点格局分析中边缘校正的一种新算法及其应用

在点格局分析中,通常选取一个矩形作为研究区域,而K(d)函数估计值的方差倾向于随着距离尺度的增加而增加.作为一种粗略的指导,距离尺度的最大值一般为矩形最小边长度的一半.在这种情况下,边缘校正的权重最小值为0.25.通过在校正圆上等弧长取点,用校正圆上落在研究区域之内的点数除以整个校正圆上的点数,作为边缘校正权重的近似值.点数越多,这种近似算法越接近传统的精确算法.这种近似算法不仅适用于计算研究区域为矩形的边缘校正权重,而且适用于计算研究区域为任意多边形的边缘校正权重.此外,当矩形研究区域中点事件的信息不足时,这种算法可以允许计算接近到距离尺度的上限(即矩形对角线长度的一半)对应的K(d)函数.     

Relative Efficiency of Estimators of the Mean of a Normal Distribution when Coefficient of Variation is Known

A biased but simple and consistent estimator of the parameter ? has been obtained for the normal distribution N(?, a?₂), ?>0 where a is a known constant. It is shown that the estimator is more efficient than the sample mean or any suitably chosen constant multiple of the sample standard deviation. It is also proved to be more efficient than the mimumum variance unbiased estimator among a typical class of unbiased estimators derived by RASUL KHAN (1968).     

Identification of potential drugs targeting L,L-diaminopimelate aminotransferase of Chlamydia trachomatis: An integrative pharmacoinformatics approach

Chlamydia trachomatis (C.t) is a gram-negative obligate intracellular bacteria, which is a major causative of infectious blindness and sexually transmitted diseases. A surge in multidrug resistance among chlamydial species has posed a challenge to adopt alternative drug targeting strategies. Recently, in C.t, L,L-diaminopimelate aminotransferase (CtDAP-AT) is proven to be a potential drug target due its essential role in cell survival and host nonspecificity. Hence, in this study, a multilevel precision-based virtual screening of CtDAP-AT was performed to identify potential inhibitors, wherein, an integrative stringent scoring and filtration were performed by coupling, glide docking score, binding free energy, ADMET (absorption, distribution, metabolism, and excretion, toxicity) prediction, density functional theory (quantum mechanics), and molecular dynamics simulation (molecular mechanics). On cumulative analysis, NSC_5485 (1,3-bis((7-chloro-4-quinolinyl)amino)-2-propanol) was found to be the most potential lead, as it showed higher order significance in terms of binding affinity, bonded interactions, favorable ADMET, chemical reactivity, and greater stabilization during complex formation. This is the first report on prioritization of small molecules from National Cancer Institute (NCI) and Maybridge data sets (341 519 compounds) towards targeting CtDAP-AT. Thus, the proposed compound shall aid in effective combating of a broad spectrum of C.t infections as it surpassed all the levels of prioritization.     

Genetic mapping of a new semi-dwarf gene, <Emphasis Type="Italic">sd-t(t)</Emphasis>, in indica rice and estimating of the physical distance of the mapping region

Application and functional study of dwarf and semi-dwarf genes are of great importance to both crop breeding and molecular biology. A new semi-dwarf gene, sd-t(t), non-allelic to sd-1, had been identified in an indica rice variety, Aitaiyin 2. In this study the gene was genetically mapped by using an F₂ population, which consisted of 474 individuals developed from a cross between Aitaiyin 2 and B30. The sd-t(t) gene was located between the RFLP markers R514 and R1408B with a distance of 1.1 cM to R514, and 4.5 cM to R1408B on chromosome 4. A physical contig covering the sd-t(t) mapping region was further constructed by screening a BAC library with R514 and R1408B as probes, and the physical distance between R514 and R1408B was estimated at approximately 147 kb. This result will facilitate map-based cloning of the sd-t(t) gene.     

A Robust Alternative to the Schemper–Henderson Estimator of Prediction Error

Summary In clinical applications, the prediction error of survival models has to be taken into consideration to assess the practical suitability of conclusions drawn from these models. Different approaches to evaluate the predictive performance of survival models have been suggested in the literature. In this article, we analyze the properties of the estimator of prediction error developed by Schemper and Henderson (2000 , Biometrics 56, 249–255), which quantifies the absolute distance between predicted and observed survival functions. We provide a formal proof that the estimator proposed by Schemper and Henderson is not robust against misspecification of the survival model, that is, the estimator will only be meaningful if the model family used for deriving predictions has been specified correctly. To remedy this problem, we construct a new estimator of the absolute distance between predicted and observed survival functions. We show that this modified Schemper–Henderson estimator is robust against model misspecification, allowing its practical application to a wide class of survival models. The properties of the Schemper–Henderson estimator and its new modification are illustrated by means of a simulation study and the analysis of two clinical data sets.     

Impact of elevated CO2 on soil organic matter dynamics as related to changes in aggregate turnover and residue quality

Increasing global atmospheric CO₂ concentration can potentially affect C cycling in terrestrial ecosystems. This study was conducted to assess the impact of elevated CO₂ concentration on soil organic matter and aggregate dynamics in Lolium perenne and Trifolium repens pastures. Soil samples from a 6 year old `free air CO₂ enrichment' (FACE) experiment were separated in four aggregate size classes (<53, 53–250, 250–2000, and > 2000 m). Free light fraction (i.e. particulate organic matter (POM) outside of aggregates; free LF) and intra-aggregate-POM (i.e. POM occluded within the aggregate structure; iPOM) were isolated. The distinct ¹³C-signature of the CO₂ used to raise the ambient CO₂ concentration in FACE allowed us to calculate proportions of recently incorporated C (< 6 yr) in the physically defined soil fractions. The proportion of new C increased with increasing aggregate size class, except the two largest aggregate size classes had a similar proportion of new C; this indicates a faster turnover of macroaggregates compared to microaggregates. In addition, higher proportions of new C in macroaggregates under T. repens compared to L. perenne indicate a faster macroaggregate turnover under T. repens. This faster macroaggregate turnover is hypothesized to be a result of the higher residue quality (C:N ratio) of T. repens compared to L. perenne and reduces the potential of sequestering C under elevated CO₂. In the L. perenne soil, elevated CO₂ did not significantly increase total C, but led to: (1) a 54% increase in aggregation and (2) a 40% increase in total iPOM-C. It is hypothesized that the sequestration of iPOM-C induced by elevated CO₂ in the low residue quality, L. perenne treatment, resulted from an increase in the proportion of large macroaggregates with a slow turnover.     

Enantiomeric NMR signal separation behavior and mechanism of samarium(III) and neodymium(III) complexes with (S,S)‐ethylenediamine‐N,N'‐disuccinate

Enantiomeric ¹H and ¹³C NMR signal separation behaviors of various α‐amino acids and DL‐tartarate were investigated by using the samarium(III) and neodymium(III) complexes with (S ,S )‐ethylenediamine‐N ,N' ‐disuccinate as chiral shift reagents. A relatively smaller concentration ratio of the lanthanide(III) complex to substrates was suitable for the neodymium(III) complex compared with the samarium(III) one, striking a balance between relatively greater signal separation and broadening. To clarify the difference in the signal separation behavior, the chemical shifts of β‐protons for fully bound D‐ and L‐alanine (δ_b(D) and δ_b(L)) and their adduct formation constants (K s) were obtained for both metal complexes. Preference for D‐alanine was similarly observed for both complexes, while it was revealed that the difference between the δ_b(D) and δ_b(L) values is the significant factor to determine the enantiomeric signal separation. The neodymium(III) and samarium(III) complexes can be used complementarily for higher and smaller concentration ranges of substrates, respectively, because the neodymium(III) complex gives the larger difference between the δ_b(D) and δ_b(L) values with greater signal broadening compared to the samarium(III) complex.     

Multiple testing with discrete data: Proportion of true null hypotheses and two adaptive FDR procedures

We consider multiple testing with false discovery rate (FDR) control when p values have discrete and heterogeneous null distributions. We propose a new estimator of the proportion of true null hypotheses and demonstrate that it is less upwardly biased than Storey's estimator and two other estimators. The new estimator induces two adaptive procedures, that is, an adaptive Benjamini–Hochberg (BH) procedure and an adaptive Benjamini–Hochberg–Heyse (BHH) procedure. We prove that the adaptive BH (aBH) procedure is conservative nonasymptotically. Through simulation studies, we show that these procedures are usually more powerful than their nonadaptive counterparts and that the adaptive BHH procedure is usually more powerful than the aBH procedure and a procedure based on randomized p‐value. The adaptive procedures are applied to a study of HIV vaccine efficacy, where they identify more differentially polymorphic positions than the BH procedure at the same FDR level.     

A long-term study on interactions between the Adh and αGpdh allozyme polymorphisms and the chromosomal inversion In(2L)t in a seminatural population of D. melanogaster

The Adh and αGpdh allozyme loci (both located on the second chromosome) showed considerable fluctuations in allele frequencies in a seminatural population of Drosophila melanogaster during 1972–97. Both long-term and short-term fluctuations were observed. The short-term fluctuations occurred within almost all years and comparison of allele frequencies between winters and summers showed significantly higher Adh^S (P < 0.001) and αGpdh^F (P < 0.01) allele frequencies in summers. Frequencies of these alleles were significantly positively correlated with environmental temperature, suggesting the adaptive significance of these allozyme polymorphisms. Frequency changes of the Odh locus (located on the third chromosome) showed no seasonal pattern and were not correlated with environmental temperature. Almost all short-term and long-term increases in Adh^S frequency were accompanied by a corresponding decrease in αGpdh^S frequency (r = –0.82, P < 0.001) and vice versa. Further analysis showed that gametic disequilibria between the Adh and αGpdh loci, which frequently occurred, were due to the presence of inversion In(2L)t located on the same chromosome arm and In(2L)t frequencies were positively correlated with environmental temperature. Gametic disequilibria between Adh and Odh and between Odh and αGpdh were hardly observed. Because In(2L)t is exclusively associated with the Adh^S/αGpdh^F allele combination, the observed correlated response in Adh/αGpdh allele frequencies is (at least partly) explained by hitchhiking effects with In(2L)t. This means that the adaptive value of the allozyme polymorphisms has been overestimated by ignoring In(2L)t polymorphism. Fluctuations in Adh allele frequencies are fully explained by selection on In(2L)t polymorphism, whereas we have shown that αGpdh frequency fluctuations are only partly explained by chromosomal hitchhiking, indicating the presence of selective differences among αGpdh genotypes in relation with temperature and independent of In(2L)t. Frequency fluctuations of αGpdh and In(2L)t are consistent with their latitudinal distributions, assuming that temperature is the main environmental factor varying with latitude that causes directly or indirectly these frequency distributions. However, the results of the tropical greenhouse population show no correlation of Adh (independent of In(2L)t) and Odh allele frequencies with environmental temperature, which may indicate that the latitudinal distribution in allele frequencies for these loci is not the result of selection on the F/S polymorphism in a direct way.     

Exact Results on the Inadmissibility of the Feasible Generalized Least Squares Estimator in Regression Models with Non‐Spherical Disturbances

In various guises, feasible generalized least squares (FGLS) estimation has occupied an important place in regression analysis for more than 35 years. Past studies on the characteristics of the FGLS estimators are largely based on large sample evaluations, and the important issue of admissibility remains unexplored in the case of the FGLS estimator. In this paper, an exact sufficient condition for the dominance of a Stein‐type shrinkage estimator over the FGLS estimator in finite samples based on squared error loss is given. In deriving the condition, we assume that the model's disturbance covariance matrix is unknown except for a scalar multiple. Further, for models with AR(1) disturbances, it is observed that the dominance condition reduces to one that involves no unknown parameter. In other words, in the case of AR(1) disturbances and where the condition for risk dominance is met, the FGLS estimator is rendered inadmissible under squared error loss.     

Synthesis,Antifungal Activity,DFT Study and Molecular Dynamics Simulation of Novel 4-(1,2,4-Oxadiazol-3-yl)-N-(4-phenoxyphenyl)benzamide Derivatives

In order to find novel potential antifungal agrochemicals, a series of new 4-(1,2,4-oxadiazol-3-yl)-N-(4-phenoxyphenyl)benzamide derivatives 3a – j were designed, synthesized and characterized by their ¹H - , ¹³C-NMR and HRMS spectra. The preliminary antifungal assay in vitro revealed that compounds 3a – j exhibited moderate to good antifungal activity against five plant pathogenic fungi. Especially, compound 3e presented significant antifungal activity against Alternaria solani, Botrytis cinerea and Sclerotinia sclerotiorum, superior to positive control boscalid. In the in vivo antifungal assay on tomato plants and cucumber leaves, compound 3e presented good inhibition rate against B. cinerea at 200 mg/L. Molecular dynamics simulation revealed that compound 3e could bind with the active site of class II histone deacetylase (HDAC).     

Estimating overdispersion in sparse multinomial data

Multinomial data arise in many areas of the life sciences, such as mark-recapture studies and phylogenetics, and will often by overdispersed, with the variance being higher than predicted by a multinomial model. The quasi-likelihood approach to modeling this overdispersion involves the assumption that the variance is proportional to that specified by the multinomial model. As this approach does not require specification of the full distribution of the response variable, it can be more robust than fitting a Dirichlet-multinomial model or adding a random effect to the linear predictor. Estimation of the amount of overdispersion is often based on Pearson's statistic X² or the deviance D. For many types of study, such as mark-recapture, the data will be sparse. The estimator based on X² can then be highly variable, and that based on D can have a large negative bias. We derive a new estimator, which has a smaller asymptotic variance than that based on X², the difference being most marked for sparse data. We illustrate the numerical difference between the three estimators using a mark-recapture study of swifts and compare their performance via a simulation study. The new estimator has the lowest root mean squared error across a range of scenarios, especially when the data are very sparse.     

Transgenic Brassica rapa plants over‐expressing eIF(iso)4E variants show broad‐spectrum Turnip mosaic virus (TuMV) resistance

The protein–protein interaction between VPg (viral protein genome‐linked) of potyviruses and eIF4E (eukaryotic initiation factor 4E) or eIF(iso)4E of their host plants is a critical step in determining viral virulence. In this study, we evaluated the approach of engineering broad‐spectrum resistance in Chinese cabbage (Brassica rapa) to Turnip mosaic virus (TuMV), which is one of the most important potyviruses, by a systematic knowledge‐based approach to interrupt the interaction between TuMV VPg and B. rapa eIF(iso)4E. The seven amino acids in the cap‐binding pocket of eIF(iso)4E were selected on the basis of other previous results and comparison of protein models of cap‐binding pockets, and mutated. Yeast two‐hybrid assay and co‐immunoprecipitation analysis demonstrated that W95L, K150L and W95L/K150E amino acid mutations of B. rapa eIF(iso)4E interrupted its interaction with TuMV VPg. All eIF(iso)4E mutants were able to complement an eIF4E‐knockout yeast strain, indicating that the mutated eIF(iso)4E proteins retained their function as a translational initiation factor. To determine whether these mutations could confer resistance, eIF(iso)4E W95L, W95L/K150E and eIF(iso)4E wild‐type were over‐expressed in a susceptible Chinese cabbage cultivar. Evaluation of the TuMV resistance of T₁ and T₂ transformants demonstrated that the over‐expression of the eIF(iso)4E mutant forms can confer resistance to multiple TuMV strains. These data demonstrate the utility of knowledge‐based approaches for the engineering of broad‐spectrum resistance in Chinese cabbage.     

Identification and fine mapping of a new bacterial blight resistance gene,Xa43(t), in Zhangpu wild rice (Oryza rufipogon)

• Bacterial blight (BB) is currently considered one of the most serious rice diseases and is caused by Xanthomonas oryzae pv. oryzae (Xoo). Numerous studies have shown that breeding resistant rice varieties is one of the most effective methods to prevent BB, and it is important to identify and isolate more BB resistance (R) genes from different rice resources.
• Using a map-based approach, we identified a new QTL/gene, Xa43(t), from ZhangPu wild rice, which was highly resistant to the BB isolate PX099. We performed bulked segregant analysis combined with candidate gene prediction to identify the candidate gene.
• The Xa43(t) gene was narrowed down to a 29-kb region containing four putative genes. More importantly, the candidate gene Xa43(t) did not affect the main agronomic traits of rice. We also identified a widely applicable molecular marker, namely Inde1-18, which co-segregates with the Xa43(t) gene.
• The Xa43(t) gene is a new broad-spectrum BB resistance gene without identified alleles and has good application prospects for rice disease resistance breeding.

     

Bifunctional Platinum(II) Complexes with Bisphosphonates Substituted Diamine Derivatives: Synthesis and In vitro Cytotoxicity

A series of N,N′‐dibisphosphonate‐containing 1,3‐propanediamine derivatives ( L1 – L6 ) and their corresponding dichloridoplatinum(II) complexes ( 1 – 6 ) have been synthesized and characterized by elemental analysis, ¹H‐NMR, ¹³C‐NMR, ³¹P‐NMR and HR‐MS spectra. The in vitro antitumor activities of compounds L1 – L6 and 1 – 6 were tested by WST‐8 assay with Cell Counting Kit‐8, indicating that platinum‐based complexes 1 – 6 showed higher cytotoxicity than corresponding ligands L1 – L6 against A549 and MG‐63, especially complex 2 which displayed comparable cytotoxicity to those of cisplatin and zoledronate after 48 h incubation. In addition, complexes 1 – 6 were more active in vitro on osteosarcoma cell line MG‐63 than normal osteoblast cell line hFOB 1.19. The structure‐activity relationship has been summarized based on the in vitro cytotoxicity of three series of platinum complexes from this and our previous studies. The in vitro bone affinity of platinum complexes was also tested by hydroxyapatite (HAP) chromatography in terms of capacity factor K′. Besides, in this paper, representative complex 2 , which has been proved to be a promising antitumor agent with high cytotoxicity and bone HAP binding property, was investigated for its mechanism of action producing cell death against MG‐63.     

Matrix-based concordance correlation coefficient for repeated measures

Summary In many clinical studies, Lin's concordance correlation coefficient (CCC) is a common tool to assess the agreement of a continuous response measured by two raters or methods. However, the need for measures of agreement may arise for more complex situations, such as when the responses are measured on more than one occasion by each rater or method. In this work, we propose a new CCC in the presence of repeated measurements, called the matrix‐based concordance correlation coefficient (MCCC) based on a matrix norm that possesses the properties needed to characterize the level of agreement between two p× 1 vectors of random variables. It can be shown that the MCCC reduces to Lin's CCC when p= 1. For inference, we propose an estimator for the MCCC based on U‐statistics. Furthermore, we derive the asymptotic distribution of the estimator of the MCCC, which is proven to be normal. The simulation studies confirm that overall in terms of accuracy, precision, and coverage probability, the estimator of the MCCC works very well in general cases especially when n is greater than 40. Finally, we use real data from an Asthma Clinical Research Network (ACRN) study and the Penn State Young Women's Health Study for demonstration.     

On Edge-Corrected Probability Density Function Estimators for Point Processes

FIKSEL (1988) provides an asymptotically unbiased kernel estimator for the density h_s (r) of the spherical contact distribution function of stationary and isotropic point processes. This paper proposes alternative estimators of h_s (r) for use with regular grid of locations. The existing estimator of h_s (r) and the alternatives proposed in this paper are then tested out in a simulation study.     

Molecular-Dynamics Simulations for the Density Autocorrelation Function in a Supercooled Fluid Phase

Abstract

We have re-calculated the self part of the density autocorrelation function F_s(k, t) (incoherent scattering function) for the binary soft-sphere fluid with a much longer molecular-dynamics (MD) simulation than our previous MD calculations, and with a larger system size (N = 4000) to a longer time window as well as to study a system-size dependence, if it exists. The full density autocorrelation function F(k, t) was also computed. It is found that all F(k, t)'s that we have computed in this work can be fitted over a wide range of time steps (at least over three figures of the decay) by a Williams-Watts stretched exponential function F_s(k, t) = A exp [— (t/t ₀)^β], where A, β and t ₀ are adjustable parameters. Other significant dynamical behaviours were also presented in mean square displacements and non-Gaussian parameters for highly supercooled fluids with N = 4000. The present results are compatible to our previous computations with N = 500, but a significant size dependence is suggested.