ALBERT

Description: Breast cancer tumor draining lymph nodes (TDLNs) display distinct morphologic changes depending on the breast cancer subtype. For triple-negative breast cancers (TNBC), draining LNs display a higher amount of secondary lymphoid follicles, which can be regarded as a surrogate marker for an activated humoral immune response. In the present study, we focus on PD1+ T-follicular helper cells (Tfh) in TDLNs of TNBC, since PD1+ Tfh are drivers of the germinal center (GC) reaction. We quantified PD1+ Tfh in 22 sentinel LNs with 853 GCs and interfollicular areas from 19 patients with TNBC by morphometry from digitalized immunostained tissue sections. Overall survival was significantly worse for patients with a higher number and area density of PD1+ Tfh within GCs of TDLNs. Further, we performed T-cell receptor gamma chain (TRG) analysis from microdissected tissue in the primary tumor and TDLNs. Eleven patients showed the same TRG clones in the tumor and the LN. Five patients shared the same TRG clones in the tumor and the GCs. In two patients, those clones were highly enriched inside the GCs. Enrichment of identical TRG clones at the tumor site vs. the TDLN was associated with improved overall survival. TDLNs are important relays of cancer immunity and enable surrogate approaches to predict the outcome of TNBC itself.

Description: This work proposes a fast and straightforward method, called natural point correspondences (NaPoCo), for the extraction of road segment shapes from trajectories of vehicles. The algorithm can be expressed with 20 lines of code in Python and can be used as a baseline for further extensions or as a heuristic initialization for more complex algorithms. In this paper, we evaluate the performance of the proposed method. We show that (1) the order of the points in a trajectory can be used to cluster points among the trajectories for road segment shape extraction and (2) that preprocessing using polygonal approximation improves the results of the approach. Furthermore, we show based on “averaging GPS segments” competition results, that the algorithm despite its simplicity and low computational complexity achieves state-of-the-art performance on the challenge dataset, which is composed of data from several cities and countries.

Description: This article addresses the question of mapping building functions jointly using both aerial and street view images via deep learning techniques. One of the central challenges here is determining a data fusion strategy that can cope with heterogeneous image modalities. We demonstrate that geometric combinations of the features of such two types of images, especially in an early stage of the convolutional layers, often lead to a destructive effect due to the spatial misalignment of the features. Therefore, we address this problem through a decision-level fusion of a diverse ensemble of models trained from each image type independently. In this way, the significant differences in appearance of aerial and street view images are taken into account. Compared to the common multi-stream end-to-end fusion approaches proposed in the literature, we are able to increase the precision scores from 68% to 76%. Another challenge is that sophisticated classification schemes needed for real applications are highly overlapping and not very well defined without sharp boundaries. As a consequence, classification using machine learning becomes significantly harder. In this work, we choose a highly compact classification scheme with four classes, commercial, residential, public, and industrial because such a classification has a very high value to urban geography being correlated with socio-demographic parameters such as population density and income.

Description: Pathological biopsy protocols require tissue marking dye (TMD) for orientation. In some cases (e.g., close margin), additional immunohistochemical analyses can be necessary. Therefore, the correlation between the applied TMD during macroscopy and the examined TMD during microscopy is crucial for the correct orientation, the residual tumour status and the subsequent therapeutic regime. In this context, our group observed colour changes during routine immunohistochemistry. Tissue specimens were marked with various TMD and processed by two different methods. TMD (blue, red, black, yellow and green) obtained from three different providers (A, B and C, and Whiteout/Tipp-Ex®) were used. Immunohistochemistry was performed manually via stepwise omission of reagents to identify the colour changing mechanism. Blue colour from provider A changed during immunohistochemistry into black, when 3,3′-Diaminobenzidine-tetrahydrochloride-dihydrate (DAB) and H2O2 was applied as an immunoperoxidase-based terminal colour signal. No other applied reagents, nor tissue texture or processing showed any influence on the colour. The remaining colours from provider A and the other colours did not show any changes during immunohistochemistry. Our results demonstrate an interesting and important pitfall in routine immunohistochemistry-based diagnostics that pathologists should be aware of. Furthermore, the chemical rationale behind the observed misleading colour change is discussed.

Description: In order to quantify the relative importance of individual boundary conditions and forcings, including greenhouse gases, ice sheets, and Earth's orbital parameters, on determining Last Glacial Maximum (LGM) climate, we have performed a series of LGM experiments using a state-of-the-art climate model AWI-ESM, in which different combinations of boundary conditions and forcings have been applied following the protocol of Paleoclimate Modelling Intercomparison Project phase 4 (PMIP4). In good agreement with observational proxy records, a general colder and drier climate is simulated in our full-forced LGM experiment as compared to the present-day simulation. Our simulated results from non-full-forced sensitivity simulations reveal that both the greenhouse gases and ice sheets play a major role in defining the anomalous LGM surface temperature compared to today. Decreased greenhouse gases in LGM as compared to present day leads to a non-uniform global cooling with polar amplification effect. The presence of LGM ice sheets favors a warming over the Arctic and northern Atlantic oceans in boreal winter, as well as a cooling over regions with the presence of ice sheets. The former is induced by a strengthening in the Atlantic meridional overturning circulation (AMOC) transporting more heat to high latitudes, whilst the latter is due to the increased surface albedo and elevation of ice sheets. We find that the Northern Hemisphere monsoon precipitation is influenced by the opposing effects of LGM greenhouse gases and ice sheets. Specifically, the presence of ice sheets leads to significant drying in the Northern Hemisphere monsoon regions, while a reduction in greenhouse gases results in increased monsoon rainfall. Based on our model results, continental ice sheets exert a major control on atmospheric dynamics and the variability of El Niño–Southern Oscillation (ENSO). Moreover, our analysis also implies a nonlinearity in climate response to LGM boundary conditions and forcings.

Description: Numerical simulations employing prognostic stable water isotopes can not only facilitate our understanding of hydrological processes and climate change but also allow for a direct comparison between isotope signals obtained from models and various archives. In the current work, we describe the performance and explore the potential of a new version of the Earth system model AWI-ESM (Alfred Wegener Institute Earth System Model), labeled AWI-ESM-2.1-wiso, in which we incorporated three isotope tracers into all relevant components of the water cycle. We present here the results of pre-industrial (PI) and mid-Holocene (MH) simulations. The model reproduces the observed PI isotope compositions in both precipitation and seawater well and captures their major differences from the MH conditions. The simulated relationship between the isotope composition in precipitation (δ18Op) and surface air temperature is very similar between the PI and MH conditions, and it is largely consistent with modern observations despite some regional model biases. The ratio of the MH–PI difference in δ18Op to the MH–PI difference in surface air temperature is comparable to proxy records over Greenland and Antarctica only when summertime air temperature is considered. An amount effect is evident over the North African monsoon domain, where a negative correlation between δ18Op and the amount of precipitation is simulated. As an example of model applications, we studied the onset and withdrawal date of the MH West African summer monsoon (WASM) using daily variables. We find that defining the WASM onset based on precipitation alone may yield erroneous results due to the substantial daily variations in precipitation, which may obscure the distinction between pre-monsoon and monsoon seasons. Combining precipitation and isotope indicators, we suggest in this work a novel method for identifying the commencement of the WASM. Moreover, we do not find an obvious difference between the MH and PI periods in terms of the mean onset of the WASM. However, an advancement in the WASM withdrawal is found in the MH compared to the PI period due to an earlier decline in insolation over the northern location of Intertropical Convergence Zone (ITCZ).

Description: Meridional atmospheric transport is an important process in the climate system and has implications for the availability of heat and moisture at high latitudes. Near-surface cold and warm temperature advection over the ocean in the context of extratropical cyclones additionally leads to important air–sea exchange. In this paper, we investigate the impact of these air–sea fluxes on the stable water isotope (SWI) composition of water vapour in the Southern Ocean’s atmospheric boundary layer. SWIs serve as a tool to trace phase change processes involved in the atmospheric water cycle and, thus, provide important insight into moist atmospheric processes associated with extratropical cyclones. Here we combine a 3-month ship-based SWI measurement data set around Antarctica with a series of regional high-resolution numerical model simulations from the isotope-enabled numerical weather prediction model COSMOiso. We objectively identify atmospheric cold and warm temperature advection associated with the cold and warm sector of extratropical cyclones, respectively, based on the air–sea temperature difference applied to the measurement and the simulation data sets. A Lagrangian composite analysis of temperature advection based on the COSMOiso simulation data is compiled to identify the main processes affecting the observed variability of the isotopic signal in marine boundary layer water vapour in the region from 35 to 70◦ S. This analysis shows that the cold and warm sectors of extratropical cyclones are associated with contrasting SWI signals. Specifically, the measurements show that the median values of δ18O and δ2H in the atmospheric water vapour are 3.8 ‰ and 27.9 ‰ higher during warm than during cold advection. The median value of the second-order isotope variable deuterium excess d, which can be used as a measure of non-equilibrium processes during phase changes, is 6.4 ‰ lower during warm than during cold advection. These characteristic isotope signals during cold and warm advection reflect the opposite air–sea fluxes associated with these large-scale transport events. The trajectory-based analysis reveals that the SWI signals in the cold sector are mainly shaped by ocean evaporation. In the warm sector, the air masses experience a net loss of moisture due to dew deposition as they are advected over the relatively colder ocean, which leads to the observed low d. We show that additionally the formation of clouds and precipitation in moist adiabatically ascending warm air parcels can decrease d in boundary layer water vapour. These findings illustrate the highly variable isotopic composition in water vapour due to contrasting air–sea interactions during cold and warm advection, respectively, induced by the circulation associated with extratropical cyclones. SWIs can thus potentially be useful as tracers for meridional air advection and other characteristics associated with the dynamics of the storm tracks over interannual timescales.

Description: Winter (October to March) precipitation δ18OP and δDP values in central Europe correlate with the winter North Atlantic Oscillation index (wNAOi), but the causal mechanisms remain poorly understood. Here we analyse the relationships between precipitation-weighted δ18OP and δDP datasets (δ18Opw and δDpw) from European GNIP and ANIP stations and the wNAOi, with a focus on isotope gradients. We demonstrate that longitudinal δ18Opw and δDpw gradients across Europe (“continental effect”) depend on the wNAOi state, with steeper gradients associated with more negative wNAOi states. Changing gradients reflect a combination of air temperature and variable amounts of precipitable water as a function of the wNAOi. The relationships between the wNAOi, δ18Opw and δDpw can provide additional information from palaeoclimate archives such as European speleothems that primarily record winter δ18Opw. Comparisons between present-day and past European longitudinal δ18O gradients inferred from Holocene speleothems suggest that atmospheric pressure configurations akin to negative wNAO modes dominated the early Holocene, whereas patterns resembling positive wNAO modes were more common in the late Holocene, possibly caused by persistent shifts in the relative locations of the Azores High and the Icelandic Low.

Description: The project MUSICA (MUlti-platform remote Sensing of Isotopologues for investigating the Cycle of Atmospheric water) has shown that the sensor IASI aboard the satellite MetOp can measure the free tropospheric {H2O,δD} pair distribution twice per day on a quasi-global scale. Such data are very promising for investigating tropospheric moisture pathways, however, the complex data characteristics compromise their usage in the context of model evaluation studies. Here we present a tool that allows for simulating MUSICA MetOp/IASI {H2O,δD} pair remote sensing data for a given model atmosphere, thereby creating model data that have the remote sensing data characteristics assimilated. This model data can then be compared to the MUSICA data. The retrieval simulation method is based on the physical principles of radiative transfer and we show that the uncertainty of the simulations is within the uncertainty of the MUSICA MetOp/IASI products, i.e. the retrieval simulations are reliable enough. We demonstrate the working principle of the simulator by applying it to ECHAM5-wiso model data. The few case studies clearly reveal the large potential of the MUSICA MetOp/IASI {H2O,δD} data pairs for evaluating modelled moisture pathways. The tool is made freely available in form of MATLAB and Python routines and can be easily connected to any atmospheric water vapour isotopologue model.

Description: This modelling study aims at an improved understanding of the processes that determine the water vapour budget in the stratosphere by means of the investigation of water isotope ratios. An additional (and separate from the actual) hydrological cycle has been introduced into the chemistry–climate model EMAC, including the water isotopologues HDO and H2 18 O and their physical fractionation processes. Additionally an explicit computation of the contribution of methane oxidation to H2O and HDO has been incorporated. The model expansions allow detailed analyses of water vapour and its isotope ratio with respect to deuterium throughout the stratosphere and in the transition region to the troposphere. In order to assure the correct representation of the water isotopologues in the model’s hydrological cycle, the expanded system has been evaluated in several steps. The physical fractionation effects have been evaluated by comparison of the simulated isotopic composition of precipitation with measurements from a ground-based network (GNIP) and with the results from the isotopologue-enabled general circulation model ECHAM5-wiso. The model’s representation of the chemical HDO precursor CH3D in the stratosphere has been confirmed by a comparison with chemical transport models (1-D, CHEM2D) and measurements from radiosonde flights. Finally, the simulated stratospheric HDO and the isotopic composition of water vapour have been evaluated, with respect to retrievals from three different satellite instruments (MIPAS, ACE-FTS, SMR). Discrepancies in stratospheric water vapour isotope ratios between two of the three satellite retrievals can now partly be explained.