Relevant bibliographies by topics / Whole-of-population

Academic literature on the topic 'Whole-of-population'

Author: Grafiati

Published: 10 December 2022

Last updated: 28 January 2023

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Journal articles on the topic "Whole-of-population"

Sahana, S., Rahul C. Bhoyar, Ambily Sivadas, Abhinav Jain, Mohamed Imran, Mercy Rophina, Vigneshwar Senthivel, et al. "Pharmacogenomic landscape of Indian population using whole genomes." Clinical and Translational Science 15, no. 4 (March 26, 2022): 866–77. http://dx.doi.org/10.1111/cts.13153.

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Gusev, A., J. K. Lowe, M. Stoffel, M. J. Daly, D. Altshuler, J. L. Breslow, J. M. Friedman, and I. Pe'er. "Whole population, genome-wide mapping of hidden relatedness." Genome Research 19, no. 2 (December 3, 2008): 318–26. http://dx.doi.org/10.1101/gr.081398.108.

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Tong, Zhijun, Sanjie Jiang, Weiming He, Xuejun Chen, Lixin Yin, Dunhuang Fang, Yafei Hu, et al. "Construction of high-density genetic map and QTL mapping in Nicotiana tabacum backcrossing BC4F3 population using whole-genome sequencing." Czech Journal of Genetics and Plant Breeding 57, No. 3 (July 14, 2021): 102–12. http://dx.doi.org/10.17221/8/2021-cjgpb.

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Backcrossing is a powerful tool for plant breeding. The improved marker-assisted backcrossing intends to transfer targeted genes or quantitative trait loci (QTLs) of interest from a donor parent into a recurrent parent. In this study, a tobacco BC4F3 population was generated using Y3 and K326 as hybrid parents and YF1-1 as F<sub>1</sub> parents. High-throughput sequencing data of 381 pedigree populations were used to construct high-density genetic maps containing 24 142 high-quality single nucleotide polymorphism (SNP) markers with an average genetic distance of 0.59 cM. A genome module analysis was then performed for all the offspring. A total of forty-three candidate QTLs for six agronomics traits were identified. This study provides original biomarkers for tobacco breeding and offers clues for prospective backcrossing applications in other plants.

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Gappy, Mavis, Malli Barremkala, and A. Celeste Farr. "Perception of the Chaldean Population Towards Whole Body Donation." FASEB Journal 34, S1 (April 2020): 1. http://dx.doi.org/10.1096/fasebj.2020.34.s1.09745.

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Carswell, Fleming. "Whole-population screening for carriers of cystic fibrosis gene." Lancet 347, no. 9013 (May 1996): 1421–22. http://dx.doi.org/10.1016/s0140-6736(96)91676-1.

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ALHARBI, K. "W14.345 Mutation scanning of LDLR in the whole population." Atherosclerosis 5, no. 1 (April 2004): 80. http://dx.doi.org/10.1016/s0021-9150(04)90344-9.

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Alharbi, K. K., L. Haddad, S. Ye, D. A. Lawlor, R. A. Whittall, E. Spanakis, X. Chen, et al. "W14.345 Mutation scanning of LDLR in the whole population." Atherosclerosis Supplements 5, no. 1 (April 2004): 80. http://dx.doi.org/10.1016/s1567-5688(04)90344-9.

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Gudbjartsson, Daniel F., Hannes Helgason, Sigurjon A. Gudjonsson, Florian Zink, Asmundur Oddson, Arnaldur Gylfason, Soren Besenbacher, et al. "Large-scale whole-genome sequencing of the Icelandic population." Nature Genetics 47, no. 5 (March 25, 2015): 435–44. http://dx.doi.org/10.1038/ng.3247.

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RASTIMESINA, Inna, Olga POSTOLACHI, and Valentina JOSAN. "Dissociation of Rhodococcus rhodochrous Population after the Whole Cells Immobilization." Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca. Agriculture 78, no. 1 (May 14, 2021): 28. http://dx.doi.org/10.15835/buasvmcn-agr:2020.0043.

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Six agricultural organic wastes and three inorganic matrices were selected for rhodococci whole cells immobilization. The degree of immobilization of rhodococci cells varied from 6.20% to 34.30% on organic matrices. A high level of Rhodococcus rhodochrous CNMN-Ac-05 cells immobilization was demonstrated on inorganic matrices, it was from 69.25% to 97.30%. After the contact with support the strain dissociated, forming, in addition to original S type, rough (R) and altercolour smooth (S) types. Immobilization of rhodococci cells on organic supports led to the appearance of phenotypic heterogeneity from 0.34% to 3.26%. On inorganic matrices the variability of rhodococci was 0.88-1.05%.

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Karimi, Karim, Duy Ngoc Do, Mehdi Sargolzaei, and Younes Miar. "Population Genomics of American Mink Using Whole Genome Sequencing Data." Genes 12, no. 2 (February 11, 2021): 258. http://dx.doi.org/10.3390/genes12020258.

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Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

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Dissertations / Theses on the topic "Whole-of-population"

Robinson, Emma Claire. "Characterising population variability in brain structure through models of whole-brain structural connectivity." Thesis, Imperial College London, 2010. http://hdl.handle.net/10044/1/5875.

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Models of whole-brain connectivity are valuable for understanding neurological function. This thesis seeks to develop an optimal framework for extracting models of whole-brain connectivity from clinically acquired diffusion data. We propose new approaches for studying these models. The aim is to develop techniques which can take models of brain connectivity and use them to identify biomarkers or phenotypes of disease. The models of connectivity are extracted using a standard probabilistic tractography algorithm, modified to assess the structural integrity of tracts, through estimates of white matter anisotropy. Connections are traced between 77 regions of interest, automatically extracted by label propagation from multiple brain atlases followed by classifier fusion. The estimates of tissue integrity for each tract are input as indices in 77x77 ”connectivity” matrices, extracted for large populations of clinical data. These are compared in subsequent studies. To date, most whole-brain connectivity studies have characterised population differences using graph theory techniques. However these can be limited in their ability to pinpoint the locations of differences in the underlying neural anatomy. Therefore, this thesis proposes new techniques. These include a spectral clustering approach for comparing population differences in the clustering properties of weighted brain networks. In addition, machine learning approaches are suggested for the first time. These are particularly advantageous as they allow classification of subjects and extraction of features which best represent the differences between groups. One limitation of the proposed approach is that errors propagate from segmentation and registration steps prior to tractography. This can cumulate in the assignment of false positive connections, where the contribution of these factors may vary across populations, causing the appearance of population differences where there are none. The final contribution of this thesis is therefore to develop a common co-ordinate space approach. This combines probabilistic models of voxel-wise diffusion for each subject into a single probabilistic model of diffusion for the population. This allows tractography to be performed only once, ensuring that there is one model of connectivity. Cross-subject differences can then be identified by mapping individual subjects’ anisotropy data to this model. The approach is used to compare populations separated by age and gender.

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Zhou, Jin, Wai-Ki Yip, Michael Cho, Dandi Qiao, Merry-Lynn McDonald, and Nan Laird. "A comparative analysis of family-based and population-based association tests using whole genome sequence data." BioMed Central, 2014. http://hdl.handle.net/10150/610090.

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The revolution in next-generation sequencing has made obtaining both common and rare high-quality sequence variants across the entire genome feasible. Because researchers are now faced with the analytical challenges of handling a massive amount of genetic variant information from sequencing studies, numerous methods have been developed to assess the impact of both common and rare variants on disease traits. In this report, whole genome sequencing data from Genetic Analysis Workshop 18 was used to compare the power of several methods, considering both family-based and population-based designs, to detect association with variants in the MAP4 gene region and on chromosome 3 with blood pressure. To prioritize variants across the genome for testing, variants were first functionally assessed using prediction algorithms and expression quantitative trait loci (eQTLs) data. Four set-based tests in the family-based association tests (FBAT) framework--FBAT-v, FBAT-lmm, FBAT-m, and FBAT-l--were used to analyze 20 pedigrees, and 2 variance component tests, sequence kernel association test (SKAT) and genome-wide complex trait analysis (GCTA), were used with 142 unrelated individuals in the sample. Both set-based and variance-component-based tests had high power and an adequate type I error rate. Of the various FBATs, FBAT-l demonstrated superior performance, indicating the potential for it to be used in rare-variant analysis. The updated FBAT package is available at: http://www.hsph.harvard.edu/fbat/ webcite.

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Manyisa, Noluthando. "Whole exome sequencing to investigate genetic variants of non-syndromic hearing impairment in a population of African ancestry." Master's thesis, University of Cape Town, 2018. http://hdl.handle.net/11427/29272.

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Introduction: Hearing impairment occurs when a child has hearing loss greater than 30dB in their better hearing ear and an adult cannot detect sound lower than 40dB in the better hearing ear. It is a common sensory disorder that affecting approximately 360 million worldwide, with an incidence of 6 in 1000 live births in developing countries such as those in Sub-Saharan Africa. 50 % of hearing impairment, in developed countries, is due to genetic factors, with 70% of genetic hearing impairment being classified as non-syndromic hearing impairment, which occurs when the hearing impairment presents with no other clinical manifestations. Hearing impairment is associated with over 150 genes, of which two connexin genes, GJB2 and GJB6, are the most prevalent genes associated with hearing impairment in European, Asian and North American of European ancestries populations. These genes have however been shown to be insignificant causes of Hearing Impairment in African populations. Aim: The aim of this study is to determine the rates for putative pathogenic variants in 172 hearing impairment associated genes, among Cameroonian patients affected by hearing impairment, and non-hearing-impaired controls. Methods: Patients and controls Patients were recruited from various schools of the Deaf and Ear, Nose and Throat (ENT) clinics in Cameroon. The patients were examined by qualified medical geneticists and ophthalmologist and detailed family history and medical history was obtained from the patients and their parents. 19 patients, who were negative for GJB2 and GJB6 mutations and presented with putative non-syndromic hearing impairment, were selected from a cohort of 582 patients for the present study. The control population consisted of 130 ethnically matched groups without any personal or familial history of hearing impairment. The controls were recruited from Yaoundé Central Hospital and Laquintinie Hospital in Cameroon. Whole exome sequencing DNA was extracted from whole blood using the salting out procedure and the Puregene Blood kit®. The DNA was subjected to spectrometry and gel electrophoresis to determine the quantity and quality of the DNA samples. The samples were then subjected to whole exome sequencing on the Illumina platform using the Nextera Rapid Capture Exome Kit at an average read depth of 30X, whereby only 18 patients were successfully sequenced. The exomes were then subjected to FastQC and SolexaQC++ for quality control measures and aligned to the hg19 reference genome using GATK and VariantMetaCaller. Bioinformatics analysis Variant annotation was performed using Annovar and the annotated variants were filtered based in rarity and pathogenicity. Tests for genetic differentiation and principle component analysis was performed on the combined patient exomes and combine control exomes. The first principle component analysis included data from African populations from the 1000 Genomes Phase 3 as well as six control samples from the Democratic Republic of Congo; and the second principle component analysis analysed on the Cameroonian patients and control population. Population structure analysis was followed by protein-protein interaction analysis using custom python and R script and pathway enrichment analysis using Enrichr combined with a second custom R script. The proportion of derived and ancestral alleles was computed by downloading the SNP ancestral alleles from Ensembl and verifying the presence of the SNPs in dbSNP database. The combined patient and control exomes were annotated using the VCFtools “fillOaa” script. The ancestral alleles were computed by dividing the number of times the alternative allele matched the ancestral allele with the number of copies of all the alternative alleles across all samples at the particular position. The ancestral alleles were categorised into six bins, based on their minor allele frequency, in the patient and control populations and this was used to contrast their proportions of derived and ancestral alleles. Furthermore, the proportion of ancestral and derived alleles in hearing impairment associated genes was computed at SNP based level for the Cameroonian population and contrasted with population from the Democratic Republic of Congo. Variants validation by Sanger sequencing Primers were designed to amplify the fragment surrounding the purported SNPs in MYO15A, MYO3A, and COL9A3 as well as for the fragments surrounding the population specific SNPs in VTN, RPL3L and DHRS4L2. Polymerase chain reaction was performed for the MYO15A, and MYO3A fragments. This was followed by purification of the PCR products and direct cycle Sanger sequencing of the PCR products. The sequencing products were then purified through ethanol precipitation and the fragments were suspended in HiDi Formamide and run on the capillary electrophoresis. The variants in MYO3A, MYO15A and COL9A3 were viewed in Integrated Genomics Viewer using the Bam files as well. Results Putative deleterious variants Single nucleotide polymorphism (SNPs) in MYO3A, MYO15A and COL9A3, were filtered out as putative causative mutations for three, four and two patients respectively. Direct Sanger Sequencing and viewing the patients BAM files did not confirm the presence of any of these putative pathogenic in the patients. Variations in USH2A, HSD17B4 and MYO1A were also filtered out but these variants were not considered disease causing, after a careful genotype to phenotypes correlations. Population genetics variants differentiations At a population level, specific variations were identified in FOXD4L2, DHRS2L6, RPL3L and VTN. Significant genetic differentiation was shown to exist between the control population and the patients’ population with regard to specific variants in VTN and RPL3L; furthermore, it was shown that these variants in VTN and RPL3L interact with other hearing impairment associated proteins with evidences that that VTN is hub protein for a hearing impairment associated pathway along with nine other genes. Conversely, this was not the case for variants described in FOXD4L2 and DHRS2L6. In known hearing Impairment genes, the proportion of ancestral alleles was lowest for the patients’ population for variations with minor allele frequencies between 0.0 and 0.1. The proportion of derived and ancestral alleles was also shown to differ between the Cameroonian and the population from the Democratic Republic of Congo, indication possible regional differences in aetiology of Hearing impairment amongst multiple African populations. Discussion Low putative pathogenic variants in known hearing impairment genes among Africans The low pick up rate for putative pathogenic variants in our patients follows a similar trend observed in the African American populations, with hearing impairment, as well as data from targeted exome sequencing from South African and Nigerian populations. This result is also in agreeance with other studies that interrogated hearing impairment in African populations utilising other means besides next generation sequencing. This result also highlights the importance of validating any results obtained from next generation sequencing through traditional approaches such as Sanger Sequencing or viewing the BAM files on IGV, specifically in African population, poorly represented in Exome databases. Bioinformatics Analysis Exhibited some Specific Variants among Cameroonian Protein-protein interactions and enrichment analysis indicated that VTN and RPL3L, and their interacting proteins, are significantly associated with osteoclast differentiation, which is associated with hearing impairment in osteogenesis imperfecta. VTN was further shown as a hub protein of a protein subnetwork, along ATPB2. The presence of a second protein acting as a hub protein may account for why aberrations in VTN have not been associated with a disease; whereby ATPB2 may ameliorate the pathogenic phenotype that ought to be observed in the presence of null mutations in VTN. Evolutionary adaptation of human hearing Data indicates the patient population carried a higher proportion of derived alleles in known hearing impairment genes, at low minor allele frequencies; possibly indicating, the interactive modifiers capacities of multiple hearing impairment genes, or alternatively, the polygenetic nature of hearing impairment in some patients. The proportion of ancestral and derived alleles was contrasted in the Cameroonian and the population from the Democratic Republic of Congo and it indicated that the variations that may result in hearing impairment in the one population may not be the same variations that result in hearing impairment in the other population Due to this, it is necessary to determine the causative variants resulting in disease in each of these populations independently. Conclusion and perspectives The results support a low pick up rate of putative variants in 172 known genes in groups of Cameroonian patients with HI, underscoring the current Targeted panel sequencing for HI may not be relevant for some African populations. The result also support the need of confirmation of variants found in WES, as well careful genotype to phenotypes correlations, particularly among African, whose sequences exome is relatively low in Exomes databases, and as a result could lead to more false positive results. Population genetic analysis has provided novel insight in the genetic architecture of HI among this group of Africans; particularly, the differential frequencies of ancestral alleles vs derived alleles in HI genes among patients vs controls underline the possibility of multigenic influence on the phenotype of Hearing Impairment that have not been well investigated, and may also signal evolutionary enrichment of some variants of HI genes in the populations as the result of natural selections, that deserve further investigation. The result supports the need of intensive familial studies in multiple African populations in order to unravel the novel genes and those variants that are relevant in clinical practice for people of African ancestry.

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Gladstein, Ariella. "Inference of Recent Demographic History of Population Isolates Using Genome-Wide High Density SNP Arrays and Whole Genome Sequences." Thesis, The University of Arizona, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10839026.

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In this dissertation I addressed the problem of SNP array bias when finding runs of ho- mozygosity. I demonstrated the pitfalls of using uninformed methods for finding runs of homozygosity and provide better alternatives, including a more reliable algorithm for identi- fying runs of homozygosity than the most commonly used program. I then provide a review of Ashkenazi population genetics. Next, I developed software to efficiently run millions of whole chromosome simulations, which is publicly available through GitHub, DockerHub, and on the CyVerse Discovery Environment. I applied my computational method to use Approximate Bayesian Computation to test models of Ashkenazi Jewish demographic his- tory. I found that the Ashkenazi Jews are comprised of genetically distinct subgroups from Eastern and Western Europe, as a result of massive population growth in the Eastern Ashkenazi Jews, but not in the Western Ashkenazi Jews. I further confirmed that the Ashkenazi Jews do not primarily originate from Khazaria. Finally, I created a correction for SNP array ascertainment bias in the median and total length of runs of homozygosity, and applied this correction to world-wide human populations. However, I found that ascertainment bias plays a minor role compared to SNP array bias in human populations.

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Benoit, Julie E. "Evaluation of Nutritional Risk in Maine's Senior Population with an Emphasis on how Whole Grain Intake Affects Nutritional Status." Fogler Library, University of Maine, 2008. http://www.library.umaine.edu/theses/pdf/BenoitJE2008.pdf.

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Sanders, G. Rashad Shabazz. ""They imprison the whole population" : U.S. and South African prison literature and the emergence of symbiotic carcerality, 1900-present /." Diss., Digital Dissertations Database. Restricted to UC campuses, 2008. http://uclibs.org/PID/11984.

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Mohamed, Mahgoub Mohamed Ahmed Mohamed. "Sporadic on/off switching of HTLV-1 Tax expression is crucial to maintain the whole population of virus-induced leukemic cells." Kyoto University, 2018. http://hdl.handle.net/2433/232139.

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Hsieh, PingHsun. "Model-Based Population Genetics in Indigenous Humans: Inferences of Demographic History, Adaptive Selection, and African Archaic Admixture using Whole-Genome/Exome Sequencing Data." Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/612540.

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Reconstructing the origins and evolutionary journey of humans is a central piece of biology. Complementary to archeology, population genetics studying genetic variation among individuals in extant populations has made considerable progress in understanding the evolution of our species. Particularly, studies in indigenous humans provide valuable insights on the prehistory of humans because their life history closely resembles that of our ancestors. Despite these efforts, it can be difficult to disentangle population genetic inferences because of the interplay among evolutionary forces, including mutation, recombination, selection, and demographic processes. To date, few studies have adopted a comprehensive framework to jointly account for these confounding effects. The shortage of such an approach inspired this dissertation work, which centered on the development of model-based analysis and demonstrated its importance in population genetic inferences. Indigenous African Pygmy hunter-gatherers have been long studied because of interest in their short stature, foraging subsistence strategy in rainforests, and long-term socio-economic relationship with nearby farmers. I proposed detailed demographic models using genomes from seven Western African Pygmies and nine Western African farmers (Appendix A). Statistical evidence was shown for a much deeper divergence than previously thought and for asymmetric migrations with a larger contribution from the farmers to Pygmies. The model-based analyses revealed significant adaption signals in the Pygmies for genes involved in muscle development, bone synthesis, immunity, reproduction, etc. I also showed that the proposed model-based approach is robust to the confounding effects of evolutionary forces (Appendix A). Contrary to the low-latitude African homeland of humans, the indigenous Siberians are long-term survivors inhabiting one of the coldest places on Earth. Leveraging whole exome sequencing data from two Siberian populations, I presented demographic models for these North Asian dwellers that include divergence, isolation, and gene flow (Appendix B). The best-fit models suggested a closer genetic affinity of these Siberians to East Asians than to Europeans. Using the model-based framework, seven NCBI BioSystems gene sets showed significance for polygenic selection in these Siberians. Interestingly, many of these candidate gene sets are heavily related to diet, indicating possible adaptations to special dietary requirements in these populations in cold, resource-limited environments. Finally, I moved beyond studying the history of extant humans to explore the origins of our species in Africa (Appendix C). Specifically, with statistical analyses using genomes only from extant Africans, I rejected the null model of no archaic admixture in Africa and in turn gave the first whole-genome evidence for interbreeding among human species in Africa. Using extensive simulation analyses under various archaic admixture models, the results suggest recurrent admixture between the ancestors of archaic and modern Africans, with evidence that at least one such event occurred in the last 30,000 years in Africa.

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Williamson, Jill Marie. "Global investigation into the population genetic structure of Ciyptosporidium hominis based on a whole genome multi-locus SNP-typing scheme; inferences about the existence of biogeographical partitions." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/15002.

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Previously considered a disease of importance strictly to veterinary medicine Cryptosporidium has emerged as a highly successful opportunistic parasitic protozoan posing a significant threat to public health. Intricate transmission dynamics, a complex epidemiology, and parasite robustness and persistence have all hampered efforts for the prevention and control of Cryptosporidium. Genetic diversity is a prerequisite to better understand the role of parasite variation in disease etiology and pathobiology. The extent of genetic structure among C. hominis and C. parvum, the two most prevalent species of Ciyptosporidium, is insufficiently understood with the population structure still largely suspect. We report on the distribution of genetic diversity and possible existence of geographic partitions among C. hominis subpopulations from Australia, Kenya, Peru and Scotland. We studied C. hominis population genetic structure using a multi-locus SNP-type (M1St) established from 45 single nucleotide polymorphic loci covering 13 bio-functionally relevant proteins. A total of 77 isolates from 4 intercontinental subpopulations were genetically typed. Twenty-four unique M1St’s were identified, 25% of which were found to be located within one or more subpopulations. Diversity statistical tests to discern the degree of ultrapopulation and inter-population diversity, genetic distance, and genetic identity variation were used to examine the population genetic structure. Within-population differences among subpopulations account for 69.6% of genetic variation; differentiation among subpopulations constitute 30.4%. Genetic distances among subpopulations averaged 0.048 and varied from 0.03 4 between the Australian and Scotland subpopulations to 0.061 between Scotland and Kenya. More broadly, our results argue that too wide of a geographic boundary can impede rather than advance genetic population studies and that the practice of sampling more regional subpopulations be adopted. A fifth subpopulation, a combination of C. hominis and C. parvum isolates, was drawn upon to determine whether or not a pre-defined allelic profile of single nucleotide polymorphisms (SNPs) was an efficient and reliable means for species specific identification. Results showed the SNP-typing approach’s ability to distinguish between different species as well as being capable of uncovering potential novel SNPs within an individual isolate. We propose that the patterns of genetic variation are influenced by geography and that the identification of host adapted geographically conserved sub-genotypes within a defined geographic cohort versus widespread dissemination of genetically stable isolates could ultimately provide a valuable basis for the predictive epidemiology of Cryptosporidiwn infection. Our fmdings provide an alternative method for species detection, a crucial element to epidemiological investigations.

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Maceda, Porto Iago 1986. "Characterization of the micro-substructure of a rural population from the Pyrenees from a geodesic and technical point of view using NGS data : Quantification of batch effects in whole genome sequence data." Doctoral thesis, TDX (Tesis Doctorals en Xarxa), 2021. http://hdl.handle.net/10803/671600.

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In this work we present a new whole genome sequencing dataset with samples gathered from the Spanish Eastern Pyrenees (SEP) with more than 40x coverage. We apply both classical and new methods to unveil their particular demographic histories and we present the use of a newly in-house developed algorithm to detect genetic barriers taking into account the use of geo-statistics. With these analyses we detect fine population substructure for the first time in this region. We also report the presence of an important batch effect in one of the most important datasets used in genomics: the 1,000 Genomes Project. We find this batch effect when considering very low frequency variants, such as loss of function mutations and the amount of singletons (both ancestral and derived) detected in each sample.
En aquest treball presentem un nou dataset de whole genome sequencing amb mostres recollides del Pirineu Oriental espanyol (SEP) amb un coverage superior a 40x. Apliquem mètodes clàssics i nous per descobrir les seves particulars històries demogràfiques i presentem l’ús d’un algorisme desenvolupat recentment en el nostre laboratori per detectar barreres genètiques tenint en compte l’ús de geoestadística. Amb aquestes anàlisis detectem, per primera vegada, una delicada subestructura de poblacions en aquesta regió. També informem de la presència d’un important batch effect en un dels datasets més importants utilitzats en genòmica: the 1.000 Genomes Project. Trobem aquest batch effect quan considerem variants rares, com per exemple mutacions que comporten pèrdua de funció i la quantitat de singletons (tant ancestrals com derivats) detectats en cada mostra.

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Books on the topic "Whole-of-population"

Twenty-one trends for the 21st century: Out of the trenches and into the future, their profound implications for students, education, communities, and the whole of society. Bethesda, MD: Education Week Press, 2014.

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name, No. Inclusive design: Design for the whole population. London: Springer, 2003.

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A guide to twenty-one trends for the 21st century: Out of the trenches and into the future : their profound implications for students, education, communities, countries and the whole of society. Bethesday, MD: Education Week Press, 2015.

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Kleiterp, Nanno. Banking for a Better World. NL Amsterdam: Amsterdam University Press, 2016. http://dx.doi.org/10.5117/9789462983519.

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When we look at all the challenges facing the world, including inequality, population migration, and climate change, we can see a role for development banking in nearly all of them. But will that role be played for good or ill? This book brings together two people who collectively draw on their forty-five years of experience in that world to argue that development banking can-and must-play a constructive role. We only need to read the news to find public outrage at tales of short-sighted greed in the financial world. But what happens when banks invest in long-term sustainability? Readers will find a fascinating example in the journey of the Dutch development bank FMO. At times global in perspective, at other moments intimately personal, Banking for a Better World interweaves candid anecdotes with development history, as well as banking lessons with client interviews, to deliver a powerful argument for a business model that generates profit through impact, and impact through profit. This is an important and accessible must-read for anyone involved in banking, business, policy making, and civil society as a whole. Banking for a Better World challenges us to start finding overlaps between our own lives and global issues and to bridge the distance between our personal needs and those of our planet.

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Hartl, Daniel L. A Primer of Population Genetics and Genomics. Oxford University Press, 2020. http://dx.doi.org/10.1093/oso/9780198862291.001.0001.

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A Primer of Population Genetics and Genomics, 4th edition, has been completely revised and updated to provide a concise but comprehensive introduction to the basic concepts of population genetics and genomics. Recent textbooks have tended to focus on such specialized topics as the coalescent, molecular evolution, human population genetics, or genomics. This primer bucks that trend by encouraging a broader familiarity with, and understanding of, population genetics and genomics as a whole. The overview ranges from mating systems through the causes of evolution, molecular population genetics, and the genomics of complex traits. Interwoven are discussions of ancient DNA, gene drive, landscape genetics, identifying risk factors for complex diseases, the genomics of adaptation and speciation, and other active areas of research. The principles are illuminated by numerous examples from a wide variety of animals, plants, microbes, and human populations. The approach also emphasizes learning by doing, which in this case means solving numerical or conceptual problems. The rationale behind this is that the use of concepts in problem-solving lead to deeper understanding and longer knowledge retention. This accessible, introductory textbook is aimed principally at students of various levels and abilities (from senior undergraduate to postgraduate) as well as practising scientists in the fields of population genetics, ecology, evolutionary biology, computational biology, bioinformatics, biostatistics, physics, and mathematics.

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Merchant, Emily Klancher. Building the Population Bomb. Oxford University Press, 2021. http://dx.doi.org/10.1093/oso/9780197558942.001.0001.

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Building the Population Bomb examines how human population came to be understood as a problem in the twentieth century, how it became an object of intervention for governments, scientists, and nongovernmental organizations, and how some forms of intervention got coded as legitimate while others were recognized as coercive. It traces the emergence and growth of two scientific perspectives on population from the 1920s to the present. The first, rooted in the natural sciences, considered the world’s population as a whole in relation to natural resources. The second, rooted in the social sciences, considered national population growth rates in relation to economic growth. These two perspectives converged briefly after World War II, convincing world leaders that population growth posed a barrier to economic development and a threat to worldwide peace and environmental integrity. The book documents how this overpopulation consensus attracted vast sums of money to demography and population control, and teases out the differences between population control, birth control, and family planning. It concludes with the fracturing of this consensus at the end of the 1960s, constituting the factions that structure today’s debates over whether the world’s population is growing too quickly or not quickly enough, and over what should be done about it. The book documents how population growth came to take the blame for the world’s most complex and pressing problems, and how efforts to solve “the population problem” have diverted attention and resources from the pursuit of economic, environmental, and reproductive justice.

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Čhamnūan prachākō̜n čhamnǣk tām ʻāchīp rāilaʻīat čhāk Sammanō prachākō̜n læ khēha, Phō̜. Sō̜. 2523, thūa rātchaʻānāčhak læ Krung Thēp Mahā Nakhō̜n =: Population by detailed classification of occupation : 1980 population and housing census, whole kingdom & Bangkok Metropolis. [Bangkok]: Samnakngān Sathiti hǣng Chāt, Samnak Nāyok Ratthamontrī, 1985.

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Thailand. Samnakngān Sathiti hǣng Chāt., ed. Čhamnūan prachākō̜n čhamnǣk tām ʻutsāhakam rāilaʻīat čhāk Sammanō prachākō̜n læ khēha, Phō̜. Sō̜. 2523, thūa rātchaʻānāčhak læ Krung Thēp Mahā Nakhō̜n =: Population by detailed classification of industry : 1980 population and housing census, whole kingdom & Bangkok Metropolis. [Bangkok]: Samnakngān Sathiti hǣng Chāt, Samnak Nāyok Ratthamontrī, 1985.

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Rostow, W. W. The Great Population Spike and After. Oxford University Press, 1998. http://dx.doi.org/10.1093/oso/9780195116915.001.0001.

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Midway through the eighteenth century, the rate of growth for the world's population was roughly at zero. Immediately after World War II, it was just above 2 percent. Ever since, it has fallen steadily. This new book, the latest offering from a distinguished expert on international economics, tells readers what this stagnation or fall in population will mean--economically, politically, and historically--for the nations of the world. W. W. Rostow not only traces the whole global arc of this "great population spike"--he looks far beyond it. What he sees will interest anyone curious about what is in store for the world's financial and governmental systems. The Great Population Spike and After: Reflections on the 21st Century contends that, as the decline in population now occurring in the industrialized world spreads to all of the presently developing countries, the global rate of population will fall to the "zero" level circa 2100. (Indeed, with the exception of Africa south of the Sahara, it could reach "zero" long before then.) This being so, how will it be possible to maintain full employment and social services with a decelerating population? What will societies do when the proportion of the working force (as now defined) diminishes radically in relation to the population of poor or elderly dependents? How will the countries of the world confront subsequent decreases in population-related investment? In answering these queries, this bold study asserts that the United States is not the "last remaining superpower" but the "critical margin" without whose support no constructive action on the world scene can succeed. Rostow takes the view that world peace will depend on our government's ability to assume responsibly this "critical margin" role. Further, he argues that, over a period of time, the execution of this strategy on the international scene will require a bipartisan, relentless effort to solve the combustible social problems that weaken not only our cities but our whole society.

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Publishing, Norman Ross, and United States Census Office. Census of the United States: First Decennial Census, 1790: Return of the Whole Number of Persons Within the Several Districts of the United States. Norman Ross Publishing, Inc., 1990.

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Book chapters on the topic "Whole-of-population"

Lacey, Jake A., Taylah B. James, Steven Y. C. Tong, and Mark R. Davies. "Whole Genome Sequence Analysis and Population Genomics of Group A Streptococci." In Methods in Molecular Biology, 81–111. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0467-0_7.

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Lehtinen, V., and M. Joukamaa. "Mental Disorders in a Sample Representative of the Whole Finnish Adult Population." In Psychiatric Epidemiology, 43–54. London: Routledge, 2021. http://dx.doi.org/10.1201/9781003134831-4.

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Kerry, Brian R., and Penny R. Hirsch. "Ecology of Pochonia chlamydosporia in the Rhizosphere at the Population, Whole Organism and Molecular Scales." In Biological Control of Plant-Parasitic Nematodes:, 171–82. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-1-4020-9648-8_7.

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Epping, Lennard, Esther-Maria Antão, and Torsten Semmler. "Population Biology and Comparative Genomics of Campylobacter Species." In Current Topics in Microbiology and Immunology, 59–78. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-65481-8_3.

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AbstractThe zoonotic pathogen Campylobacter is the leading cause for bacterial foodborne infections in humans. Campylobacters are most commonly transmitted via the consumption of undercooked poultry meat or raw milk products. The decreasing costs of whole genome sequencing enabled large genome-based analyses of the evolution and population structure of this pathogen, as well as the development of novel high-throughput molecular typing methods. Here, we review the evolutionary development and the population diversity of the two most clinically relevant Campylobacter species; C. jejuni and C. coli. The state-of-the-art phylogenetic studies showed clustering of C. jejuni lineages into host specialists and generalists with coexisting lifestyles in chicken and livestock-associated hosts, as well as the separation of C. coli isolates of riparian origin (waterfowl, water) from C. coli isolated from clinical and farm-related samples. We will give an overview of recombination between both species and the potential impact of horizontal gene transfer on host adaptation in Campylobacter. Additionally, this review briefly places the current knowledge of the population structure of other Campylobacter species such as C. lari, C. concisus and C. upsaliensis into perspective. We also provide an overview of how molecular typing methods such as multilocus sequence typing (MLST) and whole genome MLST have been used to detect and trace Campylobacter outbreaks along the food chain.

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Shumilina, Vera, and Valeria Drobotenko. "STATISTIC ANALYSIS OF LABOR MARKET IN THE RUSSIAN FEDERATION." In Problems of the labor market of the Russian Federation and its legal support in the context of economic recession and pandemic, 11–18. au: AUS PUBLISHERS, 2021. http://dx.doi.org/10.26526/chapter_60252bded22487.28151181.

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The chapter discusses such concepts as the labor market and the economically active population. The situation on the labor market in 2018-2020 is described, the number of vacancies and resumes in various fields and constituent entities of the Russian Federation is analyzed. The dynamics of the number of employment of the population both by regions and by Russia as a whole are presented. The problems arising in the labor market and ways to solve them are considered.

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Izvarina, Nataliya, Anastasiya Kosyanok, and Eduard Pashchenko. "ANALYSIS OF UNEMPLOYMENT IN THE RUSSIAN LABOR MARKET: CAUSES AND CONSEQUENCES." In Socio-economic and legal problems of modern society, 56–63. au: AUS PUBLISHERS, 2022. http://dx.doi.org/10.26526/chapter_61e7f12a856050.80567548.

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The article discusses the problems associated with unemployment in the Russian labor market. The analysis of unemployment indicators in Russia is carried out. The main reasons for the low level of employment of the population are systematized. The economic and non-economic consequences of this socio-economic phenomenon on both an individual and the economy of the country as a whole are presented

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Zeng, Qinghe, Stefano Caruso, Julien Calderaro, Nicolas Loménie, and Christophe Klein. "Prediction of Immune and Stromal Cell Population Abundance from Hepatocellular Carcinoma Whole Slide Images Using Weakly Supervised Learning." In Artificial Intelligence over Infrared Images for Medical Applications and Medical Image Assisted Biomarker Discovery, 143–53. Cham: Springer Nature Switzerland, 2022. http://dx.doi.org/10.1007/978-3-031-19660-7_14.

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Schlundt, Joergen. "Whole Genome Sequencing." In Encyclopedia of Gerontology and Population Aging, 1–10. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-319-69892-2_943-1.

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Schlundt, Joergen. "Whole Genome Sequencing." In Encyclopedia of Gerontology and Population Aging, 5424–33. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-22009-9_943.

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Boutet, Gilles, Susete Carvalho, Matthieu Falque, Pierre Peterlongo, Emeline Lhuillier, Olivier Bouchez, Clément Lavaud, Marie Pilet, Nathalie Rivière, and Alain Baranger. "SNP Discovery and Genetic Mapping Using Genotyping by Sequencing of Whole Genome Genomic DNA from a Pea RIL Population." In Crop Breeding, 223–48. Taylor & Francis Group, 6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487-2742: CRC Press, 2016. http://dx.doi.org/10.1201/9781315365084-8.

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Conference papers on the topic "Whole-of-population"

Clarke, Malcolm, Joanna Fursse, Hulya Gokalp, Urvashi Sharma, and Russell W. Jones. "Whole population management of patients with diabetes." In 2014 Health Innovations and POCT. IEEE, 2014. http://dx.doi.org/10.1109/hic.2014.7038908.

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Begum, M., CR Chittleborough, RM Pilkington, M. Mittinty, JW Lynch, M. Penno, and LG Smithers. "RF01 Educational outcomes among children with type 1 diabetes: whole-of-population study." In Society for Social Medicine and Population Health and International Epidemiology Association European Congress Annual Scientific Meeting 2019, Hosted by the Society for Social Medicine & Population Health and International Epidemiology Association (IEA), School of Public Health, University College Cork, Cork, Ireland, 4–6 September 2019. BMJ Publishing Group Ltd, 2019. http://dx.doi.org/10.1136/jech-2019-ssmabstracts.116.

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Homaira, Nusrat, Mark Hanly, Nancy Briggs, Christopher Pardy, Ju-Lee Oei, Lisa Hilder, Barbara Bajuk, et al. "RSV increases the risk of first paediatric asthma hospitalisation: whole-of-population cohort study." In ERS International Congress 2017 abstracts. European Respiratory Society, 2017. http://dx.doi.org/10.1183/1393003.congress-2017.oa498.

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Begum, M., RM Pilkington, CR Chittleborough, JW Lynch, M. Penno, and LG Smithers. "OP74 Maternal smoking during pregnancy and risk of type 1 diabetes: whole-of-population study." In Society for Social Medicine and Population Health and International Epidemiology Association European Congress Annual Scientific Meeting 2019, Hosted by the Society for Social Medicine & Population Health and International Epidemiology Association (IEA), School of Public Health, University College Cork, Cork, Ireland, 4–6 September 2019. BMJ Publishing Group Ltd, 2019. http://dx.doi.org/10.1136/jech-2019-ssmabstracts.77.

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"Whole genome sequencing and development of KASP markers for genotyping the West Siberian wheat stem rust population." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-346.

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Zhou, Guiyao, Yanyou Wu, Xianjian Xie, Deke Xing, Fang Fan, and Rui Yu. "Research on characteristics in the spatial distribution of the whole county population of Sichuan province, China via ARCGIS analysis." In 2013 International Conference on Advances in Social Science, Humanities, and Management. Paris, France: Atlantis Press, 2013. http://dx.doi.org/10.2991/asshm-13.2013.185.

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Simon, Winfried, and Giorgi Bit-Babik. "Effect of the variation in population on the whole body average SAR of persons exposed to vehicle mounted antennas." In 2012 International Conference on Electromagnetics in Advanced Applications (ICEAA). IEEE, 2012. http://dx.doi.org/10.1109/iceaa.2012.6328735.

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Lamis, Farhana, and Sara E. Wilson. "Neuromotor Effects of Whole Body Horizontal Vibration." In ASME 2008 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2008. http://dx.doi.org/10.1115/sbc2008-193167.

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Low back disorders are very common affecting up to 80% of the population in their lifetime [1]. Whole body vibration (WBV) exposure has long been identified as an important risk factor for low back disorders in industrial workers [2]. A potential mechanism has been proposed by which vibration may lead to injury. Namely, vibration-induced losses in proprioception may lead to inappropriate stabilization and poor dynamic control of the lumbar spine [3]. Increases in proprioceptive errors and in delays in neuormotor response have been demonstrated with 5 Hz, vertical seatpan vibration [3]. While vertical vibration exposure is a common occupational exposure, in some cases, such as off road vehicles and construction vehicles horizontal (fore-aft) vibration may dominate [4]. In this study, the objective was to investigate how the whole body, horizontal, seatpan vibration affects muscle response and to compare these results with the previously studied whole body vertical vibration.

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Sing Ng, Christopher Pui, Jamie Sui Lam Kwok, Junwei Zhou, Pik Yuen Belinda Cheung, Lawrence Chi Hung Tzang, and Senthil Sundaram. "IDDF2018-ABS-0204 Effect of whole grains and unsaturated fatty acids dietary intervention on health in hong kong overweight population." In International Digestive Disease Forum (IDDF) 2018, Hong Kong, 9–10 June 2018. BMJ Publishing Group Ltd and British Society of Gastroenterology, 2018. http://dx.doi.org/10.1136/gutjnl-2018-iddfabstracts.153.

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Li, Ning, Shuhang Wang, Yue Yu, Yuan Fang, Huiyao Huang, Dawei Wu, Hong Fang, et al. "Abstract LB-310: Whole-exome sequencing reveals genetic underpinnings of salivary adenoid cystic carcinoma and tongue carcinoma in Chinese population." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-lb-310.

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Reports on the topic "Whole-of-population"

Busso, Matías, Julian P. Cristia, and Julián Messina. SkillsBank Methodology Note: Adult Training Methodology. Inter-American Development Bank, September 2022. http://dx.doi.org/10.18235/0004472.

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After determining the pool of studies to be analyzed from the search protocol, we dropped all those papers that appeared twice in the dataset. Then, we focused on the title, abstract and the whole study in that order. The filters we analyzed here timing and language, population, intervention, methods, and measures, in that order.

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Sherman, Amir, Rebecca Grumet, Ron Ophir, Nurit Katzir, and Yiqun Weng. Whole genome approach for genetic analysis in cucumber: Fruit size as a test case. United States Department of Agriculture, December 2013. http://dx.doi.org/10.32747/2013.7594399.bard.

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The Cucurbitaceae family includes a broad array of economically and nutritionally important crop species that are consumed as vegetables, staple starches and desserts. Fruit of these species, and types within species, exhibit extensive diversity as evidenced by variation in size, shape, color, flavor, and others. Fruit size and shape are critical quality determinants that delineate uses and market classes and are key traits under selection in breeding programs. However, the underlying genetic bases for variation in fruit size remain to be determined. A few species the Cucurbitaceae family were sequenced during the time of this project (cucumber was already sequenced when the project started watermelon and melon sequence became available during the project) but functional genomic tools are still missing. This research program had three major goals: 1. Develop whole genome cucumber and melon SNP arrays. 2. Develop and characterize cucumber populations segregating for fruit size. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. As suggested by the reviewers the work concentrated mostly in cucumber and not both in cucumber and melon. In order to develop a SNP (single nucleotide polymorphism) array for cucumber, available and newly generated sequence from two cucumber cultivars with extreme differences in shape and size, pickling GY14 and Chinese long 9930, were analyzed for variation (SNPs). A large set of high quality SNPs was discovered between the two parents of the RILs population (GY14 and 9930) and used to design a custom SNP array with 35000 SNPs using Agilent technology. The array was validated using 9930, Gy14 and F1 progeny of the two parents. Several mapping populations were developed for linkage mapping of quantitative trait loci (QTL) for fruit size These includes 145 F3 families and 150 recombinant inbred line (RILs F7 or F8 (Gy14 X 9930) and third population contained 450 F2 plants from a cross between Gy14 and a wild plant from India. The main population that was used in this study is the RILs population of Gy14 X 9930. Phenotypic and morphological analyses of 9930, Gy14, and their segregating F2 and RIL progeny indicated that several, likely independent, factors influence cucumber fruit size and shape, including factors that act both pre-anthesis and post-pollination. These include: amount, rate, duration, and plane of cell division pre- and post-anthesis and orientation of cell expansion. Analysis of F2 and RIL progeny indicated that factors influencing fruit length were largely determined pre-anthesis, while fruit diameter was more strongly influenced by environment and growth factors post-anthesis. These results suggest involvement of multiple genetically segregating factors expected to map independently onto the cucumber genome. Using the SNP array and the phenotypic data two major QTLs for fruit size of cucumber were mapped in very high accuracy (around 300 Kb) with large set of markers that should facilitate identification and cloning of major genes that contribute to fruit size in cucumber. In addition, a highly accurate haplotype map of all RILS was created to allow fine mapping of other traits segregating in this population. A detailed cucumber genetic map with 6000 markers was also established (currently the most detailed genetic map of cucumber). The integration of genetics physiology and genomic approaches in this project yielded new major infrastructure tools that can be used for understanding fruit size and many other traits of importance in cucumber. The SNP array and genetic population with an ultra-fine map can be used for future breeding efforts, high resolution mapping and cloning of traits of interest that segregate in this population. The genetic map that was developed can be used for other breeding efforts in other populations. The study of fruit development that was done during this project will be important in dissecting function of genes that that contribute to the fruit size QTLs. The SNP array can be used as tool for mapping different traits in cucumber. The development of the tools and knowledge will thus promote genetic improvement of cucumber and related cucurbits.

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Баттахов, Петр Петрович. ПРАВОВОЕ РЕГУЛИРОВАНИЕ СОЦИАЛЬНО-ЭКОНОМИЧЕСКИХ ОТНОШЕНИЙ В АРКТИЧЕСКОЙ ЗОНЕ. DOI CODE, 2021. http://dx.doi.org/10.18411/1815-1337-2021-11862.

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nomic progress of society. In this case, legal regulation creates favourable conditions and protects the rights of small indigenous northern peoples, that is, the local population, who live permanently in the Arctic zone. Separately, on the basis of this concept, the development of the economy and social sphere of the Arctic bloc as a whole is considered. The main strategic directions for the development of the Arctic and the current regulatory framework of the Russian Federation are being investigated. The author proposes to solve issues related to the socioeconomic problems of the Arctic through the adoption of comprehensive concepts and regulatory legal acts. The main conclusion of the work is to improve the regulatory framework through the adoption of a separate codified act.

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Weller, Joel I., Harris A. Lewin, and Micha Ron. Determination of Allele Frequencies for Quantitative Trait Loci in Commercial Animal Populations. United States Department of Agriculture, February 2005. http://dx.doi.org/10.32747/2005.7586473.bard.

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Individual loci affecting economic traits in dairy cattle (ETL) have been detected via linkage to genetic markers by application of the granddaughter design in the US population and the daughter design in the Israeli population. From these analyses it is not possible to determine allelic frequencies in the population at large, or whether the same alleles are segregating in different families. We proposed to answer this question by application of the "modified granddaughter design", in which granddaughters with a common maternal grandsire are both genotyped and analyzed for the economic traits. The objectives of the proposal were: 1) to fine map three segregating ETL previously detected by a daughter design analysis of the Israeli dairy cattle population; 2) to determine the effects of ETL alleles in different families relative to the population mean; 3) for each ETL, to determine the number of alleles and allele frequencies. The ETL on Bostaurusautosome (BT A) 6 chiefly affecting protein concentration was localized to a 4 cM chromosomal segment centered on the microsatellite BM143 by the daughter design. The modified granddaughter design was applied to a single family. The frequency of the allele increasing protein percent was estimated at 0.63+0.06. The hypothesis of equal allelic frequencies was rejected at p<0.05. Segregation of this ETL in the Israeli population was confirmed. The genes IBSP, SPP1, and LAP3 located adjacent to BM143 in the whole genome cattle- human comparative map were used as anchors for the human genome sequence and bovine BAC clones. Fifteen genes within 2 cM upstream of BM143 were located in the orthologous syntenic groups on HSA4q22 and HSA4p15. Only a single gene, SLIT2, was located within 2 cM downstream of BM143 in the orthologous HSA4p15 region. The order of these genes, as derived from physical mapping of BAC end sequences, was identical to the order within the orthologous syntenic groups on HSA4: FAM13A1, HERC3. CEB1, FLJ20637, PP2C-like, ABCG2, PKD2. SPP, MEP, IBSP, LAP3, EG1. KIAA1276, HCAPG, MLR1, BM143, and SLIT2. Four hundred and twenty AI bulls with genetic evaluations were genotyped for 12 SNPs identified in 10 of these genes, and for BM143. Seven SNPs displayed highly significant linkage disequilibrium effects on protein percentage (P<0.000l) with the greatest effect for SPP1. None of SNP genotypes for two sires heterozygous for the ETL, and six sires homozygous for the ETL completely corresponded to the causative mutation. The expression of SPP 1 and ABCG2 in the mammary gland corresponded to the lactation curve, as determined by microarray and QPCR assays, but not in the liver. Anti-sense SPP1 transgenic mice displayed abnormal mammary gland differentiation and milk secretion. Thus SPP 1 is a prime candidate gene for this ETL. We confirmed that DGAT1 is the ETL segregating on BTA 14 that chiefly effects fat concentration, and that the polymorphism is due to a missense mutation in an exon. Four hundred Israeli Holstein bulls were genotyped for this polymorphism, and the change in allelic frequency over the last 20 years was monitored.

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Blum, Abraham, and Henry T. Nguyen. Molecular Tagging of Drought Resistance in Wheat: Osmotic Adjustment and Plant Productivity. United States Department of Agriculture, November 2002. http://dx.doi.org/10.32747/2002.7580672.bard.

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Drought stress is a major limitation to bread wheat (Triticumaestivum L.) productivity and its yield stability in arid and semi-arid regions of world including parts of Israel and the U.S. Currently, breeding for sustained yields under drought stress is totally dependent on the use of yield and several key physiological attributes as selection indices. The attempt to identify the optimal genotype by evaluating the phenotype is undermining progress in such breeding programs. Osmotic adjustment (OA) is an effective drought resistance mechanism in many crop plants. Evidence exists that there is a genetic variation for OA in wheat and that high OA capacity supports wheat yields under drought stress. The major objective of this research was to identify molecular markers (RFLPs, restriction fragment length polymorphisms; and AFLPs, amplified fragment length polymorph isms) linked to OA as a major attribute of drought resistance in wheat and thus to facilitate marker-assisted selection for drought resistance. We identified high and low OA lines of wheat and from their cross developed recombinant inbred lines (RILs) used in the molecular tagging of OA in relation to drought resistance in terms of plant production under stress. The significant positive co-segregation of OA, plant water status and yield under stress in this RIL population provided strong support for the important role of OA as a drought resistance mechanism sustaining wheat production under drought stress. This evidence was obtained in addition to the initial study of parental materials for constructing this RIL population, which also gave evidence for a strong correlation between OA and grain yield under stress. This research therefore provides conclusive evidence on the important role of OA in sustaining wheat yield under drought stress. The measurement of OA is difficult and the selection for drought resistance by the phenotypic expression of OA is practically impossible. This research provided information on the genetic basis of OA in wheat in relations to yield under stress. It provided the basic information to indicate that molecular marker assisted selection for OA in wheat is possible. The RIL population has been created by a cross between two agronomic spring wheat lines and the high OA recombinants in this population presented very high OA values, not commonly observed in wheat. These recombinants are therefore an immediate valuable genetic recourse for breeding well-adapted drought resistant wheat in Texas and Israel. We feel that this work taken as a whole eliminate the few previous speculated . doubts about the practical role of OA as an important mechanism of drought resistance in economic crop plants. As such it should open the way, in terms of both concept and the use of marker assisted selection, for improving drought resistance in wheat by deploying high osmotic adjustment.

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LI, Peng, and Junjun Liu. Effect of statin therapy on moderate-to-severe depression: an updated systematic review and meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, March 2022. http://dx.doi.org/10.37766/inplasy2022.3.0016.

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Review question / Objective: We aim to assess the antidepressant effects of statin therapy among patients complicated with moderate to severe depression. Condition being studied: Depression is one of the major causes of disability worldwide, and major depressive disorders (MDD) contribute to a significant heavy disease burden, which is expected to be second by 2050, only to heart disease. Despite great improvement in therapy, the treatment efficacy remains low. Therefore, alternative therapies have been intensely investigated. A substantial body of researches have suggested that inflammation is one of the operative pathways between MDD and increased risk of somatic comorbidities, and some specific depressive symptoms. Depression occurs in most patients with cardiac and cerebrovascular disease due to the long-term effects, and depression increases the risk of cardiovascular disease in the population as a whole and in patients with coronary artery disease or stroke. Several observational studies have demonstrated reduced rates of depression among patients taking statins, which may be related to its anti-inflammatory effect. However, whether statin improves the depressive symptoms and its associated mechanism is still mixed. Furthermore, there is little evidence about statin treatment effect in those with moderate to severe depression. In addition, whether the effect of statin treatment on depressive symptom changes with time or is affected by baseline depression severity or percentage change of lipid levels has not been explored in previous studies.

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Jorgensen, Frieda, Andre Charlett, Craig Swift, Anais Painset, and Nicolae Corcionivoschi. A survey of the levels of Campylobacter spp. contamination and prevalence of selected antimicrobial resistance determinants in fresh whole UK-produced chilled chickens at retail sale (non-major retailers). Food Standards Agency, June 2021. http://dx.doi.org/10.46756/sci.fsa.xls618.

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Campylobacter spp. are the most common bacterial cause of foodborne illness in the UK, with chicken considered to be the most important vehicle for this organism. The UK Food Standards Agency (FSA) agreed with industry to reduce Campylobacter spp. contamination in raw chicken and issued a target to reduce the prevalence of the most contaminated chickens (those with more than 1000 cfu per g chicken neck skin) to below 10 % at the end of the slaughter process, initially by 2016. To help monitor progress, a series of UK-wide surveys were undertaken to determine the levels of Campylobacter spp. on whole UK-produced, fresh chicken at retail sale in the UK. The data obtained for the first four years was reported in FSA projects FS241044 (2014/15) and FS102121 (2015 to 2018). The FSA has indicated that the retail proxy target for the percentage of highly contaminated raw whole retail chickens should be less than 7% and while continued monitoring has demonstrated a sustained decline for chickens from major retailer stores, chicken on sale in other stores have yet to meet this target. This report presents results from testing chickens from non-major retailer stores (only) in a fifth survey year from 2018 to 2019. In line with previous practise, samples were collected from stores distributed throughout the UK (in proportion to the population size of each country). Testing was performed by two laboratories - a Public Health England (PHE) laboratory or the Agri-Food & Biosciences Institute (AFBI), Belfast. Enumeration of Campylobacter spp. was performed using the ISO 10272-2 standard enumeration method applied with a detection limit of 10 colony forming units (cfu) per gram (g) of neck skin. Antimicrobial resistance (AMR) to selected antimicrobials in accordance with those advised in the EU harmonised monitoring protocol was predicted from genome sequence data in Campylobacter jejuni and Campylobacter coli isolates The percentage (10.8%) of fresh, whole chicken at retail sale in stores of smaller chains (for example, Iceland, McColl’s, Budgens, Nisa, Costcutter, One Stop), independents and butchers (collectively referred to as non-major retailer stores in this report) in the UK that are highly contaminated (at more than 1000 cfu per g) with Campylobacter spp. has decreased since the previous survey year but is still higher than that found in samples from major retailers. 8 whole fresh raw chickens from non-major retailer stores were collected from August 2018 to July 2019 (n = 1009). Campylobacter spp. were detected in 55.8% of the chicken skin samples obtained from non-major retailer shops, and 10.8% of the samples had counts above 1000 cfu per g chicken skin. Comparison among production plant approval codes showed significant differences of the percentages of chicken samples with more than 1000 cfu per g, ranging from 0% to 28.1%. The percentage of samples with more than 1000 cfu of Campylobacter spp. per g was significantly higher in the period May, June and July than in the period November to April. The percentage of highly contaminated samples was significantly higher for samples taken from larger compared to smaller chickens. There was no statistical difference in the percentage of highly contaminated samples between those obtained from chicken reared with access to range (for example, free-range and organic birds) and those reared under standard regime (for example, no access to range) but the small sample size for organic and to a lesser extent free-range chickens, may have limited the ability to detect important differences should they exist. Campylobacter species was determined for isolates from 93.4% of the positive samples. C. jejuni was isolated from the majority (72.6%) of samples while C. coli was identified in 22.1% of samples. A combination of both species was found in 5.3% of samples. C. coli was more frequently isolated from samples obtained from chicken reared with access to range in comparison to those reared as standard birds. C. jejuni was less prevalent during the summer months of June, July and August compared to the remaining months of the year. Resistance to ciprofloxacin (fluoroquinolone), erythromycin (macrolide), tetracycline, (tetracyclines), gentamicin and streptomycin (aminoglycosides) was predicted from WGS data by the detection of known antimicrobial resistance determinants. Resistance to ciprofloxacin was detected in 185 (51.7%) isolates of C. jejuni and 49 (42.1%) isolates of C. coli; while 220 (61.1%) isolates of C. jejuni and 73 (62.9%) isolates of C. coli isolates were resistant to tetracycline. Three C. coli (2.6%) but none of the C. jejuni isolates harboured 23S mutations predicting reduced susceptibility to erythromycin. Multidrug resistance (MDR), defined as harbouring genetic determinants for resistance to at least three unrelated antimicrobial classes, was found in 10 (8.6%) C. coli isolates but not in any C. jejuni isolates. Co-resistance to ciprofloxacin and erythromycin was predicted in 1.7% of C. coli isolates. 9 Overall, the percentages of isolates with genetic AMR determinants found in this study were similar to those reported in the previous survey year (August 2016 to July 2017) where testing was based on phenotypic break-point testing. Multi-drug resistance was similar to that found in the previous survey years. It is recommended that trends in AMR in Campylobacter spp. isolates from retail chickens continue to be monitored to realise any increasing resistance of concern, particulary to erythromycin (macrolide). Considering that the percentage of fresh, whole chicken from non-major retailer stores in the UK that are highly contaminated (at more than 1000 cfu per g) with Campylobacter spp. continues to be above that in samples from major retailers more action including consideration of interventions such as improved biosecurity and slaughterhouse measures is needed to achieve better control of Campylobacter spp. for this section of the industry. The FSA has indicated that the retail proxy target for the percentage of highly contaminated retail chickens should be less than 7% and while continued monitoring has demonstrated a sustained decline for chickens from major retailer stores, chicken on sale in other stores have yet to meet this target.

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Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7600047.bard.

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Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule sequencing and shifted the focus to Nanoporelong-read sequencing of all 25 founder lines. This analysis provides invaluable information on genome-wide structural variation across our diversity 4) Integrated analyses and development of prediction models Agricultural heterosis relates to hybrids that outperform their inbred parents for yield. First generation (F1) hybrids are produced in many crop species and it is estimated that heterosis increases yield by 15-30% globally. Melon (Cucumismelo) is an economically important species of The Cucurbitaceae family and is among the most important fleshy fruits for fresh consumption Worldwide. The major goal of this project was to explore the patterns and magnitude of yield heterosis in melon and link it to whole genome sequence variation. A core subset of 25 diverse lines was selected from the Newe-Yaar melon diversity panel for whole-genome re-sequencing (WGS) and test-crosses, to produce structured half-diallele design of 300 F1 hybrids (MelHDA25). Yield variation was measured in replicated yield trials at the whole-plant and at the rootstock levels (through a common-scion grafted experiments), across the F1s and parental lines. As part of this project we also developed an algorithmic pipeline for detection and yield estimation of melons from aerial-images, towards future implementation of such high throughput, cost-effective method for remote yield evaluation in open-field melons. We found extensive, highly heritable root-derived yield variation across the diallele population that was characterized by prominent best-parent heterosis (BPH), where hybrids rootstocks outperformed their parents by 38% and 56 % under optimal irrigation and drought- stress, respectively. Through integration of the genotypic data (~4,000,000 SNPs) and yield analyses we show that root-derived hybrids yield is independent of parental genetic distance. However, we mapped novel root-derived yield QTLs through genome-wide association (GWA) analysis and a multi-QTLs model explained more than 45% of the hybrids yield variation, providing a potential route for marker-assisted hybrid rootstock breeding. Four selected hybrid rootstocks are further studied under multiple scion varieties and their validated positive effect on yield performance is now leading to ongoing evaluation of their commercial potential. On the genomic level, this project resulted in 3 layers of data: 1) whole-genome short-read Illumina sequencing (30X) of the 25 founder lines provided us with 25 genome alignments and high-density melon HapMap that is already shown to be an effective resource for QTL annotation and candidate gene analysis in melon. 2) fast advancements in long-read single-molecule sequencing allowed us to shift focus towards this technology and generate ~50X Nanoporesequencing of the 25 founders which in combination with the short-read data now enable de novo assembly of the 25 genomes that will soon lead to construction of the first melon pan-genome. 3) Transcriptomic (3' RNA-Seq) analysis of several selected hybrids and their parents provide preliminary information on differentially expressed genes that can be further used to explain the root-derived yield variation. Taken together, this project expanded our view on yield heterosis in melon with novel specific insights on root-derived yield heterosis. To our knowledge, thus far this is the largest systematic genetic analysis of rootstock effects on yield heterosis in cucurbits or any other crop plant, and our results are now translated into potential breeding applications. The genomic resources that were developed as part of this project are putting melon in the forefront of genomic research and will continue to be useful tool for the cucurbits community in years to come.

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Hilbrecht, Margo, Sally M. Gainsbury, Nassim Tabri, Michael J. A. Wohl, Silas Xuereb, Jeffrey L. Derevensky, Simone N. Rodda, McKnight Sheila, Voll Jess, and Gottvald Brittany. Prevention and education evidence review: Gambling-related harm. Edited by Margo Hilbrecht. Greo, September 2021. http://dx.doi.org/10.33684/2021.006.

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This report supports an evidence-based approach to the prevention and education objective of the National Strategy to Reduce Harm from Gambling. Applying a public health policy lens, it considers three levels of measures: universal (for the benefit of the whole population), selective (for the benefit of at-risk groups), and indicated (for the benefit of at-risk individuals). Six measures are reviewed by drawing upon a range of evidence in the academic and grey literature. The universal level measures are “Regulatory restriction on how gambling is provided” and “Population-based safer gambling/responsible gambling efforts.” Selective measures focus on age cohorts in a chapter entitled, “Targeted safer gambling campaigns for children, youth, and older adults.” The indicated measures are “Brief internet delivered interventions for gambling,” “Systems and tools that produced actual (‘hard’) barriers and limit access to funds,” and “Self-exclusion.” Since the quantity and quality of the evidence base varied by measure, appropriate review methods were selected to assess publications using a systematic, scoping, or narrative approach. Some measures offered consistent findings regarding the effectiveness of interventions and initiatives, while others were less clear. Unintended consequences were noted since it is important to be aware of unanticipated, negative consequences resulting from prevention and education activities. After reviewing the evidence, authors identified knowledge gaps that require further research, and provided guidance for how the findings could be used to enhance the prevention and education objective. The research evidence is supplemented by consultations with third sector charity representatives who design and implement gambling harm prevention and education programmes. Their insights and experiences enhance, support, or challenge the academic evidence base, and are shared in a separate chapter. Overall, research evidence is limited for many of the measures. Quality assessments suggest that improvements are needed to support policy decisions more fully. Still, opportunities exist to advance evidence-based policy for an effective gambling harm prevention and education plan.

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Allik, Mirjam, Dandara Ramos, Marilyn Agranonik, Elzo Pereira Pinto Junior, Maria Yury Ichihara, Mauricio Barreto, Alastair Leyland, and Ruth Dundas. Developing a Small-Area Deprivation Measure for Brazil. University of Glasgow, May 2020. http://dx.doi.org/10.36399/gla.pubs.215898.

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This report describes the development of the BrazDep small-area deprivation measure for the whole of Brazil. The measure uses the 2010 Brazilian Population Census data and is calculated for the smallest possible geographical area level, the census sectors. It combines three variables – (1) percent of households with per capita income ≤ 1/2 minimum wage; (2) percent of people not literate, aged 7+; and (3) average of percent of people with inadequate access to sewage, water, garbage collection and no toilet and bath/shower – into a single measure. Similar measures have previously been developed at the census sector level for some states or municipalities, but the deprivation measure described in this report is the first one to be provided for census sectors for the whole of Brazil. BrazDep is a measure of relative deprivation, placing the census sectors on a scale of material well-being from the least to the most deprived. It is useful in comparing areas within Brazil in 2010, but cannot be used to make comparisons across countries or time. Categorical versions of the measure are also provided, placing census sectors into groups of similar levels of deprivation. Deprivation measures, such as the one developed here, have been developed for many countries and are popular tools in public health research for describing the social patterning of health outcomes and supporting the targeting and delivery of services to areas of higher need. The deprivation measure is exponentially distributed, with a large proportion of areas having a low deprivation score and a smaller number of areas experiencing very high deprivation. There is significant regional variation in deprivation; areas in the North and Northeast of Brazil have on average much higher deprivation compared to the South and Southeast. Deprivation levels in the Central-West region fall between those for the North and South. Differences are also great between urban and rural areas, with the former having lower levels of deprivation compared to the latter. The measure was validated by comparing it to other similar indices measuring health and social vulnerability at the census sector level in states and municipalities where it was possible, and at the municipal level for across the whole of Brazil. At the municipal level the deprivation measure was also compared to health outcomes. The different validation exercises showed that the developed measure produced expected results and could be considered validated. As the measure is an estimate of the “true” deprivation in Brazil, uncertainty exists about the exact level of deprivation for all of the areas. For the majority of census sectors the uncertainty is small enough that we can reliably place the area into a deprivation category. However, for some areas uncertainty is very high and the provided estimate is unreliable. These considerations should always be kept in mind when using the BrazDep measure in research or policy. The measure should be used as part of a toolkit, rather than a single basis for decision-making. The data together with documentation is available from the University of Glasgow http: //dx.doi.org/10.5525/gla.researchdata.980. The data and this report are distributed under Creative Commons Share-Alike license (CC BY-SA 4.0) and can be freely used by researchers, policy makers or members of public.

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