Browsing by Subject "REGION"

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  • Mgbeahuruike, Eunice Ego; Holm, Yvonne; Vuorela, Heikki; Amandikwa, Chinyere; Fyhrquist, Pia (2019)
    Ethnobotanical relevance: Piper guineense occurs commonly in West Africa where it is used for fungal infections instead of the costly and not always accessible conventional antifungals. Fungal, yeast-based diseases are common in West-Africa especially among those living with HIV/AIDS, and thus this study was performed in Imo state, South-Eastern Nigeria, where P. guineense is predominantly used for the treatment of fungal diseases, such as skin rashes, oral thrush and vaginosis. Aim of study: The scarce number of previous studies on the documentation of the traditional uses of P. guineense extracts for the treatment of fungal infections in Nigeria prompted this survey. The investigation focused on how traditional healers recognize and diagnose fungal infections, how P. guineense is collected, on the various parts used for the treatments, methods of preparations, administrations and treatments. In addition, an in vitro anti fungal screening of P. guineense fruit and leaf extracts of various polarities, and piperine and piperlongumine, representing the main constituents in these extracts, were performed. Methods: A house to house ethnobotanical survey was conducted using questionnaires. Twenty traditional medical practitioners (TMP) and herb sellers from ten villages were interviewed. Four human pathogenic strains of yeast and Cryptococcus neoformans, a yeast-like basidiomycete causing meningitis in immunocompromised individuals, were used for the antifungal screening. Results: The traditional medical practitioners (TMP) and herb sellers explained that the leaves and fruits are the most commonly used plant parts for the treatments. The oral intake of the extracts in locally produced bamboo alcohol (Kai-kai) is the most common method of administration. In accordance with these recorded traditional uses, we found that extracts of P. guineense were growth inhibitory against the fungal strains with MIC values ranging from 39 to 2500 g/mL. The lowest MIC value of 39 g/mL was recorded for a methanol fruit extract against Candida albicans, C. glabrata and C. tropicalis. In addition, ethanol and hexane fruit extracts were effective against the growth of C. albicans and C. glabrata, respectively, with a MIC of 78 g/mL. Piperlongumine and piperine were active against C. albicans with MIC values of 39 and 78 g/mL respectively. Conclusion: P. guineense fruit and leaf extracts, as well as their piperamide alkaloid constituents piperine and piperlongumine, have interesting antifungal properties and could have potential as new antifungal scaffolds. Our results warrant further in-depth investigations to isolate and characterize piperamide alkaloids and other compounds responsible for the antifungal activity in the extracts.
  • Rantalainen, Ville; Lahti, Jari; Kajantie, Eero; Tienari, Pentti; Eriksson, Johan G.; Raikkonen, Katri (2019)
    We tested if the epsilon 4 major isoform of the APOE gene and rs405509 and rs440446 promoter and intron-1 polymorphisms predicted risk of any dementia or Alzheimer's disease with diagnoses derived from the Hospital Discharge and Causes of Death Registers in 1453 participants of the Helsinki Birth Cohort Study. We used Cox proportional hazard models adjusted for sex, year of birth, maximum lifetime occupational status and education, and diagnoses of stroke, coronary heart disease, mood disorders, and depressive symptoms. APOE epsilon 4 predicted higher risk of any dementia (hazard ratios >3.68; 95% confidence interval [CI] 1.76, 7.70) across all statistical models, and when adjusted for rs405509 and rs440446. The number of minor alleles in rs405509 or rs440446 was not associated with dementia risk (hazard ratios
  • Rebbeck, Timothy R.; Mitra, Nandita; Wan, Fei; Sinilnikova, Olga M.; Healey, Sue; McGuffog, Lesley; Mazoyer, Sylvie; Chenevix-Trench, Georgia; Easton, Douglas F.; Antoniou, Antonis C.; Nathanson, Katherine L.; CIMBA Consortium; Nevanlinna, Heli; Aittomäki, Kristiina (2015)
    IMPORTANCE Limited information about the relationship between specific mutations in BRCA1 or BRCA2 (BRCA1/2) and cancer risk exists. OBJECTIVE To identify mutation-specific cancer risks for carriers of BRCA1/2. DESIGN, SETTING, AND PARTICIPANTS Observational study of women who were ascertained between 1937 and 2011 (median, 1999) and found to carry disease-associated BRCA1 or BRCA2 mutations. The international sample comprised 19 581 carriers of BRCA1 mutations and 11 900 carriers of BRCA2 mutations from 55 centers in 33 countries on 6 continents. We estimated hazard ratios for breast and ovarian cancer based on mutation type, function, and nucleotide position. We also estimated RHR, the ratio of breast vs ovarian cancer hazard ratios. A value of RHR greater than 1 indicated elevated breast cancer risk; a value of RHR less than 1 indicated elevated ovarian cancer risk. EXPOSURES Mutations of BRCA1 or BRCA2. MAIN OUTCOMES AND MEASURES Breast and ovarian cancer risks. RESULTS Among BRCA1 mutation carriers, 9052 women (46%) were diagnosed with breast cancer, 2317(12%) with ovarian cancer, 1041 (5%) with breast and ovarian cancer, and 7171 (37%) without cancer. Among BRCA2 mutation carriers, 6180 women (52%) were diagnosed with breast cancer, 682(6%) with ovarian cancer, 272(2%) with breast and ovarian cancer, and 4766 (40%) without cancer. In BRCA1, we identified 3 breast cancer cluster regions (BCCRs) located at c.179 to c.505 (BCCR1; RHR = 1.46; 95% Cl, 1.22-1.74; P = 2 x 10(-6)), c.4328 to c.4945 (BCCR2; RH R = 1.34; 95% Cl, 1.01-1.78; P =.04), and c. 5261 to c.5563 (BCCR2', RHR = 1.38; 95% Cl, 1.22-1.55; P = 6 x 10(-9)). We also identified an ovarian cancer cluster region (OCCR) from c.1380 to c.4062 (approximately exon 11) with RHR = 0.62 (95% Cl, 0.56-0.70; P = 9 x 10(-17)). In BRCA2, we observed multiple BCCRs spanning c.1 to c.596 (BCCR1; RHR = 1.71; 95% Cl, 1.06-2.78; P =.03), c.772 to c.1806 (BCCRI; RHR = 1.63; 95% Cl, 1.10-2.40; P =.01), and c.7394 to c.8904 (BCCR2; RHR = 2.31; 95% Cl, 1.69-3.16; P =.00002). We also identified 3 OCCRs: the first (OCCR1) spanned c.3249 to c.5681 that was adjacent to c.5946delT (6174delT; RHR = 0.51; 95% Cl, 0.44-0.60; P = 6 x 10(-17)). The second OCCR spanned c.6645 to c.7471 (OCCR2; RHR = 0.57; 95% Cl, 0.41-0.80; P =.001). Mutations conferring nonsense-mediated decay were associated with differential breast or ovarian cancer risks and an earlier age of breast cancer diagnosis for both BRCA1 and BRCA2 mutation carriers. CONCLUSIONS AND RELEVANCE Breast and ovarian cancer risks varied by type and location of BRCA1/2 mutations. With appropriate validation, these data may have implications for risk assessment and cancer prevention decision making for carriers of BRCA1 and BRCA2 mutations.
  • Marjonen, Heidi; Toivonen, Mia; Lahti, Laura; Kaminen-Ahola, Nina (2018)
    Prenatal alcohol exposure (PAE) can harm the embryonic development and cause life-long consequences in offspring's health. To clarify the molecular mechanisms of PAE we have used a mouse model of early alcohol exposure, which is based on maternal ad libitum ingestion of 10% (v/v) ethanol for the first eight days of gestation (GD 0.5-8.5). Owing to the detected postnatal growth-restricted phenotype in the offspring of this mouse model and both prenatal and postnatal growth restriction in alcohol-exposed humans, we focused on imprinted genes Insulin-like growth factor 2 (Igf2), H19, Small Nuclear Ribonucleoprotein Polypeptide N (Snrpn) and Paternally expressed gene 3 (Peg3), which all are known to be involved in embryonic and placental growth and development. We studied the effects of alcohol on DNA methylation level at the Igf2/H19 imprinting control region (ICR), Igf2 differentially methylated region 1, Snrpn ICR and Peg3 ICR in 9.5 embryonic days old (E9.5) embryos and placentas by using MassARRAY EpiTYPER. To determine alcohol-induced alterations globally, we also examined methylation in long interspersed nuclear elements (Line-1) in E9.5 placentas. We did not observe any significant alcohol-induced changes in DNA methylation levels. We explored effects of PAE on gene expression of E9.5 embryos as well as E9.5 and E16.5 placentas by using quantitative PCR. The expression of growth promoter gene Igf2 was decreased in the alcohol-exposed E9.5 and E16.5 placentas. The expression of negative growth controller H19 was significantly increased in the alcohol exposed E9.5 embryos compared to controls, and conversely, a trend of decreased expression in alcohol-exposed E9.5 and E16.5 placentas were observed. Furthermore, increased Snrpn expression in alcohol-exposed E9.5 embryos was also detected. Our study indicates that albeit no alterations in the DNA methylation levels of studied sequences were detected by EpiTYPER, early PAE can affect the expression of imprinted genes in both developing embryo and placenta.
  • Yohannes, Dawit A.; de Kauwe, Andrea; Kaukinen, Katri; Kurppa, Kalle; Mäki, Markku; Anderson, Robert P.; Linnarsson, Sten; Greco, Dario; Saavalainen, Päivi (2020)
    The pathological mechanisms that lead to the onset and reactivation of celiac disease (CD) remain largely unknown. While gluten free diet (GFD) improves the intestinal damage and associated clinical symptoms in majority of cases, it falls short of providing full recovery. Additionally, late or misdiagnosis is also common as CD presents with a wide range of symptoms. Clear understanding of CD pathogenesis is thus critical to address both diagnostic and treatment concerns. We aimed to study the molecular impact of short gluten exposure in GFD treated CD patients, as well as identify biological pathways that remain altered constitutively in CD regardless of treatment. Using RNAseq profiling of PBMC samples collected from treated CD patients and gluten challenged patient and healthy controls, we explored the peripheral transcriptome in CD patients following a short gluten exposure. Short gluten exposure of just three days was enough to alter the genome-wide PBMC transcriptome of patients. Pathway analysis revealed gluten-induced upregulation of mainly immune response related pathways, both innate and adaptive, in CD patients. We evaluated the perturbation of biological pathways in sample-specific manner. Compared to gluten exposed healthy controls, pathways related to tight junction, olfactory transduction, metabolism of unsaturated fatty acids (such as arachidonic acid), metabolism of amino acids (such as cysteine and glutamate), and microbial infection were constitutively altered in CD patients regardless of treatment, while GFD treatment appears to mostly normalize immune response pathways to "healthy" state. Upstream regulator prediction analysis using differentially expressed genes identified constitutively activated regulators relatively proximal to previously reported CD associated loci, particularly SMARCA4 on 19p13.2 and CSF2 on 5q31. We also found constitutively upregulated genes in CD that are in CD associated genetic loci such as MEF2BNB-MEF2B (BORCS8-MEF2B) on 19p13.11 and CSTB on 21q22.3. RNAseq revealed strong effects of short oral gluten challenge on whole PBMC fraction and constitutively altered pathways in CD PBMC suggesting important factors other than gluten in CD pathogenesis.
  • IDS Collaboration; Lica, R.; Greenlees, P. T.; Konki, J.; Rahkila, P. (2018)
    The occurrence of octupolar shapes in the Ba isotopic chain was recently established experimentally up to N = 90. To further extend the systematics, the evolution of shapes in the most neutron-rich members of the Z = 56 isotopic chain accessible at present, Ba-148,Ba-150, has been studied via beta decay at the ISOLDE Decay Station. This paper reports on the first measurement of the positive-and negative-parity low-spin excited states of 150Ba and presents an extension of the beta-decay scheme of Cs-148. Employing the fast timing technique, half-lives for the 2(1)(+) level in both nuclei have been determined, resulting in T-1/2 = 1.51(1) ns for Ba-148 and T-1/2 = 3.4(2) ns for Ba-150. The systematics of low-spin states, together with the experimental determination of the B(E2 : 2(+) -> 0(+)) transition probabilities, indicate an increasing collectivity in Ba148-150, towards prolate deformed shapes. The experimental data are compared to symmetry conserving configuration mixing (SCCM) calculations, confirming an evolution of increasingly quadrupole deformed shapes with a definite octupolar character.
  • Darabi, Hatef; Beesley, Jonathan; Droit, Arnaud; Kar, Siddhartha; Nord, Silje; Marjaneh, Mahdi Moradi; Soucy, Penny; Michailidou, Kyriaki; Ghoussaini, Maya; Wahl, Hanna Fues; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Alonso, M. Rosario; Andrulis, Irene L.; Anton-Culver, Hoda; Arndt, Volker; Beckmann, Matthias W.; Benitez, Javier; Bogdanova, Natalia V.; Bojesen, Stig E.; Brauch, Hiltrud; Brenner, Hermann; Broeks, Annegien; Bruening, Thomas; Burwinkel, Barbara; Chang-Claude, Jenny; Choi, Ji-Yeob; Conroy, Don M.; Couch, Fergus J.; Cox, Angela; Cross, Simon S.; Czene, Kamila; Devilee, Peter; Doerk, Thilo; Easton, Douglas F.; Fasching, Peter A.; Figueroa, Jonine; Fletcher, Olivia; Flyger, Henrik; Galle, Eva; Garcia-Closas, Montserrat; Giles, Graham G.; Goldberg, Mark S.; Gonzalez-Neira, Anna; Guenel, Pascal; Haiman, Christopher A.; Hallberg, Emily; Hamann, Ute; Hartman, Mikael; Hollestelle, Antoinette; Hopper, John L.; Ito, Hidemi; Jakubowska, Anna; Johnson, Nichola; Kang, Daehee; Khan, Sofia; Kosma, Veli-Matti; Kriege, Mieke; Kristensen, Vessela; Lambrechts, Diether; Le Marchand, Loic; Lee, Soo Chin; Lindblom, Annika; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Manoukian, Siranoush; Margolin, Sara; Matsuo, Keitaro; Mayes, Rebecca; Mckay, James; Meindl, Alfons; Milne, Roger L.; Muir, Kenneth; Neuhausen, Susan L.; Nevanlinna, Heli; Olswold, Curtis; Orr, Nick; Peterlongo, Paolo; Pita, Guillermo; Pylkaes, Katri; Rudolph, Anja; Sangrajrang, Suleeporn; Sawyer, Elinor J.; Schmidt, Marjanka K.; Schmutzler, Rita K.; Seynaeve, Caroline; Shah, Mitul; Shen, Chen-Yang; Shu, Xiao-Ou; Southey, Melissa C.; Stram, Daniel O.; Surowy, Harald; Swerdlow, Anthony; Teo, Soo H.; Tessier, Daniel C.; Tomlinson, Ian; Torres, Diana; Truong, Therese; Vachon, Celine M.; Vincent, Daniel; Winqvist, Robert; Wu, Anna H.; Wu, Pei-Ei; Yip, Cheng Har; Zheng, Wei; Pharoah, Paul D. P.; Hall, Per; Edwards, Stacey L.; Simard, Jacques; French, Juliet D.; Chenevix-Trench, Georgia; Dunning, Alison M. (2016)
    Genome-wide association studies have found SNPs at 17q22 to be associated with breast cancer risk. To identify potential causal variants related to breast cancer risk, we performed a high resolution fine-mapping analysis that involved genotyping 517 SNPs using a custom Illumina iSelect array (iCOGS) followed by imputation of genotypes for 3,134 SNPs in more than 89,000 participants of European ancestry from the Breast Cancer Association Consortium (BCAC). We identified 28 highly correlated common variants, in a 53 Kb region spanning two introns of the STXBP4 gene, that are strong candidates for driving breast cancer risk (lead SNP rs2787486 (OR = 0.92; CI 0.90-0.94; P = 8.96 x 10(-15))) and are correlated with two previously reported risk-associated variants at this locus, SNPs rs6504950 (OR = 0.94, P = 2.04 x 10-09, r(2) = 0.73 with lead SNP) and rs1156287 (OR = 0.93, P = 3.41 x 10(-11), r(2) = 0.83 with lead SNP). Analyses indicate only one causal SNP in the region and several enhancer elements targeting STXBP4 are located within the 53 kb association signal. Expression studies in breast tumor tissues found SNP rs2787486 to be associated with increased STXBP4 expression, suggesting this may be a target gene of this locus.
  • Caballero-Folch, R.; Dillmann, I.; Agramunt, J.; Tain, J. L.; Algora, A.; Äystö, J.; Calvino, F.; Canete, L.; Cortes, G.; Domingo-Pardo, C.; Eronen, T.; Ganioglu, E.; Gelletly, W.; Gorelov, D.; Guadilla, V.; Hakala, J.; Jokinen, A.; Kankainen, A.; Kolhinen, V. S; Koponen, J.; Marta, M.; Mendoza, E.; Montaner-Piza, A.; Moore, I.; Nobs, C. R.; Orrigo, S. E. A.; Penttilä, H.; Pohjalainen, J.; Reinikainen, J.; Riego, A.; Rinta-Antila, S.; Rubio, B.; Salvador-Castineira, P.; Simutkin, V.; Tarifeno-Saldivia, A.; Tolosa-Delgado, A.; Vos, A. (2018)
    Background: beta-delayed multiple neutron emission has been observed for some nuclei with A 100 to test the predictions of theoretical models and simulation tools for the decays of heavy nuclei in the region of very neutron-rich nuclei. In addition the decay properties of these nuclei are fundamental for the understanding of astrophysical nucleosynthesis processes such as the r-process and safety inputs for nuclear reactors. Purpose: To determine for the first time the two-neutron branching ratio the P-2n value for Sb-136 through a direct neutron measurement and to provide precise P-1n values for Sb-136 and Te-136. Method: A pure beam of each isotope of interest was provided by the JYFLTRAP Penning trap at the Ion Guide Isotope Separator On-Line (IGISOL) facility of the University of Jyvaskyla Finland. The purified ions were implanted into a moving tape at the end of the beam line. The detection setup consisted of a plastic scintillator placed right behind the implantation point after the tape to register the beta decays and the BELEN detector based on neutron counters embedded in a polyethylene matrix. The analysis was based on the study of the beta- and neutron-growth-and-decay curves and the beta-one-neutron and beta-two-neutron time correlations which allowed us the determination of the neutron branching ratios. Results: The P-2n value of Sb-136 was found to be 0.14(3)% and the measured P-1n values for Sb-136 and Te-136 were found to be 32.2(15)% and 1.47(6)% respectively. Conclusions: The measured P-2n value is a factor 44 smaller than predicted by the finite-range droplet model plus the quasiparticle random-phase approximation (FRDM+QRPA) model used for r-process calculations.
  • Malyshev, Sergey; Pasenko, Aleksander M.; Ivanov, Alexei; Gladkochub, Dmitrii P.; Savatenkov, Valery M.; Meffre, Sebastien; Abersteiner, Adam; Kamenetsky, Vadim S.; Shcherbakov, Vasiliy D. (2018)
    The emplacement age of the Great Udzha Dyke (northern Siberian Craton) was determined by the U-Pb dating of apatite using laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). This produced an age of 1386 +/- 30 Ma. This dyke along with two other adjacent intrusions, which cross-cut the sedimentary units of the Udzha paleo-rift, were subjected to paleomagnetic investigation. The paleomagnetic poles for the Udzha paleo-rift intrusions are consistent with previous results published for the Chieress dyke in the Anabar shield of the Siberian Craton (1384 +/- 2 Ma). Our results suggest that there was a period of intense volcanism in the northern Siberian Craton, as well as allow us to reconstruct the apparent migration of the Siberian Craton during the Mesoproterozoic.
  • Koskela, Satu; Ritari, Jarmo; Hyvärinen, Kati; Kwan, Tony; Niittyvuopio, Riitta; Itälä-Remes, Maija; Pastinen, Tomi; Partanen, Jukka (2018)
    Matching classical HLA alleles between donor and recipient is an important factor in avoiding adverse immunological effects in HSCT. Siblings with no differences in HLA alleles, either due to identical-by-state or identical-by-descent status, are considered to be optimal donors. We carried out a retrospective genomic sequence and SNP analysis of 336 fully HLA-A, -B, -DRB1 matched and 14 partially HLA-matched sibling HSCT pairs to determine the level of undetected mismatching within the MHC segment as well as to map their recombination sites. The genomic sequence of 34 genes locating in the MHC region revealed allelic mismatching at 1 to 8 additional genes in partially HLA-matched pairs. Also, fully matched pairs were found to have mismatching either at HLA-DPB1 or at non-HLA region within the MHC segment. Altogether, 3.9% of fully HLA-matched HSCT pairs had large genomic mismatching in the MHC segment. Recombination sites mapped to certain restricted locations. The number of mismatched nucleotides correlated with the risk of GvHD supporting the central role of full HLA matching in HSCT. High-density genome analysis revealed that fully HLA-matched siblings may not have identical MHC segments and even single allelic mismatching at any classical HLA gene often implies larger genomic differences along MHC.
  • Olaizola, B.; Mach, H.; Fraile, L. M.; Benito, J.; Borge, M. J. G.; Boutami, R.; Butler, P. A.; Dlouhy, Z.; Fynbo, H. O. U.; Hoff, P.; Hyldegaard, S.; Jeppesen, H. B.; Jokinen, A.; Jollet, C.; Korgul, A.; Koster, U.; Kroell, Th.; Kurcewicz, W.; Marechal, F.; Mrazek, J.; Nilsson, T.; Plociennik, W. A.; Ruchowska, E.; Schuber, R.; Schwerdtfeger, W.; Sewtz, M.; Simpson, G. S.; Stanoiu, M.; Tengblad, O.; Thirolf, P. G.; Yordanov, D. T. (2016)
    gamma-ray and fast-timing spectroscopy were used to study levels in Al-30 populated following the beta(-) decay of Mg-30. Five new transitions and three new levels were located in Al-30. A search was made to identify the third 1(+) state expected at an excitation energy of similar to 2.5 MeV. Two new levels were found, at 3163.9 and 3362.5 keV, that are firm candidates for this state. Using the advanced time-delayed (ATD) beta gamma gamma (t) method we have measured the lifetime of the 243.8-keV state to be T-1/2 = 15(4) ps, which implies that the 243.8-keV transition is mainly of M1 character. Its fast B(M1; 2(+) -> 3(+)) value of 0.10(3) W.u. is in very good agreement with the USD shell-model prediction of 0.090 W.u. The 1801.5-keV level is the only level observed in this study that could be a candidate for the second excited 2(+) state.
  • Oversti, Sanni; Onkamo, Paivi; Stoljarova, Monika; Budowle, Bruce; Sajantila, Antti; Palo, Jukka U. (2017)
    In Europe, modern mitochondrial diversity is relatively homogeneous and suggests an ubiquitous rapid population growth since the Neolithic revolution. Similar patterns also have been observed in mitochondrial control region data in Finland, which contrasts with the distinctive autosomal and Y-chromosomal diversity among Finns. A different picture emerges from the 843 whole mitochondrial genomes from modern Finns analyzed here. Up to one third of the subhaplogroups can be considered as Finn-characteristic, i.e. rather common in Finland but virtually absent or rare elsewhere in Europe. Bayesian phylogenetic analyses suggest that most of these attributed Finnish lineages date back to around 3,000-5,000 years, coinciding with the arrival of Corded Ware culture and agriculture into Finland. Bayesian estimation of past effective population sizes reveals two differing demographic histories: 1) the 'local' Finnish mtDNA haplotypes yielding small and dwindling size estimates for most of the past; and 2) the 'immigrant' haplotypes showing growth typical of most European populations. The results based on the local diversity are more in line with that known about Finns from other studies, e.g., Y-chromosome analyses and archaeology findings. The mitochondrial gene pool thus may contain signals of local population history that cannot be readily deduced from the total diversity.
  • Lica, R.; Rotaru, F.; Borge, M. J. G.; Grevy, S.; Negoita, F.; Poves, A.; Sorlin, O.; Andreyev, A. N.; Borcea, R.; Costache, C.; De Witte, H.; Fraile, L. M.; Greenlees, P. T.; Huyse, M.; Ionescu, A.; Kisyov, S.; Konki, J.; Lazarus, I.; Madurga, M.; Marginean, N.; Marginean, R.; Mihai, C.; Mihai, R. E.; Negret, A.; Page, R. D.; Pakarinen, J.; Pascu, S.; Pucknell, V.; Rahkila, P.; Rapisarda, E.; Serban, A.; Sotty, C. O.; Stan, L.; Stanoiu, M.; Tengblad, O.; Turturica, A.; Van Duppen, P.; Wadsworth, R.; Warr, N.; IDS Collaboration (2017)
    The beta(-) decay of Mg-34 was used to study the Al-34 nucleus through. spectroscopy at the Isotope Separator On-Line facility of CERN. Previous studies identified two beta-decaying states in Al-34 having spin-parity assignments J(pi) = 4(-) dominated by the normal configuration pi(d(5/2))(-1)circle times nu(f(7/2)) and J(pi) = 1(+) by the intruder configuration pi(d(5/2))(-1) circle times nu(d(3/2))(-1) (f(7/2))(2). Their unknown ordering and relative energy have been the subject of debate for the placement of Al-34 inside or outside the N = 20 "island of inversion." We report here that the 1(+) intruder lies only 46.6 keV above the 4(-) ground state. In addition, a new half-life of T-1/2 = 44.9(4) ms, that is twice as long as the previously measured 20(10) ms, has been determined for Mg-34. Large-scale shell-model calculations with the recently developed SDPF-U-MIX interaction are compared with the new data and used to interpret the mechanisms at play at the very border of the N = 20 island of inversion.
  • Fahmi, Mustafa Kamil Mahmoud; Dafa-Alla, Dafa-Alla Mohamed; Kanninen, Markku; Luukkanen, Olavi (2018)
    National food security has been a major policy goal in Sudan since the country gained its independence in 1956. One of the fundamental reasons is to ensure the social welfare for people living in rural areas. In this study we aimed to analyse how farmers secure their food and generate income in the semi-arid Sennar state in Sudan, using two selected sites, El Dali and El Mazmum, as examples. We interviewed 281 randomly sampled household heads, of which 145 at El Dali and 136 at El Mazmum, between July and November 2011. We identified four distinct land use systems, of which three consist of monocropping and one of cultivation in agroforestry parklands. Several statistical techniques and economic analysis were applied on the study data. Our results show that, in the two areas, the highest average yields over a 10-year period for the three crops studied, sorghum, pearl millet and sesame, were achieved in agroforestry system, except for the case of sesame at El Mazmum. Economic returns for the farmers, as indicated by net present value or benefit/cost ratio, followed the same pattern. The study concludes that farmers should rely more on agroforestry to improve their food security and cash income generation. Land use and land right policies, which currently discourage farmers from growing trees on their lands, should be revised, so as to give more incentive to them to adopt ecologically and economically more sustainable land use practices.
  • Abelev, B.; Adam, J.; Adamova, D.; Aggarwal, M. M.; Rinella, G. Aglieri; Agnello, M.; Agostinelli, A.; Agrawal, N.; Ahammed, Z.; Ahmad, N.; Ahmed, I.; Ahn, S. U.; Ahn, S. A.; Aimo, I.; Aiola, S.; Ajaz, M.; Akindinov, A.; Alam, S. N.; Aleksandrov, D.; Alessandro, B.; Alexandre, D.; Alici, A.; Alkin, A.; Alme, J.; Alt, T.; Altinpinar, S.; Altsybeev, I.; Prado, C. Alves Garcia; Andrei, C.; Andronic, A.; Anguelov, V.; Anielski, J.; Anticic, T.; Antinori, F.; Antonioli, P.; Aphecetche, L.; Appelshaeuser, H.; Arcelli, S.; Armesto, N.; Arnaldi, R.; Aronsson, T.; Arsene, I. C.; Chang, B.; Hilden, T. E.; Kim, D. J.; Kral, J.; Pohjoisaho, E. H. O.; Rak, J.; Räsänen, S. S.; Trzaska, W. H. (2015)
    The multiplicity and pseudorapidity distributions of inclusive photons have been measured at forward rapidities (2.3 <eta <3.9) in proton-proton collisions at three center-of-mass energies, root s = 0.9, 2.76 and 7 TeV using the ALICE detector. It is observed that the increase in the average photon multiplicity as a function of beam energy is compatible with both a logarithmic and a power-law dependence. The relative increase in average photon multiplicity produced in inelastic pp collisions at 2.76 and 7 TeV center-of-mass energies with respect to 0.9 TeV are 37.2 +/- 0.3% (stat) +/- 8.8% (sys) and 61.2 +/- 0.3% (stat) +/- 7.6% (sys), respectively. The photon multiplicity distributions for all center-of-mass energies are well described by negative binomial distributions. The multiplicity distributions are also presented in terms of KNO variables. The results are compared to model predictions, which are found in general to underestimate the data at large photon multiplicities, in particular at the highest center-of-mass energy. Limiting fragmentation behavior of photons has been explored with the data, but is not observed in the measured pseudorapidity range.
  • Rodriguez, E.; Kolmonen, P.; Virtanen, T. H.; Sogacheva, L.; Sundström, Anu-Maija; de Leeuw, G. (2015)
    The Advanced Along-Track Scanning Radiometer (AATSR) on board the ENVISAT satellite is used to study aerosol properties. The retrieval of aerosol properties from satellite data is based on the optimized fit of simulated and measured reflectances at the top of the atmosphere (TOA). The simulations are made using a radiative transfer model with a variety of representative aerosol properties. The retrieval process utilizes a combination of four aerosol components, each of which is defined by their (lognormal) size distribution and a complex refractive index: a weakly and a strongly absorbing fine-mode component, coarse mode sea salt aerosol and coarse mode desert dust aerosol). These components are externally mixed to provide the aerosol model which in turn is used to calculate the aerosol optical depth (AOD). In the AATSR aerosol retrieval algorithm, the mixing of these components is decided by minimizing the error function given by the sum of the differences between measured and calculated path radiances at 3-4 wavelengths, where the path radiances are varied by varying the aerosol component mixing ratios. The continuous variation of the fine-mode components allows for the continuous variation of the fine-mode aerosol absorption. Assuming that the correct aerosol model (i.e. the correct mixing fractions of the four components) is selected during the retrieval process, also other aerosol properties could be computed such as the single scattering albedo (SSA). Implications of this assumption regarding the ratio of the weakly/strongly absorbing fine-mode fraction are investigated in this paper by evaluating the validity of the SSA thus obtained. The SSA is indirectly estimated for aerosol plumes with moderate-to-high AOD resulting from wildfires in Russia in the summer of 2010. Together with the AOD, the SSA provides the aerosol absorbing optical depth (AAOD). The results are compared with AERONET data, i.e. AOD level 2.0 and SSA and AAOD inversion products. The RMSE (root mean square error) is 0.03 for SSA and 0.02 for AAOD lower than 0.05. The SSA is further evaluated by comparison with the SSA retrieved from the Ozone Monitoring Instrument (OMI). The SSA retrieved from both instruments show similar features, with generally lower AATSR-estimated SSA values over areas affected by wildfires.
  • Huong Thi Thanh Nguyen,; Trung Minh Doan,; Tomppo, Erkki; McRoberts, Ronald E. (2020)
    Information on land use and land cover (LULC) including forest cover is important for the development of strategies for land planning and management. Satellite remotely sensed data of varying resolutions have been an unmatched source of such information that can be used to produce estimates with a greater degree of confidence than traditional inventory estimates. However, use of these data has always been a challenge in tropical regions owing to the complexity of the biophysical environment, clouds, and haze, and atmospheric moisture content, all of which impede accurate LULC classification. We tested a parametric classifier (logistic regression) and three non-parametric machine learning classifiers (improved k-nearest neighbors, random forests, and support vector machine) for classification of multi-temporal Sentinel 2 satellite imagery into LULC categories in Dak Nong province, Vietnam. A total of 446 images, 235 from the year 2017 and 211 from the year 2018, were pre-processed to gain high quality images for mapping LULC in the 6516 km(2) study area. The Sentinel 2 images were tested and classified separately for four temporal periods: (i) dry season, (ii) rainy season, (iii) the entirety of the year 2017, and (iv) the combination of dry and rainy seasons. Eleven different LULC classes were discriminated of which five were forest classes. For each combination of temporal image set and classifier, a confusion matrix was constructed using independent reference data and pixel classifications, and the area on the ground of each class was estimated. For overall temporal periods and classifiers, overall accuracy ranged from 63.9% to 80.3%, and the Kappa coefficient ranged from 0.611 to 0.813. Area estimates for individual classes ranged from 70 km(2) (1% of the study area) to 2200 km(2) (34% of the study area) with greater uncertainties for smaller classes.
  • Ryan, A. M.; Gallagher, P. T.; Carley, E. P.; Brentjens, M. A.; Murphy, P. C.; Vocks, C.; Morosan, D. E.; Reid, H.; Magdalenic, J.; (AIP), Leibniz Institut fur Astrophysik; Zucca, P.; Fallows, R.; Mann, G.; Kerdraon, A.; Halfwerk, R. (2021)
    The solar corona is a highly-structured plasma which can reach temperatures of more than similar to 2 MK. At low frequencies (decimetric and metric wavelengths), scattering and refraction of electromagnetic waves are thought to considerably increase the imaged radio source sizes (up to a few arcminutes). However, exactly how source size relates to scattering due to turbulence is still subject to investigation. The theoretical predictions relating source broadening to propagation effects have not been fully confirmed by observations due to the rarity of high spatial resolution observations of the solar corona at low frequencies. Here, the LOw Frequency ARray (LOFAR) was used to observe the solar corona at 120-180 MHz using baselines of up to similar to 3.5 km (corresponding to a resolution of similar to 1-2 ') during the partial solar eclipse of 2015 March 20. A lunar de-occultation technique was used to achieve higher spatial resolution (similar to 0.6 ') than that attainable via standard interferometric imaging (similar to 2.4 '). This provides a means of studying the contribution of scattering to apparent source size broadening. It was found that the de-occultation technique reveals a more structured quiet corona that is not resolved from standard imaging, implying scattering may be overestimated in this region when using standard imaging techniques. However, an active region source was measured to be similar to 4 ' using both de-occultation and standard imaging. This may be explained by the increased scattering of radio waves by turbulent density fluctuations in active regions, which is more severe than in the quiet Sun.
  • Shishido, Tania Keiko; Wahlsten, Matti; Laine, Pia; Rikkinen, Jouko; Lundell, Taina; Auvinen, Petri (2021)
    Lichens have been widely used in traditional medicine, especially by indigenous communities worldwide. However, their slow growth and difficulties in the isolation of lichen symbionts and associated microbes have hindered the pharmaceutical utilisation of lichen-produced compounds. Advances in high-throughput sequencing techniques now permit detailed investigations of the complex microbial communities formed by fungi, green algae, cyanobacteria, and other bacteria within the lichen thalli. Here, we used amplicon sequencing, shotgun metagenomics, and in silico metabolomics together with compound extractions to study reindeer lichens collected from Southern Finland. Our aim was to evaluate the potential of Cladonia species as sources of novel natural products. We compared the predicted biosynthetic pathways of lichen compounds from isolated genome-sequenced lichen fungi and our environmental samples. Potential biosynthetic genes could then be further used to produce secondary metabolites in more tractable hosts. Furthermore, we detected multiple compounds by metabolite analyses, which revealed connections between the identified biosynthetic gene clusters and their products. Taken together, our results contribute to metagenomic data studies from complex lichen-symbiotic communities and provide valuable new information for use in further biochemical and pharmacological studies.