Neighbor Effects Research Articles

The Influence of Negative Orthographic Neighborhood in the Lexical Decision Task: Valence and Arousal Contributions.

This study investigated whether the visual recognition of neutral words might be influenced by the emotional dimensions (i.e., valence and arousal) of orthographically similar lexical representations, and whether this might also depend on emotional-related traits of participants (i.e., alexithymia). To this end, 108 participants performed a lexical decision task with 80 neutral words with a higher frequency orthographic neighbor that varied in valence (from neutral to negative) and arousal (from low to high). The main finding was the expected interaction effect between the valence and arousal of the neighbor on the lexical decision times of neutral stimulus words. Longer reaction times were found when the valence score of the neighbor decreased from neutral to negative for words with a low-arousal orthographic neighbor while this emotional neighbor effect was reversed for words with a high-arousal negative neighbor. This combined influence of the valence and arousal of the neighbor was interpreted in terms of increased lexical competition processes and direct influence of the affective system on the participant's response. Moreover, this interaction effect was smaller when the level of alexithymia of the participants increased, suggesting that people with a higher level of alexithymia are less sensitive to the emotional content of the neighbor. The results are discussed within an interactive activation model of visual word recognition incorporating an affective system with valence and arousal dimensions, with regard to the role of the alexithymia level of participants.

Theoretical analysis of RNA polymerase fidelity: a steady-state copolymerization approach

The fidelity of DNA transcription catalyzed by RNA polymerase (RNAP) has long been an important issue in biology. Experiments have revealed that RNAP can incorporate matched nucleotides selectively and proofread the incorporated mismatched nucleotides. However, systematic theoretical researches on RNAP fidelity are still lacking. In the last decade, several theories on RNA transcription have been proposed, but they only handled highly simplified models without considering the high-order neighbor effects and the oligonucleotides cleavage both of which are critical for the overall fidelity. In this paper, we regard RNA transcription as a binary copolymerization process and calculate the transcription fidelity by the steady-state copolymerization theory recently proposed by us for DNA replication. With this theory, the more realistic models considering higher-order neighbor effects, oligonucleotides cleavage, multi-step incorporation and multi-step cleavage can be rigorously handled.

An Easy Construction of Generalized Neighbor Designs in Minimal Circular Blocks

Neighbor designs are used in the experiments where neighbor effects may arise. Neighbor designs neutralize these effects and are, therefore, considered to be robust against neighbor effects. Minimal neighbor designs are always most economical among the neighbor designs and are, therefore, preferred by the experimenters. Method of cyclic shifts provides these designs in circular blocks only for odd v (number of treatments). For v even, minimal circular generalized neighbor designs in which only v 2 unordered pairs of distinct treatments do not appear as neighbors will be the better alternate to the minimal neighbor designs. In this article, such minimal generalized neighbor designs are constructed in circular blocks for v even.

Cooperator or supporter: how can cross-boundary Macau–Zhuhai metropolis promote regional tourism together?

PurposeThis study initiated an investigation of how the Macau–Zhuhai tourism cooperated and discussed how Macau and Zhuhai could join hands to develop tourism in the region. The study demonstrated an approach for destination marketing organizations to explore online tourist-generated content and to understand tourists' perceptions of the destination image (DI).Design/methodology/approachA total of 1,291,057 reviews (535,317 for Macau and 755,740 for Zhuhai) were collected, analyzed and examined to determine how the DI s of Macau and Zhuhai changed during the period of 2015–2019 based on tourist-generated content on travel websites (TripAdvisor, Ctrip.com and Qyer.com) through a text-mining approach.FindingsThe result revealed that Macau and Zhuhai were in a hybrid of competition and collaboration on tourism DI s. First, Macau and Zhuhai competed in hotel and catering industry. Macau was appealing to international tourists and provided high-end and prestigious offerings; while Zhuhai was impressed by cost-effective accommodation and food. Second, Macau diversified industrial structure with diverse “Tourism, Leisure and Recreation” and “Culture, History and Art” more than Zhuhai did. Meanwhile, Macau should balance the different demands of international and Chinese tourists. Third, complementary potentials were found in natural resources, urbanization technology and tourism innovation and related projects.Practical implicationsThe research provides valuable insights for policymakers and industrial managers on their endeavors to develop DIs. Policymakers should be able to develop supportive mechanisms and tourism facilitators to promote industrial collaboration and mutual DIs. Managers could refer to the components in the changing DIs and identify the developmental gaps and cooperation potentials in their targeted areas.Originality/valueThe research fulfills the gap in regional tourism studies on Macau, in which the evaluation on synergetic influence and neighbor effect from Zhuhai has been underexplored. Facilitated by up-to-date data mining techniques, the study contributes to both DI and coopetition literature in tourism marketing; and this should inspire further studies on the antecedences of DI changes, resolutions to the competing interests and DIs of different stakeholders in different forms of strategic cooperation in regional tourism. The employment of DIs is an explicit demonstration of tourists' immersion and values attached to the destination, providing effective cues on the status of coopetition.

An object kinetic Monte Carlo method to model precipitation and segregation in alloys under irradiation

A method based on object kinetic Monte Carlo that can account for segregation and precipitation in metallic alloys in the presence of both vacancies and self-interstitials is presented. Here the model has been applied specifically to FeCr alloys, but could be used for other alloys with proper parametrization. The model is based on the division of the simulation box into cells where only the local concentration of the alloy is considered and not the explicit location of each alloy atom, in a mean field type of approach. This concentration, together with those of neighboring cells, is used to bias defect migration taking into account the proper thermodynamics of the alloy at hand and the stiffness coefficient to include neighboring effects. The novelty of this implementation is, among other things, the explicit description of mixed pairs of point defects with the alloy element: vacancy-Cr (VCr) and self-interstitial-Cr (ICr) whenever necessary. This explicit description allows the temperature dependence of defect evolution to be correctly reproduced. In this paper we present the model in detail for the particular case of processes that take place in the presence of vacancies, to show the robustness and applicability of this method.

Construction of circular quasi rees neighbor designs which can be converted into minimal circular balanced and strongly balanced neighbor designs

The response of a treatment (direct effect) applied on a given unit may be affected by the treatments applied to its neighboring units (neighbor effects). Neighbor designs are considered robust to neighbor effects. Minimal neighbor designs are economical, therefore, these are preferred by the experimenters. Method of cyclic shifts (Rule I) provides the minimal neighbor designs for odd v (number of treatments). Method of cyclic shifts (Rule II) provides the minimal circular Quasi Rees neighbor designs for v even which are considered to be the good alternate to the minimal neighbor designs. In this article, for every case of v even, minimal circular Quasi Rees neighbor designs are constructed in such a way that these designs can also be converted directly into minimal circular balanced and strongly balanced neighbor designs.

Size-Induced Inversion of Selectivity in the Acylation of 1,2-Diols.

Relative rates for the Lewis base‐catalyzed acylation of aryl‐substituted 1,2‐diols with anhydrides differing in size have been determined by turnover‐limited competition experiments and absolute kinetics measurements. Depending on the structure of the anhydride reagent, the secondary hydroxyl group of the 1,2‐diol reacts faster than the primary one. This preference towards the secondary hydroxyl group is boosted in the second acylation step from the monoesters to the diester through size and additional steric effects. In absolute terms the first acylation step is found to be up to 35 times faster than the second one for the primary alcohols due to neighboring group effects.

An In Silica Model for RPE Loss Patterns in Choroideremia.

PurposeTo use empirical data to develop a model of cell loss in choroideremia that predicts the known exponential rate of RPE loss and central, scalloped preservation pattern seen in this disease.MethodsA computational model of RPE loss was created in Python 3.7, which constructed an array of RPE cells clusters, binarized as either live or atrophic. Two rules were applied to this model: the background effect gave each cell a chance of dying defined by a background function, and the neighbor effect increased the chance of RPE cell death if a neighbor were dead. The known anatomic distribution of rods, RPE, choriocapillaris density, amacrine, ganglion, and cone cells were derived from the literature and applied to this model. Atrophy growth rates were measured over arbitrary time units and fit to the known exponential decay model. The main outcome measures: included topography of atrophy over time and fit of simulated residual RPE area to exponential decay.ResultsA background effect alone can simulate exponential decay, but does not simulate the central island preservation seen in choroideremia. An additive neighbor effect alone does not simulate exponential decay. When the neighbor effect multiplies the background effect using the rod density function, our model follows an exponential decay, similar to previous observations. Also, our model predicts a residual island of RPE that resembles the topographic distribution of residual RPE seen in choroideremia.ConclusionsThe pattern of RPE loss in choroideremia can be predicted by applying simple rules. The RPE preservation pattern typically seen in choroideremia may be related to the underlying pattern of rod density. Further studies are needed to validate these findings.

The effect of neighbors on the effective inertial collision efficiency of cylindrical collectors

We investigate the effect that an upstream cylinder has on the effective inertial collision efficiency of a downstream cylinder. We consider an initially uniform distribution of particles moving past a cylindrical fiber in a potential crossflow and numerically calculate the resulting particle distribution far downstream of the fiber using finite differences. We then investigate the effect that the downstream distribution of particles has on the effective inertial collision efficiency of a downstream test cylinder oriented parallel to the first. We show that the effective collision efficiency of the test cylinder depends on its relative offset in the transverse direction (normal to the flow) with respect to the upstream cylinder. For relatively small offsets there is complete shielding, and no particles collide with the test cylinder. As the offset increases, a growing effective collision efficiency is observed leading to a significant enhancement relative to the collision efficiency of an isolated cylinder for intermediate offsets and Stokes numbers close to unity. Importantly, we observe relative gains in effective collision efficiency above 100% for a range of Stokes numbers and offset values. For larger offsets and Stokes numbers, the effect of the upstream cylinder on the effective collision efficiency of the test cylinder decreases and eventually becomes negligible. Detailed results are provided for Stokes drag acting on the particles and we also show that a non-linear drag has a negligible effect on the observed trends for the conditions relevant to air filtration systems. These results suggest that the arrangement of fibers has a substantial effect on inertial particle impaction even when neighboring fibers do not alter the flow field around each individual collector. Moreover, periodic arrangements with specific orientations with respect of the flow could lead to a significant enhancement of the inertial collision of particles on an array of collectors, thus contributing towards a better filtration performance.

Sex-specific interactions shape root phenolics and rhizosphere microbial communities in Populus cathayana

We assessed root phenolics and rhizosphere microbiomes of Populus cathayana females and males in the replicated 30-year-old plantations, including pure female plantations (PF), pure male plantations (PM), and mixed female and male plantations (MS) to reveal sex and neighbor effects, and associations between root phenolic metabolites and root-related microbes. The phenolic composition of females varied more between intrasexual and intersexual interactions compared to that of males. Thus, sexual dimorphism was present in the metabolic composition and biochemical plasticity. MS plantations enhanced the bacterial and fungal alpha diversity of both females and males. The composition of fungal communities of females and males in MS plantations was different from that in PF and PM, while such differences were not found in the composition of bacterial communities. Bacterial and fungal diversities were correlated with concentrations of specific phenolic metabolites and were most positively responsive to root benzoic acid and pinoresinol production, respectively. Our findings indicate that sex-specific interactions affect the system of plant sex - root phenolics - rhizosphere microbes, and they may contribute to sex-specific resource utilization patterns. Knowledge of such mechanisms would be helpful when establishing plantations of dioecious plants.

Interspecific relationships between submerged and emergent aquatic plants along a nitrogen gradient in a mesocosm experiment

The responses of plant populations and communities to environmental factors play a key role in the ecological protection and restoration of lakes. However, little is known about how interspecific relationships respond to environmental gradients, especially for relationships between different growth forms such as submerged and emergent aquatic plants in shallow lakes, which can further affect species composition as community dynamics. We carried out a mesocosm experiment to investigate the responses of two focal aquatic plants (Ceratophyllum demersum and Phragmites australis) at two density levels and six levels of total nitrogen (TN) levels. Our results suggested that interspecific competition exist between C. demersum and P. australis, especially at high nitrogen levels. The competition relationship was mainly influenced by variations of relative growth rates of C. demersum and population density of P. australis along the nitrogen gradient. The interspecific neighbor effect on C. demersum shifted from facilitation to competition as TN increased, whereas on P. australis showed no significant facilitation effect along the TN gradient. Ceratophyllum demersum and P. australis adopted stress-tolerance and competition strategies for nitrogen, respectively, in co-culture. As a result, the dominant species in the plant community is likely to shift from the submerged macrophyte (C. demersum) to the emergent macrophyte (P. australis) as TN increases. Moderate TN (2.5 mg/L) can potentially support high biodiversity in macrophyte-dominated shallow lakes in our study. This finding has implications for different community composition at different nitrogen levels. Furthermore, it has important implications for protecting biodiversity and guiding vegetation restoration in shallow lakes.

Study of spreading phenomenon in network population considering heterogeneous property

In practice, it is well known that the environment plays an essential role in affecting personal opinions regarding epidemics. In this paper, we assume that personal recovery rate from infected state varies and corresponding recovery value is affected by the number of aware and susceptible neighbors while this is referred to as resource for simplicity. A tunable factor, i.e., α, is introduced indicating the rate of resource utilization, while this parameter is adopted to characterize the effect of neighbors to individual’s recovery rate. For simplicity, the UAU-SIS model is adopted to study the spreading phenomenon. Later, extensive Monte Carlo simulations are conducted; for comparison, theoretical results are also derived through microscopic Markov chain approach. Regardless of the considered network topology, we can easily find that the obtained results are consistent from the epidemic level. Furthermore, the fraction of infected individuals or aware individuals seems to increase with the increase of resource utilization rate. This is incurred by the fact that a larger recovery rate will be obtained for higher resource utilization rate. We also devote our efforts deriving the epidemic spreading threshold while the threshold value decreases for larger. Thus, we can conclude that the resource utilization rate plays a negative role in eliminating epidemics. We hope the findings here can contribute the understanding about spreading phenomenon in network population given heterogeneous recovery rate.

Transition kinetics of defect patterns in confined two-dimensional smectic liquid crystals.

Topological defects in liquid crystals under confined geometries have attracted extensive research interests. Here, we perform molecular dynamics simulations to investigate the formation and transition of defect patterns in two-dimensional smectic Gay-Berne liquid crystals with a simple rectangular confinement boundary. Two typical types of defect patterns, bridge and diagonal defect patterns, are observed, which can be transformable continuously between each other over time. The transition usually starts from the line or point defect regions, and the competition between neighboring and opposite boundary effects induces the continuous realignments of the smectic layers to connect the neighboring or opposite walls. The relative stability of these two defect patterns can be controlled by changing the confinement conditions. These results deepen our understanding of transition kinetics of defect patterns in confined liquid crystals.

Exploring the real contribution of socioeconomic variation to urban PM2.5 pollution: New evidence from spatial heteroscedasticity

Making cities safe, resilient and sustainable is one of the United Nations Sustainable Development Goals (SDGs). Health risk, productivity loss and climate change caused by air pollution obstacles the present urban sustainable development, especially people living in middle-and low-income countries areas are most affected. The spatial models (such as SAR and SEM) are often considered to examine the driven factors and the spatial spillover effect of PM2.5 concentrations. Given that these spatial models assume spatially dependent second-order moments of the dependent variable without considering the possible autoregressive conditional heteroscedasticity. This present study empirically examines the heterogeneous effects of economic development, secondary industry, FDI, population density, number of buses and urbanization on PM2.5 concentrations in 269 Chinese cities using the SAR, spARCH and SARspARCH, respectively. This newly proposed Spatial ARCH model is the first attempt to be applied to environmental research. The empirical results indicate that an increasing spatial correlation with PM2.5 concentration was observed among 269 cities during 2004–2016, and the most influential cities in high-high clustering are mainly located in North China. Furthermore, except for population density, the effects of other factors are heterogeneous on the time scale. Among those socioeconomic factors, population density shows the largest contribution to urban PM2.5 pollution, the effects of secondary industry, GDP and FDI may be overestimated in the absence of spatial neighbouring effects in mean or variance. The comparative analysis could provide new enlightenments for a deeper understanding of the socioeconomic impact on PM2.5 pollution.

Species stress tolerance and community competitive effects drive differences in species composition between calcareous and siliceous plant communities

Abstract Both chemical and physical properties of soils have been used for two centuries for explaining differences in species composition and diversity between plant communities from calcareous and siliceous soils. Here, we examine the prediction from the ‘physical hypothesis’, which proposes that species from siliceous soils are absent from calcareous soils because of high drought stress, while species from calcareous soils are absent from siliceous soils because of high competition due to higher water availability. This hypothesis therefore predicts a trade‐off between stress tolerance and competitive response that allows calcareous and siliceous species to dominate their respective communities. There has been no attempt to experimentally assess these predictions. We cross‐transplanted with and without neighbours using a removal experiment, two dominant species from calcareous soils (Bromus erectus and Brachypodium sylvaticum) and two species from siliceous soils (Pseudarrhenatherum longifolium and Deschampsia flexuosa) in herbaceous communities from the two soils types. We repeated the experiment 4 years, taking advantage of inter‐annual climatic variability to test the interplay between year quality (dry vs. wet years) and soil types on survival responses with and without neighbours. We quantified species stress tolerances, their competitive responses and the competitive effect of the two community types. In the absence of neighbours, species from siliceous soils had much lower survival than species from calcareous soils during dry years, in particular on calcareous soils. It indicates a lower stress tolerance of siliceous species and a higher level of stress occurring on calcareous soils. Competition strongly reduced the survival of calcareous but not siliceous species, indicating a greater competitive response of the latter and competition was more important on siliceous soils than on calcareous soils during wet years. However, we found that species stress tolerances were more important than competitive effect of neighbours in driving differences in species composition. Synthesis. The contrasting responses found for dominant species from calcareous and siliceous soils support the trade‐off between stress tolerance and competitive response proposed by the physical hypothesis. Our results bring additional evidence that differences in water availability and stress between the two soil types are driving species responses to bedrock types.

A standard knockout procedure alters expression of adjacent loci at the translational level

The Saccharomyces cerevisiae gene deletion collection is widely used for functional gene annotation and genetic interaction analyses. However, the standard G418-resistance cassette used to produce knockout mutants delivers strong regulatory elements into the target genetic loci. To date, its side effects on the expression of neighboring genes have never been systematically assessed. Here, using ribosome profiling data, RT-qPCR, and reporter expression, we investigated perturbations induced by the KanMX module. Our analysis revealed significant alterations in the transcription efficiency of neighboring genes and, more importantly, severe impairment of their mRNA translation, leading to changes in protein abundance. In the ‘head-to-head’ orientation of the deleted and neighboring genes, knockout often led to a shift of the transcription start site of the latter, introducing new uAUG codon(s) into the expanded 5′ untranslated region (5′ UTR). In the ‘tail-to-tail’ arrangement, knockout led to activation of alternative polyadenylation signals in the neighboring gene, thus altering its 3′ UTR. These events may explain the so-called neighboring gene effect (NGE), i.e. false genetic interactions of the deleted genes. We estimate that in as much as ∼1/5 of knockout strains the expression of neighboring genes may be substantially (>2-fold) deregulated at the level of translation.

Context-aware Adaptive Surgery

Deep Neural Networks (DNNs) have made massive progress in many fields and deploying DNNs on end devices has become an emerging trend to make intelligence closer to users. However, it is challenging to deploy large-scale and computation-intensive DNNs on resource-constrained end devices due to their small size and lightweight. To this end, model partition, which aims to partition DNNs into multiple parts to realize the collaborative computing of multiple devices, has received extensive research attention. To find the optimal partition, most existing approaches need to run from scratch under given resource constraints. However, they ignore that resources of devices (e.g., storage, battery power), and performance requirements (e.g., inference latency), are often continuously changing, making the optimal partition solution change constantly during processing. Therefore, it is very important to reduce the tuning latency of model partition to realize the real-time adaption under the changing processing context. To address these problems, we propose the Context-aware Adaptive Surgery (CAS) framework to actively perceive the changing processing context, and adaptively find the appropriate partition solution in real-time. Specifically, we construct the partition state graph to comprehensively model different partition solutions of DNNs by import context resources. Then "the neighbor effect" is proposed, which provides the heuristic rule for the search process. When the processing context changes, CAS adopts the runtime search algorithm, Graph-based Adaptive DNN Surgery (GADS), to quickly find the appropriate partition that satisfies resource constraints under the guidance of the neighbor effect. The experimental results show that CAS realizes adaptively rapid tuning of the model partition solutions in 10ms scale even for large DNNs (2.25x to 221.7x search time improvement than the state-of-the-art researches), and the total inference latency still keeps the same level with baselines.

Comparative impact of light and neighbor effect on the growth of introduced speciesSonneratia apetalaand native mangrove species in China: implications for restoration

Light condition and neighbor effects are important environmental factors that need to be considered for restoration of mangroves, especially when introduced species are mixed with native species. To evaluate different mangrove species performance under various light intensities and different planting systems, we selected three native mangrove species (Avicennia marina,Aegiceras corniculatum, andKandelia obovata) and grew them withSonneratia apetalain multispecies plots and in monospecies plots withoutS. apetalaunder three light conditions in Futian Nature Reserve, south China. After 10 months of the experiment, plant functional traits were measured. The results showed thatS. apetalawas a light‐demanding species andA. corniculatumandA. marinawere suitable for growth under the medium light condition. The native species were inhibited byS. apetala. Specifically, the height and basal diameter of the native species were lower in the multispecies plots than in the monospecies plots. In the multispecies plots, native species changed their functional growth traits, with higher‐specific leaf area and chlorophyll content, and reduced leaf thickness, leaf dry‐mass content, and carotenoid content compared to those in the monospecies plots. These results indicated trade‐offs between traits that enhance light interception and traits that stimulate plant growth in native species. Our findings revealed thatS. apetalais an adequate species with good invasion capability for restoration in open‐degraded areas, but its ecological impact on the inhibited growth of native species should be carefully considered in mangrove restoration.

Intraspecific variation mediates density dependence in a genetically diverse plant species.

Interactions between neighboring plants are critical for biodiversity maintenance in plant populations and communities. Intraspecific trait variation and genome duplication are common in plant species and can drive eco-evolutionary dynamics through genotype-mediated plant-plant interactions. However, few studies have examined how species-wide intraspecific variation may alter interactions between neighboring plants. We investigate how subspecies and ploidy variation in a genetically diverse species, big sagebrush (Artemisia tridentata), can alter the demographic outcomes of plant interactions. Using a replicated, long-term common garden experiment that represents range-wide diversity of A. tridentata, we ask how intraspecific variation, environment, and stand age mediate neighbor effects on plant growth and survival. Spatially explicit models revealed that ploidy variation and subspecies identity can mediate plant-plant interactions but that the effect size varied in time and across experimental sites. We found that demographic impacts of neighbor effects were strongest during early stages of stand development and in sites with greater growth rates. Within subspecies, tetraploid populations showed greater tolerance to neighbor crowding compared to their diploid variants. Our findings provide evidence that intraspecific variation related to genome size and subspecies identity impacts spatial demography in a genetically diverse plant species. Accounting for intraspecific variation in studies of conspecific density dependence will improve our understanding of how local populations will respond to novel genotypes and biotic interaction regimes. As introduction of novel genotypes into local populations becomes more common, quantifying demographic processes in genetically diverse populations will help predict long-term consequences of plant-plant interactions.

Some useful classes of minimal weakly balanced neighbor designs in circular blocks of two different sizes

Neighbor designs (NDs) are used to balance out the neighbor effects. Among these designs, minimal NDs are economical, therefore, these are preferred by experimenters. Unfortunately, minimal NDs cannot be constructed for all combinations of v (number of treatments) and k (block sizes). Minimal weakly balanced NDs (WBNDs) are recommended in the situations where minimal NDs could not be constructed. In this article, some generators are developed to obtain minimal circular WBNDs (MCWBNDs) in blocks of two different sizes. In our proposed designs, 3v/2 unordered pairs of distinct treatments appear twice as neighbors while all other pairs appear once. In these designs, we lose % neighbor balance while saving at least % experimental material.