bluuebunny/crossref_metadata_2025 huggingface dataset:
Mastering the Sequential Organ Failure Assessment Score: Critical Choices of Score Statistic, Timing, Imputations, and Competing Risk Handling in Major Trials—A Systematic Review
Authors: Marmiere Marilena , D’Amico Filippo , Monti Giacomo , Landoni Giovanni
Published: December 2024

Objectives:

The Sequential Organ Failure Assessment (SOFA) score originated as a tool for assessing organ dysfunction in critical illness but has expanded to become an outcome measure in clinical trials. We aimed to assess how the SOFA score was used as the primary or secondary endpoint of major randomized controlled trials (RCTs).

Data Sources:

Independent reviewers searched MEDLINE/PubMed, Scopus, and Embase databases.

Study Selection:

Articles were selected when they fulfilled: 1) RCT; 2) SOFA score was primary or secondary endpoint; and 3) published in the Lancet, New England Journal of Medicine, or Journal of the American Medical Association.

Data Extraction:

Data collection included study details, outcomes, statistical differences in SOFA score, choice of score statistics, timepoints of SOFA reporting, and how missing data and competing risks analysis were managed.

Data Synthesis:

Twenty-three RCTs had SOFA score as outcome measure, eight used it as primary endpoint. Daily maximum SOFA was the key statistic in 11 RCTs, delta SOFA was used in eight, and mean SOFA in four. Mean SOFA was most frequently chosen as primary endpoint (4/8, 50%). There were 18 different outcome assessment timepoints, ranging from 1 to 28 days. Three RCTs reported statistically significant difference in SOFA between groups. Handling of missing SOFA scores was not described in ten of 23 RCTs. When described, it varied from study to study with variable imputation methods and variable accounting for the competing risk of mortality and ICU discharge.

Conclusions:

There is major variability in the choice of summary statistic for SOFA score analysis and assessment timepoints, when using it as outcome measure in RCTs. There was either no information or great variability in the handling of missing values, use of imputation, and accounting for competing risk. The current use of SOFA scores in RCTs lacks sufficient reproducibility and statistical and methodological robustness.
Hepatic real-world outcomes with obeticholic acid in primary biliary cholangitis (HEROES): A trial emulation study design
Authors: Brookhart M. Alan , Mayne Tracy J. , Coombs Charles , Breskin Alexander , Ness Erik , Bessonova Leona , Chu Yucheng Julia , Li Jing , Fried Michael W. , Hansen Bettina E. , Kowdley Kris V. , Jones David , Mells George , Trivedi Palak J. , Hiu Shaun , Kareithi Dorcas N. , Wason James , Smith Rachel , Seeger John D. , Hirschfield Gideon M.
Published: December 2024

Background and Aims:

Primary biliary cholangitis is a rare, progressive liver disease. Obeticholic acid (OCA) received accelerated approval for treating patients with primary biliary cholangitis in whom ursodeoxycholic acid failed, based on a surrogate endpoint of reduction in ALP. Analysis of the long-term safety extension with 2 external control groups demonstrated a significant increase in event-free survival in OCA-treated patients. This fully real-world evidence study assessed the effect of OCA treatment on clinical outcomes.

Approach and Results:

This trial emulation used data from the Komodo Healthcare Map claims database linked to US national laboratory, transplant, and death databases. Patients with compensated primary biliary cholangitis and intolerance/inadequate response to ursodeoxycholic acid who initiated OCA therapy were compared with patients who were OCA-eligible but not OCA-treated. The primary endpoint was time to the first occurrence of death, liver transplant, or hospitalization for hepatic decompensation, analyzed using a propensity-score weighted Cox proportional hazards model. Baseline prognostic factors were balanced using standardized morbidity ratio weighting. For the primary analysis, 4174 patients contributed 11,246 control index dates, and 403 patients contributed OCA indexes. Weighted groups were well balanced. Median (95% CI) follow-up in the OCA and non-OCA arms was 9.3 (8.4–10.6) months and 17.5 (16.2–18.6) months (weighted population; censored at discontinuation). Eight events occurred in the OCA arm and 32 in the weighted control (HR = 0.37; 95% CI = 0.14–0.75; p < 0.001). Effects were consistent for each component of the composite endpoint.

Conclusions:

We identified a 63% reduced risk of hospitalization for hepatic decompensation, liver transplant, or death in OCA-treated versus non–OCA-treated individuals.

Trial Registration:

HEROES; ClinicalTrials.gov NCT05292872.
Tissue Glue-Assisted Plaque Radiotherapy for Choroidal Tumors with Scleral Thinning
Authors: Shields Carol L. , Suribhatla Rhea , Romero Mark , Ealer Christin , Bansal Rolika , Emrich Jacqueline , Komarnicky-Kocher Lydia , Lally Sara E.
Published: December 2024

Purpose:

To evaluate tissue glue-assisted plaque placement regarding accuracy, stability, and longer-term outcomes for choroidal tumors with scleral thinning.

Methods:

All patients with tissue glue-assisted plaque radiotherapy at a single ocular oncology center were evaluated for patient demographics, tumor features, surgical details, tumor response, and glue-related complications.

Results:

There were 13 patients (mean age 72 years) treated with tissue glue-assisted plaque radiotherapy for choroidal melanoma (n=12) or choroidal metastasis (n=1). At presentation, the tumor was mean 4.3 mm to the optic disc and 2.0 mm to the foveola with mean basal diameter of 9.5 mm and thickness of 4.2 mm. In all cases, the tissue glue-assistance was employed due to extreme scleral thinning in the bed of proposed radiation. The plaque size was 15 mm (n=5), 18 mm (n=7), or 20 mm (n=1). At application, there was no immediate glue hypersensitivity, ultrasonography confirmed accuracy of placement, and the glue remained adherent for the entire treatment duration (mean 113 hours) with stable plaque location at removal. At removal, the plaque-glue composite was peeled off the globe without need for glue dissolvent and without scleral disruption. At 12 months mean melanoma thickness (2.7 mm, regression 36%). There were no conjunctival, corneal, or scleral complications.

Conclusion:

Tissue glue-assisted plaque radiotherapy is safe and effective for treatment of choroidal tumors with thin sclera.
Experience of Orofacial Injuries and Use of Mouthguards — A Survey in German Elite Sport
Authors: Merle Cordula Leonie , Rott Theresa Antonia , Rauch Angelika , Wolfarth Bernd , Wüstenfeld Jan , Haak Rainer , Schmalz Gerhard , Ziebolz Dirk
Published: December 2024

Objective:

This study aimed to assess the experience of orofacial injuries and sports mouthguard use in German elite athletes.

Design:

A questionnaire-based cross-sectional study was conducted.

Setting:

The data were collected at the Institute of Applied Training Science (IAT, Leipzig, Germany) that provides regular primary care for elite athletes.

Participants:

German elite athletes (18-35 years) from different disciplines with completed questionnaire on oral health in sports between May 2020 and April 2021 were included.

Interventions:

N/A.

Main Outcome Measures:

Number of dental, oral, and facial injuries during sports career and mouthguard use (received information, ownership, frequency) were assessed and compared between disciplines with different risks for orofacial trauma.

Results:

In total, questionnaires of 337 athletes (23 ± 4 years, 50% female) were included. Disciplines were classified into high (HT, n = 20), medium (MT, n = 48), and low (LT, n = 269) risk for orofacial trauma. Substantial rates of injuries were identified; especially a lot of HT athletes reported orofacial injuries (HT: 55%, MT: 31%, LT: 17%; P ≤ 0.076) and dental injuries (HT: 30%, MT: 10%, LT: 7%; P ≤ 0.028). Mouthguards were rare (HT: 25%, MT: 0%, LT: 3%).

Conclusions:

There is a need for more prevention of orofacial injuries in German elite sports for both HT and MT.
The push to infuse mental health education across advanced nursing curricula
Authors: Roche Rosa M. , Hidalgo Ivette , Graña Antonella , Brenes Francisco
Published: December 2024

Research indicates that knowledge gaps and unfavorable attitudes among primary care advanced practice registered nurses (APRNs) are linked to stigma surrounding psychiatric care, affecting the management of patients experiencing mental illness. Despite standards of practice and educational guidelines set forth by professional nursing organizations to increase quality of care, challenges exist when delivering care to patients with mental health disorders. Lack of integration of mental health education throughout graduate nursing courses contributes to an underestimation of its significance and applicability within advanced practice nursing in primary care. Advancing mental health education across primary care APRN curricula promotes access to psychiatric care, reduces disparities, and enhances health outcomes in the United States. Such practices increase competence and skills for primary care APRNs in the care of patients with mental health illness. This cultivates an advanced practice nursing workforce prepared to meet the evolving needs of diverse patients across the lifespan. Primary care APRNs offer a combination of clinical knowledge, holistic approach to care, and a strong focus on patient advocacy; therefore, we feel that enhancing primary care APRNs' knowledge in mental health may lead to decreased health care costs, increased access to psychiatric care, and decreased need for emergency mental health services.
Bridge to Heart Transplant With Temporary Mechanical Circulatory Support: Trends and Outcomes in the 2018 Allocation Policy Era
Authors: Dorken-Gallastegi Ander , Hong Yeahwa , Hess Nicholas R. , Ziegler Luke A. , Abdullah Mohamed , Iyanna Nidhi , Ramanan Raj , Hickey Gavin W. , Keebler Mary E. , Kaczorowski David J.
Published: December 2024

The United Network for Organ Sharing (UNOS) 2018 heart allocation policy prioritizes patients receiving temporary mechanical circulatory support (tMCS) given the high waitlist mortality rate of this group. This study evaluates national trends and waitlist outcomes for patients receiving tMCS under the UNOS 2018 allocation policy. Adult patients waitlisted for isolated heart transplantation were included using the UNOS database. The prevalence of tMCS, 90 day waitlist mortality, 90 day incidence of transplantation, and posttransplant 1 year mortality were analyzed. A total of 27,343 patients were waitlisted during the study period (pre-policy change: 13,004 vs. post-policy change: 14,339). The prevalence of tMCS increased from 7.4% (n: 956) to 22.4% (n: 3,186) after the policy change (p < 0.001). The use of Impella increased proportionally among tMCS modalities. Patients on tMCS had lower adjusted odds of waitlist mortality (p < 0.001), higher adjusted incidence of transplantation (p < 0.001), and similar posttransplant mortality (p = 0.10) under the 2018 policy. Patients on extracorporeal membrane oxygenation (ECMO) support had the highest odds of 90 day waitlist mortality (p < 0.05) but also the highest incidence of transplantation in the post-policy change cohort (p < 0.05). In conclusion, the use of tMCS as bridge to heart transplantation increased threefolds and is associated with lower waitlist mortality and higher incidence of transplantation following the UNOS 2018 allocation policy change.
Systematic Review and Meta-Analysis: Role of Proton Pump Inhibitors in Prevention of Upper Gastrointestinal Bleeding in Patients on Dual Antiplatelet Therapy
Authors: Saeed Aamir , Haider Marjan , Yousuf Saira , Ahmad Soban , Fine Michael , Yazdani Ali , Hayat Umar , Noverati Nicholas , Khan Muhammad Ali , Gangwani Manesh Kumar , Aziz Muhammad , Farooq Umer , Kamal Faisal
Published: December 2024

Background:

Dual antiplatelet therapy (DAPT) with oral P2Y12 inhibitors and aspirin is crucial for patients with acute coronary syndrome (ACS) and postpercutaneous coronary interventions (PCI). Concomitant proton pump inhibitor (PPI) therapy with DAPT can potentially reduce the risk of upper gastrointestinal bleeding (UGIB)

Aim:

We conducted a meta-analysis of randomized controlled trials to evaluate the prevention of UGIB with concomitant use of PPI with DAPT.

Methods:

We reviewed several databases to identify randomized controlled trials comparing the risk of UGIB in patients using DAPT + PPI vs. DAPT with no PPI or DAPT + Histamine 2 receptor antagonists. Our outcomes of interest were UGIB, major cardiovascular adverse events (MACE), myocardial infarction, and all-cause mortality. We calculated pooled risk ratio (RR) with 95% confidence intervals (CI) for all of the outcomes and analyzed data using random effect model. Heterogeneity was assessed using I2 statistic

Results:

Seven randomized controlled trials comprising 6708 patients were included. Rate of UGIB was significantly lower in the PPI + DAPT group, RR (95% CI): 0.39 (0.25–0.60). There was no significant difference in the rate of MACE between groups, RR (95% CI): 0.87 (0.69–1.10). Rate of MI was also not significantly different between groups, RR (95% CI): 0.93 (0.75–1.14). Rate of mortality was significantly lower in the PPI + DAPT group, RR (95% CI) 0.46 (0.27–0.80)

Conclusions:

Our meta-analysis demonstrates that adding PPI therapy to DAPT significantly lowers the risk of UGIB and all-cause mortality, without adversely affecting major cardiovascular outcomes.
Perioperative Nursing Management of Patients With Rheumatoid Arthritis Undergoing Total Joint Arthroplasty
Authors: Campbell Eileen , Schultz Jeanette
Published: December 2024

Rheumatoid arthritis (RA) is a chronic autoimmune disorder that causes joint inflammation, pain, and potential disability. Patients with RA have unique needs when undergoing total joint arthroplasty (TJA). Careful and comprehensive evaluation and management includes physical assessment, patient history, and knowledge about the medication regimen in the setting of elective TJA. Nursing care is critical to patients with RA in the perioperative period. Nursing interventions can improve patient outcomes and reduce potential risks related to the RA and the surgical procedure. Registered nurses must be knowledgeable about the pathophysiology and pharmacological management of patients with RA to provide appropriate nursing care.
Mind–Body Interventions Impact Patient Anxiety Levels After Total Knee Arthroplasty (TKA)
Authors: Vizyak Karen , Davila Lisa R. , Woods Nicole , Brou Lina
Published: December 2024

Background: Orthopedic surgery can trigger anxiety that negatively impacts patient experience and recovery. Purpose: This pilot study investigated if a compassionate interaction combined with standardized mind–body techniques could reduce patient anxiety levels during the initial postoperative phase for patients undergoing a total knee arthroplasty (TKA). Methods: Participants were 36 postsurgical hospital inpatients guided through a 10-minute mind–body breathing and visualization intervention on post-op day zero (POD 0) and on post-op day one (POD 1). Quantitative data included before and after Visual Analogue Scale for Anxiety (VAS-A) reports, heart rate values, and pulse oximetry readings. Results: Significant decreases in VAS-A and heart rate values as well as increases in pulse oximetry values were demonstrated on both POD 0 and POD 1. Conclusion: These results indicate that a brief mind–body intervention can reduce reported anxiety levels and induce physiologic benefits for hospitalized patients post-TKA and suggest the possibility that such interventions could reduce anxiety in a broader patient population.
Caregiver Perspectives on Provider Continuity During Prolonged PICU Hospitalizations: A Single-Center Qualitative Study, 2021–2022
Authors: Jiménez Patricia Peña , Phipps Wendy Leatherman , Jacob-Files Elizabeth , Lindo Elizabeth , Rakes Lauren C. , Roberts Joan S. , Clark Jonna D. , Berkman Emily R. , Nielsen Katie R.
Published: December 2024

OBJECTIVES:

To improve continuity of care, some PICUs assign a continuity attending (CA) physician for children with prolonged hospitalizations. Little is known about how this intervention impacts familial caregivers’ experiences. The objective of this study was to provide in-depth descriptions of family perspectives about continuity of care during prolonged PICU hospitalizations for children with and without a PICU CA.

DESIGN:

Qualitative semi-structured interviews.

SETTING:

Single center cohort, from October 2021 to December 2022, at an academic PICU in the United States.

PARTICIPANTS:

Familial caregivers (n = 39) of critically ill children hospitalized in the PICU for greater than or equal to 14 days were purposively sampled, stratified by group: 18 with a PICU CA and 21 without a PICU CA.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

Semi-structured interviews were audio recorded, transcribed, coded, and analyzed in the context of the continuity of care model using a realist thematic approach. Familial caregivers described six themes related to relational, informational, and management continuity: 1) familiar providers who demonstrate empathy for the child improve family members’ comfort and trust (Relational); 2) providers who know and use a child’s baseline health status to inform clinical decision-making alleviate family members’ stress (Relational, Management); 3) information loss during care team transitions frustrates families (Informational, Management); 4) known providers enhance caregiver communication (Informational); 5) familiar providers who value a family’s expertise about their child’s care (Relational, Management); and 6) take responsibility for the child’s long-term care plan (Management) decrease parental stress.

CONCLUSIONS:

As PICU patient medical complexity and length of stay increase, familial caregivers’ needs transition from understanding day-to-day management to navigating care team transitions and partnering with providers to develop long-term care plans. Targeted interventions to increase provider continuity that consider relational, informational, and management continuity are needed to optimize patient outcomes and family experiences.
Developing a Practice-Driven Taxonomy of Implementation Strategies for HIV Prevention
Authors: Golub Sarit A. , Wolfer Carly , Beacham Alexa , Lane Benjamin V. , Chastain Cody A. , Meyers Kathrine A.
Published: December 2024

Background:

Effective implementation of evidence-based HIV prevention interventions continues to be a challenge in the United States, and the field is increasingly turning to implementation science for solutions. As such, it is critical to expand the current implementation science vocabulary—and its taxonomy of implementation strategies—to increase its relevance and utility for front-line implementers.

Setting:

Community-based health centers providing HIV prevention services in the southeastern United States.

Methods:

We conducted a collective case-study analysis, combining document review and qualitative interviews with program directors, clinicians, and other providers (N = 30) at 5 sites. We used an inductive and iterative analytic approach to specify and categorize strategies, and then conducted in-depth cross-case analysis to derive a practice-driven taxonomy of HIV prevention implementation strategies.

Results:

From an initial matrix of 264 activities, we identified 50 strategies common across sites. In contrast to existing implementation science frameworks, most (68%, n = 34) strategies were designed to affect implementation outcomes (eg, acceptability, adoption, feasibility) for patients. We present a practice-driven taxonomy of these strategies, operationalized according to implementation science literature, but with terminology that more directly relates to implementers.

Conclusions:

Findings demonstrate the feasibility and utility of this method for developing a practice-driven implementation science vocabulary for HIV prevention. Our evidence-based taxonomy provides a framework for implementers seeking data about the universe of strategies they might consider for their own programs, and increases researchers' ability to measure and evaluate the effectiveness of implementation strategies being enacted in practice settings.
A Novel Approach to Aplasia Cutis Congenita With PolyNovo BTM
Authors: Pollock Michaela , Leung Rachael , Low Nelson CK
Published: December 2024

Aplasia cutis congenita (ACC) is a rare congenital condition characterized by the absence of skin and subcutaneous tissue, typically affecting the scalp. This case report presents a female infant born at 38+3 weeks with a posterior midline scalp defect measuring 15×12.5 mm, involving skin, subcutaneous tissue, and calvarium. The defect was managed with NovoSorb Biodegradable Temporising Matrix (BTM). Initially, the plan involved a subsequent skin graft; however, the defect epithelized without grafting. By 2 months, the wound had healed completely, and by 6 months, the underlying bone had ossified. ACC presents with significant variability, and management strategies range from conservative treatment to surgical intervention depending on defect size. This case demonstrates the successful use of a fully synthetic dermal substitute in managing full-thickness scalp defects, providing a novel, effective option for treating ACC without requiring grafting.
Multidisciplinary Approach to Smile Design of a Patient With Osteogenesis Imperfecta With Clear Aligners and Prosthetic Restorations
Authors: Albayrak Elif , Buyukcavus Muhammed Hilmi , Başağaoğlu Demirekin Zeynep
Published: December 2024

Osteogenesis imperfecta (OI) is an autosomal dominant disease that affects the teeth and the musculoskeletal system. Orthodontic treatment in OI patients may be risky due to the fragility of dental hard tissues. Clear aligners may be considered a suitable orthodontic treatment method for these patients. A 30-year-old female OI patient with Angle Class I malocclusion, open bite, and crowding underwent prosthetic treatment after 15 months of clear aligner orthodontic treatment. Aesthetic rehabilitation was achieved with clear aligner treatment and prosthetic restorations. It is possible to obtain more aesthetic results with orthodontic treatments before prosthetic restorations in the oral rehabilitation of patients with skeletal and dental malocclusions. In orthodontic treatments in adult patients with systemic diseases, the use of clear aligners both minimizes the risk and provides a more comfortable process.
Applying nutritional ecology to optimize diets of crickets raised for food and feed
Authors: Muzzatti Matthew J. , Harrison Sarah J. , McColville Emily R. , Brittain Caelyn T. , Brzezinski Hunter , Manivannan Sujitha , Stabile Cassandra C. , MacMillan Heath A. , Bertram Susan M.
Published: December 2024

Increasing yield is a primary goal of mass insect rearing for food and feed, and diet impacts insect life-history traits that affect yield, such as survival, development time and body size. However, experiments rarely test the nutritional requirements of insects from hatch to adulthood, and so little is known about how the full developmental macronutrient intake impacts the survival, growth and adult body size of mass-reared insects. Here, we applied the nutritional geometry framework and reared individual tropical house crickets (
Gryllodes sigillatus
) from hatch to adulthood on a wide range of protein : carbohydrate diets. We measured weekly food consumption, survival, development time to adulthood and adult body size and mass, and calculated a yield metric to extrapolate our individual-level results and predict how diet influences yield at the mass-rearing level. Yield was maximized on a 3
P
: 1
C
diet, as crickets fed this diet were most likely to develop into adults and grew maximum mass and body size. When provided with a choice between diets, crickets selected a relatively balanced 1.05
P
: 1
C
diet throughout development, but males consumed 17% more protein than females. Our results represent a crucial first step towards determining the optimal standard feed formulation required to maximize cricket farming yield.
Barycentric and pairwise Rényi quantum leakage with application to privacy-utility trade-off
Authors: Farokhi Farhad
Published: December 2024

Barycentric and pairwise quantum Rényi leakages are proposed as two measures of information leakage for privacy and security analysis in quantum computing and communication systems. These quantities both require minimal assumptions on the eavesdropper, i.e. they do not make any assumptions on the eavesdropper’s attack strategy or the statistical prior on the secret or private classical data encoded in the quantum system. They also satisfy important properties of positivity, independence, post-processing inequality and unitary invariance. The barycentric quantum Rényi leakage can be computed by solving a semi-definite program; the pairwise quantum Rényi leakage possesses an explicit formula. The barycentric and pairwise quantum Rényi leakages form upper bounds on the maximal quantum leakage, the sandwiched quantum

α

-mutual information, the accessible information and the Holevo’s information. Furthermore, differentially private quantum channels are shown to bound these measures of information leakage. Global and local depolarizing channels, that are common models of noise in quantum computing and communication, restrict private or secure information leakage. Finally, a privacy-utility trade-off formula in quantum machine learning using variational circuits is developed. The privacy guarantees can only be strengthened, i.e. information leakage can only be reduced, if the performance degradation grows larger and
vice versa
.
The human glucocorticoid receptor variant rs6190 promotes blood cholesterol and atherosclerosis
Authors: Durumutla Hima Bindu , Haller April , Noble Greta , Prabakaran Ashok Daniel , McFarland Kevin , Latimer Hannah , Akinborewa Olukunle , Namjou-Khales Bahram , Hui David Y. , Quattrocelli Mattia
Published: December 2024

Elevated cholesterol poses a significant cardiovascular risk, particularly in older women. The glucocorticoid receptor (GR), a crucial nuclear transcription factor that regulates the metabolism of virtually all major nutrients, harbors a still undefined role in cholesterol regulation. Here, we report that a coding single nucleotide polymorphism (SNP) in the gene encoding the GR,rs6190, associated with increased cholesterol levels in women according to UK Biobank and All Of Us datasets. In SNP-genocopying transgenic mice, we found that the rs6190 SNP enhanced hepatic GR activity to transactivatePcsk9andBhlhe40, negative regulators of low-density lipoprotein (LDL) and high-density lipoprotein (HDL) receptors in liver respectively. Accordingly, in mice the rs6190 SNP was sufficient to elevate circulating cholesterol levels across all lipoprotein fractions and the risk and severity of atherosclerotic lesions on the pro-atherogenichAPOE*2/*2background. The SNP effect on atherosclerosis was blocked by in vivo knockdown of Pcsk9 and Bhlhe40 in liver. Remarkably, we found that this mechanism was conserved in human hepatocyte-like cells using CRISPR-engineered, SNP-genocopying human induced pluripotent stem cells (hiPSCs). Taken together, our study leverages a non-rare human variant to uncover a novel GR-dependent mechanism contributing to atherogenic risk, particularly in women.

Abstract Figure

Graphical Abstract
Genome size estimation from long read overlaps
Authors: Hall Michael B , Coin Lachlan J M
Published: December 2024

Accurate genome size estimation is an important component of genomic analyses, though existing tools are primarily optimised for short-read data. We present LRGE, a novel tool that uses read-to-read overlap information to estimate genome size in a reference-free manner. LRGE calculates per-read genome size estimates by analysing the expected number of overlaps for each read, considering read lengths and a minimum overlap threshold. The final size is taken as the median of these estimates, ensuring robustness to outliers such as reads with no overlaps. Additionally, LRGE provides an expected confidence range for the estimate. LRGE outperformsk-mer-based methods in both accuracy and computational efficiency and produces genome size estimates comparable to those from assembly-based approaches, like Raven, while using significantly less computational resources. We validate LRGE on a large, diverse bacterial dataset and confirm it generalises to eukaryotic datasets.

Availability and implementation

Our method, LRGE (LongRead-basedGenome sizeEstimation from overlaps), is implemented in Rust and is available as a precompiled binary for most architectures, a Bioconda package, a prebuilt container image, and a crates.io package as a binary (lrge) or library (liblrge). The source code is available athttps://github.com/mbhall88/lrgeunder an MIT license.
Reevaluating the Association Between Epstein-Barr Virus (EBV) and Breast Cancer in the United States
Authors: Hu Clarence C. , Kamtam Devanish N. , Cardona Juan J.
Published: December 2024

The World Health Organization estimates 9.9% of cancers are attributable to viruses. Notably, human papillomavirus causes roughly 90% of cervical cancers, while Epstein-Barr virus (EBV) is linked to nearly 10% of gastric carcinomas. Regarding breast cancer, the association with EBV is inconclusive. While studies in some nations report an association, those in the United States largely do not. We reviewed studies from 2003 to 2023 and identified seven that analyzed EBV association with breast cancer in American patients. We observed a potential risk of not investigating novel EBV variants. Detection protocols utilized only lymphoma-derived strains, despite the current knowledge suggesting that genotype variation can influence pathogenic potential and cell tropism. Certain EBV strains, for instance, may preferentially infect epithelial cells and increase the risk of nasopharyngeal carcinoma (NPC) by up to 11 times. Stated simply, the optimal EBV detection protocol for breast cancer cells may differ from lymphoma cells. Reliance on lymphoma-derived strains assumes a level of sequence conservation among EBV genomes. Mounting evidence demonstrates greater variation than previously believed, especially in key coding and non-coding regions. Our analysis reveals that 5/7 (71%) studies used at least one assay sequence that did not exactly match more than 50% of EBV genomes in NCBI GenBank. Moreover, 98% of these GenBank entries became available after assay sequences were selected. Overall, it is possible the current understanding may be incomplete. Should breast cancer mirror gastric carcinoma and exhibit EBV influence in certain subtypes, these insights could enable targeted therapies and screening programs.

Objectives

This study examines potential limitations of prior investigations into the association between Epstein-Barr Virus (EBV) and breast cancer in the United States. Specifically, our aims are to:

Assess the cellular origin and pathogenicity of EBV strains employed in detection protocols.This objective stems from the background section’s discussion on EBV genotype variations and their potential influence on tissue tropism and pathogenic mechanisms.

Evaluate the sequence similarity between assay sequences and available EBV genomic data.This objective addresses the concern raised in the background section regarding the potential for newfound sequence variation among EBV strains and the implications for accurate detection.

Determine the extent to which detection protocols incorporate the latest EBV genomic data.
Soft, 3D printed muscle ultrasound phantom with structurally tunable B-mode echo intensity
Authors: Gillespie Samuel D , Collins Caralyn P , Perreault Eric J , Sun Cheng , Balogun Oluwaseyi , Murray Wendy M
Published: December 2024

OBJECTIVES

Imaging phantoms for training and validation are vital to improving the performance and adoption of ultrasound imaging modalities in clinical and pre-clinical applications, and the goal of this study was to assess the viability of 3D printed muscle ultrasound phantoms to meet this need.

METHODS

We used a soft stereolithography resin to 3D print phantoms that mimicked the fascicle- and perimysium-scale structure of skeletal muscle and compared the long axis B-mode imaging quality and pattern of the phantom to that of healthy, adult Biceps brachii. We used a pulse-echo, time-of-flight method to measure the acoustic impedance of the resin for comparison to skeletal muscle and common soft tissue mimicking materials. We analyzed the echo intensity (EI) of muscle images to establish a physiological range and compared the EI of different phantom designs to assess the ability to control imaging brightness through structural modification.

RESULTS

A linear, striated hyper-/hypo-echoic B-mode imaging pattern mimicking long axis Biceps brachii muscle images was achieved with two 3D structure paradigms, rod and honeycomb. Acoustic impedance of Elastic 50A resin is higher than skeletal muscle in bulk, but appears suitable for use in a 3D structured phantom. EI measured in the Biceps images were found to vary both within and across images with an overall mean ± SD of 87 ±13 AU. EI measured in honeycomb phantoms (55 ±15 AU) was higher than in rod phantoms (42 ±13 AU), and a latticed honeycomb further increased EI (90 ±11 AU).

CONCLUSIONS

This study serves as proof-of-concept for soft, 3D printed phantoms that replicate the characteristic muscle ultrasound imaging pattern with the ability to tune clinically relevant EI values via structural design.
Epigenetic study of the long-term effects of Gulf War illness
Authors: Jones B. C. , O’Callaghan J. P. , Ashbrook D. G. , Lu L. , Prins P. , Zhao W. , Mozhui K
Published: December 2024

Gulf war illness is a chronic multisymptom disorder that affects as many as many as 25-35% of the military personnel who were sent to the Persian Gulf war in 1991. The illness has many debilitating symptoms, including cognitive problems, gastrointestinal symptoms, and musculoskeletal pain. Those so afflicted have been sick for more than 30 years and, therefore, it has become imperative to understand the etiology and then produce treatments to ease the symptoms. We hypothesized that the length of the disease was reflected in epigenetic modification of possibly several genes related to the symptoms. We subjected male and female mice from 11 BXD strains to combined corticosterone and the sarin surrogate, diisopropylfluorophosphate, to emulate the physiological stress of war and the potential exposures to organophosphate pesticides and nerve agent in theater. Three hundred days after treatment, we analyzed the animals’ DNA for genome-wide methylation by MBD-seq. The analysis revealed 20 methylated genes, notablyEif2B5, that regulates myelin production. Loss of myelin with accompanying musculoskeletal pain is a major symptom of Gulf War illness. Our work demonstrates multiple genes were methylated by exposure to OPs and glucocorticoids. These genes point to biochemical mechanisms that may be targets for therapeutic intervention.
The proteome content of blood clots observed under different conditions: successful role in predicting clot amyloid(ogenicity)
Authors: Kell Douglas B. , Pretorius Etheresia
Published: December 2024

A recent analysis compared the proteome of (i) blood clots seen in two diseases – sepsis and long COVID – when blood was known to have clotted into an amyloid microclot form (as judged by staining with the fluorogenic amyloid stain thioflavin T) with (ii) that of those non-amy-loid clots considered to have formed normally. Such fibrinaloid microclots are also relatively resistant to fibrinolysis. The proteins that the amyloid microclots contained differed markedly both from the soluble proteome of typical plasma and that of normal clots, and also between the disease studies (an acute syndrome in the form of sepsis in an ITU and a chronic disease represented by Long COVID). Many proteins in the amyloid microclots were low in concentration in plasma and were effectively accumulated into the fibres, whereas many other abundant plasma proteins were excluded. The proteins found in the microclots associated with the diseases also tended to be themselves amyloidogenic. We here ask effectively the inverse question. This is: can the clot proteome tell us whether the clots associated with a particular disease contained proteins that are observed uniquely (or are highly over-represented) in known amyloid clots relative to normal clots, and thus were in fact amyloid in nature? The answer is in the affirmative in a variety of major coagulopathies, viz. venous thromboembolism, pulmonary embolism, deep vein thrombosis, various cardiac issues, and ischaemic stroke. Galectin-3-binding protein and thrombospondin-1 seem to be especially widely associated with amyloid-type clots, and the latter has indeed been shown to be incorporated into growing fibrin fibres. These may consequently provide useful biomarkers with a mechanistic basis.
Probing Nanoscale Electrochemical Phenomena with Nitrogen-Vacancy Centers in Diamond
Authors: Fulton Samuel , Stropko Jack , Vitale Robert , Sushkov Alexander O.
Published: December 2024

Nitrogen-vacancy centers in nanodiamonds exhibit photo-stability and biocompatibility that make them promising candidates for versatile biological sensors. In the present work, we study the dependence of NV-nanodiamond fluorescence on the pH of the surrounding ionic aqueous solution. Band-bending effects and modified ion migration rates may be the potential mechanisms underlying the observed pH sensitivity. Our work offers insight into diamond electrochemistry and paves the way toward nanoscale pH imaging. Additionally, the methodologies developed in this work introduce a viable approach for analyzing local electrochemical environments, with potential applications in intra-cellular pH sensing, the design of electrolytic cells, and the development of alternative fuel technologies.
Guidelines for alternative polyadenylation identification tools using single-cell and spatial transcriptomics data
Authors: Zhao Qian , Rattray Magnus
Published: December 2024

Background

Many popular single-cell and spatial transcriptomics platforms exhibit 3’ bias, making it challenging to resolve all transcripts but potentially more feasible to resolve alternative polyadenylation (APA) events. Despite the development of several tools for identifying APA events in scRNA-seq data, a neutral benchmark is lacking, complicating the choice for biologists.

Results

We categorized existing APA analysis tools into three main classes, with the alignment-based class being the largest and we further divided this category into four sub-types. We compared the performance of methods from each algorithmic subtype in terms of site identification, quantification, and differential expression analysis across four single-cell and spatial transcriptomic datasets, using matched nanopore data as ground truth. No single method showed absolute superiority in all comparisons. Therefore, we selected representative methods (Sierra, scAPAtrap, and SCAPE) to deeply analyze the impact of different algorithmic choices on performance. SCAPE which is based on the distance estimation demonstrated less sensitivity to changes in read length and sequencing depth. It identified the most sites and achieved high recall but does not account for the impact of alternative splicing on site identification, leading to a loss in precision. Sierra that fits a coverage distribution is sensitive to changes in sequencing depth and identifies relatively fewer sites, but it considers the impact of junction reads on site identification and this results in relatively high precision. scAPAtrap combines peak calling and soft clipping, both of which are sensitive to sequencing depth. Moreover, soft clipping is particularly sensitive to read length, with increased read length leading to more false positive sites. Quantification consistency was affected by Cell Ranger versions and parameters, influencing downstream analysis but having less effect on differential expression between cell types.

Conclusions

Each method has unique strengths. SCAPE is recommended for low-coverage data, scAPAtrap for moderate read lengths including intergenic sites, and Sierra for high-depth data with alternative splicing considerations. Filtering low-confidence sites, choosing appropriate mapping tools, and optimizing window size can improve performance.
Elevated plasma pTau181 in a specialty neuropsychiatric clinic is associated with opioid use and guides medication titration on a clinically relevant short-time scale
Authors: Hanson Emily , Berner Karl , Berner Jon
Published: December 2024

A combinatorial explosion of agents that delay neurodegeneration in animal models has created a crisis of abundance in human applications with too many combinations to try when time is short. Plasma biomarkers of premature neuronal aging, the amyloid-tau-neurodegeneration (ATN) profile, may provide a tool to rapidly optimize treatment in single-patient trials. We retrospectively analyzed plasma ATN profiles in patients with extensive neuropsychiatric polypharmacy and premature neuronal aging. ATN profiles were based on the biomarkers amyloid-β ratio, phosphorylated Tau 181 (pTau181), and neurofilament light chain (NfL). We investigated whether ATN profile biomarkers were associated with age, gender, metabolic syndrome markers, and medication use. Two case reports additionally provide examples of the application of ATN profiles in clinical settings. We found that in 80 patients with ATN profiles and complete clinical phenotypes, pTau181 was elevated in 31 (38.75%), amyloid-β ratio was below normal ranges in 11 (13.75%), and NfL was elevated in three (3.75%). The biomarkers correlated with age, as expected. Opioid use was significantly associated with pTau181 (p=0.004) and NfL (p=0.002), also after Bonferroni correction (both p <0.05), but not with amyloid-β ratio. No other medications were associated with the biomarkers. In conclusion, identifying the overlaps between complex behavioral phenotypes (pain and cognition), plasma endophenotypes (ATN profile), and medication-targeted components of age-related pathophysiology is now a technical problem rather than theoretical speculation. Rapid progress in single-patient trials for treatment optimization will require funding to promote using repurposed generic treatments, educate patients and providers regarding optimization principles, and continue developing sensitive biomarkers.
Detection of human brain cancers using genomic and immune cell characterization of cerebrospinal fluid through CSF-BAM
Authors: Pearlman Alexander H. , Wang Yuxuan , Kalluri Anita , Parker Megan , Cohen Joshua D , Dudley Jonathan , Rincon-Torroella Jordina , Xia Yuanxuan , Gensler Ryan , Alfonzo Horwitz Melanie , Theodore John , Dobbyn Lisa , Popoli Maria , Ptak Janine , Silliman Natalie , Judge Kathy , Groves Mari , Jackson Christopher M. , Jackson Eric M. , Jallo George I. , Lim Michael , Luciano Mark , Mukherjee Debraj , Naidoo Jarushka , Rozati Sima , Sterling Cole H. , Weingart Jon , Koschmann Carl , Mansouri Alireza , Glantz Michael , Kamson David , Schreck Karisa C. , Pardo Carlos A. , Holdhoff Matthias , Paul Suman , Kinzler Kenneth W. , Papadopoulos Nickolas , Vogelstein Bert , Douville Christopher , Bettegowda Chetan
Published: December 2024

Patients who have radiographically detectable lesions in their brain or other symptoms compatible with brain tumors pose challenges for diagnosis. The only definitive way to diagnose such patients is through brain biopsy, an obviously invasive and dangerous procedure. Here we present a new workflow termed “CSF-BAM” that simultaneously identifiesBcell or T cell receptor rearrangements,Aneuploidy, andMutationsusing PCR-mediated amplification of both strands of the DNA from CSF samples. We first describe the details of the molecular genetic assessments and then establish thresholds for positivity using training sets of libraries from patients with or without cancer. We then applied CSF-BAM to an independent set of 206 DNA samples from patients with common, aggressive cancer types as well as other forms of brain cancers. Among the 126 samples from patients with the most common aggressive cancer types (high grade gliomas, medulloblastomas, or metastatic cancers to the brain), the sensitivity of detection was >81%. None of 33 CSF-BAM assays (100% specificity, 90% to 100% credible interval) were positive in CSF samples from patients without brain cancers. The sensitivity of CSF-BAM was considerably higher than that achieved with cytology. CSF-BAM provides an integrated multi-analyte approach to identify neoplasia in the central nervous system, provides information about the immune environment in patients with or without cancer, and has the potential to inform the subsequent management of such patients.

Statement of significance

There is a paucity of technologies beyond surgical biopsy that can accurately diagnose central nervous system neoplasms. We developed a novel, sensitive and highly specific assay that can detect brain cancers by comprehensively identifying somatic mutations, chromosomal copy number changes, and adaptive immunoreceptor repertoires from samples of cerebrospinal fluid.
VEXAS anemia is a mosaic erythroblastopenia
Authors: Rodrigues François , Hardouin Giulia , El Hoss Sara , Ghoul Aya , Gautier Emilie-Fleur , Dussiot Michaël , Peltier Sandy , Amireault Pascal , Soldan Vanessa , Miccio Annarita , Debili Mounia , Jachiet Vincent , Trovati Maciel Thiago , Rossignol Julien , Allemand Eric , Mekinian Arsène , Georgin-Lavialle Sophie , Salma Mohammad , Soler Eric , Gleizes Pierre-Emmanuel , O’Donohue Marie-Françoise , Kosmider Olivier , Rodriguez Manuel S. , Hermine Olivier ,   French VEXAS group,   MINHEMON
Published: December 2024

VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) is a recently discovered autoinflammatory disorder linked to somatic mutations in theUBA1gene, resulting in a profound cytoplasm-restricted defect in ubiquitylation. The disease is characterized by a macrocytic anemia that remains poorly understood. To investigate the erythroid lineage in VEXAS, we conducted a comprehensive study combiningin vivoassessments of patients’ mature red cells and marrow erythroblasts, alongsidein vitrobase-editing models of erythropoiesis. Here we show that mature red cells do not exhibit ubiquitylation defects, and patient-derived bone marrow erythroblasts lackUBA1mutations beyond the basophilic stage of erythroid differentiation.In vitrobase editing ofUBA1variants in CD34+ primary cells resulted in high mortality during early erythroid differentiation, but not during monocytic differentiation. Edited erythroid precursors displayed TP53 overexpression linked to defective ubiquitylation and anomalies in ribosome biogenesis, reminiscent of Diamond-Blackfan anemia. We propose that VEXAS-associated anemia should be considered as a mosaic erythroblastopenia, where the severity of anemia is influenced by the quality and quantity of theUBA1-WT compartment. These insights may aid clinicians in tailoring treatment strategies.