Making the impact on research and society: a case study - open repository and crowdsourcing solutions developed for the Finno-Ugric Digitization Pilot Project at the National Library of Finland

Jussi-Pekka Hakkaraisen esitys 24. Kansainvälisessä tieteen-, teknologian ja lääketieteen historian kongressissa (24th International Congress of History of Science, Technology and Medicine) Manchesterissa 26.7.2013

A Modified phosphate-carrier protein theory is proposed as a non-target site mechanism For glyphosate resistance in weeds

Glyphosate is an herbicide that inhibits the enzyme 5-enolpyruvyl-shikimate-3-phosphate synthase (EPSPs) (EC 2.5.1.19). EPSPs is the sixth enzyme of the shikimate pathway, by which plants synthesize the aromatic amino acids phenylalanine, tyrosine, and tryptophan and many compounds used in secondary metabolism pathways. About fifteen years ago it was hypothesized that it was unlikely weeds would evolve resistance to this herbicide because of the limited degree of glyphosate metabolism observed in plants, the low resistance level attained to EPSPs gene overexpression, and because of the lower fitness in plants with an altered EPSPs enzyme. However, today 20 weed species have been described with glyphosate resistant biotypes that are found in all five continents of the world and exploit several different resistant mechanisms. The survival and adaptation of these glyphosate resistant weeds are related toresistance mechanisms that occur in plants selected through the intense selection pressure from repeated and exclusive use of glyphosate as the only control measure. In this paper the physiological, biochemical, and genetic basis of glyphosate resistance mechanisms in weed species are reviewed and a novel and innovative theory that integrates all the mechanisms of non-target site glyphosate resistance in plants is presented.

Developing Bioimage Informatics – from Microscopy to Software Solutions – with alpha2beta1 Integrin as a Case Study

Biokuvainformatiikan kehittäminen – mikroskopiasta ohjelmistoratkaisuihin – sovellusesimerkkinä α2β1-integriini Kun ihmisen genomi saatiin sekvensoitua vuonna 2003, biotieteiden päätehtäväksi tuli selvittää eri geenien tehtävät, ja erilaisista biokuvantamistekniikoista tuli keskeisiä tutkimusmenetelmiä. Teknologiset kehitysaskeleet johtivat erityisesti fluoresenssipohjaisten valomikroskopiatekniikoiden suosion räjähdysmäiseen kasvuun, mutta mikroskopian tuli muuntua kvalitatiivisesta tieteestä kvantitatiiviseksi. Tämä muutos synnytti uuden tieteenalan, biokuvainformatiikan, jonka on sanottu mahdollisesti mullistavan biotieteet. Tämä väitöskirja esittelee laajan, poikkitieteellisen työkokonaisuuden biokuvainformatiikan alalta. Väitöskirjan ensimmäinen tavoite oli kehittää protokollia elävien solujen neliulotteiseen konfokaalimikroskopiaan, joka oli yksi nopeimmin kasvavista biokuvantamismenetelmistä. Ihmisen kollageenireseptori α2β1-integriini, joka on tärkeä molekyyli monissa fysiologisissa ja patologisissa prosesseissa, oli sovellusesimerkkinä. Työssä saavutettiin selkeitä visualisointeja integriinien liikkeistä, yhteenkeräytymisestä ja solun sisään siirtymisestä, mutta työkaluja kuvainformaation kvantitatiiviseen analysointiin ei ollut. Väitöskirjan toiseksi tavoitteeksi tulikin tällaiseen analysointiin soveltuvan tietokoneohjelmiston kehittäminen. Samaan aikaan syntyi biokuvainformatiikka, ja kipeimmin uudella alalla kaivattiin erikoistuneita tietokoneohjelmistoja. Tämän väitöskirjatyön tärkeimmäksi tulokseksi muodostui näin ollen BioImageXD, uudenlainen avoimen lähdekoodin ohjelmisto moniulotteisten biokuvien visualisointiin, prosessointiin ja analysointiin. BioImageXD kasvoi yhdeksi alansa suurimmista ja monipuolisimmista. Se julkaistiin Nature Methods -lehden biokuvainformatiikkaa käsittelevässä erikoisnumerossa, ja siitä tuli tunnettu ja laajalti käytetty. Väitöskirjan kolmas tavoite oli soveltaa kehitettyjä menetelmiä johonkin käytännönläheisempään. Tehtiin keinotekoisia piidioksidinanopartikkeleita, joissa oli "osoitelappuina" α2β1-integriinin tunnistavia vasta-aineita. BioImageXD:n avulla osoitettiin, että nanopartikkeleilla on potentiaalia lääkkeiden täsmäohjaussovelluksissa. Tämän väitöskirjatyön yksi perimmäinen tavoite oli edistää uutta ja tuntematonta biokuvainformatiikan tieteenalaa, ja tämä tavoite saavutettiin erityisesti BioImageXD:n ja sen lukuisten julkaistujen sovellusten kautta. Väitöskirjatyöllä on merkittävää potentiaalia tulevaisuudessa, mutta biokuvainformatiikalla on vakavia haasteita. Ala on liian monimutkainen keskimääräisen biolääketieteen tutkijan hallittavaksi, ja alan keskeisin elementti, avoimen lähdekoodin ohjelmistokehitystyö, on aliarvostettu. Näihin seikkoihin tarvitaan useita parannuksia,

Making the impact on research and society : a case study: crowdsourcing solutions developed for the linguistic research and citizen science

Can crowdsourcing solutions serve many masters? Can they be beneficial for both, for the layman or native speakers of minority languages on the one hand and serious linguistic research on the other? How did an infrastructure that was designed to support linguistics turn out to be a solution for raising awareness of native languages? Since 2012 the National Library of Finland has been developing the Digitisation Project for Kindred Languages, in which the key objective is to support a culture of openness and interaction in linguistic research, but also to promote crowdsourcing as a tool for participation of the language community in research. In the course of the project, over 1,200 monographs and nearly 111,000 pages of newspapers in Finno-Ugric languages will be digitised and made available in the Fenno-Ugrica digital collection. This material was published in the Soviet Union in the 1920s and 1930s, and users have had only sporadic access to the material. The publication of open-access and searchable materials from this period is a goldmine for researchers. Historians, social scientists and laymen with an interest in specific local publications can now find text materials pertinent to their studies. The linguistically-oriented population can also find writings to delight them: (1) lexical items specific to a given publication, and (2) orthographically-documented specifics of phonetics. In addition to the open access collection, we developed an open source code OCR editor that enables the editing of machine-encoded text for the benefit of linguistic research. This tool was necessary since these rare and peripheral prints often include already archaic characters, which are neglected by modern OCR software developers but belong to the historical context of kindred languages, and are thus an essential part of the linguistic heritage. When modelling the OCR editor, it was essential to consider both the needs of researchers and the capabilities of lay citizens, and to have them participate in the planning and execution of the project from the very beginning. By implementing the feedback iteratively from both groups, it was possible to transform the requested changes as tools for research that not only supported the work of linguistics but also encouraged the citizen scientists to face the challenge and work with the crowdsourcing tools for the benefit of research. This presentation will not only deal with the technical aspects, developments and achievements of the infrastructure but will highlight the way in which user groups, researchers and lay citizens were engaged in a process as an active and communicative group of users and how their contributions were made to mutual benefit.

Analyses of the usefulness of Software Defined Storage Solutions for Web-based Digital Preservation Applications

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

ReShare and ReCollect: EPrints data repository solutions developed at the UK Data Archive

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Modified nano- and microcellulose based adsorption materials in water treatment

In recent decades, industrial activity growth and increasing water usage worldwide have led to the release of various pollutants, such as toxic heavy metals and nutrients, into the aquatic environment. Modified nanocellulose and microcellulose-based adsorption materials have the potential to remove these contaminants from aqueous solutions. The present research consisted of the preparation of five different nano/microcellulose-based adsorbents, their characterization, the study of adsorption kinetics and isotherms, the determination of adsorption mechanisms, and an evaluation of adsorbents’ regeneration properties. The same well known reactions and modification methods that were used for modifying conventional cellulose also worked for microfibrillated cellulose (MFC). The use of succinic anhydride modified mercerized nanocellulose, and aminosilane and hydroxyapatite modified nanostructured MFC for the removal of heavy metals from aqueous solutions exhibited promising results. Aminosilane, epoxy and hydroxyapatite modified MFC could be used as a promising alternative for H2S removal from aqueous solutions. In addition, new knowledge about the adsorption properties of carbonated hydroxyapatite modified MFC as multifunctional adsorbent for the removal of both cations and anions ions from water was obtained. The maghemite nanoparticles (Fe3O4) modified MFC was found to be a highly promising adsorbent for the removal of As(V) from aqueous solutions due to its magnetic properties, high surface area, and high adsorption capacity . The maximum removal efficiencies of each adsorbent were studied in batch mode. The results of adsorption kinetics indicated very fast removal rates for all the studied pollutants. Modeling of adsorption isotherms and adsorption kinetics using various theoretical models provided information about the adsorbent’s surface properties and the adsorption mechanisms. This knowledge is important for instance, in designing water treatment units/plants. Furthermore, the correspondence between the theory behind the model and properties of the adsorbent as well as adsorption mechanisms were also discussed. On the whole, both the experimental results and theoretical considerations supported the potential applicability of the studied nano/microcellulose-based adsorbents in water treatment applications.

Malaria vaccine: roadblocks and possible solutions

Malaria remains the most prevalent and devastating parasitic disease worldwide. Vaccination is considered to be an approach that will complement other strategies for prevention and control of the disease in the future. In the last 10 years, intense studies aimed at the development of a malaria vaccine have provided important knowledge of the nature of the host immunological mechanisms of protection and their respective target antigens. It became well established that protective immune responses can be generated against the distinct stages of Plasmodium. However, in general, protective immune responses are directed at stage-specific antigens. The elucidation of the primary structure of these antigens made possible the generation of synthetic and recombinant proteins that are being extensively used in experimental immunizations against the infection. Today, several epitopes of limited polymorphism have been described and protective immunity can be generated by immunization with them. These epitopes are being tested as primary candidates for a subunit vaccine against malaria. Here we critically review the major roadblocks for the development of a malaria vaccine and provide some insight on how these problems are being solved

Liquid cooling solutions for rotating permanent magnet synchronous machines

In the design of electrical machines, efficiency improvements have become very important. However, there are at least two significant cases in which the compactness of electrical machines is critical and the tolerance of extremely high losses is valued: vehicle traction, where very high torque density is desired at least temporarily; and direct-drive wind turbine generators, whose mass should be acceptably low. As ever higher torque density and ever more compact electrical machines are developed for these purposes, thermal issues, i.e. avoidance of over-temperatures and damage in conditions of high heat losses, are becoming of utmost importance. The excessive temperatures of critical machine components, such as insulation and permanent magnets, easily cause failures of the whole electrical equipment. In electrical machines with excitation systems based on permanent magnets, special attention must be paid to the rotor temperature because of the temperature-sensitive properties of permanent magnets. The allowable temperature of NdFeB magnets is usually significantly less than 150 ˚C. The practical problem is that the part of the machine where the permanent magnets are located should stay cooler than the copper windings, which can easily tolerate temperatures of 155 ˚C or 180 ˚C. Therefore, new cooling solutions should be developed in order to cool permanent magnet electrical machines with high torque density and because of it with high concentrated losses in stators. In this doctoral dissertation, direct and indirect liquid cooling techniques for permanent magnet synchronous electrical machines (PMSM) with high torque density are presented and discussed. The aim of this research is to analyse thermal behaviours of the machines using the most applicable and accurate thermal analysis methods and to propose new, practical machine designs based on these analyses. The Computational Fluid Dynamics (CFD) thermal simulations of the heat transfer inside the machines and lumped parameter thermal network (LPTN) simulations both presented herein are used for the analyses. Detailed descriptions of the simulated thermal models are also presented. Most of the theoretical considerations and simulations have been verified via experimental measurements on a copper tooth-coil (motorette) and on various prototypes of electrical machines. The indirect liquid cooling systems of a 100 kW axial flux (AF) PMSM and a 110 kW radial flux (RF) PMSM are analysed here by means of simplified 3D CFD conjugate thermal models of the parts of both machines. In terms of results, a significant temperature drop of 40 ̊C in the stator winding and 28 ̊C in the rotor of the AF PMSM was achieved with the addition of highly thermally conductive materials into the machine: copper bars inserted in the teeth, and potting material around the end windings. In the RF PMSM, the potting material resulted in a temperature decrease of 6 ̊C in the stator winding, and in a decrease of 10 ̊C in the rotor embedded-permanentmagnets. Two types of unique direct liquid cooling systems for low power machines are analysed herein to demonstrate the effectiveness of the cooling systems in conditions of highly concentrated heat losses. LPTN analysis and CFD thermal analysis (the latter being particularly useful for unique design) were applied to simulate the temperature distribution within the machine models. Oil-immersion cooling provided good cooling capability for a 26.6 kW PMSM of a hybrid vehicle. A direct liquid cooling system for the copper winding with inner stainless steel tubes was designed for an 8 MW directdrive PM synchronous generator. The design principles of this cooling solution are described in detail in this thesis. The thermal analyses demonstrate that the stator winding and the rotor magnet temperatures are kept significantly below their critical temperatures with demineralized water flow. A comparison study of the coolant agents indicates that propylene glycol is more effective than ethylene glycol in arctic conditions.

Inhibition of carbachol-induced inositol phosphate accumulation in the embryonic retina promoted by kainate and veratridine

In the present study, we report that low concentrations of the glutamate ionotropic agonist kainate decreased the turnover of [3H]-phosphoinositides ([3H]-InsPs) induced by muscarinic receptors in the chick embryonic retina. When 100 µM carbachol was used, the estimated IC50 value for kainate was 0.2 µM and the maximal inhibition of ~50% was obtained with 1 µM or higher concentrations of the glutamatergic agonist. Our data also show that veratridine, a neurotoxin that increases the permeability of voltage-sensitive sodium channels, had no effect on [3H]-InsPs levels of the embryonic retina. However, 50 µM veratridine, but not 50 mM KCl, inhibited ~65% of the retinal response to carbachol. While carbachol increased [3H]-InsPs levels from 241.2 ± 38.0 to 2044.5 ± 299.9 cpm/mg protein, retinal response decreased to 861.6 ± 113.9 cpm/mg protein when tissues were incubated with carbachol plus veratridine. These results suggest that the accumulation of phosphoinositides induced by activation of muscarinic receptors can be inhibited by the influx of Na+ ions triggered by activation of kainate receptors or opening of voltage-sensitive sodium channels in the chick embryonic retina.

Annual changes in serum calcium and inorganic phosphate levels and correlation with gonadal status of a freshwater murrel, Channa punctatus (Bloch)

Adult Channa punctatus murrels of both sexes (60-80 g) were collected locally from Ramgarh Lake during the second week of every month (10 individuals of each sex/month) throughout the year. Blood samples were collected and analyzed for serum calcium and phosphate levels by the methods of Trinder (1960) and Fiske and Subbarow (1925), respectively. Gonads were fixed to judge the state of maturation of the fish. Males exhibited no change in serum calcium levels throughout the year in correlation with testicular maturation. However, serum phosphate levels exhibited a rise in correlation with the increased gonadosomatic index. Females showed marked seasonal changes in serum calcium and phosphate levels which were associated with ovarian maturation (vitellogenesis).

Flavianate, an amino acid precipitant, is a competitive inhibitor of trypsin at pH 3.0

Textile dyes bind to proteins leading to selective co-precipitation of a complex involving one protein molecule and more than one dye molecule of opposite charge in acid solutions, in a process of reversible denaturation that can be utilized for protein fractionation. In order to understand what occurs before the co-precipitation, a kinetic study using bovine ß-trypsin and sodium flavianate was carried out based on reaction progress curve techniques. The experiments were carried out using a-CBZ-L-Lys-p-nitrophenyl ester as substrate which was added to 50 mM sodium citrate buffer, pH 3.0, containing varying concentrations of ß-trypsin and dye. The reaction was recorded spectrophotometrically at 340 nm for 30 min, and the families of curves obtained were analyzed simultaneously by fitting integrated Michaelis-Menten equations. The dye used behaved as a competitive inhibitor of trypsin at pH 3.0, with Ki = 99 µM; kinetic parameters for the substrate hydrolysis were: Km = 32 µM, and kcat = 0.38/min. The competitive character of the inhibition suggests a specific binding of the first dye molecule to His-57, the only positively charged residue at the active site of the enzyme.

Erythrocyte glucose-6-phosphate dehydrogenase activity assay and affinity for its substrate under "physiological" conditions

Glucose-6-phosphate dehydrogenase (G6PD) activity and the affinity for its substrate glucose-6-phosphate were investigated under conditions similar to the physiological environment in terms of ionic strength (I: 0.188), cation concentration, pH 7.34, and temperature (37oC). A 12.4, 10.4 and 21.4% decrease was observed in G6PD B, G6PD A+ and G6PD A- activities, respectively. A Km increase of 95.1, 94.4 and 95.4% was observed in G6PD B, G6PD A+ and G6PD A-, respectively, leading to a marked decrease in affinity. In conclusion, the observation of the reduced activity and affinity for its natural substrate reflects the actual pentose pathway rate. It also suggests a much lower NADPH generation, which is crucial mostly in G6PD-deficient individuals, whose NADPH availability is poor.

Zinc accumulation in phosphate granules of Ucides cordatus hepatopancreas

Amorphous phosphate granules are present in vertebrate and invertebrate organisms. The functions attributed to these structures depend on their mineral contents and organic matrix composition. In the present study we have determined zinc concentrations in the hepatopancreas of the crab Ucides cordatus from regions contaminated with zinc, and the elemental composition of hepatopancreal phosphate granules. Organisms were collected from the contaminated areas of Sepetiba Bay (SB) and Guanabara Bay (GB), and from a non-contaminated area, Ribeira Bay (RB). The first two sites are located near the metropolitan region of Rio de Janeiro city, Brazil. Atomic absorption spectroscopy (AAS) showed a significant difference (P<0.05) for zinc concentration in the hepatopancreas from organisms collected at the contaminated sites GB (210 ± 20 µg/g dry weight) and SB (181 ± 16 µg/g dry weight) compared to the non-contaminated site RB (76 ± 14 µg/g dry weight). Phosphate granules isolated from hepatopancreatic tissue were studied by electron diffraction (ED), energy dispersive X-ray analysis (EDX) and electron spectroscopic imaging (ESI). ED of granules presented no diffraction spots, indicating that these structures are in an amorphous state, while EDX of granules isolated from a contaminated area contained P, Ca and Zn. Mg, Cl and Fe were also found in some of the spectra. ESI showed that O, P and Ca were colocalized in the mineralized layers of most granules observed. The correlation between the results obtained by AAS and those obtained by microanalytical techniques suggests that the hepatopancreatic granules of U. cordatus may be related to the phenomenon of heavy metal retention.