Wilks’ dissimilarity for gene clustering: computational issues

Clustering methods are widely used in the analysis of gene expression data for their ability to uncover coordinated expression profiles. One important goal of clustering is to discover co–regulated genes because it has been postulated that co–regulation implies a similar function. In the context of agglomerative hierarchical clustering, we introduced a dissimilarity measure based on the Wilks’ Λ statistic that they called the Wilks’ dissimilarity and showed its usefulness in the identification of transcription modules. In this paper, we discuss the ability of the Wilks’ dissimilarity to identify clusters of co-expressed genes by providing an example where the most commonly used dissimilarity measures fail. Furthermore, we carry out a set of simulations aimed to investigate the use of a sparse canonical correlation technique in the estimation of the Wilks’ dissimilarity and provide guidelines for its use

Dissimilarity functions for rank-invariant hierarchical clustering of continuous variables

A theoretical framework is presented for a (copula-based) notion of dissimilarity between continuous random vectors and its main properties are studied. The proposed dissimilarity assigns the smallest value to a pair of random vectors that are comonotonic. Various properties of this dissimilarity are studied, with special attention to those that are prone to the hierarchical agglomerative methods, such as reducibility. Some insights are provided for the use of such a measure in clustering algorithms and a simulation study is presented. Real case studies illustrate the main features of the whole methodology.Comment: 38 pages, 10 figures, 7 table

Supplier's total cost of ownership evaluation: a data envelopment analysis approach

Supplier Total Cost of Ownership (TCO) is a widely-known approach for determining the overall cost generated by a supplier relationship, but its adoption is still limited. The complex calculations involved - and in particular the activity-based costing procedure for computing the cost of managing the relationship - pose a major obstacle to widespread TCO implementation. The purpose of this work is to formulate a Data Envelopment Analysis application (denoted 'TCO-based DEA') that can act as a proxy for TCO, and to test its ability to approximate the results of TCO with less effort. The study is based on the analysis of two categories of suppliers (74 in total) of a medium-sized Italian mechanical engineering company. The results show that TCO-based DEA is able to significantly approximate the outcomes of TCO, for both the efficiency indexes and rankings of suppliers, whilst requiring substantially less effort to perform the analysis. To our knowledge, this is the first study to develop a DEA-based tool for approximating TCO and to test it in a real-world setting. The research shows significant potential within the supply chain management field. In particular, TCO-based DEA can be used for analysing suppliers' performance, rationalising and reducing the supplier base, assisting the negotiation process

Global disparities in surgeons’ workloads, academic engagement and rest periods: the on-calL shIft fOr geNEral SurgeonS (LIONESS) study

: The workload of general surgeons is multifaceted, encompassing not only surgical procedures but also a myriad of other responsibilities. From April to May 2023, we conducted a CHERRIES-compliant internet-based survey analyzing clinical practice, academic engagement, and post-on-call rest. The questionnaire featured six sections with 35 questions. Statistical analysis used Chi-square tests, ANOVA, and logistic regression (SPSS® v. 28). The survey received a total of 1.046 responses (65.4%). Over 78.0% of responders came from Europe, 65.1% came from a general surgery unit; 92.8% of European and 87.5% of North American respondents were involved in research, compared to 71.7% in Africa. Europe led in publishing research studies (6.6 ± 8.6 yearly). Teaching involvement was high in North America (100%) and Africa (91.7%). Surgeons reported an average of 6.7 ± 4.9 on-call shifts per month, with European and North American surgeons experiencing 6.5 ± 4.9 and 7.8 ± 4.1 on-calls monthly, respectively. African surgeons had the highest on-call frequency (8.7 ± 6.1). Post-on-call, only 35.1% of respondents received a day off. Europeans were most likely (40%) to have a day off, while African surgeons were least likely (6.7%). On the adjusted multivariable analysis HDI (Human Development Index) (aOR 1.993) hospital capacity > 400 beds (aOR 2.423), working in a specialty surgery unit (aOR 2.087), and making the on-call in-house (aOR 5.446), significantly predicted the likelihood of having a day off after an on-call shift. Our study revealed critical insights into the disparities in workload, access to research, and professional opportunities for surgeons across different continents, underscored by the HDI

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Cluster analysis and conditional copula: a joint approach to analyse energy demand

In this work we investigate the thermal energy demand (TED) in urban areas through a copula-based approach. The proposed method enables the characterization of the probability law of TED under extreme weather conditions and for specific groups of buildings. In particular, we show how building characteristics, such as energy class and heating surface, may worsen or mitigate the impact of extreme scenarios

Clustering dependent observations with copula functions

This paper deals with the problem of clustering dependent observations according to their underlying complex generating process. Di Lascio and Giannerini (Journal of Classification 29(1):50\u201375, 2012) introduced the CoClust, a clustering algorithm based on copula function that achieves the task but has a high computational burden. Moreover, the CoClust automatically allocates all the observations to the clusters; thus, it cannot discard potentially irrelevant observations. In this paper we introduce an improved version of the CoClust that both overcomes these issues and performs better in many respects. By means of a Monte Carlo study we investigate the features of the algorithm and show that it improves consistently with respect to the old CoClust. The validity of our proposal is also supported by applications to real data sets of human breast tumor samples for which the algorithm provides a meaningful biological interpretation. The new algorithm is implemented and made available through an updated version of the R package CoClust

The impact of institutional and cultural factors on the use of non-GAAP financial measures. International evidence from the oil and gas industry

While the main aim of Non-GAAP Financial Measures (NGFMs) is to increase the compara- bility of the performance, many studies highlight an opportunistic use aimed at distorting investors\u2019 decisions. A recent stream of literature suggests that the conditions in which the company operates affect how NGFMs are used. Many studies focus on the impact of company-specific factors, while the role played by the institutional and cultural context remains scarcely investigated. This research analyses how institutional and cultural factors affect the propensity to disclose NGFMs, and both the materiality and the transparency of adjustments. The analysis is based on 1,731 quarterly press releases of 120 firms from the global Oil and Gas industry. The results show that the propensity to use NGFMs is reduced by a strong institutional system, while increased by the presence of a regulation on NGFMs\u2019 disclosure and the adoption of International Financial Reporting Standards (IFRS). A strong legal system also reduces the materiality of the adjustments. Surprisingly, the presence of a regulation on NGFMs negatively affects the transparencyof the adjustments. Cultural factors, such as uncertainty avoidance and long-term orientation, reduce the propensity to disclose NGFMs and positively increase transparency. However, compared to institutional values, cultural factors play a less relevant role