[article-cris] Perustieteiden korkeakoulu / SCI
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- (1+1)-Dimensional Scalar Field Theory on q-Deformed Space
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2023) Tadros, PoulaWe study scalar field theory in a one-space and one-time dimension on a q-deformed space with a static background.We write the Lagrangian and the equation of motion and solve it to first order in q -1, where q is the deformation parameter of the space. - 172 fs, 24.3 kW peak power pulse generation from a Ho-doped fiber laser system
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2018-10-01) Wang, Mengmeng; Zhang, Hui; Wei, Rongling; Zhu, Zexiu; Ruan, Shuangchen; Yan, Peiguang; Wang, Jinzhang; Hasan, Tawfique; Sun, ZhipeiWe demonstrate a high-peak-power femtosecond fiber laser system based on single-mode holmium (Ho)-doped fibers. 833 fs, 27.7 MHz pulses at 2083.4 nm generated in a passively mode-locked Ho fiber laser are amplified and compressed to near transform-limited 172 fs, 7.2 nJ pulses with 24.3 kW peak power. We achieve this performance level by using the soliton effect and high-order soliton compression. To the best of our knowledge, this is the first demonstration of sub-200 fs pulses, with peak power exceeding 10 kW from a Ho-doped single-mode fiber laser system without using bulk optics compressors. - 1D kinetic modelling of the JET SOL with tungsten divertor
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2013-07) Tskhakaya, D.; Groth, M.; Contributors, JET EFDAIn this work a fully kinetic model of the JET SOL with tungsten divertor plates has been developed. It includes the dynamics of main-ions (D+) and electrons, the neutrals (D, C, W) and the impurity particles (C+m, W+n). Our simulations show extremely low concentration of W impurity. We identify two reasons which are responsible for this effect: (1) for low temperature divertor plasma the energy of most of the main-ions and the impurities in a low-ionization state impinging the divertor plates is below the W-sputtering threshold energy; (2) with increasing temperature the W-sputtering increases, but the potential drop across the divertor plasma increases too, so that most of the W ions are reabsorbed at the divertors. - 2-Methylresorcinarene: a very high packing coefficient in a mono-anion based dimeric capsule and the X-ray crystal structure of the tetra-anion
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2016-05) Puttreddy, Rakesh; Beyeh, Ngong Kodiah; Kalenius, Elina; Ras, Robin H A; Rissanen, KariMono- and tetra-deprotonated 2-methylresorcinarene anions (1 and 2) as their trans-1,4-diammoniumcyclohexane (TDAC)2+ inclusion complexes are reported. The mono-anion forms a fully closed dimeric capsule [1·H2O·MeOH]2 2- with a cavity volume of 165 3 and (TDAC)2+ as the guest with an extremely high packing coefficient, PC = 84.2%, while the tetra-anion forms a close-packed structure with two structurally isomeric tetra-anions 2a and 2b with a 50:50 ratio in the crystal lattice. - The 2021 Magnonics Roadmap
A2 Katsausartikkeli tieteellisessä aikakauslehdessä(2021-10-13) Barman, Anjan; Gubbiotti, Gianluca; Ladak, S.; Adeyeye, A. O.; Krawczyk, M.; Grafe, J.; Adelmann, C.; Cotofana, S.; Naeemi, A.; Vasyuchka, V. I.; Hillebrands, B.; Nikitov, S. A.; Yu, H.; Grundler, D.; Sadovnikov, A. V.; Grachev, A. A.; Sheshukova, S. E.; Duquesne, J. Y.; Marangolo, M.; Csaba, G.; Porod, W.; Demidov, V. E.; Urazhdin, S.; Demokritov, S. O.; Albisetti, E.; Petti, D.; Bertacco, R.; Schultheiss, H.; Kruglyak, V. V.; Poimanov, V. D.; Sahoo, S.; Sinha, J.; Yang, H.; Münzenberg, M.; Moriyama, T.; Mizukami, S.; Landeros, P.; Gallardo, R. A.; Carlotti, G.; Kim, J. V.; Stamps, R. L.; Camley, R. E.; Rana, B.; Otani, Y.; Yu, W.; Yu, T.; Bauer, G. E.W.; Back, C.; Uhrig, G. S.; Dobrovolskiy, O. V.; Budinska, B.; Qin, H.; Van Dijken, S.; Chumak, A. V.; Khitun, A.; Nikonov, D. E.; Young, I. A.; Zingsem, B. W.; Winklhofer, M.Magnonics is a budding research field in nanomagnetism and nanoscience that addresses the use of spin waves (magnons) to transmit, store, and process information. The rapid advancements of this field during last one decade in terms of upsurge in research papers, review articles, citations, proposals of devices as well as introduction of new sub-topics prompted us to present the first roadmap on magnonics. This is a collection of 22 sections written by leading experts in this field who review and discuss the current status besides presenting their vision of future perspectives. Today, the principal challenges in applied magnonics are the excitation of sub-100 nm wavelength magnons, their manipulation on the nanoscale and the creation of sub-micrometre devices using low-Gilbert damping magnetic materials and its interconnections to standard electronics. To this end, magnonics offers lower energy consumption, easier integrability and compatibility with CMOS structure, reprogrammability, shorter wavelength, smaller device features, anisotropic properties, negative group velocity, non-reciprocity and efficient tunability by various external stimuli to name a few. Hence, despite being a young research field, magnonics has come a long way since its early inception. This roadmap asserts a milestone for future emerging research directions in magnonics, and hopefully, it will inspire a series of exciting new articles on the same topic in the coming years. - A 204-subject multimodal neuroimaging dataset to study language processing
Data Article(2019-04-03) Schoffelen, Jan Mathijs; Oostenveld, Robert; Lam, Nietzsche H.L.; Uddén, Julia; Hultén, Annika; Hagoort, PeterThis dataset, colloquially known as the Mother Of Unification Studies (MOUS) dataset, contains multimodal neuroimaging data that has been acquired from 204 healthy human subjects. The neuroimaging protocol consisted of magnetic resonance imaging (MRI) to derive information at high spatial resolution about brain anatomy and structural connections, and functional data during task, and at rest. In addition, magnetoencephalography (MEG) was used to obtain high temporal resolution electrophysiological measurements during task, and at rest. All subjects performed a language task, during which they processed linguistic utterances that either consisted of normal or scrambled sentences. Half of the subjects were reading the stimuli, the other half listened to the stimuli. The resting state measurements consisted of 5 minutes eyes-open for the MEG and 7 minutes eyes-closed for fMRI. The neuroimaging data, as well as the information about the experimental events are shared according to the Brain Imaging Data Structure (BIDS) format. This unprecedented neuroimaging language data collection allows for the investigation of various aspects of the neurobiological correlates of language. - 3D Genome Reconstruction from Partially Phased Hi-C Data
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2024-04) Cifuentes, Diego; Draisma, Jan; Henriksson, Oskar; Korchmaros, Annachiara; Kubjas, KaieThe 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses additional challenges compared to the better-studied haploid setting. With the help of techniques from algebraic geometry, we prove that a small amount of phased data is sufficient to ensure finite identifiability, both for noiseless and noisy data. In the light of these results, we propose a new 3D reconstruction method based on semidefinite programming, paired with numerical algebraic geometry and local optimization. The performance of this method is tested on several simulated datasets under different noise levels and with different amounts of phased data. We also apply it to a real dataset from mouse X chromosomes, and we are then able to recover previously known structural features. - 3D histopathological grading of osteochondral tissue using contrast-enhanced micro-computed tomography
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2017-10) Nieminen, H. J.; Gahunia, H. K.; Pritzker, K. P.H.; Ylitalo, Tuomo; Rieppo, L.; Karhula, S. S.; Lehenkari, P.; Hæggström, Edward; Saarakkala, S.Objective: Histopathological grading of osteochondral (OC) tissue is widely used in osteoarthritis (OA) research, and it is relatively common in post-surgery in vitro diagnostics. However, relying on thin tissue section, this approach includes a number of limitations, such as: (1) destructiveness, (2) sample processing artefacts, (3) 2D section does not represent spatial 3D structure and composition of the tissue, and (4) the final outcome is subjective. To overcome these limitations, we recently developed a contrast-enhanced μCT (CEμCT) imaging technique to visualize the collagenous extracellular matrix (ECM) of articular cartilage (AC). In the present study, we demonstrate that histopathological scoring of OC tissue from CEμCT is feasible. Moreover, we establish a new, semi-quantitative OA μCT grading system for OC tissue. Results: Pathological features were clearly visualized in AC and subchondral bone (SB) with μCT and verified with histology, as demonstrated with image atlases. Comparison of histopathological grades (OARSI or severity (0-3)) across the characterization approaches, CEμCT and histology, excellent (0.92, 95% CI = [0.84, 0.96], n = 30) or fair (0.50, 95% CI = [0.16, 0.74], n = 27) intra-class correlations (ICC), respectively. A new μCT grading system was successfully established which achieved an excellent cross-method (μCT vs histology) reader-to-reader intra-class correlation (0.78, 95% CI = [0.58, 0.89], n = 27). Conclusions: We demonstrated that histopathological information relevant to OA can reliably be obtained from CEμCT images. This new grading system could be used as a reference for 3D imaging and analysis techniques intended for volumetric evaluation of OA pathology in research and clinical applications. - 3D Mitochondria Instance Segmentation with Spatio-Temporal Transformers
A4 Artikkeli konferenssijulkaisussa(2023) Thawakar, Omkar; Anwer, Rao Muhammad; Laaksonen, Jorma; Reiner, Orly; Shah, Mubarak; Khan, Fahad ShahbazAccurate 3D mitochondria instance segmentation in electron microscopy (EM) is a challenging problem and serves as a prerequisite to empirically analyze their distributions and morphology. Most existing approaches employ 3D convolutions to obtain representative features. However, these convolution-based approaches struggle to effectively capture long-range dependencies in the volume mitochondria data, due to their limited local receptive field. To address this, we propose a hybrid encoder-decoder framework based on a split spatio-temporal attention module that efficiently computes spatial and temporal self-attentions in parallel, which are later fused through a deformable convolution. Further, we introduce a semantic foreground-background adversarial loss during training that aids in delineating the region of mitochondria instances from the background clutter. Our extensive experiments on three benchmarks, Lucchi, MitoEM-R and MitoEM-H, reveal the benefits of the proposed contributions achieving state-of-the-art results on all three datasets. Our code and models are available at https://github.com/OmkarThawakar/STT-UNET. - 3D morphometric analysis of calcified cartilage properties using micro-computed tomography
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2019-01-01) Kauppinen, S.; Karhula, S. S.; Thevenot, J.; Ylitalo, Tuomo; Rieppo, L.; Kestilä, I.; Haapea, M.; Hadjab, I.; Finnilä, M. A.; Quenneville, E.; Garon, M.; Gahunia, H. K.; Pritzker, K. P.H.; Buschmann, M. D.; Nieminen, H. J.Objective: Our aim is to establish methods for quantifying morphometric properties of calcified cartilage (CC) from micro-computed tomography (mu CT). Furthermore, we evaluated the feasibility of these methods in investigating relationships between osteoarthritis (OA), tidemark surface morphology and open subchondral channels (OSCCs). Method: Samples (n = 15) used in this study were harvested from human lateral tibial plateau (n = 8). Conventional roughness and parameters assessing local 3-dimensional (3D) surface variations were used to quantify the surface morphology of the CC. Subchondral channel properties (percentage, density, size) were also calculated. As a reference, histological sections were evaluated using Histopathological osteoarthritis grading (OARSI) and thickness of CC and subchondral bone (SCB) was quantified. Results: OARSI grade correlated with a decrease in local 3D variations of the tidemark surface (amount of different surface patterns (r(s) = -0.600, P = 0.018), entropy of patterns (EP) (r(s) = -0.648, P = 0.018), homogeneity index (HI) (r(s) = 0.555, P = 0.032)) and tidemark roughness (TMR) (r(s) = -0.579, P = 0.024). Amount of different patterns (ADP) and EP associated with channel area fraction (CAF) (r(p) = 0.876, P <0.0001; r(p) = 0.665, P = 0.007, respectively) and channel density (CD) (r(p) = 0.680, P = 0.011; r(p) = 0.582, P = 0.023, respectively). TMR was associated with CAF (r(p) = 0.926, P <0.0001) and average channel size (r(p) = 0.574, P = 0.025). CC topography differed statistically significantly in early OA vs healthy samples. Conclusion: We introduced a mu-CT image method to quantify 3D CC topography and perforations through CC. CC topography was associated with OARSI grade and OSCC properties; this suggests that the established methods can detect topographical changes in tidemark and CC perforations associated with OA. (c) 2018 The Authors. Published by Elsevier Ltd on behalf of Osteoarthritis Research Society International. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). - 3He Universe 2020
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2021-01) Volovik, G. E.The latest news from 3He Universe are presented together with the extended map of the Universe. - 3PP-R: Enabling Natural Movement in 3rd Person Virtual Reality
A4 Artikkeli konferenssijulkaisussa(2020-11-02) Evin, Inan; Pesola, Toni; Kaos, Maximus; Takala, Tuukka M.; Hämäläinen, PerttuWe propose 3PP-R, a novel Virtual Reality display and interaction technique that allows natural movement in 3rd-person perspective (3PP), including body rotation without losing sight of the avatar. A virtual display such as a World-in-Miniature model orbits around the user when the user turns, but does not rotate except for the user’s avatar. From the user’s perspective, the display appears fixed in the field of vision, while the world rotates around the avatar. 3PP-R combines the strengths of 3PP and 1st-person perspective (1PP): Similar to 1PP, it allows interacting with rich natural movements, while also reaping the benefits of 3PP, i.e., superior spatial awareness and animating the avatar without nauseating viewpoint movement, e.g., for joystick-controlled locomotion. We test 3PP-R in a maze navigation study, which indicates considerably less cybersickness in 3PP-R than in 1PP. We also demonstrate 3PP-R in dynamic game interaction including running, jumping, swinging on bars, and martial arts. - 4D and 5D phase-space tomography using slowing-down physics regularization
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2023-07) Schmidt, B. S.; Salewski, M.; Moseev, D.; Baquero-Ruiz, M.; Hansen, P. C.; Eriksson, J.; Ford, O.; Gorini, G.; Järleblad, H.; Kazakov, Ye O.; Kulla, D.; Lazerson, S.; Mencke, J. E.; Mykytchuk, D.; Nocente, M.; Poloskei, P.; Rud, M.; Snicker, A.; Stagner, L.; Äkäslompolo, S.; , W7-X TeamWe compute reconstructions of 4D and 5D fast-ion phase-space distribution functions in fusion plasmas from synthetic projections of these functions. The fast-ion phase-space distribution functions originating from neutral beam injection (NBI) at TCV and Wendelstein 7-X (W7-X) at full, half, and one-third injection energies can be distinguished and particle densities of each component inferred based on 20 synthetic spectra of projected velocities at TCV and 680 at W7-X. Further, we demonstrate that an expansion into a basis of slowing-down distribution functions is equivalent to regularization using slowing-down physics as prior information. Using this technique in a Tikhonov formulation, we infer the particle density fractions for each NBI energy for each NBI beam from synthetic measurements, resulting in six unknowns at TCV and 24 unknowns at W7-X. Additionally, we show that installing 40 LOS in each of 17 ports at W7-X, providing full beam coverage and almost full angle coverage, produces the highest quality reconstructions. - A-site deficient semiconductor electrolyte Sr1−xCoxFeO3−δ for low-temperature (450-550 °C) solid oxide fuel cells
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2022-08-30) Lu, Yuzheng; Yousaf Shah, M. A.K.; Mushtaq, Naveed; Yousaf, Muhammad; Lund, Peter D.; Zhu, Bin; Asghar, Muhammad ImranFast ionic conduction at low operating temperatures is a key factor for the high electrochemical performance of solid oxide fuel cells (SOFCs). Here an A-site deficient semiconductor electrolyte Sr1−xCoxFeO3−δ is proposed for low-temperature solid oxide fuel cells (LT-SOFCs). A fuel cell with a structure of Ni/NCAL-Sr0.7Co0.3FeO3−δ-NCAL/Ni reached a promising performance of 771 mW cm−2 at 550 °C. Moreover, appropriate doping of cobalt at the A-site resulted in enhanced charge carrier transportation yielding an ionic conductivity of >0.1 S cm−1 at 550 °C. A high OCV of 1.05 V confirmed that neither short-circuiting nor power loss occurred during the operation of the prepared SOFC device. A modified composition of Sr0.5Co0.5FeO3−δ and Sr0.3Co0.7FeO3−δ also reached good fuel cell performance of 542 and 345 mW cm−2, respectively. The energy bandgap analysis confirmed optimal cobalt doping into the A-site of the prepared perovskite structure improved the charge transportation effect. Moreover, XPS spectra showed how the Co-doping into the A-site enhanced O-vacancies, which improve the transport of oxide ions. The present work shows that Sr0.7Co0.3FeO3−δ is a promising electrolyte for LT-SOFCs. Its performance can be boosted with Co-doping to tune the energy band structure. - AaltoNLP at SemEval-2022 Task 11: Ensembling Task-adaptive Pretrained Transformers for Multilingual Complex NER
A4 Artikkeli konferenssijulkaisussa(2022) Pietiläinen, Aapo; Ji, ShaoxiongThis paper presents the system description of team AaltoNLP for SemEval-2022 shared task 11: MultiCoNER. Transformer-based models have produced high scores on standard Named Entity Recognition (NER) tasks. However, accuracy on complex named entities is still low. Complex and ambiguous named entities have been identified as a major error source in NER tasks. The shared task is about multilingual complex named entity recognition. In this paper, we describe an ensemble approach, which increases accuracy across all tested languages. The system ensembles output from multiple same architecture task-adaptive pretrained transformers trained with different random seeds. We notice a large discrepancy between performance on development and test data. Model selection based on limited development data may not yield optimal results on large test data sets. - AATOS – A configurable tool for automatic annotation
A4 Artikkeli konferenssijulkaisussa(2017) Tamper, Minna; Leskinen, Petri; Ikkala, Esko; Oksanen, Arttu; Mäkelä, Eetu; Heino, Erkki; Tuominen, Jouni; Koho, Mikko; Hyvönen, EeroThis paper presents an automatic annotation tool AATOS for providing documents with semantic annotations. The tool links entities found from the texts to ontologies defined by the user. The application is highly configurable and can be used with different natural language Finnish texts. The application was developed as a part of the WarSampo (http://seco.cs.aalto.fi/projects/sotasampo/en/) and Semantic Finlex (http://seco.cs.aalto.fi/projects/lawlod/en/) projects and tested using Kansa Taisteli magazine articles and consolidated Finnish legislation of Semantic Finlex. The quality of the automatic annotation was evaluated by measuring precision and recall against existing manual annotations. The results showed that the quality of the input text, as well as the selection and configuration of the ontologies impacted the results. - Ab initio studies of stepped Pd surfaces with and without S
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2003) Makkonen, Ilja; Salo, Petri; Alatalo, Matti; Rahman, Talat S. - Ab initio study of Cu diffusion in α-cristobalite
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2012-11) Zelený, M.; Hegedüs, J.; Foster, A. S.; Drabold, D. A.; Elliott, S. R.; Nieminen, R. M.We have studied the geometries, formation energies, migration barriers and diffusion of a copper interstitial with different charge states with and without an external electric field in the α-cristobalite crystalline form of SiO2 using ab initio computer simulation. The most stable state almost throughout the band gap is charge q = + 1. The height of the migration barrier depends slightly on the charge state and varies between 0.11 and 0.18 eV. However, the charge has a strong influence on the shape of the barrier, as metastable states exist in the middle of the diffusion path for Cu with q = + 1. The heights and shapes of barriers also depend on the density of SiO 2, because volume expansion has a similar effect to increase the positive charge on Cu. Furthermore, diffusion coefficients have been deduced from our calculations according to transition-state theory and these calculations confirm the experimental result that oxidation of Cu is a necessary condition for diffusion. Our molecular dynamics simulations show a similar ion diffusion, and dependence on charge state. These simulations also confirm the fact that diffusion of ions can be directly simulated using ab initio molecular dynamics. - Ab initio study of oxygen point defects in GaAs, and AIN
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(1996) Mattila, T.; Nieminen, R.M.We have studied oxygen point defects with the plane-wave pseudopotential method in GaAs, GaN, and AlN. The calculations demonstrate a qualitatively different behavior of oxygen impurities in these materials. OAs in GaAs acts as a deep center with an off-center displacement and negative-U behavior, in agreement with the experimental data. ON in GaN is found to be a shallow donor with a low formation energy, and is suggested to act as a partial source for the unintentional n-type conductivity commonly observed in GaN. O in AlN is also found to easily substitute for N, which is consistent with the experimentally observed large oxygen concentrations in AlN. However, ON in AlN is shown to be a deep center due to the wide band gap, in contrast with ON in GaN. Our calculations thus predict that isolated oxygen acts as a DX-type center in AlxGa1−xN alloys. Results for other oxygen point defect configurations and for the dominant native defects are also presented. - Ab initio study of point-defects in CdF2
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(1997) Mattila, T.; Pöykkö, S.; Nieminen, R.M.The plane-wave pseudopotential method is used to study point defects in CdF2. We present comprehensive results for the native defects as well as for dominant impurities. In addition to Fi, VCd and OF were found to be easily formed compensating acceptors. For In and Ga impurities the experimentally observed large Stokes shift could not be established, and the results rule out symmetric atomic relaxation as the mechanism leading to the bistable behavior. The limitations of the present approach utilizing density-functional theory and the local-density approximation in the case of ionic materials are addressed.