A New Computational Efficient Approach for Trabecular Bone Analysis using Beam Models Generated with Skeletonized Graph Technique

Micro-finite element (FE) analysis is a well established technique for the evaluation of the elastic properties of trabecular bone, but is limited in its application due to the large number of elements that it requires to represent the complex internal structure of the bone. In this paper, we present an alternative FE approach that makes use of a recently developed 3D-Line Skeleton Graph Analysis (LSGA) technique to represent the complex internal structure of trabecular bone as a network of simple straight beam elements in which the beams are assigned geometrical properties of the trabeculae that they represent. Since an enormous reduction of cputime can be obtained with this beam modeling approach, ranging from approximately 1,200 to 3,600 for the problems investigated here, we think that the FE modeling technique that we introduced could potentially constitute an interesting alternative for the evaluation of the elastic mechanical properties of trabecular bone.     

The computationalist reformulation of the mind-body problem

Computationalism, or digital mechanism, or simply mechanism, is a hypothesis in the cognitive science according to which we can be emulated by a computer without changing our private subjective feeling. We provide a weaker form of that hypothesis, weaker than the one commonly referred to in the (vast) literature and show how to recast the mind-body problem in that setting.     

暗腹雪鸡与海兰褐鸡血液生理生化指标的比较

为了解暗腹雪鸡（Tetraogallus himalayensis）正常血液生理生化特性,本文对暗腹雪鸡21项血液生理生化指标进行了测定,并与海兰褐鸡（Gallus gallus domesticus var. Hyline）进行了比较。测定结果,暗腹雪鸡的红细胞纵径及横纵径乘积、平均红细胞容积及平均红细胞血红蛋白含量极显著大于海兰褐鸡（P<0.01）;暗腹雪鸡天冬氨酸氨基转移酶和胆固醇含量均极显著高于海兰褐鸡（P<0.01）。其他各项血液生理生化指标两禽种间之间差异不显著。实验结果表明,暗腹雪鸡血液生理生化指标与家养蛋鸡之间有一定差异,暗腹雪鸡对高原低氧环境有较强的适应性可能与其红细胞体积较大、平均红细胞容积及平均红细胞血红蛋白含量较高有一定关系。     

Feeding behaviour and performance of different populations of the black currant‐lettuce aphid,Nasonovia ribisnigri,on resistant and susceptible lettuce

When crops are bred for resistance to herbivores, these herbivores are under strong selection pressure to overcome this resistance, which may result in the emergence of virulent biotypes. This is a growing problem for crop species attacked by aphids. The Nr‐gene in lettuce confers near‐complete resistance against the black currant‐lettuce aphid, Nasonovia ribisnigri (Mosely) (Hemiptera: Aphididae). Since 2007, populations of N. ribisnigri have been reported in several locations in Europe to infest resistant lettuce varieties that possess the Nr‐gene. The objective of this study was to analyse the behaviour and level of virulence of several N. ribisnigri populations observed to have colonized Nr‐locus‐containing lettuce lines. We analysed the stylet penetration and feeding behaviour, and the performance of these N. ribisnigri populations on resistant and susceptible lettuce lines. Large variation in the degree of virulence to the Nr‐locus‐containing lettuce lines was found among populations of the Nr:1 biotype. The German population was highly virulent on the Nr‐containing resistant lettuce lines, and showed similar feeding behaviour and performance on both the susceptible and resistant lettuces. The French population from Paris was the second most virulent, though reproduction on the resistant lines was reduced. The French population from Perpignan and a population from Belgium, however, showed reduced performance and feeding rate on the resistant compared to the susceptible lettuces. The lettuce background in which the Nr‐gene is expressed influences the level of resistance to the various Nr:1 aphid populations, because the performance and feeding behaviour differed between the aphids on the cultivars (romaine lettuce) compared to the near‐isogenic lines (butterhead/iceberg lettuce). This study also shows that being able to feed on a plant not automatically implies that a population can successfully develop on that plant, because aphids showed phloem ingestion during the 8‐h recording period on resistant lettuce, but were not able to survive and reproduce on the same lettuce line.     

An Ancestral Recombination Graph for Diploid Populations with Skewed Offspring Distribution

A large offspring-number diploid biparental multilocus population model of Moran type is our object of study. At each time step, a pair of diploid individuals drawn uniformly at random contributes offspring to the population. The number of offspring can be large relative to the total population size. Similar “heavily skewed” reproduction mechanisms have been recently considered by various authors (cf. e.g., Eldon and Wakeley 2006, 2008) and reviewed by Hedgecock and Pudovkin (2011). Each diploid parental individual contributes exactly one chromosome to each diploid offspring, and hence ancestral lineages can coalesce only when in distinct individuals. A separation-of-timescales phenomenon is thus observed. A result of Möhle (1998) is extended to obtain convergence of the ancestral process to an ancestral recombination graph necessarily admitting simultaneous multiple mergers of ancestral lineages. The usual ancestral recombination graph is obtained as a special case of our model when the parents contribute only one offspring to the population each time. Due to diploidy and large offspring numbers, novel effects appear. For example, the marginal genealogy at each locus admits simultaneous multiple mergers in up to four groups, and different loci remain substantially correlated even as the recombination rate grows large. Thus, genealogies for loci far apart on the same chromosome remain correlated. Correlation in coalescence times for two loci is derived and shown to be a function of the coalescence parameters of our model. Extending the observations by Eldon and Wakeley (2008), predictions of linkage disequilibrium are shown to be functions of the reproduction parameters of our model, in addition to the recombination rate. Correlations in ratios of coalescence times between loci can be high, even when the recombination rate is high and sample size is large, in large offspring-number populations, as suggested by simulations, hinting at how to distinguish between different population models.     

Protein‐fold recognition using an improved single‐source K diverse shortest paths algorithm

Protein structure prediction, when construed as a fold recognition problem, is one of the most important applications of similarity search in bioinformatics. A new protein‐fold recognition method is reported which combines a single‐source K diverse shortest path (SSKDSP) algorithm with Enrichment of Network Topological Similarity (ENTS) algorithm to search a graphic feature space generated using sequence similarity and structural similarity metrics. A modified, more efficient SSKDSP algorithm is developed to improve the performance of graph searching. The new implementation of the SSKDSP algorithm empirically requires 82% less memory and 61% less time than the current implementation, allowing for the analysis of larger, denser graphs. Furthermore, the statistical significance of fold ranking generated from SSKDSP is assessed using ENTS. The reported ENTS‐SSKDSP algorithm outperforms original ENTS that uses random walk with restart for the graph search as well as other state‐of‐the‐art protein structure prediction algorithms HHSearch and Sparks‐X, as evaluated by a benchmark of 600 query proteins. The reported methods may easily be extended to other similarity search problems in bioinformatics and chemoinformatics. The SSKDSP software is available at http://compsci.hunter.cuny.edu/~leixie/sskdsp.html . Proteins 2016; 84:467–472. © 2016 Wiley Periodicals, Inc.     

Horticultural mineral oil influences Plum pox virus transmission by Myzus persicae

The residual activity of horticultural mineral oil (HMO) on the ability of green peach aphids, Myzus persicae (Sulzer), (GPA) to transmit Plum pox virus (PPV) to peach was measured by infection rates of detached leaves from plants sprayed with either HMO or water as a control that were inoculated using transfer of 25 viruliferous aphids per leaf at 0, 2, 4, 7, 9, 11 and 14 days after treatment (DAT). Persistent effects of HMO residue on the probing and feeding behaviours of GPA were also monitored with the electrical penetration graph (EPG) system. For glasshouse‐grown peach seedlings, the residual activity of HMO reduced PPV infection rates by more than 58% for up to 4 DAT following an initial reduction of approximately 81%. EPG recordings of GPA feeding behaviour showed that HMO significantly delayed first feeding probes and first intracellular punctures by more than 50 min without changing the ensuing stylet penetration behaviour. Applying HMO reduced virus infection rates for up to a week depending on the environmental conditions. EPG monitoring of aphid probing showed that HMO reduced the mean duration and mean number of potential drop (PD) phase feeding occurrences, compared with the water control. A reduction in the PD that has been shown to be related to the transmission of non‐persistently transmitted viruses may partly explain the reduction in PPV infection rates.     

Transforming the dilemma

How does natural selection lead to cooperation between competing individuals? The Prisoner's Dilemma captures the essence of this problem. Two players can either cooperate or defect. The payoff for mutual cooperation, R, is greater than the payoff for mutual defection, P. But a defector versus a cooperator receives the highest payoff, T, where as the cooperator obtains the lowest payoff, S. Hence, the Prisoner's Dilemma is defined by the payoff ranking T > R > P > S . In a well‐mixed population, defectors always have a higher expected payoff than cooperators, and therefore natural selection favors defectors. The evolution of cooperation requires specific mechanisms. Here we discuss five mechanisms for the evolution of cooperation: direct reciprocity, indirect reciprocity, kin selection, group selection, and network reciprocity (or graph selection). Each mechanism leads to a transformation of the Prisoner's Dilemma payoff matrix. From the transformed matrices, we derive the fundamental conditions for the evolution of cooperation. The transformed matrices can be used in standard frameworks of evolutionary dynamics such as the replicator equation or stochastic processes of game dynamics in finite populations.     

Characteristics of sugarcane white leaf phytoplasma transmission by the leafhopper Matsumuratettix hiroglyphicus

The leafhopper Matsumuratettix hiroglyphicus (Matsumura) (Hemiptera: Cicadellidae) is the most important vector of sugarcane white leaf (SCWL) phytoplasma that significantly affects the sugarcane crop in Asia. Here, we aimed to study the characteristics of SCWL phytoplasma transmission by M. hiroglyphicus. To this end, the stylet penetration activities performed during the acquisition access period (AAP) and inoculation access period (IAP) were investigated by the direct current electrical penetration graph technique and confirmed by quantitative polymerase chain reaction (qPCR). Additionally, the latent period (LP) of SCWL phytoplasma in the vector was determined by qPCR and localised by fluorescent in situ hybridisation. The results indicated that the acquisition of SCWL phytoplasma occurred during phloem ingestion (waveform D), whereas its inoculation was associated with salivation into the phloem sieve element (waveform C). The minimum AAP was 15 min and the minimum duration of phloem ingestion was 2.35 min. The minimum LP of SCWL phytoplasma in the vector was at least 14 days; then, SCWL phytoplasma moved to the salivary glands of the insect, enabling the transmission of the pathogen to the host plants. The minimum IAP for a successful transmission of SCWL phytoplasma to the host plants was 11–12 min, with a minimum duration of salivation into phloem of 1.35 min. The female vectors had higher SCWL phytoplasma copy numbers than the male vectors, and displayed faster AAP, IAP, and LP. Overall, our findings provide important information related to the feeding behaviour of M. hiroglyphicus and its effect on the transmission of SCWL phytoplasma.     

Statistical quality control of variety trial data

I propose detection criteria for identifying an abnormal or erroneous data vector provided by a single variety trial in a longer series of variety trials. The test criteria are based on the linear effects estimated separately for each studied trial using global variance components estimated from the whole series of variety trials. The criteria comprise three mutually independent test statistics. The first one is a quadratic form in the estimated fixed effects, the second one is a quadratic form in the estimated realized linear random effects not including the residual effects, and the third one is a quadratic form in the estimated realized residual effects. Under the null hypothesis defining a valid data vector, the three quadratics have independent chi2 distributions. Under natural alternative hypotheses, they have noncentral chi2 distributions. Decomposing the total variation of the data vector studied into quadratic forms due to different types of the realized linear effects intuitively justifies the resulting test criteria. The decomposition may also be used to show that the resulting tests are likelihood ratio tests. I further present computational procedures that allow us to dispense with the need for prior estimation of the linear effects.