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River deltas are densely populated, ecologically vital landscapes threatened by rising sea levels. Distributary channel networks disperse sediment to build deltaic land, yet the relationship between the network organization and land building remains elusive. Inspired by Hack's law, which shows that watershed drainage area scales with channel length in tributary networks, we analyzed a global dataset of distributary networks and found a nearly identical scaling relationship between distributary channel length and nourishment area, the land-building counterpart to drainage area. Despite this apparent global scaling, we further identified two distinct local land-building patterns: uniform delta networks consistently follow Hack's law, whereas composite delta networks exhibit a scale break, transitioning from space-filling growth around the delta apex to quasi-linear growth near the coast. The unexpected growth patterns suggest that global simplicity and local variability coexist in how river deltas grow and organize.
Software bug leads to exposure of peer-review records for 10,000 papers.
Entangled atoms send data securely-neutralizing backdoor hardware threat.
Research has shown a robust inverse association between maximal aerobic capacity and muscular strength, and lifestyle related diseases and mortality. People with a substance use disorder have a higher prevalence of lifestyle-related diseases and a shorter life expectancy than the general population. There is a paucity in the literature of normative aerobic capacity and muscular strength variables in people with a substance use disorder. The main purpose of this study was to contribute to establish reference values on these key variables for this patient group, and to compare these data to normative values consisting of healthy age matched controls. A total of 179 men and women with diagnosed substance use disorder according to International Classification of Diseases-10 performed a maximal cardiopulmonary exercise test on a treadmill recording maximal oxygen uptake and maximal oxygen pulse, along with a muscular strength test in a hack squat machine assessing maximal leg strength. Patients with substance use disorder generally demonstrated lower- maximal oxygen uptake (⁓ 15%), maximal oxygen pulse (⁓ 10%) and muscular strength (⁓ 30%) across all age groups compared to comprehensive Norwegian and American reference materials of healthy age-matched populations. This could contribute to explain the higher prevalence of lifestyle related diseases and reduced longevity in this patient group.
An optogenetic split-GAL4 system, ShineGAL4, allows genes to be manipulated with unprecedented spatiotemporal precision. Here, we convert a panel of 14 GAL4 drivers widely used in Drosophila research into their ShineGAL4 counterparts. Homology assisted CRISPR knock-in (HACK) is used to replace GAL4 with the GAL4 DNA binding domain fused to a Magnet photoswitch. We show that the resulting ShineGAL4 drivers enable gene expression to be rapidly induced by light specifically in fat body, muscles, enterocytes, oenocytes, Malpighian tubules, neurons, neuroblast lineages, glial subtypes or in all glia. We also develop an optogenetic cassette for photoactivation of GAL4 in 'silent' FLP-out clones. This panel of optogenetic tools will enable precise spatiotemporal control of gene expression in a wide range of different Drosophila tissues and cell-types.
Restrictions on antibiotic growth promoters in poultry production have driven the search for safe, natural alternatives. Organic acids, herbal additives and spirulina are promising options due to their antimicrobial, antioxidant and growth-enhancing effects. The purpose of this experiment was to evaluate the effects of formic acid (FAc), herbal mixture (HMX) and spirulina powder (SPI) as potential antibiotic alternatives in broiler diets, specifically examining their impact on growth, carcass characteristics, blood biochemistry and intestinal microbial count. Six replicates of ten unsexed chicks per group comprised the eight experimental groups to which 480 one-day-old Ross 308 broiler chicks were randomly assigned. The treatments were as follows: T1 (control); T2 (0.5 g Colistin antibiotic/kg diet); T3 (2 cm3 FAc/kg diet); T4 (4 cm3 FAc/kg diet); T5 (2 g HMX/kg diet); T6 (3 g HMX/kg diet); T7 (0.5 g SPI/kg diet); and T8 (1 g SPI/kg diet). Significant differences were detected in daily body weight gain (DBWG) and live body weight (LBW), with the spirulina-treated groups (T7 and T8) showing the highest values. Also, significant influences on feed intake (FI), feed conversion ratio (FCR) and performance index (PI), with the HMX groups showing the most favourable FCR and the highest PI. Blood biochemistry and antioxidant markers were influenced by the HMX and SPI treatments. The SPI groups showed reduced liver enzyme levels, while the HMX groups demonstrated improved protein profiles and enhanced antioxidant enzyme activity. Microbial analysis revealed that FAc and HMX treatments led to a reduction in pathogenic bacteria, with T3, T4 and T5 showing the lowest levels of Escherichia coli and Salmonella. These results suggest that FAc, HMX and SPI are promising dietary supplements for enhancing both the broiler chickens' growth rates and general health.
To provide a state-of-the-art, otolaryngology-focused review of 22q11.2 deletion syndrome (22q11.2DS), emphasizing recent developments in the understanding of airway, hearing, velopharyngeal, sleep, and perioperative manifestations that directly influence contemporary ENT practice. PubMed, Scopus, and Cochrane Library were searched for English-language publications from January 2018 to September 2025. Additional data were identified through reference lists of key guidelines and landmark cohort studies. A narrative review approach was used to synthesize recent literature addressing the epidemiology, anatomy, diagnostic advances, and management of otologic, palatal, airway, sleep, swallowing, vascular, immune, and perioperative features of 22q11.2DS. Priority was given to studies published within the past 5 years, multicenter analyses, updated clinical practice guidelines, and investigations describing evolving surgical and diagnostic paradigms. Articles focusing solely on cardiac, endocrine, or psychiatric aspects were excluded unless directly relevant to otolaryngologic care. 22q11.2DS presents a uniquely high burden of ENT disease across the lifespan, including chronic otitis media, elevated cholesteatoma risk, persistent velopharyngeal dysfunction, multilevel airway anomalies, sleep-disordered breathing, dysphagia, and perioperative vulnerability due to vascular, immunologic, and hematologic anomalies. Emerging imaging techniques, updated pediatric and adult guidelines, and expanded genotype-phenotype data have reshaped diagnostic and surgical strategies. Otolaryngologists play a central role in lifelong care of individuals with 22q11.2DS. Structured surveillance, genotype-informed imaging, proactive sleep and airway assessment, and multidisciplinary perioperative planning are essential for improving outcomes. Standardized pathways and longitudinal, ENT-specific research are urgently needed to guide evidence-based management.
This study investigated the effects of supplementing broiler drinking water with Egyptian clover honey on growth performance, carcass characteristics, and blood biochemical parameters. A total of 525 one-day-old male Hubbard broilers were assigned to seven treatment groups to evaluate two concentrations of honey (13 and 26 mL L - 1 ) administered at three different frequencies (daily, every other day, and every 3 d), along with a control group receiving no honey. Supplementing drinking water with honey significantly enhanced overall broiler performance. Birds receiving honey, particularly at the higher concentration and at intermittent intervals, showed improved body weight gain and feed efficiency compared to the control group. The highest relative weights of key lymphoid organs - such as the spleen, bursa of Fabricius, and thymus - were observed in supplemented groups, indicating a positive impact on immune system development. Hematological analysis revealed increased red and white blood cell counts, hemoglobin, and packed cell volume in honey-fed birds, reflecting improved oxygen transport and immune competence. Serum biochemical profiles demonstrated a favorable shift, with significant reductions in markers of metabolic stress and liver function (uric acid, creatinine, cholesterol, triglycerides, and alanine aminotransferase (ALT)) and notable increases in total protein, albumin, and globulin levels. Additionally, honey supplementation significantly enhanced humoral immune response, as evidenced by higher hemagglutination inhibition titers against Newcastle disease virus. The results indicate that honey supplementation via drinking water, especially at 26 mL L - 1 , administered intermittently, can effectively improve growth performance, physiological health, and immune function in broiler chickens. These findings support the potential of honey as a natural antibiotic-free additive to promote sustainable poultry production.
The management of head and neck cancer relies on multidisciplinary expertise; however, access to tumor boards remains variable. Large language models (LLMs) may support guideline-based decision-making, although performance in complex oncologic scenarios is not well defined. Fourteen synthetic cases based on real tumor board encounters were evaluated. Five blinded comparator arms produced recommendations: a human expert, Non-RAG-GPT-4, Non-RAG-GPT-5, RAG-GPT-4, and RAG-GPT-5. Eight head and neck oncologic surgeons scored each recommendation for appropriateness, clarity, specificity, and feasibility using 5-point Likert scales. Paired permutation testing and inter-rater reliability were assessed. LLM outputs showed close alignment with expert recommendations. RAG-based models achieved the highest mean scores across domains, with some statistically significant differences versus the expert comparator in appropriateness and clarity; however, absolute differences were modest. Inter-rater reliability was strong (ICC 0.73-0.87). Advanced LLMs can generate guideline-concordant management recommendations in simulated head and neck cancer cases, supporting potential utility for decision support and education; prospective validation and expert oversight remain essential.
Hemangioblastomas (HGB) are the most common primary intra-axial tumors in the posterior fossa in adults, with an overall occurrence of 7-10%. They occur sporadically or as part of von Hippel-Lindau (VHL) disease. The role of stereotactic radiosurgery (SRS) as a minimally invasive treatment in larger HGB (>2cc) has not been thoroughly investigated. This multi-center study retrospectively analyzed data from 91 patients with large HGB (>2cc) treated between 1993 and 2023. Patients were stratified into VHL-associated and sporadic groups, with assessments including radiosurgical parameters, tumor response, overall survival (OS), and progression-free survival (PFS). Patients with VHL-associated HGB were younger at diagnosis (median: 33 years vs. 52 years, p < 0.001) and presented more frequently with multiple tumors (68.8% vs. 23.2%, p < 0.001). Cerebellar lesions were the most common location (70%), followed by brainstem lesions (21%). The median target tumor volume was smaller in VHL cases (3.49 cc vs. 6.5 cc, p = 0.038). Tumor control was achieved in 70% of cases across groups, with no significant differences in outcomes between VHL and sporadic cases. OS (170 months for VHL and 199 months for sporadic cases) and PFS (108 months for both groups) were comparable. Radiation necrosis was observed in 8.8% of patients. SRS may provide favorable tumor control with low morbidity in both VHL-associated and sporadic cases of larger HGB (>2 cc).Future studies should compare SRS with resection for larger HGB and explore molecular predictors of favorable response to SRS.
This study presents a detailed mechanistic investigation of the photocatalytic decomposition of different aldehydes via various Norrish reaction pathways and their subsequent role in the carbonylation of hydrocarbons, particularly toluene, using [Rh(PMe3)2(Cl)(CO)] as a catalyst. Utilizing 1H NMR spectroscopy, we quantitatively analysed the kinetics of the reaction network, focusing on the formation of key products such as alkanes and alkenes. The results reveal multiple well-explainable structure-property relationships for different aldehyde structures. In addition, the presence of [Rh(PMe3)2(Cl)(CO)] significantly suppresses the decomposition rates, suggesting intersystem crossing between photoactivated aldehydes and the Rh complex, potentially reducing the aldehyde's excited state lifetime. Furthermore, we explored the structural characterization of Rh-phosphine complexes formed during the reaction, though the exact structures remain elusive.
Enteroviruses (EVs) are a common cause of a wide spectrum of infectious diseases, ranging from mild respiratory illnesses to severe neurological conditions, particularly affecting children. Current molecular methods, such as 5'UTR-based PCR for detection and (partial) VP1 gene sequencing for typing, are widely utilized. However, Next-Generation Sequencing (NGS), and bioinformatics offer a comprehensive alternative, enabling full-genome analyses for improved virus characterization, genomic epidemiological surveillance, and outbreak investigation. Despite its advantages, implementation of NGS poses challenges, particularly in standardizing and optimizing laboratory workflows (wet-lab) and bioinformatics analyses (dry-lab), methods that are not often readily accessible in many laboratories. Here, we discuss the potential of NGS as a tool for EV detection/characterization in clinical virology, public health, and research settings. We provide practical options for actions for implementing NGS to advance the understanding and management of enterovirus infections. These recommendations are based on expert discussions during the recent European non-polio enterovirus network (ENPEN) workshop held in Corfu, Greece, on 23-24 May 2024, aiming to guide harmonization of NGS practices across clinical, public health, and research settings.
Cognitive training has arisen in the last several years as an approach to leveraging neuroplasticity toward the goals of improving cognitive performance and psychological well-being. The purpose of this review is to evaluate the potential for cognitive training to serve as a means of preventing maladaptive behaviors, particularly substance use disorder and suicidal thoughts and behaviors in a military population. We identified the outcomes of peer-reviewed, published randomized controlled trials (RCTs) using 2 common and well-validated approaches to cognitive training: SMART (and its online adaptation, SMART+) and BrainHQ. We also reviewed recent data from deploying SMART+ and BrainHQ within the National Guard, thus supplementing historical RCTs data with recent data collected in a military population. Finally, we conducted a literature review to determine whether there is evidence that the benefits of cognitive training have a documented relationship to risk of substance use and suicide. We observed 3 pathways by which cognitive training appears to reduce the risk of maladaptive behaviors: (1) improved higher order cognitive functions; (2) reduced symptoms of psychological distress; and (3) improved social connectedness. Maladaptive behaviors arise in response to a complex, highly individuated set of psychosocial and situational conditions. Prevention of maladaptive behaviors is, therefore, likely to require a wide variety of interventions. Based upon this literature review, there is a compelling case for cognitive training to be among these interventions. Not only does cognitive training bolster protective factors such as emotional regulation, problem-solving, and psychological well-being, but it reduces risk factors such as social isolation and impaired social skills. Furthermore, because cognitive training is beneficial to healthy (ie, nonclinical) populations, it can be appropriately framed as a tool to improve brain fitness, rather as a "mental health" intervention, the latter of which may be met with some resistance in military populations. Based upon this literature review, we recommend prospective research be conducted to further quantify the relationship between cognitive training and primary prevention of maladaptive behaviors in a military population.
This review explores the potential of microalgae as a sustainable feed ingredient for shrimp cultivation. Microalgae, used as nutritional supplements, offer several advantages as protein sources, including rich nutrient profiles and bioactive compounds. As shrimp production in the aquaculture sector grows and infectious diseases become more prevalent, microalgae can serve as a safe feed additive and an alternative to antibiotic overuse. This report reviews the prominent microalgae species used as feed ingredients for shrimp, examining their nutritional value, as they are widely utilized in the aquaculture industry. The focus is on the potential of microalgae as a substitute for fishmeal and fish oil in shrimp feed within a circular bioeconomic approach. Additionally, it examines how the inclusion of dietary microalgae influences shrimp growth performance, feed conversion efficiency, antioxidant activity, immune response, and disease resistance. The review also emphasizes the use of microalgae to improve water quality in shrimp culture systems. Furthermore, it aims to demonstrate effective methods of delivering vaccines to shrimp via transgenic microalgae, especially through oral vaccination, to combat pathogens. Overall, this comprehensive review provides an overview of current applications and prospects of microalgae as a sustainable feed ingredient to enhance shrimp aquaculture productivity and sustainability.
Mutations in PIK3CA are one of several actionable mutations for patients with hormone receptor positive, human epidermal growth factor receptor 2 negative breast cancer. Alpelisib in combination with fulvestrant was the first approved PI3K inhibitor and was introduced in clinical practice in 2019. A lack of evidence for the use of alpelisib in the context of current treatment options like cyclin-dependent 4/6 inhibitor (CDK4/6i), highlights the importance of this analysis. We provide a real-world analysis of the use of alpelisib with the prospective German PRAEGNANT registry (NCT02338167). 57 patients with advanced breast cancer receiving alpelisib and fulvestrant were identified. 55 Patients had received prior CDK4/6i therapy. Progression-free survival (PFS) and overall survival (OS) were calculated for all patients, and stratified according CDK4/6i pre-treatment, using the Kaplan-Meier method. Subgroups (age, line of therapy, concomitant disease among others), somatic PIK3CA mutations, reasons for discontinuation and adverse events (AEs) were analyzed. The median PFS was 5.0 (95% confidence interval [CI], 3.1-9.4) months, and the median OS was 20.1 (95% CI, 14.6-30.8) months. Line of therapy and concomitant diseases appeared to affect PFS, while the line of therapy and preexisting diabetes influenced OS. However, subgroups were too small for statistical testing. Discontinuation was mainly due to tumor progression (56.1%). Hyperglycemia, rash and diarrhea were the most documented AEs. This prospective real-world analysis shows slightly shorter median PFS and OS times compared with the pivotal trials. Patients in our analyses received alpelisib in later therapy lines, which may explain the poorer outcome.
Rising global temperatures, compounded by diminishing water resources, have escalated the incidence and severity of heat stress in poultry production, posing a critical threat to animal welfare, productivity, and food security. Heat stress represents a multifactorial physiological challenge, disrupting the thermo-immuno-endocrine axis and thereby impairing hypothalamic thermoregulation, suppressing immune responses, and altering endocrine signaling pathways. Such imbalances contribute to reduced feed intake, compromised growth and reproductive performance, elevated mortality rates, and heightened disease susceptibility. Central to this response is the hypothalamus, particularly the preoptic area and the hypothalamic-pituitary-adrenal axis, which integrates environmental and internal stress cues to regulate corticosterone release, thyroid hormone activity, and immunological cascades. This review consolidates current evidence on the pathophysiological impacts of heat stress on poultry, with emphasis on oxidative stress, cytokine imbalance, and lymphoid tissue degeneration. It also explores pharmacological strategies for heat stress mitigation e.g., nonsteroidal anti-inflammatory drugs (NSAIDs), antioxidant supplementation (vitamins C, E, selenium), and bioactive plant-derived compounds (e.g., ashwagandha, betaine, resveratrol, curcumin). These interventions demonstrate potential in restoring cellular homeostasis, modulating endocrine activity, and enhancing immune resilience; however, their efficacy is contingent upon dosage, duration, and production context. Moreover, concerns remain regarding drug residues, side effects, and variability in responses across poultry strains. In parallel, the integration of precision livestock and poultry farming tools-such as sensor-based monitoring, automated ventilation, and real-time climate control-emerges as a complementary approach, enabling proactive management of thermal loads. Collectively, the convergence of pharmacological, nutritional, and technological strategies provides a multifaceted framework to mitigate heat stress and improve poultry resilience under climate change. Nevertheless, further longitudinal and field-based studies are required to elucidate mechanistic interactions, validate interventions under commercial conditions, and align practices with sustainability and food safety goals.
For the first time, an S3 guideline on complementary medicine in oncology was published in 2021, 2024 in May version 2.0 was published. The broad spectrum of complementary and integrative medicine was presented at the highest level of evidence, the respective established interventions were comprehensively addressed, and recommendations were made in the case of sufficient data availability. The guideline also contains a questionnaire for a risk-adapted evaluation of utilized CIM (complementary and integrative medicine) interventions. In this article, the clinical validation of this questionnaire from the guideline is carried out, as well as a descriptive analysis of utilization of CIM interventions in a cohort with gynecologial cancer. The present study is a cross-sectional study conducted at the Women's Hospital of the University Hospital Erlangen. In a first stage, rolled out from January to February 2022, fifty patients completed the questionnaire for the structured assessment of the use of complementary medicine from the S3 guideline "Complementary Medicine in Oncology", as well as a validation questionnaire. The latter included the comprehensibility of the questions, the time taken to complete them, as well as any problems encountered and suggestions for improvement. After successful validation of the questionnaire, in the second phase, patients with gynecologic cancer were invited to participate in the survey.The patient population was characterized by descriptive analyses of age, educational level, lifestyle factors such as dietary habits and physical activity, as well as tumor characteristics and treatment. In addition, the frequency of complaints and the utilization of complementary interventions and procedures, classified according to their risk of interactions, were analyzed. Validation showed that forty-five out of fifty (90%) patients felt that the questionnaire was clear to understand. Forty-seven (94%) of respondents indicated that the time taken to answer the questions was reasonable. In figures, 42% needed less than five minutes and 48% less than ten minutes.When looking at the utilization of CIM in patients with gynecological tumors, most participants were suffering from ovarian cancer (n = 61, 41.8%), followed by endometrial cancer (n = 33, 22.6%), cervical cancer (n = 32, 21.9%) and vulvar cancer (n = 20, 13.7%). In total, the utilization of a CIM intervention was described 267 times. According to the traffic light classification system in the guideline questionnaire the interventions of the green category (low risk for interaction) (n = 124, 46.4%) was the most commonly used. Therapies in the yellow category were used slightly less frequently (n = 93, 34.8%). CIM interventions of the red category were mentioned 50 times (18.7%). To date, there has been a lack of standardized surveys that explicitly include CIM.The questionnaire published in the S3 guideline is well understandable and concise. It can therefore be used in a structured way not only in research, but also in everyday clinical practice to avoid interactions and increase patients' safety. However, further training of oncologists is required regarding the application of the interventions mentioned in the questionnaire. Erstmals wurde 2021 eine S3-Leitlinie zur Komplementärmedizin in der Onkologie veröffentlicht, 2024 im Mai folgte die Version 2.0. Das breite Spektrum der Komplementär- und Integrativmedizin wurde auf höchstem Evidenzniveau dargestellt, die jeweiligen etablierten Interventionen wurden umfassend behandelt und bei ausreichender Datenverfügbarkeit wurden Empfehlungen ausgesprochen. Die Leitlinie enthält auch einen Fragebogen zur risikobezogenen Bewertung der eingesetzten CIM-Interventionen (komplementäre und integrative Medizin). In diesem Artikel wird die klinische Validierung dieses Fragebogens aus der Leitlinie durchgeführt sowie eine deskriptive Analyse der Nutzung von CIM-Interventionen in einer Kohorte mit gynäkologischen Krebserkrankungen. Die vorliegende Studie ist eine Querschnittsstudie, die an der Frauenklinik des Universitätsklinikums Erlangen durchgeführt wurde. In einer ersten Phase, die von Januar bis Februar 2022 lief, füllten 50 Patientinnen den Fragebogen zur strukturierten Bewertung der Nutzung komplementärmedizinischer Verfahren aus der S3-Leitlinie „Komplementärmedizin in der Onkologie“ sowie einen Validierungsfragebogen aus. Letzterer umfasste die Verständlichkeit der Fragen, die für das Ausfüllen benötigte Zeit sowie eventuell aufgetretene Probleme und Verbesserungsvorschläge. Nach erfolgreicher Validierung des Fragebogens wurden in der zweiten Phase Patientinnen mit gynäkologischen Krebserkrankungen zur Teilnahme an der Umfrage eingeladen. Die Patientenpopulation wurde anhand deskriptiver Analysen zu Alter, Bildungsniveau, Lebensstilfaktoren wie Ernährungsgewohnheiten und körperlicher Aktivität sowie Tumoreigenschaften und Behandlung charakterisiert. Darüber hinaus wurden die Häufigkeit von Beschwerden und die Inanspruchnahme komplementärer Interventionen und Verfahren, klassifiziert nach ihrem Interaktionsrisiko, analysiert. Die Validierung ergab, dass 45 von 50 (90%) Patientinnen den Fragebogen als klar verständlich empfanden. 47 (94%) der Befragten gaben an, dass die Beantwortung der Fragen einen angemessenen Zeitaufwand erforderte. In Zahlen ausgedrückt benötigten 42% weniger als 5 Minuten und 48% weniger als 10 Minuten. Bei der Betrachtung der Anwendung von CIM bei Patientinnen mit gynäkologischen Tumoren litten die meisten Teilnehmerinnen an Ovarialkarzinom (n = 61, 41,8%), gefolgt von Endometriumkarzinom (n = 33, 22,6%), Zervixkarzinom (n = 32, 21,9%) und Vulvakarzinom (n = 20, 13,7%) . Insgesamt wurde die Anwendung einer CIM-Intervention 267-mal beschrieben. Gemäß dem Ampelsystem im Leitfaden-Fragebogen wurden die Interventionen der grünen Kategorie (geringes Interaktionsrisiko) (n = 124, 46,4%) am häufigsten angewendet. Therapien der gelben Kategorie wurden etwas seltener angewendet (n = 93, 34,8%). CIM-Interventionen der roten Kategorie wurden 50-mal (18,7%) erwähnt. Bislang gab es keinen standardisierten Fragebogen, der explizit CIM berücksichtigt. Der in der S3-Leitlinie veröffentlichte Fragebogen ist gut verständlich und prägnant. Er kann daher nicht nur in der Forschung, sondern auch in der täglichen klinischen Praxis strukturiert eingesetzt werden, um Wechselwirkungen zu vermeiden und die Sicherheit der Patienten zu erhöhen. Allerdings ist eine weitere Schulung der Onkologen hinsichtlich der Anwendung der im Fragebogen genannten Interventionen erforderlich.
Microbiology researchers rely on nucleic acid measurement techniques, such as the quantitative polymerase chain reaction (qPCR) and DNA sequencing, to address diverse scientific and practical challenges. These applications range from detecting microbial contaminants in regenerative medicine and biotherapeutic products to advancing waste remediation, pathogen detection, biosurveillance, and microbiome studies. A critical step in these techniques is DNA extraction, which involves breaking cells to release their DNA as the required input for downstream analyses. The efficiency of this process, known as DNA extraction efficiency (DEE), directly impacts the accuracy of quantitative measurements and, therefore, the interpretation of results. Unfortunately, most DNA extraction methods suffer from suboptimal efficiency that varies across microbial strains, potentially leading to inaccurate results. In this paper, we present a highly efficient DNA extraction protocol leveraging adaptive focused acoustics (AFA) technology to achieve a balance between cell lysis and DNA integrity. Using Escherichia coli as the model organism, the protocol delivers nearly 100% DEE, setting a benchmark for performance. A key innovation in this protocol is the integration of focused ultrasonication, droplet digital polymerase chain reaction (ddPCR), and flow cytometry to estimate genome copies and the corrected DNA extraction efficiency (cDEE), which accounts for the number of genome copies. The proposed protocol addresses the need for an accurate assessment of DEE and DNA quantification, as demonstrated here with E. coli, for various DNA-based techniques, including metagenomic analysis of complex microbial communities and the development of new DNA extraction protocols. This novel protocol addresses a longstanding limitation in microbiological research and has the potential to significantly enhance accuracy and reproducibility across various applications. While there is significant potential for applying this approach, the authors acknowledge that further studies using microorganisms with thicker cell walls will enhance the utility of this framework. However, the knowledge generated in this study can be readily applied and tailored to the specific objectives of individual research groups.
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