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2. Identification of depression and anxiety during pregnancy : A systematic review and meta-analysis of test accuracy

Author

Rondung, Elisabet, Massoudi, P., Nieminen, K., Wickberg, B., Peira, N., Silverstein, R., Moberg, K., Lundqvist, M., Grundberg, Å., Hultcrantz, M., Rondung, Elisabet, Massoudi, P., Nieminen, K., Wickberg, B., Peira, N., Silverstein, R., Moberg, K., Lundqvist, M., Grundberg, Å., and Hultcrantz, M.

Abstract

Introduction: Depression and anxiety are significant contributors to maternal perinatal morbidity and a range of negative child outcomes. This systematic review and meta-analysis aimed to review and assess the diagnostic test accuracy of selected screening tools (Edinburgh Postnatal Depression Scale [EPDS], EPDS-3A, Patient Health Questionnaire [PHQ-9]-, PHQ-2, Matthey Generic Mood Question [MGMQ], Generalized Anxiety Disorder scale [GAD-7], GAD-2, and the Whooley questions) used to identify women with antenatal depression or anxiety in Western countries. Material and methods: On January 16, 2023, we searched 10 databases (CINAHL, Cochrane Library, CRD Database, Embase, Epistemonikos, International HTA Database, KSR Evidence, Ovid MEDLINE, PROSPERO and PsycINFO); the references of included studies were also screened. We included studies of any design that compared case-identification with a relevant screening tool to the outcome of a diagnostic interview based on the Diagnostic and Statistical Manual of Mental Disorders, fourth or fifth edition (DSM-IV or DSM-5), or the International Statistical Classification of Diseases and Related Health Problems, 10th revision (ICD-10). Diagnoses of interest were major depressive disorder and anxiety disorders. Two authors independently screened abstracts and full-texts for relevance and evaluated the risk of bias using QUADAS-2. Data extraction was performed by one person and checked by another team member for accuracy. For synthesis, a bivariate model was used. The certainty of evidence was assessed using Grading of Recommendations Assessment, Development and Evaluation (GRADE). Registration: PROSPERO CRD42021236333. Results: We screened 8276 records for eligibility and included 16 original articles reporting on diagnostic test accuracy: 12 for the EPDS, one article each for the GAD-2, MGMQ, PHQ-9, PHQ-2, and Whooley questions, and no articles for the EPDS-3A or GAD-7. Most of the studies had moderate to high risk of bias. Ten

Published
2024
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4. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Author

Tuskan, G.A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R.R., Bhalerao, R.P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.-L., Cooper, D., Coutinho, P.M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., dePamphillis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehiting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J.-C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D.R., Nelson, D., Nieminen, K., Nilsson, O., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C., Uberbacher, E., Unneberg, P., and Vahala, J.

Subjects
Basic biological sciences
Published
2006

7. Simple inheritance of a complex trait: Figured wood in curly birch is caused by one semi-dominant and lethal Mendelian factor?

Author

Karkkainen, K., Vihera-Aarnio, A., Vakkari, P., Hagqvist, R., and Nieminen, K.

Subjects
Birches -- Genetic aspects, Plant morphology -- Genetic aspects, Earth sciences
Abstract

Even though individuals with a deviant morphology have been elemental in genetics of model species, they have thus far been largely ignored in the studies of forest trees. Here we studied the inheritance of curly-grained and brown-figured wood phenotype in curly birch (Betula pendula var. carelica (Mercklin) Hamet-Ahti). In addition of the figured wood, curly birches display reduced and aberrant growth, indicating that the causative locus (loci) is (are) vital for normal tree development. To explore the genetic basis of this mutation, we studied the inheritance of the curly birch phenotype in a progeny trial (crosses between curly birch parent trees, between curly and normal phenotypes, and from selfings of curly trees). Based on the external morphology, the phenotypes of 11-year-old progeny trees were scored as either curly or wild. Based on the phenotypic segregation ratios, we postulate a simple Mendelian inheritance model for curliness: (i) a one-locus, two-allele model in which the allele coding for curly phenotype is dominant over the allele coding for normal phenotype and (ii) the semi-dominant curly allele is lethal when homozygous. We expect that further studies on the molecular genetic basis of the curly birch phenotype will provide valuable information on the developmental pathways involved in wood formation. Key words: Betula, curly birch, figured wood, genetics, wood quality. Meme si les individus dont la morphologie est anormale ont ete incontournables en genetique des especes modeles, ils ont jusqu'a maintenant ete largement ignores dans les etudes portant sur les arbres forestiers. Nous avons etudie la transmission du phenotype au bois figure de couleur brune ou madre chez le bouleau madre (Betula pendula var. carelica (Mercklin) Hamet-Ahti). En plus du bois figure, les bouleaux madres ont une croissance reduite et aberrante, indiquant que le locus (ou loci) responsables est (ou sont) essentiels au developpement normal de l'arbre. Afin d'explorer les fondements genetiques de cette mutation, la transmission du phenotype du bouleau madre a ete etudiee a l'aide d'un test de descendances (croisements entre des bouleaux madres, entre des phenotypes normaux et madres, et auto-croisements de bouleaux madres). A partir de la morphologie externe, le phenotype de descendants ages de 11 ans a ete classe madre ou sauvage. En se basant sur les rapports de segregation des phenotypes, un modele mendelien simple de transmission du phenotype madre a ete postule : (i) un modele a un locus et deux alleles oU l'allele codant pour le phenotype madre est dominant par rapport a l'allele codant pour le phenotype normal et (ii) l'allele semi-dominant codant pour le bois madre est letal lorsque homozygote. Nous esperons que des etudes additionnelles sur les fondements genetiques moleculaires du phenotype du bouleau madre fourniront des informations precieuses sur les sentiers de developpement qui contribuent a la formation du bois. [Traduit par la Redaction] Mots-cles : Betula, bouleau madre, bois figure, genetique, qualite du bois., Introduction Wood represents a renewable source of lignocellulosic biomass with immense commercial value and the genetic regulation of wood development is an important target for tree breeding efforts. Formation of [...]

Published
2017
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13. The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

Author

Tuskan, G. A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R. R., Bhalerao, R. P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.-L., Cooper, D., Coutinho, P. M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Déjardin, A., dePamphilis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehlting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjärvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leplé, J.-C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D. R., Nelson, C., Nieminen, K., Nilsson, O., Pereda, V., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouzé, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C.-J., Uberbacher, E., Unneberg, P., Vahala, J., Wall, K., Wessler, S., Yang, G., Yin, T., Douglas, C., Marra, M., Sandberg, G., Van de Peer, Y., and Rokhsar, D.

Published
2006

19. Validation of the short forms of the Pelvic Floor Distress Inventory (PFDI-20), Pelvic Floor Impact Questionnaire (PFIQ-7), and Pelvic Organ Prolapse/Urinary Incontinence Sexual Questionnaire (PISQ-12) in Finnish

Author

Mattsson, N. K. (Nina Kristiina), Nieminen, K. (Kari), Heikkinen, A.-M. (Anna-Mari), Jalkanen, J. (Jyrki), Koivurova, S. (Sari), Eloranta, M.-L. (Marja-Liisa), Suvitie, P. (Pia), Tolppanen, A.-M. (Anna-Maija), Mattsson, N. K. (Nina Kristiina), Nieminen, K. (Kari), Heikkinen, A.-M. (Anna-Mari), Jalkanen, J. (Jyrki), Koivurova, S. (Sari), Eloranta, M.-L. (Marja-Liisa), Suvitie, P. (Pia), and Tolppanen, A.-M. (Anna-Maija)

Abstract

Background: Although several validated generic health-related quality of life instruments exist, disease-specific instruments are important as they are often more sensitive to changes in symptom severity. It is essential to validate the instruments in a new population and language before their use. The objective of the study was to translate into Finnish the short forms of three condition-specific questionnaires (PFDI-20, PFIQ-7 and PISQ-12) and to evaluate their psychometric properties in Finnish women with symptomatic pelvic organ prolapse. Methods: A multistep translation method was used followed by an evaluation of validity and reliability in prolapse patients. Convergent and discriminant validity, internal consistency and reliability via test-retest were calculated. Results: Sixty-three patients waiting for prolapse surgery filled the three questionnaires within two weeks. Response rate for each item was high in PFDI-20 and PISQ-12 (99.8 and 98.9% respectively). For PFIQ-7 response rate was only 60%. In PFIQ-7, six respondents (9.5%) reached the minimum value of zero showing floor effect. None of the instruments had ceiling effect. Based on the item-total correlations both PFIQ-7 and PFDI-20 had acceptable convergent validity, while the convergent validity of PISQ-12 was lower, r = 0.138–0.711. However, in this instrument only three questions (questions 6, 10 and 11) had r < 0.3 while others had r ≥ 0.380. In the test-retest analysis all the three instruments showed good reliability (ICC 0.75–0.92). Similarly, the internal consistency of the instruments, measured by Cronbach’s α, was good (range 0.69–0.96) indicating high homogeneity. Conclusions: Finnish validated translation of the PFDI-20 and PISQ-12 have acceptable psychometric properties and can be used for both research purposes and clinical evaluation of pelvic organ prolapse symptoms. The Finnish version of PFIQ-7 displayed low response rate and some evidence of a floor effect, and thus its

Published
2017

20. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Author

Salojärvi, J. (Jarkko), Smolander, O.-P. (Olli-Pekka), Nieminen, K. (Kaisa), Rajaraman, S. (Sitaram), Safronov, O. (Omid), Safdari, P. (Pezhman), Lamminmäki, A. (Airi), Immanen, J. (Juha), Lan, T. (Tianying), Tanskanen, J. (Jaakko), Rastas, P. (Pasi), Amiryousefi, A. (Ali), Jayaprakash, B. (Balamuralikrishna), Kammonen, J. I. (Juhana I.), Hagqvist, R. (Risto), Eswaran, G. (Gugan), Ahonen, V. H. (Viivi Helena), Serra, J. A. (Juan Alonso), Asiegbu, F. O. (Fred O.), Barajas-Lopez, J. d. (Juan de Dios), Blande, D. (Daniel), Blokhina, O. (Olga), Blomster, T. (Tiina), Broholm, S. (Suvi), Brosche, M. (Mikael), Cui, F. (Fuqiang), Dardick, C. (Chris), Ehonen, S. E. (Sanna E.), Elomaa, P. (Paula), Escamez, S. (Sacha), Fagerstedt, K. V. (Kurt V.), Fujii, H. (Hiroaki), Gauthier, A. (Adrien), Gollan, P. J. (Peter J.), Halimaa, P. (Pauliina), Heino, P. I. (Pekka I.), Himanen, K. (Kristiina), Hollender, C. (Courtney), Kangasjärvi, S. (Saijaliisa), Kauppinen, L. (Leila), Kelleher, C. T. (Colin T.), Kontunen-Soppela, S. (Sari), Koskinen, J. P. (J. Patrik), Kovalchuk, A. (Andriy), Kärenlampi, S. O. (Sirpa O.), Kärkönen, A. K. (Anna K.), Lim, K.-J. (Kean-Jin), Leppälä, J. (Johanna), Macpherson, L. (Lee), Mikola, J. (Juha), Mouhu, K. (Katriina), Mähönen, A. P. (Ari Pekka), Niinemets, Ü. (Ülo), Oksanen, E. (Elina), Overmyer, K. (Kirk), Palva, E. T. (E. Tapio), Pazouki, L. (Leila), Pennanen, V. (Ville), Puhakainen, T. (Tuula), Poczai, P. (Peter), Possen, B. J. (Boy J. H. M.), Punkkinen, M. (Matleena), Rahikainen, M. M. (Moona M.), Rousi, M. (Matti), Ruonala, R. (Raili), van der Schoot, C. (Christiaan), Shapiguzov, A. (Alexey), Sierla, M. (Maija), Sipilä, T. P. (Timo P.), Sutela, S. (Suvi), Teeri, T. H. (Teemu H.), Tervahauta, A. I. (Arja I.), Vaattovaara, A. (Aleksia), Vahala, J. (Jorma), Vetchinnikova, L. (Lidia), Welling, A. (Annikki), Wrzaczek, M. (Michael), Xu, E. (Enjun), Paulin, L. G. (Lars G.), Schulman, A. H. (Alan H.), Lascoux, M. (Martin), Albert, V. A. (Victor A.), Auvinen, P. (Petri), Helariutta, Y. (Ykä), Kangasjärvi, J. (Jaakko), Salojärvi, J. (Jarkko), Smolander, O.-P. (Olli-Pekka), Nieminen, K. (Kaisa), Rajaraman, S. (Sitaram), Safronov, O. (Omid), Safdari, P. (Pezhman), Lamminmäki, A. (Airi), Immanen, J. (Juha), Lan, T. (Tianying), Tanskanen, J. (Jaakko), Rastas, P. (Pasi), Amiryousefi, A. (Ali), Jayaprakash, B. (Balamuralikrishna), Kammonen, J. I. (Juhana I.), Hagqvist, R. (Risto), Eswaran, G. (Gugan), Ahonen, V. H. (Viivi Helena), Serra, J. A. (Juan Alonso), Asiegbu, F. O. (Fred O.), Barajas-Lopez, J. d. (Juan de Dios), Blande, D. (Daniel), Blokhina, O. (Olga), Blomster, T. (Tiina), Broholm, S. (Suvi), Brosche, M. (Mikael), Cui, F. (Fuqiang), Dardick, C. (Chris), Ehonen, S. E. (Sanna E.), Elomaa, P. (Paula), Escamez, S. (Sacha), Fagerstedt, K. V. (Kurt V.), Fujii, H. (Hiroaki), Gauthier, A. (Adrien), Gollan, P. J. (Peter J.), Halimaa, P. (Pauliina), Heino, P. I. (Pekka I.), Himanen, K. (Kristiina), Hollender, C. (Courtney), Kangasjärvi, S. (Saijaliisa), Kauppinen, L. (Leila), Kelleher, C. T. (Colin T.), Kontunen-Soppela, S. (Sari), Koskinen, J. P. (J. Patrik), Kovalchuk, A. (Andriy), Kärenlampi, S. O. (Sirpa O.), Kärkönen, A. K. (Anna K.), Lim, K.-J. (Kean-Jin), Leppälä, J. (Johanna), Macpherson, L. (Lee), Mikola, J. (Juha), Mouhu, K. (Katriina), Mähönen, A. P. (Ari Pekka), Niinemets, Ü. (Ülo), Oksanen, E. (Elina), Overmyer, K. (Kirk), Palva, E. T. (E. Tapio), Pazouki, L. (Leila), Pennanen, V. (Ville), Puhakainen, T. (Tuula), Poczai, P. (Peter), Possen, B. J. (Boy J. H. M.), Punkkinen, M. (Matleena), Rahikainen, M. M. (Moona M.), Rousi, M. (Matti), Ruonala, R. (Raili), van der Schoot, C. (Christiaan), Shapiguzov, A. (Alexey), Sierla, M. (Maija), Sipilä, T. P. (Timo P.), Sutela, S. (Suvi), Teeri, T. H. (Teemu H.), Tervahauta, A. I. (Arja I.), Vaattovaara, A. (Aleksia), Vahala, J. (Jorma), Vetchinnikova, L. (Lidia), Welling, A. (Annikki), Wrzaczek, M. (Michael), Xu, E. (Enjun), Paulin, L. G. (Lars G.), Schulman, A. H. (Alan H.), Lascoux, M. (Martin), Albert, V. A. (Victor A.), Auvinen, P. (Petri), Helariutta, Y. (Ykä), and Kangasjärvi, J. (Jaakko)

Abstract

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.

Published
2017

21. EFFECTS OF HOT WATER EXTRACTION IN A BATCH REACTOR ON THE DELIGNIFICATION OF BIRCH WOOD

Author

Marc Borrega, Nieminen, K., and Sixta, H.

Subjects
lcsh:Biotechnology, fungi, Birch, technology, industry, and agriculture, food and beverages, macromolecular substances, Lignin condensation, complex mixtures, Autohydrolysis, Delignification kinetics, lcsh:TP248.13-248.65, Hot water extraction, Wood fractionation
Abstract

The amount of residual lignin in birch wood after a hot water extraction in a batch reactor was investigated as a function of extraction temperature and time. A kinetic model fitting the experimental data was then developed to explain delignification of wood during a hot water treatment. Results showed that delignification kinetics involves simultaneous degradation and condensation reactions, with degradation of lignin being much faster than its condensation. Native lignin in wood was successfully modeled as the sum of two fractions with different degradation rates. The rates of degradation and condensation increased along with increasing extraction temperature. The proportion of acidsoluble lignin to acid-insoluble (Klason) lignin in the wood residue decreased with increasing extraction temperature and time, probably due to chemical and structural changes in the lignin during the hot water treatment. Condensed lignin was predominantly determined as Klason lignin. On the other hand, the amount of soluble lignin in the extraction liquor increased slightly with temperature, but remained mostly constant after any extraction time. An insoluble fraction in the liquor that originated from precipitated lignin fragments is believed to contain traces of degradation products from carbohydrates or other degradation compounds.

Published
2011

23. International guide to the circus. - 2015 edition

Author

Huey, R., Albrecht, E., Belbahri, N., Brunsdale, M., Christian, J., Garcia, J., Giarola, A., Jando, D., Lehmann, R., Marier, F., Nieminen, K., Parkinson, G., Pierce, R.D., Revolledo Cárdenas, J., Rodenhuis, W., Serena, A., Schlotfeldt, A., Shaina, C., Shrake, P., Simon, M., St. Leon, M., Stone, C., Cooper, J., Tamaoki, V., Winkler, G., and Universiteitsbibliotheek

Abstract

An easy-to-read publication defining 100 key circus terms translated in nine languages. The 2015 edition has been re-created in a smaller "pocket" version, 44 pages in length and weighing 63 grams per book. Additional images have been added to illustrate terms and each book is sold complete with a beautiful circus envelope that can be used for gift-giving or mailing. The full color Guide is categorized by aerial acts, acrobatics, balancing, juggling, daredevil and specialty acts, clowning and performing animals. Terms are illustrated by photographs supplied by circuses and participants in the Federation’s annual World Circus Photo Contest. Perfect for circuses and organisations to give to visiting media, special guests, school groups or politicians. Edited by R. Huey, Ph.D.

Published
2015

24. Transcription factors PRE3 and WOX11 are involved in the formation of new lateral roots from secondary growth taproot in <italic>A. thaliana</italic>.

Author

Baesso, B., Chiatante, D., Terzaghi, M., Zenga, D., Nieminen, K., Mahonen, A. P., Siligato, R., Helariutta, Y., Scippa, G. S., and Montagnoli, A.

Subjects
ARABIDOPSIS proteins, AUXIN, TRANSCRIPTION factors, PLANT proteins, ARABIDOPSIS
Abstract

Abstract: The spatial deployment of lateral roots determines the ability of a plant to interact with the surrounding environment for nutrition and anchorage. This paper shows that besides the pericycle, the vascular cambium becomes active in Arabidopsis thaliana taproot at a later stage of development and is also able to form new lateral roots. To demonstrate the above, we implemented a two‐step approach in which the first step leads to development of a secondary structure in A. thaliana taproot, and the second applies a mechanical stress on the vascular cambium to initiate formation of a new lateral root primordium. GUS staining showed PRE3, DR5 and WOX11 signals in the cambial zone of the root during new lateral root formation. An advanced level of wood formation, characterized by the presence of medullar rays, was achieved. Preliminary investigations suggest the involvement of auxin and two transcription factors (PRE3/ATBS1/bHLH135/TMO7 and WOX11) in the transition of some vascular cambium initials from a role as producers of xylem/phloem mother cells to founder cells of a new lateral root primordium. [ABSTRACT FROM AUTHOR]

Published
2018
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25. International guide to the circus

Author

Huey, R., Albrecht, E., Belbahri, N., Brunsdale, M., Christian, J., Garcia, J., Giarola, A., Jando, D., Lehmann, R., Marier, F., Nieminen, K., Parkinson, G., Pierce, R.D., Revolledo Cárdenas, J., Rodenhuis, W., Serena, A., Schlotfeldt, A., Shaina, C., Shrake, P., Simon, M., St. Leon, M., Stone, C., Cooper, J., Tamaoki, V., Winkler, G., and Universiteitsbibliotheek

Abstract

An easy-to-read publication defining 100 key circus terms translated in nine languages. The 24-page full color Guide (A4 size) is categorized by aerial acts, acrobatics, balancing, juggling, daredevil and specialty acts, clowning and performing animals. Terms are illustrated by photographs supplied by circuses and participants in the Federation’s annual World Circus Photo Contest. Perfect for circuses and organisations to give to visiting media. Edited by R. Huey, Ph.D.

Published
2012

26. A multiobjective dynamic nonlinear robot assignment problem

Author

Ruuth, S, Maros, I, and Nieminen, K

Abstract

Robots will be used under rapidly changing and highly dangerous circumstances such as rescue operations in a radioactive environment or a fire as well as military operations. The robots are sent to several targets in order to carry out various tasks. The robots we are considering here are able to send and receive messages to and from each other as well as solve nonlinear assignment problems. When the robot salvo is en-route to their targets several events may happen. A number of co- operative robots may get jammed as a consequence of disturbances. Some robots may already have reached their targets. Some robots may not be able to reach all targets. The system being investigated enables the surviving robots to work together in real time and change their pre-set tasks if necessary in order to maximize their effectiveness. In this paper we present a method which solves the reallocation problem using a piecewise linear network algorithm. Experimental results up to 493 targets and 500 robots show that the reallocation of the robots can be done in real time.

Published
2007

28. Genetic algorithm for finding a good first integer solution for MILP

Author

Nieminen, K, Ruuth, S, and Maros, I

Abstract

The paper proposes a genetic algorithm based method for nding a good rst integer solu- tion to mixed integer programming problems (MILP). The objective value corresponding to this solution can be used to e ciently prune the search tree in branch and bound type algorithms for MILP. Some preliminary computational results are also presented which support the view that this approach deserves some attention.

Published
2003

30. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).

Author

Tuskan, G A, Difazio, S, Jansson, Stefan, Bohlmann, J, Grigoriev, I, Hellsten, U, Putnam, N, Ralph, S, Rombauts, S, Salamov, A, Schein, J, Sterck, L, Aerts, A, Bhalerao, Rupali R, Bhalerao, Rishikesh P, Blaudez, D, Boerjan, W, Brun, A, Brunner, A, Busov, V, Campbell, M, Carlson, J, Chalot, M, Chapman, J, Chen, G-L, Cooper, D, Coutinho, P M, Couturier, J, Covert, S, Cronk, Q, Cunningham, R, Davis, J, Degroeve, S, Déjardin, A, Depamphilis, C, Detter, J, Dirks, B, Dubchak, I, Duplessis, S, Ehlting, J, Ellis, B, Gendler, K, Goodstein, D, Gribskov, M, Grimwood, J, Groover, A, Gunter, L, Hamberger, B, Heinze, B, Helariutta, Y, Henrissat, B, Holligan, D, Holt, R, Huang, W, Islam-Faridi, N, Jones, S, Jones-Rhoades, M, Jorgensen, R, Joshi, C, Kangasjärvi, J, Karlsson, Jan, Kelleher, C, Kirkpatrick, R, Kirst, M, Kohler, A, Kalluri, U, Larimer, F, Leebens-Mack, J, Leplé, J-C, Locascio, P, Lou, Y, Lucas, S, Martin, F, Montanini, B, Napoli, C, Nelson, D R, Nelson, C, Nieminen, K, Nilsson, Ove, Pereda, V, Peter, G, Philippe, R, Pilate, G, Poliakov, A, Razumovskaya, J, Richardson, P, Rinaldi, C, Ritland, K, Rouzé, P, Ryaboy, D, Schmutz, J, Schrader, J, Segerman, Bo, Shin, H, Siddiqui, A, Sterky, Fredrik, Terry, A, Tsai, C-J, Uberbacher, E, Unneberg, P, Vahala, J, Wall, K, Wessler, S, Yang, G, Yin, T, Douglas, C, Marra, M, Sandberg, Göran, Van de Peer, Y, Rokhsar, D, Tuskan, G A, Difazio, S, Jansson, Stefan, Bohlmann, J, Grigoriev, I, Hellsten, U, Putnam, N, Ralph, S, Rombauts, S, Salamov, A, Schein, J, Sterck, L, Aerts, A, Bhalerao, Rupali R, Bhalerao, Rishikesh P, Blaudez, D, Boerjan, W, Brun, A, Brunner, A, Busov, V, Campbell, M, Carlson, J, Chalot, M, Chapman, J, Chen, G-L, Cooper, D, Coutinho, P M, Couturier, J, Covert, S, Cronk, Q, Cunningham, R, Davis, J, Degroeve, S, Déjardin, A, Depamphilis, C, Detter, J, Dirks, B, Dubchak, I, Duplessis, S, Ehlting, J, Ellis, B, Gendler, K, Goodstein, D, Gribskov, M, Grimwood, J, Groover, A, Gunter, L, Hamberger, B, Heinze, B, Helariutta, Y, Henrissat, B, Holligan, D, Holt, R, Huang, W, Islam-Faridi, N, Jones, S, Jones-Rhoades, M, Jorgensen, R, Joshi, C, Kangasjärvi, J, Karlsson, Jan, Kelleher, C, Kirkpatrick, R, Kirst, M, Kohler, A, Kalluri, U, Larimer, F, Leebens-Mack, J, Leplé, J-C, Locascio, P, Lou, Y, Lucas, S, Martin, F, Montanini, B, Napoli, C, Nelson, D R, Nelson, C, Nieminen, K, Nilsson, Ove, Pereda, V, Peter, G, Philippe, R, Pilate, G, Poliakov, A, Razumovskaya, J, Richardson, P, Rinaldi, C, Ritland, K, Rouzé, P, Ryaboy, D, Schmutz, J, Schrader, J, Segerman, Bo, Shin, H, Siddiqui, A, Sterky, Fredrik, Terry, A, Tsai, C-J, Uberbacher, E, Unneberg, P, Vahala, J, Wall, K, Wessler, S, Yang, G, Yin, T, Douglas, C, Marra, M, Sandberg, Göran, Van de Peer, Y, and Rokhsar, D

Abstract

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Published
2006
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34. Collecting EEG Signals in the IMPROVE Data Library

Author

Thomsen, C.E., Gade, J., Nieminen, K., Langford, R.M., Ghosh, R., Jensen, K., Rosenfalck, A., Prior, P.F., White, S., van Gils, M., Thomsen, C.E., Gade, J., Nieminen, K., Langford, R.M., Ghosh, R., Jensen, K., Rosenfalck, A., Prior, P.F., White, S., and van Gils, M.

Published
1997

39. Collecting EEG signals in the IMPROVE data library

Author

Thomsen, C.E., primary, Gade, J., additional, Nieminen, K., additional, Langford, R.M., additional, Ghosh, I.R., additional, Jensen, K., additional, Van Gils, M., additional, Rosenfalck, A., additional, Prior, P., additional, and White, S., additional

Published
1997
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