Impact of fetal endoscopic tracheal occlusion in fetuses with congenital diaphragmatic hernia and moderate lung hypoplasia.

OBJECTIVE: To assess the effect of Fetal Endoscopic Tracheal Occlusion (FETO) on neonatal survival in fetuses with left congenital diaphragmatic hernia (CDH) and moderate lung hypoplasia. STUDY DESIGN: CDH fetuses with moderate pulmonary hypoplasia (observed/expected lung area to head ratio between 26% and 35%, or between 36% and 45% with liver herniation) were prospectively recruited. Included patients were matched to a control group who were ineligible for FETO. Primary outcomes were survival at 28 days, at discharge, and at 6 months of age, respectively. RESULTS: 58 cases were recruited, 29 treated with FETO and 29 matched controls. Median gestational age (GA) at balloon placement and removal were 29.6 and 33.6 weeks, respectively. FETO group showed significantly lower GA at delivery (35.2 vs. 37.1 weeks, respectively, p < 0.01), higher survival at 28 days (51.7 vs. 24.1%, respectively, p = 0.03), at discharge (48.3 vs. 24.1%, respectively, p = 0.06), and at six months of age (41.4 vs. 24.1%, respectively, p = 0.16), and significantly lower length of ventilatory support (17.8 vs. 32.3 days, p = 0.01) and NICU stay (34.2 vs. 58.3 days, p = <0.01) compared to controls. CONCLUSION: FETO was associated with a non-significant increase in survival and significantly lower neonatal respiratory morbidity among CDH fetuses with moderate lung hypoplasia.

Relationship of Patent Ductus Arteriosus Echocardiographic Markers With Descending Aorta Diastolic Flow.

OBJECTIVES: To characterize the relationship of echocardiographic markers of left heart overload and flow in peripheral major end-organ vessels (eg, celiac artery) with the presence of reversed holodiastolic flow in the descending aorta, considered a surrogate marker of an increased transductal shunt volume, in preterm patients with a patent ductus arteriosus (PDA). METHODS: This work was a retrospective study of data from echocardiography performed to investigate the hemodynamic significance of a PDA in preterm patients. We studied differences in echocardiographic markers of the PDA shunt volume according to patterns of flow in the postductal descending aorta (no PDA, PDA with antegrade diastolic flow, and PDA with reversed diastolic flow). The strength of the association between each echocardiographic marker and the presence of aortic holodiastolic flow reversal was investigated. RESULTS: We studied 137 patients with a median (interquartile range) birth weight of 850 (694-1030) g and a median gestational age of 25 (24-27) weeks. Among patients with a PDA (113), those with diastolic flow reversal in the descending aorta (44) presented had increased echocardiographic markers representative of the shunt volume (increased left ventricular output, left atrial-to-aortic ratio, pulmonary vein D wave, and shorter isovolumic relaxation time) compared to those with aortic antegrade diastolic flow. A positive, albeit weak, correlation between diastolic flow reversal and shunt volume echocardiographic markers was found. Abnormal diastolic flow in the celiac artery had the strongest correlation (R2  = 0.24). CONCLUSIONS: In preterm patients with a PDA, echocardiographic markers of the shunt volume were more abnormal in patients with reversed diastolic flow in the descending aorta. These data support the assumption that variance in these markers are related to the shunt volume, which needs consideration when adjudicating hemodynamic significance.

Dynamics of SIV-specific CXCR5+ CD8 T cells during chronic SIV infection.

A significant challenge to HIV eradication is the elimination of viral reservoirs in germinal center (GC) T follicular helper (Tfh) cells. However, GCs are considered to be immune privileged for antiviral CD8 T cells. Here, we show a population of simian immunodeficiency virus (SIV)-specific CD8 T cells express CXCR5 (C-X-C chemokine receptor type 5, a chemokine receptor required for homing to GCs) and expand in lymph nodes (LNs) following pathogenic SIV infection in a cohort of vaccinated macaques. This expansion was greater in animals that exhibited superior control of SIV. The CXCR5+ SIV-specific CD8 T cells demonstrated enhanced polyfunctionality, restricted expansion of antigen-pulsed Tfh cells in vitro, and possessed a unique gene expression pattern related to Tfh and Th2 cells. The increase in CXCR5+ CD8 T cells was associated with the presence of higher frequencies of SIV-specific CD8 T cells in the GC. Following TCR-driven stimulation in vitro, CXCR5+ but not CXCR5- CD8 T cells generated both CXCR5+ as well as CXCR5- cells. However, the addition of TGF-ß to CXCR5- CD8 T cells induced a population of CXCR5+ CD8 T cells, suggesting that this cytokine may be important in modulating these CXCR5+ CD8 T cells in vivo. Thus, CXCR5+ CD8 T cells represent a unique subset of antiviral CD8 T cells that expand in LNs during chronic SIV infection and may play a significant role in the control of pathogenic SIV infection.

A multicentre study to predict neonatal survival according to lung-to-head ratio and liver herniation in fetuses with left congenital diaphragmatic hernia (CDH): Hidden mortality from the Latin American CDH Study Group Registry.

OBJECTIVE: To evaluate natural history of fetuses congenital diaphragmatic hernia (CDH) prenatally diagnosed in countries where termination of pregnancy is not legally allowed and to predict neonatal survival according to lung area and liver herniation. METHODS: Prospective study including antenatally diagnosed CDH cases managed expectantly during pregnancy in six tertiary Latin American centres. The contribution of the observed/expected lung-to-head ratio (O/E-LHR) and liver herniation in predicting neonatal survival was assessed. RESULTS: From the total population of 380 CDH cases, 144 isolated fetuses were selected showing an overall survival rate of 31.9% (46/144). Survivors showed significantly higher O/E-LHR (56.5% vs 34.9%; P < .001), lower proportion of liver herniation (34.8% vs 80.6%, P < .001), and higher gestational age at birth (37.8 vs 36.2 weeks, P < 0.01) than nonsurvivors. Fetuses with an O/E-LHR less than 35% showed a 3.4% of survival; those with an O/E-LHR between 35% and 45% showed 28% of survival with liver up and 50% with liver down; those with an O/E-LHR greater than 45% showed 50% of survival rate with liver up and 76.9% with liver down. CONCLUSIONS: Neonatal mortality in CDH is higher in Latin American countries. The category of lung hypoplasia should be classified according to the survival rates in our Latin American CDH registry.

Accuracy and reliability of qualitative echocardiography assessment of right ventricular size and function in neonates.

BACKGROUND: Subjective assessment of right ventricular (RV) function by neonatal echocardiography lacks validation. Incorrect diagnostic assignment in patients with suspected pulmonary hypertension (PH) may lead to unnecessary treatment or missed treatment opportunities. METHODS: Six evaluators (experts [n = 3], novice [n = 3]) were asked to independently rate RV characteristics (global function, dilation, and septal flattening) based on standardized echocardiography images. We randomly selected 60 infants, ≥35 weeks gestation at birth, of whom 30 were clinically unwell with acute pulmonary hypertension (aPH) and 30 were healthy controls. aPH was defined by echocardiography presence of right-left shunting across transitional shunts or elevated right ventricular systolic pressure as estimated by the magnitude of the regurgitant jet across the tricuspid valve with impaired oxygenation. Inter-rater comparative evaluation within groups and between groups was performed using Kappa statistics. RESULTS: Global agreement between evaluators for subjective assessment of RV function (0.3 [0.03], P < 0.001), size (0.14 [0.02], P < 0.001), and septal flattening (0.2 [0.02], P < 0.001) was uniformly poor. Agreement in RV function assessment was marginally better for both expert (0.32 [0.08], P < 0.001 vs 0.13 [0.081], and P < 0.001) and novice (0.4 [0.08], P < 0.001 vs 0.06 [0.07], and P < 0.001) evaluators. Overall, the diagnosis of aPH vs control was misclassified in 18% of cases. CONCLUSION: This study demonstrated significant variability in qualitative assessment of RV size and function by trained evaluators, regardless of level of expertise attained. The reliability of objective measures of RV hemodynamics requires prospective evaluation.

Increased Abundance of M Cells in the Gut Epithelium Dramatically Enhances Oral Prion Disease Susceptibility.

Many natural prion diseases of humans and animals are considered to be acquired through oral consumption of contaminated food or pasture. Determining the route by which prions establish host infection will identify the important factors that influence oral prion disease susceptibility and to which intervention strategies can be developed. After exposure, the early accumulation and replication of prions within small intestinal Peyer's patches is essential for the efficient spread of disease to the brain. To replicate within Peyer's patches, the prions must first cross the gut epithelium. M cells are specialised epithelial cells within the epithelia covering Peyer's patches that transcytose particulate antigens and microorganisms. M cell-development is dependent upon RANKL-RANK-signalling, and mice in which RANK is deleted only in the gut epithelium completely lack M cells. In the specific absence of M cells in these mice, the accumulation of prions within Peyer's patches and the spread of disease to the brain was blocked, demonstrating a critical role for M cells in the initial transfer of prions across the gut epithelium in order to establish host infection. Since pathogens, inflammatory stimuli and aging can modify M cell-density in the gut, these factors may also influence oral prion disease susceptibility. Mice were therefore treated with RANKL to enhance M cell density in the gut. We show that prion uptake from the gut lumen was enhanced in RANKL-treated mice, resulting in shortened survival times and increased disease susceptibility, equivalent to a 10-fold higher infectious titre of prions. Together these data demonstrate that M cells are the critical gatekeepers of oral prion infection, whose density in the gut epithelium directly limits or enhances disease susceptibility. Our data suggest that factors which alter M cell-density in the gut epithelium may be important risk factors which influence host susceptibility to orally acquired prion diseases.

Relationship of Patent Ductus Arteriosus Size to Echocardiographic Markers of Shunt Volume.

OBJECTIVE: To define the technique of estimating ductal diameter (DD) that best correlates with echocardiographic markers of transductal shunt volume in preterm infants >7 days old with persistent patent ductus arteriosus (PDA). STUDY DESIGN: We conducted a retrospective study of 104 neonates born at <30 weeks gestation that had targeted neonatal echocardiography evaluation of PDA performed between 7 and 30 days. We used univariate analysis to determine the association of echocardiographic markers of shunt volume with ductal size definitions: DD, DD indexed to weight, and DD indexed to left pulmonary artery diameter. RESULTS: Two hundred echocardiograms were reviewed from 104 patients with a median gestational age of 25.4 weeks (range, 25-26.3 weeks) and a median birth weight of 810 g (range, 740-920 g). We found a weak correlation of each method of PDA size definition with individual echocardiographic markers of transductal shunt volume, of which nonindexed DD demonstrated the best correlation. The best correlation was found with markers of systemic hypoperfusion, such as diastolic flow reversal in the descending aorta (R2 = 0.24) and celiac artery (R2 = 0.21). Markers of pulmonary overcirculation, such as left ventricular end-diastolic diameter (R2 = 0.19) and left ventricular output (R2 = 0.17), showed fair correlation with nonindexed DD. CONCLUSION: In preterm infants >7 days old with PDA, nonindexed DD demonstrated weak correlations with individual echocardiographic markers of shunt volume. These data highlight the need for comprehensive echocardiographic evaluation in addition to diameter measurements to provide a better understanding of the hemodynamic consequences of PDA.

TNF-α augments RANKL-dependent intestinal M cell differentiation in enteroid cultures.

Microfold (M) cells are phagocytic intestinal epithelial cells in the follicle-associated epithelium of Peyer's patches that transport particulate antigens from the gut lumen into the subepithelial dome. Differentiation of M cells from epithelial stem cells in intestinal crypts requires the cytokine receptor activator of NF-κB ligand (RANKL) and the transcription factor Spi-B. We used three-dimensional enteroid cultures established with small intestinal crypts from mice as a model system to investigate signaling pathways involved in M cell differentiation and the influence of other cytokines on RANKL-induced M cell differentiation. Addition of RANKL to enteroids induced expression of multiple M cell-associated genes, including Spib, Ccl9 [chemokine (C-C motif) ligand 9], Tnfaip2 (TNF-α-induced protein 2), Anxa5 (annexin A5), and Marcksl1 (myristoylated alanine-rich protein kinase C substrate) in 1 day. The mature M cell marker glycoprotein 2 (Gp2) was strongly induced by 3 days and expressed by 11% of cells in enteroids. The noncanonical NF-κB pathway was required for RANKL-induced M cell differentiation in enteroids, as addition of RANKL to enteroids from mice with a null mutation in the mitogen-activated protein kinase kinase kinase 14 (Map3k14) gene encoding NF-κB-inducing kinase failed to induce M cell-associated genes. While the cytokine TNF-α alone had little, if any, effect on expression of M cell-associated genes, addition of TNF-α to RANKL consistently resulted in three- to sixfold higher levels of multiple M cell-associated genes than RANKL alone. One contributing mechanism is the rapid induction by TNF-α of Relb and Nfkb2 (NF-κB subunit 2), genes encoding the two subunits of the noncanonical NF-κB heterodimer. We conclude that endogenous activators of canonical NF-κB signaling present in the gut-associated lymphoid tissue microenvironment, including TNF-α, can play a supportive role in the RANKL-dependent differentiation of M cells in the follicle-associated epithelium.

Analysis of the tryptic search space in UniProt databases.

In this article, we provide a comprehensive study of the content of the Universal Protein Resource (UniProt) protein data sets for human and mouse. The tryptic search spaces of the UniProtKB (UniProt knowledgebase) complete proteome sets were compared with other data sets from UniProtKB and with the corresponding International Protein Index, reference sequence, Ensembl, and UniRef100 (where UniRef is UniProt reference clusters) organism-specific data sets. All protein forms annotated in UniProtKB (both the canonical sequences and isoforms) were evaluated in this study. In addition, natural and disease-associated amino acid variants annotated in UniProtKB were included in the evaluation. The peptide unicity was also evaluated for each data set. Furthermore, the peptide information in the UniProtKB data sets was also compared against the available peptide-level identifications in the main MS-based proteomics repositories. Identifying the peptides observed in these repositories is an important resource of information for protein databases as they provide supporting evidence for the existence of otherwise predicted proteins. Likewise, the repositories could use the information available in UniProtKB to direct reprocessing efforts on specific sets of peptides/proteins of interest. In summary, we provide comprehensive information about the different organism-specific sequence data sets available from UniProt, together with the pros and cons for each, in terms of search space for MS-based bottom-up proteomics workflows. The aim of the analysis is to provide a clear view of the tryptic search space of UniProt and other protein databases to enable scientists to select those most appropriate for their purposes.

The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.

The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.

Activation of gas-phase uranyl: from an oxo to a nitrido complex.

The uranyl moiety, UO2(2+), is ubiquitous in the chemistry of uranium, the most prevalent actinide. Replacing the strong uranium-oxygen bonds in uranyl with other ligands is very challenging, having met with only limited success. We report here uranyl oxo bond activation in the gas phase to form a terminal nitrido complex, a previously elusive transformation. Collision induced dissociation of gas-phase UO2(NCO)Cl2(-) in an ion trap produced the nitrido oxo complex, NUOCl2(-), and CO2. NUOCl2(-) was computed by DFT to have Cs symmetry and a singlet ground state. The computed bond length and order indicate a triple U-N bond. Endothermic activation of UO2(NCO)Cl2(-) to produce NUOCl2(-) and neutral CO2 was computed to be thermodynamically more favorable than NCO ligand loss. Complete reaction pathways for the CO2 elimination process were computed at the DFT level.

Normal curvature of glenoid surface can be restored when performing an inlay osteochondral allograft: an anatomic computed tomographic comparison.

PURPOSE: The purpose of this study was to quantitatively measure the morphology of the glenoid and to assess feasibility of using the medial tibial plateau surface as a donor for osteoarticular allograft reconstruction of the glenoid. METHODS: Using computed tomography (CT), 10 tibias and 10 scapular models from our database (5 males and 5 females in each group) were randomly selected. Commercial software (Mimics, Materialize, Inc., Plymouth, MI) was used to extract the bone contours from the CT images and to reconstruct the 3-dimensional (3D) geometry of the scapula and tibia. By utilizing the software Creo Elements/Pro 5.0 (Parametric Technology Corp., Needham, MA), mean length and width of both the glenoid and medial tibial plateau were calculated. Radius of curvature was then measured in each 3D CT model at three intermediate segment points that were established within the length line at 25, 50, and 75 percent from superior to inferior in the glenoid and from posterior to anterior in the medial tibial plateau. Statistical analysis was performed and determined to be significant for P < 0.05. RESULTS: The mean (± SD) radius of curvature values at the established 25, 50, and 75 percent segments of the glenoid were 47.4 ± 17.5 mm, 51.2 ± 12.4 mm, and 45.9 ± 17.0 mm, respectively. For the medial tibial plateau, the radius of curvature at 25, 50, and 75 percent were 43.5 ± 9.7 mm, 37.4 ± 14.3 mm and 52.3 ± 21.5 mm, respectively. Values of the glenoid length were 34.0 ± 2.9 mm, and width values were 24.4 ± 2.3 mm. For the medial tibial plateau, the length was 42.6 ± 2.7 mm, and the width was 23.3 ± 4.3 mm. There was no statistical difference in the radius of curvature and dimensional surface area between the glenoid and medial tibial plateau surfaces. CONCLUSION: The 3D CT-based anatomic study found that there is a statistically similar relationship in the radius of curvature of the glenoid and the medial tibial plateau surface. This concept may allow the medial tibial plateau to be used as a donor for osteoarticular allograft reconstruction of the glenoid, especially in young patients where previous studies have demonstrated that the success rate in shoulder replacements is not as good as in older patients.

Pulmonary Calcifying Fibrous Tumor in a Pediatric Patient: A Case Report.

A calcifying fibrous tumor (CFT), also known as calcifying fibrous pseudotumor, is an uncommon non-cancerous neoplasm usually located in the gastrointestinal tract. Its location in the lung is extremely rare, and only a few case reports have been published. This case report describes our diagnostic approach in a 9-year-old male patient with an incidental pulmonary mass. The mass was initially misdiagnosed, requiring multiple imaging tests and interventions to obtain the definitive diagnosis of pulmonary CFT. This paper aims to contribute to the limited information available on pulmonary CFT by presenting detailed findings from computed tomography and magnetic resonance imaging.

Next-generation cell-penetrating antibodies for tumor targeting and RAD51 inhibition.

Monoclonal antibody therapies for cancer have demonstrated extraordinary clinical success in recent years. However, these strategies are thus far mostly limited to specific cell surface antigens, even though many disease targets are found intracellularly. Here we report studies on the humanization of a full-length, nucleic acid binding, monoclonal lupus-derived autoantibody, 3E10, which exhibits a novel mechanism of cell penetration and tumor specific targeting. Comparing humanized variants of 3E10, we demonstrate that cell uptake depends on the nucleoside transporter ENT2, and that faster cell uptake and superior in vivo tumor targeting are associated with higher affinity nucleic acid binding. We show that one human variant retains the ability of the parental 3E10 to bind RAD51, serving as a synthetically lethal inhibitor of homology-directed repair in vitro. These results provide the basis for the rational design of a novel antibody platform for therapeutic tumor targeting with high specificity following systemic administration.

From Peptidome to PRIDE: public proteomics data migration at a large scale.

The PRIDE database, developed and maintained at the European Bioinformatics Institute (EBI), is one of the most prominent data repositories dedicated to high throughput MS-based proteomics data. Peptidome, developed by the National Center for Biotechnology Information (NCBI) as a sibling resource to PRIDE, was discontinued due to funding constraints in April 2011. A joint effort between the two teams was started soon after the Peptidome closure to ensure that data were not "lost" to the wider proteomics community by exporting it to PRIDE. As a result, data in the low terabyte range have been migrated from Peptidome to PRIDE and made publicly available under experiment accessions 17 900-18 271, representing 54 projects, ~53 million mass spectra, ~10 million peptide identifications, ~650,000 protein identifications, ~1.1 million biologically relevant protein modifications, and 28 species, from more than 30 different labs.

Ensembl 2011.

The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.

Comprehensive Arthroscopic Management (CAM) procedure: clinical results of a joint-preserving arthroscopic treatment for young, active patients with advanced shoulder osteoarthritis.

PURPOSE: The purpose of this study was to examine the surgical outcomes of 29 active patients (30 shoulders) with end-stage, symptomatic glenohumeral arthritis undergoing the comprehensive arthroscopic management (CAM) procedure. METHODS: In this institutional review board-approved study, patients with advanced glenohumeral osteoarthritis (OA) underwent the CAM procedure, a joint-preserving arthroscopic treatment. All subjects were candidates for shoulder arthroplasty. The CAM procedure involves the combination of glenohumeral chondroplasty; removal of loose bodies if present; humeral osteoplasty and osteophyte resection (goat's beard deformity); anterior, posterior, and inferior capsular release; subacromial decompression; axillary nerve neurolysis; and biceps tenodesis. Outcome measures included pain, American Shoulder and Elbow Surgeons score, Single Assessment Numeric Evaluation score, QuickDASH (short version of Disabilities of the Arm, Shoulder and Hand questionnaire) score, and satisfaction. For survivorship analysis, failure was defined as progression to shoulder arthroplasty. RESULTS: The mean age was 52 years (range, 33 to 68 years), and there were 23 men and 6 women. Of the 30 shoulders, 6 progressed to an arthroplasty at a mean of 1.9 years (range, 0.9 to 3.4 years). Patients with less than 2.0 mm of joint space on radiographs were more likely to undergo arthroplasty (P = .037). For shoulders that did not progress to arthroplasty (n = 24), the mean follow-up was 2.6 years (range, 2.1 to 4.7 years). The American Shoulder and Elbow Surgeons scores significantly improved from 58 points (SE, 2.4) to 83 points (SE, 3.3) (P < .001), and pain levels decreased with activities of daily living, work, recreation, and sleep (P < .05). The median patient satisfaction rating was 9 (range, 3 to 10). Survivorship analysis showed a 92% survival rate at 1 year and 85% at 2 years. Patients with larger osteophytes had greater improvement in postoperative range of motion but were less satisfied (r = 0.479, P = .038). CONCLUSIONS: The CAM procedure reduced pain, improved function, and provided reasonable short-term durability for our cohort of young, active patients with advanced shoulder OA and may serve as a joint-preserving alternative to arthroplasty. Patients with less than 2 mm of joint space had a significantly higher failure rate. The CAM procedure is a viable surgical option in young, active patients with advanced OA, showing survivorship of 85% at 2 years. LEVEL OF EVIDENCE: Level IV, therapeutic case series.