Miracle-dz/UniFAR-FTUs huggingface dataset:
Self-optimization, Community Stability, and Fluctuations in a Class of Individual-based Models of Biological Coevolution

We study the dynamical properties of a class of simple, individual-based models of biological coevolution. These are multispecies, stochastic population-dynamics models in which the reproduction probability for individuals of a particular species depends nonlinearly on the population densities of all the species present in the community. New species are introduced through a small probability of mutation during reproduction. For a subclass of simplified models we are able to perform exact linear stability analysis, and we compare the analytic results with large-scale kinetic Monte Carlo simulations. Based on this analysis, we present a phase diagram for the total population size as a function of an average interspecies interaction strength. Over time, the models are found to self-optimize through mutation and selection to maximize a community fitness function, subject only to constraints internal to the particular model. If the off-diagonal elements of the matrix of in-terspecies interactions are distributed independently on an interval that includes positive values, the model evolves toward mutualistic communities, in which the population is self-sustaining. In contrast, for predator/prey models the interaction matrix is antisymmetric, and the community is constrained to a region of the phase diagram where a nonzero population size can only be sustained by an external resource. Time series of the diversity and total population size for the different models show approximate 1/f noise and power-law distributions for the lifetimes of communities and species. For the mutualistic model, these two lifetime distributions have the same exponent, while their exponents are different for the predator/prey model. The difference is probably due to greater resilience toward mass extinctions exhibited by the food-web like communities produced by the predator/prey model.
Conditions for the Evolution of Gene Clusters in Bacterial Genomes

Genes encoding proteins in a common pathway are often found near each other along bacterial chromosomes. Several explanations have been proposed to account for the evolution of these structures. For instance, natural selection may directly favour gene clusters through a variety of mechanisms, such as increased efficiency of coregulation. An alternative and controversial hypothesis is the selfish operon model, which asserts that clustered arrangements of genes are more easily transferred to other species, thus improving the prospects for survival of the cluster. According to another hypothesis (the persistence model), genes that are in close proximity are less likely to be disrupted by deletions. Here we develop computational models to study the conditions under which gene clusters can evolve and persist. First, we examine the selfish operon model by re-implementing the simulation and running it under a wide range of conditions. Second, we introduce and study a Moran process in which there is natural selection for gene clustering and rearrangement occurs by genome inversion events. Finally, we develop and study a model that includes selection and inversion, which tracks the occurrence and fixation of rearrangements. Surprisingly, gene clusters fail to evolve under a wide range of conditions. Factors that promote the evolution of gene clusters include a low number of genes in the pathway, a high population size, and in the case of the selfish operon model, a high horizontal transfer rate. The computational analysis here has shown that the evolution of gene clusters can occur under both direct and indirect selection as long as certain conditions hold. Under these conditions the selfish operon model is still viable as an explanation for the evolution of gene clusters.
Heterogeneous Inflation Expectations and Learning

Using the panel component of the Michigan Survey of Consumers, we estimate a learning model of inflation expectations, allowing for heterogeneous use of private information and lifetime inflation experience. Life experience inflation has a significant impact on individual expectations, but only for 1‐year‐ahead inflation. Public information is substantially more relevant for longer horizon expectations. Even controlling for life experience inflation and public information, idiosyncratic information explains a nontrivial proportion of the inflation forecasts of agents. Women, ethnic minorities, and less educated agents have a higher degree of heterogeneity in their idiosyncratic information, and give less importance to recent movements in inflation.
Configuring Value for Internet Business Model and Competitive Advantage

In the network age, the source of economic value and wealth is no longer the production of material goods but the creation and manipulation of competitive Internet business models. When a new model changes the economics of an industry and is difficult to replicate, it can by itself create a strong competitive advantage. The purpose of this paper is to investigate the value configuration and competitive advantage on Internet business models. The business model analysis includes the business model primary components and emphasizes the value analysis. This analysis serves as a mean for developing and understanding of a model value configuration and how this value configuration can both create and maintain competitive advantages. >From case studies, we conclude that even though each model has a unique value configuration, the value creation configurations are based on the value chain, value shop, value network their integration or remodeling. The intermediary model value configurations, such as a brokerage, are based on the value network and value shop. The competitive advantage of the brokerage model is that the first mover appears in the market armed with a brand name, industry know-how, and impressive value-added service. The merchant model is based on the value chain and value shop. A strong brand name, a gigantic selection of titles, successful distribution operations, and customized services are the main competitive advantages for a virtual merchant. The value chain and value shop are the value configurations applied most appropriately to the manufacturer model. Brand name, professional manufacturing technology, superior quality product, direct sales system, successful physical distribution, and impressive service are the key competitive advantages of the manufacturer model. Only when firms build an Internet business model consistent with the correct value configuration can they develop and maintain a competitive advantage.
A parallel method for time-discretization of parabolic problems based on contour integral representation and quadrature

We treat the time discretization of an initial-value problem for a homogeneous abstract parabolic equation by first using a representation of the solution as an integral along the boundary of a sector in the right half of the complex plane, then transforming this into a real integral on the finite interval , and finally applying a standard quadrature formula to this integral. The method requires the solution of a finite set of elliptic problems with complex coefficients, which are independent and may therefore be done in parallel. The method is combined with spatial discretization by finite elements.
Research groups: How big should they be?

Understanding the relationship between scientific productivity and research group size is important for deciding how science should be funded. We have investigated the relationship between these variables in the life sciences in the United Kingdom using data from 398 principle investigators (PIs). We show that three measures of productivity, the number of publications, the impact factor of the journals in which papers are published and the number of citations, are all positively correlated to group size, although they all show a pattern of diminishing returns—doubling group size leads to less than a doubling in productivity. The relationships for the impact factor and the number of citations are extremely weak. Our analyses suggest that an increase in productivity will be achieved by funding more PIs with small research groups, unless the cost of employing post-docs and PhD students is less than 20% the cost of a PI. We also provide evidence that post-docs are more productive than PhD students both in terms of the number of papers they produce and where those papers are published.
Circulation Research an Official Journal of the American Heart Association Brief Reviews Intercellular Communication in Cardiac Muscle Intercellular Junction and the Electrical Coupling of Heart Cells

THE heart muscle was conceptualized as an anatomical syncytium for many years (Heidenhain, 1901; Godlewsky, 1902). With the development of electron microscopy, it was proved that cardiac fibers are composed of isolated cells separated by specialized zones—the so-called intercalated discs (Sjostrand and Andersson, 1954). The discs comprise three junctional specializations: (1) the macula adhaerens (desmo-some), (2) the fascia adhaerens, and (3) the gap junc-At the level of desmosomes, the apposing plasma membranes are separated by a gap of 250-300 A and a fibrillar material is seen inside the adjacent cells, and in its central area, several structures are seen bridging the gap with a periodicity of 100 A (Fig. 1). Freeze-cleaving studies indicate that the nexus is characterized by particles closely packed in a hexagonal array These particles are usually 70-80 A in diameter showing dots (20-25 A) in the central region (Gilula, 1978). Hydrophilic channels connecting the cytoplasm of adjacent cells seem to pass through the center of the As cardiac muscle consists of cells with surface membrane of high electrical resistance, it became difficult to understand how the depolarization of a myocyte could initiate activity in its neighbors. The possibility of a chemical mechanism was considered (Sperelakis et al., 1960), and the localization of acetylcholinesterase near intercalated discs (Joo and Czillik, 1962) represented an apparent support for this theory. However, the complex chemical machinery required for the synthesis of a chemical transmitter, as well as synaptic vesicles, is absent in cardiac cells. The concept that the heart cells are electrically coupled has emerged from different types of observations. When a subthreshold pulse is injected into a cardiac cell, electrotonic potentials can be recorded in In Purkinje fibers, the core resistivity is quite low (105 8cm) and the space constant is higher (1.9 mm) in comparison with the length of the cells (125 jiim) (Weidmann, 1952), which indicates that the intercellular junctions have a low electrical resistance (Weidmann, 1969). In myocardial fibers, the values of space constants are smaller [1300 jum (Kamiyama and Matsuda, 1966); 880 jum (Weidmann, 1970)], and the intracellular longitudinal resistance (470 fl/cm) higher than in Purkinje fibers (Weidmann, 1970). This higher value of Rj can be ascribed to the density of myofibrils and mitochondria, or to a smaller junctional conduct-ance (Weidmann, 1970). Barr et al. (1965), utilizing a method similar to that described by Osterhout and Hill (1930), showed that the impulse conduction along a …
The Hα luminosity function and star formation rate up to z ∼ 1 ⋆

We describe ISAAC/ESO-VLT observations of the Ha λ6563 Balmer line of 33 field galaxies from the Canada-France Redshift Survey (CFRS) with redshifts selected between 0.5 and 1.1. We detect Ha in emission in 30 galaxies and compare the properties of this sample with the low-redshift sample of CFRS galaxies at z ∼0.2. We find that the Ha luminosity, L(Hα), is tightly correlated to M(B A B ) in the same way for both the low- and high-redshift samples. L(Ha) is also correlated to L([O II]λ3727), and again the relation appears to be similar at low and high redshifts. The ratio L([O II])/L(Hα) decreases for brighter galaxies by as much as a factor of 2 on average. Derived from the Ha luminosity function, the comoving Ha luminosity density increases by a factor 12 from (z) = 0.2 to (z) = 1.3. Our results confirm a strong rise of the star formation rate (SFR) at z < 1.3, proportional to (1 + z) 4 . 1 γ 0 . 3 (with H 0 = 50 km s - 1 Mpc - 1 , q 0 = 0.5). We find an average SFR(2800 A)/SFR(Hα) ratio of 3.2 using the Kennicutt SFR transformations. This corresponds to the dust correction that is required to make the near-ultraviolet data consistent with the reddening-corrected Ha data within the self-contained, I-selected CFRS sample.
RECURSIVE CO-KRIGING MODEL FOR DESIGN OF COMPUTER EXPERIMENTS WITH MULTIPLE LEVELS OF FIDELITY

We consider in this paper the problem of building a fast-running approximation—also called surrogate model—of a complex computer code. The co-kriging based surrogate model is a promising tool to build such an approximation when the complex computer code can be run at different levels of accuracy. We present here an original approach to perform a multi-fidelity co-kriging model which is based on a recursive formulation. We prove that the predictive mean and the variance of the presented approach are identical to the ones of the original co-kriging model. However, our new approach allows to obtain original results. First, closed-form formulas for the universal co-kriging predictive mean and variance are given. Second, a fast cross-validation procedure for the multi-fidelity co-kriging model is introduced. Finally, the proposed approach has a reduced computational complexity compared to the previous one. The multi-fidelity model is successfully applied to emulate a hydrodynamic simulator.
Predicting Factors in Iron Supplement Intake among Pregnant Women in Urban Care Setting.

BACKGROUND The world health organization estimates that 58% of pregnant women in developing countries are anemic. In spite of the fact that most ministries of health in developing countries have policies to provide pregnant women with iron supplementation, prevalence of maternal anemia has not declined significantly. The aim of this study was to assess adherence to the current recommendation in the local population and to describe factors associated with taking iron supplementation during pregnancy. METHODS A questionnaire assessing the use of prenatal iron supplementation was distributed among women recently having delivered in Urmia, west Azerbaijan Province, northwest Iran. The questionnaire consisted of two sections. The first included demographic information and the second part covered questions regarding duration of iron supplementation, awareness of per partum anemia and management including benefits and side effects of iron supplementation. SPSS version 10 was used for statistical analysis; data were analyzed by Chi-Square and logistic regression. RESULTS Eighty seven percent of participants took iron supplements for at least 4 months. Training during pregnancy was associated with longer duration of iron use. In logistic regression analysis nuliparity was the only variable, which remained in the model . Knowledge of participants on anemia, was obviously poor. Health care stuffs were the main source of information. CONCLUSION The compliance was rather high but knowledge of subjects was low. Therefore, increasing effort is required to mobilize health workers to distribute information on anemia prevention and using iron supplements properly.
Prediction : A Cache Replacement Policy Based on Second-Order Trend Analysis

Caching is one of the most e ective techniques for improving the performance of Internet systems. The heart of a caching system is its page replacement policy, which decides which page to replace in a cache by a new one. Di erent caching policies have dramatically di erent e ects on the system performance. In this paper, we extend the well-known GDSF caching policies to include not only access trend information, but also the dynamics of the access trend itself to the trends on access trends. The new trend policy that we propose, called Taylor Series Prediction (TSP) policy, provides more accurate prediction on future accessing trends when the access patterns vary greatly. We back up our claims through a series of experiments using web access traces.
Implications of avian flu for economic development in Kenya

Kenya is vulnerable to avian flu given its position along migratory bird routes and proximity to other high-risk countries. This raises concerns about the effect an outbreak could have on economic development. We use a dynamic computable general equilibrium model of Kenya to simulate potential outbreaks of different severities, durations, and geographic spreads. Results indicate that even a severe outbreak does not greatly reduce economic growth. It does, however, significantly worsen poverty, because poultry is an important income source for poor farmers and a major food item in consumers' baskets. Avian flu therefore does pose a threat to future development in Kenya. Reducing the duration and geographic spread of an outbreak is found to substantially lower economic losses. However, losses are still incurred when poultry demand falls, even without a confirmed outbreak but only the threat of an outbreak. Our findings support monitoring poultry production and trade, responding rapidly to possible infections, and improving both farmers' and consumers' awareness of avian flu.
Frequency of injury and the ecology of regeneration in marine benthic invertebrates.

Many marine invertebrates are able to regenerate lost tissue following injury, but regeneration can come at a cost to individuals in terms of reproduction, behavior and physiological condition, and can have effects that reach beyond the individual to impact populations, communities, and ecosystems. For example, removal and subsequent regeneration of clams' siphons, polychaetes' segments, and brittlestars' arms can represent significant energetic input to higher trophic levels. In marine soft-sediment habitats, injury changes infaunal bioturbation rates and thus secondarily influences sediment-mediated competition, adult-larval interactions, and recruitment success. The importance of injury and regeneration as factors affecting the ecology of marine invertebrate communities depends on the frequency of injury, as well as on individual capacity for, and speed of, regeneration. A key question to answer is: "How frequently are marine benthic invertebrates injured? " Here, I review the sources and the frequencies of injury in a variety of marine invertebrates from different benthic habitats, discuss challenges, and approaches for accurately determining injury rates in the field, consider evidence for species-specific, temporal and geographic variation in injury rates, and present examples of indirect effects of injury on marine invertebrates to illustrate how injury and regeneration can modify larger-scale ecological patterns and processes.
Acquisition of L2 Japanese geminates: Training with waveform displays

Miki Motohashi-Saigo, Kansai Gaidai University Debra M. Hardison, Michigan State University The value of waveform display s as visual feedback was explored in a training study involving perception and production of L2 Japanese by beginning-level L1 English learners. A pretest-posttest design compared auditory-visual (AV) and auditory-only (Aonly) Web-based training. Stimuli were sin gleton and geminate /t ,k,s/ followed by /a,u/ in two conditions (isolated words, carrier sentences). Fillers with long vowels were included. Participants completed a forced-choice identification task involving minimal triplets: singletons, geminates, long vowels (e.g., sa su, sassu, saasu). Results revealed a) significant improvement in geminate identification following training, especially for AV; b) significant effect of geminate (lowest scores for /s/); c) no significant effect of condition; and d) no significant improvement for the control group. Most errors were misperceptions of geminates as long vowels. Test of generalization revealed 5% decline in accuracy for AV an d 14% for A-only. Geminate production improved significantly (especially for AV) based on rater judgments; improvement was greatest for /k/ and smallest for /s/. Most production errors involved substitution of a singleton for a geminate. Post-study interviews produced positive comments on Web-based training. Waveforms increased awareness of durational differences. Results support the effectiveness of auditory-visual input in L2 perception training with transfer to novel stimuli and improved production.
Intelligent model-following position control for PMSM servo drives

In this paper, an intelligent robust position controller for permanent-magnet synchronous motor (PMSM) servo drives is proposed. The intelligent robust position controller consists of a two-degrees-of-freedom integral plus proportional & rate feedback (2DOF I-PD) controller in addition to an on-line trained neural-network model-following controller (NNMFC). This controller, 2DOF I-PD NNMFC, combines the merits of the 2DOF I-PD controller and the NNMF controller for PMSM servo drives position control. A systematic mathematical procedure is derived to find the parameters of the 2DOF I-PD position controller according to the required specifications for the PMSM servo drive system. Then, the resulting closed loop transfer function of the servo drive system including the current control, speed control and position control loops is used as the reference model. In addition to the 2DOF I-PD position controller, a neural-network model-following controller whose weights are trained on-line is designed to realize high dynamic performance in disturbance rejection and tracking characteristics. According to the model-following error between the outputs of the reference model and the PMSM servo drive system, the NNMFC generates two adaptive control signal which are added to the 2DOF I-PD speed controller output to attain robust model-following characteristics under different operating conditions regardless of parameter variations and load disturbances. A computer simulation is developed to demonstrate the effectiveness of the proposed 2DOF I-PD NNMF position controller. The results confirm that the proposed 2DOF I-PD NNMF position controller produces robust performance, rapid and accurate response to the reference model regardless of load disturbances or PMSM parameter variations.
Learning Structured Appearance Models from Captioned Images of Cluttered Scenes

Given an unstructured collection of captioned images of cluttered scenes featuring a variety of objects, our goal is to learn both the names and appearances of the objects. Only a small number of local features within any given image are associated with a particular caption word. We describe a connected graph appearance model where vertices represent local features and edges encode spatial relationships. We use the repetition of feature neighborhoods across training images and a measure of correspondence with caption words to guide the search for meaningful feature configurations. We demonstrate improved results on a dataset to which an unstructured object model was previously applied. We also apply the new method to a more challenging collection of captioned images from the Web, detecting and annotating objects within highly cluttered realistic scenes.