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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Holstege, Henne; Grozeva, Detelina; Sims, Rebecca; Luckcuck, Lauren; +85 Authors

    The genetic component of Alzheimer’s disease (AD) has been mainly assessed using Genome Wide Association Studies (GWAS), which do not capture the risk contributed by rare variants. Here, we compared the gene-based burden of rare damaging variants in exome sequencing data from 32,558 individuals —16,036 AD cases and 16,522 controls— in a two-stage analysis. Next to known genes TREM2, SORL1 and ABCA7, we observed a significant association of rare, predicted damaging variants in ATP8B4 and ABCA1 with AD risk, and a suggestive signal in ADAM10. Next to these genes, the rare variant burden in RIN3, CLU, ZCWPW1 and ACE highlighted these genes as potential driver genes in AD-GWAS loci. Rare damaging variants in these genes, and in particular loss-of-function variants, have a large effect on AD-risk, and they are enriched in early onset AD cases. The newly identified AD-associated genes provide additional evidence for a major role for APP-processing, Aβ-aggregation, lipid metabolism and microglial function in AD.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ CORE (RIOXX-UK Aggre...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ CORE (RIOXX-UK Aggre...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Šidlauskienė, Virginija;

    Straipsnyje pristatoma viena Europos Sąjungos ir neabejotinai Lietuvos moterų, studijuojančių ir dirbančių mokslinį darbąinžinerinių ir technologinių (IT) mokslų srityje, trūkumo problema. Nepaisant ankstesnių iniciatyvų aukštajame moksle, moterys sudaro mažumą IT mokslų ir studijų srityje. Mokslinė tyrimo problema formuluojama keliant šiuos probleminius klausimus: ar mokslo suvokimas ir visuomenėje vykstantys procesai lemia merginų IT studijų srities pasirinkimą? Ar padidinus IT studijų programų interdiscipliniškumą ir kartu technines bei technologines kompetencijas papildžius socialiniais ir perkeliamais gebėjimais, studijos tampa merginoms patrauklesnės? Tyrimas atliktas vykdant BP7 projektą HELENA: Aukštasis mokslas, orientuojantis moteris studijuoti inžinerijos ir technologinius mokslus su mokslininkų iš Austrijos, Prancūzijos, Jungtinės Karalystės, Serbijos, Ispanijos ir Lietuvos komanda. Tyrimo metodologija grindžiama kiekybinių ir kokybinių tyrimo duomenų trianguliacija, pradedant kiekybinių ir kokybinių duomenų rinkimą, pasikartojančią (iteratyvinę) pakopinę analizę institucijos, nacionaliniame ir tarpnacionaliniame lygmenyse. Vėliau numatyta ES šalių rezultatų tarptautinė lyginamoji analizė. Šiame straipsnyje pristatomas Lietuvos atvejis. Pradiniame tyrimo etape nustatyti studijų programų tradiciškumo ir inovatyvumo (interdiscipliniškumo) parametrai. Pirmojoje hipotezėje teigiama, jog studijų programos, kurių tarpdalykiškumas viršija 25 proc, yra patrauklesnės studijuoti moterims. Nustatytas priklausomas kintamasis - studenčių dalis visų studijuojančiųjų imtyje, nepriklausomas kintamasis - studijų programos tardalykiškumo laipsnis. Remiantis Godfrey, Pinault, Thaler, Wachter (2010) tyrimo metodologija, išanalizavus 126 inžinerinių ir 41 technologinių mokslų studijų sritis, iškeltai hipotezei patvirtinti atrinktos 23 studijų programos, kuriose įstojusių, studijuojančių ir studijų baigusių merginų skaičius yra arba mažas, arba akivaizdžiai didelis. Apibendrinant galima teigti, kad Lietuvos tyrimo atveju pirmoji hipotezė, teigianti, kad studijų programos, kurių tarpdalykiškumas viršija 25 proc, yra patrauklesnės studijuoti moterims, patvirtinta. Tokios studijų programos yra inovatyvios, savo turinyje komponuoja socialinių, humanitarinių, kultūros, teisės mokslų dalykus, tokius kaip Komunikacijos pagrindai, Profesinės kalbos kultūra, Teisės pagrindai, Aplinkosaugos ekonomika ir teisė, Inžinerijos ekonomika, Vadybos pagrindai, Darni plėtra, Ekologija, Profesinė sauga ir sveikata, Aplinkosaugos chemija, Aplinkosaugos sociologija, Mikro- ir makroekonomika, Ekstremalių situacijųmodeliavimas ir saugus valdymas ir pan. Antroji hipotezė pasitvirtino Lietuvos atvejo tyrimu: moterų, studijuojančių tarpdisciplininėse studijų programose, studijos yra sėkmingesnės nei studijuojančiųjų tradicinius studijų kursus. Būsimoje tyrimų stadijoje numatyta tirti tarpdisciplininių ir tradicinių studijų programų viešinimo medžiagą ir marketingą, studijų programų tikslinės grapės numatymą, karjeros, kokybiškos praktikos, skatinimo, mobilumo užsienyje galimybių pristatymą, šiuolaikinės studijų didaktikos ir kokybiško mokymo ir mokymosi sąlygų akcentavimą. The paper summarises the Lithuanian specific case studies, providing gender specific data on traditional and innovative pilot degree courses in E&T and identifying innovative study programs in engineering, then there is a comparison of traditional and interdisciplinary study courses. For that purpose an in-depth qualitative and quantitative analysis of some engineering study programmes grounded on transnational iterative methodology has been done. From this first analysis, a set of Lithuanian case studies has been selected for further analysis of students' perception of E&T studies. The paper summarises the results found after an in-depth examination of these selected case studies for a posterior evaluation of the success of pilot projects in E&T in attracting more female engineering students. The research draws up whether women are more likely than men to study engineering because of its perceived societal and cultural impact, and whether women are more attracted to engineering programs in universities that include an interdisciplinary approach, student-centred learning and the teaching and empowering studies environment.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ “Lituanistika”, Inte...arrow_drop_down
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  • Authors: Canals, Rocío; Hammarlöf, Disa; Kröger, Carsten; Owen, Siân; +15 Authors

    Salmonella Typhimurium ST313 causes invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa, targeting susceptible HIV + , malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered the S. Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of the Salmonella expression compendium SalComD23580: bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl . We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Allardyce, Judith; Leonenko, Ganna; Hamshere, Marian L.; Pardinas, Antonio; +15 Authors

    Abstract Importance Bipolar disorder (BD) overlaps schizophrenia in its clinical presentation and genetic liability. Alternative approaches to patient stratification beyond current diagnostic categories are needed to understand the underlying disease processes/mechanisms. Objectives To investigate the relationship between common-variant liability for schizophrenia, indexed by polygenic risk scores (PRS) and psychotic presentations of BD, using clinical descriptions which consider both occurrence and level of mood-incongruent psychotic features. Design Case-control design: using multinomial logistic regression, to estimate differential associations of PRS across categories of cases and controls. Settings & Participants 4399 BDcases, mean [sd] age-at-interview 46[12] years, of which 2966 were woman (67%) from the BD Research Network (BDRN) were included in the final analyses, with data for 4976 schizophrenia cases and 9012 controls from the Type-1 diabetes genetics consortium and Generation Scotland included for comparison. Exposure Standardised PRS, calculated using alleles with an association p-value threshold < 0.05 in the second \ud \ud Psychiatric Genomics Consortium genome-wide association study of schizophrenia, adjusted for the first 10 population principal components and genotyping-platform. Main outcome measure Multinomial logit models estimated PRS associations with BD stratified by (1) Research Diagnostic Criteria (RDC) BD subtypes (2) Lifetime occurrence of psychosis.(3) Lifetime mood-incongruent psychotic features and (4) ordinal logistic regression examined PRS associations across levels of mood-incongruence. Ratings were derived from the Schedule for Clinical Assessment in Neuropsychiatry interview (SCAN) and the Bipolar Affective Disorder Dimension Scale (BADDS). Results Across clinical phenotypes, there was an exposure-response gradient with the strongest PRS association for schizophrenia (RR=1.94, (95% C.I. 1.86, 2.01)), then schizoaffective BD (RR=1.37, (95% C.I. 1.22, 1.54)), BD I (RR= 1.30, (95% C.I. 1.24, 1.36)) and BD II (RR=1.04, (95% C.I. 0.97, 1.11)). Within BD cases, there was an effect gradient, indexed by the nature of psychosis, with prominent mood-incongruent psychotic features having the strongest association (RR=1.46, (95% C.I. 1.36, 1.57)), followed by mood-congruent psychosis (RR= 1.24, (95% C.I. 1.17, 1.33)) and lastly, BD cases with no history of psychosis (RR=1.09, (95% C.I. 1.04, 1.15)). Conclusion We show for the first time a polygenic-risk gradient, across schizophrenia and bipolar disorder, indexed by the occurrence and level of mood-incongruent psychotic symptoms.

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    Authors: Marron, Alan; Cassarino, Lucie; Hatton, Jade; Curnow, Paul; +1 Authors

    The marine silicon cycle is intrinsically linked with carbon cycling in the oceans via biological production of silica by a wide range of organisms. The stable silicon isotopic composition (denoted by δ30Si) of siliceous microfossils extracted from sediment cores can be used as an archive of past oceanic silicon cycling. However, the silicon isotopic composition of biogenic silica has only been measured in diatoms, sponges and radiolarians, and isotopic fractionation relative to seawater is entirely unknown for many other silicifiers. Furthermore, the biochemical pathways and mechanisms that determine isotopic fractionation during biosilicification remain poorly understood. Here, we present the first measurements of the silicon isotopic fractionation during biosilicification by loricate choanoflagellates, a group of protists closely related to animals. We cultured two species of choanoflagellates, Diaphanoeca grandis and Stephanoeca diplocostata, which showed consistently greater isotopic fractionation (approximately −5 ‰ to −7 ‰) than cultured diatoms (−0.5 ‰ to −2.1 ‰). Instead, choanoflagellate silicon isotopic fractionation appears to be more similar to sponges grown under similar dissolved silica concentrations. Our results highlight that there is a taxonomic component to silicon isotope fractionation during biosilicification, possibly via a shared or related biochemical transport pathway. These findings have implications for the use of biogenic silica δ30Si produced by different silicifiers as proxies for past oceanic change.

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    Authors: Jain, Saurabh; Sima, Diana M.; Sanaei Nezhad, Faezeh; Hangel, Gilbert; +5 Authors

    Purpose: Magnetic resonance spectroscopic imaging (MRSI) provides complementary information to conventional magnetic resonance imaging. Acquiring high resolution MRSI is time consuming and requires complex reconstruction techniques.Methods: In this paper, a patch-based super-resolution method is presented to increase the spatial resolution of metabolite maps computed from MRSI. The proposed method uses high resolution anatomical MR images (T1-weighted and Fluid-attenuated inversion recovery) to regularize the super-resolution process. The accuracy of the method is validated against conventional interpolation techniques using a phantom, as well as simulated and in vivo acquired human brain images of multiple sclerosis subjects.Results: The method preserves tissue contrast and structural information, and matches well with the trend of acquired high resolution MRSI.Conclusions: These results suggest that the method has potential for clinically relevant neuroimaging applications.

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    Authors: Ried, Janina S.;
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    Authors: Matzaraki, Vasiliki; Kumar, Vinod; Wijmenga, Cisca; Zhernakova, Alexandra;

    In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.

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    Other ORP type . 2017
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      Other ORP type . 2017
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    Authors: Pardinas, Antonio; Holmans, Peter; Pocklington, Andrew; Escott-Price, Valentina; +31 Authors

    Schizophrenia is a debilitating psychiatric condition often associated with poor quality of life and decreased life expectancy. Lack of progress in improving treatment outcomes has been attributed to limited knowledge of the underlying biology, although large-scale genomic studies have begun to provide such insight. We report the largest single cohort genome-wide association study of schizophrenia (11,260 cases and 24,542 controls) and through meta-analysis with existing data we identify 50 novel GWAS loci. Using gene-wide association statistics we implicate an additional set of 22 novel associations that map onto a single gene. We show for the first time that the common variant association signal is highly enriched among genes that are intolerant to loss of function mutations and that variants in these genes persist in the population despite the low fecundity associated with the disorder through the process of background selection. Associations point to novel areas of biology (e.g. metabotropic GABA-B signalling and acetyl cholinesterase), reinforce those implicated in earlier GWAS studies (e.g. calcium channel function), converge with earlier rare variants studies (e.g. NRXN1, GABAergic signalling), identify novel overlaps with autism (e.g. RBFOX1, FOXP1, FOXG1), and support early controversial candidate gene hypotheses (e.g. ERBB4 implicating neuregulin signalling). We also demonstrate the involvement of six independent central nervous system functional gene sets in schizophrenia pathophysiology. These findings provide novel insights into the biology and genetic architecture of schizophrenia, highlight the importance of mutation intolerant genes and suggest a mechanism by which common risk variants are maintained in the population.

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  • Authors: Kasperaviciute, Dalia; Catarino, Claudia B.; Matarin, Mar; Leu, Costin; +67 Authors

    Epilepsy comprises several syndromes, amongst the most common being mesial temporal lobe epilepsy with hippocampal sclerosis. Seizures in mesial temporal lobe epilepsy with hippocampal sclerosis are typically drug-resistant, and mesial temporal lobe epilepsy with hippocampal sclerosis is frequently associated with important co-morbidities, mandating the search for better understanding and treatment. The cause of mesial temporal lobe epilepsy with hippocampal sclerosis is unknown, but there is an association with childhood febrile seizures. Several rarer epilepsies featuring febrile seizures are caused by mutations in SCN1A, which encodes a brain-expressed sodium channel subunit targeted by many anti-epileptic drugs. We undertook a genome-wide association study in 1018 people with mesial temporal lobe epilepsy with hippocampal sclerosis and 7552 control subjects, with validation in an independent sample set comprising 959 people with mesial temporal lobe epilepsy with hippocampal sclerosis and 3591 control subjects. To dissect out variants related to a history of febrile seizures, we tested cases with mesial temporal lobe epilepsy with hippocampal sclerosis with (overall n = 757) and without (overall n = 803) a history of febrile seizures. Meta-analysis revealed a genome-wide significant association for mesial temporal lobe epilepsy with hippocampal sclerosis with febrile seizures at the sodium channel gene cluster on chromosome 2q24.3 [rs7587026, within an intron of the SCN1A gene, P = 3.36 x 10(-9), odds ratio (A) = 1.42, 95% confidence interval: 1.26-1.59]. In a cohort of 172 individuals with febrile seizures, who did not develop epilepsy during prospective follow-up to age 13 years, and 6456 controls, no association was found for rs7587026 and febrile seizures. These findings suggest SCN1A involvement in a common epilepsy syndrome, give new direction to biological understanding of mesial temporal lobe epilepsy with hippocampal sclerosis with febrile seizures, and open avenues for investigation of prognostic factors and possible prevention of epilepsy in some children with febrile seizures.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Holstege, Henne; Grozeva, Detelina; Sims, Rebecca; Luckcuck, Lauren; +85 Authors

    The genetic component of Alzheimer’s disease (AD) has been mainly assessed using Genome Wide Association Studies (GWAS), which do not capture the risk contributed by rare variants. Here, we compared the gene-based burden of rare damaging variants in exome sequencing data from 32,558 individuals —16,036 AD cases and 16,522 controls— in a two-stage analysis. Next to known genes TREM2, SORL1 and ABCA7, we observed a significant association of rare, predicted damaging variants in ATP8B4 and ABCA1 with AD risk, and a suggestive signal in ADAM10. Next to these genes, the rare variant burden in RIN3, CLU, ZCWPW1 and ACE highlighted these genes as potential driver genes in AD-GWAS loci. Rare damaging variants in these genes, and in particular loss-of-function variants, have a large effect on AD-risk, and they are enriched in early onset AD cases. The newly identified AD-associated genes provide additional evidence for a major role for APP-processing, Aβ-aggregation, lipid metabolism and microglial function in AD.

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    Authors: Šidlauskienė, Virginija;

    Straipsnyje pristatoma viena Europos Sąjungos ir neabejotinai Lietuvos moterų, studijuojančių ir dirbančių mokslinį darbąinžinerinių ir technologinių (IT) mokslų srityje, trūkumo problema. Nepaisant ankstesnių iniciatyvų aukštajame moksle, moterys sudaro mažumą IT mokslų ir studijų srityje. Mokslinė tyrimo problema formuluojama keliant šiuos probleminius klausimus: ar mokslo suvokimas ir visuomenėje vykstantys procesai lemia merginų IT studijų srities pasirinkimą? Ar padidinus IT studijų programų interdiscipliniškumą ir kartu technines bei technologines kompetencijas papildžius socialiniais ir perkeliamais gebėjimais, studijos tampa merginoms patrauklesnės? Tyrimas atliktas vykdant BP7 projektą HELENA: Aukštasis mokslas, orientuojantis moteris studijuoti inžinerijos ir technologinius mokslus su mokslininkų iš Austrijos, Prancūzijos, Jungtinės Karalystės, Serbijos, Ispanijos ir Lietuvos komanda. Tyrimo metodologija grindžiama kiekybinių ir kokybinių tyrimo duomenų trianguliacija, pradedant kiekybinių ir kokybinių duomenų rinkimą, pasikartojančią (iteratyvinę) pakopinę analizę institucijos, nacionaliniame ir tarpnacionaliniame lygmenyse. Vėliau numatyta ES šalių rezultatų tarptautinė lyginamoji analizė. Šiame straipsnyje pristatomas Lietuvos atvejis. Pradiniame tyrimo etape nustatyti studijų programų tradiciškumo ir inovatyvumo (interdiscipliniškumo) parametrai. Pirmojoje hipotezėje teigiama, jog studijų programos, kurių tarpdalykiškumas viršija 25 proc, yra patrauklesnės studijuoti moterims. Nustatytas priklausomas kintamasis - studenčių dalis visų studijuojančiųjų imtyje, nepriklausomas kintamasis - studijų programos tardalykiškumo laipsnis. Remiantis Godfrey, Pinault, Thaler, Wachter (2010) tyrimo metodologija, išanalizavus 126 inžinerinių ir 41 technologinių mokslų studijų sritis, iškeltai hipotezei patvirtinti atrinktos 23 studijų programos, kuriose įstojusių, studijuojančių ir studijų baigusių merginų skaičius yra arba mažas, arba akivaizdžiai didelis. Apibendrinant galima teigti, kad Lietuvos tyrimo atveju pirmoji hipotezė, teigianti, kad studijų programos, kurių tarpdalykiškumas viršija 25 proc, yra patrauklesnės studijuoti moterims, patvirtinta. Tokios studijų programos yra inovatyvios, savo turinyje komponuoja socialinių, humanitarinių, kultūros, teisės mokslų dalykus, tokius kaip Komunikacijos pagrindai, Profesinės kalbos kultūra, Teisės pagrindai, Aplinkosaugos ekonomika ir teisė, Inžinerijos ekonomika, Vadybos pagrindai, Darni plėtra, Ekologija, Profesinė sauga ir sveikata, Aplinkosaugos chemija, Aplinkosaugos sociologija, Mikro- ir makroekonomika, Ekstremalių situacijųmodeliavimas ir saugus valdymas ir pan. Antroji hipotezė pasitvirtino Lietuvos atvejo tyrimu: moterų, studijuojančių tarpdisciplininėse studijų programose, studijos yra sėkmingesnės nei studijuojančiųjų tradicinius studijų kursus. Būsimoje tyrimų stadijoje numatyta tirti tarpdisciplininių ir tradicinių studijų programų viešinimo medžiagą ir marketingą, studijų programų tikslinės grapės numatymą, karjeros, kokybiškos praktikos, skatinimo, mobilumo užsienyje galimybių pristatymą, šiuolaikinės studijų didaktikos ir kokybiško mokymo ir mokymosi sąlygų akcentavimą. The paper summarises the Lithuanian specific case studies, providing gender specific data on traditional and innovative pilot degree courses in E&T and identifying innovative study programs in engineering, then there is a comparison of traditional and interdisciplinary study courses. For that purpose an in-depth qualitative and quantitative analysis of some engineering study programmes grounded on transnational iterative methodology has been done. From this first analysis, a set of Lithuanian case studies has been selected for further analysis of students' perception of E&T studies. The paper summarises the results found after an in-depth examination of these selected case studies for a posterior evaluation of the success of pilot projects in E&T in attracting more female engineering students. The research draws up whether women are more likely than men to study engineering because of its perceived societal and cultural impact, and whether women are more attracted to engineering programs in universities that include an interdisciplinary approach, student-centred learning and the teaching and empowering studies environment.

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  • Authors: Canals, Rocío; Hammarlöf, Disa; Kröger, Carsten; Owen, Siân; +15 Authors

    Salmonella Typhimurium ST313 causes invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa, targeting susceptible HIV + , malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered the S. Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of the Salmonella expression compendium SalComD23580: bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl . We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.

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    Authors: Allardyce, Judith; Leonenko, Ganna; Hamshere, Marian L.; Pardinas, Antonio; +15 Authors

    Abstract Importance Bipolar disorder (BD) overlaps schizophrenia in its clinical presentation and genetic liability. Alternative approaches to patient stratification beyond current diagnostic categories are needed to understand the underlying disease processes/mechanisms. Objectives To investigate the relationship between common-variant liability for schizophrenia, indexed by polygenic risk scores (PRS) and psychotic presentations of BD, using clinical descriptions which consider both occurrence and level of mood-incongruent psychotic features. Design Case-control design: using multinomial logistic regression, to estimate differential associations of PRS across categories of cases and controls. Settings & Participants 4399 BDcases, mean [sd] age-at-interview 46[12] years, of which 2966 were woman (67%) from the BD Research Network (BDRN) were included in the final analyses, with data for 4976 schizophrenia cases and 9012 controls from the Type-1 diabetes genetics consortium and Generation Scotland included for comparison. Exposure Standardised PRS, calculated using alleles with an association p-value threshold < 0.05 in the second \ud \ud Psychiatric Genomics Consortium genome-wide association study of schizophrenia, adjusted for the first 10 population principal components and genotyping-platform. Main outcome measure Multinomial logit models estimated PRS associations with BD stratified by (1) Research Diagnostic Criteria (RDC) BD subtypes (2) Lifetime occurrence of psychosis.(3) Lifetime mood-incongruent psychotic features and (4) ordinal logistic regression examined PRS associations across levels of mood-incongruence. Ratings were derived from the Schedule for Clinical Assessment in Neuropsychiatry interview (SCAN) and the Bipolar Affective Disorder Dimension Scale (BADDS). Results Across clinical phenotypes, there was an exposure-response gradient with the strongest PRS association for schizophrenia (RR=1.94, (95% C.I. 1.86, 2.01)), then schizoaffective BD (RR=1.37, (95% C.I. 1.22, 1.54)), BD I (RR= 1.30, (95% C.I. 1.24, 1.36)) and BD II (RR=1.04, (95% C.I. 0.97, 1.11)). Within BD cases, there was an effect gradient, indexed by the nature of psychosis, with prominent mood-incongruent psychotic features having the strongest association (RR=1.46, (95% C.I. 1.36, 1.57)), followed by mood-congruent psychosis (RR= 1.24, (95% C.I. 1.17, 1.33)) and lastly, BD cases with no history of psychosis (RR=1.09, (95% C.I. 1.04, 1.15)). Conclusion We show for the first time a polygenic-risk gradient, across schizophrenia and bipolar disorder, indexed by the occurrence and level of mood-incongruent psychotic symptoms.

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    Authors: Marron, Alan; Cassarino, Lucie; Hatton, Jade; Curnow, Paul; +1 Authors

    The marine silicon cycle is intrinsically linked with carbon cycling in the oceans via biological production of silica by a wide range of organisms. The stable silicon isotopic composition (denoted by δ30Si) of siliceous microfossils extracted from sediment cores can be used as an archive of past oceanic silicon cycling. However, the silicon isotopic composition of biogenic silica has only been measured in diatoms, sponges and radiolarians, and isotopic fractionation relative to seawater is entirely unknown for many other silicifiers. Furthermore, the biochemical pathways and mechanisms that determine isotopic fractionation during biosilicification remain poorly understood. Here, we present the first measurements of the silicon isotopic fractionation during biosilicification by loricate choanoflagellates, a group of protists closely related to animals. We cultured two species of choanoflagellates, Diaphanoeca grandis and Stephanoeca diplocostata, which showed consistently greater isotopic fractionation (approximately −5 ‰ to −7 ‰) than cultured diatoms (−0.5 ‰ to −2.1 ‰). Instead, choanoflagellate silicon isotopic fractionation appears to be more similar to sponges grown under similar dissolved silica concentrations. Our results highlight that there is a taxonomic component to silicon isotope fractionation during biosilicification, possibly via a shared or related biochemical transport pathway. These findings have implications for the use of biogenic silica δ30Si produced by different silicifiers as proxies for past oceanic change.

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    Authors: Jain, Saurabh; Sima, Diana M.; Sanaei Nezhad, Faezeh; Hangel, Gilbert; +5 Authors

    Purpose: Magnetic resonance spectroscopic imaging (MRSI) provides complementary information to conventional magnetic resonance imaging. Acquiring high resolution MRSI is time consuming and requires complex reconstruction techniques.Methods: In this paper, a patch-based super-resolution method is presented to increase the spatial resolution of metabolite maps computed from MRSI. The proposed method uses high resolution anatomical MR images (T1-weighted and Fluid-attenuated inversion recovery) to regularize the super-resolution process. The accuracy of the method is validated against conventional interpolation techniques using a phantom, as well as simulated and in vivo acquired human brain images of multiple sclerosis subjects.Results: The method preserves tissue contrast and structural information, and matches well with the trend of acquired high resolution MRSI.Conclusions: These results suggest that the method has potential for clinically relevant neuroimaging applications.

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    Authors: Ried, Janina S.;
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    Authors: Matzaraki, Vasiliki; Kumar, Vinod; Wijmenga, Cisca; Zhernakova, Alexandra;

    In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.

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    Authors: Pardinas, Antonio; Holmans, Peter; Pocklington, Andrew; Escott-Price, Valentina; +31 Authors

    Schizophrenia is a debilitating psychiatric condition often associated with poor quality of life and decreased life expectancy. Lack of progress in improving treatment outcomes has been attributed to limited knowledge of the underlying biology, although large-scale genomic studies have begun to provide such insight. We report the largest single cohort genome-wide association study of schizophrenia (11,260 cases and 24,542 controls) and through meta-analysis with existing data we identify 50 novel GWAS loci. Using gene-wide association statistics we implicate an additional set of 22 novel associations that map onto a single gene. We show for the first time that the common variant association signal is highly enriched among genes that are intolerant to loss of function mutations and that variants in these genes persist in the population despite the low fecundity associated with the disorder through the process of background selection. Associations point to novel areas of biology (e.g. metabotropic GABA-B signalling and acetyl cholinesterase), reinforce those implicated in earlier GWAS studies (e.g. calcium channel function), converge with earlier rare variants studies (e.g. NRXN1, GABAergic signalling), identify novel overlaps with autism (e.g. RBFOX1, FOXP1, FOXG1), and support early controversial candidate gene hypotheses (e.g. ERBB4 implicating neuregulin signalling). We also demonstrate the involvement of six independent central nervous system functional gene sets in schizophrenia pathophysiology. These findings provide novel insights into the biology and genetic architecture of schizophrenia, highlight the importance of mutation intolerant genes and suggest a mechanism by which common risk variants are maintained in the population.

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  • Authors: Kasperaviciute, Dalia; Catarino, Claudia B.; Matarin, Mar; Leu, Costin; +67 Authors

    Epilepsy comprises several syndromes, amongst the most common being mesial temporal lobe epilepsy with hippocampal sclerosis. Seizures in mesial temporal lobe epilepsy with hippocampal sclerosis are typically drug-resistant, and mesial temporal lobe epilepsy with hippocampal sclerosis is frequently associated with important co-morbidities, mandating the search for better understanding and treatment. The cause of mesial temporal lobe epilepsy with hippocampal sclerosis is unknown, but there is an association with childhood febrile seizures. Several rarer epilepsies featuring febrile seizures are caused by mutations in SCN1A, which encodes a brain-expressed sodium channel subunit targeted by many anti-epileptic drugs. We undertook a genome-wide association study in 1018 people with mesial temporal lobe epilepsy with hippocampal sclerosis and 7552 control subjects, with validation in an independent sample set comprising 959 people with mesial temporal lobe epilepsy with hippocampal sclerosis and 3591 control subjects. To dissect out variants related to a history of febrile seizures, we tested cases with mesial temporal lobe epilepsy with hippocampal sclerosis with (overall n = 757) and without (overall n = 803) a history of febrile seizures. Meta-analysis revealed a genome-wide significant association for mesial temporal lobe epilepsy with hippocampal sclerosis with febrile seizures at the sodium channel gene cluster on chromosome 2q24.3 [rs7587026, within an intron of the SCN1A gene, P = 3.36 x 10(-9), odds ratio (A) = 1.42, 95% confidence interval: 1.26-1.59]. In a cohort of 172 individuals with febrile seizures, who did not develop epilepsy during prospective follow-up to age 13 years, and 6456 controls, no association was found for rs7587026 and febrile seizures. These findings suggest SCN1A involvement in a common epilepsy syndrome, give new direction to biological understanding of mesial temporal lobe epilepsy with hippocampal sclerosis with febrile seizures, and open avenues for investigation of prognostic factors and possible prevention of epilepsy in some children with febrile seizures.

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