Snapshot Analysis Research Articles

Antimicrobial stewardship program in one primary care hospital, a snapshot analysis

Abstract Antimicrobic resistance (AMR) continues to rise, whereas development of new agents to counter it has slowed. A heightened need to maintain the effectiveness of currently available agents exists. Healthcare-associated infections (HAIs) are a significant cause of poor treatment outcomes and elevated healthcare and societal costs worldwide. At the beginning of 2024, we started a prospective, interventional, interrupted time-series study, based on Prospective Audit and Feedback in the Intensive Care Unit (ICU) and in the internal medicine ward of our hospital. The primary outcomes will be the difference in the antibiotic consumption, and the incidence of bloodstream infections (BSI) caused by multidrug-resistant (MDR) organisms. The secondary outcomes will include the hospital mortality rate, the mean length of stay and the antibiotic expense. We conducted a snapshot analysis of the first three months to assess the efficacy our program. In the first three months we registered a global reduction in antibiotic expense (almost by half in comparison of 2023 first quarter) and consumption, particularly in the use of carbapenems: (change in level, CL: -51,26 DDD/1000 PD,) and third- generation cephalosporins (CL: -6 DDD/1000 PD). We registered a reduction in the use of hydroalcoholic gel, probably due to the reducted perception after the waning of risk perception towards Covid-19, although no big difference was observed in BSI incidence due to MDR Gram-negative organisms (CL: +1,2 events/1000 PD). Albeit partial, once again these findings demonstrated that implementation of an antimicrobial stewardship program, no matter the level of healthcare, is critical for fighting the AMR and to lessen the burden on Public Health; in particular our program induced a significant reduction in antibiotic consumption that lead to more funds at disposal to improve our clinical practice. Key messages • Once again our findings demonstrated that implementation of an antimicrobial stewardship, no matter the level of healthcare, is critical for fighting the AMR. • Our program induced a significant reduction in antibiotic consumption.

SNaPshot minisequencing for SARS CoV 2 Variant Genotyping

Abstract Introduction/Objective The SNaPshot Multiplex System (Thermo Fisher) can investigate up to fifty SNP markers simultaneously by using PCR amplification and subsequent dideoxy single base extension of an unlabeled primer and capillary electrophoresis. After electrophoresis and fluorescence detection, the alleles of a single marker appear as different colored peaks at roughly the same size in the electropherogram plot. The size of the different allele peaks vary slightly due to differences in molecular weight of the dyes. We propose a new set of primers and probes to use this system to differentiate variants of SARs Cov 2 variants. Methods/Case Report SNAPSHOT analysis was performed using the primers designed internally and analysis was done of up to 7 mutation hot spots, which were 417, 4511, 478, 484, 501, 614, and 681. By implementing the algorithm of systems and methods herein with the traces depicted in Figures, true positive and true negative outcomes for the different COVID variants can be performed, based on the highlighted peaks, which are not necessarily the most intense peaks. 10 Positive controls achieved from in stro transcript plasmid was tested then 10 viral RNA obtained through BEI Resources, NIAID was tested after mixed into 30 pooled negative PCR-swab specimens. Genmapper was used for analysis of results. 40 Korean patient samples were tested as well. Results (if a Case Study enter NA) Both In vitro transcript and derived specimens of wild type, alpha, beta, delta, gamma, kappa, omicron, and pirola showed expected results in 78/80 of the specimens. For example,delta B.1.617.2 variant showed 1 = A (green) at Primer 452R-F, 2 = G (blue): Primer 484Q-F, and 3 = A (green) at Primer 614-F. Of note, hetero type was noted in a few of the patient strains but none of the BEI strains and this may be due to a transfromation of the virus and worth investigation. Conclusion The SNaPshot® Multiplex System is a accurate system that may be applied to multiple applications including viral strain anylsis and here we can show how it may be effectively used for SARS-Cov-2 gentotyping. Using this technique, it is possible to analyze more than 50 SNPs distributed throughout the genome in a single multiplex reaction, making it an advantage when compared with traditional sequencing reaction. This is a important study that shows that this technique may be used in multiple field applictions.

Keeping up with the decarbonization: Conceptualizing and investigating incumbents’ responses to transition pressures in the post-Paris world

Incumbents are central regime actors who simultaneously adapt to transitions and actively shape them. This study has two objectives: advance the conceptualization around these actors’ behaviors in contemporary transition processes and demonstrate a novel research approach to study this behavior in practice. The focus is on incumbents’ responses to transition-related external pressures. These responses are studied by reviewing related work from organization and management literature, as well as conducting an empirical case study in the aviation sector. The theoretical and empirical insights are combined through flexible pattern matching into a conceptual framework, which simultaneously accommodates a holistic view of different types of responses incumbents use to navigate the complex operating environment, while also supporting particularity that goes beyond strategy talk. For the empirical investigation, this research utilizes incumbent airlines’ transition risk work as a source of information on what external pressures these actors themselves perceive and the responses they operationalize. The empirical case study illustrates how by distinguishing between standard, inconsistent, and unconventional response areas that incumbents take part in, even a snapshot analysis of a contemporary transition phenomenon can reveal what is happening in socio-technical regimes. The analysis also pinpoints how responses have two important characteristics that signify the importance of acknowledging the variety of responses that incumbents have at their disposal: multi-functionality and parallelity. Together, the insights of this paper can support the study and understanding of the complex, heterogeneous, and nuanced behavior of incumbent organizations, and encourage more research efforts on transitions in the making.

Effectiveness and safety of secukinumab updosing in patients with moderate to severe plaque psoriasis: data from the PURE registry

Secukinumab is a fully human IgG1 antibody that selectively binds to and neutralizes the proinflammatory cytokine interleukin-17A. Secukinumab is an effective and well-tolerated treatment for plaque psoriasis. There is a limited real-word evidence for dose optimisation of secukinumab based on clinical response. PURE is a multi-national, prospective, observational study in patients with moderate to severe chronic plaque psoriasis in Canada and Latin America, assessing the real-world safety and effectiveness of secukinumab and other indicated therapies. The aim of the current snapshot analysis was to evaluate the effectiveness and safety of on-label dose and updosed secukinumab in patients with plaque psoriasis enrolled in the PURE study. At the time of analysis, 676 patients received secukinumab, of which 84.6% (n = 572) remained on the on-label dose, while 15.4% (n = 104) were updosed. With on-label secukinumab, the absolute Psoriasis Area and Severity Index (PASI) score was reduced from 13.6 at baseline to 1.2 over 36 months, with treatment persistence of 73% at 40 months. At Month 36, 73.2% of the patients receiving on-label secukinumab achieved Investigator’s Global Assessment (IGA) 0/1. With updosed secukinumab (300 mg every 2 weeks, 300 mg every 3 weeks, 450 mg every 4 weeks, or 450 mg every 3 weeks), 57.9% of the patients showed improvement in the absolute PASI score at the first visit after updosing, with treatment persistence of 50% at 12 months after updosing. At Month 15, 40% of patients receiving updosed secukinumab achieved IGA 0/1. Patients with previous biologic exposure (odds ratio [OR]: 3.25; 95% confidence interval [CI]: 2.03, 5.18, p < 0.0001) were more likely to be updosed while those with a body weight < 90 kg (OR: 0.49; 95% CI [0.31, 0.77], p = 0.0019) were less likely to be updosed. Previous biologic exposure (HR [hazard ratio]: 1.47; 95% CI [1.24, 1.75], p < 0.0001) and current biologic exposure (secukinumab vs. other indicated therapies: HR 0.57; 95% CI [0.43, 0.75], p = 0.0001) were significantly associated with time to secukinumab updosing. No new or unexpected safety signals were observed with updosed secukinumab. Secukinumab updosing was efficacious and well-tolerated in patients with psoriasis who failed to respond to the approved on-label regimen, suggesting that updosing may be a useful therapeutic option for approved dose non-responders.

The artification of fossils in commercial art spaces: Dinosaurs in a desirescape

In this article we consider the movement of fossils into art commercial spaces as a process of artification underpinned by the deep object associations that art spaces foster. We combine observational data gathering at art and fossil fairs, dealerships, and auctions with snapshot analysis of the online market for Tyrannosaurus rex fossils, contextualized by interviews with palaeontologists and fossil dealers, to understand the increasing appearance of fossils within art commercial spaces. We believe that the placement of fossils within the art market desirescape, so within a network of alluring, provocative, affective art objects, allows the fossils to transform into what consumers would consider art. The fossils then gain the social associations that artworks have for these consumers. We believe that art and fossil consumers are not simply drawn to individual objects of desire, but to the myriad associations those objects have with other objects and the deep meanings those associations overlay. Those associations and the network they form can, in turn, transform the objects within it. When a fossil is artified, it can be desired like art, and can command art prices.

Rapid Initiation of Antiretroviral Therapy With Coformulated Bictegravir, Emtricitabine, and Tenofovir Alafenamide Versus Efavirenz, Lamivudine, and Tenofovir Disoproxil Fumarate in HIV-Positive Men Who Have Sex With Men in China: Week 48 Results of the Multicenter, Randomized Clinical Trial.

Most international treatment guidelines recommend rapid initiation of antiretroviral therapy (ART) for people newly diagnosed with human immunodeficiency virus (HIV)-1 infection, but experiences with rapid ART initiation remain limited in China. We aimed to evaluate the efficacy and safety of efavirenz (400 mg) plus lamivudine and tenofovir disoproxil fumarate (EFV + 3TC + TDF) versus coformulated bictegravir, emtricitabine, and tenofovir alafenamide (BIC/FTC/TAF) in rapid ART initiation among men who have sex with men (MSM) who have been diagnosed with HIV. This multicenter, open-label, randomized clinical trial enrolled MSM aged ≥18 years to start ART within 14 days of confirmed HIV diagnosis. The participants were randomly assigned in a 1:1 ratio to receive EFV (400 mg) + 3TC + TDF or BIC/FTC/TAF. The primary end point was viral suppression (<50 copies/mL) at 48 weeks per US Food and Drug Administration Snapshot analysis. Between March 2021 and July 2022, 300 participants were enrolled; 154 were assigned to receive EFV + 3TC + TDF (EFV group) and 146 BIC/FTC/TAF (BIC group). At week 48, 118 (79.2%) and 140 (95.9%) participants in the EFV and BIC group, respectively, were retained in care with viral suppression, and 24 (16.1%) and 1 (0.7%) participant in the EFV and BIC group (P < .001), respectively, discontinued treatment because of adverse effects, death, or lost to follow-up. The median increase of CD4 count was 181 and 223 cells/μL (P = .020), respectively, for the EFV and BIC group, at week 48. The overall incidence of adverse effects was significantly higher for the EFV group (65.8% vs 37.7%, P < .001). BIC/FTC/TAF was more efficacious and safer than EFV (400 mg) + 3TC + TDF for rapid ART initiation among HIV-positive MSM in China.

Very-Low-Level Viremia, Inflammatory Biomarkers, and Associated Baseline Variables: Three-Year Results of the Randomized TANGO Study.

We compared proportions of participants with target detected, target not detected (TND), and elevated viral load (VL) and assessed baseline variables associated with week 144 inflammatory biomarker levels between dolutegravir-lamivudine (DTG/3TC) and tenofovir alafenamide-based regimens (TBRs) in the TANGO study (post hoc). TANGO is an open-label, multicenter, phase 3 study that randomized adults with VL <50 copies/mL to switch to once-daily fixed-dose DTG/3TC or continue TBR. At baseline and each study visit, the VL was measured. Elevated VL event frequencies were assessed, including "blips." Interleukin 6, D-dimer, high-sensitivity C-reactive protein, soluble CD14, and soluble CD163 were measured at baseline and at week 144. Loge-transformed week 144 biomarker levels were compared between treatment groups using an analysis of covariance model adjusting for baseline variables. High, comparable proportions of participants had VL <40 copies/mL and TND at week 144 (DTG/3TC, 279 of 369 [76%]; TBR, 267 of 372 [72%], intention-to-treat exposed Snapshot analysis; adjusted difference, 3.9% [95% confidence interval, -2.5% to 10.2%]), with similar TND proportions at all postbaseline visits (123 of 369 [33%] vs 101 of 372 [27%], respectively). Similar proportions of DTG/3TC participants had ≥1 postbaseline VL ≥50 copies/mL (28 of 369 [8%] vs 42 of 372 [11%] for TBR), primarily blips (18 of 369 [5%] and 26 of 372 [7%], respectively). Week 144 inflammatory biomarker levels were low and comparable between groups and associated with multiple demographic and baseline characteristics, including baseline biomarker levels, indicating a multifactorial inflammatory response. Week 144 biomarker levels were low and generally comparable between treatment groups, reflecting similar, robust, and durable viral suppression observed using the stringent TND end point. Trial registration: ClinicalTrials.gov, NCT03446573.

Characterization of Hematopoietic Stem Cell Diversity Using Spatiotemporal Quantitative Phase Imaging

Cells undergo continual transformations, never retaining their original state. Hematopoietic stem cells (HSCs), at the apex of the hematopoietic hierarchy, are not exempt from this dynamic process. In recent years, the advent of single-cell analysis techniques such as scRNAseq has progressively unveiled the heterogeneity within cell populations previously presumed to be homogeneous. However, these techniques are limited to evaluating the cellular state at a single temporal point based on snapshot analysis, thus failing to account for temporal changes and dynamic behavior of cells. Therefore, the true diversity inherent to the ever-changing HSCs remains uncertain. In this study, we comprehensively elucidate HSC diversity, including temporal changes, by integrating our recently established ex vivo HSC expansion techniques (Wilkinson et al., Nature, Becker et al., Cell Stem Cell), single-cell quantitative phase imaging (QPI), and post-transplantation dynamics analysis. For live imaging, HSCs were harvested from hepatic leukemia factor ( Hlf)-tdTomato reporter mice, which specifically marks long-term HSCs. Index sorted single Hlf-tdTomato + HSC were expanded with a single-HSC culture system and monitored by QPI fluorescence time-lapse imaging. Surprisingly, even though the cells were derived from the same HSC fraction, significant variations in mitotic rate, motility, morphological changes, and Hlf expression levels were observed at the single-cell level. Stemness did not decrease stepwise over time, but always exhibited continuous changes. Thus, analysis including the temporal dimension illuminated the infinitely branched nature of HSC diversity. Interestingly, Hlf expression level correlated with the dynamic behavior of HSCs in the expansion culture system. Hlf-high HSCs exhibited a slow division rate, small, rounded morphology and low motility, while Hlf-low HSCs actively divided and differentiated, displayed larger morphological size with low sphericity, and exhibited high motility. Furthermore, spatiotemporal dynamics analysis of Hlf-high/low HSCs after transplantation, employing the highly sensitive in vivo imaging system Akaluc bioluminescence imaging (AkaBLI), revealed that Hlf-high HSCs initiate systemic hematopoiesis slowly, while Hlf-low HSCs expanded quickly, characterized by short-term explosive hematopoiesis in the spleen. As expected, only Hlf-high HSCs had long-term bone marrow reconstitution ability. Thus, based on the expression level of Hlf, it is possible to predict the dynamic behavior of the cells in the expansion medium and in the post-transplant body. Next, we investigated whether Hlf expression level could be predicted based on the kinetic features of cells during HSC ex vivo expansion. Interestingly, multidimensional analysis based on kinetic features extracted from time-lapse imaging showed multiple clusters, each linked to Hlf expression levels. In human HSCs, the dynamic diversity of HSCs was also observed in our recently established ex vivo expansion system (Sakurai et al., Nature). Notably, the kinetic features of human HSCs differed from those of mouse HSCs. Transplantation of human HSCs exhibiting specific morphological characteristics showed long-term reconstitution ability. Thus, classification of HSCs based on kinetic features facilitated enrichment of functional HSCs. This study demonstrates the importance of characterizing cells, including the temporal dimension, and illustrates the existence of infinite dynamic individuality in mouse and human HSCs.

HPB P35 A snapshot analysis to identify ideal interval between liver imaging and resection

Abstract Background An increase in waiting times has been seen across all NHS service provisions in the last few years due to post-pandemic backlog, staffing issues, bed and theatre pressures. This has led to increasing intervals between cancer diagnosis and surgery, which may negatively impact patient outcomes. The ideal interval between final cross-sectional imaging and liver resection for hepatocellular carcinoma (HCC) and colorectal liver metastases (CRLM) is not well established.The aim of the study was to explore the most appropriate interval between scan and operation and its effect on outcomes; Tumour growth, resectability, R0 rates, disease free survival and overall survival. Methods A retrospective analysis of our prospective maintained liver resectional database was performed. Patients undergoing resection for HCC or CRLM between January 2020 and December 2021 were included. Patients were followed up until June 2023. Groups were split into a &amp;lt;6-week interval and ≥6-week interval group. Scans and radiology reports and post-op histology were reviewed to identify interval changes of individual tumours. We analysed outcomes of gross and percentage increase in tumour size, recurrence rates, median disease-free survival and overall survival. Patient demographics including age (≥18), gender, BMI, neoadjuvant chemotherapy, type of scan, initial size and number of lesions were analysed. Results 53 patients were included in the analysis (19 female). Disease free survival was 27.4 months in &amp;lt;6 week group vs. 24.9 months in ≥6 week group. Average tumour growth was 5.9mm higher (range 3.7-9.6mm) when interval time was &amp;gt;6 weeks. Tumour percentage growth was 11.5% in &amp;lt;6 week group vs 32% in ≥6 week group. Recurrence rate in &amp;lt;6 week group was 23.5% VS 30.5% in ≥6 week group. There was no difference in percentage overall survival, non-resectability rate or R1 rates. Conclusions In this snapshot study of liver resections over a two-year period we did find an expected bigger increase in tumour size in patients where the interval between last cross-sectional imaging and actual resection was longer. The ≥6week interval group seems to have more tumour recurrence but this did not impact overall survival. This pilot cohort was not powered to firmly establish guidance for maximum interval between last scan and surgery, but it prompts further investigation to get clarity to guide clinical practice. A larger cohort would ideally look at HCC and CRLM separately.

Effectiveness and safety of bempedoic acid in routine clinical practice: 1-year follow-up snapshot of the MILOS German cohort

Abstract Background Low-density lipoprotein cholesterol (LDL-C) has an established role in the development of atherosclerotic cardiovascular disease. The 2019 ESC/EAS dyslipidaemia guidelines recommended more intensive treatment goals, however, many patients do not reach them. Bempedoic acid (BA) is a first-in-class ATP citrate lyase inhibitor that lowers LDL-C levels. There is limited data on the use of BA and BA + ezetimibe (EZE) fixed-dose combination (FDC) in clinical practice. Purpose The purpose of this snapshot of 1-year follow-up data from the MILOS study is to evaluate the effectiveness and safety of BA and its FDC in routine clinical practice in Germany. Methods MILOS is a European, prospective, observational, non-interventional study in adult patients with primary hypercholesterolaemia or mixed dyslipidaemia. Patients were recruited from 126 sites in Germany between January 2021 and January 2022, and are followed up for 1–2 years after baseline measurements. Here, we summarise 1-year follow-up data from a snapshot taken on January 13th, 2023. Results Of 992 patients enrolled in Germany, 714 had either completed their 1-year follow-up or discontinued the study prematurely, and 524 of these 714 patients attended their 1-year follow-up visit. For this snapshot, 714 patients are used when determining cardiovascular (CV) outcomes and safety endpoints, and 524 patients are used when reporting efficacy data. The overall mean (SD) age of the population (n=524) was 64.7 (10.0) years, and 60.7% were male. Patients treated with BA/BA+EZE FDC had an overall mean LDL-C level of 2.18 mmol/L (84.1 mg/dL) at 1 year compared with 3.20 mmol/L (123.6 mg/dL) pre-treatment, representing a mean relative LDL-C reduction of 27.3%. Overall, 25.8% (135/524) of patients had reached their LDL-C goal after 1 year of treatment compared with 4.0% (21/524) pre-treatment (Figure 1A and 1B). The overall incidence rate of the composite endpoint of major adverse cardiovascular event (4-component MACE) including CV death, non-fatal myocardial infarction, non-fatal stroke, and coronary revascularisation (n=714) was 3.36%. At 1-year follow-up, 19% (136/714) of patients had an adverse drug reaction (ADR) suspected to be related to BA/BA+EZE FDC, and 0.8% (6/714) had serious ADRs, as deemed by the investigator. Conclusion This snapshot analysis of 1-year follow-up data suggests that the addition of BA to other lipid-lowering therapies increases the proportion of patients at LDL-C goal by ∼6-fold in the observed cohort. The safety and tolerability profile of bempedoic acid are in line with data from randomised controlled trials.

Current practice in assessment and management of malnutrition in surgical oncology practice – An ESSO-EYSAC snapshot analysis

IntroductionMalnutrition is common in patients suffering from malignant diseases and has a major impact on patient outcomes. Prevention and early detection are crucial for effective treatment. This study aimed to investigate current international practice in the assessment and management of malnutrition in surgical oncology departments. Material and methodsThe survey was designed by European Society of Surgical Oncology (ESSO) and ESSO Young Surgeons and Alumni Club (EYSAC) Research Academy as an online questionnaire with 41 questions addressing three main areas: participant demographics, malnutrition assessment, and perioperative nutritional standards. The survey was distributed from October to November 2021 via emails, social media and the ESSO website to surgical networks focussing on surgical oncologists. Results were collected and analysed by an independent team. ResultsA total of 156 participants from 39 different countries answered the survey, reflecting a response rate of 1.4%. Surgeons reported treating a mean of 22.4 patients per month. 38% of all patients treated in surgical oncology departments were routinely screened for malnutrition. 52% of patients were perceived as being at risk for malnutrition. The most used screening tool was the “Malnutrition Universal Screening Tool” (MUST). 68% of participants agreed that the surgeon is responsible for assessing preoperative nutritional status. 49% of patients were routinely seen by dieticians. In cases of severe malnutrition, 56% considered postponing the operation. ConclusionsThe reported rate of malnutrition screening by surgical oncologists is lower than expected (38%). This indicates a need for improved awareness of malnutrition in surgical oncology, and nutritional screening.

Current approaches to the treatment of patients with dyslipidemia in the real practice in the outpatient stage

Aim To evaluate the frequency and structure of lipid-lowering therapy and of achieving the goal of low-density lipoprotein cholesterol (LDL-C) in patients with very high cardiovascular risk (CVR) who were monitored at the outpatient stage.Material and methods A retrospective snapshot analysis was performed by continuous sampling method for 136 medical records of outpatient patients (71 men, 65 women) aged 42 to 91 years [median, 68 years; 25th and 75th percentiles (59; 78)].Results 134 (98,53 %) patients took statins; 8 (5.88 %) patients took a combination of statin and ezetimibe; 2 (1.47 %) patients took proprotein convertase subtilisin/kexin type 9 enzyme inhibitors (PCSK9): 2 (1.47 %) patients took evolocumab and 1 (0.74%) of 2 PCSK9-treated patients took a combination of PCSK9 inhibitor and statin. Atorvastatin at a dose of 20 (20; 40) mg as recommended at the hospital was the most frequently prescribed statin. 5 (3.68%) patients achieved the goal LDL-C of ≤1.4 mmol/l.Conclusion Statins prevail in the structure of lipid-lowering therapy in patients with very high CVR. The frequency of combination therapy (statin/ezetimibe, 5.88%; PCSK9 inhibitor/statin, 0.74%) and PCSK9 inhibitors was noted to be low. Only 3.68% of patients achieved the goal LDL-C during the lipid-lowering treatment.

Development of SNP markers for Cucurbita species discrimination

There are five domesticated species in the genus Cucurbita. These are Cucurbita. pepo, Cucurbita maxima, Cucurbita moschata, Cucurbita ficifolia, and Cucurbita argyrosperma. Cucurbita has a large genetic diversity, with various growth forms, sizes, shapes, colors, compositions, tastes, and resistance to biotic and abiotic factors. Maintaining the biological diversity of genetic resources and managing the right historical information are important first steps in the development of new varieties with desirable traits. This study presents the classification of Cucurbita species using DNA barcodes and the development of powerful single nucleotide polymorphism (SNP) markers that can distinguish the five Cucurbita species. A total of 54 accessions from five Cucurbita species (C. pepo, C. maxima, C. moschata, C. ficifolia, and C. argyrosperma) were used for SNP marker development. The chloroplast DNA was extracted, and the three universal barcoding regions (matK, trnH-psbA, and rbcL) were sequenced. Neighbor-joining (NJ) trees were constructed using the nucleotide sequence of the cpDNA barcodes. The rbcL and trnH-psbA barcodes failed to differentiate between C. moschata and C. argyrosperma, whereas the matK region efficiently differentiated with 87% bootstrap support. Moreover, the matK region showed a species identification rate of 100%, making it an efficient marker for identifying the five domesticated Cucurbita species. Multiplex SNaPShot (mini sequencing) analysis of four SNPs in the matK region revealed four species-specific SNPs that effectively classify Cucurbita species into five groups. When all four markers are used together, they are effective. These four species specific SNP markers were validated using known Cucurbita germplasm (111 accessions) and applied for the species identification of unknown Cucurbita germplasm (370 accessions) available at the RDA gene bank in the Republic of Korea. These markers were 100% effective for identifying the five Cucurbita species. Therefore, these SNP markers can be used for effective management of Cucurbita genetic resources in genebanks around the world.

Rotary mechanism of V/A-ATPases-how is ATP hydrolysis converted into a mechanical step rotation in rotary ATPases?

V/A-ATPase is a rotary molecular motor protein that produces ATP through the rotation of its central rotor. The soluble part of this protein, the V1 domain, rotates upon ATP hydrolysis. However, the mechanism by which ATP hydrolysis in the V1 domain couples with the mechanical rotation of the rotor is still unclear. Cryo-EM snapshot analysis of V/A-ATPase indicated that three independent and simultaneous catalytic events occurred at the three catalytic dimers (ABopen, ABsemi, and ABclosed), leading to a 120° rotation of the central rotor. Besides the closing motion caused by ATP bound to ABopen, the hydrolysis of ATP bound to ABsemi drives the 120° step. Our recent time-resolved cryo-EM snapshot analysis provides further evidence for this model. This review aimed to provide a comprehensive overview of the structure and function of V/A-ATPase from a thermophilic bacterium, one of the most well-studied rotary ATPases to date.

Abstract 6625: Mathematical modeling of single-cell data reveals the key role of stochasticity - not fitness - in determining the clonal origins of relapse in childhood leukemia

Abstract Acute lymphoblastic leukemia (cALL) is the most common pediatric cancer, and since up to 20% of children relapse after initially responding to chemotherapy treatment, the largest cause of cancer-related childhood deaths in the western world. With the idea that dissecting the evolutionary population dynamics leading to relapse would help explain treatment failure from a mechanistic standpoint, several studies have performed comparisons of genetic heterogeneity at diagnosis and relapse. These showed that as many as 70% of relapses are dominated by a single diagnostic subclone or one of its evolutionary progeny; leading to the prevailing view that treatment selection in cALL primarily operates at the genotype level. However, a crucial caveat of these studies is their reliance, due primarily to technical and economic constraints, on very limited data timepoints. While the dynamics linking said timepoints are often interpreted based on simple intuition. To overcome this sparse data challenge and reconstruct the entire spatial and temporal evolutionary trajectories of individual cALL cells from diagnosis to relapse, we have integrated experimental data with an in silico model. Single-cell WGS and RNAseq data were obtained from primary and xenografted leukemic cells before and after chemotherapy. These were then used to parameterize an agent-based mathematical model allowing tracking of the genotype and evolving phenotype of individual cells over time. When short treatment courses akin to those we delivered in vivo were used, the in silico model closely recapitulated the experimental results. Since cALL treatment lasts several years, it cannot be entirely modelled in vivo. Due to the rarity of post-treatment residual cells and the lack of universal cell surface markers to isolate them, direct analysis of clinical samples is also challenging. However, based on the initial treatment data, our calibrated model provided a unique opportunity to simulate longer remission-relapse dynamics of several leukemias. Mechanistic analysis of the collected data showed that, strikingly, in most cases, clonal dominance at relapse results from stochastic sweeps rather than deterministic differences in clonal fitness. Indeed, independent treatment of the same leukemia with an identical drug regimen more frequently ended with a considerably different clonal landscape (either polyclonal disease or a different dominant clone) than with the same outcome initially observed. Rather than genotype differences, the size of residual disease and a founder effect linked to the stochastic exit, post-treatment, of individual cells from quiescence were the key determinants of the relapse genetic landscape. Altogether, our data highlight the misinterpretation risk associated with snapshot analysis and might inform promising alternative treatment schedules. Citation Format: Virginia Turati, Javier Herrero, Mark Robertson-Tessi, Tariq Enver, Andriy Marusyk, Alexander RA Anderson. Mathematical modeling of single-cell data reveals the key role of stochasticity - not fitness - in determining the clonal origins of relapse in childhood leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6625.

An indirect comparison of 144-week efficacy, safety, and tolerability of dolutegravir plus lamivudine and second-generation integrase inhibitor–based, 3-drug, single-tablet regimens in therapy-naive people with HIV-1

BackgroundThe long-term efficacy and safety of the 2-drug regimen dolutegravir (DTG) + lamivudine (3TC) and 3-drug single-tablet regimens recommended for antiretroviral therapy (ART)-naive people with HIV-1 (PWH) have yet to be compared directly in clinical trials. This indirect treatment comparison (ITC) was conducted to compare the durability of efficacy and long-term safety of DTG + 3TC vs second-generation, integrase strand transfer inhibitor (INSTI)-based, 3-drug, single-tablet regimens bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF) and DTG/abacavir/3TC (DTG/ABC/3TC) at Week 144 after treatment initiation.MethodsA systematic literature review identified 4 trials evaluating the treatment regimens of interest in ART-naive PWH (GEMINI-1, GEMINI-2, GS-US-380-1489, and GS-US-380-1490). Safety, efficacy, and tolerability results were compared using fixed-effects Bucher ITC methodology to calculate relative outcomes.ResultsRates of virologic suppression (HIV-1 RNA < 50 copies/mL, US Food and Drug Administration Snapshot analysis) and virologic failure (HIV-1 RNA ≥ 50 copies/mL) as well as mean change in CD4 + cell count were similar with DTG + 3TC, BIC/FTC/TAF, and DTG/ABC/3TC at Week 144. Serious adverse events occurred less frequently with DTG + 3TC compared with both BIC/FTC/TAF (odds ratio [OR], 0.51; 95% CI 0.29–0.87; P = 0.014) and DTG/ABC/3TC (OR, 0.38; 95% CI 0.19–0.75; P = 0.006). Discontinuations and overall adverse events were similar across all 3 regimens.ConclusionsThese results suggest that the 2-drug regimen DTG + 3TC offers comparable and durable efficacy with fewer serious adverse events vs BIC/FTC/TAF and DTG/ABC/3TC through 144 weeks of treatment in ART-naive PWH. These long-term comparative data support the therapeutic value of DTG + 3TC for PWH.

The assessment and treatment strategies of malnutrition in patients with cancer treated by surgical oncologist – an EYSAC snapshot analysis

The assessment and treatment strategies of malnutrition in patients with cancer treated by surgical oncologist – an EYSAC snapshot analysis

Same-day initiation of bictegravir/emtricitabine/tenofovir alafenamide: Week 48 results of the FAST study-IMEA 055.

Initiating same-day ART for newly HIV-diagnosed individuals reduces secondary HIV transmissions and the risk of them being lost to follow-up between diagnosis and initiation of ART. The FAST study was a national, prospective, single-arm study assessing the efficacy, safety and feasibility of bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF) in a same-day initiation model. ART had to be started on the first medical appointment, before any laboratory results were available. Participants completed a self-administered questionnaire at each visit including a HIV anxiety 5-point Likert scale. The primary outcome was the proportion of participants in the ITT population with plasma HIV RNA (pVL) < 50 copies/mL at Week (W) 24 using the FDA Snapshot algorithm. Overall, 112 participants were included in the ITT population. During follow-up, seven participants discontinued the study drug but remained on the study, and seven others discontinued follow-up. According to FDA Snapshot analysis, at W24 and W48, 90/112, (80.4%; 95% CI: 71.8-87.3) and 95/112 (84.8%; 95% CI: 76.8-90.9) of participants achieved pVL < 50 copies/mL, respectively. The protocol-defined virological failure (PDVF, 2 consecutive pVL ≥ 50 copies/mL as of W24) was observed in 11/112 (9.8%) at W24 and 14/112 (12.5%) at W48. No emergent resistance-associated mutation was detected in those with PDVF at W24 and W48. BIC/FTC/TAF was well tolerated through to W48, with a low incidence of grade 3-4 adverse events (15/100 person-years). Patient opinion of same-day treatment initiation and continuing BIC/FTC/TAF was very favourable. These results suggest that BIC/FTC/TAF is safe, effective and well accepted for same-day initiation.

Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding

Vacuolar/archaeal-type ATPase (V/A-ATPase) is a rotary ATPase that shares a common rotary catalytic mechanism with FoF1 ATP synthase. Structural images of V/A-ATPase obtained by single-particle cryo-electron microscopy during ATP hydrolysis identified several intermediates, revealing the rotary mechanism under steady-state conditions. However, further characterization is needed to understand the transition from the ground state to the steady state. Here, we identified the cryo-electron microscopy structures of V/A-ATPase corresponding to short-lived initial intermediates during the activation of the ground state structure by time-resolving snapshot analysis. These intermediate structures provide insights into how the ground-state structure changes to the active, steady state through the sequential binding of ATP to its three catalytic sites. All the intermediate structures of V/A-ATPase adopt the same asymmetric structure, whereas the three catalytic dimers adopt different conformations. This is significantly different from the initial activation process of FoF1, where the overall structure of the F1 domain changes during the transition from a pseudo-symmetric to a canonical asymmetric structure (PNAS NEXUS, pgac116, 2022). In conclusion, our findings provide dynamical information that will enhance the future prospects for studying the initial activation processes of the enzymes, which have unknown intermediate structures in their functional pathway.

Associations of genes of DNA repair systems with Parkinson’s disease

Background. Approximately 5–10 % of cases of Parkinson’s disease (PD) are monogenic, in other cases the pathology has a multifactorial etiology. One of recognized pathogenetic pathways of PD is mitochondrial dysfunction, in particular the accumulation of damage in mitochondrial DNA. Hence, the genes of DNA repair proteins are promising candidate genes for multifactorial forms of PD.The aim. To study the involvement of genes of DNA repair proteins in the development of Parkinson’s disease.Materials and methods. The associative analysis was carried out while comparing a group of patients with PD (n = 133) with a Tomsk population sample (n = 344). SNaPshot analysis was used to study 8 SNPs in genes of DNA repair proteins (rs560191 (TP53BP1); rs1805800 and rs709816 (NBN); rs473297 (MRE11A); rs1189037 and rs1801516 (ATM); rs1799977 (MLH1); rs1805321 (PMS2)).Results. Common alleles and homozygous rs1801516 genotypes in the ATM gene predispose the development of PD (odds ratio (OR) – 3.27 (p = 0.000004) and OR = 3.46 (p = 0.00008) for risk alleles and genotype respectively) and rs1799977 in the MLH1 gene (OR = 1.88 (p = 0.0004) and OR = 2.42 (p = 0.00007) respectively); heterozygotes have a protective effect (OR = 0.33 (p = 0.0007) and OR = 0.46 (p = 0.0007) for ATM and MLH1, respectively). The rare rs1805800 allele in the NBN gene (OR = 1.62 (p = 0.019)) and a homozygous genotype for it (OR = 2.28 (p = 0.016)) also predispose to PD. Associations with PD of the ATM, MLH1, NBN genes were revealed for the first time.Conclusion. Mitochondrial dysfunction is one of the key factors in the pathogenesis of PD, while at least two of the three protein products of associated genes are involved in the development of mitochondrial dysfunction. Accordingly, it can be assumed that associated genes are involved in the pathogenesis of PD precisely through mitochondrial dysfunction.