Browsing by Subject "IN-SITU"

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  • Pandolfi, Marco; Alados-Arboledas, Lucas; Alastuey, Andres; Andrade, Marcos; Angelov, Christo; Artinano, Begona; Backman, John; Baltensperger, Urs; Bonasoni, Paolo; Bukowiecki, Nicolas; Coen, Martine Collaud; Conil, Sebastien; Coz, Esther; Crenn, Vincent; Dudoitis, Vadimas; Ealo, Marina; Eleftheriadis, Kostas; Favez, Olivier; Fetfatzis, Prodromos; Fiebig, Markus; Flentje, Harald; Ginot, Patrick; Gysel, Martin; Henzing, Bas; Hoffer, Andras; Smejkalova, Adela Holubova; Kalapov, Ivo; Kalivitis, Nikos; Kouvarakis, Giorgos; Kristensson, Adam; Kulmala, Markku; Lihavainen, Heikki; Lunder, Chris; Luoma, Krista; Lyamani, Hassan; Marinoni, Angela; Mihalopoulos, Nikos; Moerman, Marcel; Nicolas, Jose; O'Dowd, Colin; Petäjä, Tuukka; Petit, Jean-Eudes; Pichon, Jean Marc; Prokopciuk, Nina; Putaud, Jean-Philippe; Rodriguez, Sergio; Sciare, Jean; Sellegri, Karine; Swietlicki, Erik; Titos, Gloria; Tuch, Thomas; Tunved, Peter; Ulevicius, Vidmantas; Vaishya, Aditya; Vana, Milan; Virkkula, Aki; Vratolis, Stergios; Weingartner, Ernest; Wiedensohler, Alfred; Laj, Paolo (2018)
    This paper presents the light-scattering properties of atmospheric aerosol particles measured over the past decade at 28 ACTRIS observatories, which are located mainly in Europe. The data include particle light scattering (sigma(sp)) and hemispheric backscattering (sigma(bsp)) coefficients, scattering Angstrom exponent (SAE), backscatter fraction (BF) and asymmetry parameter (g). An increasing gradient of sigma(sp) is observed when moving from remote environments (arctic/mountain) to regional and to urban environments. At a regional level in Europe, sigma(sp) also increases when moving from Nordic and Baltic countries and from western Europe to central/eastern Europe, whereas no clear spatial gradient is observed for other station environments. The SAE does not show a clear gradient as a function of the placement of the station. However, a west-to-east-increasing gradient is observed for both regional and mountain placements, suggesting a lower fraction of fine-mode particle in western/south-western Europe compared to central and eastern Europe, where the fine-mode particles dominate the scattering. The g does not show any clear gradient by station placement or geographical location reflecting the complex relationship of this parameter with the physical properties of the aerosol particles. Both the station placement and the geographical location are important factors affecting the intraannual variability. At mountain sites, higher sigma(sp) and SAE values are measured in the summer due to the enhanced boundary layer influence and/or new particle-formation episodes. Conversely, the lower horizontal and vertical dispersion during winter leads to higher sigma(sp) values at all low-altitude sites in central and eastern Europe compared to summer. These sites also show SAE maxima in the summer (with corresponding g minima). At all sites, both SAE and g show a strong variation with aerosol particle loading. The lowest values of g are always observed together with low sigma(sp) values, indicating a larger contribution from particles in the smaller accumulation mode. During periods of high sigma(sp) values, the variation of g is less pronounced, whereas the SAE increases or decreases, suggesting changes mostly in the coarse aerosol particle mode rather than in the fine mode. Statistically significant decreasing trends of sigma(sp) are observed at 5 out of the 13 stations included in the trend analyses. The total reductions of sigma(sp) are consistent with those reported for PM2.5 and PM10 mass concentrations over similar periods across Europe.
  • Kneis, David; Hiltunen, Teppo; Hess, Stefanie (2019)
    Horizontal gene transfer is an essential component of bacterial evolution. Quantitative information on transfer rates is particularly useful to better understand and possibly predict the spread of antimicrobial resistance. A variety of methods has been proposed to estimate the rates of plasmid-mediated gene transfer all of which require substantial labor input or financial resources. A cheap but reliable method with high-throughput capabilities is yet to be developed in order to better capture the variability of plasmid transfer rates, e.g. among strains or in response to environmental cues. We explored a new approach to the culture-based estimation of plasmid transfer rates in liquid media allowing for a large number of parallel experiments. It deviates from established approaches in the fact that it exploits data on the absence/presence of transconjugant cells in the wells of a well plate observed over time. Specifically, the binary observations are compared to the probability of transconjugant detection as predicted by a dynamic model. The bulk transfer rate is found as the best-fit value of a designated model parameter. The feasibility of the approach is demonstrated on mating experiments where the RP4 plasmid is transfered from Serratia marcescens to several Escherichia coil recipients. The methods uncertainty is explored via split sampling and virtual experiments.
  • Li, Xiaodong; Meng, Shuo; Puhakka, Eini; Ikonen, Jussi; Liu, Longcheng; Siitari-Kauppi, Marja (2020)
    To determine the diffusion and sorption properties of radionuclides in intact crystalline rocks, a new electromigration device was built and tested by running with I- and Se(IV) ions. By introducing a potentiostat to impose a constant voltage over the studied rock sample, the electromigration device can give more stable and accurate experimental results than those from the traditional electromigration devices. In addition, the variation in the pH of the background electrolytes was minimised by adding a small amount of NaHCO3 as buffers. To interpret the experimental results with more confidence, an advection-dispersion model was also developed in this study, which accounts for the most important mechanisms governing ionic transport in the electromigration experiments. Data analysis of the breakthrough curves by the advection-dispersion model, instead of the traditional ideal plug-flow model, suggest that the effective diffusivities of I- and Se(IV) are (1.15 +/- 0.06) x 10(-13) m(2)/s and (3.50 +/- 0.86) x 10(-14) m(2)/s, respectively. The results also show that I- is more mobile than Se(IV) ions when migrating through the same intact rock sample and that their sorption properties are almost identical.
  • Hautala, Laura C.; Pang, Poh-Choo; Antonopoulos, Aristotelis; Pasanen, Annukka; Lee, Cheuk-Lun; Chiu, Philip C. N.; Yeung, William S. B.; Loukovaara, Mikko; Bützow, Ralf; Haslam, Stuart M.; Dell, Anne; Koistinen, Hannu (2020)
    Glycodelin is a major glycoprotein expressed in reproductive tissues, like secretory and decidualized endometrium. It has several reproduction related functions that are dependent on specific glycosylation, but it has also been found to drive differentiation of endometrial carcinoma cells toward a less malignant phenotype. Here we aimed to elucidate whether the glycosylation and function of glycodelin is altered in endometrial carcinoma as compared with a normal endometrium. We carried out glycan structure analysis of glycodelin expressed in HEC-1B human endometrial carcinoma cells (HEC-1B Gd) by mass spectrometry glycomics strategies. Glycans of HEC-1B Gd were found to comprise a typical mixture of high-mannose, hybrid, and complex-type N-glycans, often containing undecorated LacNAc (Gal beta 1-4GlcNAc) antennae. However, several differences, as compared with previously reported glycan structures of normal human decidualized endometrium-derived glycodelin isoform, glycodelin-A (GdA), were also found. These included a lower level of sialylation and more abundant poly-LacNAc antennae, some of which are fucosylated. This allowed us to select lectins that showed different binding to these classes of glycodelin. Despite the differences in glycosylation between HEC-1B Gd and GdA, both showed similar inhibitory activity on trophoblast cell invasion and peripheral blood mononuclear cell proliferation. For the detection of cancer associated glycodelin, we established a novel in situ proximity-ligation based histochemical staining method using a specific glycodelin antibody and UEAI lectin. We found that the UEAI reactive glycodelin was abundant in endometrial carcinoma, but virtually absent in normal endometrial tissue even when glycodelin was strongly expressed. In conclusion, we established a histochemical staining method for the detection of endometrial carcinoma-associated glycodelin and showed that this specific glycodelin is exclusively expressed in cancer, not in normal endometrium. Similar methods can be used for studies of other glycoproteins. Glycodelin is a major endometrial glycoprotein. The authors analyzed glycan structures of endometrial carcinoma associated glycodelin and established a novel glycodelin-glycoform specific histochemical staining method. With this, they showed that glycodelin is differentially glycosylated in endometrial carcinoma tissue, as compared to normal endometrium, representing a neoantigen with potential clinical applications.
  • Kajos, M. K.; Rantala, P.; Hill, M.; Hellen, H.; Aalto, J.; Patokoski, J.; Taipale, R.; Hoerger, C. C.; Reimann, S.; Ruuskanen, T. M.; Rinne, J.; Petäjä, T. (2015)
    Proton transfer reaction mass spectrometry (PTR-MS) and gas chromatography mass spectrometry GC-MS) are commonly used methods for automated in situ measurements of various volatile organic compounds (VOCs) in the atmosphere. In order to investigate the reliability of such measurements, we operated four automated analyzers using their normal field measurement protocol side by side at a boreal forest site. We measured methanol, acetaldehyde, acetone, benzene and toluene by two PTR-MS and two GC-MS instruments. The measurements were conducted in southern Finland between 13 April and 14 May 2012. This paper presents correlations and biases between the concentrations measured using the four instruments. A very good correlation was found for benzene and acetone measurements between all instruments (the mean R value was 0.88 for both compounds), while for acetaldehyde and toluene the correlation was weaker (with a mean R value of 0.50 and 0.62, respectively). For some compounds, notably for methanol, there were considerable systematic differences in the mixing ratios measured by the different instruments, despite the very good correlation between the instruments (mean R = 0.90). The systematic difference manifests as a difference in the linear regression slope between measurements conducted between instruments, rather than as an offset. This mismatch indicates that the systematic uncertainty in the sensitivity of a given instrument can lead to an uncertainty of 50-100% in the methanol emissions measured by commonly used methods.
  • Nionelli, Luana; Wang, Yaqin; Pontonio, Erica; Immonen, Mikko; Rizzello, Carlo; Maina, Ndegwa; Katina, Kati; Coda, Rossana (2020)
    Bread is one of the most consumed food products in the world and one of the most discarded, due to its intrinsic short shelf-life and susceptibility to mold spoilage. Additionally, bread waste is generated during production and distribution, leading to the disposal of bread otherwise still fit for consumption. To avoid generating huge amount of bread waste, strategies to enable its reutilization should be sought. In this study, surplus bread, still suitable for consumption, was bioprocessed with enzymes and fermented by selected lactic acid bacteria generating an ingredient with antifungal properties. Bread hydrolysate fermented by Lactobacillus brevis AM7 showed broad inhibitory spectrum against the fungal species tested and antifungal activity ranging from 20 to 70%. Nine antifungal peptides were identified via Liquid Chromatography-Electrospray Ionisation-Mass Spectra/ Mass Spectra (nano-LC-ESI-MS/MS), having 10-17 amino acid residues and mass ranging from 1083.6 to 1980.7 Da, all of them encrypted in wheat proteins sequences. Bread hydrolysate fermented by Lb. brevis AM7, non fermented bread hydrolysate and a slurry consisting of water-bread mixture were used as ingredients in bread making and compared to regular wheat bread. Breads containing the fermented hydrolysate (18 and 22% of the dough weight) showed the longest mold-free shelf-life compared to the other breads, lasting up to 10 days before mold appearance. Additionally, the fermented hydrolysate was the least detrimental on bread quality, emphasizing the positive impact and potential of the studied biotechnology.
  • Guo, Lishu; Carraro, Michela; Sartori, Geppo; Minervini, Giovanni; Eriksson, Ove; Petronilli, Valeria; Bernardi, Paolo (2018)
    Modification with arginine-specific glyoxals modulates the permeability transition (PT) of rat liver mitochondria, with inhibitory or inducing effects that depend on the net charge of the adduct(s). Here, we show that phenylglyoxal (PGO) affects the PT in a species-specific manner (inhibition in mouse and yeast, induction in human and Drosophila mitochondria). Following the hypotheses (i) that the effects are mediated by conserved arginine(s) and (ii) that the PT is mediated by the F-ATP synthase, we have narrowed the search to 60 arginines. Most of these residues are located in subunits alpha, beta, gamma, epsilon, a, and c and were excluded because PGO modification did not significantly affect enzyme catalysis. On the other hand, yeast mitochondria lacking subunit g or bearing a subunit g R107A mutation were totally resistant to PT inhibition by PGO. Thus, the effect of PGO on the PT is specifically mediated by Arg-107, the only subunit g arginine that has been conserved across species. These findings are evidence that the PT is mediated by F-ATP synthase.
  • Mattinen, Miika; Hatanpaa, Timo; Sarnet, Tiina; Mizohata, Kenichiro; Meinander, Kristoffer; King, Peter J.; Khriachtchev, Leonid; Räisänen, Jyrki; Ritala, Mikko; Leskelä, Markku (2017)
    Molybdenum disulfide (MoS2) is a semiconducting 2D material, which has evoked wide interest due to its unique properties. However, the lack of controlled and scalable methods for the production of MoS2 films at low temperatures remains a major hindrance on its way to applications. In this work, atomic layer deposition (ALD) is used to deposit crystalline MoS2 thin films at a relatively low temperature of 300 degrees C. A new molybdenum precursor, Mo(thd)(3) (thd = 2,2,6,6-tetramethylheptane-3,5-dionato), is synthesized, characterized, and used for film deposition with H2S as the sulfur precursor. Self-limiting growth with a low growth rate of approximate to 0.025 angstrom cycle(-1), straightforward thickness control, and large-area uniformity are demonstrated. Film crystallinity is found to be relatively good considering the low deposition temperature, but the films have significant surface roughness. Additionally, chemical composition as well as optical and wetting properties are evaluated. MoS2 films are deposited on a variety of substrates, which reveal notable differences in growth rate, surface morphology, and crystallinity. The growth of crystalline MoS2 films at comparably low temperatures by ALD contributes toward the use of MoS2 for applications with a limited thermal budget.
  • Lauer, Axel; Eyring, Veronika; Righi, Mattia; Buchwitz, Michael; Defourny, Pierre; Evaldsson, Martin; Friedlingstein, Pierre; de Jeu, Richard; de Leeuw, Gerrit; Loew, Alexander; Merchant, Christopher J.; Mueller, Benjamin; Popp, Thomas; Reuter, Maximilian; Sandven, Stein; Senftleben, Daniel; Stengel, Martin; Van Roozendael, Michel; Wenzel, Sabrina; Willen, Ulrika (2017)
    The Coupled Model Intercomparison Project (CMIP) is now moving into its sixth phase and aims at a more routine evaluation of the models as soon as the model output is published to the Earth System Grid Federation (ESGF). To meet this goal the Earth System Model Evaluation Tool (ESMValTool), a community diagnostics and performance metrics tool for the systematic evaluation of Earth system models (ESMs) in CMIP, has been developed and a first version (1.0) released as open source software in 2015. Here, an enhanced version of the ESMValTool is presented that exploits a subset of Essential Climate Variables (ECVs) from the European Space Agency's Climate Change Initiative (ESA CCI) Phase 2 and this version is used to demonstrate the value of the data for model evaluation. This subset includes consistent, long-term time series of ECVs obtained from harmonized, reprocessed products from different satellite instruments for sea surface temperature, sea ice, cloud, soil moisture, land cover, aerosol, ozone, and greenhouse gases. The ESA CCI data allow 'extending the calculation of performance metrics as summary statistics for some variables and add an important alternative data set in other cases where observations are already available. The provision of uncertainty estimates on a per grid basis for the ESA CCI data sets is used in a new extended version of the Taylor diagram and provides important additional information for a more objective evaluation of the models. In our analysis we place a specific focus on the comparability of model and satellite data both in time and space. The ESA CCI data are well suited for an evaluation of results from global climate models across ESM compartments as well as an analysis of long-term trends, variability and change in the context of a changing climate. The enhanced version of the ESMValTool is released as open source software and ready to support routine model evaluation in CMIP6 and at individual modeling centers. (C) 2017 Elsevier Inc. All rights reserved.
  • Hedenbjork-Lager, Anders; Hamberg, Kristina; Paakkonen, Virve; Tjaderhane, Leo; Ericson, Dan (2016)
    Objective: Dental caries is a process driven by acids produced by oral microorganisms followed by degradation of the dentine collagen matrix by proteolytic enzymes. Matrix metalloproteinases (MMPs) have been suggested to contribute to caries by degrading collagen. The aim of this study was to develop a method for generating demineralized dentine matrix substrate (DDM) maintaining MMP-8 bioactivity and no interference with later assays. Such a substrate would allow study of the effects of various treatments on MMP-8 activity and collagen degradation in demineralized dentine. Design: Human dentine was powderized in a tissue grinder and frozen (-80 degrees C). The powder was demineralized in dialysis tubes, using EDTA or acetic acid. The demineralized dentine matrix (DDM) was harvested and analyzed for collagen content using SDS-PAGE. The DDM was subsequently suspended in PBS or TESCA buffer. Protein, MMP-8 (ELISA) and collagen (HYP) was analyzed directly or after 1 wk. Results: EDTA or acid demineralization of dentine using dialysis yielded a substrate rich in collagen coupled with preserved MMP-8 activity. Collagen degraded in room temperature, assessed by higher HYP amounts in the soluble fraction of DDM after one wk, indicating that the methods used preserved active DDM-components after the demineralization process. Conclusions: The presented demineralization methods both provided insoluble DDM substrates suitable for further intervention studies. However, it was found that the substrates differed depending on the demineralization method and buffers used. This needs further study to find an optimal technique for generating DDM with retained proteins as well as enzymatic bioactivity. (C) 2016 Elsevier Ltd. All rights reserved.
  • Kögler, Martin; Paul, Andrea; Anane, Emmanuel; Birkholz, Mario; Bunker, Alex; Viitala, Tapani; Maiwald, Michael; Junne, Stefan; Neubauer, Peter (2018)
    The application of Raman spectroscopy as a monitoring technique for bioprocesses is severely limited by a large background signal originating from fluorescing compounds in the culture media. Here, we compare time-gated Raman (TG-Raman)-, continuous wave NIR-process Raman (NIR-Raman), and continuous wave micro-Raman (micro-Raman) approaches in combination with surface enhanced Raman spectroscopy (SERS) for their potential to overcome this limit. For that purpose, we monitored metabolite concentrations of Escherichia coli bioreactor cultivations in cell-free supernatant samples. We investigated concentration transients of glucose, acetate, AMP, and cAMP at alternating substrate availability, from deficiency to excess. Raman and SERS signals were compared to off-line metabolite analysis of carbohydrates, carboxylic acids, and nucleotides. Results demonstrate that SERS, in almost all cases, led to a higher number of identifiable signals and better resolved spectra. Spectra derived from the TG-Raman were comparable to those of micro-Raman resulting in well-discernable Raman peaks, which allowed for the identification of a higher number of compounds. In contrast, NIR-Raman provided a superior performance for the quantitative evaluation of analytes, both with and without SERS nanoparticles when using multivariate data analysis. (c) 2018 American Institute of Chemical Engineers
  • Cairns, Johannes; Jokela, Roosa; Hultman, Jenni; Tamminen, Manu; Virta, Marko; Hiltunen, Teppo (2018)
    Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work.
  • Deckwirth, Vivi; Rajakylä, Eeva Kaisa; Cattavarayane, Sandhanakrishnan; Acheva, Anna; Schaible, Niccole; Krishnan, Ramaswamy; Valle-Delgado, Juan Jose; Osterberg, Monika; Björkenheim, Pia; Sukura, Antti; Tojkander, Sari (2021)
    At invasion, transformed mammary epithelial cells expand into the stroma through a disrupted myoepithelial (ME) cell layer and basement membrane (BM). The intact ME cell layer has thus been suggested to act as a barrier against invasion. Here, we investigate the mechanisms behind the disruption of ME cell layer. We show that the expression of basal/ME proteins CK5, CK14, and alpha-SMA altered along increasing grade of malignancy, and their loss affected the maintenance of organotypic 3D mammary architecture. Furthermore, our data suggests that loss of CK5 prior to invasive stage causes decreased levels of Zinc finger protein SNAI2 (SLUG), a key regulator of the mammary epithelial cell lineage determination. Consequently, a differentiation bias toward luminal epithelial cell type was detected with loss of mature, alpha-SMA-expressing ME cells and reduced deposition of basement membrane protein laminin-5. Therefore, our data discloses the central role of CK5 in mammary epithelial differentiation and maintenance of normal ME layer.
  • Hellquist, Henrik; Ferlito, Alfio; Mäkitie, Antti A.; Thompson, Lester D. R.; Bishop, Justin A.; Agaimy, Abbas; Hernandez-Prera, Juan C.; Gnepp, Douglas R.; Willems, Stefan M.; Slootweg, Pieter J.; Rinaldo, Alessandra (2020)
    During the last 60 years numerous significant attempts have been made to achieve a widely acceptable terminology and histological grading for laryngeal squamous intraepithelial lesions. While dysplasia was included in the pathology of the uterine cervix already in 1953, the term dysplasia was accepted in laryngeal pathology first after the Toronto Centennial Conference on Laryngeal Cancer in 1974. In 1963 Kleinsasser proposed a three-tier classification, and in 1971 Kambic and Lenart proposed a four-tier classification. Since then, four editions of the World Health Organisation (WHO) classification have been proposed (1978, 1991, 2005 and 2017). Several terms such as squamous intraepithelial neoplasia (SIN) and laryngeal intraepithelial neoplasia (LIN) are now being abandoned and replaced by squamous intraepithelial lesions (SIL). The essential change between the 2005 and 2017 WHO classifications is the attempt to induce a simplification from a four- to a two-tier system. The current WHO classification (2017) thus recommends the use of a two-tier system with reasonably clear histopathological criteria for the two groups: low-grade and high-grade dysplasia. Problems with interobserver variability apart, subjectivities and uncertainties remain, but to a lesser degree. Ongoing and additional molecular studies may help to clarify underlying events that will increase our understanding and possibly can facilitate our attempts to obtain an even better classification. The classification needs to be easier for the general pathologist to perform and easier for the clinician to interpret. These two objectives are equally important to provide each patient the best personalised treatment available for squamous intraepithelial lesions.
  • Puukko, Esa; Lehto, Jukka; Lindberg, Antero; Voutilainen, Mikko (2018)
    This study aims to determine upscaling factors for the radionuclides' distribution coefficients (Kd) on crushed rocks to intact rock for the safety analysis of radionuclide migration from spent nuclear fuel in bedrock towards biosphere. Here we report the distribution coefficients for intact rock determined by electromigration sorption experiments and compare the results with those from recently performed batch sorption experiments. In total 34 rock samples, representing three typical rock types from Olkiluoto Finland, were studied in order to determine distribution coefficients, effective diffusion coefficients and porosities using the electromigration sorption experiments, formation factor experiments and porosity measurement. The parameters determined represent the three main parameters of geosphere used in the safety assessment of spent nuclear fuel disposal. The distribution coefficients of cesium and strontium on intact rock varied between (0.12–26.2) × 10−3 m3/kg and (1.4–13.3) × 10−3 m3/kg, respectively, whereas recent results for crushed rock varied between (2–57) × 10−3 m3/kg and (17–40) × 10−3 m3/kg, respectively. This implies that crushing increases the distribution coefficient significantly and upscaling factors from 3 to 33 were determined for scaling the distribution coefficients of crushed rock to ones of intact rock. The determined distribution coefficients of cesium and strontium for intact rock can be directly applied in the safety assessment whereas the upscaling factors can be used to convert distribution coefficients determined for crushed rock into ones for intact rock. Based on the results for porosities and effective diffusion coefficients it was concluded that they do not seem to correlate with sorption parameters. However, an alteration state, heterogeneity and mineral content seem to be important factors affecting the distribution coefficients and upscaling factors.
  • Jääskeläinen, Anniina; Roininen, Nelli; Karihtala, Peeter; Jukkola, Arja (2020)
    While breast cancer prognoses are generally good, different molecular subtypes are known to have varying outcomes. Previous studies using breast cancer registries have suggested that high parity may be an adverse prognostic factor in luminal breast cancer, but breast cancer subtype definitions have varied and there have been few prospective studies. We therefore collected prospective data from patients diagnosed with early breast cancer at a single institution and followed them for a median of 8.5 years. All patients (N= 594) were treated according to Finnish national guidelines using modern treatment modalities in a Finnish university hospital. Clinicopathological surrogates of the intrinsic breast cancer subtypes were updated to match European Society for Medical Oncology 2015 Early Breast Cancer Clinical Practice Guidelines. The overall 10-year breast cancer-specific survival (BCSS) was 91.4%, with the longest 10-year BCSS observed in luminal A-like cancers (97.9%) and the worst in luminal B-like (HER2 positive) cancers (80.6%). Parity of >= 5 deliveries was also associated with poor BCSS (univariateP= 0.0020). However, when the subtypes were assessed separately in a multivariate analysis that included tumor size and nodal status, high parity remained significant only in luminal B-like (HER2 negative) cancers (HR = 2.63; 95% confidence interval = 1.04-6.62;P= 0.040). Our results suggest excellent overall 10-year BCSS but indicate that high parity is an adverse prognostic factor in luminal B-like (HER2 negative) breast cancers.
  • Huiskonen, Juha T. (2018)
    Cryogenic transmission electron microscopy (cryo-TEM) is a high-resolution biological imaging method, whereby biological samples, such as purified proteins, macromolecular complexes, viral particles, organelles and cells, are embedded in vitreous ice preserving their native structures. Due to sensitivity of biological materials to the electron beam of the microscope, only relatively low electron doses can be applied during imaging. As a result, the signal arising from the structure of interest is overpowered by noise in the images. To increase the signal-to-noise ratio, different image processing-based strategies that aim at coherent averaging of signal have been devised. In such strategies, images are generally assumed to arise from multiple identical copies of the structure. Prior to averaging, the images must be grouped according to the view of the structure they represent and images representing the same view must be simultaneously aligned relatively to each other. For computational reconstruction of the 3D structure, images must contain different views of the original structure. Structures with multiple symmetry-related substructures are advantageous in averaging approaches because each image provides multiple views of the substructures. However, the symmetry assumption may be valid for only parts of the structure, leading to incoherent averaging of the other parts. Several image processing approaches have been adapted to tackle symmetry-mismatched substructures with increasing success. Such structures are ubiquitous in nature and further computational method development is needed to understanding their biological functions.
  • Chattopadhyay, S.; Zheng, G.; Hemminki, A.; Försti, A.; Sundquist, K.; Sundquist, J.; Hemminki, K. (2020)
    Summary Background Patients with squamous cell skin cancer (SCC) have an excellent prognosis but second primary cancers (SPCs) weaken survival prospects. Family history is a known risk factor for cancer but whether it is a risk factor for SPC in patients with SCC is not known. Objectives To quantify the risk of family history on SPCs in patients with SCC and estimate survival probabilities of patients with SPCs depending on family history. Methods With 13 945 histologically verified SCCs, relative risks (RRs) were estimated for family history using a generalized regression model. For survival analysis, hazard ratios (HRs) were assessed using a multivariable Cox proportional-hazards model. Results Family history of invasive SCC increased risk of second invasive SCC [RR = 42·92, 95% confidence interval (CI) 33·69?50·32] compared with risk without family history (RR 19·12, 95% CI 17·88?21·08). Family history of any nonskin cancer in invasive SCC increased risk of the same cancers to be diagnosed as SPC (RRFH = 1·48, 95% CI 1·35?1·61 vs. RRno FH = 1·40, 95% CI 1·32?1·48); significant increases were observed for seven different nonskin cancers. Most results were replicated for in situ SCC. SPC was deleterious for survival irrespective of family history; HR for patients with SPC was 4·28 (95% CI 3·83?4·72) vs. those without SPC (1·04). Conclusions Family history of nonskin cancer was associated with approximately a doubling of risk for SPCs in patients with SCC. SPC increases the death rate in patients with SCC 3?4 times, irrespective of family history. Taking family history into account at SCC diagnosis may help prevention or early detection of SPCs. What's already known about this topic? Second primary cancers (SPCs) are frequently diagnosed in patients with invasive and in situ squamous cell carcinoma (SCC); some epidemiological studies suggest a link to immune dysfunction. Family history of cancer is a risk factor for practically all first primary cancers but whether it also influences risk of SPCs in patients with SCC is not known. The possible influence of family history on survival in patients with SCC remains to be established.
  • Wlodarski, Maksymilian; Putkonen, Matti; Norek, Malgorzata (2020)
    Infrared (IR) spectroscopy is a powerful technique to characterize the chemical structure and dynamics of various types of samples. However, the signal-to-noise-ratio drops rapidly when the sample thickness gets much smaller than penetration depth, which is proportional to wavelength. This poses serious problems in analysis of thin films. In this work, an approach is demonstrated to overcome these problems. It is shown that a standard IR spectroscopy can be successfully employed to study the structure and composition of films as thin as 20 nm, when the layers were grown on porous substrates with a well-developed surface area. In contrast to IR spectra of the films deposited on flat Si substrates, the IR spectra of the same films but deposited on porous ceramic support show distinct bands that enabled reliable chemical analysis. The analysis of Zn-S ultrathin films synthesized by atomic layer deposition (ALD) from diethylzinc (DEZ) and 1,5-pentanedithiol (PDT) as precursors of Zn and S, respectively, served as proof of concept. However, the approach presented in this study can be applied to analysis of any ultrathin film deposited on target substrate and simultaneously on porous support, where the latter sample would be a reference sample dedicated for IR analysis of this film.
  • Friess, U.; Baltink, H. Klein; Beirle, S.; Clemer, K.; Hendrick, F.; Henzing, B.; Irie, H.; de Leeuw, G.; Li, A.; Moerman, M. M.; van Roozendael, M.; Shaiganfar, R.; Wagner, T.; Wang, Y.; Xie, P.; Yilmaz, S.; Zieger, P. (2016)
    A first direct intercomparison of aerosol vertical profiles from Multi-Axis Differential Optical Absorption Spectroscopy (MAX-DOAS) observations, performed during the Cabauw Intercomparison Campaign of Nitrogen Dioxide measuring Instruments (CINDI) in summer 2009, is presented. Five out of 14 participants of the CINDI campaign reported aerosol extinction profiles and aerosol optical thickness (AOT) as deduced from observations of differential slant column densities of the oxygen collision complex (O-4) at different elevation angles. Aerosol extinction vertical profiles and AOT are compared to backscatter profiles from a ceilometer instrument and to sun photometer measurements, respectively. Furthermore, the near-surface aerosol extinction coefficient is compared to in situ measurements of a humidity-controlled nephelometer and dry aerosol absorption measurements. The participants of this intercomparison exercise use different approaches for the retrieval of aerosol information, including the retrieval of the full vertical profile using optimal estimation and a parametrised approach with a prescribed profile shape. Despite these large conceptual differences, and also differences in the wavelength of the observed O-4 absorption band, good agreement in terms of the vertical structure of aerosols within the boundary layer is achieved between the aerosol extinction profiles retrieved by the different groups and the backscatter profiles observed by the ceilometer instrument. AOTs from MAX-DOAS and sun photometer show a good correlation (R > 0.8), but all participants systematically underestimate the AOT. Substantial differences between the near-surface aerosol extinction from MAX-DOAS and from the humidified nephelometer remain largely unresolved.