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"en": "Abstract Background In otosurgical training, cadaveric temporal bones are primarily used to provide a realistic tactile experience. However, using cadaveric temporal bones is challenging due to their limited availability, high cost, and potential for infection. Utilizing current three-dimensional (3D) technologies could overcome the limitations associated with cadaveric bones. This study focused on how a 3D-printed middle ear model can be used in otosurgical training. Methods A cadaveric temporal bone was imaged using microcomputed tomography (micro-CT) to generate a 3D model of the middle ear. The final model was printed from transparent photopolymers using a laser-based 3D printer (vat photopolymerization), yielding a 3D-printed phantom of the external ear canal and middle ear. The feasibility of this phantom for otosurgical training was evaluated through an ossiculoplasty simulation involving ten otosurgeons and ten otolaryngology–head and neck surgery (ORL-HNS) residents. The participants were tasked with drilling, scooping, and placing a 3D-printed partial ossicular replacement prosthesis (PORP). Following the simulation, a questionnaire was used to collect the participants' opinions and feedback. Results A transparent photopolymer was deemed suitable for both the middle ear phantom and PORP. The printing procedure was precise, and the anatomical landmarks were recognizable. Based on the evaluations, the phantom had realistic maneuverability, although the haptic feedback during drilling and scooping received some criticism from ORL-HNS residents. Both otosurgeons and ORL-HNS residents were optimistic about the application of these 3D-printed models as training tools. Conclusions The 3D-printed middle ear phantom and PORP used in this study can be used for low-threshold training in the future. The integration of 3D-printed models in conventional otosurgical training holds significant promise."
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"en": "Abstract Background Microbial expansins (EXLXs) are non-lytic proteins homologous to plant expansins involved in plant cell wall formation. Due to their non-lytic cell wall loosening properties and potential to disaggregate cellulosic structures, there is considerable interest in exploring the ability of microbial expansins (EXLX) to assist the processing of cellulosic biomass for broader biotechnological applications. Herein, EXLXs with different modular structure and from diverse phylogenetic origin were compared in terms of ability to bind cellulosic, xylosic, and chitinous substrates, to structurally modify cellulosic fibrils, and to boost enzymatic deconstruction of hardwood pulp. Results Five heterogeneously produced EXLXs (Clavibacter michiganensis; CmiEXLX2, Dickeya aquatica; DaqEXLX1, Xanthomonas sacchari; XsaEXLX1, Nothophytophthora sp.; NspEXLX1 and Phytophthora cactorum; PcaEXLX1) were shown to bind xylan and hardwood pulp at pH 5.5 and CmiEXLX2 (harboring a family-2 carbohydrate-binding module) also bound well to crystalline cellulose. Small-angle X-ray scattering revealed a 20–25% increase in interfibrillar distance between neighboring cellulose microfibrils following treatment with CmiEXLX2, DaqEXLX1, or NspEXLX1. Correspondingly, combining xylanase with CmiEXLX2 and DaqEXLX1 increased product yield from hardwood pulp by ~ 25%, while supplementing the TrAA9A LPMO from Trichoderma reesei with CmiEXLX2, DaqEXLX1, and NspEXLX1 increased total product yield by over 35%. Conclusion This direct comparison of diverse EXLXs revealed consistent impacts on interfibrillar spacing of cellulose microfibers and performance of carbohydrate-active enzymes predicted to act on fiber surfaces. These findings uncover new possibilities to employ EXLXs in the creation of value-added materials from cellulosic biomass."
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"en": "Abstract Background CRISPR-Cas9-based genome engineering represents a powerful therapeutic tool for cartilage tissue engineering and for understanding molecular pathways driving cartilage diseases. However, primary chondrocytes are difficult to transfect and rapidly dedifferentiate during monolayer (2D) cell culture, making the lengthy expansion of a single-cell-derived edited clonal population not feasible. For this reason, functional genetics studies focused on cartilage and rheumatic diseases have long been carried out in cellular models that poorly recapitulate the native molecular properties of human cartilaginous tissue (e.g., cell lines, induced pluripotent stem cells). Here, we set out to develop a non-viral CRISPR-Cas9, bulk-gene editing method suitable for chondrocyte populations from different cartilaginous sources. Methods We screened electroporation and lipid nanoparticles for ribonucleoprotein (RNP) delivery in primary polydactyly chondrocytes, and optimized RNP reagents assembly. We knocked out RELA (also known as p65), a subunit of the nuclear factor kappa B (NF-κB), in polydactyly chondrocytes and further characterized knockout (KO) cells with RT-qPCR and Western Blot. We tested RELA KO in chondrocytes from diverse cartilaginous sources and characterized their phenotype with RT-qPCR. We examined the chondrogenic potential of wild-type (WT) and KO cell pellets in presence and absence of interleukin-1β (IL-1β). Results We established electroporation as the optimal transfection technique for chondrocytes enhancing transfection and editing efficiency, while preserving high cell viability. We knocked out RELA with an unprecedented efficiency of ~90%, confirming lower inflammatory pathways activation upon IL-1β stimulation compared to unedited cells. Our protocol could be easily transferred to primary human chondrocytes harvested from osteoarthritis (OA) patients, human FE002 chondroprogenitor cells, bovine chondrocytes, and a human chondrocyte cell line, achieving comparable mean RELA KO editing levels using the same protocol. All KO pellets from primary human chondrocytes retained chondrogenic ability equivalent to WT cells, and additionally displayed enhanced matrix retention under inflamed conditions. Conclusions We showcased the applicability of our bulk gene editing method to develop effective autologous and allogeneic off-the-shelf gene therapies strategies and to enable functional genetics studies in human chondrocytes to unravel molecular mechanisms of cartilage diseases."
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"en": "The examination of the comprehensive effects of flagship projects on adjacent neighborhoods remains inadequately explored, particularly within developing countries. This scholarly void is expanding despite limited research on public space flagship projects. The current study delves into a problematic case study: Atigh Square, located within the historical center of Isfahan, Iran. This site has undergone substantial efforts to transform into a pedestrian-oriented public space, aimed at recapturing its original configuration fro the eleventh century. The 5 criteria of identity, economy, social, physical, and tourism features and 22 indicators attributed to them were extracted from the theoretical literature. Mixed methods research was pursued, using seminal publications, quantitative data from a questionnaire, and qualitative analysis of interviews conducted with several experts. Furthermore, the integration and connectivity of the area before and after regeneration was compared using Depth map software package. The results of the analysis show that the impact of the project in social, identity-related, infrastructural, and economic sub-criteria was weak, but it achieved relative success in terms of planning and tourism indicators. Besides, the sanitation sub-class received the highest rank whereas facilities and public services had the lowest rank among the sub-classes. As with the subjective and objective quality of life, the project was not a great success. Overall, although the project has considerably enhanced the physical and visual conditions of the area, it has failed to solve the social and economic problems of the surrounding fabric. The findings significantly contribute to the existing body of global literature concerning the impacts of flagship projects on surrounding areas, as the research explores diverse facets of these effects. The results underscore the necessity for flagship projects to be meticulously planned, taking into account not only the specific circumstances and challenges of local communities but also their integration into the broader socio-economic dynamics of the entire city."
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"en": "Abstract Background Patients’ online record access (ORA) enables patients to read and use their health data through online digital solutions. One such solution, patient-accessible electronic health records (PAEHRs) have been implemented in Estonia, Finland, Norway, and Sweden. While accumulated research has pointed to many potential benefits of ORA, its application in mental healthcare (MHC) continues to be contested. The present study aimed to describe MHC users’ overall experiences with national PAEHR services. Methods The study analysed the MHC-part of the NORDeHEALTH 2022 Patient Survey, a large-scale multi-country survey. The survey consisted of 45 questions, including demographic variables and questions related to users’ experiences with ORA. We focused on the questions concerning positive experiences (benefits), negative experiences (errors, omissions, offence), and breaches of security and privacy. Participants were included in this analysis if they reported receiving mental healthcare within the past two years. Descriptive statistics were used to summarise data, and percentages were calculated on available data. Results 6,157 respondents were included. In line with previous research, almost half (45%) reported very positive experiences with ORA. A majority in each country also reported improved trust (at least 69%) and communication (at least 71%) with healthcare providers. One-third (29.5%) reported very negative experiences with ORA. In total, half of the respondents (47.9%) found errors and a third (35.5%) found omissions in their medical documentation. One-third (34.8%) of all respondents also reported being offended by the content. When errors or omissions were identified, about half (46.5%) reported that they took no action. There seems to be differences in how patients experience errors, omissions, and missing information between the countries. A small proportion reported instances where family or others demanded access to their records (3.1%), and about one in ten (10.7%) noted that unauthorised individuals had seen their health information. Conclusions Overall, MHC patients reported more positive experiences than negative, but a large portion of respondents reported problems with the content of the PAEHR. Further research on best practice in implementation of ORA in MHC is therefore needed, to ensure that all patients may reap the benefits while limiting potential negative consequences."
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"en": "This dataset contains the data and code that enable reproducing the results reported in article **Hovi, A., Janoutová, R., Malenovský, Z., Schraik, D., Gastellu-Etchegorry, J-P., Lauret, N., Novotný, J., Rautiainen, M. Physically-based modeling of spectral transmittance through forest canopies. Methods in Ecology and Evolution**. The data and code are organized in six folders as follows. See the README.txt in each folder for more detailed description. - **0_spectral_transmittance_data/** - In situ measurements of forest canopy spectral transmittance. - **1_model_input_data/** - Input data for the PARAS and DART models. - **2_PAI_calculation/** - Calculation of plant area index (plant area volume density) by inverting a ray tracing model against hemispherical photographs. Used as input in the DART model. - **3_DART/** - Input data processed in formats required by the DART model, and the results of forest canopy spectral transmittance simulations with the DART model. - The DART model is available as an executable file after a license agreement acceptance at https://dart.omp.eu/. - **4_PARAS/** - Code for running forest canopy spectral transmittance simulations with the PARAS model, and results from those simulations. - **5_figures_and_tables/** - Code for producing the figures and tables of the article. UTF-8 encoding was used in all .txt and .csv files. **Citation:** If using the code provided in this dataset, please cite this dataset and the accompanying scientific article (**DOI**). The input data (i.e., the .csv files in folders **0_spectral_transmittance_data/** and **1_model_input_data/**) were obtained from the following published open data sources. If you use the data given in the files listed below, please credit the original data sources. Some of the listed datasets have specific instructions for how to cite the data. Refer to the original datasets for accurate citation information. - Canopy transmittance and forest floor spectra, forest inventory data, hemispherical photograph, and terrestrial laser scanning data in 21 forest plots in four study areas in Finland, Estonia, and the Czech Republic, as well as accompanying foliage spectral data from the same study areas (**canopytransmittance_measurements.csv**, **canopygaps_for_PARAS.csv**, **forest_structure.csv**, **forestfloor_R.csv**, **leaf_R.csv**, **leaf_R-C1.csv**, **leaf_R-REDUCED.csv**, **leaf_R-SUNEXP.csv**, **leaf_T.csv**, **leaf_T-C1.csv**, **leaf_T-REDUCED.csv**, **leaf_T-SUNEXP.csv**, **shoot_R.csv**, **shoot_R-C1.csv**, **shoot_R-REDUCED.csv**, **shoot_R-SUNEXP.csv**, **shoot_T.csv**, **shoot_T-C1.csv**, **shoot_T-REDUCED.csv**, **shoot_T-SUNEXP.csv**, **tree_crown_dimensions_from_TLS-FINAL.csv**) were obtained from: - Hovi, A., Schraik, D., Hanuš, J., Lukeš, P., Lhotáková, Z., Homolová, L., & Rautiainen, M. (2024). A spectral-structural characterization of European temperate, hemiboreal and boreal forests: Laboratory and field data. Aalto University. https://doi.org/10.23729/9a8d90cd-73e2-438d-9230-94e10e61adc9 - Tree stem reflectance spectra (**trunk_R.csv**, **trunk_R-REDUCED.csv**) were obtained from: - Juola, J., Hovi, A., & Rautiainen, M. (2022). A dataset of stem bark reflectance spectra for boreal and temperate tree species. Mendeley Data, V2. https://doi.org/10.17632/pwfxgzz5fj.2 - Lang, M., Kuusk, A., Nilson, T., Lükk, T., Pehk, M., & Alm, G. (2002). Reflectance spectra of ground vegetation in sub-boreal forests. Tartu Observatory, Estonia. http://www.aai.ee/bgf/ger2600/ (Accessed 8 October 2023). - Spencer, S., & Rock, B.N. (1999). BOREAS TE-08 Aspen bark spectral reflectance data. Data set. Oak Ridge National Laboratory Distributed Active Archive Center, Oak Ridge, Tennessee, U.S.A. https://doi.org/10.3334/ORNLDAAC/336 (Accessed 8 October 2023). - Beta distribution parameters specifying the leaf and shoot angle distributions (**beta_distribution_parameters.csv**) were obtained from: - Janoutová, R., Homolová, L., Malenovský, Z., Hanuš, J., Lauret, N., & Gastellu-Etchegorry, J.P. (2019). Influence of 3D spruce tree representation on accuracy of airborne and satellite forest reflectance simulated in DART. Forests, 10, 292. https://doi.org/10.3390/f10030292 - Pisek, J., Diaz-Pines, E., Matteucci, G., Noe, S., & Rebmann, C. (2022). On the leaf inclination angle distribution as a plant trait for the most abundant broadleaf tree species in Europe. Agricultural and Forest Meteorology, 323, 109030. https://doi.org/10.1016/j.agrformet.2022.109030 - Pisek, J., Sonnentag, O., Richardson, A.D., & Mõttus, M. (2013). Is the spherical leaf angle distribution a valid assumption for temperate and boreal broadleaf tree species? Agricultural and Forest Meteorology, 169, 186-194. https://doi.org/10.1016/j.agrformet.2012.10.011 - Raabe, K., Pisek, J., Sonnentag, O., & Annuk, K. (2015). Variations of leaf inclination angle distribution with height over the growing season and light exposure for eight broadleaf tree species. Agricultural and Forest Meteorology, 214-215, 2–11. http://dx.doi.org/10.1016/j.agrformet.2015.07.008 - Stenberg, P., Smolander, H., & Kellomäki, S. (1993). Description of crown structure for light interception models: angular and spatial distribution of shoots in young Scots pine. In S. Linder and S. Kellomäki (Eds.), Management of structure and productivity of boreal and subalpine forests (pp. 43–50). Studia Forestalia Suecica 191. - Top-of-canopy spectral irradiance and diffuse to total irradiance ratio (**total_irradiance.csv**, **diffuse_to_total_irradiance.csv**) were obtained by simulating with the libRadtran atmospheric model, with atmospheric aerosol optical depth and water vapor content derived from the data in: - CAMS (2023). CAMS global reanalysis (EAC4). Web page. https://ads.atmosphere.copernicus.eu/cdsapp#!/dataset/cams-global-reanalysis-eac4 (Accessed 7 October 2023). **A note on plot naming:** Note that the identification codes (IDs) that we used for the forest plots differ from the original dataset (https://doi.org/10.23729/9a8d90cd-73e2-438d-9230-94e10e61adc9) Furthermore, in the published article the plots are identified just by numbers from 1 to 21 instead of full identification codes. A conversion table is provided below. | Plot nr in the article | Plot ID used in our computation code and in the input files (i.e., this dataset) | Plot ID used in the original dataset | |----|--------------|--------------| | 1 | HY_BIRCH2 | HY_BIRCH2 | | 2 | HY_BIRCH3 | HY_BIRCH3 | | 3 | HY_BIRCH4 | HY_BIRCH4 | | 4 | JS_11 | JS_ALDER1 | | 5 | JS_31 | JS_BIRCH1 | | 6 | JS_40 | JS_BIRCH2 | | 7 | LZ_HORNBEAM1 | LZ_HORNBEAM1 | | 8 | LZ_MIXED3 | LZ_ASH1 | | 9 | LZ_OAK1 | LZ_OAK1 | | 10 | LZ_OAK4 | LZ_OAK4 | | 11 | HY_PINE4 | HY_PINE4 | | 12 | HY_PINE5 | HY_PINE5 | | 13 | HY_SPRUCE3 | HY_SPRUCE3 | | 14 | HY_SPRUCE5 | HY_SPRUCE5 | | 15 | HY_SPRUCE6 | HY_SPRUCE6 | | 16 | JS_21 | JS_SPRUCE1 | | 17 | JS_37 | JS_PINE2 | | 18 | BK_SPRUCE2 | BK_SPRUCE2 | | 19 | BK_SPRUCE4 | BK_SPRUCE4 | | 20 | BK_SPRUCE5 | BK_SPRUCE5 | | 21 | BK_SPRUCE6 | BK_SPRUCE6 | Note also that in some of the input data files there are data for one extra plot (plot ID JS_44, which corresponds to JS_BIRCH3 in the original dataset). This plot was not used in the article, because the data from it included only one terrestrial laser scan instead of 16 scans in the other plots."
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