Levels of agreement between clinical examination and transabdominal ultrasound evaluation of fetal head position in the second stage of labor

Aim: To compare transvaginal digital examination performed by residents and attending physicians to transabdominal suprapubic ultrasound in the evaluation of fetal head position in the second stage of labor.

Methods: A prospective study was conducted at a tertiary center and included pregnant women at term, with normal singleton cephalic presentation fetuses. All patients had ruptured membranes and were evaluated during the second stage of labor. Fetal head position was assessed consecutively by two clinicians (one resident and one attending physician). Afterwards, transabdominal suprapubic ultrasound was performed by another observer. Examiners were blinded to each other’s findings. Cohen’s kappa test was used to assess the degree of agreement between the evaluation methods.

Results: One-hundred sixty-one women were included. Transvaginal examination was consistent with the ultrasound in 45.0% of cases (95% CI: 37–53%) when the examination was performed by residents (k?=?0.349) and in 67% (95% CI: 60–74%) if the attending physician carried out the evaluation (k?=?0.604). When considering only the anterior positions, the Cohen’s kappa test was 0.426 and 0.709, respectively.

Conclusion: Transabdominal suprapubic ultrasound improved the accuracy of the evaluation of fetal head position, namely when transvaginal digital examination was performed by residents. This may be important especially when instrumental deliveries are considered.     

Development-dependent inheritance of 5-azacytidine-induced epimutations in triticale: analysis of rDNA expression patterns

Genomic imprinting of rye origin rDNA sequences in triticale is modulated by DNA methylation responsible for ontogenic expression patterns of those sequences. Considering the dynamic nature of these phenomena, we evaluated the influence of plant development on the inheritance of modified rye rDNA expression patterns. DNA hypomethylation was induced in triticale by 5-azacytidine (5AC) treatments at distinct developmental stages of M₁ plants, and expression patterns were analysed in M₂. The activity of rye origin rRNA genes in progeny of untreated and 5AC-treated plants was evaluated by silver staining in meristematic root tip cells and in meiocytes at diplotene. In the progeny of 5AC-treated plants, a significant increase in rye rDNA expression was observed, contrasting with the residual activity in untreated plants. Significant differential effects of 5AC treatments were observed in M₂ plants and correlated with the M₁ plant developmental stage in which DNA hypomethylation was induced. Hypotheses to explain the origin of those differences are discussed here.This revised version was published online in November 2005 with corrections to the Cover Date.     

Basic emotion profiles in healthy, chronic pain, depressed and PTSD individuals

Objectives: To compare self‐reports of five basic emotions across four samples: healthy, chronic pain, depressed and post‐traumatic stress disorder (PTSD), and to investigate the extent to which basic emotion reports discriminate between individuals in healthy or clinical groups. Methods: In total, 439 participants took part in this study: healthy (n = 131), chronic pain (n = 220), depressed (n = 24) and PTSD (n = 64). The participants completed the trait version of the Basic Emotion Scale. Basic emotion profiles were compared both within each group and between the healthy group and each of the three other groups. Discriminant analysis was used to assess the extent to which basic emotions can be used to classify the participants as belonging to the healthy group or one of the clinical groups. Results: In the healthy group, happiness was experienced more than any other basic emotion. This was not found in the clinical groups. In comparison to the healthy participants, the chronic pain group experienced more fear, anger and sadness, the depressed group reported more sadness and the PTSD group experienced all of the negative emotions more frequently. Discriminant analysis revealed that happiness was the most important variable in determining whether an individual belonged to the healthy group or one of the clinical groups. Anger was found to further discriminate between depressed and chronic pain individuals. Conclusion: The findings demonstrate that basic emotion profile analysis can provide a useful foundation for the exploration of emotional experience both within and between healthy and clinical groups. Copyright © 2011 John Wiley & Sons, Ltd. Key Practitioner Message: ? More frequent experiences of happiness relative to discrete negative emotions most clearly discriminate between individuals in healthy and clinical groups. More frequent anger experiences further discriminate between individuals with chronic pain and those with depression while disgust levels help discriminate between those with post‐traumatic stress disorder (PTSD) and depression. ? More frequent experiences of high arousal negative emotions—fear, anger and disgust—are characteristic of individuals with PTSD. ? Fear is the most frequently experienced negative emotion in both healthy and clinical groups. Higher levels of fear compared with other discrete negative emotions are not necessarily an indicator of psychopathology. Consideration of emotional profiles more generally and the relative frequency with which happiness is experienced relative to negative emotions may be more useful in delineating between healthy individuals and those with chronic pain, depression or PTSD.     

Assemblathon 1: a competitive assessment of de novo short read assembly methods

Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/.     

The Photobacterium damselae subsp. damselae hemolysins damselysin and HlyA are encoded within a new virulence plasmid

Photobacterium damselae subsp. damselae (formerly Vibrio damsela) is a marine bacterium that causes infections and fatal disease in a wide range of marine animals and in humans. Highly hemolytic strains produce damselysin (Dly), a cytolysin encoded by the dly gene that is lethal for mice and has hemolytic activity. We found that Dly is encoded in the highly hemolytic strain RM-71 within a 153,429-bp conjugative plasmid that we dubbed pPHDD1. In addition to Dly, pPHDD1 also encodes a homologue of the pore-forming toxin HlyA. We found a direct correlation between presence of pPHDD1 and a strong hemolytic phenotype in a collection of P. damselae subsp. damselae isolates. Hemolysis was strongly reduced in a double dly hlyA mutant, demonstrating the role of the two pPHDD1-encoded genes in hemolysis. Interestingly, although single hlyA and dly mutants showed different levels of hemolysis reduction depending on the erythrocyte source, hemolysis was not abolished in any of the single mutants, suggesting that the hemolytic phenotype is the result of the additive effect of Dly and HlyA. We found that pPHDD1-encoded dly and hlyA genes are necessary for full virulence for mice and fish. Our results suggest that pPHDD1 can be considered as a driving force for the emergence of a highly hemolytic lineage of P. damselae subsp. damselae.     

Route of delivery following successful external cephalic version

Objective

To evaluate the delivery route and the indications for cesarean delivery after successful external cephalic version (ECV).

Methods

A retrospective matched case–control study was conducted at a hospital in Lisbon, Portugal, between 2002 and 2012. Each woman who underwent successful ECV (n = 44) was compared with the previous and next women who presented for labor management and who had the same parity and a singleton vertex pregnancy at term (n = 88). The outcome measures were route of delivery, indications for cesarean delivery, and incidence of nonreassuring fetal status.

Results

Attempts at ECV were successful in 62 (46%) of 134 women, and 44 women whose fetuses remained in a cephalic presentation until delivery were included in the study. The rates of intrapartum cesarean delivery and operative vaginal delivery did not differ significantly between cases and controls (intrapartum cesarean delivery, 9 [20%] vs 16 [18%], P = 0.75; operative vaginal delivery, 14 [32%] vs 19 [22%], P = 0.20). The indications for cesarean delivery after successful ECV did not differ; in both groups, cesarean delivery was mainly performed for labor arrest disorders (cases, 6 [67%] vs controls, 13 [81%]; P = 0.63).

Conclusion

Successful ECV was not associated with increased rates of intrapartum cesarean delivery or operative vaginal delivery.     

T-cell selection in the thymus: New routes toward the identification of the self-peptide ligandome presented by thymic epithelial cells

Within the thymus, thymic epithelial cells (TECs) provide a dedicated niche for the selection of functional T cells expressing a highly variable and self-tolerant T-cell receptor (TCR) repertoire. In this minireview, we start by summarizing recent studies that have improved our understanding on the composition of cortical TEC and medullary TEC microenvironments. Next, we focus on the molecular processes that control the function of TECs in T-cell selection. In particular, we discuss the role of cortical TECs in positive selection and the pathways employed by these cells to generate and present selecting self-peptides:MHC II complexes. Several studies have underscored the role of the β5t-containing thymoproteasome in the production of unique MHC I-bound peptides critical for CD8 T-cell selection. Contrarily, the identity of the molecular determinants that regulate the generation of MHC II-bound self-peptides capable of positive selecting CD4 T cells is far more uncertain. We highlight recent advances that interconnect the autophagy-lysosomal pathway, the presentation of specific sets of self-peptide:MHC II complexes, and the diversification of CD4 TCR repertoire. Lastly, we discuss how these findings may open up new avenues for deciphering the identity of the MHC I and MHC II ligandome in the thymus.     

Yeasts identification in microfluidic devices using peptide nucleic acid fluorescence <Emphasis Type="Italic">in situ</Emphasis> hybridization (PNA-FISH)

Peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) is a highly specific molecular method widely used for microbial identification. Nonetheless, and due to the detection limit of this technique, a time-consuming pre-enrichment step is typically required before identification. In here we have developed a lab-on-a-chip device to concentrate cell suspensions and speed up the identification process in yeasts. The PNA-FISH protocol was optimized to target Saccharomyces cerevisiae, a common yeast that is very relevant for several types of food industries. Then, several coin-sized microfluidic devices with different geometries were developed. Using Computational fluid dynamics (CFD), we modeled the hydrodynamics inside the microchannels and selected the most promising options. SU-8 structures were fabricated based on the selected designs and used to produce polydimethylsiloxane-based microchips by soft lithography. As a result, an integrated approach combining microfluidics and PNA-FISH for the rapid identification of S. cerevisiae was achieved. To improve fluid flow inside microchannels and the PNA-FISH labeling, oxygen plasma treatment was applied to the microfluidic devices and a new methodology to introduce the cell suspension and solutions into the microchannels was devised. A strong PNA-FISH signal was observed in cells trapped inside the microchannels, proving that the proposed methodology works as intended. The microfluidic designs and PNA-FISH procedure described in here should be easily adaptable for detection of other microorganisms of similar size.     

Immunohistochemical classification of non-BRCA1/2 tumors identifies different groups that demonstrate the heterogeneity of BRCAX families.

Around 25% of hereditary breast and ovarian cancer families have mutations in the BRCA1 and BRCA2 genes. The search for other genes has until now failed, probably because there is not one single BRCAX gene, but rather various genes that may each be responsible for a small number of breast cancer families and/or may interact according to a polygenic model. We have studied 50 tumors from probands belonging to non-BRCA1/2 breast cancer families (BRCAX), using 25 immunohistochemical markers. The objective was to classify these tumors and confirm that they are heterogeneous. Unsupervised cluster analysis showed the existence of the following two main groups of tumors: high-grade and estrogen receptor (ER)-negative tumors (50%), and low-grade and ER-positive tumors (50%). In addition we identified five subgroups, three among the high-grade and two among the low-grade groups; one overexpressing HER-2 (18%); one with a basal-like phenotype (14%); one with a normal breast-like phenotype (18%); a luminal A subgroup (36%), and a luminal B subgroup (14%). Hypermethylation of the BRCA1 gene was observed in 42% of the cases, spread across all five subgroups, but only 37% of those had loss of heterozygosity as well. These latter cases were all clustered in the high-grade group and the majority of them in the basal-like subgroup. Our results show that familial non-BRCA1/2 tumors are heterogeneous and suggest a polygenic model for explaining the majority of BRCAX families. In addition we have defined a subset of them that have somatic inactivation of the BRCA1 gene.