Browsing by Subject "FREQUENCY"

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  • Brugnara, Y.; Auchmann, R.; Broennimann, S.; Allan, R. J.; Auer, I.; Barriendos, M.; Bergstrom, H.; Bhend, J.; Brazdil, R.; Compo, G. P.; Cornes, R. C.; Dominguez-Castro, F.; van Engelen, A. F. V.; Filipiak, J.; Holopainen, J.; Jourdain, S.; Kunz, M.; Luterbacher, J.; Maugeri, M.; Mercalli, L.; Moberg, A.; Mock, C. J.; Pichard, G.; Reznckova, L.; van der Schrier, G.; Slonosky, V.; Ustrnul, Z.; Valente, M. A.; Wypych, A.; Yin, X. (2015)
    The eruption of Mount Tambora (Indonesia) in April 1815 is the largest documented volcanic eruption in history. It is associated with a large global cooling during the following year, felt particularly in parts of Europe and North America, where the year 1816 became known as the "year without a summer". This paper describes an effort made to collect surface meteorological observations from the early instrumental period, with a focus on the years of and immediately following the eruption (1815-1817). Although the collection aimed in particular at pressure observations, correspondent temperature observations were also recovered. Some of the series had already been described in the literature, but a large part of the data, recently digitised from original weather diaries and contemporary magazines and newspapers, is presented here for the first time. The collection puts together more than 50 sub-daily series from land observatories in Europe and North America and from ships in the tropics. The pressure observations have been corrected for temperature and gravity and reduced to mean sea level. Moreover, an additional statistical correction was applied to take into account common error sources in mercury barometers. To assess the reliability of the corrected data set, the variance in the pressure observations is compared with modern climatologies, and single observations are used for synoptic analyses of three case studies in Europe. All raw observations will be made available to the scientific community in the International Surface Pressure Databank.
  • Nikolaev, Alexandre; Lehtonen, Minna; Higby, Eve; Hyun, JungMoon; Ashaie, Sameer (2018)
    The aim of the present study was to investigate whether the recognition speed of Finnish nominal base forms varies as a function of their paradigmatic complexity (stem allomorphy) or productivity status. Nikolaev et al. (2014) showed that words with greater stem allomorphy from an unproductive inflectional class arc recognized faster than words with lower stein allomorphy from a productive inflectional class. Productivity of an inflectional paradigm correlates with the number of stem allomorphs in languages like Finnish in that unproductive inflectional classes tend to have higher stem allomorphy. We wanted to distinguish which of these two characteristics provides the benefit to speed of recognition found by Nikolaev et al. (2014). The current study involved a lexical decision task comparing three categories of words: unproductive with three or more stem allomorphs, unproductive with two stem allomorphs, and productive with two stein allomorphs. We observed a facilitation effect for word recognition only for unproductive words with three or more stem allomorphs, but not for unproductive words with two allomorphs. This effect was observed particularly in words of low to moderate familiarity. The findings suggest that high stem allomorphy, rather than productivity of the inflectional class, is driving the facilitation effect in word recognition.
  • Van Horebeek, Lies; Hilven, Kelly; Mallants, Klara; Van Nieuwenhuijze, Annemarie; Kelkka, Tiina; Savola, Paula; Mustjoki, Satu; Schlenner, Susan M.; Liston, Adrian; Dubois, Benedicte; Goris, An (2019)
    The role of somatic variants in diseases beyond cancer is increasingly being recognized, with potential roles in autoinflammatory and autoimmune diseases. However, as mutation rates and allele fractions are lower, studies in these diseases are substantially less tolerant of false positives, and bio-informatics algorithms require high replication rates. We developed a pipeline combining two variant callers, MuTect2 and VarScan2, with technical filtering and prioritization. Our pipeline detects somatic variants with allele fractions as low as 0.5% and achieves a replication rate of > 55%. Validation in an independent data set demonstrates excellent performance (sensitivity > 57%, specificity > 98%, replication rate > 80%). We applied this pipeline to the autoimmune disease multiple sclerosis (MS) as a proof-of-principle. We demonstrate that 60% of MS patients carry 2-10 exonic somatic variants in their peripheral blood T and B cells, with the vast majority (80%) occurring in T cells and variants persisting over time. Synonymous variants significantly co-occur with non-synonymous variants. Systematic characterization indicates somatic variants are enriched for being novel or very rare in public databases of germline variants and trend towards being more damaging and conserved, as reflected by higher phred-scaled combined annotation-dependent depletion (CADD) and genomic evolutionary rate profiling (GERP) scores. Our pipeline and proof-of-principle now warrant further investigation of common somatic genetic variation on top of inherited genetic variation in the context of autoimmune disease, where it may offer subtle survival advantages to immune cells and contribute to the capacity of these cells to participate in the autoimmune reaction.
  • Kauppi, Jukka-Pekka; Pajula, Juha; Tohka, Jussi (2014)
    In the inter-subject correlation (ISC) based analysis of the functional magnetic resonance imaging (fMRI) data, the extent of shared processing across subjects during the experiment is determined by calculating correlation coefficients between the fMRI time series of the subjects in the corresponding brain locations. This implies that ISC can be used to analyze fMRI data without explicitly modeling the stimulus and thus ISC is a potential method to analyze fMRI data acquired under complex naturalistic stimuli. Despite of the suitability of ISC based approach to analyze complex fMRI data, no generic software tools have been made available for this purpose, limiting a widespread use of ISC based analysis techniques among neuroimaging community. In this paper, we present a graphical user interface (GUI) based software package, ISC Toolbox, implemented in Matlab for computing various ISC based analyses. Many advanced computations such as comparison of ISCs between different stimuli, time window ISC, and inter-subject phase synchronization are supported by the toolbox. The analyses are coupled with resampling based statistical inference. The ISC based analyses are data and computation intensive and the ISC toolbox is equipped with mechanisms to execute the parallel computations in a cluster environment automatically and with an automatic detection of the cluster environment in use. Currently, SGE-based (Oracle Grid Engine, Son of a Grid Engine, or Open Grid Scheduler) and Slurm environments are supported. In this paper, we present a detailed account on the methods behind the ISC Toolbox, the implementation of the toolbox and demonstrate the possible use of the toolbox by summarizing selected example applications. We also report the computation time experiments both using a single desktop computer and two grid environments demonstrating that parallelization effectively reduces the computing time.
  • Haider, Zahra; Larsson, Pär; Landfors, Mattias; Köhn, Linda; Schmiegelow, Kjeld; Flægstad, Trond; Kanerva, Jukka; Heyman, Mats; Hultdin, Magnus; Degerman, Sofie (2019)
    Classification of pediatric T-cell acute lymphoblastic leukemia (T-ALL) patients into CIMP (CpG Island Methylator Phenotype) subgroups has the potential to improve current risk stratification. To investigate the biology behind these CIMP subgroups, diagnostic samples from Nordic pediatric T-ALL patients were characterized by genome-wide methylation arrays, followed by targeted exome sequencing, telomere length measurement, and RNA sequencing. The CIMP subgroups did not correlate significantly with variations in epigenetic regulators. However, the CIMP+ subgroup, associated with better prognosis, showed indicators of longer replicative history, including shorter telomere length (P = 0.015) and older epigenetic (P <0.001) and mitotic age (P <0.001). Moreover, the CIMP+ subgroup had significantly higher expression of ANTP homeobox oncogenes, namely TLX3, HOXA9, HOXA10, and NKX2-1, and novel genes in T-ALL biology including PLCB4, PLXND1, and MYO18B. The CIMP- subgroup, with worse prognosis, was associated with higher expression of TAL1 along with frequent STIL-TAL1 fusions (2/40 in CIMP+ vs 11/24 in CIMP-), as well as stronger expression of BEX1. Altogether, our findings suggest different routes for leukemogenic transformation in the T-ALL CIMP subgroups, indicated by different replicative histories and distinct methylomic and transcriptomic profiles. These novel findings can lead to new therapeutic strategies.
  • Virtanen, Eunice; Nurmi, Tapio; Soder, Per-Osten; Airila-Mansson, Stella; Soder, Birgitta; Meurman, Jukka H. (2017)
    Background: Periodontal disease associates with systemic diseases but corresponding links regarding apical periodontitis (AP) are not so clear. Hence our aim was to study association between AP and the prevalence of systemic diseases in a study population from Sweden. Methods: The subjects were 150 patients from a randomly selected epidemiological sample of 1676 individuals. 120 accepted to participate and their basic and clinical examination data were available for these secondary analyses where dental radiographs were used to record signs for endodontic treatments and AP. Periapical Index and modified Total Dental Index scores were calculated from the x-rays to classify the severity of AP and dental infection burden, respectively. Demographic and hospital record data were collected from the Swedish National Statistics Center. T-test, chi-square and univariate analysis of covariance (ANCOVA) and regressions analyses were used for statistics. Results: Of the 120 patients 41% had AP and 61% had received endodontic treatments of which 52% were radiographically unsatisfactory. AP patients were older and half of them were smokers. AP and periodontitis often appeared in the same patient (32.5%). From all hospital diagnoses, cardiovascular diseases (CVD) were most common, showing 20.4% prevalence in AP patients. Regression analyses, controlled for age, gender, income, smoking and periodontitis, showed AP to associate with CVD with odds ratio 3.83 (95% confidence interval 1.18-12.40; p = 0.025). Conclusions: The results confirmed our hypothesis by showing that AP statistically associated with cardiovascular diseases. The finding that subjects with AP also often had periodontitis indicates an increased oral inflammatory burden.
  • Salonen, Anne H.; Kontto, Jukka; Perhoniemi, Riku; Alho, Hannu; Castren, Sari (2018)
    Background: Excessive expenditure and financial harms are core features of problem gambling. There are various forms of gambling and their nature varies. The aim was to measure gambling expenditure by game type while controlling for demographics and other gambling participation factors. A further aim was to find out how each game type was associated with gambling expenditure when the number of game types played is adjusted for. Methods: Using data from the 2015 Finnish Gambling survey on adult gamblers (n = 3555), multiple log-linear regression was used to examine the effects of demographics, gambling participation, and engaging in different game types on weekly gambling expenditure (WGE) and relative gambling expenditure (RGE). Background: Excessive expenditure and financial harms are core features of problem gambling. There are various forms of gambling and their nature varies. The aim was to measure gambling expenditure by game type while controlling for demographics and other gambling participation factors. A further aim was to find out how each game type was associated with gambling expenditure when the number of game types played is adjusted for. Conclusions: It seems that overall gambling frequency is the strongest indicator of high gambling expenditure. Our results showed that different game types had different effect sizes on gambling expenditure. Weekly gambling on horse races and non-monopoly games had the greatest increasing effect on expenditure. However, different game types also varied based on their popularity. The extent of potential harms caused by high expenditure therefore also varies on the population level. Based on our results, future prevention and harm minimization efforts should be tailored to different game types for greater effectiveness.
  • Roberts, Sean G.; Killin, Anton; Deb, Angarika; Sheard, Catherine; Greenhill, Simon J.; Sinnemäki, Kaius; Segovia Martín, José; Nölle, Jonas; Berdicevskis, Aleksandrs; Humphreys-Balkwill, Archie; Little, Hannah; Opie, Kit; Jacques, Guillaume; Bromham, Lindell; Tinits, Peeter; Ross, Robert M.; Lee, Sean; Gasser, Emily; Calladine, Jasmine; Spike, Matthew; Mann, Stephen; Shcherbakova, Olena; Singer, Ruth; Zhang, Shuya; Benítez-Burraco, Antonio; Kliesch, Christian; Thomas-Colquhoun, Ewan; Skirgård, Hedvig; Tamariz, Monica; Passmore, Sam; Pellard, Thomas; Jordan, Fiona (2020)
    Language is one of the most complex of human traits. There are many hypotheses about how it originated, what factors shaped its diversity, and what ongoing processes drive how it changes. We present the Causal Hypotheses in Evolutionary Linguistics Database (CHIELD, https://chield.excd.org/), a tool for expressing, exploring, and evaluating hypotheses. It allows researchers to integrate multiple theories into a coherent narrative, helping to design future research. We present design goals, a formal specification, and an implementation for this database. Source code is freely available for other fields to take advantage of this tool. Some initial results are presented, including identifying conflicts in theories about gossip and ritual, comparing hypotheses relating population size and morphological complexity, and an author relation network.
  • Rasouli, B.; Ahlqvist, E.; Alfredsson, L.; Andersson, T.; Carlsson, P.-O.; Groop, L.; Löfvenborg, J.E.; Martinell, M.; Rosengren, A.; Tuomi, T.; Wolk, A.; Carlsson, S. (2018)
    Aim. - Coffee consumption is inversely related to risk of type 2 diabetes (T2D). In contrast, an increased risk of latent autoimmune diabetes in adults (LADA) has been reported in heavy coffee consumers, primarily in a subgroup with stronger autoimmune characteristics. Our study aimed to investigate whether coffee consumption interacts with HLA genotypes in relation to risk of LADA. Methods. - This population-based study comprised incident cases of LADA (n = 484) and T2D (n = 1609), and also 885 healthy controls. Information on coffee consumption was collected by food frequency questionnaire. Odds ratios (ORs) with 95% CIs of diabetes were calculated and adjusted for age, gender, BMI, education level, smoking and alcohol intake. Potential interactions between coffee consumption and high-risk HLA genotypes were calculated by attributable proportion (AP) due to interaction. Results. - Coffee intake was positively associated with LADA in carriers of high-risk HLA genotypes (OR: 1.14 per cup/day, 95% CI: 1.02-1.28), whereas no association was observed in non-carriers (OR: 1.04, 95% CI: 0.93-1.17). Subjects with both heavy coffee consumption (>= 4 cups day) and high-risk HLA genotypes had an OR of 5.74 (95% Cl: 3.34-9.88) with an estimated AP of 0.36 (95% CI: 0.01-0.71; P = 0.04370). Conclusion. - Our findings suggest that coffee consumption interacts with HLA to promote LADA. (C) 2018 Elsevier Masson SAS. All rights reserved.
  • Gaudet, Mia M.; Kirchhoff, Tomas; Green, Todd; Vijai, Joseph; Korn, Joshua M.; Guiducci, Candace; Segre, Ayellet V.; McGee, Kate; McGuffog, Lesley; Kartsonaki, Christiana; Morrison, Jonathan; Healey, Sue; Sinilnikova, Olga M.; Stoppa-Lyonnet, Dominique; Mazoyer, Sylvie; Gauthier-Villars, Marion; Sobol, Hagay; Longy, Michel; Frenay, Marc; Hogervorst, Frans B. L.; Rookus, Matti A.; Collee, J. Margriet; Hoogerbrugge, Nicoline; van Roozendaal, Kees E. P.; Piedmonte, Marion; Rubinstein, Wendy; Nerenstone, Stacy; Van Le, Linda; Blank, Stephanie V.; Caldes, Trinidad; de la Hoya, Miguel; Nevanlinna, Heli; Aittomäki, Kristiina; Lazaro, Conxi; Blanco, Ignacio; Arason, Adalgeir; Johannsson, Oskar T.; Barkardottir, Rosa B.; Devilee, Peter; Olopade, Olofunmilayo I.; Neuhausen, Susan L.; Wang, Xianshu; Fredericksen, Zachary S.; Peterlongo, Paolo; Manoukian, Siranoush; Barile, Monica; Viel, Alessandra; Radice, Paolo; Phelan, Catherine M.; Narod, Steven; kConFab, OCGN, HEBON Study Collaborators, GEMO Study Collaborators (2010)
  • Kuusimäki, Tomi; Korpela, Jaana; Pekkonen, Eero; Martikainen, Mika H.; Antonini, Angelo; Kaasinen, Valtteri (2020)
    Deep brain stimulation (DBS) is an effective treatment for Parkinson's disease (PD) patients with motor fluctuations and dyskinesias. The key DBS efficacy studies were performed in PD patients with unknown genotypes; however, given the estimated monogenic mutation prevalence of approximately 5-10%, most commonly LRRK2, PRKN, PINK1 and SNCA, and risk-increasing genetic factors such as GBA, proper characterization is becoming increasingly relevant. We performed a systematic review of 46 studies that reported DBS effects in 221 genetic PD patients. The results suggest that monogenic PD patients have variable DBS benefit depending on the mutated gene. Outcome appears excellent in patients with the most common LRRK2 mutation, p.G2019S, and good in patients with PRKN mutations but poor in patients with the more rare LRRK2 p.R1441G mutation. The overall benefit of DBS in SNCA, GBA and LRRK2 p.T2031S mutations may be compromised due to rapid progression of cognitive and neuropsychiatric symptoms. In the presence of other mutations, the motor changes in DBS-treated monogenic PD patients appear comparable to those of the general PD population.
  • Unruptured Aneurysms SAH CDE; Hackenberg, Katharina A. M.; Algra, Ale; Salman, Rustam Al-Shahi; Frosen, Juhana; Hasan, David; Juvela, Seppo; Langer, David; Meyers, Philip; Morita, Akio (2019)
    IntroductionVariability in usage and definition of data characteristics in previous cohort studies on unruptured intracranial aneurysms (UIA) complicated pooling and proper interpretation of these data. The aim of the National Institute of Health/National Institute of Neurological Disorders and Stroke UIA and Subarachnoid Hemorrhage (SAH) Common Data Elements (CDE) Project was to provide a common structure for data collection in future research on UIA and SAH.MethodsThis paper describes the development and summarization of the recommendations of the working groups (WGs) on UIAs, which consisted of an international and multidisciplinary panel of cerebrovascular specialists on research and treatment of UIAs. Consensus recommendations were developed by review of previously published CDEs for other neurological diseases and the literature on UIAs. Recommendations for CDEs were classified by priority into Core,' SupplementalHighly Recommended,' Supplemental,' and Exploratory.'ResultsNinety-one CDEs were compiled; 69 were newly created and 22 were existing CDEs. The CDEs were assigned to eight subcategories and were classified as Core (8), SupplementalHighly Recommended (23), Supplemental (25), and Exploratory (35) elements. Additionally, the WG developed and agreed on a classification for aneurysm morphology.ConclusionThe proposed CDEs have been distilled from a broad pool of characteristics, measures, or outcomes. The usage of these CDEs will facilitate pooling of data from cohort studies or clinical trials on patients with UIAs.
  • Tšuiko, Olga; Dmitrijeva, Tuuli; Kask, Katrin; Tammur, Pille; Tõnisson, Neeme; Salumets, Andres; Jatsenko, Tatjana (2019)
    Balanced translocation carriers are burdened with fertility issues due to improper chromosome segregation in gametes, resulting in either implantation failure, miscarriage or birth of a child with chromosomal disorders. At the same time, these individuals are typically healthy with no signs of developmental problems, hence they often are unaware of their condition. Yet, because of difficulties in conceiving, balanced translocation carriers often turn to assisted reproduction, some of whom may also undergo preimplantation genetic testing for aneuploidy (PGT-A) to improve the likelihood of achieving a successful pregnancy.
  • Harju, Jarkko; Vehkaoja, Antti; Lindroos, Ville; Kumpulainen, Pekka; Liuhanen, Sasu; Yli-Hankala, Arvi; Oksala, Niku (2017)
    Alterations in arterial blood oxygen saturation, heart rate (HR), and respiratory rate (RR) are strongly associated with intra-hospital cardiac arrests and resuscitations. A wireless, easy-to-use, and comfortable method for monitoring these important clinical signs would be highly useful. We investigated whether the Nellcor (TM) OxiMask MAX-FAST forehead sensor could provide data for vital sign measurements when located at the distal forearm instead of its intended location at the forehead to provide improved comfortability and easy placement. In a prospective setting, we recruited 30 patients undergoing surgery requiring postoperative care. At the postoperative care unit, patients were monitored for two hours using a standard patient monitor and with a study device equipped with a Nellcor (TM) Forehead SpO(2) sensor. The readings were electronically recorded and compared in post hoc analysis using Bland-Altman plots, Spearman's correlation, and root-mean-square error (RMSE). Bland-Altman plot showed that saturation (SpO(2)) differed by a mean of -0.2 % points (SD, 4.6), with a patient-weighted Spearman's correlation (r) of 0.142, and an RMSE of 4.2 points. For HR measurements, the mean difference was 0.6 bpm (SD, 2.5), r = 0.997, and RMSE = 1.8. For RR, the mean difference was -0.5 1/min (4.1), r = 0.586, and RMSE = 4.0. The SpO(2) readings showed a low mean difference, but also a low correlation and high RMSE, indicating that the Nellcor (TM) saturation sensor cannot reliably assess oxygen saturation at the forearm when compared to finger PPG measurements.
  • Cardiomyopathy Myocarditis; Asselbergs, Folkert W.; Sammani, Arjan; Elliott, Perry; Heliö, Tiina; Charron, Philippe (2021)
    Aims Dilated cardiomyopathy (DCM) is a complex disease where genetics interplay with extrinsic factors. This study aims to compare the phenotype, management, and outcome of familial DCM (FDCM) and non-familial (sporadic) DCM (SDCM) across Europe. Methods and results Patients with DCM that were enrolled in the prospective ESC EORP Cardiomyopathy & Myocarditis Registry were included. Baseline characteristics, genetic testing, genetic yield, and outcome were analysed comparing FDCM and SDCM; 1260 adult patients were studied (238 FDCM, 707 SDCM, and 315 not disclosed). Patients with FDCM were younger (P <0.01), had less severe disease phenotype at presentation (P <0.02), more favourable baseline cardiovascular risk profiles (P Conclusions We observed that FDCM and SDCM have significant differences at baseline but similar short-term prognosis. Whether modification of associated cardiovascular risk factors provide opportunities for treatment remains to be investigated. Our results also show a prevalent role of genetics in FDCM and a non-marginal yield in SDCM although genetic testing is largely neglected in SDCM. Limited genetic testing and heterogeneity in panels provides a scaffold for improvement of guideline adherence.
  • Leppaaho, Eemeli; Renvall, Hanna; Salmela, Elina; Kere, Juha; Salmelin, Riitta; Kaski, Samuel (2019)
    Brain structure and many brain functions are known to be genetically controlled, but direct links between neuroimaging measures and their underlying cellular-level determinants remain largely undiscovered. Here, we adopt a novel computational method for examining potential similarities in high-dimensional brain imaging data between siblings. We examine oscillatory brain activity measured with magnetoencephalography (MEG) in 201 healthy siblings and apply Bayesian reduced-rank regression to extract a low-dimensional representation of familial features in the participants' spectral power structure. Our results show that the structure of the overall spectral power at 1-90Hz is a highly conspicuous feature that not only relates siblings to each other but also has very high consistency within participants' own data, irrespective of the exact experimental state of the participant. The analysis is extended by seeking genetic associations for low-dimensional descriptions of the oscillatory brain activity. The observed variability in the MEG spectral power structure was associated with SDK1 (sidekick cell adhesion molecule 1) and suggestively with several other genes that function, for example, in brain development. The current results highlight the potential of sophisticated computational methods in combining molecular and neuroimaging levels for exploring brain functions, even for high-dimensional data limited to a few hundred participants.
  • Surendran, Praveen; Feofanova, Elena; Lahrouchi, Najim; Ntalla, Ioanna; Karthikeyan, Savita; Cook, James; Chen, Lingyan; Mifsud, Borbala; Yao, Chen; Kraja, Aldi T.; Cartwright, James H.; Hellwege, Jacklyn N.; Giri, Ayush; Tragante, Vinicius; Thorleifsson, Gudmar; Liu, Dajiang J.; Prins, Bram P.; Stewart, Isobel D.; Cabrera, Claudia P.; Eales, James M.; Akbarov, Artur; Auer, Paul L.; Bielak, Lawrence F.; Bis, Joshua C.; Braithwaite, Vickie S.; Brody, Jennifer A.; Daw, E. Warwick; Warren, Helen R.; Drenos, Fotios; Nielsen, Sune Fallgaard; Faul, Jessica D.; Fauman, Eric B.; Fava, Cristiano; Ferreira, Teresa; Foley, Christopher N.; Franceschini, Nora; Gao, He; Giannakopoulou, Olga; Giulianini, Franco; Gudbjartsson, Daniel F.; Guo, Xiuqing; Harris, Sarah E.; Havulinna, Aki S.; Helgadottir, Anna; Huffman, Jennifer E.; Hwang, Shih-Jen; Kanoni, Stavroula; Kontto, Jukka; Larson, Martin G.; Li-Gao, Ruifang; Lindström, Jaana; Lotta, Luca A.; Lu, Yingchang; Luan, Jian'an; Mahajan, Anubha; Malerba, Giovanni; Masca, Nicholas G. D.; Mei, Hao; Menni, Cristina; Mook-Kanamori, Dennis O.; Mosen-Ansorena, David; Muller-Nurasyid, Martina; Pare, Guillaume; Paul, Dirk S.; Perola, Markus; Poveda, Alaitz; Rauramaa, Rainer; Richard, Melissa; Richardson, Tom G.; Sepulveda, Nuno; Sim, Xueling; Smith, Albert; Smith, Jennifer A.; Staley, James R.; Stanakova, Alena; Sulem, Patrick; Theriault, Sebastien; Thorsteinsdottir, Unnur; Trompet, Stella; Varga, Tibor V.; Edwards, Digna R. Velez; Veronesi, Giovanni; Weiss, Stefan; Willems, Sara M.; Yao, Jie; Young, Robin; Yu, Bing; Zhang, Weihua; Zhao, Jing-Hua; Zhao, Wei; Zhao, Wei; Evangelou, Evangelos; Aeschbacher, Stefanie; Asllanaj, Eralda; Blankenberg, Stefan; Bonnycastle, Lori L.; Bork-Jensen, Jette; Brandslund, Ivan; Braund, Peter S.; Burgess, Stephen; Cho, Kelly; Christensen, Cramer; Connell, John; de Mutsert, Renee; Dominiczak, Anna F.; Dorr, Marcus; Eiriksdottir, Gudny; Farmaki, Aliki-Eleni; Gaziano, J. Michael; Grarup, Niels; Grove, Megan L.; Hallmans, Goran; Hansen, Torben; Have, Christian T.; Heiss, Gerardo; Jorgensen, Marit E.; Jousilahti, Pekka; Kajantie, Eero; Kamat, Mihir; Karajamaki, AnneMari; Karpe, Fredrik; Koistinen, Heikki A.; Kovesdy, Csaba P.; Kuulasmaa, Kari; Laatikainen, Tiina; Lannfelt, Lars; Lee, I-Te; Lee, Wen-Jane; Linneberg, Allan; Martin, Lisa W.; Moitry, Marie; Nadkarni, Girish; Neville, Matt J.; Palmer, Colin N. A.; Papanicolaou, George J.; Pedersen, Oluf; Peters, James; Poulter, Neil; Rasheed, Asif; Rasmussen, Katrine L.; Rayner, N. William; Magi, Reedik; Renstrom, Frida; Rettig, Rainer; Rossouw, Jacques; Schreiner, Pamela J.; Sever, Peter S.; Sigurdsson, Emil L.; Skaaby, Tea; Sun, Yan; Sundstrom, Johan; Thorgeirsson, Gudmundur; Esko, Tonu; Trabetti, Elisabetta; Tsao, Philip S.; Tuomi, Tiinamaija; Turner, Stephen T.; Tzoulaki, Ioanna; Vaartjes, Ilonca; Vergnaud, Anne-Claire; Willer, Cristen J.; Wilson, Peter W. F.; Witte, Daniel R.; Yonova-Doing, Ekaterina; Zhang, He; Aliya, Naheed; Almgren, Peter; Amouyel, Philippe; Asselbergs, Folkert W.; Barnes, Michael R.; Blakemore, Alexandra; Boehnke, Michael; Bots, Michiel L.; Bottinger, Erwin P.; Buring, Julie E.; Chambers, John C.; Chen, Yii-Der Ida; Chowdhury, Rajiv; Conen, David; Correa, Adolfo; Smith, George Davey; de Boer, Rudolf A.; Deary, Ian J.; Dedoussis, George; Deloukas, Panos; Di Angelantonio, Emanuele; Elliott, Paul; Felix, Stephan B.; Ferrieres, Jean; Ford, Ian; Fornage, Myriam; Franks, Paul W.; Franks, Stephen; Frossard, Philippe; Gambaro, Giovanni; Gaunt, Tom R.; Groop, Leif; Gudnason, Vilmundur; Harris, Tamara B.; Hayward, Caroline; Hennig, Branwen J.; Herzig, Karl-Heinz; Ingelsson, Erik; Tuomilehto, Jaakko; Jarvelin, Marjo-Riitta; Jukema, J. Wouter; Kardia, Sharon L. R.; Kee, Frank; Kooner, Jaspal S.; Kooperberg, Charles; Launer, Lenore J.; Lind, Lars; Loos, Ruth J. F.; Majumder, Abdulla Al Shafi; Laakso, Markku; McCarthy, Mark; Melander, Olle; Mohlke, Karen L.; Murray, Alison D.; Nordestgaard, Borge Gronne; Orho-Melander, Marju; Packard, Chris J.; Padmanabhan, Sandosh; Palmas, Walter; Polasek, Ozren; Porteous, David J.; Prentice, Andrew M.; Province, Michael A.; Relton, Caroline L.; Rice, Kenneth; Ridker, Paul M.; Rolandsson, Olov; Rosendaal, Frits R.; Rotter, Jerome; Rudan, Igor; Salomaa, Veikko; Samani, Nilesh J.; Sattar, Naveed; Sheu, Wayne H-H; Smith, Blair H.; Soranzo, Nicole; Spector, Timothy D.; Starr, John M.; Sebert, Sylvain; Taylor, Kent D.; Lakka, Timo A.; Timpson, Nicholas J.; Tobin, Martin D.; van der Harst, Pim; van der Meer, Peter; Ramachandran, Vasan S.; Verweij, Niek; Virtamo, Jarmo; Volker, Uwe; Weir, David R.; Zeggini, Eleftheria; Charchar, Fadi J.; Wareham, Nicholas J.; Langenberg, Claudia; Tomaszewski, Maciej; Butterworth, Adam S.; Caulfield, Mark J.; Danesh, John; Edwards, Todd L.; Holm, Hilma; Hung, Adriana M.; Lindgren, Cecilia M.; Liu, Chunyu; Manning, Alisa K.; Morris, Andrew P.; Morrison, Alanna C.; O'Donnell, Christopher J.; Psaty, Bruce M.; Saleheen, Danish; Stefansson, Kari; Boerwinkle, Eric; Chasman, Daniel; Levy, Daniel; Newton-Cheh, Christopher; Munroe, Patricia B.; Howson, Joanna M. M. (2020)
    Genetic studies of blood pressure (BP) to date have mainly analyzed common variants (minor allele frequency > 0.05). In a meta-analysis of up to similar to 1.3 million participants, we discovered 106 new BP-associated genomic regions and 87 rare (minor allele frequency
  • Huang, Gwo-Jong; Bringi, Viswanathan N.; Newman, Andrew J.; Lee, Gyuwon; Moisseev, Dmitri; Notaros, Branislav M. (2019)
    Quantitative precipitation estimation (QPE) of snowfall has generally been expressed in power-law form between equivalent radar reflectivity factor (Z(e)) and liquid equivalent snow rate (SR). It is known that there is large variability in the prefactor of the power law due to changes in particle size distribution (PSD), density, and fall velocity, whereas the variability of the exponent is considerably smaller. The dual-wavelength radar reflectivity ratio (DWR) technique can improve SR accuracy by estimating one of the PSD parameters (characteristic diameter), thus reducing the variability due to the prefactor. The two frequencies commonly used in dual-wavelength techniques are Ku- and Kabands. The basic idea of DWR is that the snow particle size-to-wavelength ratio is falls in the Rayleigh region at Ku-band but in the Mie region at Ka-band. We propose a method for snow rate estimation by using NASA D3R radar DWR and Ka-band reflectivity observations collected during a long-duration synoptic snow event on 30-31 January 2012 during the GCPEx (GPM Cold-season Precipitation Experiment). Since the particle mass can be estimated using 2-D video disdrometer (2DVD) fall speed data and hydrodynamic theory, we simulate the DWR and compare it directly with D3R radar measurements. We also use the 2DVD-based mass to compute the 2DVD-based SR. Using three different mass estimation methods, we arrive at three respective sets of Z-SR and SR(Z(h), DWR) relationships. We then use these relationships with D3R measurements to compute radar-based SR. Finally, we validate our method by comparing the D3R radar-retrieved SR with accumulated SR directly measured by a well-shielded Pluvio gauge for the entire synoptic event.
  • Kazakov, Ye. O.; Alcator C-Mod Team; JET Contributors; Ahlgren, Tommy Juha; Aho-Mantila, L.; Airila, M.; Asunta, O.; Björkas, Carolina Maria Isabel; Groth, M.; Hakola, A.; Järvinen, A.; Karhunen, J.; Koivuranta, S.; Lahtinen, Aki Alvar; Lasa Esquisabel, Ane; Nordlund, Kai Henrik; Safi, Elnaz (2017)
    We describe a new technique for the efficient generation of high-energy ions with electromagnetic ion cyclotron waves in multi-ion plasmas. The discussed three-ion scenarios are especially suited for strong wave absorption by a very low number of resonant ions. To observe this effect, the plasma composition has to be properly adjusted, as prescribed by theory. We demonstrate the potential of the method on the world-largest plasma magnetic confinement device, JET (Joint European Torus, Culham, UK), and the high-magnetic-field tokamak Alcator C-Mod (Cambridge, USA). The obtained results demonstrate efficient acceleration of He-3 ions to high energies in dedicated hydrogendeuterium mixtures. Simultaneously, effective plasma heating is observed, as a result of the slowing-down of the fast He-3 ions. The developed technique is not only limited to laboratory plasmas, but can also be applied to explain observations of energetic ions in space-plasma environments, in particular, He-3-rich solar flares.
  • Porkka, Noora; Lahtinen, Laura; Ahtiainen, Maarit; Böhm, Jan P.; Kuopio, Teijo; Eldfors, Samuli; Mecklin, Jukka-Pekka; Seppälä, Toni T.; Peltomäki, Päivi (2019)
    Colorectal carcinomas that are mismatch repair (MMR)-deficient in the absence of MLH1 promoter methylation or germline mutations represent Lynch-like syndrome (LLS). Double somatic events inactivating MMR genes are involved in the etiology of LLS tumors. Our purpose was to define the clinical and broader molecular hallmarks of LLS tumors and the population incidence of LLS, which remain poorly characterized. We investigated 762 consecutive colorectal carcinomas operated in Central Finland in 2000-2010. LLS cases were identified by a stepwise protocol based on MMR protein expression, MLH1 methylation and MMR gene mutation status. LLS tumors were profiled for CpG Island Methylator Phenotype (CIMP) and somatic mutations in 578 cancer-relevant genes. Among 107 MMR-deficient tumors, 81 (76%) were attributable to MLH1 promoter methylation and 9 (8%) to germline mutations (Lynch syndrome, LS), leaving 14 LLS cases (13%) (3 remained unclassified). LLS carcinomas were diagnosed at a mean age of 65 years (vs. 44 years in LS, p <0.001), had a proximal to distal ratio of 1:1, and all were BRAF V600E-negative. Two somatic events in MMR genes were identifiable in 11 tumors (79%). As novel findings, the tumors contained an average of 31 nonsynonymous somatic mutations/Mb and 13/14 were CIMP-positive. In conclusion, we establish the epidemiological, clinical and molecular characteristics of LLS in a population-based study design. Significantly more frequent CIMP-positivity and lower rates of somatic mutations make a distinction to LS. The absence of BRAF V600E mutation separates LLS colorectal carcinomas from MLH1-methylated colorectal carcinomas with CIMP-positive phenotype.