Comprehensive analysis of the complete mitochondrial genome of Lilium tsingtauense reveals a novel multichromosome structure

KEY MESSAGE

Lilium tsingtauense mitogenome comprises 27 independent chromosome molecules, it undergoes frequent genomic recombination, and the rate of recombination and mutation between different repetitive sequences affects the formation of multichromosomal structures. Given the extremely large genome of Lily, which likely harbors additional genetic resources, it serves as an ideal material for studying the phylogenetic evolution of organisms. Although the Lilium chloroplast genome has been documented, the sequence of its mitochondrial genome (mitogenome) remains uncharted. Using BGI short reads and Nanopore long reads, we sequenced, assembled, and annotated the mitogenome of Lilium tsingtauense. This effort culminated in the characterization of Lilium's first complete mitogenome. Comparative analysis with other angiosperms revealed the unique multichromosomal structure of the L. tsingtauense mitogenome, spanning 1,125,108 bp and comprising 27 independent circular chromosomes. It contains 36 protein-coding genes, 12 tRNA genes, and 3 rRNA genes, with a GC content of 44.90%. Notably, three chromosomes in the L. tsingtauense mitogenome lack identifiable genes, hinting at the potential existence of novel genes and noncoding elements. The high degree of observed genome fragmentation implies frequent reorganization, with recombination and mutation rates among diverse repetitive sequences likely driving the formation of multichromosomal structures. Our comprehensive analysis, covering genome size, coding genes, structure, RNA editing, repetitive sequences, and sequence migration, sheds light on the evolutionary and molecular biology of multichromosomal mitochondria in Lilium. This high-quality mitogenome of L. tsingtauense not only enriches our understanding of multichromosomal mitogenomes but also establishes a solid foundation for future genome breeding and germplasm innovation in Lilium.

Genomic divergence and demographic history of Quercus aliena populations

BACKGROUND

Quercus aliena is a major montane tree species of subtropical and temperate forests in China, with important ecological and economic value. In order to reveal the species' population dynamics, genetic diversity, genetic structure, and association with mountain habitats during the evolutionary process, we re-sequenced the genomes of 72 Q. aliena individuals.

RESULTS

The whole chloroplast and nuclear genomes were used for this study. Phylogenetic analysis using the chloroplast genome dataset supported four clades of Q. aliena, while the nuclear dataset supported three major clades. Sex-biased dispersal had a critical role in causing discordance between the chloroplast and nuclear genomes. Population structure analysis showed two groups in Q. aliena. The effective population size sharply declined 1 Mya, coinciding with the Poyang Glaciation in Eastern China. Using genotype-climate association analyses, we found a positive correlation between allele frequency variation in SNPs and temperature, suggesting the species has the capacity to adapt to changing temperatures.

CONCLUSION

Overall, this study illustrates the genetic divergence, genomic variation, and evolutionary processes behind the demographic history of Q. aliena.

Genome-wide analysis of the heat shock transcription factor family reveals saline-alkali stress responses in Xanthoceras sorbifolium

The heat shock transcription factor (HSF) family is involved in regulating growth, development, and abiotic stress. The characteristics and biological functions of HSF family member in X. sorbifolium, an important oil and ornamental plant, have never been reported. In this study, 21 XsHSF genes were identified from the genome of X. sorbifolium and named XsHSF1-XsHSF21 based on their chromosomal positions. Those genes were divided into three groups, A, B, and C, containing 12, one, and eight genes, respectively. Among them, 20 XsHSF genes are located on 11 chromosomes. Protein structure analysis suggested that XsHSF proteins were conserved, displaying typical DNA binding domains (DBD) and oligomerization domains (OD). Moreover, HSF proteins within the same group contain specific motifs, such as motif 5 in the HSFC group. All XsHSF genes have one intron in the CDS region, except XsHSF1 which has two introns. Promoter analysis revealed that in addition to defense and stress responsiveness elements, some promoters also contained a MYB binding site and elements involved in multiple hormones responsiveness and anaerobic induction. Duplication analysis revealed that XsHSF1 and XsHSF4 genes were segmentally duplicated while XsHSF2, XsHSF9, and XsHSF13 genes might have arisen from transposition. Expression pattern analysis of leaves and roots following salt-alkali treatment using qRT-PCR indicated that five XsHSF genes were upregulated and one XsHSF gene was downregulated in leaves upon NaCl treatment suggesting these genes may play important roles in salt response. Additionally, the expression levels of most XsHSFs were decreased in leaves and roots following alkali-induced stress, indicating that those XsHSFs may function as negative regulators in alkali tolerance. MicroRNA target site prediction indicated that 16 of the XsHSF genes may be regulated by multiple microRNAs, for example XsHSF2 might be regulated by miR156, miR394, miR395, miR408, miR7129, and miR854. And miR164 may effect the mRNA levels of XsHSF3 and XsHSF17, XsHSF9 gene may be regulated by miR172. The expression trends of miR172 and miR164 in leaves and roots on salt treatments were opposite to the expression trend of XsHSF9 and XsHSF3 genes, respectively. Promoter analysis showed that XsHSFs might be involved in light and hormone responses, plant development, as well as abiotic stress responses. Our results thus provide an overview of the HSF family in X. sorbifolium and lay a foundation for future functional studies to reveal its roles in saline-alkali response.

Resequencing of Rosa rugosa accessions revealed the history of population dynamics, breed origin, and domestication pathways

BACKGROUND

Rosa rugosa is a shrub that originated in China and has economic and ecological value. However, during the development of R. rugosa, the genetic background was chaotic, and the genetic structure among different wild populations was unclear, as well as wild and cultivated accessions. Here, we report whole-genome resequencing of wild and cultivated R. rugosa accessions.

RESULTS

A total of 19,041,284 SNPs were identified in 188 R. rugosa accessions and 3 R. chinensis accessions by resequencing. Population genetic analysis revealed that cultivated and wild groups were separated very early. All R. rugosa accessions were divided into 8 categories based on genetic structure: (1) Weihai, Yantai, and Liaoning category, (2) Jilin category, and (3) Hammonasset category (above three are wild); (4) traditional varieties, (5) hybrids between R. rugosa and R. chinensis, (6) Zizhi Rose, (7) Kushui Rose, (8) hybrids between R. rugosa and R. multiflora. We found that the heterozygosity and genetic diversity of wild accessions were generally lower than those of cultivated individuals. The genes that were selected during cultivation were identified, and it was found that these genes were mainly related to environmental adaptation and growth.

CONCLUSIONS

The Jilin population was the oldest population and later migrated to Liaoning and then migrated to Yantai and Weihai by sea regression in the Bohai Basin. The Hammonasset naturalized population probably originated from the Jilin population and then experienced separate differentiation. The long-term asexual reproduction pattern of R. rugosa decreased genetic diversity in the wild population. During R. rugosa cultivation, the ancestors of the Jilin population were involved in breeding traditional varieties, after which almost no wild individuals were engaged in breeding. However, in recent decades, cross breeding of R. rugosa started the utilization of wild germplasms. In comparison, some other species play important roles in variety formation. Few genes related to economic traits were selected, suggesting no directional domestication in the R. rugosa cultivation process.

Sporogenesis, gametophyte development and embryogenesis in Glehnia littoralis

BACKGROUND

Glehnia littoralis is an economic herb with both medicinal and edible uses. It also has important ecological value and special phylogenetic status as it is a monotypic genus species distributing around beach. Little information on its reproductive biology has been reported so far, which has hindered conservation and application of this species. In this study, we observed morphological changes from buds emergence to seeds formation and internal changes during sporogenesis, gametophyte development and embryo and endosperm development of G. littoralis using paraffin-embedded-sectioning and stereo microscope.

RESULTS

The results showed that the stages of internal development events of G. littoralis corresponded to obvious external morphological changes, most of developmental features were consistent with other Apiaceae species. The development of male and female gametophytes was not synchronized in the same flower, however, exhibited temporal overlap. From mid-late April to mid-May, the anther primordial and ovule primordial developed into the trinucleate pollen grain and eight-nuclear embryo sac, respectively. From late-May to mid-July, the zygote developed into mature embryo. In addition, some defects in gynoecium or ovule development and abnormal embryo and endosperm development were found. We induced that the possible causes of abortion in G. littoralis were as follows: nutrient limitation, poor pollination and fertilization, and bad weather.

CONCLUSIONS

This study revealed the whole process and morphological characteristics of the development of reproductive organ in G. littoralis, which not only provided important data for the study of systematic and conservation biology, but also provided a theoretical basis for cross breeding.

The role and molecular mechanism of gut microbiota in Graves' orbitopathy

PURPOSE

Graves' orbitopathy (GO) is an autoimmune orbital disorder. Gut microbiota dysfunction plays a vital role in autoimmune diseases, including Graves' disease (GD) and GO. In the present study, we aimed to investigate the change of gut microbiota in GD/GO using mouse model.

METHODS

The murine model of GD/GO was established by the challenge of adenovirus expressing thyroid-stimulating hormone (TSH) receptor (TSHR) (Ad-TSHR). The histological changes of orbital and thyroid tissues were analyzed by hematoxylin and eosin (H&E), Masson staining, and immunohistochemistry (IHC) staining. The fecal samples were collected for 16S rRNA gene sequencing and bioinformatics analysis.

RESULTS

The GD/GO model was established successfully, as manifested as the broadened eyelid, exophthalmia and conjunctive redness, severe inflammatory infiltration among thyroid glands and between extraocular muscle space, hypertrophic extraocular muscles, elevated thyroxine (T4) and decreased TSH, and positive CD34, CD40, collagen I, and α-SMA staining. A total of 222 operational taxonomic units (OUTs) were overlapped between mice in the Ad-NC and Ad-TSHR groups. The microbial composition of the samples in the two groups was mainly Bacteroidia and Clostridia, and the Ad-NC group had a significantly lower content of Bacteroidia and higher content of Clostridia. KEGG orthology analysis results revealed differences in dehydrogenase, aspartic acid, bile acid, chalcone synthase, acetyltransferase, glutamylcyclotransferase, glycogenin, and 1-phosphatidylinositol-4-phosphate 5-kinase between two groups; enzyme commission (EC) analysis results revealed differences in several dehydrogenase, oxidase, thioxy/reductase between two groups; MetaCyc pathways analysis results revealed differences in isoleucine degradation, oxidation of C1 compounds, tricarboxylic acid (TCA) cycle IV, taurine degradation, and biosynthesis of paromamine, heme, colonic acid building blocks, butanediol, lysine/threonine/methionine, and histidine/purine/pyrimidine between two groups.

CONCLUSION

This study induced a mouse model of GD/GO by Ad-TSHR challenge, and gut microbiota characteristics were identified in the GD/GO mice. The Bacteroidia and Clostridia abundance was changed in the GD/GO mice. These findings may lay a solid experimental foundation for developing personalized treatment regimens for GD patients according to the individual gut microbiota. Given the potential impact of regional differences on intestinal microbiota, this study in China may provide a reference for the global overview of the gut-thyroid axis hypothesis.

Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus

Clematis is one of the large worldwide genera of the Ranunculaceae Juss. Family, with high ornamental and medicinal value. China is the modern distribution centre of Clematis with abundant natural populations. Due to the complexity and high morphological diversity of Clematis, the genus is difficult to classify systematically, and in particular, the phylogenetic position of the endangered Clematis acerifolia is highly controversial. The use of the mitochondrial complete genome is a powerful molecular method that is frequently used for inferring plants phylogenies. However, studies on Clematis mitogenome are rare, thus limiting our full understanding of its phylogeny and genome evolution. Here, we sequenced and annotated the C. acerifolia mt genome using Illumina short- and Nanopore long-reads, characterized the species first complete mitogenome, and performed a comparative phylogenetic analysis with its close relatives. The total length of the C. acerifolia mitogenome is 698,247 bp and the main structure is multi-branched (linear molecule 1 and circular molecule 2). We annotated 55 genes, including 35 protein-coding, 17 tRNA, and 3 rRNA genes. The C. acerifolia mitogenome has extremely unconserved structurally, with extensive sequence transfer between the chloroplast and mitochondrial organelles, sequence repeats, and RNA editing. The phylogenetic position of C. acerifolia was determined by constructing the species mitogenome with 24 angiosperms. Further, our C. acerifolia mitogenome characteristics investigation included GC contents, codon usage, repeats and synteny analysis. Overall, our results are expected to provide fundamental information for C. acerifolia mitogenome evolution and confirm the validity of mitochondrial analysis in determining the phylogenetic positioning of Clematis plants.

Genome-Wide Identification and Expression Profiling of Heat Shock Protein 20 Gene Family in Sorbus pohuashanensis (Hance) Hedl under Abiotic Stress

Small heat shock proteins (HSP20s) are a significant factor in plant growth and development in response to abiotic stress. In this study, we investigated the role of HSP20s' response to the heat stress of Sorbus pohuashanensis introduced into low-altitude areas. The HSP20 gene family was identified based on the genome-wide data of S. pohuashanensis, and the expression patterns of tissue specificity and the response to abiotic stresses were evaluated. Finally, we identified 38 HSP20 genes that were distributed on 16 chromosomes. Phylogenetic analysis of HSP20s showed that the closest genetic relationship to S. pohuashanensis (SpHSP20s) is Malus domestica, followed by Populus trichocarpa and Arabidopsis thaliana. According to phylogenetic analysis and subcellular localization prediction, the 38 SpHSP20s belonged to 10 subfamilies. Analysis of the gene structure and conserved motifs indicated that HSP20 gene family members are relatively conserved. Synteny analysis showed that the expansion of the SpHSP20 gene family was mainly caused by segmental duplication. In addition, many cis-acting elements connected with growth and development, hormones, and stress responsiveness were found in the SpHSP20 promoter region. Analysis of expression patterns showed that these genes were closely related to high temperature, drought, salt, growth, and developmental processes. These results provide information and a theoretical basis for the exploration of HSP20 gene family resources, as well as the domestication and genetic improvement of S. pohuashanensis.

A high-quality genome assembly and annotation of Quercus acutissima Carruth

INTRODUCTION

Quercus acutissima is an economic and ecological tree species often used for afforestation of arid and semi-arid lands and is considered as an excellent tree for soil and water conservation.

METHODS

Here, we combined PacBio long reads, Hi-C, and Illumina short reads to assemble Q. acutissima genome.

RESULTS

We generated a 957.1 Mb genome with a contig N50 of 1.2 Mb and scaffold N50 of 77.0 Mb. The repetitive sequences constituted 55.63% of the genome, among which long terminal repeats were the majority and accounted for 23.07% of the genome. Ab initio, homology-based and RNA sequence-based gene prediction identified 29,889 protein-coding genes, of which 82.6% could be functionally annotated. Phylogenetic analysis showed that Q. acutissima and Q. variabilis were differentiated around 3.6 million years ago, and showed no evidence of species-specific whole genome duplication.

CONCLUSION

The assembled and annotated high-quality Q. acutissima genome not only promises to accelerate the species molecular biology studies and breeding, but also promotes genome level evolutionary studies.

Genome-wide analysis of BURP genes and identification of a BURP-V gene RcBURP4 in Rosa chinensis

Nine RcBURPs have been identified in Rosa chinensis, and overexpression of RcBURP4 increased ABA, NaCl sensitivity, and drought tolerance in transgenic Arabidopsis. BURP proteins are unique to plants and may contribute greatly to growth, development, and stress responses of plants. Despite the vital role of BURP proteins, little is known about these proteins in rose (Rosa spp.). In the present study, nine genes belonging to the BURP family in R. chinensis were identified using multiple bioinformatic approaches against the rose genome database. The nine RcBURPs, with diverse structures, were located on all chromosomes of the rose genome, except for Chr2 and Chr3. Phylogenic analysis revealed that these RcBURPs can be classified into eight subfamilies, including BNM2-like, PG1β-like, USP-like, RD22-like, BURP-V, BURP-VI, BURP-VII, and BURP-VIII. Conserved motif and exon-intron analyses indicated a conserved pattern within the same subfamily. The presumed cis-regulatory elements (CREs) within the promoter region of each RcBURP were analyzed and the results showed that all RcBURPs contained different types of CREs, including abiotic stress-, light response-, phytohormones response-, and plant growth and development-related CREs. Transcriptomic analysis revealed that a BURP-V member, RcBURP4, was induced in rose leaves and roots under mild and severe drought treatments. We then overexpressed RcBURP4 in Arabidopsis and examined its role under abscisic acid (ABA), NaCl, polyethylene glycol (PEG), and drought treatments. Nine stress-responsive genes expression were changed in RcBURP4-overexpressing leaves and roots. Furthermore, RcBURP4-silenced rose plants exhibited decreased tolerance to dehydration. The results obtained from this study provide the first comprehensive overview of RcBURPs and highlight the importance of RcBURP4 in rose plant.

[A prospective cohort study on BMI levels and risk of acute pancreatitis]

Objective: To investigate the effects of body mass index (BMI) levels at different baseline on the risk of new-onset acute pancreatitis (AP). Methods: The subjects were from the Kailuan Study Cohort and divided into 3 groups according to baseline BMI levels: BMI<24 kg/m², normal weight; BMI 24-28 kg/m², overweight; BMI≥28 kg/m², obesity. The incidence of new-onset AP in these three groups was analyzed. The survival curve was plotted by Kaplan-Meier method, the cumulative incidence was calculated and tested by log-rank method. Multivariate Cox proportional hazards regression model was used to calculate HR of baseline BMI levels for AP. Results: A total of 123 841 subjects were included and followed up for (11.94±2.13) years, during which, 395 cases were found with AP. The incidence of AP was 2.67 per 10 000 person years in total population, and the incidences of AP were 2.20, 2.72 and 3.58 per 10 000 person-years in the normal, overweight and obesity groups, respectively. The cumulative incidences of AP was 0.32%, 0.40% and 0.49% in normal, overweight and obesity groups, respectively, which showed a significant inter-group difference by log-rank test (χ ²=13.17,P<0.01). The results of multivariable adjusted Cox proportional hazards regression model analysis indicated that obesity group (HR=1.45, 95%CI: 1.10-1.92) had a higher risk for AP compared with the normal BMI group. The subgroup analyses by age and sex showed that compared with the normal weight group,the HRs for AP in the obesity group was 1.58(95%CI:1.14-2.19) and 1.40(95%CI:1.03-1.90) among subjects younger than 60 years old and male subjects, respectively. After excluded onset AP within two years from baseline,with a control group from normal weight,the results of multivariate Cox proportional hazards regression model analysis indicated that the AP in the obesity group was 1.60 (95%CI: 1.18-2.15). Conclusion: Obesity may increase the risk of developing AP, particularly among young and middle-aged men.

Measurement of the Lund Jet Plane Using Charged Particles in 13 TeV Proton-Proton Collisions with the ATLAS Detector

The prevalence of hadronic jets at the LHC requires that a deep understanding of jet formation and structure is achieved in order to reach the highest levels of experimental and theoretical precision. There have been many measurements of jet substructure at the LHC and previous colliders, but the targeted observables mix physical effects from various origins. Based on a recent proposal to factorize physical effects, this Letter presents a double-differential cross-section measurement of the Lund jet plane using 139  fb^{-1} of sqrt[s]=13  TeV proton-proton collision data collected with the ATLAS detector using jets with transverse momentum above 675 GeV. The measurement uses charged particles to achieve a fine angular resolution and is corrected for acceptance and detector effects. Several parton shower Monte Carlo models are compared with the data. No single model is found to be in agreement with the measured data across the entire plane.

Measurement of Azimuthal Anisotropy of Muons from Charm and Bottom Hadrons in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

The elliptic flow of muons from the decay of charm and bottom hadrons is measured in pp collisions at sqrt[s]=13  TeV using a data sample with an integrated luminosity of 150  pb^{-1} recorded by the ATLAS detector at the LHC. The muons from heavy-flavor decay are separated from light-hadron decay muons using momentum imbalance between the tracking and muon spectrometers. The heavy-flavor decay muons are further separated into those from charm decay and those from bottom decay using the distance-of-closest-approach to the collision vertex. The measurement is performed for muons in the transverse momentum range 4-7 GeV and pseudorapidity range |η|<2.4. A significant nonzero elliptic anisotropy coefficient v_{2} is observed for muons from charm decays, while the v_{2} value for muons from bottom decays is consistent with zero within uncertainties.

Search for Magnetic Monopoles and Stable High-Electric-Charge Objects in 13 Tev Proton-Proton Collisions with the ATLAS Detector

A search for magnetic monopoles and high-electric-charge objects is presented using 34.4  fb^{-1} of 13 TeV pp collision data collected by the ATLAS detector at the LHC during 2015 and 2016. The considered signature is based upon high ionization in the transition radiation tracker of the inner detector associated with a pencil-shape energy deposit in the electromagnetic calorimeter. The data were collected by a dedicated trigger based on the tracker high-threshold hit capability. The results are interpreted in models of Drell-Yan pair production of stable particles with two spin hypotheses (0 and 1/2) and masses ranging from 200 to 4000 GeV. The search improves by approximately a factor of 5 the constraints on the direct production of magnetic monopoles carrying one or two Dirac magnetic charges and stable objects with electric charge in the range 20≤|z|≤60 and extends the charge range to 60<|z|≤100.

Observation of Electroweak Production of a Same-Sign W Boson Pair in Association with Two Jets in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

This Letter presents the observation and measurement of electroweak production of a same-sign W boson pair in association with two jets using 36.1  fb^{-1} of proton-proton collision data recorded at a center-of-mass energy of sqrt[s]=13  TeV by the ATLAS detector at the Large Hadron Collider. The analysis is performed in the detector fiducial phase-space region, defined by the presence of two same-sign leptons, electron or muon, and at least two jets with a large invariant mass and rapidity difference. A total of 122 candidate events are observed for a background expectation of 69±7 events, corresponding to an observed signal significance of 6.5 standard deviations. The measured fiducial signal cross section is σ^{fid}=2.89_{-0.48}^{+0.51}(stat)_{-0.28}^{+0.29}(syst)  fb.

Observation of Light-by-Light Scattering in Ultraperipheral Pb+Pb Collisions with the ATLAS Detector

This Letter describes the observation of the light-by-light scattering process, γγ→γγ, in Pb+Pb collisions at sqrt[s_{NN}]=5.02  TeV. The analysis is conducted using a data sample corresponding to an integrated luminosity of 1.73  nb^{-1}, collected in November 2018 by the ATLAS experiment at the LHC. Light-by-light scattering candidates are selected in events with two photons produced exclusively, each with transverse energy E_{T}^{γ}>3  GeV and pseudorapidity |η_{γ}|<2.4, diphoton invariant mass above 6 GeV, and small diphoton transverse momentum and acoplanarity. After applying all selection criteria, 59 candidate events are observed for a background expectation of 12±3 events. The observed excess of events over the expected background has a significance of 8.2 standard deviations. The measured fiducial cross section is 78±13(stat)±7(syst)±3(lumi)  nb.

Comparison of Fragmentation Functions for Jets Dominated by Light Quarks and Gluons from pp and Pb+Pb Collisions in ATLAS

Charged-particle fragmentation functions for jets azimuthally balanced by a high-transverse-momentum, prompt, isolated photon are measured in 25  pb^{-1} of pp and 0.49  nb^{-1} of Pb+Pb collision data at 5.02 TeV per nucleon pair recorded with the ATLAS detector at the Large Hadron Collider. The measurements are compared to predictions of Monte Carlo generators and to measurements of inclusively selected jets. In pp collisions, a different jet fragmentation function in photon-tagged events from that in inclusive jet events arises from the difference in fragmentation between light quarks and gluons. The ratios of the fragmentation functions in Pb+Pb events to that in pp events are used to explore the parton color-charge dependence of jet quenching in the hot medium. In relatively peripheral collisions, fragmentation functions exhibit a similar modification pattern for photon-tagged and inclusive jets. However, photon-tagged jets are observed to have larger modifications than inclusive jets in central Pb+Pb events.

Complete chloroplast genome of Prunus canescens: an endemic shrub in China

Prunus canescens is an endemic cherry species in China, which is distributed in Shaanxi, Gansu, Hubei, and Sichuan provinces of China. The chloroplast (cp) genome of P. canescens is 157,890 bp in size containing 125 unique genes, including 8 rRNA genes, 37 tRNA genes, and 80 protein-coding genes (PCGs). Phylogenetic analysis exhibited that P. canescens is most related to P. pseudocerasus.

Combination of Searches for Invisible Higgs Boson Decays with the ATLAS Experiment

Dark matter particles, if sufficiently light, may be produced in decays of the Higgs boson. This Letter presents a statistical combination of searches for H→invisible decays where H is produced according to the standard model via vector boson fusion, Z(ℓℓ)H, and W/Z(had)H, all performed with the ATLAS detector using 36.1  fb^{-1} of pp collisions at a center-of-mass energy of sqrt[s]=13  TeV at the LHC. In combination with the results at sqrt[s]=7 and 8 TeV, an exclusion limit on the H→invisible branching ratio of 0.26(0.17_{-0.05}^{+0.07}) at 95% confidence level is observed (expected).

Different genetic and morphological outcomes for phages targeted by single or multiple CRISPR-Cas spacers

CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against genetic invaders, such as bacteriophages. The systems integrate short sequences from the phage genome into the bacterial CRISPR array. These 'spacers' provide sequence-specific immunity but drive natural selection of evolved phage mutants that escape the CRISPR-Cas defence. Spacer acquisition occurs by either naive or primed adaptation. Naive adaptation typically results in the incorporation of a single spacer. By contrast, priming is a positive feedback loop that often results in acquisition of multiple spacers, which occurs when a pre-existing spacer matches the invading phage. We predicted that single and multiple spacers, representative of naive and primed adaptation, respectively, would cause differing outcomes after phage infection. We investigated the response of two phages, ϕTE and ϕM1, to the Pectobacterium atrosepticum type I-F CRISPR-Cas system and observed that escape from single spacers typically occurred via point mutations. Alternatively, phages escaped multiple spacers through deletions, which can occur in genes encoding structural proteins. Cryo-EM analysis of the ϕTE structure revealed shortened tails in escape mutants with tape measure protein deletions. We conclude that CRISPR-Cas systems can drive phage genetic diversity, altering morphology and fitness, through selective pressures arising from naive and primed acquisition events. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.

Search for the Production of a Long-Lived Neutral Particle Decaying within the ATLAS Hadronic Calorimeter in Association with a Z Boson from pp Collisions at sqrt[s]=13 TeV

This Letter presents a search for the production of a long-lived neutral particle (Z_{d}) decaying within the ATLAS hadronic calorimeter, in association with a standard model (SM) Z boson produced via an intermediate scalar boson, where Z→ℓ^{+}ℓ^{-} (ℓ=e, μ). The data used were collected by the ATLAS detector during 2015 and 2016 pp collisions with a center-of-mass energy of sqrt[s]=13  TeV at the Large Hadron Collider and correspond to an integrated luminosity of 36.1±0.8  fb^{-1}. No significant excess of events is observed above the expected background. Limits on the production cross section of the scalar boson times its decay branching fraction into the long-lived neutral particle are derived as a function of the mass of the intermediate scalar boson, the mass of the long-lived neutral particle, and its cτ from a few centimeters to one hundred meters. In the case that the intermediate scalar boson is the SM Higgs boson, its decay branching fraction to a long-lived neutral particle with a cτ approximately between 0.1 and 7 m is excluded with a 95% confidence level up to 10% for m_{Z_{d}} between 5 and 15 GeV.

Abstract OT2-08-01: Personalized breast cancer screening in a population based study: Women Informed to Screen Depending On Measures of risk (WISDOM)

Background: WISDOM is a 100,000 healthy women preference-tolerant, pragmatic study comparing annual to personalized risk-based breast screening. The novelty of WISDOM personalized screening is the integration of previously validated genetic and clinical risk factors (age, family history, breast biopsy results, ethnicity, mammographic density) into a single risk assessment model that directs the starting age, timing, and frequency of screening. The goal of WISDOM is to determine if personalized screening, compared to annual screening, is as safe, less morbid, enables prevention, and is preferred by women. The study is registered on ClinicalTrials.gov, NCT02620852.

Methods: Women aged 40-74 years with no history of breast cancer or DCIS, and no previous double mastectomy can join the study online at wisdomstudy.org. Participants can elect randomization or self-select a study arm, and provide electronic consent and Release for Medical Information using DocuSign. For all participants, 5-year risk of developing breast cancer is calculated according to the Breast Cancer Screening Consortium (BCSC) model. Participants in the personalized arm undergo panel-based mutation testing, and their 5-year risk is calculated using the BCSC score combined with a Polygenic Risk Score (BCSC-PRS) that includes 75 single nucleotide polymorphisms (SNPs, increase to 229) known to increase breast cancer risk. SNPs and mutations (BRCA1, BRCA2, TP53, PTEN, STK11, CDH1, ATM, PALB2, and CHEK2) are assessed by saliva-based testing through Color Genomics. 5-year risk level thresholds are used to stratify for low-, moderate- and high risk. Risk stratification determines age to start, stop, and frequency of screening.

Enrollment: As of July 2018, the WISDOM study is open to all eligible women in California, North Dakota, South Dakota, Minnesota and Iowa. To date, 23,329 eligible women have registered and 14,393 women have consented to participate in the trial. We analyzed 3,255 participants who have completed risk assessment in the personalized arm. The median age was 56 years. 82% were Caucasian, 1% African-American, and 6% Asian. 9% self-reported as Hispanic. We are partnering with health insurers and self-insured companies using coverage with evidence progression. To strengthen generalizability, we are expanding to other states. WISDOM enrollment will continue past 2019.

Feasibility: To evaluate the addition of PRS, we used paired statistical tests (McNemar) to compare the distributions of BCSC, and BCSC-PRS risk estimates around low-risk (&lt;1.3%), and very-high risk (&gt;6%) thresholds, the latter corresponding to 5-year risk of a BRCA mutation carrier. The median 5-year risk was 1.5% (IQR 1.0-2.1%) using the BCSC model, and 1.4% (IQR 0.8-2.5%) using the BCSC-PRS model. The BCSC-PRS model classified more women into the low (&lt;1%) and very high (≥6%) risk categories compared to the BCSC model (p &lt; 0.001).

Conclusions: Our findings demonstrate that incorporating genetic variants into a validated clinical model is feasible and impacts risk classification compared to a model without genetic risk factors. Results at 5 years will reveal if this classification improves healthcare value by reducing screen volumes and costs without jeopardizing outcomes.

Citation Format: Acerbi I, Shieh Y, Madlensky L, Tice J, Ziv E, Eklund M, Blanco A, DeRosa D, Tong B, Goodman D, Nassereddine L, Anderson N, Harvey H, Layton T, Park HL, Petruse A, Stewart S, Wernisch J, Risty L, Koenig B, Sarrafan S, Firouzian R, Kaplan C, Hiatt R, Parker BA, Wenger N, Lee V, Heditsian D, Brain S, Stover Fiscalini A, Borowsky AD, Anton-Culver H, Naeim A, Kaster A, Talley M, van 't Veer LJ, LaCroix A, Wisdom Study and Athena Breast Health Network Investigators and Advocate Partners, Esserman LJ. Personalized breast cancer screening in a population based study: Women Informed to Screen Depending On Measures of risk (WISDOM) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr OT2-08-01.

Search for doubly charged scalar bosons decaying into same-sign W boson pairs with the ATLAS detector

A search for doubly charged scalar bosons decaying into W boson pairs is presented. It uses a data sample from proton-proton collisions corresponding to an integrated luminosity of 36.1 fb - 1 collected by the ATLAS detector at the LHC at a centre-of-mass energy of 13 TeV in 2015 and 2016. This search is guided by a model that includes an extension of the Higgs sector through a scalar triplet, leading to a rich phenomenology that includes doubly charged scalar bosons H ± ± . Those bosons are produced in pairs in proton-proton collisions and decay predominantly into electroweak gauge bosons H ± ± → W ± W ± . Experimental signatures with several leptons, missing transverse energy and jets are explored. No significant deviations from the Standard Model predictions are found. The parameter space of the benchmark model is excluded at 95% confidence level for H ± ± bosons with masses between 200 and 220 GeV.

Erratum to: Measurement of the W boson polarisation in t t ¯ events from pp collisions at s = 8 TeV in the lepton + jets channel with ATLAS

[This corrects the article DOI: 10.1140/epjc/s10052-017-4819-4.].

Search for Higgs boson pair production in the γ γ W W ∗ channel using pp collision data recorded at s = 13 TeV with the ATLAS detector

Searches for non-resonant and resonant Higgs boson pair production are performed in the γ γ W W ∗ channel with the final state of γ γ ℓ ν j j using 36.1  fb - 1 of proton-proton collision data recorded at a centre-of-mass energy ofs = 13 TeV by the ATLAS detector at the Large Hadron Collider. No significant deviation from the Standard Model prediction is observed. A 95% confidence-level observed upper limit of 7.7 pb is set on the cross section for non-resonant production, while the expected limit is 5.4 pb. A search for a narrow-width resonance X decaying to a pair of Standard Model Higgs bosons HH is performed with the same set of data, and the observed upper limits on σ ( p p → X ) × B ( X → H H ) range between 40.0 and 6.1 pb for masses of the resonance between 260 and 500 GeV, while the expected limits range between 17.6 and 4.4 pb. When deriving the limits above, the Standard Model branching ratios of the H → γ γ and H → W W ∗ are assumed.

Measurement of the azimuthal anisotropy of charged particles produced in s NN = 5.02 TeV Pb+Pb collisions with the ATLAS detector

Measurements of the azimuthal anisotropy in lead-lead collisions ats NN = 5.02 TeV are presented using a data sample corresponding to 0.49nb - 1 integrated luminosity collected by the ATLAS experiment at the LHC in 2015. The recorded minimum-bias sample is enhanced by triggers for "ultra-central" collisions, providing an opportunity to perform detailed study of flow harmonics in the regime where the initial state is dominated by fluctuations. The anisotropy of the charged-particle azimuthal angle distributions is characterized by the Fourier coefficients, v 2 - v 7 , which are measured using the two-particle correlation, scalar-product and event-plane methods. The goal of the paper is to provide measurements of the differential as well as integrated flow harmonics v n over wide ranges of the transverse momentum, 0.5  < p T <  60 GeV, the pseudorapidity, | η | <  2.5, and the collision centrality 0-80%. Results from different methods are compared and discussed in the context of previous and recent measurements in Pb+Pb collisions ats NN = 2.76  TeV and 5.02  TeV . In particular, the shape of the p T dependence of elliptic or triangular flow harmonics is observed to be very similar at different centralities after scaling the v n and p T values by constant factors over the centrality interval 0-60% and the p T range 0.5  < p T <  5 GeV.

Search for electroweak production of supersymmetric particles in final states with two or three leptons at s = 13 TeV with the ATLAS detector

A search for the electroweak production of charginos, neutralinos and sleptons decaying into final states involving two or three electrons or muons is presented. The analysis is based on 36.1 fb- 1 ofs = 13  TeV proton-proton collisions recorded by the ATLAS detector at the Large Hadron Collider. Several scenarios based on simplified models are considered. These include the associated production of the next-to-lightest neutralino and the lightest chargino, followed by their decays into final states with leptons and the lightest neutralino via either sleptons or Standard Model gauge bosons; direct production of chargino pairs, which in turn decay into leptons and the lightest neutralino via intermediate sleptons; and slepton pair production, where each slepton decays directly into the lightest neutralino and a lepton. No significant deviations from the Standard Model expectation are observed and stringent limits at 95% confidence level are placed on the masses of relevant supersymmetric particles in each of these scenarios. For a massless lightest neutralino, masses up to 580 GeV are excluded for the associated production of the next-to-lightest neutralino and the lightest chargino, assuming gauge-boson mediated decays, whereas for slepton-pair production masses up to 500 GeV are excluded assuming three generations of mass-degenerate sleptons.

Operation and performance of the ATLAS Tile Calorimeter in Run 1

The Tile Calorimeter is the hadron calorimeter covering the central region of the ATLAS experiment at the Large Hadron Collider. Approximately 10,000 photomultipliers collect light from scintillating tiles acting as the active material sandwiched between slabs of steel absorber. This paper gives an overview of the calorimeter's performance during the years 2008-2012 using cosmic-ray muon events and proton-proton collision data at centre-of-mass energies of 7 and 8 TeV with a total integrated luminosity of nearly 30 fb - 1 . The signal reconstruction methods, calibration systems as well as the detector operation status are presented. The energy and time calibration methods performed excellently, resulting in good stability of the calorimeter response under varying conditions during the LHC Run 1. Finally, the Tile Calorimeter response to isolated muons and hadrons as well as to jets from proton-proton collisions is presented. The results demonstrate excellent performance in accord with specifications mentioned in the Technical Design Report.

Combination of the Searches for Pair-Produced Vectorlike Partners of the Third-Generation Quarks at sqrt[s]=13 TeV with the ATLAS Detector

A combination of the searches for pair-produced vectorlike partners of the top and bottom quarks in various decay channels (T→Zt/Wb/Ht, B→Zb/Wt/Hb) is performed using 36.1  fb^{-1} of pp collision data at sqrt[s]=13  TeV with the ATLAS detector at the Large Hadron Collider. The observed data are found to be in good agreement with the standard model background prediction in all individual searches. Therefore, combined 95% confidence-level upper limits are set on the production cross section for a range of vectorlike quark scenarios, significantly improving upon the reach of the individual searches. Model-independent limits are set assuming the vectorlike quarks decay to standard model particles. A singlet T is excluded for masses below 1.31 TeV and a singlet B is excluded for masses below 1.22 TeV. Assuming a weak isospin (T,B) doublet and |V_{Tb}|≪|V_{tB}|, T and B masses below 1.37 TeV are excluded.

Observation of Centrality-Dependent Acoplanarity for Muon Pairs Produced via Two-Photon Scattering in Pb+Pb Collisions at sqrt[s_{NN}]=5.02 TeV with the ATLAS Detector

This Letter presents a measurement of γγ→μ^{+}μ^{-} production in Pb+Pb collisions recorded by the ATLAS detector at the Large Hadron Collider at sqrt[s_{NN}]=5.02  TeV with an integrated luminosity of 0.49  nb^{-1}. The azimuthal angle and transverse momentum correlations between the muons are measured as a function of collision centrality. The muon pairs are produced from γγ through the interaction of the large electromagnetic fields of the nuclei. The contribution from background sources of muon pairs is removed using a template fit method. In peripheral collisions, the muons exhibit a strong back-to-back correlation consistent with previous measurements of muon pair production in ultraperipheral collisions. The angular correlations are observed to broaden significantly in central collisions. The modifications are qualitatively consistent with rescattering of the muons while passing through the hot matter produced in the collision.

Search for Resonant and Nonresonant Higgs Boson Pair Production in the bb[over ¯]τ^{+}τ^{-} Decay Channel in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

A search for resonant and nonresonant pair production of Higgs bosons in the bb[over ¯]τ^{+}τ^{-} final state is presented. The search uses 36.1  fb^{-1} of pp collision data with sqrt[s]=13  TeV recorded by the ATLAS experiment at the LHC in 2015 and 2016. Decays of the τ-lepton pairs with at least one τ lepton decaying to final states with hadrons and a neutrino are considered. No significant excess above the expected background is observed in the data. The cross-section times branching ratio for nonresonant Higgs boson pair production is constrained to be less than 30.9 fb, 12.7 times the standard model expectation, at 95% confidence level. The data are also analyzed to probe resonant Higgs boson pair production, constraining a model with an extended Higgs sector based on two doublets and a Randall-Sundrum bulk graviton model. Upper limits are placed on the resonant Higgs boson pair production cross-section times branching ratio, excluding resonances X in the mass range 305  GeV<m_{X}<402  GeV in the simplified hMSSM minimal supersymmetric model for tanβ=2 and excluding bulk Randall-Sundrum gravitons G_{KK} in the mass range 325  GeV<m_{G_{KK}}<885  GeV for k/M[over ¯]_{Pl}=1.

Performance of missing transverse momentum reconstruction with the ATLAS detector using proton-proton collisions at s = 13 TeV

The performance of the missing transverse momentum ( E T miss ) reconstruction with the ATLAS detector is evaluated using data collected in proton-proton collisions at the LHC at a centre-of-mass energy of 13 TeV in 2015. To reconstruct E T miss , fully calibrated electrons, muons, photons, hadronically decaying τ -leptons , and jets reconstructed from calorimeter energy deposits and charged-particle tracks are used. These are combined with the soft hadronic activity measured by reconstructed charged-particle tracks not associated with the hard objects. Possible double counting of contributions from reconstructed charged-particle tracks from the inner detector, energy deposits in the calorimeter, and reconstructed muons from the muon spectrometer is avoided by applying a signal ambiguity resolution procedure which rejects already used signals when combining the various E T miss contributions. The individual terms as well as the overall reconstructed E T miss are evaluated with various performance metrics for scale (linearity), resolution, and sensitivity to the data-taking conditions. The method developed to determine the systematic uncertainties of the E T miss scale and resolution is discussed. Results are shown based on the full 2015 data sample corresponding to an integrated luminosity of 3.2 fb - 1 .

Measurement of colour flow using jet-pull observables in t t ¯ events with the ATLAS experiment at s = 13 TeV

Previous studies have shown that weighted angular moments derived from jet constituents encode the colour connections between partons that seed the jets. This paper presents measurements of two such distributions, the jet-pull angle and jet-pull magnitude, both of which are derived from the jet-pull angular moment. The measurement is performed in t t ¯ events with one leptonically decaying W boson and one hadronically decaying W boson, using 36.1 fb - 1 of pp collision data recorded by the ATLAS detector ats = 13 TeV delivered by the Large Hadron Collider. The observables are measured for two dijet systems, corresponding to the colour-connected daughters of the W boson and the two b-jets from the top-quark decays, which are not expected to be colour connected. To allow the comparison of the measured distributions to colour model predictions, the measured distributions are unfolded to particle level, after correcting for experimental effects introduced by the detector. While good agreement can be found for some combinations of predictions and observables, none of the predictions describes the data well across all observables.

Probing the Quantum Interference between Singly and Doubly Resonant Top-Quark Production in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

This Letter presents a normalized differential cross-section measurement in a fiducial phase-space region where interference effects between top-quark pair production and associated production of a single top quark with a W boson and a b-quark are significant. Events with exactly two leptons (ee, μμ, or eμ) and two b-tagged jets that satisfy a multiparticle invariant mass requirement are selected from 36.1  fb^{-1} of proton-proton collision data taken at sqrt[s]=13  TeV with the ATLAS detector at the LHC in 2015 and 2016. The results are compared with predictions from simulations using various strategies for the interference. The standard prescriptions for interference modeling are significantly different from each other but are within 2σ of the data. State-of-the-art predictions that naturally incorporate interference effects provide the best description of the data in the measured region of phase space most sensitive to these effects. These results provide an important constraint on interference models and will guide future model development and tuning.

Prompt and non-prompt J / ψ elliptic flow in Pb+Pb collisions at s NN = 5.02 Tev with the ATLAS detector

The elliptic flow of prompt and non-prompt J / ψ was measured in the dimuon decay channel in Pb+Pb collisions ats NN = 5.02   TeV with an integrated luminosity of 0.42 nb - 1 with the ATLAS detector at the LHC. The prompt and non-prompt signals are separated using a two-dimensional simultaneous fit of the invariant mass and pseudo-proper decay time of the dimuon system from the J / ψ decay. The measurement is performed in the kinematic range of dimuon transverse momentum and rapidity 9 < p T < 30   GeV , | y | < 2 , and 0-60% collision centrality. The elliptic flow coefficient, v 2 , is evaluated relative to the event plane and the results are presented as a function of transverse momentum, rapidity and centrality. It is found that prompt and non-prompt J / ψ mesons have non-zero elliptic flow. Prompt J / ψ v 2 decreases as a function of p T , while for non-prompt J / ψ it is, with limited statistical significance, consistent with a flat behaviour over the studied kinematic region. There is no observed dependence on rapidity or centrality.

Prompt and non-prompt J / ψ and ψ ( 2 S ) suppression at high transverse momentum in 5.02 TeV Pb+Pb collisions with the ATLAS experiment

A measurement of J / ψ and ψ ( 2 S ) production is presented. It is based on a data sample from Pb+Pb collisions at s NN = 5.02 TeV and pp collisions at s = 5.02 TeV recorded by the ATLAS detector at the LHC in 2015, corresponding to an integrated luminosity of 0.42 nb - 1 and 25 pb - 1 in Pb+Pb and pp, respectively. The measurements of per-event yields, nuclear modification factors, and non-prompt fractions are performed in the dimuon decay channel for 9 < p T μ μ < 40 GeV in dimuon transverse momentum, and - 2 < y μ μ < 2 in rapidity. Strong suppression is found in Pb+Pb collisions for both prompt and non-prompt J / ψ , increasing with event centrality. The suppression of prompt ψ ( 2 S ) is observed to be stronger than that of J / ψ , while the suppression of non-prompt ψ ( 2 S ) is equal to that of the non-prompt J / ψ within uncertainties, consistent with the expectation that both arise from b-quarks propagating through the medium. Despite prompt and non-prompt J / ψ arising from different mechanisms, the dependence of their nuclear modification factors on centrality is found to be quite similar.

Measurement of the Soft-Drop Jet Mass in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

Jet substructure observables have significantly extended the search program for physics beyond the standard model at the Large Hadron Collider. The state-of-the-art tools have been motivated by theoretical calculations, but there has never been a direct comparison between data and calculations of jet substructure observables that are accurate beyond leading-logarithm approximation. Such observables are significant not only for probing the collinear regime of QCD that is largely unexplored at a hadron collider, but also for improving the understanding of jet substructure properties that are used in many studies at the Large Hadron Collider. This Letter documents a measurement of the first jet substructure quantity at a hadron collider to be calculated at next-to-next-to-leading-logarithm accuracy. The normalized, differential cross section is measured as a function of log_{10}ρ^{2}, where ρ is the ratio of the soft-drop mass to the ungroomed jet transverse momentum. This quantity is measured in dijet events from 32.9  fb^{-1} of sqrt[s]=13  TeV proton-proton collisions recorded by the ATLAS detector. The data are unfolded to correct for detector effects and compared to precise QCD calculations and leading-logarithm particle-level Monte Carlo simulations.

Search for Low-Mass Dijet Resonances Using Trigger-Level Jets with the ATLAS Detector in pp Collisions at sqrt[s]=13 TeV

Searches for dijet resonances with sub-TeV masses using the ATLAS detector at the Large Hadron Collider can be statistically limited by the bandwidth available to inclusive single-jet triggers, whose data-collection rates at low transverse momentum are much lower than the rate from standard model multijet production. This Letter describes a new search for dijet resonances where this limitation is overcome by recording only the event information calculated by the jet trigger algorithms, thereby allowing much higher event rates with reduced storage needs. The search targets low-mass dijet resonances in the range 450-1800 GeV. The analyzed data set has an integrated luminosity of up to 29.3  fb^{-1} and was recorded at a center-of-mass energy of 13 TeV. No excesses are found; limits are set on Gaussian-shaped contributions to the dijet mass distribution from new particles and on a model of dark-matter particles with axial-vector couplings to quarks.