Complete genomes of Pasteurella multocida isolates from porcine, bovine, and cervine samples found in New Zealand farms

Here, we present complete genome assemblies of Pasteurella multocida strains isolated from porcine, bovine, and cervine farms as part of bacteriology incursion investigations to identify pathogens that might present a sanitary risk to New Zealand.

Molecular characterisation of the Australian and New Zealand livestock Chlamydia pecorum strains confirms novel but clonal ST23 in association with ovine foetal loss

Chlamydia pecorum is a veterinary pathogen associated with abortions and perinatal mortality in sheep. Recent studies investigating foetal and perinatal lamb mortality in sheep from Australia and New Zealand identified C. pecorum clonal sequence type (ST)23 strains in aborted and stillborn lambs. Presently, there is limited genotypic information on C. pecorum strains associated with reproductive disease, although whole genome sequencing (WGS) of one abortigenic ST23 C. pecorum strain identified unique features, including a deletion in the CDS1 locus of the chlamydial plasmid. We applied WGS on two ST23 strains detected in aborted and stillborn lambs from Australia and used phylogenetic and comparative analyses to compare these to the other available C. pecorum genomes. To re-evaluate the genetic diversity of contemporary strains, we applied C. pecorum genotyping, and chlamydial plasmid sequencing to a range of C. pecorum positive samples and isolates from ewes, aborted foetuses and stillborn lambs, cattle and a goat from diverse geographical regions across Australia and New Zealand.The two new C. pecorum genomes are nearly identical to the genome of the Australian abortigenic strain including the unique deletion in the chlamydial plasmid. Genotyping revealed that these novel C. pecorum ST23 strains are widespread and associated with sheep abortions on Australian and New Zealand farms. In addition, a goat C. pecorum strain (denoted ST 304) from New Zealand was also characterised. This study expands the C. pecorum genome catalogue and describes a comprehensive molecular characterisation of the novel livestock ST23 strains associated with foetal and lamb mortality.

Next generation high resolution perovskite direct conversion detector: Monte Carlo design optimisation and virtual clinical trial

We implement virtual clinical integration of next-generation perovskite detectors into common x-ray imaging devices. This was achieved by performing Monte Carlo (MC) optimisation of the design and benchmarking of low cost, high spatial resolution, direct conversion perovskite crystal x-ray flat panel imagers for a next generation of breast-, MV-, and kV-cone beam CT detectors. Semiconductor methylammonium lead bromide perovskite crystals energy deposition efficiencies calculated in TOPAS were benchmarked against four common detector materials for twelve detector crystal thicknesses between 40 to 15 mm and ten beam energies ranging from 20 keV to 6 MeV. Based on these simulations, Koning's dedicated breast CT, and Varian's Truebeam kV- and MV-cone beam CT systems were designated as suitable applications for perovskite detectors. System specific Fastcat hybrid MC cone beam CT image simulation was subsequently used to optimise the perovskite detector design and conduct virtual clinical trials. Device-specific optimal perovskite crystal thicknesses were calculated to be 0.30, 0.86, and 1.99 mm for Koning breast CT and Truebeam kV- and MV-cone beam CT systems, respectively. Replacing the current detectors on these machines with low cost perovskite crystal detectors could be advantageous as it would simultaneously yield 12.1%, 9.5% and 86.1% improvements in detective quantum efficiency as well as increases in contrast to noise ratio in brain, lung, and bone tissues.

Vancomycin-Resistant Enterococci in Patients Attending for Colonoscopy: An Estimate of Community Prevalence

Aims Ireland has the highest vancomycin-resistant Enterococcus faecium (VRE) bloodstream infection prevalence in Europe. Two patterns of VRE carriage are recognised. European, with widespread community prevalence and North American, where carriage is predominantly nosocomial. It is unclear which pattern is dominant in Ireland. This uncertainty limits infection control measures. This study sought to explore this issue via a cross sectional point prevalence study. Methods Asymptomatic community volunteers, represented by patients undergoing elective outpatient colonoscopy testing, were opportunistically screened for VRE. Demographic and risk factor data were collected via a patient survey. Rectal swabs were collected before colonoscopy and VRE was identified using the VITEK MS system. Results 102 patients were cultured. A single patient tested positive, representing a prevalence rate of 0.98% (95% CI <0.01-5.8%). This patient demonstrated traditional risk factors, suggesting nosocomial rather than community acquisition. 94% (N=94) of patients had no knowledge of VRE, while 83% (N=83) had low levels of concern regarding hospital acquired infections. Conclusion There is a low incidence of VRE in the Irish community setting, in contrast to other European Countries, suggesting asymptomatic community colonization is not responsible for the high rates of VRE seen in Ireland. Wider screening or atypical infection control measures would not be supported by this data.

Influence of viral transport media and freeze-thaw cycling on the sensitivity of qRT-PCR detection of SARS-CoV-2 nucleic acids

Objective: The events of the last year have highlighted the complexity of implementing large-scale molecular diagnostic testing for novel pathogens. The purpose of this study was to determine the chemical influences of sample collection media and storage on the stability and detection of viral nucleic acids by qRT-PCR. We studied the mechanism(s) through which viral transport media (VTM) and number of freeze-thaw cycles influenced the analytical sensitivity of qRT-PCR detection of SARS-CoV-2. Our goal is to reinforce testing capabilities and identify weaknesses that could arise in resource-limited environments that do not have well-controlled cold chains. Method: The sensitivity of qRT-PCR analysis was studied in four VTM for synthetic single-stranded RNA (ssRNA) and double-stranded DNA (dsDNA) simulants of the SARS-CoV-2 genome. Results: The sensitivity and reproducibility of qRT-PCR for the synthetic ssRNA and dsDNA were found to be highly sensitive to VTM with the best results observed for ssRNA in HBSS and PBS-G. Surprisingly, the presence of epithelial cellular material with the ssRNA increased the sensitivity of the qRT-PCR assay. Repeated freeze-thaw cycling decreased the sensitivity of the qRT-PCR with two noted exceptions. Conclusions: The choice of VTM is critically important to defining the sensitivity of COVID-19 molecular diagnostics assays and this study suggests they can impact upon the stability of the SARS-CoV-2 viral genome. This becomes increasingly important if the virus structure is destabilised before analysis, which can occur due to poor storage conditions. This study suggests that COVID-19 testing performed with glycerol-containing PBS will produce a high level of stability and sensitivity. These results are in agreement with clinical studies reported for patient-derived samples.

Short-Term Concerns Primarily Determine Patient Preference for Abdominal Aortic Aneurysm Repair

INTRODUCTION

Abdominal aortic aneurysm (AAA) repair may be performed through open or endovascular approaches, but the factors influencing a patient's repair-type preference are not well characterized. Here we performed a qualitative analysis to better understand factors influencing patient preference within the Preference for Open Versus Endovascular Repair of AAA Trial.

METHODS

Open-ended responses regarding primary (n = 21) and secondary (n = 47) factors influencing patient preference underwent qualitative analysis using the constant comparative method with iterative reviews. Codes were used to generate themes and themes grouped into categories, with each step conducted via consensus agreement between three researchers. Relative prevalence of themes were compared to ascertain trends in patient preference.

RESULTS

Patient responses regarding both primary and secondary factors fell into four categories: Short-term concerns, long-term concerns, advice & experience, and other. Patients most frequently described short-term concerns (23) as their primary influence, with themes including post-op complications, hospitalization & recovery, and intraoperative concerns. Long-term concerns were more prevalent (20) as secondary factors, which included themes such as survival, and chronic management. The average age of patients voicing only long-term concerns as a primary factor was 11 years younger than those listing only short-term concerns.

CONCLUSION

Short-term concerns relating to the procedure and recovery are more often the primary factor influencing patient preference, while long term concerns play a more secondary role. Long-term concerns are more often a primary factor in younger patients. Vascular surgeons should consider this information in shared decision making to reach an optimal outcome.

A Survey of Latent Tuberculosis Screening and Treatment Practices in a Tertiary Centre

Aim Knowledge of latent tuberculosis infection (LTBI) screening and treatment practices are lacking in Ireland, where LTBI is not programmatically surveyed or managed. The aim of this research was to describe current clinical practice when screening and treating patients for LTBI in a tertiary referral centre in Ireland. Methods A 17-question survey relating to LTBI screening and management practices with both open-ended questions and close ended multiple-choice questions was created using SurveyMonkey. The survey target sample was healthcare workers in the tertiary centre who direct LTBI screening and treatment for patients at risk of TB disease in their respective departments. Results The response rate to the survey was 45% (21/47). Seventy-one percent (15/21) of those surveyed responded to the question "What barriers exist to screening patients for latent TB in your clinical practice?". Fifty-three percent (8/15) said that they found it difficult to access LTBI testing and 27% (4/15) cited accessing the interferon-gamma release assay (IGRA) result as a barrier. Forty-three percent (9/21) responded that there was not a clear referral pathway for patients that they would like specialist input on when diagnosing and managing patients with LTBI. Conclusion Access to LTBI testing, LTBI test results, TB specialist services and the use of rifamycin-based regimens should be improved in this tertiary centre. Consideration should be given to developing a national LTBI education programme for healthcare professionals and updating national LTBI treatment guidelines.

Characteristics and outcomes of acute colitis diagnosed on cross-sectional imaging presenting via the emergency department in an Irish academic medical centre

BACKGROUND AND AIMS

A significant proportion of patients presenting to the Emergency Department with gastrointestinal symptoms that result in cross-sectional imaging receive a radiological diagnosis of colitis. We aimed to review the characteristics, outcomes, and final diagnoses of new emergency department presentations with colitis diagnosed on cross-sectional imaging.

METHODS

A radiology database was interrogated to identify patients admitted from the Emergency Department of St James's Hospital whose cross-sectional imaging demonstrated colitis. Baseline demographic data, information on inpatient investigations, final diagnoses, and outcomes were recorded. Adverse outcomes were defined as a requirement for surgery, intensive care unit (ICU) stay, or mortality RESULTS: A total of 118 patients, 67% female, were identified with a median age of 64 years (range 16.9-101.2). Median (range) admission duration was 10 days (1-241). Final colitis diagnoses were infectious (28%), undefined (27%), reactive (18%), inflammatory bowel disease (11%), ischaemic (9%), chemotherapy-associated (3%), diverticular (3%), and medication-associated (1%). Colonic perforation, colectomy, and mortality occurred in 1%, 5%, and 13% of the cohort respectively. On univariate analysis, low haemoglobin, low albumin, high lactate, and male gender were associated with adverse outcomes with the following odds ratios (OR) and 95% confidence intervals (95%CI) were low haemoglobin 1.49 [1.15-1.92] P = 0.002, low albumin 1.16 [1.07-1.25] P = 0.0002, lactate 1.65 [1.13-2.42] P = 0.009, and male gender 3.09 [1.23-7.77] P = 0.019. On multivariate analysis, male gender was associated with adverse outcomes.

CONCLUSION

Patients presenting to the Emergency Department with a colitis, requiring an abdominal CT are a heterogenous group with a proportion having concomitant intra-abdominal pathology resulting in critical illness. Hence their is a significant morbidity and mortality observed in this cohort which should not be extrapolated to a general population of patients presenting with colitis. In this cohort of patients, anaemia, hypoalbuminaemia, and elevated lactate in patients presenting to the ED with acute colitis are significantly associated with adverse outcomes. Early recognition of these prognostic factors may identify the cohort of patients who are best managed in a high-dependency setting.

Biopsychosocial factors associated with depression and anxiety in older adults with intellectual disability: results of the wave 3 Intellectual Disability Supplement to The Irish Longitudinal Study on Ageing

BACKGROUND

Depression and anxiety are amongst the most prevalent mental health disorders in the older population with intellectual disability (ID). There is a paucity of research that pertains to associative biopsychosocial factors for depression and anxiety in this population. The aim of this study is to determine the biopsychosocial factors associated with depression and anxiety in a population of older adults with ID in Ireland.

METHODS

The study was part of 'The Intellectual Disability Supplement to The Irish Longitudinal Study on Ageing'. Depressive symptoms were assessed using the Glasgow Depression Scale for people with a Learning Disability. Anxiety symptoms were measured using the Glasgow Anxiety Scale for people with a Learning Disability. The cross-sectional associations of depression and anxiety with biopsychosocial parameters were measured using a variety of self-report and proxy-completed questionnaires.

RESULTS

For the study population, 9.97% met the criteria for depression, and 15.12% met the criteria for an anxiety disorder. Participants meeting criteria for depression were more likely to be taking regular mood stabiliser medications and to exhibit aggressive challenging behaviour. Participants meeting criteria for anxiety were more likely to have sleep difficulties and report loneliness. Participants meeting criteria for either/both depression and anxiety were more likely to report loneliness.

CONCLUSIONS

This study identified both treatable and modifiable, as well as unmodifiable, biopsychosocial factors associated with depression and/or anxiety in older adults with ID. A longitudinal study follow-up will further develop our knowledge on the causality and direction of associated biopsychosocial factors with depression and anxiety in older adults with ID and better inform management strategies, prevention policies and funding of services.

Cytokinetic bridge triggers de novo lumen formation in vivo

Multicellular rosettes are transient epithelial structures that serve as intermediates during diverse organ formation. We have identified a unique contributor to rosette formation in zebrafish Kupffer's vesicle (KV) that requires cell division, specifically the final stage of mitosis termed abscission. KV utilizes a rosette as a prerequisite before forming a lumen surrounded by ciliated epithelial cells. Our studies identify that KV-destined cells remain interconnected by cytokinetic bridges that position at the rosette's center. These bridges act as a landmark for directed Rab11 vesicle motility to deliver an essential cargo for lumen formation, CFTR (cystic fibrosis transmembrane conductance regulator). Here we report that premature bridge cleavage through laser ablation or inhibiting abscission using optogenetic clustering of Rab11 result in disrupted lumen formation. We present a model in which KV mitotic cells strategically place their cytokinetic bridges at the rosette center, where Rab11-associated vesicles transport CFTR to aid in lumen establishment.

The association of life events and mental ill health in older adults with intellectual disability: results of the wave 3 Intellectual Disability Supplement to The Irish Longitudinal Study on Ageing

BACKGROUND

Exposures to life events are associated with emotional, psychological and behavioural problems in those with intellectual disability (ID). Older adults with ID may experience different life events given differences in living circumstances, cognitive decline, greater dependency on others and less autonomy. This study examines the relationship of life events and mental ill health in an older ID population in Ireland.

METHODS

The study was part of 'The Intellectual Disability Supplement to The Irish Longitudinal Study on Ageing'. The frequency of life events was assessed using a 20-item checklist, and the level of stress experienced was assessed using a three-point Likert scale measuring the burden of the life event. The associations of life events with factors associated with mental ill health were measured using a variety of self-report and proxy completed questionnaires.

RESULTS

For the study population, 88.1% had been exposed to at least one life event in the preceding 12 months and 64.5% to two or more life events. Frequency and burden of life events were significantly higher in individuals living in institutional settings and in individuals with any current psychiatric condition, increased depressive and anxiety symptoms, challenging behaviour and reported poorer self-rated mental and physical health. More life events were significantly associated with new psychiatric diagnoses as well as initiation and increased dosage of mood stabilising, hypnotic and sedative medications.

CONCLUSIONS

Life events are significantly associated with mental ill health in the older ID population. Service providers must focus on limiting the exposure to these events and, in situations where they cannot be avoided, should support and manage individuals compassionately and effectively, prioritising their mental and physical well-being.

Chemical approaches for doping nanodevice architectures

Advanced doping technologies are key for the continued scaling of semiconductor devices and the maintenance of device performance beyond the 14 nm technology node. Due to limitations of conventional ion-beam implantation with thin body and 3D device geometries, techniques which allow precise control over dopant diffusion and concentration, in addition to excellent conformality on 3D device surfaces, are required. Spin-on doping has shown promise as a conventional technique for doping new materials, particularly through application with other dopant methods, but may not be suitable for conformal doping of nanostructures. Additionally, residues remain after most spin-on-doping processes which are often difficult to remove. In situ doping of nanostructures is especially common for bottom-up grown nanostructures but problems associated with concentration gradients and morphology changes are commonly experienced. Monolayer doping has been shown to satisfy the requirements for extended defect-free, conformal and controllable doping on many materials ranging from traditional silicon and germanium devices to emerging replacement materials such as III-V compounds but challenges still remain, especially with regard to metrology and surface chemistry at such small feature sizes. This article summarises and critically assesses developments over the last number of years regarding the application of gas and solution phase techniques to dope silicon-, germanium- and III-V-based materials and nanostructures to obtain shallow diffusion depths coupled with high carrier concentrations and abrupt junctions.

A phase II study (ARCHER 1042) to evaluate prophylactic treatment of dacomitinib-induced dermatologic and gastrointestinal adverse events in advanced non-small-cell lung cancer

BACKGROUND

ARCHER 1042, a randomized phase II trial, explored the impact of prophylactic treatment on select dermatologic adverse events of interest (SDAEI), diarrhea, and mucositis associated with dacomitinib, an oral irreversible pan-human epidermal growth factor receptor (HER) inhibitor, in development for advanced non-small-cell lung cancer (NSCLC).

PATIENTS AND METHODS

Patients with advanced NSCLC treated with dacomitinib were enrolled in two cohorts. Cohort I patients were randomized 1:1 to receive oral doxycycline or placebo (4 weeks). Cohort II patients received oral VSL#3 probiotic plus topical alclometasone. Primary end points for Cohorts I and II were incidence of all grade and grade ≥2 SDAEI in the first 8 weeks of treatment and quality of life (QoL) assessed by the Skindex-16 survey. Additional primary end points for Cohort II were incidence of all grade and grade ≥2 diarrhea and mucositis in the first 8 weeks of treatment; QoL regarding diarrhea and mucositis incidence was assessed by the modified-Oral Mucositis Daily Questionnaire.

RESULTS

Cohort I randomized 114 evaluable patients: 56 in the doxycycline arm, 58 in the placebo arm. Cohort II enrolled 59 evaluable patients. Doxycycline significantly reduced the incidence of grade ≥2 SDAEI by 50% (P = 0.016) compared with placebo. The incidence of all grade SDAEI was lower with doxycycline than with placebo but did not reach statistical significance. Doxycycline was associated with less deterioration in QoL compared with placebo. Alclometasone was associated with less deterioration in QoL compared with placebo but did not statistically significantly reduce the incidence of all grade or grade ≥2 SDAEI. VSL#3 did not reduce the incidence of all grade or grade ≥2 diarrhea and did not impact mucositis scores.

CONCLUSIONS

Doxycycline was effective as a prophylactic treatment for dacomitinib-induced grade ≥2 SDAEI. Both doxycycline and alclometasone reduced the negative impact in patient-reported dermatologic AEs. The probiotic was not effective for preventing diarrhea or mucositis.

Monolayer Doping of Si with Improved Oxidation Resistance

In this article, the functionalization of planar silicon with arsenic- and phosphorus-based azides was investigated. Covalently bonded and well-ordered alkyne-terminated monolayers were prepared from a range of commercially available dialkyne precursors using a well-known thermal hydrosilylation mechanism to form an acetylene-terminated monolayer. The terminal acetylene moieties were further functionalized through the application of copper-catalyzed azide-alkyne cycloaddition (CuAAC) reactions between dopant-containing azides and the terminal acetylene groups. The introduction of dopant molecules via this method does not require harsh conditions typically employed in traditional monolayer doping approaches, enabling greater surface coverage with improved resistance toward reoxidation. X-ray photoelectron spectroscopy studies showed successful dialkyne incorporation with minimal Si surface oxidation, and monitoring of the C 1s and N 1s core-level spectra showed successful azide-alkyne cycloaddition. Electrochemical capacitance-voltage measurements showed effective diffusion of the activated dopant atoms into the Si substrates.

Fabrication of ultra-dense sub-10 nm in-plane Si nanowire arrays by using a novel block copolymer method: optical properties

The use of a low-χ, symmetric block copolymer as an alternative to the high-χ systems currently being translated towards industrial silicon chip manufacture has been demonstrated. Here, the methodology for generating on-chip, etch resistant masks and subsequent pattern transfer to the substrate using ultra-small dimension, lamellar, microphase separated polystyrene-b-poly(ethylene oxide) (PS-b-PEO) block copolymer (BCP) is described. Well-controlled films of a perpendicularly oriented lamellar pattern with a domain size of ∼8 nm were achieved through amplification of an effective interaction parameter (χeff) of the BCP system. The self-assembled films were used as 'templates' for the generation of inorganic oxides nanowire arrays through selective metal ion inclusion and subsequent processing. Inclusion is a significant challenge because the lamellar systems have less chemical and mechanical robustness than the cylinder forming materials. The oxide nanowires of uniform diameter (∼8 nm) were isolated and their structure mimics the original BCP nanopatterns. We demonstrate that these lamellar phase iron oxide nanowire arrays could be used as a resist mask to fabricate densely packed, identical ordered, good fidelity silicon nanowire arrays on the substrate. Possible applications of the materials prepared are discussed, in particular, in the area of photonics and photoluminescence where the properties are found to be similar to those of surface-oxidized silicon nanocrystals and porous silicon.

Embedding colloidal nanoparticles inside mesoporous silica using gas expanded liquids for high loading recyclable catalysts

Size and composition controlled alloy nanoparticles can be easily incorporated into porous SiO₂ supports using carbon dioxide expanded hexane. Embedding NPs into porous networks increase catalyst stability and recyclability compared to immobilisation on non-porous SiO₂ supports.

An enhanced surface passivation effect in InGaN/GaN disk-in-nanowire light emitting diodes for mitigating Shockley-Read-Hall recombination

We present a detailed study of the effects of dangling bond passivation and the comparison of different sulfide passivation processes on the properties of InGaN/GaN quantum-disk (Qdisk)-in-nanowire based light emitting diodes (NW-LEDs). Our results demonstrated the first organic sulfide passivation process for nitride nanowires (NWs). The results from Raman spectroscopy, photoluminescence (PL) measurements, and X-ray photoelectron spectroscopy (XPS) showed that octadecylthiol (ODT) effectively passivated the surface states, and altered the surface dynamic charge, and thereby recovered the band-edge emission. The effectiveness of the process with passivation duration was also studied. Moreover, we also compared the electro-optical performance of NW-LEDs emitting at green wavelength before and after ODT passivation. We have shown that the Shockley-Read-Hall (SRH) non-radiative recombination of NW-LEDs can be greatly reduced after passivation by ODT, which led to a much faster increasing trend of quantum efficiency and higher peak efficiency. Our results highlighted the possibility of employing this technique to further design and produce high performance NW-LEDs and NW-lasers.

Organo-arsenic molecular layers on silicon for high-density doping

This article describes for the first time the controlled monolayer doping (MLD) of bulk and nanostructured crystalline silicon with As at concentrations approaching 2 × 10(20) atoms cm(-3). Characterization of doped structures after the MLD process confirmed that they remained defect- and damage-free, with no indication of increased roughness or a change in morphology. Electrical characterization of the doped substrates and nanowire test structures allowed determination of resistivity, sheet resistance, and active doping levels. Extremely high As-doped Si substrates and nanowire devices could be obtained and controlled using specific capping and annealing steps. Significantly, the As-doped nanowires exhibited resistances several orders of magnitude lower than the predoped materials.

The prevalence of cardiovascular risk factors in obese children

Childhood Obesity poses a public health problem in Ireland. Complications associated include metabolic disease and cardiovascular disease risk. Our aim was to determine the prevalence of cardiovascular risk factors in a cohort of obese Irish children. Assessments were performed on obese children attending weight management clinic. Pedometers and self report physical activity questionnaires were administered to each participant to determine physical activity levels. Fifty-nine children (21 prepubertal and 38 pubertal/post-pubertal) were metabolically profiled. Mean ± SD of z scores for BMI, Waist Circumference and Body Fat % were +3.29 ± 0.48, +3.98 ± 0.73 and +2.75 ± 0.50 respectively. 43% (n = 9) prepubertal and 68% (n = 26) pubertal/postpubertal children had at least one other cardiovascular risk factor in addition to obesity. Increased moderate-vigorous physical activity levels correlated with reduced incidence of cardiovascular risk factors. There is a significant prevalence of cardiovascular risk factors among obese pre-pubertal children and pubertal/post-pubertal adolescents attending an Irish obesity clinic.

Targeting HER2 aberrations as actionable drivers in lung cancers: phase II trial of the pan-HER tyrosine kinase inhibitor dacomitinib in patients with HER2-mutant or amplified tumors

BACKGROUND

HER2 mutations and amplifications have been identified as oncogenic drivers in lung cancers. Dacomitinib, an irreversible inhibitor of HER2, EGFR (HER1), and HER4 tyrosine kinases, has demonstrated activity in cell-line models with HER2 exon 20 insertions or amplifications. Here, we studied dacomitinib in patients with HER2-mutant or amplified lung cancers.

PATIENTS AND METHODS

As a prespecified cohort of a phase II study, we included patients with stage IIIB/IV lung cancers with HER2 mutations or amplification. We gave oral dacomitinib at 30-45 mg daily in 28-day cycles. End points included partial response rate, overall survival, and toxicity.

RESULTS

We enrolled 30 patients with HER2-mutant (n = 26, all in exon 20 including 25 insertions and 1 missense mutation) or HER2-amplified lung cancers (n = 4). Three of 26 patients with tumors harboring HER2 exon 20 mutations [12%; 95% confidence interval (CI) 2% to 30%] had partial responses lasting 3+, 11, and 14 months. No partial responses occurred in four patients with tumors with HER2 amplifications. The median overall survival was 9 months from the start of dacomitinib (95% CI 7-21 months) for patients with HER2 mutations and ranged from 5 to 22 months with amplifications. Treatment-related toxicities included diarrhea (90%; grade 3/4: 20%/3%), dermatitis (73%; grade 3/4: 3%/0%), and fatigue (57%; grade 3/4: 3%/0%). One patient died on study likely due to an interaction of dacomitinib with mirtazapine.

CONCLUSIONS

Dacomitinib produced objective responses in patients with lung cancers with specific HER2 exon 20 insertions. This observation validates HER2 exon 20 insertions as actionable targets and justifies further study of HER2-targeted agents in specific HER2-driven lung cancers.

CLINICALTRIALSGOV

NCT00818441.

Aligned silicon nanofins via the directed self-assembly of PS-b-P4VP block copolymer and metal oxide enhanced pattern transfer

'Directing' block copolymer (BCP) patterns is a possible option for future semiconductor device patterning, but pattern transfer of BCP masks is somewhat hindered by the inherently low etch contrast between blocks. Here, we demonstrate a 'fab' friendly methodology for forming well-registered and aligned silicon (Si) nanofins following pattern transfer of robust metal oxide nanowire masks through the directed self-assembly (DSA) of BCPs. A cylindrical forming poly(styrene)-block-poly(4-vinyl-pyridine) (PS-b-P4VP) BCP was employed producing 'fingerprint' line patterns over macroscopic areas following solvent vapor annealing treatment. The directed assembly of PS-b-P4VP line patterns was enabled by electron-beam lithographically defined hydrogen silsequioxane (HSQ) gratings. We developed metal oxide nanowire features using PS-b-P4VP structures which facilitated high quality pattern transfer to the underlying Si substrate. This work highlights the precision at which long range ordered ∼10 nm Si nanofin features with 32 nm pitch can be defined using a cylindrical BCP system for nanolithography application. The results show promise for future nanocircuitry fabrication to access sub-16 nm critical dimensions using cylindrical systems as surface interfaces are easier to tailor than lamellar systems. Additionally, the work helps to demonstrate the extension of these methods to a 'high χ' BCP beyond the size limitations of the more well-studied PS-b-poly(methyl methylacrylate) (PS-b-PMMA) system.

Tissue specific regulation of glucocorticoids in severe obesity and the response to significant weight loss following bariatric surgery (BARICORT)

CONTEXT

Tissue cortisol exposure is under the control of the isozymes of 11β-hydroxysteroid dehydrogenase (11β-HSD). 11β-HSD1 in vivo, acts as an oxoreductase converting inactive cortisone to active cortisol. We hypothesized that 11β-HSD1 activity is dysregulated in obesity and alters following bariatric surgery induced weight loss in different tissues.

METHODS

We recruited 21 patients prior to undergoing bariatric surgery and performed cortisol generation profiles (following oral cortisone administration), urinary corticosteroid metabolite analysis, adipose tissue microdialysis, and tissue gene expression before and after weight loss, following bariatric surgery. Archived tissue samples from 20 previous bariatric surgery patients were also used for tissue gene expression studies.

RESULTS

Gene expression showed a positive correlation with 11β-HSD1 and BMI in omental adipose tissue (OM) (r = +0.52, P = .0001) but not sc adipose tissue (r = +0.28, P = .17). 11β-HSD1 expression in liver negatively correlated with body mass index (BMI) (r = -0.37, P = .04). 11β-HSD1 expression in sc adipose tissue was significantly reduced after weight loss (0.41 ± 0.28 vs 0.17 ± 0.1 arbitrary units, P = .02). Following weight loss, serum cortisol generation increased during a cortisol generation profile (area under the curve 26 768 ± 16 880 vs 47 579 ± 16 086 nmol/L/minute, P ≤ .0001.) Urinary corticosteroid metabolites demonstrated a significant reduction in total cortisol metabolites after bariatric surgery (15 224 ± 6595 vs 8814 ± 4824 μg/24 h, P = .01). Microdialysis of sc adipose tissue showed a threefold reduction in cortisol/cortisone ratio after weight loss.

CONCLUSIONS

This study highlights the differences in tissue specific regulation of cortisol metabolism in obesity and after weight loss. Following bariatric surgery hepatic 11β-HSD1 activity increases, sc adipose tissue 11β-HSD1 activity is reduced and total urinary cortisol metabolites are reduced indicating a possible reduction in hypothalamic pituitary adrenal axis drive. 11β-HSD1 expression correlates positively with BMI in omental adipose tissue and negatively within hepatic tissue. 11β-HSD1 expression is reduced in sc adipose tissue after weight loss.

Comparison of cryopreserved amniotic membrane and umbilical cord tissue with dehydrated amniotic membrane/chorion tissue

OBJECTIVE

To evaluate how the different processing methods cryopreservation and dehydration affect the structural integrity and biological composition of key signalling molecules within amniotic membrane and umbilical cord tissues.

METHOD

We directly compared cryopreserved amniotic membrane (AM) and umbilical cord (UC) tissues with dehydrated amniotic membrane/chorion (dHACM) tissue using biochemical and functional assays including histological and histochemical staining, BCA, agarose gel electrophoresis, western blot, ELISA, and proliferation and cell death assays.

RESULTS

Cryopreservation retains the native architecture of the AM/UC extracellular matrix and maintains the quantity and activity of key biological signals present in fresh AM/UC, including high molecular weight hyaluronic acid, heavy chain-HA complex, and pentraxin 3. In contrast, dehydrated tissues were structurally compromised and almost completely lacked these crucial components.

CONCLUSION

The results presented here indicate that cryopreservation better preserves the structural and biological signaling molecules of foetal tissues.

An analysis of radiation therapy medical events in New York State: the role of the state radiation programs in patient safety

From 2001 through 2009, the New York State Department of Health (NYSDOH) has documented 244 reports of radiation therapy events, of which 228 have resulted from the delivery of radiation beam therapy using linear accelerators (LINACs). Historically, radiation therapy events involving LINACs have not been uniformly reported across the country because LINACs are regulated by state radiation control programs, and reporting requirements vary among states. The Nuclear Regulatory Commission's Nuclear Material Events Database (NMED) only tracks events involving radioactive materials (RAM). Efforts to track medical events involving LINACs at a national level have begun only recently. This article highlights the importance of tracking and analyzing all medical radiation events in order to improve quality of care and patient safety. An analysis of a subset of the data collected by the NYSDOH from 2001-2009 is presented. This subset consists of only events arising from the use of LINACs in radiation therapy. There are very few publications on errors and error rates in the use of medical accelerators in radiation therapy. This analysis highlights the most common types of errors, causes and contributing factors, areas for improvement and actions taken to bring this information to the regulated community. An error rate of 0.07% per patient receiving radiation treatment is estimated using these data and the New York State Tumor Registry data for the same period. NY State Regulations governing the practice of Radiation Oncology have been revised recently to reflect the increased complexity in the delivery of therapeutic radiation. Collaboration and sharing of data such as those presented here, between federal, state and local regulators, professional organizations such as the Conference of Radiation Control Program Directors (CRCPD), American Society for Radiation Oncology (ASTRO), American Association of Physicists in Medicine (AAPM), American College of Radiology (ACR), American College of Radiation Oncology (ACRO), manufacturers of medical radiation equipment and software developers and the regulated community has begun and will contribute to improved quality of care and patient safety.

Optimizing vanadium pentoxide thin films and multilayers from dip-coated nanofluid precursors

Using an alkoxide-based precursor, a strategy for producing highly uniform thin films and multilayers of V2O5 is demonstrated using dip coating. Defect-free and smooth films of V2O5 on different surfaces can be deposited from liquid precursors. We show how pinholes are formed due to heterogeneous nucleation during hydrolysis as the precursor forms a nanofluid. Using knowledge of instability formation often found in composite nanofluid films and the influence of cluster formation on the stability of these films, we show how polymer-precursor mixtures provide optimum uniformity and very low surface roughness in amorphous V2O5 and also orthorhombic V2O5 after crystallization by heating. Pinhole and roughness instability formation during the liquid stage of the nanofluid on gold and ITO substrates is suppressed giving a uniform coating. Practically, understanding evolution pathways that involve dewetting processes, nucleation, decomposition, or hydrolysis in complex nanofluids provides a route for improved uniformity of thin films. The method could be extended to improve the consistency in sequential or iterative multilayer deposits of a range of liquid precursors for functional materials and coatings.

Changes in human dendritic cell number and function in severe obesity may contribute to increased susceptibility to viral infection

Dendritic cells (DCs) are key immune sentinels linking the innate and adaptive immune systems. DCs recognise danger signals and initiate T-cell tolerance, memory and polarisation. They are critical cells in responding to a viral illness. Obese individuals have been shown to have an impaired response to vaccinations against virally mediated conditions and to have an increased susceptibility to multi-organ failure in response to viral illness. We investigated if DCs are altered in an obese cohort (mean body mass index 51.7±7.3 kg m(-2)), ultimately resulting in differential T-cell responses. Circulating DCs were found to be significantly decreased in the obese compared with the lean cohort (0.82% vs 2.53%). Following Toll-like receptor stimulation, compared with lean controls, DCs generated from the obese cohort upregulated significantly less CD83 (40% vs 17% mean fluorescence intensity), a molecule implicated in the elicitation of T-cell responses, particularly viral responses. Obese DCs produced twofold more of the immunosuppressive cytokine interleukin (IL)-10 than lean controls, and in turn stimulated fourfold more IL-4-production from allogenic naive T cells. We conclude that obesity negatively impacts the ability of DCs to mature and elicit appropriate T-cell responses to a general stimulus. This may contribute to the increased susceptibility to viral infection observed in severe obesity.

Comparison of intensity-modulated radiotherapy, adaptive radiotherapy, proton radiotherapy, and adaptive proton radiotherapy for treatment of locally advanced head and neck cancer

BACKGROUND AND PURPOSE

Various radiotherapy planning methods for locally advanced squamous cell carcinoma of the head and neck (SCCHN) have been proposed to decrease normal tissue toxicity. We compare IMRT, adaptive IMRT, proton therapy (IMPT), and adaptive IMPT for SCCHN.

MATERIALS AND METHODS

Initial and re-simulation CT images from 10 consecutive patients with SCCHN were used to quantify dosimetric differences between photon and proton therapy. Contouring was performed on both CTs, and plans (n=40 plans) and dose-volume histograms were generated.

RESULTS

The mean GTV volume decreased 53.4% with re-simulation. All plans provided comparable PTV coverage. Compared with IMRT, adaptive IMRT significantly reduced the maximum dose to the mandible (p=0.020) and mean doses to the contralateral parotid gland (p=0.049) and larynx (p=0.049). Compared with IMRT and adaptive IMRT, IMPT significantly lowered the maximum doses to the spinal cord (p<0.002 for both) and brainstem (p<0.002 for both) and mean doses to the larynx (p<0.002 for both) and ipsilateral (p=0.004 IMRT, p=0.050 adaptive) and contralateral (p<0.002 IMRT, p=0.010 adaptive) parotid glands. Adaptive IMPT significantly reduced doses to all critical structures compared with IMRT and adaptive IMRT and several critical structures compared with non-adaptive IMPT.

CONCLUSIONS

Although adaptive IMRT reduced dose to several normal structures compared with standard IMRT, non-adaptive proton therapy had a more favorable dosimetric profile than IMRT or adaptive IMRT and may obviate the need for adaptive planning. Protons allowed significant sparing of the spinal cord, parotid glands, larynx, and brainstem and should be considered for SCCHN to decrease normal tissue toxicity while still providing optimal tumor coverage.

Preadipocyte factor-1 is associated with metabolic profile in severe obesity

CONTEXT

Dysfunctional adipose tissue has been proposed as a key pathological process linking obesity and metabolic disease. Preadipocyte factor-1 (Pref-1) has been shown to inhibit differentiation in adipocyte precursor cells and could thereby play a role in determining adipocyte size, adipose tissue functioning, and metabolic profile in obese individuals.

OBJECTIVE

We hypothesized that adipose tissue from metabolically healthy obese (MHO) and matched metabolically unhealthy obese individuals would demonstrate distinct differences in relation to Pref-1 expression, adipocyte size, and inflammatory markers.

DESIGN, SETTING, AND PATIENTS

This was a cross-sectional study, investigating obese patients undergoing bariatric surgery at a tertiary referral centre. Patients included 12 MHO and 17 age- and body mass index-matched metabolically unhealthy obese individuals.

MAIN OUTCOME MEASURES

Pref-1, monocyte chemotactic protein-1, TNF-α, granulocyte colony-stimulating factor, IL-6, and adiponectin levels, macrophage numbers, and adipocyte size were measured in omental and subcutaneous adipose tissue.

RESULTS

The MHO group had a lower level of Pref-1 (per 1000 adipocytes) in both subcutaneous [160 (136-177) versus 194 (153-355); P < 0.05] and omental adipose tissue [102 (32-175) versus 194 (100-350); P < 0.005]. This was associated with lower numbers of macrophages, lower levels of TNF-α, monocyte chemotactic protein-1, and granulocyte colony-stimulating factor, and higher levels of adiponectin. Omental Pref-1 showed strong correlations with adipocyte size (r = 0.67, P < 0.0005) and metabolic and adipokine parameters, including percent fatty liver (r = 0.62, P < 0.005), fasting glucose (r = 0.68, P < 0.0005), triglyceride (r = 0.60, P < 0.005), high-density lipoprotein cholesterol (r = -0.46, P < 0.05), and adiponectin (r = -0.71, P < 0.05).

CONCLUSION

Adipose tissue in MHO individuals had lower levels of Pref-1, a known inhibitor of preadipocyte differentiation, and a more favorable inflammatory profile. These factors may be key to protecting this subgroup of obese individuals from the adverse metabolic profile associated with excess adiposity.

Predicted rates of secondary malignancies from proton versus photon radiation therapy for stage I seminoma

PURPOSE

Photon radiotherapy has been the standard adjuvant treatment for stage I seminoma. Single-dose carboplatin therapy and observation have emerged as alternative options due to concerns for acute toxicities and secondary malignancies from radiation. In this institutional review board-approved study, we compared photon and proton radiotherapy for stage I seminoma and the predicted rates of excess secondary malignancies for both treatment modalities.

METHODS AND MATERIAL

Computed tomography images from 10 consecutive patients with stage I seminoma were used to quantify dosimetric differences between photon and proton therapies. Structures reported to be at increased risk for secondary malignancies and in-field critical structures were contoured. Reported models of organ-specific radiation-induced cancer incidence rates based on organ equivalent dose were used to determine the excess absolute risk of secondary malignancies. Calculated values were compared with tumor registry reports of excess secondary malignancies among testicular cancer survivors.

RESULTS

Photon and proton plans provided comparable target volume coverage. Proton plans delivered significantly lower mean doses to all examined normal tissues, except for the kidneys. The greatest absolute reduction in mean dose was observed for the stomach (119 cGy for proton plans vs. 768 cGy for photon plans; p < 0.0001). Significantly more excess secondary cancers per 10,000 patients/year were predicted for photon radiation than for proton radiation to the stomach (4.11; 95% confidence interval [CI], 3.22-5.01), large bowel (0.81; 95% CI, 0.39-1.01), and bladder (0.03; 95% CI, 0.01-0.58), while no difference was demonstrated for radiation to the pancreas (0.02; 95% CI, -0.01-0.06).

CONCLUSIONS

For patients with stage I seminoma, proton radiation therapy reduced the predicted secondary cancer risk compared with photon therapy. We predict a reduction of one additional secondary cancer for every 50 patients with a life expectancy of 40 years from the time of radiation treatment with protons instead of photons. Proton radiation therapy also allowed significant sparing of most critical structures examined and warrants further study for patients with seminoma, to decrease radiation-induced toxicity.

Genetic counselor opinions of, and experiences with telephone communication of BRCA1/2 test results

BRCA1/2 test disclosure has, historically, been conducted in-person by genetics professionals. Given increasing demand for, and access to, genetic testing, interest in telephone and Internet genetic services, including disclosure of test results, has increased. Semi-structured interviews with genetic counselors were conducted to determine interest in, and experiences with telephone disclosure of BRCA1/2 test results. Descriptive data are summarized with response proportions. One hundred and ninety-four genetic counselors completed self-administered surveys via the web. Although 98% had provided BRCA1/2 results by telephone, 77% had never provided pre-test counseling by telephone. Genetic counselors reported perceived advantages and disadvantages to telephone disclosure. Thirty-two percent of participants described experiences that made them question this practice. Genetic counselors more frequently reported discomfort with telephone disclosure of a positive result or variant of uncertain significance (p < 0.01) than other results. Overall, 73% of participants reported interest in telephone disclosure. Many genetic counselors have provided telephone disclosure, however, most, infrequently. Genetic counselors identify potential advantages and disadvantages to telephone disclosure, and recognize the potential for testing and patient factors to impact patient outcomes. Further research evaluating the impact of testing and patient factors on cognitive, affective, social and behavioral outcomes of alternative models of communicating genetic information is warranted.