A general hidden Markov model for multi-parent populations

Mapping Intimacies ◽

10.1101/2021.08.03.454963 ◽

2021 ◽

Author(s):

Karl W Broman

Keyword(s):

Relative Frequency ◽

Hidden Markov ◽

Exchange Process ◽

Approximate Model ◽

Experimental Designs ◽

Marker Data ◽

Diversity Outbred ◽

Precise Characterization ◽

Dense Marker

A common step in the analysis of multi-parent populations is genotype reconstruction: identifying the founder origin of haplotypes from dense marker data. This process often makes use of a model for the exchange process along chromosomes, including the relative frequency of founder alleles and of the probability of exchanges among them. While the precise experimental design used to generate the population may be used to derive a precise characterization of the exchange process, this can be tedious, particularly given the great variety of experimental designs that have been proposed. We describe an approximate model that can be applied for a variety of multi-parent populations. We have implemented the approach in the R/qtl2 software, and we illustrate its use in applications to publicly available data on Diversity Outbred and Collaborative Cross mice.

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A generic hidden Markov model for multi-parent populations

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab396 ◽

2021 ◽

Author(s):

Karl W Broman

Keyword(s):

Meiotic Recombination ◽

Relative Frequency ◽

Hidden Markov ◽

Probability Model ◽

Approximate Model ◽

Marker Data ◽

Diversity Outbred ◽

Precise Characterization ◽

Dense Marker

Abstract A common step in the analysis of multi-parent populations is genotype reconstruction: identifying the founder origin of haplotypes from dense marker data. This process often makes use of a probability model for the pattern of founder alleles along chromosomes, including the relative frequency of founder alleles and the probability of exchanges among them, which depend on a model for meiotic recombination and on the mating design for the population. While the precise experimental design used to generate the population may be used to derive a precise characterization of the model for exchanges among founder alleles, this can be tedious, particularly given the great variety of experimental designs that have been proposed. We describe an approximate model that can be applied for a variety of multi-parent populations. We have implemented the approach in the R/qtl2 software, and we illustrate its use in applications to publicly-available data on Diversity Outbred and Collaborative Cross mice.

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Water Tunnel to test and characterization of experimental designs of Hydrokinetics Turbines

Workrooms Journal ◽

10.15592/workrooms.2018.0005 ◽

2018 ◽

Vol 1 (6) ◽

Author(s):

Eduardo Alvarez-Alvarez ◽

Aitor Fernandez-Jimenez ◽

Manuel Rico-Secades ◽

Antonio Javier Calleja-Rodriguez ◽

Joaquin Fernandez-Francos ◽

...

Keyword(s):

Experimental Designs ◽

Water Tunnel

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Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor

Physical Chemistry Chemical Physics ◽

10.1039/d0cp02265a ◽

2020 ◽

Vol 22 (35) ◽

pp. 19468-19479 ◽

Cited By ~ 1

Author(s):

Keiichiro Shiraga ◽

Mako Urabe ◽

Takeshi Matsui ◽

Shojiro Kikuchi ◽

Yuichi Ogawa

Keyword(s):

Human Serum Albumin ◽

Serum Albumin ◽

Human Serum ◽

Thermal Denaturation ◽

Hydration Water ◽

Biological Functions ◽

Dielectric Sensor ◽

Hydration State ◽

Precise Characterization

The biological functions of proteins depend on harmonization with hydration water surrounding them.

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Distorted chiolite crystal structures of α-Na5M3F14 (M=Cr,Fe,Ga) studied by X-ray powder diffraction

Powder Diffraction ◽

10.1154/1.1556990 ◽

2003 ◽

Vol 18 (2) ◽

pp. 128-134 ◽

Cited By ~ 4

Author(s):

A. Le Bail ◽

A.-M. Mercier

Keyword(s):

Crystal Structures ◽

Powder Diffraction ◽

Room Temperature ◽

Rietveld Refinements ◽

Space Group ◽

X Ray ◽

Precise Characterization

The crystal structures of the chiolite-related room temperature phases α-Na5M3F14 (MIII=Cr,Fe,Ga) are determined. For all of them, the space group is P21/n, Z=2; a=10.5096(3) Å, b=7.2253(2) Å, c=7.2713(2) Å, β=90.6753(7)° (M=Cr); a=10.4342(7) Å, b=7.3418(6) Å, c=7.4023(6) Å, β=90.799(5)° (M=Fe), and a=10.4052(1) Å, b=7.2251(1) Å, c=7.2689(1), β=90.6640(4)° (M=Ga). Rietveld refinements produce final RF factors 0.036, 0.033, and 0.035, and RWP factors, 0.125, 0.116, and 0.096, for MIII=Cr, Fe, and Ga, respectively. The MF6 polyhedra in the defective isolated perovskite-like layers deviate very few from perfect octahedra. Subtle octahedra tiltings lead to the symmetry decrease from the P4/mnc space group adopted by the Na5Al3F14 chiolite aristotype to the P21/n space group adopted by the title series. Facile twinning precluded till now the precise characterization of these compounds.

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Synthesis and Characterization of Pd exchanged MMT Clay for Mizoroki-Heck Reaction

Open Chemistry ◽

10.1515/chem-2018-0065 ◽

2018 ◽

Vol 16 (1) ◽

pp. 605-613 ◽

Cited By ~ 2

Author(s):

Vivek Srivastava

Keyword(s):

Heck Reaction ◽

Exchange Process ◽

Reaction Medium ◽

Analytical Techniques ◽

Catalyst Loading ◽

Catalyst Recycling ◽

Mmt Clay ◽

Vinyl Phosphonates ◽

Low Catalyst Loading

AbstractWe successfully synthesized Pd@MMT clay using a cation exchange process. We characterized all the synthesized Pd@MMT clays using sophisticated analytical techniques before testing them as a heterogeneous catalyst for the Mizoroki - Heck reaction (mono and double). The highest yield of the Mizoroki-Heck reaction product was recovered using thermally stable and highly reactive Pd@ MMT-1 clay catalyst in the functionalized ionic liquid reaction medium. We successfully isolated 2-aryl-vinyl phosphonates (mono-Mizoroki-Heck reaction product) and 2,2-diaryl-vinylphosphonates (double-Mizoroki-Heck reaction product) using aryl halides and dialkyl vinyl phosphonates in higher yields. The low catalyst loading, easy recovery of reaction product and 8 times catalyst recycling are the major highlights of this proposed protocol.

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Simple and Precise Characterization of Differential Modal Group Delay arising in Few-Mode Fiber

Optics Letters ◽

10.1364/ol.423950 ◽

2021 ◽

Author(s):

Zhe Fu ◽

Junjie Zhang ◽

Ziheng Zhang ◽

Songnian Fu ◽

Yuwen Qin ◽

...

Keyword(s):

Group Delay ◽

Precise Characterization ◽

Modal Group

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Children hospitalized due to maltreatment in the ICU of a Public Health Service

Revista Brasileira de Enfermagem ◽

10.1590/0034-7167-2017-0502 ◽

2018 ◽

Vol 71 (suppl 3) ◽

pp. 1420-1427

Author(s):

Letícia Medeiros Santomé ◽

Sandra Maria Cezar Leal ◽

Joel Rolim Mancia ◽

Antônio Marcos Freire Gomes

Keyword(s):

Medical Records ◽

Relative Frequency ◽

Life Histories ◽

Public Health Service ◽

Physical Violence ◽

First Aid ◽

Porto Alegre ◽

Chi Square ◽

Pediatric Icu

ABSRACT Objective: to characterize children hospitalized due to violence in a pediatric ICU in 2011; to relate violence and the mechanisms of trauma with death; to know the contextualization of violence, from the records in the medical records. Method: retrospective cohort, performed in a first aid hospital, Porto Alegre city, in the records of 22 children hospitalized in the ICU due to violence. Quantitative analysis was performed by absolute and relative frequency rates, chi-square and relative risk. Results: 54.5% were boys, 81.8% were white and 50% were up to three years old. Physical violence 50% and neglect 36.4%, family of children (77.3%), highlighting the mother (35.3%). Mechanisms of aggression: fall (22.7%), burns (18.2%). Burns were at high risk for death. Discharge to go home after ICU admission (59.1%). Conclusion: It is considered that the characterization of the cases of violence reflects the complexity of the theme, mainly, in face of the life histories that surround each case of children hospitalized by this aggravation.

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