Molecular profiling and feasibility using a comprehensive hybrid capture panel on a consecutive series of non-small-cell lung cancer patients from a single centre

BACKGROUND

Targeted next-generation sequencing (NGS) is recommended to screen actionable genomic alterations (GAs) in patients with non-small-cell lung cancer (NSCLC). We determined the feasibility to detect actionable GAs using TruSight™ Oncology 500 (TSO500) in 200 consecutive patients with NSCLC.

MATERIALS AND METHODS

DNA and RNA were sequenced on an Illumina® NextSeq 550 instrument and processed using the TSO500 Docker pipeline. Clinical actionability was defined within the molecular tumour board following European Society for Medical Oncology (ESMO) guidelines for oncogene-addicted NSCLC. Overall survival (OS) was estimated as per the presence of druggable GAs and treatment with targeted therapy.

RESULTS

Most patients were males (69.5%) and former or current smokers (86.5%). Median age was 64 years. The most common histological type and tumour stage were lung adenocarcinoma (81%) and stage IV (64%), respectively. Sequencing was feasible in most patients (93.5%) and actionable GAs were found in 26.5% of patients. A high concordance was observed between single-gene testing and TSO500 NGS panel. Patients harbouring druggable GAs and receiving targeted therapy achieved longer OS compared to patients without druggable GAs. Conversely, patients with druggable GAs not receiving targeted therapy had a trend toward shorter OS compared with driver-negative patients.

CONCLUSIONS

Hybrid capture sequencing using TSO500 panel is feasible to analyse clinical samples from patients with NSCLC and is an efficient tool for screening actionable GAs.

Critical appraisal beyond clinical guidelines for intraabdominal candidiasis

BACKGROUND

Regardless of the available antifungals, intraabdominal candidiasis (IAC) mortality continues to be high and represents a challenge for clinicians.

MAIN BODY

This opinion paper discusses alternative antifungal options for treating IAC. This clinical entity should be addressed separately from candidemia due to the peculiarity of the required penetration of antifungals into the peritoneal cavity. Intraabdominal concentrations may be further restricted in critically ill patients where pathophysiological facts alter normal drug distribution. Echinocandins are recommended as first-line treatment in guidelines for invasive candidiasis. However, considering published data, our pharmacodynamic analysis suggests the required increase of doses, postulated by some authors, to attain adequate pharmacokinetic (PK) levels in peritoneal fluid. Given the limited evidence in the literature on PK/PD-based treatments of IAC, an algorithm is proposed to guide antifungal treatment. Liposomal amphotericin B is advocated as first-line therapy in patients with sepsis/septic shock presenting candidemia or endophthalmitis, or with prior exposure to echinocandins and/or fluconazole, or with infections by Candida glabrata. Other situations and alternatives, such as new compounds or combination therapy, are also analysed.

CONCLUSION

There is a critical need for more robust clinical trials, studies examining patient heterogeneity and surveillance of antifungal resistance to enhance patient care and optimise treatment outcomes. Such evidence will help refine the existing guidelines and contribute to a more personalised and effective approach to treating this serious medical condition. Meanwhile, it is suggested to broaden the consideration of other options, such as liposomal amphotericin B, as first-line treatment until the results of the fungogram are available and antifungal stewardship could be implemented to prevent the development of resistance.

Utility of Molecular Analysis of Peritoneal Fluid in Staging Laparoscopy of Advanced Esophagogastric Junction and Gastric Cancer Prior to Neoadjuvant Treatment

PURPOSE

Molecular analysis of peritoneal fluid in staging laparoscopy of gastric cancer is performed to improve the detection of free intraperitoneal tumor cells. Nevertheless, its significance is controversial, especially in patients with negative cytology but positive molecular analysis. The aim of this study was to analyze the sensitivity of molecular analysis and its prognostic value.

METHODS

A retrospective analysis from April 2011 to October 2019 was performed. Cytology (Cyt) and molecular analysis were analyzed by real-time reverse transcriptase polymerase chain reaction (RT-PCR) of the carcinoembryonic antigen (CEA) and cytokeratin 20 (CK20) tumor makers.

RESULTS

During the study period, 138 staging laparoscopies were performed. Macroscopic carcinomatosis was found in 12.3%. Of the remaining 87.7%, 9.9% were Cyt + and 11.6% were Cyt- RT-PCR + . Of the latter, 9 responded to chemotherapy and underwent radical surgery. The sensitivity of cytology and molecular analysis was 0.70 and 0.76, respectively (p = 0.67). The 2-year overall survival (OS) of Cyt- RT-PCR + vs. Cyt + was similar (p = 0.1). The 2-year OS of Cyt-RT-PCR + subgroup who underwent radical surgery vs. Cyt-RT-PCR- patients was similar (p = 0.69), but disease-free survival was shorter in the first group (p = 0.005).

CONCLUSION

Our results show that the sensitivity of molecular analysis is similar to that of cytology. The prognostic value of positive molecular analysis was similar to positive cytology in terms of 2-year overall survival, except in the subgroup of operated patients in whom the overall survival was similar to that of those with a negative molecular analysis, albeit with a shorter disease-free survival.

Critical patients COVID-19 has changed the management and outcomes in the ICU after 1 year of the pandemic? A multicenter, prospective, observational study

OBJECTIVE

To compare the clinical characteristics, treatments, and evolution of critical patients with COVID-19 pneumonia treated in Intensive Care Units (ICU) after one year of pandemic.

METHODOLOGY

Multicenter, prospective study, which included critical COVID-19 patients in 9 ICUs in northwestern Spain. The clinical characteristics, treatments, and evolution of patients admitted to the ICU during the months of March-April 2020 (period 1) were compared with patients admitted in January-February 2021 (period 2).

RESULTS

337 patients were included (98 in period 1 and 239 in period 2). In period 2, fewer patients required invasive mechanical ventilation (IMV) (65% vs 84%, p < 0.001), using high-flow nasal cannulas (CNAF) more frequently (70% vs 7%, p < 0.001), ventilation non-invasive mechanical (NIMV) (40% vs 14%, p < 0.001), corticosteroids (100% vs 96%, p = 0.007) and prone position in both awake (42% vs 28%, p = 0.012), and intubated patients (67% vs 54%, p = 0.034). The days of IMV, ICU stay and hospital stay were lower in period 2. Mortality was similar in the two periods studied (16% vs 17%).

CONCLUSIONS

After 1 year of pandemic, we observed that in patients admitted to the ICU, CNAF, NIMV, use of the prone position, and corticosteroids have been used more frequently, reducing the number of patients in IMV, and the length of stay in the ICU and hospital stay. Mortality was similar in the two study periods.

[Critical patients COVID-19 has changed the management and outcomes in the ICU after 1 year of the pandemic? A multicenter, prospective, observational study]

Objective

To compare the clinical characteristics, treatments, and evolution of critical patients with COVID-19 pneumonia treated in intensive care units (ICU) after one year of pandemic.

Methodology

Multicenter, prospective study, which included critical COVID-19 patients in 9 ICUs in northwestern Spain. The clinical characteristics, treatments, and evolution of patients admitted to the ICU during the months of March-April 2020 (period 1) were compared with patients admitted in January-February 2021 (period 2).

Results

337 patients were included (98 in period 1 and 239 in period 2). In period 2, fewer patients required invasive mechanical ventilation (IMV) (65% vs. 84%, P < .001), using high-flow nasal cannulas (CNAF) more frequently (70% vs. 7%, P < .001), ventilation non-invasive mechanical (NIMV) (40% vs. 14%, P < .001), corticosteroids (100% vs. 96%, P = .007) and prone position in both awake (42% vs. 28%, P = .012), and intubated patients (67% vs. 54%, P = .034). The days of IMV, ICU stay and hospital stay were lower in period 2. Mortality was similar in the two periods studied (16% vs. 17%).

Conclusions

After one year of pandemic, we observed that in patients admitted to the ICU, CNAF, NIMV, use of the prone position, and corticosteroids have been used more frequently, reducing the number of patients in IMV, and the length of stay in the ICU and hospital stay. Mortality was similar in the two study periods.

Framework for large-scale automatic curation of heterogeneous cardiac MRI (ACUR MRI)

Funding Acknowledgements

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): UKRI CDT in AI for Healthcare http://ai4health.io and British Heart Foundation

Background 

Data curation is an important process that structures and organises data, supporting research and the development of artificial intelligence models. However, manually curating a large volume of medical data is a time-consuming, repetitive and costly process that puts additional strain on clinical experts. The curation becomes more complex and demanding as more data sources are used. This leads to an introduction of disparity in the data structure and protocols. 

Purpose 

Here, we propose an automatic framework to curate large volumes of heterogenous cardiac MRI scans acquired across different sites and scanner vendors. Our framework requires minimal expert involvement throughout and works directly on DICOM images from the scanner or PACS.  The resulting structured standardised data allow for straightforward image analysis, hypothesis testing and the training and application of artificial intelligence models. 

Methods 

It is broken down into three main components

anonymisation, cataloguing and outlier detection (see Figure 1). Anonymisation automatically removes any identifiable patient information from the DICOM image attributes. These data are replaced with anonymised labels, whilst maintaining relevant longitudinal information from each patient. DICOM attributes are also used to automatically group the different images according to imaging sequence (e.g. CINE, Delayed-Enhancement, T1 maps), acquisition geometry (e.g. short-axis, 2-chamber, 4-chamber) and imaging attributes (e.g. slice thickness, TE, TR), for easier querying. The sorting characteristics are flexible and can easily be defined by the user. Finally, we detect and flag, for subsequent manual inspection, any outliers within those groups, based on the similarity levels of chosen DICOM attributes. This framework additionally offers interactive image visualisation to allow users to assess its performance in real time. 

Results 

We tested the performance of ACUR CMRI on 26,668 CMR image series (723,531 images) from 858 patient examinations, which took place across two sites in four different scanners. With an average execution time per patient of 100 seconds, ACUR was able to sort imaging data with 1191 different sequence names into 43 categories. The framework can be freely downloaded from https://bitbucket.org/cmr-ai-working-group/acur/. 

Conclusions 

We present ACUR, an automatic framework to curate large volumes of heterogeneous cardiac MRI data. We show how it can quickly and automatically curate data, grouping it according to desired imaging characteristics defined in DICOM attributes. The proposed framework is flexible and ideally suited as a pre-processing tool for large biomedical imaging data studies.

Structural and optical properties of self-assembled AlN nanowires grown on SiO2/Si substrates by molecular beam epitaxy

Self-assembled AlN nanowires (NWs) are grown by plasma-assisted molecular beam epitaxy (PAMBE) on SiO₂/Si (111) substrates. Using a combination of in situ reflective high energy electron diffraction and ex situ x-ray diffraction (XRD), we show that the NWs grow nearly strain-free, preferentially perpendicular to the amorphous SiO₂ interlayer and without epitaxial relationship to Si(111) substrate, as expected. Scanning electron microscopy investigation reveals significant NWs coalescence, which results in their progressively increasing diameter and formation of columnar structures with non-hexagonal cross-section. Making use of scanning transmission electron microscopy (STEM), the NWs initial diameters are found in the 20-30 nm range. In addition, the formation of a thin (≈30 nm) polycrystalline AlN layer is observed on the substrate surface. Regarding the structural quality of the AlN NWs, STEM measurements reveal the formation of extended columnar regions, which grow with a virtually perfect metal-polarity wurtzite arrangement and with extended defects only sporadically observed. Combination of STEM and electron energy loss spectroscopy reveals the formation of continuous aluminum oxide (1-2 nm) on the NW surface. Low temperature photoluminescence measurements reveal a single near-band-edge (NBE) emission peak, positioned at 6.03 eV (at 2 K), a value consistent with nearly zero NW strain evidenced by XRD and in agreement with the values obtained on AlN bulk layers synthesized by other growth techniques. The significant full-width-at-half-maximum of NBE emission, found at ≈20 meV (at 2 K), suggests that free and bound excitons are mixed together within this single emission band. Finally, the optical properties of the hereby reported AlN NWs grown by PAMBE are comprehensively compared to optical properties of bulk, epitaxial and/or columnar AlN grown by various techniques such as: physical vapor transport, metal organic vapor phase epitaxy, metal organic chemical vapor deposition and molecular beam epitaxy.

Critically ill COVID-19 patients attended by anesthesiologists in northwestern Spain: a multicenter prospective observational study

BACKGROUND AND OBJECTIVES

There are limited information on outcome, complications and treatments of critically ill COVID-19 patients requiring admission to an intensive care unit (ICU). The aim of this study is to describe the clinical ICU course, treatments used, complications and outcomes, of critically ill COVID-19 patients admitted in seven ICU in Galicia region during the 2020 March-April pandemic peak.

METHODS

Between March 21 and April 19, 2020, we evaluated critically ill COVID-19 patients admitted to the ICU of Anesthesia of seven hospitals in Galicia, northwestern Spain. Outcome, complications, and treatments were monitored until May 6, 2020, the final date of follow-up.

RESULTS

A total of 97 critically ill COVID-19 patients were included. During ICU stay, mechanical ventilation became necessary in 80 (82.5%) patients, and tracheostomy in 22 (22.7%) patients. Prone position was used frequently in both intubated (67.5%) and awake (27.8%) patients. Medications consisted of antivirals agents (92.7%), corticosteroids (93.8%), tocilizumab (57.7%), and intermediate or high doses of anticoagulants (83.5%). The most frequent complications were ICU-acquired infection (52.6%), thrombosis events (16.5%), and reintubation (9.3%). After a median follow-up of 42 (34-45) days, 15 patients (15.5%) deceased, 73 patients (75.2%) had been discharged from ICU, and nine patients (9.3%) were still in the ICU.

CONCLUSIONS

A high proportion of our critically ill COVID-19 patients required mechanical ventilation, prone positioning, antiviral medication, corticosteroids, and anticoagulants. ICU complications were frequent, mainly infections and thrombotic events. We had a relatively low mortality of 15,5%.

Controlled Sign Reversal of Electroresistance in Oxide Tunnel Junctions by Electrochemical-Ferroelectric Coupling

The persistence of ferroelectricity in ultrathin layers relies critically on screening or compensation of polarization charges which otherwise destabilize the ferroelectric state. At surfaces, charged defects play a crucial role in the screening mechanism triggering novel mixed electrochemical-ferroelectric states. At interfaces, however, the coupling between ferroelectric and electrochemical states has remained unexplored. Here, we make use of the dynamic formation of the oxygen vacancy profile in the nanometer-thick barrier of a ferroelectric tunnel junction to demonstrate the interplay between electrochemical and ferroelectric degrees of freedom at an oxide interface. We fabricate ferroelectric tunnel junctions with a La_{0.7}Sr_{0.3}MnO_{3} bottom electrode and BaTiO_{3} ferroelectric barrier. We use poling strategies to promote the generation and transport of oxygen vacancies at the metallic top electrode. Generated oxygen vacancies control the stability of the ferroelectric polarization and modify its coercive fields. The ferroelectric polarization, in turn, controls the ionization of oxygen vacancies well above the limits of thermodynamic equilibrium, triggering the build up of a Schottky barrier at the interface which can be turned on and off with ferroelectric switching. This interplay between electronic and electrochemical degrees of freedom yields very large values of the electroresistance (more than 10^{6}% at low temperatures) and enables a controlled switching between clockwise and counterclockwise switching modes in the same junction (and consequently, a change of the sign of the electroresistance). The strong coupling found between electrochemical and electronic degrees of freedom sheds light on the growing debate between resistive and ferroelectric switching in ferroelectric tunnel junctions, and moreover, can be the source of novel concepts in memory devices and neuromorphic computing.

High-resolution CINE MRI allows estimation of 3D regional atrial strains

Introduction

It is increasingly evident that atrial function is an important marker of cardiovascular health. Impaired global left atrial strain has been associated with risk of thromboembolic events, atrial fibrillation and heart failure. When performed at high spatial resolution, CINE MRI allows the estimation of regional atrial strains, which may facilitate earlier identification of atrial disease and improved (non-contrast) characterisation of atrial fibrosis. Nevertheless, to date, high resolution regional atrial strains has not been assessed using CINE MRI.

Purpose

We introduce a novel rapid 2.2-mm isotropic atrial CINE MRI protocol used to image healthy subjects and patients with cardiovascular disease (CVD). We additionally present a dedicated image analysis pipeline to estimate regional 3D atrial strains from these images.

Methods

We imaged 10 healthy subjects (5 female, 24–36 years old) and 6 patients referred for cardiac MRI due to known or suspected CVD (2 female, 25–80 years old). All subjects were scanned in a 1.5T Philips Ingenia MRI scanner in a single breath-hold (&lt;25 s), using a short-axis 3D bSSFP protocol (flip angle: 60°, TE/TR: 1.6/3.3 ms) with retrospective cardiac gating, SENSE = 2.3 (along both phase encode directions), typical FOV: 400 x 270 x 70 mm3, isotropic acquisition resolution of 2.2 mm3. Images were reconstructed to 20 cardiac phases with 55% view sharing.

The left atrium (LA) was manually segmented in atrial diastole. We tracked the position of evenly spaced points along the LA contour across all phases of the cardiac cycle using the Medical Image Tracking Toolbox. This was used to create a series of deforming smooth triangular meshes, from which Lagrange strain tensors were estimated.

Results

Figs a-c show 3 orthogonal views of the proposed high-resolution atrial CINE MRI scans for a representative CVD patient, with the LA segmentation overlaid in red. Representative LA principal strain directions (as arrows) with the colour indicating the amount of strain observed along this direction are shown in Fig d for active atrial contraction (posterior view). The calculated strain directions varied smoothly in space and time, as expected, and were largest in amplitude in the regions closest to the mitral valve.

Overall, principal strains were larger in healthy subjects (AC strains: 0.12±0.06) than in the CVD cohort (AC strains: 0.04±0.01). This difference was statistically significant during AC (p-value: 0.02), but not during atrial diastole (p-value: 0.06).

Conclusions

We present a novel high-resolution CINE-MRI protocol for estimating regional atrial strains in 3D, with pilot data from 10 healthy subjects and 6 cardiovascular patients. Future studies will compare regions of abnormal atrial strain with fibrosis identified in late gadolinium enhanced MRI to assess whether regional strains can provide a better characterisation of atrial tissue and improved stratification of patients at risk.

Figure 1

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): British Heart Foundation, EPSRC/Wellcome Trust Centre for Medical Engineering

Automatic estimation of left atrial function from short axis CINE-MRI using machine learning

Introduction

The importance of atrial mechanical dysfunction in atrial and ventricular pathologies is becoming increasingly recognised. Although machine learning (ML) tools have the ability to automatically estimate atrial function, to date ML techniques have not been used to automatically estimate atrial volumes and functional parameters directly from short axis CINE MRI.

Purpose

We introduce a convolutional neural network (CNN) to automatically segment the left atria (LA) in CINE-MRI. As a demonstration of the clinical utility of this technique, we calculated LA and left ventricular (LV) ejection fractions automatically from CINE images.

Methods

Short axis CINE MRI stacks, covering both ventricles and atria, were obtained in a 1.5T Philips Ingenia scanner. A 2D bSSFP ECG-gated protocol was used (FA=60°, TE/TR=1.5/2.9 ms), typical FOV =385 x 310 x 150 mm3, acquisition matrix = 172 x 140, slice thickness = 10 mm, reconstructed with resolution 1.25 x 1.25 x 10 mm3, 30–50 cardiac phases. Images were collected from 37 AF patients in sinus rythm at the time of scan (31–72 years old, 75% male, 18 with paroxysmal AF (PAF), 19 with persistent AF (persAF)).

To automatically segment the LA, we used a dedicated CNN that follows a U-Net architecture and was trained in 715 images of the LA, manually segmented by an expert. Data augmentation techniques that included noise addition and linear and non-linear image transforms were also used to increase the training dataset. Ventricular structures, including the LV blood pool, were automatically segmented in these images using a CNN previously trained for this task.

Volumetric time plots of LA and LV volume were produced and used to automatically compute maximal and minimal volumes, from which LA and LV ejection fractions (EFs) were assessed. A Bland-Altman analysis compared these automatically computed LA volumes and LA EFs with clinical manual estimates from the same scanning session.

Results

The CNN achieved very good quality LA segmentations when compared to manual ones (Fig a,b): Dice coefficients (0.90±0.07), median contour distances (0.50±1.12mm) and Hausdorff distances (6.70±6.16mm). Bland-Altman analyses show very good agreement between automatic and manual LA volumes and EFs (Fig e). A moderate linear correlation between LA and LV EFs in AF patients was found (Fig d). The measured LA EF was higher for PAF (29±8%) than PersAF patients (21±11%), although non-significantly (t-test p-value: 0.10).

Conclusions

We present a reliable automatic method to perform LA segmentations from CINE MRI across the entire cardiac cycle. This approachs opens up the possibility of automatically calculating more sophisticated biomarkers of LA function which take into account information about LA volumes across the entire cardiac cycle, including biomarkers of LA booster pump function.

Figure 1

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): British Heart Foundation; EPSRC/Wellcome Centre for Medical Engineering

Quasiparticle tunnel electroresistance in superconducting junctions

The term tunnel electroresistance (TER) denotes a fast, non-volatile, reversible resistance switching triggered by voltage pulses in ferroelectric tunnel junctions. It is explained by subtle mechanisms connected to the voltage-induced reversal of the ferroelectric polarization. Here we demonstrate that effects functionally indistinguishable from the TER can be produced in a simpler junction scheme—a direct contact between a metal and an oxide—through a different mechanism: a reversible redox reaction that modifies the oxide’s ground-state. This is shown in junctions based on a cuprate superconductor, whose ground-state is sensitive to the oxygen stoichiometry and can be tracked in operando via changes in the conductance spectra. Furthermore, we find that electrochemistry is the governing mechanism even if a ferroelectric is placed between the metal and the oxide. Finally, we extend the concept of electroresistance to the tunnelling of superconducting quasiparticles, for which the switching effects are much stronger than for normal electrons. Besides providing crucial understanding, our results provide a basis for non-volatile Josephson memory devices.

The non-volatile switching of tunnel electroresistance in ferroelectric junctions provides the basis for memory and neuromorphic computing devices. Rouco et al. show tunnel electroresistance in superconductor-based junctions that arises from a redox rather than ferroelectric mechanism and is enhanced by superconductivity.

P5739Venoarterial Extracorporeal Membrane Oxygenation in Cardiogenic Shock: exploring prognostic variables and risk prediction tools

Introduction

The use of venoarterial extracorporeal membrane oxygenation (VA-ECMO) to support patients in cardiogenic shock has been increasing in Portugal over the past few years. Nonetheless, epidemiologic, prognostic and clinical outcome data are scarce.

Purpose

We aim to identify clinical variables with prognostic significance in this challenging population, as well as the performance of various risk scores in mortality prediction.

Methods

All patients that underwent VA-ECMO support at our Cardiac ICU between 2011 and 2018 were included in the analysis. Logistic regression analysis was used to assess the relationship between clinical variables and outcomes.

Results

Short-term mechanical support with VA-ECMO was given to 40 patients, with a mean age of 52±11 years. At the time of the implant, the mean SOFA score was 11.2±4.0, and mean SAVE score was −4.75±4.6. Mean ECMO support duration was 116±96 hours. In 70% (N=28) of patients, VA-ECMO was successfully weaned. In-hospital mortality was observed in 52.5% of patients, which was in accordance with the predicted mortality by SOFA score (22.5% to 82% in our population risk range) and by SAVE score (60 to 70%). Those who placed the VA-ECMO as a bridge to transplant or to long-term mechanical LV assist device had greater in-hospital mortality rates (91.6 vs 41.9%, p=0.013), as well as those under ≥2 inotropic/vasopressors (69.2 vs 21.4%, p=0.012) or when adrenaline use was needed (100% vs 44.1%, p=0.01). No other between-group differences were observed in what concerns short-term mortality. After logistic regression analysis, independent predictors of in-hospital mortality included AMI setting, number of vasoactive amines used, and necessity of a LV venting device. SAVE score had the greater predictive ability in these patients (AUC = 0.638) among the most utilized clinical risk scores (SOFA score AUC = 0.37; APACHE II score AUC = 0.59; SAPS II score AUC = 0.54).

Conclusion

In our analysis, patients in profound cardiogenic shock on VA-ECMO support had slightly better survival rates than predicted by classical Risk Scores. The SAVE score may be the most accurate tool to predict in-hospital mortality in this specific, and yet heterogeneous, clinical subset. Other well recognized clinical markers of severity may also help refine short-term prognosis, and potentially improve organ transplant or other destination therapy prioritization.

Structural, magnetic and electronic properties of pulsed-laser-deposition grown SrFeO3-δ thin films and SrFeO3-δ /La2/3Ca1/3MnO3 multilayers

We studied the structural, magnetic and electronic properties of [Formula: see text] (SFO) thin films and [Formula: see text]/[Formula: see text] [Formula: see text]MnO₃ (LCMO) superlattices that have been grown with pulsed laser deposition (PLD) on [Formula: see text] [Formula: see text] [Formula: see text] [Formula: see text] [Formula: see text] (LSAT) substrates. X-ray reflectometry and scanning transmission electron microscopy (STEM) confirm the high structural quality of the films and flat and atomically sharp interfaces of the superlattices. The STEM data also reveal a difference in the interfacial layer stacking with a SrO layer at the LCMO/SFO and a LaO layer at the SFO/LCMO interfaces along the PLD growth direction. The x-ray diffraction (XRD) data suggest that the as grown SFO films and SFO/LCMO superlattices have an oxygen-deficient [Formula: see text] structure with I4/ mmm space group symmetry ([Formula: see text]). Subsequent ozone annealed SFO films are consistent with an almost oxygen stoichiometric structure ([Formula: see text]). The electronic and magnetic properties of these SFO films are similar to the ones of corresponding single crystals. In particular, the as grown [Formula: see text] films are insulating whereas the ozone annealed films are metallic. The magneto-resistance effects of the as grown SFO films have a similar magnitude as in the single crystals, but extend over a much wider temperature range. Last but not least, for the SFO/LCMO superlattices we observe a rather large exchange bias effect that varies as a function of the cooling field.

Origin of the magnetic transition at 100 K in ε-Fe2O3 nanoparticles studied by x-ray absorption fine structure spectroscopy

The current study unveils the structural origin of the magnetic transition of the ε-Fe₂O₃ polymorph from an incommensurate magnetic order to a collinear ferrimagnetic state at low temperature. The high crystallinity of the samples and the absence of other iron oxide polymorphs have allowed us to carry out temperature-dependent x-ray absorption fine structure spectroscopy experiments out. The deformation of the structure is followed by the Debye-Waller factor for each selected Fe-O and Fe-Fe sub-shell. For nanoparticle sizes between 7 and 15 nm, the structural distortions between the Fe_te and Fe-D1_oc sites are localized in a temperature range before the magnetic transition starts. On the contrary, the inherent interaction between the other sub-shells (named Fe-O1,2 and Fe-Fe1) provokes cooperative magneto-structural changes in the same temperature range. This means that the Fe_te with Fe-D1_oc polyhedron interaction seems to be uncoupled with temperature dealing with these nanoparticle sizes wherein the structural distortions are likely moderate due to surface effects.

Epitaxial Growth of SrTiO3 Films on Cube-Textured Cu-Clad Substrates by PLD at Low Temperature Under Reducing Atmosphere

The growth of epitaxial {001}<100> SrTiO₃ (STO) on low-cost cube-textured Cu-based clad substrate at low temperature was carried out by means of pulsed laser deposition (PLD). STO film was deposited in one step under a reducing atmosphere (5% H₂ and 95% Ar mixture) to prevent the oxidation of the metal surface. The optimization of PLD parameters leads to a sharpest biaxial texture at a temperature as low as 500 °C and a thickness of 500 nm with a (100) STO layer. The upper limit of highly textured STO thickness was also investigated. The maximum thickness which retains the best quality {001}<100> texture is 800 nm, since the texture is preserved not only through the layer but also on the surface. Atomic force microscopy (AFM) and scanning electron microscopy (SEM) measurements showed that STO films are continuous, dense, and smooth with very low roughness (between 5 and 7 nm). This paper describes the development of STO layer by means of PLD in absence of oxygen throughout the process, suggesting an alternative and effective method for growing highly {001}<100> textured STO layer on low-cost metal substrates.

Competition between Polar and Nonpolar Lattice Distortions in Oxide Quantum Wells: New Critical Thickness at Polar Interfaces

Two basic lattice distortions permeate the structural phase diagram of oxide perovskites: antiferrodistortive (AFD) rotations and tilts of the oxygen octahedral network and polar ferroelectric modes. With some notable exceptions, these two order parameters rarely coexist in a bulk crystal, and understanding their competition is a lively area of active research. Here we demonstrate, by using the LaAlO_{3}/SrTiO_{3} system as a test case, that quantum confinement can be a viable tool to shift the balance between AFD and polar modes and selectively stabilize one of the two phases. By combining scanning transmission electron microscopy (STEM) and first-principles-based models, we find a crossover between a bulklike LaAlO_{3} structure where AFD rotations prevail, to a strongly polar state with no AFD tilts at a thickness of approximately three unit cells; therefore, in addition to the celebrated electronic reconstruction, our work unveils a second critical thickness, related not to the electronic properties but to the structural ones. We discuss the implications of these findings, both for the specifics of the LaAlO_{3}/SrTiO_{3} system and for the general quest towards nanoscale control of material properties.

Conserved gene regulation during acute inflammation between zebrafish and mammals

Zebrafish (Danio rerio), largely used as a model for studying developmental processes, has also emerged as a valuable system for modelling human inflammatory diseases. However, in a context where even mice have been questioned as a valid model for these analysis, a systematic study evaluating the reproducibility of human and mammalian inflammatory diseases in zebrafish is still lacking. In this report, we characterize the transcriptomic regulation to lipopolysaccharide in adult zebrafish kidney, liver, and muscle tissues using microarrays and demonstrate how the zebrafish genomic responses can effectively reproduce the mammalian inflammatory process induced by acute endotoxin stress. We provide evidence that immune signaling pathways and single gene expression is well conserved throughout evolution and that the zebrafish and mammal acute genomic responses after lipopolysaccharide stimulation are highly correlated despite the differential susceptibility between species to that compound. Therefore, we formally confirm that zebrafish inflammatory models are suited to study the basic mechanisms of inflammation in human inflammatory diseases, with great translational impact potential.

Hybridization-controlled charge transfer and induced magnetism at correlated oxide interfaces

At interfaces between conventional materials, band bending and alignment are classically controlled by differences in electrochemical potential. Applying this concept to oxides in which interfaces can be polar and cations may adopt a mixed valence has led to the discovery of novel two-dimensional states between simple band insulators such as LaAlO3 and SrTiO3. However, many oxides have a more complex electronic structure, with charge, orbital and/or spin orders arising from strong Coulomb interactions between transition metal and oxygen ions. Such electronic correlations offer a rich playground to engineer functional interfaces but their compatibility with the classical band alignment picture remains an open question. Here we show that beyond differences in electron affinities and polar effects, a key parameter determining charge transfer at correlated oxide interfaces is the energy required to alter the covalence of the metal-oxygen bond. Using the perovskite nickelate (RNiO3) family as a template, we probe charge reconstruction at interfaces with gadolinium titanate GdTiO3. X-ray absorption spectroscopy shows that the charge transfer is thwarted by hybridization effects tuned by the rare-earth (R) size. Charge transfer results in an induced ferromagnetic-like state in the nickelate, exemplifying the potential of correlated interfaces to design novel phases. Further, our work clarifies strategies to engineer two-dimensional systems through the control of both doping and covalence.

Abstract P2-08-31: Tumor and axillar downstaging as a prognostic factor and evaluation of effectiveness to primary chemotherapy in breast cancer: A retrospective analysis

Introduction: Evaluation of the benefit of primary chemotherapy (PC) is not easy to establish. Pathologic complete response (pCR) has been considered the main surrogate prognostic factor of patient's survival. However, patients achieving a pCR are not the only ones who benefit from PC. The purpose of our study is to find a measure of response that includes the maximum of patients that benefit from PC in terms of survival.

Patients and methods: 224 breast cancer patients were treated in Breast Cancer Unit from Institut Català d'Oncologia (ICO) L'Hospitalet with taxans and antracyclines-based PC +/- trastuzumab between 2009 and 2011. pCR was defined as no invasive carcinoma found in the tumor and in the axillary lymph nodes (ypT0/ypTis ypN0). Tumor and nodal downstaging (TNDS) was calculated according to the "neoadjuvant response index" (NRI) from Rodenhuis and also as a dichotomic variable: Positive includes those patients achieving dowstaging of both T and N plus T downstaging N0 and negatives those patients without downstaging in any of both variables. Those parameters were related to patient's overall survival (OS). Statistical analysis was performed with SPSS version 15.

Results: Median age 45.5 years (24-83). Main tumor characteristics: T2 (62.6%); N1 (50%); ductal infiltrating carcinoma (95.5%) and grade III (57.1%). Biological sub-type according to the last St Gallen classification: luminal A: 28 patients (pts); luminal B/Her2-: 61 pts; luminal B/HER2+: 34 pts; HER2+: 33 pts and triple negative: 69 pts. Pathologic complete response was achieved in 49 pts (22.5%). TNDS was evaluated in 181 patients and of those 90 was positive. According to NRI 74 patients presented cut-off&gt; 0.5 and 52 pts &gt; 0.7. Parameters related to OS were: biological subtype (P: 0.007); achieving a pCR (p: 0.007); NRI cut-off 0.5 (P: 0.001) and TNDS (p:0.000). In the multivariate analysis only TNDS and biological subtype remained statistically significant. When comparing those patients with positive vs. negative TNDS, the HR for recurrence was of 10.05 (IC 2.33 -43.57). The median OS of the series has not been reached. OS at 5y was 82.7% (IC: 77.1%-88%) and specific breast cancer OS at 5 y was 85% (IC:79.5%-90%). The number of events (breast cancer deaths) for each biological subtype according to positive vs. negative TNDS was: luminal A: 0/5 vs. 0/18; luminal B Her2-: 0/10 vs. 8/43; luminal B HER2+:0/23 vs. 2/9; HER2+: 0/22 vs. 0/2 and TN: 2/30 vs. 8/18. Survival data per subtypes and TNDS is immature due to the scarce number of events. Estimated 5y OS for TNDS positive vs. negative in luminal A: 100% vs. 100%; luminal B Her2-: 100% vs. 82%; luminal B HER2+:100 vs.77.7%; HER2+: 100% vs. 100% and TN: 93% vs. 55%, respectively.

Conclusion: In our series, TNDS measured either with the NRI from Rodenhuis or as a dichotomic variable was the best parameter to evaluate response to PC in terms of OS. OS of luminal A and luminal B/Her2 negative is less influenced by PC than the rest of subgroups. In fact both subgroups have good prognosis despite their poor sensitivity to chemotherapy. Those tumors that benefit most from PC were luminal B/ Her2+; Her2+ and triple negative patients who achieved a positive TNDS.

Citation Format: Falo C, Ventura LM, Petit A, Perez J, Cañellas J, Perez L, Loayza C, Gil M, Varela M, Garcia A, Pla MJ, Lopez A, Guma A, Pernas S. Tumor and axillar downstaging as a prognostic factor and evaluation of effectiveness to primary chemotherapy in breast cancer: A retrospective analysis. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-08-31.

Zebrafish Nk-lysins: First insights about their cellular and functional diversification

Nk-lysins are antimicrobial proteins produced by cytotoxic T lymphocytes and natural killer cells with a broad antimicrobial spectrum (including bacteria, fungi and parasites). Nevertheless, the implication of these proteins in the protection against viral infections is still poorly understood. In this work, four different Nk-lysin genes (nkla, nklb, nklc and nkld) were identified in the zebrafish genome. That means that zebrafish is the species with the higher repertoire of Nk-lysin genes described so far. The differential expression pattern of the Nk-lysins in several tissues, during ontogeny, among the different kidney cell populations, as well as between Rag1(-/-) and Rag1(+/+) individuals, could suggest a certain specialization of different cell types in the production of different Nk-lysin. Moreover, only two of these genes (nkla and nkld) were significantly up-regulated after viral infection, and this observation could be also a consequence of a functional diversification of the zebrafish Nk-lysins.

Bismuth labeling for the CT assessment of local administration of magnetic nanoparticles

Many therapeutic applications of magnetic nanoparticles involve the local administration of nanometric iron oxide based materials as seeds for magnetothermia or drug carriers. A simple and widespread way of controlling the process using x-ray computed tomography (CT) scanners is desirable. The combination of iron and bismuth in one entity will increase the atenuation of x-rays, offering such a possibility. In order to check this possibility core-shell nanocrystals of iron oxide@bismuth oxide have been synthesized by an aqueous route and stabilized in water by polyethylene glycol (PEG), and we have evaluated their ability to generate contrast by CT and magnetic resonance imaging (MRI) to measure the radiopacity and proton relaxivities using phantoms. High-resolution scanning transmission electron microscopy (STEM) revealed that the material consists of a highly crystalline 8 nm core of maghemite and a 1 nm shell of bismuth atoms either isolated or clustered on the nanocrystal's surface. The comparison of μCT and MRI images of mice acquired in the presence of the contrast shows that when local accumulations of the magnetic nanoparticles take place, CT images are more superior in the localization of the magnetic nanoparticles than MRI images, which results in magnetic field inhomogeneity artifacts.

Synthetic magnetoelectric coupling in a nanocomposite multiferroic

Given the paucity of single phase multiferroic materials (with large ferromagnetic moment), composite systems seem an attractive solution to realize magnetoelectric coupling between ferromagnetic and ferroelectric order parameters. Despite having antiferromagnetic order, BiFeO₃ (BFO) has nevertheless been a key material due to excellent ferroelectric properties at room temperature. We studied a superlattice composed of 8 repetitions of 6 unit cells of La_0.7Sr_0.3MnO₃ (LSMO) grown on 5 unit cells of BFO. Significant net uncompensated magnetization in BFO, an insulating superlattice, is demonstrated using polarized neutron reflectometry. Remarkably, the magnetization enables magnetic field to change the dielectric properties of the superlattice, which we cite as an example of synthetic magnetoelectric coupling. Importantly, controlled creation of magnetic moment in BFO is a much needed path toward design and implementation of integrated oxide devices for next generation magnetoelectric data storage platforms.

Insight into spin transport in oxide heterostructures from interface-resolved magnetic mapping

At interfaces between complex oxides, electronic, orbital and magnetic reconstructions may produce states of matter absent from the materials involved, offering novel possibilities for electronic and spintronic devices. Here we show that magnetic reconstruction has a strong influence on the interfacial spin selectivity, a key parameter controlling spin transport in magnetic tunnel junctions. In epitaxial heterostructures combining layers of antiferromagnetic LaFeO(3) (LFO) and ferromagnetic La(0.7)Sr(0.3)MnO(3) (LSMO), we find that a net magnetic moment is induced in the first few unit planes of LFO near the interface with LSMO. Using X-ray photoemission electron microscopy, we show that the ferromagnetic domain structure of the manganite electrodes is imprinted into the antiferromagnetic tunnel barrier, endowing it with spin selectivity. Finally, we find that the spin arrangement resulting from coexisting ferromagnetic and antiferromagnetic interactions strongly influences the tunnel magnetoresistance of LSMO/LFO/LSMO junctions through competing spin-polarization and spin-filtering effects.