A heterodyne dispersion interferometer for wide bandwidth density measurements on DIII-D

In order to improve both the density and particularly the temporal resolution beyond previous dispersion interferometers (DIs), a heterodyne technique based on an acousto-optic (AO) cell has been added to the DI. A 40 MHz drive frequency for the AO cell allows density fluctuation measurements into the MHz range. A CO₂ laser-based heterodyne DI (HDI) installed on DIII-D has demonstrated that the HDI is capable of tracking the density evolution throughout DIII-D discharges, including disruption events and other rapid transient phenomena. The data also show good agreement with independent density measurements obtained with the existing DIII-D two-color interferometer. The HDI line-integrated density resolution sampled over a 1 s interval is ∼9 × 10¹⁷ m^-2. Density fluctuations induced by MHD instabilities are also successfully measured by the HDI.

Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans

The emergence of Clostridium difficile as a significant human diarrheal pathogen is associated with the production of highly transmissible spores and the acquisition of antimicrobial resistance genes (ARGs) and virulence factors. Unlike the hospital-associated C. difficile RT027 lineage, the community-associated C. difficile RT078 lineage is isolated from both humans and farm animals; however, the geographical population structure and transmission networks remain unknown. Here, we applied whole-genome phylogenetic analysis of 248 C. difficile RT078 strains from 22 countries. Our results demonstrate limited geographical clustering for C. difficile RT078 and extensive coclustering of human and animal strains, thereby revealing a highly linked intercontinental transmission network between humans and animals. Comparative whole-genome analysis reveals indistinguishable accessory genomes between human and animal strains and a variety of antimicrobial resistance genes in the pangenome of C. difficile RT078. Thus, bidirectional spread of C. difficile RT078 between farm animals and humans may represent an unappreciated route disseminating antimicrobial resistance genes between humans and animals. These results highlight the importance of the "One Health" concept to monitor infectious disease emergence and the dissemination of antimicrobial resistance genes.

Abstract SY10-02: Pan-cancer study of recurrent and heterogeneous RNA aberrations and association with whole-genome variants

Whole-exome sequencing studies have transformed our understanding of recurrent somatic mutations that contribute to cancer pathogenesis; however, these studies limit our ability to identify cancer-associated mutations to those that cause protein-coding changes. To more comprehensively catalogue cancer-associated gene alterations, we have extensively characterized tumor transcriptomes from 1,220 donors with matched whole-genome sequence data to identify recurrent RNA-level aberrations. Specifically, we created a unified RNA-Seq analysis pipeline including sequence alignment and quality control and subsequently identified gene alterations through outlier detection from estimated gene expression levels, alternative splicing, alternative transcription starts, and allele-specific expression and through identified RNA-edited sites and gene fusions. Our data represent an extensive catalog of RNA aberrations for each gene across 27 cancer types. We have also tested for genetic associations with these RNA phenotypes. Using an integrative analysis approach, we have mapped genome-wide cis and trans effects on individual RNA phenotypes, considering both common germline variants as well as somatic SNVs in gene promoters, enhancers, and intronic and other regions. Many of the regulatory associations we identify are not accessible by exome sequencing, underlining the importance of whole-genome sequence data. Utilizing this RNA-centric view, we have identified genes that are recurrently altered, yet have not been previously characterized as cancer genes or identified through DNA-level driver gene analysis. To identify further supporting evidence that these recurrent alterations are potential drivers, we identified genes with mutually exclusive RNA-level alterations. Our findings reveal new insights into selective advantages of somatic changes and molecular mechanisms of cancer. This work is by the Transcriptome Working Group of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium and authors are listed in alphabetical order.

Citation Format: Samirkumar Amin, Philip Awadalla, Andrew Biankin, Paul Boutros, Alvis Brazma, Angela Norie Brooks, Claudia Calabrese, David Chang, Aurélien Chateigner, Ken Chen, Zechen Chong, Brian Craft, Chad Creighton, Deniz Demircioğlu, Nuno Fonseca, Milana Frenkel-Morgenstern, Gad Getz, Jonathan Göke, Mary Goldman, Liliana Greger, Syed Haider, Yao He, Katherine Hoadley, Yuan Ji, Andre Kahles, Ekta Khurana, Jan Korbel, Kjong Lehmann, Han Liang, Fenglin Liu, Maximillian Marin, Matthew Meyerson, Akinyemi Ojesina, Francis Ouellette, Chandra Pedamallu, Marc Perry, Gunnar Rätsch, Roland Schwarz, Yuichi Shiraishi, Cameron Soulette, Oliver Stegle, Patrick Tan, Alfonso Valencia, Linda Xiang, Christina Yung, Junjun Zhang, Fan Zhang, Zemin Zhang, Jingchun Zhu. Pan-cancer study of recurrent and heterogeneous RNA aberrations and association with whole-genome variants [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr SY10-02. doi:10.1158/1538-7445.AM2017-SY10-02

Asynchronously Calibrated Quantitative Bone Densitometry

Conventional quantitative computed tomography (QCT) uses a phantom scanned simultaneously with the anatomical region of interest. A newly developed method called asynchronous QCT does not require a phantom to be present during the patient scan. This allows the inclusion of computer tomography scans performed without any calibration standard in a different clinical context than bone densitometry, for example, in a screening context. In the present study, the asynchronous and the conventional quantitative computed tomographies were compared. Specifically, short-term precision, a phantom-induced bias, methodical equivalence of the asynchronous and the conventional methods, and interobserver variability were investigated. Ten phantom scans served for investigation of short-term precision. A prospective dataset of 43 study participants (44-80 years, mean 63.8 ± 8.6 years) was acquired over 3 clinical sites. Trabecular regions of the spine as well as cortical and trabecular regions of the hip (femoral neck, trochanter, intertrochanter, and shaft) were analyzed with respect to the presence or absence of a phantom and with regard to the synchronous and asynchronous calibration methods. Regarding precision, all variations of the mean areal and volumetric densities were lower for the asynchronous method than for the conventional method. The presence of the phantom resulted in a bias of 2.3 mg/cm³, and the choice of the asynchronously or synchronously calibrated analysis resulted in a bias of 3.7 mg/cm³ at the spine. Both were statistically, but not clinically, significant. The total hip was statistically, but not clinically, significantly different by 0.008 g/cm². The bone density values between the 2 techniques correlated highly with one another at all regions investigated. Interobserver variability between 2 trained observers showed a difference of 0.2 mg/cm³ (spine) and differences less or equal to 0.009 g/cm² (hip), which again was regarded as clinically nonsignificant. In summary, the asynchronously calibrated QCT provides results comparable to the established synchronously calibrated QCT.

Bench testing of a heterodyne CO2 laser dispersion interferometer for high temporal resolution plasma density measurements

A heterodyne detection scheme is combined with a 10.59 μm CO₂ laser dispersion interferometer for the first time to allow large bandwidth measurements in the 10-100 MHz range. The approach employed utilizes a 40 MHz acousto-optic cell operating on the frequency doubled CO₂ beam which is obtained using a high 2nd harmonic conversion efficiency orientation patterned gallium arsenide crystal. The measured standard deviation of the line integrated electron density equivalent phase resolution obtained with digital phase demodulation technique, is 4 × 10¹⁷ m^-2. Air flow was found to significantly affect the baseline of the phase signal, which an optical table cover was able to reduce considerably. The heterodyne dispersion interferometer (DI) approach is found to be robustly insensitive to motion, with measured phase shifts below baseline drifts even in the presence of several centimeters of retroreflector induced path length variations. Plasma induced dispersion was simulated with a wedged ZnSe plate and the measured DI phase shifts are consistent with expectations.

Emergency management for orbital compartment syndrome-is decompression mandatory?

Current guidelines for the urgent management of patients with orbital compartment syndrome include immediate lateral canthotomy and cantholysis, followed by surgical decompression. Medical treatment is also advocated to 'buy time' while preparing the patient for theatre. This consists of high-dose steroids, mannitol, and acetazolamide diuretics to reduce swelling and orbital pressure. It is generally recognized that late or delayed intervention is associated with poor outcomes including blindness. With early presentation, given the potential risk to sight, there is generally a low threshold for treating suspected cases. However, whether or not to treat late cases is more controversial, partly because clinicians could face accusations of medical negligence if they do nothing. The case of a patient who sustained an orbital trauma to his only seeing eye, which resulted in acute proptosis and loss of vision, is presented here. He received no treatment at all for what appeared to be an orbital compartment syndrome secondary to retrobulbar haemorrhage, but surprisingly made a full recovery of vision within 48h. In contrast to the current literature in favour of urgent treatment, this case would appear to cast some doubt over the concept of 'always' treating orbital compartment syndrome and our understanding of the condition.