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In this study, we present the results of a genome-wide scan for signatures of positive selection using data from four tribal groups (Kokana, Warli, Bhil, and Pawara) and two caste groups (Deshastha Brahmin and Kunbi Maratha) from West of the Maharashtra State In India, as well as two samples of South Asian ancestry from the 1KG project (Gujarati Indian from Houston, Texas and Indian Telugu from UK). We used an outlier approach based on different statistics, including PBS, xpEHH, iHS, CLR, Tajima’s D, as well as two recently developed methods: Graph-aware Retrieval of Selective Sweeps (GRoSS) and Ascertained Sequentially Markovian Coalescent (ASMC). In order to minimize the risk of false positives, we selected regions that are outliers in all the samples included in the study using more than one method. We identified putative selection signals in 107 regions encompassing 434 genes. Many of the regions overlap with only one gene. The signals observed using microarray-based data are very consistent with our analyses using high-coverage sequencing data, as well as those identified with a novel coalescence-based method (ASMC). Importantly, at least 24 of these genomic regions have been identified in previous selection scans in South Asian populations or in other population groups. Our study highlights genomic regions that may have played a role in the adaptation of anatomically modern humans to novel environmental conditions after the out of Africa migration.

Modern humans and archaic hominins, namely Denisovans and Neanderthals, have a long history of admixture. Some of these admixture events have allowed modern humans to adapt to new environments outside of Africa. Little research has been done on the impact of archaic introgression on genes associated with reproduction. In this study we report evidence of adaptive introgression of 118 genes within modern humans that have been previously associated with reproduction in mice or modern humans. We identified 11 archaic core haplotypes, three that have been positively selected, with 327 archaic alleles being genome-wide significant for a variety of traits. Over 300 of these variants were discovered to be eQTLs regulating 176 genes with 81% of the archaic eQTLs overlapping a core haplotype region regulating genes expressed in reproductive tissues. Several of the adaptively introgressed genes in our results are enriched in developmental and cancer pathways, while some have been associated with embryo development and reproductive-inhibiting phenotypes like endometriosis and preeclampsia. Lastly, we find that archaic alleles overlapping an introgressed segment on chromosome 2 are protective against prostate cancer. Our results highlight that archaic alleles show connections with important developmental pathways throughout the lifespan and may help regulate these critical processes. Modern human reproductive genes show evidence of adaptive introgression due to gene flow from Neanderthals and Denisovans in the past.

Interbreeding between modern humans and archaic hominins, including Neanderthals and Denisovans, occurred as modern humans migrated outside of Africa. Here, we report on evidence of adaptive introgression from archaic hominins within genomic regions associated with circadian rhythm cycling, chronotype, and sleep using 76 worldwide modern human populations from the Human Genome Diversity Project and 1000 Genomes Project. We identified 265 independent segments suggestive of adaptive introgression, where 22 of these segments show evidence of positive selection. We tested for evidence of a latitudinal cline within 35 core haplotypes, finding no clear latitude gradient, and identified the likely archaic donor for each of these haplotypes. We found that several genes with evidence of adaptive introgression are associated with affective disorders, chronotype, and respiratory diseases. Lastly, many of the variants are eQTLs for several genes that are significantly enriched in immunity pathways.

\"This volume commemorates the eclectic research of Douglas James Shearman into evaporites, which was initiated by his studies of the prograding UAE coastal sabkhas or salt flats that incorporate evaporite minerals which displace and replace earlier carbonate sediments. His subsequent proselytization of the study of ancient evaporites in sedimentary sections all over the world led to fundamental advances in our understanding of arid zone carbonate sedimentology. The papers presented here are based on presentations made in Abu Dhabi, UAE 12-14th October 2004 and 7th -8th November 2006. They provide a retrospective from the 1960's and 70's of Holocene evaporites and carbonates, recapturing Shearman's contribution by revisiting the Holocene coastal evaporite and carbonate sediments of the Arabian/Persian Gulf from Abu Dhabi, Qatar, and Oman. The first set of papers considers these sediments from the perspective of their coastal geomorphology, sedimentary character and their geochemistry. Later papers examine the significance of these settings in the ancient geological section world-wide, including examples from the Mesozoic-Cenozoic of the Moroccan Atlantic margin and the Upper Jurassic Arab Formation of the Arabian Gulf\"--

Using the 2000 Little Sisters v Customs Canada case as a springboard, Kendall argues that gay male pornography violates the legal right to sex equality, and that there is little to be gained from sexualized conformity.

This paper seeks to arrive at a consistent interpretation of (1) the age model, (2) the grain size record, and (3) seismic reflection data from Lake Hovsgol (a.k.a Khubsugul or Hövsgöl), Mongolia, reported by Fedotov et al. ( 2007 , earlier by Fedotov et al. 2002 , 2004 ). In their most recent contribution, the grain size record of the KDP-01 drill core is interpreted as a climatic signal while little consideration is given to lake-level changes and hence to basin-wide changes in depositional setting evident from seismic profiles; also, a nearly linear age model is at odds with the seismic evidence for a major angular unconformity in the sediment strata. The lack of regional seismic stratigraphic analysis has thus led to an improbable interpretation of the Lake Hovsgol sediment grain size record and ultimately to an improbable scenario of Mongolian glaciation history. Using the available seismic profiles, here we show that the drill core penetrated several transgressive/regressive sedimentary sequences and a major angular unconformity. Therefore, the drilled sediment section cannot represent continuous sediment accumulation and the Brunhes age model across the unconformity cannot be nearly linear; the time interval representing a hiatus remains to be determined. The assumed nearly linear age/depth relationship in the upper 23 m above the angular unconformity is also an unlikely relationship, given the evidence of repeated changes in lake level, and hence in the depositional setting and sedimentation rates. We further propose a qualitative reference model for changes in the Lake Hovsgol depositional setting (presented as a step-by-step animation – see supplementary material) based on manually ‘backstripping and rebuilding’ the seismic pattern. We argue that this model provides a useful template of the likely sediment facies changes in the deep axial part of the Hovsgol basin: our crude model in fact captures the major depositional trends in the KDP-01 drill core section located some 10 km NW along the seismic line. We contend that changes in the depositional setting provide the first-order control on sediment grain size in the Hovsgol record. Our study provides important new constraints on the nature of sedimentary proxy records in Lake Hovsgol and on their interpretation as a record of Mongolian glaciation history.

Cardiovascular disease (CVD) is the number one killer in the USA, yet it is largely preventable (World Health Organization 2011). To prevent CVD, carotid intima-media thickness (CIMT) imaging, a noninvasive ultrasonography method, has proven to be clinically valuable in identifying at-risk persons before adverse events. Researchers are developing systems to automate CIMT video interpretation based on deep learning, but such efforts are impeded by the lack of large annotated CIMT video datasets. CIMT video annotation is not only tedious, laborious, and time consuming, but also demanding of costly, specialty-oriented knowledge and skills, which are not easily accessible. To dramatically reduce the cost of CIMT video annotation, this paper makes three main contributions. Our first contribution is a new concept, called Annotation Unit (AU), which simplifies the entire CIMT video annotation process down to six simple mouse clicks. Our second contribution is a new algorithm, called AFT (active fine-tuning), which naturally integrates active learning and transfer learning (fine-tuning) into a single framework. AFT starts directly with a pre-trained convolutional neural network (CNN), focuses on selecting the most informative and representative AU s from the unannotated pool for annotation, and then fine-tunes the CNN by incorporating newly annotated AU s in each iteration to enhance the CNN’s performance gradually. Our third contribution is a systematic evaluation, which shows that, in comparison with the state-of-the-art method (Tajbakhsh et al., IEEE Trans Med Imaging 35(5):1299–1312, 2016), our method can cut the annotation cost by >81% relative to their training from scratch and >50% relative to their random selection. This performance is attributed to the several advantages derived from the advanced active, continuous learning capability of our AFT method.

The last couple of decades have highlighted the importance of studying hybridization, particularly among primate species, as it allows us to better understand our own evolutionary trajectory. Here, we report on genetic ancestry estimates using dense, full genome data from 881 olive ( Papio anubus ), yellow ( Papio cynocephalus ), or olive-yellow crossed captive baboons from the Southwest National Primate Research Center. We calculated global and local ancestry information, imputed low coverage genomes (n = 830) to improve marker quality, and updated the genetic resources of baboons available to assist future studies. We found evidence of historical admixture in some putatively purebred animals and identified errors within the Southwest National Primate Research Center pedigree. We also compared the outputs between two different phasing and imputation pipelines along with two different global ancestry estimation software. There was good agreement between the global ancestry estimation software, with R 2 > 0.88, while evidence of phase switch errors increased depending on what phasing and imputation pipeline was used. We also generated updated genetic maps and created a concise set of ancestry informative markers (n = 1,747) to accurately obtain global ancestry estimates.

Hybridisation is a widespread phenomenon, documented extensively across animals, insects, and plants. Specifically, within primates, hybridisation was once thought to occur in only rare instances. However, more recent analyses using genomic methods have uncovered that hybridisation occurs in primates likely at higher rates than previously estimated. Additionally, research on hybrids has highlighted that novel loci can be subject to positive natural selection leading to adaptive introgression within populations post-admixture. Therefore, examination of the extent of hybridisation within primate taxa is needed to better understand the complex nature of admixture and to test for evidence of adaptive introgression. Here, I report on instances of admixture within two primate groups, Papio and Homo, using high-coverage, whole-genome analysis and bioinformatic methods. In the first chapter, I outline the occurrences of hybridisation and adaptive introgression in primates. In the second chapter, I describe the extent of cryptic admixture within a pedigreed, captive baboon colony using 881 high-coverage, phased and imputed whole genomes of olive, yellow, and olive-yellow hybrid baboons. I found that over 10 percent of the sequenced animals were incorrectly labelled in the pedigree, which has implications for future research done at the colony. In the third and fourth chapters I use high coverage, phased modern human genomes from 76 worldwide populations to identify archaic introgression within modern human circadian rhythm genes, and secondarily, within genes that have been associated with reproduction in both mice and modern humans. I found evidence that archaic segments introgressed into modern humans were likely adaptive in both circadian rhythm- and reproductive-associated genes and contributed to assisting modern humans as they adjusted to their new environments outside of Africa. In the last chapter, I summarise my findings and provide a concise list of limitations and suggestions for future research.