Using joint models for longitudinal and time-to-event data to investigate the causal effect of salvage therapy after prostatectomy

Prostate cancer patients who undergo prostatectomy are closely monitored for recurrence and metastasis using routine prostate-specific antigen measurements. When prostate-specific antigen levels rise, salvage therapies are recommended in order to decrease the risk of metastasis. However, due to the side effects of these therapies and to avoid over-treatment, it is important to understand which patients and when to initiate these salvage therapies. In this work, we use the University of Michigan Prostatectomy Registry Data to tackle this question. Due to the observational nature of this data, we face the challenge that prostate-specific antigen is simultaneously a time-varying confounder and an intermediate variable for salvage therapy. We define different causal salvage therapy effects defined conditionally on different specifications of the longitudinal prostate-specific antigen history. We then illustrate how these effects can be estimated using the framework of joint models for longitudinal and time-to-event data. All proposed methodology is implemented in the freely-available R package JMbayes2.

Varicella in the Neonatal ICU due to the Varicella Vaccine Oka Strain

BACKGROUND

Varicella vaccination of non-immune post-partum women is recommended to reduce the risk of chickenpox in mothers and their infants. Though rare, transmission of the varicella vaccine strain vOka can occur from recent vaccinees to non-immune contacts who usually develop mild chickenpox.

METHODS/RESULTS

Here we describe an infant hospitalized in the neonatal ICU with vaccine-strain varicella due to transmission from their mother who received the varicella vaccine post-partum. We describe the infection prevention and control strategies implemented to prevent further transmission.

CONCLUSION

Vaccine-strain varicella transmission from mother to infant is a rare event and its occurrence in the neonatal ICU setting can be challenging. Anticipatory guidance for mothers vaccinated in the postpartum period and support of parents of an infected infant are recommended.

Impact of Nodal Metastases in HPV-negative Oropharyngeal Cancer

BACKGROUND

The updated American Joint Committee on Cancer (AJCC) 8th Edition staging manual restructured nodal classification and staging by placing less prognostic emphasis on nodal metastases for HPV-positive oropharyngeal squamous cell carcinoma (OPSCC). However, there was no change for HPV-negative OPSCC. The purpose of our study is to examine the impact of nodal metastases on survival in HPV-negative OPSCC.

METHODS

HPV-negative OPSCC were queried from the NCDB and SEER databases. Univariable and multivariable models were utilized to determine the impact of nodal status on overall survival. These patients were reclassified according to AJCC 8 HPV-positive criteria (TNM8+) and risk stratification was quantified with C-statistics.

RESULTS

There were 11,147 cases of HPV-negative OPSCC in the NCDB and 3,613 cases in SEER that were included in the nodal classification analysis. Unlike non-oropharyngeal malignancies, increased nodal stage is not clearly associated with survival for patients with OPSCC independent of HPV status. When the TNM8+ was applied to HPV-negative patients, there was improved concordance in the NCDB cohort, 0.561 {plus minus} 0.004 to 0.624 {plus minus} 0.004 (difference +0.063) and the SEER cohort, 0.561 {plus minus} 0.008 to 0.625 {plus minus} 0.008 (difference +0.065).

CONCLUSIONS

We demonstrated a reduced impact of nodal metastasis on OPSCC survival, independent of HPV-status and specific to OPSCC.

IMPACT

We demonstrate, that when nodal staging is de-emphasized as a part of overall staging, we see improved concordance and risk stratification for HPV-negative OPSCC. The exact mechanism of this differential impact remains unknown but offers a novel area of study.

Multiple imputation with missing data indicators

Multiple imputation is a well-established general technique for analyzing data with missing values. A convenient way to implement multiple imputation is sequential regression multiple imputation, also called chained equations multiple imputation. In this approach, we impute missing values using regression models for each variable, conditional on the other variables in the data. This approach, however, assumes that the missingness mechanism is missing at random, and it is not well-justified under not-at-random missingness without additional modification. In this paper, we describe how we can generalize the sequential regression multiple imputation imputation procedure to handle missingness not at random in the setting where missingness may depend on other variables that are also missing but not on the missing variable itself, conditioning on fully observed variables. We provide algebraic justification for several generalizations of standard sequential regression multiple imputation using Taylor series and other approximations of the target imputation distribution under missingness not at random. Resulting regression model approximations include indicators for missingness, interactions, or other functions of the missingness not at random missingness model and observed data. In a simulation study, we demonstrate that the proposed sequential regression multiple imputation modifications result in reduced bias in the final analysis compared to standard sequential regression multiple imputation, with an approximation strategy involving inclusion of an offset in the imputation model performing the best overall. The method is illustrated in a breast cancer study, where the goal is to estimate the prevalence of a specific genetic pathogenic variant.

A Bayesian dose-finding design for outcomes evaluated with uncertainty

INTRODUCTION

In some phase I trial settings, there is uncertainty in assessing whether a given patient meets the criteria for dose-limiting toxicity.

METHODS

We present a design which accommodates dose-limiting toxicity outcomes that are assessed with uncertainty for some patients. Our approach could be utilized in many available phase I trial designs, but we focus on the continual reassessment method due to its popularity. We assume that for some patients, instead of the usual binary dose-limiting toxicity outcome, we observe a physician-assessed probability of dose-limiting toxicity specific to a given patient. Data augmentation is used to estimate the posterior probabilities of dose-limiting toxicity at each dose level based on both the fully observed and partially observed patient outcomes. A simulation study is used to assess the performance of the design relative to using the continual reassessment method on the true dose-limiting toxicity outcomes (available in simulation setting only) and relative to simple thresholding approaches.

RESULTS

Among the designs utilizing the partially observed outcomes, our proposed design has the best overall performance in terms of probability of selecting correct maximum tolerated dose and number of patients treated at the maximum tolerated dose.

CONCLUSION

Incorporating uncertainty in dose-limiting toxicity assessment can improve the performance of the continual reassessment method design.

Using multiple imputation to classify potential outcomes subgroups

With medical tests becoming increasingly available, concerns about over-testing, over-treatment and health care cost dramatically increase. Hence, it is important to understand the influence of testing on treatment selection in general practice. Most statistical methods focus on average effects of testing on treatment decisions. However, this may be ill-advised, particularly for patient subgroups that tend not to benefit from such tests. Furthermore, missing data are common, representing large and often unaddressed threats to the validity of most statistical methods. Finally, it is often desirable to conduct analyses that can be interpreted causally. Using the Rubin Causal Model framework, we propose to classify patients into four potential outcomes subgroups, defined by whether or not a patient's treatment selection is changed by the test result and by the direction of how the test result changes treatment selection. This subgroup classification naturally captures the differential influence of medical testing on treatment selections for different patients, which can suggest targets to improve the utilization of medical tests. We can then examine patient characteristics associated with patient potential outcomes subgroup memberships. We used multiple imputation methods to simultaneously impute the missing potential outcomes as well as regular missing values. This approach can also provide estimates of many traditional causal quantities of interest. We find that explicitly incorporating causal inference assumptions into the multiple imputation process can improve the precision for some causal estimates of interest. We also find that bias can occur when the potential outcomes conditional independence assumption is violated; sensitivity analyses are proposed to assess the impact of this violation. We applied the proposed methods to examine the influence of 21-gene assay, the most commonly used genomic test in the United States, on chemotherapy selection among breast cancer patients.

Pretreatment Dietary Patterns, Serum Carotenoids and Tocopherols Influence Tumor Immune Response in Head and Neck Squamous Cell Carcinoma

BACKGROUND

Tumor infiltrating lymphocytes (TILs) aid in informing treatment for head and neck squamous cell carcinoma (HNSCC). Nevertheless, little is known about the role of diet on TILs.

METHODS

Immunohistologic expression of CD4, CD8, CD68, CD103, CD104 and FOXP3 were assessed in tissue microarrays from 233 previously untreated HNSCC patients. Associations between these markers and pretreatment dietary patterns were evaluated using linear regression. Associations between baseline serum carotenoids, tocopherols and TILs were assessed using logistic regression. Cox models evaluated the association between diet and TILs on overall and recurrence-free survival.

RESULTS

Consumption of a Western dietary pattern was associated with lower CD8+ and FOXP3+ infiltrates (p-value:0.03 and 0.02, respectively). Multivariable logistic regression models demonstrated significantly higher CD8+ (OR:2.21;p-value:0.001) and FOXP3+ (OR:4.26;p-value:<0.0001) among patients with high gamma tocopherol. Conversely, high levels of xanthophylls (OR:0.12;p-value:<0.0001), lycopene (OR:0.36;p-value:0.0001) and total carotenoids(OR:0.31;p-value: <0.0001) were associated with significantly lower CD68+. Among those with high CD4+ (HR:1.77;p-value:0.03), CD68+ (HR:2.42;p-value:0.004), CD103+ (HR:3.64;p-value:0.03) and FOXP3+ (HR:3.09;p-value:0.05), having a high Western dietary pattern increased the risk of overall mortality when compared to a low Western dietary pattern.

CONCLUSION

Dietary patterns and serum carotenoids may play an important role in modifying TILs, and ultimately, outcome after diagnosis with HNSCC.

Modeling adverse event counts in phase I clinical trials of a cytotoxic agent

Background/Aims The goal of phase I clinical trials for cytotoxic agents is to find the maximum dose with an acceptable risk of severe toxicity. The most common designs for these dose-finding trials use a binary outcome indicating whether a patient had a dose-limiting toxicity. However, a patient may experience multiple toxicities, with each toxicity assigned an ordinal severity score. The binary response is then obtained by dichotomizing a patient's richer set of data. We contribute to the growing literature on new models to exploit this richer toxicity data, with the goal of improving the efficiency in estimating the maximum tolerated dose. Methods We develop three new, related models that make use of the total number of dose-limiting and low-level toxicities a patient experiences. We use these models to estimate the probability of having at least one dose-limiting toxicity as a function of dose. In a simulation study, we evaluate how often our models select the true maximum tolerated dose, and we compare our models with the continual reassessment method, which uses binary data. Results Across a variety of simulation settings, we find that our models compare well against the continual reassessment method in terms of selecting the true optimal dose. In particular, one of our models which uses dose-limiting and low-level toxicity counts beats or ties the other models, including the continual reassessment method, in all scenarios except the one in which the true optimal dose is the highest dose available. We also find that our models, when not selecting the true optimal dose, tend to err by picking lower, safer doses, while the continual reassessment method errs more toward toxic doses. Conclusion Using dose-limiting and low-level toxicity counts, which are easily obtained from data already routinely collected, is a promising way to improve the efficiency in finding the true maximum tolerated dose in phase I trials.

Efimov States of Strongly Interacting Photons

We demonstrate the emergence of universal Efimov physics for interacting photons in cold gases of Rydberg atoms. We consider the behavior of three photons injected into the gas in their propagating frame, where a paraxial approximation allows us to consider them as massive particles. In contrast to atoms and nuclei, the photons have a large anisotropy between their longitudinal mass, arising from dispersion, and their transverse mass, arising from diffraction. Nevertheless, we show that, in suitably rescaled coordinates, the effective interactions become dominated by s-wave scattering near threshold and, as a result, give rise to an Efimov effect near unitarity. We show that the three-body loss of these Efimov trimers can be strongly suppressed and determine conditions under which these states are observable in current experiments. These effects can be naturally extended to probe few-body universality beyond three bodies, as well as the role of Efimov physics in the nonequilibrium, many-body regime.

Threshold Dynamics of a Semiconductor Single Atom Maser

We demonstrate a single atom maser consisting of a semiconductor double quantum dot (DQD) that is embedded in a high-quality-factor microwave cavity. A finite bias drives the DQD out of equilibrium, resulting in sequential single electron tunneling and masing. We develop a dynamic tuning protocol that allows us to controllably increase the time-averaged repumping rate of the DQD at a fixed level detuning, and quantitatively study the transition through the masing threshold. We further examine the crossover from incoherent to coherent emission by measuring the photon statistics across the masing transition. The observed threshold behavior is in agreement with an existing single atom maser theory when small corrections from lead emission are taken into account.

Precise spatio-temporal control of rapid optogenetic cell ablation with mem-KillerRed in Zebrafish

The ability to kill individual or groups of cells in vivo is important for studying cellular processes and their physiological function. Cell-specific genetically encoded photosensitizing proteins, such as KillerRed, permit spatiotemporal optogenetic ablation with low-power laser light. We report dramatically improved resolution and speed of cell targeting in the zebrafish kidney through the use of a selective plane illumination microscope (SPIM). Furthermore, through the novel incorporation of a Bessel beam into the SPIM imaging arm, we were able to improve on targeting speed and precision. The low diffraction of the Bessel beam coupled with the ability to tightly focus it through a high NA lens allowed precise, rapid targeting of subsets of cells at anatomical depth in live, developing zebrafish kidneys. We demonstrate that these specific targeting strategies significantly increase the speed of optoablation as well as fish survival.

Observation of optomechanical buckling transitions

Correlated phases of matter provide long-term stability for systems as diverse as solids, magnets and potential exotic quantum materials. Mechanical systems, such as buckling transition spring switches, can have engineered, stable configurations whose dependence on a control variable is reminiscent of non-equilibrium phase transitions. In hybrid optomechanical systems, light and matter are strongly coupled, allowing engineering of rapid changes in the force landscape, storing and processing information, and ultimately probing and controlling behaviour at the quantum level. Here we report the observation of first- and second-order buckling transitions between stable mechanical states in an optomechanical system, in which full control of the nature of the transition is obtained by means of the laser power and detuning. The underlying multiwell confining potential we create is highly tunable, with a sub-nanometre distance between potential wells. Our results enable new applications in photonics and information technology, and may enable explorations of quantum phase transitions and macroscopic quantum tunnelling in mechanical systems.

Optomechanical systems could form logic gates, but key requirements are two stable static states and the ability to switch between them. Here, the authors observe radiation-pressure induced buckling transitions in an optomechanical system, and control this transition by varying laser power and detuning.

Sisyphus Thermalization of Photons in a Cavity-Coupled Double Quantum Dot

We investigate the nonclassical states of light that emerge in a microwave resonator coupled to a periodically driven electron in a nanowire double quantum dot (DQD). Under certain drive configurations, we find that the resonator approaches a thermal state at the temperature of the surrounding substrate with a chemical potential given by a harmonic of the drive frequency. Away from these thermal regions we find regions of gain and loss, where the system can lase, or regions where the DQD acts as a single-photon source. These effects are observable in current devices and have broad utility for quantum optics with microwave photons.

Optical Control of Donor Spin Qubits in Silicon

We show how to achieve optical, spin-selective transitions from the ground state to excited orbital states of group-V donors (P, As, Sb, Bi) in silicon. We consider two approaches based on either resonant, far-infrared (IR) transitions of the neutral donor or resonant, near-IR excitonic transitions. For far-IR light, we calculate the dipole matrix elements between the valley-orbit and spin-orbit split states for all the goup-V donors using effective mass theory. We then calculate the maximum rate and amount of electron-nuclear spin-polarization achievable through optical pumping with circularly polarized light. We find this approach is most promising for Bi donors due to their large spin-orbit and valley-orbit interactions. Using near-IR light, spin-selective excitation is possible for all the donors by driving a two-photon Λ-transition from the ground state to higher orbitals with even parity. We show that externally applied electric fields or strain allow similar, spin-selective Λ-transition to odd-parity excited states. We anticipate these results will be useful for future spectroscopic investigations of donors, quantum control and state preparation of donor spin qubits, and for developing a coherent interface between donor spin qubits and single photons.

Injection Locking of a Semiconductor Double Quantum Dot Micromaser

Emission linewidth is an important figure of merit for masers and lasers. We recently demonstrated a semiconductor double quantum dot (DQD) micromaser where photons are generated through single electron tunneling events. Charge noise directly couples to the DQD energy levels, resulting in a maser linewidth that is more than 100 times larger than the Schawlow-Townes prediction. Here we demonstrate a linewidth narrowing of more than a factor 10 by locking the DQD emission to a coherent tone that is injected to the input port of the cavity. We measure the injection locking range as a function of cavity input power and show that it is in agreement with the Adler equation. The position and amplitude of distortion sidebands that appear outside of the injection locking range are quantitatively examined. Our results show that this unconventional maser, which is impacted by strong charge noise and electron-phonon coupling, is well described by standard laser models.

NDN and CD1A are novel prognostic methylation markers in patients with head and neck squamous carcinomas

BACKGROUND

HPV-associated HNSCCs have a distinct etiologic mechanism and better prognosis than those with non-HPV associated HNSCCs. However, even within the each group, there is heterogeneity in survival time. Here, we test the hypothesis that specific candidate gene methylation markers (CCNA1, NDN, CD1A, DCC, p16, GADD45A) are associated with tumor recurrence and survival, in a well-characterized, prospective, cohort of 346 HNSCC patients.

METHODS

Kaplan-Meier curves were used to estimate survival time distributions. Multivariable Cox Proportional Hazards models were used to test associations between each methylation marker and OST/RPFT after adjusting for known or identified prognostic factors. Stratified Cox models included an interaction term between HPV and methylation marker to test for differences in the associations of the biomarker with OST or RPFT across HPV status.

RESULTS

Methylation markers were differentially associated with patient characteristics. DNA hypermethylation of NDN and CD1A was found to be significantly associated with overall survival time (OST) in all HNSCC patients (NDN hazard ratio (HR): 2.35, 95% CI: 1.40-3.94; CD1A HR: 1.31, 95% CI: 1.01-1.71). Stratification by HPV status revealed hypermethylation of CD1A was associated with better OST and recurrence/persistence-free time (RPFT) (OST HR: 3.34, 95% CI: 1.88-5.93; RPFT HR: 2.06, 95% CI: 1.21-3.49), while hypomethylation of CCNA1 was associated with increased RPFT in HPV (+) patients only (HR: 0.31, 95% CI: 0.13-0.74).

CONCLUSIONS

This study is the first to describe novel epigenetic alterations associated with survival in an unselected, prospectively collected, consecutive cohort of patients with HNSCC. DNA hypermethylation of NDN and CD1A was found to be significantly associated with increased overall survival time in all HNSCC patients. However, stratification by the important prognostic factor of HPV status revealed the immune marker, CD1A, and the cell cycle regulator, CCNA1 to be associated with prognosis in HPV (+) patients, specifically. Here, we identified novel methylation markers and specific, epigenetic molecular differences associated with HPV status, which warrant further investigation.

Tibiotalocalcaneal arthrodesis with a compressive retrograde nail: A retrospective study of 59 nails

BACKGROUND

Tibiotalocalcaneal arthrodesis is an important salvage method for patients with complex hindfoot problems. This study reports the elective results of combined subtalar and ankle arthrodesis using one design of retrograde intramedullary compression nail.

METHODS

Retrospective review identified 58 patients undergoing 59 tibiotalocalcaneal arthrodesis procedures. Mean follow up was 9.15 (3-36) months with average age 60.7 (22-89) years. A function and subjective patient satisfaction questionnaire was achieved in 89%.

RESULTS

53 patients (93%) achieved union at a mean time of 4.17 months. Four patients (8%) subjectively thought the procedure was of no benefit while 42 (84%) had an excellent or good result. The mean visual analogue scale (VAS) score for preoperative functional pain was 7.46 compared to 1.98 post-operatively (p<0.001).

CONCLUSIONS

This device and technique offers an effective treatment of hindfoot pathology giving reliable compression and subsequent fusion with excellent patient satisfaction and pain relief.

LEVEL OF EVIDENCE

IV case series.

Retrospective Study of Sirolimus and Cyclophosphamide in Patients with Advanced Differentiated Thyroid Cancers

BACKGROUND

We hypothesize that the combination of an mTOR inhibitor, sirolimus, with a well-known cytotoxic agent, cyclophosphamide, provides a well-tolerated and promising alternative treatment for advanced, differentiated thyroid cancers (DTC).

METHODS

This retrospective review extracted data from patients treated for advanced DTC at the University of Michigan Comprehensive Cancer Center from 1995 through 2013. Fifteen patients treated with combination sirolimus and cyclophosphamide were identified as the sirolimus+cyp group. Seventeen patients treated with standard of care and enrolled in clinical trials were identified as the comparison group.

RESULTS

The one-year progression free survival rate (PFS) was 0.45, 95% CI [0.26, 0.80] in the sirolimus+cyp population and 0.30, 95% CI [0.13, 0.67] in the comparison population. The hazard ratio for PFS from initiation of treatment was 1.47, 95% CI [0.57, and 3.78]. In patients treated as first line, one-year PFS rate was 0.57, 95% CI [0.30, 1.00] in the sirolimus+cyp group and relatively unchanged at 0.29, 95% CI [0.11, 0.74] in the comparison group. The hazard ratio for PFS for first line patients was 1.10, 95% CI[ 0.4, and 3.5]. In patients with 3 or fewer sites of metastases, the one year PFS was 0.58, 95% CI [0.33, 1.00] in the sirolimus+cyp group, and 0.37, 95% CI [0.17, 0.80] in the comparison group. The average number of toxicities was 0.87 in the sirolimus+cyp patients and 1.71 in the comparison group.

CONCLUSIONS

The combination of sirolimus and cyclophosphamide was generally well tolerated with similar progression free survival, highlighting its applicability in patients with limited options.

Phonon-assisted gain in a semiconductor double quantum dot maser

We develop a microscopic model for the recently demonstrated double-quantum-dot maser. In characterizing the gain of this device we find that, in addition to the direct stimulated emission of photons, there is a large contribution from the simultaneous emission of a photon and a phonon, i.e., the phonon sideband. We show that this phonon-assisted gain typically dominates the overall gain, which leads to masing. Recent experimental data are well fit with our model.

Transcription of the Rous sarcoma virus genome in vitro and in vivo

RNA-directed DNA synthesis by detergent-disrupted virions of Rous sarcoma virus (RSV) initiates by the covalent attachment of pdA to the 3'-terminal rA of a 4S RNA hydrogen-bonded to the 70S RNA template. This 4S "primer" has structural features of tRNA and can be aminoacylated with methionine. Synthesis and integration of provirus DNA can be monitored in both permissive (duck) and nonpermissive (mouse) cells acutely infected with RSV. The results of these studies, as well as data obtained with RSV-infected mammalian cells which have reverted from a transformed to a pheno-typically normal state, indicate that integration of viral genes into the host chromosome is not sufficient cause for transformation. Pertinent features of virus-specific RNA-directed DNA synthesis in vitro and in vivo are reviewed and compared.

Smoking, internalized heterosexism, and HIV disease management among male couples

High rates of cigarette smoking have been observed among HIV-positive individuals. Smoking has been linked to HIV-related medical complications and non-AIDS defining cancers and negatively impacts on immune function and virologic control. Although internalized heterosexism has been related to smoking behaviors, little is known about associations between partners' reports of smoking, internalized heterosexism, and HIV medication management in male couples with HIV. A sample of 266 male couples completed baseline assessments for a cohort study examining relationship factors and HIV treatment. A computer-based survey assessed self-reported smoking behaviors, alcohol use, internalized heterosexism, and antiretroviral therapy (ART) adherence. HIV-positive men also provided blood samples to assess viral load. Approximately 30% of the sample reported that they are currently smoking cigarettes. After adjusting for demographic characteristics, men in a primary relationship with a partner who reported currently smoking had more than five-fold greater odds of reporting smoking. Higher levels of internalized heterosexism and financial hardship were each independently associated with greater odds of reporting smoking. Among HIV-positive men on ART (n = 371), having a partner who reported smoking was associated with almost three-fold greater odds of having a detectable viral load. Our findings add new support to the evidence of romantic partners influencing each other's health behaviors, and demonstrate an association between smoking and disease management within male couples. Future research should explore the interpersonal and social contexts of smoking in order to develop interventions that meet the unique needs of male couples.

Topologically robust transport of photons in a synthetic gauge field

Electronic transport is localized in low-dimensional disordered media. The addition of gauge fields to disordered media leads to fundamental changes in the transport properties. We implement a synthetic gauge field for photons using silicon-on-insulator technology. By determining the distribution of transport properties, we confirm that waves are localized in the bulk and localization is suppressed in edge states. Our system provides a new platform for investigating the transport properties of photons in the presence of synthetic gauge fields.

Photon emission from a cavity-coupled double quantum dot

We study a voltage biased InAs double quantum dot (DQD) that is coupled to a superconducting transmission line resonator. Inelastic tunneling in the DQD is mediated by electron phonon coupling and coupling to the cavity mode. We show that electronic transport through the DQD leads to photon emission from the cavity at a rate of 10 MHz. With a small cavity drive field, we observe a gain of up to 15 in the cavity transmission. Our results are analyzed in the context of existing theoretical models and suggest that it may be necessary to account for inelastic tunneling processes that proceed via simultaneous emission of a phonon and a photon.

Increasing efficiency for estimating treatment-biomarker interactions with historical data

Detecting a treatment-biomarker interaction, which is a task better suited for large sample sizes, in a phase II trial, which has a small sample size, is challenging. In this paper, we investigate how two plausibly available sources of historical data may contain partial information to help estimate the treatment-biomarker interaction parameter in a randomized phase II study. The parameter is not identified in either historical dataset alone; nonetheless, both can provide some information about the parameter and, consequently, increase the precision of its estimate. To illustrate the potential for gains in efficiency and implications for the design of the study, we consider Gaussian outcomes and biomarker data and calculate the asymptotic variance using the expected Fisher information matrix. We quantify the gain in efficiency both through a numerical study and, in a simplified setting, insights derived from an algebraic development of the problem. We find that a non-negligible gain in precision is possible, even if the historical and prospective data do not arise from identical underlying models.

Individualized dynamic prediction of prostate cancer recurrence with and without the initiation of a second treatment: Development and validation

With the emergence of rich information on biomarkers after treatments, new types of prognostic tools are being developed: dynamic prognostic tools that can be updated at each new biomarker measurement. Such predictions are of interest in oncology where after an initial treatment, patients are monitored with repeated biomarker data. However, in such setting, patients may receive second treatments to slow down the progression of the disease. This paper aims to develop and validate dynamic individual predictions that allow the possibility of a new treatment in order to help understand the benefit of initiating new treatments during the monitoring period. The prediction of the event in the next x years is done under two scenarios: (1) the patient initiates immediately a second treatment, (2) the patient does not initiate any treatment in the next x years. Predictions are derived from shared random-effect models. Applied to prostate cancer data, different specifications for the dependence between the prostate-specific antigen repeated measures, the initiation of a second treatment (hormonal therapy), and the risk of clinical recurrence are investigated and compared. The predictive accuracy of the dynamic predictions is evaluated with two measures (Brier score and prognostic cross-entropy) for which approximated cross-validated estimators are proposed.

Ultra-sensitive chip-based photonic temperature sensor using ring resonator structures

Resistance thermometry provides a time-tested method for taking temperature measurements. However, fundamental limits to resistance-based approaches has produced considerable interest in developing photonic temperature sensors to leverage advances in frequency metrology and to achieve greater mechanical and environmental stability. Here we show that silicon-based optical ring resonator devices can resolve temperature differences of 1 mK using the traditional wavelength scanning methodology. An even lower noise floor of 80 μK for measuring temperature difference is achieved in the side-of-fringe, constant power mode measurement.

Personal or relational? Examining sexual health in the context of HIV serodiscordant same-sex male couples

Couples' ability to adopt a "we" orientation has been associated with optimal health outcomes. This study examined how personal and relational motivations are uniquely associated with unprotected anal intercourse (UAI), protected anal intercourse (PAI), and the absence of sexual activity within HIV-serodiscordant same-sex male couples. HIV-positive men and their HIV-negative partners (N = 116 couples, 232 men) completed questionnaires and HIV-positive men had blood drawn for viral load. Results of a multinomial logistic regression illustrated that sexual satisfaction was positively associated with PAI among HIV-negative partners and negatively associated with PAI among HIV-positive partners. Endorsing a "we" orientation was positively associated with PAI among HIV-positive partners. Findings suggest that HIV-positive partners who espouse a "we" orientation may be willing to forgo their personal interests to protect their HIV-negative partners from HIV transmission. Couples-based interventions are warranted to help strengthen relationship dynamics to enhance the sexual health of serodiscordant couples.

Personal or relational? Examining sexual health in the context of HIV serodiscordant same-sex male couples

Couples' ability to adopt a "we" orientation has been associated with optimal health outcomes. This study examined how personal and relational motivations are uniquely associated with unprotected anal intercourse (UAI), protected anal intercourse (PAI), and the absence of sexual activity within HIV-serodiscordant same-sex male couples. HIV-positive men and their HIV-negative partners (N = 116 couples, 232 men) completed questionnaires and HIV-positive men had blood drawn for viral load. Results of a multinomial logistic regression illustrated that sexual satisfaction was positively associated with PAI among HIV-negative partners and negatively associated with PAI among HIV-positive partners. Endorsing a "we" orientation was positively associated with PAI among HIV-positive partners. Findings suggest that HIV-positive partners who espouse a "we" orientation may be willing to forgo their personal interests to protect their HIV-negative partners from HIV transmission. Couples-based interventions are warranted to help strengthen relationship dynamics to enhance the sexual health of serodiscordant couples.

BAYESIAN SHRINKAGE METHODS FOR PARTIALLY OBSERVED DATA WITH MANY PREDICTORS

Motivated by the increasing use of and rapid changes in array technologies, we consider the prediction problem of fitting a linear regression relating a continuous outcome Y to a large number of covariates X , eg measurements from current, state-of-the-art technology. For most of the samples, only the outcome Y and surrogate covariates, W , are available. These surrogates may be data from prior studies using older technologies. Owing to the dimension of the problem and the large fraction of missing information, a critical issue is appropriate shrinkage of model parameters for an optimal bias-variance tradeoff. We discuss a variety of fully Bayesian and Empirical Bayes algorithms which account for uncertainty in the missing data and adaptively shrink parameter estimates for superior prediction. These methods are evaluated via a comprehensive simulation study. In addition, we apply our methods to a lung cancer dataset, predicting survival time (Y) using qRT-PCR ( X ) and microarray ( W ) measurements.

Long-term clinical and functional outcome following treatment for Paget–Schroetter syndrome

Background

Effort-related thrombosis of the axillosubclavian vein (Paget–Schroetter syndrome, PSS) is uncommon. It tends to affect young, active individuals and yet consensus on management is lacking. The aim here was to analyse late outcomes in a series of patients treated for PSS using a standard protocol.

Methods

The medical records of patients treated for PSS over 16 years were analysed. Patients were divided into four groups according to their management. Clinical and functional outcomes were analysed regarding residual venous defects after treatment, and Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire scores, respectively.

Results

Some 117 patients (52 men and 65 women, mean age 32 years) were included. Catheter-directed thrombolysis was successful in 42 of 56 treated patients. Thoracic outlet decompression surgery was performed in 95 patients. DASH scores improved significantly in patients treated surgically (P &lt; 0.001 to P = 0·009); early surgery had a better outcome than delayed surgery (P = 0·040). Patients who were managed conservatively showed no improvement (P = 0·116). Where venoplasty was necessary, it was successful in 18 of 25 patients. A short duration of lysis (less than 24 h) increased the risk of rethrombosis (P = 0·020). The method of postoperative anticoagulation had no influence on the rate of rethrombosis.

Conclusion

Patients treated surgically for PSS had better functional outcomes than those managed conservatively. Prompt thrombolysis and surgery was superior to delayed management with respect to rethrombosis and functional outcome.

Self-consistent measurement and state tomography of an exchange-only spin qubit

Quantum-dot spin qubits characteristically use oscillating magnetic or electric fields, or quasi-static Zeeman field gradients, to realize full qubit control. For the case of three confined electrons, exchange interaction between two pairs allows qubit rotation around two axes, hence full control, using only electrostatic gates. Here, we report initialization, full control, and single-shot readout of a three-electron exchange-driven spin qubit. Control via the exchange interaction is fast, yielding a demonstrated 75 qubit rotations in less than 2 ns. Measurement and state tomography are performed using a maximum-likelihood estimator method, allowing decoherence, leakage out of the qubit state space, and measurement fidelity to be quantified. The methods developed here are generally applicable to systems with state leakage, noisy measurements and non-orthogonal control axes.

Electrically protected resonant exchange qubits in triple quantum dots

We present a modulated microwave approach for quantum computing with qubits comprising three spins in a triple quantum dot. This approach includes single- and two-qubit gates that are protected against low-frequency electrical noise, due to an operating point with a narrowband response to high frequency electric fields. Furthermore, existing double quantum dot advances, including robust preparation and measurement via spin-to-charge conversion, are immediately applicable to the new qubit. Finally, the electric dipole terms implicit in the high frequency coupling enable strong coupling with superconducting microwave resonators, leading to more robust two-qubit gates.

Quantum-dot-based resonant exchange qubit

We introduce a solid-state qubit in which exchange interactions among confined electrons provide both the static longitudinal field and the oscillatory transverse field, allowing rapid and full qubit control via rf gate-voltage pulses. We demonstrate two-axis control at a detuning sweet spot, where leakage due to hyperfine coupling is suppressed by the large exchange gap. A π/2-gate time of 2.5 ns and a coherence time of 19 μs, using multipulse echo, are also demonstrated. Model calculations that include effects of hyperfine noise are in excellent quantitative agreement with experiment.

Performance of coagulation tests in patients on therapeutic doses of dabigatran: a cross-sectional pharmacodynamic study based on peak and trough plasma levels

BACKGROUND

Knowledge of anticoagulation status during dabigatran therapy may be desirable in certain clinical situations.

OBJECTIVE

To determine the coagulation tests that are most useful for assessing dabigatran's anticoagulant effect.

METHODS

Peak and trough blood samples from 35 patients taking dabigatran 150 mg twice daily, and one sample each from 30 non-anticoagulated individuals, were collected. Mass spectrometry and various coagulation assays were performed. 'Therapeutic range' was defined as the range of plasma dabigatran concentrations determined by mass spectrometry between the 2.5th and 97.5th percentiles of all values.

RESULTS

The therapeutic range was 27-411 ng mL(-1) . The prothrombin time (PT) and activated partial thromboplastin time (APTT), determined with multiple reagents, and activated clotting time (ACT) were insensitive to therapeutic dabigatran: 29%, 18% and 40% of samples had a normal PT, APTT, and ACT, respectively. However, normal PT, ACT and APTT ruled out dabigatran levels above the 75th percentile. The thrombin clotting time (TCT) correlated well and linearly with dabigatran levels below the 50th percentile, but was unmeasurable above it. The dilute thrombin time, ecarin clotting time and ecarin chromogenic assay showed linear correlations with dabigatran levels over a broad range, and identified therapeutic and supratherapeutic levels.

CONCLUSIONS

The prothrombin time, APTT and ACT are often normal in spite of therapeutic dabigatran plasma levels. The TCT is useful for detecting minimal dabigatran levels. The dilute thrombin time and chromogenic and clotting ecarin assays accurately identify therapeutic and supratherapeutic dabigatran levels. This trial is registered at www.clinicaltrials.gov (#NCT01588327).

Cardiac damage induced by immunization with heat-killed Trypanosoma cruzi is not antibody mediated

Cardiac inflammation that develops during infection with Trypanosoma cruzi may result in part from autoimmunity, which may occur after bystander activation, after parasite-induced cardiomyocyte damage, or molecular mimicry. A/J mice infected with T. cruzi or immunized with heat-killed T. cruzi (HKTC) develop strong autoimmunity accompanied by cardiac damage. To determine whether this cardiac damage occurs via an antibody-dependent mechanism, we analysed T. cruzi-infected and HKTC-immunized mice for the presence of autoantibodies, cardiac antibody deposition, and serum cardiac troponin I as a measure of cardiac damage. We also performed a serum transfer experiment in which sera from T. cruzi-infected and T. cruzi-immunized mice (and controls) were transferred into naïve recipients, which were then analysed for the presence of antibodies and serum troponin. Unlike T. cruzi-infected mice, T. cruzi-immunized mice did not show significant antibody deposition in the myocardium. These results indicate that antibody deposition does not precede cardiac damage and inflammation in mice immunized with or infected with T. cruzi. Serum adoptive transfer did not induce cardiac damage in any recipients. Based on these findings, we conclude that the cardiac damage induced by immunization with HKTC is not mediated by antibodies.

Simultaneous spin-charge relaxation in double quantum dots

We investigate phonon-induced spin and charge relaxation mediated by spin-orbit and hyperfine interactions for a single electron confined within a double quantum dot. A simple toy model incorporating both direct decay to the ground state of the double dot and indirect decay via an intermediate excited state yields an electron spin relaxation rate that varies nonmonotonically with the detuning between the dots. We confirm this model with experiments performed on a GaAs double dot, demonstrating that the relaxation rate exhibits the expected detuning dependence and can be electrically tuned over several orders of magnitude. Our analysis suggests that spin-orbit mediated relaxation via phonons serves as the dominant mechanism through which the double-dot electron spin-flip rate varies with detuning.

Nonlinear optics quantum computing with circuit QED

One approach to quantum information processing is to use photons as quantum bits and rely on linear optical elements for most operations. However, some optical nonlinearity is necessary to enable universal quantum computing. Here, we suggest a circuit-QED approach to nonlinear optics quantum computing in the microwave regime, including a deterministic two-photon phase gate. Our specific example uses a hybrid quantum system comprising a LC resonator coupled to a superconducting flux qubit to implement a nonlinear coupling. Compared to the self-Kerr nonlinearity, we find that our approach has improved tolerance to noise in the qubit while maintaining fast operation.

A Phase I/II trial design when response is unobserved in subjects with dose-limiting toxicity

We propose a Phase I/II trial design in which subjects with dose-limiting toxicity are not followed for response, leading to three possible outcomes for each subject: dose-limiting toxicity, absence of therapeutic response without dose-limiting toxicity, and presence of therapeutic response without dose-limiting toxicity. We define the latter outcome as a 'success,' and the goal of the trial is to identify the dose with the largest probability of success. This dose is commonly referred to as the most successful dose. We propose a design that accumulates information on subjects with regard to both dose-limiting toxicity and response conditional on no dose-limiting toxicity. Bayesian methods are used to update the estimates of dose-limiting toxicity and response probabilities when each subject is enrolled, and we use these methods to determine the dose level assigned to each subject. Due to the need to explore doses more fully, each subject is not necessarily assigned the current estimate of the most successful dose; our algorithm may instead assign a dose that is in a neighborhood of the current most successful dose. We examine the ability of our design to correctly identify the most successful dose in a variety of settings via simulation and compare the performance of our design to that of competing approaches.

Quantum interface between an electrical circuit and a single atom

We show how to bridge the divide between atomic systems and electronic devices by engineering a coupling between the motion of a single ion and the quantized electric field of a resonant circuit. Our method can be used to couple the internal state of an ion to the quantized circuit with the same speed as the internal-state coupling between two ions. All the well-known quantum information protocols linking ion internal and motional states can be converted to protocols between circuit photons and ion internal states. Our results enable quantum interfaces between solid state qubits, atomic qubits, and light, and lay the groundwork for a direct quantum connection between electrical and atomic metrology standards.

Laser cooling and optical detection of excitations in a LC electrical circuit

We explore a method for laser cooling and optical detection of excitations in a room temperature LC electrical circuit. Our approach uses a nanomechanical oscillator as a transducer between optical and electronic excitations. An experimentally feasible system with the oscillator capacitively coupled to the LC and at the same time interacting with light via an optomechanical force is shown to provide strong electromechanical coupling. Conditions for improved sensitivity and quantum limited readout of electrical signals with such an "optical loud speaker" are outlined.

Nanoscale optical electrometer

We propose and demonstrate an all-optical approach to single-electron sensing using the optical transitions of a semiconductor quantum dot. The measured electric-field sensitivity of 5 (V/m)/√Hz corresponds to detecting a single electron located 5 μm from the quantum dot-nearly 10 times greater than the diffraction limited spot size of the excitation laser-in 1 s. The quantum-dot-based electrometer is more sensitive than other devices operating at a temperature of 4.2 K or higher and further offers suppressed backaction on the measured system.

Coupling nitrogen-vacancy centers in diamond to superconducting flux qubits

We propose a method to achieve coherent coupling between nitrogen-vacancy (NV) centers in diamond and superconducting (SC) flux qubits. The resulting coupling can be used to create a coherent interaction between the spin states of distant NV centers mediated by the flux qubit. Furthermore, the magnetic coupling can be used to achieve a coherent transfer of quantum information between the flux qubit and an ensemble of NV centers. This enables a long-term memory for a SC quantum processor and possibly an interface between SC qubits and light.

Exchange control of nuclear spin diffusion in a double quantum dot

The influence of gate-controlled two-electron exchange on the relaxation of nuclear polarization in small ensembles (N∼10(6)) of nuclear spins is examined in a GaAs double quantum dot system. Waiting in the (2,0) charge configuration, which has large exchange splitting, reduces the nuclear diffusion rate compared to that of the (1,1) configuration. Matching exchange to Zeeman splitting significantly increases the nuclear diffusion rate.

Dynamic nuclear polarization in double quantum dots

We theoretically investigate the controlled dynamic polarization of lattice nuclear spins in GaAs double quantum dots containing two electrons. Three regimes of long-term dynamics are identified, including the buildup of a large difference in the Overhauser fields across the dots, the saturation of the nuclear polarization process associated with formation of so-called "dark states", and the elimination of the difference field. We show that in the case of unequal dots, buildup of difference fields generally accompanies the nuclear polarization process, whereas for nearly identical dots, buildup of difference fields competes with polarization saturation in dark states. The elimination of the difference field does not, in general, correspond to a stable steady state of the polarization process.

Repetitive readout of a single electronic spin via quantum logic with nuclear spin ancillae

Robust measurement of single quantum bits plays a key role in the realization of quantum computation and communication as well as in quantum metrology and sensing. We have implemented a method for the improved readout of single electronic spin qubits in solid-state systems. The method makes use of quantum logic operations on a system consisting of a single electronic spin and several proximal nuclear spin ancillae in order to repetitively readout the state of the electronic spin. Using coherent manipulation of a single nitrogen vacancy center in room-temperature diamond, full quantum control of an electronic-nuclear system consisting of up to three spins was achieved. We took advantage of a single nuclear-spin memory in order to obtain a 10-fold enhancement in the signal amplitude of the electronic spin readout. We also present a two-level, concatenated procedure to improve the readout by use of a pair of nuclear spin ancillae, an important step toward the realization of robust quantum information processors using electronic- and nuclear-spin qubits. Our technique can be used to improve the sensitivity and speed of spin-based nanoscale diamond magnetometers.

Optical binding mechanisms: a conceptual model for Gaussian beam traps

Optical binding interactions between laser-trapped spherical microparticles are familiar in a wide range of trapping configurations. Recently it has been demonstrated that these experiments can be accurately modeled using Mie scattering or coupled dipole models. This can help confirm the physical phenomena underlying the inter-particle interactions, but does not necessarily develop a conceptual understanding of the effects that can lead to future predictions. Here we interpret results from a Mie scattering model to obtain a physical description which predict the behavior and trends for chains of trapped particles in Gaussian beam traps. In particular, it describes the non-uniform particle spacing and how it changes with the number of particles. We go further than simply demonstrating agreement, by showing that the mechanisms "hidden" within a mathematically and computationally demanding Mie scattering description can be explained in easily-understood terms.

Qubit protection in nuclear-spin quantum dot memories

We present a mechanism to protect quantum information stored in an ensemble of nuclear spins in a semiconductor quantum dot. When the dot is charged the nuclei interact with the spin of the excess electron through the hyperfine coupling. If this coupling is made off-resonant, it leads to an energy gap between the collective storage states and all other states. We show that the energy gap protects the quantum memory from local spin-flip and spin-dephasing noise. Effects of nonperfect initial spin polarization and inhomogeneous hyperfine coupling are discussed.

Multipole expansion of Bessel and Gaussian beams for Mie scattering calculations

Multipole expansions of Bessel and Gaussian beams, suitable for use in Mie scattering calculations, are derived. These results allow Mie scattering calculations to be carried out considerably faster than existing methods, something that is of particular interest for time evolution simulations where large numbers of scattering calculations must be performed. An analytic result is derived for the Bessel beam that improves on a previously published expression requiring the evaluation of an integral. An analogous expression containing a single integral, similar to existing results quoted, but not derived, in literature, is derived for a Gaussian beam, valid from the paraxial limit all the way to arbitrarily high numerical apertures.

Atomic three-body loss as a dynamical three-body interaction

We discuss how large three-body loss of atoms in an optical lattice can give rise to effective hard-core three-body interactions. For bosons, in addition to the usual atomic superfluid, a dimer superfluid can then be observed for attractive two-body interactions. The nonequilibrium dynamics of preparation and stability of these phases are studied in 1D by combining time-dependent density matrix renormalization group techniques with a quantum trajectories method.