Detection of recurrence of large-bowel carcinoma by radioimmunoassay of circulating carcinoembryonic antigen (C.E.A.).

The usefulness and limitations of the carcinoembryonic antigen (C.E.A.) radioimmunoassay for the evaluation of tumour resection and for the detection of tumour relapse were studied in patients with large-bowel carcinoma. The level of plasma-C.E.A. was determined before any treatment in a group of 101 patients with histologically proven adenocarcinoma of the colon and rectum. 71% of all patients and 63% of cases with localised tumour (Dukes A and B) had a preoperative C.E.A. value of 5 ng. per ml. or higher. This limit was reached by only 1 of 90 apparently healthy, non-smoking blood-donors. Among 45 patients for whom a complete tumour resection was reported, all patients except 5 showed a drop of C.E.A. to normal values after surgery. The 5 patients whose C.E.A. did not fall to below 5 ng. per ml. showed a subsequent rise in C.E.A. level and were all found later to have a tumour relapse. The results indicate that an incomplete drop of circulating C.E.A. level one month after surgery has a bad prognostic significance. 22 of these patients were followed up by repeated C.E.A. radioimmunoassay for several months after surgery. 8 showed a progressive increase in C.E.A. levels preceding clinical diagnosis of tumour relapse by two to ten months. 6 other patients showed a moderate increase in C.E.A. levels, suggesting a tumour relapse not yet clinically detectable. The remaining 8 patients showed no increase in C.E.A. level above 5 ng. per ml. and no clinical symptoms of relapse. The results demonstrate that relapses of colon and rectum carcinoma can be detected by increased C.E.A. levels months before the appearance of any clinical evidence.

Pore size distribution in soils irrigated with sodic water and wastewater

Soil porosity, especially pore size distribution, is an important controlling factor for soil infiltration, hydraulic conductivity, and water retention. This study aimed to verify the effect of secondary-treated domestic wastewater (STW) on the porosity of a sandy loam Oxisol in the city of Lins, state of São Paulo, Brazil. The two-year experiment was divided into three plots: soil cultivated with corn and sunflower and irrigated with STW, soil cultivated and irrigated with sodic groundwater, and non-irrigated and non-cultivated soil (control). At the end of the experiment, undisturbed core samples were sampled from 0 to 2.0 m (8 depths). The water retention curves were obtained by tension plates and Richard's pressure plate apparatus, and the pore size distribution inferred from the retention curves. It was found that irrigation with treated wastewater and treated groundwater led to a decrease in microporosity (V MI), defined as the pore class ranging from 0.2 to 50 μm diameter. On the other hand, a significant increase in cryptoporosity (V CRI) (< 0.2 μm) was identified throughout the soil profile. The presence of Na+ in both waters confirmed the role of this ion on pore size distribution and soil moisture (higher water retention).

Irrigation with domestic wastewater: a multivariate analysis of main soil changes

Irrigation with treated domestic sewage wastewater (TSE) is an agricultural practice to reduce water requirements of agroecossystems and the nutrient load impact on freshwaters, but adverse effects on soil chemical (salinization, sodification, etc.) and soil physical properties (alteration in soil porosity and hydraulic conductivity, etc.) have been reported. This study aimed to define some relationships among these changes in an Oxisol using multivariate analysis. Corn (Zea mays L.) and sunflower (Helianthus annuus L.) were grown for two years, irrigated with TSE. The following soil properties were determined: Ca2+; Mg2+; Na+; K+ and H + Al contents, cationic exchangeable capacity (CEC), sum of bases (SB), base saturation (V), texture (sand, silt and clay), macro-, micro-, and cryptoporosity (V MA, V MI and V CRI), water content at soil saturation (θS) and at field capacity (θFC), residual water content (θR), soil bulk density (d s), water dispersed clay (WDC) and saturated hydraulic conductivity (K SAT). Factor analysis revealed the following six principal factors: Fine Porosity (composed of Na+; K+; WDC, θR, θRFC, and V CRI); Large Porosity (θS, d s, V MA, Vs); Soil CEC (Ca2+; Mg2+; CEC, SB, V); Soil Acidity (H + Al); and Soil Texture (factors 5 and 6). A dual pore structure appears clearly to the factors 1 and 2, with an apparent relationship between fine porosity and the monovalent cations Na+ and K+. The irrigation (with potable sodic tap water or sewage wastewater) only had a significant effect on Fine Porosity and Large Porosity factors, while factors 3 and 4 (Soil CEC and Soil Acidity) were correlated with soil depth. The main conclusion was a shift in pore distribution (large to fine pores) during irrigation with TSE, which induces an increase of water storage and reduces the capacity of drainage of salts.

Flank stability and processes off the western Canary Islands: a review from El Hierro and La Palma

The morphological characterisation of the western submarine island flanks of El Hierro and La Palma differentiates four type-zones that may give new insights into the evolution of oceanic island slopes. The different type-zones result from the interplay between constructive volcanic processes, hemipelagic settling and volcano collapses. The latter results in massive debris avalanche deposits, which form large volcaniclastic aprons. In most cases, the headwall scarps are clearly exposed on the emerged part of the islands. The events that occurred in the youngest and westernmost islands of El Hierro and La Palma have vertical runouts exceeding 6,000 m and volumes that can reach several hundred km3. The landslide frequency for the entire Canaries is one major event per 90 ka. Triggering mechanisms are closely related to magmatic processes. The increase in the shear stress is directly linked with the forceful intrusion of magma along ridge-rift systems, while in the western Canary Islands it seems that the main process reducing shear resistance may be related to the rise in pore pressure due to hydrothermal circulation.

Current-density-functional approach to large quantum dots in intense magnetic fields

Within current-density-functional theory, we have studied a quantum dot made of 210 electrons confined in a disk geometry. The ground state of this large dot exhibits some features as a function of the magnetic field (Beta) that can be attributed in a clear way to the formation of compressible and incompressible states of the system. The orbital and spin angular momenta, the total energy, ionization and electron chemical potentials of the ground state, as well as the frequencies of far-infrared edge modes are calculated as a function of Beta, and compared with available experimental and theoretical results.

Large scale assessment of regulatory evolution and transcriptome complexity in mammals

AbstractIn addition to genetic changes affecting the function of gene products, changes in gene expression have been suggested to underlie many or even most of the phenotypic differences among mammals. However, detailed gene expression comparisons were, until recently, restricted to closely related species, owing to technological limitations. Thus, we took advantage of the latest technologies (RNA-Seq) to generate extensive qualitative and quantitative transcriptome data for a unique collection of somatic and germline tissues from representatives of all major mammalian lineages (placental mammals, marsupials and monotremes) and birds, the evolutionary outgroup.In the first major project of my thesis, we performed global comparative analyses of gene expression levels based on these data. Our analyses provided fundamental insights into the dynamics of transcriptome change during mammalian evolution (e.g., the rate of expression change across species, tissues and chromosomes) and allowed the exploration of the functional relevance and phenotypic implications of transcription changes at a genome-wide scale (e.g., we identified numerous potentially selectively driven expression switches).In a second project of my thesis, which was also based on the unique transcriptome data generated in the context of the first project we focused on the evolution of alternative splicing in mammals. Alternative splicing contributes to transcriptome complexity by generating several transcript isoforms from a single gene, which can, thus, perform various functions. To complete the global comparative analysis of gene expression changes, we explored patterns of alternative splicing evolution. This work uncovered several general and unexpected patterns of alternative splicing evolution (e.g., we found that alternative splicing evolves extremely rapidly) as well as a large number of conserved alternative isoforms that may be crucial for the functioning of mammalian organs.Finally, the third and final project of my PhD consisted in analyzing in detail the unique functional and evolutionary properties of the testis by exploring the extent of its transcriptome complexity. This organ was previously shown to evolve rapidly both at the phenotypic and molecular level, apparently because of the specific pressures that act on this organ and are associated with its reproductive function. Moreover, my analyses of the amniote tissue transcriptome data described above, revealed strikingly widespread transcriptional activity of both functional and nonfunctional genomic elements in the testis compared to the other organs. To elucidate the cellular source and mechanisms underlying this promiscuous transcription in the testis, we generated deep coverage RNA-Seq data for all major testis cell types as well as epigenetic data (DNA and histone methylation) using the mouse as model system. The integration of these complete dataset revealed that meiotic and especially post-meiotic germ cells are the major contributors to the widespread functional and nonfunctional transcriptome complexity of the testis, and that this "promiscuous" spermatogenic transcription is resulting, at least partially, from an overall transcriptionally permissive chromatin state. We hypothesize that this particular open state of the chromatin results from the extensive chromatin remodeling that occurs during spermatogenesis which ultimately leads to the replacement of histones by protamines in the mature spermatozoa. Our results have important functional and evolutionary implications (e.g., regarding new gene birth and testicular gene expression evolution).Generally, these three large-scale projects of my thesis provide complete and massive datasets that constitute valuables resources for further functional and evolutionary analyses of mammalian genomes.

Escape over a potential barrier driven by colored noise: Large but finite correlation times

The recent theory of Tsironis and Grigolini for the mean first-passage time from one metastable state to another of a bistable potential for long correlation times of the noise is extended to large but finite correlation times.

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.

This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5' rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5' distal to the annotated 5' terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be "noncoding," ultimately relating to the identification of disease-related sequence alterations.