Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparison of incorporation of dissipation in the FDTD analysis of transmission lines using stability analysis

A comparison of incorporation schemes of dissipation in the FDTD analysis of transmission lines using stability analysis is described. In the leapfrog type FDTD method, the calculation points of the voltage and the current are different in the time space. Therefore, how dissipation is included in the update equation becomes a problem. We find that incorporation of dissipation by using average value is more stable and lower numerical dispersion than that of Yee when discretization interval is large. Oppositely, Yee's scheme is more accurate in case of discretization interval is small. This is confirmed from the accuracy in numerical analysis of pulse responses.
Trace-based method for big data memory characteristics research

Big data has exacerbated the so-called “memory wall” problem. To study the memory characteristics of big data applications has become an important issue in the high end computing community. In this paper, we propose a trace-based method based on the trace files generated by simulators, which captures memory access information in different memory hierarchies and aggregates information to get memory performance statistics. Simulations were conducted to research the impact of cache size and hardware prefetch on big data applications, and our trace-based method was used to obtain the desired memory performance metrics. Experimental results show that big data benchmarks are less sensitive to cache size than traditional benchmarks, and hardware prefetching is effective in improving L2 cache hit rate. In terms of memory access address range, big data benchmarks have wider address range and the address distribution is more irregular than traditional benchmarks.
Data Modeling and Data Management for the Biological Enterprise

RECENT TECHNOLOGICAL ADVANCES in computational biology have had a fundamental impact on the vast amount of data that is available to the biological enterprise. To date, technological advances in data modeling and data management have not focused on the special needs and challenges of data management for cellular and molecular biology. These needs as well as the strengths and weaknesses of existing solutions for biological data integration are summarized. Next, we discuss challenges and potential solutions to the emerging data management needs of biologists. If these issues are not addressed satisfactorily, it is unclear if the adoption of data management technology will be of benefit to the biological scientist.
Borrelia burgdorferi and Interleukin-1 Promote the Transendothelial Migration of Monocytes In Vitro by Different Mechanisms

ABSTRACT A prominent feature of Lyme disease is the perivascular accumulation of mononuclear leukocytes. Incubation of human umbilical vein endothelial cells (HUVEC) cultured on amniotic tissue with either interleukin-1 (IL-1) or Borrelia burgdorferi, the spirochetal agent of Lyme disease, increased the rate at which human monocytes migrated across the endothelial monolayers. Very late antigen 4 (VLA-4) and CD11/CD18 integrins mediated migration of monocytes across HUVEC exposed to either B. burgdorferi or IL-1 in similar manners. Neutralizing antibodies to the chemokine monocyte chemoattractant protein 1 (MCP-1) inhibited the migration of monocytes across unstimulated, IL-1-treated, or B. burgdorferi-stimulated HUVEC by 91% ± 3%, 65% ± 2%, or 25% ± 22%, respectively. Stimulation of HUVEC with B. burgdorferi also promoted a 6-fold ± 2-fold increase in the migration of human CD4+ T lymphocytes. Although MCP-1 played only a limited role in the migration of monocytes acrossB. burgdorferi-treated HUVEC, migration of CD4+T lymphocytes across HUVEC exposed to spirochetes was highly dependent on this chemokine. The anti-inflammatory cytokine IL-10 reduced both migration of monocytes and endothelial production of MCP-1 in response to B. burgdorferi by approximately 50%, yet IL-10 inhibited neither migration nor secretion of MCP-1 when HUVEC were stimulated with IL-1. Our results suggest that activation of endothelium by B. burgdorferi may contribute to formation of the chronic inflammatory infiltrates associated with Lyme disease. The transendothelial migration of monocytes that is induced by B. burgdorferi is significantly less dependent on MCP-1 than is migration induced by IL-1. Selective inhibition by IL-10 further indicates that B. burgdorferi and IL-1 employ distinct mechanisms to activate endothelial cells.
Integrated Bi-directional Trench Lateral Power MOSFETs for One Chip Lithium-ion Battery Protection ICs

A low specific on-resistance bi-directional trench lateral power MOSFET (BTLPM) has been integrated with a controller in a 0.6mum BiCDMOS process for single-cell lithium-ion battery protector, downsizing the footprint of the protector in chip-scale package to 3mm 2, one-third of its multi-chip counterparts. The first-silicon results of the BTLPM switches demonstrated a breakdown voltage of 22V, a specific on-resistance of 6.8mOmegamm2 at a gate voltage of 4V (a gate electrical field of 2.3MV/cm)
VAST 2011 Mini Challenge #3 Award: "Good Analysis & Support Debrief"

nSpace2 is an innovative visual analytics tool that was the primary platform used to search, evaluate, and organize the data in the VAST 2011 Mini Challenge #3 dataset. nSpace2 is a web-based tool that is designed to facilitate the back-and-forth-flow of the multiple steps of an analysis workflow, including search, data triage, organization, sense-making, and reporting. This paper describes how nSpace2 was used to assist every step of the analysis process for this VAST challenge.
Does probability of occurrence relate to population dynamics?

Hutchinson defined species' realized niche as the set of environmental conditions in which populations can persist in the presence of competitors. In terms of demography, the realized niche corresponds to the environments where the intrinsic growth rate (r) of populations is positive. Observed species occurrences should reflect the realized niche when additional processes like dispersal and local extinction lags do not have overwhelming effects. Despite the foundational nature of these ideas, quantitative assessments of the relationship between range-wide demographic performance and occurrence probability have not been made. This assessment is needed both to improve our conceptual understanding of species' niches and ranges and to develop reliable mechanistic models of species geographic distributions that incorporate demography and species interactions. The objective of this study is to analyse how demographic parameters (intrinsic growth rate r and carrying capacity K) and population density (N) relate to occurrence probability (Pocc ). We hypothesized that these relationships vary with species' competitive ability. Demographic parameters, density, and occurrence probability were estimated for 108 tree species from four temperate forest inventory surveys (Québec, Western US, France and Switzerland). We used published information of shade tolerance as indicators of light competition strategy, assuming that high tolerance denotes high competitive capacity in stable forest environments. Interestingly, relationships between demographic parameters and occurrence probability did not vary substantially across degrees of shade tolerance and regions. Although they were influenced by the uncertainty in the estimation of the demographic parameters, we found that r was generally negatively correlated with Pocc , while N, and for most regions K, was generally positively correlated with Pocc . Thus, in temperate forest trees the regions of highest occurrence probability are those with high densities but slow intrinsic population growth rates. The uncertain relationships between demography and occurrence probability suggests caution when linking species distribution and demographic models.
A novel 3D anisotropic diffusion filter

We propose a 3D anisotropic diffusion filter for denoising and enhancing oriented data. The approach is a generalization of a previous contribution and it is based on a novel, more precise orientation estimation step. The orientation in the 3D space is computed using an asymmetric Isotropic Recursive Oriented Network (IRON) operator that can handle in a natural way junctions and corners. In the experimental section we employ a set of 3D synthetic blocks to illustrate the efficiency of the new method through quantitative and visual comparisons with other 3D-extended classical models or recently proposed 3D Partial Differential Equations (PDE).
A systematic analysis of the resistance and sensitivity of HER2YVMA receptor tyrosine kinase mutant to tyrosine kinase inhibitors in HER2-positive lung cancer

Abstract Human epidermal growth factor receptor 2 (HER2) has become a well-established target for the treatment of HER2-positive lung cancer. However, a frequently observed in-frame mutation that inserts amino acid quadruplex Tyr776-Val777-Met778-Ala779 at G776 (G776YVMA) in HER2 kinase domain can cause drug resistance and sensitivity, largely limiting the application of reversible tyrosine kinase inhibitors in lung cancer therapy. A systematic investigation of the intermolecular interactions between the HER2YVMA mutant and clinical small-molecule inhibitors would help to establish a complete picture of drug response to HER2 G776YVMA insertion in lung cancer, and to design new tyrosine kinase inhibitors with high potency and selectivity to target the lung cancer-related HER2YVMA mutant. Here, we combined homology modeling, ligand grafting, structure minimization, molecular simulation and binding affinity analysis to profile a number of tyrosine kinase inhibitors against the G776YVMA insertion in HER2. It is found that the insertion is far away from HER2 active pocket and thus cannot contact inhibitor ligand directly. However, the insertion is expected to induce marked allosteric effect on some regions around the pocket, including A-loop and hinges connecting between the N- and C-lobes of HER2 kinase domain, which may exert indirect influence to inhibitor binding. Most investigated inhibitors exhibit weak binding strength to both wild-type and mutant HER2, which can be attributed to steric hindrance that impairs ligand compatibility with HER2 active pocket. However, the cognate inhibitor lapatinib and the non-cognate inhibitor bosutinib were predicted to have low affinity for wild-type HER2 but high affinity for HER2YVMA mutant, which was confirmed by subsequent kinase assay experiments; the inhibitory potencies of bosutinib against wild-type and mutant HER2 were determined to be IC50 > 1000 and =27 nM, respectively, suggesting that the bosutinib might be exploited as a selective inhibitor for mutant over wild-type HER2. Structural examination revealed that formation of additional non-bonded interactions such as hydrogen bonds and hydrophobic contacts with HER2 A-loop region due to G776YVMA insertion is the primary factor to improve bosutinib affinity upon the mutation.
Dentistry in Sweden - Healthy work or ruthless efficiency?

The general objective of this thesis is to provide an understanding of the organization of Sweden's Public Dental Health Service (PDHS) and the problems it has faced, e.g. dentists’ job dissatisfaction. This is done against the background of the historical development of the Service. The thesis comprises five papers, based on two empirical studies. Questionnaires were used for both studies: respondents for Study 1 were 769 dentists and 493 dental nurses in the PDHS; and for Study 2, 472 dentists and 3,595 other Swedish professionals (response rates 66%-88%). The materials were analyzed using multiple regression models and other statistical methods. Properties of "healthy work" among professionals were investigated. Graduate workers in general emphasized the intellectuality and value of work. Dentists in the PDHS, showed the greatest discrepancy between ideal and reality of all professional groups. Staff opinions on the managerial control system employed in the PDHS were analyzed. Dentists reported that their pace of work was adapted to surveillance, competition and demands of the employer. On analysis of perceived changes in managerial control systems, it was found that such changes tend to be distributed along two dimensions, interpreted here as mirroring "hard" and "soft" Human Resource Management (HRM). The combined effects of "hard" and "soft" HRM on work conditions were more negative for dentists than for other professionals. It became apparent that a duality in managerial changes contributed to a polarization between human-service and other professional work. While opportunities for healthy work increased among graduates who worked with things and data, the same changes led to a deteriorated effort-reward balance for human-service workers. Negative effects were found to be more pronounced for dentists in the PDHS than for human-service workers as a whole. The results are discussed in terms of dentists enclosure within the profession and their scope of action, to leave or protest.
Accelerometry and self-report in sedentary populations.

OBJECTIVES To determine whether self-reported exercise duration and intensity matched accelerometer data in sedentary endometrial cancer survivors and age-matched controls. METHODS Participants were asked to wear an accelerometer and self-report exercise bouts, duration, and intensity for one week. Self-reported duration was compared with accelerometer data. RESULTS Self-reported exercise-bout duration matched accelerometer duration 93% for survivors and 99% for controls. Self-reported exercise-bout intensity matched accelerometer intensity 70% for survivors and 66% for controls. There were no significant differences between groups. CONCLUSIONS Sedentary endometrial cancer survivors and controls self-reported duration and intensity of physical activity consistent with accelerometer data.
Mobile telephone use is associated with changes in cognitive function in young adolescents

As part of the Mobile Radiofrequency Phone Exposed Users' Study (MoRPhEUS), a cross‐sectional epidemiological study examined cognitive function in secondary school students. We recruited 317, 7th grade students (144 boys, 173 girls, median age 13 years) from 20 schools around Melbourne, Australia. Participants completed an exposure questionnaire based on the Interphone study, a computerised cognitive test battery, and the Stroop colour‐word test. The principal exposure metric was the total number of reported mobile phone voice calls per week. Linear regression models were fitted to cognitive test response times and accuracies. Age, gender, ethnicity, socio‐economic status and handedness were fitted as covariates and standard errors were adjusted for clustering by school. The accuracy of working memory was poorer, reaction time for a simple learning task shorter, associative learning response time shorter and accuracy poorer in children reporting more mobile phone voice calls. There were no significant relationships between exposure and signal detection, movement monitoring or estimation. The completion time for Stroop word naming tasks was longer for those reporting more mobile phone voice calls. The findings were similar for total short message service (SMS, also known as text) messages per week, suggesting these cognitive changes were unlikely due to radiofrequency (RF) exposure. Overall, mobile phone use was associated with faster and less accurate responding to higher level cognitive tasks. These behaviours may have been learned through frequent use of a mobile phone. Bioelectromagnetics 30:678–686, 2009. © 2009 Wiley‐Liss, Inc.
Evidence for a functional role of calsequestrin 2 in mouse atrium

Several genetically modified mice models were studied so far to investigate the role of cardiac calsequestrin (CSQ2) for the contractile function of the ventricle and for the occurrence of ventricular tachycardia. Using a CSQ2 knockout mouse, we wanted to study also the atrial function of CSQ2.
Stress Response of Pancreatic Islets from Diabetes Prone BB Rats of Different Age

Protective and/or repair mechanisms are thought to be activated in pancreatic beta cells in response to injury during insulitis. Manifestation of type-1 diabetes may depend on an imbalance between beta cell damage and repair. To prove this hypothesis, the ability of collagenase-isolated islets to respond to heat stress depending on the age of BB rats was investigated. The islets were exposed either to 44°C (HS) or 37°C (control) for 30 min and then kept at 37°C for 5 h. Immediately and 5 h after heat shock, insulin secretion in response to 20 mmol/l glucose and total protein synthesis of heat-exposed islets were significantly diminished as compared with controls. The islet proteins were separated by SDS-PAGE followed by immunoblotting. Islets from BB rats at an age of 6-90 days responded to heat shock with the expression of major heat shock protein 70 (HSP 70). Islets from 3-day old rats, however, did not respond with induction of HSP 70. In contrast we could detect inducible HSP 70 in islets from 3-day old diabetes-resistant LEW rats. In islets from 90-day old BB rats we observed a decreased amount of HSP 70 compared with islets from 9-, 12-, 30- and 60-day old animals. There was also a higher extent of HSP 70 to observe in islets from 90-day old LEW rats as compared with 90-day old BB rats. Differences in HSP 70 expression between islets of 3-day old BB and LEW rats and other age groups of BB rats might represent distinct stages of maturation of islets whereas diminished expression of HSP 70 in islets of 90-day old BB rats at the age of high probability of developing diabetes might result from reduced ability to induce protective mechanisms.
Evidence Based Periodontology – A Compressive Conspectus

Periodontology has a rich history and a strong passion for science. Evidence-based periodontology is the application of evidence-based health care to periodontology. The substantial and extensive periodontal information base, developed over the years, has provided a rational basis for choosing the best treatment for patients. The goal of evidence-based dentistry is to help practitioners provide their patients with optimal care. The practice-related element in evidence-based dentistry is the clinician's integration of the resulting knowledge with clinical expertise and patient preferences to determine the treatment to be recommended to individual patients. Various components of evidence-based periodontology include the production of best available evidence, the critical appraisal and interpretation of the evidence, the communication and discussion of the evidence to individuals seeking care and the integration of the evidence with clinical skills and patient values. Evidenced based approach offers a bridge from science to clinical practice.
Power and sample assessments for tests of hypotheses on cost-effectiveness ratios.

We address the issue of statistical power and sample size for cost-effectiveness studies. Tests of hypotheses on the cost-effectiveness ratio (CER) are constructed from the net cost and incremental effectiveness measures. When the difference in effectiveness is known, we derive formulae for statistical power and sample size assessments for one- and two-sided tests of hypotheses of the CER. We also construct a test of the joint hypothesis of cost-effectiveness and effectiveness and derive an expression connecting power and sample size. Our methods account for the correlation between cost and effectiveness and lead to smaller sample size requirements than comparative methods that ignore the correlation. The implications of our formulae for cost-effectiveness studies are illustrated through numerical examples. When compared with trials designed to demonstrate effectiveness alone, our results indicate that a trial appropriately powered to demonstrate cost-effectiveness might require sample sizes many times greater.
Dislocation density reduction of virtual Ge substrates by CW diode laser treatment

Ge wafers have been employed as substrates for high efficiency III-V multi-junction solar cells because of the almost ideal lattice match. However, the cost of Ge wafers is high and the Ge bandgap is too small which limits its contribution to the overall voltage output. Since Si has much higher bandgap and lower cost than Ge, using epitaxial Ge on Si as virtual substrates for III-V material growth is a promising solution. However, the challenge is the high threading dislocation density (TDD) in the Ge layer generated by the large lattice mismatch (4%) between Ge and Si. Thermal annealing has been intensively investigated in order to reduce TDD in the Ge layer deposited on Si. Two-step low temperature - high temperature Ge deposition followed by thermal annealing and cycled epitaxial Ge growth and annealing have been studied using CVD systems. Compared with conventional thermal processes, the CW diode laser treatment offers a fast and low-cost alternative to effectively reduce the TDD in Ge films. By laser scanning the sample, the Ge layer can be melted and recrystallized. After the laser treatment, the TDD of Ge films can be reduced by three orders of magnitude to 106 cm-2 which may be suitable for fabrication of III-V solar cells. Raman spectroscopy and Transmission Electron Microscopy measurements are employed to investigate the TDD reduction of the virtual Ge substrates.
Importance of disrupted intestinal barrier in inflammatory bowel diseases

&NA; The current paradigm of inflammatory bowel diseases (IBD), both Crohn's disease (CD) and ulcerative colitis (UC), involves the interaction between environmental factors in the intestinal lumen and inappropriate host immune responses in genetically predisposed individuals. The intestinal mucosal barrier has evolved to maintain a delicate balance between absorbing essential nutrients while preventing the entry and responding to harmful contents. In IBD, disruptions of essential elements of the intestinal barrier lead to permeability defects. These barrier defects exacerbate the underlying immune system, subsequently resulting in tissue damage. The epithelial phenotype in active IBD is very similar in CD and UC. It is characterized by increased secretion of chloride and water, leading to diarrhea, increased permeability via both the transcellular and paracellular routes, and increased apoptosis of epithelial cells. The main cytokine that seems to drive these changes is tumor necrosis factor alpha in CD, whereas interleukin (IL)‐13 may be more important in UC. Therapeutic restoration of the mucosal barrier would provide protection and prevent antigenic overload due to intestinal “leakiness. ” Here we give an overview of the key players of the intestinal mucosal barrier and review the current literature from studies in humans and human systems on mechanisms underlying mucosal barrier dysfunction in IBD. (Inflamm Bowel Dis 2011;)