Succinct Indexable Dictionaries with Applications to Encoding kk-ary Trees, Prefix Sums and Multisets

We consider the {\it indexable dictionary} problem, which consists of storing a set $S \subseteq \{0,...,m-1\}$ for some integer $m$, while supporting the operations of \Rank(x), which returns the number of elements in $S$ that are less than $x$ if $x \in S$, and -1 otherwise; and \Select(i) which returns the $i$-th smallest element in $S$. We give a data structure that supports both operations in O(1) time on the RAM model and requires ${\cal B}(n,m) + o(n) + O(\lg \lg m)$ bits to store a set of size $n$, where {\cal B}(n,m) = \ceil{\lg {m \choose n}} is the minimum number of bits required to store any $n$-element subset from a universe of size $m$. Previous dictionaries taking this space only supported (yes/no) membership queries in O(1) time. In the cell probe model we can remove the $O(\lg \lg m)$ additive term in the space bound, answering a question raised by Fich and Miltersen, and Pagh. We present extensions and applications of our indexable dictionary data structure, including: An information-theoretically optimal representation of a $k$-ary cardinal tree that supports standard operations in constant time, A representation of a multiset of size $n$ from $\{0,...,m-1\}$ in ${\cal B}(n,m+n) + o(n)$ bits that supports (appropriate generalizations of) \Rank and \Select operations in constant time, and A representation of a sequence of $n$ non-negative integers summing up to $m$ in ${\cal B}(n,m+n) + o(n)$ bits that supports prefix sum queries in constant time.Comment: Final version of SODA 2002 paper; supersedes Leicester Tech report 2002/1

Risk of diabetes mellitus among users of immune checkpoint inhibitors: A population‐based cohort study

Background Immune checkpoint inhibitors (ICIs) are increasingly established cancer therapeutics, but they are associated with new-onset diabetes mellitus (DM). Such risks have not been adequately quantified, and between-class and -sex differences remain unexplored. Methods This was a prospective cohort study of cancer patients receiving any ICI in Hong Kong between 2013 and 2021. Patients with known DM were excluded. Due to few patients using other ICIs, only programmed cell death 1 inhibitors (PD-1i) and programmed death ligand 1 inhibitors (PD-L1i) were compared, alongside between-sex comparison. When comparing PD-1i against PD-L1i, patients with the use of other ICIs or both PD-1i and PD-L1 were further excluded. Inverse probability treatment weighting (IPTW) was used to minimize between-group covariate imbalances. Results Altogether, 3375 patients were analyzed (65.2% males, median age 62.2 [interquartile range 53.8–69.5] years old). Over a median follow-up of 1.0 [0.4–2.4] years, new-onset DM occurred in 457 patients (13.5%), with a 3-year risk of 14.5% [95% confidence interval 13.3%, 15.8%]. IPTW achieve acceptable covariate balance between sexes, and between PD-1i (N = 622) and PD-L1i (N = 2426) users. Males had significantly higher risk of new-onset DM (hazard ratio 1.35 [1.09, 1.67], p = 0.006), while PD-1i and PD-L1i users did not have significantly different risks (hazard ratio vs PD-L1i 0.81 [0.59, 1.11], p = 0.182). These were consistent in those with at least 1 year of follow-up, and on competing risk regression. Conclusion Users of ICI may have a substantial risk of new-onset DM, which may be higher in males but did not differ between PD-1i and PD-L1i

Intracellular cytokine staining and flow cytometry: Considerations for application in clinical trials of novel tuberculosis vaccines

Intracellular cytokine staining combined with flow cytometry is one of a number of assays designed to assess T-cell immune responses. It has the specific advantage of enabling the simultaneous assessment of multiple phenotypic, differentiation and functional parameters pertaining to responding T-cells, most notably, the expression of multiple effector cytokines. These attributes make the technique particularly suitable for the assessment of T-cell immune responses induced by novel tuberculosis vaccines in clinical trials. However, depending upon the particular nature of a given vaccine and trial setting, there are approaches that may be taken at different stages of the assay that are more suitable than other alternatives. In this paper, the Tuberculosis Vaccine Initiative (TBVI) TB Biomarker Working group reports on efforts to assess the conditions that will determine when particular assay approaches should be employed. We have found that choices relating to the use of fresh whole blood or peripheral blood mononuclear cells (PBMC) and frozen PBMC; use of serum-containing or serum-free medium; length of stimulation period and use of co-stimulatory antibodies can all affect the sensitivity of intracellular cytokine assays. In the case of sample material, frozen PBMC, despite some loss of sensitivity, may be more advantageous for batch analysis. We also recommend that for multi-site studies, common antibody panels, gating strategies and analysis approaches should be employed for better comparability

Controlled One-Pot Synthesis of Polystyrene-block-Polycaprolactone Copolymers by Simultaneous RAFT and ROP

A convenient one-pot method for the controlled synthesis of polystyrene- block -polycaprolactone (PS- b -PCL) copolymers by simultaneous reversible addition?fragmentation chain transfer (RAFT) and ring-opening polymerization (ROP) processes is reported. The strategy involves the use of 2-(benzylsulfanylthiocarbonylsulfanyl)ethanol (1) for the dual roles of chain transfer agent (CTA) in the RAFT polymerization of styrene and co-initiator in the ROP of ε -caprolactone. One-pot poly merizations using the electrochemically stable ROP catalyst diphenyl phosphate (DPP) yield well-defi ned PS- b -PCL in a relatively short reaction time (≈4 h; Mn = 9600−43 600 g mol−1 ; Mw/Mn = 1.21−1.57). Because the hydroxyl group is strategically located on the Z substituent of the CTA, segments of these diblock copolymers are connected through a trithiocarbonate group, thus offering an easy way for subsequent growth of a third segment between PS and PCL. In contrast, an oxidatively unstable Sn(Oct) 2 ROP catalyst reacts with (1) leading to multimodal distributions of polymer chains with variable composition.Fil: de Freitas, Augusto G. O.. Universidade Federal de Santa Maria; BrasilFil: Trindade, Suelen G.. Universidade Federal de Santa Maria; BrasilFil: Muraro, Paulo I. R.. Universidade Federal de Santa Maria; BrasilFil: Schmidt, Vanessa. Universidade Federal de Santa Maria; BrasilFil: Satti, Angel Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Bahía Blanca. Planta Piloto de Ingeniería Química (i); ArgentinaFil: Villar, Marcelo Armando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Bahía Blanca. Planta Piloto de Ingeniería Química (i); ArgentinaFil: Ciolino, Andrés Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Bahía Blanca. Planta Piloto de Ingeniería Química (i); ArgentinaFil: Giacomelli, Cristiano. Universidade Federal de Santa Maria; Brasi

Immunological correlates of mycobacterial growth inhibition describe a spectrum of tuberculosis infection

© 2018, The Author(s). A major contribution to the burden of Tuberculosis (TB) comes from latent Mycobacterium tuberculosis infections (LTBI) becoming clinically active. TB and LTBI probably exist as a spectrum and currently there are no correlates available to identify individuals with LTBI most at risk of developing active disease. We set out to identify immune parameters associated with ex vivo mycobacterial growth control among individuals with active TB disease or LTBI to define the spectrum of TB infection. We used a whole blood mycobacterial growth inhibition assay to generate a functional profile of growth control among individuals with TB, LTBI or uninfected controls. We subsequently used a multi-platform approach to identify an immune signature associated with this profile. We show, for the first time, that patients with active disease had the greatest control of mycobacterial growth, whilst there was a continuum of responses among latently infected patients, likely related to the degree of immune activation in response to bacillary load. Control correlated with multiple factors including inflammatory monocytes, activated and atypical memory B cells, IgG1 responses to TB-specific antigens and serum cytokines/chemokines. Our findings offer a method to stratify subclinical TB infections and the future potential to identify individuals most at risk of progressing to active disease and benefit from chemoprophylaxis.Wellcome Trust (grant number 103420/Z/13/Z to M.K.O.) and the British Lung Foundation (grant number BHPG13-2 to M.K.O.

Artemisinin derivatives versus quinine in treating severe malaria in children: a systematic review

<p>Abstract</p> <p>Background</p> <p>The efficacy of intravenous quinine, which is the mainstay for treating severe malaria in children, is decreasing in South East Asia and Africa. Artemisinin derivatives are a potential alternative to quinine. However, their efficacy compared to quinine in treating severe malaria in children is not clearly understood. The objective of this review was to assess the efficacy of parenteral artemisinin derivatives versus parenteral quinine in treating severe malaria in children.</p> <p>Methods</p> <p>All randomized controlled studies comparing parenteral artemisinin derivatives with parenteral quinine in treating severe malaria in children were included in the review. Data bases searched were: The Cochrane Central Register of Controlled Trials (The Cochrane Library Issue 4, 2007), MEDLINE (1966 to February 2008), EMBASE (1980 to February 2008), and LILACS (1982 to February 2008). Dichotomous variables were compared using risk ratios (RR) and the continuous data using weighted mean difference (WMD).</p> <p>Results</p> <p>Twelve trials were included (1,524 subjects). There was no difference in mortality between artemisinin derivatives and quinine (RR = 0.90, 95% CI 0.73 to 1.12). The artemisinin derivatives resolved coma faster than quinine (WMD = -4.61, 95% CI: -7.21 to -2.00, fixed effect model), but when trials with adequate concealment only were considered this differences disappeared. There was no statistically significant difference between the two groups in parasite clearance time, fever clearance time, incidence of neurological sequelae and 28^thday cure rate. One trial reported significantly more local reactions at the injection site with intramuscular quinine compared to artemether. None of the trials was adequately powered to demonstrate equivalence.</p> <p>Conclusion</p> <p>There was no evidence that treatment of children with severe malaria with parenteral artemisinin derivatives was associated with lower mortality or long-term morbidity compared to parenteral quinine. Future studies require adequately powered equivalence trial design to decide whether both drugs are equally effective.</p

Induction of Functional Specific Antibodies, IgG-Secreting Plasmablasts and Memory B Cells Following BCG Vaccination

Data Availability Statement: The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.Copyright © 2022 Bitencourt, Peralta-Álvarez, Wilkie, Jacobs, Wright, Salman Almujri, Li, Harris, Smith, Elias, White, Satti, Sharpe, O’Shea, McShane and Tanner. Tuberculosis (TB) is a major global health problem and the only currently-licensed vaccine, BCG, is inadequate. Many TB vaccine candidates are designed to be given as a boost to BCG; an understanding of the BCG-induced immune response is therefore critical, and the opportunity to relate this to circumstances where BCG does confer protection may direct the design of more efficacious vaccines. While the T cell response to BCG vaccination has been well-characterized, there is a paucity of literature on the humoral response. We demonstrate BCG vaccine-mediated induction of specific antibodies in different human populations and macaque species which represent important preclinical models for TB vaccine development. We observe a strong correlation between antibody titers in serum versus plasma with modestly higher titers in serum. We also report for the first time the rapid and transient induction of antibody-secreting plasmablasts following BCG vaccination, together with a robust and durable memory B cell response in humans. Finally, we demonstrate a functional role for BCG vaccine-induced specific antibodies in opsonizing mycobacteria and enhancing macrophage phagocytosis in vitro, which may contribute to the BCG vaccine-mediated control of mycobacterial growth observed. Taken together, our findings indicate that the humoral immune response in the context of BCG vaccination merits further attention to determine whether TB vaccine candidates could benefit from the induction of humoral as well as cellular immunity.This work was funded in part by a small grant awarded to RT from the Royal Society of Tropical Medicine and Hygiene (RSTMH); the European Research Infrastructures for Poverty Related Diseases (EURIPRED), an EC seventh framework program (grant number 312661); TBVAC2020 (grant number 643381); and the Wellcome Trust (HMcS is a Wellcome Trust Investigator, grant code WT 206331/Z/17/Z). Human Study 1 was funded by the Bill & Melinda Gates Foundation (grant number OPP1112389) and human Study 2 was funded by a grant awarded to MO’S from the Wellcome Trust (grant number 103420/Z/13/Z). For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. This work was also supported by the National Institute for Health Research (NIHR) Oxford Biomedical Research Center (BRC)

Effect of praziquantel treatment of Schistosoma mansoni during pregnancy on intensity of infection and antibody responses to schistosome antigens: results of a randomised, placebo-controlled trial

BACKGROUND: Praziquantel treatment of schistosomiasis during pregnancy was only recommended in 2002; hence the effects of treatment during pregnancy are not fully known. We have therefore evaluated the effects on infection intensity and the immunological effects of praziquantel treatment against Schistosoma mansoni during pregnancy, compared with treatment after delivery. METHODS: A nested cohort of 387 Schistosoma mansoni infected women was recruited within a larger trial of de-worming during pregnancy. Women were randomised to receive praziquantel or placebo during pregnancy. All women were treated after delivery. Infection intensity after treatment was assessed by a single Kato-Katz examination of stool samples with duplicate slides and categorised as undetected, light (1-99 eggs per gram (epg)), moderate (100-399 epg) or heavy (>or=400 epg). Antibodies against S. mansoni worm and egg antigens were measured by ELISA. Results were compared between women first treated during pregnancy and women first treated after delivery. RESULTS: At enrollment, 252 (65.1%) of the women had light infection (median (IQR) epg: 35 (11, 59)), 75 (19.3%) moderate (median (IQR) epg: 179(131, 227)) and 60 (15.5%) had heavy infection (median (IQR) epg: 749 (521, 1169)) with S. mansoni. At six weeks after praziquantel treatment during pregnancy S. mansoni infection was not detectable in 81.9% of the women and prevalence and intensity had decreased to 11.8% light, 4.7% moderate and 1.6% heavy a similar reduction when compared with those first treated after delivery (undetected (88.5%), light (10.6%), moderate (0.9%) and heavy (0%), p = 0.16). Parasite specific antibody levels were lower during pregnancy than after delivery. Praziquantel treatment during pregnancy boosted anti-worm IgG isotypes and to a lesser extent IgE, but these boosts were less pronounced than in women whose treatment was delayed until after delivery. Praziquantel had limited effects on antibodies against egg antigens. CONCLUSION: S mansoni antigen-specific antibody levels and praziquantel-induced boosts in antibody levels were broadly suppressed during pregnancy, but this was not associated with major reduction in the efficacy of praziquantel. Long-term implications of these findings in relation to resistance to re-infection remain to be explored

Modified Vaccinia Virus Ankara Preferentially Targets Antigen Presenting Cells In Vitro, Ex Vivo and In Vivo

Modified Vaccinia virus Ankara (MVA) is a promising vaccine vector with an excellent safety profile. However, despite extensive pre-clinical and clinical testing, surprisingly little is known about the cellular tropism of MVA, especially in relevant animal species. Here, we performed in vitro, ex vivo and in vivo experiments with recombinant MVA expressing green fluorescent protein (rMVA-GFP). In both human peripheral blood mononuclear cells and mouse lung explants, rMVA-GFP predominantly infected antigen presenting cells. Subsequent in vivo experiments performed in mice, ferrets and non-human primates indicated that preferential targeting of dendritic cells and alveolar macrophages was observed after respiratory administration, although subtle differences were observed between the respective animal species. Following intramuscular injection, rMVA-GFP was detected in interdigitating cells between myocytes, but also in myocytes themselves. These data are important in advancing our understanding of the basis for the immunogenicity of MVA-based vaccines and aid rational vaccine design and delivery strategies