Risk‐adjusted monitoring of time to event in the presence of long‐term survivors

The use of control charts for monitoring schemes in medical context should consider adjustments to incorporate the specific risk for each individual. Some authors propose the use of a risk‐adjusted survival time cumulative sum (RAST CUSUM) control chart to monitor a time‐to‐event outcome, possibly right censored, using conventional survival models, which do not contemplate the possibility of cure of a patient. We propose to extend this approach considering a risk‐adjusted CUSUM chart, based on a cure rate model. We consider a regression model in which the covariates affect the cure fraction. The CUSUM scores are obtained for Weibull and log‐logistic promotion time model to monitor a scale parameter for nonimmune individuals. A simulation study was conducted to evaluate and compare the performance of the proposed chart (RACUF CUSUM) with RAST CUSUM, based on optimal control limits and average run length in different situations. As a result, we note that the RAST CUSUM chart is inappropriate when applied to data with a cure rate, while the proposed RACUF CUSUM chart seems to have similar performance if applied to data without a cure rate. The proposed chart is illustrated with simulated data and with a real data set of patients with heart failure treated at the Heart Institute (InCor), at the University of São Paulo, Brazil.     

Enhanced Cumulative Sum Charts for Monitoring Process Dispersion

The cumulative sum (CUSUM) control chart is widely used in industry for the detection of small and moderate shifts in process location and dispersion. For efficient monitoring of process variability, we present several CUSUM control charts for monitoring changes in standard deviation of a normal process. The newly developed control charts based on well-structured sampling techniques - extreme ranked set sampling, extreme double ranked set sampling and double extreme ranked set sampling, have significantly enhanced CUSUM chart ability to detect a wide range of shifts in process variability. The relative performances of the proposed CUSUM scale charts are evaluated in terms of the average run length (ARL) and standard deviation of run length, for point shift in variability. Moreover, for overall performance, we implore the use of the average ratio ARL and average extra quadratic loss. A comparison of the proposed CUSUM control charts with the classical CUSUM R chart, the classical CUSUM S chart, the fast initial response (FIR) CUSUM R chart, the FIR CUSUM S chart, the ranked set sampling (RSS) based CUSUM R chart and the RSS based CUSUM S chart, among others, are presented. An illustrative example using real dataset is given to demonstrate the practicability of the application of the proposed schemes.     

CUSUM chart method for continuous monitoring of antifouling treatment of tubular heat exchangers in open-loop cooling seawater systems

Abstract

A CUSUM chart method is presented as an alternative tool for continuous monitoring of an electromagnetic field-based (EMF) antifouling (AF) treatment of a heat exchanger cooled by seawater. During an initial experimental phase, biofilm growth was allowed in a heat exchanger formed of four tubes until sufficient growth had been established. In two of the tubes, continuous EMF treatment was then applied. The heat transfer resistance and heat duty (heat transfer per unit time) results showed that biofilm adhesion was reduced by the EMF treatment. EMF treatments resulted in a 35% improvement in the heat transfer resistance values. The proposed CUSUM chart method showed that the EMF treatment increased the useful life of the heat exchanger by ～20?days. Thus, CUSUM charts proved to be an efficient tool for continuous monitoring of an AF treatment using data collected online and can also be used to reduce operation and maintenance costs.     

Cumulative sum procedure in evaluation of EUS-guided FNA cytology: the learning curve and diagnostic performance beyond sensitivity and specificity

Background: Using cumulative sum (CUSUM) chart, we address two questions: (i) Over time, how will an EUS‐FNA (endoscopic ultrasound guided fine needle aspiration) service maintain an acceptable non‐diagnostic rate defined as technical failures, unsatisfactory specimens and atypical and suspicious diagnoses? (ii) Over time, how will EUS‐FNA maintain acceptable diagnostic errors (false‐positives plus false‐negative diagnosis)? Methods: The study included all consecutive patients who underwent EUS‐FNA at our institution from July 2000 to October 2003 and were followed up until December 2004. Using a simple spread sheet, we designed CUSUM charts and used them to track trends and assess performance at a preset acceptable rate of 10% and a preset unacceptable rate of 15% for non‐diagnostic rate and diagnostic errors. We assessed all cases collectively and then in groups defined by site, size and cytopathologist. Results: Of 876 patients undergoing EUS‐FNA, 83 (9.5%) had non‐diagnostic results: 43 (51%) of these diagnoses were ‘atypical’, 27(33%) were ‘suspicious for malignancy’, eight (10%) were ‘insufficient material for diagnosis’ and five (6%) were ‘technical failure’. In 585 cases with adequate follow up, there were 26 (6.3%) diagnostic errors: three (0.5%) were false positive and 23 (3.1) were false negative. The overall CUSUM charts for both non‐diagnostic rate and for diagnostic error rate start with a small period of learning then cross to a significantly acceptable level at case numbers 121 and 97 respectively. Our diagnostic performance was better in lymph nodes than in the pancreas and other organs and was not significantly different for lesions ≤25 mm compared with lesion >25 mm in diameter. Performance was better for pathologists with prior experience than for pathologists without experience. Conclusion: In the current climate of proficiency testing, error tracking and competence evaluation, there is a great potential for the use of CUSUM charts to assess procedure failure and error tracking in quality control programs, particularly when a new procedure such as EUS‐FNA is introduced in the laboratory. Additionally, the method can be used to assess trainee competency and to track the proficiency of practicing cytologists.     

Retrospective study on performance of constancy check device in Linac beam monitoring using Statistical Process Control

AimTo examine the application of Statistical Process Control (SPC) and Ishikawa diagrams for retrospective evaluation of machine Quality Assurance (QA) performance in radiotherapyBackgroundSPC is a popular method for supplementing the performance of QA techniques in healthcare. This work investigates the applicability of SPC techniques and Ishikawa charts in machine QA.Materials and MethodsSPC has been applied to recommend QA limits on the particular beam parameters using the QUICKCHECK^webline QA portable constancy check device for 6 MV and 10 MV flattened photon beams from the Elekta Versa HD linear accelerator (Linac). Four machine QA parameters – beam flatness, beam symmetry along gun target direction and left-right direction, and beam quality factor (BQF) – were selected for retrospective analysis. Shewhart charts, Exponentially Weighted Moving Average (EWMA) charts and Cumulative Sum (CUSUM) charts were obtained for each parameter. The root causes for a failure in machine QA were broken down into an Ishikawa diagram enabling the user to identify the root cause of error and rectify the problem subsequently.ResultsShewhart charts and EWMA charts applied could detect loss in control in one variable in the 6 MV beams and in all four variables in 10 MV beams. CUSUM charts detected offsets in the readings. The Ishikawa chart exhaustively included the possible errors that lead to loss of control.ConclusionSPC is proven to be effective for detection of loss in control in machine QA. The Ishikawa chart provides the set of probable root causes of machine error useful while troubleshooting.     

Use of CUSUM and Shewhart charts to monitor regional trends of birth defect reports in New York State

BACKGROUND: Cumulative sum (CUSUM) charts were originally developed for industrial quality control, but may be adapted for the surveillance of health outcome data, such as birth defects. The reported prevalence of birth defects can vary due to differences in case ascertainment, surveillance practices, or true changes in prevalence. We examined the utility of CUSUM and Shewhart charts for detect-ing changes in prevalence of two different birth defect groups. We chose obstructive renal defects because we expected an increase in reporting due to improved diagnosis. We chose oral clefts for comparison because we expected reporting to be unaffected by changes in diagnostic technologies. METHODS: Data from the New York State Congenital Malformations Registry from 1992-1999 were analyzed using self-starting binomial CUSUM and Shewhart charts for four regions of New York State. RESULTS: CUSUM charts show that reports of obstructive urinary defects have increased from 1992-1999 in all regions of New York State. Reports of oral clefts increased only on Long Island. CONCLUSIONS: The CUSUM method proved useful for identifying changes in birth defect reporting and was able to detect the expected increases in obstructive renal defects. The apparent increase is likely due to improvements in diagnostic imaging techniques. In contrast, we only detected an increase in oral clefts on Long Island, which may be related to under report-ing of cases in the earlier years. CUSUM charts are useful in detecting small, sustained increases in prevalences over time while Shewhart charts are easier to interpret and can detect large sharp increases.     

Raman spectroscopy and chemometrics for on‐line control of glucose fermentation by Saccharomyces cerevisiae

This work presents the use of Raman spectroscopy and chemometrics for on‐line control of the fermentation process of glucose by Saccharomyces cerevisiae. In a first approach, an on‐line determination of glucose, ethanol, glycerol, and cells was accomplished using multivariate calibration based on partial least squares (PLS). The PLS models presented values of root mean square error of prediction (RMSEP) of 0.53, 0.25, and 0.02% for glucose, ethanol and glycerol, respectively, and RMSEP of 1.02 g L^?1 for cells. In a second approach, multivariate control charts based on multiway principal component analysis (MPCA) were developed for detection of fermentation fault‐batch. Two multivariate control charts were developed, based on the squared prediction error (Q) and Hotelling's T². The use of the Q control chart in on‐line monitoring was efficient for detection of the faults caused by temperature, type of substrate and contamination, but the T² control chart was not able to monitor these faults. On‐line monitoring by Raman spectroscopy in conjunction with chemometric procedures allows control of the fermentative process with advantages in relation to reference methods, which require pretreatment, manipulation of samples and are time consuming. Also, the use of multivariate control charts made possible the detection of faults in a simple way, based only on the spectra of the system. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Can recreational hunting contribute to pest mammal control on public land in Australia?

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Change point estimation in monitoring survival time

Precise identification of the time when a change in a hospital outcome has occurred enables clinical experts to search for a potential special cause more effectively. In this paper, we develop change point estimation methods for survival time of a clinical procedure in the presence of patient mix in a Bayesian framework. We apply Bayesian hierarchical models to formulate the change point where there exists a step change in the mean survival time of patients who underwent cardiac surgery. The data are right censored since the monitoring is conducted over a limited follow-up period. We capture the effect of risk factors prior to the surgery using a Weibull accelerated failure time regression model. Markov Chain Monte Carlo is used to obtain posterior distributions of the change point parameters including location and magnitude of changes and also corresponding probabilistic intervals and inferences. The performance of the Bayesian estimator is investigated through simulations and the result shows that precise estimates can be obtained when they are used in conjunction with the risk-adjusted survival time CUSUM control charts for different magnitude scenarios. The proposed estimator shows a better performance where a longer follow-up period, censoring time, is applied. In comparison with the alternative built-in CUSUM estimator, more accurate and precise estimates are obtained by the Bayesian estimator. These superiorities are enhanced when probability quantification, flexibility and generalizability of the Bayesian change point detection model are also considered.     

CUSUM charts in the quality control of colon cancer lymph node analysis: a population-registry study

Background

The most important determinant of survival in patients with colon cancer is the presence or absence of regional lymph node metastases. This factor is consistently associated with long-term and disease-specific survival. Cumulative summation of differences (CUSUM) charts can help to discriminate abnormalities that cannot be explained by the general variability of a process. We used CUSUM charts to analyse the quality of nodal analysis in colon cancer and to use a population-registry cancer database to estimate the optimal number of lymph nodes for adequate prognostic analysis.

Methods

This was a multicentre population-registry cancer study from January 2004 to December 2007. We used these data to produce the different CUSUM curves, focusing on the main variables. To calculate survival, we used the Kaplan–Meier method.

Results

In this study, we examined 548 patients. The CUSUM curves were calculated for overall mortality, specific mortality, and recurrence according to (1) the number of lymph nodes analysed and affected and (2) compared the ratio of the number of lymph nodes affected to the number analysed. Finally, the lymph node ratio was compared to the overall survival CUSUM curve.

Discussion

This CUSUM control chart analysis reinforces the unquestionable importance of analysing at least 12 lymph nodes in patients with colon cancer in order to accurately estimate their prognosis. However, our findings indicate that the analysis of at least 20 lymph nodes is a more appropriate cutoff point for accomplishing the demanding objective of diagnosing a high-quality prognosis in colon cancer patients.

     

Establishment of laboratory quality control indicators for NAT on blood donors' samples

In order to establish and screen nucleic acid test (NAT) quality control indicators for blood donor samples, C_T value of each test item were detected by NAT, internal and external quality controls, the number of unsuccessful mixed samples, the split positive rate, the rate of detection efficiency, and the equipment failure rate were collected. The "instant method" is used to establish the Levey-Jennings quality control chart, the mixed test positive rate, the rate of unqualified sample. Possion distribution is used to establish the quality control chart, and it is easily to operate and monitor NAT effectively. The results displayed that quality control charts were established, including unqualified sample Possion distribution quality control chart, the rate of equipment failure quality control chart, the failure rate of reagent batch and inefficient quality control chart, test result positive of Possion distribution quality control chart, quality control charts of NAT positive Possion distribution probability, the rate of split positive quality control charts, quality control charts of unsuccessful mixed samples, quality control chart of reagents effective rate, internal quality control chart, correctness, and NAT qualitative quality control chart. The study established quality control indicators throughout the whole NAT process, which were able to effectively improve NAT quality control and the efficacy of laboratory management.     

Warming experiments elucidate the drivers of observed directional changes in tundra vegetation

Few studies have clearly linked long‐term monitoring with in situ experiments to clarify potential drivers of observed change at a given site. This is especially necessary when findings from a site are applied to a much broader geographic area. Here, we document vegetation change at Barrow and Atqasuk, Alaska, occurring naturally and due to experimental warming over nearly two decades. An examination of plant cover, canopy height, and community indices showed more significant differences between years than due to experimental warming. However, changes with warming were more consistent than changes between years and were cumulative in many cases. Most cases of directional change observed in the control plots over time corresponded with a directional change in response to experimental warming. These included increases in canopy height and decreases in lichen cover. Experimental warming resulted in additional increases in evergreen shrub cover and decreases in diversity and bryophyte cover. This study suggests that the directional changes occurring at the sites are primarily due to warming and indicates that further changes are likely in the next two decades if the regional warming trend continues. These findings provide an example of the utility of coupling in situ experiments with long‐term monitoring to accurately document vegetation change in response to global change and to identify the underlying mechanisms driving observed changes.     

Grain subproteome responses to nitrogen and sulfur supply in diploid wheat Triticum monococcum ssp. monococcum

Wheat grain storage proteins (GSPs) make up most of the protein content of grain and determine flour end‐use value. The synthesis and accumulation of GSPs depend highly on nitrogen (N) and sulfur (S) availability and it is important to understand the underlying control mechanisms. Here we studied how the einkorn (Triticum monococcum ssp. monococcum) grain proteome responds to different amounts of N and S supply during grain development. GSP composition at grain maturity was clearly impacted by nutrition treatments, due to early changes in the rate of GSP accumulation during grain filling. Large‐scale analysis of the nuclear and albumin‐globulin subproteomes during this key developmental phase revealed that the abundance of 203 proteins was significantly modified by the nutrition treatments. Our results showed that the grain proteome was highly affected by perturbation in the N:S balance. S supply strongly increased the rate of accumulation of S‐rich α/β‐gliadin and γ‐gliadin, and the abundance of several other proteins involved in glutathione metabolism. Post‐anthesis N supply resulted in the activation of amino acid metabolism at the expense of carbohydrate metabolism and the activation of transport processes including nucleocytoplasmic transit. Protein accumulation networks were analyzed. Several central actors in the response were identified whose variation in abundance was related to variation in the amounts of many other proteins and are thus potentially important for GSP accumulation. This detailed analysis of grain subproteomes provides information on how wheat GSP composition can possibly be controlled in low‐level fertilization condition.     

Ongoing changes in migration phenology and winter residency at Bracken Bat Cave

Bats play an important role in agroecology and are effective bioindicators of environmental conditions, but little is known about their fundamental migration ecology, much less how these systems are responding to global change. Some of the world's largest bat populations occur during the summer in the south‐central United States, when millions of pregnant females migrate from lower latitudes to give birth in communal maternity colonies. Despite a relatively large volume of research into these colonies, many fundamental questions regarding their abundance—including their intra‐ and interseasonal variability—remain unanswered, and even estimating the size of individual populations has been a long‐running challenge. Overall, monitoring these bat populations at high temporal resolution (e.g., nightly) and across long time spans (e.g., decades) has been impossible. Here, we show 22 continuous years of nightly population counts at Bracken Cave, a large bat colony in south‐central Texas, enabling the first climate‐scale phenological analysis. Using quantitative radar monitoring, we found that spring migration and the summer reproductive cycle have advanced by approximately 2 weeks over the study period. Furthermore, we quantify the ongoing growth of a newly—established overwintering population that indicates a system‐wide response to changing environmental conditions. Our observations reveal behavioral plasticity in bats’ ability to adapt to changing resource availability, and provide the first long‐term quantification of their response to a changing climate. As aerial insectivores, these changes in bat phenology and propensity for overwintering indicate probable shifts in prey availability, with clear implications for pest management across wider regional agrisystems.     

Minimizing the cost of environmental management decisions by optimizing statistical thresholds

Environmental management decisions are prone to expensive mistakes if they are triggered by hypothesis tests using the conventional Type I error rate (α) of 0.05. We derive optimal α‐levels for decision‐making by minimizing a cost function that specifies the overall cost of monitoring and management. When managing an economically valuable koala population, it shows that a decision based on α = 0.05 carries an expected cost over $5 million greater than the optimal decision. For a species of such value, there is never any benefit in guarding against the spurious detection of declines and therefore management should proceed directly to recovery action. This result holds in most circumstances where the species’ value substantially exceeds its recovery costs. For species of lower economic value, we show that the conventional α‐level of 0.05 rarely approximates the optimal decision‐making threshold. This analysis supports calls for reversing the statistical ‘burden of proof’ in environmental decision‐making when the cost of Type II errors is relatively high.     

Train crash crinoids revisited

‘Train crash crinoids’ represent an unusual mode of preservation of crinoid columns, superficially resembling to the carriages of a crashed train. They were exhumed from the White Peak (Mississippian limestones) of the Peak District in the Treak Cliff area of Castleton, Derbyshire, north‐central England, and were presented by Broadhurst & Simpson as part of a varied suite of observations supporting the recognition of an ancient apron reef (= fore‐reef slope). A re‐examination of these specimens shows that they were not live crinoids at or near the reef crest, but were recently dead specimens, recumbent on the sediment surface. Something triggered their movement into deeper water, and some travelled downslope parallel to the direction of movement and broke into a ‘train crash pattern’ when the lower end impacted on an immovable object.     

The effect of targeted high‐threat weed control on wet forest understorey vegetation in the Central Highlands region,Victoria

The effective control of highly invasive weeds in Australia is an important conservation management action. In this study, we monitored the outcome of herbicide control on high‐threat weeds in the wet forests of the Central Highlands of Victoria. Twenty‐two control (no weed control) and 32 treatment (weed control) plots were surveyed annually over 24 months. Initial results show that weed cover and frequency decreased substantially in response to weed control; however, it is too early to determine the response of native species. We recommend that herbicide control and the associated monitoring programme be continued, and depending on the outcomes, data should be used to develop a more integrated management strategy.     

Drought and recovery effects on belowground respiration dynamics and the partitioning of recent carbon in managed and abandoned grassland

The supply of soil respiration with recent photoassimilates is an important and fast pathway for respiratory loss of carbon (C). To date it is unknown how drought and land‐use change interactively influence the dynamics of recent C in soil‐respired CO₂. In an in situ common‐garden experiment, we exposed soil‐vegetation monoliths from a managed and a nearby abandoned mountain grassland to an experimental drought. Based on two ¹³CO₂ pulse‐labelling campaigns, we traced recently assimilated C in soil respiration during drought, rewetting and early recovery. Independent of grassland management, drought reduced the absolute allocation of recent C to soil respiration. Rewetting triggered a respiration pulse, which was strongly fuelled by C assimilated during drought. In comparison to the managed grassland, the abandoned grassland partitioned more recent C to belowground respiration than to root C storage under ample water supply. Interestingly, this pattern was reversed under drought. We suggest that these different response patterns reflect strategies of the managed and the abandoned grassland to enhance their respective resilience to drought, by fostering their resistance and recovery respectively. We conclude that while severe drought can override the effects of abandonment of grassland management on the respiratory dynamics of recent C, abandonment alters strategies of belowground assimilate investment, with consequences for soil‐CO₂ fluxes during drought and drought‐recovery.     

Use of home range behaviour to assess establishment in translocated giraffes

Conservation translocation is a management technique employed to introduce, re‐introduce or reinforce wild animal and plant populations. Giraffe translocations are being conducted throughout Africa, but the lack of effective post‐translocation monitoring limits our ability to assess translocation outcomes. One potential indicator of translocation success is the establishment of characteristic movement and home range behaviour in the new location. We analysed the post‐translocation movement patterns of six Global Positioning System‐collared Angolan giraffes (Giraffa camelopardalis angolensis) in three regions of Namibia. We estimated home range size with minimum convex polygon (MCP) and adaptive local convex hull estimators, and assessed home range behaviour with the localizing tendency model and a home range Monte Carlo bootstrap analysis. Four of the six giraffes appeared to establish home ranges, indicating short‐term translocation success. The other two giraffes exhibited long‐distance linear movements throughout the observation period, suggesting they did not establish home ranges. Home range sizes varied greatly among regions. Our results suggest monitoring translocated animals for the establishment of characteristic movement behaviour could be a useful early indicator of translocation success.     

Two in one: cryptic species discovered in biological control agent populations using molecular data and crossbreeding experiments

There are many examples of cryptic species that have been identified through DNA‐barcoding or other genetic techniques. There are, however, very few confirmations of cryptic species being reproductively isolated. This study presents one of the few cases of cryptic species that has been confirmed to be reproductively isolated and therefore true species according to the biological species concept. The cryptic species are of special interest because they were discovered within biological control agent populations. Two geographically isolated populations of Eccritotarsus catarinensis (Carvalho) [Hemiptera: Miridae], a biological control agent for the invasive aquatic macrophyte, water hyacinth, Eichhornia crassipes (Mart.) Solms [Pontederiaceae], in South Africa, were sampled from the native range of the species in South America. Morphological characteristics indicated that both populations were the same species according to the current taxonomy, but subsequent DNA analysis and breeding experiments revealed that the two populations are reproductively isolated. Crossbreeding experiments resulted in very few hybrid offspring when individuals were forced to interbreed with individuals of the other population, and no hybrid offspring were recorded when a choice of mate from either population was offered. The data indicate that the two populations are cryptic species that are reproductively incompatible. Subtle but reliable diagnostic characteristics were then identified to distinguish between the two species which would have been considered intraspecific variation without the data from the genetics and interbreeding experiments. These findings suggest that all consignments of biological control agents from allopatric populations should be screened for cryptic species using genetic techniques and that the importation of multiple consignments of the same species for biological control should be conducted with caution.