Long-term recovery of macroinvertebrate biota in grossly polluted streams: Re-colonisation as a constraint to ecological quality

To meet targets imposed by the European Water Framework Directive (2000/60/EC) it is vital that measures to improve the status of rivers are both effective and economically viable. Achievement of such aims needs robust understanding of biological responses to changes in water quality vis-à-vis mechanisms of and constraints to the colonization of previously polluted sites. This study therefore examined the long-term chemical and biological changes in historically polluted rivers to elucidate the responses of macroinvertebrate biota to improvements in chemical water quality. For three historically polluted sites in the English Midlands, data from surveys over a period of ca. 50 years were analysed. Ammonia (NH₃) and 5-day biochemical oxygen demand (BOD₅) were used as chemical water quality indicators. Variations in the ecological recovery of the study sites were assessed using an average pollution sensitivity score (Average Score Per Taxon) and the number of taxa present (usually to family level) present in hand-net samples. Ecological recovery varied widely and was influenced by the intensity and spatial extent of the pollution and the proximity of available sources of potential colonisers. At the site most isolated from potential sources of colonizing taxa, no clean-water macroinvertebrate taxa were recorded 30 years after the major sources of pollution ceased. Where clean-water colonisers were more readily available, significant improvements in ecological quality followed within 2–5 years of the improvements in chemical quality. Macroinvertebrate communities and hence monitoring data may thus be indicative of long past conditions or of biological isolation rather than contemporaneous chemical conditions. Combined chemical and biological data were used to explore a generic model for predicting recovery rates and success. Neither BOD₅ nor NH₃ were found to provide a consistent and meaningful prediction of either average pollution tolerance of macroinvertebrate taxa or of the number of taxa present. Long-term relationships between macroinvertebrate variables and chemical water quality variables, however, were non-linear, suggesting that water quality thresholds may have to be exceeded before biological recovery can occur. Even when chemical water quality has been improved substantially, the apparent ecological status of macroinvertebrate communities may not reflect reduced pollution levels attained until adequate time to allow for re-colonisation (possibly decades) has elapsed.     

Confidence intervals for the mean of diagnostic test charge data containing zeros

In this paper, we consider the problem of interval estimation for the mean of diagnostic test charges. Diagnostic test charge data may contain zero values, and the nonzero values can often be modeled by a log-normal distribution. Under such a model, we propose three different interval estimation procedures: a percentile-t bootstrap interval based on sufficient statistics and two likelihood-based confidence intervals. For theoretical properties, we show that the two likelihood-based one-sided confidence intervals are only first-order accurate and that the bootstrap-based one-sided confidence interval is second-order accurate. For two-sided confidence intervals, all three proposed methods are second-order accurate. A simulation study in finite-sample sizes suggests all three proposed intervals outperform a widely used minimum variance unbiased estimator (MVUE)-based interval except for the case of one-sided lower end-point intervals when the skewness is very small. Among the proposed one-sided intervals, the bootstrap interval has the best coverage accuracy. For the two-sided intervals, when the sample size is small, the bootstrap method still yields the best coverage accuracy unless the skewness is very small, in which case the bias-corrected ML method has the best accuracy. When the sample size is large, all three proposed intervals have similar coverage accuracy. Finally, we analyze with the proposed methods one real example assessing diagnostic test charges among older adults with depression.     

Upper bound estimators of the population size based on ordinal models for capture‐recapture experiments

Capture‐recapture studies have attracted a lot of attention over the past few decades, especially in applied disciplines where a direct estimate for the size of a population of interest is not available. Epidemiology, ecology, public health, and biodiversity are just a few examples. The estimation of the number of unseen units has been a challenge for theoretical statisticians, and considerable progress has been made in providing lower bound estimators for the population size. In fact, it is well known that consistent estimators for this cannot be provided in the very general case. Considering a case where capture‐recapture studies are summarized by a frequency of frequencies distribution, we derive a simple upper bound of the population size based on the cumulative distribution function. We introduce two estimators of this bound, without any specific parametric assumption on the distribution of the observed frequency counts. The behavior of the proposed estimators is investigated using several benchmark datasets and a large‐scale simulation experiment based on the scheme discussed by Pledger.     

Homozygosity Haplotype and Whole-Exome Sequencing Analysis to Identify Potentially Functional Rare Variants Involved in Multiple Sclerosis among Sardinian Families

Multiple Sclerosis (MS) is a complex multifactorial autoimmune disease, whose sex- and age-adjusted prevalence in Sardinia (Italy) is among the highest worldwide. To date, 233 loci were associated with MS and almost 20% of risk heritability is attributable to common genetic variants, but many low-frequency and rare variants remain to be discovered. Here, we aimed to contribute to the understanding of the genetic basis of MS by investigating potentially functional rare variants. To this end, we analyzed thirteen multiplex Sardinian families with Immunochip genotyping data. For five families, Whole Exome Sequencing (WES) data were also available. Firstly, we performed a non-parametric Homozygosity Haplotype analysis for identifying the Region from Common Ancestor (RCA). Then, on these potential disease-linked RCA, we searched for the presence of rare variants shared by the affected individuals by analyzing WES data. We found: (i) a variant (43181034 T > G) in the splicing region on exon 27 of CUL9; (ii) a variant (50245517 A > C) in the splicing region on exon 16 of ATP9A; (iii) a non-synonymous variant (43223539 A > C), on exon 9 of TTBK1; (iv) a non-synonymous variant (42976917 A > C) on exon 9 of PPP2R5D; and v) a variant (109859349-109859354) in 3′UTR of MYO16.     

Methylerythritol phosphate pathway to isoprenoids: Kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum

The methylerythritol phosphate (MEP) pathway of Plasmodium falciparum (P. falciparum) has become an attractive target for anti-malarial drug discovery. This study describes a kinetic model of this pathway, its use in validating 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) as drug target from the systemic perspective, and additional target identification, using metabolic control analysis and in silico inhibition studies. In addition to DXR, 1-deoxy-d-xylulose 5-phosphate synthase (DXS) can be targeted because it is the first enzyme of the pathway and has the highest flux control coefficient followed by that of DXR. In silico inhibition of both enzymes caused large decrement in the pathway flux. An added advantage of targeting DXS is its influence on vitamin B1 and B6 biosynthesis. Two more potential targets, 2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase and 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, were also identified. Their inhibition caused large accumulation of their substrates causing instability of the system.     

MicroPhenoDB Associates Metagenomic Datawith Pathogenic Microbes,Microbial Core Genes,and Human Disease Phenotypes

Microbes play important roles in human health and disease. The interaction between microbes and hosts is a reciprocal relationship, which remains largely under-explored. Current computational resources lack manually and consistently curated data to connect metagenomic data to pathogenic microbes, microbial core genes, and disease phenotypes. We developed the MicroPhenoDB database by manually curating and consistently integrating microbe-disease association data. MicroPhenoDB provides 5677 non-redundant associations between 1781 microbes and 542 human disease phenotypes across more than 22 human body sites. MicroPhenoDB also provides 696,934 relationships between 27,277 unique clade-specific core genes and 685 microbes. Disease phenotypes are classified and described using the Experimental Factor Ontology (EFO). A refined score model was developed to prioritize the associations based on evidential metrics. The sequence search option in MicroPhenoDB enables rapid identification of existing pathogenic microbes in samples without running the usual metagenomic data processing and assembly. MicroPhenoDB offers data browsing, searching, and visualization through user-friendly web interfaces and web service application programming interfaces. MicroPhenoDB is the first database platform to detail the relationships between pathogenic microbes, core genes, and disease phenotypes. It will accelerate metagenomic data analysis and assist studies in decoding microbes related to human diseases. MicroPhenoDB is available through http://www.liwzlab.cn/microphenodb and http://lilab2.sysu.edu.cn/microphenodb.     

Kronecker积在分析多因子非平衡实验中的应用

以Kroneckert积和效应矩阵为工具,阐明了一种分析多因子缺值实验的严格、有效、方便的新方法。     

The Relation Between Growth of Gastrodia elata Protocorms and Fungi

Armillaria mellea penetrated protocorms from seed germination and vegetative multiplication corms of Gastrodia elata with rhizomorph. At beginning, they formed a hypha passing road and a hypha flow in the inner cells of cortex, and then, they both penetrated inside of large cells and penetrated outside of cortical cells. Gastrodia elata seeds depended on digesting Mycenct osmundicola etc gain nutrition to germinate at the stage of sexual reproduction, but its corms of vegetative multiplication must be penetrated by Armillaria mellea obtaining nutrition for normal growth at the stage of vegetative propagation.