Spin Motion in Electron Transmission through Ultrathin Ferromagnetic Films Accessed by Photoelectron Spectroscopy

Ab initio and model calculations demonstrate that the spin motion of electrons transmitted through ferromagnetic films can be analyzed in detail by means of angle- and spin-resolved core-level photoelectron spectroscopy. The spin motion appears as precession of the photoelectron spin polarization around and as relaxation towards the magnetization direction. In a systematic study for ultrathin Fe films on Pd(001) we elucidate its dependence on the Fe film thickness and on the Fe electronic structure. In addition to elastic and inelastic scattering, the effect of band gaps on the spin motion is addressed in particular.Comment: 4 pages, 5 figure

Evolution of spectral function in a doped Mott insulator : surface vs. bulk contributions

We study the evolution of the spectral function with progressive hole doping in a Mott insulator, $La_{1-x}Ca_xVO_3$ with $x$ = 0.0 - 0.5. The spectral features indicate a bulk-to-surface metal-insulator transition in this system. Doping dependent changes in the bulk electronic structure are shown to be incompatible with existing theoretical predictions. An empirical description based on the single parameter, $U/W$, is shown to describe consistently the spectral evolution.Comment: Revtex, 4 pages, 3 postscript figures. To appear in Phys. Rev. Let

Performance characteristics of next-generation sequencing for the detection of antimicrobial resistance determinants in Escherichia coli genomes and metagenomes

Short-read sequencing can provide detection of multiple genomic determinants of antimicrobial resistance from single bacterial genomes and metagenomic samples. Despite its increasing application in human, animal, and environmental microbiology, including human clinical trials, the performance of short-read Illumina sequencing for antimicrobial resistance gene (ARG) detection, including resistance-conferring single nucleotide polymorphisms (SNPs), has not been systematically characterized. Using paired-end 2 x 150 bp (base pair) Illumina sequencing and an assembly-based method for ARG prediction, we determined sensitivity, positive predictive value (PPV), and sequencing depths required for ARG detection in an Escherichia coli isolate of sequence type (ST) 38 spiked into a synthetic microbial community at varying abundances. Approximately 300,000 reads or 15x genome coverage was sufficient to detect ARGs in E. coli ST38, with comparable sensitivity and PPV to ~100x genome coverage. Using metagenome assembly of mixed microbial communities, ARG detection at E. coli relative abundances of 1% would require assembly of approximately 30 million reads to achieve 15x target coverage. The minimum sequencing depths were validated using public data sets of 948 E. coli genomes and 10 metagenomic rectal swab samples. A read-based approach using k-mer alignment (KMA) for ARG prediction did not substantially improve minimum sequencing depths for ARG detection compared to assembly of the E. coli ST38 genome or the combined metagenomic samples. Analysis of sequencing depths from recent studies assessing ARG content in metagenomic samples demonstrated that sequencing depths had a median estimated detection frequency of 84% (interquartile range: 30%-92%) for a relative abundance of 1%. IMPORTANCE Systematically determining Illumina sequencing performance characteristics for detection of ARGs in metagenomic samples is essential to inform study design and appraisal of human, animal, and environmental metagenomic antimicrobial resistance studies. In this study, we quantified the performance characteristics of ARG detection in E. coli genomes and metagenomes and established a benchmark of ~15x coverage for ARG detection for E. coli in metagenomes. We demonstrate that for low relative abundances, sequencing depths of ~30 million reads or more may be required for adequate sensitivity for many applications

Concomitant CIS on TURBT does not impact oncological outcomes in patients treated with neoadjuvant or induction chemotherapy followed by radical cystectomy

© Springer-Verlag GmbH Germany, part of Springer Nature 2018Background: Cisplatin-based neoadjuvant chemotherapy (NAC) for muscle invasive bladder cancer improves all-cause and cancer specific survival. We aimed to evaluate whether the detection of carcinoma in situ (CIS) at the time of initial transurethral resection of bladder tumor (TURBT) has an oncological impact on the response to NAC prior to radical cystectomy. Patients and methods: Patients were identified retrospectively from 19 centers who received at least three cycles of NAC or induction chemotherapy for cT2-T4aN0-3M0 urothelial carcinoma of the bladder followed by radical cystectomy between 2000 and 2013. The primary and secondary outcomes were pathological response and overall survival, respectively. Multivariable analysis was performed to determine the independent predictive value of CIS on these outcomes. Results: Of 1213 patients included in the analysis, 21.8% had concomitant CIS. Baseline clinical and pathologic characteristics of the ‘CIS’ versus ‘no-CIS’ groups were similar. The pathological response did not differ between the two arms when response was defined as pT0N0 (17.9% with CIS vs 21.9% without CIS; p = 0.16) which may indicate that patients with CIS may be less sensitive to NAC or ≤ pT1N0 (42.8% with CIS vs 37.8% without CIS; p = 0.15). On Cox regression model for overall survival for the cN0 cohort, the presence of CIS was not associated with survival (HR 0.86 (95% CI 0.63–1.18; p = 0.35). The presence of LVI (HR 1.41, 95% CI 1.01–1.96; p = 0.04), hydronephrosis (HR 1.63, 95% CI 1.23–2.16; p = 0.001) and use of chemotherapy other than ddMVAC (HR 0.57, 95% CI 0.34–0.94; p = 0.03) were associated with shorter overall survival. For the whole cohort, the presence of CIS was also not associated with survival (HR 1.05 (95% CI 0.82–1.35; p = 0.70). Conclusion: In this multicenter, real-world cohort, CIS status at TURBT did not affect pathologic response to neoadjuvant or induction chemotherapy. This study is limited by its retrospective nature as well as variability in chemotherapy regimens and surveillance regimens.Peer reviewedFinal Accepted Versio

Comprehensive Researcher Achievement Model (CRAM): A framework for measuring researcher achievement, impact and influence derived from a systematic literature review of metrics and models

Objectives Effective researcher assessment is key to decisions about funding allocations, promotion and tenure. We aimed to identify what is known about methods for assessing researcher achievements, leading to a new composite assessment model. Design We systematically reviewed the literature via the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols framework. Data sources All Web of Science databases (including Core Collection, MEDLINE and BIOSIS Citation Index) to the end of 2017. Eligibility criteria (1) English language, (2) published in the last 10 years (2007-2017), (3) full text was available and (4) the article discussed an approach to the assessment of an individual researcher's achievements. Data extraction and synthesis Articles were allocated among four pairs of reviewers for screening, with each pair randomly assigned 5% of their allocation to review concurrently against inclusion criteria. Inter-rater reliability was assessed using Cohen's Kappa (A). The A statistic showed agreement ranging from moderate to almost perfect (0.4848-0.9039). Following screening, selected articles underwent full-text review and bias was assessed. Results Four hundred and seventy-eight articles were included in the final review. Established approaches developed prior to our inclusion period (eg, citations and outputs, h-index and journal impact factor) remained dominant in the literature and in practice. New bibliometric methods and models emerged in the last 10 years including: measures based on PageRank algorithms or 'altmetric' data, methods to apply peer judgement and techniques to assign values to publication quantity and quality. Each assessment method tended to prioritise certain aspects of achievement over others. Conclusions All metrics and models focus on an element or elements at the expense of others. A new composite design, the Comprehensive Researcher Achievement Model (CRAM), is presented, which supersedes past anachronistic models. The CRAM is modifiable to a range of applications

Opportunities and challenges for data physicalization

Physical representations of data have existed for thousands of years. Yet it is now that advances in digital fabrication, actuated tangible interfaces, and shape-changing displays are spurring an emerging area of research that we call Data Physicalization. It aims to help people explore, understand, and communicate data using computer-supported physical data representations. We call these representations physicalizations, analogously to visualizations -- their purely visual counterpart. In this article, we go beyond the focused research questions addressed so far by delineating the research area, synthesizing its open challenges and laying out a research agenda

Loss of ATRX in Chondrocytes Has Minimal Effects on Skeletal Development

BACKGROUND:Mutations in the human ATRX gene cause developmental defects, including skeletal deformities and dwarfism. ATRX encodes a chromatin remodeling protein, however the role of ATRX in skeletal development is currently unknown. METHODOLOGY/PRINCIPAL FINDINGS:We induced Atrx deletion in mouse cartilage using the Cre-loxP system, with Cre expression driven by the collagen II (Col2a1) promoter. Growth rate, body size and weight, and long bone length did not differ in Atrx(Col2cre) mice compared to control littermates. Histological analyses of the growth plate did not reveal any differences between control and mutant mice. Expression patterns of Sox9, a transcription factor required for cartilage morphogenesis, and p57, a marker of cell cycle arrest and hypertrophic chondrocyte differentiation, was unaffected. However, loss of ATRX in cartilage led to a delay in the ossification of the hips in some mice. We also observed hindlimb polydactily in one out of 61 mutants. CONCLUSIONS/SIGNIFICANCE:These findings indicate that ATRX is not directly required for development or growth of cartilage in the mouse, suggesting that the short stature in ATR-X patients is caused by defects in cartilage-extrinsic mechanisms