The somatic mutation landscape of premalignant colorectal adenoma.

OBJECTIVE: There are few studies which characterised the molecular alterations in premalignant colorectal adenomas. Our major goal was to establish colorectal adenoma genome atlas and identify molecular markers of progression from colorectal adenoma to adenocarcinoma. DESIGN: Whole-exome sequencing and targeted sequencing were carried out in 149 adenoma samples and paired blood from patients with conventional adenoma or sessile serrated adenoma to characterise the somatic mutation landscape for premalignant colorectal lesions. The identified somatic mutations were compared with those in colorectal cancer (CRC) samples from The Cancer Genome Atlas. A supervised random forest model was employed to identify gene panels differentiating adenoma from CRC. RESULTS: Similar somatic mutation frequencies, but distinctive driver mutations, were observed in sessile serrated adenomas and conventional adenomas. The final model included 20 genes and was able to separate the somatic mutation profile of colorectal adenoma and adenocarcinoma with an area under the curve of 0.941. CONCLUSION: The findings of this project hold potential to better identify patients with adenoma who may be candidates for targeted surveillance programmes and preventive interventions to reduce the incidence of CRC.

Adaptive optics correction into single mode fiber for a low Earth orbiting space to ground optical communication link using the OPALS downlink.

An adaptive optics (AO) testbed was integrated to the Optical PAyload for Lasercomm Science (OPALS) ground station telescope at the Optical Communications Telescope Laboratory (OCTL) as part of the free space laser communications experiment with the flight system on board the International Space Station (ISS). Atmospheric turbulence induced aberrations on the optical downlink were adaptively corrected during an overflight of the ISS so that the transmitted laser signal could be efficiently coupled into a single mode fiber continuously. A stable output Strehl ratio of around 0.6 was demonstrated along with the recovery of a 50 Mbps encoded high definition (HD) video transmission from the ISS at the output of the single mode fiber. This proof of concept demonstration validates multi-Gbps optical downlinks from fast slewing low-Earth orbiting (LEO) spacecraft to ground assets in a manner that potentially allows seamless space to ground connectivity for future high data-rates network.

A multi-stakeholder perspective on the use of alternative test strategies for nanomaterial safety assessment.

There has been a conceptual shift in toxicological studies from describing what happens to explaining how the adverse outcome occurs, thereby enabling a deeper and improved understanding of how biomolecular and mechanistic profiling can inform hazard identification and improve risk assessment. Compared to traditional toxicology methods, which have a heavy reliance on animals, new approaches to generate toxicological data are becoming available for the safety assessment of chemicals, including high-throughput and high-content screening (HTS, HCS). With the emergence of nanotechnology, the exponential increase in the total number of engineered nanomaterials (ENMs) in research, development, and commercialization requires a robust scientific approach to screen ENM safety in humans and the environment rapidly and efficiently. Spurred by the developments in chemical testing, a promising new toxicological paradigm for ENMs is to use alternative test strategies (ATS), which reduce reliance on animal testing through the use of in vitro and in silico methods such as HTS, HCS, and computational modeling. Furthermore, this allows for the comparative analysis of large numbers of ENMs simultaneously and for hazard assessment at various stages of the product development process and overall life cycle. Using carbon nanotubes as a case study, a workshop bringing together national and international leaders from government, industry, and academia was convened at the University of California, Los Angeles, to discuss the utility of ATS for decision-making analyses of ENMs. After lively discussions, a short list of generally shared viewpoints on this topic was generated, including a general view that ATS approaches for ENMs can significantly benefit chemical safety analysis.

t4 workshop report. Nanotoxicology: "the end of the beginning" - signs on the roadmap to a strategy for assuring the safe application and use of nanomaterials.

In October 2010, a group of experts met as part of the transatlantic think tank for toxicology (t4) to exchange ideas about the current status and future of safety testing of nanomaterials. At present, there is no widely accepted path forward to assure appropriate and effective hazard identification for engineered nanomaterials. The group discussed needs for characterization of nanomaterials and identified testing protocols that incorporate the use of innovative alternative whole models such as zebrafish or C. elegans, as well as in vitro or alternative methods to examine specific functional pathways and modes of action. The group proposed elements of a potential testing scheme for nanomaterials that works towards an integrated testing strategy, incorporating the goals of the NRC report Toxicity Testing in the 21st Century: A Vision and a Strategy by focusing on pathways of toxic response, and utilizing an evidence-based strategy for developing the knowledge base for safety assessment. Finally, the group recommended that a reliable, open, curated database be developed that interfaces with existing databases to enable sharing of information.

An experimental and theoretical study of the mixing characteristics of a periodically reoriented irrotational flow.

The minimum-energy method to generate chaotic advection should be to use an irrotational flow. However, irrotational flows have no saddle connections to perturb in order to generate chaotic orbits. To the early work of Jones & Aref (Jones & Aref 1988 Phys. Fluids 31, 469-485 (doi:10.1063/1.866828)) on potential flow chaos, we add periodic reorientation to generate chaotic advection with irrotational experimental flows. Our experimental irrotational flow is a dipole potential flow in a disc-shaped Hele-Shaw cell called the rotated potential mixing flow; it leads to chaotic advection and transport in the disc. We derive an analytical map for the flow. This is a partially open flow, in which parts of the flow remain in the cell forever, and parts of it pass through with residence-time and exit-time distributions that have self-similar features in the control parameter space of the stirring. The theory compares well with the experiment.

A partially open porous media flow with chaotic advection: towards a model of coupled fields.

In nature, dissipative fluxes of fluid, heat and/or reacting species couple to each other and may also couple to deformation of a surrounding porous matrix. We use the well-known analogy of Hele-Shaw flow to Darcy flow to make a model porous medium with porosity proportional to local cell height. Time- and space-varying fluid injection from multiple source/sink wells lets us create many different kinds of chaotic flows and chemical concentration patterns. Results of an initial time-dependent potential flow model illustrate that this is a partially open flow, in which parts of the material transported by the flow remain in the cell forever and parts pass through with residence time and exit time distributions that have self-similar features in the control parameter space of the stirring. We derive analytically the existence boundary in stirring control parameter space between where isolated fluid regions can and cannot remain forever in the open flow. Experiments confirm the predictions.

Value of baseline positron emission tomography for predicting overall survival in patient with nonmetastatic esophageal or gastroesophageal junction carcinoma.

BACKGROUND: The value of baseline positron emission tomography (PET) for predicting overall survival (OS) or disease-free survival (DFS) is unclear in patients with nondistant metastatic (locoregional only) esophageal carcinoma. The authors tested the hypothesis that, in this setting, the number of PET abnormalities (NPA) would correlate with OS and DFS. METHODS: The authors of the current study analyzed patients with localized esophageal carcinoma (Stages II and III) who had a baseline PET and endoscopic ultrasonography (EUS) and were all treated with chemoradiotherapy followed by surgery. The standardized uptake value (SUV) of PET avid lesions were evaluated for: SUV of the primary, NPA, peak SUV, and total SUV. Correlations were performed with baseline EUS results, OS, DFS, and clinical and pathologic response. RESULTS: Forty-seven patients who underwent chemoradiotherapy followed by surgery were analyzed. Most patients had clinical Stage III cancer. NPA was significantly associated with OS (Cox model, P = 0.02; log-rank test, P = 0.04) and DFS (P = 0.04). Patients with NPA > 1 had a death hazard ratio of 4.49 (reference, NPA = 1). In a multivariate analysis, NPA was independently predictive of OS (P = 0.03). Alternatively, SUV of the primary tumor, peak SUV, total SUV, and EUS clinical stage did not correlate with the type of response, OS or DFS. CONCLUSIONS: Data from the current study suggest that for nondistant metastatic esophageal carcinoma, baseline PET can predict patient outcome. Baseline NPA (> 1), reflecting the regional nodal metastases, is an independent predictor of OS. Baseline PET may become a useful stratification factor in randomized trials and for individualizing therapy.

Combined resection and radiofrequency ablation for advanced hepatic malignancies: results in 172 patients.

BACKGROUND: Resection combined with radiofrequency ablation (RFA) is a novel approach in patients who are otherwise unresectable. The objective of this study was to investigate the safety and efficacy of hepatic resection combined with RFA. METHODS: Patients with multifocal hepatic malignancies were treated with surgical resection combined with RFA. All patients were followed prospectively to assess complications, treatment response, and recurrence. RESULTS: Seven hundred thirty seven tumors in 172 patients were treated (124 with colorectal metastases; 48 with noncolorectal metastases). RFA was used to treat 350 tumors. Combined modality treatment was well tolerated with low operative times and minimal blood loss. The postoperative complication rate was 19.8% with a mortality rate of 2.3%. At a median follow-up of 21.3 months, tumors had recurred in 98 patients (56.9%). Failure at the RFA site was uncommon (2.3%). A combined total number of tumors treated with resection and RFA >10 was associated with a faster time to recurrence (P =.02). The median actuarial survival time was 45.5 months. Patients with noncolorectal metastases and those with less operative blood loss had an improved survival (P =.03 and P =.04, respectively), whereas radiofrequency ablating a lesion >3 cm adversely impacted survival (HR = 1.85, P =.04). CONCLUSIONS: Resection combined with RFA provides a surgical option to a group of patients with liver metastases who traditionally are unresectable, and may increase long-term survival.

Cutaneous angiosarcoma of the scalp: a multidisciplinary approach.

BACKGROUND: Angiosarcoma is a malignant tumor of vascular endothelial cells that arises in the head and neck. It is a rare, difficult to treat, and lethal tumor. METHODS: Clinical data from patients who were diagnosed with angiosarcoma of the scalp between 1975 and 2002 at the University of Michigan were reviewed. Analysis was performed to assess for factors impacting time to recurrence and survival. RESULTS: The study was comprised of 29 patients with a median age of 71.0 years. Most patients presented after a delay in diagnosis with either a bruise-like macule (48.3%) or a nonbruise-like nodule (51.7%). Seventy-five percent of patients had pathologic Stage T2 disease, and 76% of patients had high-grade tumors. Virtually all patients underwent surgical excision (96.6%); however, negative surgical margins were achieved in only 21.4% of patients. Multiple lesions on presentation were associated with a shorter time to recurrence (P = 0.02). The median actuarial survival was 28.4 months. Younger patients and patients with Stage T1 disease had improved survival (P = 0.024 and P = 0.013, respectively). Radiation therapy was associated significantly with a decreased chance of death (hazard ratio, 0.16; P = 0.006). CONCLUSIONS: Although surgery remains the first option for the treatment of patients with angiosarcoma of the scalp, achieving negative margins often is impossible. Patients who are younger and who have less extensive disease fare better. Postoperative radiation therapy should be employed routinely, as it may lead to improved survival.