Miracle-dz/UniFAR-FTUs huggingface dataset:
Experience in Aligning Anatomical Ontologies

An ontology is a formal representation of a domain modeling the entities in the domain and their relations. When a domain is represented by multiple ontologies, there is need for creating mappings among these ontologies in order to facilitate the integration of data annotated with these ontologies and reasoning across ontologies. The objective of this paper is to recapitulate our experience in aligning large anatomical ontologies and to reflect on some of the issues and challenges encountered along the way. The four anatomical ontologies under investigation are the Foundational Model of Anatomy, GALEN, the Adult Mouse Anatomical Dictionary and the NCI Thesaurus. Their underlying representation formalisms are all different. Our approach to aligning concepts (directly) is automatic, rule-based, and operates at the schema level, generating mostly point-to-point mappings. It uses a combination of domain-specific lexical techniques and structural and semantic techniques (to validate the mappings suggested lexically). It also takes advantage of domain-specific knowledge (lexical knowledge from external resources such as the Unified Medical Language System, as well as knowledge augmentation and inference techniques). In addition to point-to-point mapping of concepts, we present the alignment of relationships and the mapping of concepts group-to-group. We have also successfully tested an indirect alignment through a domain-specific reference ontology. We present an evaluation of our techniques, both against a gold standard established manually and against a generic schema matching system. The advantages and limitations of our approach are analyzed and discussed throughout the paper.
e-Learning as an Object of Study

The article seeks to typify e-learning as a transversal object of study particular to the development of the network society. To that end, the article presents the conceptual premises, the institutional framework, the study levels and the working focal points of Scopeo, a new Observatory of Activity, Innovation and Trends in e-Learning. The article also presents the results of the first two research projects on e-learning in four basic study contexts: pre-university, higher education, public administration and private enterprise. El artículo busca caracterizar la formación en red como objeto de investigación transversal propio del desarrollo de la sociedad en red. Para ello se presentan las premisas conceptuales, el marco institucional, los niveles de estudio y los enfoques de trabajo del nuevo Observatorio de la Actividad, la Innovación y las Tendencias en la Formación en Red, Scopeo. Se presentan también los resultados de las dos primeras investigaciones sobre la formación en red en los cuatro ámbitos básicos de estudio: el nivel preuniversitario, el nivel superior, la Administración pública y la empresa privada.
In vitro and in vivo studies on the metabolism of tirofiban.

Tirofiban hydrochloride [L-tyrosine-N-(butylsulfonyl)-O-[4-(4-piperidinebutyl)] monohydrochloride, is a potent and specific fibrinogen receptor antagonist. Radiolabeled tirofiban was synthesized with either (3)H-label incorporated into the phenyl ring of the tyrosinyl residue or (14)C-label in the butane sulfonyl moiety. Neither human liver microsomes nor liver slices metabolized [(14)C]tirofiban. However, male rat liver microsomes converted a limited amount of the substrate to a more polar metabolite (I) and a relatively less polar metabolite (II). The formation of I was sex dependent and resulted from an O-dealkylation reaction catalyzed by CYP3A2. Metabolite II was identified as a 2-piperidone analog of tirofiban. There was no evidence for Phase II biotransformation of tirofiban by microsomes fortified with uridine-5'-diphospho-alpha-D-glucuronic acid. After a 1 mg/kg i.v. dose of [(14)C]tirofiban, recoveries of radioactivity in rat urine and bile were 23 and 73%, respectively. Metabolite I and unchanged tirofiban represented 70 and 30% of the urinary radioactivity, respectively. Tirofiban represented >90% of the biliary radioactivity. At least three minor biliary metabolites represented the remainder of the radioactivity. One of them was identified as I. Another was identified as II. When dogs received 1 mg/kg i.v. of [(3)H]tirofiban, most of the radioactivity was recovered in the feces as unchanged tirofiban. The plasma half-life of tirofiban was short in both rats and dogs, and tirofiban was not concentrated in tissues other than those of the vasculature and excretory organs.
Work ability: Concept and assessment from a physiotherapeutic perspective. An interview study

The aim of this study was to ascertain experiences and perceptions among physiotherapists (PTs) in Sweden regarding the concept of work ability as well as their perspectives of their professional role in work ability assessments. We conducted an in-depth interview study with four male and twelve female physiotherapists working in the field of occupational health care, orthopaedics, primary health care or rehabilitation. Qualitative content analysis was applied to the data. Work ability was perceived as the ability to perform work tasks as requested. Having the potential to adjust at work and to allocate resources, having an attachment to the workplace and time factors were vital. The physiotherapists were striving for a well-defined role within a multiprofessional team, where work ability assessments were performed in a real work environment. The PTs experienced contradictory roles in relation to the patient but believed they could contribute with valuable material for assessments; this professional help was not always requested. It was noted that there was a need for experience and further education to enable PTs to further engage in work ability assessments. It is important to improve collaboration and to further discuss the work ability concept from the viewpoints of different professionals.
Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.)

All above-ground plant organs are derived from shoot apical meristems (SAMs). Global analyses of gene expression were conducted on maize (Zea mays L.) SAMs to identify genes preferentially expressed in the SAM. The SAMs were collected from 14-day-old B73 seedlings via laser capture microdissection (LCM). The RNA samples extracted from LCM-collected SAMs and from seedlings were hybridized to microarrays spotted with 37 660 maize cDNAs. Approximately 30% (10 816) of these cDNAs were prepared as part of this study from manually dissected B73 maize apices. Over 5000 expressed sequence tags (ESTs) (about 13% of the total) were differentially expressed (P<0.0001) between SAMs and seedlings. Of these, 2783 and 2248 ESTs were up- and down-regulated in the SAM, respectively. The expression in the SAM of several of the differentially expressed ESTs was validated via quantitative RT-PCR and/or in situ hybridization. The up-regulated ESTs included many regulatory genes including transcription factors, chromatin remodeling factors and components of the gene-silencing machinery, as well as about 900 genes with unknown functions. Surprisingly, transcripts that hybridized to 62 retrotransposon-related cDNAs were also substantially up-regulated in the SAM. Complementary DNAs derived from the LCM-collected SAMs were sequenced to identify additional genes that are expressed in the SAM. This generated around 550 000 ESTs (454-SAM ESTs) from two genotypes. Consistent with the microarray results, approximately 14% of the 454-SAM ESTs from B73 were retrotransposon-related. Possible roles of genes that are preferentially expressed in the SAM are discussed.
HLA Class I and Class II Conserved Extended Haplotypes and Their Fragments or Blocks in Mexicans: Implications for the Study of Genetic Diversity in Admixed Populations

Major histocompatibility complex (MHC) genes are highly polymorphic and informative in disease association, transplantation, and population genetics studies with particular importance in the understanding of human population diversity and evolution. The aim of this study was to describe the HLA diversity in Mexican admixed individuals. We studied the polymorphism of MHC class I (HLA-A, -B, -C), and class II (HLA-DRB1, -DQB1) genes using high-resolution sequence based typing (SBT) method and we structured the blocks and conserved extended haplotypes (CEHs) in 234 non-related admixed Mexican individuals (468 haplotypes) by a maximum likelihood method. We found that HLA blocks and CEHs are primarily from Amerindian and Caucasian origin, with smaller participation of African and recent Asian ancestry, demonstrating a great diversity of HLA blocks and CEHs in Mexicans from the central area of Mexico. We also analyzed the degree of admixture in this group using short tandem repeats (STRs) and HLA-B that correlated with the frequency of most probable ancestral HLA-C/−B and -DRB1/−DQB1 blocks and CEHs. Our results contribute to the analysis of the diversity and ancestral contribution of HLA class I and HLA class II alleles and haplotypes of Mexican admixed individuals from Mexico City. This work will help as a reference to improve future studies in Mexicans regarding allotransplantation, immune responses and disease associations.
Canonical parameterization of excess motor degrees of freedom with self-organizing maps

The problem of sensorimotor control is underdetermined due to excess (or "redundant") degrees of freedom when there are more joint variables than the minimum needed for positioning an end-effector. A method is presented for solving the nonlinear inverse kinematics problem for a redundant manipulator by learning a natural parameterization of the inverse solution manifolds with self-organizing maps. The parameterization approximates the topological structure of the joint space, which is that of a fiber bundle. The fibers represent the "self-motion manifolds" along which the manipulator can change configuration while keeping the end-effector at a fixed location. The method is demonstrated for the case of the redundant planar manipulator. Data samples along the self-motion manifolds are selected from a large set of measured input-output data. This is done by taking points in the joint space corresponding to end-effector locations near "query points", which define small neighborhoods in the end-effector work space. Self-organizing maps are used to construct an approximate parameterization of each manifold which is consistent for all of the query points. The resulting parameterization is used to augment the overall kinematics map so that it is locally invertible. Joint-angle and end-effector position data, along with the learned parameterizations, are used to train neural networks to approximate direct inverse functions.
Aging and death-associated changes in serum albumin variability over the course of chronic hemodialysis treatment

Background Several epidemiological studies have demonstrated associations between variability in a number of biological parameters and adverse outcomes. As the variability may reflect impaired homeostatic regulation, we assessed albumin variability over time in chronic hemodialysis (HD) patients. Methods Data from 1346 subjects who received chronic HD treatment from May 2001 to February 2015 were analyzed according to three phases of HD treatment: post-HD initiation, during maintenance HD treatment, and before death. The serum albumin values were grouped according to the time interval from HD initiation or death, and the yearly trends for both the albumin levels and the intra-individual albumin variability (quantified by the residual coefficient of variation: Alb-rCV) were examined. The HD initiation and death-associated changes were also analyzed using generalized additive mixed models. Furthermore, the long-term trend throughout the maintenance treatment period was evaluated separately using linear regression models. Results Albumin levels and variability showed distinctive changes during each of the 3 periods. After HD initiation, albumin variability decreased and reached a nadir within a year. During the subsequent maintenance treatment period (interquartile range = 5.2–11.0 years), the log Alb-rCV showed a significant upward trend (mean slope: 0.011 ± 0.035 /year), and its overall mean was -1.49 ± 0.08 (equivalent to an Alb-rCV of 3.22%). During the 1–2 years before death, this upward trend clearly accelerated, and the mean log Alb-rCV in the last year of life was -1.36 ± 0.17. The albumin levels and variability were negatively correlated with each other and exhibited exactly opposite movements throughout the course of chronic HD treatment. Different from the albumin levels, albumin variability was not dependent on chronological age but was independently associated with an individual’s aging and death process. Conclusion The observed upward trend in albumin variability seems to be consistent with a presumed aging-related decline in homeostatic capacity.
Functional characterization of the α‐glucoside transporter Sut1p from Schizosaccharomyces pombe, the first fungal homologue of plant sucrose transporters

Disaccharide transporters have not previously been identified in Schizosaccharomyces pombe. This is in contrast to Saccharomyces cerevisiae in which several maltose permeases belonging to the sugar porter (SP) family have been characterized. Here we report that a novel S. pombe gene, sut1+, encodes a proton‐coupled disaccharide uptake transporter in the glycoside–pentoside–hexuronide (GPH):cation symporter family. Previously, members of the GPH family were restricted to bacteria and plants. The closest homologues of sut1+ are the sucrose uptake transporters (SUTs) from higher plants that transport sucrose with a higher affinity than maltose. The transport function of Sut1p was analysed by expression in S. cerevisiae. Sut1p was found to transport maltose with a Km of 6.5 ± 0.4 mM and sucrose with a Km of 36.3 ± 9.7 mM. Therefore, the substrate specificity of Sut1p from S. pombe is different from that of its plant homologues. Glucose repression of sut1+ at the transcriptional level is also consistent with a physiological function for Sut1p in maltose uptake. These results indicate that, unlike S. cerevisiae, S. pombe utilizes maltose transporters derived from a common ancestor with the plant SUTs.
Economic MPC with periodic terminal constraints of nonlinear differential-algebraic-equation systems: Application to drinking water networks

In this paper, an Economic Model Predictive Control (EMPC) strategy with periodic terminal constraints is addressed for nonlinear differential-algebraic-equation systems with an application to Drinking Water Networks (DWNs). DWNs have some periodic behaviours because of the daily seasonality of water demands and electrical energy price. The periodic terminal constraint and economic terminal cost are implemented in the EMPC controller design for the purpose of achieving convergence. The feasibility of the proposed EMPC strategy when disturbances are considered is guaranteed by means of soft constraints implemented by using slack variables. Finally, the comparison results in a case study of the D-Town water network is provided by applying the EMPC strategy with or without periodic terminal constraints.
Surface Doping of Steel with an Intense Pulsed Electron Beam

Surface doping of AISI420 steel is carried out in a single vacuum cycle, and consisted of spraying a thin (0.5 μm) film of Zr-Ti-Cu alloy by electric-arc sputtering of a cathode of the composition Zr-6 at. % Ti-6 at. % Cu, and the subsequent irradiation of the system “film (Zr-Ti-Cu alloy) / (AISI420 steel) substrate” with an intense pulsed electron beam. It is shown that the concentration of zirconium in the surface layer of steel decreases with an increase in the energy density of the electron beam (ES). It is established that formation of a surface alloy is accompanied by the following: formation of a cellular crystallization structure (the average cell size increases from 150 nm at ES = 20 J/cm2 to 370 nm at ES = 40 J/cm2); formation of a dendritic crystallization structure in the presence of refractory element particles (titanium or zirconium); decomposition of a solid solution with the release of zirconium carbide particles (particle sizes increase from (10-15) nm at ES = 20 J/cm2 to (30-40) nm at ES = 40 J/cm2). Particles of the carbide phase based on chromium of the composition Cr3C2, Cr7C3 and (Cr, Fe)23С6, along with zirconium carbide particles, are revealed upon the irradiation of the system “film (Zr-Ti-Cu alloy) / (AISI420 steel) substrate” with an intense pulsed electron beam (ES = 40 J/cm2). Chromium carbide particles have a round shape; their sizes vary from 40 nm to 60 nm. The analysis of phase transformation diagrams taking place under equilibrium conditions in systems Fe-Zr-C; Cr-Zr-C; Fe-Cr-Zr is carried out. It is established that ultra-high cooling rates that occur during the irradiation of the system “film (Zr-Ti-Cu alloy) / (AISI420 steel) substrate” with an intense pulsed electron beam impose restrictions on formation of phases of the intermetallic type. It is suggested that formation of predominantly carbide phases in the surface layer of the material is conditioned upon high mobility of carbon atoms in steel.
Liveness in Timed and Untimed Systems

We present a coordinated pair of general labeled transition system models for describing timed and untimed concurrent systems. Both of the models incorporate liveness properties as well as safety properties. The models are related via an embedding of the untimed model into the timed model, which preserves all the interesting attributes of the untimed model. Both models include notions of environment-freedom, which express the idea that the liveness properties can be guaranteed by the system, independently of the behavior of the environment in which it operates. These environment-freedom conditions are used to prove compositionality results for both models. This pair of models, which generalize several existing models, is intended to comprise a general formalism for the verification of timed and untimed concurrent systems.
Creating Dynamic Story Plots with Continual Multiagent Planning

An AI system that is to create a story (autonomously or in interaction with human users) requires capabilities from many subfields of AI in order to create characters that themselves appear to act intelligently and believably in a coherent story world. Specifically, the system must be able to reason about the physical actions and verbal interactions of the characters as well as their perceptions of the world. Furthermore it must make the characters act believably--i.e. in a goal-directed yet emotionally plausible fashion. Finally, it must cope with (and embrace! ) the dynamics of a multiagent environment where beliefs, sentiments, and goals may change during the course of a story and where plans are thwarted, adapted and dropped all the time. In this paper, we describe a representational and algorithmic framework for modelling such dynamic story worlds, Continual Multiagent Planning. It combines continual planning (i.e. an integrated approach to planning and execution) with a rich description language for modelling epistemic and affective states, desires and intentions, sensing and communication. Analysing story examples generated by our implemented system we show the benefits of such an integrated approach for dynamic plot generation.
Upper Bounds for Unsupervised Parsing with Unambiguous Non-Terminally Separated Grammars

Unambiguous Non-Terminally Separated (UNTS) grammars have properties that make them attractive for grammatical inference. However, these properties do not state the maximal performance they can achieve when they are evaluated against a gold treebank that is not produced by an UNTS grammar. In this paper we investigate such an upper bound. We develop a method to find an upper bound for the unlabeled F1 performance that any UNTS grammar can achieve over a given tree-bank. Our strategy is to characterize all possible versions of the gold treebank that UNTS grammars can produce and to find the one that optimizes a metric we define. We show a way to translate this score into an upper bound for the F1. In particular, we show that the F1 parsing score of any UNTS grammar can not be beyond 82.2% when the gold treebank is the WSJ10 corpus.
Automatic Chinese Confusion Words Extraction Using Conditional Random Fields and the Web

A ready set of commonly confused words plays an important role in spelling error detection and correction in texts. In this paper, we present a system named ACE (Automatic Confusion words Extraction), which takes a Chinese word as input (e.g., “不脛而走 ”) and automatically outputs its easily confused words (e.g., “不徑 徑 ”, “不逕 逕 逕 逕而走 ”). The purpose of ACE is similar to web-based set expansion ‐ the problem of finding all instances (e.g. “Halloween”, “Thanksgiving Day”, “Independence Day”, etc.) of a set given a small number of class names (e.g. “holidays”). Unlike set expansion , our system is used to produce commonly confused words of a given Chinese word. In brief, we use some handcoded patterns to find a set of sentence fragments from search engine, and then assign an array of tags to each character in each sentence fragment. Finally, these tagged fragments are served as inputs to a pre-learned conditional random fields (CRFs) model. We present experiment results on 3,211 test cases, showing that our system can achieve 95.2% precision rate while maintaining 91.2% recall rate.
Miler: a toolset for exploring email data

Source code is the target and final outcome of software development. By focusing our research and analysis on source code only, we risk forgetting that software is the product of human efforts, where communication plays a pivotal role. One of the most used communications means are emails, which have become vital for any distributed development project. Analyzing email archives is non-trivial, due to the noisy and unstructured nature of emails, the vast amounts of information, the unstandardized storage systems, and the gap with development tools. We present Miler, a toolset that allows the exploration of this form of communication, in the context of software maintenance and evolution. With Miler we can retrieve data from mailing list repositories in different formats, model emails as first-class entities, and transparently store them in databases. Miler offers tools and support for navigating the content, manually labelling emails with discussed source code entities, automatically linking emails to source code, measuring code entities' popularity in mailing lists, exposing structured content in the unstructured content, and integrating email communication in an IDE.