Ensuring progress on sustainable access to effective antibiotics at the 2024 UN General Assembly: a target-based approach.

Rising antimicrobial resistance (AMR) is a global health crisis for countries of all economic levels, alongside the broader challenge of access to antibiotics. As a result, development goals for child survival, healthy ageing, poverty reduction, and food security are at risk. Preserving antimicrobial effectiveness, a global public good, requires political will, targets, accountability frameworks, and funding. The upcoming second high-level meeting on AMR at the UN General Assembly (UNGA) in September, 2024, is evidence of political interest in addressing the problem of AMR, but action on targets, accountability, and funding, absent from the 2016 UNGA resolution, is needed. We propose ambitious yet achievable global targets for 2030 (relative to a prepandemic 2019 baseline): a 10% reduction in mortality from AMR; a 20% reduction in inappropriate human antibiotic use; and a 30% reduction in inappropriate animal antibiotic use. Given national variation in current levels of antibiotic use, these goals (termed the 10-20-30 by 2030) should be met within a framework of universal access to effective antibiotics. The WHO Access, Watch, Reserve (AWARE) system can be used to define, monitor, and evaluate appropriate levels of antibiotic use and access. Some countries should increase access to narrow-spectrum, safe, and affordable (Access) antibiotics, whereas others should discourage the inappropriate use of broader-spectrum (Watch) and last-resort (Reserve) antibiotics; AWARE targets should use a risk-based, burden-adjusted approach. Improved infection prevention and control, access to clean water and sanitation, and vaccination coverage can offset the selection effects of increased antibiotic use in low-income settings. To ensure accountability and global scientific guidance and consensus, we call for the establishment of the Independent Panel on Antimicrobial Access and Resistance and the support of leaders from low-income and middle-income countries.

CIndex: compressed indexes for fast retrieval of FASTQ files.

MOTIVATION: Ultrahigh-throughput next-generation sequencing instruments continue to generate vast amounts of genomic data. These data are generally stored in FASTQ format. Two important simultaneous goals are space-efficient compressed storage of the genomic data and fast query performance. Toward that end, we introduce compressed indexing to store and retrieve FASTQ files. RESULTS: We propose a compressed index for FASTQ files called CIndex. CIndex uses the Burrows-Wheeler transform and the wavelet tree, combined with hybrid encoding, succinct data structures and tables REF and Rγ, to achieve minimal space usage and fast retrieval on the compressed FASTQ files. Experiments conducted over real publicly available datasets from various sequencing instruments demonstrate that our proposed index substantially outperforms existing state-of-the-art solutions. For count, locate and extract queries on reads, our method uses 2.7-41.66% points less space and provides a speedup of 70-167.16 times, 1.44-35.57 times and 1.3-55.4 times. For extracting records in FASTQ files, our method uses 2.86-14.88% points less space and provides a speedup of 3.13-20.1 times. CIndex has an additional advantage in that it can be readily adapted to work as a general-purpose text index; experiments show that it performs very well in practice. AVAILABILITY AND IMPLEMENTATION: The software is available on Github: https://github.com/Hongweihuo-Lab/CIndex. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Predictors of Recurrence, and Progression-Free and Overall Survival following Open versus Robotic Radical Cystectomy: Analysis from the RAZOR Trial with a 3-Year Followup.

PURPOSE: The RAZOR (Randomized Open versus Robotic Cystectomy) trial revealed noninferior 2-year progression-free survival for robotic radical cystectomy. This update was performed with extended followup for 3 years to determine potential differences between the approaches. We also report 3-year overall survival and sought to identify factors predicting recurrence, and progression-free and overall survival. MATERIALS AND METHODS: We analyzed the per protocol population of 302 patients from the RAZOR study. Cumulative recurrence was estimated using nonbladder cancer death as the competing risk event and the Gray test was applied to assess significance in differences. Progression-free survival and overall survival were estimated by the Kaplan-Meier method and compared with the log rank test. Predictors of outcomes were determined by Cox proportional hazard analysis. RESULTS: Estimated progression-free survival at 36 months was 68.4% (95% CI 60.1-75.3) and 65.4% (95% CI 56.8-72.7) in the robotic and open groups, respectively (p=0.600). At 36 months overall survival was 73.9% (95% CI 65.5-80.5) and 68.5% (95% CI 59.8-75.7) in the robotic and open groups, respectively (p=0.334). There was no significant difference in the cumulative incidence rates of recurrence (p=0.802). Patient age greater than 70 years, poor performance status and major complications were significant predictors of 36-month progression-free survival. Stage and positive margins were significant predictors of recurrence, and progression-free and overall survival. Surgical approach was not a significant predictor of any outcome. CONCLUSIONS: This analysis showed no difference in recurrence, 3-year progression-free survival or 3-year overall survival for robotic vs open radical cystectomy. It provides important prospective data on the oncologic efficacy of robotic radical cystectomy and high level data for patient counseling.

Structure-activity relationships of tubulysin analogues.

The tubulysins are an emerging antibody-drug conjugate (ADC) payload that maintain potent anti-proliferative activity against cells that exhibit the multi-drug resistant (MDR) phenotype. These drugs possess a C-11 acetate known to be hydrolytically unstable in plasma, and loss of the acetate significantly attenuates cytotoxicity. Structure-activity relationship studies were undertaken to identify stable C-11 tubulysin analogues that maintain affinity for tubulin and potent cytotoxicity. After identifying several C-11 alkoxy analogues that possess comparable biological activity to tubulysin M with significantly improved plasma stability, additional analogues of both the Ile residue and N-terminal position were synthesized. These studies revealed that minor changes within the tubulin binding site of tubulysin can profoundly alter the activity of this chemotype, particularly against MDR-positive cell types.

Head-to-head competition does not affect pacing or performance in 1 km cycling time trials.

Previous research has shown enhanced performance and altered pacing behaviour in the presence of a virtual opponent during middle-distance cycling time trials with a duration of 2 min and longer. The purpose of this study was to determine whether these effects are also present in cycling time trials of shorter duration. Twelve physically active men completed three 1-km time trials. After a familiarisation trial (FAM), participants performed two experimental conditions: one without opponent (NO) and one with a virtual opponent (OP). Repeated-measures ANOVAs were used to assess differences in pacing and performance using power output and duration (p<0.05). No differences in mean finishing times (FAM: 91.5 ± 7.7 s; NO: 91.6 ± 6.4 s; OP: 90.9 ± 4.9 s; p=0.907) or power output (FAM: 382 ± 111 W; NO: 363 ± 80 W; OP: 367 ± 67; p=0.564) were found between experimental conditions. Furthermore, no differences in pacing profiles between experimental conditions were found (p=0.199). Similarly, rate of perceived exertion did not differ between experimental conditions at any moment (p=0.831). In conclusion, unlike events of a more prolonged duration (>2 min), the presence of an opponent did not affect participants' pacing behaviour in short duration 1-km time trials.

Robot-assisted radical cystectomy versus open radical cystectomy in patients with bladder cancer (RAZOR): an open-label, randomised, phase 3, non-inferiority trial.

BACKGROUND: Radical cystectomy is the surgical standard for invasive bladder cancer. Robot-assisted cystectomy has been proposed to provide similar oncological outcomes with lower morbidity. We aimed to compare progression-free survival in patients with bladder cancer treated with open cystectomy and robot-assisted cystectomy. METHODS: The RAZOR study is a randomised, open-label, non-inferiority, phase 3 trial done in 15 medical centres in the USA. Eligible participants (aged ≥18 years) had biopsy-proven clinical stage T1-T4, N0-N1, M0 bladder cancer or refractory carcinoma in situ. Individuals who had previously had open abdominal or pelvic surgery, or who had any pre-existing health conditions that would preclude safe initiation or maintenance of pneumoperitoneum were excluded. Patients were centrally assigned (1:1) via a web-based system, with block randomisation by institution, stratified by type of urinary diversion, clinical T stage, and Eastern Cooperative Oncology Group performance status, to receive robot-assisted radical cystectomy or open radical cystectomy with extracorporeal urinary diversion. Treatment allocation was only masked from pathologists. The primary endpoint was 2-year progression-free survival, with non-inferiority established if the lower bound of the one-sided 97·5% CI for the treatment difference (robotic cystectomy minus open cystectomy) was greater than -15 percentage points. The primary analysis was done in the per-protocol population. Safety was assessed in the same population. This trial is registered with ClinicalTrials.gov, number NCT01157676. FINDINGS: Between July 1, 2011, and Nov 18, 2014, 350 participants were randomly assigned to treatment. The intended treatment was robotic cystectomy in 176 patients and open cystectomy in 174 patients. 17 (10%) of 176 patients in the robotic cystectomy group did not have surgery and nine (5%) patients had a different surgery to that they were assigned. 21 (12%) of 174 patients in the open cystectomy group did not have surgery and one (1%) patient had robotic cystectomy instead of open cystectomy. Thus, 302 patients (150 in the robotic cystectomy group and 152 in the open cystectomy group) were included in the per-protocol analysis set. 2-year progression-free survival was 72·3% (95% CI 64·3 to 78·8) in the robotic cystectomy group and 71·6% (95% CI 63·6 to 78·2) in the open cystectomy group (difference 0·7%, 95% CI -9·6% to 10·9%; pnon-inferiority=0·001), indicating non-inferiority of robotic cystectomy. Adverse events occurred in 101 (67%) of 150 patients in the robotic cystectomy group and 105 (69%) of 152 patients in the open cystectomy group. The most common adverse events were urinary tract infection (53 [35%] in the robotic cystectomy group vs 39 [26%] in the open cystectomy group) and postoperative ileus (33 [22%] in the robotic cystectomy group vs 31 [20%] in the open cystectomy group). INTERPRETATION: In patients with bladder cancer, robotic cystectomy was non-inferior to open cystectomy for 2-year progression-free survival. Increased adoption of robotic surgery in clinical practice should lead to future randomised trials to assess the true value of this surgical approach in patients with other cancer types. FUNDING: National Institutes of Health National Cancer Institute.

The Digitization of Patient Care: A Review of the Effects of Electronic Health Records on Health Care Quality and Utilization.

Electronic health records (EHRs) adoption has become nearly universal during the past decade. Academic research into the effects of EHRs has examined factors influencing adoption, clinical care benefits, financial and cost implications, and more. We provide an interdisciplinary overview and synthesis of this literature, drawing on work in public and population health, informatics, medicine, management information systems, and economics. We then chart paths forward for policy, practice, and research.

Why Professional Football Players Chose Not to Reveal Their Concussion Symptoms During a Practice or Game.

OBJECTIVE: To determine why professional football players in Canada decided not to seek medical attention during a game or practice when they believed they had suffered a concussion. DESIGN: Retrospective survey. SETTING: Preseason Canadian Football League training camps. PARTICIPANTS: Four hundred fifty-four male professional football players. MAIN OUTCOME MEASURES: Reasons athletes did not seek medical attention for a presumed concussion during the previous season, how often this occurred and how important these reasons were in the decision process. RESULTS: One hundred six of the 454 respondents (23.4%) believed they had suffered a concussion during their previous football season and 87 of the 106 (82.1%) did not seek medical attention for a concussion at least once during that season. The response "Did not feel the concussion was serious/severe and felt you could still continue to play with little danger to yourself" was the most commonly listed reason (49/106) for not seeking medical attention for a presumed concussion. Many players answered that they did not seek medical attention because they did not want to be removed from a game (42/106) and/or they did not want to risk missing future games (41/106) by being diagnosed with a concussion. CONCLUSIONS: Some professional football players who believed they had suffered a concussion chose not to seek medical attention at the time of injury. Players seemed educated about the concussion evaluation process and possible treatment guidelines, but this knowledge did not necessarily translate into safe and appropriate behavior at the time of injury.

Understanding the Intestinal Microbiome in Health and Disease.

This article provides readers with the basic concepts necessary to understand studies using recent molecular methods performed in intestinal microbiome assessment, with special emphasis on the high throughput sequencing. This review also summarizes the current knowledge on this topic and discusses future insights on the interaction between the intestinal microbiome and equine health.

Exosomal RNA from Mycobacterium tuberculosis-Infected Cells Is Functional in Recipient Macrophages.

Exosomes are extracellular vesicles released by cells that carry proteins, lipids and nucleic acids and function in intercellular communication. Previously, we determined that exosomes released from Mycobacterium tuberculosis (M.tb)-infected macrophages carry mycobacterial proteins and lipids. However, the RNA composition within these exosomes has not been defined. In this study, we characterized the exosomes released from M.tb-infected macrophages and identified a cohort of mouse messenger RNA (mRNA) and microRNA (miRNA). Quantitative reverse-transcriptase polymerase chain reaction analysis showed less abundance of miRNAs in exosomes released from infected compared with uninfected macrophages. Moreover, more than 100 transcripts were found to be enriched or unique to exosomes from infected cells including transcripts involved in regulating an immune response. The exosomal RNA could be transferred and expressed in naïve macrophages and was biologically active, stimulating production of inflammatory mediators and inducing apoptosis in recipient cells. Interestingly, we also identified mycobacterial transcripts in exosomes released from infected macrophages. To our knowledge, this is the first study to identify bacterial-derived RNA in exosomes. Our results suggest that exosomal RNA released from M.tb-infected macrophages may have functional and diagnostic potential in the context of a mycobacterial infection.

RefSelect: a reference sequence selection algorithm for planted (l, d) motif search.

BACKGROUND: The planted (l, d) motif search (PMS) is an important yet challenging problem in computational biology. Pattern-driven PMS algorithms usually use k out of t input sequences as reference sequences to generate candidate motifs, and they can find all the (l, d) motifs in the input sequences. However, most of them simply take the first k sequences in the input as reference sequences without elaborate selection processes, and thus they may exhibit sharp fluctuations in running time, especially for large alphabets. RESULTS: In this paper, we build the reference sequence selection problem and propose a method named RefSelect to quickly solve it by evaluating the number of candidate motifs for the reference sequences. RefSelect can bring a practical time improvement of the state-of-the-art pattern-driven PMS algorithms. Experimental results show that RefSelect (1) makes the tested algorithms solve the PMS problem steadily in an efficient way, (2) particularly, makes them achieve a speedup of up to about 100× on the protein data, and (3) is also suitable for large data sets which contain hundreds or more sequences. CONCLUSIONS: The proposed algorithm RefSelect can be used to solve the problem that many pattern-driven PMS algorithms present execution time instability. RefSelect requires a small amount of storage space and is capable of selecting reference sequences efficiently and effectively. Also, the parallel version of RefSelect is provided for handling large data sets.

Recovery of strength is dependent on mTORC1 signaling after eccentric muscle injury.

INTRODUCTION: Eccentric contractions may cause immediate and long-term reductions in muscle strength that can be recovered through increased protein synthesis rates. The purpose of this study was to determine whether the mechanistic target-of-rapamycin complex 1 (mTORC1), a vital controller of protein synthesis rates, is required for return of muscle strength after injury. METHODS: Isometric muscle strength was assessed before, immediately after, and then 3, 7, and 14 days after a single bout of 150 eccentric contractions in mice that received daily injections of saline or rapamycin. RESULTS: The bout of eccentric contractions increased the phosphorylation of mTORC1 (1.8-fold) and p70s6k1 (13.8-fold), mTORC1's downstream effector, 3 days post-injury. Rapamycin blocked mTORC1 and p70s6k1 phosphorylation and attenuated recovery of muscle strength (∼20%) at 7 and 14 days. CONCLUSION: mTORC1 signaling is instrumental in the return of muscle strength after a single bout of eccentric contractions in mice. Muscle Nerve 54: 914-924, 2016.

Identifying factors of activities of daily living important for cost and caregiver outcomes in Alzheimer's disease.

BACKGROUND: We aimed to obtain a better understanding of how different aspects of patient functioning affect key cost and caregiver outcomes in Alzheimer's disease (AD). METHODS: Baseline data from a prospective observational study of community-living AD patients (GERAS) were used. Functioning was assessed using the Alzheimer's Disease Cooperative Study-Activities of Daily Living Scale. Generalized linear models were conducted to analyze the relationship between scores for total activities of daily living (ADL), basic ADL (BADL), instrumental ADL (IADL), ADL subdomains (confirmed through factor analysis) and individual ADL questions, and total societal costs, patient healthcare and social care costs, total and supervision caregiver time, and caregiver burden. RESULTS: Four distinct ADL subdomains were confirmed: basic activities, domestic/household activities, communication, and outside activities. Higher total societal costs were associated with impairments in all aspects of ADL, including all subdomains; patient costs were associated with total ADL and BADL, and basic activities subdomain scores. Both total and supervision caregiver hours were associated with total ADL and IADL scores, and domestic/household and outside activities subdomain scores (greater hours associated with greater functional impairments). There was no association between caregiver burden and BADL or basic activities subdomain scores. The relationship between total ADL, IADL, and the outside activities subdomain and outcomes differed between patients with mild and moderate-to-severe AD. CONCLUSIONS: Identification of ADL subdomains may lead to a better understanding of the association between patient function and costs and caregiver outcomes at different stages of AD, in particular the outside activities subdomain within mild AD.

Development of orally active inhibitors of protein and cellular fucosylation.

The key role played by fucose in glycoprotein and cellular function has prompted significant research toward identifying recombinant and biochemical strategies for blocking its incorporation into proteins and membrane structures. Technologies surrounding engineered cell lines have evolved for the inhibition of in vitro fucosylation, but they are not applicable for in vivo use and drug development. To address this, we screened a panel of fucose analogues and identified 2-fluorofucose and 5-alkynylfucose derivatives that depleted cells of GDP-fucose, the substrate used by fucosyltransferases to incorporate fucose into protein and cellular glycans. The inhibitors were used in vitro to generate fucose-deficient antibodies with enhanced antibody-dependent cellular cytotoxicity activities. When given orally to mice, 2-fluorofucose inhibited fucosylation of endogenously produced antibodies, tumor xenograft membranes, and neutrophil adhesion glycans. We show that oral 2-fluorofucose treatment afforded complete protection from tumor engraftment in a syngeneic tumor vaccine model, inhibited neutrophil extravasation, and delayed the outgrowth of tumor xenografts in immune-deficient mice. The results point to several potential therapeutic applications for molecules that selectively block the endogenous generation of fucosylated glycan structures.

The Methylene Alkoxy Carbamate Self-Immolative Unit: Utilization for the Targeted Delivery of Alcohol-Containing Payloads with Antibody-Drug Conjugates.

A strategy for the conjugation of alcohol-containing payloads to antibodies has been developed and involves the methylene alkoxy carbamate (MAC) self-immolative unit. A series of MAC ß-glucuronide model constructs were prepared to evaluate stability and enzymatic release, and the results demonstrated high stability at physiological pH in a substitution-dependent manner. All the MAC model compounds efficiently released alcohol drug surrogates under the action of ß-glucuronidase. To assess the MAC technology for ADCs, the potent microtubule-disrupting agent auristatin E (AE) was incorporated through the norephedrine alcohol. Conjugation of the MAC ß-glucuronide AE drug linker to the anti-CD30 antibody cAC10, and an IgG control antibody, gave potent and immunologically specific activities in vitro and in vivo. These studies validate the MAC self-immolative unit for alcohol-containing payloads within ADCs, a class that has not been widely exploited.

Endothelial trauma from mechanical thrombectomy in acute stroke: in vitro live-cell platform with animal validation.

BACKGROUND AND PURPOSE: Endovascular thrombectomy has shown promise for the treatment of acute strokes resulting from large-vessel occlusion. Reperfusion-related injury may contribute to the observed decoupling of angiographic and clinical outcomes. Iatrogenic disruption of the endothelium during thrombectomy is potentially a key mediator of this process that requires further study. METHODS: An in vitro live-cell platform was developed to study the effect of various commercially available endovascular devices on the endothelium. In vivo validation was performed using porcine subjects. RESULTS: This novel in vitro platform permitted high-resolution quantification and characterization of the pattern and timing of endothelial-cell injury among endovascular thrombectomy devices and vessel diameters. Thrombectomy devices displayed heterogeneous effects on the endothelium; the device performance assessed in vitro was substantiated by in vivo findings. CONCLUSIONS: In vitro live-cell artificial vessel modeling enables a detailed study of the endothelium after thrombectomy and may contribute to future device design. Large animal studies confirm the relevance of this in vitro system to investigate endothelial physiology. This artificial vessel model may represent a practical, scalable, and physiologically relevant system to assess new endovascular technologies.

SGN-CD33A: a novel CD33-targeting antibody-drug conjugate using a pyrrolobenzodiazepine dimer is active in models of drug-resistant AML.

Outcomes in acute myeloid leukemia (AML) remain unsatisfactory, and novel treatments are urgently needed. One strategy explores antibodies and their drug conjugates, particularly those targeting CD33. Emerging data with gemtuzumab ozogamicin (GO) demonstrate target validity and activity in some patients with AML, but efficacy is limited by heterogeneous drug conjugation, linker instability, and a high incidence of multidrug resistance. We describe here the development of SGN-CD33A, a humanized anti-CD33 antibody with engineered cysteines conjugated to a highly potent, synthetic DNA cross-linking pyrrolobenzodiazepine dimer via a protease-cleavable linker. The use of engineered cysteine residues at the sites of drug linker attachment results in a drug loading of approximately 2 pyrrolobenzodiazepine dimers per antibody. In preclinical testing, SGN-CD33A is more potent than GO against a panel of AML cell lines and primary AML cells in vitro and in xenotransplantation studies in mice. Unlike GO, antileukemic activity is observed with SGN-CD33A in AML models with the multidrug-resistant phenotype. Mechanistic studies indicate that the cytotoxic effects of SGN-CD33A involve DNA damage with ensuing cell cycle arrest and apoptotic cell death. Together, these data suggest that SGN-CD33A has CD33-directed antitumor activity and support clinical testing of this novel therapeutic in patients with AML.

Identification of novel markers for mouse CD4(+) T follicular helper cells.

CD4(+) T follicular helper (TFH) cells are central for generation of long-term B-cell immunity. A defining phenotypic attribute of TFH cells is the expression of the chemokine R CXCR5, and TFH cells are typically identified by co-expression of CXCR5 together with other markers such as PD-1, ICOS, and Bcl-6. Herein, we report high-level expression of the nutrient transporter folate R 4 (FR4) on TFH cells in acute viral infection. Distinct from the expression profile of conventional TFH markers, FR4 was highly expressed by naive CD4(+) T cells, was downregulated after activation and subsequently re-expressed on TFH cells. Furthermore, FR4 expression was maintained, albeit at lower levels, on memory TFH cells. Comparative gene expression profiling of FR4(hi) versus FR4(lo) Ag-specific CD4(+) effector T cells revealed a molecular signature consistent with TFH and TH1 subsets, respectively. Interestingly, genes involved in the purine metabolic pathway, including the ecto-enzyme CD73, were enriched in TFH cells compared with TH1 cells, and phenotypic analysis confirmed expression of CD73 on TFH cells. As there is now considerable interest in developing vaccines that would induce optimal TFH cell responses, the identification of two novel cell surface markers should be useful in characterization and identification of TFH cells following vaccination and infection.

Comparison of vials and prefilled pens of a rapid-acting insulin analog on pharmacy budgets in a long-term care setting.

OBJECTIVE: Estimate budgetary impact for skilled nursing facility converting from individual patient supply (IPS) delivery of rapid-acting insulin analog (RAIA) 10-mL vials or 3-mL prefilled pens to 3-mL vials. DESIGN: A budget-impact model used insulin volume purchased and assumptions of length of stay (LOS), daily RAIA dose, and delivery protocol to estimate the cost impact of using 3-mL vials. SETTING: Skilled nursing facility. PARTICIPANTS: Medicare Part A patients. INTERVENTIONS: Simulations conducted using 12-month current and future scenarios. Comparisons of RAIA use for 13- and 28-day LOS. MAIN OUTCOME MEASURES: RAIA costs and savings, waste reduction. RESULTS: For patients with 13-day LOS using 20 units/day of IPS insulin, the model estimated a 70% reduction in RAIA costs and units purchased and a 95% waste reduction for the 3-mL vial compared with the 10-mL vial. The estimated costs for prefilled pen use were 58% lower than for use of 10-mL vials. The incremental savings associated with 3-mL vial use instead of prefilled pens was 28%, attributable to differences in per-unit cost of insulin in vials versus prefilled pens. Using a more conservative scenario of 28-day LOS at 20 units/day, the model estimated a 40% reduction in RAIA costs and units purchased, resulting in a 91% reduction in RAIA waste for the 3-mL vial, compared with 10-mL vial. CONCLUSION: Budget-impact analysis of conversion from RAIA 10-mL vials or 3-mL prefilled pens to 3-mL vials estimated reductions in both insulin costs and waste across multiple scenarios of varying LOS and patient daily doses for skilled nursing facility stays.