Partially linear censored quantile regression

Censored regression quantile (CRQ) methods provide a powerful and flexible approach to the analysis of censored survival data when standard linear models are felt to be appropriate. In many cases however, greater flexibility is desired to go beyond the usual multiple regression paradigm. One area of common interest is that of partially linear models: one (or more) of the explanatory covariates are assumed to act on the response through a non-linear function. Here the CRQ approach of Portnoy (J Am Stat Assoc 98:1001–1012, 2003) is extended to this partially linear setting. Basic consistency results are presented. A simulation experiment and unemployment example justify the value of the partially linear approach over methods based on the Cox proportional hazards model and on methods not permitting nonlinearity

The Universe out of an Elementary Particle?

We consider a model of an elementary particle as a 2 + 1 dimensional brane evolving in a 3 + 1 dimensional space. Introducing gauge fields that live in the brane as well as normal surface tension can lead to a stable "elementary particle" configuration. Considering the possibility of non vanishing vacuum energy inside the bubble leads, when gravitational effects are considered, to the possibility of a quantum decay of such "elementary particle" into an infinite universe. Some remarkable features of the quantum mechanics of this process are discussed, in particular the relation between possible boundary conditions and the question of instability towards Universe formation is analyzed

These aren’t the loci you’re looking for: Principles of effective SNP filtering for molecular ecologists

Sequencing reduced‐representation libraries of restriction site‐associated DNA (RADseq) to identify single nucleotide polymorphisms (SNPs) is quickly becoming a standard methodology for molecular ecologists. Because of the scale of RADseq data sets, putative loci cannot be assessed individually, making the process of filtering noise and correctly identifying biologically meaningful signal more difficult. Artefacts introduced during library preparation and/or bioinformatic processing of SNP data can create patterns that are incorrectly interpreted as indicative of population structure or natural selection. Therefore, it is crucial to carefully consider types of errors that may be introduced during laboratory work and data processing, and how to minimize, detect and remove these errors. Here, we discuss issues inherent to RADseq methodologies that can result in artefacts during library preparation and locus reconstruction resulting in erroneous SNP calls and, ultimately, genotyping error. Further, we describe steps that can be implemented to create a rigorously filtered data set consisting of markers accurately representing independent loci and compare the effect of different combinations of filters on four RAD data sets. At last, we stress the importance of publishing raw sequence data along with final filtered data sets in addition to detailed documentation of filtering steps and quality control measures

Kin-Aggregations Explain Chaotic Genetic Patchiness, a Commonly Observed Genetic Pattern, in a Marine Fish

The phenomenon of chaotic genetic patchiness is a pattern commonly seen in marine organisms, particularly those with demersal adults and pelagic larvae. This pattern is usually associated with sweepstakes recruitment and variable reproductive success. Here we investigate the biological underpinnings of this pattern in a species of marine goby Coryphopterus personatus. We find that populations of this species show tell-tale signs of chaotic genetic patchiness including: small, but significant, differences in genetic structure over short distances; a non-equilibrium or “chaotic” pattern of differentiation among locations in space; and within locus, within population deviations from the expectations of Hardy-Weinberg equilibrium (HWE). We show that despite having a pelagic larval stage, and a wide distribution across Caribbean coral reefs, this species forms groups of highly related individuals at small spatial scales (metres). These spatially clustered family groups cause the observed deviations from HWE and local population differentiation, a finding that is rarely demonstrated, but could be more common than previously thought

Breast conserving surgery in the treatment of breast cancer stage III

This study evaluated the ability to perform organ-operation in breast cancer stage III. Highlight 2 similar groups of patients, depending on the extent of the procedure: in the 1st (main) were performed breast conserving surgery (BCS), in the 2nd (control) radical mastectomy (RM) with preservation of the pectoral muscles. It was analyzed overall survival (OS), disease-free survival (DFS); the frequency of postoperative complications and aesthetic results of the treatment. The 3-, 5- and 10-year OS group did not differ significantly and amounted to 80.0 ± 8.0, 87.0 ± 4.6 %; 70.2 ± 9.7, 67.8 ± 6.7 %; 61.4 ± 11.8, 62.2 ± 7.2 %, respectively (p > 0.05). The 3-, 5- and 10-year DFS group did not differ significantly and amounted to 68.1 ± 9.2, 80.7 ± 5.5 %; 58.9 ± 10.9, 67.2 ± 6.6 %; 58.9 ± 10.9, 60.3 ± 7.2 %), respectively (p > 0.05). The frequency of postoperative complications was in the group of BCS 7.7 %, in the group of RM – 6.9 % (p > 0.05). The aesthetic results of the treatment: satisfactory when BCS, unsatisfactory at RM

CP and related phenomena in the context of Stellar Evolution

We review the interaction in intermediate and high mass stars between their evolution and magnetic and chemical properties. We describe the theory of Ap-star `fossil' fields, before touching on the expected secular diffusive processes which give rise to evolution of the field. We then present recent results from a spectropolarimetric survey of Herbig Ae/Be stars, showing that magnetic fields of the kind seen on the main-sequence already exist during the pre-main sequence phase, in agreement with fossil field theory, and that the origin of the slow rotation of Ap/Bp stars also lies early in the pre-main sequence evolution; we also present results confirming a lack of stars with fields below a few hundred gauss. We then seek which macroscopic motions compete with atomic diffusion in determining the surface abundances of AmFm stars. While turbulent transport and mass loss, in competition with atomic diffusion, are both able to explain observed surface abundances, the interior abundance distribution is different enough to potentially lead to a test using asterosismology. Finally we review progress on the turbulence-driving and mixing processes in stellar radiative zones.Comment: Proceedings of IAU GA in Rio, JD4 on Ap stars; 10 pages, 7 figure

Centerscope

Centerscope, formerly Scope, was published by the Boston University Medical Center "to communicate the concern of the Medical Center for the development and maintenance of improved health care in contemporary society.

Placental syncytiotrophoblast constitutes a major barrier to vertical transmission of Listeria monocytogenes.

Listeria monocytogenes is an important cause of maternal-fetal infections and serves as a model organism to study these important but poorly understood events. L. monocytogenes can infect non-phagocytic cells by two means: direct invasion and cell-to-cell spread. The relative contribution of each method to placental infection is controversial, as is the anatomical site of invasion. Here, we report for the first time the use of first trimester placental organ cultures to quantitatively analyze L. monocytogenes infection of the human placenta. Contrary to previous reports, we found that the syncytiotrophoblast, which constitutes most of the placental surface and is bathed in maternal blood, was highly resistant to L. monocytogenes infection by either internalin-mediated invasion or cell-to-cell spread. Instead, extravillous cytotrophoblasts-which anchor the placenta in the decidua (uterine lining) and abundantly express E-cadherin-served as the primary portal of entry for L. monocytogenes from both extracellular and intracellular compartments. Subsequent bacterial dissemination to the villous stroma, where fetal capillaries are found, was hampered by further cellular and histological barriers. Our study suggests the placenta has evolved multiple mechanisms to resist pathogen infection, especially from maternal blood. These findings provide a novel explanation why almost all placental pathogens have intracellular life cycles: they may need maternal cells to reach the decidua and infect the placenta

Listeriolysin O Is Necessary and Sufficient to Induce Autophagy during Listeria monocytogenes Infection

Recent studies have suggested that autophagy is utilized by cells as a protective mechanism against Listeria monocytogenes infection.However we find autophagy has no measurable role in vacuolar escape and intracellular growth in primary cultured bone marrow derived macrophages (BMDMs) deficient for autophagy (atg5-/-). Nevertheless, we provide evidence that the pore forming activity of the cholesterol-dependent cytolysin listeriolysin O (LLO) can induce autophagy subsequent to infection by L. monocytogenes. Infection of BMDMs with L. monocytogenes induced microtubule-associated protein light chain 3 (LC3) lipidation, consistent with autophagy activation, whereas a mutant lacking LLO did not. Infection of BMDMs that express LC3-GFP demonstrated that wild-type L. monocytogenes was encapsulated by LC3-GFP, consistent with autophagy activation, whereas a mutant lacking LLO was not. Bacillus subtilis expressing either LLO or a related cytolysin, perfringolysin O (PFO), induced LC3 colocalization and LC3 lipidation. Further, LLO-containing liposomes also recruited LC3-GFP, indicating that LLO was sufficient to induce targeted autophagy in the absence of infection. The role of autophagy had variable effects depending on the cell type assayed. In atg5-/- mouse embryonic fibroblasts, L. monocytogenes had a primary vacuole escape defect. However, the bacteria escaped and grew normally in atg5-/- BMDMs.We propose that membrane damage, such as that caused by LLO, triggers bacterial-targeted autophagy, although autophagy does not affect the fate of wild-type intracellular L. monocytogenes in primary BMDMs