Miracle-dz/UniFAR-FTUs huggingface dataset:
Ontological Analysis of Integrated Process Models: testing hypotheses

Integrated process modeling is achieving prominence in helping to document and manage business administration and IT processes in organizations. The ARIS framework is a popular example for a framework of integrated process modeling not least because it underlies the 800 or more reference models embedded in the world's most popular ERP package, SAP R/3. This paper demonstrates the usefulness of the Bunge-Wand-Weber (BWW) representation model for evaluating modeling grammars such as those constituting ARIS. It reports some initial insights gained from pilot testing Green and Rosemann's (2000) evaluative propositions. Even when considering all five views of ARIS, modelers have problems representing business rules, the scope and boundary of systems, and decomposing models. However, even though it is completely ontologically redundant, users still find the function view useful in modeling.
Coordination between T helper cells, iNKT cells, and their follicular helper subsets in the humoral immune response against Clostridium difficile toxin B

Activation of iNKT cells with the CD1d‐binding glycolipid adjuvant α‐galactosylceramide (α‐GC) enhances humoral immunity specific for coadministered T‐dependent Ag. However, the relationship between the iNKT cell and the classic T helper (Th) or T follicular helper (Tfh) function following this immunization modality remains unclear. We show that immunization with the C‐terminal domain (CTD) of Clostridium difficile toxin B (TcdB), accompanied by activation of iNKT cells with α‐GC, led to enhanced production of CTD‐specific IgG, which was CD1d‐ and iNKT cell‐dependent and associated with increased neutralization of active TcdB. Immunization with CTD plus α‐GC followed by NP hapten‐linked CTD increased NP‐specific IgG1 titers in an NKT‐dependent manner, suggesting that iNKT activation could enhance Th or Tfh function or that iNKT and iNKTfh cells could provide supplemental, yet independent, B cell help. Th, Tfh, iNKT, and iNKTfh cells were, therefore, examined quantitatively, phenotypically, and functionally following immunization with CTD or with CTD plus α‐GC. Our results demonstrated that α‐GC–activated iNKT cells had no direct effect on the numbers, phenotype, or function of Th or Tfh cells. However, CD4+ T cell–specific ablation of the Bcl6 transcription factor demonstrated that Tfh and iNKTfh cells both contributed to B cell help. This work extends our understanding of the immune response to vaccination and demonstrates an important contribution by NKTfh cells to humoral immunity.
Bovine Lactoferricin-induced Anti-inflammation Is, in Part, via Up-regulation of Interleukin-11 by Secondary Activation of STAT3 in Human Articular Cartilage*

Background: Bovine lactoferricin (LfcinB) promotes anti-catabolism and anti-inflammation in articular cartilage. Results: LfcinB induces IL-11 via AP-1, which in turn induces TIMP-1 via STAT3. Conclusion: LfcinB sequentially regulates IL-11 and TIMP-1 expression through distinct mechanisms in articular chondrocytes. Significance: These findings further suggest the potential of LfcinB as a novel therapeutic agent in osteoarthritis. Bovine lactoferricin (LfcinB), a multifunctional peptide, was recently demonstrated to be anti-catabolic and anti-inflammatory in human articular cartilage. LfcinB blocks IL-1-mediated proteoglycan depletion, matrix-degrading enzyme expression, and pro-inflammatory mediator induction. LfcinB selectively activates ERK1/2, p38 (but not JNK), and Akt signaling. However, the relationship between these pathways and LfcinB target genes has never been explored. In this study, we uncovered the remarkable ability of LfcinB in the induction of an anti-inflammatory cytokine, IL-11. LfcinB binds to cell surface heparan sulfate to initiate ERK1/2 signaling and activate AP-1 complexes composed of c-Fos and JunD, which transactivate the IL-11 gene. The induced IL-11 functions as an anti-inflammatory and chondroprotective cytokine in articular chondrocytes. Our data show that IL-11 directly attenuates IL-1-mediated catabolic and inflammatory processes ex vivo and in vitro. Moreover, IL-11 activates STAT3 signaling pathway to critically up-regulate TIMP-1 expression, as a consecutive secondary cellular response after IL-11 induction by LfcinB-ERK-AP-1 axis in human adult articular chondrocytes. The pathological relevance of IL-11 signaling to osteoarthritis is evidenced by significant down-regulation of its cognate receptor expression in osteoarthritic chondrocytes. Together, our results suggest a two-step mechanism, whereby LfcinB induces TIMP-1 through an IL-11-dependent pathway involving transcription factor AP-1 and STAT3.
Smoking Diminishes the Beneficial Effect of Statins: Observations from the Landmark Trials

The landmark statin trials showed a significant reduction in morbidity and mortality associated with ischemic heart disease. However, it may not be widely appreciated that smoking had a marked adverse effect on outcome in these trials. In both the primary and secondary preven tion setting, the effect of smoking was broadly similar. Smoking markedly increased the risk of events in the placebo and treatment groups. For example, in the primary prevention trials, this risk was 74-86% higher when smokers were compared with nonsmokers in the placebo groups. The corresponding figures for the secondary prevention trials were 23-61%. The risk of events in untreated nonsmokers was of a similar order to that seen in smokers taking statins. Although statin treatment was associated with a significant reduction in events in smokers, the best outcome was observed in nonsmokers treated with statins (primary preven tion : lovastatin or pravastatin; secondary prevention: pravastatin or simvastatin). The highest risk of events in any group was in the smokers on placebo. This information may increase clinician and patient awareness as to the marked harmful effect of smoking relative to effective, evidence-based treatment (ie, the use of statins).
Chaos around a Hénon-Heiles-inspired exact perturbation of a black hole.

We find that the model of a black hole plus an exterior halo of quadrupoles and octopoles recently proposed by us is more chaotic than previously detected. In fact, the quadrupolar component gives rise also to a chaotic behavior, found after further numerical search. This fact reinforces even more the role of chaos in relativistic core--halo models.
Heavy metal and associated antibiotic resistance of fecal coliforms, fecal streptococci and pathogens isolated from wastewaters of abattoirs in Nairobi, Kenya

Objective: The pollution of the environment with toxic heavy metals is increasing globally with industrial progress. Microorganisms can be good bio-accumulators of particulate and soluble forms of heavy metals and subsequently resist antibiotics. The present study aimed at assessing the resistance pattern to multiple heavy metals by wastewater bacteria and associated antibiotic resistance. Methodology and results: Standard microbiological methods were used to isolate fecal streptococci, fecal coliforms, Vibrio and Salmonella species from raw animal wastewaters and sludge samples obtained from three abattoirs around Nairobi city. A total of 30 samples were collected. Agar diffusion and tube dilution methods were used to assess the heavy metal resistance while sensitivity to antibiotics was determined by the agar diffusion method. From the 40 isolates obtained, 27 showed multiple resistance to heavy metals. Resistance pattern was as follows; Hg 9 (33.3%), Co 11 (40.7%), Cu 18 (66.7%), Zn 19 (70.4%), Pb 21 (77.8%), and Ni 24 (88.9%). Out of the 27 resistant strains, 5 (18.5%) showed resistance to 5 different metal ions and only 1 (3.7%) showed resistance to two different metal ions. With each of the six metals tested, there was a tendency towards a high frequency of resistance among the isolates to lincomycin (77.8%), tetracycline (70.4%) and ampicillin (66.7%). Conclusion and application of findings: In the present study, heavy metal resistance associated with multiple drug resistance was detected in the bacterial isolates from the wastewater and sludge of the cattle, sheep and goat abattoirs. The high degree of resistance to common antibiotics could be attributed to the contamination of the wastewaters and sludge with heavy metals possibly from animal feeds or drinking waters, leading to co-selection of both metal tolerant and antibiotic resistant microbial species. This requires intervention measures to curb the potential health hazard that heavy metal pollution pose in the environment. The identified heavy metal resistant bacteria could be useful for bioremediation of heavy metals contaminated sewage and wastewaters, but the coupled antibiotic resistance is a worrying phenomenon. Keywords: Heavy metal resistant bacteria, antibiotic resistance, wastewaters, sludge, animals
Long‐Term Effects of Safe Patient Handling Program on Staff Injuries

Purpose: This study evaluated the effectiveness of a safe patient handling program (STEPS) at an inpatient rehabilitation unit in reducing injury due to patient transfers. Our objectives were to compare number of staff injuries during the 1.5‐year period post training to pre training (baseline) and to determine whether reduction in injuries was sustained long term during a 2.5‐year post training period. Methods: All nursing and therapy staff as well as new hires received STEPS training. Periodic retraining was not provided. Findings: The number of injuries was significantly reduced at post training compared to baseline (p = 0.01). However, the reductions in injuries were not sustained long term. Conclusion: We estimated a cost benefit of $3.71 for every dollar invested in retraining based on injury reduction realized during the post training period. Clinical Relevance: Retraining is likely to have a positive cost benefit when it results in maintaining reduction in staff injuries.
Proteomic Analysis of Chicken Skeletal Muscle during Embryonic Development

Embryonic growth and development of skeletal muscle is a major determinant of muscle mass, and has a significant effect on meat production in chicken. To assess the protein expression profiles during embryonic skeletal muscle development, we performed a proteomics analysis using isobaric tags for relative and absolute quantification (iTRAQ) in leg muscle tissues of female Xinghua chicken at embryonic age (E) 11, E16, and 1-day post hatch (D1). We identified 3,240 proteins in chicken embryonic muscle and 491 of them were differentially expressed (fold change ≥ 1.5 or ≤ 0.666 and p < 0.05). There were 19 up- and 32 down-regulated proteins in E11 vs. E16 group, 238 up- and 227 down-regulated proteins in E11 vs. D1 group, and 13 up- and 5 down-regulated proteins in E16 vs. D1 group. Protein interaction network analyses indicated that these differentially expressed proteins were mainly involved in the pathway of protein synthesis, muscle contraction, and oxidative phosphorylation. Integrative analysis of proteome and our previous transcriptome data found 189 differentially expressed proteins that correlated with their mRNA level. The interactions between these proteins were also involved in muscle contraction and oxidative phosphorylation pathways. The lncRNA-protein interaction network found four proteins DMD, MYL3, TNNI2, and TNNT3 that are all involved in muscle contraction and may be lncRNA regulated. These results provide several candidate genes for further investigation into the molecular mechanisms of chicken embryonic muscle development, and enable us to better understanding their regulation networks and biochemical pathways.
Integration of Social Information by Human Groups

We consider a situation in which individuals search for accurate decisions without direct feedback on their accuracy, but with information about the decisions made by peers in their group. The "wisdom of crowds" hypothesis states that the average judgment of many individuals can give a good estimate of, for example, the outcomes of sporting events and the answers to trivia questions. Two conditions for the application of wisdom of crowds are that estimates should be independent and unbiased. Here, we study how individuals integrate social information when answering trivia questions with answers that range between 0% and 100% (e.g., "What percentage of Americans are left-handed? "). We find that, consistent with the wisdom of crowds hypothesis, average performance improves with group size. However, individuals show a consistent bias to produce estimates that are insufficiently extreme. We find that social information provides significant, albeit small, improvement to group performance. Outliers with answers far from the correct answer move toward the position of the group mean. Given that these outliers also tend to be nearer to 50% than do the answers of other group members, this move creates group polarization away from 50%. By looking at individual performance over different questions we find that some people are more likely to be affected by social influence than others. There is also evidence that people differ in their competence in answering questions, but lack of competence is not significantly correlated with willingness to change guesses. We develop a mathematical model based on these results that postulates a cognitive process in which people first decide whether to take into account peer guesses, and if so, to move in the direction of these guesses. The size of the move is proportional to the distance between their own guess and the average guess of the group. This model closely approximates the distribution of guess movements and shows how outlying incorrect opinions can be systematically removed from a group resulting, in some situations, in improved group performance. However, improvement is only predicted for cases in which the initial guesses of individuals in the group are biased.
Scene Reconstruction and Visualization from Internet Photo Collections: A Survey

The Internet is becoming an unprecedented source of visual information, with billions of images instantly accessible through image search engines such as Google Images and Flickr. These include thousands of photographs of virtually every famous place, taken from a multitude of viewpoints, at many different times of day, and under a variety of weather conditions. This thesis addresses the problem of leveraging such photos to create new 3D interfaces for virtually exploring our world. One key challenge is that recreating 3D scenes from photo collections requires knowing where each photo was taken. This thesis introduces new computer vision techniques that robustly recover such information from photo collections without requiring GPS or other instrumentation. These methods are the first to be demonstrated on Internet imagery, and show that 3D reconstruction techniques can be successfully applied to this rich, largely untapped resource. For this problem scale is a particular concern, as Internet collections can be extremely large. I introduce an efficient reconstruction algorithm that selects a small skeletal set of images as a preprocess. This approach can reduce reconstruction time by an order of magnitude with little or no loss in completeness or accuracy. A second challenge is to build interfaces that take these reconstructions and provide effective scene visualizations. Towards this end, I describe two new 3D user interfaces. Photo Tourism is a 3D photo browser with new geometric controls for moving between photos. These include zooming in to find details, zooming out for more context, and selecting an image region to find photos of an object. The second interface, Pathfinder, takes advantage of the fact that people tend to take photos of interesting views and along interesting paths. Pathfinder creates navigation controls tailored to each location by analyzing the distribution of photos to discover such characteristic views and paths. These controls make it easy to find and explore the important parts of each scene. Together these techniques enable the automatic creation of 3D experiences for famous sites. A user simply enters relevant keywords and the system automatically downloads images, reconstructs the site, derives navigation controls, and provides an immersive interface.
Behavioral/systems/cognitive Effective Deep Brain Stimulation Suppresses Low-frequency Network Oscillations in the Basal Ganglia by Regularizing Neural Firing Patterns

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is an effective treatment for the motor symptoms of Parkinson's disease (PD). The effects of DBS depend strongly on stimulation frequency: high frequencies (Ͼ90 Hz) improve motor symptoms, while low frequencies (Ͻ50 Hz) are either ineffective or exacerbate symptoms. The neuronal basis for these frequency-dependent effects of DBS is unclear. The effects of different frequencies of STN-DBS on behavior and single-unit neuronal activity in the basal ganglia were studied in the unilateral 6-hydroxydopamine lesioned rat model of PD. Only high-frequency DBS reversed motor symptoms, and the effectiveness of DBS depended strongly on stimulation frequency in a manner reminiscent of its clinical effects in persons with PD. Quantification of single-unit activity in the globus pallidus externa (GPe) and substantia nigra reticulata (SNr) revealed that high-frequency DBS, but not low-frequency DBS, reduced pathological low-frequency oscillations (ϳ9 Hz) and entrained neurons to fire at the stimulation frequency. Similarly, the coherence between simultaneously recorded pairs of neurons within and across GPe and SNr shifted from the pathological low-frequency band to the stimulation frequency during high-frequency DBS, but not during low-frequency DBS. The changes in firing patterns in basal ganglia neurons were not correlated with changes in firing rate. These results indicate that high-frequency DBS is more effective than low-frequency DBS, not as a result of changes in firing rate, but rather due to its ability to replace pathological low-frequency network oscillations with a regularized pattern of neuronal firing.
S0 galaxies in Fornax: data and kinematics

We have obtained long-slit spectroscopy for a sample of nine S0 galaxies in the Fornax Cluster using the FORS2 spectrograph at the 8.2-m European Southern Observatory (ESO) Very Large Telescope (VLT). From these data, we have extracted the kinematic parameters, comprising the mean velocity, velocity dispersion and higher moment h3 and h4 coefficients, as a function of position along the major axes of these galaxies. Comparison with published kinematics indicates that earlier data are often limited by their lower signal-to-noise ratio and relatively poor spectral resolution. The greater depth and higher dispersion of the new data mean that we reach well beyond the bulges of these systems, probing their disc kinematics in some detail for the first time. Qualitative inspection of the results for individual galaxies shows that they are not entirely simple systems, perhaps indicating a turbulent past. None the less, we are able to derive reliable circular velocities for most of these systems, which points the way towards a study of their Tully–Fisher relation. This study, along with an analysis of the stellar populations of these systems out to large galactocentric distances, will form the bases of future papers exploiting these new high-quality data, hopefully shedding new light on the evolutionary history of these systems.
Which Type of Citation Analysis Generates the Most Accurate Taxonomy of Scientific and Technical Knowledge?

In 1965, Price foresaw the day when a citation‐based taxonomy of science and technology would be delineated and correspondingly used for science policy. A taxonomy needs to be comprehensive and accurate if it is to be useful for policy making, especially now that policy makers are utilizing citation‐based indicators to evaluate people, institutions and laboratories. Determining the accuracy of a taxonomy, however, remains a challenge. Previous work on the accuracy of partition solutions is sparse, and the results of those studies, although useful, have not been definitive. In this study we compare the accuracies of topic‐level taxonomies based on the clustering of documents using direct citation, bibliographic coupling, and co‐citation. Using a set of new gold standards—articles with at least 100 references—we find that direct citation is better at concentrating references than either bibliographic coupling or co‐citation. Using the assumption that higher concentrations of references denote more accurate clusters, direct citation thus provides a more accurate representation of the taxonomy of scientific and technical knowledge than either bibliographic coupling or co‐citation. We also find that discipline‐level taxonomies based on journal schema are highly inaccurate compared to topic‐level taxonomies, and recommend against their use.
Travel-related Dengue Virus Infection, the Netherlands, 2006–2007

To assess the incidence of and risk factors for clinical and subclinical dengue virus (DENV) infection, we prospectively studied 1,207 adult short-term travelers from the Netherlands to dengue-endemic areas. Participants donated blood samples for serologic testing before and after travel. Blood samples were tested for antibodies against DENV. Seroconversion occurred in 14 (1.2%) travelers at risk. The incidence rate was 14.6 per 1,000 person-months. The incidence rate was significantly higher for travel during the rainy months. Dengue-like illness occurred in 5 of the 14 travelers who seroconverted. Seroconversion was significantly related to fever, retro-orbital pain, myalgia, arthralgia, and skin rash. The risk for DENV infection for short-term travelers to dengue-endemic areas is substantial. The incidence rate for this study is comparable with that in 2 other serology-based prospective studies conducted in the 1990s.
Queering young adult literature: Examining sexual minorities in contemporary realistic fiction between 2000--2005

Queering Young Adult Literature: Examining Sexual Minorities in Contemporary Realistic Fiction Between 2000-2005. (December 2007) Corrine Marie Wickens, B.A., Indiana University; M.Ed., Texas A&M University Co-Chairs of Advisory Committee: Dr. Donna E. Norton Dr. Gaile S. Cannella Fiction that incorporates gay, lesbian, bisexual, transgender, or questioning of heterosexuality itself (GLBTQ) themes and characters has been noted among the most widely censored novels for young adults (ALA, 2007; Finnessy, 2002; Karolides, 2002). Despite many teachers’ and librarians’ anxiety about even recommending a novel that includes homosexual characters, more novels with GLBTQ characters and themes are receiving significant literary accolades and awards. Furthermore, acclaimed researcher and young adult literary historian, Michael Cart (2004) notes that reading young adult literature, “the quintessential literature of the outsider,” provides “the lifesaving necessity of seeing one’s own face reflected in the pages of a good book and the corollary comfort that derives from the knowledge that one is not alone” (p. 46). For GLBTQ youth, this is exceptionally important given the heteronormative structures in place to monitor and control sexual and gender identities and expressions. With this in mind, I utilized a dynamic and multi-faceted analytic approach, including interpretivist, textual discursive, and literary analyses, to examine seventeen GLBTQ themed novels for images, characterizations, and messages depicted about