GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

Background: With its simple library preparation and robust approach to genome reduction, genotyping-by-sequencing (GBS) is a flexible and cost-effective strategy for SNP discovery and genotyping, provided an appropriate reference genome is available. For resource-limited curation, research, and breeding programs of underutilized plant genetic resources, however, even low-depth references may not be within reach, despite declining sequencing costs. Such programs would find value in an open-source bioinformatics pipeline that can maximize GBS data usage and perform high-density SNP genotyping in the absence of a reference. Results: The GBS SNP-Calling Reference Optional Pipeline (GBS-SNP-CROP) developed and presented here adopts a clustering strategy to build a population-tailored “Mock Reference” from the same GBS data used for downstream SNP calling and genotyping. Designed for libraries of paired-end (PE) reads, GBS-SNP-CROP maximizes data usage by eliminating unnecessary data culling due to imposed read-length uniformity requirements. Using 150 bp PE reads from a GBS library of 48 accessions of tetraploid kiwiberry (Actinidia arguta), GBS-SNP-CROP yielded on average three times as many SNPs as TASSEL-GBS analyses (32 and 64 bp tag lengths) and over 18 times as many as TASSEL-UNEAK, with fewer genotyping errors in all cases, as evidenced by comparing the genotypic characterizations of biological replicates. Using the published reference genome of a related diploid species (A. chinensis), the reference-based version of GBS-SNP-CROP behaved similarly to TASSEL-GBS in terms of the number of SNPs called but had an improved read depth distribution and fewer genotyping errors. Our results also indicate that the sets of SNPs detected by the different pipelines above are largely orthogonal to one another; thus GBS-SNP-CROP may be used to augment the results of alternative analyses, whether or not a reference is available. Conclusions: By achieving high-density SNP genotyping in populations for which no reference genome is available, GBS-SNP-CROP is worth consideration by curators, researchers, and breeders of under-researched plant genetic resources. In cases where a reference is available, especially if from a related species or when the target population is particularly diverse, GBS-SNP-CROP may complement other reference-based pipelines by extracting more information per sequencing dollar spent. The current version of GBS-SNP-CROP is available at https://github.com/halelab/GBS-SNP-CROP.gi

Changing the Construct: Promoting Cross-Cultural Conversations in the Law School Classroom

Promoting cross-cultural awareness should be an important aspect of professionalism training in legal education. Cross-cultural awareness is essential to our students as they prepare to practice in an increasingly diverse domestic and international legal marketplace with competence and confidence. At the very least, faculty should help students avoid becoming the next lawyer or judge to be sanctioned for culturally off ensive behavior. More broadly, early and repeated faculty attention to cross-cultural issues can improve the learning environment for all students while they are still in law school. Although such training can be diffi cult and uncomfortable for both the professor and the students, it is far better for our students to make mistakes within the safety of the classroom, where the ramifications of their errors will not be career ending, and better if by learning from mistakes students develop cultural competencies that will serve them and their clients in their future careers. In short, promoting cross-cultural awareness is part of our obligation to educate our students in professionalism. Accordingly, this article provides a blueprint for incorporating these valuable but challenging discussions into the law school classroom. Part II of this article identifies the pedagogical and institutional advantages of infusing legal instruction with discussions designed to promote crosscultural awareness. Part III discusses how to create an effective and safe classroom environment for conducting cross-cultural discussions by assessing the classroom climate, establishing a respectful and approachable relationship with students, and developing the cultural literacy and emotional knowledge to lead cross-cultural conversations with sensitivity and openness. Part IV explores specific techniques and best practices for promoting cross-cultural conversations that raise or implicate diverse cultural assumptions and expectations. Part V suggests techniques for dealing with student resistance and classroom incivility, and Part VI concludes the article

Has a Higgs-flavon with a 750750 GeV mass been detected at the LHC13?

Higgs-flavon fields appear as a part of the Froggatt-Nielsen (FN) mechanism, which attempts to explain the hierarchy of Yukawa couplings. We explore the possibility that the 750 GeV diphoton resonance recently reported at the LHC13, could be identified with a low-scale Higgs-flavon field $H_F$ and find the region of the parameter space consistent with CMS and ATLAS data. It is found that the extra vector-like fermions of the ultraviolet completion of the FN mechanism are necessary in order to reproduce the observed signal. We consider a standard model (SM) extension that contains two Higgs doublets (a standard one and an inert one) and one complex FN singlet. The inert doublet includes a stable neutral boson, which provides a viable dark matter candidate, while the mixing of the standard doublet and the FN singlet induces flavor violation in the Higgs sector at the tree-level. Constraints on the parameters of the model are derived from the LHC Higgs data, which include the search for the lepton flavor violating decay of the SM Higgs boson $h\to \bar{\mu}\tau$. It is also found that in some region of the parameter space the model may give rise to a large branching ratio for the $H_F \to hh$ decay, of the order of 0.1, which could be searched for at the LHC.Comment: 18 pages, 7 Figures, includes updated files to match published versio

Topological defects in lattice models and affine Temperley-Lieb algebra

This paper is the first in a series where we attempt to define defects in critical lattice models that give rise to conformal field theory topological defects in the continuum limit. We focus mostly on models based on the Temperley-Lieb algebra, with future applications to restricted solid-on-solid (also called anyonic chains) models, as well as non-unitary models like percolation or self-avoiding walks. Our approach is essentially algebraic and focusses on the defects from two points of view: the "crossed channel" where the defect is seen as an operator acting on the Hilbert space of the models, and the "direct channel" where it corresponds to a modification of the basic Hamiltonian with some sort of impurity. Algebraic characterizations and constructions are proposed in both points of view. In the crossed channel, this leads us to new results about the center of the affine Temperley-Lieb algebra; in particular we find there a special subalgebra with non-negative integer structure constants that are interpreted as fusion rules of defects. In the direct channel, meanwhile, this leads to the introduction of fusion products and fusion quotients, with interesting mathematical properties that allow to describe representations content of the lattice model with a defect, and to describe its spectrum.Comment: 41