A diagnostic for Cox regression with discrete failure-time models

Changes in maximum likelihood parameter estimates due to deletion of individual observations are useful statistics, both for regression diagnostics and for computing robust estimates of covariance. For many likelihoods, including those in the exponential family, these delete-one statistics can be approximated analytically from a one-step Newton-Raphson iteration on the full maximum likelihood solution. But for general conditional likelihoods and the related Cox partial likelihood, the one-step method does not reduce to an analytic solution. For these likelihoods, an alternative analytic approximation that relies on an appropriately augmented design matrix has been proposed. In this paper, we extend the augmentation approach to explicitly deal with discrete failure-time models. In these models, an individual subject may contribute information at several time points, thereby appearing in multiple risk sets before eventually experiencing a failure or being censored. Our extension also allows the covariates to be time dependent. The new augmentation requires no additional computational resources while improving results.     

In situ experiments on predatory regulation of a bivalve mollusc (Dreissena polymorpha) in the Mississippi and Ohio Rivers

1. In situ exclosure experiments in the Mississippi and Ohio Rivers determined the importance of fish predation in regulating zebra mussels (Dreissena polymorpha), an increasingly important constituent of the benthic invertebrate assemblages in both rivers. 2. We evaluated the effects of predatory fish on the density, biomass and size distribution of zebra mussels in a floodplain reach of the upper Mississippi River and in a naturally constrained reach of the Ohio River. Fifty, six-sided, predator-exclusion cages and fifty ‘partial’ cages (mesh at the upstream end only) were deployed, with half the cages containing willow snags and half clay tiles suspended 12–16 cm above the bottom. A single snag or tile sample unit was removed from each cage at approximately monthly intervals from July to October 1994. Types and relative abundances of molluscivorous fish were evaluated by electrofishing near the cages in both rivers. Actual and potential recruitment of young zebra mussels on to the substrata were measured using benthic samples in both rivers and estimated (Ohio River only) from counts of planktonic veligers. 3. Zebra mussels were consumed by at least three fish species in the upper Mississippi River (mostly carp, Cyprinus carpio, and redhorse suckers, Moxostoma sp.) and five species in the Ohio River (primarily smallmouth buffalo, Ictiobus bubalus, and channel catfish, Ictalurus punctatus), but potential recruitment seemed adequate to replace consumed mussels, at least in the Ohio River. The number of juvenile benthic mussels showed no apparent link with the density of veligers soon after initiation of reproduction. Recruitment of juveniles on snags and tiles was not affected by cage type (thus eliminating a potentially confounding ‘cage effect’). 4. Fish significantly influenced mussel populations, but the impact was often greatest among low density populations in the upper Mississippi. Density and biomass differed in both rivers for cage type (higher inside cages), substratum (greater on tiles), and date (increased over time). Presumed size-selective predation was present in the Mississippi (greater on larger size classes) but was not evident in the Ohio. We hypothesize that fish in the Mississippi can more easily select larger prey from the low density populations; whereas size-selective predation on tightly packed zebra mussels in the Ohio would be difficult. 5. Although fish can reduce numbers of Dreissena polymorpha in the two rivers, current levels of fish predation seem insufficient to regulate zebra mussel densities because of its great reproductive capacity. The recent invasion of zebra mussels, however, could lead to larger fish populations while promoting greater carbon retention and overall ecosystem secondary production.     

Transcriptional profiling of CD133(+) cells in coronary artery disease and effects of exercise on gene expression

Background aimsBone marrow (BM)-derived progenitor cells are under investigation for cardiovascular repair but may be altered by disease. Our aim was to identify differences in gene expression in CD133⁺ cells of patients with coronary artery disease (CAD) and healthy controls, and determine whether exercise modifies gene expression.MethodsCD133⁺ cells were flow-sorted from 10 CAD patients and four controls, and total RNA was isolated for microarray-based gene expression profiling. Genes that were found to be differentially regulated in patients were analyzed further to investigate whether exercise had any normalizing effect on CD133⁺ cells in CAD patients following 3 months of an exercise program.ResultsImprovement in effort tolerance and increases in the number of CD133⁺ cells were observed in CAD patients after 3 months of exercise. Gene expression analysis of the CD133⁺ cells identified 82 differentially expressed genes (2-fold cut-off, 25% false-discovery rate and % present calls) in patients compared with controls, of which 59 were found to be up-regulated and 23 down-regulated. These genes were found to be involved in carbohydrate metabolism, cell cycle, cellular development and signaling, and molecular transport. Following completion of the exercise program, gene expression patterns resembled those of controls in seven of 10 patients.ConclusionsAlterations in gene expression of BM-derived CD133⁺ progenitor cells were found in CAD patients, which in part may be normalized by exercise.     

野生鸟类对禽流感爆发与传播的影响

2003—2005年高致病性禽流感在亚洲、欧洲多个国家大范围爆发,引起了全世界的关注,并将视线集中在候鸟身上。结合最近疫情,文章对野生鸟类在禽流感爆发和传播中的作用予以简要分析。     

Deep brain stimulation for movement and other neurologic disorders

Deep brain stimulation (DBS) was introduced as a treatment for patients with parkinsonism and other movement disorders in the early 1990s. The technique rapidly became the treatment of choice for these conditions, and is now also being explored for other diseases, including Tourette syndrome, gait disorders, epilepsy, obsessive-compulsive disorder, and depression. Although the mechanism of action of DBS remains unclear, it is recognized that DBS works through focal modulation of functionally specific circuits. The fact that the same DBS parameters and targets can be used in multiple diseases suggests that DBS does not counteract the pathophysiology of any specific disorder, but acts to replace pathologic activities in disease-affected brain circuits with activity that is more easily tolerated. Despite the progress made in the use of DBS, much remains to be done to fully realize the potential of this therapy. We describe some of the most active areas of research in this field, both in terms of exploration of new targets and stimulation parameters, and in terms of new electrode or stimulator designs.     

培养时间对蛹拟青霉(Paecilomyces militaris)菌丝体中代谢产物的影响

[目的]通过测定不同培养时间蛹拟青霉(Paecilomyces militaris)菌丝体中次级代谢产物的变化,分析蛹拟青霉次级代谢产物与培养时间之间的关系.[方法]液体种子接入SDAY固体培养基 ;培养温度为25℃,培养周期为9d,从第2天开始每天取样 ;用甲醇与乙酸乙酯分别提取菌丝体中次级代谢产物,离心、过滤后合并提取液,用液质联用仪进行分析,用MetaboAnalyst software软件进行数据采集分析.[结果]主成分分析结果表明供试菌株在不同培养时间内其菌丝中次级代谢产物差异显著.聚类分析结果显示,供试拟青霉对生物碱、肽类和核苷等易形成阳离子类物质的代谢物可分为前中后三个阶段.供试拟青霉对糖类和有机酸等易形成阴离子类物质的代谢主要分为前后两个阶段.差异代谢物及热图分析结果表明,在培养的第2和第3天含量显著增加的代谢产物种类较多,主要有酯类及其水解产物、细胞破坏素B和拟青霉素,以及多种尚未鉴定的含氮化合物等 ;在培养第4和第5天含量显著增加的差异代谢物质种类较少,主要有细胞破坏素A和团囊虫草素等肽类抗菌杀虫物质 ;在培养第6天至第9天含量显著增加的代谢物种类较多,除多种白僵菌交酯和细胞破坏素等肽类抗生素外,显著增加的还有多种脂肪酸、氨基酸、鼠李糖、海藻糖、脑苷脂类化合物和核黄素等物质.[结论]培养时间对蛹拟青霉菌丝中次级代谢产物的产生有显著影响.在培养初期,菌体中酯类及细胞破坏素B和拟青霉素等含氮化合物的合成旺盛.在培养中期,次生代谢物明显减少,但细胞破坏素A2和团囊虫草素等肽类抗生素的合成却仍显著增多.在培养后期,供试蛹拟青霉除代谢出多种白僵菌交酯等肽类抗生素外,还大量产生有机酸、氨基酸和海藻糖等物质.虽然在整个培养过程中都有肽类抗生素产生,但这些抗生素并不相同,同时后一阶段新的抗生素的产生常常伴随着前一阶段的抗生素减少,因此前期的抗生素可能是后期产生的抗生素的前体.     

In vitro symplasmata formation in the rice diazotrophic endophyte Pantoea agglomerans YS19

Pantoea (formerly Enterobacter) agglomerans YS19 is an endophytic diazotrophic bacterium isolated from rice (Oryza sativa cv. Yuefu) grown in temperate climatic regions in west Beijing (China). The bacterium forms aggregate structures called `symplasmata'. A symplasmatum is a multicellular aggregate structure in which several (at least two) to hundreds of individual cells tightly bind together. The studies on the symplasmata formation of YS19 showed that there were two growth stages for YS19, including the single cell stage existing before exponential growth phase and the symplasmata forming stage starting at the early stationary growth phase in liquid GY (glucose yeast extract) medium or at the end of the exponential growth phase in liquid LB (Luria-Bertani) medium. There was a correlation between symplasmata formation and bacterial growth phase. When the medium was acidified, the cell growth rate was affected by the low pH of the medium, but the time required for symplasmata formation was not influenced by it. YS19 also formed symplasmata on agar medium, where more symplasmata were formed than in liquid medium. The volume of individual constitutional cells of symplasmata was sharply decreased by more than a half in comparison with that of the single cells existing before symplasmata formation. On all the media tested, YS19 formed symplasmata in most of the cell growth phases. The genome DNA/DNA homology between P. agglomerans YS19 and type strain P. agglomerans JCM1236^T (ATCC27155^T) was determined as 90.1%, confirming its membership of P. agglomerans. In order to investigate the phylogenetic relationships of YS19 at the intraspecific, intrageneric and super-generic level, the 16S rDNA similarities between strain YS19 and 17 other strains of Pantoea and 4 representatives of the closely related genera were analyzed. All the strains of Pantoea were clustered into 5 groups, and YS19 was clustered in a unique branch. The 16S rDNA similarity between YS19 and type strain JCM1236^T was 93.9%, much lower than the generally accepted value (=97%) for members of the same species, indicating that the 16S rDNA of YS19 has a distinct molecular characteristic.     

Isolation of the lux genes from Photobacterium leiognathi and expression in Escherichia coli

Genes necessary for luminescence (lux genes) in the marine bacterium Photobacterium leiognathi, strain PL721, were isolated and expressed in Escherichia coli. A 15-kb fragment obtained from a partial digestion of PL721 DNA with HindIII was cloned into the plasmid pACYC184, resulting in the hybrid plasmid pSD721. When pSD721 was transformed into E. coli ED8654, the resulting transformants were luminous with no additions to the cells, indicating that it contained the structural genes coding for the alpha and beta subunits of luciferase (luxA and luxB), and for components involved in aldehyde biosynthesis. Hybridization analysis with luxA and luxB 32P probes confirmed the location of these two genes on the 15-kb insert. When pSD721 was transformed into four different strains of E. coli, luminescence expression varied widely in amount and in pattern. In some strains, luminescence developed like an autoinducible system, and at maximum induction was very bright, even with no addition of aldehyde, while in others, luminescence was 100-fold less, and no induction was seen. In no case was luminescence affected by shifts in temperature, osmolarity, or iron concentration. These results indicate that, while the complete lux regulon is apparently contained on the 15-kb cloned fragment, the regulation of the lux regulon in pSD721 is subject to host controls by E. coli, controls which vary widely among different E. coli strains.