Miracle-dz/UniFAR-FTUs huggingface dataset:
Optical flow estimation on coarse-to-fine region-trees using discrete optimization

In this paper, we propose a new region-based method for accurate motion estimation using discrete optimization. In particular, the input image is represented as a tree of over-segmented regions and the optical flow is estimated by optimizing an energy function defined on such a region-tree using dynamic programming. To accommodate the sampling-inefficiency problem intrinsic to discrete optimization compared to the continuous optimization based methods, both spatial and solution domain coarse-to-fine (C2F) strategies are used. That is, multiple region-trees are built using different over-segmentation granularities. Starting from a global displacement label discretization, optical flow estimation on the coarser level region-tree is used for defining region-wise finer displacement samplings for finer level region-trees. Furthermore, cross-checking based occlusion detection and correction and continuous optimization are also used to improve accuracy. Extensive experiments using the Middlebury benchmark datasets have shown that our proposed method can produce top-ranking results.
Linked Data based applications for Learning Analytics Research: faceted searches, enriched contexts, graph browsing and dynamic graphic visualisation of data

We present a case of exploitation of Linked Data about learning analytics research through innovative end-user applications built on GNOSS, a semantic and social software platform. It allows users to find and discover knowledge from two datasets, Learning Analytics Knowledge (LAK) and Educational Data Mining (EDM), and also reach some related external information thanks to the correlation with other datasets. We used four additional datasets, either to supplement information or to generate enriched contexts: Dbpedia, Geonames, DBLP-GNOSS (an index of scientific publications in Computer Science from DBLP) and DeustoTech Publications (publications of the Institute of Technology of the University of Deusto, and more specifically a selection of works by the DeustoTech Learning research unit). The featured applications are: faceted searches, enriched contexts, navigation through graphs and graphic visualization in charts or geographic maps. Faceted searches can be performed on three basic items: scientific publications, researchers (authors of the publications) and organizations in the learning analytics area. The search engine enables aggregated searches by different facets and summarization of results for each successive search. Analytics on data are provided firstly through that summarization given for results in every facet, and secondly through dynamic graphic representations for some attributes. Several charts are available to show the distribution of publications depending on different attributes (e.g. per publication type and year or per organization). The search results for organizations and researchers can be visualized in geographic maps. This work was presented to the LAK Data Challenge 2013.
Human papillomavirus type 16 DNA-induced malignant transformation of NIH 3T3 cells

A biological function for human papillomavirus 16 (HPV 16) DNA was demonstrated by transformation of NIH 3T3 cells. HPV 16 DNA has been found frequently in genital cancer and has been classified as a papillomavirus on the basis of DNA homology. A recombinant HPV 16 DNA (pSHPV16d), which contains a head-to-tail dimer of the full-length HPV 16 genome, induced morphologic transformation; the transformed cells were tumorigenic in nude mice. Expression of transforming activity was unique because of the long latency period (more than 4 weeks) required for induction of morphologic transformation and because the transfected DNA existed primarily in a multimeric form with some rearrangements. Furthermore, virus-specific RNAs were expressed in the transformants. The transformation of NIH 3T3 cells provides a model for analyzing the functions of HPV 16, which is associated with cervical carcinomas.
The Documentalist Support System: a Web-Services based Tool for Semantic Annotation and Browsing

The Documentalist Support System (DocSS) is developed to suite novel needs of documentalists working within the Dutch archive for Sound and Vision, broadcasters working outside of Sound and Vision and people interested in the Cultural Heritage value of the archive, who want to perform search in context. The documentalists (and to some extent the other users mentioned) need an environment in which they can view and manipulate multiple types of information (documents and metadata), receive annotation suggestions from their controlled vocabularies, create catalogue descriptions and browse for semantically similar documents within their collection. The open architecture, the publicly published annotation format and the SKOS representation requirement for the controlled vocabularies make the generated annotations interoperable with other annotation databases and the DocSS usable for any documentalist annotating material with controlled vocabularies, for which a digital textual representation of the data exists.
Expression of the circadian clock gene Period 1 in neuroendocrine cells: an investigation using mice with a Per1::GFP transgene

The circadian clock located in the suprachiasmatic nuclei (SCN) of the hypothalamus regulates daily temporal organization in behaviour and neuroendocrine function. The molecular basis for circadian rhythm generation is an interacting transcriptional/translational feedback loop comprised of several ‘clock genes’ and their respective protein products. Clock genes are expressed not only in the SCN but also in numerous other locations throughout the brain, including regions rich in neuroendocrine cells. In order to investigate whether neuroendocrine cells function as autonomous oscillators, we used female transgenic mice in which an unstable, degradable jellyfish green fluorescent protein (GFP) gene is driven by a mouse Period 1 (Per1) gene promoter. Mice were injected (s.c.) with fluorogold (FG) in order to label neuroendocrine cells and brain sections were double‐labelled for either FG and Per1 mRNA (labelled by GFP immunostaining) or FG and PER1 protein using fluorescence immunocytochemistry. Mice were killed during either the day or night. Neuroendocrine cells contained Per1 mRNA and PER1 protein in several brain regions with the greatest proportion of double‐labelled cells occurring in the arcuate nucleus (Arc). The number of neuroendocrine cells labelled was not affected by the stage of the estrous cycle. Fewer FG‐labelled cells expressed Per1 message and protein during the night compared to the day. In the Arc, staining for tyrosine hydroxylase revealed that neuroendocrine cells expressing Per1 message and protein were dopaminergic. Together, these findings suggest that neuroendocrine cells contain the molecular machinery necessary to oscillate independently. It remains to be determined whether these cells actually function as autonomous oscillators or whether these rhythms are driven by signals from the SCN. These findings also indicate that the endocrine system represents an opportunity to study the interactions between central (SCN and neuroendocrine cells) and peripheral circadian (endocrine gland) oscillators.
Unfolding the Blanket of Understanding in the Listening Space: A Phenomenological Exploration of 'Being-With' in the Nursing Student-Teacher Relationship

Title of Dissertation: UNFOLDING THE BLANKET OF UNDERSTANDING IN THE LISTENING SPACE: A PHENOMENOLOGICAL EXPLORATION OF ‘BEING-WITH’ IN THE NURSING STUDENT-TEACHER RELATIONSHIP Mary T. Packard PhD 2004 Dissertation Directed By: Professor Francine H. Hultgren Department of Education Policy and Leadership College of Education University of Maryland This hermeneutic phenomenological inquiry is called by the question, What is the lived experience of ‘being-with’ in the nursing student-teacher relationship? I engage with eight senior baccalaureate nursing students in teaching and learning together in a psychiatric-mental health nursing course. Text is gathered through their narrative work in reflective journals and taped classroom conversations, as well as through taped individual hermeneutic conversations. The exploration into the phenomenon of ‘being-with’ is philosophically grounded in the work of Martin Heidegger, Hans-Georg Gadamer, and David Levin. The framework of activities as identified by Max van Manen (1990) brings the research to a practical possibility. As the students and I dwell together through listening, ‘being-with’ in the context of our pedagogical relationship is opened up for our understanding. Accounts of lived experiences are offered and become opportunities for deep interpretation. Through this hermeneutic work experiential structures of the phenomenon of ‘beingwith’ are brought forward and named in the presence of listening. Students and teacher alike risk vulnerability, enter into silence, and engage in profound meaning making of being in teaching and learning together. ‘Being-with’ in the nursing student-teacher relationship unravels as the following dimensions: creating soul space, flowing and blending in community, soulfriendship, hand of comfort in the midst of anxiety, opening an inn-between, and holding eternal echoes. Transformation through the experience and language of ‘being-with’ offers up possibilities for being in pedagogy and curriculum. This hermeneutic phenomenological inquiry into the phenomenon of ‘being-with’ in the nursing student-teacher relationship unfolds as a blanket of understanding and necessarily leads toward a pedagogy of ‘being-with’ the world of nursing education. UNFOLDING THE BLANKET OF UNDERSTANDING IN THE LISTENING SPACE: A PHENOMENOLOGICAL EXPLORATION OF ‘BEING-WITH’ IN THE NURSING STUDENT-TEACHER RELATIONSHIP
A practical hypertext catergorization method using links and incrementally available class information

As WWW grows at an increasing speed, a classifier targeted at hypertext has become in high demand. While document categorization is quite a mature, the issue of utilizing hypertext structure and hyperlinks has been relatively unexplored. In this paper, we propose a practical method for enhancing both the speed and the quality of hypertext categorization using hyperlinks. In comparison against a recently proposed technique that appears to be the only one of the kind, we obtained up to 18.5% of improvement in effectiveness while reducing the processing time dramatically. We attempt to explain through experiments what factors contribute to the improvement.
Definition of the Interaction Domain for Cytochrome con Cytochrome c Oxidase

To determine the interaction site for cytochromec (Cc) on cytochrome c oxidase (CcO), a number of conserved carboxyl residues in subunit II of Rhodobacter sphaeroides CcO were mutated to neutral forms. A highly conserved tryptophan, Trp143, was also mutated to phenylalanine and alanine. Spectroscopic and metal analyses of the surface carboxyl mutants revealed no overall structural changes. The double mutants D188Q/E189N and D151Q/E152N exhibit similar steady-state kinetic behavior as wild-type oxidase with horse Cc and R. sphaeroides Cc2, showing that these residues are not involved in Cc binding. The single mutants E148Q, E157Q, D195N, and D214N have decreased activities and increased K m values, indicating they contribute to the Cc:CcO interface. However, their reactions with horse and R. sphaeroides Cc are different, as expected from the different distribution of surface lysines on these cytochromes c. Mutations at Trp143 severely inhibit activity without changing theK m for Cc or disturbing the adjacent CuA center. From these data, we identify a Cc binding area on CcO with Trp143 and Asp214 close to the site of electron transfer and Glu148, Glu157, and Asp195 providing electrostatic guidance. The results are completely consistent with time-resolved kinetic measurements (Wang, K., Zhen, Y., Sadoski, R., Grinnell, S., Geren, L., Ferguson-Miller, S., Durham, B., and Millett, F. (1999) J. Biol. Chem.274, 38042–38050) and computational docking analysis (Roberts, V. A., and Pique, M. E. (1999) J. Biol. Chem. 274, 38051–38060).
Nutritional status and eating habits of bus drivers during the day and night

The aim of this study was to compare anthropometry and food intake patterns in bus drivers working during the day and night. One hundred and fifty males (81 night workers and 69 day workers) participated in the study. Dietary intake was assessed using a validated semi-quantitative food frequency questionnaire. Measurements of height, weight, waist circumference (WC), systolic and diastolic blood pressure, blood glucose, and lipid profile were obtained. A significant difference between groups was observed for mean WC (98.5 ± 10.7 cm in day workers versus 103.2 ± 9.7 cm in night workers; p = 0.005). Night workers had higher prevalence of being overweight and obese (BMI ≥ 25 kg/m2) than day workers (78.2% day workers versus 90.2% night workers; p = 0.004) and increased WC (>94 cm) (72.4% day workers versus 86.4% night workers; p = 0.03). Significant differences were found for meat consumption (2.3 servings ±0.9 for night workers versus 2.0 servings ±0.7 day workers, p = 0.04) and fruit intake (0.9 servings ±0.4 for night workers versus 0.7 servings for day workers ±0.5; p = 0.006). Night workers had a lower intake of vegetables than recommended compared to day workers (100 versus 92.7%, respectively, p = 0.01) and higher intake of oil (40.7 versus 24.6%, p = 0.03). Multivariate logistic regression analysis indicated that night work was associated with being overweight (OR = 2.94, 95% IC: 1.14–7.66, p = 0.03) and abnormal values of WC (OR = 2.82, 95% IC: 1.20–6.69, p = 0.009) after adjusting for potential confounders. It is concluded that night workers had a higher prevalence and risk of being overweight/obese and increased WC compared with day workers. Night workers also presented a higher proportion of inappropriate intakes of food groups when compared to day workers, even though both groups were eating poor diets. These results demonstrate the need of lifestyle-intervention programs in these workers.
From neurological soft signs to functional outcome in young individuals in treatment with secondary services for non-psychotic disorders: a path analysis

Background Functional decline among patients with mental illness is not unique to individuals with psychotic disorders. Despite this, research on early predictors of functional outcome mainly focused on individuals thought to have an ‘at risk mental state’ (ARMS) for psychosis. There is evidence suggesting that certain early vulnerability markers, such as neurological soft signs (NSS), may explain variability in functional outcomes independent of the level of psychosis risk and the traditional diagnostic classification. Method Structural equation modeling was applied to baseline data from a prospective longitudinal study of 138 young individuals in treatment with secondary services for non-psychotic disorders. We evaluated theoretically based models of pathways to functional outcome starting from NSS. The intervening variables were established according to previous evidence and drawn from two general categories: cognition (neuro- and social-) and negative symptoms (expressive and experiential). Results A final trimmed model was a single path running from NSS to neurocognition to experiential negative symptoms to outcome. It could not be improved by adding or dropping connections that would change the single path to multiple paths. The indirect effect from NSS to outcome was significant. The validity of the model was independent of the ARMS status and the psychiatric diagnosis. Conclusions Our results provide evidence for a single pathway model in which the starting and intervening variables represent modifiable trans-diagnostic therapeutic targets to improve functional trajectories in young individuals with a recent-onset psychiatric diagnosis and different levels of psychosis risk.
Aligning Pharmacologic Classes Between MeSH and ATC

Objective: To align pharmacologic classes in ATC and MeSH with lexical and instance-based techniques. Methods: Lexical alignment: we map the names of ATC classes to MeSH through the UMLS, leveraging normalization and additional synonymy. Instance-based alignment: we associate ATC and MeSH classes through the drugs they share, using the Jaccard coefficient to measure class-class similarity. We use a metric to distinguish between equivalence and inclusion mappings. Results: We found 221 lexical mappings, as well as 343 instance-based mappings, with a limited overlap (61). From the 343 instance-based mappings we classify 113 as equivalence mappings and 230 as inclusion mappings. A limited failure analysis is presented. Conclusion: Our instance-based approach to aligning pharmacologic classes has the prospect of effectively supporting the creation of a mapping of pharmacologic classes between ATC and MeSH. This exploratory investigation needs to be evaluated in order to adapt the thresholds for similarity.
Specificity for block by saxitoxin and divalent cations at a residue which determines sensitivity of sodium channel subtypes to guanidinium toxins

bTyrosine 401 of the skeletal muscle isoform (mu 1) of the rat muscle Na channel is an important determinant of high affinity block by tetrodotoxin (TTX) and saxitoxin (STX) in Na-channel isoforms. In mammalian heart Na channels, this residue is substituted by cysteine, which results in low affinity for TTX/STX and enhanced sensitivity to block by Zn2+ and Cd2+. In this study, we investigated the molecular basis for high affinity block of Na channels by STX and divalent cations by measuring inhibition of macroscopic Na+ current for a series of point mutations at residue Tyr401 of the rat mu 1 Na channel expressed in Xenopus oocytes. Substitution of Tyr401 by Gly, Ala, Ser, Cys, Asp, His, Trp, and Phe produced functional Na+ currents without major perturbation of gating or ionic selectivity. High affinity block by STX and neosaxitoxin (NEO) with Ki values in the range of 2.6-18 nM required Tyr, Phe, or Trp, suggestive of an interaction between an aromatic ring and a guanidinium group of the toxin. The Cys mutation resulted in a 7- and 23-fold enhancement of the dissociation rate of STX and NEO, respectively, corresponding to rapid toxin dissociation rates of cardiac Na channels. High affinity block by Zn2+ (Ki = 8-23 microM) required Cys, His, or Asp, three residues commonly found to coordinate directly with Zn2+ in metalloproteins. For the Cys mutant of mu 1 and also for the cardiac isoform Na channel (rh1) expressed in the L6 rat muscle cell line, inhibition of macroscopic Na+ conductance by Zn2+ reached a plateau at 85-90% inhibition, suggesting the presence of a substate current. The Asp mutant also displayed enhanced affinity for inhibition of conductance by Ca2+ (Ki = 0.3 mM vs approximately 40 mM in wild type), but block by Ca2+ was incomplete, saturating at approximately 69% inhibition. In contrast, Cd2+ completely blocked macroscopic current in the Cys mutant and the L6 cell line. These results imply that the magnitude of substate current depends on the particular residue at position 401 and the species of divalent cation. The His mutant also exhibited enhanced sensitivity to block by H+ with a pKa of approximately 7.5 for the His imidazole group. Our findings provide further evidence that residue 401 of mu 1 is located within the outer vestibule of the Na channel but external to the single-filing region for permeant ions.
Implementation of golden section search method in SAGE algorithm

The SAGE algorithm gives the chance to divide the multi-dimension optimization problem, which one confronts when the maximum likelihood (ML) estimation is performed, into iterations of one-dimension optimization problems. The progress to find out the maximum of the log-likelihood function during Maximization-step (M-step) of the algorithm is yet to be refined with purpose of reducing the time cost of the computation and also path management for channel parameter estimation. In this contribution, we try to improve the performance of the SAGE algorithm by using Golden Section search method in the M-step. Numerical and experimental results demonstrate that the effectiveness of the SAGE algorithm is improved.
Causal Broadcast Protocol for Very Large Group Communication Systems

The paper presents a causal protocol for very large group communication systems. The protocol does not make any assumption concerning the group structure nor the network topology. It aims to minimize and control the flow of causal information through two mechanisms. First, it reduces the amount of causal information (CI) timestamped per message by avoiding the transmission of redundant information. The second original mechanism we propose controls and bounds the size of transmitted CI, without losing causality, through the use of additional control messages. Our protocol guarantees a great flexibility, as well as the minimization of exchanged causal information. In addition, it accelerates the knowledge of the system concerning its causal past.
An Algorithm for Probabilistic Least-Commitment Planning

We define the probabilistic planning problem in terms of a probability distribution over initial world states, a boolean combination of goal propositions, a probability threshold, and actions whose effects depend on the execution-time state of the world and on random chance. Adopting a probabilistic model complicates the definition of plan success: instead of demanding a plan that provably achieves the goal, we seek plans whose probability of success exceeds the threshold. This paper describes a probabilistic semantics for planning under uncertainty, and presents a fully implemented algorithm that generates plans that succeed with probability no less than a user-supplied probability threshold. The algorithm is sound (if it terminates then the generated plan is sufficiently likely to achieve the goal) and complete (the algorithm will generate a solution if one exists).
Parameter extraction from DFB lasers by means of a simple expression for the spontaneous emission spectrum

A simple expression for the amplified spontaneous emission from a laser biased below lasing threshold is applied to semiconductor laser parameter extraction. We demonstrate that accurate measurement of the coupling coefficient for distributed feedback (DFB) lasers with phaseshifts and end reflections is a practical possibility. It is also shown that the used expression, for a reciprocal device, can be derived directly from the wave equation using the Green's function. <<ETX>>