A Profunctorial Scott Semantics

In this paper, we study the bicategory of profunctors with the free finite coproduct pseudo-comonad and show that it constitutes a model of linear logic that generalizes the Scott model. We formalize the connection between the two models as a change of base for enriched categories which induces a pseudo-functor that preserves all the linear logic structure. We prove that morphisms in the co-Kleisli bicategory correspond to the concept of strongly finitary functors (sifted colimits preserving functors) between presheaf categories. We further show that this model provides solutions of recursive type equations which provides 2-dimensional models of the pure lambda calculus and we also exhibit a fixed point operator on terms

A Bicategorical Model for Finite Nondeterminism

Finiteness spaces were introduced by Ehrhard as a refinement of the relational model of linear logic. A finiteness space is a set equipped with a class of finitary subsets which can be thought of being subsets that behave like finite sets. A morphism between finiteness spaces is a relation that preserves the finitary structure. This model provided a semantics for finite non-determism and it gave a semantical motivation for differential linear logic and the syntactic notion of Taylor expansion. In this paper, we present a bicategorical extension of this construction where the relational model is replaced with the model of generalized species of structures introduced by Fiore et al. and the finiteness property now relies on finite presentability

Stabilized profunctors and stable species of structures

We introduce a bicategorical model of linear logic which is a novel variation of the bicategory of groupoids, profunctors, and natural transformations. Our model is obtained by endowing groupoids with additional structure, called a kit, to stabilize the profunctors by controlling the freeness of the groupoid action on profunctor elements. The theory of generalized species of structures, based on profunctors, is refined to a new theory of \emph{stable species} of structures between groupoids with Boolean kits. Generalized species are in correspondence with analytic functors between presheaf categories; in our refined model, stable species are shown to be in correspondence with restrictions of analytic functors, which we characterize as being stable, to full subcategories of stabilized presheaves. Our motivating example is the class of finitary polynomial functors between categories of indexed sets, also known as normal functors, that arises from kits enforcing free actions. We show that the bicategory of groupoids with Boolean kits, stable species, and natural transformations is cartesian closed. This makes essential use of the logical structure of Boolean kits and explains the well-known failure of cartesian closure for the bicategory of finitary polynomial functors between categories of set-indexed families and cartesian natural transformations. The paper additionally develops the model of classical linear logic underlying the cartesian closed structure and clarifies the connection to stable domain theory.Comment: FSCD 2022 special issue of Logical Methods in Computer Science, minor changes (incorporated reviewers comments

Stabilized profunctors and stable species of structures

We introduce a bicategorical model of linear logic which is a novel variation of the bicategory of groupoids, profunctors, and natural transformations. Our model is obtained by endowing groupoids with additional structure, called a kit, to stabilize the profunctors by controlling the freeness of the groupoid action on profunctor elements. The theory of generalized species of structures, based on profunctors, is refined to a new theory of \emph{stable species} of structures between groupoids with Boolean kits. Generalized species are in correspondence with analytic functors between presheaf categories; in our refined model, stable species are shown to be in correspondence with restrictions of analytic functors, which we characterize as being stable, to full subcategories of stabilized presheaves. Our motivating example is the class of finitary polynomial functors between categories of indexed sets, also known as normal functors, that arises from kits enforcing free actions. We show that the bicategory of groupoids with Boolean kits, stable species, and natural transformations is cartesian closed. This makes essential use of the logical structure of Boolean kits and explains the well-known failure of cartesian closure for the bicategory of finitary polynomial functors between categories of set-indexed families and cartesian natural transformations. The paper additionally develops the model of classical linear logic underlying the cartesian closed structure and clarifies the connection to stable domain theory

Global, regional, and national incidence of six major immune-mediated inflammatory diseases: findings from the global burden of disease study 2019

BACKGROUND: The causes for immune-mediated inflammatory diseases (IMIDs) are diverse and the incidence trends of IMIDs from specific causes are rarely studied. The study aims to investigate the pattern and trend of IMIDs from 1990 to 2019. METHODS: We collected detailed information on six major causes of IMIDs, including asthma, inflammatory bowel disease, multiple sclerosis, rheumatoid arthritis, psoriasis, and atopic dermatitis, between 1990 and 2019, derived from the Global Burden of Disease study in 2019. The average annual percent change (AAPC) in number of incidents and age standardized incidence rate (ASR) on IMIDs, by sex, age, region, and causes, were calculated to quantify the temporal trends. FINDINGS: In 2019, rheumatoid arthritis, atopic dermatitis, asthma, multiple sclerosis, psoriasis, inflammatory bowel disease accounted 1.59%, 36.17%, 54.71%, 0.09%, 6.84%, 0.60% of overall new IMIDs cases, respectively. The ASR of IMIDs showed substantial regional and global variation with the highest in High SDI region, High-income North America, and United States of America. Throughout human lifespan, the age distribution of incident cases from six IMIDs was quite different. Globally, incident cases of IMIDs increased with an AAPC of 0.68 and the ASR decreased with an AAPC of −0.34 from 1990 to 2019. The incident cases increased across six IMIDs, the ASR of rheumatoid arthritis increased (0.21, 95% CI 0.18, 0.25), while the ASR of asthma (AAPC = −0.41), inflammatory bowel disease (AAPC = −0.72), multiple sclerosis (AAPC = −0.26), psoriasis (AAPC = −0.77), and atopic dermatitis (AAPC = −0.15) decreased. The ASR of overall and six individual IMID increased with SDI at regional and global level. Countries with higher ASR in 1990 experienced a more rapid decrease in ASR. INTERPRETATION: The incidence patterns of IMIDs varied considerably across the world. Innovative prevention and integrative management strategy are urgently needed to mitigate the increasing ASR of rheumatoid arthritis and upsurging new cases of other five IMIDs, respectively. FUNDING: The Global Burden of Disease Study is funded by the Bill and Melinda Gates Foundation. The project funded by Scientific Research Fund of Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital (2022QN38)

X-linked agammaglobulinemia (XLA) : Phenotype, diagnosis, and therapeutic challenges around the world

Background: X-linked agammaglobulinemia is an inherited immunodeficiency recognized since 1952. In spite of seven decades of experience, there is still a limited understanding of regional differences in presentation and complications. This study was designed by the Primary Immunodeficiencies Committee of the World Allergy Organization to better understand regional needs, challenges and unique patient features. Methods: A survey instrument was designed by the Primary Immunodeficiencies Committee of the World Allergy Organization to collect both structured and semi-structured data on X-linked agammaglobulinemia. The survey was sent to 54 centers around the world chosen on the basis of World Allergy Organization participation and/or registration in the European Society for Immunodeficiencies. There were 40 centers that responded, comprising 32 countries. Results: This study reports on 783 patients from 40 centers around the world. Problems with diagnosis are highlighted by the reported delays in diagnosis>24 months in 34% of patients and the lack of genetic studies in 39% of centers Two infections exhibited regional variation. Vaccine-associated paralytic poliomyelitis was seen only in countries with live polio vaccination and two centers reported mycobacteria. High rates of morbidity were reported. Acute and chronic lung diseases accounted for 41% of the deaths. Unusual complications such as inflammatory bowel disease and large granular lymphocyte disease, among others were specifically enumerated, and while individually uncommon, they were collectively seen in 20.3% of patients. These data suggest that a broad range of both inflammatory, infectious, and autoimmune conditions can occur in patients. The breadth of complications and lack of data on management subsequently appeared as a significant challenge reported by centers. Survival above 20 years of age was lowest in Africa (22%) and reached above 70% in Australia, Europe and the Americas. Centers were asked to report their challenges and responses (n = 116) emphasized the difficulties in access to immunoglobulin products (16%) and reflected the ongoing need for education of both patients and referring physicians. Conclusions: This is the largest study of patients with X-linked agammaglobulinemia and emphasizes the continued morbidity and mortality of XLA despite progress in diagnosis and treatment. It presents a world view of the successes and challenges for patients and physicians alike. A pivotal finding is the need for education of physicians regarding typical symptoms suggesting a possible diagnosis of X-linked agammaglobulinemia and sharing of best practices for the less common complications.Peer reviewe

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P < 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Constructions d'orthogonalité bicatégoriques pour la logique linéaire

Cette thèse porte sur la sémantique bicatégorique de la logique linéaire. Elle s'incrit dans le cadre de catégorification des modèles de calculs où l'on remplace des sémantiques où les types sont interprétés par des ensembles ou des préordres par des structures catégoriques plus riches permettant d'obtenir des invariants mathématiques plus fins. Nous nous intéressons spécifiquement à la catégorification du modèle relationel de la logique linéaire par le modèle des espèces généralisées introduit par Fiore, Gambino, Hyland et Winskel ansi qu'à ses raffinements par des constructions d'orthogonalité. Nous présentons dans un premier temps une généralisation bicatégorique du modèle des espaces de finitude introduit par Ehrhard où nous introduisons une orthogonalité sur la bicatégorie des espèces nous permettant d'obtenir une bicatégorie où les interactions entre programmes et environnements sont finies. Toute la structure de logique linéaire du modèle des espèces peut alors être transposée dans cette nouvelle bicatégorie. Nous considérons ensuite la catégorification de la notion de stabilité des fonctions stables à la Berry vers les foncteurs stables. Nous combinons les espèces de structure avec la stabilité grâce à une orthogonalité sur les sous-groupes d'endomorphismes pour chaque objet d'un groupoïde. Cette orthogonalité peut aussi être traduite en une orthogonalité sur la catégorie de préfaiscaux d'un groupoïde nous permettant de restreindre les foncteurs analytiques associés aux espèces à des foncteurs stables et nous montrons qu'ils forment une bicatégorie cartésienne fermée. Nous étudions dernièrement la catégorification du modèle de Scott de la logique linéaire et son lien avec le modèle des espèces. Nous commençons par montrer que la bicatégorie des profoncteurs équipée de la pseudo-comonade des coproduits finis est un modèle de la logique linéaire catégorifiant le modèle de Scott. Nous introduisons ensuite une orthogonalité entre la bicatégorie de Scott obtenue et la bicatégorie des espèces et obtenons une nouvelle bicatégorie constituant une première étape afin de relier la substitution linéaire et non-linéaire dans ce contexte.This thesis is concerned with the bicategorical semantics of linear logic. We follow the line of research of categorifying models of linear logic by replacing semantics where types are sets or preorders with richer categorical structures providing finer mathematical invariants. In this thesis, we are interested in the categorification of the relational model of linear logic with the generalized species model introduced by Fiore, Gambino, Hyland and Winskel; and its refinements using orthogonality constructions. We first present a bicategorical generalization of the model of finiteness spaces introduced by Ehrhard where we introduce an orthogonality construction on the bicategory of profunctors based on finite presentability to obtain a new bicategory where all interactions between programs and environments are enforced to be finite. We show that all the linear logic structure in the bicategory of profunctors can be refined to this new bicategory. We then consider the categorication of the computational notion of stability from stable functions to stable functors. We bring together generalized species of structures and stability by refining the species model with an orthogonality on subgroups of endomorphisms for each object in a groupoid. We show that this orthogonality can also be translated to an orthogonality on the category of presheaves associated with a groupoid that allows us to restrict the analytic functors to stable functors and prove that they form a cartesian closed bicategory. We lastly study the categorification of the qualitative Scott model of linear logic and its connection with the quantitative species model of Fiore et al. We start by showing that the bicategory of profunctors with the finite coproduct pseudo-comonad is a model of linear logic that categorifies the Scott model. We then define an orthogonality between the Scott bicategory and the species bicategory that allows us to construct a new bicategory giving us a first step towards connecting linear and non-linear substitution in this setting