Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast

Gene expression varies between individuals and corresponds to a key step linking genotypes to phenotypes. However, our knowledge regarding the species-wide genetic control of protein abundance, including its dependency on transcript levels, is very limited. Here, we have determined quantitative proteomes of a large population of 942 diverse natural Saccharomyces cerevisiae yeast isolates. We found that mRNA and protein abundances are weakly correlated at the population gene level. While the protein co-expression network recapitulates major biological functions, differential expression patterns reveal proteomic signatures related to specific populations. Comprehensive genetic association analyses highlight that genetic variants associated with variation in protein (pQTL) and transcript (eQTL) levels poorly overlap (3.6%). Our results demonstrate that transcriptome and proteome are governed by distinct genetic bases, likely explained by protein turnover. It also highlights the importance of integrating these different levels of gene expression to better understand the genotype-phenotype relationship.

Highlights

At the level of individual genes, the abundance of transcripts and proteins is weakly correlated within a species ( ρ = 0.165). While the proteome is not imprinted by population structure, co-expression patterns recapitulate the cellular functional landscapeWild populations exhibit a higher abundance of respiration-related proteins compared to domesticated populationsLoci that influence protein abundance differ from those that impact transcript levels, likely because of protein turnover.

POS1547-HPR CREATION OF A MULTI-DISCIPLINARY TEAM (MDT) RHEUMATOLOGY CLINIC AT UNIVERSITY COLLEGE LONDON HOSPITAL (UCLH) TO TACKLE THE BACKLOG OF PATIENTS WAITING FOR TREATMENT AS A RESULT OF THE COVID-19 PANDEMIC

Background

Covid-19 has consumed hospital resources since January 2020. In the UK, routine care has been disrupted with an estimated 30 million fewer outpatient attendances (2020/21) and over 6 million patients waiting for consultant led care (1). The British Society for Rheumatology ‘Rheumatology Workforce: a crisis in numbers (2021)’ highlights the challenges facing National Health Service rheumatology departments in managing rising caseloads (2). In 2021, UCLH wait time for follow up rheumatology appointments was 9 months. We were inundated with patients requiring urgent treatment. Innovative ways of running outpatients were required which led to the formation of an MDT clinic.

Objectives

Create a Rheumatology MDT clinic to:

Reduce follow up time

Increase clinic capacity

Reduce number of hospital attendances

Add value to each clinic encounter

Methods

The consultant lead identified an existing clinical nurse specialist (CNS) interested in supporting the MDT. With a UCLH Outpatient Transformation grant of £15,000 we recruited an advanced physiotherapy practitioner (APP) and administrator for a 6 month trial period. Managerial support was provided by the board. We met weekly to agree aims and allocate responsibilities. We did the following:

•Reviewed clinic lists for 6 months to identify duplicate appointments.

•Identified patients with CNS and consultant follow up scheduled in a short time frame and cancelled unnecessary appointments.

•Reviewed the clinic list weekly to identify patients suitable for APP management. This allowed overbooking of urgent cases.

•Embedded hand ultrasound appointments in the clinic template.

•Created CNS ‘Zoom’ virtual drop-ins for routine enquiries to reduce the administrative burden of patient emails/phone calls occurring outside the clinic.

•Organised patient participation sessions to help shape the service and collected patient feedback questionnaires.

Results

We reduced our waiting time for follow up appointments from 9 months to 2 months. Pre-MDT the average wait from consultant referral to physiotherapist appointment was 55 days. The MDT allows for same day assessment (reducing 2-3 patient journeys a clinic) and where suitable, facilitates discharge or onwards referral to the appropriate service i.e. pain management, hand therapy, APP-led hypermobility programme. A dedicated MDT CNS has shortened treatment times, reduced email traffic between CNS and consultant and allows for same day, joint decision making resulting in fewer appointments. Patients welcomed the Zoom sessions as an efficient, reliable method of raising concerns/queries. Our administrator helps to facilitate communication between patients and clinicians and streamline MDT processes. Embedding point of care ultrasound reduces hospital visits and enhances treatment decision making thereby reducing follow up attendances.

Conclusion

Our MDT model has reduced waiting lists, decreased treatment delays and cut the number of hospital visits. Performing ultrasound in clinic helped prevent patients being sent for scans at private providers. This cost saving likely covers the APP, ensuring the project is close to cost neutral. Shared decision making added value to outpatient attendances, reflected in patients positive feedback. The MDT enhances the role of APP and CNS, utilising their unique skill set. Administrative support is crucial, enhances team working and places added value on this often underappreciated role. We encourage other Rheumatology departments to adopt an MDT approach to tackle the backlog of patients awaiting treatment, add value to clinic encounters and maximise the skill set of clinicians involved in patient care.

References

[1]NHS backlog data analysis. British Medical Association. Online; NHS backlog data analysis (bma.org.uk)

[2]Rheumatology workforce: a crisis in numbers. British Society for Rheumatology. Workforce Policy Report 2021. BSR-workforce-report-crisis-numbers.pdf (rheumatology.org.uk)

Acknowledgements

I would like to thank the UCLH Outpatient Transformation Team for their support and funding to carry out this pilot project.

Disclosure of Interests

None declared

Laboratory biomarkers associated with COVID-19 severity and management

The heterogeneous disease course of COVID-19 is unpredictable, ranging from mild self-limiting symptoms to cytokine storms, acute respiratory distress syndrome (ARDS), multi-organ failure and death. Identification of high-risk cases will enable appropriate intervention and escalation. This study investigates the routine laboratory tests and cytokines implicated in COVID-19 for their potential application as biomarkers of disease severity, respiratory failure and need of higher-level care.

From analysis of 203 samples, CRP, IL-6, IL-10 and LDH were most strongly correlated with the WHO ordinal scale of illness severity, the fraction of inspired oxygen delivery, radiological evidence of ARDS and level of respiratory support (p ≤ 0.001). IL-6 levels of ≥3.27 pg/ml provide a sensitivity of 0.87 and specificity of 0.64 for a requirement of ventilation, and a CRP of ≥37 mg/l of 0.91 and 0.66.

Reliable stratification of high-risk cases has significant implications on patient triage, resource management and potentially the initiation of novel therapies in severe patients.

AB0501 THREE CASES OF VERTEBRAL ARTERITIS IDENTIFIED ON FDG-PET IN PATIENTS WITH SUSPECTED GCA AT UNIVERSITY COLLEGE LONDON HOSPITAL (UCLH)

Background:

Giant cell arteritis (GCA) may affect both cranial and extra-cranial vessels; where the latter occurs, it can be termed large-vessel GCA (LV-GCA). Large vessel involvement is common: histological evidence has been seen in 80% of autopsies of patients with known GCA, and imaging studies suggest large vessel involvement in over 80%1. LV-GCA is important to diagnose due to the risks of vascular complications such as occlusion and ischaemic stroke. The clinical diagnosis can be challenging, and the American College of Rheumatology (ACR) GCA classification criteria often underperform in cases of LV-GCA1. F-fluorodeoxyglucose positron emission tomography (FDG-PET) has been found to be useful in the detection of extra-cranial involvement to support the diagnosis of LV-GCA.2

Objectives:

To appreciate the variability in presentation of cases of LV-GCA, and to further characterise a subgroup of patients with vertebral arteritis.

To explore the use of FDG-PET imaging in GCA patients in addition to or in place of traditional diagnostic tools (temporal artery ultrasound / biopsy).

Methods:

Through evaluation of the new GCA fast-track pathway implemented at UCLH, a subgroup of patients diagnosed with vertebral arteritis was identified. The history and presentation of these patients were analysed.

Results:

Three patients were diagnosed with vertebral arteritis. All three were male, Caucasian and aged over 70. All were investigated for GCA due to a history of severe headache (frontal in one, occipital in one, bi-temporal in one) with associated red flag symptoms. Two had a history of jaw claudication and visual disturbances (unilateral visual loss in one, transient diplopia in the other). Both of these patients had positive temporal artery biopsies. The third patient had no ischaemic symptoms but a strong history of prominent polymyalgic features and a positive temporal artery ultrasound. Inflammatory markers were raised in two, and normal in one, of the patients. Only one had systemic symptoms (weight loss). All three proceeded to FDG-PET scans which showed vertebral arteritis and were commenced on immunosuppressive treatment.

Conclusion:

The cases discussed illustrate the heterogeneity of the presentation of LV-GCA, and the diagnostic challenge this poses. FDG-PET imaging is useful in confirming extra-cranial involvement and therefore guiding treatment.

References:

[1]Large-vessel giant cell arteritis: diagnosis, monitoring and management.Matthew J Koster, Eric L Matteson, Kenneth J Warrington.2018, Rheumatology, Vol. 57, pp. 32-42.

[2]EULAR recommendations for the use of imaging in large vessel vasculitis in clinical practice.Dejaco C, Ramiro S, Duftner C, et al.2018, Annals of the Rheumatic Diseases, Vol. 77, pp. 636-643.

Disclosure of Interests: :

None declared

AB0948 TIME TO CONSIDER HYPERMOBILITY AS A CAUSE OF SYMPTOMS IN PATIENTS PRESENTING TO EARLY ARTHRITIS CLINICS: A RETROSPECTIVE ANALYSIS OF 279 PATIENTS

Background:

Joint hypermobility is a common, although largely ignored physical sign. It is often asymptomatic but can be associated with significant musculoskeletal symptoms. Joint hypermobility may also be a feature of an underlying genetic disorder and patients may present with arthralgia, recurrent soft tissue injuries and intermittent joint swelling due to mechanical instability and poor proprioception. At University College London Hospital, we run a national service for the diagnosis and management of patients with hypermobility related disorders including hypermobility spectrum disorders, Ehlers-Danlos syndromes and Marfan syndrome. Over the years we observed that a significant number of our patients had been referred to the early arthritis clinics years prior to the recognition of their hypermobility. For example, one patient with a vascular type of Ehlers-Danlos syndrome EDS (confirmed COL3A mutation) presented to 3 different hospitals over a 5-year period, with possible inflammatory arthritis prior to the EDS diagnosis. Several studies have shown that a significant proportion of patients attending early arthritis clinics do not have inflammatory rheumatic diseases. In our experience, heritable disorders of connective tissue and hypermobility spectrum disorders are often overlooked and should be included in the differential diagnosis in patients seen in the early arthritis clinics.

Objectives:

We aimed to audit the outcome of patients who were seen in the early arthritis clinics focusing on those who were not found to have inflammatory rheumatic diseases and to explore if joint hypermobility was considered as a possible cause of patient’s symptoms.

Methods:

A retrospective analysis of medical records was conducted of patients attending the early arthritis clinics at University College London Hospital between May 2018 and December 2019.

Results:

279 patients (90 males, 189 females) were seen in the early arthritis clinics with a mean age of 48 (range 19-91). 131 patients (47%) did not have inflammatory rheumatic diseases. Sixty-three of these patients (48%) were not given any diagnosis and joint hypermobility was not assessed during the appointment. Eleven patients (8%) had features of hypermobility, 11 patients (8%) were diagnosed with fibromyalgia, 20 patients (15%) received a diagnosis of osteoarthritis, and 27 patients (21%) were given other diagnoses including tendonitis and soft tissue pathology.

Conclusion:

Almost 50 % of patients who were seen in the early arthritis clinics did not have inflammatory rheumatic diseases and 21 % of patients were discharged without a clear diagnosis. In these patients, hypermobility was not assessed and this is consistent with our observation. In our experience recognising joint hypermobility as a cause of arthralgia and intermittent joint swelling usually reassures patients and motivates them to follow appropriate treatment protocols including physiotherapy and occupational therapy thus allowing a more efficient utilization of early arthritis clinic resources towards those with true inflammatory rheumatic diseases. Going forward, we have planned to embed a cognisant attitude towards hypermobility within the relevant clinics to ensure that patients who do not have inflammatory arthritis are assessed for hypermobility and directed towards appropriate management.

References:

[1]Castori M, Hakim A. Contemporary approach to joint hypermobility & related disorders. Current Opinion in Pediatrics. 2017;29(6):640-649.

[2]Emma Connelly, Alan Hakim, Sally Davenportc & Jane Simmonds, A study exploring the prevalence of Joint Hypermobility Syndrome in patients attending a Musculoskeletal Triage Clinic. Physiotherapy Practice & Research 36 (2015) 43–53

[3]Feuchtenberger M, Nigg A, Kraus M, Schäfer A. Rate of Proven Rheumatic Diseases in a Large Collective of Referrals to an Outpatient Rheumatology Clinic under Routine Conditions. Clin Med Insights Arthritis Musculoskelet Disord. 2016; 9: 181–187.

Disclosure of Interests:

None declared

AB0502 EVALUATION OF A NOVEL FAST TRACK PATHWAY FOR GIANT CELL ARTERITIS USING PET IN ADDITION TO TAUS AND TAB FOR EARLY DIAGNOSIS

Background: :

Giant Cell Arteritis (GCA) is a common primary systemic vasculitis (1). Its predilection for the temporal artery can result in permanent visual loss if left untreated. Over 25% of patients have involvement of large vessels, such as the aorta, resulting in an increased risk of aneurysm formation and dissection. (3)

Diagnosis of GCA is largely clinical and temporal artery biopsy (TAB) has long been the gold standard for diagnosis. In recent years temporal artery ultrasound (TAUS) has emerged as an effective, non-invasive tool to aid diagnosis. Positron-emission tomography (PET) can also be utilised to detect the presence of large vessel involvement but is currently not used in many centres for diagnostic purposes and requires further standardisation and validation (2). The challenge arises from these investigations losing sensitivity in the days following steroid treatment, meaning that rapid access is key to confirm diagnosis.

Objectives:

To evaluate the impact of the introduction of a fast track pathway (FTP) on prompt diagnostics and treatment.

To improve our understanding of the use of PET at diagnosis and compare this to the gold standard TAB, and to TAUS, in our institution.

Methods:

Cohort 1: 32 patients, all presenting before FTP implementation, identified from outpatient clinics and referrals to the Rheumatology team. Time taken from steroid initiation to TAUS/TAB was extracted from clinical records. Outcomes for this group included number of years on steroid (steroid burden).

Cohort 2: 21 patients all referred after implementation of a new GCA FTP. This group contains all patients referred as query GCA, not just those with positive diagnoses. Time from steroid initiation to TAUS/TAB was recorded. The FTP included the addition of PET imaging within 72 hours.

Results:

Cohort 1: 20 (63%) patients had TAB and 3 (9%) had TAUS. The average time from starting steroid to investigation was 5.2 days and 2 days respectively. The average steroid burden in patients with no confirmatory test was 11 years. If patients had just a single diagnostic test this value dropped to 3 years.

Cohort 2: 11 (52%) had TAB, 10 (48%) had TAUS and 11 (52%) had PET. In positive GCA diagnoses, time from steroid start to investigations was 7.2 days, 1 day and 3.2 days respectively. In patients with a negative diagnosis the time frames were 13 days, 1 day and 1.7 days respectively. Sensitivity for TAB was 45.5% and TAUS 40%. Specificity for TAB and TAUS was 100%. These results are comparable to similar studies (4). PET sensitivity was 63.6% and specificity 100%.

Table 1.

Sensitivity, specificity, predictive values

TABTAUSPET CTSensitivity (%)45.540.063.6Specificity (%)100100100PPV (%)100100100NPV (%)33.357.155.6

Conclusion:

Prompt diagnostics, best facilitated through a FTP, can reduce steroid burden in GCA even if only one confirmatory test is available. Patients with a low clinical suspicion of GCA and negative TAUS or a high clinical suspicion and positive TAUS stand little to gain from TAB. These findings summarise the first 6 months of our GCA FTP. Continued evaluation of PET in our FTP is needed to understand its role in diagnosis, particularly in patients at risk of vascular complications.

References:

[1]Crowson CS, Matteson EL. Contemporary prevalence estimates for giant cell arteritis and polymyalgia rheumatica 2015. Semin Arthritis Rheum. 2017; 47 (2) 253–6

[2]Camellino D, Dejaco C. Should 18 F FDG PET imaging be used in the diagnosis of GCA? Nature Reviews Rheumatology 2019; 15 (7) 388–90

[3]Nuenninghoff DM et al. Incidence and predictors of large-artery complication (aortic aneurysm, aortic dissection, and/or large artery stenosis) in patients with giant cell arteritis: a population-based study over 50 years. Arthritis Rheum 2003; 48:3522-3531

[4]Luqmani, R. et al. The Role of Ultrasound Compared to Biopsy of Temporal Arteries in the Diagnosis and Treatment of Giant Cell Arteritis (TABUL): A Diagnostic Accuracy and Cost-Effectiveness Study. Health Technol Assess 2016; 20 (90) 1-238

Disclosure of Interests:

None declared

The accuracy of the diffusion approximation to the expected time to extinction for some discrete stochastic processes

Asymptotic approximations and numerical computations are used to estimate the accuracy of the diffusion approximation for the expected time to extinction for some stochastic processes. The results differ for processes with a continuant transition matrix (e.g. a birth and death process), and those with a noncontinuant transition matrix (e.g. a non-linear branching process). In the latter case, the diffusion equation does not hold near the point of exit. Consequently, high-order corrections do not result in substantial improvement over the diffusion approximation.

Measurement of the centrality dependence of the charged-particle pseudorapidity distribution in proton-lead collisions at [Formula: see text] TeV with the ATLAS detector

The centrality dependence of the mean charged-particle multiplicity as a function of pseudorapidity is measured in approximately 1 [Formula: see text]b[Formula: see text] of proton-lead collisions at a nucleon-nucleon centre-of-mass energy of [Formula: see text] [Formula: see text] using the ATLAS detector at the Large Hadron Collider. Charged particles with absolute pseudorapidity less than 2.7 are reconstructed using the ATLAS pixel detector. The [Formula: see text] collision centrality is characterised by the total transverse energy measured in the Pb-going direction of the forward calorimeter. The charged-particle pseudorapidity distributions are found to vary strongly with centrality, with an increasing asymmetry between the proton-going and Pb-going directions as the collisions become more central. Three different estimations of the number of nucleons participating in the [Formula: see text] collision have been carried out using the Glauber model as well as two Glauber-Gribov inspired extensions to the Glauber model. Charged-particle multiplicities per participant pair are found to vary differently for these three models, highlighting the importance of including colour fluctuations in nucleon-nucleon collisions in the modelling of the initial state of [Formula: see text] collisions.

Jet energy measurement and its systematic uncertainty in proton-proton collisions at [Formula: see text] TeV with the ATLAS detector

The jet energy scale (JES) and its systematic uncertainty are determined for jets measured with the ATLAS detector using proton-proton collision data with a centre-of-mass energy of [Formula: see text] TeV corresponding to an integrated luminosity of [Formula: see text][Formula: see text]. Jets are reconstructed from energy deposits forming topological clusters of calorimeter cells using the anti-[Formula: see text] algorithm with distance parameters [Formula: see text] or [Formula: see text], and are calibrated using MC simulations. A residual JES correction is applied to account for differences between data and MC simulations. This correction and its systematic uncertainty are estimated using a combination of in situ techniques exploiting the transverse momentum balance between a jet and a reference object such as a photon or a [Formula: see text] boson, for [Formula: see text] and pseudorapidities [Formula: see text]. The effect of multiple proton-proton interactions is corrected for, and an uncertainty is evaluated using in situ techniques. The smallest JES uncertainty of less than 1 % is found in the central calorimeter region ([Formula: see text]) for jets with [Formula: see text]. For central jets at lower [Formula: see text], the uncertainty is about 3 %. A consistent JES estimate is found using measurements of the calorimeter response of single hadrons in proton-proton collisions and test-beam data, which also provide the estimate for [Formula: see text] TeV. The calibration of forward jets is derived from dijet [Formula: see text] balance measurements. The resulting uncertainty reaches its largest value of 6 % for low-[Formula: see text] jets at [Formula: see text]. Additional JES uncertainties due to specific event topologies, such as close-by jets or selections of event samples with an enhanced content of jets originating from light quarks or gluons, are also discussed. The magnitude of these uncertainties depends on the event sample used in a given physics analysis, but typically amounts to 0.5-3 %.

[Classification of canine intervertebral disc degeneration using high-field magnetic resonance imaging and computed tomography]

OBJECTIVE

Although the classification of canine intervertebral disc degeneration using magnetic resonance imaging (MRI) has been described in the literature, there is no such classification using computed tomographic imaging. Because computed tomography (CT) is a frequently used diagnostic imaging tool in veterinary medicine, the aim of this study was the introduction and validation of such a scoring system. T2-weighted magnetic resonance images were available for comparative analysis.

MATERIAL AND METHODS

A total of 43 dogs were examined using CT and MRI. Image data records of 144 intervertebral discs were blinded, randomized and evaluated twice by three observers. CT data were analyzed using a self-developed scoring system, while MRI data sets were evaluated using the Pfirrmann scoring system. Intra- and interobserver agreement were determined using Statistical Analysis Software (SAS).

RESULTS

Intra- and interobserver agreement were mostly substantial in the Pfirrmann (0.58-0.77) and self-developed (0.60-0.81) scoring systems. A slight agreement was found between both classification systems (κ scores 0.26-0.29).

CONCLUSION AND CLINICAL RELEVANCE

The self-developed scoring system allows a reliable assessment of canine intervertebral disc degeneration using CT imaging. Therefore, further diagnostic and prognostic information can be obtained. Degenerative changes in the intervertebral discs could be identified at an earlier stage when using MRI in comparison with CT.

Muon reconstruction efficiency and momentum resolution of the ATLAS experiment in proton-proton collisions at [Formula: see text] TeV in 2010

This paper presents a study of the performance of the muon reconstruction in the analysis of proton-proton collisions at [Formula: see text] TeV at the LHC, recorded by the ATLAS detector in 2010. This performance is described in terms of reconstruction and isolation efficiencies and momentum resolutions for different classes of reconstructed muons. The results are obtained from an analysis of [Formula: see text] meson and [Formula: see text] boson decays to dimuons, reconstructed from a data sample corresponding to an integrated luminosity of 40 pb[Formula: see text]. The measured performance is compared to Monte Carlo predictions and deviations from the predicted performance are discussed.

The differential production cross section of the [Formula: see text](1020) meson in [Formula: see text] = 7 TeV [Formula: see text] collisions measured with the ATLAS detector

A measurement is presented of the [Formula: see text] production cross section at [Formula: see text] = 7 TeV using [Formula: see text] collision data corresponding to an integrated luminosity of 383 [Formula: see text], collected with the ATLAS experiment at the LHC. Selection of [Formula: see text](1020) mesons is based on the identification of charged kaons by their energy loss in the pixel detector. The differential cross section is measured as a function of the transverse momentum, [Formula: see text], and rapidity, [Formula: see text], of the [Formula: see text](1020) meson in the fiducial region 500 [Formula: see text] 1200 MeV, [Formula: see text] 0.8, kaon [Formula: see text] 230 MeV and kaon momentum [Formula: see text] 800 MeV. The integrated [Formula: see text]-meson production cross section in this fiducial range is measured to be [Formula: see text] = 570 [Formula: see text] 8 (stat) [Formula: see text] 66 (syst) [Formula: see text] 20 (lumi) [Formula: see text].

Search for quantum black hole production in high-invariant-mass lepton+jet final states using pp collisions at √s=8 TeV and the ATLAS detector

This Letter presents a search for quantum black-hole production using 20.3 fb-1 of data collected with the ATLAS detector in pp collisions at the LHC at √s = 8 TeV. The quantum black holes are assumed to decay into a final state characterized by a lepton (electron or muon) and a jet. In either channel, no event with a lepton-jet invariant mass of 3.5 TeV or more is observed, consistent with the expected background. Limits are set on the product of cross sections and branching fractions for the lepton+jet final states of quantum black holes produced in a search region for invariant masses above 1 TeV. The combined 95% confidence level upper limit on this product for quantum black holes with threshold mass above 3.5 TeV is 0.18 fb. This limit constrains the threshold quantum black-hole mass to be above 5.3 TeV in the model considered.

Search for dark matter in events with a hadronically decaying W or Z boson and missing transverse momentum in pp collisions at √s=8 TeV with the ATLAS detector

A search is presented for dark matter pair production in association with a W or Z boson in pp collisions representing 20.3  fb(-1) of integrated luminosity at √s=8  TeV using data recorded with the ATLAS detector at the Large Hadron Collider. Events with a hadronic jet with the jet mass consistent with a W or Z boson, and with large missing transverse momentum are analyzed. The data are consistent with the standard model expectations. Limits are set on the mass scale in effective field theories that describe the interaction of dark matter and standard model particles, and on the cross section of Higgs production and decay to invisible particles. In addition, cross section limits on the anomalous production of W or Z bosons with large missing transverse momentum are set in two fiducial regions.

Measurement of jet shapes in top-quark pair events at [Formula: see text] using the ATLAS detector

A measurement of jet shapes in top-quark pair events using 1.8 fb-1 of [Formula: see text]pp collision data recorded by the ATLAS detector at the LHC is presented. Samples of top-quark pair events are selected in both the single-lepton and dilepton final states. The differential and integrated shapes of the jets initiated by bottom-quarks from the top-quark decays are compared with those of the jets originated by light-quarks from the hadronic W-boson decays [Formula: see text] in the single-lepton channel. The light-quark jets are found to have a narrower distribution of the momentum flow inside the jet area than b-quark jets.

Measurement of top quark polarization in top-antitop events from proton-proton collisions at √s=7 TeV using the ATLAS detector

This Letter presents measurements of the polarization of the top quark in top-antitop quark pair events, using 4.7  fb(-1) of proton-proton collision data recorded with the ATLAS detector at the Large Hadron Collider at √s=7  TeV. Final states containing one or two isolated leptons (electrons or muons) and jets are considered. Two measurements of α(ℓ)P, the product of the leptonic spin-analyzing power and the top quark polarization, are performed assuming that the polarization is introduced by either a CP conserving or a maximally CP violating production process. The measurements obtained, α(ℓ)P(CPC)=-0.035±0.014(stat)±0.037(syst) and α(ℓ)P(CPV)=0.020±0.016(stat)(-0.017)(+0.013)(syst), are in good agreement with the standard model prediction of negligible top quark polarization.

Measurement of the azimuthal angle dependence of inclusive jet yields in Pb+Pb collisions at √(sNN)=2.76 TeV with the ATLAS detector

Measurements of the variation of inclusive jet suppression as a function of relative azimuthal angle, Δφ, with respect to the elliptic event plane provide insight into the path-length dependence of jet quenching. ATLAS has measured the Δφ dependence of jet yields in 0.14 nb(-1) of √(s(NN))=2.76 TeV Pb+Pb collisions at the LHC for jet transverse momenta p(T)>45 GeV in different collision centrality bins using an underlying event subtraction procedure that accounts for elliptic flow. The variation of the jet yield with Δφ was characterized by the parameter, v(2)(jet), and the ratio of out-of-plane (Δφ~π/2) to in-plane (Δφ~0) yields. Nonzero v(2)(jet) values were measured in all centrality bins for p(T)<160 GeV. The jet yields are observed to vary by as much as 20% between in-plane and out-of-plane directions.

Improved luminosity determination in pp collisions at [Formula: see text] using the ATLAS detector at the LHC

The luminosity calibration for the ATLAS detector at the LHC during pp collisions at [Formula: see text] in 2010 and 2011 is presented. Evaluation of the luminosity scale is performed using several luminosity-sensitive detectors, and comparisons are made of the long-term stability and accuracy of this calibration applied to the pp collisions at [Formula: see text]. A luminosity uncertainty of [Formula: see text] is obtained for the 47 pb-1 of data delivered to ATLAS in 2010, and an uncertainty of [Formula: see text] is obtained for the 5.5 fb-1 delivered in 2011.

Measurement of the inclusive jet cross-section in pp collisions at [Formula: see text] and comparison to the inclusive jet cross-section at [Formula: see text] using the ATLAS detector

The inclusive jet cross-section has been measured in proton-proton collisions at [Formula: see text] in a dataset corresponding to an integrated luminosity of [Formula: see text] collected with the ATLAS detector at the Large Hadron Collider in 2011. Jets are identified using the anti-kt algorithm with two radius parameters of 0.4 and 0.6. The inclusive jet double-differential cross-section is presented as a function of the jet transverse momentum pT and jet rapidity y, covering a range of 20≤pT<430 GeV and |y|<4.4. The ratio of the cross-section to the inclusive jet cross-section measurement at [Formula: see text], published by the ATLAS Collaboration, is calculated as a function of both transverse momentum and the dimensionless quantity [Formula: see text], in bins of jet rapidity. The systematic uncertainties on the ratios are significantly reduced due to the cancellation of correlated uncertainties in the two measurements. Results are compared to the prediction from next-to-leading order perturbative QCD calculations corrected for non-perturbative effects, and next-to-leading order Monte Carlo simulation. Furthermore, the ATLAS jet cross-section measurements at [Formula: see text] and [Formula: see text] are analysed within a framework of next-to-leading order perturbative QCD calculations to determine parton distribution functions of the proton, taking into account the correlations between the measurements.

Search for a light charged Higgs boson in the decay channel [Formula: see text] in [Formula: see text] events using pp collisions at [Formula: see text] with the ATLAS detector

A search for a charged Higgs boson (H+) in [Formula: see text] decays is presented, where one of the top quarks decays via t→H+b, followed by H+→ two jets ([Formula: see text]). The other top quark decays to Wb, where the W boson then decays into a lepton (e/μ) and a neutrino. The data were recorded in pp collisions at [Formula: see text] by the ATLAS detector at the LHC in 2011, and correspond to an integrated luminosity of 4.7 fb-1. With no observation of a signal, 95 % confidence level (CL) upper limits are set on the decay branching ratio of top quarks to charged Higgs bosons varying between 5 % and 1 % for H+ masses between 90 GeV and 150 GeV, assuming [Formula: see text].

Measurement of kT splitting scales in W→ℓν events at [Formula: see text] with the ATLAS detector

A measurement of splitting scales, as defined by the kT clustering algorithm, is presented for final states containing a W boson produced in proton-proton collisions at a centre-of-mass energy of 7 TeV. The measurement is based on the full 2010 data sample corresponding to an integrated luminosity of 36 pb-1 which was collected using the ATLAS detector at the CERN Large Hadron Collider. Cluster splitting scales are measured in events containing W bosons decaying to electrons or muons. The measurement comprises the four hardest splitting scales in a kT cluster sequence of the hadronic activity accompanying the W boson, and ratios of these splitting scales. Backgrounds such as multi-jet and top-quark-pair production are subtracted and the results are corrected for detector effects. Predictions from various Monte Carlo event generators at particle level are compared to the data. Overall, reasonable agreement is found with all generators, but larger deviations between the predictions and the data are evident in the soft regions of the splitting scales.

Observation of associated near-side and away-side long-range correlations in sqrt[s(NN)]=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δø) and pseudorapidity (Δη) are measured in sqrt[s(NN)] = 5.02 TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1 μb(-1) of data as a function of transverse momentum (p(T)) and the transverse energy (ΣE(T)(Pb)) summed over 3.1 < η < 4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2 < |Δ η | < 5) "near-side" (Δø ~ 0) correlation that grows rapidly with increasing ΣE(T)(Pb). A long-range "away-side" (Δø ~ π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣE(T)(Pb), is found to match the near-side correlation in magnitude, shape (in Δη and Δø) and ΣE(T)(Pb) dependence. The resultant Δø correlation is approximately symmetric about π/2, and is consistent with a dominant cos2Δø modulation for all ΣE(T)(Pb) ranges and particle p(T).

Multi-channel search for squarks and gluinos in [Formula: see text]pp collisions with the ATLAS detector at the LHC

A search for supersymmetric particles in final states with zero, one, and two leptons, with and without jets identified as originating from b-quarks, in 4.7 fb-1 of [Formula: see text]pp collisions produced by the Large Hadron Collider and recorded by the ATLAS detector is presented. The search uses a set of variables carrying information on the event kinematics transverse and parallel to the beam line that are sensitive to several topologies expected in supersymmetry. Mutually exclusive final states are defined, allowing a combination of all channels to increase the search sensitivity. No deviation from the Standard Model expectation is observed. Upper limits at 95 % confidence level on visible cross-sections for the production of new particles are extracted. Results are interpreted in the context of the constrained minimal supersymmetric extension to the Standard Model and in supersymmetry-inspired models with diverse, high-multiplicity final states.

Measurement of the [Formula: see text] production cross section in the tau + jets channel using the ATLAS detector

A measurement of the top quark pair production cross section in the final state with a hadronically decaying tau lepton and jets is presented. The analysis is based on proton-proton collision data recorded by the ATLAS experiment at the LHC, with a centre-of-mass energy of 7 TeV. The data sample corresponds to an integrated luminosity of 1.67 fb-1. The cross section is measured to be [Formula: see text] and is in agreement with other measurements and with the Standard Model prediction.

Jet energy resolution in proton-proton collisions at [Formula: see text] recorded in 2010 with the ATLAS detector

The measurement of the jet energy resolution is presented using data recorded with the ATLAS detector in proton-proton collisions at [Formula: see text]. The sample corresponds to an integrated luminosity of 35 pb-1. Jets are reconstructed from energy deposits measured by the calorimeters and calibrated using different jet calibration schemes. The jet energy resolution is measured with two different in situ methods which are found to be in agreement within uncertainties. The total uncertainties on these measurements range from 20 % to 10 % for jets within |y|<2.8 and with transverse momenta increasing from 30 GeV to 500 GeV. Overall, the Monte Carlo simulation of the jet energy resolution agrees with the data within 10 %.

Measurement of Z boson production in Pb-Pb collisions at sqrt[s(NN)]=2.76 TeV with the ATLAS detector

The ATLAS experiment has observed 1995 Z boson candidates in data corresponding to 0.15  nb(-1) of integrated luminosity obtained in the 2011 LHC Pb+Pb run at sqrt[s(NN)]=2.76  TeV. The Z bosons are reconstructed via dielectron and dimuon decay channels, with a background contamination of less than 3%. Results from the two channels are consistent and are combined. Within the statistical and systematic uncertainties, the per-event Z boson yield is proportional to the number of binary collisions estimated by the Glauber model. The elliptic anisotropy of the azimuthal distribution of the Z boson with respect to the event plane is found to be consistent with zero.

Search for dark matter candidates and large extra dimensions in events with a photon and missing transverse momentum in pp collision data at sqrt[s]=7 TeV with the ATLAS detector

Results of a search for new phenomena in events with an energetic photon and large missing transverse momentum in proton-proton collisions at sqrt[s] = 7 TeV are reported. Data collected by the ATLAS experiment at the LHC corresponding to an integrated luminosity of 4.6 fb(-1) are used. Good agreement is observed between the data and the standard model predictions. The results are translated into exclusion limits on models with large extra spatial dimensions and on pair production of weakly interacting dark matter candidates.

Search for magnetic monopoles in sqrt[s]=7 TeV pp collisions with the ATLAS detector

This Letter presents a search for magnetic monopoles with the ATLAS detector at the CERN Large Hadron Collider using an integrated luminosity of 2.0  fb(-1) of pp collisions recorded at a center-of-mass energy of sqrt[s]=7  TeV. No event is found in the signal region, leading to an upper limit on the production cross section at 95% confidence level of 1.6/ϵ  fb for Dirac magnetic monopoles with the minimum unit magnetic charge and with mass between 200 GeV and 1500 GeV, where ϵ is the monopole reconstruction efficiency. The efficiency ϵ is high and uniform in the fiducial region given by pseudorapidity |η|<1.37 and transverse kinetic energy 600-700<E(kin)sinθ<1400  GeV. The minimum value of 700 GeV is for monopoles of mass 200 GeV, whereas the minimum value of 600 GeV is applicable for higher mass monopoles. Therefore, the upper limit on the production cross section at 95% confidence level is 2 fb in this fiducial region. Assuming the kinematic distributions from Drell-Yan pair production of spin-1/2 Dirac magnetic monopoles, the efficiency is in the range 1%-10%, leading to an upper limit on the cross section at 95% confidence level that varies from 145 fb to 16 fb for monopoles with mass between 200 GeV and 1200 GeV. This limit is weaker than the fiducial limit because most of these monopoles lie outside the fiducial region.

Search for direct top squark pair production in final states with one isolated lepton, jets, and missing transverse momentum in sqrt[s] = 7 TeV pp collisions using 4.7 fb(-10 of ATLAS data

A search is presented for direct top squark pair production in final states with one isolated electron or muon, jets, and missing transverse momentum in proton-proton collisions at sqrt[s] = 7 TeV. The measurement is based on 4.7 fb(-1) of data collected with the ATLAS detector at the LHC. Each top squark is assumed to decay to a top quark and the lightest supersymmetric particle (LSP). The data are found to be consistent with standard model expectations. Top squark masses between 230 GeV and 440 GeV are excluded with 95% confidence for massless LSPs, and top squark masses around 400 GeV are excluded for LSP masses up to 125 GeV.

Search for a supersymmetric partner to the top quark in final states with jets and missing transverse momentum at sqrt[s] = 7 TeV with the ATLAS detector

A search for direct pair production of supersymmetric top squarks (t(1)) is presented, assuming the t(1) decays into a top quark and the lightest supersymmetric particle, χ(1)(0), and that both top quarks decay to purely hadronic final states. A total of 16 (4) events are observed compared to a predicted standard model background of 13.5(-3.6)(+3.7)(4.4(-1.3)(+1.7)) events in two signal regions based on ∫Ldt = 4.7 fb(-1) of pp collision data taken at sqrt[s] = 7 TeV with the ATLAS detector at the LHC. An exclusion region in the t(1) versus χ(1)(0) mass plane is evaluated: 370<m(t)(1)}<465 GeV is excluded for m(χ)(1)(0) ~ 0 GeV while m(t)(1) = 445 GeV is excluded for m(χ)(1)(0) ≤ 50 GeV.

A search for [Formula: see text] resonances with the ATLAS detector in 2.05 fb-1 of proton-proton collisions at [Formula: see text]

A search for top quark pair resonances in final states containing at least one electron or muon has been performed with the ATLAS experiment at the CERN Large Hadron Collider. The search uses a data sample corresponding to an integrated luminosity of 2.05 fb-1, which was recorded in 2011 at a proton-proton centre-of-mass energy of 7 TeV. No evidence for a resonance is found and limits are set on the production cross-section times branching ratio to [Formula: see text] for narrow and wide resonances. For narrow Z' bosons, the observed 95 % Bayesian credibility level limits range from 9.3 pb to 0.95 pb for masses in the range of mZ'=500 GeV to mZ'=1300 GeV. The corresponding excluded mass region for a leptophobic topcolour Z' boson (Kaluza-Klein gluon excitation in the Randall-Sundrum model) is mZ'<880 GeV ([Formula: see text]).

Search for supersymmetry in events with three leptons and missing transverse momentum in √[s]=7 TeV pp collisions with the ATLAS detector

A search for the weak production of charginos and neutralinos decaying to a final state with three leptons (electrons or muons) and missing transverse momentum is presented. The analysis uses 2.06 fb(-1) of √[s]=7 TeV proton-proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with standard model expectations in two signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric and simplified models. For the simplified models, degenerate lightest chargino and next-to-lightest neutralino masses up to 300 GeV are excluded for mass differences from the lightest neutralino up to 300 GeV.

Search for lepton flavour violation in the eμ continuum with the ATLAS detector in [Formula: see text]pp collisions at the LHC

This paper presents a search for the t-channel exchange of an R-parity violating scalar top quark ([Formula: see text]) in the e±μ∓ continuum using 2.1 fb-1 of data collected by the ATLAS detector in [Formula: see text]pp collisions at the Large Hadron Collider. Data are found to be consistent with the expectation from the Standard Model backgrounds. Limits on R-parity-violating couplings at 95 % C.L. are calculated as a function of the scalar top mass ([Formula: see text]). The upper limits on the production cross section for pp→eμX, through the t-channel exchange of a scalar top quark, ranges from 170 fb for [Formula: see text] to 30 fb for [Formula: see text].

Measurement of the ZZ production cross section and limits on anomalous neutral triple gauge couplings in proton-proton collisions at sqrt[s] = 7 TeV with the ATLAS detector

A measurement of the ZZ production cross section in proton-proton collisions at sqrt[s] = 7 TeV using data corresponding to an integrated luminosity of 1.02 fb(-1) recorded by the ATLAS experiment at the LHC is presented. Twelve events containing two Z boson candidates decaying to electrons and/or muons are observed, with an expected background of 0.3 ± 0.3(stat)(-0.3)(+0.4)(syst) events. The cross section measured in a phase-space region with good detector acceptance and for dilepton masses within the range 66 to 116 GeV is σ(ZZ → ℓ+ ℓ- ℓ+ ℓ-)(fid) = 19.4(-5.2)(+6.3)(stat)(-0.7)(+0.9)(syst) ± 0.7(lumi) fb. The resulting total cross section for on-shell ZZ production, σ(ZZ)(tot) = 8.5(-2.3)(+2.7)(stat)(-0.3)(+0.4)(syst) ± 0.3(lumi) pb, is consistent with the standard model expectation of 6.5(-0.2)(+0.3) pb calculated at the next-to-leading order in QCD. Limits on anomalous neutral triple gauge boson couplings are derived.

Clinical trial: cyclophosphamide pulse therapy - a promising therapeutic alternative in refractory Crohn's disease

BACKGROUND

In severe steroid-refractory Crohn's disease (CD), established therapies fail in a relevant proportion of patients. Recent pilot studies indicated the efficacy of cyclophosphamide pulse therapy in these patients.

AIM

To provide further and substantial evidence for the rationale to apply cyclophosphamide pulse therapy as therapeutic option in severe courses of CD.

METHODS

Fifteen patients with steroid-refractory (n = 13) or steroid-dependent (n = 2) CD received 2-6 (median 3) monthly pulses of 750 mg cyclophosphamide in an open-label fashion. Eleven patients were on concomitant immunosuppression (azathioprine/mercaptopurine n = 9; methotrexate n = 2).

RESULTS

Thirteen of 15 patients (87%) had a clinical response (CDAI decrease >100). Ten patients (67%) went into remission (CDAI <150) after 8 weeks. Steroid-free remission was achieved in eight patients (54%). Two patients (13%) failed to respond. Median CDAI decreased from 420 (245-550) to 100 (26-538) at week 8. Remission lasted 16 months (median, range 4-40). In three patients, arthritis, erythema nodosum and episcleritis completely resolved. Cyclophosphamide pulse therapy administration was well tolerated in all subjects.

CONCLUSIONS

Cyclophosphamide pulse therapy is safe and highly effective for induction and maintenance of remission in steroid-refractory/-dependent CD. There is a strong need for additional experience to improve the setting of the encouraging cyclophosphamide treatment in CD.