Consensus clustering methodology to improve molecular stratification of non-small cell lung cancer

Recent advances in machine learning research, combined with the reduced sequencing costs enabled by modern next-generation sequencing, paved the way to the implementation of precision medicine through routine multi-omics molecular profiling of tumours. Thus, there is an emerging need of reliable models exploiting such data to retrieve clinically useful information. Here, we introduce an original consensus clustering approach, overcoming the intrinsic instability of common clustering methods based on molecular data. This approach is applied to the case of non-small cell lung cancer (NSCLC), integrating data of an ongoing clinical study (PROMOLE) with those made available by The Cancer Genome Atlas, to define a molecular-based stratification of the patients beyond, but still preserving, histological subtyping. The resulting subgroups are biologically characterized by well-defined mutational and gene-expression profiles and are significantly related to disease-free survival (DFS). Interestingly, it was observed that (1) cluster B, characterized by a short DFS, is enriched in KEAP1 and SKP2 mutations, that makes it an ideal candidate for further studies with inhibitors, and (2) over- and under-representation of inflammation and immune systems pathways in squamous-cell carcinomas subgroups could be potentially exploited to stratify patients treated with immunotherapy.

Long-term results after surgical treatment of the dominant lung adenocarcinoma associated with ground-glass opacities

Background

To evaluate the effect of first-time and eventual reiterative surgery on overall survival (OS) and disease-free survival (DFS) in Caucasian patients affected by an invasive adenocarcinoma (ADC) with at least another ground-glass opacity (GGO).

Methods

We analysed 47 patients operated on for lung ADC, identified as main cancer (MC), with at least one synchronous GGO, from January 2003 to March 2017. Characteristics associated with the evolution of GGOs were investigated with logistic regression and overall and DFS were evaluated with Kaplan-Meier method.

Results

Forty-two (89%) patients received an anatomic resection of the MC, 5 patients were treated by a single or multiple wedge resections. In total, 9 (19.1%) patients had all the lesions resected undergoing simultaneous resection of ipsilateral GGOs at first surgery while the remaining 38 (80.9%) patients still had at least one GGO that was followed up by serial CT scan. At the median follow-up of 41 months, GGO evolved in 16 (42.1%) patients. The presence of solid component at the initial CT scan was the only risk factor for evolution of the GGO. Thirteen patients underwent surgical resection showing an invasive ADC in 9 patients, MIA in 3 and AIS in 1. New GGOs developed in 7 (14.9%) patients, in which three underwent surgery showing the presence of solid ADC, MIA and AAH. OS rate at 5 years was 97.4%. DFS at 3 years was 82% and was significantly influenced by the stage of MC.

Conclusions

Patients affected by an invasive ADC with at least another GGO nodule enjoy good OS and DFS with a surgical reiterative approach. Part-solid GGO is associated with GGO progression requiring treatment, but OS is not influenced by the new onset or evolution of GGOs. DFS is affected by the stage of the MC which dictates the treatment strategy.

Using overbooking to manage no-shows in an Italian healthcare center

Background

In almost all healthcare systems, no-shows (scheduled appointments missed without any notice from patients) have a negative impact on waiting lists, costs and resource utilization, impairing the quality and quantity of cares that could be provided, as well as the revenues from the corresponding activity. Overbooking is a tool healthcare providers can resort to reduce the impact of no-shows.

Methods

We develop an overbooking algorithm, and we assess its effectiveness using two methods: an analysis of the data coming from a practical implementation in an healthcare center; a simulation experiment to check the robustness and the potential of the strategy under different conditions. The data of the study, which includes personal and administrative information of patients, together with their scheduled and attended examinations, was taken from the electronic database of a big outpatient center. The attention was focused on the Magnetic Resonance (MR) ward because it uses expensive equipment, its services need long execution times, and the center has actually used it to implement an overbooking strategy aimed at reducing the impact of no-shows. We propose a statistical model for the patient’s show/no-show behavior and we evaluate the ensuing overbooking procedure implemented in the MR ward. Finally, a simulation study investigates the effects of the overbooking strategy under different scenarios.

Results

The first contribution is a list of variables to identify the factors performing the best to predict no-shows. We classified the variables in three groups: “Patient’s intrinsic factors”, “Exogenous factors” and “Factors associated with the examination”. The second contribution is a predictive model of no-shows, which is estimated on context-specific data using the variables just discussed. Such a model represents a fundamental ingredient of the overbooking strategy we propose to reduce the negative effects of no-shows. The third contribution is the assessment of that strategy by means of a simulation study under different scenarios in terms of number of resources and no-show rates. The same overbooking strategy was also implemented in practice (giving the opportunity to consider it as a quasi-experiment) to reduce the negative impact caused by non attendance in the MR ward. Both the quasi-experiment and the simulation study demonstrated that the strategy improved the center’s productivity and reduced idle time of resources, although it increased slightly the patient’s waiting time and the staff’s overtime. This represents an evidence that overbooking can be suitable to improve the management of healthcare centers without adversely affecting their costs and the quality of cares offered.

Conclusions

We shown that a well designed overbooking procedure can improve the management of medical centers, in terms of a significant increase of revenue, while keeping patient’s waiting time and overtime under control. This was demonstrated by the results of a quasi-experiment (practical implementation of the strategy in the MR ward) and a simulation study (under different scenarios). Such positive results took advantage from a predictive model of no-show carefully designed around the medical center data.

Electronic supplementary material

The online version of this article (10.1186/s12913-018-2979-z) contains supplementary material, which is available to authorized users.

Detection of infarct size safety threshold for left ventricular ejection fraction impairment in acute myocardial infarction successfully treated with primary percutaneous coronary intervention

PURPOSE

In acute myocardial infarction (AMI) treated by primary percutaneous coronary intervention (PCI), there is a direct relationship between myocardial damage and consequent left ventricular (LV) functional impairment. It is however unclear whether there is a safety threshold below which infarct size does not significantly affect LV ejection fraction (EF). The aim of this study was to evaluate the relationship between infarct size and LVEF in AMI patients treated by successful PCI using a specific statistical approach to identify a possible safety threshold.

METHODS

Among patients with recent AMI submitted to perfusion gated single photon emission computed tomography (SPECT) to define the infarct size, the data of 427 subjects with sizable infarct size were considered. The relationship between infarct size and LVEF was analysed using a simple segmented regression (SSR) model and an iterative algorithm based on robust least squares (RLS) for parameter estimation.

RESULTS

The RLS algorithm detected two break points in the SSR model, set at infarct size values of 11.0 and 51.5 %. Because the slope coefficients of the two extreme segments of the regression line were not significant, by constraining such segments to zero slope in the SSR model, the lower break point was identified at infarct size = 8 % and the upper one at 45 %.

CONCLUSION

Using a rigorous statistical approach, it is possible to demonstrate that below a threshold of 8 % the infarct size apparently does not affect the LVEF and therefore a safety threshold could be set at this value. Furthermore, the same analysis suggests that the relationship between infarct size and LVEF impairment is lost for an infarct size > 45 %.

Use, Attitudes and Knowledge of Complementary and Alternative Drugs (CADs) Among Pregnant Women: a Preliminary Survey in Tuscany

To explore pregnant women's use, attitudes, knowledge and beliefs of complementary and alternative drugs (CADs) defined as products manufactured from herbs or with a natural origin. A preliminary survey was conducted among 172 pregnant women in their third trimester of pregnancy, consecutively recruited in two obstetrical settings; 15 women were randomly selected to compute a test-to-retest analysis. Response rate was 87.2%. Test-to-retest analysis showed a questionnaire's reproducibility exceeding a K-value of 0.7 for all items. Mean age was 32.4 ± 0.4 years; most women were nulliparae (62.7%). The majority of subjects (68%) declared to have used one or more CADs during their lifetime; 48% of pregnant women reported taking at least one CAD previously and during the current pregnancy. Women's habitual use of CADs meant they were at higher risk of taking CADs also during pregnancy (adjusted odds ratio = 10.8; 95% confidence interval: 4.7-25.0). Moreover, 59.1% of the subjects were unable to correctly identify the type of CADs they were using. The majority of women resorted to gynecologists as the primary information source for CADs during pregnancy, while they mainly referred to herbalists when not pregnant. Habitual use of CADs seems to be a strong predictor for their ingestion also during pregnancy; in addition most subjects were unable to correctly identify the products they were taking. In the light of the scanty data concerning the safety of CADs during pregnancy, these preliminary results confirm the need to investigate thoroughly the situation of pregnant women and CADs consumption.

SDH Mutations in Patients Affected by Paraganglioma Syndromes: A Personal Experience

Mutations in genes encoding mitochondrial succinate dehydrogenase (SDH) are frequently involved in the development of neural crest-derived (NCD) tumors, such as pheochromocytomas (PHEOs) or paragangliomas (PGLs). In this study we report the results of sequencing analysis in leukocyte DNA of patients affected by PHEO/PGL who turned out to be SDH mutation carriers. A nonsense germline heterozygous mutation (Q109X) was found in the exon 4 of the SDHD gene in the index cases of six unrelated families affected by PHEO/PGL. Haplotype analysis showed the presence of a founder effect. Affected patients showed high clinical variability, ranging from monolateral to bilateral glomus tumors, variably associated or not with PGLs or PHEOs. A novel missense SDHD variant, T112I, was also found in one of our families. A new missense G106D mutation, involving a highly conserved amino acid, was found in two sisters affected by bilateral glomus tumors. A P81L mutation associated with abdominal and head and neck PGL was detected in three families. A G12S variant of the SDHD gene was found in one patient affected by a PHEO. The finding of this variant in 3 of 100 control subjects suggests that it is a polymorphism and not a mutation. A novel IVS2-1G>T variant was found at intron 2 of SDHD gene in one patient affected by a glomus tumor. All the tumors associated with SDHD mutations were benign. Conversely, the only mutation we found in SDHB gene (IVS3+1G>A) was associated with a malignant PHEO.

Increased risk for gallstone disease in subjects operated on for partial gastrectomy with gastro-jejunostomy (BII operation)

The prevalence of cholelithiasis has been investigated in 301 male subjects (age range 35-60 years) operated on for partial gastrectomy with gastro-jejunostomy (BII), in 277 unoperated peptic ulcer patients (age range 30-60 years) and in a control population of 281 factory's workers (age range 31-58 years). The prevalence of gallstone disease resulted significantly higher in BII operated subjects (23.9%) than in unoperated (9%) and controls (8.5%). No difference was found between unoperated peptic ulcer patients and controls. These results indicate that BII operation is a high risk condition for cholelithiasis while peptic ulcer disease does not constitute a favourable factor for gallstone formation.

Candida albicans infection of gastric ulcer frequency and correlation with medical treatment. Results of a multicenter study

This paper reports the results of a multicenter prospective study of 188 consecutive patients affected by gastric ulcer, verified by endoscopy, in whom the frequency of a mycotic infection of the lesion was evaluated as well as the eventual influence of such pathology on the efficiency of medical treatment, the healing rate, and the healing time. A mycotic infection, defined as penetration of the periulcerous mucosa by the fungi, was found in only 13 patients (6.9%). No significant differences were found in the healing rate and healing time among these patients treated with H2-receptor antagonists and a control group of 43 matched gastric ulcer patients treated in the same period with the same therapy. It would appear from the data that mycotic infections of the gastric ulcer do not modify the efficiency of medical treatment.