A low coverage investigation on Al adsorption on the (111) surface of Pt, Ir and Au

The effect of temperature and structure of the palladium surfaces on acetylene chemisorption was studied along with the interaction of the adsorbed layers with molecular and atomic hydrogen. The work function changes were measured and combined with the volumetric measurements and analysis of the products. At temperature below 100 °C, acetylene is adsorbed almost without dissociation and forms at least two different types of thermally stable adsorption complexes. Acetylene adsorbed at 200 °C is partly decomposed, especially in the low coverage region. Besides the above mentioned effects, the template effect of adsorbed acetylene was studied in the temperature range from -80° to 25 °C. It has been shown that this effect is a typical phenomenon of the palladium-acetylene system which is not due to surface impurities.

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Overuse of Health Care in the Emergency Services in Chile

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18063082 ◽

2021 ◽

Vol 18 (6) ◽

pp. 3082

Author(s):

Ximena Alvial ◽

Alejandra Rojas ◽

Raúl Carrasco ◽

Claudia Durán ◽

Christian Fernández-Campusano

Keyword(s):

Public Health ◽

Emergency Services ◽

Clinical Care ◽

Tertiary Care ◽

Public Health Policies ◽

The Public ◽

Healthcare Network ◽

Use Of Emergency Services ◽

Low Coverage ◽

Different Levels

The Public Health Service in Chile consists of different levels of complexity and coverage depending on the severity and degree of specialization of the pathology to be treated. From primary to tertiary care, tertiary care is highly complex and has low coverage. This work focuses on an analysis of the public health system with emphasis on the healthcare network and tertiary care, whose objectives are designed to respond to the needs of each patient. A review of the literature and a field study of the problem of studying the perception of internal and external users is presented. This study intends to be a contribution in the detection of opportunities for the relevant actors and the processes involved through the performance of Triage. The main causes and limitations of the excessive use of emergency services in Chile are analyzed and concrete proposals are generated aiming to benefit clinical care in emergency services. Finally, improvements related to management are proposed and the main aspects are determined to improve decision-making in hospitals, which could be a contribution to public health policies.

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Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Animals ◽

10.3390/ani11030899 ◽

2021 ◽

Vol 11 (3) ◽

pp. 899

Author(s):

Fotis Pappas ◽

Christos Palaiokostas

Keyword(s):

Genetic Diversity ◽

Salvelinus Alpinus ◽

Arctic Charr ◽

Cost Effective ◽

Limiting Factors ◽

Phenotypic Traits ◽

Production Volume ◽

High Coverage ◽

Genomic Relationships ◽

Low Coverage

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.

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Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data

BMC Bioinformatics ◽

10.1186/s12859-020-03924-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xinping Fan ◽

Guanghao Luo ◽

Yu S. Huang

Keyword(s):

Copy Number ◽

Bayesian Learning ◽

Kernel Smoothing ◽

Gaussian Mixture ◽

Copy Number Alterations ◽

Sequencing Data ◽

Copy Numbers ◽

Allele Specific ◽

Tumor Sequencing ◽

Low Coverage

Abstract Background Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task. Results We introduce Accucopy, a method to infer total copy numbers (TCNs) and allele-specific copy numbers (ASCNs) from challenging low-purity and low-coverage tumor samples. Accucopy adopts many robust statistical techniques such as kernel smoothing of coverage differentiation information to discern signals from noise and combines ideas from time-series analysis and the signal-processing field to derive a range of estimates for the period in a histogram of coverage differentiation information. Statistical learning models such as the tiered Gaussian mixture model, the expectation–maximization algorithm, and sparse Bayesian learning were customized and built into the model. Accucopy is implemented in C++ /Rust, packaged in a docker image, and supports non-human samples, more at http://www.yfish.org/software/. Conclusions We describe Accucopy, a method that can predict both TCNs and ASCNs from low-coverage low-purity tumor sequencing data. Through comparative analyses in both simulated and real-sequencing samples, we demonstrate that Accucopy is more accurate than Sclust, ABSOLUTE, and Sequenza.

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353 ASAS-EAAP Talk: Low-coverage whole-genome sequencing in local livestock breeds

Journal of Animal Science ◽

10.1093/jas/skaa278.149 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 81-82

Author(s):

Joaquim Casellas ◽

Melani Martín de Hijas-Villalba ◽

Marta Vázquez-Gómez ◽

Samir Id Lahoucine

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Error Rate ◽

Allele Frequencies ◽

Paternity Testing ◽

Sequencing Error ◽

Whole Genome ◽

Genomic Evaluation ◽

Sequencing Error Rate ◽

Low Coverage

Abstract Current European regulations for autochthonous livestock breeds put a special emphasis on pedigree completeness, which requires laboratory paternity testing by genetic markers in most cases. This entails significant economic expenditure for breed societies and precludes other investments in breeding programs, such as genomic evaluation. Within this context, we developed paternity testing through low-coverage whole-genome data in order to reuse these data for genomic evaluation at no cost. Simulations relied on diploid genomes composed by 30 chromosomes (100 cM each) with 3,000,000 SNP per chromosome. Each population evolved during 1,000 non-overlapping generations with effective size 100, mutation rate 10–4, and recombination by Kosambi’s function. Only those populations with 1,000,000 ± 10% polymorphic SNP per chromosome in generation 1,000 were retained for further analyses, and expanded to the required number of parents and offspring. Individuals were sequenced at 0.01, 0.05, 0.1, 0.5 and 1X depth, with 100, 500, 1,000 or 10,000 base-pair reads and by assuming a random sequencing error rate per SNP between 10–2 and 10–5. Assuming known allele frequencies in the population and sequencing error rate, 0.05X depth sufficed to corroborate the true father (85,0%) and to discard other candidates (96,3%). Those percentages increased up to 99,6% and 99,9% with 0,1X depth, respectively (read length = 10,000 bp; smaller read lengths slightly improved the results because they increase the number of sequenced SNP). Results were highly sensitive to biases in allele frequencies and robust to inaccuracies regarding sequencing error rate. Low-coverage whole-genome sequencing data could be subsequently integrated into genomic BLUP equations by appropriately constructing the genomic relationship matrix. This approach increased the correlation between simulated and predicted breeding values by 1.21% (h2 = 0.25; 100 parents and 900 offspring; 0.1X depth by 10,000 bp reads). Although small, this increase opens the door to genomic evaluation in local livestock breeds.

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Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab024 ◽

2021 ◽

Author(s):

Rajanikanth Govindarajulu ◽

Ashley N Hostetler ◽

Yuguo Xiao ◽

Srinivasa R Chaluvadi ◽

Margarita Mauro-Herrera ◽

...

Keyword(s):

Agronomic Traits ◽

Interspecific Cross ◽

Crop Improvement ◽

Differentially Expressed ◽

Plant Domestication ◽

Sorghum Propinquum ◽

Ril Population ◽

Trait Locus ◽

Genomic Regions ◽

Low Coverage

Abstract Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ∼1920 bin markers spanning ∼875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.

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COVID-19 Infection and Previous BCG Vaccination Coverage in the Ecuadorian Population

Vaccines ◽

10.3390/vaccines9020091 ◽

2021 ◽

Vol 9 (2) ◽

pp. 91

Author(s):

Daniel Garzon-Chavez ◽

Jackson Rivas-Condo ◽

Adriana Echeverria ◽

Jhoanna Mozo ◽

Emmanuelle Quentin ◽

...

Keyword(s):

Vaccination Coverage ◽

Vaccine Coverage ◽

National Level ◽

Kendall Test ◽

Amino Acid Sequences ◽

Bcg Vaccination ◽

High Prevalence ◽

Health Organization ◽

Low Coverage ◽

Homologous Amino Acid

The Bacillus Calmette–Guérin (BCG) is a well-known vaccine with almost a century of use, with the apparent capability to improve cytokine production and epigenetics changes that could develop a better response to pathogens. It has been postulated that BCG protection against SARS-CoV-2 has a potential role in the pandemic, through the presence of homologous amino acid sequences. To identify a possible link between BCG vaccination coverage and COVID-19 cases, we used official epidemic data and Ecuadorian Ministry of Health and Pan American Health Organization vaccination information. BCG information before 1979 was available only at a national level. Therefore, projections based on the last 20 years were performed, to compare by specific geographic units. We used a Mann–Kendall test to identify BCG coverage variations, and mapping was conducted with a free geographic information system (QGIS). Nine provinces where BCG vaccine coverage was lower than 74.25% show a significant statistical association (χ2 Pearson’s = 4.800, df = 1, p = 0.028), with a higher prevalence of cases for people aged 50 to 64 years than in younger people aged 20 to 49 years. Despite the availability of BCG vaccination data and the mathematical models needed to compare these data with COVID-19 cases, our results show that, in geographic areas where BCG coverage was low, 50% presented a high prevalence of COVID-19 cases that were young; thus, low-coverage years were more affected.

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