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Modeling a reactor's antineutrino flux spectrum is a critical step in studying its detector response. The first objective of this paper is to study the importance of fission product libraries in the construction of the antineutrino spectrum using the summation method and with various other corrections, including excited states in fission products, finite size, weak magnetism, and radiative corrections. We have used the ENDF/B-VIII.0 and JEFF-3.3 nuclear libraries as our base data to model the antineutrino spectrum. We have also included the total absorption gamma spectroscopy (TAGS) data, which is free from the pandemonium effect, when such data are available. Our analysis includes the newest TAGS data sets from Gombas et al. [Phys. Rev. C, Vol. 103, p. 35803 (2021)] with additions made after the Estienne et al. [EPJ Web Conf., Vol. 211, p. 01001 (2019)] reactor antineutrino spectra study involving TAGS data. The excited state correction has the highest impact on the antineutrino energy spectra, increasing the values 29% to 37% on average in the energy range of 0.5 to 2 MeV. This antineutrino spectra correction also shows an increase of 4.71% to 7.13% in the range of 0 to 2 MeV, with improving excited states using the TAGS data from published literature. Next, antineutrino spectra including the excited state correction using the Gross Theory causes reduction by 11.56% to 69.46% for all four fissionable isotopes in the range of 6 to 8 MeV. The finite size correction, radiative correction, and weak magnetism corrections cause no more than a 3.27% difference between the corrected and uncorrected spectra. We studied the impact of various corrections to the antineutrino spectra and quantified the improvements made in the antineutrino spectrum calculation due to these changes. However, we have not included forbidden decays to simplify the calculations. The second objective of this work is to determine the impact of spectrum improvements on the coherent-elastic-neutrino-nucleus-scatter (CEνNS)-based detector response because this detection mechanism is more sensitive to lower energy antineutrinos, as expected from a nuclear reactor. We calculate pulse height distributions of Ge- and Si-based CEνNS sensors assuming a 20-eV nuclear recoil threshold. Toward this objective, we formulate pulse height distribution probabilities for different incident antineutrino energies in Ge and Si for a 100-kg detector placed 10 m away from the 1-MW TRIGA reactor with a 20-eV nuclear recoil energy threshold. Our results show that the reaction rate with corrected spectra for a CEνNS-based natural Ge detector is 20.6 events/day and a natural Si detector is 7.18 events/day. The biggest impact on the reaction rates between 38% and 41% is observed due to the excited state corrections. To benchmark our results, we show excellent agreement with the previous antineutrino spectrum calculated by Huber [Phys. Rev. C, Vo. 84, p. 24617 (2011)] and Hayes et al. [Phys. Rev. Lett., Vol. 112, p. 202501 (2014)]. [ABSTRACT FROM AUTHOR]

SUMMARY: Sorghum is an important food and feed crop globally; its production is hampered by anthracnose disease caused by the fungal pathogen Colletotrichum sublineola (Cs). Here, we report identification and characterization of ANTHRACNOSE RESISTANCE GENE 2 (ARG2) encoding a nucleotide‐binding leucine‐rich repeat (NLR) protein that confers race‐specific resistance to Cs strains. ARG2 is one of a cluster of several NLR genes initially identified in the sorghum differential line SC328C that is resistant to some Cs strains. This cluster shows structural and copy number variations in different sorghum genotypes. Different sorghum lines carrying independent ARG2 alleles provided the genetic validation for the identity of the ARG2 gene. ARG2 expression is induced by Cs, and chitin induces ARG2 expression in resistant but not in susceptible lines. ARG2‐mediated resistance is accompanied by higher expression of defense and secondary metabolite genes at early stages of infection, and anthocyanin and zeatin metabolisms are upregulated in resistant plants. Interestingly, ARG2 localizes to the plasma membrane when transiently expressed in Nicotiana benthamiana. Importantly, ARG2 plants produced higher shoot dry matter than near‐isogenic lines carrying the susceptible allele suggesting an absence of an ARG2 associated growth trade‐off. Furthermore, ARG2‐mediated resistance is stable at a wide range of temperatures. Our observations open avenues for resistance breeding and for dissecting mechanisms of resistance. Significance Statement: Sorghum is a crop of global importance that is used for food, feed and biofuel. The crop feeds millions of people, especially small holder framers around the world. The productivity of sorghum is constrained by anthracnose diseases caused by the fungus Colletotrichum sublineola. Genetic resistance provides the most sustainable disease control method. We identified and characterized a sorghum anthracnose resistance gene encoding a nucleotide‐binding leucine‐rich repeat protein by exploring natural variation in the crop. Our findings will have significant implications for improvement of disease resistance in sorghum, as well as for future studies in the molecular genetics of pathogen resistance. [ABSTRACT FROM AUTHOR]

Genetic similarity matrices are commonly used to assess population substructure (PS) in genetic studies. Through simulation studies and by the application to whole-genome sequencing (WGS) data, we evaluate the performance of three genetic similarity matrices: the unweighted and weighted Jaccard similarity matrices and the genetic relationship matrix. We describe different scenarios that can create numerical pitfalls and lead to incorrect conclusions in some instances. We consider scenarios in which PS is assessed based on loci that are located across the genome ('globally') and based on loci from a specific genomic region ('locally'). We also compare scenarios in which PS is evaluated based on loci from different minor allele frequency bins: common (>5%), low-frequency (5–0.5%) and rare (<0.5%) single-nucleotide variations (SNVs). Overall, we observe that all approaches provide the best clustering performance when computed based on rare SNVs. The performance of the similarity matrices is very similar for common and low-frequency variants, but for rare variants, the unweighted Jaccard matrix provides preferable clustering features. Based on visual inspection and in terms of standard clustering metrics, its clusters are the densest and the best separated in the principal component analysis of variants with rare SNVs compared with the other methods and different allele frequency cutoffs. In an application, we assessed the role of rare variants on local and global PS, using WGS data from multiethnic Alzheimer's disease data sets and European or East Asian populations from the 1000 Genome Project. [ABSTRACT FROM AUTHOR]

Background: Seasonal influenza virus infection causes a range of disease severity, including lower respiratory tract infection with respiratory failure. We evaluated the association of common variants in interferon (IFN) regulatory genes with susceptibility to critical influenza infection in children.Methods: We performed targeted sequencing of 69 influenza-associated candidate genes in 348 children from 24 US centers admitted to the intensive care unit with influenza infection and lacking risk factors for severe influenza infection (PICFlu cohort, 59.4% male). As controls, whole genome sequencing from 675 children with asthma (CAMP cohort, 62.5% male) was compared. We assessed functional relevance using PICFlu whole blood gene expression levels for the gene and calculated IFN gene signature score.Results: Common variants in DDX58, encoding the retinoic acid-inducible gene I (RIG-I) receptor, demonstrated association above or around the Bonferroni-corrected threshold (synonymous variant rs3205166; intronic variant rs4487862). The intronic single-nucleotide polymorphism rs4487862 minor allele was associated with decreased DDX58 expression and IFN signature (P < .05 and P = .0009, respectively) which provided evidence supporting the genetic variants' impact on RIG-I and IFN immunity.Conclusions: We provide evidence associating common gene variants in DDX58 with susceptibility to severe influenza infection in children. RIG-I may be essential for preventing life-threatening influenza-associated disease. [ABSTRACT FROM AUTHOR]