Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Delayed colorectal cancer care during covid-19 pandemic (decor-19). Global perspective from an international survey

Background The widespread nature of coronavirus disease 2019 (COVID-19) has been unprecedented. We sought to analyze its global impact with a survey on colorectal cancer (CRC) care during the pandemic. Methods The impact of COVID-19 on preoperative assessment, elective surgery, and postoperative management of CRC patients was explored by a 35-item survey, which was distributed worldwide to members of surgical societies with an interest in CRC care. Respondents were divided into two comparator groups: 1) ‘delay’ group: CRC care affected by the pandemic; 2) ‘no delay’ group: unaltered CRC practice. Results A total of 1,051 respondents from 84 countries completed the survey. No substantial differences in demographics were found between the ‘delay’ (745, 70.9%) and ‘no delay’ (306, 29.1%) groups. Suspension of multidisciplinary team meetings, staff members quarantined or relocated to COVID-19 units, units fully dedicated to COVID-19 care, personal protective equipment not readily available were factors significantly associated to delays in endoscopy, radiology, surgery, histopathology and prolonged chemoradiation therapy-to-surgery intervals. In the ‘delay’ group, 48.9% of respondents reported a change in the initial surgical plan and 26.3% reported a shift from elective to urgent operations. Recovery of CRC care was associated with the status of the outbreak. Practicing in COVID-free units, no change in operative slots and staff members not relocated to COVID-19 units were statistically associated with unaltered CRC care in the ‘no delay’ group, while the geographical distribution was not. Conclusions Global changes in diagnostic and therapeutic CRC practices were evident. Changes were associated with differences in health-care delivery systems, hospital’s preparedness, resources availability, and local COVID-19 prevalence rather than geographical factors. Strategic planning is required to optimize CRC care

Exclusive photon-photon production of muon pairs in proton-proton collisions at sqrt(s) = 7 TeV

Abstract A measurement of the exclusive two-photon production of muon pairs in protonproton collisions at √ s = 7 TeV, pp → pµ + µ − p, is reported using data corresponding to an integrated luminosity of 40 pb −1 . For muon pairs with invariant mass greater than 11.5 GeV, transverse momentum p T (µ) > 4 GeV and pseudorapidity |η(µ)| < 2.1, a fit to the dimuon p T (µ + µ − ) distribution results in a measured cross section of σ(p → pµ + µ − p) = 3.38 +0.58 −0.55 (stat.) ± 0.16 (syst.) ± 0.14 (lumi.) pb, consistent with the theoretical prediction evaluated with the event generator LPAIR. The ratio to the predicted cross section is 0.83 +0.14 −0.13 (stat.) ± 0.04 (syst.) ± 0.03 (lumi.). The characteristic distributions of the muon pairs produced via γγ fusion, such as the muon acoplanarity, the muon pair invariant mass and transverse momentum agree with those from the theory. Submitted to the Journal of High Energy Physics Introduction The exclusive two-photon production of lepton pairs may be reliably calculated within the framework of quantum electrodynamics (QED) At the Tevatron, the exclusive two-photon production of electron [4, 5] and muon [5, 6] pairs in pp collisions has been measured with the CDF detector. Observations have been made of QED signals, leading to measurements of exclusive charmonium photoproduction [6] and searches for anomalous high-mass exclusive dilepton production [5]. However, all such measurements have very limited numbers of selected events because the data samples were restricted to single interaction bunch crossings. The higher energies and increased luminosity available at the Large Hadron Collider (LHC) will allow significant improvements in these measurements, if this limitation can be avoided. As a result of the small theoretical uncertainties and characteristic kinematic distributions in γγ → µ + µ − , this process has been proposed as a candidate for a complementary absolute calibration of the luminosity of pp collisions Unless both outgoing protons are detected, the semi-exclusive two-photon production, involving single or double proton dissociation 3 Simulated Samples The paper is organized as follows. In Section 2, a brief description of the CMS detector is provided. Section 3 describes the data and samples of simulated events used in the analysis. Section 4 documents the criteria used to select events, and Section 5 the method used to extract the signal yield from the data. The systematic uncertainties and cross-checks performed are discussed in Section 6, while Section 7 contains plots comparing the selected events in data and simulation. Finally, the results of the measurement are given in Section 8 and summarized in Section 9. The CMS detector A detailed description of the CMS experiment can be found elsewhere Simulated Samples The LPAIR 4.0 event generator [9, 10] is used to produce simulated samples of two-photon production of muon pairs. The generator uses full leading-order QED matrix elements, and the cross sections for the exclusive events depend on the proton electromagnetic form-factors to account for the distribution of charge within the proton. For proton dissociation, the cross sections depend on the proton structure function. In order to simulate the fragmentation of the dissociated proton into a low-mass system N, the LUND model shower routine Event selection The analysis uses a sample of pp collisions at √ s = 7 TeV, collected during 2010 at the LHC and corresponding to an integrated luminosity of 40 pb −1 . The sample includes 36 pb −1 of data passing the standard CMS quality criteria for all detector subsystems, and 4 pb −1 in which the quality criteria are satisfied for the tracking and muon systems used in the analysis. From the sample of triggered events, the presence of two reconstructed muons is required. Then the exclusivity selection is performed to keep only events with a vertex having no tracks other than those from the two muons. Finally, the signal muons are required to satisfy identification criteria, and kinematic constraints are imposed using their four-momentum. All selection steps are described in the following sections. Trigger and muon reconstruction Events are selected online by triggers requiring the presence of two muons with a minimum p T of 3 GeV. No requirement on the charge of the muons is applied at the trigger level. Muons are reconstructed offline by combining information from the muon chambers with that on chargedparticle tracks reconstructed in the silicon tracker Vertex and track exclusivity selection With single interactions, the exclusive signal is characterized by the presence of two muons, no additional tracks, and no activity above the noise threshold in the calorimeters. The presence of additional interactions in the same bunch crossing will spoil this signature by producing additional tracks and energy deposits in the calorimeters. In the 2010 data, less than 20% of the total luminosity was estimated to have been collected from bunch crossings where only a single interaction look place, leading to a significant decrease in signal efficiency if the conditions of no extra tracks or calorimeter energy are required. The selection of exclusive events is therefore applied using the pixel and silicon tracker only, since the primary vertex reconstruction In order to reduce the background from inclusive DY and QCD dimuon production, which typically have many tracks originating from the same vertex as a prompt muon pair, the dimuon vertex is required to be separated in three dimensions by more than 2 mm from any additional tracks in the event. This value is selected to optimize the signal efficiency and background rejection found in events triggered only by the presence of colliding bunches ("zero-bias" events), and in DY Monte Carlo simulation. For the zero-bias data, this is accomplished by introducing an artificial additional dimuon vertex into each event as a proxy for an exclusive dimuon interaction. Thus, in this study, beam crossings with no real vertex present are counted as "single vertex" events, and crossings with one real vertex are counted as having an additional pileup event. Event selection The effects of the track veto on the signal efficiency and on the efficiency for misidentifying background as signal are studied as a function of the distance to the closest track for the zerobias sample and DY background Muon identification Each muon of the pair is required to pass a "tight" muon selection Kinematic selection In order to minimize the systematic uncertainties related to the knowledge of the low-p T and large-η muon efficiencies, only muons with p T > 4 GeV and |η| < 2.1 are selected. The p T and |η| requirements retain muon pairs from exclusive photoproduction of upsilon mesons, γp → Υp → µ + µ − p. This process occurs when a photon emitted from one proton fluctuates into a qq pair, which interacts with the second proton via a color-singlet exchange. This contribution is removed by requiring that the muons have an invariant mass m(µ + µ − ) > 11.5 GeV. In order to suppress further the proton dissociation background, the muon pair is required to be back-to-back in azimuthal angle (1 − |∆φ(µ + µ − )/π| < 0.1) and balanced in the scalar difference in the p T of the two muons (|∆p T (µ + µ − )| < 1.0 GeV). A possible contamination could arise from cosmic-ray muons, which would produce a signature similar to the exclusive γγ → µ + µ − signal. The three-dimensional opening angle of the pair, defined as the arccosine of the normalized scalar product of the muon momentum vectors, is therefore required to be smaller than 0.95 π, to reduce any contribution from cosmic-ray muons. The effect of each step of the selection on the data and simulated signal and background samples is shown in Signal extraction Efficiency corrections A correction is applied to account for the presence of extra proton-proton interactions in the same bunch crossing as a signal event. These pileup interactions will result in an inefficiency if they produce a track with a position within the nominal 2 mm veto distance around the dimuon vertex. This effect is studied in zero-bias data using the method described in Section 4.2. The nominal 2 mm veto is then applied around the dimuon vertex, and the event is accepted if no tracks fall within the veto distance. The efficiency is measured as a function of the instantaneous luminosity per colliding bunch. The average efficiency is calculated based on 6 5 Signal extraction The trigger, tracking, and offline muon selection efficiencies are each obtained from the tagand-probe The effect of the vertexing efficiency is studied both in inclusive dimuon data and signal simulation, by performing an independent selection of all muon pairs with a longitudinal separation of less than 0.5 mm. A Kalman filter Maximum likelihood fit The elastic pp → pµ + µ − p contribution is extracted by performing a binned maximum-likelihood fit to the measured p T (µ + µ − ) distribution. Shapes from Monte Carlo simulation are used for the signal, single-proton dissociation, double-proton dissociation, and DY contributions, with all corrections described in Section 4.4 applied. Three parameters are determined from the fit: the elastic signal yield relative to the LPAIR prediction for an integrated luminosity of 40 pb −1 (R El−El ), the single-proton dissociation yield relative to the LPAIR single-proton dissociation prediction for 40 pb −1 (R diss−El ), and an exponential modification factor for the shape of the p T distribution, characterized by the parameter a. The modification parameter is included to account for possible rescattering effects not included in the simulation, as described in Section 3. Given the small number of events expected in 40 pb −1 , the double-proton dissociation and DY contributions cannot be treated as free parameters and are fixed from simulation to their predicted values. The contribution from exclusive γγ → τ + τ − production is estimated to be 0.1 events from the simulation, and is neglected. The p T (µ + µ − ) distribution in data is shown overlaid with the result of the fit to the shapes from Monte Carlo simulation in data-theory signal ratio: R El−El = 0.83 +0.14 −0.13 ; single-proton dissociation yield ratio: R diss−El = 0.73 +0.16 −0.14 ; modification parameter: a = 0.04 with asymmetric statistical uncertainties computed using MINOS As a cross-check, a fit to the 1 − |∆φ(µ + µ − )/π| distribution is performed, with the signal and single-proton dissociation yields as free parameters, and the shape of the single-proton dissociation component fixed from the simulation. The resulting value of the data-theory signal ratio is 0.81 +0.14 −0.13 , consistent with the nominal fit result. The central values of the signal and single-proton dissociation yields from the fit are both below the mean number expected for 40 pb −1 , consistent with the deficit shown in The fits to the data with these looser selection requirements are shown in Control plots The dimuon invariant mass and acoplanarity distributions for events passing all selection criteria listed in In Systematic uncertainties and cross-checks Systematic uncertainties related to the pileup efficiency correction, muon trigger and reconstruction efficiency corrections, momentum scale, LHC crossing angle, and description of the backgrounds in the fit are considered. The systematic uncertainties related to the muon identification, trigger, and tracking efficiencies are determined from the statistical uncertainties of the J/ψ and Z control samples used to derive the corrections. The remaining systematic uncertainties are evaluated by varying each contribution as described in the following sections, and repeating the fit with the same three free parameters R El−El , R diss−El , and the shape correction a. The relative difference of the data-theory signal ratio between the modified and the nominal fit result is taken as a systematic uncertainty. Pileup correction systematic uncertainties Charged tracks from pileup interactions more than 2.0 mm from the dimuon vertex may induce a signal inefficiency, if they are misreconstructed to originate from within the 2.0 mm veto window. The η-dependent single-track impact parameter resolution in CMS has been measured to be less than 0.2 mm in the transverse direction, and less than 1.0 mm in the longitudinal direction As a further check, the same variations are applied to the selected sample of dimuon events, removing the Υ mass cut m < 11.5 GeV to increase the statistics with photo-produced exclusive upsilon events. The change in the number of events selected in the dimuon sample is found to be consistent with the expectation from the zero-bias sample. Muon efficiencies and momentum scale The statistical uncertainty on the muon efficiency correction is evaluated by performing a fast Monte Carlo study in which each single-muon correction evaluated from the tag-andprobe study is varied independently using a Gaussian distribution having a width equal to the measured uncertainty. The r.m.s. of the distribution of the resulting variations in the overall dimuon efficiency correction is taken as the systematic uncertainty. From 1000 pseudoexperiments, this results in an uncertainty of 0.8%. In addition, we study the effect of correlations in the dimuon efficiency. The tag-and-probe study is only sensitive to single-muon efficiencies. Since we take the dimuon efficiency as the product of the single-muon efficiencies, the effect of correlations in the efficiency are not modeled. To evaluate the size of this effect, the efficiency corrections are computed after removing events in the J/ψ control sample in which the two muons bend towards each other in the r-φ plane, potentially becoming very close or overlapping. Such events may introduce larger correlations in the efficiency of the dimuon pair than would be present in the well separated signal muons. Repeating the signal extraction with this change results in a relative difference of 0.7% from the nominal efficiency, which is taken as a systematic uncertainty. Using studies of the muon momentum scale derived from Z → µ + µ − [23], the muon p T is shifted by the observed p T -dependent bias, and the nominal fit is performed again. The resulting relative change in the signal yield is 0.1%, which is taken as a systematic uncertainty. As a cross-check using a sample kinematically closer to the signal, we apply all the selections except for the veto on the Υ mass region, and perform a fit to the Υ(1S) resonance. The resulting mass is consistent with the PDG value Vertexing and tracking efficiencies Since the study described in Section 4.4 shows no significant difference in the vertexing efficiency between data and simulation, the 0.1% statistical uncertainty of the measurement in data is taken as a systematic uncertainty. For the tracking efficiency, the difference between data and simulation is applied as a single correction without binning in p T or η. The statistical uncertainty of 0.1% on the correction for the dimuon is taken as a systematic uncertainty. Crossing angle The non-zero crossing angle of the LHC beams leads to a boost of the dimuon system in the x direction. Consequently, the p T of the pair is over-estimated by a few MeV, especially for high-mass dimuon events. This effect is estimated by applying a correction for the Lorentz boost, using a half-angle of 100 µrad in the x-z plane. This results in a 1.0% variation from the nominal fit value, and is taken as an additional systematic uncertainty. Fit stability Checks of the fit stability are performed by testing different bin widths and fit ranges. Starting from the nominal number of 20 bins in the range 0-3 GeV, variations in the bin width from 0.1 to 0.2 GeV and fit range [0, 2] to [0, 4] GeV show deviations by at most 3.3% with respect to the nominal yield. The fit bias is studied by performing a series of Monte Carlo pseudoexperiments for different input values of the signal and proton-dissociation yields, using events drawn from the fully simulated samples. The means of the pull distributions are found to be 7.6 Backgrounds 13 consistent with zero. Since the pseudo-experiments with the nominal binning and fit range show no significant bias, no additional systematics are assigned in this case. Backgrounds The yields of the double-proton dissociation and DY contributions are fixed in the nominal fit. To estimate the systematic uncertainty from this constraint, the fit is repeated with each of these varied independently by a factor of 2. The resulting changes in the fitted signal yield are 0.9% and 0.4%, respectively, where because of the similar shapes of the single and double proton dissociation components, this variation is partly absorbed into the fitted single-proton dissociation yield. As a cross-check of this procedure, the |∆p T (µ + µ − )| and 1 − |∆φ(µ + µ − )/π| requirements are inverted to select samples of events expected to be dominated by doubleproton dissociation and DY backgrounds. The agreement between data and simulation in these regions is found to be within the factor of 2 used as a systematic variation. The possibility of a large contamination from cosmic-ray muons, which may fake a signal since they will not be correlated with other tracks in the event, is studied by comparing the vertex position and three-dimensional opening angle in data and simulations of collision backgrounds. A total of three events fail the vertex position selection in data, after all other selection criteria are applied. All three also fail the opening angle selection, which is consistent with the expected signature from cosmic muons. We conclude that the opening angle requirement effectively rejects cosmic muons, and do not assign a systematic uncertainty for this possible contamination. A similar check for contamination from beam-halo muons is performed by applying the nominal analysis selection to non-collision events triggered by the presence of a single beam. Within the limited statistics, zero events pass all the analysis selections, and therefore no additional systematic uncertainty is assigned in this case. Summary of systematic uncertainties The individual variations in the definition of the track-veto are taken as correlated uncertainties, with the largest variation taken as a contribution to the systematic uncertainty. The largest variation related to the track quality, obtained when requiring high-purity tracks with > 10 hits instead of the nominal value of > 3 hits, is also taken as a contribution. The larger variation resulting from increasing or decreasing the double-proton dissociation background normalization by a factor of 2, and the larger variation resulting from increasing or decreasing the DY background normalization by a factor of 2, are each taken as contributions to the systematic uncertainty. The variation in the crossing angle, muon identification and trigger efficiencies, tracking efficiency, bias due to correlations in the J/ψ control sample, and vertexing efficiency are treated as uncorrelated uncertainties. Summing quadratically all uncorrelated contributions gives an overall relative systematic uncertainty of 4.8% on the signal yield Results For muon pairs with invariant mass greater than 11.5 GeV, single-muon transverse momentum p T (µ) > 4 GeV, and single-muon pseudorapidity in the range |η(µ)| < 2.1, 148 events pass all selections. Approximately half of these are ascribed to fully exclusive (elastic) production. The number of events expected from Monte Carlo simulation of signal, proton dissociation, and DY backgrounds for an integrated luminosity of 40 pb −1 is 184. +0.58 −0.55 (stat.) ± 0.16 (syst.) ± 0.14 (lumi.) pb, and the corresponding data-theory signal ratio is 0.83 +0.14 −0.13 (stat.) ± 0.04 (syst.) ± 0.03 (lumi.), where the statistical uncertainties are strongly correlated with the single-proton dissociation background. Summary A measurement is reported of the exclusive two-photon production of muon pairs, pp → pµ + µ − p, in a 40 pb −1 sample of proton-proton collisions collected at √ s = 7 TeV during 2010 at the LHC. The measured cross section +0.58 −0.55 (stat.) ± 0.16 (syst.) ± 0.14 (lumi.) pb, is consistent with the predicted value, and the characteristic distributions of the muon pairs produced via γγ fusion, such as the pair acoplanarity and transverse momentum, are well described by the full simulation using the matrix-element event generator LPAIR. The detection efficiencies are determined from control samples in data, including corrections for the significant event pileup. The signal yield is correlated with the dominant background from two-photon production with proton dissociation, for which the current estimate from a fit to the p T (µ + µ − ) distribution can be improved with additional data. The efficiency for the exclusivity selection is above 90% in the full data sample collected by CMS during the 2010 LHC run. With increasing instantaneous luminosity this efficiency will decrease, but without possible improvements to the selection remains above 60% with up to 8 additional pileup vertices. Since the process may be calculated reliably in the framework of QED, within uncertainties associated with the proton form factor, this represents a first step towards a complementary luminosity measurement, and a reference for other exclusive production measurements to be performed with pileup. Acknowledgments We wish to congratulate our colleagues in the CERN accelerator departments for the excellent performance of the LHC machine. [10] S. P. Baranov et al., "LPAIR -A generator

Alignment of the CMS Muon System with Cosmic-Ray and Beam-Halo Muons

Abstract The CMS muon system has been aligned using cosmic-ray muons collected in 2008 and beam-halo muons from the 2008 LHC circulating beam tests. After alignment, the resolution of the most sensitive coordinate is 80 microns for the relative positions of superlayers in the same barrel chamber and 270 microns for the relative positions of endcap chambers in the same ring structure. The resolution on the position of the central barrel chambers relative to the tracker is comprised between two extreme estimates, 200 and 700 microns, provided by two complementary studies. With minor modifications, the alignment procedures can be applied using muons from LHC collisions, leading to additional significant improvements. * See Appendix A for the list of collaboration members arXiv:0911.4022v2 [physics.ins-det] 8 Feb 2010 FERMILAB-PUB-10-163-CMS Introduction The primary goal of the Compact Muon Solenoid (CMS) experiment [1] is to explore particle physics at the TeV energy scale exploiting the proton-proton collisions delivered by the Large Hadron Collider (LHC) The muon system consists of hundreds of independent tracking chambers mounted within the CMS magnetic field return yoke. Three technologies are employed: Drift Tube (DT) chambers on the five modular wheels of the barrel section, Cathode Strip Chambers (CSC) on the six endcap disks (illustrated in Figs. 1 and 2) and Resistive Plate Chambers (RPC) throughout. The DTs and CSCs are sufficiently precise to contribute to the momentum resolution of highmomentum muons (several hundred GeV/c) assuming that these chambers are well-aligned relative to the CMS tracker, a one-meter radius silicon strip and pixel detector. Between the tracker and the muon system are electromagnetic and hadronic calorimeters (ECAL and HCAL, respectively) for particle identification and energy measurement, as well as the solenoid coil for producing an operating magnetic field strength of 3.8 T in which to measure charged-particle momenta (all shown in The CMS collaboration is developing multiple techniques to align the DT and CSC chambers and their internal layers. Photogrammetry and in-situ measurement devices [3] provide realtime monitoring of potential chamber movements on short timescales and measurements of degrees of freedom to which tracks are only weakly sensitive. Track-based alignment, the subject of this paper, optimizes component positions for a given set of tracks, directly relating the active elements of the detectors traversed by the charged particles in a shared coordinate frame. Methods using tracks are employed both to align nearby components relative to one another and to align all muon chambers relative to the tracker. A challenge to track-based alignment in the CMS muon system is the presence of large quantities of material between the chambers. As a central design feature of the detector, 20-60 cm layers of steel are sandwiched between the chambers to concentrate the magnetic field and absorb beam-produced hadrons. Consequently, uncertainties in track trajectories become significant as muons propagate through the material, making it necessary to develop alignment procedures that are insensitive to scattering, even though typical deviations in the muon trajectories (3-8 mm) are large compared to the intrinsic spatial resolution (100-300 µm). Two types of approaches are presented in this paper: the relative alignment of nearby structures, which avoids extrapolation of tracks through material but does not relate distant coordinate frames to each other, and the alignment using tracks reconstructed in the tracker, which allows for a more sophisticated treatment of propagation effects by simplifying the interdependence of alignment parameters. This paper begins with a brief overview of the geometry of the muon system and conventions to be used thereafter (Section 2), followed by presentations of three alignment procedures: (a) internal alignment of layers within DT chambers using a combination of locally fitted track segments and survey measurements (Section 3); (b) alignment of groups of overlapping CSC chambers relative to one another, using only (c) alignment of each chamber relative to the tracker, using the tracks from the tracker, propagated to the muon system with a detailed map of the magnetic field and material distribution of CMS (Section 5). Procedure (c), above, completes the alignment, relating all local coordinate frames to a shared frame. Its performance is greatly improved by supplying internally aligned chambers from procedure (a), such that only rigid-body transformations of whole chambers need to be considered. Procedures (b) and (c) both align CSC chambers relative to one another, but in different ways: (b) does not need many tracks, only about 1000 per chamber, to achieve high precision, and (c) additionally links the chambers to the tracker. With the first LHC collisions, groups of CSCs will be interaligned using (b) and these rigidbody groups will be aligned relative to the tracker with (c). As more data become available, comparisons of results from (b) and (c) yield highly sensitive tests of systematic errors in (c). Although the ideal tracks for these procedures are muons from LHC collisions, this paper focuses on application of the procedures using currently available data, namely cosmic rays (a and c) and beam-halo muons from circulating LHC beam tests in September 2008 (b). In particular, (c) requires a magnetic field to select high-quality, high-momentum muons and concurrent operation of the tracker and muon systems. The CMS Collaboration conducted a monthlong data-taking exercise known as the Cosmic Run At Four Tesla (CRAFT) during OctoberNovember 2008, with the goal of commissioning the experiment for extended operation The formalism and results of each procedure are presented together. Details of the data transfer and the computing model which were used to implement these procedures are described in Ref. Geometry of the Muon System and Definitions Muon chambers are independent, modular track detectors, each containing 6-12 measurement layers, sufficient to determine the position and direction of a passing muon from the intersections of its trajectory with the layer planes ("hits"). The DT layers are oriented nearly perpendicular to lines radially projected from the beamline, and CSC layers are perpendicular to lines parallel with the beamline. Hits are initially expressed in a local coordinate frame (x, y, z) defined by the layers: z = 0 is the plane of the layer and x is the more precisely measured (or the only measured) of the two plane coordinates. On CSC layers, the most precise measurement is given by cathode strips, which fan radially from the beamline A semi-local coordinate system for the entire chamber is defined with x, y, and z axes nominally parallel to the layers' axes, but with a single origin. Within this common frame, the positions of hits from different layers can be related to each other and combined by a linear fit into segments with position (x,ȳ) and direction ( dx dz , dy dz ). The nominal x direction of every chamber is perpendicular to the beamline and radial projections from the beamline