Vara-Paleosoikumi linguliformsete käsijalgsete kodade bakulaarne struktuur

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Käsijalgsed on rühm merelisi selgrootuid, kes asustasid merepõhja juba Kambriumi ajastul ning elavad ka tänapäeval. Nende keha on peidus kahe (selgmise ja kõhtmise) kojapoolme vahel, mis alamhõimkonna Linguliformea esindajatel koosneb kaltsiumfosfaadist (apatiidist). Linguliformsed käsijalgsed on sageli uurimisobjektideks skeletitekke, biomineralisatsiooni, evolutsiooni ning mineviku kliima uurimisel, kuid nende kasutamiseks on vaja teada, kuidas kojad geoloogilise aja jooksul muutuvad. Käesoleva doktoritöö eesmärgiks oli uurida käsijalgsete koja struktuuri ja keemilis-mineraloogilise koostise post mortem muutusi. Uuritud liikide koda iseloomustab bakulaarne struktuur, mida kujundavad apatiitsed pulgataolistest moodustistest (baakulatest) poorsemad kihid, mis esinevad vaheldumisi kompaktsete kihtidega. Kambriumi vanusega Obolus ruchini ja Ungula inornata ning Devoni vanusega Bicarinatina bicarinata kojapoolmete detailuuringud näitavad nii struktuuri kui ka keemilise koostise kojasisest varieerumist. Tüüpiliste baakulate kõrval avastati väga peened, 100–200 nanomeetrise diameetriga niitjad moodustised (nanofiibrid), mis moodustasid tõenäoliselt bakulaarse struktuuri orgaanilise raamistiku ja on säilinud kiire varajase fosfatiseerumise tulemusena. Nanofiibrite sarnane iseloom retsentsetes ja fossiilsetes kodades näitab, et linguliformsete käsijalgsete baakulate arengus ei ole Fanerosoikumi vältel toimunud olulisi muutusi. Eesti fosforiidikihindi ühe olulisema kivistise – käsijalgse Ungula ingrica kojapoolmete keemilis-mineraloogilised uuringud näitasid, et koja kompaktsetes kihtides esinev apatiit on nii keemilise koostise kui apatiidi morfoloogia poolest väga sarnane tänapäevaste linguliformsete käsijalgsete kojaapatiidile ning selle koostis võib kajastada looma eluaegseid keskkonnatingimusi. Bakulaarsete kihtide apatiit erineb nii koostiselt kui ka morfoloogialt, selle päritolu vajab edasist uurimist ning tõenäoliselt ei ole see kasutatav paleokeskkonna interpreteerimisel. Käsijalgsete kodade diageneesi põhilisteks etappideks on fosfatiseerumine, kojaapatiidi stabiliseerumine, apatiidi morfoloogia muutused ning lõpuks koja massiivseks muutumine sekundaarse apatiidi ladestumise tulemusel. Eesti fosforiit koosneb linguliformsete käsijalgsete kojapoolmetest, seega aitavad saadud tulemused paremini mõista fosforiidi omadusi ning kujunemise põhjusi ning võivad olla olulised fosforiidi tehnoloogiliste omaduste ning kaevandamisega seotud keskkonnaprobleemide analüüsimisel.Brachiopods are bivalved benthic marine invertebrates colonizing the seafloor since the Cambrian Period. The valves in the subphylum Linguliformea are composed of calcium phosphate (apatite). Linguliform brachiopods are important research objects for revealing the biomineralization patterns and evolution of mineralized skeletons as well as for gaining palaeoclimatic information stored in linguliform shell apatite. All these studies require understanding of taphonomic changes in biominerals and mineralized structures. The aim of this thesis was to study the structural and chemical variability of fossil linguliform brachiopod shells. The studied species are characterized by baculate shell structure that consists of porous laminae with small apatitic rods (bacula) alternating with compact laminae. Detailed studies of the valves of Cambrian Obolus ruchini and Ungula inornata as well as Devonian Bicarinatina bicarinata demonstrated remarkable variability in the shell structure and chemical composition. Narrow fibrils of 100–200 nm in diameter (nanofibrils) were discovered. These are similar to nanostructures shaping the baculate structure in modern linguliforms and likely represent originally non-mineralized (organic) fibrils preserved through rapid phosphatization. This suggests that the development of bacula has not much changed throughout the Phanerozoic. The studies of chemical composition and mineral morphology in the valves of Cambrian Ungula ingrica – one of the most characteristic fossil composing Estonian shelly phosphorite – revealed different chemical composition of the apatite in compact and baculate laminae. The apatite in compact laminae is morphologically and chemically similar to the shell apatite of modern linguliforms and may likely be used for biological or palaeoenvironmental interpretations. The apatite in baculate laminae is significantly different having only a limited potential for palaeoenvironmental analysis. The origin of this phase needs additional study. The successive stages of diagenetic changes in linguliform brachiopods are phosphatization, stabilization of original bioapatite, apatite transformations and structural homogenization. Estonian shelly phosphorite is mainly composed of the remains of linguliform shells and the new data on the structure and chemical composition of the shells may help to understand the properties and history of formation of phosphorite deposit, which may further provide information on technological characteristics of the phosphorite and help to solve environmental problems arising in course of mining

Constraining the conditions of phosphogenesis : stable isotope and trace element systematics of Recent Namibian phosphatic sediments

This study was supported by the Estonian Science Agency project PRG447 and the Estonian Centre of Analytical Chemistry. K. Paiste was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 894831. We would also like to thank the organizers and participants of the Regional Graduate Network in Oceanography Discovery Camp 2015, funded by the Agouron Institute and the Scientific Committee for Oceanographic Research (SCOR), as well as the Namibian Ministry of Fisheries and Marine Resources and the captain and crew of R/V Mirabilis for access to the coring site.Modern phosphogenesis occurs on continental margins influenced by upwelling and high primary productivity. The formation of phosphatic sediments is coupled to global climate fluctuations, biological cycling of phosphorus and local redox conditions. Although the processes involved in phosphogenesis are well described, high-resolution data on the redox and stable isotope systematics in Recent in-situ phosphorites are scarce. In this contribution, we investigate the trace element and sulfur, nitrogen and organic carbon stable isotope composition of Recent in-situ phosphatic sediments off the coast of Namibia. Also, we examine the reliability of different widely used geochemical proxies in phosphatic sediments. Our results suggest a shift from sulfidic to suboxic conditions, coinciding with the maximum in solid calcium phosphate mineral concentration. This shift is accompanied by unidirectional changes in Mo and Re enrichments and TOC abundance. Relatively low pyrite δ34S values (ca -20‰) of phosphatic sediments indicate open system fractionation during phosphogenesis. The initiation of phosphogenesis is also accompanied by negative shifts in sedimentary δ13Corg and δ15N values. Phosphate associated sulfate (PAS) δ34S values are lower than modern seawater sulfate values, suggesting the involvement of chemolithotrophic sulfur oxidation. Our results show a shift in redox conditions from sulfidic to (sub)oxic, coupled with active sulfur cycling are prerequisites for phosphogenesis. Phosphatic sediments show substantial enrichments in U and V highlighting the complexity of using these elements, as well as V/(V+Ni) and V/Cr, as redox proxies particularly in phosphorites and phosphatic sediments.PostprintPostprintPeer reviewe

TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)

The TBestDB database contains ∼370 000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and includes experimental information, consensus sequences, gene annotations and metabolic pathway predictions. Most of these ESTs have been generated by the Protist EST Program, a collaboration among six Canadian research groups. EST sequences are read from trace files up to a minimum quality cut-off, vector and linker sequence is masked, and the ESTs are clustered using phrap. The resulting consensus sequences are automatically annotated by using the AutoFACT program. The datasets are automatically checked for clustering errors due to chimerism and potential cross-contamination between organisms, and suspect data are flagged in or removed from the database. Access to data deposited in TBestDB by individual users can be restricted to those users for a limited period. With this first report on TBestDB, we open the database to the research community for free processing, annotation, interspecies comparisons and GenBank submission of EST data generated in individual laboratories. For instructions on submission to TBestDB, contact [email protected]. The database can be queried at

Prevalence study of abuse and violence against older women: results of a multi-cultural survey conducted in Austria, Belgium, Finland, Lithuania, and Portugal

Introduction • The study included women aged between 60 and 97 years who were living in private households. The survey asked about violence and abuse in the last 12 months. 2880 women were surveyed across five countries during 2010. • So-called “stranger violence” was ruled out and only perpetrators who were in the women's close circles were considered. • Response rates ranged from 26.1% (Belgium) to 49.1% (Austria). Prevalence of violence and abuse • Overall, 28.1% of older women had experienced some kind of violence or abuse. By country the prevalence rates were as follows: • Portugal 39.4% (postal survey) • Belgium 32.0% (postal survey and face-to-face interviews) • Finland 25.1% (postal survey) • Austria 23.8% (telephone survey (CATI)) • Lithuania 21.8% (face-to-face interviews) • Generally, emotional abuse was the most common form of violence experienced (23.6%) followed by financial abuse (8.8%), violation of rights (6.4%) and neglect (5.4%). Sexual abuse (3.1%) and physical violence (2.5%) were the least reported forms. Perpetrators • In most cases, perpetrators of emotional abuse, financial abuse, sexual abuse and violation of rights were the women's partners or spouses. The exception to this was in relation to neglect, where in most cases older women were abused by their adult children or children-in-law. Intensity of violence • 7.6% of older women had experienced a single form of abuse, but infrequently. • 13.5% had experienced several forms of abuse, but infrequently. • 1.2% had experienced a single form of abuse very often. • 5.8% had experienced multiple forms of abuse very often. Prevalence Study of Abuse and Violence against Older Women – Final Report 8 Risk factors • There were considerable differences between countries with regard to prevalence rates. However, connections between risk factors and abuse and violence were apparent regardless of country. • The likelihood of abuse is lower in higher age groups. • There was a significant association between abuse and violence and reduced physical health, poor mental health, managing poorly with household income, not participating in social activities, living with spouse or partner or with adult children, and loneliness. After the abuse • The most common effects of violence and abuse were tension, anger, hatred and feelings of powerlessness. • Nearly half of the abused women (44.7%) talked with somebody they knew about the most serious incident or reported it to an official agency. In Portugal and Lithuania, however, only a quarter of the abused women talked about the incident with anyone else. • The majority of older women did not talk with anybody else about the abusive incident(s). Mostly women thought the incident was too trivial to report or discuss or considered that nobody could do anything about the situation. Quality of Life • In relation to abuse in overall terms, the findings are unambiguous: older women who had experienced any kind of abuse reported having significantly lower quality of life than older women who had not experienced abuse.Daphne II

Research and innovation as a catalyst for food system transformation

Background: Food systems are associated with severe and persistent problems worldwide. Governance approaches aiming to foster sustainable transformation of food systems face several challenges due to the complex nature of food systems. Scope and approach: In this commentary we argue that addressing these governance challenges requires the development and adoption of novel research and innovation (R&I) approaches that will provide evidence to inform food system transformation and will serve as catalysts for change. We first elaborate on the complexity of food systems (transformation) and stress the need to move beyond traditional linear R&I approaches to be able to respond to persistent problems that affect food systems. Though integrated transdisciplinary approaches are promising, current R&I systems do not sufficiently support such endeavors. As such, we argue, we need strategies that trigger a double transformation - of food systems and of their R&I systems. Key Findings and Conclusions: Seizing the opportunities to transform R&I systems has implications for how research is done - pointing to the need for competence development among researchers, policy makers and society in general - and requires specific governance interventions that stimulate a systemic approach. Such interventions should foster transdisciplinary and transformative research agendas that stimulate portfolios of projects that will reinforce one another, and stimulate innovative experiments to shape conditions for systemic change. In short, a thorough rethinking of the role of R&I as well as how it is funded is a crucial step towards the development of the integrative policies that are necessary to engender systemic change - in the food system and beyond

Subsequent Event Risk in Individuals with Established Coronary Heart Disease:Design and Rationale of the GENIUS-CHD Consortium

BACKGROUND: The "GENetIcs of sUbSequent Coronary Heart Disease" (GENIUS-CHD) consortium was established to facilitate discovery and validation of genetic variants and biomarkers for risk of subsequent CHD events, in individuals with established CHD. METHODS: The consortium currently includes 57 studies from 18 countries, recruiting 185,614 participants with either acute coronary syndrome, stable CHD or a mixture of both at baseline. All studies collected biological samples and followed-up study participants prospectively for subsequent events. RESULTS: Enrollment into the individual studies took place between 1985 to present day with duration of follow up ranging from 9 months to 15 years. Within each study, participants with CHD are predominantly of self-reported European descent (38%-100%), mostly male (44%-91%) with mean ages at recruitment ranging from 40 to 75 years. Initial feasibility analyses, using a federated analysis approach, yielded expected associations between age (HR 1.15 95% CI 1.14-1.16) per 5-year increase, male sex (HR 1.17, 95% CI 1.13-1.21) and smoking (HR 1.43, 95% CI 1.35-1.51) with risk of subsequent CHD death or myocardial infarction, and differing associations with other individual and composite cardiovascular endpoints. CONCLUSIONS: GENIUS-CHD is a global collaboration seeking to elucidate genetic and non-genetic determinants of subsequent event risk in individuals with established CHD, in order to improve residual risk prediction and identify novel drug targets for secondary prevention. Initial analyses demonstrate the feasibility and reliability of a federated analysis approach. The consortium now plans to initiate and test novel hypotheses as well as supporting replication and validation analyses for other investigators

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Large meta-analysis of genome-wide association studies identifies five loci for lean body mass

Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 x 10(-8)) or suggestively genome wide (p < 2.3 x 10(-6)). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/ near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/ near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass