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https://www.readbyqxmd.com/read/29026650/accurate-quantification-of-within-and-between-host-hbv-evolutionary-rates-requires-explicit-transmission-chain-modelling
#1
Bram Vrancken, Marc A Suchard, Philippe Lemey
Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, Journal of Virology, 89/7: 3512-22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the 'colonization-adaptation-transmission' model can explain the differential impact of transmission on synonymous and non-synonymous substitution rates...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/29024178/familial-clustering-of-oropharyngeal-squamous-cell-carcinoma-in-the-utah-population
#2
Marcus M Monroe, Mia Hashibe, Quinn Orb, Jeremiah Alt, Luke Buchmann, Jason Hunt, Lisa A Cannon-Albright
BACKGROUND: The main purpose of the current study was to define the familial aggregation of oropharyngeal squamous cell carcinoma (SCC) and risk to relatives of patients with oropharyngeal SCC. METHODS: We conducted a retrospective study utilizing linked population-based genealogy and state cancer registry databases between 1966 and 2012. Relative risks for oropharyngeal SCC and other malignancies among patients with oropharyngeal SCC and their relatives were estimated...
October 11, 2017: Head & Neck
https://www.readbyqxmd.com/read/29017623/the-genealogy-of-the-clinical-syndrome-of-mania-signs-and-symptoms-described-in-psychiatric-texts-from-1880-to-1900
#3
K S Kendler
In 1800, mania was conceptualized as an agitated psychotic state. By 1900, it closely resembled its modern form. This paper reviews the descriptions of mania in Western psychiatry from 1880 to 1900, when Kraepelin was training and developing his concept of manic-depressive illness. Psychiatric textbooks published 1900-1960 described 22 characteristic manic symptoms/signs the presence of which were recorded in 25 psychiatric textbooks and three other key documents published 1880-1900. Descriptions of mania in these nineteenth century textbooks closely resembled those in the twentieth century, recording a mean (s...
October 11, 2017: Psychological Medicine
https://www.readbyqxmd.com/read/29016976/a-description-of-familial-clustering-of-meningiomas-in-the-utah-population
#4
William T Couldwell, Lisa A Cannon-Albright
Background: Meningiomas are common intracranial tumors in adults, yet the genetics and cause of sporadic meningiomas are not well understood. Few familial clusters have been reported. The aim of this study was to investigate the familiality of meningiomas within the Utah Population Database. Methods: Meningioma cases reported in the Utah Cancer Registry were identified. Relative risk of their relatives was calculated. All possible cases were assessed with the Genealogical Index of Familiality (GIF), which measures average pairwise relatedness of all possible pairs using the Malecot coefficient of kinship...
July 7, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28993198/wright-fisher-diffusion-bridges
#5
Robert Griffiths, Paul A Jenkins, Dario Spanò
This paper considers the coalescent genealogy in a Wright-Fisher diffusion process, modelling the frequency of an allele, when the frequency is fixed in a bridge at two times 0 and T. Particular attention is paid to beginning and ending at zero frequency. The coalescent genealogy of the population at time t is described by two coalescent processes from t to 0 and from t to T. If the frequencies are fixed at zero then the coalescent processes have single lineages at 0 and T. Genealogy of the neutral Wright-Fisher bridge is also modelled by branching Pólya urns, extending a representation in a Wright-Fisher diffusion...
October 6, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28981849/the-genetic-diversity-haplotype-analysis-and-phylogenetic-relationship-of-aedes-albopictus-diptera-culicidae-based-on-the-cytochrome-oxidase-1-marker-a-malaysian-scenario
#6
Nurul-Ain Ismail, Nurul Adilah-Amrannudin, Mayamin Hamsidi, Rodziah Ismail, Nazri Che Dom, Abu Hassan Ahmad, Mohd Fahmi Mastuki, Siti Nazrina Camalxaman
The global expansion of Ae. albopictus from its native range in Southeast Asia has been implicated in the recent emergence of dengue endemicity in Malaysia. Genetic variability studies of Ae. albopictus are currently lacking in the Malaysian setting, yet are crucial to enhancing the existing vector control strategies. The study was conducted to establish the genetic variability of maternally inherited mitochondrial DNA encoding for cytochrome oxidase subunit 1 (CO1) gene in Ae. albopictus. Twelve localities were selected in the Subang Jaya district based on temporal indices utilizing 120 mosquito samples...
July 17, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/28980899/oesophageal-disease-in-systemic-sclerosis-does-heritability-play-a-role
#7
Tracy Frech, Latifa Fakoya, Andrew J Gawron, Jathine Wong, Mary Beth Scholand, Allen Sawitzke, Kathryn Peterson
OBJECTIVES: In systemic sclerosis (SSc) the most common gastrointestinal tract (GIT) complaint is gastroesophageal reflux disease (GERD), which may contribute to oesophagitis, stricture, Barrett's oesophagus, and oesophageal adenocarcinoma. We used a genealogical resource the Utah Population Database (UPDB) to analyse SSc pedigrees for hereditability of oesophageal disease. METHODS: SSc, GERD, oesophagitis, stricture, Barrett's, and oesophageal adenocarcinoma were defined by ICD Ninth and Tenth Revision codes...
October 2, 2017: Clinical and Experimental Rheumatology
https://www.readbyqxmd.com/read/28980240/detecting-pedigree-relationship-errors
#8
Lei Sun
Pedigree relationship errors often occur in family data collected for genetic studies, and unidentified errors can lead to either increased false positives or decreased power in both linkage and association analyses. Here, we review several allele sharing as well as likelihood-based statistics that were proposed to efficiently extract genealogical information from available genome-wide marker data, and the software package PREST that implements these methods. We provide the detailed analytical steps involved using two application examples, and we discuss various practical issues, including result interpretation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28975624/genesis-and-profanation-of-the-other-world-the-interpretation-of-dreams
#9
Leandro Drivet
This paper addresses Nietzsche's reflections on the phenomenon of dreams as a crucial precedent of Freud's Die Traumdeutung. The works of Nietzsche and Freud are scrutinized to establish and compare the most relevant aspects of their understanding of dreams. The philosophical impact of both accounts is assessed in terms of the transvaluation of religious and metaphysical values, which reveals three epistemological shifts: the replacement of Metaphysics by History/Genealogy (Nietzsche) and by Metapsychology (Freud), and the expansion of rationality beyond the limits of consciousness (Nietzsche and Freud)...
October 4, 2017: International Journal of Psycho-analysis
https://www.readbyqxmd.com/read/28964318/environmental-contributions-to-otitis-media-requiring-tympanostomy-tubes
#10
Reema Padia, Jeremiah A Alt, Karen Curtin, Harlan R Muntz, Richard R Orlandi, Justin Berger, Jeremy D Meier
OBJECTIVE: Otitis media requiring tympanostomy tubes (OMwTT) is a prevalent disease process that has been previously shown to have a strong familial link. The impact from the environmental versus genetic contributions to this link is unknown. The objective was to determine the environmental involvement in the development of OMwTT. METHODS: Using an extensive genealogical database linked to medical records, we evaluated the risk of OMwTT in children of probands as compared to children of controls, individually matched 5:1 on sex and birth year, from a conditional logistic regression model...
October 2017: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/28956315/hyperphenylalaninaemias-in-estonia-genotype-phenotype-correlation-and-comparative-overview-of-the-patient-cohort-before-and-after-nation-wide-neonatal-screening
#11
Hardo Lilleväli, Karit Reinson, Kai Muru, Kristi Simenson, Ülle Murumets, Tõnu Möls, Katrin Õunap
The present study provides a retrospective overview of the cohort of phenylketonuria (PKU) patients in Estonia. Based on the available data, the patients clearly cluster into two distinct groups: the patients with late diagnosis and start of therapy (N = 46), who were born before 1993 when the national newborn screening programme was launched, and the screened babies (N = 48) getting their diagnoses at least in a couple of weeks after birth.Altogether 153 independent phenylalanine hydroxylase (PAH) alleles from 92 patients were analysed in the study, wherein 80% of them were carrying the p...
September 28, 2017: JIMD Reports
https://www.readbyqxmd.com/read/28943126/computing-the-joint-distribution-of-the-total-tree-length-across-loci-in-populations-with-variable-size
#12
Alexey Miroshnikov, Matthias Steinrücken
In recent years, a number of methods have been developed to infer complex demographic histories, especially historical population size changes, from genomic sequence data. Coalescent Hidden Markov Models have proven to be particularly useful for this type of inference. Due to the Markovian structure of these models, an essential building block is the joint distribution of local genealogical trees, or statistics of these genealogies, at two neighboring loci in populations of variable size. Here, we present a novel method to compute the marginal and the joint distribution of the total length of the genealogical trees at two loci separated by at most one recombination event for samples of arbitrary size...
September 21, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28926096/the-ambivert-a-failed-attempt-at-a-normal-personality
#13
Ian J Davidson
Recently, attention has been drawn toward an overlooked and nearly forgotten personality type: the ambivert. This paper presents a genealogy of the ambivert, locating the various contexts it traversed in order to highlight the ways in which these places and times have interacted and changed-ultimately elucidating our current situation. Proposed by Edmund S. Conklin in 1923, the ambivert only was meant for normal persons in between the introvert and extravert extremes. Although the ambivert could have been taken up by early personality psychologists who were transitioning from the study of the abnormal to the normal, it largely failed to gain traction...
September 19, 2017: Journal of the History of the Behavioral Sciences
https://www.readbyqxmd.com/read/28923029/mitochondrial-genomes-reveal-recombination-in-the-presumed-asexual-fusarium-oxysporum-species-complex
#14
Balázs Brankovics, Peter van Dam, Martijn Rep, G Sybren de Hoog, Theo A J van der Lee, Cees Waalwijk, Anne D van Diepeningen
BACKGROUND: The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. RESULTS: A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28919319/a-population-based-description-of-familial-clustering-of-hirschsprung-s-disease
#15
Craig C Teerlink, Ryan Bernhisel, Lisa A Cannon-Albright, Michael D Rollins
BACKGROUND: Familial recurrence of Hirschsprung's disease (HSCR) is well documented, and risk estimates for relatives have been reported from various populations. We describe the familial clustering of HSCR cases using well-established unbiased familial aggregation techniques within the context of a population genealogy. METHODS: Patients included 264 HSCR cases identified using ICD-9 diagnosis coding from the two largest healthcare providers in Utah who also had linked genealogy data...
September 1, 2017: Journal of Pediatric Surgery
https://www.readbyqxmd.com/read/28884289/dispersals-of-the-siberian-y-chromosome-haplogroup-q-in-eurasia
#16
Yun-Zhi Huang, Horolma Pamjav, Pavel Flegontov, Vlastimil Stenzl, Shao-Qing Wen, Xin-Zhu Tong, Chuan-Chao Wang, Ling-Xiang Wang, Lan-Hai Wei, Jing-Yi Gao, Li Jin, Hui Li
The human Y-chromosome has proven to be a powerful tool for tracing the paternal history of human populations and genealogical ancestors. The human Y-chromosome haplogroup Q is the most frequent haplogroup in the Americas. Previous studies have traced the origin of haplogroup Q to the region around Central Asia and Southern Siberia. Although the diversity of haplogroup Q in the Americas has been studied in detail, investigations on the diffusion of haplogroup Q in Eurasia and Africa are still limited. In this study, we collected 39 samples from China and Russia, investigated 432 samples from previous studies of haplogroup Q, and analyzed the single nucleotide polymorphism (SNP) subclades Q1a1a1-M120, Q1a2a1-L54, Q1a1b-M25, Q1a2-M346, Q1a2a1a2-L804, Q1a2b2-F1161, Q1b1a-M378, and Q1b1a1-L245...
September 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28877583/leaf-lims-a-flexible-laboratory-information-management-system-with-a-synthetic-biology-focus
#17
Thomas Craig, Richard Holland, Rosalinda D'Amore, James Johnson, Hannah V McCue, Anthony West, Valentin Zulkower, Hille Tekotte, Yizhi Cai, Daniel Swan, Robert P Davey, Christiane Hertz-Fowler, Anthony Hall, Mark Caddick
This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most LIMS systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture...
September 6, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28852243/genealogy-study-of-three-generations-of-patients-with-bipolar-mood-disorder-type-i
#18
Bahman Salehi, Sara Khoz, Bahman Sadeghi, Manouchehr Amanat, Mona Salehi
INTRODUCTION: The purpose of this research is genealogy examination of three generation of bipolar mood disorder Type I patients. METHODS: Patients selected using Poisson sampling method from 100 patients with bipolar mood disorder Type I, referring to a psychiatric center of Amir Kabir Hospital of Arak, Iran. Examine issues such as physical ailments, psychological review of living and deceased family members of each patient, drawn family pedigree using pedigree chart, check the relationship of the different pattern of the autosomal dominant and recessive disease, sex-linked dominant and recessive and linked to Y chromosome have been performed on patients...
July 2017: Indian Journal of Psychological Medicine
https://www.readbyqxmd.com/read/28827797/composite-likelihood-method-for-inferring-local-pedigrees
#19
Amy Ko, Rasmus Nielsen
Pedigrees contain information about the genealogical relationships among individuals and are of fundamental importance in many areas of genetic studies. However, pedigrees are often unknown and must be inferred from genetic data. Despite the importance of pedigree inference, existing methods are limited to inferring only close relationships or analyzing a small number of individuals or loci. We present a simulated annealing method for estimating pedigrees in large samples of otherwise seemingly unrelated individuals using genome-wide SNP data...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28817696/phenotypic-and-molecular-characterization-of-sweet-sorghum-accessions-for-bioenergy-production
#20
Michele Jorge da Silva, Maria Marta Pastina, Vander Fillipe de Souza, Robert Eugene Schaffert, Pedro Crescêncio Souza Carneiro, Roberto Willians Noda, José Eustáquio de Souza Carneiro, Cynthia Maria Borges Damasceno, Rafael Augusto da Costa Parrella
Sweet sorghum [Sorghum bicolor (L.) Moench] is a type of cultivated sorghum characterized by the accumulation of high levels of sugar in the stems and high biomass accumulation, making this crop an important feedstock for bioenergy production. Sweet sorghum breeding programs that focus on bioenergy have two main goals: to improve quantity and quality of sugars in the juicy stem and to increase fresh biomass productivity. Genetic diversity studies are very important for the success of a breeding program, especially in the early stages, where understanding the genetic relationship between accessions is essential to identify superior parents for the development of improved breeding lines...
2017: PloS One
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