Miracle-dz/UniFAR-FTUs huggingface dataset:
From System Dynamics and Discrete Event to Practical Agent Based Modeling: Reasons, Techniques, Tools

This paper may be considered as a practical reference for those who wish to add (now sufficiently matured) Agent Based modeling to their analysis toolkit and may or may not have some System Dynamics or Discrete Event modeling background. We focus on systems that contain large numbers of active objects (people, business units, animals, vehicles, or even things like projects, stocks, products, etc. that have timing, event ordering or other kind of individual behavior associated with them). We compare the three major paradigms in simulation modeling: System Dynamics, Discrete Event and Agent Based Modeling with respect to how they approach such systems. We show in detail how an Agent Based model can be built from an existing System Dynamics or a Discrete Event model and then show how easily it can be further enhanced to capture much more complicated behavior, dependencies and interactions thus providing for deeper insight in the system being modeled. Commonly understood examples are used throughout the paper; all models are specified in the visual language supported by AnyLogic TM tool. We view and present Agent Based modeling not as a substitution to older modeling paradigms but as a useful add-on that can be efficiently combined with System Dynamics and Discrete Event modeling. Several multi-paradigm model architectures are suggested.
Purposeful underestimation of demands for the airline seat allocation with incomplete information

We study stochastic programming formulations for the origin destination model in airline seat allocation under uncertainty. In particular, we focus on solving the stability issues of the traditional probabilistic model by purposefully underestimating the demands. The stochastic seat allocation models assume at least the possession of the distributional information, which is usually difficult to satisfy in a constantly changing environment. We propose a heuristic that consists of dynamically incorporating available information by solving a sequence of stochastic programming models. We show that the proposed method, named 'seat reservation (SR)', can ease most negative effects of incomplete distributional information and under some restrictive conditions, the SR will yield optimal revenue. The seat reservation method suggests that a revenue management company must (1) obtain timely results using adequately up–to–date computational facilities; (2) be conservative when allocating resources and (3) actively and continually revise previous estimations.
Endoscopic Determination of Location of Gastric Cancer in Bangladesh

The incidence of gastric cancer has declined from half a century ago in the west. However, contrary to general trend of steady decline in the incidence of gastric cancer, many western countries have noticed in recent decades an increase in gastric cancer in cardia with declining trend in distal involvement. In the developed world including the Japan, the highest prevalent country of gastric cancer, the distal stomach has remained predominant although a trend toward a proximal shift has been noted. So the study was performed to estimate the cancer by tumour location in Bangladesh. One hundred and sixty five patient were endoscopically assessed for location of cancer. The age range of the patients were 19 to 70 years and male outnumbered the female (2:1). The stomach is divided apparently into upper, middle and lower third by dividing the lesser and greater curvature in two equidistant points and joining the points. Distal or antral gastric carcinoma was found to be the commonest location (56.9%) followed by body (29.6%), cardia (9.09%) and diffusely involved (4.2%). The study also depicted no significant change in location of tumour with age of the patients. All patients were subjected to serological test for H. pylori and 106(64.2%) gave positive results. In conclusion, Bangladeshi population has shown no change in age predilection with site specificities of gastric carcinoma and the antrum continues to be the commonest site of malignancy. doi: 10.3329/taj.v20i2. 3067 TAJ 2007; 20(2): 95-98
Transformational and transactional leadership: a meta-analytic test of their relative validity.

This study provided a comprehensive examination of the full range of transformational, transactional, and laissez-faire leadership. Results (based on 626 correlations from 87 sources) revealed an overall validity of . 44 for transformational leadership, and this validity generalized over longitudinal and multisource designs. Contingent reward (.39) and laissez-faire (-.37) leadership had the next highest overall relations; management by exception (active and passive) was inconsistently related to the criteria. Surprisingly, there were several criteria for which contingent reward leadership had stronger relations than did transformational leadership. Furthermore, transformational leadership was strongly correlated with contingent reward (.80) and laissez-faire (-.65) leadership. Transformational and contingent reward leadership generally predicted criteria controlling for the other leadership dimensions, although transformational leadership failed to predict leader job performance.
The Streptococcal Cysteine Protease SpeB Is Not a Natural Immunoglobulin-Cleaving Enzyme

ABSTRACT The human bacterial pathogen Streptococcus pyogenes has developed a broad variety of virulence mechanisms to evade the actions of the host immune defense. One of the best-characterized factors is the streptococcal cysteine protease SpeB, an important multifunctional protease that contributes to group A streptococcal pathogenesis in vivo. Among many suggested activities, SpeB has been described to degrade various human plasma proteins, including immunoglobulins (Igs). In this study, we show that SpeB has no Ig-cleaving activity under physiological conditions and that only Igs in a reduced state, i.e., semimonomeric molecules, are cleaved and degraded by SpeB. Since reducing conditions outside eukaryotic cells have to be considered nonphysiological and IgG in a reduced state lacks biological effector functions, we conclude that SpeB does not contribute to S. pyogenes virulence through the proteolytic degradation of Igs.
Spatio-Temporal Analysis of Forest Fire Risk and Danger Using LANDSAT Imagery

Computing fire danger and fire risk on a spatio-temporal scale is of crucial importance in fire management planning, and in the simulation of fire growth and development across a landscape. However, due to the complex nature of forests, fire risk and danger potential maps are considered one of the most difficult thematic layers to build up. Remote sensing and digital terrain data have been introduced for efficient discrete classification of fire risk and fire danger potential. In this study, two time-series data of Landsat imagery were used for determining spatio-temporal change of fire risk and danger potential in Korudag forest planning unit in northwestern Turkey. The method comprised the following two steps: (1) creation of indices of the factors influencing fire risk and danger; (2) evaluation of spatio-temporal changes in fire risk and danger of given areas using remote sensing as a quick and inexpensive means and determining the pace of forest cover change. Fire risk and danger potential indices were based on species composition, stand crown closure, stand development stage, insolation, slope and, proximity of agricultural lands to forest and distance from settlement areas. Using the indices generated, fire risk and danger maps were produced for the years 1987 and 2000. Spatio-temporal analyses were then realized based on the maps produced. Results obtained from the study showed that the use of Landsat imagery provided a valuable characterization and mapping of vegetation structure and type with overall classification accuracy higher than 83%.
COSMOLOGY FROM GRAVITATIONAL LENS TIME DELAYS AND PLANCK DATA

Under the assumption of a flat ΛCDM cosmology, recent data from the Planck satellite point toward a Hubble constant that is in tension with that measured by gravitational lens time delays and by the local distance ladder. Prosaically, this difference could arise from unknown systematic uncertainties in some of the measurements. More interestingly—if systematics were ruled out—resolving the tension would require a departure from the flat ΛCDM cosmology, introducing, for example, a modest amount of spatial curvature, or a non-trivial dark energy equation of state. To begin to address these issues, we present an analysis of the gravitational lens RXJ1131−1231 that is improved in one particular regard: we examine the issue of systematic error introduced by an assumed lens model density profile. We use more flexible gravitational lens models with baryonic and dark matter components, and find that the exquisite Hubble Space Telescope image with thousands of intensity pixels in the Einstein ring and the stellar velocity dispersion of the lens contain sufficient information to constrain these more flexible models. The total uncertainty on the time-delay distance is 6.6% for a single system. We proceed to combine our improved time-delay distance measurement with the WMAP9 and Planck posteriors. In an open ΛCDM model, the data for RXJ1131−1231 in combination with Planck favor a flat universe with (68% credible interval (CI)). In a flat wCDM model, the combination of RXJ1131−1231 and Planck yields (68% CI).
The Maguk protein, Pals1, functions as an adapter, linking mammalian homologues of Crumbs and Discs Lost

Membrane-associated guanylate kinase (Maguk) proteins are scaffold proteins that contain PSD-95–Discs Large–zona occludens-1 (PDZ), Src homology 3, and guanylate kinase domains. A subset of Maguk proteins, such as mLin-2 and protein associated with Lin-7 (Pals)1, also contain two L27 domains: an L27C domain that binds mLin-7 and an L27N domain of unknown function. Here, we demonstrate that the L27N domain targets Pals1 to tight junctions by binding to a PDZ domain protein, Pals1-associated tight junction (PATJ) protein, via a unique Maguk recruitment domain. PATJ is a homologue of Drosophila Discs Lost, a protein that is crucial for epithelial polarity and that exists in a complex with the apical polarity determinant, Crumbs. PATJ and a human Crumbs homologue, CRB1, colocalize with Pals1 to tight junctions, and CRB1 interacts with PATJ albeit indirectly via binding the Pals1 PDZ domain. In agreement, we find that a Drosophila homologue of Pals1 participates in identical interactions with Drosophila Crumbs and Discs Lost. This Drosophila Pals1 homologue has been demonstrated recently to represent Stardust, a crucial polarity gene in Drosophila. Thus, our data identifies a new multiprotein complex that appears to be evolutionarily conserved and likely plays an important role in protein targeting and cell polarity.
A Randomized Trial of the Effect of Single-Vision vs. Bifocal Lenses on Myopia Progression in Children with Esophoria

Background Bifocals have long been thought to reduce progression of childhood myopia. However, this hypothesis has not been definitively evaluated. Methods We conducted a randomized clinical trial to test the hypothesis that bifocals slow myopia progression in children with near-point esophoria. Eighty-two myopic children were randomized to single-vision glasses (n = 40) or to bifocals with a +1.50 D add (n = 42) and were followed for 30 months. Refraction was measured by an automated refractor after cycloplegia. The primary outcome was myopia progression defined as the difference between the spherical equivalent at baseline and at the 30-month examination, averaged over both eyes. Results Follow-up was incomplete for six children in the bifocal group and one child in the single-vision group. Among the children completing the 30 months of follow up, myopia progression (mean spherical equivalent of the two eyes) averaged 0.99 D for bifocals and 1.24 D for single vision (unadjusted, p = 0.106; adjusted for age, p = 0.046). Treatment groups differed in their cumulative distributions (Kolmogorov-Smirnov procedure, p = 0.031). Evidence for a treatment effect on growth in vitreous chamber depth was similar (p = 0.046 by K.S.). Conclusion Use of bifocals, instead of single-vision glasses, by children with near-point esophoria seemed to slow myopia progression to a slight degree.
A Novel Approach to Beam Steering Using Arrays Composed of Multiple Unique Radiating Modes

A novel approach to beam steering is presented using an array composed of elements each supporting a unique radiating mode. The one-dimensional (1-D) beam synthesis properties of the novel ideal multiple mode dipole array are quantified using Fourier synthesis and shown to have significant improvement in scan range compared to a conventional linear dipole reference array. A hybrid phased array composed of multiple mode subarrays is also proposed and shown to be an efficient tradeoff between performance improvement and design complexity. Reasonable agreement is obtained between the simulated and measured impedance and radiation pattern properties of a fourelement multiple mode array. Finally, a 16-element hybrid phased array composed of four four-element multiple mode subarrays is fabricated and measured. The array is shown to have a 3-dB scan range of ±68°, which is in good agreement with the simulated value of ±69° at the design frequency of 4.6 GHz. Additionally, the 3-dB bandwidth of the array is more than 1 GHz at broadside. This bandwidth reduces to approximately 300 MHz at the widest scan angles, which is consistent with an equivalent conventional linear array.
Cost effectiveness of paliperidone palmitate versus risperidone long-acting injectable and olanzapine pamoate for the treatment of patients with schizophrenia in Sweden

Abstract Objective: To model the cost effectiveness of paliperidone palmitate (paliperidone long-acting injectable; PLAI), a new once-monthly long-acting antipsychotic therapy, compared with risperidone long-acting injectable (RLAI) and olanzapine pamoate (OLAI), in multi-episode patients (two or more relapses) with schizophrenia in Sweden. Methods: A Markov decision analytic model was developed to simulate the history of a cohort of multi-episode patients transitioning through different health states on a monthly basis over a 5-year time horizon from the perspective of the Swedish healthcare system. Therapeutic strategies consisted of starting treatment with RLAI (mean dose 37.5 mg every 2 weeks), PLAI (mean dose 75 mg equivalent (eq.) every month) or OLAI (150 mg every 2 weeks or 300 mg every 4 weeks). Probability of relapse, level of adherence, side-effects (extrapyramidal symptoms, tardive dyskinesia, weight gain and diabetes) and treatment discontinuation (switch) were derived from long-term observational data when feasible. Incremental cost-effectiveness outcomes, discounted at 3% annually, included cost per quality-adjusted life-year (QALY) and cost per relapse avoided (expressed in 2009 Swedish Krona SEK). Results: Relative to RLAI and OLAI, PLAI is economically dominant: more effective (additional QALYs, less relapses) and less costly treatment option over a 5-year time horizon. The results were robust when tested in sensitivity analysis. Limitations: The impact of once-monthly treatment on adherence levels is not yet known, and not all variables that could impact on real-world outcomes and costs were included in this model. Conclusion: PLAI was cost saving from a Swedish payer perspective compared with RLAI and OLAI in the long-term treatment of multi-episode (two or more relapses) schizophrenia patients.
A Depth-Adjustment Deployment Algorithm Based on Two-Dimensional Convex Hull and Spanning Tree for Underwater Wireless Sensor Networks

Most of the existing node depth-adjustment deployment algorithms for underwater wireless sensor networks (UWSNs) just consider how to optimize network coverage and connectivity rate. However, these literatures don’t discuss full network connectivity, while optimization of network energy efficiency and network reliability are vital topics for UWSN deployment. Therefore, in this study, a depth-adjustment deployment algorithm based on two-dimensional (2D) convex hull and spanning tree (NDACS) for UWSNs is proposed. First, the proposed algorithm uses the geometric characteristics of a 2D convex hull and empty circle to find the optimal location of a sleep node and activate it, minimizes the network coverage overlaps of the 2D plane, and then increases the coverage rate until the first layer coverage threshold is reached. Second, the sink node acts as a root node of all active nodes on the 2D convex hull and then forms a small spanning tree gradually. Finally, the depth-adjustment strategy based on time marker is used to achieve the three-dimensional overall network deployment. Compared with existing depth-adjustment deployment algorithms, the simulation results show that the NDACS algorithm can maintain full network connectivity with high network coverage rate, as well as improved network average node degree, thus increasing network reliability.
A Click Away: News Choice On the Internet.

This dissertation examines the technological shifts that influence the dynamics of information consumption and their implications for democratic citizenship. I focus on two factors that drive selective news exposure: attitude consistency and personal issue importance. First, by drawing from the research on selective exposure, I investigate how people seek out and avoid news messages based on their predispositions. To increase the generalizability of research findings, both political and science news stories are considered. In addition, I explore how multitasking activities influence selective exposure. Behavior tracking software is used to observe media selection behavior. Second, using two national data from the Kaiser Family Foundation’s health tracking survey and 2008 American National Election Data, I examine how people who rely on the Internet as a primary source of information tend to engage in selective learning and become issue specialists. I contextualized the results within the understanding of media and audience evolution. I also discuss the political implications of the findings and suggest future directions for research.
Transitions Clinic: Creating a Community-Based Model of Health Care for Recently Released California Prisoners

Most California prisoners experience discontinuity of health care upon return to the community. In January 2006, physicians working with community organizations and representatives of the San Francisco Department of Public Health's safety-net health system opened the Transitions Clinic (TC) to provide transitional and primary care as well as case management for prisoners returning to San Francisco. This article provides a complete description of TC, including an illustrative case, and reports information about the recently released individuals who participated in the program. From January 2006 to October 2007, TC saw 185 patients with chronic medical conditions. TC patients are socially and economically disenfranchised; 86% belong to ethnic minority groups and 38% are homeless. Eighty-nine percent of patients did not have a primary care provider prior to their incarceration. Preliminary findings demonstrate that a community-based model of care tailored to this disenfranchised population successfully engages them in seeking health care.
Maximum likelihood estimation of haplotype effects and haplotype‐environment interactions in association studies

The associations between haplotypes and disease phenotypes offer valuable clues about the genetic determinants of complex diseases. It is highly challenging to make statistical inferences about these associations because of the unknown gametic phase in genotype data. We describe a general likelihood‐based approach to inferring haplotype‐disease associations in studies of unrelated individuals. We consider all possible phenotypes (including disease indicator, quantitative trait, and potentially censored age at onset of disease) and all commonly used study designs (including cross‐sectional, case‐control, cohort, nested case‐control, and case‐cohort). The effects of haplotypes on phenotype are characterized by appropriate regression models, which allow various genetic mechanisms and gene‐environment interactions. We present the likelihood functions for all study designs and disease phenotypes under Hardy‐Weinberg disequilibrium. The corresponding maximum likelihood estimators are approximately unbiased, normally distributed, and statistically efficient. We provide simple and efficient numerical algorithms to calculate the maximum likelihood estimators and their variances, and implement these algorithms in a freely available computer program. Extensive simulation studies demonstrate that the proposed methods perform well in realistic situations. An application to the Carolina Breast Cancer Study reveals significant haplotype effects and haplotype‐smoking interactions in the development of breast cancer. Genet. Epidemiol. 2005. © 2005 Wiley‐Liss, Inc.
Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model

Beginning in 2003, highly pathogenic avian influenza (HPAI) H5N1 virus spread across Southeast Asia, causing unprecedented epidemics. Thailand was massively infected in 2004 and 2005 and continues today to experience sporadic outbreaks. While research findings suggest that the spread of HPAI H5N1 is influenced primarily by trade patterns, identifying the anthropogenic risk factors involved remains a challenge. In this study, we investigated which anthropogenic factors played a role in the risk of HPAI in Thailand using outbreak data from the “second wave” of the epidemic (3 July 2004 to 5 May 2005) in the country. We first performed a spatial analysis of the relative risk of HPAI H5N1 at the subdistrict level based on a hierarchical Bayesian model. We observed a strong spatial heterogeneity of the relative risk. We then tested a set of potential risk factors in a multivariable linear model. The results confirmed the role of free-grazing ducks and rice-cropping intensity but showed a weak association with fighting cock density. The results also revealed a set of anthropogenic factors significantly linked with the risk of HPAI. High risk was associated strongly with densely populated areas, short distances to a highway junction, and short distances to large cities. These findings highlight a new explanatory pattern for the risk of HPAI and indicate that, in addition to agro-environmental factors, anthropogenic factors play an important role in the spread of H5N1. To limit the spread of future outbreaks, efforts to control the movement of poultry products must be sustained.