Articles from TUHAT CRIS

 

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This collection contains Open Access articles deposited from the University of Helsinki TUHAT CRIS

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  • Athukorala, Kumaripaba Miyurusara; Glowacka, Dorota; Jacucci, Giulio; Oulasvirta, Antti; Vreeken, Jilles (John Wiley & Sons Ltd., 2016)
    Exploratory search is an increasingly important activity yet challenging for users. Although there exists an ample amount of research into understanding exploration, most of the major information retrieval (IR) systems do not provide tailored and adaptive support for such tasks. One reason is the lack of empirical knowledge on how to distinguish exploratory and lookup search behaviors in IR systems. The goal of this paper is to investigate how to separate the two types of tasks in an IR system using easily measurable behaviors. In this paper, we first review characteristics of exploratory search behavior. We then report on a controlled study of six search tasks with three exploratory – comparison, knowledge acquisition, planning – and three lookup tasks – fact-finding, navigational, question answering. The results are encouraging, showing that IR systems can distinguish the two search categories in the course of a search session. The most distinctive indicators that characterize exploratory search behaviors are query length, maximum scroll depth, and task completion time. However, two tasks are borderline and exhibit mixed characteristics. We assess the applicability of this finding by reporting on several classification experiments. Our results have valuable implications for designing tailored and adaptive IR systems.
  • Lepola, Pirkko; Needham, Allison; Mendum, Jo; Sallabank, Peter; Neubauer, David; de Wildt, Saskia (BMJ PUBLISHING GROUP, 2016)
    Objective Paediatric clinical trials are often conducted as multinational trials. Informed consent or assent is part of the ethics committee approval for clinical trials. The consent requirements vary between countries due to national laws and regulations, which are not harmonised in Europe. These discrepancies can present challenges for paediatric clinical trials. The aim of this study was to assemble these consent and assent requirements across the European Economic Area. The collated national requirements have not been publicly available before, despite a real need for this data. Methods National consent and assent requirements for paediatric clinical trials were analysed and collated for 25 European Union Member States and 2 European Free Trade Association countries until the end of 2014. The data were retrieved from existing databases and through communication with the competent authorities and selected ethics committees. Results from a literature search for international or national guidelines, declarations and conventions and academic societies' publications served as comparison material. Results Consent and assent requirements are heterogeneous across these countries. We compiled our findings in 'The Informed Consent and Assent Tool Kit', a table including 27 national consent and assent requirements listed by individual country. Conclusions Wide variation in paediatric consents and assents presents challenges for multinational paediatric trials in Europe. The toolkit is available for all those involved in paediatric clinical trials and ethics committees, providing a new platform for proactive feedback on informed consent requirements, and may finally lead to a needed harmonisation process, including uniform standards accepted across Europe.
  • Raj, Rahul; Bendel, Stepani; Reinikainen, Matti; Hoppu, Sanna; Luoto, Teemu; Ala-Kokko, Tero; Tetri, Sami; Laitio, Ruut; Koivisto, Timo; Rinne, Jaakko; Kivisaari, Riku; Siironen, Jari; Skrifvars, Markus (BioMed Central, 2016)
    Background: Differences in outcomes after traumatic brain injury (TBI) between neurosurgical centers exist, although the reasons for this are not clear. Thus, our aim was to assess the association between the annual volume of TBI patients and mortality in neurosurgical intensive care units (NICUs). Methods: We collected data on all patients treated in the five Finnish university hospitals to examine all patients with TBI treated in NICUs in Finland from 2009 to 2012. We used a random effect logistic regression model to adjust for important prognostic factors to assess the independent effect of ICU volume on 6-month mortality. Subgroup analyses were performed for patients with severe TBI, moderate-to-severe TBI, and those who were undergoing mechanical ventilation or intracranial pressure monitoring. Results: Altogether 2,328 TBI patients were treated during the study period in five NICUs. The annual TBI patient volume ranged from 61 to 206 patients between the NICUs. Univariate analysis, showed no association between the NICUs' annual TBI patient volume and 6-month mortality (p = 0.063). The random effect model showed no independent association between the NICUs' annual TBI patient volume and 6-month mortality (OR = 1.000, 95% CI = 0.996-1.004, p = 0.876). None of the pre-defined subgroup analyses indicated any association between NICU volume and patient mortality (p > 0.05 for all). Discussion and Conclusion: We did not find any association between annual TBI patient volume and 6-month mortality in NICUs. These findings should be interpreted taking into account that we only included NICUs, which by international standards all treated high volumes of TBI patients, and that we were not able to study the effect of NICU volume on neurological outcome.
  • Liu, Jingjing; Loncar, Ivona; Collee, J. Margriet; Bolla, Manjeet K.; Dennis, Joe; Michailidou, Kyriaki; Wang, Qin; Andrulis, Irene L.; Barile, Monica; Beckmann, Matthias W.; Behrens, Sabine; Benitez, Javier; Blomqvist, Carl; Boeckx, Bram; Bogdanova, Natalia V.; Bojesen, Stig E.; Brauch, Hiltrud; Brennan, Paul; Brenner, Hermann; Broeks, Annegien; Burwinkel, Barbara; Chang-Claude, Jenny; Chen, Shou-Tung; Chenevix-Trench, Georgia; Cheng, Ching Y.; Choi, Ji-Yeob; Couch, Fergus J.; Cox, Angela; Cross, Simon S.; Cuk, Katarina; Czene, Kamila; Doerk, Thilo; Dos-Santos-Silva, Isabel; Fasching, Peter A.; Figueroa, Jonine; Flyger, Henrik; Garcia-Closas, Montserrat; Giles, Graham G.; Glendon, Gord; Goldberg, Mark S.; Gonzalez-Neira, Anna; Guenel, Pascal; Haiman, Christopher A.; Hamann, Ute; Hart, Steven N.; Hartman, Mikael; Hatse, Sigrid; Hopper, John L.; Ito, Hidemi; Jakubowska, Anna; Kabisch, Maria; Kang, Daehee; Kosma, Veli-Matti; Kristensen, Vessela N.; Le Marchand, Loic; Lee, Eunjung; Li, Jingmei; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Matsuo, Keitaro; Milne, Roger L.; Neuhausen, Susan L.; Nevanlinna, Heli; Orr, Nick; Perez, Jose I. A.; Peto, Julian; Putti, Thomas C.; Pylkas, Katri; Radice, Paolo; Sangrajrang, Suleeporn; Sawyer, Elinor J.; Schmidt, Marjanka K.; Schneeweiss, Andreas; Shen, Chen-Yang; Shrubsole, Martha J.; Shu, Xiao-Ou; Simard, Jacques; Southey, Melissa C.; Swerdlow, Anthony; Teo, Soo H.; Tessier, Daniel C.; Thanasitthichai, Somchai; Tomlinson, Ian; Torres, Diana; Truong, Therese; Tseng, Chiu-Chen; Vachon, Celine; Winqvist, Robert; Wu, Anna H.; Yannoukakos, Drakoulis; Zheng, Wei; Hall, Per; Dunning, Alison M.; Easton, Douglas F.; Hooning, Maartje J.; van den Ouweland, Ans M. W.; Martens, John W. M.; Hollestelle, Antoinette; NBCS Collaborators (NATURE PUBLISHING GROUP, 2016)
    NBS1, also known as NBN, plays an important role in maintaining genomic stability. Interestingly, rs2735383 G > C, located in a microRNA binding site in the 3'-untranslated region (UTR) of NBS1, was shown to be associated with increased susceptibility to lung and colorectal cancer. However, the relation between rs2735383 and susceptibility to breast cancer is not yet clear. Therefore, we genotyped rs2735383 in 1,170 familial non-BRCA1/2 breast cancer cases and 1,077 controls using PCR-based restriction fragment length polymorphism (RFLP-PCR) analysis, but found no association between rs2735383CC and breast cancer risk (OR = 1.214, 95% CI = 0.936-1.574, P = 0.144). Because we could not exclude a small effect size due to a limited sample size, we further analyzed imputed rs2735383 genotypes (r(2) > 0.999) of 47,640 breast cancer cases and 46,656 controls from the Breast Cancer Association Consortium (BCAC). However, rs2735383CC was not associated with overall breast cancer risk in European (OR = 1.014, 95% CI = 0.969-1.060, P = 0.556) nor in Asian women (OR = 0.998, 95% CI = 0.905-1.100, P = 0.961). Subgroup analyses by age, age at menarche, age at menopause, menopausal status, number of pregnancies, breast feeding, family history and receptor status also did not reveal a significant association. This study therefore does not support the involvement of the genotype at NBS1 rs2735383 in breast cancer susceptibility.
  • Rausalu, Kai; Utt, Age; Quirin, Tania; Varghese, Finny S.; Zusinaite, Eva; Das, Pratyush Kumar; Ahola, Tero; Merits, Andres (NATURE PUBLISHING GROUP, 2016)
    Chikungunya virus (CHIKV), genus Alphavirus, family Togaviridae, has a positive-stand RNA genome approximately 12 kb in length. In infected cells, the genome is translated into non-structural polyprotein P1234, an inactive precursor of the viral replicase, which is activated by cleavages carried out by the non-structural protease, nsP2. We have characterized CHIKV nsP2 using both cell-free and cell-based assays. First, we show that Cys478 residue in the active site of CHIKV nsP2 is indispensable for P1234 processing. Second, the substrate requirements of CHIKV nsP2 are quite similar to those of nsP2 of related Semliki Forest virus (SFV). Third, substitution of Ser482 residue, recently reported to contribute to the protease activity of nsP2, with Ala has almost no negative effect on the protease activity of CHIKV nsP2. Fourth, Cys478 to Ala as well as Trp479 to Ala mutations in nsP2 completely abolished RNA replication in CHIKV and SFV trans-replication systems. In contrast, trans-replicases with Ser482 to Ala mutation were similar to wild type counterparts. Fifth, Cys478 to Ala as well as Trp479 to Ala mutations in nsP2 abolished the rescue of infectious virus from CHIKV RNA transcripts while Ser482 to Ala mutation had no effect. Thus, CHIKV nsP2 is a cysteine protease.
  • Hemilä, Harri (Suomen matematiikan ja fysiikan opettajien liitto, 1983)
  • Hemilä, Harri (Zhonghua Yixuehui Beijing Fenhui, 2002)
  • Hemilä, Harri (Tieteen tiedotus, 1982)
  • Hemilä, Harri (Tieteen tiedotus, 1981)
  • Hemilä, Harri (1982)
  • Hemilä, Harri (TERVEYDENHUOLLON MENETELMIEN ARVIOINTIYKSIKKÖ, 1999)
    Käsitys C-vitamiinin hyödyllisyydestä nuhakuumeen eli flunssan ehkäisyssä ja hoidossa elää sitkeänä. Asia ei ole kokonaan vailla tieteellistäkään näyttöä, mutta lopullinen vastaus tuntuu edelleen jäävän ilmaan. Tutkimus jatkuu, sillä flunssan kourissa vietettyjen sairaspäivien vähentämisellä olisi suuri merkitys sekä potilaille itselleen että koko kansantaloudelle.
  • Terho, Petra Maria; Leppaniemi, Ari Kalevi; Mentula, Panu Juhani (BioMed Central, 2016)
    Background: The purpose of the study was to identify risk factors for conversion of laparoscopic cholecystectomy and risk factors for postoperative complications in acute calculous cholecystitis. The most common complications arising from cholecystectomy were also to be identified. Methods: A total of 499 consecutive patients, who had undergone emergent cholecystectomy with diagnosis of cholecystitis in Meilahti Hospital in 2013-2014, were identified from the hospital database. Of the identified patients, 400 had acute calculous cholecystitis of which 27 patients with surgery initiated as open cholecystectomy were excluded, resulting in 373 patients for the final analysis. The Clavien-Dindo classification of surgical complications was used. Results: Laparoscopic cholecystectomy was initiated in 373 patients of which 84 (22.5%) were converted to open surgery. Multivariate logistic regression identified C-reactive protein (CRP) over 150 mg/l, age over 65 years, diabetes, gangrene of the gallbladder and an abscess as risk factors for conversion. Complications were experienced by 67 (18.0%) patients. Multivariate logistic regression identified age over 65 years, male gender, impaired renal function and conversion as risk factors for complications. Conclusions: Advanced cholecystitis with high CRP, gangrene or an abscess increase the risk of conversion. The risk of postoperative complications is higher after conversion. Early identification and treatment of acute calculous cholecystitis might reduce the number of patients with advanced cholecystitis and thus improve outcomes.
  • Hemilä, Harri (2000)
    Edellisessä Skeptikko-lehdessä (2/2000) käsiteltiin vaihtoehtohoitoja. OIen itse pohdiskellut tätä kenttää pitkään ja esitän tässä joitakin kommentteja Skeptikon kirjoitusten motivoimana.
  • Hemilä, Harri (Sanoma Magazines, 2006)
    Hyvä Terveys (2/06) käsitteli lyhyesti C-vitamiinin vaikutusta flunssaan, mutta kirjoitus antoi jonkin verran harhaanjohtavan käsityksen aiheesta. Siinä viitattiin kotimaiseen katsaustutkimukseen, joka on minun laatimani. Lisäksi olen kirjoittanut väitöskirjan, joka käsittelee C-vitamiinia ja flunssaa.
  • Louhiala, Pekka; Hemilä, Harri (Kustannus Oy Duodecim, 2005)
    Kiitämme Janne Kurkea mielenkiinnosta artikkeliamme kohtaan ja kommentoimme joitakin hänen huomautuksiansa. Kurki ei kiistä pääväitteitämme vaan kiinnittää lähinnä huomioita eräiden käsitteiden käyttöön ja toivoo syvällisempää pohdiskelua, joka ammentaisi nykyfilosofian klassikoista. ...