Effects of circadian rhythm phase alteration on physiological and psychological variables: Implications to pilot performance (including a partially annotated bibliography)

The effects of environmental synchronizers upon circadian rhythmic stability in man and the deleterious alterations in performance and which result from changes in this stability are points of interest in a review of selected literature published between 1972 and 1980. A total of 2,084 references relevant to pilot performance and circadian phase alteration are cited and arranged in the following categories: (1) human performance, with focus on the effects of sleep loss or disturbance and fatigue; (2) phase shift in which ground based light/dark alteration and transmeridian flight studies are discussed; (3) shiftwork; (4)internal desynchronization which includes the effect of evironmental factors on rhythmic stability, and of rhythm disturbances on sleep and psychopathology; (5) chronotherapy, the application of methods to ameliorate desynchronization symptomatology; and (6) biorythm theory, in which the birthdate based biorythm method for predicting aircraft accident susceptability is critically analyzed. Annotations are provided for most citations

The impact of mineral dust on cloud formation during the Saharan dust event in April 2014 over Europe

A regional modeling study on the impact of desert dust on cloud formation is presented for a major Saharan dust outbreak over Europe from 2 to 5 April 2014. The dust event coincided with an extensive and dense cirrus cloud layer, suggesting an influence of dust on atmospheric ice nucleation. Using interactive simulation with the regional dust model COSMO-MUSCAT, we investigate cloud and precipitation representation in the model and test the sensitivity of cloud parameters to dust–cloud and dust–radiation interactions of the simulated dust plume. We evaluate model results with ground-based and spaceborne remote sensing measurements of aerosol and cloud properties, as well as the in situ measurements obtained during the ML-CIRRUS aircraft campaign. A run of the model with single-moment bulk microphysics without online dust feedback considerably underestimated cirrus cloud cover over Germany in the comparison with infrared satellite imagery. This was also reflected in simulated upper-tropospheric ice water content (IWC), which accounted for only 20&thinsp;% of the observed values. The interactive dust simulation with COSMO-MUSCAT, including a two-moment bulk microphysics scheme and dust–cloud as well as dust–radiation feedback, in contrast, led to significant improvements. The modeled cirrus cloud cover and IWC were by at least a factor of 2 higher in the relevant altitudes compared to the noninteractive model run. We attributed these improvements mainly to enhanced deposition freezing in response to the high mineral dust concentrations. This was corroborated further in a significant decrease in ice particle radii towards more realistic values, compared to in situ measurements from the ML-CIRRUS aircraft campaign. By testing different empirical ice nucleation parameterizations, we further demonstrate that remaining uncertainties in the ice-nucleating properties of mineral dust affect the model performance at least as significantly as including the online representation of the mineral dust distribution. Dust–radiation interactions played a secondary role for cirrus cloud formation, but contributed to a more realistic representation of precipitation by suppressing moist convection in southern Germany. In addition, a too-low specific humidity in the 7 to 10&thinsp;km altitude range in the boundary conditions was identified as one of the main reasons for misrepresentation of cirrus clouds in this model study.</p

Meteorological conditions during the ACLOUD/PASCAL field campaign near Svalbard in early summer 2017

The two concerted field campaigns, Arctic CLoud Observations Using airborne measurements during polar Day (ACLOUD) and the Physical feedbacks of Arctic planetary boundary level Sea ice, Cloud and AerosoL (PASCAL), took place near Svalbard from 23 May to 26 June 2017. They were focused on studying Arctic mixed-phase clouds and involved observations from two airplanes (ACLOUD), an icebreaker (PASCAL) and a tethered balloon, as well as ground-based stations. Here, we present the synoptic development during the 35-day period of the campaigns, using near-surface and upper-air meteorological observations, as well as operational satellite, analysis, and reanalysis data. Over the campaign period, short-term synoptic variability was substantial, dominating over the seasonal cycle. During the first campaign week, cold and dry Arctic air from the north persisted, with a distinct but seasonally unusual cold air outbreak. Cloudy conditions with mostly low-level clouds prevailed. The subsequent 2 weeks were characterized by warm and moist maritime air from the south and east, which included two events of warm air advection. These synoptical disturbances caused lower cloud cover fractions and higher-reaching cloud systems. In the final 2 weeks, adiabatically warmed air from the west dominated, with cloud properties strongly varying within the range of the two other periods. Results presented here provide synoptic information needed to analyze and interpret data of upcoming studies from ACLOUD/PASCAL, while also offering unprecedented measurements in a sparsely observed region.</p

Characterization of organic aerosol across the global remote troposphere: A comparison of ATom measurements and global chemistry models

The spatial distribution and properties of submicron organic aerosol (OA) are among the key sources of uncertainty in our understanding of aerosol effects on climate. Uncertainties are particularly large over remote regions of the free troposphere and Southern Ocean, where very few data have been available and where OA predictions from AeroCom Phase II global models span 2 to 3 orders of magnitude, greatly exceeding the model spread over source regions. The (nearly) pole-to-pole vertical distribution of nonrefractory aerosols was measured with an aerosol mass spectrometer onboard the NASA DC-8 aircraft as part of the Atmospheric Tomography (ATom) mission during the Northern Hemisphere summer (August 2016) and winter (February 2017). This study presents the first extensive characterization of OA mass concentrations and their level of oxidation in the remote atmosphere. OA and sulfate are the major contributors by mass to submicron aerosols in the remote troposphere, together with sea salt in the marine boundary layer. Sulfate was dominant in the lower stratosphere. OA concentrations have a strong seasonal and zonal variability, with the highest levels measured in the lower troposphere in the summer and over the regions influenced by biomass burning from Africa (up to 10 μgsm-3). Lower concentrations (~ 0:1 0.3 μgsm-3) are observed in the northern middle and high latitudes and very low concentrations (< 0:1 μgsm-3) in the southern middle and high latitudes. The ATom dataset is used to evaluate predictions of eight current global chemistry models that implement a variety of commonly used representations of OA sources and chemistry, as well as of the AeroCom-II ensemble. The current model ensemble captures the average vertical and spatial distribution of measured OA concentrations, and the spread of the individual models remains within a factor of 5. These results are significantly improved over the AeroCom-II model ensemble, which shows large overestimations over these regions. However, some of the improved agreement with observations occurs for the wrong reasons, as models have the tendency to greatly overestimate the primary OA fraction and underestimate the sec-ondary fraction. Measured OA in the remote free troposphere is highly oxygenated, with organic aerosol to organic carbon (OA= OC) ratios of ~ 2.2 2.8, and is 30 % 60% more oxygenated than in current models, which can lead to significant errors in OA concentrations. The model measurement comparisons presented here support the concept of a more dynamic OA system as proposed by Hodzic et al. (2016), with enhanced removal of primary OA and a stronger production of secondary OA in global models needed to provide better agreement with observations. © 2020 IEEE Computer Society. All rights reserved

FEBUKO and MODMEP: Field measurements and modelling of aerosol and cloud multiphase processes

An overview of the two FEBUKO aerosol–cloud interaction field experiments in the Thüringer Wald (Germany) in October 2001 and 2002 and the corresponding modelling project MODMEP is given. Experimentally, a variety of measurement methods were deployed to probe the gas phase, particles and cloud droplets at three sites upwind, downwind and within an orographic cloud with special emphasis on the budgets and interconversions of organic gas and particle phase constituents. Out of a total of 14 sampling periods within 30 cloud events three events (EI, EII and EIII) are selected for detailed analysis. At various occasions an impact of the cloud process on particle chemical composition such as on the organic compounds content, sulphate and nitrate and also on particle size distributions and particle mass is observed. Moreover, direct phase transfer of polar organic compound from the gas phase is found to be very important for the understanding of cloudwater composition. For the modelling side, a main result of the MODMEP project is the development of a cloud model, which combines a complex multiphase chemistry with detailed microphysics. Both components are described in a fine-resolved particle/drop spectrum. New numerical methods are developed for an efficient solution of the entire complex model. A further development of the CAPRAM mechanism has lead to a more detailed description of tropospheric aqueous phase organic chemistry. In parallel, effective tools for the reduction of highly complex reaction schemes are provided. Techniques are provided and tested which allow the description of complex multiphase chemistry and of detailed microphysics in multidimensional chemistry-transport models

Prevalence of bisphosphonate associated osteonecrosis of the jaws in multiple myeloma patients

<p>Abstract</p> <p>Background</p> <p>Bisphosphonate-associated osteonecrosis of the jaws (BP-ONJ) is an adverse effect of bisphosphonate treatment with varying reported incidence rates.</p> <p>Methods</p> <p>In two neighboring German cities, prevalence and additional factors of the development of BP-ONJ in multiple myeloma patients with bisphosphonates therapy were recorded using a retrospective (RS) and cross-sectional study (CSS) design. For the RS, all patients treated from Jan. 2000 - Feb. 2006 were contacted by letter. In the CSS, all patients treated from Oct. 2006 - Mar. 2008 had a physical and dental examination. Additionally, a literature review was conducted to evaluate all articles reporting on BP-ONJ prevalence. PubMed search terms were: bisphosphonat, diphosphonate, osteonecrosis, prevalence and incidence.</p> <p>Results</p> <p>In the RS, data from 81 of 161 patients could be obtained; four patients (4.9%) developed BP-ONJ. In the CSS, 16 of 78 patients (20.5%) developed BP-ONJ. All patients with BP-ONJ had received zoledronate; 12 of these had had additional bisphosphonates. All except one had an additional trigger factor (tooth extraction [n = 14], dental surgical procedure [n = 2], sharp mylohyoid ridge [n = 3]).</p> <p>Conclusion</p> <p>The prevalence of BP-ONJ may have been underestimated to date. The oral examination of all patients in this CSS might explain the higher prevalence, since even early asymptomatic stages of BP-ONJ and previously unnoticed symptomatic BP-ONJ were recorded. Since nearly all patients with BP-ONJ had an additional trigger factor, oral hygiene and dental care might help to reduce BP-ONJ incidence.</p

Amino acid substitutions within HLA-B*27- restricted T cell epitopes prevent recognition by hepatitis delta virus-specific CD8+ T cells

Virus-specific CD8 T cell response seems to play a significant role in the outcome of hepatitis delta virus (HDV) infection. However, the HDV-specific T cell epitope repertoire and mechanisms of CD8 T cell failure in HDV infection have been poorly characterized. We therefore aimed to characterize HDV-specific CD8 T cell epitopes and the impacts of viral mutations on immune escape. In this study, we predicted peptide epitopes binding the most frequent human leukocyte antigen (HLA) types and assessed their HLA binding capacities. These epitopes were characterized in HDV-infected patients by intracellular gamma interferon (IFN-γ) staining. Sequence analysis of large hepatitis delta antigen (L-HDAg) and HLA typing were performed in 104 patients. The impacts of substitutions within epitopes on the CD8 T cell response were evaluated experimentally and by in silico studies. We identified two HLA-B*27-restricted CD8 T cell epitopes within L-HDAg. These novel epitopes are located in a relatively conserved region of L-HDAg. However, we detected molecular footprints within the epitopes in HLA-B*27-positive patients with chronic HDV infections. The variant peptides were not cross-recognized in HLA-B*27-positive patients with resolved HDV infections, indicating that the substitutions represent viral escape mutations. Molecular modeling of HLA-B*27 complexes with the L-HDAg epitope and its potential viral escape mutations indicated that the structural and electrostatic properties of the bound peptides differ considerably at the T cell receptor interface, which provides a possible molecular explanation for the escape mechanism. This viral escape from the HLA-B*27-restricted CD8 T cell response correlates with a chronic outcome of hepatitis D infection. T cell failure resulting from immune escape may contribute to the high chronicity rate in HDV infection. © 2018 American Society for Microbiology

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.We thank the DKFZ Genomics and Proteomics Core Facility and the OICR Genome Technologies Platform for provision of sequencing services. Financial support was provided by the consortium projects READNA under grant agreement FP7 Health-F4-2008-201418, ESGI under grant agreement 262055, GEUVADIS under grant agreement 261123 of the European Commission Framework Programme 7, ICGC-CLL through the Spanish Ministry of Science and Innovation (MICINN), the Instituto de Salud Carlos III (ISCIII) and the Generalitat de Catalunya. Additional financial support was provided by the PedBrain Tumor Project contributing to the International Cancer Genome Consortium, funded by German Cancer Aid (109252) and by the German Federal Ministry of Education and Research (BMBF, grants #01KU1201A, MedSys #0315416C and NGFNplus #01GS0883; the Ontario Institute for Cancer Research to PCB and JDM through funding provided by the Government of Ontario, Ministry of Research and Innovation; Genome Canada; the Canada Foundation for Innovation and Prostate Cancer Canada with funding from the Movember Foundation (PCB). PCB was also supported by a Terry Fox Research Institute New Investigator Award, a CIHR New Investigator Award and a Genome Canada Large-Scale Applied Project Contract. The Synergie Lyon Cancer platform has received support from the French National Institute of Cancer (INCa) and from the ABS4NGS ANR project (ANR-11-BINF-0001-06). The ICGC RIKEN study was supported partially by RIKEN President’s Fund 2011, and the supercomputing resource for the RIKEN study was provided by the Human Genome Center, University of Tokyo. MDE, LB, AGL and CLA were supported by Cancer Research UK, the University of Cambridge and Hutchison-Whampoa Limited. SD is supported by the Torres Quevedo subprogram (MI CINN) under grant agreement PTQ-12-05391. EH is supported by the Research Council of Norway under grant agreements 221580 and 218241 and by the Norwegian Cancer Society under grant agreement 71220-PR-2006-0433. Very special thanks go to Jennifer Jennings for administrating the activity of the ICGC Verification Working Group and Anna Borrell for administrative support.This is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/ncomms1000

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Characterization of organic aerosol across the global remote troposphere: a comparison of ATom measurements and global chemistry models

The spatial distribution and properties of submicron organic aerosol (OA) are among the key sources of uncertainty in our understanding of aerosol effects on climate. Uncertainties are particularly large over remote regions of the free troposphere and Southern Ocean, where very few data have been available and where OA predictions from AeroCom Phase II global models span 2&nbsp;to 3&nbsp;orders of magnitude, greatly exceeding the model spread over source regions. The (nearly) pole-to-pole vertical distribution of non-refractory aerosols was measured with an aerosol mass spectrometer onboard the NASA DC-8 aircraft as part of the Atmospheric Tomography (ATom) mission during the Northern Hemisphere summer (August&nbsp;2016) and winter (February&nbsp;2017). This study presents the first extensive characterization of OA mass concentrations and their level of oxidation in the remote atmosphere. OA and sulfate are the major contributors by mass to submicron aerosols in the remote troposphere, together with sea salt in the marine boundary layer. Sulfate was dominant in the lower stratosphere. OA concentrations have a strong seasonal and zonal variability, with the highest levels measured in the lower troposphere in the summer and over the regions influenced by biomass burning from Africa (up to 10&thinsp;&micro;g&thinsp;sm&minus;3). Lower concentrations (&sim;0.1&ndash;0.3&thinsp;&micro;g&thinsp;sm&minus;3) are observed in the northern middle and high latitudes and very low concentrations (&lt;0.1&thinsp;&micro;g&thinsp;sm&minus;3) in the southern middle and high latitudes. The ATom dataset is used to evaluate predictions of eight current global chemistry models that implement a variety of commonly used representations of OA sources and chemistry, as well as of the AeroCom-II ensemble. The current model ensemble captures the average vertical and spatial distribution of measured OA concentrations, and the spread of the individual models remains within a factor of 5. These results are significantly improved over the AeroCom-II model ensemble, which shows large overestimations over these regions. However, some of the improved agreement with observations occurs for the wrong reasons, as models have the tendency to greatly overestimate the primary OA fraction and underestimate the secondary fraction. Measured OA in the remote free troposphere is highly oxygenated, with organic aerosol to organic carbon (OA&thinsp;∕&thinsp;OC) ratios of &sim;2.2&ndash;2.8, and is 30&thinsp;%&ndash;60&thinsp;% more oxygenated than in current models, which can lead to significant errors in OA concentrations. The model&ndash;measurement comparisons presented here support the concept of a more dynamic OA system as proposed by Hodzic et al. (2016), with enhanced removal of primary OA and a stronger production of secondary OA in global models needed to provide better agreement with observations. </div