Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

Leiomyosarcoma (LMS) is a soft tissue tumor with a significant degree of morphologic and molecular heterogeneity. We used integrative molecular profiling to discover and characterize molecular subtypes of LMS. Gene expression profiling was performed on 51 LMS samples. Unsupervised clustering showed three reproducible LMS clusters. Array comparative genomic hybridization (aCGH) was performed on 20 LMS samples and showed that the molecular subtypes defined by gene expression showed distinct genomic changes. Tumors from the muscle-enriched cluster showed significantly increased copy number changes (P=0.04). A majority of the muscle-enriched cases showed loss at 16q24, which contains Fanconi anemia, complementation group A, known to have an important role in DNA repair, and loss at 1p36, which contains PRDM16, of which loss promotes muscle differentiation. Immunohistochemistry (IHC) was performed on LMS tissue microarrays (n=377) for five markers with high levels of messenger RNA in the muscle-enriched cluster (ACTG2, CASQ2, SLMAP, CFL2 and MYLK) and showed significantly correlated expression of the five proteins (all pairwise P<0.005). Expression of the five markers was associated with improved disease-specific survival in a multivariate Cox regression analysis (P<0.04). In this analysis that combined gene expression profiling, aCGH and IHC, we characterized distinct molecular LMS subtypes, provided insight into their pathogenesis, and identified prognostic biomarkers

The effects of iCVD film thickness and conformality on the permeability and wetting of MD membranes

Membranes possessing high permeability to water vapor and high liquid entry pressure (LEP) are necessary for efficient membrane distillation (MD) desalination. A common technique to prepare specialized MD membranes consists of coating a hydrophilic or hydrophobic base membrane with a low surface-energy material. This increases its liquid entry pressure, making the membrane suitable for MD. However, in addition to increasing LEP, the surface-coating may also decrease permeability of the membrane by reducing its average pore size. In this study, we quantify the effects of initiated chemical vapor deposition (iCVD) polymer coatings on membrane permeability and LEP. We consider whether the iCVD films should have minimized thickness or maximized non-conformality, in order to maximize the permeability achieved for a given value of LEP. We determined theoretically that permeability of a single pore is maximized with a highly non-conformal iCVD coating. However, the overall permeability of a membrane consisting of many pores is maximized when iCVD film thickness is minimized. We applied the findings experimentally, preparing an iCVD-treated track-etched polycarbonate (PCTE) membrane and testing it in a permeate gap membrane distillation (PCMD) system. This study focuses on membranes with clearly defined, cylindrical pores. However, we believe that the principles we discuss will extend to membranes with more complex pore architectures. Overall, this work indicates that the focus of surface-coating development should be on minimizing film thickness, not on increasing their non-conformality.MIT & Masdar Institute Cooperative Program (02/MI/MI/CP/11/07633/GEN/G/00)Massachusetts Institute of Technology. Institute for Soldier Nanotechnologies (W911NF-13-d-0001

Finite precision measurement nullifies the Kochen-Specker theorem

Only finite precision measurements are experimentally reasonable, and they cannot distinguish a dense subset from its closure. We show that the rational vectors, which are dense in S^2, can be colored so that the contradiction with hidden variable theories provided by Kochen-Specker constructions does not obtain. Thus, in contrast to violation of the Bell inequalities, no quantum-over-classical advantage for information processing can be derived from the Kochen-Specker theorem alone.Comment: 7 pages, plain TeX; minor corrections, interpretation clarified, references update

Industrial relations in the UK shipping industry since the Second World War

The shipping industry has undergone a period of rapid and fundamental change during the three decades since the end of the Second World War. While these changes have been experienced world-wide and have promoted the implementation of technological advances and the growth of the world fleet, they have occurred during a period which has also witnessed a substantial relative decline in Britain's maritime position. It is the aim of this study to analyse their effect on industrial relations in the U.K. shipping industry

The advanced LIGO input optics

The advanced LIGO gravitational wave detectors are nearing their design sensitivity and should begin taking meaningful astrophysical data in the fall of 2015. These resonant optical interferometers will have unprecedented sensitivity to the strains caused by passing gravitational waves. The input optics play a significant part in allowing these devices to reach such sensitivities. Residing between the pre-stabilized laser and the main interferometer, the input optics subsystem is tasked with preparing the laser beam for interferometry at the sub-attometer level while operating at continuous wave input power levels ranging from 100 mW to 150 W. These extreme operating conditions required every major component to be custom designed. These designs draw heavily on the experience and understanding gained during the operation of Initial LIGO and Enhanced LIGO. In this article, we report on how the components of the input optics were designed to meet their stringent requirements and present measurements showing how well they have lived up to their design

Coordination changes in liquid tin under shock compression determined using in situ femtosecond x-ray diffraction

Little is known regarding the liquid structure of materials compressed to extreme conditions, and even less is known about liquid structures undergoing rapid compression on nanosecond timescales. Here, we report on liquid structure factor and radial distribution function measurements of tin shock compressed to 84(19) GPa. High-quality, femtosecond x-ray diffraction measurements at the Linac Coherent Light Source were used to extract the liquid diffuse scattering signal. From the radial distribution function, we find that the structural evolution of the liquid with increasing pressure mimics the evolution of the solid phase. With increasing pressure, we find that the liquid structure evolves from a complex structure, with a low coordination number, to a simple liquid structure with a coordination number of 12. We provide a pathway for future experiments to study liquids at elevated pressures using high-energy lasers to shock compress materials beyond the reach of static diamond anvil cell techniques

The Advanced LIGO Input Optics

The advanced LIGO gravitational wave detectors are nearing their design sensitivity and should begin taking meaningful astrophysical data in the fall of 2015. These resonant optical interferometers will have unprecedented sensitivity to the strains caused by passing gravitational waves. The input optics play a significant part in allowing these devices to reach such sensitivities. Residing between the pre-stabilized laser and the main interferometer, the input optics subsystem is tasked with preparing the laser beam for interferometry at the sub-attometer level while operating at continuous wave input power levels ranging from 100 mW to 150 W. These extreme operating conditions required every major component to be custom designed. These designs draw heavily on the experience and understanding gained during the operation of Initial LIGO and Enhanced LIGO. In this article, we report on how the components of the input optics were designed to meet their stringent requirements and present measurements showing how well they have lived up to their design

Recovery of Metastable Dense Bi Synthesized by Shock Compression

X-ray free electron laser (XFEL) sources have revolutionized our capability to study ultrafast material behavior. Using an XFEL, we revisit the structural dynamics of shock compressed bismuth, resolving the transition sequence on shock release in unprecedented details. Unlike previous studies that found the phase-transition sequence on shock release to largely adhere to the equilibrium phase diagram (i.e., Bi-V → Bi-III → Bi-II → Bi-I), our results clearly reveal previously unseen, non-equilibrium behavior at these conditions. On pressure release from the Bi-V phase at 5 GPa, the Bi-III phase is not formed but rather a new metastable form of Bi. This new phase transforms into the Bi-II phase which in turn transforms into a phase of Bi which is not observed on compression. We determine this phase to be isostructural with β-Sn and recover it to ambient pressure where it exists for 20 ns before transforming back to the Bi-I phase. The structural relationship between the tetragonal β-Sn phase and the Bi-II phase (from which it forms) is discussed. Our results show the effect that rapid compression rates can have on the phase selection in a transforming material and show great promise for recovering high-pressure polymorphs with novel material properties in the future

Validation of a contemporary prostate cancer grading system using prostate cancer death as outcome

BACKGROUND: Gleason scoring (GS) has major deficiencies and a novel system of five grade groups (GS⩽6; 3+4; 4+3; 8; ⩾9) has been recently agreed and included in the WHO 2016 classification. Although verified in radical prostatectomies using PSA relapse for outcome, it has not been validated using prostate cancer death as an outcome in biopsy series. There is debate whether an ‘overall' or ‘worst' GS in biopsies series should be used. METHODS: Nine hundred and eighty-eight prostate cancer biopsy cases were identified between 1990 and 2003, and treated conservatively. Diagnosis and grade was assigned to each core as well as an overall grade. Follow-up for prostate cancer death was until 31 December 2012. A log-rank test assessed univariable differences between the five grade groups based on overall and worst grade seen, and using univariable and multivariable Cox proportional hazards. Regression was used to quantify differences in outcome. RESULTS: Using both ‘worst' and ‘overall' GS yielded highly significant results on univariate and multivariate analysis with overall GS slightly but insignificantly outperforming worst GS. There was a strong correlation with the five grade groups and prostate cancer death. CONCLUSIONS: This is the largest conservatively treated prostate cancer cohort with long-term follow-up and contemporary assessment of grade. It validates the formation of five grade groups and suggests that the ‘worst' grade is a valid prognostic measure

Stunting and lead: using causal mediation analysis to better understand how environmental lead exposure affects cognitive outcomes in children

Background Many children in Bangladesh experience poor nutritional status and environmental lead exposure, both of which are associated with lower scores on neurodevelopmental assessments. Recent studies have suggested that part of lead’s adverse effects on neurodevelopment are caused in part by lead’s effect on growth. New statistical methods are now available to evaluate potential causal pathways in observational studies. This study used a novel statistical method to test the hypothesis that stunting, a measure of linear growth related to poor nutrition, is a mediator and/or an effect modifier of the lead exposure’s adverse effect on cognitive development. Methods Participants were 734 children from a longitudinal birth cohort established in rural Bangladesh to study the health effects of prenatal and early childhood environmental metal exposures. Lead exposure was estimated using umbilical cord blood samples obtained at birth and blood obtained via venipuncture at age 20–40 months. Stunting was determined using the World Health Organization’s standards. Neurodevelopment was assessed at age 20–40 months years using the Bayley Scales of Infant and Toddler Development, Third Edition (BSID-III). We evaluated the effect of lead on stunting and whether the effect of lead on cognitive scores is modified by stunting status in multivariable regression analyses. We then conducted a novel 4-way mediation analysis that allows for exposure-mediator interaction to assess how much of the effect of lead on cognitive scores is explained by the pathway through stunting (mediation) and how much is explained by the interaction between lead and stunt (effect modification). Results Stunting was not a mediator of the effect of lead in our analyses. Results suggested effect modification by stunting. In an area of Bangladesh with lower lead exposures (median umbilical cord blood lead concentration, 1.7 μg/dL), stunting modified the relationship between prenatal blood lead concentrations and cognitive score at age 2–3 years. A 1-unit increase in natural log cord blood lead concentration in the presence of stunting was associated with a 2.1-unit decrease in cognitive scores (β = − 2.10, SE = 0.71, P = 0.003). This interaction was not found in a second study site where lead exposures were higher (median umbilical cord blood lead concentration, 6.1 μg/dL, β = − 0.45, SE = 0.49, P = 0.360). Conclusions We used a novel method of mediation analysis to test whether stunting mediated the adverse effect of prenatal lead exposure on cognitive outcomes in Bangladesh. While we did not find that stunting acted as mediator of lead’s effect on cognitive development, we found significant effect modification by stunting. Our results suggest that children with stunting are more vulnerable to the adverse effects of low-level lead exposure