Estimation of the highest chromosome number of eukaryotes based on the minimum interaction theory

According to the minimum interaction theory, the chromosome evolution of eukaryotes proceeds as a whole toward increasing the chromosome number. This raises the following two questions: what was the starting chromosome number of eukaryotes and does the chromosome number increase infinitely? We attempted to provide a theoretical framework to resolve these questions. We propose that the species with n=2 observed in Protozoa, Platyhelminthes, Annelid, Algae, Fungi and higher plants would be chromosomal relicts conserving the karyotypes of ancestral eukaryotes. We also propose that the ideal highest number of eukaryotes (n(max)) can be given by an inverse of the minimum terminal interference distance (It(min)) in crossing-over (n(max)=100/It(min)). AsIt(min) =0.6 in mammals, n(max) approximately 166. On the other hand, the value estimated by computer simulations is somewhat lower with n(max)=133-138. Our arguments can be applied to other eukaryotes, if they have a localized centromere and the ratio of total synaptonemal complex/nuclear volume is comparable to that of mammals. We revealed that the index of gene shuffling per karyotypes (G) by means of the total number of gamete types with different gene combinations can be formulated asG =2(n+Fxi), where Fxi means interstitial chiasma frequency per cell corresponding to crossing-over mediated by the recombination nodule. The Fxi value increases in proportion to the n value in areas where n<40, but decreases gradually when n>40 and becomes zero when n>83. Therefore, in the ultimate karyotype with n(max)=166, FXi=0 andG =2(n)=2(166), where gene shuffling is guaranteed by the random orientation of chromosomes at the equatorial plate of meiotic metaphase I.     

Soybean biotic pollination and its relationship to linear forest fragments of subtropical dry Chaco

The delivery of ecosystem services, such as biotic pollination is a benefit that nature provides us. Pollinators increase the quantity, quality and stability of crops for food production. Previous works show that proximity to natural habitats increases crop production through the delivery of pollination services. However, similar researches in subtropical regions is largely lacking. In this study we evaluated the role of linear forest fragments (LFFs) on the provision of biotic pollination service to soybean crops (Glycine max) and explored whether this service changes with increasing distance to LFFs in subtropical dry Chaco (Argentina). In three agricultural farms and testing two soybean varieties, we covered plots of 0.75 m² with soybean plants and compared them with equally sized open plots. Plots were placed near (60 m) and far (600 m) from LFFs. We found that plants from the open treatment produced 32% more pods, 41% more seeds and had 42% higher yield (kg/ha) than plants from the covered plots. The difference between open and covered plots in seeds and yield did not change significantly with the distance to LFFs, but the number of pods, contrary to what we expected, was higher far from LFFs. Our findings highlight the possible impact of pollinators on soybean yield in both varieties tested here; but the proximity to LFFs was not directly related to a larger difference in production. Observed patterns are explained by edge effects and competition between soybean plants and trees near LFFs, combined with an underestimation of the distance from the natural hives to which honeybees can efficiently exploit the crops. In this subtropical region, soybean expansion is the most important driver of land cover change and this study represents a first step towards a better understanding of the functioning of these remnants of natural areas within the agricultural land in the region of dry Chaco forests.     

Gradients in the number of species at reef-seagrass ecotones explained by gradients in abundance

Gradients in the composition and diversity (e.g. number of species) of faunal assemblages are common at ecotones between juxtaposed habitats. Patterns in the number of species, however, can be confounded by patterns in abundance of individuals, because more species tend to be found wherever there are more individuals. We tested whether proximity to reefs influenced patterns in the composition and diversity ('species density' = number of species per area and 'species richness' = number of species per number of individuals) of prosobranch gastropods in meadows of two seagrasses with different physiognomy: Posidonia and Amphibolis. A change in the species composition was observed from reef-seagrass edges towards the interiors of Amphibolis, but not in Posidonia meadows. Similarly, the abundance of gastropods and species density was higher at edges relative to interiors of Amphibolis meadows, but not in Posidonia meadows. However, species richness was not affected by proximity to reefs in either type of seagrass meadow. The higher number of species at the reef-Amphibolis edge was therefore a consequence of higher abundance, rather than species richness per se. These results suggest that patterns in the composition and diversity of fauna with proximity to adjacent habitats, and the underlying processes that they reflect, likely depend on the physiognomy of the habitat.     

Patchy populations in stochastic environments: critical number of patches for persistence

We introduce a model for the dynamics of a patchy population in a stochastic environment and derive a criterion for its persistence. This criterion is based on the geometric mean (GM) through time of the spatial-arithmetic mean of growth rates. For the population to persist, the GM has to be >/=1. The GM increases with the number of patches (because the sampling error is reduced) and decreases with both the variance and the spatial covariance of growth rates. We derive analytical expressions for the minimum number of patches (and the maximum harvesting rate) required for the persistence of the population. As the magnitude of environmental fluctuations increases, the number of patches required for persistence increases, and the fraction of individuals that can be harvested decreases. The novelty of our approach is that we focus on Malthusian local population dynamics with high dispersal and strong environmental variability from year to year. Unlike previous models of patchy populations that assume an infinite number of patches, we focus specifically on the effect that the number of patches has on population persistence. Our work is therefore directly relevant to patchily distributed organisms that are restricted to a small number of habitat patches.     

Effect of the buck on number of services per conception,service period and litter size at birth in Bauscat rabbits

A non-significant buck effect on the number of services per conception, service period and litter size at birth in Bauscat rabbits was found using 66 bucks. The within-buck repeatability of number of services per conception and service period of 0.027 ± 0.028 and 0.035 ± 0.029, respectively, were non-significant. The same parameter for litter size at birth could not be obtained because of the negative buck component of variance observed. For this population of rabbits it appeared that no difference in these traits existed among bucks and, as a result, improvement in these traits could not be made by selection of bucks based on their own performance.     

Threshold, wave and cell-cell avalanche behaviour in a class of substrate inhibition oscillators.

Two molecules of IgG need to be in close proximity upon a cell surface in order to bind complement. Here we obtain approximate results for the probability that two or more IgG molecules are closer than some minimum separation distance, given that N IgG molecules are bound to the cell. Determining this probability exactly is a classical unsolved problem in geometrical probability. We also estimate the probability of having n pairs of IgG molecules in close proximity and compute the expected number of IgG pairs. Our theoretical results are compared with experimental measurements on complement fixation by IgG.     

Effect of service number on estrus duration in dairy goats

The object of this research was to study the effect of sterile service number on estrus duration in dairy goats. Twenty-four Nubian goats (20 nulliparous and 4 multiparous) were randomly assigned to 1 of 4 treatment groups (n = 6 animals per group). The following Groups were formed: no service (GS-0); 1 service (GS-1); 2 services (GS-2); 3 services (GS-3). Estrus was synchronized by using fluorogestone acetate intravaginal pessaries (40 mg) over a 12-d period plus 400 IU im pregnant mare serum gonadotropin (PMSG) at pessary removal. Estrus was detected by using a vasectomized buck at 6-h intervals over 5 d after pessary removal (at 0600, 1200, 1800 and 2400 h). In the GS-0 group the teaser was outfitted with an apron and was permitted to mount. In the GS-1, GS-2 and GS-3 groups, the teaser was permitted to mount and service 1, 2 and 3 times, respectively, within the first 12 h after initiation of estrus. The duration of estrus for the 4 groups (GS-0, GS-1, GS-2 and GS-3) was (mean +/- SD) 41.0 +/- 5.9, 24.0 +/- 5.4, 22.0 +/- 4.9 and 22.0 +/- 7.2 h, respectively. These results show differences between the serviced groups and the nonserviced group (P<0.01), but they fail to show differences among the serviced groups (P>0.05). It is concluded that sterile service shortens estrus duration and that service number (1, 2 or 3) does not affect estrus duration.     

Ovule number per flower in a world of unpredictable pollination

The number of ovules per flower varies over several orders of magnitude among angiosperms. Here we consider evidence that stochastic uncertainty in pollen receipt and ovule fertilization has been a selective factor in the evolution of ovule number per flower. We hypothesize that stochastic variation in floral mating success creates an advantage to producing many ovules per flower because a plant will often gain more fitness from occasional abundant seed production in randomly successful flowers than it loses in resource commitment to less successful flowers. Greater statistical dispersion in pollination and fertilization among flowers increases the frequency of windfall success, which should increase the strength of selection for greater ovule number per flower. We therefore looked for evidence of a positive relationship between ovule number per flower and the statistical dispersion of pollen receipt or seed number per flower in a comparative analysis involving 187 angiosperm species. We found strong evidence of such a relationship. Our results support the hypothesis that unpredictable variation in mating success at the floral level has been a factor in the evolution of ovule packaging in angiosperms.     

Cost-aware job scheduling for cloud instances using deep reinforcement learning

As the services provided by cloud vendors are providing better performance, achieving auto-scaling, load-balancing, and optimized performance along with low infrastructure maintenance, more and more companies migrate their services to the cloud. Since the cloud workload is dynamic and complex, scheduling the jobs submitted by users in an effective way is proving to be a challenging task. Although a lot of advanced job scheduling approaches have been proposed in the past years, almost all of them are designed to handle batch jobs rather than real-time workloads, such as that user requests are submitted at any time with any amount of numbers. In this work, we have proposed a Deep Reinforcement Learning (DRL) based job scheduler that dispatches the jobs in real time to tackle this problem. Specifically, we focus on scheduling user requests in such a way as to provide the quality of service (QoS) to the end-user along with a significant reduction of the cost spent on the execution of jobs on the virtual instances. We have implemented our method by Deep Q-learning Network (DQN) model, and our experimental results demonstrate that our approach can significantly outperform the commonly used real-time scheduling algorithms.

     

Response of ecosystem services to socioeconomic development in the Yangtze River Basin,China

The provision of ecosystem services from multifunctional landscapes has contributed to human well-being. However, a general tendency exists to consider only marketed ecosystem services and to ignore non-marketed services, which has become more common when evaluating multiple-ecosystem services at the local level. In this study, we present an integrative index of multiple-ecosystem services (IMES) that avoids this tendency. Our main objective is to evaluate how socioeconomic factors interact with the spatial differences between the supply of and demand for multiple-ecosystem services. GlobCover data and a modified ecosystem service “matrix” are used to quantify and map ecosystem service supply and demand at the municipality level in the Yangtze River Basin, China. We used multiple regression analysis to detect relationships between ecosystem services and socioeconomic factors in municipalities to identify the main drivers of change in the supply of and demand for multiple-ecosystem services at the local level, respectively. The results revealed that 111 municipalities in the Yangtze River Basin (84.7% of the area) had an oversupply of multiple-ecosystem services; these municipalities were primarily situated in the western part of the upper reach and the southeast parts of the middle reach. Undersupplied areas were mainly situated in densely populated municipalities in the northern part of the lower reach and in agricultural municipalities in the northeastern part of the middle reach. The driving factors of changes in multiple-ecosystem services are significantly different not only in terms of the supply, demand and balance between the two but also among the three reaches. These differences in the driving factors among the three reaches can produce incorrect conclusions if an entire basin is considered, particularly for large basins. This information may be of interest to policymakers. The first principal component for the supply of and demand for multiple-ecosystem services exhibits a good correlation with the IMES in the Yangtze River Basin. Additionally, the integrative index of multiple-ecosystem services (including IMES_s and IMES_d) in the study area is relatively reliable according to the sensitivity analysis. Therefore, IMES is an effective tool for aggregating the value of multiple-ecosystem services at local scales. This tool can be used to identify the drivers of changes in multiple-ecosystem services based on the relationships between IMES and socioeconomic factors at the municipality scale. IMES should be useful for policymakers and stakeholders because it can provide important information for local decision-making.     

Scheduling unrelated parallel machines in semiconductor manufacturing by problem reduction and local search heuristics

We investigate a difficult scheduling problem in a semiconductor manufacturing process that seeks to minimize the number of tardy jobs and makespan with sequence-dependent setup time, release time, due dates and tool constraints. We propose a mixed integer programming (MIP) formulation which treats tardy jobs as soft constraints so that our objective seeks the minimum weighted sum of makespan and heavily penalized tardy jobs. Although our polynomial-sized MIP formulation can correctly model this scheduling problem, it is so difficult that even a feasible solution can not be calculated efficiently for small-scale problems. We then propose a technique to estimate the upper bound for the number of jobs processed by a machine, and use it to effectively reduce the size of the MIP formulation. In order to handle real-world large-scale scheduling problems, we propose an efficient dispatching rule that assigns a job of the earliest due date to a machine with least recipe changeover (EDDLC) and try to re-optimize the solution by local search heuristics which involves interchange, translocation and transposition between assigned jobs. Our computational experiments indicate that EDDLC and our proposed reoptimization techniques are very efficient and effective. In particular, our method usually gives solutions very close to the exact optimum for smaller scheduling problems, and calculates good solutions for scheduling up to 200 jobs on 40 machines within 10 min.     

Enhancing service capability with multiple finite capacity server queues in cloud data centers

Cloud computing took a step forward in the efficient use of hardware through virtualization technology. And as a result, cloud brings evident benefits for both users and providers. While users can acquire computational resources on-demand elastically, cloud vendors can also utilize maximally the investment costs for data centers infrastructure. In the Internet era, the number of appliances and services migrated to cloud environment increases exponentially. This leads to the expansion of data centers, which become bigger and bigger. Not just that these data centers must have the architecture with a high elasticity in order to serve the huge upsurge of tasks and balance the energy consumption. Although in recent times, many research works have dealt with finite capacity for single job queue in data centers, the multiple finite-capacity queues architecture receives less attention. In reality, the multiple queues architecture is widely used in large data centers. In this paper, we propose a novel three-state model for cloud servers. The model is deployed in both single and multiple finite capacity queues. We also bring forward several strategies to control multiple queues at the same time. This approach allows to reduce service waiting time for jobs and managing elastically the service capability for the whole system. We use CloudSim to simulate the cloud environment and to carry out the experiments in order to demonstrate the operability and effectiveness of the proposed method and strategies. The power consumption is also evaluated to provide insights into the system performance in respect of performance-energy trade-off.     

The control of chloroplast number in wheat mesophyll cells

Chloroplast number per cell and mesophyll cell plan area were determined in populations of separated cells from the primary leaves of different wheat species representing three levels of ploidy. Mean chloroplast number per cell increases with ploidy level as mean cell size increases. But in addition the analysis of individual cells clearly shows that cells of a similar size but from species of different ploidies have similar numbers of chloroplasts. We conclude that the number of chloroplasts within a cell is closely correlated (P<0.001) with the size of the cell and this relationship is consistent for species of different ploidies over a wide range of cell sizes. These results are discussed in relation to the hypothesis that chloroplast number in leaf mesophyll cells is determined by the size of the cell.     

The trade balance of grooming and its coordination of reciprocation and tolerance in Indonesian long-tailed macaques (<Emphasis Type="Italic">Macaca fascicularis</Emphasis>)

We collected data on grooming, proximity, and aggression in long-tailed macaques (Macaca fascicularis) in Kalimantan, Indonesia. We used this data to study how grooming influenced a receiver's (B) behavior towards the bout's initiator (A). In our first analysis, post-grooming samples were collected after A groomed B. These were compared to matched-control samples of similar conditions but A had not previously groomed B. This comparison was performed on 26 individuals (16 female, 3 male, 7 immature) and tested whether A's initial act of grooming increased the pair's time in proximity and the amount of time B groomed A. We also tested if A's grooming decreased B's aggression towards A per time in proximity. Rates of B-->A aggression per time in proximity with A for 39 individuals (18 female, 5 male, 16 immature) were compared between post-grooming and focal sample data. Finally, we studied 248 grooming bouts to test if the first two grooming episodes were time matched. We assessed the influence of age, sex, rank and inferred kinship on time matching, and controlled for individual variation and tendency to groom using a general linear mixed model. Our results showed that A-->B grooming acted to increase B-->A grooming and the pair's proximity, while lowering B-->A aggression. Despite these effects, episodes in grooming bouts were generally not matched, except weakly among similar partners (i.e., female pairs and immature pairs). Grooming imbalance was greatest across age-sex class (i.e., male-female and adult-immature pairs). In similar pairs, grooming duration was skewed in favor of high-ranking individuals. We conclude grooming established tolerance and increased the likelihood that grooming reciprocation would occur, but grooming durations were not typically matched within bouts. Lack of time matching may be the result of grooming that is performed to coordinate interchanges of other social services.     

Postnatal variations in the number and size of C-cells in the rat thyroid gland

The heterogeneous distribution of thyroid C-cells has until now hindered an objective evaluation of changes caused by age or experimental stimuli. To overcome this, a rigorous methodology has been designed to detect variations in shape, size, and number of C-cells throughout development. Using this methodology, we have demonstrated that C-cells do not significantly alter their shape with age. However, their volume increases gradually from 472 m³ in newborn rats to 1653 m³ in 120-day-old animals. Over the same time period, the mean number of C-cells within the thyroid gland increased 9-fold (from 1.6x10⁴ to 1.5x10⁵), and the number of C-cells per unit area decreased (from 6.15x10⁴/mm³ to 2.6x10⁴/mm³). We conclude that there are marked variations in size, total number, and number of C-cells per unit area in the rat thyroid gland after birth.     

Persistence and availability of Web services in computational biology

We have conducted a study on the long-term availability of bioinformatics Web services: an observation of 927 Web services published in the annual Nucleic Acids Research Web Server Issues between 2003 and 2009. We found that 72% of Web sites are still available at the published addresses, only 9% of services are completely unavailable. Older addresses often redirect to new pages. We checked the functionality of all available services: for 33%, we could not test functionality because there was no example data or a related problem; 13% were truly no longer working as expected; we could positively confirm functionality only for 45% of all services. Additionally, we conducted a survey among 872 Web Server Issue corresponding authors; 274 replied. 78% of all respondents indicate their services have been developed solely by students and researchers without a permanent position. Consequently, these services are in danger of falling into disrepair after the original developers move to another institution, and indeed, for 24% of services, there is no plan for maintenance, according to the respondents. We introduce a Web service quality scoring system that correlates with the number of citations: services with a high score are cited 1.8 times more often than low-scoring services. We have identified key characteristics that are predictive of a service's survival, providing reviewers, editors, and Web service developers with the means to assess or improve Web services. A Web service conforming to these criteria receives more citations and provides more reliable service for its users. The most effective way of ensuring continued access to a service is a persistent Web address, offered either by the publishing journal, or created on the authors' own initiative, for example at http://bioweb.me. The community would benefit the most from a policy requiring any source code needed to reproduce results to be deposited in a public repository.     

Trade-off between number and length of remote videos for rapid assessments of reef fish assemblages

Remote underwater videos are widely employed to assess the structure and composition of reef fish assemblages but the sampling effort employed on each survey differs considerably, indicating that both the number of assessments and video length could be optimized. We searched for this optimal sampling effort in remote video samples to conduct rapid assessments of community composition and discussed the relation between number of replicates and video length, and how it impacts the method's efficiency to characterize species assemblages. Remote video recordings from tropical reefs in northeastern Brazil were used to investigate how fish species richness and composition builds across time and number of assays. Videos as short as 5 min successfully recorded species richness, requiring about five repetitions to record most species that compose 80% of the total biomass. Recording species composition required even less time in these reefs, setting a minimum of 3 min with the same five videos. By comparing the detected richness per analysed time unit, we found several shorter videos recorded for more species than a few longer videos, indicating that increasing the sampling coverage in the reef area might be better than just extending the video length for rapid assessments.     

Estimation of the reproduction number of dengue fever from spatial epidemic data

Dengue, a vector-borne disease, thrives in tropical and subtropical regions worldwide. A retrospective analysis of the 2002 dengue epidemic in Colima located on the Mexican central Pacific coast is carried out. We estimate the reproduction number from spatial epidemic data at the level of municipalities using two different methods: (1) Using a standard dengue epidemic model and assuming pure exponential initial epidemic growth and (2) Fitting a more realistic epidemic model to the initial phase of the dengue epidemic curve. Using Method I, we estimate an overall mean reproduction number of 3.09 (95% CI: 2.34,3.84) as well as local reproduction numbers whose values range from 1.24 (1.15,1.33) to 4.22 (2.90,5.54). Using Method II, the overall mean reproduction number is estimated to be 2.0 (1.75,2.23) and local reproduction numbers ranging from 0.49 (0.0,1.0) to 3.30 (1.63,4.97). Method I systematically overestimates the reproduction number relative to the refined Method II, and hence it would overestimate the intensity of interventions required for containment. Moreover, optimal intervention with defined resources demands different levels of locally tailored mitigation. Local epidemic peaks occur between the 24th and 35th week of the year, and correlate positively with the final local epidemic sizes (rho=0.92, P-value<0.001). Moreover, final local epidemic sizes are found to be linearly related to the local population size (P-value<0.001). This observation supports a roughly constant number of female mosquitoes per person across urban and rural regions.     

Integrating the spatial proximity effect into the assessment of changes in ecosystem services for biodiversity conservation

The assessment of the value of ecosystem services is a valuable tool for biodiversity conservation that can facilitate better environmental policy decision-making and land management, and can help land managers develop interventions to compensate for biodiversity loss at the patch level. Previous studies have suggested that it is appropriate to assess the value of biodiversity for conservation planning by considering both the condition of the landscape and the spatial configuration of adjacent land uses that can be reflected as a proximity effect. This research examines the influence of spatial proximity on biodiversity conservation from the ecosystem service perspective based on the assumption that the variation in the proximity effect caused by land cover change has positive or negative impacts on ecological services. Three factors related to the spatial characteristics of the landscape were considered in this approach: the relative artificiality of the land cover types, the distance decay effect of patches and the impact of one land cover type on others. The proximity effect change (PE_C) parameter reflected the relationship between the spatial proximity effect and biodiversity conservation. The results of a quantitative and spatial comparative analysis of the proposed method and the conventional method in Yingkou for the periods of 2000–2005 and 2005–2010 showed that the former can account for the temporal and spatial changes in ecosystem services for biodiversity conservation that were caused by patch-level changes as well as the interaction between the altered and adjacent patches from a spatial perspective. The metric can also identify the most critical areas for biodiversity protection and inform the efficient allocation of limited land resources for nature conservation to maximize the benefit to biodiversity by guiding the process of land-use change, particularly urbanization and agriculture. Future studies should focus on the other important factors that are applicable to the assessment of the value of biodiversity conservation in socio-ecological systems, where society and nature are mutually capable of fulfilling their roles.     

Distance-dependent differences in synapse number and AMPA receptor expression in hippocampal CA1 pyramidal neurons

The ability of synapses throughout the dendritic tree to influence neuronal output is crucial for information processing in the brain. Synaptic potentials attenuate dramatically, however, as they propagate along dendrites toward the soma. To examine whether excitatory axospinous synapses on CA1 pyramidal neurons compensate for their distance from the soma to counteract such dendritic filtering, we evaluated axospinous synapse number and receptor expression in three progressively distal regions: proximal and distal stratum radiatum (SR), and stratum lacunosum-moleculare (SLM). We found that the proportion of perforated synapses increases as a function of distance from the soma and that their AMPAR, but not NMDAR, expression is highest in distal SR and lowest in SLM. Computational models of pyramidal neurons derived from these results suggest that they arise from the compartment-specific use of conductance scaling in SR and dendritic spikes in SLM to minimize the influence of distance on synaptic efficacy.