Experimentation with Combinatorial Hopf Algebras in Sage

Abstract. We present a Sage patch for computing with Combinatorial Hopf algebras. It includes a new Category (pattern), several concrete Hopf algebras: FQSym, WQSym, PQSym, PBT, FSym, and easily allows implementation of other ones

External replication of urinary bladder cancer prognostic polymorphisms in the UK Biobank

Introduction: Multiple studies have reported genetic associations with prognostic outcomes of urinary bladder cancer. However, the lack of replication of these associations prohibits establishing further evidence-based research directions. Moreover, there is a lack of independent bladder cancer patient samples that contain prognostic measures, making genetic replication analyses even more challenging. Materials and Methods: We have identified 1,534 eligible patients and used data on Hospital Episode Statistics in the UK Biobank to model variables of otherwise non-collected events on bladder cancer recurrence and progression. Data on survival was extracted from the Death Registry. We have used SNPTEST software to replicate previously reported genetic associations with bladder cancer recurrence (N = 69), progression (N = 23), survival (N = 53), and age at the time of diagnosis (N = 20). Results: Using our algorithm, we have identified 618 recurrence and 58 UBC progression events. In total, there were 209 deaths (106 UBC-specific). In replication analyses, eight SNPs have reached nominal statistical significance (p <0.05). Rs2042329 (CWC27) for UBC recurrence; rs804256, rs4639, and rs804276 (in/close to NEIL2) for NMIBC recurrence; rs2293347 (EGFR) for UBC OS; rs3756712 (PDCD6) for NMIBC OS; rs2344673 (RGS5) for MIBC OS, and rs2297518 (NOS2) for UBC progression. However, none have remained significant after adjustments for multiple comparisons. Discussion: External replication in genetic epidemiology is an essential step to identify credible findings. In our study, we identify potential genetic targets of higher interest for UBC prognosis. In addition, we propose an algorithm for identifying UBC recurrence and progression using routinely-collected data on patient interventions

Improving Ergonomics at Work with Personalized Multi-Objective Optimization of Human Movements

International audienc

BUSM News and Notes

Monthly newsletter providing updates of interest to the Boston University School of Medicine community

Genome-wide association study for tumour stage, grade, size, and age at diagnosis of non-muscle-invasive bladder cancer

BACKGROUND: Non-muscle-invasive bladder cancer (NMIBC) causes a considerable health burden due to the high recurrence and progression rates. Past studies have identified multiple candidate loci associated with NMIBC prognosis, albeit lacking validation. Moreover, scarce reports exist on genetic susceptibility to independent prognostic predictors of NMIBC, such as stage or grade. OBJECTIVE: To investigate genetic associations with NMIBC tumour and patient characteristics at the time of diagnosis. DESIGN, SETTING, AND PARTICIPANTS: A sample of 653 NMIBC cases comes from the Bladder Cancer Prognosis Programme. Replication of the significant findings was conducted in the Nijmegen Bladder Cancer Study cohort (N=1470). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: A genome-wide association study (GWAS) was carried out for outcomes of tumour size (as a continuous variable in centimetres), stage (Tis and T1 vs Ta), grade (G3 vs G2 and G1), and age (as continuous [years] and dichotomous [70.2 yr as a cut-off] variables). RESULTS AND LIMITATIONS: Significant (p<5E-08) associations (N=61) with tumour size, stage, grade, and age were identified in the GWAS discovery stage. None of the variants were independently significantly associated in the replication cohort. A meta-analysis of both cohorts suggests that rs180940944 (13q13.3 locus, NBEA) was associated with tumour size as a continuous variable (ss=0.9cm, p=2.92E-09). However, other single nucleotide polymorphisms in this region did not show evidence of association in the meta-analysis. CONCLUSIONS: Our study suggests that rs180940944 (NBEA) is associated with an increased NMIBC tumour size at the time of diagnosis. Given study limitations, further replication is essential to validate the finding. PATIENT SUMMARY: The current study reports on a genome-wide association study on non-muscle-invasive bladder cancer tumour and patient characteristics. We suggest that NBEA gene might be associated with increased tumour size at the time of diagnosis. The result must be replicated to establish validity

Molecular gas in high redshift QSOs

We review cm and mm observations of thermal molecular line emission from high redshift QSOs. These observations reveal the massive gas reservoirs (10^{10} to 10^{11} M_sun) required to fuel star formation at high rates. We discuss evidence for active star formation in QSO host galaxies, and we show that these high redshift, FIR-luminous QSOs follow the non-linear trend of increasing L_{FIR}/L'(CO) with increasing L_{FIR}. We conclude with a brief discussion of the recent CO detection of the most distant QSO at z=6.42, and its implications for cosmic reionization.Comment: To appear in: Multiwavelength AGN Surveys, eds. Maiolino and Mujica (World Scientific), 8 page

Reducing two-level system dissipations in 3D superconducting Niobium resonators by atomic layer deposition and high temperature heat treatment

Superconducting qubits have arisen as a leading technology platform for quantum computing which is on the verge of revolutionizing the world's calculation capacities. Nonetheless, the fabrication of computationally reliable qubit circuits requires increasing the quantum coherence lifetimes, which are predominantly limited by the dissipations of two-level system (TLS) defects present in the thin superconducting film and the adjacent dielectric regions. In this paper, we demonstrate the reduction of two-level system losses in three-dimensional superconducting radio frequency (SRF) niobium resonators by atomic layer deposition (ALD) of a 10 nm aluminum oxide Al2O3 thin films followed by a high vacuum (HV) heat treatment at 650 {\deg}C for few hours. By probing the effect of several heat treatments on Al2O3-coated niobium samples by X-ray photoelectron spectroscopy (XPS) plus scanning and conventional high resolution transmission electron microscopy (STEM/HRTEM) coupled with electron energy loss spectroscopy (EELS) and (EDX) , we witness a dissolution of niobium native oxides and the modification of the Al2O3-Nb interface, which correlates with the enhancement of the quality factor at low fields of two 1.3 GHz niobium cavities coated with 10 nm of Al2O3

Direct measurement of local constitutive relations, at the micrometre scale, in bulk metallic alloys

Multiscale models involving crystal plasticity are essential to predict the elastoplastic behavior of structural materials with respect to their microstructure. However, those models are often limited by a poor knowledge of the local constitutive behavior. This article reports a method to measure the mechanical behavior directly, at the micrometre scale, in bulk crystalline materials. Local strain and stress states were evaluated at the surface of a bent stainless steel crystal by combining total strain measurements – performed with the digital image correlation technique on optical images – with elastic strain measurements obtained by Laue microdiffraction. A local constitutive relation was measured, in an efficient nondestructive way, without the need for full-field simulations. The method was validated by a comparison between the measured local behavior and the macroscopic behavior of the single crystal

Validity of Crystal Plasticity Models Near Grain Boundaries: Contribution of Elastic Strain Measurements at Micron Scale

Synchrotron Laue microdiffraction and digital image correlation measurements were coupled to track the elastic strain field (or stress field) and the total strain field near a general grain boundary in a bent bicrystal. A 316L stainless steel bicrystal was deformed in situ into the elasto-plastic regime using a four-point bending setup. The test was then simulated using finite elements with a crystal plasticity model comprising internal variables (dislocation densities on discrete slip systems). The predictions of the model are compared with both the total strain field and the elastic strain field obtained experimentally. While activated slip systems and total strains are reasonably well predicted, elastic strains appear overestimated next to the grain boundary. This suggests that conventional crystal plasticity models need improvement to correctly model stresses at grain boundaries

On the Accuracy of Elastic Strain Field Measurements by Laue Microdiffraction and High-Resolution EBSD: a Cross-Validation Experiment

Determining the accuracy of elastic strain measurements in plastically deformed alloys is an experimental challenge. To develop a novel cross-validation procedure, a controlled elasto-plastic strain gradient was created in a stainless steel single crystal by four point bending deformation. The corresponding elastic strain field was probed, with an intragranular spatial resolution, in-situ by Laue microdiffraction and ex-situ by High Resolution EBSD. Good agreement is found for the two independent measurements and the predictions of a mechanical model, at plastic strains below 0.5 %. The accuracy of the measurements is estimated at 3.2 × 10 − 4