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Strong families and declining fertility : a comparative study of family relations and reproductive careers in Soviet Ukraine
Hilevych, Yuliya - \ 2016
University. Promotor(en): Hilde Bras; Theo Engelen. - Wageningen : Wageningen University - ISBN 9789462579385 - 191
families - demography - family environment - family size - sociology of the family - contraception - ukraine - gezinnen - demografie - gezinsmilieu - gezinsgrootte - gezinssociologie - contraceptie - oekraïne

This dissertation focuses on the role of family and social relationships in individuals’ reproductive careers during the fertility decline in Soviet Ukraine from around 1950 to 1975. These three decades after the Second World War signified the end of the First Demographic Transition in Ukraine and other European republics of the Soviet Union, and some even define the period after the 1960s as the start of a latent depopulation in this part of Europe. However, this fertility decline that had already begun to manifest itself in the early 1920s gained speed within only a few generations as those who were born in families of six siblings in the 1920s and 1930s had only two children themselves in the 1950s, the 1960s and the 1970s.

Previous research has discussed these demographic changes on a macro-level for the Soviet and post-Soviet periods by typically linking these changes to the processes of modernisation and transformation. However, this singular focus on structural changes ignores the fact that relationships between people also adjust to politico-economic changes according to the social and family values that al- ready exist in society. As a result, old and new social (in)equalities, both outside and within the household, (re-) emerge alongside the politico-economic modernisation, which, in tandem, contribute to the formation of different demographic realities on a micro-level and different fertility trends on a macro-level. In this respect, social relationships should be seen as playing an intermediary role in the interplay between the formation of interpersonal inequalities and the politico- economic reality. Because they surround our everyday lives and choices, social relationships form a coherent social structure that helps us to interpret, to under- stand and to adjust to everyday reality, including state legal regulations, political ideology, and economic crises. The primary aim of this dissertation is to study the effects of family relationships and their continuities on changes in reproductive behaviour through a comparative regional perspective in Ukraine during the post-war fertility decline.The role of social relationships in reproductive behaviour is particularly important in the specific context of Ukraine as well as in the broader context of Eastern Europe, where family relationships have provided welfare in critical situations, such as childbearing, childcare and elderly care, both in the past and today. Sim- ilar to Southern Europe, the prevalence of strong family ties in Eastern Europe is also often connected to the high fertility rates in the pre-transitional context and to the rapid fertility decline to the lowest-low level in the 1990s and 2000s. The lowest-low fertility phenomenon is often referred to as a paradox of strong family and low fertility. Moreover, in the context of Ukraine, where regional dif- ferences remain pronounced in many aspects of social life, regional variations in fertility could also be linked to local family values. Considering this, the main research questions that I address in this dissertation are the following: (1) How did family and social relationships influence individual reproductive careers in Soviet Ukraine from around the 1950s to the 1970s? (2) How can local family systems and their associated power dynamics and social interdependencies help to understand fertility decline in Soviet Ukraine? Focusing on these post-war decades is also relevant for our understanding of historical and contemporary fertility decline in this part of Europe because these three decades were significant for the beginning of the Cold War, general liberalisation of the regime and the introduction of some family policies that are still enacted today.

On the theoretical level, I frame the empirical analysis of family and social influences on individual reproductive careers in a broader framework of local con- tinuities in family relationships and values, the so-called family systems. In this respect, individual reproductive careers are studied as processual characteristics of reproductive behaviour and long life experiences and include such life events as marriage, entrance into parenthood, abortion and birth control, and transition to second birth. By social influences I understand the ‘process by which attitudes, values or behaviour of an individual are determined by the attitudes, values or behaviour of others with whom he or she interacts’ (Bernardi, 2003, p. 535). I examine different patterns of social relationships, such as those between spouses, generations, siblings and peers. Based on the social influences stemming from family and social relationships, I try to characterise different power relationships and other social interdependencies underlying these relationships, which I then connect to the context of local family systems.

On the methodological level, this study is based on the analysis of various qual- itative methods, such as in-depth biographical interviews, life history calendars (LHC) and family photographs. The interviews were collected in two Ukrainian borderland cities: Lviv in western Ukraine and Kharkiv in eastern Ukraine. These sites allowed me to compare how family relationships were historically organised in Ukraine and how they actually shaped the informants’ reproductive decisions. This study also uses archival demographic data and secondary ethnographic materials as supplementary sources.

The empirical findings of this dissertation discuss different transitions of individual reproductive careers, namely marriage, entrance into parenthood, birth control and abortion, and transitions to second and later births, all of which I discuss in the context of family and peer relationships. In Soviet Ukraine, the transition to marriage was characterised by strong parental control over men’s and women’s pre-marital practices and sometimes also marital decisions. This strong parental control before marriage was not without consequences, as it seems to have created an imaginary dependency of children on their parents not only be- fore but also after marriage, which I associate with the persistence of paternalistic intergenerational values in family relationships in the two localities.

Similarly, the entrance into parenthood was also surrounded by frequent parental assistance, particularly when a couple tried to postpone their entrance into par- enthood. This pattern was also reinforced by the social learning from peers among the Kharkiv informants and social contagion from siblings(in-law) among the Lviv informants. That said, the actual decision to give birth was connected to the ex- pectations of help with childcare in the future. In this respect, I observed that if after the marriage a couple resided separately from their parents, they would also take greater responsibility for childcare, and grandparental support became an additional and temporary option, as it often was in Lviv. However, when spouses resided with either set of parents, they also tended to rely more on the parents in terms of childcare, which I more often observed in Kharkiv and less in Lviv.

These differences in dynamics of spousal and intergenerational relationships between the two localities became even more pronounced around abortion and birth control decisions and their practices after first birth. Spousal cooperation in birth control decision-making played an important role in how women exercised their agency in these decisions and which birth control methods the couple used and how effectively they used them. In couples where spouses communicated about birth control and abortion decisions, the women had fewer abortions, as was often the case in Lviv. These women did not feel the need to exercise their agency, as the husbands took over the responsibility of both birth control and abortion. When abortion was practiced as a routine method to limit family size, spouses did not communicate about birth control and abortion, as was the case in Kharkiv. In this situation, birth control was the husband’s responsibility and abortion was the wife’s. These women sought abortions to fulfil their own goals and, at the same time, to maintain the dominant patriarchal order in marital relationships as they understood it.

These differences in spousal cooperation with regard to birth control seem to have had direct implications for the transition to second and later births in the two localities. In Lviv, spouses continued to negotiate the timing of second and third births and the childcare arrangements, while still mainly relying on each other in these matters. In doing so, the Lviv informants often adopted a traditional male-breadwinning model, which allowed spouses to share the costs of childcare: husbands were responsible for material costs and wives for the emotional and instrumental costs. However, some women resumed working part-time or worked on jobs with more flexible working schedules after their child’s birth, and then spouses divided the material and instrumental costs of childcare more equally and without a traditional gender bias. In either case, the accumulated costs of childcare were often shared between spouses. This strategy often allowed couples to combine childcare after their first and second/third child, which seems to have been reinforcing for many couples in Lviv to adopt a shorter birth spacing strategy. In Kharkiv, in contrast, the timing of second and later births and childcare were mainly the women’s responsibility. Some continued to rely on grandparental support even after starting to reside separately. However, this support was not always available due to different factors such as the few possibilities for multi- generational co-residence or parental health issues. When women received little intergenerational and spousal support, they tended to delay transition to second birth until they felt more secure. Additionally, women in Kharkiv seem to have learned from each other’s experiences about the benefits of this strategy. As such, the adoption of the waiting strategy seems to have resulted in a more prolonged interval between first and second births, sometimes ten to fifteen years, which in other studies is defined as postponement as opposed to spacing. However, those women who did not meet the deadline for parenthood because they were still feeling too insecure to proceed with another birth never had a second child.

Overall, my findings illustrate that the ways in which family relationships were organised over the life course formulated different responses in the two local- ities to the emerging socio-economic conditions. Subsequently, these differences in responses were reflected in regional reproductive strategies. I suggest that these differences in responses have to do with the intrafamilial dependencies in the two localities: more couple-oriented (horizontal intrafamilial interdependen- cies) in Lviv and generations-oriented (vertical intrafamilial interdependencies) in Kharkiv. I also observe continuity in these two social interdependencies with the historical family systems and the intrafamilial (in)equalities produced within them in the past, namely a mix of nuclear-stem family system in Lviv and a joint family system in Kharkiv. In the early life, strong intergenerational connections characterising both family systems seem to have promoted early and universal entrance into marriage and parenthood in the past and during the Soviet time. Additionally, the Soviet family policy adopted many of these paternalistic and pronatalist values on the level of legal regulations, which meant that this re-productive ideology was reinforced within and outside the family. In later life, however, the intrafamily interdependencies start to differ in the two contexts, and this aspect is crucial to understand regional patterns in fertility decline. During the Soviet time, even though socio-economic constraints created more or less sim- ilar structural uncertainties in the both localities, these structural factors did not equally challenge intrafamilial interdependencies between spouse and generations. Subsequently, these local intrafamilial interdependencies resulted in different re- productive strategies on the micro-level and in their reflection on the macro-level fertility trends.

Altogether, these findings provide a fruitful ground for formulating future hy- potheses to be tested on larger and representative population samples. They also formulate important clues for policy makers by suggesting that a more relativist perspective that incorporates intrafamilial social inequalities and communication strategies is needed to regulate the issues of fertility decline and subsequently the process of population ageing, the latter of which may soon become a vital issue in this part of the world as well.

Family systems and fertility : fertility behaviour in Europe from a network perspective
Moenkediek, Bastian - \ 2016
University. Promotor(en): Hilde Bras; J. de Kok. - Wageningen : Wageningen University - ISBN 9789462577978 - 278 p.
demography - families - human fertility - network analysis - europe - demografie - gezinnen - menselijke vruchtbaarheid - netwerkanalyse - europa
Local institutions and rural development : evidence from Liberia
Beekman, G. - \ 2015
University. Promotor(en): Erwin Bulte, co-promotor(en): Lonneke Nillesen. - Wageningen : Wageningen University - ISBN 9789462575080 - 200
plattelandsontwikkeling - gezinnen - netwerken - lokale netwerken - sociale netwerken - instellingen - micro-economische analyse - micro-economie - economische ontwikkeling - landbouwontwikkeling - liberia - west-afrika - rural development - families - networks - local area networks - social networks - institutions - microeconomic analysis - microeconomics - economic development - agricultural development - west africa

Local institutions and rural development: Evidence from Liberia

This thesis focusses on the role of local (informal) institutions for development, based on data from Liberia. I show that dense family networks can be an obstacle for economic decision making, due to strict income sharing obligations that often belong to them. I also demonstrate the importance of local governance quality: corrupt village leaders negatively affect daily investment decisions by villagers. Finally, I evaluate the impact of a rural development project that aims to strengthen food security and social cohesion between villagers. The results indicate that the impact is marginal at most, and local institutions again do play a role.

Institutions are difficult to change, as they are rooted in an historical context. However, policy makers could support the emergence of alternative institutions. Either way, a deeper understanding of the far-going impact of local institutions is important: this research contributes to that.

The IncI1 plasmid carrying the bla CTX-M-1 gene persists in in vitro culture of a Escherichia coli strain from broilers
Fischer, E.A.J. ; Dierikx, C.M. ; Essen-Zandbergen, A. van; Roermund, H.J.W. van; Mevius, D.J. ; Stegeman, A. ; Klinkenberg, D. - \ 2014
BMC Microbiology 14 (2014)77. - ISSN 1471-2180 - p. 1471 - 2180.
spectrum beta-lactamases - extended-spectrum - salmonella-enterica - bacterial plasmids - systems - existence - selection - families
Commensal bacteria are a reservoir for antimicrobial-resistance genes. In the Netherlands, bacteria producing Extended Spectrum Beta-Lactamases (ESBL) are found on chicken-meat and in the gut of broilers at a high prevalence and the predominant ESBL-gene is the blaCTX-M-1 located on IncI1 plasmids. We aim to determine the fitness costs of this plasmid for the bacterium. We investigated the conjugation dynamics of IncI1 plasmids carrying the blaCTX-M-1 gene in a batch culture and its impact on the population dynamics of three E. coli populations: donors, recipients and transconjugants. The intrinsic growth rate (¿), maximum density (K) and lag-phase (¿) of the populations were estimated as well as the conjugation coefficient. Loss of the plasmid by transconjugants was either assumed constant or depended on the effective growth rate of the transconjugants. Parameters were estimated from experiments with pure culture of donors, recipients and transconjugants and with mixed culture of donors and recipients with a duration of 24 or 48 hours. Extrapolation of the results was compared to a 3-months experiment in which a mixed culture of recipient and transconjugant was regularly diluted in new medium.
Colorectal cancer risk variants on 11q23 and 15q13 are associated with unexplained adenomatous polyposis
Hes, F.J. ; Ruano, D. ; Nieuwenhuis, M. ; Tops, C.M.J. ; Schrumpf, M. ; Nielsen, M. ; Huijts, P.E. ; Wijnen, J. ; Wagner, A. ; Gomet Garcia, E.B. ; Sijmons, R.H. ; Menko, F.H. ; Letteboer, T.G. ; Hoogerbrugge, N. ; Harryvan, J.L. ; Kampman, E. ; Morreau, H. ; Vasen, H.F. ; Wezel, T.G. van - \ 2014
Journal of Medical Genetics 51 (2014)1. - ISSN 0022-2593 - p. 55 - 60.
genome-wide association - susceptibility loci - genetic-variants - apc - mutations - hereditary - families - metaanalysis - mechanisms - phenotype
Background Colorectal adenomatous polyposis is associated with a high risk of colorectal cancer (CRC) and is frequently caused by germline mutations in APC or MUTYH. However, in about 20–30% of patients no underlying gene defect can be identified. In this study, we tested if recently identified CRC risk variants play a role in patients with >10 adenomas. Methods We analysed a total of 16 SNPs with a reported association with CRC in a cohort of 252 genetically unexplained index patients with >10 colorectal adenomas and 745 controls. In addition, we collected detailed clinical information from index patients and their first-degree relatives (FDRs). Results We found a statistically significant association with two of the variants tested: rs3802842 (at chromosome 11q23, OR=1.60, 95% CI 1.3 to 2.0) and rs4779584 (at chromosome 15q13, OR=1.50, 95% CI 1.2 to 1.9). The majority of index patients (84%) had between 10 and 100 adenomas and 15% had >100 adenomas. Only two index patients (1%), both with >100 adenomas, had FDRs with polyposis. Forty-one per cent of the index patients had one or more FDRs with CRC. Conclusions These SNPs are the first common, low-penetrant variants reported to be associated with adenomatous polyposis not caused by a defect in the APC, MUTYH, POLD1 and POLE genes. Even though familial occurrence of polyposis was very rare, CRC was over-represented in FDRs of polyposis patients and, if confirmed, these relatives will therefore benefit from surveillance.
Characterization of an acetyl esterase from Myceliophthorathermophila C1 able to deacetylate xanthan
Kool, M.M. ; Schols, H.A. ; Wagenknecht, M. ; Hinz, S.W.A. ; Moerschbacher, B.M. ; Gruppen, H. - \ 2014
Carbohydrate Polymers 111 (2014). - ISSN 0144-8617 - p. 222 - 229.
bacterial polysaccharide xanthan - xylan esterases - carbohydrate esterases - xanthomonas-campestris - rheological properties - plant polysaccharides - enzymatic-hydrolysis - gum - transition - families
Screening of eight carbohydrate acetyl esterases for their activity towards xanthan resulted in the recogni-tion of one active esterase. AXE3, a CAZy family CE1 acetyl xylan esterase originating from Myceliophthorathermophila C1, removed 31% of all acetyl groups present in xanthan after a 48 h incubation. AXE3 activ-ity towards xanthan was only observed when xanthan molecules were in the disordered conformation.Optimal performance towards xanthan was observed at 53¿C in the complete absence of salt, a condi-tion favouring the disordered conformation. AXE3-deacetylated xanthan was hydrolyzed using cellulasesand analyzed for its repeating units using UPLC–HILIC–ELSD/ESI–MS. This showed that AXE3 specificallyremoves the acetyl groups positioned on the inner mannose and that acetyl groups positioned on theouter mannose are not removed at all. After a prolonged incubation at optimal conditions, 57% of allacetyl groups, representing 70% of all acetyl groups on the inner mannose units, were hydrolyzed.
Dietary Supplement Use and Colorectal Adenoma Risk in Individuals with Lynch Syndrome: The GEOLynch Cohort Study
Heine-Bröring, R.C. ; Winkels, R.M. ; Botma, A. ; Duijnhoven, F.J.B. van; Jung, A.Y. ; Kampman, E. - \ 2013
PLoS One 8 (2013)6. - ISSN 1932-6203
cancer - prevention - validity - families - vitamin - gene - omega-3-fatty-acids - questionnaire - metaanalysis - population
Background and Aims: Individuals with Lynch syndrome have a high lifetime risk of developing colorectal tumors. In this prospective cohort study of individuals with Lynch syndrome, we examined associations between use of dietary supplements and occurrence of colorectal adenomas. Materials and Methods: Using data of 470 individuals with Lynch syndrome in a prospective cohort study, associations between dietary supplement use and colorectal adenoma risk were evaluated by calculating hazard ratios (HR) and 95% confidence intervals (CI) using cox regression models adjusted for age, sex, and number of colonoscopies during person time. Robust sandwich covariance estimation was used to account for dependency within families. Results: Of the 470 mismatch repair gene mutation carriers, 122 (26.0%) developed a colorectal adenoma during an overall median person time of 39.1 months. 40% of the study population used a dietary supplement. Use of any dietary supplement was not statistically significantly associated with colorectal adenoma risk (HR = 1.18; 95% CI 0.80-1.73). Multivitamin supplement use (HR = 1.15; 95% CI 0.72-1.84), vitamin C supplement use (HR = 1.57; 95% CI 0.93-2.63), calcium supplement use (HR = 0.69; 95% CI 0.25-1.92), and supplements containing fish oil (HR = 1.60; 95% CI 0.79-3.23) were also not associated with occurrence of colorectal adenomas. Conclusion: This prospective cohort study does not show inverse associations between dietary supplement use and occurrence of colorectal adenomas among individuals with Lynch syndrome. Further research is warranted to determine whether or not dietary supplement use is associated to colorectal adenoma and colorectal cancer risk in MMR gene mutation carriers.
A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology
Seidl, M.F. ; Schneider, A. ; Govers, F. ; Snel, B. - \ 2013
BMC Genomics 14 (2013). - ISSN 1471-2164 - 16 p.
protein-protein interactions - zoospore motility - complexes - reveals - yeast - families - tool - organization - translation - innovations
Background - Associations between proteins are essential to understand cell biology. While this complex interplay between proteins has been studied in model organisms, it has not yet been described for the oomycete late blight pathogen Phytophthora infestans. Results - We present an integrative probabilistic functional gene network that provides associations for 37 percent of the predicted P. infestans proteome. Our method unifies available genomic, transcriptomic and comparative genomic data into a single comprehensive network using a Bayesian approach. Enrichment of proteins residing in the same or related subcellular localization validates the biological coherence of our predictions. The network serves as a framework to query existing genomic data using network-based methods, which thus far was not possible in Phytophthora. We used the network to study the set of interacting proteins that are encoded by genes co-expressed during sporulation. This identified potential novel roles for proteins in spore formation through their links to proteins known to be involved in this process such as the phosphatase Cdc14. Conclusions - The functional association network represents a novel genome-wide data source for P. infestans that also acts as a framework to interrogate other system-wide data. In both capacities it will improve our understanding of the complex biology of P. infestans and related oomycete pathogens
Two novel GH11 endo-xylanases from Myceliophthora thermophila C1 act differently toward soluble and insoluble xylans
Gool, M.P. van; Muiswinkel, G.C.J. van; Hinz, S.W.A. ; Schols, H.A. ; Sinitsyn, A.P. ; Gruppen, H. - \ 2013
Enzyme and Microbial Technology 53 (2013)1. - ISSN 0141-0229 - p. 25 - 32.
chrysosporium-lucknowense - families - arabinoxylan - hydrolases
Two novel GH11 endo-xylanases from Myceliophthora thermophila C1 (C1), Xyl7 and Xyl8, were purified and the influence of solubility and molecular structure of various xylans on their efficiency was investigated. Both endo-xylanases were hindered by a high degree of substitution of a xylan. The two GH11 xylanases released different products from the xylans, in which Xyl7 displayed a degradation product composition closer to GH10 xylanases. A correlation of the degradation product composition with a specific residue at position 163 in the amino acid sequence of Xyl8 is suggested: tyrosine in Xyl8; valine in Xyl7. This is confirmed with examples of various endo-xylanases reported in literature. The C1 GH11 xylanases were more efficient on self-associated xylan compared to C1 GH10 endo-xylanases and they released more small xylooligomers from these xylans. This is contrary to the general assumption that GH10 xylanases degrade xylans to a higher degree than GH11 xylanases
Dietary Patterns and Colorectal Adenomas in Lynch Syndrome: The GEOLynch Cohort Study
Botma, A. ; Vasen, H.F. ; Duijnhoven, F.J.B. van; Kleibeuker, J.H. ; Nagengast, F.M. ; Kampman, E. - \ 2013
Cancer 119 (2013)3. - ISSN 0008-543X - p. 512 - 521.
colon-cancer - endometrial cancer - risk - hnpcc - gene - families - questionnaire - consumption - population - recurrence
BACKGROUND: Patients with Lynch syndrome (LS) have a high risk of developing colorectal cancer due to mutations in mismatch repair genes. Because dietary factors, alone and in combination, influence sporadic colorectal carcinogenesis, the association of dietary patterns with colorectal adenomas in LS patients was assessed. METHODS: In the GEOLynch cohort of 486 persons with LS, dietary information was collected, using a food frequency questionnaire. Dietary pattern scores were obtained by principal components analysis. Hazard ratios (HR) between dietary patterns and colorectal adenomas were calculated using Cox regression models. Robust sandwich variance estimates were used to control for dependency within families. Final models were adjusted for age, sex, smoking habits, colorectal adenoma history, and extent of colon resection. RESULTS: During a median follow-up of 20 months, colorectal adenomas were detected in 58 persons. Four dietary patterns were identified: a Prudent, Meat, Snack, and Cosmopolitan pattern. Individuals within the highest tertile of the Prudent pattern had a HR of 0.73 (95% confidence interval [CI], 0.32-1.66) for colorectal adenomas, compared with the lowest tertile. Those with high Meat pattern scores had a HR of 1.70 (95% CI, 0.83-3.52). A high Snack pattern was associated with an increased risk of colorectal adenomas (HR, 2.16; 95% CI, 1.03-4.49). A HR of 1.25 (95% CI, 0.61-2.55) was observed for persons in the highest tertile of the Cosmopolitan pattern. CONCLUSIONS: These findings suggest that dietary patterns may be associated with development of colorectal adenoma in patients with Lynch syndrome. The directions of these findings are corroborative with those observed in studies investigating sporadic colorectal cancer. Cancer 2013. (C) 2012 American Cancer Society.
Promoter propagation in prokaryotes
Matus-Garcia, M. ; Nijveen, H. ; Passel, M.W.J. van - \ 2012
Nucleic Acids Research 40 (2012)20. - ISSN 0305-1048 - p. 10032 - 10040.
horizontal gene-transfer - escherichia-coli - adaptive evolution - lactococcus-lactis - sequences - genomes - networks - identification - mutations - families
Transcriptional activation or 'rewiring' of silent genes is an important, yet poorly understood, phenomenon in prokaryotic genomes. Anecdotal evidence coming from experimental evolution studies in bacterial systems has shown the promptness of adaptation upon appropriate selective pressure. In many cases, a partial or complete promoter is mobilized to silent genes from elsewhere in the genome. We term hereafter such recruited regulatory sequences as Putative Mobile Promoters (PMPs) and we hypothesize they have a large impact on rapid adaptation of novel or cryptic functions. Querying all publicly available prokaryotic genomes (1362) uncovered >4000 families of highly conserved PMPs (50 to 100 long with =80% nt identity) in 1043 genomes from 424 different genera. The genomes with the largest number of PMP families are Anabaena variabilis (28 families), Geobacter uraniireducens (27 families) and Cyanothece PCC7424 (25 families). Family size varied from 2 to 93 homologous promoters (in Desulfurivibrio alkaliphilus). Some PMPs are present in particular species, but some are conserved across distant genera. The identified PMPs represent a conservative dataset of very recent or conserved events of mobilization of non-coding DNA and thus they constitute evidence of an extensive reservoir of recyclable regulatory sequences for rapid transcriptional rewiring
Smoking increases the risk for colorectal adenomas in patients with Lynch syndrome
Winkels, R.M. ; Botma, A. ; Duijnhoven, F.J.B. van; Nagengast, F.M. ; Kleibeuker, J.H. ; Vasen, H.F.A. ; Kampman, E. - \ 2012
Gastroenterology 142 (2012)2. - ISSN 0016-5085 - p. 241 - 247.
microsatellite instability - cigarette-smoking - cancer-risk - lung-cancer - gene - hypermethylation - metaanalysis - mutations - carcinoma - families
Background & Aims Individuals with Lynch syndrome have a high risk of developing colorectal carcinomas and adenomas at a young age, due to inherited mutations in mismatch repair genes. We investigated whether modifiable lifestyle factors, such as smoking and alcohol intake, increase this risk. Methods Using data from the GeoLynch cohort study, a prospective analysis of 386 subjects with Lynch syndrome, we calculated hazard ratios for the association between smoking and alcohol intake and development of colorectal adenoma. We used robust variance estimates in the calculation of 95% confidence intervals to account for dependency within families and adjusted for confounding by age, sex, smoking (in the analyses of alcohol intake), number of colonoscopies during the follow-up, colonic resection, and body mass index. Results During a median follow-up of 10 months, 58 subjects developed a histologically confirmed colorectal adenoma. The hazard ratio for current smokers was 6.13 (95% confidence interval, 2.84-13.22) and for former smokers was 3.03 (95% confidence interval, 1.49-6.16) compared with never smokers. Among ever smokers, a higher number of pack-years was associated with an increased risk for colorectal adenoma (P for trend = .03). There was a trend of alcohol intake increasing the risk of colorectal adenomas, although this was not statistically significant; the hazard ratio for the highest tertile of intake (median, 22 g/day) vs the lowest tertile (median, 0.4 g/day) was 1.56 (95% confidence interval, 0.71-3.43). Conclusions Among people with Lynch syndrome, current smokers have an increased risk of colorectal adenomas. Former smokers have a lower risk than current smokers, but greater risk than never smokers. Individuals with Lynch syndrome should be encouraged to avoid smoking
Macrophotographic wood atlas of Annonaceae.
Koek-Noorman, J. ; Westra, L.I.T. - \ 2012
Botanical Journal of the Linnean Society 169 (2012)1. - ISSN 0024-4074 - p. 135 - 189.
flowering plants - genera - classification - evolution - families - genus
In this article, a general description of the microscopic wood anatomy of Annonaceae is given. We provide a description of the wood anatomical features of the family and of all subfamilies and tribes, all from material in the Utrecht Wood collection. Hand-lens images can be an important help in identification, not only at the family level, but also at the level of genera or below, notwithstanding the fact that the number of characters that can be easily observed in end-grain photographs is restricted. The differences are often slight and difficult to summarize in a few words, making illustrations an indispensable tool. Therefore, we provide end-grain photographs of cross-sections of wood of 66 genera and > 90 species of Annonaceae. The variation seen in lens key characters is discussed against the framework of the current phylogenetic tree of the family. Additional remarks on microscopic features are given when appropriate
Editorial: The natural history of Annonaceae.
Chatrou, L.W. ; Erkens, R.H.J. ; Richardson, J.E. ; Saunders, R.M.K. ; Fay, M.F. - \ 2012
Botanical Journal of the Linnean Society 169 (2012)1. - ISSN 0024-4074 - p. 1 - 4.
phylogeny group classification - cladistic-analysis - uvaria annonaceae - flowering plants - apg iii - families - genera - genus - update - orders
Care farms as a short-break service for children with Autism Spectrum Disorders
Ferwerda-van Zonneveld, R.T. ; Oosting, S.J. ; Kijlstra, A. - \ 2012
NJAS Wageningen Journal of Life Sciences 59 (2012)1-2. - ISSN 1573-5214 - p. 35 - 40.
special educational treatment - animal-assisted therapy - families
Farms are enjoying an increasing popularity as a short-break service for children with Autism Spectrum Disorders (ASDs). The characteristics required on such care farms are currently unknown. To identify these characteristics, farmers of seven Dutch care farms with livestock were interviewed using a semi-structured questionnaire. These farmers play a key role in care by offering structure, clarity and attention to ASD-children. They use a variety of farm animals with the children, as icebreakers, co-therapists or transitional objects. Our main conclusion is that for children with ASDs, visiting care farms forms an important addition to the current short-break opportunities. At the same time, the farmers expressed needs related to the quality of care, which could be improved by offering them special training. --------------------------------------------------------------------------------
QTL linkage analysis of connected populations using ancestral marker and pedigree information
Bink, M.C.A.M. ; Radu Totir, L. ; Braak, C.J.F. ter; Winkler, C.R. ; Boer, M.P. ; Smith, O.S. - \ 2012
Theoretical and Applied Genetics 124 (2012)6. - ISSN 0040-5752 - p. 1097 - 1113.
quantitative trait loci - plant-populations - kernel hardness - dough strength - model - maize - selection - families - wheat - identity
The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the current mapping populations from locus-specific identity by descent (IBD) matrices that capture ancestral marker and pedigree information. Moreover, we demonstrate how the parental IBD data can be incorporated into a QTL linkage analysis framework by using two approaches: a Threshold IBD model (TIBD) and a Latent Ancestral Allele Model (LAAM). The TIBD and LAAM models are empirically tested via numerical simulation based on the structure of a commercial maize breeding program. The simulations included a pilot dataset with closely linked QTL on a single linkage group and 100 replicated datasets with five linkage groups harboring four unlinked QTL. The simulation results show that including parental IBD data (similarly for TIBD and LAAM) significantly improves the power and particularly accuracy of QTL mapping, e.g., position, effect size and individuals’ genotype probability without significantly increasing computational demand.
Correlated mutations via regularized multinomial regression
Sreekumar, J. ; Braak, C.J.F. ter; Ham, R.C.H.J. van; Dijk, A.D.J. van - \ 2011
BMC Bioinformatics 12 (2011). - ISSN 1471-2105 - 13 p.
multiple sequence alignments - protein-protein interaction - mutual information - graphical models - prediction - families - identification - specificity - dimension - selection
Background In addition to sequence conservation, protein multiple sequence alignments contain evolutionary signal in the form of correlated variation among amino acid positions. This signal indicates positions in the sequence that influence each other, and can be applied for the prediction of intra- or intermolecular contacts. Although various approaches exist for the detection of such correlated mutations, in general these methods utilize only pairwise correlations. Hence, they tend to conflate direct and indirect dependencies. Results We propose RMRCM, a method for Regularized Multinomial Regression in order to obtain Correlated Mutations from protein multiple sequence alignments. Importantly, our method is not restricted to pairwise (column-column) comparisons only, but takes into account the network nature of relationships between protein residues in order to predict residue-residue contacts. The use of regularization ensures that the number of predicted links between columns in the multiple sequence alignment remains limited, preventing overprediction. Using simulated datasets we analyzed the performance of our approach in predicting residue-residue contacts, and studied how it is influenced by various types of noise. For various biological datasets, validation with protein structure data indicates a good performance of the proposed algorithm for the prediction of residue-residue contacts, in comparison to previous results. RMRCM can also be applied to predict interactions (in addition to only predicting interaction sites or contact sites), as demonstrated by predicting PDZ-peptide interactions. Conclusions A novel method is presented, which uses regularized multinomial regression in order to obtain correlated mutations from protein multiple sequence alignments.
Revision of the African Genus Hexalobus (Annonaceae)
Botermans, M. ; Sosef, M.S.M. ; Chatrou, L.W. ; Couvreur, T.L.P. - \ 2011
Systematic Botany 36 (2011)1. - ISSN 0363-6445 - p. 33 - 48.
pollen morphology - families - diversity - evolution - monodora
The genus Hexalobus consists of five species characterized by six basally fused petal lobes that are transversally folded in bud, which is unique within Annonaceae. The genus is widespread across tropical Africa occurring in rain forest, savanna, and woodland. The species H. callicarpus, occurring in Madagascar, is excluded from Hexalobus, so the genus is now restricted to continental Africa. The present revision provides a synthesis of previously published information and discussions on morphology, taxonomy, phylogeny, and palynology. Conservation status assessments are provided for each species, as well as a diagnostic key and detailed species descriptions. Furthermore, four species are illustrated and all species are mapped
A new species of Uvariopsis (Annonaceae), endemic to the Eastern Arc Mountains of Tanzania
Couvreur, T.L.P. ; Luke, W.R.Q. - \ 2010
Blumea 55 (2010)1. - ISSN 0006-5196 - p. 68 - 72.
tropical africa - biodiversity - conservation - families
The Eastern Arc Mountains of Tanzania enclose high levels of plant and animal diversity with many yet to be described species. Here we describe a new species of the pan-tropical plant family Annonaceae named Uvariopsis lovettiana. It closely resembles another Eastern Arc endemic species, U. bisexualis, and its possible relationships with this species are discussed. A description with illustrations is presented as well as a suggestion for the IUCN conservation status of this new taxon
Families on the balance: eating behaviour and weight status of adolescents and their families
Snoek, H.M. - \ 2010
Radboud University Nijmegen. Promotor(en): R.C.M.E. Engels; J.M.A.M. Janssens; T. van Strien. - Den Haag : Radboud Universiteit Nijmegen - ISBN 9789090249452 - 238
voedingsgewoonten - eten - dwangmatig eten - mentale stress - emoties - gedrag - adolescenten - gezinnen - feeding habits - eating - compulsive eating - mental stress - emotions - behaviour - adolescents - families
This dissertation focusses on three eating styles: Emotional eating which is the tendency to eat in response to emotional (dis)stress, external eating which is the tendency to eat in response to food cues, and restrained eating which is the tendency to restrict food intake in order to loose weight or prevent weight gain.
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