Infrared light extinction by charged dielectric core-coat particles

We study the effect of surplus electrons on the infrared extinction of dielectric particles with a core-coat structure and propose to use it for an optical measurement of the particle charge in a dusty plasma. The particles consist of an inner core with negative and an outer coat with positive electron affinity. Both the core and the coat give rise to strong transverse optical phonon resonances, leading to anomalous light scattering in the infrared. Due to the radial profile of the electron affinity electrons accumulate in the coat region making the infrared extinction of this type of particles very charge-sensitive, in particular, the extinction due to a resonance arising solely due to the core-coat structure. The maximum of this resonance is in the far-infrared and responds to particle charges realizable in ordinary dusty laboratory plasmas.Comment: 12 pages, 8 figure

Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (, , ) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors. Overall, this large-scale analysis reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining sarcoma therapy and relationships to other cancer types

Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.

BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

Recent genomic analyses of pathologically-defined tumor types identify “within-a-tissue” disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head & neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multi-platform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All datasets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Licht- und Elektronenstreuung an dielektrischen Strukturen im Plasma

Motiviert durch den Vorschlag einer direkten, optischen Ladungsmessung an Staubteilchen wird die Lichtstreuung an den dielektrischen Kern-Schale-Teilchen tiefgehend untersucht. Das Streuregime wird durch Analyse des Nah- und Fernfeldes unter Verwendung von Methoden, die für homogene Teilchen entwickelt wurden, eingehend charakterisiert und eine Verallgemeinerung der dazu verwendeten Funktionen auf ein k-fach beschichtetes Teilchen angegeben. Dabei werden die sich im Teilcheninneren manifestierenden Effekte der Hybridisierung der beiden Oberflächenphononen des Kern-Schale-Teilchens herausgearbeitet und visualisiert. Die vorliegende Untersuchung der unterschiedlichen Kenngrößen ermöglicht ein detailliertes und umfangreiches Verständnis der Lichtstreuung an dielektrischen Kern-Schale-Teilchen und der Art und Weise, wie sich die Hybridisierung der Oberflächenphononen auf diese auswirkt. Die dabei analysierte Interferenzstruktur des elektromagnetischen Feldes in der Teilchenschale, berechnet mittels der vollen Mie-Rechnung, passt zur Interpretation der optischen Antwort des Kern-Schale-Teilchens mithilfe der Hybridisierungstheorie. Dieses Hybridisierungsbild und somit die Subsysteme und ihre Wechselwirkung werden in dieser Arbeit aus den analytisch exakten Mie-Koeffizienten heraus präpariert, um die neue Sichtweise mit der alten Mie-Theorie zusammenzubringen. Die Idee einer spektroskopische Ladungsmessung wird im Hinblick auf die Bestimmung der Wandladung aufgegriffen. Die bisherigen Methoden zur Ladungsmessung sind zwar vielfältig, bieten jedoch nur Zugang zur absoluten Wandladung und liefern keine Informationen über ihre Verteilung senkrecht zur Oberfläche oder über die Dynamik der Aufladung. Beides wäre jedoch für ein mikroskopisches Verständnis der Plasma-Wand-Wechselwirkung notwendig, sodass die Elektronenenergieverlustspektroskopie zur Ladungsbestimmung vorgeschlagen wird. Die Methode wird zunächst anhand einer lokalen Antworttheorie für verschiedene in die Wand eingesetzte Schichtstrukturen ausgelotet und aufgrund vielversprechender Resultate anschließend mittels der im betrachteten Parameterbereich notwendigen nichtlokalen Antworttheorie eingehend untersucht. Diese Theorie erfasst die Anregung von Resonanzen höherer Moden, die sich als besonders sensitiv auf die zusätzlichen Ladungsträger erweisen. Insgesamt wird ein experimenteller Aufbau mit einer geeigneten, in die Plasmakammerwand einsetzbaren Schichtstruktur vorgeschlagen, mit dem die Wandladung durch Elektronenenergieverlustspektroskopie bestimmt werden könnte.Motivated by the proposal for a direct optical charge measurement on dust particle we investigate light scattering on dielectric core-shell particles. The scattering regime is characterized by methods developed for homogenous particles, thereby the used function are generalized to arbitrary coated spheres. The hybridization effects of the two surface phonons dominating the inside of core-shell-particle is worked out and visualized. The results enable a detailed and comprehensive understanding of light scattering on dielectric core-shell particles and the way in which the hybridization of surface phonons affects it. The analysed interference structure of the electromagnetic field in the shell, calculated using the full Mie theory, corresponds to the interpretation of the optical response of the core-shell particle within the hybridization theory. In this work the hybridization picture and thus the subsystems and their interaction are derived from the analytically exact Mie coefficients in order to bring the new perspective together with the old Mie theory. The idea of a spectroscopic charge measurement is adopted the determination of wall charge. The available methods for charge measurement only offer access to the absolute wall charge and do not provide any information about its distribution perpendicular to the surface or about the charge dynamics. As both is necessary for a microscopic understanding of the plasma-wall interaction, the electron energy loss spectroscopy is proposed for determining the charge. First the method is analysed using a local response theory for different layered structures inserted into the wall and, based on promising results, then examined in detail using the non-local response theory required in the parameter range under consideration. This theory enable the excitation of higher modes, which are particularly sensitive to the additional charge carriers. Overall, an experimental setup with a suitable layered structure inserted into the wall is proposed, which enables to determine the wall charge by electron energy loss spectroscopy

Electron energy loss spectroscopy of wall charges in plasma-facing dielectrics

Abstract We propose a setup enabling electron energy loss spectroscopy to determine the density of the electrons accumulated by an electropositive dielectric in contact with a plasma. It is based on a two-layer structure inserted into a recess of the wall. Consisting of a plasma-facing film made out of the dielectric of interest and a substrate layer, the structure is designed to confine the plasma-induced surplus electrons to the region of the film. The charge fluctuations they give rise to can then be read out from the backside of the substrate by near specular electron reflection. To obtain in this scattering geometry a strong charge-sensitive reflection maximum due to the surplus electrons, the film has to be most probably pre-n-doped and sufficiently thin with the mechanical stability maintained by the substrate. Taking electronegative CaO as a substrate layer we demonstrate the feasibility of the proposal by calculating the loss spectra for Al2O3, SiO2, and ZnO films. In all three cases we find a reflection maximum strongly shifting with the density of the surplus electrons and suggest to use it for charge diagnostics