Solving Operating Room Scheduling Problems with Surgical Teams via Answer Set Programming

The optimization of daily operating room surgery schedule can be problematic because of many constraints, like to determine the starting time of different surgeries and allocating the required resources, including the availability of surgical teams for complete surgical procedures. Recently, Answer Set Programming (ASP) has been successfully employed for addressing and solving real-life scheduling and planning problems in the healthcare domain. In this paper we present an enhanced solution using ASP for scheduling operating rooms taking explicitly into consideration availability of surgical teams, that include a surgeon and an anesthetist in different specialties for the entire duration of the surgery. We tested our solution on different benchmarks with realistic parameters for schedule’s length up to the target 5-days planning. The results of our experiments show that ASP is a suitable methodology for solving also such enhanced problem

Operating Room (Re)Scheduling with Bed Management via ASP

The Operating Room Scheduling (ORS) problem is the task of assigning patients to operating rooms (ORs), taking into account different specialties, lengths, and priority scores of each planned surgery, OR session durations, and the availability of beds for the entire length of stay (LOS) both in the Intensive Care Unit (ICU) and in the wards. A proper solution to the ORS problem is of primary importance for the healthcare service quality and the satisfaction of patients in hospital environments. In this paper we first present a solution to the problem based on Answer Set Programming (ASP). The solution is tested on benchmarks with realistic sizes and parameters, on three scenarios for the target length on 5-day scheduling, common in small-medium-sized hospitals, and results show that ASP is a suitable solving methodology for the ORS problem in such setting. Then, we also performed a scalability analysis on the schedule length up to 15 days, which still shows the suitability of our solution also on longer plan horizons. Moreover, we also present an ASP solution for the rescheduling problem, that is, when the offline schedule cannot be completed for some reason. Finally, we introduce a web framework for managing ORS problems via ASP that allows a user to insert the main parameters of the problem, solve a specific instance, and show results graphically in real time

An ASP-based Solution to the Chemotherapy Treatment Scheduling problem

The problem of scheduling chemotherapy treatments in oncology clinics is a complex problem, given that the solution has to satisfy (as much as possible) several requirements such as the cyclic nature of chemotherapy treatment plans, maintaining a constant number of patients, and the availability of resources, for example, treatment time, nurses, and drugs. At the same time, realizing a satisfying schedule is of upmost importance for obtaining the best health outcomes. In this paper we first consider a specific instance of the problem which is employed in the San Martino Hospital in Genova, Italy, and present a solution to the problem based on Answer Set Programming (ASP). Then, we enrich the problem and the related ASP encoding considering further features often employed in other hospitals, desirable also in S. Martino, and/or considered in related papers. Results of an experimental analysis, conducted on the real data provided by the San Martino Hospital, show that ASP is an effective solving methodology also for this important scheduling problem

A Two-Phase ASP Encoding for Solving Rehabilitation Scheduling

The rehabilitation scheduling process consists of planning rehabilitation physiotherapy sessions for patients, by assigning proper operators to them in a certain time slot of a given day, taking into account several requirements and optimizations, e.g., patient’s preferences and operator’s work balancing. Being able to efficiently solve such problem is of upmost importance, in particular after the COVID-19 pandemic that significantly increased rehabilitation’s needs. In this paper, we present a solution to rehabilitation scheduling based on Answer Set Programming (ASP), which proved to be an effective tool for solving practical scheduling problems. Results of experiments performed on both synthetic and real benchmarks, the latter provided by ICS Maugeri, show the effectiveness of our solution

Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situ biofilm model

Dental caries is caused by acids released from bacterial biofilms. However, the in vivo formation of initial biofilms in relation to caries remains largely unexplored. The aim of this study was to compare the oral microbiome during the initial phase of bacterial colonization for individuals with (CC) and without (NC) cavitated dentin caries lesions. Bovine enamel slabs on acrylic splints were worn by the volunteers (CC: 14, NC: 13) for in situ biofilm formation (2 h, 4 h, 8 h, 1 ml saliva as reference). Sequencing of the V1/V2 regions of the 16S rRNA gene was performed (MiSeq). The relative abundances of individual operational taxonomic units (OTUs) were compared between samples from the CC group and the NC group. Random forests models were furthermore trained to separate the groups. While the overall heterogeneity did not differ substantially between CC and NC individuals, several individual OTUs were found to have significantly different relative abundances. For the 8 h samples, most of the significant OTUs showed higher relative abundances in the CC group, while the majority of significant OTUs in the saliva samples were more abundant in the NC group. Furthermore, using OTU signatures enabled a separation between both groups, with area-under-the-curve (AUC) values of ~0.8. In summary, the results suggest that initial oral biofilms provide the potential to differentiate between CC and NC individuals

Search for muon-neutrino emission from GeV and TeV gamma-ray flaring blazars using five years of data of the ANTARES telescope

The ANTARES telescope is well-suited for detecting astrophysical transient neutrino sources as it can observe a full hemisphere of the sky at all times with a high duty cycle. The background due to atmospheric particles can be drastically reduced, and the point-source sensitivity improved, by selecting a narrow time window around possible neutrino production periods. Blazars, being radio-loud active galactic nuclei with their jets pointing almost directly towards the observer, are particularly attractive potential neutrino point sources, since they are among the most likely sources of the very high-energy cosmic rays. Neutrinos and gamma rays may be produced in hadronic interactions with the surrounding medium. Moreover, blazars generally show high time variability in their light curves at different wavelengths and on various time scales. This paper presents a time-dependent analysis applied to a selection of flaring gamma-ray blazars observed by the FERMI/LAT experiment and by TeV Cherenkov telescopes using five years of ANTARES data taken from 2008 to 2012. The results are compatible with fluctuations of the background. Upper limits on the neutrino fluence have been produced and compared to the measured gamma-ray spectral energy distribution.Comment: 27 pages, 16 figure

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum.

Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org

Artificial intelligence for detection of microsatellite instability in colorectal cancer-a multicentric analysis of a pre-screening tool for clinical application.

BACKGROUND Microsatellite instability (MSI)/mismatch repair deficiency (dMMR) is a key genetic feature which should be tested in every patient with colorectal cancer (CRC) according to medical guidelines. Artificial intelligence (AI) methods can detect MSI/dMMR directly in routine pathology slides, but the test performance has not been systematically investigated with predefined test thresholds. METHOD We trained and validated AI-based MSI/dMMR detectors and evaluated predefined performance metrics using nine patient cohorts of 8343 patients across different countries and ethnicities. RESULTS Classifiers achieved clinical-grade performance, yielding an area under the receiver operating curve (AUROC) of up to 0.96 without using any manual annotations. Subsequently, we show that the AI system can be applied as a rule-out test: by using cohort-specific thresholds, on average 52.73% of tumors in each surgical cohort [total number of MSI/dMMR = 1020, microsatellite stable (MSS)/ proficient mismatch repair (pMMR) = 7323 patients] could be identified as MSS/pMMR with a fixed sensitivity at 95%. In an additional cohort of N = 1530 (MSI/dMMR = 211, MSS/pMMR = 1319) endoscopy biopsy samples, the system achieved an AUROC of 0.89, and the cohort-specific threshold ruled out 44.12% of tumors with a fixed sensitivity at 95%. As a more robust alternative to cohort-specific thresholds, we showed that with a fixed threshold of 0.25 for all the cohorts, we can rule-out 25.51% in surgical specimens and 6.10% in biopsies. INTERPRETATION When applied in a clinical setting, this means that the AI system can rule out MSI/dMMR in a quarter (with global thresholds) or half of all CRC patients (with local fine-tuning), thereby reducing cost and turnaround time for molecular profiling

Identifying Prototypical Components in Behaviour Using Clustering Algorithms

Quantitative analysis of animal behaviour is a requirement to understand the task solving strategies of animals and the underlying control mechanisms. The identification of repeatedly occurring behavioural components is thereby a key element of a structured quantitative description. However, the complexity of most behaviours makes the identification of such behavioural components a challenging problem. We propose an automatic and objective approach for determining and evaluating prototypical behavioural components. Behavioural prototypes are identified using clustering algorithms and finally evaluated with respect to their ability to represent the whole behavioural data set. The prototypes allow for a meaningful segmentation of behavioural sequences. We applied our clustering approach to identify prototypical movements of the head of blowflies during cruising flight. The results confirm the previously established saccadic gaze strategy by the set of prototypes being divided into either predominantly translational or rotational movements, respectively. The prototypes reveal additional details about the saccadic and intersaccadic flight sections that could not be unravelled so far. Successful application of the proposed approach to behavioural data shows its ability to automatically identify prototypical behavioural components within a large and noisy database and to evaluate these with respect to their quality and stability. Hence, this approach might be applied to a broad range of behavioural and neural data obtained from different animals and in different contexts

Analysis Tools for Next-Generation Hadron Spectroscopy Experiments

The series of workshops on New Partial-Wave Analysis Tools for Next-Generation Hadron Spectroscopy Experiments was initiated with the ATHOS 2012 meeting, which took place in Camogli, Italy, June 20-22, 2012. It was followed by ATHOS 2013 in Kloster Seeon near Munich, Germany, May 21-24, 2013. The third, ATHOS3, meeting is planned for April 13-17, 2015 at The George Washington University Virginia Science and Technology Campus, USA. The workshops focus on the development of amplitude analysis tools for meson and baryon spectroscopy, and complement other programs in hadron spectroscopy organized in the recent past including the INT-JLab Workshop on Hadron Spectroscopy in Seattle in 2009, the International Workshop on Amplitude Analysis in Hadron Spectroscopy at the ECT*-Trento in 2011, the School on Amplitude Analysis in Modern Physics in Bad Honnef in 2011, the Jefferson Lab Advanced Study Institute Summer School in 2012, and the School on Concepts of Modern Amplitude Analysis Techniques in Flecken-Zechlin near Berlin in September 2013. The aim of this document is to summarize the discussions that took place at the ATHOS 2012 and ATHOS 2013 meetings. We do not attempt a comprehensive review of the field of amplitude analysis, but offer a collection of thoughts that we hope may lay the ground for such a document.Comment: 28 pages, 11 figures, proceedings of the ATHOS 2012 and ATHOS 2013 meeting