Self-navigated isotropic three-dimensional cardiac T2 mapping.

PURPOSE: To implement and characterize an isotropic three-dimensional cardiac T2 mapping technique. METHODS: A self-navigated three-dimensional radial segmented balanced steady-state free precession pulse sequence with an isotropic 1.7-mm spatial resolution was implemented at 3T with a variable T2 preparation module. Bloch equation and Monte Carlo simulations were performed to determine the influence of the heart rate, B1 inhomogeneity and noise on the T2 fitting accuracy. In a phantom study, the accuracy of the pulse sequence was studied through comparison with a gold-standard spin-echo T2 mapping method. The robustness and homogeneity of the technique were ascertained in a study of 10 healthy adult human volunteers, while first results obtained in patients are reported. RESULTS: The numerical simulations demonstrated that the heart rate and B1 inhomogeneity cause only minor deviations in the T2 fitting, whereas the phantom study showed good agreement of the technique with the gold standard. The volunteer study demonstrated an average myocardial T2 of 40.5 ± 3.3 ms and a <15% T2 gradient in the base-apex and anterior-inferior direction. In three patients, elevated T2 values were measured in regions with expected edema. CONCLUSION: This respiratory self-navigated isotropic three-dimensional technique allows for accurate and robust in vitro and in vivo T2 quantification. Magn Reson Med 73:1549-1554, 2015. © 2014 Wiley Periodicals, Inc.

Diagnosis and Management of Upper Tract Urothelial Carcinoma.

While UTUC is relatively uncommon, it has an aggressive natural history and poor prognosis, which has not substantially improved over the past two decades. Nevertheless, continued research has led to the discovery of risk factors improving the prevention and early detection of UTUC. Although RNU remains the standard treatment for localized invasive UTUC, nephron-sparing surgery for selected patients has made considerable progress in the recent years. The stagnation in the prognosis of UTUC over the past two decades highlights the necessity for incorporating multimodal approaches including refinements in systemic chemotherapy and radiotherapy to attain better outcomes for patients with UTUC.

Reexposure and advection of C-14-depleted organic carbon from old deposits at the upper continental slope

Outcrops of old strata at the shelf edge resulting from erosive gravity-driven flows have been globally described on continental margins. The reexposure of old strata allows for the reintroduction of aged organic carbon (OC), sequestered in marine sediments for thousands of years, into the modern carbon cycle. This pool of reworked material represents an additional source of C-14-depleted organic carbon supplied to the ocean, in parallel with the weathering of fossil organic carbon delivered by rivers from land. To understand the dynamics and implications of this reexposure at the shelf edge, a biogeochemical study was carried out in the Gulf of Lions (Mediterranean Sea) where erosive processes, driven by shelf dense water cascading, are currently shaping the seafloor at the canyon heads. Mooring lines equipped with sediment traps and current meters were deployed during the cascading season in the southwestern canyon heads, whereas sediment cores were collected along the sediment dispersal system from the prodelta regions down to the canyon heads. Evidence from grain-size, X-radiographs and Pb-210 activity indicate the presence in the upper slope of a shelly-coarse surface stratum overlying a consolidated deposit. This erosive discontinuity was interpreted as being a result of dense water cascading that is able to generate sufficient shear stress at the canyon heads to mobilize the coarse surface layer, eroding the basal strata. As a result, a pool of aged organic carbon (Delta C-14 = -944.5 +/- 24.7%; mean age 23,650 +/- 3,321 ybp) outcrops at the modern seafloor and is reexposed to the contemporary carbon cycle. This basal deposit was found to have relatively high terrigenous organic carbon (lignin = 1.48 +/- 0.14 mg/100 mg OC), suggesting that this material was deposited during the last low sea-level stand. A few sediment trap samples showed anomalously depleted radiocarbon concentrations (Delta C-14 = -704.4 +/- 62.5%) relative to inner shelf (Delta C-14 = -293.4 +/- 134.0%), mid-shelf (Delta C-14 = -366.6 +/- 51.1%), and outer shelf (Delta C-14 = -384 +/- 47.8%) surface sediments. Therefore, although the major source of particulate material during the cascading season is resuspended shelf deposits, there is evidence that this aged pool of organic carbon can be eroded and laterally advected downslope.

Single acquisition electrical property mapping based on relative coil sensitivities: A proof-of-concept demonstration.

PURPOSE: All methods presented to date to map both conductivity and permittivity rely on multiple acquisitions to compute quantitatively the magnitude of radiofrequency transmit fields, B1+. In this work, we propose a method to compute both conductivity and permittivity based solely on relative receive coil sensitivities ( B1-) that can be obtained in one single measurement without the need to neither explicitly perform transmit/receive phase separation nor make assumptions regarding those phases. THEORY AND METHODS: To demonstrate the validity and the noise sensitivity of our method we used electromagnetic finite differences simulations of a 16-channel transceiver array. To experimentally validate our methodology at 7 Tesla, multi compartment phantom data was acquired using a standard 32-channel receive coil system and two-dimensional (2D) and 3D gradient echo acquisition. The reconstructed electric properties were correlated to those measured using dielectric probes. RESULTS: The method was demonstrated both in simulations and in phantom data with correlations to both the modeled and bench measurements being close to identity. The noise properties were modeled and understood. CONCLUSION: The proposed methodology allows to quantitatively determine the electrical properties of a sample using any MR contrast, with the only constraint being the need to have 4 or more receive coils and high SNR. Magn Reson Med, 2014. © 2014 Wiley Periodicals, Inc.

Bioavailability of sinking organic matter in the Blanes canyon and the adjacent open slope (NW Mediterranean Sea)

Submarine canyons are sites of intense energy and material exchange between the shelf and the deep adjacent basins. To test the hypothesis that active submarine canyons represent preferential conduits of available food for the deep-sea benthos, two mooring lines were deployed at 1200 m depth from November 2008 to November 2009 inside the Blanes canyon and on the adjacent open slope (Catalan Margin, NW Mediterranean Sea). We investigated the fluxes, biochemical composition and food quality of sinking organic carbon (OC). OC fluxes in the canyon and the open slope varied among sampling periods, though not onsistently in the two sites. In particular, while in the open slope the highest OC fluxes were observed in August 2009, in the canyon the highest OC fluxes occurred in April-May 2009. For almost the entire study period, the OC fluxes in the canyon were significantly higher than those in the open slope, whereas OC contents of sinking particles collected in the open slope were consistently higher than those in the canyon. This result confirms that submarine canyons are effective conveyors of OC to the deep sea. Particles transferred to the deep sea floor through the canyons are predominantly of inorganic origin, significantly higher than that reaching the open slope at a similar water depth. Using multivariate statistical tests, two major clusters of sampling periods were identified: one in the canyon that grouped trap samples collected in December 2008, oncurrently with the occurrence of a major storm at the sea surface, and associated with increased fluxes of nutritionally available particles from the upper shelf. Another cluster grouped samples from both the canyon and the open slope collected in March 2009, concurrently with the occurrence of the seasonal phytoplankton bloom at the sea surface, and associated with increased fluxes of total phytopigments. Our results confirm the key ecological role of submarine canyons for the functioning of deep-sea ecosystems, and highlight the importance of canyons in linking episodic storms and primary production occurring at the sea surface to the deep sea floor.

Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data.

Next-generation sequencing (NGS) technologies have become the standard for data generation in studies of population genomics, as the 1000 Genomes Project (1000G). However, these techniques are known to be problematic when applied to highly polymorphic genomic regions, such as the human leukocyte antigen (HLA) genes. Because accurate genotype calls and allele frequency estimations are crucial to population genomics analyses, it is important to assess the reliability of NGS data. Here, we evaluate the reliability of genotype calls and allele frequency estimates of the single-nucleotide polymorphisms (SNPs) reported by 1000G (phase I) at five HLA genes (HLA-A, -B, -C, -DRB1, and -DQB1). We take advantage of the availability of HLA Sanger sequencing of 930 of the 1092 1000G samples and use this as a gold standard to benchmark the 1000G data. We document that 18.6% of SNP genotype calls in HLA genes are incorrect and that allele frequencies are estimated with an error greater than ±0.1 at approximately 25% of the SNPs in HLA genes. We found a bias toward overestimation of reference allele frequency for the 1000G data, indicating mapping bias is an important cause of error in frequency estimation in this dataset. We provide a list of sites that have poor allele frequency estimates and discuss the outcomes of including those sites in different kinds of analyses. Because the HLA region is the most polymorphic in the human genome, our results provide insights into the challenges of using of NGS data at other genomic regions of high diversity.

Homozygosity mapping reveals novel and known mutations in Pakistani families with inherited retinal dystrophies.

Inherited retinal dystrophies are phenotypically and genetically heterogeneous. This extensive heterogeneity poses a challenge when performing molecular diagnosis of patients, especially in developing countries. In this study, we applied homozygosity mapping as a tool to reduce the complexity given by genetic heterogeneity and identify disease-causing variants in consanguineous Pakistani pedigrees. DNA samples from eight families with autosomal recessive retinal dystrophies were subjected to genome wide homozygosity mapping (seven by SNP arrays and one by STR markers) and genes comprised within the detected homozygous regions were analyzed by Sanger sequencing. All families displayed consistent autozygous genomic regions. Sequence analysis of candidate genes identified four previously-reported mutations in CNGB3, CNGA3, RHO, and PDE6A, as well as three novel mutations: c.2656C > T (p.L886F) in RPGRIP1, c.991G > C (p.G331R) in CNGA3, and c.413-1G > A (IVS6-1G > A) in CNGB1. This latter mutation impacted pre-mRNA splicing of CNGB1 by creating a -1 frameshift leading to a premature termination codon. In addition to better delineating the genetic landscape of inherited retinal dystrophies in Pakistan, our data confirm that combining homozygosity mapping and candidate gene sequencing is a powerful approach for mutation identification in populations where consanguineous unions are common.

Yield mapping, soil fertility and tree gaps in an orange orchard

The current high competition on Citrus industry demands from growers new management technologies for superior efficiency and sustainability. In this context, precision agriculture (PA) has developed techniques based on yield mapping and management systems that recognize field spatial variability, which contribute to increase profitability of commercial crops. Because spatial variability is often not perceived the orange orchards are still managed as uniform and adoption of PA technology on citrus farms is low. Thus, the objective of the present study was to characterize the spatial variability of three factors: fruit yield, soil fertility and occurrence of plant gaps caused by either citrus blight or huanglongbing (HLB) in a commercial Valencia orchard in Brotas, São Paulo State, Brazil. Data from volume, geographic coordinates and representative area of the bags used on harvest were recorded to generate yield points that were then interpolated to produce the yield map. Soil chemical characteristics were studied by analyzing samples collected along planting rows and inter-rows in 24 points distributed in the field. A map of density of tree gaps was produced by georeferencing individual gaps and later by counting the number of gaps within 500 m² cells. Data were submitted to statistical and geostatistical analyses. A t test was used to compare means of soil chemical characteristics between sampling regions. High variation on yield and density of tree gaps was observed from the maps. It was also demonstrated overlapping regions of high density of plant absence and low fruit yield. Soil fertility varied depending on the sampling region in the orchard. The spatial variability found on yield, soil fertility and on disease occurrence demonstrated the importance to adopt site specific nutrient management and disease control as tools to guarantee efficiency of fruit production.

Pilomatrixoma. Review of 205 cases

Aims: To determine the incidence and clinical features of patients diagnosed with pilomatrixoma. Patients and Method: A retrospective analysis was made of 205 cases of pilomatrixoma diagnosed according to clinical and histological criteria, with an evaluation of the incidence, patient age at presentation, gender, lesion location and size, single or multiple presentation, differential diagnosis, histopathological and clinical findings and relapses. Results: Pilomatrixoma was seen to account for 1.04% of all benign skin lesions. It tended to present in pediatric patients- almost 50% corresponding to individuals under 20 years of age- with a slight male predilection (107/98). Approximately 75% of all cases presented as single lesions measuring less than 15 mm in diameter. Multiple presentations were seen in 2.43% of cases. The most frequent locations were the head and orofacial zones (particularly the parotid region), with over 50% of all cases, followed by the upper (23.9%) and lower limbs (12.7%). Only one relapse was documented following simple lesion excision. Conclusions: The frequency of pilomatrixomas was 1.04% of all benign skin lesions- the lesions being predominantly located in the maxillofacial area. Due to the benign features of this disorder, simple removal of the lesion is considered to be the treatment of choice, and is associated with a very low relapse rate.

Mapping the diagnosis axis of an interface terminology to the NANDA International Taxonomy

Background: Nursing terminologies are designed to support nursing practice but, as with any other clinical tool, they should be evaluated. Cross-mapping is a formal method for examining the validity of the existing controlled vocabularies. Objectives: The study aims to assess the inclusiveness and expressiveness of the nursing diagnosis axis of a newly implemented interface terminology by cross-mapping with the NANDA-I taxonomy. Design/Methods: The study applied a descriptive design, using a cross-sectional, bidirectional mapping strategy. The sample included 728 concepts from both vocabularies. Concept cross-mapping was carried out to identify one-to-one, negative, and hierarchical connections. The analysis was conducted using descriptive statistics. Results: Agreement of the raters" mapping achieved 97%. More than 60% of the nursing diagnosis concepts in the NANDA-I taxonomy were mapped to concepts in the diagnosis axis of the new interface terminology; 71.1% were reversely mapped. Conclusions: Main results for outcome measures suggest that the diagnosis axis of this interface terminology meets the validity criterion of cross-mapping when mapped from and to the NANDA-I taxonomy.

Spatial mapping of exciton lifetimes in single ZnO nanowires

We investigate the spatial dependence of the exciton lifetimes in single ZnO nanowires. We have found that the free exciton and bound exciton lifetimes exhibit a maximum at the center of nanowires, while they decrease by 30% towards the tips. This dependence is explained by considering the cavity-like properties of the nanowires in combination with the Purcell effect. We show that the lifetime of the bound-excitons scales with the localization energy to the power of 3/2, which validates the model of Rashba and Gurgenishvili at the nanoscale.