Dust trapping in inviscid vortex pairs

The motion of tiny heavy particles transported in a co-rotating vortex pair, with or without particle inertia and sedimentation, is investigated. The dynamics of non-inertial sedimenting particles is shown to be chaotic, under the combined effect of gravity and of the circular displacement of the vortices. This phenomenon is very sensitive to particle inertia, if any. By using nearly hamiltonian dynamical system theory for the particle motion equation written in the rotating reference frame, one can show that small inertia terms of the particle motion equation strongly modify the Melnikov function of the homoclinic trajectories and heteroclinic cycles of the unperturbed system, as soon as the particle response time is of the order of the settling time (Froude number of order unity). The critical Froude number above which chaotic motion vanishes and a regular centrifugation takes place is obtained from this Melnikov analysis and compared to numerical simulations. Particles with a finite inertia, and in the absence of gravity, are not necessarily centrifugated away from the vortex system. Indeed, these particles can have various equilibrium positions in the rotating reference frame, like the Lagrange points of celestial mechanics, according to whether their Stokes number is smaller or larger than some critical value. An analytical stability analysis reveals that two of these points are stable attracting points, so that permanent trapping can occur for inertial particles injected in an isolated co-rotating vortex pair. Particle trapping is observed to persist when viscosity, and therefore vortex coalescence, is taken into account. Numerical experiments at large but finite Reynolds number show that particles can indeed be trapped temporarily during vortex roll-up, and are eventually centrifugated away once vortex coalescence occurs.Comment: 7 figure

Pregnancy Outcomes After Endometrioma Excision in Patients Undergoing In Vitro Fertilization and Embryo Transfer: A Historical Cohort Study

Objective: The objective of the study was to examine the effect of endometrioma excision on pregnancy outcomes in women with advanced-stage endometriosis who underwent in vitro fertilization and embryo transfer (IVF-ET). Design: This is a historical cohort study. Materials and Methods: We compared the pregnancy outcomes of 141 women undergoing IVF-ET. The study group consisted of 25 patients who had stage III/IV endometriosis and endometrioma excision (group 1). The control groups included 40 patients who had stage III/IV endometriosis, but no endometrioma and who underwent ovariolysis (group 2) and 76 patients with tubal factors infertility who underwent tubal surgery (group 3). After surgery up to two IVF-ET cycles in each group were analyzed. Results: Our study showed that the mean total dose of gonadotropin administered in IVF-ET cycle I was higher in group 1 compared with groups 2 and 3 (p=0.03). Otherwise, there was no significant difference in the ovarian responses among the three groups. There was a statistically significant increase in clinical pregnancy rate per cycle in the endometrioma group (69.7%) versus the ovariolysis group (48.1%) and tubal factor group (48.0%). However, there was no significant difference in delivery rate per cycle among the three groups. There was a statistically significant higher miscarriage rate in the endometrioma group (39.1%) compared with the ovariolysis group (11.5%) and tubal factor group (14.3%). Conclusion: In conclusion, our study suggests that endometrioma excision surgery does not compromise the overall ovarian reserve or pregnancy outcomes after IVF-ET. (J GYNECOL SURG 31:214)Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140100/1/gyn.2015.0013.pd

Post-Translational Regulation via Clp Protease Is Critical for Survival of Mycobacterium tuberculosis

Unlike most bacterial species, Mycobacterium tuberculosis depends on the Clp proteolysis system for survival even in in vitro conditions. We hypothesized that Clp is required for the physiologic turnover of mycobacterial proteins whose accumulation is deleterious to bacterial growth and survival. To identify cellular substrates, we employed quantitative proteomics and transcriptomics to identify the set of proteins that accumulated upon the loss of functional Clp protease. Among the set of potential Clp substrates uncovered, we were able to unambiguously identify WhiB1, an essential transcriptional repressor capable of auto-repression, as a substrate of the mycobacterial Clp protease. Dysregulation of WhiB1 turnover had a toxic effect that was not rescued by repression of whiB1 transcription. Thus, under normal growth conditions, Clp protease is the predominant regulatory check on the levels of potentially toxic cellular proteins. Our findings add to the growing evidence of how post-translational regulation plays a critical role in the regulation of bacterial physiology

Breast feeding and intergenerational social mobility: what are the mechanisms?

Objective To investigate the association between breast feeding and intergenerational social mobility and the possible mediating role of neurological and stress mechanisms. Design Secondary analysis of data from the 1958 and the 1970 British Cohort Studies. Setting Longitudinal study of individuals born in Britain during 1 week in 1958 and 1970. Participants 17 419 individuals participated in the 1958 cohort and 16 771 in the 1970 cohort. The effect of breast feeding on intergenerational social mobility from age 10/11 to age 33/34 was analysed after multiple imputations to fill in missing data and propensity score matching on a wide range of confounders measured in childhood (1958 cohort N=16 039-16 154; 1970 cohort N=16 255-16 361). Main outcome measures Own Registrar General's Social Class (RGSC) at 33/34 years adjusted for father's RGSC at 10/11 years, gender and their interaction. Results Breastfed individuals were more likely to be upwardly mobile (1958 cohort: OR 1.24 95% CI 1.12 to 1.38; 1970 cohort: OR 1.24 95% CI 1.12 to 1.37) and less likely to be downwardly mobile (1958 cohort: OR 0.81 95% CI 0.73 to 0.90; 1970 cohort: OR 0.79 95% CI 0.71 to 0.88). In an ordinal regression model, markers of neurological development (cognitive test scores) and stress (emotional stress scores) accounted for approximately 36% of the relationship between breast feeding and social mobility. Conclusions Breast feeding increased the odds of upward social mobility and decreased the odds of downward mobility. Consistent with a causal explanation, the findings were robust to matching on a large number of observable variables and effect sizes were alike for two cohorts with different social distributions of breast feeding. The effect was mediated in part through neurological and stress mechanisms

A new implicit review instrument for measuring quality of care delivered to pediatric patients in the emergency department

BackgroundThere are few outcomes experienced by children receiving care in the Emergency Department (ED) that are amenable to measuring for the purposes of assessing of quality of care. The purpose of this study was to develop, test, and validate a new implicit review instrument that measures quality of care delivered to children in EDs.MethodsWe developed a 7-point structured implicit review instrument that encompasses four aspects of care, including the physician's initial data gathering, integration of information and development of appropriate diagnoses; initial treatment plan and orders; and plan for disposition and follow-up. Two pediatric emergency medicine physicians applied the 5-item instrument to children presenting in the highest triage category to four rural EDs, and we assessed the reliability of the average summary scores (possible range of 5-35) across the two reviewers using standard measures. We also validated the instrument by comparing this mean summary score between those with and without medication errors (ascertained independently by two pharmacists) using a two-sample t-test.ResultsWe reviewed the medical records of 178 pediatric patients for the study. The mean and median summary score for this cohort of patients were 27.4 and 28.5, respectively. Internal consistency was high (Cronbach's alpha of 0.92 and 0.89). All items showed a significant (p < 0.005) positive correlation between reviewers using the Spearman rank correlation (range 0.24 to 0.39). Exact agreement on individual items between reviewers ranged from 70.2% to 85.4%. The Intra-class Correlation Coefficient for the mean of the total summary score across the two reviewers was 0.65. The validity of the instrument was supported by the finding of a higher score for children without medication errors compared to those with medication errors which trended toward significance (mean score = 28.5 vs. 26.0, p = 0.076).ConclusionThe instrument we developed to measure quality of care provided to children in the ED has high internal consistency, fair to good inter-rater reliability and inter-rater correlation, and high content validity. The validity of the instrument is supported by the fact that the instrument's average summary score was lower in the presence of medication errors, which trended towards statistical significance

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment