Interacting Epidemics and Coinfection on Contact Networks

The spread of certain diseases can be promoted, in some cases substantially, by prior infection with another disease. One example is that of HIV, whose immunosuppressant effects significantly increase the chances of infection with other pathogens. Such coinfection processes, when combined with nontrivial structure in the contact networks over which diseases spread, can lead to complex patterns of epidemiological behavior. Here we consider a mathematical model of two diseases spreading through a single population, where infection with one disease is dependent on prior infection with the other. We solve exactly for the sizes of the outbreaks of both diseases in the limit of large population size, along with the complete phase diagram of the system. Among other things, we use our model to demonstrate how diseases can be controlled not only by reducing the rate of their spread, but also by reducing the spread of other infections upon which they depend.     

白灵菇液体发酵条件研究初报

通过对白灵菇液体摇瓶发酵的研究 ,确定了适宜白灵菇液体培养的条件为 :装液量为 15 0ml(5 0 0ml)、接种量为 10 %、pH值为 5 .0～ 6 .0、CMC浓度为 0 .4 % ;并通过发酵罐培养 ,研究其发酵过程中的pH值、溶氧值 (DO)的变化。     

Cable Theory for Finite Length Dendritic Cylinders with Initial and Boundary Conditions

The cable equation is solved in the Laplace transform domain for arbitrary initial and boundary conditions. The cable potential is expressed directly in terms of the impedance of the terminations and the cable electrotonic length. A computer program is given to invert the transform. Numerical solutions may be obtained for any particular model by inserting expressions describing the terminations and parameter values into the program, without further computation by the modeler. For a finite length cable, sealed at one end, the solution is expressed in terms of the ratio of the termination impedance to the impedance of the finite length cable, a generalization of the steady-state conductance ratio. Analysis of a model of a soma with several primary dendrites shows that the dendrites may be lumped into one equivalent cylinder if they have the same electrotonic length, even though they may vary in diameter. Responses obtained under voltage clamp are conceptually predictable from measurements made under current clamp, and vice versa. The equalizing time constants of an infinite series expression of the solution are the negative reciprocals of the roots of the characteristic equation. Examination of computed solutions shows that solutions which differ theoretically may be indistinguishable experimentally.     

Transmission Dynamics of an SIS Model with Age Structure on Heterogeneous Networks

Infection age is often an important factor in epidemic dynamics. In order to realistically analyze the spreading mechanism and dynamical behavior of epidemic diseases, in this paper, a generalized disease transmission model of SIS type with age-dependent infection and birth and death on a heterogeneous network is discussed. The model allows the infection and recovery rates to vary and depend on the age of infection, the time since an individual becomes infected. We address uniform persistence and find that the model has the sharp threshold property, that is, for the basic reproduction number less than one, the disease-free equilibrium is globally asymptotically stable, while for the basic reproduction number is above one, a Lyapunov functional is used to show that the endemic equilibrium is globally stable. Finally, some numerical simulations are carried out to illustrate and complement the main results. The disease dynamics rely not only on the network structure, but also on an age-dependent factor (for some key functions concerned in the model).     

Structure and Disorder in an Unfolded State under Nondenaturing Conditions from Ensemble Models Consistent with a Large Number of Experimental Restraints

Obtaining detailed structural models of disordered states of proteins under nondenaturing conditions is important for a better understanding of both functional intrinsically disordered proteins and unfolded states of folded proteins. Extensive experimental characterization of the drk N-terminal SH3 domain unfolded state has shown that, although it appears to be highly disordered, it possesses significant nonrandom secondary and tertiary structure. In our previous attempts to generate structural models of the unfolded state using the program ENSEMBLE, we were limited by insufficient experimental restraints and conformational sampling. In this study, we have vastly expanded our experimental restraint set to include ¹H-¹⁵N residual dipolar couplings, small-angle X-ray scattering measurements, nitroxide paramagnetic relaxation enhancements, O₂-induced ¹³C paramagnetic shifts, hydrogen-exchange protection factors, and ¹⁵N R₂ data, in addition to the previously used nuclear Overhauser effects, amino terminal Cu²⁺-Ni²⁺ binding paramagnetic relaxation enhancements, J-couplings, chemical shifts, hydrodynamic radius, and solvent accessibility restraints. We have also implemented a new ensemble calculation methodology that uses iterative conformational sampling and seeks to calculate the simplest possible ensemble models. As a result, we can now generate ensembles that are consistent with much larger experimental data sets than was previously possible. Although highly heterogeneous and having broad molecular size distributions, the calculated drk N-terminal SH3 domain unfolded-state ensembles have very different properties than expected for random or statistical coils and possess significant nonnative α-helical structure and both native-like and nonnative tertiary structure.     

The Effect of Changing Sowing Date on Leaf Structure and Gas Exchange Characteristics of Wheat Flag Leaves Grown under Mediterranean Climate Conditions

Comparisons of leaf structure and gas exchange characteristicshave been made between flag leaves of four old genotypes ofcultivated tetraploid wheats and three current varieties ofhexaploid Triticum aestivum grown under Mediterranean climateconditions. For some genotypes the effect of varying the sowingdate was investigated. In the hexaploid wheat Kolibri the effectof sowing date on leaf structure and gas exchange of the penultimateleaf was also studied. Flag leaves differed significantly in photosynthetic capacityand leaf structure characteristics between genotypes, withineach ploidy level. When the mean values for each ploidy levelwere considered, there were no significant differences in valuesfor photosynthesis per unit leaf area, stomatal conductance,intercellular CO₂ concentration, residual CO₂ conductance andwater-use efficiency between the tetraploid and hexaploid wheatssown on the same date. When comparisons were made of leaf structurethe only significant differences observed were in adaxial andabaxial stomatal frequencies and leaf area: mean values of theseparameters were higher in tetraploid than in hexaploid wheats. The changes in leaf structure in response to varying sowingdate were significant and followed the same pattern in all thegenotypes studied: a xeromorphic adaptation was observed inlater sowings in response to warmer climate. Such structuralchanges affected some gas exchange characteristics. For example,the area of flag leaves decreased by 60% in the hexaploid wheatKolibri from first to last sowing, which led to a transpirativeloss of 49% per single leaf, in spite of the fact that transpirationrate per unit leaf area increased by 26%. Penultimate leavesof cv. Kolibri followed a fairly similar adaptive pattern inlater sowings as compared with flag leaves. The adaptive significanceof changes in leaf structure and gas exchange characteristicswith varying sowing date under Mediterranean climate conditionsis discussed. Key words: Photosynthesis, leaf structure, wheat     

Dynamics and Control of Diseases in Networks with Community Structure

The dynamics of infectious diseases spread via direct person-to-person transmission (such as influenza, smallpox, HIV/AIDS, etc.) depends on the underlying host contact network. Human contact networks exhibit strong community structure. Understanding how such community structure affects epidemics may provide insights for preventing the spread of disease between communities by changing the structure of the contact network through pharmaceutical or non-pharmaceutical interventions. We use empirical and simulated networks to investigate the spread of disease in networks with community structure. We find that community structure has a major impact on disease dynamics, and we show that in networks with strong community structure, immunization interventions targeted at individuals bridging communities are more effective than those simply targeting highly connected individuals. Because the structure of relevant contact networks is generally not known, and vaccine supply is often limited, there is great need for efficient vaccination algorithms that do not require full knowledge of the network. We developed an algorithm that acts only on locally available network information and is able to quickly identify targets for successful immunization intervention. The algorithm generally outperforms existing algorithms when vaccine supply is limited, particularly in networks with strong community structure. Understanding the spread of infectious diseases and designing optimal control strategies is a major goal of public health. Social networks show marked patterns of community structure, and our results, based on empirical and simulated data, demonstrate that community structure strongly affects disease dynamics. These results have implications for the design of control strategies.     

A Stochastic Model for BOD and DO with Random Initial Conditions and Distance Dependent Velocity

A random differential equation arises in stream pollution models when the initial conditions are stochastic and the stream velocity is distance dependent. The mean squared solution gives the biochemical oxygen demand (BOD) and the dissolved oxygen (DO) at any distance downstream from the pollution source. The probability density function and some of the moments of the BOD and DO are obtained, thus completely characterizing the BOD and DO process. An example illustrates the results and compares them with previous ones.     

改善植物大规模组织培养条件的研究进展

植物组织培养技术具有巨大的应用价值,传统组织培养存在许多缺点,许多学者从培养基、培养容器、环境条件(光照、气体等)进行了研究和改善,取得了一定的成效。综述了这些方面的研究进展。     

Structure Identification of Uncertain Complex Networks Based on Anticipatory Projective Synchronization

This paper investigates a method to identify uncertain system parameters and unknown topological structure in general complex networks with or without time delay. A complex network, which has uncertain topology and unknown parameters, is designed as a drive network, and a known response complex network with an input controller is designed to identify the drive network. Under the proposed input controller, the drive network and the response network can achieve anticipatory projective synchronization when the system is steady. Lyapunov theorem and Barbǎlat’s lemma guarantee the stability of synchronization manifold between two networks. When the synchronization is achieved, the system parameters and topology in response network can be changed to equal with the parameters and topology in drive network. A numerical example is given to show the effectiveness of the proposed method.     

Structure of Protein Interaction Networks and Their Implications on Drug Design

Protein-protein interaction networks (PINs) are rich sources of information that enable the network properties of biological systems to be understood. A study of the topological and statistical properties of budding yeast and human PINs revealed that they are scale-rich and configured as highly optimized tolerance (HOT) networks that are similar to the router-level topology of the Internet. This is different from claims that such networks are scale-free and configured through simple preferential-attachment processes. Further analysis revealed that there are extensive interconnections among middle-degree nodes that form the backbone of the networks. Degree distributions of essential genes, synthetic lethal genes, synthetic sick genes, and human drug-target genes indicate that there are advantageous drug targets among nodes with middle- to low-degree nodes. Such network properties provide the rationale for combinatorial drugs that target less prominent nodes to increase synergetic efficacy and create fewer side effects.     

A Novel Top-k Strategy for Influence Maximization in Complex Networks with Community Structure

In complex networks, it is of great theoretical and practical significance to identify a set of critical spreaders which help to control the spreading process. Some classic methods are proposed to identify multiple spreaders. However, they sometimes have limitations for the networks with community structure because many chosen spreaders may be clustered in a community. In this paper, we suggest a novel method to identify multiple spreaders from communities in a balanced way. The network is first divided into a great many super nodes and then k spreaders are selected from these super nodes. Experimental results on real and synthetic networks with community structure show that our method outperforms the classic methods for degree centrality, k-core and ClusterRank in most cases.     

放射形土壤杆菌突变株发酵条件及其可溶性胞外多糖结构的研究

目的:提高放射形土壤杆菌X1166101突变株发酵生产可溶性胞外多糖的产量,并探明所产多糖的化学结构。方法:采用单因素分析的方法对X1166101株的发酵产多糖条件进行了优化,采用色谱分析与波谱分析相结合的方法对多糖的结构进行了初步研究。结果:放射形土壤杆菌X1166101株产糖的最佳发酵条件为温度30℃、pH7.0、转速200r/min、装液量100mL(500mL摇瓶)、接种量8%,多糖产量达24.2g/L。该多糖是由葡萄糖单体以β-1,6糖苷键连接而成的带有丙酮酸分枝的高聚物。结论:放射形土壤杆菌X1166101突变株所产多糖极有可能是一种新型的细菌胞外多糖,具有较好的研发价值。     

125 Changing Environmental Conditions and Changes in the Abundances of Rocky Intertidal Seaweeds on Southern California Shores

In a recent study of the North American biogeography of the red algae genus Hildenbrandia , the presence of group I introns were noted in the nuclear SSU rRNA gene of the marine species H. rubra (Hildenbrandiales). Group I introns in the nuclear encoded rRNAs have been previously reported in the Hildenbrandiales as well as the Bangiales. All reported introns within the red algae have been identified as belonging to the IC1 subclass and occur at two insertion sites in the nuclear small subunit rRNA (516 and 1506). However, an unclassified intron was discovered at position 989 in the nuclear SSU rRNA gene of a collection of H. rubra from British Columbia, Canada. We have determined that the intron is a member of the IE subclass and this is the first report of an IE intron and an intron in position 989 in the red algae. Phylogenetic analyses of the intron sequences reveal a close relationship between this group IE intron and similar ascomycete and basidiomycete fungal IE introns in the nuclear SSU rRNA genes at positions 989 and 1199. In addition, a common unique helix (structural signature) in the P13 domain of the Hildenbrandia intron and those of the fungi at the 989 and 1199 IE positions in the nuclear SSU rRNA gene also indicates a close relationship. Hence, this study provides evidence for a possible lateral transfer of the IE intron in position 989 between fungal and red algal nuclear SSU rRNA genes.     

Gene Networks Underlying Convergent and Pleiotropic Phenotypes in a Large and Systematically-Phenotyped Cohort with Heterogeneous Developmental Disorders

Readily-accessible and standardised capture of genotypic variation has revolutionised our understanding of the genetic contribution to disease. Unfortunately, the corresponding systematic capture of patient phenotypic variation needed to fully interpret the impact of genetic variation has lagged far behind. Exploiting deep and systematic phenotyping of a cohort of 197 patients presenting with heterogeneous developmental disorders and whose genomes harbour de novo CNVs, we systematically applied a range of commonly-used functional genomics approaches to identify the underlying molecular perturbations and their phenotypic impact. Grouping patients into 408 non-exclusive patient-phenotype groups, we identified a functional association amongst the genes disrupted in 209 (51%) groups. We find evidence for a significant number of molecular interactions amongst the association-contributing genes, including a single highly-interconnected network disrupted in 20% of patients with intellectual disability, and show using microcephaly how these molecular networks can be used as baits to identify additional members whose genes are variant in other patients with the same phenotype. Exploiting the systematic phenotyping of this cohort, we observe phenotypic concordance amongst patients whose variant genes contribute to the same functional association but note that (i) this relationship shows significant variation across the different approaches used to infer a commonly perturbed molecular pathway, and (ii) that the phenotypic similarities detected amongst patients who share the same inferred pathway perturbation result from these patients sharing many distinct phenotypes, rather than sharing a more specific phenotype, inferring that these pathways are best characterized by their pleiotropic effects.