Browsing by Subject "TESTS"

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  • Prokic, Ivana; Lahousse, Lies; de Vries, Maaike; Liu, Jun; Kalaoja, Marita; Vonk, Judith M.; van der Plaat, Diana A.; van Diemen, Cleo C.; van der Spek, Ashley; Zhernakova, Alexandra; Fu, Jingyuan; Ghanbari, Mohsen; Ala-Korpela, Mika; Kettunen, Johannes; Havulinna, Aki S.; Perola, Markus; Salomaa, Veikko; Lind, Lars; Arnlov, Johan; Stricker, Bruno H. C.; Brusselle, Guy G.; Boezen, H. Marike; van Duijn, Cornelia M.; Amin, Najaf (2020)
    Background Chronic obstructive pulmonary disease (COPD) is a common lung disorder characterized by persistent and progressive airflow limitation as well as systemic changes. Metabolic changes in blood may help detect COPD in an earlier stage and predict prognosis. Methods We conducted a comprehensive study of circulating metabolites, measured by proton Nuclear Magnetic Resonance Spectroscopy, in relation with COPD and lung function. The discovery sample consisted of 5557 individuals from two large population-based studies in the Netherlands, the Rotterdam Study and the Erasmus Rucphen Family study. Significant findings were replicated in 12,205 individuals from the Lifelines-DEEP study, FINRISK and the Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) studies. For replicated metabolites further investigation of causality was performed, utilizing genetics in the Mendelian randomization approach. Results There were 602 cases of COPD and 4955 controls used in the discovery meta-analysis. Our logistic regression results showed that higher levels of plasma Glycoprotein acetyls (GlycA) are significantly associated with COPD (OR = 1.16,P = 5.6 x 10(- 4)in the discovery and OR = 1.30,P = 1.8 x 10(- 6)in the replication sample). A bi-directional two-sample Mendelian randomization analysis suggested that circulating blood GlycA is not causally related to COPD, but that COPD causally increases GlycA levels. Using the prospective data of the same sample of Rotterdam Study in Cox-regression, we show that the circulating GlycA level is a predictive biomarker of COPD incidence (HR = 1.99, 95%CI 1.52-2.60, comparing those in the highest and lowest quartile of GlycA) but is not significantly associated with mortality in COPD patients (HR = 1.07, 95%CI 0.94-1.20). Conclusions Our study shows that circulating blood GlycA is a biomarker of early COPD pathology.
  • Kyrgiou, Maria; Arbyn, Marc; Bergeron, Christine; Bosch, F. Xavier; Dillner, Joakim; Jit, Mark; Kim, Jane; Poljak, Mario; Nieminen, Pekka; Sasieni, Peter; Kesic, Vesna; Cuzick, Jack; Gultekin, Murat (2020)
    This paper summarises the position of ESGO and EFC on cervical screening based on existing guidelines and opinions of a team of lead experts. HPV test is replacing cytology as this offers greater protection against cervical cancer and allows longer screening intervals. Only a dozen of HPV tests are considered as clinically validated for screening. The lower specificity of HPV test dictates the use of triage tests that can select women for colposcopy. Reflex cytology is currently the only well validated triage test; HPV genotyping and p16 immunostaining may be used in the future, although methylation assays and viral load also look promising. A summary of quality assurance benchmarks is provided, and the importance to audit the screening histories of women who developed cancer is noted as a key objective. HPV-based screening is more cost-effective than cytology or cotesting. HPV-based screening should continue in the post-vaccination era. Only a fraction of the female population is vaccinated, and this varies across countries. A major challenge will be to personalise screening frequency according to vaccination status. Still the most important factor for successful prevention by screening is high population coverage and organised screening. Screening with self-sampling to reach under-screened women is promising.
  • Roettenbacher, Rachael M.; Monnier, John D.; Korhonen, Heidi; Harmon, Robert O.; Baron, Fabien; Hackman, Thomas; Henry, Gregory W.; Schaefer, Gail H.; Strassmeier, Klaus G.; Weber, Michael; ten Brummelaar, Theo A. (2017)
    Nearby active stars with relatively rapid rotation and large starspot structures offer the opportunity to compare interferometric, spectroscopic, and photometric imaging techniques. In this paper, we image a spotted star with three different methods for the first time. The giant primary star of the RS Canum Venaticorum binary sigma. Geminorum (sigma Gem) was imaged for two epochs of interferometric, high-resolution spectroscopic, and photometric observations. The light curves from the reconstructions show good agreement with the observed light curves, supported by the longitudinally consistent spot features on the different maps. However, there is strong disagreement in the spot latitudes across the methods.
  • Toivonen, H T T; Onkamo, P; Vasko, K; Ollikainen, V; Sevon, P; Mannila, H; Herr, M; Kere, J (2000)
  • Gasbarra, Dario; Pajevic, Sinisa; Basser, Peter J. (2017)
    Tensor-valued and matrix-valued measurements of different physical properties are increasingly available in material sciences and medical imaging applications. The eigenvalues and eigenvectors of such multivariate data provide novel and unique information, but at the cost of requiring a more complex statistical analysis. In this work we derive the distributions of eigenvalues and eigenvectors in the special but important case of m x m symmetric random matrices, D, observed with isotropic matrix-variate Gaussian noise. The properties of these distributions depend strongly on the symmetries of the mean tensor/matrix, (D) over bar. When (D) over bar has repeated eigenvalues, the eigenvalues of D are not asymptotically Gaussian, and repulsion is observed between the eigenvalues corresponding to the same (D) over bar eigenspaces. We apply these results to diffusion tensor imaging (DTI), with m = 3, addressing an important problem of detecting the symmetries of the diffusion tensor, and seeking an experimental design that could potentially yield an isotropic Gaussian distribution. In the 3-dimensional case, when the mean tensor is spherically symmetric and the noise is Gaussian and isotropic, the asymptotic distribution of the first three eigenvalue central moment statistics is simple and can be used to test for isotropy. In order to apply such tests, we use quadrature rules of order t >= 4 with constant weights on the unit sphere to design a DTI-experiment with the property that isotropy of the underlying true tensor implies isotropy of the Fisher information. We also explain the potential implications of the methods using simulated DTI data with a Rician noise model.
  • Määttänen, Ilmari; Makkonen, Emilia; Jokela, Markus; Närväinen, Johanna; Väliaho, Julius; Seppälä, Vilja; Kylmälä, Julia; Henttonen, Pentti (2021)
    The aim was to create and study a possible behavioural measure for trait(s) in humans that reflect the ability and motivation to continue an unpleasant behaviour, i.e., behavioural perseverance or persistence (BP). We utilised six different tasks with 54 subjects to measure the possible BP trait(s): cold pressor task, hand grip endurance task, impossible anagram task, impossible verbal reasoning task, thread and needle task, and boring video task. The task performances formed two BP factors. Together, the two-factor solution is responsible for the common variance constituting 37.3% of the total variance in the performances i.e., performance times. Excluding the impossible anagram task, the performance in any given task was better explained by performances in the other tasks (i.e., “trait”, η2 range = 0.131–0.253) than by the rank order variable (“depletion”, i.e., getting tired from the previous tasks, η2 range = 0–0.096).
  • Goharipour, Muhammad; Khanpour, Hamzeh; Guzey, Vadim (2018)
    We present GKG18-DPDFs, a next-to-leading order (NLO) QCD analysis of diffractive parton distribution functions (diffractive PDFs) and their uncertainties. This is the first global set of diffractive PDFs determined within the xFitter framework. This analysis is motivated by all available and most up-to-date data on inclusive diffractive deep inelastic scattering (diffractive DIS). Heavy quark contributions are considered within the framework of the Thorne-Roberts (TR) general mass variable flavor number scheme (GM-VFNS). We form a mutually consistent set of diffractive PDFs due to the inclusion of high-precision data from H1/ZEUS combined inclusive diffractive cross sections measurements. We study the impact of the H1/ZEUS combined data by producing a variety of determinations based on reduced data sets. We find that these data sets have a significant impact on the diffractive PDFs with some substantial reductions in uncertainties. The predictions based on the extracted diffractive PDFs are compared to the analyzed diffractive DIS data and with other determinations of the diffractive PDFs.
  • Koskenpato, Katja; Lehikoinen, Aleksi; Lindstedt, Carita; Karell, Patrik (2020)
    Camouflage may promote fitness of given phenotypes in different environments. The tawny owl (Strix aluco) is a color polymorphic species with a gray and brown morph resident in the Western Palearctic. A strong selection pressure against the brown morph during snowy and cold winters has been documented earlier, but the selection mechanisms remain unresolved. Here, we hypothesize that selection favors the gray morph because it is better camouflaged against predators and mobbers in snowy conditions compared to the brown one. We conducted an online citizen science experiment where volunteers were asked to locate a gray or a brown tawny owl specimen from pictures taken in snowy and snowless landscapes. Our results show that the gray morph in snowy landscapes is the hardest to detect whereas the brown morph in snowy landscapes is the easiest to detect. With an avian vision model, we show that, similar to human perceivers, the brown morph is more conspicuous than the gray against coniferous tree trunks for a mobbing passerine. We suggest that with better camouflage, the gray morph may avoid mobbers and predators more efficiently than the brown morph and thus survive better in snowy environments. As winters are getting milder and shorter in the species range, the selection periods against brown coloration may eventually disappear or shift poleward.
  • Lassmann-Klee, Paul G.; Sundblad, Britt-Marie; Malmberg, Leo P.; Sovijarvi, Anssi R. A.; Piirilä, Päivi (2020)
    Clinical testing of bronchial hyperreactivity (BHR) provides valuable information in asthma diagnostics. Nevertheless, the test results depend to a great extent on the testing procedure: test substance, apparatus and protocol. In Nordic countries, three protocols predominate in the testing field: Per Malmberg, Nieminen and Sovijarvi methods. However, knowledge of their equivalence is limited. We aimed to find equivalent provocative doses (PD) to obtain similar bronchoconstrictive responses for the three protocols. We recruited 31 patients with suspected asthma and health care workers and performed BHR testing with methacholine according to Malmberg and Nieminen methods, and with histamine according to Sovijarvi. We obtained the individual response-dose slopes for each method and predicted equivalent PD values. Applying a mixed-model, we found significant differences in the mean (standard error of mean) response-dose (forced expiratory volume in one second (FEV1)%/mg): Sovijarvi 7.2 (1.5), Nieminen 13.8 (4.2) and Malmberg 26 (7.3). We found that the earlier reported cut-point values for moderate BHR and marked BHR between the Sovijarvi (PD15) and Nieminen (PD20) methods were similar, but with the Malmberg method a significant bronchoconstrictive reaction was measured with lower PD20 values. We obtained a relationship between slope values and PD (mg) between different methods, useful in epidemiological research and clinical practice.
  • He, Siwen; Soininen, Janne; Deng, Guiping; Wang, Beixin (2020)
    A major challenge in community ecology is to understand the underlying factors driving metacommunity (i.e., a set of local communities connected through species dispersal) dynamics. However, little is known about the effects of varying spatial scale on the relative importance of environmental and spatial (i.e., dispersal related) factors in shaping metacommunities and on the relevance of different dispersal pathways. Using a hierarchy of insect metacommunities at three spatial scales (a small, within-stream scale, intermediate, among-stream scale, and large, among-sub-basin scale), we assessed whether the relative importance of environmental and spatial factors shaping metacommunity structure varies predictably across spatial scales, and tested how the importance of different dispersal routes vary across spatial scales. We also studied if different dispersal ability groups differ in the balance between environmental and spatial control. Variation partitioning showed that environmental factors relative to spatial factors were more important for community composition at the within-stream scale. In contrast, spatial factors (i.e., eigenvectors from Moran's eigenvector maps) relative to environmental factors were more important at the among-sub-basin scale. These results indicate that environmental filtering is likely to be more important at the smallest scale with highest connectivity, while dispersal limitation seems to be more important at the largest scale with lowest connectivity. Community variation at the among-stream and among-sub-basin scales were strongly explained by geographical and topographical distances, indicating that overland pathways might be the main dispersal route at the larger scales among more isolated sites. The relative effect of environmental and spatial factors on insect communities varied between low and high dispersal ability groups; this variation was inconsistent among three hierarchical scales. In sum, our study indicates that spatial scale, connectivity, and dispersal ability jointly shape stream metacommunities.
  • Kivelä, Jesper M.; Lempinen, Marko; Holmberg, Christer; Jalanko, Hannu; Pakarinen, Mikko P.; Isoniemi, Helena; Lauronen, Jouni (2019)
    It has been proposed that the liver protects the kidney in CLKT. However, few studies have examined long-term renal function after CLKT and contrasted renal function of CLKT patients to KT patients beyond one year after transplantation. We studied long-term renal function of CLKT patients and compared renal function of CLKT patients to KT patients between one and five years after transplantation. Patients who underwent CLKT between 1993 and 2011 were included (n = 34; 11 children and 23 adults). Ninety-six (27 children and 69 adults) KT patients were selected as controls. GFR was estimated (eGFR) and measured (mGFR) with Cr-51-EDTA clearance. Mean mGFR was 63 at one and 70 at ten years after pediatric CLKT. Mean eGFR was 75 at one and 50 at ten years after adult CLKT. Difference in mean mGFR between pediatric CLKT and KT patients was 8 (95% CI -7 to 23) and 11 (95% CI -4 to 26) at one and five years after transplantation, respectively. Difference in mean eGFR between adult CLKT and KT patients was 8 (95% CI -5 to 20) and 1 (95% CI -10 to 12) at one and five years after transplantation, respectively. Longitudinal changes in GFRs were somewhat similar in CLKT and KT patients in both age-groups but pediatric CLKT patients had on average higher GFRs than pediatric KT patients. In long-term follow-up, renal function remains stable in pediatric CLKT patients but declines in adult CLKT patients.
  • Pour-Aboughadareh, Alireza; Yousefian, Mohsen; Moradkhani, Hoda; Poczai, Péter; Siddique, Kadambot HM (2019)
    PREMISE OF THE STUDY: Access to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are determined by quantitative and qualitative traits. Genotype-by-environment interactions (GEI) occur for quantitative traits such as reproductive fitness, longevity, height, weight, yield, and disease resistance. The stability of genotypes across a range of environments can be analyzed using GEI analysis. GEI analysis includes univariate and multivariate analyses with both parametric and non-parametric models. METHODS AND RESULTS: The program STABILITYSOFT is online software based on JavaScript and R to calculate several univariate parametric and non-parametric statistics for various crop traits. These statistics include Plaisted and Peterson’s mean variance component (θi), Plaisted’s GE variance component (θ(i)), Wricke’s ecovalence stability index (Wi2), regression coefficient (bi), deviation from regression (Sdi2), Shukla’s stability variance (σi2), environmental coefficient of variance (CVi), Nassar and Huhn’s statistics (S(1), S(2)), Huhn’s equation (S(3) and S(6)), Thennarasu’s non-parametric statistics (NP(i)), and Kang’s rank-sum. These statistics are important in the identification of stable genotypes; hence, this program can compare and select genotypes across multiple environment trials for a given data set. This program supports both the repeated data across environments and matrix data types. The accuracy of the results obtained from this software was tested on several crop plants. CONCLUSIONS: This new software provides a user-friendly interface to estimate stability statistics accurately for plant scientists, agronomists, and breeders who deal with large volumes of quantitative data. This software can also show ranking patterns of genotypes and describe associations among different statistics with yield performance through a heat map plot. The software is available at
  • Lange, Alexander; Dalheimer, Bernhard; Herwartz, Helmut; Maxand, Simone (2021)
    Structural vector autoregressive (SVAR) models are frequently applied to trace the contemporaneous linkages among (macroeconomic) variables back to an interplay of orthogonal structural shocks. Under Gaussianity the structural parameters are unidentified without additional (often external and not data-based) information. In contrast, the often reasonable assumption of heteroskedastic and/or non-Gaussian model disturbances offers the possibility to identify unique structural shocks. We describe the R package svars which implements statistical identification techniques that can be both heteroskedasticity-based or independence-based. Moreover, it includes a rich variety of analysis tools that are well known in the SVAR literature. Next to a comprehensive review of the theoretical background, we provide a detailed description of the associated R functions. Furthermore, a macroeconomic application serves as a step-by-step guide on how to apply these functions to the identification and interpretation of structural VAR models.
  • Seoane, Pau Amaro; Sedda, Manuel Arca; Babak, Stanislav; Berry, Christopher P. L.; Berti, Emanuele; Bertone, Gianfranco; Blas, Diego; Bogdanovic, Tamara; Bonetti, Matteo; Breivik, Katelyn; Brito, Richard; Caldwell, Robert; Capelo, Pedro R.; Caprini, Chiara; Cardoso, Vitor; Carson, Zack; Chen, Hsin-Yu; Chua, Alvin J. K.; Dvorkin, Irina; Haiman, Zoltan; Heisenberg, Lavinia; Isi, Maximiliano; Karnesis, Nikolaos; Kavanagh, Bradley J.; Littenberg, Tyson B.; Mangiagli, Alberto; Marcoccia, Paolo; Maselli, Andrea; Nardini, Germano; Pani, Paolo; Peloso, Marco; Pieroni, Mauro; Ricciardone, Angelo; Sesana, Alberto; Tamanini, Nicola; Toubiana, Alexandre; Valiante, Rosa; Vretinaris, Stamatis; Weir, David J.; Yagi, Kent; Zimmerman, Aaron (2022)
    The science objectives of the LISA mission have been defined under the implicit assumption of a 4-years continuous data stream. Based on the performance of LISA Pathfinder, it is now expected that LISA will have a duty cycle of approximate to 0.75, which would reduce the effective span of usable data to 3 years. This paper reports the results of a study by the LISA Science Group, which was charged with assessing the additional science return of increasing the mission lifetime. We explore various observational scenarios to assess the impact of mission duration on the main science objectives of the mission. We find that the science investigations most affected by mission duration concern the search for seed black holes at cosmic dawn, as well as the study of stellar-origin black holes and of their formation channels via multi-band and multi-messenger observations. We conclude that an extension to 6 years of mission operations is recommended.
  • Dey, Lankeswar; Gopakumar, Achamveedu; Valtonen, Mauri; Zola, Stanislaw; Susobhanan, Abhimanyu; Hudec, Rene; Pihajoki, Pauli; Pursimo, Tapio; Berdyugin, Andrei; Piirola, Vilppu; Ciprini, Stefano; Nilsson, Kari; Jermak, Helen; Kidger, Mark; Komossa, Stefanie (2019)
    The bright blazar OJ 287 is the best-known candidate for hosting a nanohertz gravitational wave (GW) emitting supermassive binary black hole (SMBBH) in the present observable universe. The binary black hole (BBH) central engine model, proposed by Lehto and Valtonen in 1996, was influenced by the two distinct periodicities inferred from the optical light curve of OJ 287. The current improved model employs an accurate general relativistic description to track the trajectory of the secondary black hole (BH) which is crucial to predict the inherent impact flares of OJ 287. The successful observations of three predicted impact flares open up the possibility of using this BBH system to test general relativity in a hitherto unexplored strong field regime. Additionally, we briefly describe an ongoing effort to interpret observations of OJ 287 in a Bayesian framework.
  • Hyytinen, Heidi; Toom, Auli; Postareff, Liisa (2018)
    Critical thinking is a key capability for academic experts and for developing one’s expertise from the very beginning of studying at university. Self-efficacy beliefs and approaches to learning are important in this process, although their relationships with critical thinking are not clear. This study explores the relationship between critical thinking, approaches to learning and self-efficacy beliefs among Finnish first-year students in educational sciences (n=92). The self-reported data were used to measure approaches to learning and self-efficacy beliefs, and performance-based assessment data of critical thinking skills were analysed by using both quantitative and qualitative procedures. The results showed that most of the new students applied the deep approach to learning and had high self-efficacy beliefs related to learning. However, there were great differences in the quality of their critical thinking. Three groups with remarkable differences in critical thinking skills were detected. There were no connections between critical thinking, approaches to learning and self-efficacy beliefs. The results imply that the development of critical thinking needs to be facilitated systematically during study at university.
  • Sirkka, Jani; Parviainen, Marita; Jyrkkänen, Henna-Kaisa; Koivisto, Anne M.; Säisänen, Laura; Rauramaa, Tuomas; Leinonen, Ville; Danner, Nils (2021)
    Background Idiopathic normal pressure hydrocephalus (iNPH) is a neurodegenerative disease with a characteristic symptom triad of gait disturbance, cognitive decline, and incontinence. Recently, also dysfunctions in upper limbs have been described in iNPH and reported to improve after shunt surgery. We aim to describe the role of upper limb motor function in the clinical assessment of iNPH patients and its influence on activities of daily living (ADL). Methods Seventy-five consecutive patients with probable iNPH were studied pre-operatively and at 3 and 12 months after shunt surgery. The pre-operative evaluation included lumbar drainage of cerebrospinal fluid (tap test). Motor functions were assessed in upper and lower limbs with Grooved Pegboard Test (GPT), Box & Block Test (BBT), Total Score of Gait (TSG), and balance test. ADL was assessed with Barthel's index and cognition in accordance with the Consortium to Establish a Registry for Alzheimer's Disease (CERAD). Results Patients showed improvement in all motor tests and ADL at 3 months after shunt surgery. The improvement remained stable during the 12-month post-operative follow-up. The motor function tests correlated with each other and with ADL. Conclusions A 3-month follow-up period after shunt surgery is adequate to show improvement in motor tasks, and a positive outcome will last for at least 12 months. A shunt-responsive dysfunction of upper limb motor performance plays a major role in ADL of iNPH patients. Therefore, we suggest an evaluation of upper limb motor performance to be included in routine evaluation of iNPH patients.