Temporal Percolation of the Susceptible Network in an Epidemic Spreading

In this work, we study the evolution of the susceptible individuals during the spread of an epidemic modeled by the susceptible-infected-recovered (SIR) process spreading on the top of complex networks. Using an edge-based compartmental approach and percolation tools, we find that a time-dependent quantity , namely, the probability that a given neighbor of a node is susceptible at time , is the control parameter of a node void percolation process involving those nodes on the network not-reached by the disease. We show that there exists a critical time above which the giant susceptible component is destroyed. As a consequence, in order to preserve a macroscopic connected fraction of the network composed by healthy individuals which guarantee its functionality, any mitigation strategy should be implemented before this critical time . Our theoretical results are confirmed by extensive simulations of the SIR process.     

Effects of Light Adaptation on the Temporal Resolution of Deep-sea Crustaceans

The effects of light adaptation on flicker fusion frequencywere examined in the photoreceptors of 13 species of deep-seacrustaceans. Light adaptation produced a significant increasein the maximum critical flicker fusion frequency (CFF_max) in7 species—all 6 species of euphausiids in the study, and1 species of oplophorid (Group 1). This is the first exampleof an increase in temporal resolution due to light adaptationin a deep-sea species. In the other six species—2 oplophorids,1 pandalid, 1 pasiphaeid, 1 penaeid and 1 sergestid (Group 2)—lightadaptation had no effect, or resulted in a decrease in the flickerfusion frequency. The mean dark-adapted CFF_max of the Group1 species was significantly higher, and the mean response latencysignificantly lower, than those of the Group 2 species. Possibleexplanations for these differences include the activity andbioluminescence mode of preferred prey items, as well as theretention of larval/juvenile adaptations in adult eyes.     

Single-Leaf Resolution of the Temporal Population Dynamics of Aureobasidium pullulans on Apple Leaves

The abundance of phylloplane microorganisms typically varies over several orders of magnitude among leaves sampled concurrently. Because the methods traditionally used to sample leaves are destructive, it has remained unclear whether this high variability is due to fixed differences in habitat quality among leaves or to asynchronous temporal variation in the microbial population density on individual leaves. We developed a novel semidestructive assay to repeatedly sample the same apple leaves from orchard trees over time by removing progressively more proximal ~1-cm-wide transverse segments. Aureobasidium pullulans densities were determined by standard leaf homogenization and plating procedures and were expressed as CFU per square centimeter of segment. The A. pullulans population densities among leaves were lognormally distributed. The variability in A. pullulans population densities among subsections of a given leaf was one-third to one-ninth the variability among whole leaves harvested concurrently. Sequential harvesting of leaf segments did not result in detectable changes in A. pullulans density on residual leaf surfaces. These findings implied that we could infer whole-leaf A. pullulans densities over time by using partial leaves. When this successive sampling regimen was applied over the course of multiple 7- to 8-day experiments, the among-leaf effects were virtually always the predominant source of variance in A. pullulans density estimates. Changes in A. pullulans density tended to be synchronous among leaves, such that the rank order of leaves arrayed with respect to A. pullulans density was largely maintained through time. Occasional periods of asynchrony were observed, but idiosyncratic changes in A. pullulans density did not contribute appreciably to variation in the distribution of populations among leaves. This suggests that persistent differences in habitat (leaf) quality are primarily responsible for the variation in A. pullulans density among leaves in nature.     

人代谢网络巨强连通体的复杂网络分析

采用复杂网络理论分析了人代谢网络的巨强连通体。通过对高质量人代谢网络数据的整理,获取了该网络巨强连通体中的所有代谢反应。用代谢物图表示这些反应形成了一个网络,它包含了256个节点和648条连线。选用模拟退火算法对该网络进行社团结构分析,发现得到的模块具备重要的生物学功能。通过多种不同的中心化方法,分析了该网络的关键节点,并讨论了它们的生物学和理疗意义。     

Strong Epistatic Selection on the RNA Secondary Structure of HIV

A key question in evolutionary genomics is how populations navigate the adaptive landscape in the presence of epistasis, or interactions among loci. This problem can be directly addressed by studying the evolution of RNA secondary structures, for which there is constraint to maintain pairing between Watson-Crick (WC) sites. Replacement of a nucleotide at one site of a WC pair reduces fitness by disrupting binding, which can be restored via a compensatory replacement at the interacting site. Here, I present the first genome-scale analysis of epistasis on the RNA secondary structure of human immunodeficiency virus type 1 (HIV-1). Comparison of polymorphism frequencies at ancestrally conserved sites reveals that selection against replacements is ∼2.7 times stronger at WC than at non-WC sites, such that nearly 50% of constraint can be attributed to epistasis. However, almost all epistatic constraint is due to selection against conversions of WC pairs to unpaired (UP) nucleotides, whereas conversions to GU wobbles are only slightly deleterious. This disparity is also evident in pairs with second-site compensatory replacements; conversions from UP nucleotides to WC pairs increase median fitness by ∼4.2%, whereas conversions from GU wobbles to WC pairs only increase median fitness by ∼0.3%. Moreover, second-site replacements that convert UP nucleotides to GU wobbles also increase median fitness by ∼4%, indicating that such replacements are nearly as compensatory as those that restore WC pairing. Thus, WC peaks of the HIV-1 epistatic adaptive landscape are connected by high GU ridges, enabling the viral population to rapidly explore distant peaks without traversing deep UP valleys.     

Effects of NMR Spectral Resolution on Protein Structure Calculation

Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.     

Indicators of the Ecological Impact of Bottom-Trawl Disturbance on Seabed Communities

The Ecosystem Approach to Fisheries requires that managers take account of the environmental impacts of fishing. We develop linked state and pressure indicators that show the impact of bottom-trawling on benthic communities. The state indicator measures the proportion of an area where benthic invertebrate biomass (B) or production (P) is more than 90% of pristine benthic biomass (B _0.9) or production (P_0.9). The pressure indicator measures the proportion of the area where trawling frequency is sufficiently high to prevent reaching predicted B_0.9 or P_0.9. Time to recovery to B_0.9 and P_0.9 after trawling, depending on the habitat, was estimated using a validated size-based model of the benthic community. Based on trawling intensity in 2003, 53.5% of the southern North Sea was trawled too frequently for biomass to reach B_0.9, and 27.1% was trawled too frequently for production to reach P_0.9. As a result of bottom-trawling in 2003, in 56% of the southern North Sea benthic biomass was below B_0.9, whereas in 27% of the southern North Sea benthic production was below P_0.9. Modeled recovery times were comparable to literature estimates (2.5 to more than 6 years). The advantages of using the area with an ecological impact of trawling as a pressure indicator are that it is conceptually easy to understand, it responds quickly to changes in management action, it can be implemented at a relevant scale for fisheries management, and the necessary effort distribution data are centrally collected. One of this approach’s greatest utilities, therefore, will be to communicate to policy makers and fishing enterprises the expected medium- to long-term ecological benefits that will accrue if the frequency of trawling in particular parts of fishing grounds is reduced.     

Low Resolution Structure of Yeast Phosphoglycerate Kinase

Yeast phosphoglycerate kinase, like the same enzyme from horse muscle, has two structural lobes, reminiscent of a dimer rather than a monomer.     

Low Resolution Structure of Yeast Phosphoglycerate Mutase

The structure of phosphoglycerate mutase shows that the four chemically identical subunits are arranged in the molecule with almost perfect 222 symmetry.     

Temporal Reliability and Lateralization of the Resting-State Language Network

The neural processing loop of language is complex but highly associated with Broca''s and Wernicke''s areas. The left dominance of these two areas was the earliest observation of brain asymmetry. It was demonstrated that the language network and its functional asymmetry during resting state were reproducible across institutions. However, the temporal reliability of resting-state language network and its functional asymmetry are still short of knowledge. In this study, we established a seed-based resting-state functional connectivity analysis of language network with seed regions located at Broca''s and Wernicke''s areas, and investigated temporal reliability of language network and its functional asymmetry. The language network was found to be temporally reliable in both short- and long-term. In the aspect of functional asymmetry, the Broca''s area was found to be left lateralized, while the Wernicke''s area is mainly right lateralized. Functional asymmetry of these two areas revealed high short- and long-term reliability as well. In addition, the impact of global signal regression (GSR) on reliability of the resting-state language network was investigated, and our results demonstrated that GSR had negligible effect on the temporal reliability of the resting-state language network. Our study provided methodology basis for future cross-culture and clinical researches of resting-state language network and suggested priority of adopting seed-based functional connectivity for its high reliability.     

Decoding Multiple Sound Categories in the Human Temporal Cortex Using High Resolution fMRI

Perception of sound categories is an important aspect of auditory perception. The extent to which the brain’s representation of sound categories is encoded in specialized subregions or distributed across the auditory cortex remains unclear. Recent studies using multivariate pattern analysis (MVPA) of brain activations have provided important insights into how the brain decodes perceptual information. In the large existing literature on brain decoding using MVPA methods, relatively few studies have been conducted on multi-class categorization in the auditory domain. Here, we investigated the representation and processing of auditory categories within the human temporal cortex using high resolution fMRI and MVPA methods. More importantly, we considered decoding multiple sound categories simultaneously through multi-class support vector machine-recursive feature elimination (MSVM-RFE) as our MVPA tool. Results show that for all classifications the model MSVM-RFE was able to learn the functional relation between the multiple sound categories and the corresponding evoked spatial patterns and classify the unlabeled sound-evoked patterns significantly above chance. This indicates the feasibility of decoding multiple sound categories not only within but across subjects. However, the across-subject variation affects classification performance more than the within-subject variation, as the across-subject analysis has significantly lower classification accuracies. Sound category-selective brain maps were identified based on multi-class classification and revealed distributed patterns of brain activity in the superior temporal gyrus and the middle temporal gyrus. This is in accordance with previous studies, indicating that information in the spatially distributed patterns may reflect a more abstract perceptual level of representation of sound categories. Further, we show that the across-subject classification performance can be significantly improved by averaging the fMRI images over items, because the irrelevant variations between different items of the same sound category are reduced and in turn the proportion of signals relevant to sound categorization increases.     

Impact of Noise on Molecular Network Inference

Molecular entities work in concert as a system and mediate phenotypic outcomes and disease states. There has been recent interest in modelling the associations between molecular entities from their observed expression profiles as networks using a battery of algorithms. These networks have proven to be useful abstractions of the underlying pathways and signalling mechanisms. Noise is ubiquitous in molecular data and can have a pronounced effect on the inferred network. Noise can be an outcome of several factors including: inherent stochastic mechanisms at the molecular level, variation in the abundance of molecules, heterogeneity, sensitivity of the biological assay or measurement artefacts prevalent especially in high-throughput settings. The present study investigates the impact of discrepancies in noise variance on pair-wise dependencies, conditional dependencies and constraint-based Bayesian network structure learning algorithms that incorporate conditional independence tests as a part of the learning process. Popular network motifs and fundamental connections, namely: (a) common-effect, (b) three-chain, and (c) coherent type-I feed-forward loop (FFL) are investigated. The choice of these elementary networks can be attributed to their prevalence across more complex networks. Analytical expressions elucidating the impact of discrepancies in noise variance on pairwise dependencies and conditional dependencies for special cases of these motifs are presented. Subsequently, the impact of noise on two popular constraint-based Bayesian network structure learning algorithms such as Grow-Shrink (GS) and Incremental Association Markov Blanket (IAMB) that implicitly incorporate tests for conditional independence is investigated. Finally, the impact of noise on networks inferred from publicly available single cell molecular expression profiles is investigated. While discrepancies in noise variance are overlooked in routine molecular network inference, the results presented clearly elucidate their non-trivial impact on the conclusions that in turn can challenge the biological significance of the findings. The analytical treatment and arguments presented are generic and not restricted to molecular data sets.     

The Structure of the Two Ecological Paradigms

Ecological theory is built upon assumptions about the fundamental nature of organism-environment interactions. We argue that two mutually exclusive sets of such assumptions are available and that they have given rise to alternative approaches to studying ecology. The fundamentally different premises of these approaches render them irreconcilable with one another. In this paper, we present the first logical formalisation of these two paradigms.The more widely-accepted approach - which we label the demographic paradigm - includes both population ecology and community ecology (synecology). Demographic ecology assumes that the environment is relatively stable and that biotic processes, governed predominantly by resource availability, are the most important of ecological and evolutionary influences. Moreover, ecological processes are assumed to translate into directional selection pressures that drive significant evolutionary change on a local scale through the process of optimisation.Serious deficiencies in aspects of the demographic approach have been identified over the past few decades by various ecologists, including Gleason, Andrewartha and Birch, White, Den Boer, Strong, Simberloff, and others. Short-term evolutionary optimisation has also been seriously questioned.The development of the alternative approach (autecology) has been subverted by the prominence of demographic ecology. Moreover, it has not been recognised that autecology is underpinned by robust principles and that they are independent of the underlying demographic principles. Components of the autecological approach have been developed to some extent, but they have not been integrated with ancillary fields of study. We therefore articulate the assumptions from which autecology is derived, and use this as a basis for integrating the various spheres of autecological research.We add to the ongoing development of autecology by linking autecological understanding, in so far as it is developed, with the evolutionary justification for species' characteristics being stable in an environment that is continuously dynamic in space and time. The ecology of organisms is essentially an ongoing matching of their species-specific characteristics to the prevailing environmental factors and dynamics. We thus provide a consistent logic through the following subject areas; climate and climate change, spatial and temporal environmental heterogeneity and dynamic theory, physiology, behaviour, migration, and evolution. We demonstrate why adaptation cannot be an ongoing process, but takes place only when organisms are prevented, by incidental influences, from matching the overall dynamics of the environment.     

The Temporal Structure of Vertical Arm Movements

The present study investigates how the CNS deals with the omnipresent force of gravity during arm motor planning. Previous studies have reported direction-dependent kinematic differences in the vertical plane; notably, acceleration duration was greater during a downward than an upward arm movement. Although the analysis of acceleration and deceleration phases has permitted to explore the integration of gravity force, further investigation is necessary to conclude whether feedforward or feedback control processes are at the origin of this incorporation. We considered that a more detailed analysis of the temporal features of vertical arm movements could provide additional information about gravity force integration into the motor planning. Eight subjects performed single joint vertical arm movements (45° rotation around the shoulder joint) in two opposite directions (upwards and downwards) and at three different speeds (slow, natural and fast). We calculated different parameters of hand acceleration profiles: movement duration (MD), duration to peak acceleration (D PA), duration from peak acceleration to peak velocity (D PA-PV), duration from peak velocity to peak deceleration (D PV-PD), duration from peak deceleration to the movement end (D PD-End), acceleration duration (AD), deceleration duration (DD), peak acceleration (PA), peak velocity (PV), and peak deceleration (PD). While movement durations and amplitudes were similar for upward and downward movements, the temporal structure of acceleration profiles differed between the two directions. More specifically, subjects performed upward movements faster than downward movements; these direction-dependent asymmetries appeared early in the movement (i.e., before PA) and lasted until the moment of PD. Additionally, PA and PV were greater for upward than downward movements. Movement speed also changed the temporal structure of acceleration profiles. The effect of speed and direction on the form of acceleration profiles is consistent with the premise that the CNS optimises motor commands with respect to both gravitational and inertial constraints.     

Ecological Risk Assessment of Regions Along the Roadside of the Qinghai-Tibet Highway and Railway Based on an Artificial Neural Network

A concept model of regional risk was constructed for the characteristics of ecosystems alongside the Qinghai-Tibet highway and railway based on the MLP (Multilayer perceptron) model. Seven indices such as snow hazard, drought hazard, and landslide were selected in order to evaluate the integrated ecological risk of the ecosystems along the study area. Results show that the Qaidam montane desert zone had the greatest average risk value (4.26), followed by the Golog-Nagqu high-cold scrub meadow zone (2.80) and the East Qinghai and Qilian montane steppe zone (2.73) among the ecosystems within the six natural zones within the study region. As far as land cover types are concerned, the top three ecological risk values appear in the needle-leaved forest (4.31), desert (4.12), and land without vegetation (3.62), which are higher than those in the other seven types in the study site. Although the risk values are influenced by natural factors and human activities, they are more strongly controlled by natural factors. According to the ecological risk characteristics, the ecosystems within the study area are subdivided into four subregions, including the Qaidam basin region (high risk), the Xidatan to Damxung region (moderate risk), and the Eastern Qinghai-Qilian (slight risk) and Southern Xizang (Tibet) region (slighter risk).     

Low Resolution Structure of Glyceraldehyde 3-Phosphate Dehydrogenase

The structure of the holo enzyme shows that the four chemically identical sub-units are arranged with almost perfect 222 symmetry. There are indications, however, that the active centre regions might only be related in pairs.     

High Resolution Structure and Double Electron-Electron Resonance of the Zebrafish Voltage-dependent Anion Channel 2 Reveal an Oligomeric Population

In recent years, there has been a vast increase in structural and functional understanding of VDAC1, but VDAC2 and -3 have been understudied despite having many unique phenotypes. One reason for the paucity of structural and biochemical characterization of the VDAC2 and -3 isoforms stems from the inability of obtaining purified, functional protein. Here we demonstrate the expression, isolation, and basic characterization of zebrafish VDAC2 (zfVDAC2). Further, we resolved the structure of zfVDAC2 at 2.8 Å resolution, revealing a crystallographic dimer. The dimer orientation was confirmed in solution by double electron-electron resonance spectroscopy and by cross-linking experiments disclosing a dimer population of ∼20% in lauryldimethine amine oxide detergent micelles, whereas in lipidic bicelles a higher population of dimeric and higher order oligomers species were observed. The present study allows for a more accurate structural comparison between VDAC2 and its better-studied counterpart VDAC1.     

空间分辨率对绿潮覆盖面积、密集度卫星遥感信息提取的影响

研究表明,多源卫星数据提取的绿潮信息存在较大差异,通常认为可能的主要原因是不同卫星遥感器的的空间分辨率、过境时间差、波段设置等各不相同,但对此仍缺乏深入的研究。本文采用波段设置和过境时间完全相同、仅空间分辨率不同的四景 MERIS 全、降分辨率（300 m 和1200 m）影像,利用统一的算法（NDVI）进行绿潮信息提取,量化了空间分辨率对绿潮覆盖面积、密集度（由斑块个数、聚合度表征）卫星遥感信息提取的影响。结果表明：空间分辨率对绿潮覆盖面积卫星遥感信息提取影响显著,全、降分辨率 MERIS 影像提取的绿潮覆盖面积最大相对偏差可达67％,遥感影像的空间分辨率对绿潮面积提取结果的影响既与绿潮 NDVI 探测阈值有关,还可能与绿潮发展阶段有关。绿潮密集度卫星遥感提取结果也受遥感影像空间分辨率的影响,全分辨率 MERIS 影像提取的绿潮斑块个数为降分辨率影像的7～21倍,绿潮聚合度较降分辨率影像高15％～25％。