Automatic quantitation of hybridization signals on cDNA arrays.

Large-scale hybridization of simple or complex cDNA probes to cDNA clones arrayed on high-density filters is a method frequently used to determine systematically the expression profiles of thousands of genes. Hybridization signal intensities, which reflect the level of transcription of the corresponding genes, are captured on phosphor screens with an imaging system. We describe a high-throughput system, Xdots-Reader, that performs automatic detection and quantitation of each signal on hundreds of images. Reproducibility of spot detection and quantitation within filters and between filters has been assessed in analysis of more than 850000 hybridization signals on 436 filters. The automatic analysis success was greater than 97%, with 424 of the 436 tested filters fully analyzed without any human intervention. XdotsReader is available from the Software Library at www.BioTechniques.com or at http://www. ami. univ-evry. fr/approximately tahi/XDotsReader. It runs on SUN workstations under UNIX (SunOS or Solaris) and on PC under LINUX. No particular hardware is required, and the software is compatible with any other software. It supports the main standard image formats.

The Genexpress IMAGE knowledge base of the human brain transcriptome: a prototype integrated resource for functional and computational genomics.

Expression profiles of 5058 human gene transcripts represented by an array of 7451 clones from the first IMAGE Consortium cDNA library from infant brain have been collected by semiquantitative hybridization of the array with complex probes derived by reverse transcription of mRNA from brain and five other human tissues. Twenty-one percent of the clones corresponded to transcripts that could be classified in general categories of low, moderate, or high abundance. These expression profiles were integrated with cDNA clone and sequence clustering and gene mapping information from an upgraded version of the Genexpress Index. For seven gene transcripts found to be transcribed preferentially or specifically in brain, the expression profiles were confirmed by Northern blot analyses of mRNA from eight adult and four fetal tissues, and 15 distinct regions of brain. In four instances, further documentation of the sites of expression was obtained by in situ hybridization of rat-brain tissue sections. A systematic effort was undertaken to further integrate available cytogenetic, genetic, physical, and genic map informations through radiation-hybrid mapping to provide a unique validated map location for each of these genes in relation to the disease map. The resulting Genexpress IMAGE Knowledge Base is illustrated by five examples presented in the printed article with additional data available on a dedicated Web site at the address http://idefix.upr420.vjf.cnrs.fr/EXPR++ +/ welcome.html.

[No solution for neonatal mortality in sub-saharan Africa? Evaluation and perspectives in the urban environment of Niamey, Niger]. / La mortalité néonatale sans solution en Afrique sahélienne? Bilan et perspectives en milieu urbain à Niamey, Niger.

Niger has one of the highest mortality rates of infants (222/1000) and children under five years old (318/1000), with 15% of them suffering from malnutrition. Yet, neonatal mortality was not considered as the top priority of public health in Niger, where 85 to 90% of the deliveries succeed without any medical care and 70% of the population live more than 10 kilometers from the nearest medical center. Also, in the African countries which have adopted expensive neonatal care centers following the occidental model, the lethality rate is high and maintenance is difficult. Thus, alternative strategies should be considered to reduce the neonatal mortality, according to the local possibilities. This was carried out in Niamey, the capital of Niger. A retrospective study of the activities in the pediatric and obstetric wards was carried out from 1985 to 1992. This was associated with a descriptive prospective survey of a sample of 149 pregnant women followed from the first prenatal consultation to the end of the neonatal period. Results showed that possibilities exist in Niamey to reduce neonatal mortality. The concentration of medical personnel was high compared to the rest of the country, and the health infrastructure was diversified. However, the knowledge of neonatal care was lacking. Use of prenatal care was high and deliveries at home without medical assistance concerned only 14.3% of the total births. Mortality observed in the obstetrical ward (6.7/1000) corresponded to less than a quarter of the estimated neonatal mortality (28.6/1000). Neonatal mortality in the pediatric ward was high (43.8%), predominantly on the first day of admittance (45% of the deaths), especially for the low birth weights (under 2,500 g) (62.4%). These figures underline the necessity to improve the care of the newborns and to link prenatal prevention, obstetrical care and pediatrics. The prospective survey showed that although the ratio of prenatal visits per woman was high (3.8), the quality of the care was inadequate. Correct newborn care was rare and no examination could detect or prevent complications during the short stay of less than 24 hours in the obstetrical ward. To lower the neonatal mortality, service could be improved concerning the material conditions of prenatal consultations, reorientation of prenatal consultations towards detection, correct treatment of the risk factors of neonatal mortality, obstetrical screening and care, and training of the midwives. The adoption of inexpensive measures was suggested, including the training of pediatric nurses in each maternity ward, screening and treatment of newborns at risk in small units integrated within the obstetrical ward, and the requirement of a consultation before the traditional feast of giving names, which occurs on the seventh day of life in Niger. These measures were considered as priorities before considering construction of expensive neonatal centers and assume the participation of the public health personnel and policy makers. Some of these suggestions are now being implemented.