Quantifying acceptable artefact ranges for dermatologic classification algorithms

Background

Many classifiers have been developed that can distinguish different types of skin lesions (e.g., benign nevi, melanoma) with varying degrees of success.^1–5 However, even successfully trained classifiers may perform poorly on images that include artefacts. While problems created by hair and ink markings have been published, quantitative measurements of blur, colour and lighting variations on classification accuracy has not yet been reported to our knowledge.

Objectives

We created a system that measures the impact of various artefacts on machine learning accuracy. Our objectives were to (1) quantitatively identify the most egregious artefacts and (2) demonstrate how to assess a classification algorithm's accuracy when input images include artefacts.

Methods

We injected artefacts into dermatologic images using techniques that could be controlled with a single variable. This allows us to quantitatively evaluate the impact on the accuracy. We trained two convolutional neural networks on two different binary classification tasks and measured the impact on dermoscopy images over a range of parameter values. The area under the curve and specificity‐at‐a‐given‐sensitivity values were measured for each artefact induced at each parameter.

Results

General blur had the strongest negative effect on the melanoma versus other task. Conversely, shifting the hue towards blue had a more pronounced effect on the suspicious versus follow task.

Conclusions

Classifiers should either mitigate artefacts or detect them. Images should be excluded from diagnosis/recommendation when artefacts are present in amounts outside the machine perceived quality range. Failure to do so will reduce accuracy and impede approval from regulatory agencies.

Association of Intestinal Alkaline Phosphatase With Necrotizing Enterocolitis Among Premature Infants

IMPORTANCE

Necrotizing enterocolitis (NEC) in preterm infants is an often-fatal gastrointestinal tract emergency. A robust NEC biomarker that is not confounded by sepsis could improve bedside management, lead to lower morbidity and mortality, and permit patient selection in randomized clinical trials of possible therapeutic approaches.

OBJECTIVE

To evaluate whether aberrant intestinal alkaline phosphatase (IAP) biochemistry in infant stool is a molecular biomarker for NEC and not associated with sepsis.

DESIGN, SETTING, AND PARTICIPANTS

This multicenter diagnostic study enrolled 136 premature infants (gestational age, <37 weeks) in 2 hospitals in Louisiana and 1 hospital in Missouri. Data were collected and analyzed from May 2015 to November 2018.

EXPOSURES

Infant stool samples were collected between 24 and 40 or more weeks postconceptual age. Enrolled infants underwent abdominal radiography at physician and hospital site discretion.

MAIN OUTCOMES AND MEASURES

Enzyme activity and relative abundance of IAP were measured using fluorometric detection and immunoassays, respectively. After measurements were performed, biochemical data were evaluated against clinical entries from infants' hospital stay.

RESULTS

Of 136 infants, 68 (50.0%) were male infants, median (interquartile range [IQR]) birth weight was 1050 (790-1350) g, and median (IQR) gestational age was 28.4 (26.0-30.9) weeks. A total of 25 infants (18.4%) were diagnosed with severe NEC, 19 (14.0%) were suspected of having NEC, and 92 (66.9%) did not have NEC; 26 patients (19.1%) were diagnosed with late-onset sepsis, and 14 (10.3%) had other non-gastrointestinal tract infections. For severe NEC, suspected NEC, and no NEC samples, median (IQR) fecal IAP content, relative to the amount of IAP in human small intestinal lysate, was 99.0% (51.0%-187.8%) (95% CI, 54.0%-163.0%), 123.0% (31.0%-224.0%) (95% CI, 31.0%-224.0%), and 4.8% (2.4%-9.8%) (95% CI, 3.4%-5.9%), respectively. For severe NEC, suspected NEC, and no NEC samples, median (IQR) enzyme activity was 183 (56-507) μmol/min/g (95% CI, 63-478 μmol/min/g) of stool protein, 355 (172-608) μmol/min/g (95% CI, 172-608 μmol/min/g) of stool protein, and 613 (210-1465) μmol/min/g (95% CI, 386-723 μmol/min/g) of stool protein, respectively. Mean (SE) area under the receiver operating characteristic curve values for IAP content measurements were 0.97 (0.02) (95% CI, 0.93-1.00; P < .001) at time of severe NEC, 0.97 (0.02) (95% CI, 0.93-1.00; P < .001) at time of suspected NEC, 0.52 (0.07) (95% CI, 0.38-0.66; P = .75) at time of sepsis, and 0.58 (0.08) (95% CI, 0.42-0.75; P = .06) at time of other non-gastrointestinal tract infections. Mean (SE) area under the receiver operating characteristic curve values for IAP activity were 0.76 (0.06) (95% CI, 0.64-0.86; P < .001), 0.62 (0.07) (95% CI, 0.48-0.77; P = .13), 0.52 (0.07) (95% CI, 0.39-0.67; P = .68), and 0.57 (0.08) (95% CI, 0.39-0.69; P = .66), respectively.

CONCLUSIONS AND RELEVANCE

In this diagnostic study, high amounts of IAP protein in stool and low IAP enzyme activity were associated with diagnosis of NEC and may serve as useful biomarkers for NEC. Our findings indicated that IAP biochemistry was uniquely able to distinguish NEC from sepsis.

Event-related brain potentials during the visuomotor mental rotation task: The contingent negative variation scales to angle of rotation

Perceptual judgments about the angular disparity of a character from its standard upright (i.e., mental rotation task) result in a concurrent increase in reaction time (RT) and modulation of the amplitude of the P300 event-related brain potential (ERP). It has therefore been proposed that the P300 represents the neural processes associated with a visual rotation. In turn, the visuomotor mental rotation (VMR) task requires reaching to a location that deviates from a target by a predetermined angle. Although the VMR task exhibits a linear increase in RT with increasing oblique angles of rotation, work has not examined whether the task is supported via a visual rotation analogous to its mental rotation task counterpart. This represents a notable issue because seminal work involving non-human primates has ascribed VMR performance to the motor-related rotation of directionally tuned neurons in the primary motor cortex. Here we examined the concurrent behavioral and ERP characteristics of a standard reaching task and VMR tasks of 35°, 70°, and 105° of rotation. Results showed that the P300 amplitude was larger for the standard compared to each VMR task--an effect independent of the angle of rotation. In turn, the amplitude of the contingent negative variation (CNV)--an ERP related to cognitive and visuomotor integration for movement preparation--was systematically modulated with angle of rotation. Thus, we propose that the CNV represents an ERP correlate related to the cognitive and/or visuomotor transformation demands of increasing the angular separation between a stimulus and a movement goal.

Nurse-led clinic: effective and efficient delivery of assessment and review of patients with hepatitis B and C

BACKGROUND

Hepatology and gastroenterology services are increasingly utilising the skills and experience of nurse practitioners and nurse specialists to help meet the increasing demand for healthcare. A new nurse-led assessment clinic has been established in the liver clinic at Geelong Hospital to utilise the expertise of nurses to assess and triage new patients and streamline their pathway through the healthcare system.

AIM

The aim of this study is to assess quantitatively the first 2 years of operation of the nurse assessment clinic at Geelong Hospital, and to assess advantages and disadvantages of the nurse-led clinic.

METHODS

Data were extracted retrospectively from clinical records of new patients at the liver clinic. Quarterly 1-month periods were recorded over 2 years. Patients were categorised according to the path through which they saw a physician, including missed and rescheduled appointments. The number of appointments, the waiting time from referral to appointments and the number of 'did-not-attend' occasions were analysed before and after the institution of the nurse-led assessment clinic. The Mann-Whitney rank sum test of ordinal data was used to generate median wait times.

RESULTS

There was shown to be a statistically significant longer waiting time for physician appointment if seen by the nurse first. The difference in waiting time was 10 days. However, there was also a reduction in the number of missed appointments at the subsequent physician clinic. Other advantages have also been identified, including effective triage of patients and organisation of appropriate investigations from the initial nurse assessment.

Time Course Analysis of Closed- and Open-Loop Grasping of the Müller-Lyer Illusion

The authors investigated whether the early or later stages of closed-loop (CL) and open-loop (OL) grasping movements were differentially influenced by the Müller-Lyer (ML) illusion. Participants (N = 21) reached out and grasped small (5 cm) and large (7 cm) objects embedded within fins-in and fins-out ML configurations. Grasping time (GT) was normalized, and absolute grip aperture (GA) as well as scaled illusion effects were computed at 20%, 40%, 60%, and 80% of GT. The results indicated that CL trials were refractory to the illusory array (i.e., from 20% to 80% of GT), whereas OL trials were influenced by the ML figure during that same time. Those findings suggest that CL trials were supported by unitary and metrical visual information, whereas OL trials were entirely supported by perception-based visual information.

Online corrections can produce illusory bias during closed-loop pointing

This experiment examined whether the impact of pictorial illusions during the execution of goal-directed reaching movements is attributable to ocular motor signaling. We analyzed eye and hand movements directed toward both the vertex of the Müller-Lyer (ML) figure in a closed-loop procedure. Participants pointed to the right vertex of a visual stimulus in two conditions: a control condition wherein the figure (in-ML, neutral, out-ML) presented at response planning remained unchanged throughout the movement, and an experimental condition wherein a neutral figure presented at response planning was perturbed to an illusory figure (in-ML, out-ML) at movement onset. Consistent with previous work from our group (Heath et al. in Exp Brain Res 158:378-384, 2004; Heath et al. in J Mot Behav 37:179-185, 2005b), action-bias present in both conditions; thus illusory bias was introduced into during online control. Although primary saccades were influenced by illusory configurations (control conditions; see Binsted and Elliott in Hum Mov Sci 18:103-117, 1999a), illusory bias developed within the secondary "corrective" saccades during experimental trials (i.e., following a veridical primary saccade). These results support the position that a unitary spatial representation underlies both action and perception and this representation is common to both the manual and oculomotor systems.

Interhemispheric transmission time in persons with Down syndrome

BACKGROUND

The study of cerebral specialization in persons with Down syndrome (DS) has revealed an anomalous pattern of organization. Specifically, persons with DS elicit a right cerebral hemisphere lateralization for receptive language and a left cerebral hemisphere lateralization for the production of simple and complex movements: a pattern quite different from the left hemisphere lateralization typically characterizing the aforementioned processes in the non-DS population. It is thought that the putative separation between speech perception and movement planning systems as well as the cost of interhemispheric integration impedes verbal-motor behaviours in persons with DS. Moreover, morphological anomalies of callosal structure may further amplify between-hemisphere communication difficulties in the DS population. In the present investigation, we employed a behavioural technique (i.e. the Poffenberger paradigm; Poffenberger) to determine whether global anomalies of callosal structure further amplify deficits in interhemispheric communication.

METHODS

Fourteen individuals with DS and 25 chronological age-matched and gender-equated participants without intellectual disability performed a visuomotor reaction time (RT) test with their left or right hand to visual stimuli appearing left or right of visual fixation. Typically it is reported that responses to visual stimuli appearing ipsilateral to the responding hand (i.e. the uncrossed condition) are faster than responses wherein visual stimuli and responding hand are contralaterally mapped (i.e. the crossed condition). The increased RT associated with the crossed condition is reported on the order of 4 ms and has been interpreted to reflect the physiological result of interhemispheric transmission.

RESULTS

Not surprisingly persons with DS exhibited slower and more variable RTs relative to control counterparts. In addition, a reliable RT advantage favouring the uncrossed conditions was observed among control participants but not persons with DS.

CONCLUSIONS

In keeping with the extant literature, RT performance of the DS group was slower and more variable than control counterparts. This finding has been interpreted to reflect an 'adaptive reaction' wherein the perceptual-motor abilities of persons with DS are not optimized to respond to externally paced stimuli. In terms of evaluating interhemispheric transmission via the Poffenberger paradigm, our results show the finite measures of explicit brain-behaviour relations characterizing so-called healthy controls are not always tenable in the DS population. Indeed, we believe such a finding underpins the aforementioned 'adaptive reaction' exemplifying preferred movement control in persons with DS.

Slimline vs. glass pH electrodes: what degree of accuracy should we expect?

BACKGROUND

Ambulatory pH monitoring is considered the gold standard for measuring oesophageal acid exposure, however, data comparing antimony and glass electrodes are limited.

AIM

To compare the accuracy of the Slimline antimony pH monitoring system and a conventional glass electrode catheter pH monitoring system during ambulatory conditions.

METHODS

Eighteen subjects (13 males, 23-45 years) underwent simultaneous pH monitoring using the Slimline antimony pH electrode and MIC M3 glass pH electrode pH monitoring systems for 12 h. Acid exposure was analysed and compared by manual extraction of the data onto an excel spreadsheet.

RESULTS

There was no statistical difference in the median per cent time the pH was <4 recorded by the two systems (Slimline, 3%, Glass MIC M3, 2%, P = 0.77) and the correlation was excellent (r = 0.84). The difference in recorded reflux events was also not significantly different between the two systems, with the absolute difference being 23 events (s.d., 26). Point-by-point discrepancy was 28% (s.d., 18%), however, the agreement in terms of reflex events was excellent (Kappa value, 0.89, s.d., 0.09).

CONCLUSION

Despite substantial point-by-point disagreement, the antimony Slimline pH catheter compares favourably to the Glass MIC M3 pH catheter in terms of measuring standard pH parameters.

The influence of letrozole on serum lipid concentrations in postmenopausal women with primary breast cancer who have completed 5 years of adjuvant tamoxifen (NCIC CTG MA.17L)

BACKGROUND

The purpose of this study was to evaluate changes in serum lipid parameters {cholesterol, high-density lipoprotein (HDL) cholesterol, low-density lipoprotein (LDL) cholesterol, triglycerides and lipoprotein(a) [Lp(a)]}, in postmenopausal women receiving letrozole or placebo after adjuvant tamoxifen for early stage breast cancer (NCIC CTG MA.17L).

PATIENTS AND METHODS

MA.17L is a substudy of MA.17, a randomized, double-blind, placebo-controlled trial of letrozole 2.5 mg taken daily for 5 years in postmenopausal women with primary breast cancer completing approximately 5 years of prior adjuvant tamoxifen. Patients consenting to participate in this companion study had blood drawn and lipid parameters (total cholesterol, HDL cholesterol, LDL cholesterol, Lp(a), triglycerides) evaluated at baseline, 6 months, 12 months and yearly thereafter until completion of protocol therapy. It was required that women be non-hyperlipidemic and not taking lipid-lowering drugs at time of entry on this trial.

RESULTS

Three hundred and forty seven women were enrolled in the study. The letrozole and the placebo groups demonstrated marginally significant differences in the percentage change from baseline in HDL cholesterol at 6 months (P=0.049), in LDL cholesterol at 12 months (P=0.033) and triglycerides at 24 months (P=0.036). All comparisons of lipid parameters at other time points were not significantly different between the two treatment groups. No statistically significant differences in the number of patients exceeding the thresholds defined for the lipid parameters were found between the two treatment groups.

CONCLUSIONS

The MA.17 trial demonstrated a significant improvement in disease-free survival with the use of letrozole as extended adjuvant therapy post tamoxifen. Results from this study suggests that letrozole does not significantly alter serum cholesterol, HDL cholesterol, LDL cholesterol, triglycerides or Lp(a) in non-hyperlidiemic postmenopausal women with primary breast cancer treated up to 36 months following at least 5 years of adjuvant tamoxifen therapy. These findings further support the tolerability of extended adjuvant letrozole in postmenopausal women following standard tamoxifen therapy.

Cacao domestication II: progenitor germplasm of the Trinitario cacao cultivar

Cacao (Theobroma cacao L.) has been cultivated in Central America since pre-Columbian times. The type of cacao cultivated in this region was called Criollo; cacao populations from the Amazon basin were called Forastero. The type of Forastero most commonly cultivated until 1950 was named Amelonado. Historical data show Trinitario cacao to have originated in Trinidad, resulting from natural hybridisation between Criollo and Amelonado Forastero. Doubts persist on the source of the Amelonado Forastero involved in the origin of Trinitario; the Amelonado parent may have come from the Lower Amazon, the Orinoco or the Guyanas. Most of the cacao cultivated worldwide until 1950 consisted of Criollo, Trinitario and Amelonado. From the early 1950s, Forastero material collected in the Upper Amazon region during the 1930s and 1940s began to be employed in breeding programmes. To gain a better understanding of the origin and the genetic basis of the cacao cultivars exploited before the utilisation of germplasm collected in the Upper Amazon, a study was carried out using restriction fragment length polymorphism and microsatellite markers. Trinitario samples from 17 countries were analysed. With molecular markers, it was possible to clearly identify three main genotypes (represented by clones SP1, MAT1-6 and SIAL70) implicated in the origin of most Trinitario clones.

Resistance gene homologues in Theobroma cacao as useful genetic markers

Resistance gene homologue (RGH) sequences have been developed into useful genetic markers for marker-assisted selection (MAS) of disease resistant Theobroma cacao. A plasmid library of amplified fragments was created from seven different cultivars of cacao. Over 600 cloned recombinant amplicons were evaluated. From these, 74 unique RGHs were identified that could be placed into 11 categories based on sequence analysis. Primers specific to each category were designed. The primers specific for a single RGH category amplified fragments of equal length from the seven different cultivars used to create the library. However, these fragments exhibited single-strand conformational polymorphism (SSCP), which allowed us to map six of the RGH categories in an F(2) population of T. cacao. RGHs 1, 4 and 5 were in the same linkage group, with RGH 4 and 5 separated by less than 4 cM. As SSCP can be efficiently performed on our automated sequencer, we have developed a convenient and rapid high throughput assay for RGH alleles.