Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of the MELD allocation after its implementation in liver transplantation

Abstract Objective . On 16 December 2006, most Eurotransplant countries changed waiting time oriented liver allocation policy to the urgency oriented Model for End-stage Liver Disease (MELD) system. There are limited data on the effects of this policy change within the Eurotransplant community. Patients and methods. A total of 154 patients who had undergone deceased donor liver transplantation (LT) were retrospectively analyzed in three time periods: period A (1-year pre-MELD, n = 42) versus period B (1-year post-MELD, n = 52) versus period C (2 years after MELD implementation, n = 60). Results. The median MELD score at the time of LT increased from 16.3 points in period A to 22.4 and 20.4 in periods B and C, respectively (p = 0.007). Waitlist mortality decreased from 18.4% in period A to 10.4% and 9.4% in periods B and C, respectively (p = 0.015). Three-month mortality did not change significantly (10% each for periods A, B and C). One-year survival was 84% for the MELD 6–19 group compared with 81% in the MELD 20–29 group and 74% in the MELD ≥30 group (p = 0.823). Analyzing MELD score and previously described prognostic scores [i.e. survival after liver transplantation (SALT) score and donor-MELD (D-MELD) score] with regard to 1-year survival, only a high risk SALT score was predictive (p = 0.038). In our center, 2 years after implementation of the MELD system, waitlist mortality decreased, while 90-day mortality did not change significantly. Conclusion. Up to now, only the SALT score proved to be of prognostic relevance post-transplant.
Microstructural evaluation of Ni-SDC cermet from a representative 2D image and/or a 3D reconstruction based on a stack of images

Gregor Kapun1,3, Marjan Marin{ek2, Franci Merzel1, Sa{o [turm3,4, Miran Gaber{~ek1, Tina Skalar2 1National Institute of Chemistry, Laboratory for Materials Chemistry, Hajdrihova 19, Ljubljana, Slovenia 2University of Ljubljana, Faculty for Chemistry and Chemical Technology, Ve~na pot 113, Ljubljana, Slovenia 3Jo`ef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia 4Jo`ef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia Tina.Skalar@fkkt.uni-lj.si
Extended application of suffix trees to data compression

A practical scheme for maintaining an index for a sliding window in optimal time and space, by use of a suffix tree, is presented. The index supports location of the longest matching substring in time proportional to the length of the match. The total time for build and update operations is proportional to the size of the input. The algorithm, which is simple and straightforward, is presented in detail. The most prominent lossless data compression scheme, when considering compression performance, is prediction by partial matching with unbounded context lengths (PPM). However, previously presented algorithms are hardly practical, considering their extensive use of computational resources. We show that our scheme can be applied to PPM-style compression, obtaining an algorithm that runs in linear time, and in space bounded by an arbitrarily chosen window size. Application to Ziv-Lempel (1977) compression methods is straightforward and the resulting algorithm runs in linear time.
Computational visual ecology in the pelagic realm

Visual performance and visual interactions in pelagic animals are notoriously hard to investigate because of our restricted access to the habitat. The pelagic visual world is also dramatically different from benthic or terrestrial habitats, and our intuition is less helpful in understanding vision in unfamiliar environments. Here, we develop a computational approach to investigate visual ecology in the pelagic realm. Using information on eye size, key retinal properties, optical properties of the water and radiance, we develop expressions for calculating the visual range for detection of important types of pelagic targets. We also briefly apply the computations to a number of central questions in pelagic visual ecology, such as the relationship between eye size and visual performance, the maximum depth at which daylight is useful for vision, visual range relations between prey and predators, counter-illumination and the importance of various aspects of retinal physiology. We also argue that our present addition to computational visual ecology can be developed further, and that a computational approach offers plenty of unused potential for investigations of visual ecology in both aquatic and terrestrial habitats.
Possibility to use iPS-technology in age-related diseases

When applying the iPSCs for regenerative therapy in elderly patients, it is necessary to establish the iPSCs from elderly patients themselves then differentiate the iPSCs to specific cell types for transplantation treatments. The mouse is a perfect model to study aging in mammals. Bone marrow (BM) cells from aged C57BL/6 mice (15 months to 21 months) were cultured with granulocyte macrophage-colony stimulating factor (GM-CSF). The efficiency to produce iPSCs from aged mice BM cells was lower than that of young mice. We established several clones of iPSCs from aged mice. All the established clones have pluripotent markers. Aged-iPSCs could differentiate to three germ layers in vitro and made teratoma in vivo. We are currently making chimeric mice between Aged-iPSC-1 and ICR mice.
Three‐dimensional FDTD modeling of neurons to solve EEG and MEG forward problem

Neuronal activities including calcium sodium current, ligands current, and synaptic transmembrane current create electromagnetic fields. Here, an analytic method is suggested to obtain the electromagnetic fields and potential signals resulting from the function of nerve cells inside the brain. Modeling simulates the behavior of cells three‐dimensionally. The proposed method employs the electric scalar potential and magnetic vector potential to solve the time‐domain three‐dimensional equations using the partial differential method. All ion flows are considered as electrical current densities. In this method, the brain and desired cells are meshed to solve the problem using the numerical method. As an example, the electric fields, magnetic fields, and signals generated by cingulum nerve fibers are illustrated and compared in Cz, Fz, and T3 electrode positions. A direct analysis method based on the same mechanism and biophysics of the nervous system is proposed. Employing this direct method leads not only to a better understanding of neuronal activity but also to a more accurate vision regarding the accuracy/inaccuracy of experimental and inverse methods. The analysis of these data provides insights into the brain function processes.
Molecular dynamics study of the membrane interaction of a membranotropic dengue virus C protein-derived peptide

Dengue virus C protein, essential in the dengue virus life cycle, possesses a segment, peptide PepC, known to bind membranes composed of negatively charged phospholipids. To characterize its interaction with the membrane, we have used the molecular dynamics HMMM membrane model system. This approach is capable of achieving a stable system and sampling the peptide/lipid interactions which determine the orientation and insertion of the peptide upon membrane binding. We have been able to demonstrate spontaneous binding of PepC to the 1,2-divaleryl-sn-glycero-3-phosphate/1,2-divaleryl-sn-glycero-3-phosphocholine membrane model system, whereas no binding was observed at all for the 1,2-divaleryl-sn-glycero-3-phosphocholine one. PepC, adopting an α-helix profile, did not insert into the membrane but did bind to its surface through a charge anchor formed by its three positively charged residues. PepC, maintaining its three-dimensional structure along the whole simulation, presented a nearly parallel orientation with respect to the membrane when bound to it. The positively charged amino acid residues Arg-2, Lys-6, and Arg-16 are mainly responsible for the peptide binding to the membrane stabilizing the structure of the bound peptide. The segment of dengue virus C protein where PepC resides is a fundamental protein–membrane interface which might control protein/membrane interaction, and its positive amino acids are responsible for membrane binding defining its specific location in the bound state. These data should help in our understanding of the molecular mechanism of DENV life cycle as well as making possible the future development of potent inhibitor molecules, which target dengue virus C protein structures involved in membrane binding.
Computational Millimeter Wave Imaging: Problems, progress, and prospects

Imaging using millimeter waves (mmWs) has many advantages and applications in the defense, security, and aviation markets. All terrestrial bodies emit mmW radiation, and these wavelengths are able to penetrate smoke, blowing dust or sand, fog/clouds/marine layers, and even clothing. However, there are many obstacles to imaging in this spectrum that have to be overcome before mmW imaging systems can be successfully realized for surveillance and defense applications. Recent developments in computational imaging have the potential to significantly improve capabilities of mmW imaging systems. Our article provides an overview of computational imaging and its implication to mmW imaging in various operation modes. We discuss the merits and drawbacks of available computational mmW imaging approaches and identify avenues of research in this rapidly evolving field.
Diaqua(triethanolamine)copper(II) sulfate monohydrate

The asymmetric unit of the title compound, [Cu(C6H15NO3)(H2O)2]SO4·H2O, contains a complex cation, a sulfate anion and one uncoordinated water molecule. In the complex cation, the CuII ion is coordinated by five O atoms (three of which are from the triethanolamine ligand and two from coordinated water molecules) and one N atom of the triethanolamine ligand in a typical Jahn–Teller-distorted octahedral geometry. Classical intermolecular O—H⋯O hydrogen bonds link the cation, the sulfate anion and the water molecule into a two-dimensional network.
A Simple Trapezoid Sweep Algorithm for Reporting Red/Blue Segment Intersections

We present a new simple algorithm for computing all intersections between two collections of disjoint line segments. The algorithm runs in O(n log n + k) time and O(n) space, where n and k are the number of segments and intersections respectively. We also show that the algorithm can be extended to handle single-valued curve segments with the same time and space bound.
Dependency-Guided Service Composition for User-Centric SOA

Service-Oriented Architecture (SOA) is characterized by dynamic service discovery and composition. For user-centric SOA, not only services, workflows and application templates can be published and discovered for composition. Furthermore, a user can publish an application template and let providers supply the needed services. A key issue in user-centric service composition is to intelligently and effectively discover the subset of correlated services that best match the users’ requirements. This paper proposes a two-steps composition process. In the first step, users choose templates from ontology with its dependency. The dependency information identifies a set of candidate services and workflows that may be applicable for composition. In the send step, after the templates are selected, users can finalize the selection of services and workflows from a set of candidate services or workflows based on their preference. This 2-step process is supported by dependency identification algorithms and is illustrated using a case study.
A model for carbon management of supplier selection in green supply chain management

This study aims to utilize the Decision-making Trial and Evaluation Laboratory (DEMATEL) and Analytic Network Process (ANP) approach to recognize the causality and determine relative weights of evaluation criteria of carbon management in green supply chain for improving the overall performance of suppliers in terms of carbon management. Thirteen criteria of carbon management with three dimensions were identified from literature review and interview with three experts at an electronics manufacturer. Results indicated that the four most important criteria of supplier selection in terms of carbon management were carbon governance (0.180), management systems of carbon information (0.163), training related to carbon management (0.142), and carbon policy (0.125). The proposed framework of supplier selection that can offer an insight for managers to understand cause-effort relationship and to select appropriate suppliers that is capable of having competence in carbon management and to improve suppliers' performance.
Optimizing and Modeling Dynamics in Networks

The Internet has grown very large. No one knows exactly how large, but rough estimates indicate billions of users (around 1.8B in 2009, according to eTForecasts [4]), hundreds of millions of web sites (over 200M in February 2009, according to Netcraft [19]), and hundreds of billions of web pages (over 240B, according to the Internet archive [1]). The Internet is also very dynamic — users log in and out, new services get added, routing policies change, normal traffic gets mixed with denial-of-service (DoS) attack traffic, etc. An important question is: How do we manage such a huge and highly dynamic structure like the Internet? As a corollary, how can we build a network of the future unless we understand the steady-state and dynamics of what we build? In this chapter, we resort to two mathematical frameworks: optimization theory to study optimal steady states of networks, and control theory to study the dynamic behavior of networks as they evolve toward steady state. Our emphasis will be on congestion control using the notion of prices to model the level of congestion, such as delays and losses, observed by users or traffic sources.
OsNucleolin1-L Expression in Arabidopsis Enhances Photosynthesis via Transcriptome Modification under Salt Stress Conditions

OsNUC1 encodes rice nucleolin, which has been shown to be involved in salt stress responses. Expression of the full-length OsNUC1 gene in Arabidopsis resulted in hypersensitivity to ABA during germination. Transcriptome analysis of the transgenic lines, in comparison with the wild type, revealed that the RNA abundance of >1,900 genes was significantly changed under normal growth conditions, while under salt stress conditions the RNAs of 999 genes were found to be significantly regulated. Gene enrichment analysis showed that under normal conditions OsNUC1 resulted in repression of genes involved in photosynthesis, while in salt stress conditions OsNUC1 increased expression of the genes involved in the light-harvesting complex. Correspondingly, the net rate of photosynthesis of the transgenic lines was increased under salt stress. Transgenic rice lines with overexpression of the OsNUC1-L gene were generated and tested for photosynthetic performance under salt stress conditions. The transgenic rice lines treated with salt stress at the booting stage had a higher photosynthetic rate and stomatal conductance in flag leaves and second leaves than the wild type. Moreover, higher contents of Chl a and carotenoids were found in flag leaves of the transgenic rice. These results suggest a role for OsNUC1 in the modification of the transcriptome, especially the gene transcripts responsible for photosynthesis, leading to stabilization of photosynthesis under salt stress conditions.
Bit coir fiber and sugarcane bagasse fiber reinforced eco-friendly polypropylene composites: Development and property evaluation thereof

Waste natural fibers, bit coir fiber residue of traditional coir industries, and sugarcane bagasse fibers were subjected to chemical modifications via alkaline steam explosion treatments toward the extraction of reinforcing fibers with better compatibility and reinforcing characteristics in the polymer matrix. The treated fibers were utilized in the fabrication of composites with polypropylene (PP) as the base polymer with the aid of maleic anhydride–grafted PP as the compatibilizer. Percent composition of fiber in the composites was decided to facilitate maximum replacement of the matrix and further applicability in large-scale continuous polymeric production processes. Mechanical, thermal, and morphological characterization of the composites reveals the best composition to be of 30% composition, in the added view of maximum replacement of polymer matrix with the reinforcing filler, retention of requisite properties, reduced cost of manufacture and inventory, and reduction in the carbon footprint per unit dimensions in comparison with the wholly polymer component. The thermal properties of coir fiber-reinforced composites showed good improvement up to 134.5°C increase in onset degradation temperature while retaining matrix properties for sugarcane bagasse-reinforced composites.
Tests for mortality and recruitment in a K-sample tag-recapture experiment.

SUMMARY In tag-recapture experiments the appropriate procedure to be used for estimation of the population size depends on whether there is mortality or recruitment between the times of sampling. Tests for mortality and for recruitment in a K-sample tag-recapture experiment are developed. A possible sequence for using the derived test procedures is suggested to assist in selecting an estimation scheme.
Management of Sequence Data

One of the challenges facing today's database systems is the need to support complex data types, which are of growing importance in new application areas. The thesis addresses this problem, with a speciic focus on supporting sequence data. A large part of the thesis deals with the details of sequences. Issues covered include the model for sequence data, an algebra of operators to query the data, a query language to express the queries, optimization techniques and query processing algorithms. Performance results are presented from an implementation of these ideas, demonstrating the eeects of the various optimizations. This detailed exploration of sequence data is one contribution of the thesis. The second contribution is a solution to the problem of integrating diierent data types, including sequences and relations, in a general-purpose database system. The thesis discusses the drawbacks of existing solutions, and then proposes a solution based on a novel E-ADT paradigm. This paradigm has been used in the development of the PREDATOR database system, and the implementation brings to light several advantages as well as limitations of this paradigm. The support for sequences has been implemented as a component of this larger system. The conclusion drawn from the sequence implementation is that it is important to provide specialized support for queries over sequences. By extrapolation, similar conclusions may be drawn about support for other complex data types like matrixes and images. The E-ADT paradigm provides a mechanism to integrate all these types within a single general-purpose database system. The conclusion of the thesis is that database systems should adopt some of the E-ADT ideas so as to provide more eecient support for complex data types like sequences. ii Acknowledgements
Evidence for a Xer/dif System for Chromosome Resolution in Archaea

Homologous recombination events between circular chromosomes, occurring during or after replication, can generate dimers that need to be converted to monomers prior to their segregation at cell division. In Escherichia coli, chromosome dimers are converted to monomers by two paralogous site-specific tyrosine recombinases of the Xer family (XerC/D). The Xer recombinases act at a specific dif site located in the replication termination region, assisted by the cell division protein FtsK. This chromosome resolution system has been predicted in most Bacteria and further characterized for some species. Archaea have circular chromosomes and an active homologous recombination system and should therefore resolve chromosome dimers. Most archaea harbour a single homologue of bacterial XerC/D proteins (XerA), but not of FtsK. Therefore, the role of XerA in chromosome resolution was unclear. Here, we have identified dif-like sites in archaeal genomes by using a combination of modeling and comparative genomics approaches. These sites are systematically located in replication termination regions. We validated our in silico prediction by showing that the XerA protein of Pyrococcus abyssi specifically recombines plasmids containing the predicted dif site in vitro. In contrast to the bacterial system, XerA can recombine dif sites in the absence of protein partners. Whereas Archaea and Bacteria use a completely different set of proteins for chromosome replication, our data strongly suggest that XerA is most likely used for chromosome resolution in Archaea.
Emotion Detection in Email Customer Care

Prompt and knowledgeable responses to customers’ email are critical in maximizing customer satisfaction. Such messages often contain complaints about unfair treatment due to negligence, incompetence, rigid protocols, unfriendly systems, and unresponsive personnel. In this paper, we refer to these email messages as emotional email. They provide valuable feedback to improve contact center efficiency and the quality of the overall customer care experience, which in turn results in increased customer retention. We describe a method that uses salient features to identify emotional email in the customer care domain. Salient features in customer care related email are expressions of customer frustration, dissatisfaction with the business, and threats to either leave, take legal action, and/or report to authorities. Compared to a baseline system using word unigram features, our proposed approach significantly improves emotional email detection performance.
A Unified Probabilistic Approach to Improve Spelling in an Event-Related Potential-Based Brain–Computer Interface

In recent years, in an attempt to maximize performance, machine learning approaches for event-related potential (ERP) spelling have become more and more complex. In this paper, we have taken a step back as we wanted to improve the performance without building an overly complex model, that cannot be used by the community. Our research resulted in a unified probabilistic model for ERP spelling, which is based on only three assumptions and incorporates language information. On top of that, the probabilistic nature of our classifier yields a natural dynamic stopping strategy. Furthermore, our method uses the same parameters across 25 subjects from three different datasets. We show that our classifier, when enhanced with language models and dynamic stopping, improves the spelling speed and accuracy drastically. Additionally, we would like to point out that as our model is entirely probabilistic, it can easily be used as the foundation for complex systems in future work. All our experiments are executed on publicly available datasets to allow for future comparison with similar techniques.