Certified Quantum Computation in Isabelle/HOL

Abstract: In this article we present an ongoing effort to formalise quantum algorithms and results in quantum information theory using the proof assistant Isabelle/HOL. Formal methods being critical for the safety and security of algorithms and protocols, we foresee their widespread use for quantum computing in the future. We have developed a large library for quantum computing in Isabelle based on a matrix representation for quantum circuits, successfully formalising the no-cloning theorem, quantum teleportation, Deutsch’s algorithm, the Deutsch–Jozsa algorithm and the quantum Prisoner’s Dilemma. We discuss the design choices made and report on an outcome of our work in the field of quantum game theory

Whole-genome sequencing and the clinician: a tale of two cities

Clinicians are faced with unprecedented opportunities to identify the genetic aetiologies of hitherto molecularly uncharacterised conditions via the use of high-throughput sequencing. Access to genomic technology and resultant data is no longer limited to clinicians, geneticists and bioinformaticians, however; ongoing commercialisation gives patients themselves ever greater access to sequencing services. We report an increasingly common medical scenario by describing two neuromuscular patients-a mother and adult son-whose consumer access to whole-genome sequencing affected their diagnostic journey

Psychometric Evaluation and Design of Patient-Centered Communication Measures for Cancer Care Settings

Objective To evaluate the psychometric properties of questions that assess patient perceptions of patient-provider communication and design measures of patient-centered communication (PCC). Methods Participants (adults with colon or rectal cancer living in North Carolina) completed a survey at 2 to 3 months post-diagnosis. The survey included 87 questions in six PCC Functions: Exchanging Information, Fostering Health Relationships, Making Decisions, Responding to Emotions, Enabling Patient Self-Management, and Managing Uncertainty. For each Function we conducted factor analyses, item response theory modeling, and tests for differential item functioning, and assessed reliability and construct validity. Results Participants included 501 respondents; 46% had a high school education or less. Reliability within each Function ranged from 0.90 to 0.96. The PCC-Ca-36 (36-question survey; reliability=0.94) and PCC-Ca-6 (6-question survey; reliability=0.92) measures differentiated between individuals with poor and good health (i.e., known-groups validity) and were highly correlated with the HINTS communication scale (i.e., convergent validity). Conclusion This study provides theory-grounded PCC measures found to be reliable and valid in colorectal cancer patients in North Carolina. Future work should evaluate measure validity over time and in other cancer populations. Practice implications The PCC-Ca-36 and PCC-Ca-6 measures may be used for surveillance, intervention research, and quality improvement initiatives

Annotation and Information Extraction of Consumer-Friendly Health Articles for Enhancing Laboratory Test Reporting

Viewing laboratory test results is patients\u27 most frequent activity when accessing patient portals, but lab results can be very confusing for patients. Previous research has explored various ways to present lab results, but few have attempted to provide tailored information support based on individual patient\u27s medical context. In this study, we collected and annotated interpretations of textual lab result in 251 health articles about laboratory tests from AHealthyMe.com. Then we evaluated transformer-based language models including BioBERT, ClinicalBERT, RoBERTa, and PubMedBERT for recognizing key terms and their types. Using BioPortal\u27s term search API, we mapped the annotated terms to concepts in major controlled terminologies. Results showed that PubMedBERT achieved the best F1 on both strict and lenient matching criteria. SNOMED CT had the best coverage of the terms, followed by LOINC and ICD-10-CM. This work lays the foundation for enhancing the presentation of lab results in patient portals by providing patients with contextualized interpretations of their lab results and individualized question prompts that they can, in turn, refer to during physician consults

Adenosine-5′-phosphosulfate - a multifaceted modulator of bifunctional 3′-phospho-adenosine-5′-phosphosulfate synthases and related enzymes

All sulfation reactions rely on active sulfate in the form of 3′-phosphoadenosine-5′-phosphosulfate (PAPS). In fungi, bacteria, and plants, the enzymes responsible for PAPS synthesis, ATP sulfurylase and adenosine-5′-phosphosulfate (APS) kinase, reside on separate polypeptide chains. In metazoans, however, bifunctional PAPS synthases catalyze the consecutive steps of sulfate activation by converting sulfate to PAPS via the intermediate APS. This intricate molecule and the related nucleotides PAPS and 3′-phospho-adenosine-5′-phosphate modulate the function of various enzymes from sulfation pathways, and these effects are summarized in this review. On the ATP sulfurylase domain that initially produces APS from sulfate and ATP, APS acts as a potent product inhibitor, being competitive with both ATP and sulfate. For the APS kinase domain that phosphorylates APS to PAPS, APS is an uncompetitive substrate inhibitor that can bind both at the ATP/ADP binding site and the PAPS/APS-binding site. For human PAPS synthase 1, the steady-state concentration of APS has been modelled to be 1.6 lM, but this may increase up to 60 lM under conditions of sulfate excess. It is noteworthy that the APS concentration for maximal APS kinase activity is 15 lM. Finally, we recognized APS as a highly specific stabilizer of bifunctional PAPS synthases. APS most likely stabilizes the APS kinase part of these proteins by forming a dead-end enzyme–ADP–APS complex at APS concentrations between 0.5 and 5 lM; at higher concentrations, APS may bind to the catalytic centers of ATP sulfurylase. Based on the assumption that cellular concentrations of APS fluctuate within this range, APS can therefore be regarded as a key modulator of PAPS synthase functions

Trajectories of disease-modifying therapies and associated sickness absence and disability pension among 1923 people with multiple sclerosis in Sweden

BACKGROUND: There is limited information on the trajectories of disease-modifying therapy (DMT) use and their association with sickness absence and/or disability pension (SADP) among people with multiple sclerosis (PwMS). The objective of the study was to identify trajectories of DMT use over 10 years among PwMS, identify sociodemographic and clinical factors associated with the trajectories, and to assess the association between identified trajectories and SADP days. METHODS: A longitudinal register-based study was conducted, on a prospective data set linked across six nationwide registers, assessing treatment courses of PwMS with DMTs for the 10 years following multiple sclerosis (MS) onset. The study included 1923 PwMS with MS onset in 2007-2010, when aged 19-56 years. In each 6-month-period, their treatment was categorized as before treatment, high-efficacy, non-high-efficacy, or no DMT. Sequence analysis was performed to identify sequences of the treatment categories and cluster them into different DMT trajectories. Cluster belonging, in relation to demographic and clinical characteristics, was assessed through log-multinomial regression analysis. The association of trajectories/cluster-belonging with SADP net days was assessed using generalized estimating equation (GEE) models. RESULTS: Cluster analyses identified 4 trajectories of DMT use: long-term non-high-efficacy DMTs (38.6%), escalation to high-efficacy DMTs (31.2%), delayed start and escalation to high-efficacy DMTs (15.4%), and discontinued/ no DMT (14.2%). Age, MS type, expanded disability status scale (EDSS) score and the number of DMT switches were associated with cluster belonging. The youngest age group (18-25) were more likely to be in the escalation to high-efficacy cluster. People with primary progressive MS were more likely to be in the delayed start or discontinued/ no DMT cluster. Higher EDSS scores were associated to being in the other three clusters than in the long-term non-high-efficacy DMTs cluster. Higher number of DMT switches were associated with being in the escalation to high-efficacy DMTs cluster but less likely to be in the delayed start or discontinued/ no DMT clusters. Descriptive analyses showed a trend of fewer mean SADP days among PwMS using non-high-efficacy DMT than the other clusters about 9 years after onset. PwMS in the escalation to high-efficacy and discontinued/no DMT clusters had more SADP days. PwMS in the delayed start and escalation to high-efficacy DMTs cluster, started with fewer SADP days which increased over time. SADP days adjusted through GEE models showed trends comparable with the descriptive analysis. CONCLUSION: This study described the long-term real-world trajectories of DMT use among PwMS in Sweden using sequence analysis and showed the association of the trajectories with SADP days as well as sociodemographic and clinical characteristics

Composite Fermions and the Fermion-Chern-Simons Theory

The concept of composite fermions, and the related Fermion-Chern-Simons theory, have been powerful tools for understanding quantum Hall systems with a partially full lowest Landau level. We shall review some of the successes of the Fermion-Chern-Simons theory, as well as some limitations and outstanding issues.Comment: 13 pages, including 2 figures. Invited talk at International Symposium, Quantum Hall Effect: Past, Present and Future, Stuttgart, July 2003. Proceedings to appear in Physica

Temperature-dependent phenology of the parasitoid Fopius arisanus on the host Bactrocera dorsalis

Fopius arisanus (Sonan), an egg-pupal parasitoid of numerous fruit fly species, was recently introduced into Africa for the control of the Oriental fruit fly, Bactrocera dorsalis (Hendel). In this study, life-table data of F. arisanus were generated under laboratory conditions at six constant temperatures (15, 20, 25, 30, 28 and 35 °C; 75% RH, L12:D12 photoperiod) and under variable conditions in a screenhouse on B. dorsalis. Several non-linear functions were fitted to model species development, mortality, longevity and oviposition using the Insect Life Cycle Modeling (ILCYM) software. The established phenology models were stochastically simulated at variable temperatures to estimate the life table parameters. Fopius arisanus completed development from egg to adult at all the temperatures tested except at 35 °C. Mean developmental time from egg to adult was inversely proportional to the temperature. The minimum temperature threshold (Tmin) from egg to adult was 8.15 °C, while the maximum temperature threshold (Tmax) was estimated at 34.2 °C. The optimal temperature for immature stages survival was predicted for 20-30 °C. The optimum fecundity estimated was 251 eggs/female at 22 °C. Following the stochastic simulations under natural conditions of the selected agro-ecological zones, it appears that the Humid Forest with Bimodal Rainfall provides a suitable thermal condition for potential population growth of F. arisanus. The present study shows the importance of temperature on the demographic parameters of F. arisanus. Implications of present findings on the biological control of B. dorsalis under climate change scenarios is discussed