Abnormal preschool Lung Clearance Index (LCI) reflects clinical status and predicts lower spirometry later in childhood in cystic fibrosis.

BACKGROUND: Clinical and prognostic value of preschool Multiple Breath Washout (MBW) remains unclear. METHODS: Initial MBW results (Exhalyzer® D, EcoMedics AG) in preschool Cystic Fibrosis (CF) subjects (age 2-6 years) at a time of clinical stability were compared to (1) concurrent clinical status measures and (2) later spirometry outcomes. Abnormal Lung Clearance Index (LCI) was defined using published reference data (ULN for LCI 8.0). RESULTS: LCI was abnormal in 56% (28/50), with mean (SD) LCI 8.61(1.85) at age 4.71(1.3) years. Abnormal LCI was associated with higher dornase alfa use, previous positive bacterial cultures and pF508.del homozygous genotype. Later spirometry (n = 44; mean (SD) 2.3(0.5) years after MBW) demonstrated that abnormal initial preschool LCI was a strong predictor of lower later spirometry outcomes. CONCLUSION: Abnormal preschool LCI was associated with concurrent measures of clinical status and later spirometry deficits, suggesting early prognostic utility of MBW testing in this age range.

BRAF V600E mutation in early-stage multiple myeloma: good response to broad acting drugs and no relation to prognosis.

In this study, we analyzed the prevalence and clone size of BRAF V600E mutation in 209 patients with multiple myeloma and related the results to clinical phenotype, response and survival. Biopsies were screened for BRAF V600E by allele-specific real-time PCR (AS-PCR). Positive results were confirmed by immunohistochemistry, Sanger sequencing and, in three patients from whom we had stored purified myeloma cells, whole-exome sequencing. Eleven patients (5.3%) were BRAF V600E mutation positive by AS-PCR and at least one other method. The fraction of mutated cells varied from 4 to 100%. BRAF V600E-positive patients had no characteristic clinical phenotype except for significantly higher levels of serum creatinine (125 versus 86 µmol/l) Seven of eleven patients responded with at least very good partial response to alkylators, immunomodulatory agents or proteasome inhibitors. Progression-free and overall survival were similar in patients with and without the mutation. By this integrated approach, we found that patients with BRAF V600E mutation responded very well to broad acting drugs and there was no relation to prognosis in early-stage myeloma. In particular, a large mutated cell fraction did not correlate with aggressive disease.

HIV-1 and HIV-2 LTR nucleotide sequences: assessment of the alignment by N-block presentation, "retroviral signatures" of overrepeated oligonucleotides, and a probable important role of scrambled stepwise duplications/deletions in molecular evolution.

Previous analyses of retroviral nucleotide sequences, suggest a so-called "scrambled duplicative stepwise molecular evolution" (many sectors with successive duplications/deletions of short and longer motifs) that could have stemmed from one or several starter tandemly repeated short sequence(s). In the present report, we tested this hypothesis by focusing on the long terminal repeats (LTRs) (and flanking sequences) of 24 human and 3 simian immunodeficiency viruses. By using a calculation strategy applicable to short sequences, we found consensus overrepresented motifs (often containing CTG or CAG) that were congruent with the previously defined "retroviral signature." We also show many local repetition patterns that are significant when compared with simply shuffled sequences. First- and second-order Markov chain analyses demonstrate that a major portion of the overrepresented oligonucleotides can be predicted from the dinucleotide compositions of the sequences, but by no means can biological mechanisms be deduced from these results: some of the listed local repetitions remain significant against dinucleotide-conserving shuffled sequences; together with previous results, this suggests that interspersed and/or local mononucleotide and oligonucleotide repetitions could have biased the dinucleotide compositions of the sequences. We searched for suggestive evolutionary patterns by scrutinizing a reliable multiple alignment of the 27 sequences. A manually constructed alignment based on homology blocks was in good agreement with the polypeptide alignment in the coding sectors and has been exhaustively assessed by using a multiplied alphabet obtained by the promising mathematical strategy called the N-block presentation (taking into account the environment of each nucleotide in a sequence). Sector by sector, we hypothesize many successive duplication/deletion scenarios that fit our previous evolutionary hypotheses. This suggests an important duplication/deletion role for the reverse transcriptase, particularly in inducing stuttering cryptic simplicity patterns.

Detecting localized repeats in genomic sequences: a new strategy and its application to Bacillus subtilis and Arabidopsis thaliana sequences.

A new method for the search of local repeats in long DNA sequences, such as complete genomes, is presented. It detects a large variety of repeats varying in length from one to several hundred bases, which may contain many mutations. By mutations we mean substitutions, insertions or deletions of one or more bases. The method is based on counting occurrences of short words (3-12 bases) in sequence fragments called windows. A score is computed for each window, based on calculating exact word occurrence probabilities for all the words of a given length in the window. The probabilities are defined using a Bernoulli model (independent letters) for the sequence, using the actual letter frequencies from each window. A plot of the probabilities along the sequence for high-scoring windows facilitates the identification of the repeated patterns. We applied the method to the 1.87 Mb sequence of chromosome 4 of Arabidopsis thaliana and to the complete genome of Bacillus subtilis (4.2 Mb). The repeats that we found were classified according to their size, number of occurrences, distance between occurrences, and location with respect to genes. The method proves particularly useful in detecting long, inexact repeats that are local, but not necessarily tandem. The method is implemented as a C program called EXCEP, which is available on request from the authors.

Shufflet: shuffling sequences while conserving the k-let counts.

Shufflet is a program and a web-application that generates fast random shufflings of sequences (DNA, protein or others), conserving the exact k-let counts for a given k. The sequences are sampled uniformly from all the valid permutations.

Detecting periodic patterns in biological sequences.

MOTIVATION: The search for repeated patterns in DNA and protein sequences is important in sequence analysis. The rapid increase in available sequences, in particular from large-scale genome sequencing projects, makes it relevant to develop sensitive automatic methods for the identification of repeats. RESULTS: A new method for finding periodic patterns in biological sequences is presented. The method is based on evolutionary distance and 'phase shifts' corresponding to insertions and deletions. A given sequence is aligned to itself in a certain sense, trying to minimize a distance to periodicity. Relationships between different such periodicity measures are discussed. An iterative algorithm is used, and the running time is nearly proportional to the sequence length. The alignment produces a periodic consensus pattern. A 'phase score' is used to indicate a statistical significance of the periodicity. Three examples using both DNA and protein sequences illustrate how the method can be used to find patterns. AVAILABILITY: On request from the authors. CONTACT: evindc@mat nu.no; finn.drablos@unimed.sintef.no

Agriculture and behavioral science: emerging orientations.

New research orientations are emerging in behavioral science approaches to agricultural development. These new orientations are the product of both experience gained during the era that followed the Green Revolution and a response to changing goals in agricultural development that now place a greater emphasis on considerations of participation and equity. They also reflect a more general concern with the relation of technology and society growing out of efforts to understand energy and environmental problems. These orientations are characterized by a shift away from a conceptual perspective emphasizing communication to one in which technology and social organization are deemed essential in understanding and promoting agricultural development. This changing conceptual perspective is being manifested in the research process from which technology develops. Use of ecological systems approaches to the study of farming systems is increasing. The importance of understanding traditional agriculture is becoming evident and technology development methodologies are beginning to simulate farm conditions at the research center and to conduct experimental research on the farm. The appreciation of technology as a variable is leading to the development of alternative technologies adapted to different socionatural situations. As these emerging orientations become elaborated, they enhance the contributions which behavioral scientists can make to agricultural development.