Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Analysis of the Exon-Intron Structure in Eukaryotic Genomes

The exon numbers and lengths vary in different eukaryotic species. With increasing completed genomic sequences, it is indispensable to reanalyze the gene organization in diverse eukaryotic genomes. We performed a large-scale comparative analysis of the exon-intron structure in 72 eukaryotic organisms, including plants, fungi and animals. We confirmed that the exon-intron structure varies massively among eukaryotic genomes and revealed some lineage-specific features of eukaryotic genes. These include a teleost-specific exon-intron structure pattern, relatively small introns and large exons in fungi and algae, and a gradual expansion of introns in vertebrates. Furthermore, the conservation analysis of exon-intron boundaries indicates that several bases near splice site junctions are different in introns with variable length among different species. After comparison, we identified a trend showing increases in intron densities and lengths in diverse species from fungi, plants, invertebrates to vertebrates, while it was the opposite in relation to exon lengths. The statistical properties of eukaryotic genomic organization suggest that genome-specific features are preserved by diverse evolutionary processes, which paves way for further research on the diversification of eukaryotic evolution.
Cost Implications of Using Inhaled Nitric Oxide Compared with Epoprostenol for Pulmonary Hypertension

Objective: To compare the cost of using intravenous epoprostenol with that of inhaled nitric oxide (NO) for treating episodes of pulmonary hypertension in children with congenital heart disease. Design: An analysis of the cost of epoprostenol and NO use over the previous 18 months was performed. Three 6-month periods were identified, two in which epoprostenol was used and the third in which inhaled NO was introduced for the treatment of pulmonary hypertension. Setting: A 10-bed pediatric cardiac intensive care unit, Royal Liverpool Children's Hospital, Alder Hey, Liverpool, England. Subjects: Children with congenital heart disease and persistently elevated pulmonary artery pressure following cardiac surgery. Main Outcome Measures: The total duration of use of epoprostenol and inhaled NO was documented. The costs per hour for epoprostenol and inhaled NO were calculated and the annual cost of each agent was estimated. Results: In the two 6-month periods prior to the introduction of inhaled NO, epoprostenol was used on 14 occasions (5 in the first period, 3 in the second). In the last 6-month period, nine children required pulmonary vasodilator therapy on 14 occasions. All nine children were treated successfully with inhaled NO; none were given or needed epoprostenol, as NO always was effective in providing pulmonary vasodilatation. For resistant pulmonary hypertension, increasing the concentration of NO would have been the next therapeutic option. The cost for the two 6-month periods using epoprostenol was $19,483.48 for the drug and $283.25 for equipment costs (total cost $19,766.73). There was no expenditure on epoprostenol in the final 6-month period. The cost of NO was $465. However, the total expenditure, including the delivery and monitoring system, was $4,722.85. Conclusions: Using inhaled NO in our pediatric cardiac intensive care unit abolished the use of epoprostenol during the reported monitoring period. The cost savings were significant, amounting to 12% of the annual drug budget for the unit. The cost of setting up the inhaled NO delivery system is recouped rapidly. The ease of delivery and measurement of inhaled NO also may have contributed to its increased clinical use.
ASSOCIATION OF CYTOMEGALOVIRUS DNA CONCENTRATION IN EPITHELIAL LINING FLUID AND SYMPTOMATIC CYTOMEGALOVIRUS INFECTION IN LUNG TRANSPLANT RECIPIENTS

Background. The authors have investigated the effectiveness of virus detection from bronchoalveolar lavage (BAL) samples for the identification of symptomatic cytomegalovirus (CMV) infection in lung transplant recipients. Methods. Thus, 275 BAL samples taken from 105 lung transplant recipients during follow-up were analyzed by quantitative polymerase chain reaction (PCR) and virus isolation. Results. Quantitative PCR detected virus in all 24 BAL samples taken at onset of symptomatic disease, and virus culture in only 7 samples (29.2%). Twenty-three of 251 BAL samples (9.2%) were positive by PCR, although they were obtained in an asymptomatic phase. Quantitation of CMV DNA from BAL allowed no discrimination between symptomatic and asymptomatic infection in individual cases. However, when the urea dilution method was used to recalculate the CMV DNA concentration for the epithelial lining fluid (ELF) diluted in the BAL, a CMV DNA level of more than 104 copies/mL ELF was clearly associated with symptomatic disease. Conclusion. The CMV DNA level in ELF may be a marker for symptomatic CMV infection.
Coping with chronic pain: In‐depth interviews with children suffering from Juvenile Chronic Arthritis

This study examined from the perspective of children with Juvenile Chronic Arthritis, their experiences of coping with chronic pain in daily life. In‐depth interviews were conducted with 22 children (6–17 years). The grounded theory method was applied for analysing the taped and transcribed interviews. Seven descriptive categories were grounded in the data, labelled (1) “controlling strategies”, (2) “avoidance strategies”, (3) “cognitive strategies”, (4) “compliance with the treatment”, (5) “seeking social support”, and (6) “recovering”. A core category was identified and labelled “making me different”. The children seem to be caught in a dilemma. In one way the chosen coping strategy reduces chronic pain and in another way the strategy increases stress and feelings of being different from non‐disabled peers. Our results indicate the great importance of social support from the children's environment.
Business process modeling languages: Sorting through the alphabet soup

Requirements capture is arguably the most important step in software engineering, and yet the most difficult and the least formalized one [Phalp and Shepperd 2000]. Enterprises build information systems to support their business processes. Software engineering research has typically focused on the development process, starting with user requirements—if that—with business modeling often confused with software system modeling [Isoda 2001]. Researchers and practitioners in management information systems have long recognized that understanding the business processes that an information system must support is key to eliciting the needs of its users (see e.g., Eriksson and Penker 2000]), but lacked the tools to model such business processes or to relate such models to software requirements. Researchers and practitioners in business administration have long been interested in modeling the processes of organizations for the purposes of understanding, analyzing, and improving such processes [Hammer and Champy 1993], but their models were often too coarse to be of use to software engineers. The advent of ecommerce and workflow management systems, among other things, has led to a convergence of interests and tools, within the broad IT community, for modeling and enabling business processes. In this article we present an overview of business process modeling languages. We first propose a categorization of the various languages and then describe representative languages from each family.
Growth Performance of Lambs Fed Diet Supplemented with Rice Bran Oil as Such or as Calcium Soap

Forty two Malpura lambs (21 d old) were divided into three groups of 14 each consisting of 8 females and 6 males. Lambs were allowed to suckle their respective dams twice daily up to weaning (13 wks) and offered free choice concentrate and roughage in a cafeteria system. The lambs in control group were fed conventional concentrate mixture, in RBO group concentrate mixture fortified with 4% industrial grade rice bran oil and in Ca-soap rice bran oil (as in RBO group) was supplemented in the form of calcium soap. The concentrate intake decreased(p≤0.05) in RBO group as a result total dry matter, crude protein and metabolizable energy intake decreased compared to control whereas Ca-soap prepared from the same rice bran oil stimulated the concentrate intake leading to higher total dry matter, crude protein and energy intakes. The digestibility of dry matter (p≤0.05), organic matter (p≤0.05) and crude protein (p≤0.05) was higher in RBO group followed by Ca-soap and control whereas no effect was observed for ether extract digestibility. Higher cholesterol (p≤0.05) content was recorded in serum of oil supplemented groups (RBO and Ca-soap) while no effect was recorded for other blood parameters. Rice bran oil as such adversely affected and reduced the body weight gain (p≤0.001) of lambs in comparison to control whereas the Ca-soap of rice bran oil improved body weight gain and feed conversion efficiency in lambs. Fat supplementation decreased total volatile fatty acids (p≤0.05) and individual volatile fatty acid concentration which increased at 4 h post feeding. Fat supplementation also reduced (p≤0.05) total protozoa count. Ca-soap of rice bran oil improved pre slaughter weight (p≤0.05) and hot carcass weight (p≤0.05). It is concluded from the study that rice bran oil in the form of calcium soap at 40 g/kg of concentrate improved growth, feed conversion efficiency and carcass quality as compared to rice bran oil as such and control groups.
Visualising data in web observatories: a proposal for visual analytics development & evaluation

Web Observatories use innovative analytic processes to gather insights from observed data and use the Web as a platform for publishing interactive data visualisations. Recordable events associated with interactivity on the Web provide an opportunity to openly evaluate the utility of these artefacts, assessing fitness for purpose and observing their use. The three principles presented in this paper propose a community evaluation approach to innovation in visual analytics and visualisation for Web Observatories through code sharing, the capturing of semantically enriched interaction data and by openly stating the intended goals of all visualisation work. The potential of this approach is exampled with a set of front-end tools suitable for adoption by the majority of Web Observatories as a means of visualising data on the Web as part the shared, open, and community-driven developmental process. The paper outlines the method for capturing user interaction data as a series of semantic events, which can be used to identify improvements in both the structure and functionality of visualisations. Such refinements in user behaviour are proposed as part of a new methodology that introduces Economics as an evaluation tool for visual analytics.
AN ANALYSIS OF THE REPRESENTATIONS OF THE MAPPING CLASS GROUP OF A MULTIGEON THREE-MANIFOLD

It is known that the distinct unitary irreducible representations (UIR's) of the mapping class group G of a three-manifold ℳ give rise to distinct quantum sectors ("θ sectors") in quantum theories of gravity based on a product space–time of the form ℝ×ℳ. In this paper, we study the UIR's of G in an effort to understand the physical implications of these quantum sectors. The mapping class group of a three-manifold which is the connected sum of ℝ3 with a finite number of irreducible primes is a semidirect product group. Following Mackey's theory of induced representations, we provide an analysis of the structure of the general finite-dimensional UIR of such a group. In the picture of quantized primes as particles (topological geons), this general group-theoretic analysis enables one to draw several qualitative conclusions about the geons' behavior in different quantum sectors, without requiring an explicit knowledge of the UIR's corresponding to the individual primes. An important general result is that the classification of the UIR's of the so-called particle subgroup (equivalently, the UIR's of G in which the slide diffeomorphisms are represented trivially) is reduced to the problem of finding the UIR's of the internal diffeomorphism groups of the individual primes. Moreover, this reduction is entirely consistent with the geon picture, in which the UIR of the internal group of a prime determines the species of the corresponding quantum geon, and the remaining freedom in the overall UIR of G expresses the possibility of choosing an arbitrary statistics (Bose, Fermi or para) for the geons of each species. For UIR's which represent the slides nontrivially, we do not provide a complete classification, but we find some new types of efforts due to the slides, including quantum breaking of internal symmetry and of particle indistinguishability. In connection with the latter, a novel kind of statistics arises which is determined by representations of proper subgroups of the permutation group, rather than of the group as a whole. Finally, we observe that for a generic three-manifold there will be an infinity of inequivalent UIR's and hence an infinity of "consistent" theories, when topology change is neglected.
Impact of H.264 Advanced Video Coding Inter-frame Block Sizes on Video Quality

In this paper, we present a perceptual-based encoding benchmarking of the H.264 Advanced Video Coding (AVC) inter-frame prediction variable block sizes for various spatial and temporal contents. This paper in order to quantify the impact on the video quality of the AVC inter-frame variable block sizes and the responsible prediction algorithm has disabled the motion estimation mechanism of the encoder and manually each block size is selected. Thus each time only one available block size out of the total seven is available to be searched for each MB and it is possible to examine the video quality impact of each block size independently to the remaining ones. The scope of this paper is to study if the use of sophisticated predictions algorithms and variable block sizes enhance the perceived quality of the encoded video signal or if there is not any significant quality degradation when the option of variable size is disabled.
Lipschitz Bandits: Regret Lower Bound and Optimal Algorithms

We consider stochastic multi-armed bandit problems where the expected reward is a Lipschitzfunction of the arm, and where the set of arms is either discrete or continuous. For discrete Lipschitzbandits, we derive asymptotic problem specific lower bounds for the regret satisfied by anyalgorithm, and propose OSLB and CKL-UCB, two algorithms that efficiently exploit the Lipschitzstructure of the problem. In fact, we prove that OSLB is asymptotically optimal, as its asymptoticregret matches the lower bound. The regret analysis of our algorithms relies on a new concentrationinequality for weighted sums of KL divergences between the empirical distributions of rewards andtheir true distributions. For continuous Lipschitz bandits, we propose to first discretize the actionspace, and then apply OSLB or CKL-UCB, algorithms that provably exploit the structure efficiently.This approach is shown, through numerical experiments, to significantly outperform existing algorithmsthat directly deal with the continuous set of arms. Finally the results and algorithms areextended to contextual bandits with similarities.
Workplace Harassment — A Health Issue: Anti-Discrimination Cases and Workers' Compensation Claims

This article describes the adverse health-related effects of racial and sexual harassment elicited from files held by the Western Australian Equal Opportunity Commission where the complainant has nominated sexual or racial harassment as a ground of discrimination. Those results are compared with publicly available data on work-related stress claims obtained from the Compendium of Workers' Compensation Statistics Australia 2004–06, arising from allegations of harassment. Information gleaned from a survey of unreported court decisions (from publicly available legal data bases, such as www.austlii.edu.au and www.ohs.alert.com) is also reviewed. The purpose of examining this data is to consider the links between various forms of unlawful harassment, workplace stress and the evidence of adverse effect upon worker health. The results of this triangulation of data are consistent with that body of research which shows that workplace harassment can give rise to a range of adverse health outcomes. This paper explores how the inter-relationship of antidiscrimination and workers compensation laws may affect claimant behaviours.
Meeting the Challenges of the Future: Integrating Public Health and Public Education for Mental Health Promotion

The 2002 Future of School Psychology Conference called for reform of current models of professional school psychology, including a paradigm shift toward a public health model of practice. This article explores the role of school psychologists in efforts to achieve an integrated public health and public education model for delivering comprehensive school-based mental health services. Building on expertise as psychological and educational consultants, school psychooogists can play a unique role in facilitating the necessary systemic reform and capacity building for comprehensive mental health service delivery. This revised role requires redefining school-based consultation to include consultation for capacity building, and rethinking professional preparation to ensure expertise in public health models, inter-agency and interdisciplinary collaboration, participatory action research, and comprehensive service delivery.
CD28 Costimulation Is Required for In Vivo Induction of Peripheral Tolerance in CD8 T Cells

Whereas ligation of CD28 is known to provide a critical costimulatory signal for activation of CD4 T cells, the requirement for CD28 as a costimulatory signal during activation of CD8 cells is less well defined. Even less is known about the involvement of CD28 signals during peripheral tolerance induction in CD8 T cells. In this study, comparison of T cell responses from CD28-deficient and CD28 wild-type H-Y–specific T cell receptor transgenic mice reveals that CD8 cells can proliferate, secrete cytokines, and generate cytotoxic T lymphocytes efficiently in the absence of CD28 costimulation in vitro. Surprisingly, using pregnancy as a model to study the H-Y–specific response of maternal T cells in the presence or absence of CD28 costimulation in vivo, it was found that peripheral tolerance does not occur in CD28KO pregnants in contrast to the partial clonal deletion and hyporesponsiveness of remaining T cells observed in CD28WT pregnants. These data demonstrate for the first time that CD28 is critical for tolerance induction of CD8 T cells, contrasting markedly with CD28 independence of in vitro activation, and suggest that the role of CD28/B7 interactions in peripheral tolerance of CD8 T cells may differ significantly from that of CD4 T cells.
Pseudomonas aeruginosa pilin activates the inflammasome

IL‐1β is produced from inactive pro‐IL‐1β by activation of caspase‐1 brought about by a multi‐subunit protein platform called the inflammasome. Many bacteria can trigger inflammasome activity through flagellin activation of the host protein NLRC4. However, strains of the common human pathogen Pseudomonas aeruginosa lacking flagellin can still activate the inflammasome. We set out to identify what non‐flagellin components could produce this activation. Using mass spectroscopy, we identified an inflammasome‐activating factor from P. aeruginosa as pilin, the major component of the type IV bacterial pilus. Purified pilin introduced into mouse macrophages by liposomal delivery activated caspase‐1 and led to secretion of mature IL‐1β, as did recombinant pilin purified from Escherichia coli. This was dependent on caspase‐1 but not on the host inflammasome proteins NLRC4, NLRP3 or ASC. Mutants of P. aeruginosa strain PA103 lacking pilin did not activate the inflammasome following infection of macrophages with live bacteria. Type III secretion remained intact in the absence of pili, showing this was not due to a lack of effector delivery. Our observations show pilin is a novel activator of the inflammasome in addition to flagellin and the recently described PrgJ protein family, the basal body rod component of the type III apparatus.
RAPID MORPHOLOGICAL CHANGE IN CHANNEL ISLAND DEER MICE

Deer mice, Peromyscus maniculatus, collected over 90 years from three California Channel Islands, were examined for evidence of morphological change. Rapid morphological change has occurred in the endemic subspecies from Santa Barbara (P. m. elusus), Anacapa (P. m. anacapae), and Santa Cruz Island (P. m. santacruzae). Data were divided into two temporal classes, 1897–1941 and 1955–1988. Of the 16 morphological characters measured, between five and 10 measures changed significantly (P ⩽ 0.05) with temporal class in each subspecies, and multivariate test statistics were significant (P ⩽ 0.05) for all three subspecies. For each subspecies, depth of braincase, total length, tail length, and hind foot length became smaller over time, except depth of braincase, which became larger in P. m. elusus. The rates of change dramatically exceed those estimated from paleontological records and are even higher than those reported in some experimental selection studies. Temporal change in two characters exceeds differentiation between subspecies. Although changing, each subspecies remained well differentiated, and incorporation of temporal change allowed correct classification of most specimens. Unlike nearly all previous reports of rapid evolution, the changes in these populations were not associated with a founder events or recent introductions. This study demonstrates that rapid phenotypic change can occur in long‐established natural populations and temporal stability of morphological characters in such populations, even over short evolutionary time periods, cannot be assumed.
A Study on the Performance of a Three-Stage Load-Balancing Switch

There has been a great deal of interest recently in load-balancing switches due to their simple architecture and high forwarding bandwidth. Nevertheless, the mis-sequencing problem of the original load-balancing switch hinders the performance of underlying TCP applications. Several load-balancing switch designs have been proposed to address this mis-sequencing issue. They solve this mis-sequencing problem at the cost of either algorithmic complexity or special hardware requirements. In this paper, we address the mis-sequencing problem by introducing a three-stage load-balancing switch architecture enhanced with an output load-balancing mechanism. This three-stage load-balancing switch achieves a high forwarding capacity while preserving the order of packets without the need of costly online scheduling algorithms. Theoretical analyses and simulation results show that this three-stage load-balancing switch provides a transmission delay that is upper-bounded by that of an output-queued switch plus a constant that depends only on the number of input/output ports, indicating the same forwarding capacity as an output-queued switch.
Mentoring Women in Organizations: Practice in Search of Theory

Does mentoring really increase an individual's or an organization's capacity to develop? In response to proponents who assume that mentonng is automatically helpful to women, this research argues that deficiencies in the literature keep us from informing and improving the practice of mentorship, particularly for women. In juxtaposing what we know about mentoring women in the work-place with what we do not know, this article suggests the theoretical implications of mentoring and the related areas of inquiry that we should explore. I note that we need certain kinds of inquiry to increase our understanding of how mentoring enhances the individual's and organization's capacity to change and develop and urge scholars and practitioners to work together in developing and testing mentoring theory to answer these questions. Doing so will advance our knowledge of how mentoring helps individuals, particularly women, and organizations reach development goals.