Bayesian Quantile Regression for Longitudinal Studies with Nonignorable Missing Data

Summary .  We study quantile regression (QR) for longitudinal measurements with nonignorable intermittent missing data and dropout. Compared to conventional mean regression, quantile regression can characterize the entire conditional distribution of the outcome variable, and is more robust to outliers and misspecification of the error distribution. We account for the within-subject correlation by introducing a   ℓ₂   penalty in the usual QR check function to shrink the subject-specific intercepts and slopes toward the common population values. The informative missing data are assumed to be related to the longitudinal outcome process through the shared latent random effects. We assess the performance of the proposed method using simulation studies, and illustrate it with data from a pediatric AIDS clinical trial.     

Periplasmic superoxide dismutases in Aquaspirillum magnetotacticum

Aquaspirillum magnetotacticum MS-1 cells cultured microaerobically (dissolved O₂ tension 1% of saturation), expressed proteins with superoxide dismutase (SOD) activity. The majority (roughly 95%) of total cell superoxide dismutase activity was located in the cell periplasm with little or no activity in the cell cytoplasm. Irontype SOD (FeSOD) contributed 88% of the total activity activity detected, although a manganese-type SOD (MnSOD) was present in the periplasm as well. Cells cultured at a higher dissolved O₂ tension (10% of saturation) expressed increased activity of the MnSOD relative to that of the FeSOD.     

Parametric and Nonparametric Analyses of Repeated Ordinal Categorical Data

We compare two models for the analysis of repeated ordinal categorical data: the classical parametric model for means of scores assigned to the categories of the response variable and a nonparametric model based on relative effects derived from the marginal distribution functions of the response. An example in the field of Dentistry is used to illustrate and to compare the models. We also consider a simulation study to evaluate the type‐I error rates and the power of tests under both models in a balanced design setup. The simulation results suggest that both approaches behave similarly for equally spaced scores but may perform differently otherwise. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Effect of Repeated Convulsive Seizures on Brain γ-Aminobutyric Acid Metabolism in Three Sublines of Mice Differing by Their Response to Acoustic Stimulations

The turnover rates and steady-state levels of gamma-aminobutyric acid (GABA) have been determined in 15 brain areas of three sublines of inbred mice differing in their susceptibility to audiogenic seizures: Rb3, which is seizure resistant; Rb2, which develops clonic seizures; and Rb1, which develops tonic-clonic seizures. In the Rb1 subline, GABA steady-state levels are lower than in the Rb3 subline in three of the 15 areas examined (cerebellum, anterior colliculus, and amygdala), whereas in the Rb2 subline, steady-state levels are either higher (posterior colliculus and hippocampus) or lower (amygdala) than in the Rb3 subline. GABA turnover rates differ in three brain areas in Rb1 (amygdala, raphe, and hypothalamus) and in a single area (amygdala) in Rb2 when compared with Rb3. Only one area has similar variations of GABA turnover rate and steady-state levels in the two susceptible sublines: the amygdala. After 2 weeks of repeated auditory stimulations (two times a day, 8,000 Hz, 100 dB), additional alterations in GABA metabolism are observed: mainly large increases in GABA turnover rates (from 40% to three- to fourfold). The Rb2 subline displays a greater number of alterations (increases of turnover rates in pons, cerebellum, anterior and posterior colliculus, amygdala, olfactory bulbs and tubercles, striatum, and frontal cortex) than the Rb1 subline (increases of turnover rates in cerebellum, posterior colliculus, olfactory tubercles, raphe, and frontal cortex and a decrease in hypothalamus). In the Rb3 subline, increases of the turnover rate in amygdala and olfactory tubercles and decreases in olfactory bulbs and hippocampus are observed.(ABSTRACT TRUNCATED AT 250 WORDS)     

An unusual wheat insertion sequence (WIS1) lies upstream of an alpha-amylase gene in hexaploid wheat, and carries a "minisatellite" array

Summary Comparison of the 5′ flanking regions of three α-amylase genes from chromosome 6B of hexaploid wheat by heteroduplex and sequence analysis revealed the presence of a 1.6 kb stem-loop insertion sequence (WIS1) in one of them. Polymorphism among hexaploid wheat varieties suggests the relatively recent insertion/excision of this sequence from its present position. The complete sequence of the stem-loop insertion shows that it has many of the features found in transposable elements, including target site duplication and terminal inverted repeats. One unusual feature is a tandem array of direct repeats comprising a wheat “minisatellite” sequence. Both the insertion sequence and the minisatellite are found at multiple locations in the wheat genome, but the functional significance of their association in WIS1 is unknown. The minisatellite arrays share a common core structure, and long arrays are polymorphic between different hexaploid varieties.     

A BamHI family of highly repeated DNA sequences of Nicotiana tabacum

Summary HRS60.1, a monomer unit (184 bp) of a highly repeated nuclear DNA sequence of Nicotiana tabacum, has been cloned and sequenced. Following BamHI digestion of tobacco DNA, Southern hybridization with HRS60.1 revealed a ladder of hybridization bands corresponding to multiples of the basic monomer unit. If the tobacco DNA was digested with restriction endonucleases which have no target site in HRS60.1, the larger part of DNA homologous to HRS60.1 remained as uncleaved relic DNA. These results suggest a tandem arrangement of this DNA repeat unit. Four other clones of tobacco nuclear DNA cross-hybridized with HRS60.1, thus forming a HRS60-family. Sequencing their inserts has shown their strong mutual homology. HRS60-family comprised about 2% of the nuclear genome of N. tabacum. Computer comparisons with other tandem plant-repeated DNA sequences could not detect any other homologous sequence.     

A molecular and cytogenetic survey of major repeated DNA sequences in tomato (Lycopersicon esculentum)

Summary The major families of repeated DNA sequences in the genome of tomato (Lycopersicon esculentum) were isolated from a sheared DNA library. One thousand clones, representing one million base pairs, or 0.15% of the genome, were surveyed for repeated DNA sequences by hybridization to total nuclear DNA. Four major repeat classes were identified and characterized with respect to copy number, chromosomal localization by in situ hybridization, and evolution in the family Solanaceae. The most highly repeated sequence, with approximately 77000 copies, consists of a 162 bp tandemly repeated satellite DNA. This repeat is clustered at or near the telomeres of most chromosomes and also at the centromeres and interstitial sites of a few chromosomes. Another family of tandemly repeated sequences consists of the genes coding for the 45 S ribosomal RNA. The 9.1 kb repeating unit in L. esculentum was estimated to be present in approximately 2300 copies. The single locus, previously mapped using restriction fragment length polymorphisms, was shown by in situ hybridization as a very intense signal at the end of chromosome 2. The third family of repeated sequences was interspersed throughout nearly all chromosomes with an average of 133 kb between elements. The total copy number in the genome is approximately 4200. The fourth class consists of another interspersed repeat showing clustering at or near the centromeres in several chromosomes. This repeat had a copy number of approximately 2100. Sequences homologous to the 45 S ribosomal DNA showed cross-hybridization to DNA from all solanaceous species examined including potato, Datura, Petunia, tobacco and pepper. In contrast, with the exception of one class of interspersed repeats which is present in potato, all other repetitive sequences appear to be limited to the crossing-range of tomato. These results, along with those from a companion paper (Zamir and Tanksley 1988), indicate that tomato possesses few highly repetitive DNA sequences and those that do exist are evolving at a rate higher than most other genomic sequences.     

Repeated larval diapause and diapause-free development in geographic strains of the burnet moth Zygaena trifolii Esp. (Insecta,Lepidoptera)

Summary Zygaena trifolii is a long-day insect with temperature-dependent photoperiodic responses. All larval instars are sensitive to photoperiod; however, diapause may occur at the third larval stage or any subsequent larval instars. There were quantitative differences within populations in the threshold photoperiod for diapause induction. The diapause response was polymorphic, so that larvae might enter diapause at different instars under the same culture conditions. Furthermore, decreasing photoperiods below a critical daylength shifted the diapausing instar towards earlier stages. Geographic strains of Z. trifolii showed discontinuous clinal variation. Near the northern edge of the distribution [Cologne (Köln), FRG], there is first an obligatory diapause, mainly during early instars, and additional facultative (repeat) diapauses during later larval instars in subsequent years. In the southern part of its distribution, this burnet moth is partially bivoltine in the field with a facultative first developmental arrest and a decreased capacity for repeated diapause (Valencia, Spain; Marseille, France). Further experiments indicated that the photoperiodically controlled diapause reaction is also influenced by the number of photoperiodic cycles experienced during the period spent in each larval instar, which depends on temperature. The adaptive significance of obligatory and facultative repeated diapause, varying even among the offspring of a single female, may be to buffer the populations against the more extreme and, from year to year, unpredictable fluctuations in climatic conditions at the northern edge of the distribution.Abbreviations L₃ feeding 3rd larval instar - L₄D diapausing 4th larval instar - L₅D2 repeat-diapausing larval instar with second diapause at the 5th larval stage - LD light-dark cycle - KT shortday conditions (e.g. LD 8:16) - LT long-day conditions (e.g. LD 16:8)     

磁场对大豆共生固氮的效应

恒定磁场处理慢生大豆根瘤菌“005”和接种后的大豆植株,发现磁场可以提高根瘤的固氮活性。在一定的磁场强度(70—100mT)下,固氮活性平均可以提高4—5倍,植株的结瘤数和根瘤重量平均提高2—3倍。从这样的根瘤中所分离出的根瘤菌,由慢生型转变成快生型,在100植株中有17株的根瘤分离出快生菌。生长世代时间和培养溶液中的pH值与慢生型不同,而与快生型相同。