X-ray absorption and phase contrast imaging to study the interplay between plant roots and soil structure

Plant performance is, at least partly, linked to the location of roots with respect to soil structure features and the micro-environment surrounding roots. Measurements of root distributions from intact samples, using optical microscopy and field tracings have been partially successful but are imprecise and labour-intensive. Theoretically, X-ray computed micro-tomography represents an ideal solution for non-invasive imaging of plant roots and soil structure. However, before it becomes fast enough and affordable or easily accessible, there is still a need for a diagnostic tool to investigate root/soil interplay. Here, a method for detection of undisturbed plant roots and their immediate physical environment is presented. X-ray absorption and phase contrast imaging are combined to produce projection images of soil sections from which root distributions and soil structure can be analyzed. The clarity of roots on the X-ray film is sufficient to allow manual tracing on an acetate sheet fixed over the film. In its current version, the method suffers limitations mainly related to (i) the degree of subjectivity associated with manual tracing and (ii) the difficulty of separating live and dead roots. The method represents a simple and relatively inexpensive way to detect and quantify roots from intact samples and has scope for further improvements. In this paper, the main steps of the method, sampling, image acquisition and image processing are documented. The potential use of the method in an agronomic perspective is illustrated using surface and sub-surface soil samples from a controlled wheat trial. Quantitative characterization of root attributes, e.g. radius, length density, branching intensity and the complex interplay between roots and soil structure, is presented and discussed.

Dual processes in recognition: Does a focus on measurement operations provide a sufficient foundation?

Current theoretical thinking about dual processes in recognition relies heavily on the measurement operations embodied within the process dissociation procedure. We critically evaluate the ability of this procedure to support this theoretical enterprise. We show that there are alternative processes that would produce a rough invariance in familiarity (a key prediction of the dual-processing approach) and that the process dissociation procedure does not have the power to differentiate between these alternative possibilities. We also show that attempts to relate parameters estimated by the process dissociation procedure to subjective reports (remember-know judgments) cannot differentiate between alternative dual-processing models and that there are problems with some of the historical evidence and with obtaining converging evidence. Our conclusion is that more specific theories incorporating ideas about representation and process are required.

Comprehensive structural characterization of MCM-41: From mesopores to particles

In the present work the meso- and macro-structural characteristics of the mesoporous adsorbent MCM-41 have been estimated with the help of various techniques. The structure is found to comprise four different length scales: that of the mesopores, the crystallites, the grains and of the particles. It was found that the surface area estimated by the use of small angle scattering techniques is higher, while that estimated by mercury porosimetry is much lower, than that obtained from gas adsorption methods. Based on the macropore characterization by mercury porosimetry, and the considerable macropore area determined, it is seen that the actual mesopore area of MCM-41 may be significantly lower than the BET area. TEM studies indicated that MCM-41 does not have an ideal mesopore structure; however, it may still be treated as a model mesoporous material for gas adsorption studies because of the large radius of curvature of the channels.

An object-oriented neural network approach to short-term traffic forecasting

This paper discusses an object-oriented neural network model that was developed for predicting short-term traffic conditions on a section of the Pacific Highway between Brisbane and the Gold Coast in Queensland, Australia. The feasibility of this approach is demonstrated through a time-lag recurrent network (TLRN) which was developed for predicting speed data up to 15 minutes into the future. The results obtained indicate that the TLRN is capable of predicting speed up to 5 minutes into the future with a high degree of accuracy (90-94%). Similar models, which were developed for predicting freeway travel times on the same facility, were successful in predicting travel times up to 15 minutes into the future with a similar degree of accuracy (93-95%). These results represent substantial improvements on conventional model performance and clearly demonstrate the feasibility of using the object-oriented approach for short-term traffic prediction. (C) 2001 Elsevier Science B.V. All rights reserved.

Similitude applied to centrifugal scaling of unsaturated flow

Centrifuge experiments modeling single-phase flow in prototype porous media typically use the same porous medium and permeant. Then, well-known scaling laws are used to transfer the results to the prototype. More general scaling laws that relax these restrictions are presented. For permeants that are immiscible with an accompanying gas phase, model-prototype (i.e., centrifuge model experiment-target system) scaling is demonstrated. Scaling is shown to be feasible for Miller-similar (or geometrically similar) media. Scalings are presented for a more, general class, Lisle-similar media, based on the equivalence mapping of Richards' equation onto itself. Whereas model-prototype scaling of Miller-similar media can be realized easily for arbitrary boundary conditions, Lisle-similarity in a finite length medium generally, but not always, involves a mapping to a moving boundary problem. An exception occurs for redistribution in Lisle-similar porous media, which is shown to map to spatially fixed boundary conditions. Complete model-prototype scalings for this example are derived.

Cytokine-related genes identified from the RIKEN full-length mouse cDNA data set

To identify novel cytokine-related genes, we searched the set of 60,770 annotated RIKEN mouse cDNA clones (FANTOM2 clones), using keywords such as cytokine itself or cytokine names (such as interferon, interleukin, epidermal growth factor, fibroblast growth factor, and transforming growth factor). This search produced 108 known cytokines and cytokine-related products such as cytokine receptors, cytokine-associated genes, or their products (enhancers, accessory proteins, cytokine-induced genes). We found 15 clusters of FANTOM2 clones that are candidates for novel cytokine-related genes. These encoded products with strong sequence similarity to guanylate-binding protein (GBP-5), interleukin-1 receptor-associated kinase 2 (IRAK-2), interleukin 20 receptor alpha isoform 3, a member of the interferon-inducible proteins of the Ifi 200 cluster, four members of the membrane-associated family 1-8 of interferon-inducible proteins, one p27-like protein, and a hypothetical protein containing a Toll/Interleukin receptor domain. All four clones representing novel candidates of gene products from the family contain a novel highly conserved cross-species domain. Clones similar to growth factor-related products included transforming growth factor beta-inducible early growth response protein 2 (TIEG-2), TGFbeta-induced factor 2, integrin beta-like 1, latent TGF-binding protein 4S, and FGF receptor 4B. We performed a detailed sequence analysis of the candidate novel genes to elucidate their likely functional properties.

Identification of novel "pathologs" (human disease-related gene candidates) from the RIKEN full-length mouse cDNA data set

The majority of common diseases such as cancer, allergy, diabetes, or heart disease are characterized by complex genetic traits, in which genetic and environmental components contribute to disease susceptibility. Our knowledge of the genetic factors underlying most of such diseases is limited. A major goal in the post-genomic era is to identify and characterize disease susceptibility genes and to use this knowledge for disease treatment and prevention. More than 500 genes are conserved across the invertebrate and vertebrate genomes. Because of gene conservation, various organisms including yeast, fruitfly, zebrafish, rat, and mouse have been used as genetic models.

Folate-sensitive fragile site FRA10A is due to an expansion of a CGG repeat in a novel gene, FRA10AC1, encoding a nuclear protein

Fragile sites appear visually as nonstaining gaps on chromosomes that are inducible by specific cell culture conditions. Expansion of CGG/ CCG repeats has been shown to be the molecular basis of all five folate-sensitive fragile sites characterized molecularly so far, i.e., FRAXA, FRAXE, FRAXF, FRA11B, and FRA16A. In the present study we have refined the localization of the FRA10A folate-sensitive fragile site by fluorescence in situ hybridization. Sequence analysis of a BAC clone spanning FRA10A identified a single, imperfect, but polymorphic CGG repeat that is part of a CpG island in the 5'UTR of a novel gene named FRA10ACl. The number of CGG repeats varied in the population from 8 to 13. Expansions exceeding 200 repeat units were methylated in all FRA10A fragile site carriers tested. The FRA10ACl gene consists of 19 exons and is transcribed in the centromeric direction from the FRA10A repeat. The major transcript of similar to 1450 nt is ubiquitously expressed and codes for a highly conserved protein, FRA10ACl, of unknown function. Several splice variants leading to alternative 3' ends were identified (particularly in testis). These give rise to FRA10ACl proteins with altered COOH-termini. Immunofluorescence analysis of full-length, recombinant EGFP-tagged FRA10ACl protein showed that it was present exclusively in the nucleoplasm. We show that the expression of FRA10A, in parallel to the other cloned folate-sensitive fragile sites, is caused by an expansion and subsequent methylation of an unstable CGG trinucleotide repeat. Taking advantage of three cSNPs within the FRA10ACl gene we demonstrate that one allele of the gene is not transcribed in a FRA10A carrier. Our data also suggest that in the heterozygous state FRA10A is likely a benign folate-sensitive fragile site. (C) 2004 Elsevier Inc. All rights reserved.

Sequence analysis, chromosomal distribution and long-range organization show that rapid turnover of new and old pBuM satellite DNA repeats leads to different patterns of variation in seven species of the Drosophila buzzatii cluster

We aimed to study patterns of variation and factors influencing the evolutionary dynamics of a satellite DNA, pBuM, in all seven Drosophila species from the buzzatii cluster (repleta group). We analyzed 117 alpha pBuM-1 (monomer length 190 bp) and 119 composite alpha/beta (370 bp) pBuM-2 repeats and determined the chromosome location and long-range organization on DNA fibers of major sequence variants. Such combined methodologies in the study of satDNAs have been used in very few organisms. In most species, concerted evolution is linked to high copy number of pBuM repeats. Species presenting low-abundance and scattered distributed pBuM repeats did not undergo concerted evolution and maintained part of the ancestral inter-repeat variability. The alpha and alpha/beta repeats colocalized in heterochromatic regions and were distributed on multiple chromosomes, with notable differences between species. High-resolution FISH revealed array sizes of a few kilobases to over 0.7 Mb and mutual arrangements of alpha and alpha/beta repeats along the same DNA fibers, but with considerable changes in the amount of each variant across species. From sequence, chromosomal and phylogenetic data, we could infer that homogenization and amplification events involved both new and ancestral pBuM variants. Altogether, the data on the structure and organization of the pBuM satDNA give insights into genome evolution including mechanisms that contribute to concerted evolution and diversification.

Association of haplotypes in the IL8 gene with susceptibility to chronic periodontitis in a Brazilian population

Background: Interleukin 8 (IL-8) is a chemokine related to the initiation and amplification of acute and chronic inflammatory processes. Polymorphisms in the IL8 gene have been associated with inflammatory diseases. We investigated whether the - 845(T/C) and - 738(T/A) single nucleotide polymorphisms (SNPs) in the IL8 gene, as well as the haplotypes they form together with the previously investigated -353(A/T), are associated with susceptibility to chronic periodontitis. Methods: DNA was extracted from buccal epithelial cells of 400 Brazilian individuals (control n =182, periodontitis n=218). SNPs were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Disease associations were analyzed by the chi(2) test, Exact Fisher test and Clump program. Haplotypes were reconstructed using the expectation-maximization algorithm and differences in haplotype distribution between the groups were analyzed to estimate genetic susceptibility for chronic periodontitis development. Results: When analyzed individually, no SNPs showed different distributions between the control and chronic periodontitis groups. Although, nonsmokers carrying the TTA/CAT (OR = 2.35, 95% CI = 1.03-5.36) and TAT/CTA (OR= 6.05, 95% CI = 1.32-27.7) haplotypes were genetically susceptible to chronic periodontitis. The ITT/TAA haplotype was associated with protection against the development of periodontitis (for nonsmokers OR= 0.22, 95% CI = 0.10-0.46). Conclusion: Although none of the investigated SNPs in the IL8 gene was individually associated with periodontitis, some haplotypes showed significant association with susceptibility to, or protection against, chronic periodontitis in a Brazilian population. (C) 2010 Elsevier B.V. All rights reserved.

Population demography and spatial distribution of the mantis shrimp Squilla biformis (Stomatopoda, Squillidae) from Pacific Costa Rica

The mantis shrimp Squilla biformis is the most conspicuous and abundant stomatopod captured during benthic trawling operations off the Pacific coast of Costa Rica. Due to its abundance, this species is considered a potential fisheries resource for the region. Nevertheless, its life history is practically unknown. The present study describes the population demography, spatial distribution and behaviour of S. biformis from Pacific Costa Rica. The population was principally composed of individuals between 20 and 32 mm carapace length (CL), forming 2 age groups. Individuals of 35 to 45 mm CL and > 45 mm CL were poorly represented. We assume that larger individuals are more frequent at greater depths (probably on the continental slope), thus out of the reach of the fishing vessels used in our study. Males outnumbered females, as observed in other stomatopods. Visual evidence of their behaviour demonstrates that the adults in this species possess a benthic and pelagic life style. Largest numbers of individuals (50% of the total) were found between 240 to 260 m, the same bathymetric range that was historically occupied by commercial shrimps. This shift may be related to intense fishing activities. We observed a synchronized moulting of females and males during less luminous (third and fourth) lunar phases. The evolutionary development of a group moulting system could confer advantages to S. biformis in comparison to other stomatopods whose moulting process is individual and asynchronous.

Use of pleopod morphology to determine sexual dimorphism and maturity in hermit crabs: Isocheles sawayai as a model

In the Anomura, studies on growth patterns are infrequent, possibly because the heterogeneity of the group, especially in terms of morphology, makes it difficult to construct generalized growth models. Particularly hermit crabs are an interesting group to evaluate aspects of growth, because of their unique body. Isocheles sawayai, a hermit crab found only in the western Atlantic Ocean, poorly known with respect to its sexual dimorphism and maturity, was investigated here based on morphometry. Monthly collections (July 2001 through June 2003) were made from a shrimp fishing boat in the Caraguatatuba region on the northern coast of the state of SA o pound Paulo, Brazil. The specimens were measured and weighed, and had their sex checked. Throughout the sampling period, 374 specimens of I. sawayai were collected (11.23% nonovigerous females, 6.69% ovigerous females, 79.41% males and 2.67% intersexes). The size at which morphological sexual maturity was reached by both sexes ranged from 4.0 to 4.3 mm shield length, according to the relative growth and the size of the smallest ovigerous female. Sexual dimorphism was shown by males, which were significantly larger than females, and by differences in growth pattern between the sexes, especially for relationships that involved the pleopods, which is related to their different functions in males and females. The present study is one of the first to use pleopod morphometry to determine sexual maturity and dimorphism in hermit crabs, especially for species with intersexuality such as I. sawayai.

Use of AST platelet ratio index (APRI Score) as an alternative to liver biopsy for treatment indication in chronic hepatitis C

Chronic hepatitis C (CHC) is one of the most important causes of chronic liver disease in the world, potentially resulting in cirrhosis, hepatocellular carcinoma, and the need for liver transplantation. Liver biopsy is currently performed before therapy indication. Although, it is the golden standard there are many reasons to avoid or delay the procedure. APRI Score is an easy, low cost and practice alternative method which was described as an alternative for assessing structural changes in chronic hepatitis C (CHC). The rationale of this study was to observe the accuracy of APRI Score in comparison to liver biopsy in 400 patients divided into two groups of 200 carriers (Validation and Experimental groups respectively) selected at random or according to liver fibrosis staging (METAVIR). The ROC curves showed a concordance among these two methods of 92% and 88.5% when 1.05 was the cut off (F3 and F4), and 87% and 83%, on 0.75 cut offs (F2-F4). The discordance in advanced fibrosis staging (F3 and F4) was only 16 (8%) and 22 (11%) out of 200 patients in the experimental and validation groups, respectively. In 26 (13%) out of 200 patients in the experimental group and 34 (17%) out of 200 patients in the validation group, there was discordance between APRI Score and liver biopsy in moderate and advanced fibrosis (F2-F4). In conclusion APRI is a serological marker that has satisfactory sensitivity and specificity together with a high predictive value and it can be useful either in the absence of a biopsy or to reduce the frequency with which biopsies need to be carried out to monitor the evolution of chronic hepatitis C and the right moment for treatment indication.

Cognitive deficits, length of illness and symptom severity in schizophrenia

Background Research using neuropsychological testing has demonstrated that patients with schizophrenia show deficits in multiple neurocognitive domains. The aim of this study is to identify cognitive deficits that correlate with length of illness and symptom severity. Method Twenty clinically stable outpatients with chronic schizophrenia (18M : 2F) and 14 healthy controls (13M : 1F), matched on age, gender and parental education, were administered a neuropsychological battery consisting of the Hayling Sentence Completion Test (HSCT), WMS-III Verbal Paired Associates & Letter Number Sequencing, Modified Card Sort Test (MCST), Pyramids & Palm Trees Test, National Adult Reading Test (NART), Controlled Oral Word Association Test (COWAT), and WAIS-III. Severity of symptoms was rated with the Structured Clinical Interview – Positive and Negative Syndromes Scale (SCI-PANSS). Results In comparison to controls, patients showed significant deficits on all of the neuropsychological tasks except for the COWAT. MCST total categories, NART, Verbal IQ and arithmetic, similarities & digit symbol of the WAIS-III had the largest effect size between the groups. The longer the illness duration, the poorer the performance on WAISIII block design and the lower the performance IQ score. The poorer the performance on WMS-III letter number sequencing, the greater the positive symptoms, negative symptoms and general psychopathology. Conclusion Compared to controls, patients showed large effect sizes on measures of executive functioning, intelligence, working memory, verbal comprehension and speed of processing. The findings suggest that impairment in executive functioning and performance IQ is associated with length of illness, while impairment in working memory is associated with heightened symptom severity.

Surgical Treatment of Morbid Obesity: Mid-term Outcomes of the Laparoscopic Ileal Interposition Associated to a Sleeve Gastrectomy in 120 Patients

The aim of this study was to evaluate the mid-term outcomes of the laparoscopic ileal interposition associated to a sleeve gastrectomy (LII-SG) for the treatment of morbid obesity. The procedure was performed in 120 patients: 71 women and 49 men with mean age of 41.4 years. Mean body mass index (BMI) was 43.4 +/- 4.2 kg/m(2). Patients had to meet requirements of the 1991 NIH conference criteria for bariatric operations. Associated comorbidities were observed in all patients, including dyslipidemia in 51.7%, hypertension in 35.8%, type 2 diabetes in 15.8%, degenerative joint disease in 55%, gastroesophageal reflux disease in 36.7%, sleep apnea in 10%, and cardiovascular problems in 5.8%. Mean follow-up was 38.4 +/- 10.2 months, range 25.2-61.1. There was no conversion to open surgery nor operative mortality. Early major complications were diagnosed in five patients (4.2%). Postoperatively, 118 patients were evaluated. Late major complications were observed in seven patients (5.9%). Reoperations were performed in six (5.1%). Mean postoperative BMI was 25.7 +/- 3.17 kg/m(2), and 86.4% were no longer obese. Mean %EWL was 84.5 +/- 19.5%. Hypertension was resolved in 88.4% of the patients, dyslipidemia in 82.3%, and T2DM in 84.2%. The LII-SG provided an adequate weight loss and resolution of associated diseases during mid-term outcomes evaluation. There was an acceptable morbidity with no operative mortality. It seems that chronic ileal brake activation determined sustained reduced food intake and increased satiety over time. LII-SG could be regularly used as a surgical alternative for the treatment of morbid obesity.