Open access articles by University of Helsinki researchers. Contains final versions and manuscripts of research articles as well as professional publications and publications aimed at general public.

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  • Torkko, Jussi; Poom, Age; Willberg, Elias; Toivonen, Tuuli (2023)
    Urban greenery has been shown to impact the quality of life in our urbanizing societies. While greenery is traditionally mapped top-down, alternative computational approaches have emerged for mapping greenery from the street level to mimic human sight. Despite the variety of these novel mapping approaches, it has remained unclear how well they reflect human perception in reality. We compared a range of both novel and traditional mapping methods with the self-reported perception of urban greenery at randomly selected study sites across Helsinki, the capital of Finland. The mapping methods included both image segmentation and point cloud-based methods to capture human perspective as well as traditional approaches taking the top-down perspective, i.e., land cover and remote sensing-based mapping methods. The results suggest that all the methods tested are strongly associated with the human perception of greenery at the street-level. However, mapped greenery values were consistently lower than the perceived values. Our results support the use of semantic image segmentation methods over color segmentation methods for greenery extraction to be closer to human perception. Point cloud-based approaches and top-down methods can be used as alternatives to image segmentation in case data coverage for the latter is limited. The results highlight a further research need for a comprehensive evaluation on how human perspective should be mimicked in different temporal and spatial conditions.
  • Giri, Subarna; Ghimire, Anup; Mishra, Ashish; Acharya, Kshitiz; Kuikel, Sandip; Tiwari, Ananda; Mishra, Shyam Kumar (2022)
    Background This study aimed to estimate the pooled prevalence and sub-group-specific prevalence of Methicillin-resistant Staphylococcus aureus (MRSA) carrier rate among Healthcare Workers (HCWs) in South Asia. Methodology We considered prospective and cross-sectional studies published in the English language with participants ≥ 50 by searching different electronic databases to locate the relevant articles that reported the epidemiology of MRSA. The participants were healthy South Asian nationality HCWs (asymptomatic for any infectious disease) of any age and gender with a definitive diagnosis of MRSA carriage. The result was synthesized for the pooled prevalence of MRSA carriers among HCWs using 95% confidence interval (CI) with DerSimonian and Laird random-effects models. Results The pooled prevalence of MRSA carriage among HCWs was 9.23% (95%CI; 6.50%, 12.35%) with a range from 0.67% to 36.06%. The prevalence in India, Nepal, Pakistan, Sri Lanka, and Bangladesh was 5.65% (95%CI; 3.65%, 8.03%), 8.83% (95%CI; 6.77%, 11.11%), 17.20% (95%CI; 10.70%, 24.85%), 22.56% (95%CI; 4.93%, 47.83%) and 4.93% (95%CI; 1.88%, 9.20%) respectively. The pooled prevalence of MRSA carriage among nurses and doctors was 8.90% (95%CI; 6.00%, 12.24%) and 6.53% (95%CI; 3.63%, 10.06%) respectively. Conclusion The findings from our study suggests that if the propagation of MRSA continues, then it can lead to a situation of an outbreak. Hence, proper preventive measures are to be adopted to prevent this outbreak.
  • Ekstedt, Andreas; Schicho, Philipp; Tenkanen, Tuomas V. I. (2023)
    DRalgo is an algorithmic implementation that constructs an effective, dimensionally reduced, high-temperature field theory for generic models. The corresponding Mathematica package automatically performs the matching to next-to-leading order. This includes two-loop thermal corrections to scalar and Debye masses as well as one-loop thermal corrections to couplings. DRalgo also allows for integrating out additional heavy scalars. Along the way, the package provides leading-order beta functions for general gauge-charges and fermion-families; both in the fundamental and in the effective theory. Finally, the package computes the finite-temperature effective potential within the effective theory. The article explains the theory of the underlying algorithm while introducing the software on a pedagogical level.
  • Tykhonov, Andrii; Winkler, Alexander; Smoliar, Volodymyr (2023)
    We perform a detailed simulation of a pixelated CdTe detector using the GEANT4 toolkit completed with a custom code emulating the detector's electronic response. We demonstrate that a measured tungsten X-ray spectrum can be majorly restored back to the original incident spectrum using the developed model, without requiring the dedicated hardware charge sharing correction.
  • Jaroszynski, P.; Grzanka, E.; Grabowski, M.; Staszczak, G.; Prozheev, I.; Jakiela, R.; Tuomisto, F.; Bockowski, M. (2023)
    Europium doping of gallium nitride using a novel ultra-high pressure annealing method was investigated. Ammonothermal gallium nitride substrates (n-type) were used as europium ion implantation targets using beam energy of 490 keV and ion fluences ranging from 1 x 1015 to 1 x 1016 Eu/cm2. The implanted samples were annealed at temperatures between 1473 K and 1753 K in high nitrogen pressure. Europium concentration profiles were analyzed along the [0001] crystallographic direction. The morphology and structural quality of implanted and annealed samples were examined. The "out-diffusion" phenomenon was noted. The presence of optically active EuGa-X defect complexes was suggested based on the analysis of photoluminescence spectra measured at low temperature (20 K). Limitations of diffusion-based europium doping of ammonothermal gallium nitride are discussed.
  • Hemminki, Kari; Sundquist, Kristina; Sundquist, Jan; Försti, Asta; Liska, Vaclav; Hemminki, Akseli; Li, Xinjun (Multidisciplinary Digital Publishing Institute, 2023)
    Background: We aim to estimate population-attributable fractions (PAF) for 13 comorbidities potentially predisposing to hepatobiliary cancer of hepatocellular carcinoma (HCC), gallbladder cancer (GBC), cancers of the intrahepatic and extrahepatic bile ducts (ICC and ECC), and ampullary cancer. Methods: Patients were identified from the Swedish Inpatient Register from 1987 to 2018 and cancers from the Swedish Cancer Registry from 1997 through 2018. PAFs were calculated for each comorbidity-associated cancer using a cohort study design. Results: For male HCC, the major individual comorbidities (PAF > 10) were diabetes, alcohol-related liver disease, and hepatitis C virus infection. For female HCC, diabetes and autoimmune diseases were important contributors. For female GBC, gallstone disease was an overwhelming contributor, with a PAF of 30.57%, which was also important for men. The overall PAF for male ICC was almost two times higher than the female one. For ECC and ampullary cancer, infection of bile ducts was associated with the highest PAF. Conclusions: The 13 comorbidities accounted for 50% or more of the potential etiological pathways of each hepatobiliary cancer except female ICC. The underlying convergent mechanism for these cancers may be chronic inflammation lasting for decades and thus offering possibilities for intervention and disease monitoring.
  • Thomas, Leon-Friedrich; Änäkkälä, Mikael; Lajunen, Antti (Multidisciplinary Digital Publishing Institute, 2023)
    In the field of precision agriculture, weed detection models combined with selective spraying by ground or aerial robotics are seen as promising approaches for increasing yield harvests while simultaneously minimizing herbicide use. The available labeled training data are a major bottleneck for developing and applying supervised deep learning models, and more automated methods for labeled data generation are therefore needed. Our research aims to address this need by introducing a rule-based method for label data generation for perennial weeds. For this research, a dataset of a barley field was collected using an unmanned aerial vehicle (UAV) with a flight altitude of 10 m. A multispectral and a thermal camera were used for the data collection. The preprocessed dataset consists of multispectral and thermal orthomosaic images along with a canopy height model. The methodological part of this article introduces a proposed rule-based method for labeled data generation for perennial weeds based on the Normalized Difference Vegetation Index (NDVI), and this approach is further used to generate labels for the measured data. The preprocessed data combined with the generated labels was used to train U-net models. Three data combinations are used for the training and testing: multispectral, multispectral–thermal and multispectral–thermal–canopy–height–model. This approach was used to evaluate whether additional data improve model performance. To evaluate the models on ground truth labels, they are tested on a manually annotated test dataset, which consists of 10% of the whole dataset. The tested models achieved an F1 score of 0.82–0.83 on the test dataset. This finding demonstrates that the rule-based labeling method generates valid labels for the perennial weed detection task. Furthermore, our study shows that data fusion improved the model slightly. The data combination of multispectral–thermal–canopy–height–model as input resulted in the best-performing model, with an F1 score of 0.835.
  • Zhao, Chi; Penttinen, Petri; Zhang, Lingzi; Dong, Ling; Zhang, Fengju; Li, Zhihua; Zhang, Xiaoping (Multidisciplinary Digital Publishing Institute, 2023)
    Phenyllactic acid (PLA), a promising food preservative, is safe and effective against a broad spectrum of food-borne pathogens. However, its mechanisms against toxigenic fungi are still poorly understood. In this study, we applied physicochemical, morphological, metabolomics, and transcriptomics analyses to investigate the activity and mechanism of PLA inhibition of a typical food-contaminating mold, Aspergillus flavus. The results showed that PLA effectively inhibited the growth of A. flavus spores and reduced aflatoxin B1 (AFB1) production by downregulating key genes associated with AFB1 biosynthesis. Propidium iodide staining and transmission electron microscopy analysis demonstrated a dose-dependent disruption of the integrity and morphology of the A. flavus spore cell membrane by PLA. Multi-omics analyses showed that subinhibitory concentrations of PLA induced significant changes in A. flavus spores at the transcriptional and metabolic levels, as 980 genes and 30 metabolites were differentially expressed. Moreover, KEGG pathway enrichment analysis indicated PLA-induced cell membrane damage, energy-metabolism disruption, and central-dogma abnormality in A. flavus spores. The results provided new insights into the anti-A. flavus and -AFB1 mechanisms of PLA.
  • Ingram, Stephen; Jansen, Steven; Schenk, H. Jochen (Multidisciplinary Digital Publishing Institute, 2023)
    One of the more surprising occurrences of bulk nanobubbles is in the sap inside the vascular transport system of flowering plants, the xylem. In plants, nanobubbles are subjected to negative pressure in the water and to large pressure fluctuations, sometimes encompassing pressure changes of several MPa over the course of a single day, as well as wide temperature fluctuations. Here, we review the evidence for nanobubbles in plants and for polar lipids that coat them, allowing nanobubbles to persist in this dynamic environment. The review addresses how the dynamic surface tension of polar lipid monolayers allows nanobubbles to avoid dissolution or unstable expansion under negative liquid pressure. In addition, we discuss theoretical considerations about the formation of lipid-coated nanobubbles in plants from gas-filled spaces in the xylem and the role of mesoporous fibrous pit membranes between xylem conduits in creating the bubbles, driven by the pressure gradient between the gas and liquid phase. We discuss the role of surface charges in preventing nanobubble coalescence, and conclude by addressing a number of open questions about nanobubbles in plants.
  • Sarfraz, Sonia; Tamminen, Anni-Maria; Leikola, Junnu; Salmi, Sonja; Kaakinen, Mika; Sorsa, Timo; Suojanen, Juho; Reunanen, Justus (Multidisciplinary Digital Publishing Institute, 2023)
    The aim of this study was to evaluate and compare the biofilm formation properties of common pathogens associated with implant-related infections on two different implant material types. Bacterial strains tested in this study were Staphylococcus aureus, Streptococcus mutans, Enterococcus faecalis, and Escherichia coli. Implant materials tested and compared were PLA Resorb × polymer of Poly DL-lactide (PDLLA) comprising 50% poly-L-lactic acid and 50% poly-D-lactic acid) and Ti grade 2 (tooled with a Planmeca CAD-CAM milling device). Biofilm assays were done with and without saliva treatment to evaluate the effect of saliva on bacterial adhesion and to mimic the intraoral and extraoral surgical routes of implant placement, respectively. Five specimens of each implant type were tested for each bacterial strain. Autoclaved material specimens were first treated with 1:1 saliva-PBS solution for 30 min, followed by washing of specimens and the addition of bacterial suspension. Specimens with bacterial suspension were incubated for 24 h at 37 °C for biofilm formation. After 24 h, non-adhered bacteria were removed, and specimens were washed, followed by removal and calculation of adhered bacterial biofilm. S. aureus and E. faecalis showed more attachment to Ti grade 2, whereas S. mutans showed higher adherence to PLA in a statistically significant manner. The salivary coating of specimens enhanced the bacterial attachment by all the bacterial strains tested. In conclusion, both implant materials showed significant levels of bacterial adhesion, but saliva treatment played a vital role in bacterial attachment, therefore, saliva contamination of the implant materials should be minimized and considered when placing implant materials inside the body.
  • Valtonen, Joona; Prajapati, Chandra; Cherian, Reeja Maria; Vanninen, Sari; Ojala, Marisa; Leivo, Krista; Heliö, Tiina; Koskenvuo, Juha; Aalto-Setälä, Katriina (Multidisciplinary Digital Publishing Institute, 2023)
    Hypertrophic cardiomyopathy (HCM) is one of the most common genetic cardiac diseases; it is primarily caused by mutations in sarcomeric genes. However, HCM is also associated with mutations in non-sarcomeric proteins and a Finnish founder mutation for HCM in non-sarcomeric protein junctophilin-2 (JPH2) has been identified. This study aimed at assessing the issue of modelling the rare Finnish founder mutation in cardiomyocytes (CMs) differentiated from iPSCs; therefore, presenting the same cardiac abnormalities observed in the patients. To explore the abnormal functions in JPH2-HCM, skin fibroblasts from a Finnish patient with JPH2 p.(Thr161Lys) were reprogrammed into iPSCs and further differentiated into CMs. As a control line, an isogenic counterpart was generated using the CRISPR/Cas9 genome editing method. Finally, iPSC-CMs were evaluated for the morphological and functional characteristics associated with JPH2 mutation. JPH2-hiPSC-CMs displayed key HCM hallmarks (cellular hypertrophy, multi-nucleation, sarcomeric disarray). Moreover, JPH2-hiPSC-CMs exhibit a higher degree of arrhythmia and longer action potential duration associated with slower inactivation of calcium channels. Functional evaluation supported clinical observations, with differences in beating characteristics when compared with isogenic-hiPSC-CMs. Thus, the iPSC-derived, disease-specific cardiomyocytes could serve as a translationally relevant platform to study genetic cardiac diseases.
  • Hilander, Markus (Multidisciplinary Digital Publishing Institute, 2023)
    Geography textbooks have many visuals, such as maps, graphs, tables, photographs, and illustrations, which makes geography a highly visual school subject. However, previous studies show that geography students can pay surprisingly little attention to textbook visuals. In this article, it is asked what sorts of visuals are there in geography textbooks if they do not attract students’ attention. In order to answer the research question, a visual method to approach textbook visuals is developed. The visual method is motivated by Stephen Kellert’s concept of direct, indirect, and symbolic experience of nature. Based on the three types of experience of nature, three categories for geography textbook visuals are established respectively: snapshot visuals (deriving from direct experience), landscape visuals (deriving from indirect experience), and abstract visuals (deriving from symbolic experience). The sample covers eight Finnish geography textbooks for grades 7–9 and for one upper secondary school course. The results show that most of the visuals depict landscapes. In addition, there are many abstract visuals, such as maps and illustrations, depicting geographical processes. Instead, only a few snapshots of people in action and snapshots of geographical hazards were identified. In the article, it is suggested that enhancing the role of snapshot visuals in geography education could increase students’ interest towards textbook visuals, as well. This is because snapshot visuals can draw students’ attention and enable students to express their own feelings and thoughts.
  • Bouslama, Rim; Dumont, Vincent; Lindfors, Sonja; Paavolainen, Lassi; Tienari, Jukka; Nisen, Harry; Mirtti, Tuomas; Saleem, Moin A.; Gordin, Daniel; Groop, Per-Henrik; Suetsugu, Shiro; Lehtonen, Sanna (Multidisciplinary Digital Publishing Institute, 2023)
    Changes in the dynamic architecture of podocytes, the glomerular epithelial cells, lead to kidney dysfunction. Previous studies on protein kinase C and casein kinase 2 substrates in neurons 2 (PACSIN2), a known regulator of endocytosis and cytoskeletal organization, reveal a connection between PACSIN2 and kidney pathogenesis. Here, we show that the phosphorylation of PACSIN2 at serine 313 (S313) is increased in the glomeruli of rats with diabetic kidney disease. We found that phosphorylation at S313 is associated with kidney dysfunction and increased free fatty acids rather than with high glucose and diabetes alone. Phosphorylation of PACSIN2 emerged as a dynamic process that fine-tunes cell morphology and cytoskeletal arrangement, in cooperation with the regulator of the actin cytoskeleton, Neural Wiskott–Aldrich syndrome protein (N-WASP). PACSIN2 phosphorylation decreased N-WASP degradation while N-WASP inhibition triggered PACSIN2 phosphorylation at S313. Functionally, pS313-PACSIN2 regulated actin cytoskeleton rearrangement depending on the type of cell injury and the signaling pathways involved. Collectively, this study indicates that N-WASP induces phosphorylation of PACSIN2 at S313, which serves as a mechanism whereby cells regulate active actin-related processes. The dynamic phosphorylation of S313 is needed to regulate cytoskeletal reorganization.
  • Berg, Anton; Valaskivi, Katja (2023)
    Artikkeli jäsentää teknologian ja uskonnon välistä suhdetta tarkastelemalla empiirisesti, miten kolmen suurimman konenäköä kaupallistavan ja kehittävän yhdysvaltalaisen teknologiayrityksen, Googlen, Amazonin ja Microsoftin, kuvantunnistuspalvelut luokittelevat uskonnollisia kuvia ja millaisin seurauksin. Aineisto on kerätty Googlen kuvapalvelusta, ja se koostuu kristinuskoon, islamiin, hindulaisuuteen, buddhalaisuuteen ja shintolaisuuteen liittyvistä kuvista. Poikkitieteellisen ja eksploratiivisen artikkelin metodologinen ja teoreettinen asetelma yhdistää datatieteellisiä laskennallisen yhteiskuntatieteen menetelmiä uskonnon- ja mediatutkimuksen alan teorioihin ja laadullisiin menetelmiin. Tutkimuksemme päätulos on, että kuvantunnistuspalvelut tuottavat uskonnon kontekstissa sekularistisia, kristillisiä, kaupallisia ja rasistisia vinoumia.
  • Sumiala, Johanna; Hoover, Stewart M.; Laughlin, Corrina (2023)
    This introduction to a Special Section, Global Populism: Its Roots in Media and Religion, advances scholarly understanding of the present dynamics of global politics in the hybrid media environment from a perspective that is often neglected or undermined in media and communication studies: religion and/or "the religious" dimension. To incorporate better scholarship of religion into media and communication studies on populism, this introduction argues for a need to analyze more closely the interplay between the three and place special emphasis on (1) definitions concerning religion and populism, (2) the scale of analysis, and (3) transformations in the present media environment as hybrid. The articles address populism, media, and religion in a variety of media-related political and cultural contexts ranging from Europe to India and Brazil. The authors address populism in multiple political and religious contexts with a special focus on nationalist and right-wing politics.
  • Salonen, Jannika Maria; Slama, Ulla Susanna; Haavisto, Anu Marika; Rosenqvist, Johanna (2023)
    The Wechsler scales are among the most widely used tests in cognitive and neuropsychological assessments. When assessing children aged 6:0-7:7 years the clinician can choose between Wechsler Preschool and Primary Scale of Intelligence - Fourth Edition (WPPSI-IV) and Wechsler Intelligence Scale for Children - Fifth Edition (WISC-V). Information about how the tests function and differ in this overlapping age range is limited. Using a between-subjects design, the present study compared the cognitive profiles of typically developing Swedish-speaking children in Finland in this overlapping age range (6:1 - 7:2 years), assessed with the Swedish versions of either WPPSI-IV (n = 38) or WISC-V (n = 24). Profile analyses and one-way ANCOVA were performed to investigate differences in the comparable subtests, indexes and Full Scale IQ. On the subtest level, children assessed with WISC-V had significantly lower scores on the subtests Vocabulary, Matrix Reasoning, and Bug/Symbol Search compared to children assessed with WPPSI-IV. On the index level, scores for the Verbal Comprehension Index and the Fluid Reasoning Index were significantly lower for children assessed with WISC-V. The Full Scale IQ was significantly lower on WISC-V. Taken together, the findings indicate that WPPSI-IV and WISC-V produce partly different cognitive profiles. These differences are important to recognize when choosing which test to use and when interpreting the results of clinical assessments of children in this age group.
  • Kaaronen, Roope Oskari (2023)
    Collective intelligence, broadly conceived, refers to the adaptive behavior achieved by groups through the interactions of their members, often involving phenomena such as consensus building, cooperation, and competition. The standard view of collective intelligence is that it is a distinct phenomenon from supposed individual intelligence. In this position piece, we argue that a more parsimonious stance is to consider all intelligent adaptive behavior as being driven by similar abstract principles of collective dynamics. To illustrate this point, we highlight how similar principles are at work in the intelligent behavior of groups of non-human animals, multicellular organisms, brains, small groups of humans, cultures, and even evolution itself. If intelligent behavior in all of these systems is best understood as the emergent result of collective interactions, we ask what is left to be called “individual intelligence”? We believe that viewing all intelligence as collective intelligence offers greater explanatory power and generality, and may promote fruitful cross-disciplinary exchange in the study of intelligent adaptive behavior.
  • Pajulahti, Riikka Elisa; Ray, Carola; Korkalo, Liisa; Lehto, Reetta; Vepsäläinen, Henna; Nissinen, Kaija M; Roos, Eva; Sajaniemi, Nina; Salmela-Aro, Katariina; Erkkola, Maijaliisa (2023)
  • Abdollahi, Anna Minerva; Li, Xinyue; Merikanto, Ilona; Leppanen, Marja H.; Vepsäläinen, Henna; Lehto, Reetta; Ray, Carola; Erkkola, Maijaliisa; Roos, Eva (2023)

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