythroid differentiation (11, 12, 13).
Trade Openness and Investment Instability

In the presence of lumpy investment cost of adjustment, globalization may have non-conventional effects on the level of investment and its cyclical behavior. Trade openness may lead to a discrete 'jump' in the level of investment, as it may trigger a discrete change in the terms of trade. Such a shift creates a sizeable boost in aggregate investment. But trade openness may also lead to boom-bust cycles of investment (namely, multiple equilibrium) supported by self-validating expectations. In this sense globalization destabilizes the economy. There can be substantial gains from globalization in the investment-boom equilibrium. However, gains could be small, or negative, in the investment-bust equilibrium.
Adding a Little Reality to Building Ontologies for Biology

Background Many areas of biology are open to mathematical and computational modelling. The application of discrete, logical formalisms defines the field of biomedical ontologies. Ontologies have been put to many uses in bioinformatics. The most widespread is for description of entities about which data have been collected, allowing integration and analysis across multiple resources. There are now over 60 ontologies in active use, increasingly developed as large, international collaborations. There are, however, many opinions on how ontologies should be authored; that is, what is appropriate for representation. Recently, a common opinion has been the “realist” approach that places restrictions upon the style of modelling considered to be appropriate. Methodology/Principal Findings Here, we use a number of case studies for describing the results of biological experiments. We investigate the ways in which these could be represented using both realist and non-realist approaches; we consider the limitations and advantages of each of these models. Conclusions/Significance From our analysis, we conclude that while realist principles may enable straight-forward modelling for some topics, there are crucial aspects of science and the phenomena it studies that do not fit into this approach; realism appears to be over-simplistic which, perversely, results in overly complex ontological models. We suggest that it is impossible to avoid compromise in modelling ontology; a clearer understanding of these compromises will better enable appropriate modelling, fulfilling the many needs for discrete mathematical models within computational biology.
On linear infinite-dimensional feedback systems

The paper studies a class of linear (infinite-dimensional control) systems where system (controlled, controlling and observed) variables and external disturbances are picked up in equations with the help of bounded (‘weight’) linear operators in resolution extended normed linear spaces. Under the given conditions the set of all bounded (stable) transfer operators (acting from external disturbances to system variables) is obtained; in general not all of them prove to be realizable with the help of the feedback and separation principles.
CONVERSATIONAL AGENCY: THE TRAINS-93 DIALOGUE MANAGER

Designing an agent to participate in natural conversation requires more than just adapting a standard agent model to perceive and produce language. In particular, the model must be augmented with social attitudes (including mutual belief, shared plans, and obligations) and a notion of discourse context. The dialogue manager of the TRAINS-93 NL conversation system embodies such an augmented theory of agency. This paper focuses on the representation of mental state and discourse context and the deliberation strategies used in the agent model of the dialogue manager.
Fingerprinting Numeric Databases with Information Preservation and Collusion Avoidance

Information age demands omnipresence of data. Large data sets are created, maintained and outsourced to the third party experts for data mining. Knowledge and patterns are extracted by using advanced data mining algorithms that assist the decision makers to ensure quick, correct and effective decisions to be made in this world of competition. The outsourcing of these large data sets faces the problem of theft and loss of ownership. The problem of data theft can be handled by fingerprinting i.e. embedding buyer specific marks along with ownership identification marks which further leads to the challenge of knowledge preservation. Thus, a technique which performs fingerprinting with knowledge preservation on numeric relational data to be outsourced is proposed here. It is ensured that the usability constraints are not violated. Knowledge preservation is achieved by optimizing the error to be inserted using Particle Swarm Optimization (PSO), a nature – inspired optimization algorithm. Collusion attack is very well-known in the context of fingerprinting techniques. Here, the proposed system provides a mechanism for avoiding collusion. The proposed system is independent of the primary key. General Terms Information Security, Copyright Protection of Relational Databases.
Business Implications of Integrated Product and Service Offerings

This paper explores the business implications of Integrated Product and Service Offerings (IPSOs). The objective is to show examples of the business implications of IPSOs from a supplier’s perspective, and to suggest specifications for supporting methods needed for such an industrial company. The paper is largely based on empirical case studies of 120 Swedish manufacturing companies of all sizes. Results from the case studies show that both small and large companies that conduct the transition towards IPSOs face several important strategic challenges, some of them associated with high risk.
On the Orbits of Computable Enumerable Sets

The goal of this paper is to show there is a single orbit of the c.e. sets with inclusion, E , such that the question of membership in this orbit is Σ1-complete. This result and proof have a number of nice corollaries: the Scott rank of E is ω 1 + 1; not all orbits are elementarily definable; there is no arithmetic description of all orbits of E ; for all finite α ≥ 9, there is a properly ∆α orbit (from the proof).
The presence of fever in adults with influenza and other viral respiratory infections

SUMMARY We compared the rates of fever in adult subjects with laboratory-confirmed influenza and other respiratory viruses and examined the factors that predict fever in adults. Symptom data on 158 healthcare workers (HCWs) with a laboratory-confirmed respiratory virus infection were collected using standardized data collection forms from three separate studies. Overall, the rate of fever in confirmed viral respiratory infections in adult HCWs was 23·4% (37/158). Rates varied by virus: human rhinovirus (25·3%, 19/75), influenza A virus (30%, 3/10), coronavirus (28·6%, 2/7), human metapneumovirus (28·6%, 2/7), respiratory syncytial virus (14·3%, 4/28) and parainfluenza virus (8·3%, 1/12). Smoking [relative risk (RR) 4·65, 95% confidence interval (CI) 1·33–16·25] and co-infection with two or more viruses (RR 4·19, 95% CI 1·21–14·52) were significant predictors of fever. Fever is less common in adults with confirmed viral respiratory infections, including influenza, than described in children. More than 75% of adults with a viral respiratory infection do not have fever, which is an important finding for clinical triage of adult patients with respiratory infections. The accepted definition of ‘influenza-like illness’ includes fever and may be insensitive for surveillance when high case-finding is required. A more sensitive case definition could be used to identify adult cases, particularly in event of an emerging viral infection.
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II

Since the availability of assembled eukaryotic genomes, the first one being a budding yeast, many computational methods for the reconstruction of ancestral karyotypes and gene orders have been developed. The difficulty has always been to assess their reliability, since we often miss a good knowledge of the true ancestral genomes to compare their results to, as well as a good knowledge of the evolutionary mechanisms to test them on realistic simulated data. In this study, we propose some measures of reliability of several kinds of methods, and apply them to infer and analyse the architectures of two ancestral yeast genomes, based on the sequence of seven assembled extant ones. The pre-duplication common ancestor of S. cerevisiae and C. glabrata has been inferred manually by Gordon et al. (Plos Genet. 2009). We show why, in this case, a good convergence of the methods is explained by some properties of the data, and why results are reliable. In another study, Jean et al. (J. Comput Biol. 2009) proposed an ancestral architecture of the last common ancestor of S. kluyveri, K. thermotolerans, K. lactis, A. gossypii, and Z. rouxii inferred by a computational method. In this case, we show that the dataset does not seem to contain enough information to infer a reliable architecture, and we construct a higher resolution dataset which gives a good reliability on a new ancestral configuration.
Site-specific reverse splicing of a HEG-containing group I intron in ribosomal RNA

The wide, but scattered distribution of group I introns in nature is a result of two processes; the vertical inheritance of introns with or without losses, and the occasional transfer of introns across species barriers. Reversal of the group I intron self-splicing reaction, termed reverse splicing, coupled with reverse transcription and genomic integration potentially mediate an RNA-based intron mobility pathway. Compared to the well characterized endonuclease-mediated intron homing, reverse splicing is less specific and represents a likely explanation for many intron transpositions into new genomic sites. However, the frequency and general role of an RNA-based mobility pathway in the spread of natural group I introns is still unclear. We have used the twin-ribozyme intron (Dir.S956-1) from the myxomycete Didymium iridis to test how a mobile group I intron containing a homing endonuclease gene (HEG) selects between potential insertion sites in the small subunit (SSU) rRNA in vitro, in Escherichia coli and in yeast. Surprisingly, the results show a site-specific RNA-based targeting of Dir.S956-1 into its natural (S956) SSU rRNA site. Our results suggest that reverse splicing, in addition to the established endonuclease-mediated homing mechanism, potentially accounts for group I intron spread into the homologous sites of different strains and species.
Is There a Threshold Concentration of Cat Allergen Exposure on Respiratory Symptoms in Adults?

Background and Objective Cat allergen concentrations higher than 8 μg/g in settled house dust, have been suggested to provoke exacerbation of allergic respiratory symptoms. However, whether the 8μg/g of indoor cat allergen concentration is indeed the minimal exposure required for triggering the asthma related respiratory symptoms or the development of sensitization has not yet been confirmed. We studied the associations between domestic cat allergen concentrations and allergic symptoms in the European Community Respiratory Health Survey II, with the aim of confirming this suggested threshold. Methods Cat allergen concentrations were measured in the mattress dust of 3003 participants from 22 study centres. Levels of specific immunoglobulin E to cat allergens were measured in serum samples using an immunoassay. Information on allergic symptoms, medication use, home environment and smoking was obtained from a face-to-face interview. Results Domestic cat allergen concentrations were not associated with allergic/ asthmatic symptoms in the entire study population, nor in the subset sensitized to cat allergen. We also found no association among individuals exposed to concentrations higher than 8 μg/g. However, exposure to medium cat allergen concentrations (0.24-0.63 μg/g) was positively associated with reported asthmatic respiratory symptoms in subjects who have experienced allergic symptoms when near animals. Conclusions The proposed 8 μg/g threshold of cat allergen concentrations for the exacerbation of allergic/ respiratory symptoms was not confirmed in a general European adult population. Potential biases attributable to avoidance behaviours and an imprecise exposure assessment cannot be excluded.
Investigation of the effect of hollow cathode neutralizer location on hall effect thruster efficiency

Neutralization of ions is important for all electric thruster types when considering thruster efficiency and life. Hollow cathode is responsible for both creating plasma discharge and neutralization of the beam ions for Hall Effect Thruster (HET). In this study, appropriate placement of the cathode is investigated by taking into account that the decrease in cathode coupling voltage increases thruster efficiency. Regarding this, the effects of mass flow rate of the cathode and keeper current on the coupling voltage are investigated, according to available experimental results from the literature.
Power Control Strategies of On-Road Charging for Electric Vehicles

On-road charging systems for electric vehicles (EVs) have shown revolutionary potential in extending driving range and reducing battery capacities. The optimal equivalent load resistances to maximize receiving power of each EV according to different EV amounts are investigated. This paper introduces a typical on-road charging system with a single transmitting coil and multiple receiving coils. The equivalent circuit models according to different numbers of EVs are built. Power control strategies with regard to a varying number of EVs are then presented. Specifically, self-adaptive source voltage based on primary current detection is utilized to charge EVs, while the source can support enough EVs by providing the rated power. Otherwise, the source voltage is regulated to its maximum value and the charging energy of each EV is suggested to be controlled by adjusting the individual driving speed. A remarkable feature of the power control strategies is that the charging power for each EV is stable and can compensate for energy losses efficiently. As for urgent power demand from a particular EV with a low battery capacity, the adjustment of the corresponding load resistance is applied to alter the power distribution. The proposed technique has been verified in an experimental prototype.
Consensus answers for queries over probabilistic databases

We address the problem of finding a "best" deterministic query answer to a query over a probabilistic database. For this purpose, we propose the notion of a consensus world (or a consensus answer) which is a deterministic world (answer) that minimizes the expected distance to the possible worlds (answers). This problem can be seen as a generalization of the well-studied inconsistent information aggregation problems (e.g. rank aggregation) to probabilistic databases. We consider this problem for various types of queries including SPJ queries, Top-k ranking queries, group-by aggregate queries, and clustering. For different distance metrics, we obtain polynomial time optimal or approximation algorithms for computing the consensus answers (or prove NP-hardness). Most of our results are for a general probabilistic database model, called and/xor tree model, which significantly generalizes previous probabilistic database models like x-tuples and block-independent disjoint models, and is of independent interest.
Creating a Fine-Grained Corpus for Chinese Sentiment Analysis

Writing comments on products or news has become a popular activity in social media. The amount of opinionated text available online has been growing rapidly, increasing the need for techniques that can analyze opinions expressed in such text so that reviews can be easily absorbed by users. To date, most techniques depend on annotated corpora. However, existing corpora are almost sentence-level works that ignore important global sentiment information in other sentences. Given the rise of advanced applications, more fine-grained corpora are needed, even at the sentence level. The authors aim to create a fine-grained corpus for Chinese sentiment analysis, and more importantly, explore new sentiment analysis tasks by analyzing the annotated corpus. The proposed fine-grained annotation scheme not only introduces cross-sentence and global sentiment information (such as "target entity"') but also includes new sentence-level elements (such as "implicit aspect"). Based on this scheme, this corpus can provide a more fine-grained platform for researchers to study algorithms for advanced applications. In addition, an in-depth analysis on the annotated corpus is made and several important but ignored tasks, such as the target-aspect pair extraction task, are explored, which can give useful hints about future directions.
Three‐dimensional diffusion tensor microscopy of fixed mouse hearts

The relative utility of 3D, microscopic resolution assessments of fixed mouse myocardial structure via diffusion tensor imaging is demonstrated in this study. Isotropic 100‐μm resolution fiber orientation mapping within 5.5° accuracy was achieved in 9.1 hr scan time. Preliminary characterization of the diffusion tensor primary eigenvector reveals a smooth and largely linear angular rotation across the left ventricular wall. Moreover, a higher level of structural hierarchy is evident from the organized secondary and tertiary eigenvector fields. These findings are consistent with the known myocardial fiber and laminar structures reported in the literature and suggest an essential role of diffusion tensor microscopy in developing quantitative atlases for studying the structure–function relationships of mouse hearts. Magn Reson Med 52:453–460, 2004. © 2004 Wiley‐Liss, Inc.
THE EFFECT OF DIFFERENT CONCENTRATIONS OF LIBERASE H 1 835 Diseases to the Laboratory for Pancreatic Islet Culture in the Institute for Endocrinology , Diabetes and Metabolic Diseases

Liberase HI has many advantages over traditional collagenases. Liberase performs the rapid dissociation of human pancreata and allows for the preservation of the morphological and functional integrity of isolated islets. The aim of this study was to investigate the effect of different concentrations of Liberase HI (1.5, 2.5 and 3.5 mg/ml) on the yield, viability and function of islets isolated by a non-automated method. Based on our results, the Liberase HI concentration 1.5 mg/ml is recommended for this method of isolation.