Browsing by Subject "EXTRACTION"

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  • van den Hoogen, Johan; Geisen, Stefan; Wall, Diana H.; Wardle, David A.; Traunspurger, Walter; de Goede, Ron G. M.; Adams, Byron J.; Ahmad, Wasim; Ferris, Howard; Bardgett, Richard D.; Bonkowski, Michael; Campos-Herrera, Raquel; Cares, Juvenil E.; Caruso, Tancredi; de Brito Caixeta, Larissa; Chen, Xiaoyun; Costa, Sofia R.; Creamer, Rachel; da Cunha e Castro, José Mauro; Dam, Marie; Djigal, Djibril; Escuer, Miguel; Griffiths, Bryan S.; Gutiérrez, Carmen; Hohberg, Karin; Kalinkina, Daria; Kardol, Paul; Kergunteuil, Alan; Korthals, Gerard; Krashevska, Valentyna; Kudrin, Alexey A.; Li, Qi; Liang, Wenju; Magilton, Matthew; Marais, Mariette; Martín, José Antonio Rodríguez; Matveeva, Elizaveta; Mayad, El Hassan; Mzough, E.; Mulder, Christian; Mullin, Peter; Neilson, Roy; Nguyen, T. A. Duong; Nielsen, Uffe N.; Okada, Hiroaki; Rius, Juan Emilio Palomares; Pan, Kaiwen; Peneva, Vlada; Pellissier, Loïc; da Silva, Julio Carlos Pereira; Pitteloud, Camille; Powers, Thomas O.; Powers, Kirsten; Quist, Casper W.; Rasmann, Sergio; Moreno, Sara Sánchez; Scheu, Stefan; Setälä, Heikki; Sushchuk, Anna; Tiunov, Alexei V.; Trap, Jean; Vestergård, Mette; Villenave, Cecile; Waeyenberge, Lieven; Wilschut, Rutger A.; Wright, Daniel G.; Keith, Aidan M.; Yang, Jiue-in; Schmidt, Olaf; Bouharroud, R.; Ferji, Z.; van der Putten, Wim H.; Routh, Devin; Crowther, Thomas W. (2020)
    As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.
  • Ambat, Indu; Bec, Sabina; Peltomaa, Elina; Srivastava, Varsha; Ojala, Anne; Sillanpaa, Mika (2019)
    The combination of wastewater treatment and biodiesel production using algal cultivation was studied in the present work. The two main goals of the work were achieved by the cultivation of freshwater microalgae such as Chlamydomonas sp., Scenedesmus ecornis, and Scenedesmus communis in two different dilutions of fertilizer plant wastewater (FWWD1 and FWWD2) collected from Yara Suomi 0y, Finland. The growth pattern of different algal species in FWWD1 and FWWD2 was observed. The effect of pH on biomass concentration, lipid content, biomass productivity, and lipid productivity by all three algal species in FWWD1 and FWWD2 were monitored. The maximum biomass concentration and productivity were observed in FWWD1 at pH7.5 for Chlamydomonas sp. and at pH 8.5 for S. ecornis and S. communis. The maximum lipid content was detected in Chlamydomonas sp at pH5.5, followed by S. ecornis and then S. communis at pH 7.5 in FWWD2 obtained after co-solvent extraction method. The most significant removal percentage of COD by all algal species were observed in FWWD1, whereas the highest removal percentage of TN and TP were detected in FWWD2, respectively. The fatty acid methyl ester (FAME) characterization of each algal species in FWWD1 and FWWD2 at their optimum pH was investigated to determine the quality of obtained biodiesel.
  • Avela, Henri F.; Siren, Heli (2020)
    The review concentrates on the properties of analytical and statistical ultrahigh-performance liquid chromatographic (UHPLC) - mass spectrometric (MS) methods suitable for glycero-, glycerophospho- and sphingolipids in lipidomics published between the years 2017 2019. Trends and fluctuations of conventional and nano-UHPLC methods with MS and tandem MS detection were observed in context of analysis conditions and tools used for data-analysis. Whereas general workflow characteristics are agreed upon, more details related to the chromatographic methodology (i.e. stationary and mobile phase conditions) need evidently agreements. Lipid quantitation relies upon isotope-labelled standards in targeted analyses and fully standardless algorithm-based untargeted analyses. Furthermore, a wide spectrum of setups have shown potential for the elucidation of complex and large datasets by minimizing the risks of systematic misinterpretation like false positives. This kind of evaluation was shown to have increased importance and usage for cross-validation and data-analysis. (C) 2020 Elsevier B.V. All rights reserved.
  • Yu, Xiaowei; Litkey, Paula; Hyyppa, Juha; Holopainen, Markus; Vastaranta, Mikko (2014)
  • Huang, Xin; Ma, Kaiyue; Leinonen, Sara; Sontag-Strohm, Tuula (2020)
    The lack of certified reference materials has been one major challenge for gluten quantification in gluten-free products. In this study, the feasibility of using barley C-hordein as the calibrant for wheat gluten in R5 sandwich enzyme-linked immunosorbent assay (ELISA) was investigated. The gluten composition and total gluten R5 reactivity ranged largely depending on the genotypes and the growing environment. The conversion factor of gliadin to gluten averaged 1.31 for common wheat, which is smaller than the theoretical factor of 2. Each gluten group had varying reactivity against the R5 antibody, where omega 1.2-, gamma- and alpha-gliadins were the main reactive groups from wheat gluten. A mixture of wheat cultivars or one single cultivar as the reference material can be difficult to keep current. Based on the average R5 reactivity of total gluten from the 27 common wheat cultivars, here we proposed 10% C-hordein mixed with an inert protein as the calibrant for wheat gluten quantification. In spiking tests of gluten-free oat flour and biscuits, calibration using 10% C-hordein achieved the same recovery as the gliadin standard with its cultivar-specific conversion factor. For its good solubility and good affinity to the R5 antibody, the application of C-hordein increases the probability of developing a series of reference materials for various food matrices.
  • Aaen, Ragnhild; Lehtonen, Mari; Mikkonen, Kirsi S.; Syverud, Kristin (2021)
    The use of wood-derived cellulose nanofibrils (CNFs) or galactoglucomannans (GGM) for emulsion stabilization may be a way to obtain new environmentally friendly emulsifiers. Both have previously been shown to act as emulsifiers, offering physical, and in the case of GGM, oxidative stability to the emulsions. Oil-in-water emulsions were prepared using highly charged (1352 ± 5 µmol/g) CNFs prepared by TEMPO-mediated oxidation, or a coarser commercial CNF, less charged (≈ 70 µmol/g) quality (Exilva forte), and the physical emulsion stability was evaluated by use of droplet size distributions, micrographs and visual appearance. The highly charged, finely fibrillated CNFs stabilized the emulsions more effectively than the coarser, lower charged CNFs, probably due to higher electrostatic repulsions between the fibrils, and a higher surface coverage of the oil droplets due to thinner fibrils. At a constant CNF/oil ratio, the lowest CNF and oil concentration of 0.01 wt % CNFs and 5 wt % oil gave the most stable emulsion, with good stability toward coalescence, but not towards creaming. GGM (0.5 or 1.0 wt %) stabilized emulsions (5 wt % oil) showed no creaming behavior, but a clear bimodal distribution with some destabilization over the storage time of 1 month. Combinations of CNFs and GGM for stabilization of emulsions with 5 wt % oil, provided good stability towards creaming and a slower emulsion destabilization than for GGM alone. GGM could also improve the stability towards oxidation by delaying the initiation of lipid oxidation. Use of CNFs and combinations of GGM and CNFs can thus be away to obtain stable emulsions, such as mayonnaise and beverage emulsions.
  • Becker, Anna; Schalin-Jäntti, Camilla; Itkonen, Outi (2021)
    Context: Patients with serotonin-secreting neuroendocrine neoplasms (NENs) have increased serum 5-hydroxyindoleacetic acid (5HIAA) concentrations. Serum 5HIAA thus serves as a biomarker in NEN. Objective: To evaluate an improved tandem mass spectrometric serum 5HIAA assay for diagnosis and follow-up of NEN in a clinical cohort. Design: A retrospective study during 2016-2018 at the Diagnostic Center and Department of Endocrinology at Helsinki University Hospital, Finland. Methods: Detailed patient data was obtained from 116 patients. Serum 5HIAA was analyzed by 2 different liquid chromatography with tandem mass spectrometry (LC-MS/MS) assays with samples prepared either by protein precipitation or solid phase extraction. Twenty-four-hour urine 5HIAA samples (n = 33) were analyzed by amperometric LC, and the results were compared. Specificity and sensitivity were calculated by receiver operating characteristic (ROC) analysis. Results: We achieved 5 to 10 000 nmol/L linearity and Conclusion: Serum 5HIAA by LC-MS/MS after protein precipitation performs equally well for the diagnosis of NEN as urinary 5HIAA LC assay. The outcome and sensitivity for serum and 24-h urine assays are convergent. Due to much more reliable and convenient sampling, we recommend serum instead of 24-h urine 5HIAA for diagnosis and follow-up of NEN patients.
  • Rytkönen, Kaisa; Ventä, Irja (2018)
    The aim of the study was to evaluate the proximity of the mandibular third molar (M3) and the inferior alveolar canal (IAC) in a panoramic radiograph of 20-year-old subjects. The specific aim was to assess differences in this proximity over time. Two similar samples of panoramic radiographs taken in a routine oral health examination with 20-year time interval were examined retrospectively and images with both mandibular M3s were included. The material consisted of 300 subjects (25% men, mean age 20.5 +/- 0.6 years). The radiographic relationship between the mandibular M3 root and the IAC was assessed as follows: the M3 root was either apart from, tangential to, superimposed with, or inferior to the IAC. Differences between frequencies were tested using the chi-squared test. In the combined samples, only 16% of the M3s located apart from the IAC, 15% located tangential to, 61% superimposed with, and 8% inferior to the IAC. The proportion of the intimate locations had increased during the 20-year time interval from 79 to 88% (P <0.01) and especially in females (P <0.05). The vast majority of the mandibular M3s situated very close to the mandibular canal. Our results suggest that in the cohort of 20-year-old non-extraction subjects, most of the M3s are possibly at risk for inferior alveolar nerve injury at removal, as judged from the panoramic radiograph, and also the number of such teeth has increased over the 20-year period.
  • Rahikainen, Anna-Liina; Palo, Jukka U.; de Leeuw, Wiljo; Budowle, Bruce; Sajantila, Antti (2016)
    Blood samples preserved on FTA cards offer unique opportunities for genetic research. DNA recovered from these cards should be stable for long periods of time. However, it is not well established as how well the DNA stored on FTA card for substantial time periods meets the demands of forensic or genomic DNA analyses and especially so for from post-mortem (PM) samples in which the quality can vary upon initial collection. The aim of this study was to evaluate the time-dependent degradation on DNA quality and quantity extracted from up to 16 years old post-mortem bloodstained FTA cards. Four random FTA samples from eight time points spanning 1998 to 2013 (n = 32) were collected and extracted in triplicate. The quantity and quality of the extracted DNA samples were determined with Quantifiler (R) Human Plus (HP) Quantification kit. Internal sample and sample-to-sample variation were evaluated by comparing recovered DNA yields. The DNA from the triplicate samplings were subsequently combined and normalized for further analysis. The practical effect of degradation on DNA quality was evaluated from normalized samples both with forensic and pharmacogenetic target markers. Our results suggest that (1) a PM change, e.g. blood clotting prior to sampling, affects the recovered DNA yield, creating both internal and sample-to-sample variation; (2) a negative correlation between the FTA card storage time and DNA quantity (r = -0.836 at the 0.01 level) was observed; (3) a positive correlation (r = 0.738 at the level 0.01) was found between FTA card storage time and degradation levels. However, no inhibition was observed with the method used. The effect of degradation was manifested clearly with functional applications. Although complete STR-profiles were obtained for all samples, there was evidence of degradation manifested as decreased peak heights in the larger-sized amplicons. Lower amplification success was notable with the large 5.1 kb CYP2D6 gene fragment which strongly supports degradation of the stored samples. According to our results, DNA stored on FTA cards is rather stable over a long time period. DNA extracted from this storage medium can be used as human identification purposes as the method used is sufficiently sensitive and amplicon sizes tend to be <400 bp. However, DNA integrity was affected during storage. This effect should be taken into account depending on the intended application especially if high quality DNA and long PCR amplicons are required. (C) 2016 Elsevier Ireland Ltd. All rights reserved.
  • Astikainen, Piia; Mällo, Tanel; Ruusuvirta, Timo; Naatanen, Risto (2014)
  • Khazaei, Hamid; Purves, Randy W.; Hughes, Jessa; Link, Wolfgang; O'Sullivan, Donal M.; Schulman, Alan H.; Bjornsdotter, Emilie; Geu-Flores, Fernando; Nadzieja, Marcin; Andersen, Stig U.; Stougaard, Jens; Vandenberg, Albert; Stoddard, Frederick L. (2019)
    Background: Faba bean (Vicia faba L.) seeds are an excellent source of plant-based protein. In spite of the vast nutritional and environmental benefits provided by faba bean cultivation, its use as a food crop has been restricted, primarily due to the presence of the pyrimidine glycosides vicine and convicine (v-c). Ingestion of v-c can cause favism in individuals with a genetically inherited deficiency in glucose-6-phosphate dehydrogenase (G6PD). In monogastric animals, v-c can cause decreased feeding efficiency. The elimination of these glucosides is a goal of most faba bean breeding programs worldwide. Scope and approach: Our review focuses on the current genetic, molecular and biochemical knowledge surrounding the accumulation of v-c in faba beans. The gap between the current knowledge and what remains unknown is discussed. This review also explores historical and obscure information on v-c in faba bean. Key findings and conclusions: A low-v-c faba bean line was identified in the 1980s and this trait has been introduced into several modern cultivars. It has been shown that low-v-c faba beans are safe for G6PD-deficient individuals. A robust molecular marker is now available for marker-assisted breeding to reduce levels of v-c. The biosynthetic pathway of v-c is not yet understood and is currently under investigation. An international coordinated effort, led by the authors of this paper, is making progress towards full elucidation of the pathway. Further efforts in this direction could lead to lower levels of these compounds than the current low v-c genotypes offer, perhaps even complete elimination.
  • Jyske, Tuula; Brännström, Hanna; Sarjala, Tytti; Hellström, Jarkko; Halmemies, Eelis; Raitanen, Jan-Erik; Kaseva, Janne; Lagerquist, Lucas; Eklund, Patrik; Nurmi, Juha (2020)
    Softwood bark is an important by-product of forest industry. Currently, bark is under-utilized and mainly directed for energy production, although it can be extracted with hot water to obtain compounds for value-added use. In Norway spruce (Picea abies[L.] Karst.) bark, condensed tannins and stilbene glycosides are among the compounds that comprise majority of the antioxidative extractives. For developing feasible production chain for softwood bark extractives, knowledge on raw material quality is critical. This study examined the fate of spruce bark tannins and stilbenes during storage treatment with two seasonal replications (i.e., during winter and summer). In the experiment, mature logs were harvested and stored outside. During six-month-storage periods, samples were periodically collected for chemical analysis from both inner and outer bark layers. Additionally, bark extractives were analyzed for antioxidative activities by FRAP, ORAC, and H(2)O(2)scavenging assays. According to the results, stilbenes rapidly degraded during storage, whereas tannins were more stable: only 5-7% of the original stilbene amount and ca. 30-50% of the original amount of condensed tannins were found after 24-week-storage. Summer conditions led to the faster modification of bark chemistry than winter conditions. Changes in antioxidative activity were less pronounced than those of analyzed chemical compounds, indicating that the derivatives of the compounds contribute to the antioxidative activity. The results of the assays showed that, on average, ca. 27% of the original antioxidative capacity remained 24 weeks after the onset of the storage treatment, while a large variation (2-95% of the original capacity remaining) was found between assays, seasons, and bark layers. Inner bark preserved its activities longer than outer bark, and intact bark attached to timber is expected to maintain its activities longer than a debarked one. Thus, to ensure prolonged quality, no debarking before storage is suggested: outer bark protects the inner bark, and debarking enhances the degradation.
  • Koskinen, Janne; Roslin, Tomas; Nyman, Tommi; Abrego, Nerea; Michell, Craig; Vesterinen, Eero J. (2019)
    Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour-intensive methods involving cultivation and morphology-based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties of fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (a) initial salt-isopropanol extraction of all nucleic acids in the sample is followed by (b) an extra clean-up step using solid-phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples-regardless of biomass or other properties-being successfully PCR-amplified using metabarcoding primers and subsequently sequenced. As a proof of concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus-associated communities, that is, do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing 10 species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology-based identifications, we find a species-rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus-associated interaction webs and communities.
  • Santangeli, Andrea; Toivonen, Tuuli; Pouzols, Federico Montesino; Pogson, Mark; Hastings, Astley; Smith, Pete; Moilanen, Atte (2016)
    Reliance on fossil fuels is causing unprecedented climate change and is accelerating environmental degradation and global biodiversity loss. Together, climate change and biodiversity loss, if not averted urgently, may inflict severe damage on ecosystem processes, functions and services that support the welfare of modern societies. Increasing renewable energy deployment and expanding the current protected area network represent key solutions to these challenges, but conflicts may arise over the use of limited land for energy production as opposed to biodiversity conservation. Here, we compare recently identified core areas for the expansion of the global protected area network with the renewable energy potential available from land-based solar photovoltaic, wind energy and bioenergy (in the form of Miscanthusxgiganteus). We show that these energy sources have very different biodiversity impacts and net energy contributions. The extent of risks and opportunities deriving from renewable energy development is highly dependent on the type of renewable source harvested, the restrictions imposed on energy harvest and the region considered, with Central America appearing at particularly high potential risk from renewable energy expansion. Without restrictions on power generation due to factors such as production and transport costs, we show that bioenergy production is a major potential threat to biodiversity, while the potential impact of wind and solar appears smaller than that of bioenergy. However, these differences become reduced when energy potential is restricted by external factors including local energy demand. Overall, we found that areas of opportunity for developing solar and wind energy with little harm to biodiversity could exist in several regions of the world, with the magnitude of potential impact being particularly dependent on restrictions imposed by local energy demand. The evidence provided here helps guide sustainable development of renewable energy and contributes to the targeting of global efforts in climate mitigation and biodiversity conservation.
  • Driver, Gordon W.; Sprakel, Lisette J. M.; Kilpelainen, Ilkka; Schuur, Boelo (2021)
    Isothermal titration calorimetry (ITC) experiments were performed for investigation of binary mixtures comprised of the Bronsted superbase DBN with hydrogen ethanoate (AcOH). The heat of mixing (H-E) profile was recorded at (343.15 +/- 0.1) K and fitted with a 5-parameter Redlich-Kister (RK) polynomial. RK fit parameters were subsequently used to quantify partial molar heats of mixing, x(i)H(i)(E), for each component i. ITC-based complexometric titration data for the binary mixtures were recorded separately in methyl isobutyl ketone (mibk) and dodecane, to investigate the energetics of non random clustering phenomena. Variable temperature H-1-NMR in combination with ATR-FTIR spectroscopic analyses were employed in parallel for elucidation and verification of liquid state ion speciation. These investigations reveal a strongly non ideal system, and indicate "superbase" character of DBN is preserved for specific compositions where stoichiometric ionic liquids (ILs) form. Available ion speciation has been found to include [DBN-H](+), [AcO] as well as mu 2 -hydrogen-bridged, hydrogen-bonded homoassociate anions, of the type [H(OAc)(2)], with double liquid salt formation characterising various compositions based on spectroscopic determinations. (C) 2021 The Authors. Published by Elsevier Ltd.
  • Cai, Zongping; Sun, Yan; Deng, Yanghong; Zheng, Xiaojie; Sun, Shuiyu; Romantschuk, Martin; Sinkkonen, Aki (2021)
    Electrokinetic (EK) remediation has been widely studied at laboratory scales. However, field-scale research is far less. In this study, a 14-day EK remediation was carried out, in a field pilot (4 m2) test and a full-scale (200 m2) application for the first time, in a cadmium (Cd) contaminated paddy agricultural field near a mining area. A low voltage of 20 V was applied at both scales; voltage gradient was 20 V m & minus;1 and 4 V m & minus;1 at the pilot and full scales, respectively. Samples were taken from near the anode and cathode, and in the middle of the electric field, in the soil layers 0-10 cm, 10-20 cm, and 40-50 cm. After the EK remediation, a significant portion of the total Cd was removed in all the layers at the pilot scale, by 87%, 72%, and 54% from the top down, but only in the 0-10 cm layer at the full scale by 74%. As for the plant available (exchangeable and soluble) Cd, significant removal (64%) was only observed in the 0-10 cm layer at the pilot scale. The percentage reduction of the electrical conductivity and removal efficiency of the total Cd was higher near the anode than the cathode. The soil pH was elevated near the cathode but stayed below pH 6 due to the sufficient supply of lactic acid. After the EK remediation, the concentration of the total Cd dropped below the hazard threshold, i.e. 0.4 mg (kg dry wt soil)& minus;1 for agricultural paddy fields in China. A total energy of 2 kW & middot;h and 0.6 kW & middot;h was consumed at the pilot and full scales, respec-tively. This study showed a successful in situ EK remediation of Cd contaminated paddy agricultural soil, espe-cially in the surface layer, with low voltage and energy demand. (c) 2021 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
  • Vesth, Tammi C.; Nybo, Jane L.; Theobald, Sebastian; Frisvad, Jens C.; Larsen, Thomas O.; Nielsen, Kristian F.; Hoof, Jakob B.; Brandl, Julian; Salamov, Asaf; Riley, Robert; Gladden, John M.; Phatale, Pallavi; Nielsen, Morten T.; Lyhne, Ellen K.; Kogle, Martin E.; Strasser, Kimchi; McDonnell, Erin; Barry, Kerrie; Clum, Alicia; Chen, Cindy; LaButti, Kurt; Haridas, Sajeet; Nolan, Matt; Sandor, Laura; Kuo, Alan; Hainaut, Matthieu; Drula, Elodie; Tsang, Adrian; Magnuson, Jon K.; Henrissat, Bernard; Wiebenga, Ad; Simmons, Blake A.; Makela, Miia R.; de Vries, Ronald P.; Grigoriev, Igor V.; Mortensen, Uffe H.; Baker, Scott E.; Andersen, Mikael R. (2018)
    Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter-and intraspecies genomic variation. We further predicted 17,903 carbohydrateactive enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.
  • Vesala, Tommi; Ekholm, Marja; Ventä, Irja (2021)
    Objective:The purpose of this study was to determine, if a dental panoramic tomograph (DPT) is appropriate for every young adult due to third molars. Materials and methods:The study sample consisted of 217 university students (20% men and 80% women; mean age 20.7 years; SD +/- 0.6 years) and included a questionnaire about symptoms caused by third molars, clinical oral examination of third molars, and a DPT. Subjects were divided into the following groups: subjects with a clinical indication for a DPT and subjects without such indication. The DPTs were then examined for findings regarding third molars. Results:Clinical indication for a DPT was observed in 64% of the subjects. Radiography revealed an additional 1.4% of the subjects with >= 1 radiographic signs of disease in relation to their third molars. Also, an additional 27% of the subjects had >= 1 other radiographic findings in relation to third molars that may have affected the clinical decision making. Conclusions:In our study population, clinically undetectable pathology cannot be considered as an indication for a DPT. However, if prevailing clinical practice supports preventive removals and detecting or monitoring of unerupted third molars, a referral to DPT can be considered as good clinical practice.
  • Scala, Giovanni; Federico, Antonio; Fortino, Vittorio; Greco, Dario; Majello, Barbara (2020)
    The explosion of omics data availability in cancer research has boosted the knowledge of the molecular basis of cancer, although the strategies for its definitive resolution are still not well established. The complexity of cancer biology, given by the high heterogeneity of cancer cells, leads to the development of pharmacoresistance for many patients, hampering the efficacy of therapeutic approaches. Machine learning techniques have been implemented to extract knowledge from cancer omics data in order to address fundamental issues in cancer research, as well as the classification of clinically relevant sub-groups of patients and for the identification of biomarkers for disease risk and prognosis. Rule induction algorithms are a group of pattern discovery approaches that represents discovered relationships in the form of human readable associative rules. The application of such techniques to the modern plethora of collected cancer omics data can effectively boost our understanding of cancer-related mechanisms. In fact, the capability of these methods to extract a huge amount of human readable knowledge will eventually help to uncover unknown relationships between molecular attributes and the malignant phenotype. In this review, we describe applications and strategies for the usage of rule induction approaches in cancer omics data analysis. In particular, we explore the canonical applications and the future challenges and opportunities posed by multi-omics integration problems.
  • Li, Xinpei; Lan, Hangzhen; Hartonen, Kari; Jussila, Matti; Wang, Xinghua; Riekkola, Marja-Liisa (2020)
    Today, wide variety of adsorbents have been developed for sample pretreatment to concentrate and separate harmful substances. However, only a few solid phase microextraction Arrow adsorbents are commercially available. In this study, we developed a new solid phase microextraction Arrow coating, in which nanosheets layered double hydroxides and poly(vinylpyrrolidone) were utilized as the extraction phase and poly(vinyl chloride) as the adhesive. This new coating entailed higher extraction capacity for several volatile organic compounds (allyl methyl sulfide, methyl propyl sulfide, 3-pentanone, 2-butanone, and methyl isobutyl ketone) compared to the commercial Carboxen 1000/polydimethylsiloxane coating. Fabrication parameters for the coating were optimized and extraction and desorption conditions were investigated. The validation of the new solid phase microextraction Arrow coating was accomplished using water sample spiked with volatile organic compounds. Under the optimal conditions, the limits of quantification for the five volatile organic compounds by the new solid phase microextraction Arrow coating and developed gas chromatography with mass spectrometry method were in the range of 0.2-4.6 ng/mL. The proposed method was briefly applied for enrichment of volatile organic compounds in sludge.