High-throughput RNA isoform sequencing using programmed cDNA concatenation.

Full-length RNA-sequencing methods using long-read technologies can capture complete transcript isoforms, but their throughput is limited. We introduce multiplexed arrays isoform sequencing (MAS-ISO-seq), a technique for programmably concatenating complementary DNAs (cDNAs) into molecules optimal for long-read sequencing, increasing the throughput >15-fold to nearly 40 million cDNA reads per run on the Sequel IIe sequencer. When applied to single-cell RNA sequencing of tumor-infiltrating T cells, MAS-ISO-seq demonstrated a 12- to 32-fold increase in the discovery of differentially spliced genes.

Burden and Unmet Needs with Portable Oxygen in Patients on Long-Term Oxygen Therapy.

Rationale: Over 1.5 million Americans receive long-term oxygen therapy (LTOT) for the treatment of chronic hypoxemia to optimize functional status and quality of life. However, current portable oxygen equipment, including portable gas tanks (GTs), portable liquid tanks (LTs), and portable oxygen concentrators (POCs), each have limitations that can hinder patient mobility and daily activities. Objectives: To examine patient experiences with portable oxygen to guide equipment innovation and thereby improve patient care on oxygen therapy. Methods: The burden and unmet needs with portable oxygen equipment were assessed in 836 LTOT patients with chronic lung disease (chronic obstructive pulmonary disease [COPD], interstitial lung disease, and pulmonary hypertension) through an online survey. The survey included a combination of multiple-choice, Likert-scale, short-answer, and open-ended questions. Distribution was achieved through patient support organizations, including the U.S. COPD Coalition, the Pulmonary Fibrosis Foundation, and the Pulmonary Hypertension Association. Results: Improvements in portability were ranked as the highest priority by patients across all equipment types, followed by increases in the duration of oxygen supply for GTs, accessibility for LTs, and flow capabilities for POCs. All device types were found to be burdensome, with the greatest burden among GT users, 51% of whom characterized GT use as "strenuous" or "extremely strenuous" (high burden). POCs ranked as the most common (61%) and least burdensome devices; however, 29% of POC users still reported a high associated burden. Forty-seven percent of POC respondents described using a POC despite it not meeting their oxygen needs to benefit from advantages over alternative equipment. Among non-POC users, limited oxygen flow rate capabilities and cost were the top reasons preventing POC use. Conclusions: Although improvements have been made to portable oxygen equipment, this study highlights the burden that remains and reveals a clear need for advances in technology to improve the functional status and quality of life of portable LTOT users.

Repeat expansions confer WRN dependence in microsatellite-unstable cancers.

The RecQ DNA helicase WRN is a synthetic lethal target for cancer cells with microsatellite instability (MSI), a form of genetic hypermutability that arises from impaired mismatch repair1-4. Depletion of WRN induces widespread DNA double-strand breaks in MSI cells, leading to cell cycle arrest and/or apoptosis. However, the mechanism by which WRN protects MSI-associated cancers from double-strand breaks remains unclear. Here we show that TA-dinucleotide repeats are highly unstable in MSI cells and undergo large-scale expansions, distinct from previously described insertion or deletion mutations of a few nucleotides5. Expanded TA repeats form non-B DNA secondary structures that stall replication forks, activate the ATR checkpoint kinase, and require unwinding by the WRN helicase. In the absence of WRN, the expanded TA-dinucleotide repeats are susceptible to cleavage by the MUS81 nuclease, leading to massive chromosome shattering. These findings identify a distinct biomarker that underlies the synthetic lethal dependence on WRN, and support the development of therapeutic agents that target WRN for MSI-associated cancers.

Biomimetic anisotropic polymeric nanoparticles coated with red blood cell membranes for enhanced circulation and toxin removal.

The design of next-generation nanobiomaterials requires precise engineering of both physical properties of the core material and chemical properties of the material's surface to meet a biological function. A bio-inspired modular and versatile technology was developed to allow biodegradable polymeric nanoparticles to circulate through the blood for extended periods of time while also acting as a detoxification device. To mimic red blood cells, physical and chemical biomimicry are combined to enhance the biological function of nanomaterials in vitro and in vivo. The anisotropic shape and membrane coating synergize to resist cellular uptake and reduce clearance from the blood. This approach enhances the detoxification properties of nanoparticles, markedly improving survival in a mouse model of sepsis. The anisotropic membrane-coated nanoparticles have enhanced biodistribution and therapeutic efficacy. These biomimetic biodegradable nanodevices and their derivatives have promise for applications ranging from detoxification agents, to drug delivery vehicles, and to biological sensors.

Does learning from mistakes have to be painful? Analysis of 5 years' experience from the Leeds radiology educational cases meetings identifies common repetitive reporting errors and suggests acknowledging and celebrating excellence (ACE) as a more positive way of teaching the same lessons.

BACKGROUND: The Royal College of Radiologists (RCR) and General Medical Council (GMC) encourage learning from mistakes. But negative feedback can be a demoralising process with adverse implications for staff morale, clinical engagement, team working and perhaps even patient outcomes. We first reviewed the literature regarding positive feedback and teamworking. We wanted to see if we could reconcile our guidance to review and learn from mistakes with evidence that positive interactions had a better effect on teamworking and outcomes than negative interactions. We then aimed to review and categorise the over 600 (mainly discrepancy) cases discussed in our educational cases meeting into educational 'themes'. Finally, we explored whether we could use these educational themes to deliver the same teaching points in a more positive way. METHODS AND RESULTS: The attendance records, programmes and educational cases from 30 consecutive bimonthly meetings between 2011 and 2017 were prospectively collated and retrospectively analysed. Six hundred and thirty-two cases were collated over the study period where 76% of the cases submitted were discrepancies, or perceived errors. Eight percent were 'good spots' where examples of good calls, excellent reporting, exemplary practice or subtle findings that were successfully reported. Eight percent were educational cases in which no mistake had been made. The remaining 7% included procedural complications or system errors. CONCLUSION: By analysing the pattern of discrepancies in a department and delivering the teaching in a less negative way, the 'lead' of clinical errors can be turned in to the 'gold' of useful educational tools. Interrogating the whole database periodically can enable a more constructive, wider view of the meeting itself, highlight recurrent deficiencies in practice, and point to where the need for continuing medical training is greatest. Three ways in which our department have utilised this material are outlined: the use of 'good spots', arrangement of targeted teaching and production of specialist educational material. These techniques can all contribute to a more positive learning experience with the emphasis on acknowledging and celebrating excellence (ACE).

The proliferation of multidisciplinary team meetings (MDTMs): how can radiology departments continue to support them all?

OBJECTIVES: To quantify the changes in multidisciplinary team meeting (MDTM) workload for consultant radiologists working in a single UK tertiary referral cancer institution, assess its impact and suggest solutions to these challenges. METHODS: The annual number of MDTM cases was collated over a 5-year period (2009 - 2013). Qualitative information was obtained through questionnaire-based interviews of 47 consultant radiologists. Data analysed included number of MDTMs involved with, type of MDTM (oncological or non-oncological), time allocation for preparation and perceived deficiencies in the current MDTM. RESULTS: Thirteen thousand and forty-nine cases were discussed in MDTMs in 2009 with a continued yearly increase over the 5-year period. Fifty-five percent of MDTM attendances were at oncological MDTMs. Consultant radiologists attended a median of two MDTMs per week, each requiring 4 hours time commitment; 60 % used out-of-hours time for MDTM preparation. The most frequently cited MDTM deficiency was lack of sufficient clinical input. CONCLUSIONS: The MDTM is a challenging but worthwhile demand on the modern radiologist's time. Solutions to the increasing MDTM workload include demonstration of the benefits of MDTMs to hospital administrators to justify additional resources required, improving MDTM efficiency and ensuring this increased workload is accurately represented and remunerated in individual job plans. KEY POINTS: • MDTMs improve cancer outcomes and are being recommended for non-oncological conditions. • MDTM cases have more than doubled over 5 years at our institution. • Incorporating MDTM workload into current consultant radiologist job plans is difficult. • Solutions include demonstrating MDTM related benefits, improved efficiency, and accurate job planning.

Clinical impact of (18)F-FDG PET-CT in recurrent stage III/IV melanoma: a tertiary centre Specialist Skin Cancer Multidisciplinary Team (SSMDT) experience.

OBJECTIVES: To assess the clinical impact of (18)F-fluorodeoxyglucose positron emission tomography-computed tomography (FDG PET-CT) compared with contrast-enhanced computed tomography (CECT) in patients referred via the Specialist Skin Cancer Multidisciplinary Team (SSMDT) with recurrent stage III/IV malignant melanoma (MM). METHODS: Forty-five patients were referred for further evaluation with FDG PET-CT. Findings on FDG PET-CT were compared with prior CECT and the clinical impact on subsequent management decisions was determined retrospectively. A major clinical impact was defined as a change in treatment plan resulting from identification of additional sites of disease or by characterisation of indeterminate findings on prior imaging. A minor impact was defined as confirmation of known sites of disease as identified on prior CECT. RESULTS: Fifty-one PET-CT examinations were performed. FDG PET-CT had a major clinical impact in 21 cases (41.2 %), of which 18 examinations were performed in patients with proven or suspected stage IV MM. FDG PET-CT had a minor impact in 23 cases (45.1 %), and there were five false-positive cases (9.8 %) and two false-negative cases (3.9 %). CONCLUSION: FDG PET-CT is an effective tool in recurrent stage III/IV MM with a significant clinical impact on management decisions in patients who are appropriately referred via the highly specialised forum of the SSMDT. KEY POINTS: • FDG PET-CT is an effective tool in recurrent stage III/IV malignant melanoma. • FDG PET-CT has a significant clinical impact on management decisions. • Effective use of FDG PET-CT is via referral from the Specialist Skin Cancer Multidisciplinary Team.

Detection of colorectal metastases in patients being treated with chemotherapy utilising SPIO-MRI: a radiological-pathological study.

OBJECTIVE: Chemotherapy commonly causes liver injury through sinusoidal obstructive syndrome and steatosis. Chemotherapy-induced liver injury may make it more difficult to detect metastases secondary to reduced contrast between the injured liver and metastases. The aim of this study was to determine the sensitivity of superparamagnetic iron oxide (SPIO) contrast-enhanced imaging in patients who have undergone chemotherapy prior to liver surgery. METHODS: Local ethics committee approval was obtained. Thirty-one patients with hepatic metastases completing preoperative chemotherapy were prospectively recruited. Images were reviewed independently by two blinded observers who identified and localized lesions with a four-point confidence scale. The alternative free-response receiver operator characteristic method was used to analyze the results. RESULTS: The sensitivity in detecting colorectal metastases following chemotherapy was 78% and 76%, respectively, for observers 1 and 2 (95% confidence interval: 71%-85% and 68%-82%). The areas under the alternative free-response receiver operator curves were 0.73 and 0.80 for observers 1 and 2, respectively. CONCLUSION: Compared to previously published work on chemotherapy-naïve patients, it is clear that the sensitivity of SPIO-enhanced magnetic resonance imaging (MRI) in detecting colorectal metastases following chemotherapy is reduced. It is therefore critical that all imaging--pre-, during and postchemotherapy--is reviewed when reporting liver MRI prior to surgery.

The potential energy surface of isomerising disilyne.

A (semi-)global, analytical potential energy surface is reported for the ground electronic state of the isomerising disilyne molecule, Si2H2. The surface reproduces well ab initio energies calculated at the CCSD(T) level with a cc-pV(Q+d)Z basis set for over 50 000 symmetrically unique molecular geometries. Of these ab initio points, 33 000 were used in a least-squares fit to determine the parameters of the analytical surface and the remainder to provide an independent test/validation set. The fitted surface includes: the four known isomeric forms of disilyne, dibridged, monobridged, disilavinylidene and trans-bent; the three most important transition states and four other critical points. The surface reproduces accurately existing experimental spectroscopic data for the dibridged and monobridged isomers and predictions are made for the disilavinylidene and trans-bent forms. The surface has the correct symmetry properties with respect to permutation of like atoms and is suitable for detailed dynamics studies of the isomerising Si2H2 system. Also reported is a systematic investigation of the critical points using the CCSD(T) and MRCI methods and basis sets up to 6-zeta quality: the effects of core-correlation, augmentation with diffuse functions and tight-d functions have been studied. The basis sets include the correlation consistent core-valence, cc-pCV(n+d)Z, basis sets recently developed by Yockel and Wilson [Theor. Chem. Acc., 2008, 120, 119]. Very good agreement is obtained between the theoretical and experimental equilibrium geometries, rotational constants and three available vibration frequencies for the dibridged isomer and for the rotational constants of the monobridged isomer. Multireference character, as measured by the T1 diagnostic, is found to vary significantly across the 12 critical points investigated.

F-18 FDG PET/CT imaging of follicular dendritic cell sarcoma of the mediastinum.

A 52-year-old female smoker presenting with unexplained weight loss underwent CT and FDG PET/CT imaging, which demonstrated an extremely hypermetabolic mediastinal mass with calcification, necrosis, and features of local invasiveness. Mediastinoscopy and biopsy were followed by successful surgical resection of an encapsulated mass showing the typical histologic features of follicular dendritic cell sarcoma (FDCS). FDCS of the mediastinum is a rare neoplasm arising from accessory cells of the immune system. Integrated FDG PET/CT of mediastinal FDCS highlights the importance of histologic assessment of mediastinal tumors that may seem unresectable on initial imaging.

F-18 FDG PET/CT can help differentiate SAPHO syndrome from suspected metastatic bone disease.

A 20-year-old woman underwent magnetic resonance imaging of the spine for back pain, which demonstrated a solitary lesion in the T2 vertebral body suspicious for a metastasis. Subsequent computed tomography and bone scintigraphy identified several further sites of bony involvement but no primary malignancy. The patient was referred for F-18 FDG PET/CT which demonstrated intense FDG activity in the sternoclavicular and sacroiliac joints, in addition to the known thoracic vertebral body involvement suggesting spondyloarthropathy rather than malignant disease. During the course of investigations, the patient developed palmoplantar pustulosis leading to a diagnosis of SAPHO syndrome.

Sinusoidal obstructive syndrome diagnosed with superparamagnetic iron oxide-enhanced magnetic resonance imaging in patients with chemotherapy-treated colorectal liver metastases.

PURPOSE: To assess the predictive value of superparamagnetic iron oxide (SPIO) -enhanced T2-weighted gradient echo (GRE) imaging to determine the presence and severity of sinusoidal obstructive syndrome (SOS). PATIENTS AND METHODS: Sixty hepatic resection patients with colorectal metastases treated with chemotherapy underwent unenhanced magnetic resonance imaging (MRI) followed by T2-weighted GRE sequences obtained after SPIO. The images were reviewed in consensus by two experienced observers who determined the presence and severity of linear and reticular hyperintensities, indicating SOS-type liver injury, using a 4-point ordinal scale. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) with 95% CIs for the detection of SOS were calculated. RESULTS: Twenty-four of 60 patients had moderate to severe SOS on MRI. MRI achieved a sensitivity of 87% (95% CI, 66% to 97%), specificity of 89% (95% CI, 75% to 97%), PPV of 83% (95% CI, 63% to 95%), and NPV of 92% (95% CI, 77% to 98%). SOS was never found at surgery or histology in patients whose background liver parenchyma was normal on SPIO-enhanced MRI. CONCLUSION: SOS is present in a significant proportion of patients with treated colorectal metastases and is effectively detected on SPIO-enhanced T2-weighted GRE images.

Cardiac dose from tangential breast cancer radiotherapy in the year 2006.

PURPOSE: To quantify the radiation doses received by the heart and coronary arteries from contemporary tangential breast or chest wall radiotherapy. METHODS AND MATERIALS: Fifty consecutive patients with left-sided breast cancer and 5 consecutive patients with right-sided breast cancer treated at a large United Kingdom radiotherapy center during the year 2006 were selected. All patients were irradiated with 6- or 8-MV tangential beams to the breast or chest wall. For each dose plan, dose-volume histograms for the heart and left anterior descending (LAD) coronary artery were calculated. For 5 of the left-sided and all 5 right-sided patients, dose-volume histograms for the right and circumflex coronary arteries were also calculated. Detailed spatial assessment of dose to the LAD coronary artery was performed for 3 left-sided patients. RESULTS: For the 50 patients given left-sided irradiation, the average mean (SD) dose was 2.3 (0.7) Gy to the heart and 7.6 (4.5) Gy to the LAD coronary artery, with the distal LAD receiving the highest doses. The right and circumflex coronary arteries received approximately 2 Gy mean dose. Part of the heart received >20 Gy in 22 left-sided patients (44%). For the 5 patients given right-sided irradiation, average mean doses to all cardiac structures were in the range 1.2 to 2 Gy. CONCLUSIONS: Heart dose from left-tangential radiotherapy has decreased considerably over the past 40 years, but part of the heart still receives >20 Gy for approximately half of left-sided patients. Cardiac dose for right-sided patients was generally from scattered irradiation alone.