Enhanced charge density wave coherence in a light-quenched, high-temperature superconductor.

Superconductivity and charge density waves (CDWs) are competitive, yet coexisting, orders in cuprate superconductors. To understand their microscopic interdependence, a probe capable of discerning their interaction on its natural length and time scale is necessary. We use ultrafast resonant soft x-ray scattering to track the transient evolution of CDW correlations in YBa2Cu3O6+x after the quench of superconductivity by an infrared laser pulse. We observe a nonthermal response of the CDW order characterized by a near doubling of the correlation length within ≈1 picosecond of the superconducting quench. Our results are consistent with a model in which the interaction between superconductivity and CDWs manifests inhomogeneously through disruption of spatial coherence, with superconductivity playing the dominant role in stabilizing CDW topological defects, such as discommensurations.

dfpk: An R-package for Bayesian dose-finding designs using pharmacokinetics (PK) for phase I clinical trials.

BACKGROUND AND OBJECTIVE: Dose-finding, aiming at finding the maximum tolerated dose, and pharmacokinetics studies are the first in human studies in the development process of a new pharmacological treatment. In the literature, to date only few attempts have been made to combine pharmacokinetics and dose-finding and to our knowledge no software implementation is generally available. In previous papers, we proposed several Bayesian adaptive pharmacokinetics-based dose-finding designs in small populations. The objective of this work is to implement these dose-finding methods in an R package, called dfpk. METHODS: All methods were developed in a sequential Bayesian setting and Bayesian parameter estimation is carried out using the rstan package. All available pharmacokinetics and toxicity data are used to suggest the dose of the next cohort with a constraint regarding the probability of toxicity. Stopping rules are also considered for each method. The ggplot2 package is used to create summary plots of toxicities or concentration curves. RESULTS: For all implemented methods, dfpk provides a function (nextDose) to estimate the probability of efficacy and to suggest the dose to give to the next cohort, and a function to run trial simulations to design a trial (nsim). The sim.data function generates at each dose the toxicity value related to a pharmacokinetic measure of exposure, the AUC, with an underlying pharmacokinetic one compartmental model with linear absorption. It is included as an example since similar data-frames can be generated directly by the user and passed to nsim. CONCLUSION: The developed user-friendly R package dfpk, available on the CRAN repository, supports the design of innovative dose-finding studies using PK information.

Rapid in situ X-ray position stabilization via extremum seeking feedback.

X-ray beam stability is crucial for acquiring high-quality data at synchrotron beamline facilities. When the X-ray beam and defining apertures are of similar dimensions, small misalignments driven by position instabilities give rise to large intensity fluctuations. This problem is solved using extremum seeking feedback control (ESFC) for in situ vertical beam position stabilization. In this setup, the intensity spatial gradient required for ESFC is determined by phase comparison of intensity oscillations downstream from the sample with pre-existing vertical beam oscillations. This approach compensates for vertical position drift from all sources with position recovery times <6 s and intensity stability through a 5 µm aperture measured at 1.5% FWHM over a period of 8 hours.

A Bayesian Hybrid Adaptive Randomisation Design for Clinical Trials with Survival Outcomes.

BACKGROUND: Response-adaptive randomisation designs have been proposed to improve the efficiency of phase III randomised clinical trials and improve the outcomes of the clinical trial population. In the setting of failure time outcomes, Zhang and Rosenberger (2007) developed a response-adaptive randomisation approach that targets an optimal allocation, based on a fixed sample size. OBJECTIVES: The aim of this research is to propose a response-adaptive randomisation procedure for survival trials with an interim monitoring plan, based on the following optimal criterion: for fixed variance of the estimated log hazard ratio, what allocation minimizes the expected hazard of failure? We demonstrate the utility of the design by redesigning a clinical trial on multiple myeloma. METHODS: To handle continuous monitoring of data, we propose a Bayesian response-adaptive randomisation procedure, where the log hazard ratio is the effect measure of interest. Combining the prior with the normal likelihood, the mean posterior estimate of the log hazard ratio allows derivation of the optimal target allocation. We perform a simulation study to assess and compare the performance of this proposed Bayesian hybrid adaptive design to those of fixed, sequential or adaptive - either frequentist or fully Bayesian - designs. Non informative normal priors of the log hazard ratio were used, as well as mixture of enthusiastic and skeptical priors. Stopping rules based on the posterior distribution of the log hazard ratio were computed. The method is then illustrated by redesigning a phase III randomised clinical trial of chemotherapy in patients with multiple myeloma, with mixture of normal priors elicited from experts. RESULTS: As expected, there was a reduction in the proportion of observed deaths in the adaptive vs. non-adaptive designs; this reduction was maximized using a Bayes mixture prior, with no clear-cut improvement by using a fully Bayesian procedure. The use of stopping rules allows a slight decrease in the observed proportion of deaths under the alternate hypothesis compared with the adaptive designs with no stopping rules. CONCLUSIONS: Such Bayesian hybrid adaptive survival trials may be promising alternatives to traditional designs, reducing the duration of survival trials, as well as optimizing the ethical concerns for patients enrolled in the trial.

Designs of drug-combination phase I trials in oncology: a systematic review of the literature.

BACKGROUND: Combining several anticancer agents can increase the overall antitumor action, but at the same time, it can also increase the overall observed toxicity. Adaptive dose-escalation designs for drug combinations have recently emerged as an attractive alternative to algorithm-based designs, and they seem more effective in combination recommendations. These methods are not used in practice currently. Our aim is to describe international scientific practices in the setting of phase I drug combinations in oncology. MATERIAL AND METHODS: A bibliometric study on phase I dose-finding combination trials was conducted using the Medline(®) PubMed database between 1 January, 2011, and 31 December 2013. Sorting by abstract, we selected all papers involving a minimum of two agents and then retained only those in which at least two agents were dose-escalated. RESULTS: Among the 847 references retrieved, 162 papers reported drug-combination phase I trials in which at least two agents were dose-escalated. In 88% of trials, a traditional or modified 3 + 3 dose-escalation design was used. All except one trial used a design developed for single-agent evaluation. Our study suggests that drug-combination phase I trials in oncology are very safe, as revealed by the calculated median dose-limiting toxicity rate of 6% at the recommended dose, which is far below the target rate in these trials (33%). We also examined requirements of phase I clinical trials in oncology with drug combinations and the potential advantages of novel approaches in early phases. CONCLUSION: Efforts to promote novel and innovative approaches among statisticians and clinicians appear valuable. Adaptive designs have an important role to play in early phase development.

Competing designs for drug combination in phase I dose-finding clinical trials.

The aim of phase I combination dose-finding studies in oncology is to estimate one or several maximum tolerated doses (MTDs) from a set of available dose levels of two or more agents. Combining several agents can indeed increase the overall anti-tumor action but at the same time also increase the toxicity. It is, however, unreasonable to assume the same dose-toxicity relationship for the combination as for the simple addition of each single agent because of a potential antagonist or synergistic effect. Therefore, using single-agent dose-finding methods for combination therapies is not appropriate. In recent years, several authors have proposed novel dose-finding designs for combination studies, which use either algorithm-based or model-based methods. The aim of our work was to compare, via a simulation study, six dose-finding methods for combinations proposed in recent years. We chose eight scenarios that differ in terms of the number and location of the true MTD(s) in the combination space. We then compared the performance of each design in terms of correct combination selection, patient allocation, and mean number of observed toxicities during the trials. Our results showed that the model-based methods performed better than the algorithm-based ones. However, none of the compared model-based designs gave consistently better results than the others.

Major histocompatibility complex class I core promoter elements are not essential for transcription in vivo.

The role of core promoter elements in regulating transcription initiation is largely unknown for genes subject to complex regulation. Major histocompatibility complex class I genes are ubiquitously expressed and governed by tissue-specific and hormonal signals. Transcription initiates at multiple sites within the core promoter, which contains elements homologous to the canonical elements CCAAT, TATAA, Sp1 binding site (Sp1BS), and Initiator (Inr). To determine their functions, expression of class I transgenes with individually mutated elements was assessed. Surprisingly, all mutant promoters supported transcription. However, each mutated core promoter element had a distinct effect on expression: CAAT box mutations modulated constitutive expression in nonlymphoid tissues, whereas TATAA-like element mutations dysregulated transcription in lymphoid tissues. Inr mutations aberrantly elevated expression. Sp1BS element mutations resulted in variegated transgene expression. RNA polymerase II binding and histone H3K4me3 patterns correlated with transgene expression; H3K9me3 marks partially correlated. Whereas the wild-type, TATAA-like, and CAAT mutant promoters were activated by gamma interferon, the Sp1 and Inr mutants were repressed, implicating these elements in regulation of hormonal responses. These results lead to the surprising conclusion that no single element is required for promoter activity. Rather, each plays a distinct role in promoter activity, chromatin structure, tissue-specific expression, and extracellular signaling.

Detection of microwave phase variation in nanometre-scale magnetic heterostructures.

The internal phase profile of electromagnetic radiation determines many functional properties of metal, oxide or semiconductor heterostructures. In magnetic heterostructures, emerging spin electronic phenomena depend strongly upon the phase profile of the magnetic field H at gigahertz frequencies. Here we demonstrate nanometre-scale, layer-resolved detection of electromagnetic phase through the radio frequency magnetic field H(rf) in magnetic heterostructures. Time-resolved X-ray magnetic circular dichroism reveals the local phase of the radio frequency magnetic field acting on individual magnetizations M(i) through the susceptibility as M = χH(rf). An unexpectedly large phase variation, ~40°, is detected across spin-valve trilayers driven at 3 GHz. The results have implications for the identification of novel effects in spintronics and suggest general possibilities for electromagnetic-phase profile measurement in heterostructures.

What is the ED95 of prilocaine for femoral nerve block using ultrasound?

BACKGROUND: Our aim was to estimate the ED95 of prilocaine 1% w/v for femoral nerve block. METHODS: This two-stage dose-finding sequential clinical trial followed an adaptive design based on the continual reassessment method (CRM). Adult patients undergoing Vastus medialis muscle biopsy under ultrasound-guided femoral nerve block were recruited. Data from previously published studies and our own previous experience were used to set the dose levels and their guesstimate probabilities of response. RESULTS: Forty patients were recruited in the trial (n=26 in the first stage and n=14 in the second stage). Using the CRM, the estimated response probabilities with 13 and 17 ml prilocaine 1% w/v were 90.4% (95% credibility interval: 68-98%) and 99.1% (95% credibility interval: 89-100%), respectively. CONCLUSION: Our study demonstrates that the dose closest to the ED(95) of prilocaine 1% w/v for ultrasound-guided femoral nerve block is 17 ml. The study also illustrates the value of CRM in dose-finding experiments.

Elemental and magnetic sensitive imaging using x-ray excited luminescence microscopy.

We demonstrate the potential of x-ray excited luminescence microscopy for full-field elemental and magnetic sensitive imaging using a commercially available optical microscope, mounted on preexisting synchrotron radiation (SR) beamline end stations. The principal components of the instrument will be described. Bench top measurements indicate that a resolution of 1 µm or better is possible; this value was degraded in practice due to vibrations and/or drift in the end station and associated manipulator. X-ray energy dependent measurements performed on model solar cell materials and lithographically patterned magnetic thin film structures reveal clear elemental and magnetic signatures. The merits of the apparatus will be discussed in terms of conventional SR imaging techniques.

Risk factors for conversion and complications after unilateral laparoscopic adrenalectomy.

BACKGROUND: Laparoscopic adrenalectomy (LA) is the procedure of choice for surgical management of most benign adrenal tumours, with a reported overall complication rate around 10 per cent. The aim of this study was to determine predictive factors for postoperative complications and conversion to open surgery after unilateral LA. METHODS: From 1994 to 2009, consecutive patients undergoing unilateral LA by the lateral transabdominal approach were analysed from a prospectively maintained database. A mass larger than 12 cm in diameter and suspected primary adrenal carcinoma were considered contraindications to LA. Predictive factors for postoperative complications and conversion to open surgery were analysed. RESULTS: Some 462 patients were analysed. There were no postoperative deaths. Postoperative complications occurred in 53 patients (11·5 per cent), medical complications in 28, and surgical complications in 33 patients. Six patients underwent reoperation for complications. Multivariable logistic regression analysis showed that conversion to open surgery (odds ratio (OR) 6·20, 95 per cent confidence interval 2·08 to 18·53; P = 0·001) and left-sided tumour (OR 1·89, 1·02 to 3·52; P = 0·044) were independent predictive factors for overall complications. Conversion to open surgery was the only independent predictive factor for medical complications (OR 12·88, 4·21 to 39·41; P = 0·001), and left-sided LA was the only predictive factor for surgical complications (OR 2·22, 1·01 to 4·89; P = 0·047). No factor was predictive of conversion to open surgery. CONCLUSION: In this single-institution study, conversion to open surgery and left-sided tumours were independent predictive factors for overall complications, but none of the variables analysed was predictive of conversion.

Posterior maximization and averaging for Bayesian working model choice in the continual reassessment method.

The continual reassessment method (CRM) is a method for estimating the maximum tolerated dose in a dose-finding study. Traditionally, use is made of a single working model or 'skeleton' idealizing an underlying true dose-toxicity relationship. This working model is chosen either by discussion with investigators or published data, before the beginning of the trial or simply on the basis of operating characteristics. To overcome the arbitrariness of the choice of such a single working model, Yin and Yuan (biJ. Am. Statist. Assoc. 2009; 104:954-968) propose a model averaging over a set of working models. Here, instead of averaging, we investigate some alternative Bayesian model criteria that maximize the posterior distribution. We propose three adaptive model-selecting CRMs using the Bayesian model selection criteria, in which we specify in advance a collection of candidate working models for the dose-toxicity relationship, especially initial guesses of toxicity probabilities, and adaptively select the only one working model among the candidates updated by using the original CRM for each working model, based on the posterior model probability, the posterior predictive loss or the deviance information criteria, during the course of the trial. These approaches were compared via a simulation study with the model averaging approach.

Dose-finding approach for dose escalation with overdose control considering incomplete observations.

We propose a hybrid design, the time-to-event dose-escalation method with overdose control (TITE-EWOC), introducing the time-to-event approach, developed by Cheungit et al., in the EWOC method, developed by Babb et al. The aim of this new design is to decrease the dose-finding trial duration, without impairing the characteristics of the EWOC design, especially the overdose control ability. We conducted a simulation study, exploring four dose­toxicity relationships and three mean inter-patient arrival times. Performances of TITE-EWOC were compared with those of the EWOC method. This study shows that the trial duration can be greatly decreased with the TITE-EWOC, without impacting the proportion of overdosed patients or the number of dose-limiting toxicities by trial, for all explored dose­toxicity relationships, except for very short inter-patient arrival times. The ability of the method to find the true maximum tolerated dose remains unchanged.

A compact apparatus for studies of element and phase-resolved ferromagnetic resonance.

We present a compact sample holder equipped with electromagnets and high frequency transmission lines; the sample holder is intended for combined x-ray magnetic circular dichroism (XMCD) and ferromagnetic resonance measurements (FMR). Time-resolved measurements of resonant x-ray detected FMR during forced precession are enabled by use of a rf excitation that is phase-locked to the storage ring bunch clock. Several applications of the combined XMCD+FMR technique are presented, demonstrating the flexibility of the experimental design.

Hematopoietic progenitor cell mobilization and harvesting in children with malignancies: do the advantages of pegfilgrastim really translate into clinical benefit?

Our purpose was to assess success rates in children of achieving optimal hematopoietic progenitor cells (HPCs) harvest after mobilization with 300 microg/kg pegfilgrastim. Between January 2005 and January 2007, 26 children with solid malignancies who were referred for HPC collection were consecutively included. Hematopoietic progenitor cell mobilization consisted of one s.c. injection of 300 microg/kg body weight (BW) of pegfilgrastim. The success criterion was defined as at least 5 x 10(6) CD34+ cells/kg during the first standard apheresis (less than 3 blood volumes processed (BVP)). After 26 inclusions, the Bayesian analysis gave a mean estimated success rate of 60.7% (95% credibility interval: 42.0-78.0%). The first apheresis allowed the collection of 8.3 x 10(6) CD34+ cells/kg BW (range 0.6-37.8), with a median of 2.8 BVP (range 1.4-3.0). Overall, the median of CD34+ cells collected was 12.4 x 10(6)/kg (range 2.7-37.8). The cumulative dose of anthracyclin was the only variable associated with the total number of CD34+ collected cells (P<0.05). Mobilization was clinically well tolerated in 20 patients. No drug-related adverse events of grade > or =3 occurred. We conclude that a single injection of 300 microg/kg pegfilgrastim in the hematological steady state is an efficient and well-tolerated method of HPC mobilization in children with solid malignancies.

Long-term follow-up results after autologous haematopoietic stem cell transplantation for severe systemic sclerosis.

OBJECTIVE: Systemic sclerosis (SSc) is a generalised autoimmune disease, causing morbidity and a reduced life expectancy, especially in patients with rapidly progressive diffuse cutaneous SSc. As no proven treatment exists, autologous haematopoietic stem cell transplantation (HSCT) is employed as a new therapeutic strategy in patients with a poor prognosis. This study reports the effects on survival, skin and major organ function of HSCT in patients with severe diffuse cutaneous SSc. PATIENTS AND METHODS: A total of 26 patients were evaluated. Peripheral blood stem cells were collected using cyclophosphamide (4 g/m2) and rHu G-CSF (5 to 10 microg/kg/day) and were reinfused after positive CD34+ selection. For conditioning, cyclophosphamide 200 mg/kg was used. RESULTS: After a median follow-up of 5.3 (1-7.5) years, 81% (n = 21/26) of the patients demonstrated a clinically beneficial response. The Kaplan-Meier estimated survival at 5 years was 96.2% (95% CI 89-100%) and at 7 years 84.8% (95% CI 70.2-100%) and event-free survival, defined as survival without mortality, relapse or progression of SSc, resulting in major organ dysfunction was 64.3% (95% CI 47.9-86%) at 5 years and 57.1% (95% CI 39.3-83%) at 7 years. CONCLUSION: This study confirms that autologous HSCT in selected patients with severe diffuse cutaneous SSc results in sustained improvement of skin thickening and stabilisation of organ function up to 7 years after transplantation.

Altered adenosine-to-inosine RNA editing in human cancer.

Adenosine-to-inosine (A-to-I) RNA editing was recently shown to be abundant in the human transcriptome, affecting thousands of genes. Employing a bioinformatic approach, we identified significant global hypoediting of Alu repetitive elements in brain, prostate, lung, kidney, and testis tumors. Experimental validation confirmed this finding, showing significantly reduced editing in Alu sequences within MED13 transcripts in brain tissues. Looking at editing of specific recoding and noncoding sites, including in cancer-related genes, a more complex picture emerged, with a gene-specific editing pattern in tumors vs. normal tissues. Additionally, we found reduced RNA levels of all three editing mediating enzymes, ADAR, ADARB1, and ADARB2, in brain tumors. The reduction of ADARB2 correlated with the grade of malignancy of glioblastoma multiforme, the most aggressive of brain tumors, displaying a 99% decrease in ADARB2 RNA levels. Consistently, overexpression of ADAR and ADARB1 in the U87 glioblastoma multiforme cell line resulted in decreased proliferation rate, suggesting that reduced A-to-I editing in brain tumors is involved in the pathogenesis of cancer. Altered epigenetic control was recently shown to play a central role in oncogenesis. We suggest that A-to-I RNA editing may serve as an additional epigenetic mechanism relevant to cancer development and progression.

A phase I dose-finding and pharmacokinetic study of subcutaneous semisynthetic homoharringtonine (ssHHT) in patients with advanced acute myeloid leukaemia.

To determine the maximum-tolerated dose (MTD), dose-limiting toxicities and pharmacokinetic of semisynthetic homoharringtonine (ssHHT), given as a twice daily subcutaneous (s.c.) injections for 9 days, in patients with advanced acute leukaemia, 18 patients with advanced acute myeloid leukaemia were included in this sequential Bayesian phase I dose-finding trial. A starting dose of 0.5 mg m(-2) day(-1) was explored with subsequent dose escalations of 1, 3, 5 and 6 mg m(-2) day(-1). Myelosuppression was constant. The MTD was estimated as the dose level of 5 mg m(-2) day(-1) for 9 consecutive days by s.c. route. Dose-limiting toxicities were hyperglycaemia with hyperosmolar coma at 3 mg m(-2), and (i) one anasarque and haematemesis, (ii) one life-threatening pulmonary aspergillosis, (iii) one skin rash and (iv) one scalp pain at dose level of 5 mg m(-2) day(-1). The mean half-life of ssHHT was 11.01+/-3.4 h, the volume of distribution at steady state was 2+/-1.4 l kg(-1) and the plasma clearance was 11.6+/-10.4 l h(-1). Eleven of the 12 patients with circulating leukaemic cells had blood blast clearance, two achieved complete remission and one with blast crisis of CMML returned in chronic phase. The recommended daily dose of ssHHT on the 9-day schedule is 5 mg m(-2) day(-1).

The VAD chemotherapy regimen plus a G-CSF dose of 10 microg/kg is as effective and less toxic than high-dose cyclophosphamide plus a G-CSF dose of 5 microg/kg for progenitor cell mobilization: results from a monocentric study of 82 patients.

A study was conducted to compare the efficiency and toxicity of two peripheral blood stem cell (PBSC) mobilization procedures for newly diagnosed patients with multiple myeloma. Patients from group 1 (n=51) were treated by high-dose cyclophosphamide (HD-CY) plus G-CSF (5 microg/kg/day), and the second group (n=31) by VAD regimen plus G-CSF administration (10 microg/kg/day). Successful mobilization, defined by a minimal count of 2.5 x 10(6) CD34(+) cells/kg collected, was achieved in 96 and 90% of patients in groups 1 and 2, respectively (P=0.15). The mean peripheral blood CD34(+) cells concentration and the mean CD34(+) cells/kg collected were higher in group 2 than in the group 1 (P=0.05). The mean number of leukaphereses necessary to collect a count of 2.5 x 10(6) CD34(+) cells/kg was reduced in group 2 compared to group 1. Adverse events, blood products consumption and time spent in the hospital were significantly greater after HD-CY. In conclusion, VAD plus a G-CSF dose of 10 microg/kg administration seems preferential to HD-CY plus a G-CSF dose of 5 microg/kg for PBSC collection because of equivalent or better efficiency in stem cell mobilization, strong favorable toxicity profile and reduced cost.

Experimental designs for phase I and phase I/II dose-finding studies.

We review the rationale behind the statistical design of dose-finding studies as used in phase I and phase I/II clinical trials. We underline what the objectives of such dose-finding studies should be and why the widely used standard design fails to meet any of these objectives. The standard design is a "memoryless" design and we discuss how this impacts on practical behaviour. Designs introduced over the last two decades can be viewed as designs with memory and we discuss how these designs are superior to memoryless designs. By superior we mean that they require less patients overall, less patients to attain the maximum tolerated dose (MTD), and concentrate a higher percentage of patients at and near to the MTD. We reanalyse some recently published studies in order to provide support to our contention that markedly better results could have been achieved had a design with memory been used instead of a memoryless design.