Comparison theorems for deformation functors via invariant theory

We compare deformations of algebras to deformations of schemes in the setting of invariant theory. Our results generalize comparison theorems of Schlessinger and the second author for projective schemes. We consider deformations (abstract and embedded) of a scheme $X$ which is a good quotient of a quasi-affine scheme $X^\prime$ by a linearly reductive group $G$ and compare them to invariant deformations of an affine $G$-scheme containing $X^\prime$ as an open invariant subset. The main theorems give conditions for when the comparison morphisms are smooth or isomorphisms.Comment: Minor improvements and corrections. Improved presentation. Changed some definitions and term

Associations between the human immune system and gut microbiome with neurodevelopment in the first 5 years of life: A systematic scoping review

The aim of this review was to map the literature assessing associations between maternal or infant immune or gut microbiome biomarkers and child neurodevelopmental outcomes within the first 5 years of life. We conducted a PRISMA-ScR compliant review of peer-reviewed, English-language journal articles. Studies reporting gut microbiome or immune system biomarkers and child neurodevelopmental outcomes prior to 5 years were eligible. Sixty-nine of 23,495 retrieved studies were included. Of these, 18 reported on the maternal immune system, 40 on the infant immune system, and 13 on the infant gut microbiome. No studies examined the maternal microbiome, and only one study examined biomarkers from both the immune system and the gut microbiome. Additionally, only one study included both maternal and infant biomarkers. Neurodevelopmental outcomes were assessed from 6 days to 5 years. Associations between biomarkers and neurodevelopmental outcomes were largely nonsignificant and small in effect size. While the immune system and gut microbiome are thought to have interactive impacts on the developing brain, there remains a paucity of published studies that report biomarkers from both systems and associations with child development outcomes. Heterogeneity of research designs and methodologies may also contribute to inconsistent findings. Future studies should integrate data across biological systems to generate novel insights into the biological underpinnings of early development

The ethics of uncertainty for data subjects

Modern health data practices come with many practical uncertainties. In this paper, I argue that data subjects’ trust in the institutions and organizations that control their data, and their ability to know their own moral obligations in relation to their data, are undermined by significant uncertainties regarding the what, how, and who of mass data collection and analysis. I conclude by considering how proposals for managing situations of high uncertainty might be applied to this problem. These emphasize increasing organizational flexibility, knowledge, and capacity, and reducing hazard

Rethinking justice beyond human rights. Anti-colonialism and intersectionality in the politics of the Palestinian Youth Movement

This article discusses the politics of the Palestinian Youth Movement (PYM) – a contemporary social movement operating across a number of Arab and western countries. Unlike analysis on the Arab Uprisings which focused on the national dimension of youth activism, we explore how the PYM politics fosters and upholds an explicitly transnational anti-colonial and intersectional solidarity framework, which foregrounds a radical critique of conventional notions of self-determination based on state-framed human rights discourses and international law paradigms. The struggle becomes instead framed as an issue of justice, freedom and liberation from interlocking forms and hierarchies of oppression. KEYWORDS: Palestine, transnational social movements, intersectionality, human rights, anti-colonialis

Runoff sources and land cover change in the Amazon : an end-member mixing analysis from small watersheds

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Biogeochemistry 105 (2011): 7-18, doi:10.1007/s10533-011-9597-8.The flowpaths by which water moves from watersheds to streams has important consequences for the runoff dynamics and biogeochemistry of surface waters in the Amazon Basin. The clearing of Amazon forest to cattle pasture has the potential to change runoff sources to streams by shifting runoff to more surficial flow pathways. We applied end member mixing analysis (EMMA) to ten small watersheds throughout the Amazon in which solute composition of streamwater and groundwater, overland flow, soil solution, throughfall and rainwater were measured, largely as part of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia. We found a range in the extent to which streamwater samples fell within the mixing space determined by potential flowpath end members, suggesting that some water sources to streams were not sampled. The contribution of overland flow as a source of stream flow was greater in pasture watersheds than in forest watersheds of comparable size. Increases in overland flow contribution to pasture streams ranged in some cases from 0% in forest to 27 to 28% in pasture and were broadly consistent with results from hydrometric sampling of Amazon forest and pasture watersheds that indicate 17- to 18-fold increase in the overland flow contribution to stream flow in pastures. In forest, overland flow was an important contribution to stream flow (45 to 57%) in ephemeral streams where flows were dominated by stormflow. Overland flow contribution to stream flow decreased in importance with increasing watershed area, from 21 to 57% in forest and 60 to 89% in pasture watersheds 100 ha. Soil solution contributions to stream flow were similar across watershed area and groundwater inputs generally increased in proportion to decreases in overland flow. Application of EMMA across multiple watersheds indicated patterns across gradients of stream size and land cover that were consistent with patterns determined by detailed hydrometric sampling.This work was supported by National Science Foundation (DEB-0315656, DEB-0640661), the NASA LBA Program (NCC5-686, NCC5-69, NCC5-705, NNG066E88A) and by grants from Brazilian agencies FAPESP (03/13172-2) and CNPq (20199/2005-5)

Association between mortality from suicide in England and antidepressant prescribing: an ecological study

BACKGROUND: Antidepressant prescribing has been increasing in England. Studies in other countries suggest that while this may be associated with reduced suicide rates, it may also be associated with increased fatal poisoning from antidepressant drugs. We therefore conducted an ecological study to assess the association between prescription rates for antidepressants and suicide or fatal antidepressant-related poisoning in England. METHODS: The Office for National Statistics provided information on the number of suicides, antidepressant-related poisoning deaths and populations for England between 1993 and 2002. The Department of Health supplied data on prescriptions for all antidepressants dispensed in England. Associations between prescriptions and deaths were assessed using Spearman's rank correlation coefficient. RESULTS: There were 46,747 suicides, 3,987 deaths involving tricyclic antidepressants and 430 involving selective serotonin re-uptake inhibitors and other antidepressants. Increased antidepressant prescribing was statistically associated with a fall in suicide rates (Spearman's r(s )= -0.73, p = 0.02) and fatal poisoning involving tricyclic antidepressants (r(s )= -0.64, p = 0.05). In contrast, increased prescribing of selective serotonin re-uptake inhibitors and other antidepressants was statistically associated with an increase in fatal poisoning involving these drugs (r(s )= 0.99, p < 0.001). CONCLUSION: Increased prescribing of antidepressants may indicate improved diagnosis and treatment of depression in primary care. Our analysis suggests that this was accompanied by lower suicide rates. A decrease in poisoning deaths involving tricyclic antidepressants may suggest a change in preference for using serotonin reuptake inhibitors and other antidepressant drugs for high-risk patients. This may also partially explain the increase in deaths involving these drugs. Due to the ecological nature of the design, we cannot say conclusively whether reduced suicide rates are a direct consequence of increased antidepressant prescribing rates. To confirm these associations, individual level data on prescribing and suicide is needed

DNA-Methylation Profiling of Fetal Tissues Reveals Marked Epigenetic Differences between Chorionic and Amniotic Samples

Epigenetic mechanisms including DNA methylation are supposed to play a key role in fetal development. Here we have investigated fetal DNA-methylation levels of 27,578 CpG loci in 47 chorionic villi (CVS) and 16 amniotic cell (AC) samples. Methylation levels differed significantly between karyotypically normal AC and CVS for 2,014 genes. AC showed more extreme DNA-methylation levels of these genes than CVS and the differentially methylated genes are significantly enriched for processes characteristic for the different cell types sampled. Furthermore, we identified 404 genes differentially methylated in CVS with trisomy 21. These genes were significantly enriched for high CG dinucleotid (CpG) content and developmental processes associated with Down syndrome. Our study points to major tissue-specific differences of fetal DNA-methylation and gives rise to the hypothesis that part of the Down syndrome phenotype is epigenetically programmed in the first trimester of pregnancy

Genome-Wide Association Study Singles Out SCD and LEPR as the Two Main Loci Influencing Intramuscular Fat Content and Fatty Acid Composition in Duroc Pigs

[EN] Intramuscular fat (IMF) content and fatty acid composition affect the organoleptic quality and nutritional value of pork. A genome-wide association study was performed on 138 Duroc pigs genotyped with a 60k SNP chip to detect biologically relevant genomic variants influencing fat content and composition. Despite the limited sample size, the genome-wide association study was powerful enough to detect the association between fatty acid composition and a known haplotypic variant in SCD (SSC14) and to reveal an association of IMF and fatty acid composition in the LEPR region (SSC6). The association of LEPR was later validated with an independent set of 853 pigs using a candidate quantitative trait nucleotide. The SCD gene is responsible for the biosynthesis of oleic acid (C18:1) from stearic acid. This locus affected the stearic to oleic desaturation index (C18:1/C18:0), C18: 1, and saturated (SFA) and monounsaturated (MUFA) fatty acids content. These effects were consistently detected in gluteus medius, longissimus dorsi, and subcutaneous fat. The association of LEPR with fatty acid composition was detected only in muscle and was, at least in part, a consequence of its effect on IMF content, with increased IMF resulting in more SFA, less polyunsaturated fatty acids (PUFA), and greater SFA/PUFA ratio. Marker substitution effects estimated with a subset of 65 animals were used to predict the genomic estimated breeding values of 70 animals born 7 years later. Although predictions with the whole SNP chip information were in relatively high correlation with observed SFA, MUFA, and C18: 1/C18: 0 (0.48-0.60), IMF content and composition were in general better predicted by using only SNPs at the SCD and LEPR loci, in which case the correlation between predicted and observed values was in the range of 0.36 to 0.54 for all traits. Results indicate that markers in the SCD and LEPR genes can be useful to select for optimum fatty acid profiles of pork.This research was funded by the Spanish Ministry of Economy and Competitiveness (MINECO; grants AGL2012-33529 and AGL2015-65846-R).Ros-Freixedes, R.; Gol, S.; Pena, R.; Tor, M.; Ibañez Escriche, N.; Dekkers, J.; Estany, J. (2016). Genome-Wide Association Study Singles Out SCD and LEPR as the Two Main Loci Influencing Intramuscular Fat Content and Fatty Acid Composition in Duroc Pigs. PLoS ONE. 11(3). https://doi.org/10.1371/journal.pone.0152496S113Cameron, N. ., Enser, M., Nute, G. ., Whittington, F. ., Penman, J. ., Fisken, A. ., … Wood, J. . (2000). Genotype with nutrition interaction on fatty acid composition of intramuscular fat and the relationship with flavour of pig meat. Meat Science, 55(2), 187-195. doi:10.1016/s0309-1740(99)00142-4Christophersen, O. A., & Haug, A. (2011). Animal products, diseases and drugs: a plea for better integration between agricultural sciences, human nutrition and human pharmacology. Lipids in Health and Disease, 10(1), 16. doi:10.1186/1476-511x-10-16Ntawubizi, M., Colman, E., Janssens, S., Raes, K., Buys, N., & De Smet, S. (2010). Genetic parameters for intramuscular fatty acid composition and metabolism in pigs1. Journal of Animal Science, 88(4), 1286-1294. doi:10.2527/jas.2009-2355Ros-Freixedes, R., Reixach, J., Tor, M., & Estany, J. (2012). Expected genetic response for oleic acid content in pork1. Journal of Animal Science, 90(12), 4230-4238. doi:10.2527/jas.2011-5063Clop, A., Ovilo, C., Perez-Enciso, M., Cercos, A., Tomas, A., Fernandez, A., … Noguera, J. L. (2003). Detection of QTL affecting fatty acid composition in the pig. Mammalian Genome, 14(9), 650-656. doi:10.1007/s00335-002-2210-7Kim, Y., Kong, M., Nam, Y. J., & Lee, C. (2006). A Quantitative Trait Locus for Oleic Fatty Acid Content on Sus scrofa Chromosome 7. Journal of Heredity, 97(5), 535-537. doi:10.1093/jhered/esl026Sanchez, M.-P., Iannuccelli, N., Basso, B., Bidanel, J.-P., Billon, Y., Gandemer, G., … Le Roy, P. (2007). Identification of QTL with effects on intramuscular fat content and fatty acid composition in a Duroc × Large White cross. BMC Genetics, 8(1), 55. doi:10.1186/1471-2156-8-55Guo, T., Ren, J., Yang, K., Ma, J., Zhang, Z., & Huang, L. (2009). Quantitative trait loci for fatty acid composition in longissimus dorsi and abdominal fat: results from a White Duroc × Erhualian intercross F2population. Animal Genetics, 40(2), 185-191. doi:10.1111/j.1365-2052.2008.01819.xC.M. Dekkers, J. (2012). Application of Genomics Tools to Animal Breeding. Current Genomics, 13(3), 207-212. doi:10.2174/138920212800543057Uemoto, Y., Nakano, H., Kikuchi, T., Sato, S., Ishida, M., Shibata, T., … Suzuki, K. (2011). Fine mapping of porcine SSC14 QTL and SCD gene effects on fatty acid composition and melting point of fat in a Duroc purebred population. Animal Genetics, 43(2), 225-228. doi:10.1111/j.1365-2052.2011.02236.xUemoto, Y., Soma, Y., Sato, S., Ishida, M., Shibata, T., Kadowaki, H., … Suzuki, K. (2011). Genome-wide mapping for fatty acid composition and melting point of fat in a purebred Duroc pig population. Animal Genetics, 43(1), 27-34. doi:10.1111/j.1365-2052.2011.02218.xEstany, J., Ros-Freixedes, R., Tor, M., & Pena, R. N. (2014). A Functional Variant in the Stearoyl-CoA Desaturase Gene Promoter Enhances Fatty Acid Desaturation in Pork. PLoS ONE, 9(1), e86177. doi:10.1371/journal.pone.0086177Ramayo-Caldas, Y., Mercadé, A., Castelló, A., Yang, B., Rodríguez, C., Alves, E., … Folch, J. M. (2012). Genome-wide association study for intramuscular fatty acid composition in an Iberian × Landrace cross1. Journal of Animal Science, 90(9), 2883-2893. doi:10.2527/jas.2011-4900Muñoz, M., Rodríguez, M. C., Alves, E., Folch, J. M., Ibañez-Escriche, N., Silió, L., & Fernández, A. I. (2013). Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data. BMC Genomics, 14(1), 845. doi:10.1186/1471-2164-14-845Yang, B., Zhang, W., Zhang, Z., Fan, Y., Xie, X., Ai, H., … Ren, J. (2013). Genome-Wide Association Analyses for Fatty Acid Composition in Porcine Muscle and Abdominal Fat Tissues. PLoS ONE, 8(6), e65554. doi:10.1371/journal.pone.0065554Zhang, W., Zhang, J., Cui, L., Ma, J., Chen, C., Ai, H., … Yang, B. (2016). Genetic architecture of fatty acid composition in the longissimus dorsi muscle revealed by genome-wide association studies on diverse pig populations. Genetics Selection Evolution, 48(1). doi:10.1186/s12711-016-0184-2Kim, E.-S., Ros-Freixedes, R., Pena, R. N., Baas, T. J., Estany, J., & Rothschild, M. F. (2015). Identification of signatures of selection for intramuscular fat and backfat thickness in two Duroc populations1. Journal of Animal Science, 93(7), 3292-3302. doi:10.2527/jas.2015-8879Bosch, L., Tor, M., Reixach, J., & Estany, J. (2009). Estimating intramuscular fat content and fatty acid composition in live and post-mortem samples in pigs. Meat Science, 82(4), 432-437. doi:10.1016/j.meatsci.2009.02.013AOAC. 1997. Supplement to AOAC Official Method 996.06: Fat (total, saturated, and monounsaturated) in foods hydrolytic extraction gas chromatographic method. Page 18 in Official Methods of Analysis (16th ed). Association of Official Analytical Chemists, Arlington, VA.ÓVILO, C., FERNÁNDEZ, A., NOGUERA, J. L., BARRAGÁN, C., LETÓN, R., RODRÍGUEZ, C., … TORO, M. (2005). Fine mapping of porcine chromosome 6 QTL and LEPR effects on body composition in multiple generations of an Iberian by Landrace intercross. Genetical Research, 85(1), 57-67. doi:10.1017/s0016672305007330Amills, M., Villalba, D., Tor, M., Mercad, A., Gallardo, D., Cabrera, B., … Estany, J. (2008). Plasma leptin levels in pigs with different leptin and leptin receptor genotypes. Journal of Animal Breeding and Genetics, 125(4), 228-233. doi:10.1111/j.1439-0388.2007.00715.xPurcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., … Sham, P. C. (2007). PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. The American Journal of Human Genetics, 81(3), 559-575. doi:10.1086/519795Bouwman, A. C., Janss, L. L., & Heuven, H. C. (2011). A Bayesian approach to detect QTL affecting a simulated binary and quantitative trait. BMC Proceedings, 5(S3). doi:10.1186/1753-6561-5-s3-s4Legarra, A., Croiseau, P., Sanchez, M., Teyssèdre, S., Sallé, G., Allais, S., … Elsen, J.-M. (2015). A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species. Genetics Selection Evolution, 47(1), 6. doi:10.1186/s12711-015-0087-7Kass, R. E., & Raftery, A. E. (1995). Bayes Factors. Journal of the American Statistical Association, 90(430), 773-795. doi:10.1080/01621459.1995.10476572Barrett, J. C., Fry, B., Maller, J., & Daly, M. J. (2004). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21(2), 263-265. doi:10.1093/bioinformatics/bth457Wolc, A., Arango, J., Settar, P., Fulton, J. E., O’Sullivan, N. P., Preisinger, R., … Dekkers, J. C. M. (2012). Genome-wide association analysis and genetic architecture of egg weight and egg uniformity in layer chickens. Animal Genetics, 43, 87-96. doi:10.1111/j.1365-2052.2012.02381.xChen, E. Y., Tan, C. M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G., … Ma’ayan, A. (2013). Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics, 14(1), 128. doi:10.1186/1471-2105-14-128Rabbit programme. 2012. Available from: http://www.dcam.upv.es/dcia/ablasco/Programas/THE%20PROGRAM%20Rabbit.pdfHu, Z.-L., Park, C. A., & Reecy, J. M. (2015). Developmental progress and current status of the Animal QTLdb. Nucleic Acids Research, 44(D1), D827-D833. doi:10.1093/nar/gkv1233Óvilo, C., Fernández, A., Fernández, A. I., Folch, J. M., Varona, L., Benítez, R., … Silió, L. (2010). Hypothalamic expression of porcine leptin receptor (LEPR), neuropeptide Y (NPY), and cocaine- and amphetamine-regulated transcript (CART) genes is influenced by LEPR genotype. Mammalian Genome, 21(11-12), 583-591. doi:10.1007/s00335-010-9307-1Muñoz, G., Alcázar, E., Fernández, A., Barragán, C., Carrasco, A., de Pedro, E., … Rodríguez, M. C. (2011). Effects of porcine MC4R and LEPR polymorphisms, gender and Duroc sire line on economic traits in Duroc×Iberian crossbred pigs. Meat Science, 88(1), 169-173. doi:10.1016/j.meatsci.2010.12.018Galve, A., Burgos, C., Silió, L., Varona, L., Rodríguez, C., Ovilo, C., & López-Buesa, P. (2012). The effects of leptin receptor (LEPR) and melanocortin-4 receptor (MC4R) polymorphisms on fat content, fat distribution and fat composition in a Duroc×Landrace/Large White cross. Livestock Science, 145(1-3), 145-152. doi:10.1016/j.livsci.2012.01.010UEMOTO, Y., KIKUCHI, T., NAKANO, H., SATO, S., SHIBATA, T., KADOWAKI, H., … SUZUKI, K. (2011). Effects of porcine leptin receptor gene polymorphisms on backfat thickness, fat area ratios by image analysis, and serum leptin concentrations in a Duroc purebred population. Animal Science Journal, 83(5), 375-385. doi:10.1111/j.1740-0929.2011.00963.xHirose, K., Ito, T., Fukawa, K., Arakawa, A., Mikawa, S., Hayashi, Y., & Tanaka, K. (2013). Evaluation of effects of multiple candidate genes (LEP,LEPR,MC4R,PIK3C3, andVRTN) on production traits in Duroc pigs. Animal Science Journal, 85(3), 198-206. doi:10.1111/asj.12134López-Buesa, P., Burgos, C., Galve, A., & Varona, L. (2013). Joint analysis of additive, dominant and first-order epistatic effects of four genes (IGF2,MC4R,PRKAG3andLEPR) with known effects on fat content and fat distribution in pigs. Animal Genetics, 45(1), 133-137. doi:10.1111/age.12091Mackowski, M., Szymoniak, K., Szydlowski, M., Kamyczek, M., Eckert, R., Rozycki, M., & Switonski, M. (2005). Missense mutations in exon 4 of the porcine LEPR gene encoding extracellular domain and their association with fatness traits. Animal Genetics, 36(2), 135-137. doi:10.1111/j.1365-2052.2005.01247.xLi, X., Kim, S.-W., Choi, J.-S., Lee, Y.-M., Lee, C.-K., Choi, B.-H., … Kim, K.-S. (2010). Investigation of porcine FABP3 and LEPR gene polymorphisms and mRNA expression for variation in intramuscular fat content. Molecular Biology Reports, 37(8), 3931-3939. doi:10.1007/s11033-010-0050-1Tyra, M., & Ropka-Molik, K. (2011). Effect of the FABP3 and LEPR gene polymorphisms and expression levels on intramuscular fat (IMF) content and fat cover degree in pigs. 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The population genomic legacy of the second plague pandemic

SummaryHuman populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%–40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th–19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.Results and discussion STAR★Method