Interobserver and intraobserver variability of the apparent diffusion coefficient in treated malignant hepatic lesions on a 3.0T machine: measurements in the whole lesion versus in the area with the most restricted diffusion.

PURPOSE: To assess the inter/intraobserver variability of apparent diffusion coefficient (ADC) measurements in treated hepatic lesions and to compare ADC measurements in the whole lesion and in the area with the most restricted diffusion (MRDA). MATERIALS AND METHODS: Twenty-five patients with treated malignant liver lesions were examined on a 3.0T machine. After agreeing on the best ADC image, two readers independently measured the ADC values in the whole lesion and in the MRDA. These measurements were repeated 1 month later. The Bland-Altman method, Spearman correlation coefficients, and the Wilcoxon signed-rank test were used to evaluate the measurements. RESULTS: Interobserver variability for ADC measurements in the whole lesion and in the MRDA was 0.17 x 10(-3) mm(2)/s [-0.17, +0.17] and 0.43 x 10(-3) mm(2)/s [-0.45, +0.41], respectively. Intraobserver limits of agreement could be as low as [-0.10, +0.12] 10(-3) mm(2)/s and [-0.20, +0.33] 10(-3) mm(2)/s for measurements in the whole lesion and in the MRDA, respectively. CONCLUSION: A limited variability in ADC measurements does exist, and it should be considered when interpreting ADC values of hepatic malignancies. This is especially true for the measurements of the minimal ADC.

Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705.

BACKGROUND: Analysis of the first reported complete genome sequence of Bifidobacterium longum NCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness to Streptomyces coelicolor and Mycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes. RESULTS: Generally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of the B. longum NCC2705 chromosome yielded six, instead of two, linear segments, while its dnaA locus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low. Comparison with closely related actinobacteria strongly suggested that the chromosome of B. longum was misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10A B. longum strain. Recently, a corrected sequence of B. longum NCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions. CONCLUSION: Genometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly.

Whole genome sequencing in patients with retinitis pigmentosa reveals pathogenic DNA structural changes and NEK2 as a new disease gene.

We performed whole genome sequencing in 16 unrelated patients with autosomal recessive retinitis pigmentosa (ARRP), a disease characterized by progressive retinal degeneration and caused by mutations in over 50 genes, in search of pathogenic DNA variants. Eight patients were from North America, whereas eight were Japanese, a population for which ARRP seems to have different genetic drivers. Using a specific workflow, we assessed both the coding and noncoding regions of the human genome, including the evaluation of highly polymorphic SNPs, structural and copy number variations, as well as 69 control genomes sequenced by the same procedures. We detected homozygous or compound heterozygous mutations in 7 genes associated with ARRP (USH2A, RDH12, CNGB1, EYS, PDE6B, DFNB31, and CERKL) in eight patients, three Japanese and five Americans. Fourteen of the 16 mutant alleles identified were previously unknown. Among these, there was a 2.3-kb deletion in USH2A and an inverted duplication of ∼446 kb in EYS, which would have likely escaped conventional screening techniques or exome sequencing. Moreover, in another Japanese patient, we identified a homozygous frameshift (p.L206fs), absent in more than 2,500 chromosomes from ethnically matched controls, in the ciliary gene NEK2, encoding a serine/threonine-protein kinase. Inactivation of this gene in zebrafish induced retinal photoreceptor defects that were rescued by human NEK2 mRNA. In addition to identifying a previously undescribed ARRP gene, our study highlights the importance of rare structural DNA variations in Mendelian diseases and advocates the need for screening approaches that transcend the analysis of the coding sequences of the human genome.

Whole-body protein turnover and resting energy expenditure in obese, prepubertal children.

BACKGROUND: Obesity is becoming more frequent in children; understanding the extent to which this condition affects not only carbohydrate and lipid metabolism but also protein metabolism is of paramount importance. OBJECTIVE: We evaluated the kinetics of protein metabolism in obese, prepubertal children in the static phase of obesity. DESIGN: In this cross-sectional study, 9 obese children (x +/- SE: 44+/-4 kg, 30.9+/-1.5% body fat) were compared with 8 lean (28+/-2 kg ,16.8+/-1.2% body fat), age-matched (8.5+/-0.2 y) control children. Whole-body nitrogen flux, protein synthesis, and protein breakdown were calculated postprandially over 9 h from 15N abundance in urinary ammonia by using a single oral dose of [15N]glycine; resting energy expenditure (REE) was assessed by indirect calorimetry (canopy) and body composition by multiple skinfold-thickness measurements. RESULTS: Absolute rates of protein synthesis and breakdown were significantly greater in obese children than in control children (x +/- SE: 208+/-24 compared with 137+/-14 g/d, P < 0.05, and 149+/-20 compared with 89+/-13 g/d, P < 0.05, respectively). When these variables were adjusted for fat-free mass by analysis of covariance, however, the differences between groups disappeared. There was a significant relation between protein synthesis and fat-free mass (r = 0.83, P < 0.001) as well as between protein synthesis and REE (r = 0.79, P < 0.005). CONCLUSIONS: Obesity in prepubertal children is associated with an absolute increase in whole-body protein turnover that is consistent with an absolute increase in fat-free mass, both of which contribute to explaining the greater absolute REE in obese children than in control children.

Diet-induced thermogenesis measured over a whole day in obese and nonobese women.

The overall thermogenic response to food intake measured over a whole day in 20 young nondiabetic obese women (body fat mean +/- SEM: 38.6 +/- 0.7%), was compared with that obtained in eight nonobese control women (body fat: 24.7 +/- 0.9%). The energy expenditure of the subjects was continuously measured over 24 h with a respiration chamber, and the spontaneous activity was assessed by a radar system. A new approach was used to obtain the integrated thermogenic response to the three meals ingested over the day (from 8:30 AM to 10:30 PM). This method allows to subtract the energy expended for physical activity from total energy expenditure and to calculate the integrated dietary-induced thermogenesis as the difference between the energy expended without physical activity and basal metabolic rate. The thermogenic response to the three meals (expressed in percentage of the total energy ingested) was found to be blunted in obese women (8.7 +/- 0.8%) as compared with that of controls (14.8 +/- 1.1%). There was an inverse correlation between the percentage body fat and the diet-induced thermogenesis (r = -0.61, p less than 0.001). In addition, the relative increase in diurnal urinary norepinephrine excretion was lower in obese than in the control subjects. It is concluded that a low overall thermogenic response to feeding may be a contributing factor for energy storage in some obese subjects; a blunted response of the sympathetic nervous system could explain this low thermogenic response.

Selective suppression of cytokine secretion in whole blood cell cultures of patients with colorectal cancer.

We have investigated the secretion of interferon alpha (IFN-alpha), IFN-gamma, interleukin-1alpha (IL-1alpha), IL-1beta, IL-2 and tumour necrosis factor alpha (TNF-alpha) in whole blood cell cultures (WBCCs) of colorectal cancer patients upon mitogen stimulation. Whereas the values for IL-1beta and TNF-alpha remained virtually unchanged in comparison with healthy control subjects, WBCCs of colorectal cancer patients secreted significantly lower amounts of IFN-alpha (P < 0.005), IFN-gamma (P < 0.0001), IL-1alpha (P < 0.0001) and IL-2 (P < 0.05). This reduction correlated with the progression of the disease. The total leucocyte and monocyte population were almost identical in both groups. In contrast, a dramatic depletion of lymphocytes was observed in colorectal cancer patients, which affected both lymphocyte counts (P < 0.0005) and their distribution (P < 0.0001). Our results suggest a selective suppression of cytokines in colorectal cancer patients that is related to tumour burden. Several mechanisms might account for this phenomenon, one of which might be lymphocyte depletion.

High-resolution 3D whole-heart coronary MRA: a study on the combination of data acquisition in multiple breath-holds and 1D residual respiratory motion compensation.

OBJECT: To study a scan protocol for coronary magnetic resonance angiography based on multiple breath-holds featuring 1D motion compensation and to compare the resulting image quality to a navigator-gated free-breathing acquisition. Image reconstruction was performed using L1 regularized iterative SENSE. MATERIALS AND METHODS: The effects of respiratory motion on the Cartesian sampling scheme were minimized by performing data acquisition in multiple breath-holds. During the scan, repetitive readouts through a k-space center were used to detect and correct the respiratory displacement of the heart by exploiting the self-navigation principle in image reconstruction. In vivo experiments were performed in nine healthy volunteers and the resulting image quality was compared to a navigator-gated reference in terms of vessel length and sharpness. RESULTS: Acquisition in breath-hold is an effective method to reduce the scan time by more than 30 % compared to the navigator-gated reference. Although an equivalent mean image quality with respect to the reference was achieved with the proposed method, the 1D motion compensation did not work equally well in all cases. CONCLUSION: In general, the image quality scaled with the robustness of the motion compensation. Nevertheless, the featured setup provides a positive basis for future extension with more advanced motion compensation methods.

Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers.

Genes underlying mutant phenotypes can be isolated by combining marker discovery, genetic mapping and resequencing, but a more straightforward strategy for mapping mutations would be the direct comparison of mutant and wild-type genomes. Applying such an approach, however, is hampered by the need for reference sequences and by mutational loads that confound the unambiguous identification of causal mutations. Here we introduce NIKS (needle in the k-stack), a reference-free algorithm based on comparing k-mers in whole-genome sequencing data for precise discovery of homozygous mutations. We applied NIKS to eight mutants induced in nonreference rice cultivars and to two mutants of the nonmodel species Arabis alpina. In both species, comparing pooled F2 individuals selected for mutant phenotypes revealed small sets of mutations including the causal changes. Moreover, comparing M3 seedlings of two allelic mutants unambiguously identified the causal gene. Thus, for any species amenable to mutagenesis, NIKS enables forward genetics without requiring segregating populations, genetic maps and reference sequences.

Ultrastructure of the eggs of two species of Anopheles (Anopheles) Meigen (Diptera, Culicidae)

Egg ultrastructure of two morphologicaly similar species of the Arribalzagia Series, Anopheles (A.) costai Fonseca & Ramos, 1939 and A. (A.) mediopunctatus (Lutz, 1903) are described and illustrated using scanning electron micrographs. Although similar in the adult stage, male genitalia structures and larval and pupal stages, the eggs of these species are distinct. The eggs of A. costai and A. mediopunctatus are compared with that of A. forattinii Wilkerson & Sallum, 1999. Incomplete illustration of egg of A. forattinii is provided for comparison.

Cannibalism studies on eggs and newly hatched caterpillars in a wild population of Ascia monuste (Godart) (Lepidoptera, Pieridae)

Ascia monuste (Godart), also known as cabbage caterpillar, is considered herbivorous and specialist in Brassicaceae; however, it performs cannibalism. Experiments carried out in this work aimed to quantify the cannibalism occurrence in A. monuste, to verify whether cannibalism interferes in the species performance and to check whether cannibalism is influenced by the population size. The parameters used in order to evaluate the performance were time of development, adults weight and size, fecundity, oviposition and survival rate. Cannibalism occurred in all larval instars. There was a tendency to increase the cannibalism practice as the number of co-specific increased (potential preys). Cannibalism was more intense in larvae at the end of larval development. Generally, cannibalism did not interfere in the population performance. The most probable hypothesis for the occurrence of cannibalism in the conditions here studied would be the hypothesis of cannibalism as having the function of population control.

Natural parasitism in eggs of Anticarsia gemmatalis Hübner (Lepidoptera, Noctuidae) by Trichogramma spp. (Hymenoptera, Trichogrammatidae) in Brazil

Field surveys were carried during four soybean seasons in Southern Brazil to evaluate the occurrence of parasitoids in eggs of Anticarsia gemmatalis Hübner, 1818 and their incidence along the crop season. Eggs were collected by visual search on soybean leaves and from plants kept inside cages where A. gemmatalis moths were allowed to lay eggs. Trichogramma acacioi Brun, Moraes & Soares, 1984 was recorded for the first time in eggs of A. gemmatalis and the citations in the literature of Trichogramma lasallei Pinto, 1998 in Brazil where based on the material collected in this survey. Apart from these species, Trichogramma pretiosum Riley, 1879, Trichogramma rojasi Nagaraja & Nagarkatti, 1973 and Trichogramma atopovirilia Oatman & Platner, 1983 were also collected, all of which have been previously recorded in this host. Parasitized eggs were collected all over the period of occurrence of A. gemmatalis, from January to April each year. Total parasitism ranged from 4.8% in 2000 and 2002, 23.3% in 2001 and 28.9% in 2003. T. pretiosum and T. acacioi accounted for more than 80% of the parasitoids emerged each year, followed by T. atopovirilia, T. rojasi and T. lasallei, with less than 20% of incidence. Both the sex ratio and the mean number of parasitoids/egg did not differ among the species. Searching for A. gemmatalis eggs proved to be time consuming in comparison to the collection of eggs laid by moths inside the cages, which showed to be a useful method to provide qualitative estimates of parasitism in eggs of A. gemmatalis.

Trunk neuromuscular responses to a single whole-body vibration session in patients with chronic low back pain: a cross-sectional study.

OBJECTIVE: Whole-body vibration (WBV) exercise is progressively adopted as an alternative therapeutic modality for enhancing muscle force and muscle activity via neurogenic potentiation. So far, possible changes in the recruitment patterns of the trunk musculature after WBV remain undetermined. The main objective of this study was to evaluate the short-term effects of a single WBV session on trunk neuromuscular responses in patients with chronic low back pain (cLBP) and healthy participants. METHODS: Twenty patients with cLBP and 21 healthy participants performed 10 trunk flexion-extensions before and after a single WBV session consisting of five 1-minute vibration sets. Surface electromyography (EMG) of erector spinae at L2-L3 and L4-L5 and lumbopelvic kinematic variables were collected during the trials. Data were analyzed using 2-way mixed analysis of variance models. RESULTS: The WBV session led to increased lumbar EMG activity during the flexion and extension phases but yielded no change in the quiet standing and fully flexed phases. Kinematic data showed a decreased contribution to the movement of the lumbar region in the second extension quartile. These effects were not different between patients with cLBP and healthy participants. CONCLUSIONS: Increased lumbar EMG activity after a single WBV session most probably results from potentiation effects of WBV on lumbar muscles reflex responses. Decreased EMG activity in full trunk flexion, usually observed in healthy individuals, was still present after WBV, suggesting that the ability of the spine stabilizing mechanisms to transfer the extension torque from muscles to passive structures was not affected.

Biological characteristics and parasitism capacity of Trichogramma pretiosum Riley (Hymenoptera, Trichogrammatidae) on eggs of Spodoptera frugiperda (J. E. Smith) (Lepidoptera, Noctuidae)

This study aimed at evaluating the biological characteristics and the capacity of parasitism of a Trichogramma pretiosum Riley, 1869 (Hymenoptera, Trichogrammatidae) strain (T. pretiosum RV) collected in Rio Verde County, State of Goiás, Brazil. The study was carried out on eggs of Spodoptera frugiperda (J. E. Smith, 1797) (Lepidoptera, Noctuidae) and conducted under controlled environmental conditions at different constant temperatures. The biological parameters determined were: developmental time (egg-adult; days); emergence (%); sex ratio; number of progeny/egg; number of generation/year; thermal constant (K); temperature threshold (Tb); daily number of parasitized eggs; cumulative parasitism (%); total number of eggs parasitized by T. pretiosum; and female longevity. To study the T. pretiosum parasitism capacity, 20 S. frugiperda eggs (< 24 h old) were placed into 8.0 cm x 2.0 cm glass vials containing one female (< 24 h old) each. Trials were carried out in a completely randomized experimental design, with 20 replications at each temperature. The environmental chambers (BOD type) were set at 18ºC, 20ºC, 22ºC, 25ºC, 28ºC and 32ºC ± 1ºC, 70 ±10% relative humidity, and 14/10 h (L:D) photoperiod. The eggs of S. frugiperda were replaced daily until parasitoid death. Results have shown an inverse correlation between developmental time and temperature, with statistically significant differences among means, except at 25ºC and 28ºC (10 days). Parasitoid emergence (%) was also influenced by temperature. The lowest percent emergence was observed at 32ºC, and the highest ones at 18ºC and 20ºC temperatures. The temperature did not affect T. pretiosum sex ratio and number of parasitoids per egg, thus allowing changes in the temperature to control insect mass production in the laboratory to meet the needs for field releases.

Functional response of Telenomus remus Nixon(Hymenoptera, Scelionidae) to Spodoptera frugiperda (J. E. Smith) (Lepidoptera, Noctuidae) eggs: effect of female age

Functional response of Telenomus remus Nixon (Hymenoptera, Scelionidae) to Spodoptera frugiperda (J. E. Smith) (Lepidoptera, Noctuidae) eggs: effect of female age. Functional response of 24-h and 48-h-old Telenomus remus adults was studied on Spodoptera frugiperda eggs. The study was carried out in climatic chamber regulated at 25 ± 1°C, 70 ± 10% RH and 12:12h (L: D). Females of T. remus were honey fed and individualized in glass vials along with 25, 50, 75, 100, 150, 200, 250 or 300 eggs of S. frugiperda for 24 h. Complete randomized design with ten replications was adopted. The parameters evaluated to construct the functional response curve were daily average parasitism, searching rate and oviposition time. It was observed that the higher the egg density, the higher the parasitism for 24-h and 48-h-old females although there was a tendency of parasitism stabilization at 150-egg density. The results showed a type II functional response curve for both 24-h and 48-h-old female.

Whole brain radiotherapy with a conformational external beam radiation boost for lung cancer patients with 1-3 brain metastasis: a multi institutional study.

BACKGROUND: To determine the outcome of patients with brain metastasis (BM) from lung cancer treated with an external beam radiotherapy boost (RTB) after whole brain radiotherapy (WBRT). METHODS: A total of 53 BM patients with lung cancer were treated sequentially with WBRT and RTB between 1996 and 2008 according to our institutional protocol. Mean age was 58.8 years. The median KPS was 90. Median recursive partitioning analysis (RPA) and graded prognostic assessment (GPA) grouping were 2 and 2.5, respectively. Surgery was performed on 38 (71%) patients. The median number of BM was 1 (range, 1-3). Median WBRT and RTB combined dose was 39 Gy (range, 37.5-54). Median follow-up was 12.0 months. RESULTS: During the period of follow-up, 37 (70%) patients died. The median overall survival (OS) was 14.5 months. Only 13 patients failed in the brain. The majority of patients (n = 29) failed distantly. The 1-year OS, -local control, extracranial failure rates were 61.2%, 75.2% and 60.8%, respectively. On univariate analysis, improved OS was found to be significantly associated with total dose (< or = 39 Gy vs. > 39 Gy; p < 0.01), age < 65 (p < 0.01), absence of extracranial metastasis (p < 0.01), GPA > or = 2.5 (p = 0.01), KPS > or = 90 (p = 0.01), and RPA < 2 (p = 0.04). On multivariate analysis, total dose (p < 0.01) and the absence of extracranial metastasis (p = 0.03) retained statistical significance. CONCLUSIONS: The majority of lung cancer patients treated with WBRT and RTB progressed extracranially. There might be a subgroup of younger patients with good performance status and no extracranial disease who may benefit from dose escalation after WBRT to the metastatic site.