1,451 research outputs found
How do you design randomised trials for smaller populations? A framework.
How should we approach trial design when we can get some, but not all, of the way to the numbers required for a randomised phase III trial?We present an ordered framework for designing randomised trials to address the problem when the ideal sample size is considered larger than the number of participants that can be recruited in a reasonable time frame. Staying with the frequentist approach that is well accepted and understood in large trials, we propose a framework that includes small alterations to the design parameters. These aim to increase the numbers achievable and also potentially reduce the sample size target. The first step should always be to attempt to extend collaborations, consider broadening eligibility criteria and increase the accrual time or follow-up time. The second set of ordered considerations are the choice of research arm, outcome measures, power and target effect. If the revised design is still not feasible, in the third step we propose moving from two- to one-sided significance tests, changing the type I error rate, using covariate information at the design stage, re-randomising patients and borrowing external information.We discuss the benefits of some of these possible changes and warn against others. We illustrate, with a worked example based on the Euramos-1 trial, the application of this framework in designing a trial that is feasible, while still providing a good evidence base to evaluate a research treatment.This framework would allow appropriate evaluation of treatments when large-scale phase III trials are not possible, but where the need for high-quality randomised data is as pressing as it is for common diseases
How to design a MAMS-ROCI (aka DURATIONS) randomised trial: the REFINE-Lung case study
Background. The DURATIONS design has been recently proposed as a practical
alternative to a standard two-arm non-inferiority design when the goal is to
optimise some continuous aspect of treatment administration, e.g. duration or
frequency, preserving efficacy but improving on secondary outcomes such as
safety, costs or convenience. The main features of this design are that (i) it
randomises patients to a moderate number of arms across the continuum and (ii)
it uses a model to share information across arms. While papers published to
date about the design have focused on analysis aspects, here we show how to
design such a trial in practice. We use the REFINE-Lung trial as an example;
this is a trial seeking the optimal frequency of immunotherapy treatment for
non-small cell lung cancer patients. Because the aspect of treatment
administration to optimise is frequency, rather than duration, we propose to
rename the design as Multi-Arm Multi-Stage Response Over Continuous
Intervention (MAMS-ROCI). Methods. We show how simulations can be used to
design such a trial. We propose to use the ADEMP framework to plan such
simulations, clearly specifying aims, data generating mechanisms, estimands,
methods and performance measures before coding and analysing the simulations.
We discuss the possible choices to be made using the REFINE-Lung trial as an
example. Results. We describe all the choices made while designing the
REFINE-Lung trial, and the results of the simulations performed. We justify our
choice of total sample size based on these results. Conclusions. MAMS-ROCI
trials can be designed using simulation studies that have to be carefully
planned and conducted. REFINE-Lung has been designed using such an approach and
we have shown how researchers could similarly design their own MAMS-ROCI trial.Comment: 25 pages, 1 table, 5 figure
artcat: Sample-size calculation for an ordered categorical outcome
We describe a new command, artcat, that calculates sample size or power for a randomized controlled trial or similar experiment with an ordered categorical outcome, where analysis is by the proportional-odds model. artcat implements the method of Whitehead (1993, Statistics in Medicine 12: 2257–2271). We also propose and implement a new method that 1) allows the user to specify a treatment effect that does not obey the proportional-odds assumption, 2) offers greater accuracy for large treatment effects, and 3) allows for noninferiority trials. We illustrate the command and explore the value of an ordered categorical outcome over a binary outcome in various settings. We show by simulation that the methods perform well and that the new method is more accurate than Whitehead’s method
From Rotating Atomic Rings to Quantum Hall States
Considerable efforts are currently devoted to the preparation of ultracold
neutral atoms in the emblematic strongly correlated quantum Hall regime. The
routes followed so far essentially rely on thermodynamics, i.e. imposing the
proper Hamiltonian and cooling the system towards its ground state. In rapidly
rotating 2D harmonic traps the role of the transverse magnetic field is played
by the angular velocity. For particle numbers significantly larger than unity,
the required angular momentum is very large and it can be obtained only for
spinning frequencies extremely near to the deconfinement limit; consequently,
the required control on experimental parameters turns out to be far too
stringent. Here we propose to follow instead a dynamic path starting from the
gas confined in a rotating ring. The large moment of inertia of the fluid
facilitates the access to states with a large angular momentum, corresponding
to a giant vortex. The initial ring-shaped trapping potential is then
adiabatically transformed into a harmonic confinement, which brings the
interacting atomic gas in the desired quantum Hall regime. We provide clear
numerical evidence that for a relatively broad range of initial angular
frequencies, the giant vortex state is adiabatically connected to the bosonic
Laughlin state, and we discuss the scaling to many particles.Comment: 9 pages, 5 figure
Human Cytomegalovirus: detection of congenital and perinatal infection in Argentina
BACKGROUND: Human cytomegalovirus (CMV) is one of the most commonly found agents of congenital infections. Primary maternal infection is associated with risk of symptomatic congenital diseases, and high morbidity is frequently associated with very low birth weight. Neonates with asymptomatic infection develop various sequelae during infancy. This is the first Argentine study performed in neonates with congenital and postnatal HCMV infection. The purpose of this study was to evaluate the performance of the polymerase chain reaction (PCR) technique with different pairs of primers, to detect cytomegalovirus isolated in tissue cultures and directly in urine and dried blood spot (DBS) specimens. Results were compared with IgM detection. METHODS: The study was performed between 1999 and 2001 on routine samples in the Laboratory. A total of 61 urine and 56 serum samples were selected from 61 newborns/infants, 33 patients whose samples were analyzed during the first two to three weeks of life were considered congenital infections; the remaining 28 patients whose samples were taken later than the third week were grouped as perinatal infections, although only in 4 the perinatal transmission of infection was determined unequivocally Cytomegalovirus diagnosis was made by isolating the virus from urine samples in human foreskin fibroblast cells. Three different primer pairs directed to IE, LA and gB genes were used for the HCMV PCR assay in viral isolates. Subsequently, PCR and nested PCR (nPCR) assays with gB primers were performed directly in urine and in 11 samples of dried blood spot (DBS) on Guthrie Card, these results were then compared with serology. RESULTS: The main clinical manifestations of the 33 patients with congenital infection were purpura, jaundice, hepatomegaly and anaemia. Three patients presented low birth weight as single symptom, 10, intracranial calcifications, and 2, kidney failure. In the 28 patients grouped as with perinatal infection, anaemia, hepatosplenomegaly and enzymatic alteration were predominant, and 4 patients were HIV positive. The primers used to amplify the gB region had a PCR positivity rate of 100%, whereas those that amplified IE and LA regions had a PCR positivity rate of 54% and 61% respectively, in CMV isolates. Amplification by PCR of urine samples (with no previous DNA extraction), using primers for the gB region, detected 34/61 positive samples. Out of the 33 samples from patients with congenital infection, 24 (73%) were positive. When nPCR was used in these samples, all were positive, whereas in the remaining 28 patients, two negative cases were found. Cytomegalovirus DNA detection in 11 samples was also carried out in DBS: 7 DBS samples were positive and 4 were negative. CONCLUSIONS: Primers directed to the gB fragment region were the best choice for the detection of CMV DNA in positive isolates. In congenital infections, direct PCR in urine was positive in a high percentage (73%) of samples; however, in patients grouped as with perinatal infection only 36% of the cases were positive. With n-PCR, total sample positivity reached 97%. PCR technique performed in DBS allowed identifying congenital infection in four patients and to be confirmed in 3. These results show the value of nPCR for the detection of all cases of CMV infection. The assay offers the advantage that it may be performed within the normal working day and provides reliable results in a much shorter time frame than that required for either traditional tissue culture or the shell-viral assay
Relationship between Tibial conformation, cage size and advancement achieved in TTA procedure
Previous studies have suggested that there is a theoretical discrepancy between the cage size and the resultant tibial tuberosity advancement, with the cage size consistently providing less tibial tuberosity advancement than predicted. The purpose of this study was to test and quantify this in clinical cases. The hypothesis was that the advancement of the tibial tuberosity as measured by the widening of the proximal tibia at the tibial tuberosity level after a standard TTA, will be less than the cage sized used, with no particular cage size providing a relative smaller or higher under-advancement, and that the conformation of the proximal tibia will have an influence on the amount of advancement achieved
The usefulness of rapid diagnostic tests in the new context of low malaria transmission in zanzibar.
BACKGROUND\ud
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We assessed if histidine-rich-protein-2 (HRP2) based rapid diagnostic test (RDT) remains an efficient tool for Plasmodium falciparum case detection among fever patients in Zanzibar and if primary health care workers continue to adhere to RDT results in the new epidemiological context of low malaria transmission. Further, we evaluated the performance of RDT within the newly adopted integrated management of childhood illness (IMCI) algorithm in Zanzibar.\ud
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METHODS AND FINDINGS\ud
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We enrolled 3890 patients aged ≥2 months with uncomplicated febrile illness in this health facility based observational study conducted in 12 primary health care facilities in Zanzibar, between May-July 2010. One patient had an inconclusive RDT result. Overall 121/3889 (3.1%) patients were RDT positive. The highest RDT positivity rate, 32/528 (6.1%), was found in children aged 5-14 years. RDT sensitivity and specificity against PCR was 76.5% (95% CI 69.0-83.9%) and 99.9% (95% CI 99.7-100%), and against blood smear microscopy 78.6% (95% CI 70.8-85.1%) and 99.7% (95% CI 99.6-99.9%), respectively. All RDT positive, but only 3/3768 RDT negative patients received anti-malarial treatment. Adherence to RDT results was thus 3887/3889 (99.9%). RDT performed well in the IMCI algorithm with equally high adherence among children <5 years as compared with other age groups.\ud
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CONCLUSIONS\ud
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The sensitivity of HRP-2 based RDT in the hands of health care workers compared with both PCR and microscopy for P. falciparum case detection was relatively low, whereas adherence to test results with anti-malarial treatment was excellent. Moreover, the results provide evidence that RDT can be reliably integrated in IMCI as a tool for improved childhood fever management. However, the relatively low RDT sensitivity highlights the need for improved quality control of RDT use in primary health care facilities, but also for more sensitive point-of-care malaria diagnostic tools in the new epidemiological context of low malaria transmission in Zanzibar.\ud
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TRIAL REGISTRATION\ud
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ClinicalTrials.gov NCT01002066
Predictability of evolutionary trajectories in fitness landscapes
Experimental studies on enzyme evolution show that only a small fraction of
all possible mutation trajectories are accessible to evolution. However, these
experiments deal with individual enzymes and explore a tiny part of the fitness
landscape. We report an exhaustive analysis of fitness landscapes constructed
with an off-lattice model of protein folding where fitness is equated with
robustness to misfolding. This model mimics the essential features of the
interactions between amino acids, is consistent with the key paradigms of
protein folding and reproduces the universal distribution of evolutionary rates
among orthologous proteins. We introduce mean path divergence as a quantitative
measure of the degree to which the starting and ending points determine the
path of evolution in fitness landscapes. Global measures of landscape roughness
are good predictors of path divergence in all studied landscapes: the mean path
divergence is greater in smooth landscapes than in rough ones. The
model-derived and experimental landscapes are significantly smoother than
random landscapes and resemble additive landscapes perturbed with moderate
amounts of noise; thus, these landscapes are substantially robust to mutation.
The model landscapes show a deficit of suboptimal peaks even compared with
noisy additive landscapes with similar overall roughness. We suggest that
smoothness and the substantial deficit of peaks in the fitness landscapes of
protein evolution are fundamental consequences of the physics of protein
folding.Comment: 14 pages, 7 figure
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