TauDecay: a library to simulate polarized tau decays via FeynRules and MadGraph5

TauDecay is a library of helicity amplitudes to simulate polarized tau decays, constructed in the FeynRules and MadGraph5 framework. Together with the leptonic mode, the decay library includes the main hadronic modes, \tau \to \nu_{\tau}+\pi, 2\pi, and 3\pi, which are introduced as effective vertices by using FeynRules. The model file allows us to simulate tau decays when the on-shell tau production is kinematically forbidden. We also demonstrate that all possible correlations among the decay products of pair-produced taus through a Z boson and a scalar/pseudoscalar Higgs boson are produced automatically. The program has been tested carefully by making use of the standard tau decay library Tauola.Comment: 10 pages, 12 figures, 3 tables; v2: typo in Eq.(20b) corrected, references added, version accepted by EPJC. 'Note added' also included for the brief TauDecay instruction in MadGraph5_aMC@NL

Large linear magnetoresistance in Dirac semi-metal Cd3As2 with Fermi surfaces close to the Dirac points

We have investigated the magnetoresistive behavior of Dirac semi-metal Cd3As2 down to low temperatures and in high magnetic fields. A positive and linear magnetoresistance (LMR) as large as 3100% is observed in a magnetic field of 14 T, on high-quality single crystals of Cd3As2 with ultra-low electron density and large Lande g factor. Such a large LMR occurs when the magnetic field is applied perpendicular to both the current and the (100) surface, and when the temperature is low such that the thermal energy is smaller than the Zeeman splitting energy. Tilting the magnetic field or raising the temperature all degrade the LMR, leading to a less pronounced quadratic behavior. We propose that the phenomenon of LMR is related to the peculiar field-induced shifting/distortion of the helical electrons' Fermi surfaces in momentum space.Comment: 5 pages, 4 figure

The genome evolution and domestication of tropical fruit mango

Background: Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. Results: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes. Conclusions: Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces

Microscopic approach to current-driven domain wall dynamics

This review describes in detail the essential techniques used in microscopic theories on spintronics. We have investigated the domain wall dynamics induced by electric current based on the $s$-$d$ exchange model. The domain wall is treated as rigid and planar and is described by two collective coordinates: the position and angle of wall magnetization. The effect of conduction electrons on the domain wall dynamics is calculated in the case of slowly varying spin structure (close to the adiabatic limit) by use of a gauge transformation. The spin-transfer torque and force on the wall are expressed by Feynman diagrams and calculated systematically using non-equilibrium Green's functions, treating electrons fully quantum mechanically. The wall dynamics is discussed based on two coupled equations of motion derived for two collective coordinates. The force is related to electron transport properties, resistivity, and the Hall effect. Effect of conduction electron spin relaxation on the torque and wall dynamics is also studied.Comment: manucript accepted to Phys. Re

Waste prevention for sustainable resource and waste management

Although the 2Rs (reduce and reuse) are considered high-priority approaches, there has not been enough quantitative research on effective 2R management. The purpose of this paper is to provide information obtained through the International Workshop in Kyoto, Japan, on 11–13 November 2015, which included invited experts and researchers in several countries who were in charge of 3R policies, and an additional review of 245 previous studies. It was found that, regarding policy development, the decoupling between environmental pressures and economy growth was recognized as an essential step towards a sustainable society. 3R and resource management policies, including waste prevention, will play a crucial role. Approaches using material/substance flow analyses have become sophisticated enough to describe the fate of resources and/or hazardous substances based on human activity and the environment, including the final sink. Life-cycle assessment has also been developed to evaluate waste prevention activities. Regarding target products for waste prevention, food loss is one of the waste fractions with the highest priority because its countermeasures have significant upstream and downstream effects. Persistent organic pollutants and hazardous compounds should also be taken into account in the situation where recycling activities are globally widespread for the promotion of a material-cycling society

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN