bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in emergency healthcare use following intervention by Navigator, an emergency department social support programme: a multi-centre retrospective before-and-after study
Authors: McHenry Ryan D. , Goodall Christine A.
Published: December 2024

Background and importance

Patients living with social deprivation, and those with experiences of violence, substance misuse, mental ill-health and homelessness are known to use emergency departments (EDs) more often. It is not known whether a programme of social support initiated during ED attendance may lead to a reduction in healthcare use.

Objective(s)

The objective of this study is to determine the change in emergency, inpatient and outpatient healthcare use following a social support programme, Navigator, initiated during an ED attendance.

Design

Retrospective before-and-after study.

Settings and participants

Adult patients ≥16 years, attending EDs in the West of Scotland from 14th September 2016 to 10th March 2023, with a Navigator programme encounter.

Intervention or exposure (if any)

The Navigator social support programme, delivered by trained support workers, initiated during ED attendance, and targeting patients affected by issues including violence, substance misuse, mental ill-health, domestic abuse and homelessness.

Outcome measures and analysis

Healthcare use rates in the 365 days following intervention, as change compared to those in the 365 days prior to the intervention. The primary outcome was the number of ED attendances in the year following intervention compared with the year prior to intervention. Secondary outcomes included inpatient admissions, inpatient bed days, outpatient appointments and outpatient appointments where the patient did not attend. Changes in use rates were analysed with negative binomial regression and reported as incidence rate ratios for interpretation as percentage change. Analysis was repeated for a subgroup of frequent attenders to the ED.

Main results

Of 1421 Navigator programme encounters, 1056 were included for analysis. Median attendance in the year prior to intervention was 3 [interquartile range (IQR) 1–5], and in the year following intervention was 2 (IQR 0–4). Negative binomial regression demonstrated that in the year following Navigator intervention, there was a 29% (95% confidence interval: 24–33%) reduction in ED attendances.

Conclusion

The Navigator programme was associated with reduced emergency and acute healthcare use in the year following intervention, with increased scheduled outpatient care. There is the potential for a social support programme, delivered from the ED, to change patterns of healthcare use, and future work should consider prospectively assessing the impact of such an intervention.
Enhancing Primary Care by Investing in Interprofessional Education
Authors: Bakerjian Deb , Edwards Jennifer J. , Cachu Ana Marin , Kwan Jonathan
Published: December 2024

The System-transforming, Patient centered Longitudinal Interprofessional Community-based Education (SPLICE) Initiative was a Health Resources and Services Administration (HRSA) funded project designed to educate and train health professions learners in team-based primary care within a clinical environment. The SPLICE project team developed multiple learning activities including case studies and simulations that integrated the IPEC Core Competencies within clinical scenarios. The interprofessional aspects were also modeled by faculty facilitators from different professions. Each activity was thoroughly evaluated by the learners using mixed methods processes including data from retrospective pretest-posttest self-assessments, open-ended surveys, and focus groups. Faculty, staff, and learners invested countless hours of volunteer time due to the enthusiasm and passion for the work supported with HRSA funding to implement and evaluate the SPLICE initiative. Outcomes include the development of an enhanced primary care simulation template; the creation of 21 unique primary care simulations that integrated the IPEC competencies; improved confidence and competence in over 700 learners; over 110 faculty trained in simulation and debriefing skills; clinical skills training for Federally Qualified Health Center (FQHC) staff; improved quality improvement processes at a local FQHC; and a high rate of retention of the graduates in primary care. This project demonstrated a significant return on the investment beyond the initial HRSA funding.
Economic Evaluation of Delivering an Evidence-Based Online HIV Prevention Program to MSM via Direct-To-Consumer Marketing Versus Community-Based Organization Recruitment
Authors: Munroe Sarah , Schackman Bruce R. , Madkins Krystal , Saber Rana , Macapagal Kathryn , Vititow Jocelyn , Sweeney Nicholas , Feder Noah M. , Benbow Nanette , Mustanski Brian , Linas Benjamin P.
Published: December 2024

Purpose:

This study, conducted as part of the Keep It Up! (KIU!) 3.0 trial, compares the implementation costs of 2 strategies—centralized direct-to-consumer (DTC) marketing and decentralized distribution through community-based organizations (CBO)—in delivering an evidence-based online HIV prevention program.

Methods:

We conducted interviews and collected data to identify and quantify all costs for both delivery strategies. Costs were then categorized into start-up and ongoing (time-dependent and variable) costs and assigned dollar values based on established microcosting protocols.

Results:

In the DTC arm (1468 enrollees), the program was implemented from October 2019 through August 2022. Total ongoing costs including overhead and excluding start-up costs were $735,953, averaging $501 per participant. Start-up costs were $398,384 ($376,393 for content design and development and $21,991 for other costs), time-dependent costs were $219,177 ($149 per participant), and variable costs were $491,658 ($335 per participant). In the CBO arm (656 enrollees across 22 sites), KIU! was implemented for a 2-year period between October 2019 and December 2022. Total ongoing costs including overhead and excluding start-up costs were $2,780,682 ($4239 per participant). Start-up costs were $511,528 ($401,141 for content design and development and $110,386 for other costs), time-dependent costs were $1,926,958 ($2937 per participant), and variable costs were $256,543 ($391 per participant).

Conclusions:

The DTC arm demonstrated a lower overall cost and a lower cost per participant than distribution by the CBO arm. Understanding these cost dynamics is pivotal for guiding decisions on program sustainability and determining funding requirements for future large-scale implementation.
Contrast-Enhanced Digital Breast Tomosynthesis Compared With Contrast-Enhanced Mammography and Magnetic Resonance Imaging in the Assessment of Breast Lesions
Authors: Clauser Paola , Pötsch Nina , Santonocito Ambra , Ferrara Francesca , Zeitouni Layla , Hörnig Mathias , Weber Michael , Baltzer Pascal A.T. , Helbich Thomas H.
Published: December 2024

Objectives

Contrast-enhanced mammography (CEM) is an accurate competitor for contrast-enhanced breast magnetic resonance imaging (CE-MRI), but the examination is limited by the lack of 3D information. Digital breast tomosynthesis (DBT) allows better lesion detection and characterization compared with mammography. The availability of quasi-3D contrast imaging could further improve the performance of CEM. The aim of our analysis was to compare the diagnostic performance of a contrast-enhanced digital breast tomosynthesis prototype (CE-DBTp) to CEM and to CE-MRI.

Materials and Methods

This prospective study was approved by the ethics committee, and all patients gave written informed consent. Women who presented with suspicious findings on mammography, DBT, or ultrasound were invited to participate in the study. Participants underwent CEM and CE-DBTp of the breast with the suspicious findings as well as bilateral CE-MRI. Histology was used as the standard of reference. Four readers (R1 and R2 non-experienced; R3 and R4 experienced) evaluated the images, blinded to patients' history, previous imaging, and histology. The readers evaluated CEM, CE-DBTp, and CE-MRI in separate sessions and gave a BI-RADS score for each finding. Sensitivity, specificity, lesion conspicuity, and readers' confidence were calculated and compared.

Results

We included 84 patients (mean age, 56 years; range, 39–70) with 91 histologically verified breast lesions (27 benign, 64 malignant). The accuracy of the CE-DBTp was high, but significant differences were seen between experienced (both 86.8%) and non-experienced readers (76.9% and 78%, P = 0.021). No differences were found between CEM and CE-DBTp, whereas the accuracy of CE-MRI was higher (P = 0.002). Sensitivity with CE-DBTp varied (89.1% to 100%) between experienced and non-experienced readers (P = 0.074), and it was comparable to CEM but lower than CE-MRI (P = 0.003). Specificity was variable between readers with all modalities. Lesion conspicuity was higher for the CE-DBTp and CE-MRI than for CEM, and confidence was significantly higher with the CE-DBTp than with CEM for one of the readers (P < 0.001).

Conclusions

A high sensitivity and good accuracy were achieved with the CE-DBTp. Lesion conspicuity and readers' confidence were higher with the CE-DBTp compared with CEM. However, CE-MRI had the highest sensitivity and accuracy.
Modified Technique of Temporal Osteotomy in Fronto-Orbital Advancement in Anterior Plagiocephaly
Authors: Hassanpour Seyed E. , Kalantar-Hormozi Abdoljalil , Mousavizadeh Seyed M. , Farzan Abdolnaser , Noori Mehran
Published: December 2024

Background:

Nonsyndromic anterior plagiocephaly is one of the most common types of craniosynostosis. In recent years, various surgical techniques have been introduced to correct this deformity, which many surgeons believe have not been associated with adequate clinical and aesthetic results. The aim of the study was to introduce a new surgical technique (modified Z-technique of temporal region osteotomy) and to evaluate the aesthetic and anthropometric outcomes of frontal orbital correction for the management of patients with nonsyndromic anterior plagiocephaly.

Methods:

In this cohort study, 47 patients with nonsyndromic anterior plagiocephaly who were operated on in 15-Khordad and Mofid Hospital affiliated to Shahid Beheshti University of Medical Sciences during the years 2018 to 2023 with the modified z-technique of temporal region osteotomy, were investigated. Aesthetic outcomes and changes in anthropometric parameters of the skull were evaluated 2 years after surgery. Also, the length of surgery, the mean length of stay in the hospital and ICU, the amount of bleeding and postoperative complications were evaluated. Postoperative recurrence of deformity was evaluated according to the Whitaker classification.

Results:

The mean age of the patients was 11.1±4.15 months. Twenty-seven (57.44%) patients were female and 20 patients were male. The mean follow-up period of the patients was 19.3±3.54 months. The mean weight of the patients was 13.12±7.45 kg. The mean length of hospital stay and ICU stay were 5.44±0.50 and 1.78±0.63 days, respectively. A significant positive correlation was observed between the duration of surgery and the duration of stay in ICU (r=0.23, P=0.023). According to Whitaker’s classification, 39 (82.97%) patients were classified in class I, 4 (8.51%) in class II, 2 (4.25%) in class III, and 2 (4.25) in class IV. Aesthetically, the surgical results were excellent (class I Whitaker) in 82.97%. No serious complications such as infection, CSF rhinorrhea, hematoma occurrence, skull defect occurrence, fever, bleeding, and postoperative mortality were reported.

Conclusion:

Our study showed that the modified z-technique of temporal region osteotomy was associated with good and excellent aesthetic and clinical results. Bleeding rate, average length of hospital stay, and average length of ICU stay in patients with nonsyndromic anterior plagiocephaly treated with modified Z-technique of temporal region osteotomy were low and comparable with other with other reported series. No cases of serious complication and death were reported during the follow-up period. Nonsyndromic anterior plagiocephaly can be successfully treated with modified Z-technique of temporal region osteotomy with good results and low complication rates.
Surgical Treatment of Synkinetic Eyelid Closure in Marin-amat Syndrome Complicated by Facial Palsy After COVID-19 Vaccination
Authors: Hsieh Meng-Chien Willie , Lai Chung-Sheng , Chang Yang-Pei , Lai Ya-Wei
Published: December 2024

Background:

Marin-Amat syndrome is a rare, irreversible, and hard-to-treat neurological sequalae that has recently been associated with COVID-19 vaccination. Given the rarity of this condition and the absence of curative treatment to date, the authors herein review the literature to date and report the first ever successful surgical treatment of 2 patients who developed Marin-Amat syndrome after ChAdOx1 nCoV-19 vaccination.

Materials and Methods:

In this case study, the authors treated Marin-Amat syndrome in a 45-year-old woman and a 75-year-old woman with facial palsy that developed 24 days and 4 months after receiving COVID-19 vaccination, respectively. The patients’ clinical histories and physical examination results were reviewed. A literature review was performed using PUBMED for the years 1990 to the present.

Results:

It is noteworthy that these are the first reported cases of Marin-Amat Syndrome to be successfully treated by surgery. The patient’s neurological symptoms improved after surgical intervention in contrast with the lack of response after botulinum toxin injection and intensive rehabilitation.

Conclusion:

This study is the first to demonstrate the successful treatment of the extremely rare Marin-Amat syndrome after ChAdOx1 nCoV-19 vaccination through surgery. Selective myectomy and myotomy in situ in combination with levator plication proves to be highly effective and favorable in treating this condition as the surgery overtakes the limited effectiveness of and directly obviates the need for botulinum toxin injections, thereby improving patient satisfaction and quality of life.
The Utility of Prophylactic Muscle Flaps in Complex Pediatric Spine Surgery
Authors: Zhang Wesley Q. , Elver Ashlie A. , Humphries Laura S. , Hoppe Ian C.
Published: December 2024

Purpose:

Complex spinal surgery in the pediatric population can lead to devastating complications and morbidity. Paraspinal muscle flaps are commonly performed after complications to optimize wound closure. However, some advocate for their prophylactic use at the index surgery. The aim of this study is to determine the utility of prophylactic muscle flaps in pediatric spine surgery.

Methods:

A retrospective cohort study was performed using data from the Pediatric National Surgical Quality Improvement Program (PNSQIP) database. Patients who underwent complex spinal surgery from 2016 to 2021 were queried and split into cohorts based on whether muscle flaps were performed at the index surgery. Primary outcomes compared the incidence of surgical site infections (SSI) and wound complications. Regression modeling and propensity score matching were performed to account for baseline characteristics.

Results:

There were 43,678 patients who underwent spinal surgery. Of these, 847 (1.9%) had concomitant paraspinal flaps. Comorbidities were significantly higher in the flap group. Overall SSI, deep and organ space SSI, and wound disruption were higher in flap patients (P<0.001). Muscle flaps were performed more in high-risk patients determined by ASA (American Society of Anesthesiologists) class, and these patients experienced significantly more complications overall (rate of SSI- ASA 1: 1.1% versus ASA 4: 5.6%; P<0.001). When propensity score matching was controlled for baseline characteristics, there were no significant differences in outcomes.

Conclusions:

Patient selection may determine the need for prophylactic muscle flaps, favoring more complex patients. These patients may experience more complications, supporting the decision to perform a muscle flap at the time of index operation.
Superficial Circumflex Iliac Artery Perforator Flap With Iliac Bone—An Alternative Option for Maxilla Reconstruction
Authors: Walczak Dominik A. , Bula Daniel , Hadasik Grzegorz
Published: December 2024

A superficial circumflex iliac perforator (SCIP) flap is gaining popularity in microsurgical free flap reconstruction, especially for extremity defects. However, its application in the head and neck region is still uncommon. Besides a thin, pliable skin paddle, the SCIP flap can be elevated with a part of the iliac bone. In this brief clinical study, the authors describe 3 different reconstructions of maxilla defects, ranging from small to very extensive, using an osteocutaneous SCIP flap. In their opinion, this flap provides many advantages, such as a relatively large bony element that is highly mobile in relation to other components and minimal donor site morbidity. Therefore, it is worthwhile to consider utilizing the SCIP flap in reconstructions after maxillectomies.
Cervical spine clearance in the pediatric trauma population: What you need to know
Authors: Russell Katie W. , Kahan Anastasia , Eldredge R. Scott
Published: December 2024

Evaluation of the pediatric cervical spine after blunt trauma is an important topic that requires special consideration. In this article, we will review background information and differences between the pediatric and adult cervical spine. We will then give up-to-date guidance on best practice for screening and clearance of the cervical spine in children, including the advantages and disadvantages of different imaging techniques. Finally, we will introduce current topics of study and surmise what changes or innovations may be coming in the future.

LEVEL OF EVIDENCE

Expert Review, Level VI.
Cell-free mitochondria are detected in high concentrations in the plasma of orthopedic trauma patients
Authors: Briggs Gabrielle D. , Meakes Simone , King Kate L. , Balogh Zsolt J.
Published: December 2024

BACKGROUND

Trauma and surgery can derange inflammatory and hemostasis responses, potentially leading to multiple organ failure. Mitochondrial damage-associated molecular patterns are known to be part of the pathomechanism, but their exact origin remains uncertain. Recently, intact mitochondria were detected in healthy individuals' peripheral blood, which suggested a potential role in inflammation.

METHODS

In this case-control study, we quantitated cell-free mitochondria in the blood of healthy subjects (n = 4) and trauma patients (n = 25) and assessed their relationship with patient demographics, injury and shock severity, markers of tissue injury, inflammation, and blood transfusions. Blood samples were collected before and after major orthopedic trauma surgery, and cell-free mitochondria were quantified using flow cytometry, targeting the outer mitochondrial membrane protein, TOMM70. Mitotracker Deep Red staining was used to assess mitochondrial membrane potential.

RESULTS

Trauma patients had significantly more cell-free mitochondria in their plasma compared with healthy controls, with highest counts immediately after surgery. The number of cell-free mitochondria decreased by day 5 postoperatively. Trauma patients exhibited a higher proportion of active cell-free mitochondria compared with healthy controls, especially immediately after surgery, and this proportion correlated with tissue injury markers. Associations were also found with acute thrombocytopenia, Denver multiple organ failure score, and transfusion of fresh frozen plasma and cryoprecipitate.

CONCLUSION

Our findings indicate that the mere high number of cell-free mitochondria in the circulation of trauma patients is not necessarily pro-inflammatory, but their active status is associated with more severe secondary tissue injury. The natural history of cell-free mitochondria in trauma needs to be characterized, including their potential cause-effect relationship with major postinjury complications.

LEVEL OF EVIDENCE

Prognostic and Epidemiological; Level III.
Magnetic signals from oceanic tides: new satellite observations and applications
Authors: Grayver Alexander , Finlay Christopher C. , Olsen Nils
Published: December 2024

The tidal flow of seawater across the Earth’s magnetic field induces electric currents and magnetic fields within the ocean and solid Earth. The amplitude and phase of the induced fields depend on the electrical properties of both seawater and the solid Earth, and thus can be used as proxies to study the seabed properties or potentially for monitoring long-term trends in the global ocean climatology. This article presents new global oceanic tidal magnetic field models and their uncertainties for four tidal constituents, including

M
2

,

N
2

,

O
1

and even

Q
1

, which was not reliably retrieved previously. Models are obtained through a robust least-squares analysis of magnetic field observations from the
Swarm
and CHAMP satellites using a specially designed data selection scheme. We compare the retrieved magnetic signals with several alternative models reported in the literature. Additionally, we validate them using a series of high-resolution global three-dimensional (3D) electromagnetic simulations and place constraints on the conductivity of the sub-oceanic mantle for all tidal constituents, revealing an excellent agreement between all tidal constituents and the oceanic upper mantle structure.

This article is part of the theme issue ‘Magnetometric remote sensing of Earth and planetary oceans’.
Insights into the genome of Azotobacter sp. strain CWF10, isolated from an agricultural field in Central India, India
Authors: Roy Arindam , Ghosh Anwesha , Yash Yash , Mehra Prateeksha , Roy Sumit , Bhadury Punyasloke
Published: December 2024

Azotobacter sp. strain CWF10, an aerobic gram negative, oval shaped and motile bacterium, was isolated from a lateritic agricultural soil of Madhya Pradesh, India. The draft genome of the isolate is 5.7 Mb in size, consisting of 14 contigs with 65.09 % G+C content. Average nucleotide identity (94.66%) and digital DNA-DNA hybridization (62%) calculation with closest reference strains underpin the bacterium as a potential novel species. The bacterium has a plethora of plant growth promoting genes that point towards potential ability for enhancement of nitrogen, biosynthesis of folic acid, among others. Siderophores such as vibrioferrin and crochelin A are also present in the genome which are known to regulate iron uptake.
Identification and Mitigation of microbial contaminant reads from long-read metagenomic samples
Authors: Ayala-Montano Stefany , Afolayan Ayorinde O. , Kociurzynski Raisa , Loeber Ulrike , Reuter Sandra
Published: December 2024

Metagenomic sequencing has revolutionized our understanding of microbial communities, but the presence of contaminant DNA, particularly from the host, poses a significant challenge to accurate data interpretation. We present a methodology for the detection and removal of contaminant sequences in metagenomic datasets, focusing on microbial DNA as a primary contaminant. By integrating metrics such as the prevalence method proposed in decontam, and the coverage value per species per sample, we contributed to the remaining challenge of microbial contaminants that mislead the biological findings. We have emphasized the relevance of human DNA contamination removal (hDNA) in the laboratory and bioinformatically, especially in low-biomass environments.

We highlight that failure to account for human and microbial DNA can lead to erroneous conclusions about the microbial diversity and community composition in the metagenomes. Our approach provides a solution for contamination management for people with moderate bioinformatics skills to ensure more reliable and reproducible results in metagenomic research. The implications of this study for clinical microbiome and pathogen surveillance employing long-read sequencing are relevant and needed for comprehensive contamination control strategies.
TEAL-seq: Targeted Expression Analysis Sequencing
Authors: Doing Georgia , Shanbhag Priya , Bell Isaac , Cassidy Sara , Motakis Efthymios , Aiken Elizabeth , Oh Julia , Adams Mark D.
Published: December 2024

Metagenome sequencing enables genetic characterization of complex microbial communities. However, determining theactivityof isolates within a community presents several challenges including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed “targeted expression analysis sequencing” or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof-of-concept we targeted about 1,700 core and accessory genes ofStaphylococcus aureusandS. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstrated excellent correlation in inferred expression levels with bulk RNA-seq. Further, we show that a linear pre-amplification step to increase the amount of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.

IMPORTANCE

The gene expression patterns of bacteria in microbial communities reflect their activity and interactions with other community members. Measuring gene expression in complex microbiome contexts is challenging, however, due to the large dynamic range of microbial abundances and transcript levels. Here we describe an approach to assessing gene expression for specific species of interest using highly multiplexed pools of targeting probes. We show that an isothermal amplification step can allow profiling of low biomass samples. TEAL-seq should be widely adaptable to the study of microbial activity in natural environments.
Deep-leaning and shallow hybrid Nanopore-Illumina sequencing for affordable and accurate detection of germline variants
Authors: Gambardella Gennaro
Published: December 2024

Despite the complementary strengths of short- and long-read sequencing approaches, variant calling methods still rely on a single data type. Here, leveraging harmonized Nanopore and Illumina data from the genome in a bottle consortium, we explore the benefits of combining Illumina and Nanopore data through a hybrid approach based on deep learning. By reducing sequencing costs, we show that a shallow hybrid sequencing approach can improve germline variant detection accuracy. Our findings offer promising potential for molecular diagnostics in clinical settings, particularly for rare genetic disease screenings.
Differential Remodeling of the BRCA1 Interactome by a Unique Minimal Clinical Truncation Mutation
Authors: Chen Jingjing , Sardiu Mihaela E. , Rekowski Michaella J. , Nde Jules , Clark Zachary S. , Anant Shrikant , Washburn Michael P. , Jensen Roy A.
Published: December 2024

BRCA1, a critical tumor suppressor gene, plays an essential role in maintaining genomic stability through its involvement in DNA double-strand break repair, particularly via homologous recombination. Loss or impairment of BRCA1 function disrupts this repair pathway, resulting in genomic instability and significantly increased susceptibility to breast and ovarian cancers. To elucidate the molecular mechanisms by which BRCA1 mutations contribute to tumorigenesis, we employed quantitative mass spectrometry-based proximity labeling and affinity purification to identify cancer-specific protein-protein interactions (PPIs). Our integrated omics and visualization analysis of interactors revealed that the BRCA1-Y1853ter mutant, through its interaction with BARD1, perturbs the interactome and impacts cellular processes within the cytoplasm and nucleoplasm. Structural data further corroborated these findings, showing enhanced binding between the mutant BRCA1 and specific interactors, suggesting an altered functional profile. Together, these observations raise the hypothesis that the BRCA1-Y1853ter mutant may exhibit gain-of-function characteristics, providing new insights into the molecular and cellular effects of mutations in the BRCA1 C-Terminal (BRCT) domain and their implications for the pathogenesis of breast and ovarian cancers.
Enriched Methylomes of Low-input and Fragmented DNA Using Fragment Ligation EXclusive Methylation Sequencing (FLEXseq)
Authors: Yu Jingru , Ahmann Lauren S. , Yao Yvette Y. , Gu Wei
Published: December 2024

Methylome profiling is an emerging clinical tool for tumor classification and liquid biopsies. Here, we developed FLEXseq, a genome-wide methylation profiler that enriches and sequences the fragments of DNA flanking the CCGG motif. FLEXseq strongly correlates (Pearson’s r = 0.97) with whole genome bisulfite sequencing (WGBS) while enriching 18-fold. To demonstrate the broad applicability of FLEXseq, we verified its usage across cells, body fluids, and formalin-fixed paraffin-embedded (FFPE) tissues. DNA dilutions down to 250 pg decreased CpG coverage, but bias in methylation remained low (Pearson’s r ≥ 0.90) compared to a 10 ng input. FLEXseq offers a cost-efficient, base-pair resolution methylome with potential as a diagnostic tool for tissue and liquid biopsies.
Methods for safely sharing dual-use genetic data
Authors: Sawaya Sterling , Lo Chien-Chi , Li Po-E , Hovde Blake , Chain Patrick
Published: December 2024

Background

Some genetic data has dual-use potential. Sharing pathogen data has shown tremendous value. For example therapeutic development and lineage tracking during the COVID pandemic. This data sharing is complicated by the fact that these data have the potential to be used for harm. The genome sequence of a pathogen can be used to enable malicious genetic engineering approaches or to recreate the pathogen from synthetic DNA. Standard data security methods can be applied to genetic data, but when data is shared between institutions, ensuring appropriate security can be difficult. Sensitive data that is shared internationally among a wide array of institutions can be especially difficult to control. Methods for securely storing and sharing genetic data with potential for dual-use are needed to mitigate this potential harm.

Results

Here we propose new methods that allow genetic data to be shared in a data format that prevents a nefarious actor from accessing sensitive aspects of the data. Our methods obfuscate raw sequence data by pooling reads from different samples. This approach can ensure that data is secure while stored and during electronic transfer. We demonstrate that by pooling raw sequence data from multiple samples of the same organism, the ability to fully reconstruct any individual sample is prevented. In the pooled data, most genomic information remains, but reads or mutations cannot be directly attributed to any individual sample. To further restrict access to information, regions of a genome can be removed from the reads.

Conclusion

Our methods obscure genomic information within raw sequence reads. This method can allow genetic data to be stored and shared while preventing a nefarious actor from being able to perfectly reconstruct an organism. Broad-scale sequence information remains, while fine scale details about specific samples are difficult or impossible to reconstruct.
EUROPEAN SUBTYPE TICK-BORNE ENCEPHALITIS VIRUS EMERGENCE IN SOUTH KOREA (2005 – 2014) CAN BE ASSOCIATED WITH HUMAN ACTIVITY
Authors: Kovalev S.Y.
Published: December 2024

Tick-borne encephalitis virus (TBEV) is the etiological agent of tick-borne encephalitis. TBEV is maintained in nature by the ixodid ticksIxodes ricinusandI. persulcatus, which are its hosts and main vectors. The classification distinguishes three TBEV subtypes: Far Eastern, European (TBEV-Eu) and Siberian. Each subtype is characterized by its own range, reflected in its name. Nevertheless, numerous findings of TBEV subtypes in non-endemic areas have been reported. This phenomenon may be the result of virus introduction due to natural causes such as bird and mammal migrations. Detection of TBEV-Eu in South Korea in 2005 and in Siberia in the second half of the 20th century are significantly different from other cases of virus introduction. This paper presents the results of a comprehensive study including phylogenetic analysis, clusteron approach, establishing specificity of viral population dynamics, etc. The age of viral populations and the probable time of their emergence in non-endemic regions were determined. Using the example of TBEV-Eu in South Korea, we conclude that there is negative population dynamics of the virus after its introduction. This conclusion, in conjunction with several other features, indicates that human activity played a pivotal role in the TBEV-Eu introduction into South Korea and Siberia.
POLYGENIC DETERMINANTS OF H5N1 ADAPTATION TO BOVINE CELLS
Authors: Turnbull Matthew L , Zakaria Mohammad Khalid , Upfold Nicole S , Bakshi Siddharth , Das Udeet Ranjan , Magill Callum , Mojsiejczuk Laura , Herder Vanessa , Dee Kieran , Liu Nancy , Folwarczna Monika , Ilia Georgios , Furnon Wilhelm , Schultz Verena , Chen Hanting , Devlin Ryan , McCowan Jack , Young Alex L , Po Wai-Wai , Smollett Katherine , Yaseen Muhammad Ahsan , da Silva Filipe Ana , Iqbal Munir , Roberts Ed , Hughes Joseph , Werling Dirk , Murcia Pablo R. , Palmarini Massimo
Published: December 2024

H5N1 avian influenza virus (lineage 2.3.4.4b, B3.13 genotype) has caused, unexpectedly, a large outbreak in dairy cattle in North America. It is critical to ascertain how this virus has specifically adapted to bovine cells and the molecular determinants of this process. Here, we focused on the contribution of the viral “internal” genomic segments of H5N1 B3.13 to bovine cells adaptation. We generated 45 reassortant viruses harbouring the haemagglutinin and neuraminidase from A/Puerto Rico/8/1934 and internal gene constellations from several influenza A viruses (IAV) or carrying segment swaps between distinct H5N1 strains. The recombinant B3.13 viruses displayed faster replication kinetics in bovine cells compared to other IAV. Importantly, multiple genomic segments of B3.13 viruses contribute to their faster replicative fitness. Further, recombinants with the B3.13 internal genes were less susceptible than ancestral 2.3.4.4b strain to the bovine IFN response. However, bovine (and human) MX1, a key restriction factor for avian IAV, restricted both ancestral 2.3.4.4b and B3.13 recombinant viruses. Interestingly, the latter escape restriction from human BTN3A3. Finally, recombinant B3.13 was virulent in mice unlike the ancestor 2.3.4.4b recombinant virus. Our results highlight the polygenic nature of influenza host range as multiple internal genes of B3.13 contribute to bovine adaptation.
Indel-driven evolution of the canavanine tRNA-editing deacetylase enzyme CtdA
Authors: Mayans Olga , Tabagari Nino , Hauth Franziskus , Fleming Jennifer , Hartig Joerg
Published: December 2024

Proteins are heteropolymers composed of twenty standard amino acids. However, over 500 non-proteogenic amino acids exist in nature that can get misincorporated into proteins. Canavanine is an antimetabolite of L-arginine, with which it shares high chemical similarity. It can be utilized by bacteria such as Pseudomonas canavaninivorans in the legume rhizome as a sole source of carbon and nitrogen. However, canavanine is also incorporated in proteins of this bacterium as its arginyl-tRNA synthetase loads tRNAArg with both canavanine and arginine. The recently discovered canavanyl-tRNAArg deacetylase (CtdA) removes canavanine from misloaded tRNAArg and thereby prevents its incorporation in proteins. CtdA is the first enzyme known to edit tRNA mischarged with a non-proteinogenic amino acid. We have elucidated its crystal structure to 1.5 A resolution and studied its active site using site-directed mutagenesis. We found that CtdA is a small monomeric enzyme that presents a central, deep cavity that predictably constitutes the canavanine binding site and a positively charged surface area that likely coordinates the CCA-3(prime) tRNA attachment sequence. The stand-alone, trans-editing CtdA is distantly related to the B3/B4 cis-editing domains of the large multi-subunit enzyme Phenylalanine tRNA synthetase (PheRS). Our comparative study reveals that CdtA and B3/B4 domains from bacterial and archeal/eukaryotic origin are three subclasses of a same conserved 3D-fold that differ in type-specific indels, which distinctly shape the substrate binding cleft of these proteins. We propose a unifying nomenclature of secondary structure elements for this 3D-fold. In CtdA, residues E191, Y104, N105 and E118 prove to be relevant for catalysis, of which N105 is conserved in bacterial B3/B4 domains. No other shared residues of catalytic relevance could be identified across enzymes of this class, so that a shared mechanism of catalysis appears unlikely in these editing enzymes.
The mechanisms by which miRNAs critically contribute to differential roles of Nrf1 and Nrf2 in modulating the epithelial-mesenchymal transformation of hepatocellular carcinoma
Authors: Chen Juan , Feng Jing , Zhu Yu-ping , Hu Shaofan , Zhang Yiguo
Published: December 2024

Accumulation of various genetics and epigenetics alterations are accepted to result in the initiation and progression of hepatocellular carcinoma (HCC), and its high metastasis is viewed as a critical bottleneck leading to its treatment failure. Amongst them, the abnormal expression of several microRNAs arising from lack of antioxidant transcription factor Nrf2 (encoded byNfe2l2) leads to cancer metastasis. However, much less known is about regulation of microRNAs by Nrf1 (encoded byNfe2l1), even though it acts as an essential determinon of cell homeostasis by governing the transcriptional expression of those driver genes contributing to the epithelial–mesenchymal transition (EMT) involved in its metastasis. In this study, distinctive EMT phenotypes were unveiled to result from specific knockout of Nrf1 and Nrf2 in HepG2 cells, as accompanied by differential migratory and invasive capabilities. TheNrf1α−/−-leading EMT results from a significantly decrease in the epithelialCDH1expression, plus another increased expression of the mesenchymalCDH2. Such distinct phenotypes ofNrf1α−/−fromNrf2−/−cell lines were also attributable to differential regulation of two key microRNAs, i.e.,miR3187-3PandmiR1247-5p. Further experiments unraveled that Nrf1 activates the expression ofmiR-3187-3p, directly targeting for the inhibition ofSNAI1, leading to CDH1 activation but CDH2 inhibition insomuch as to prevent the process of EMT. By contrast, Nrf2 inhibits the expression ofmiR1247-5p,relieving its inhibitory effect on MMP15 and MMP17 to promote the EMT. Collectively, these demonstrate that the EMT of liver cancer cells is likely prevented by Nrf1viathe miR3187-3P signaling to the SNAI1-CDH1/2 axis, but conversely promoted by Nrf2 through the miR1247-5p-MMP15/17 signaling axis.
Improving Automated Deep Phenotyping Through Large Language Models Using Retrieval Augmented Generation
Authors: Garcia Brandon T. , Westerfield Lauren , Yelemali Priya , Gogate Nikhita , Rivera-Munoz E. Andres , Du Haowei , Dawood Moez , Jolly Angad , Lupski James R. , Posey Jennifer E.
Published: December 2024

Background

Diagnosing rare genetic disorders relies on precise phenotypic and genotypic analysis, with the Human Phenotype Ontology (HPO) providing a standardized language for capturing clinical phenotypes. Traditional HPO tools, such as Doc2HPO and ClinPhen, employ concept recognition to automate phenotype extraction but struggle with incomplete phenotype assignment, often requiring intensive manual review. While large language models (LLMs) hold promise for more context-driven phenotype extraction, they are prone to errors and “hallucinations,” making them less reliable without further refinement. We present RAG-HPO, a Python-based tool that leverages Retrieval-Augmented Generation (RAG) to elevate LLM accuracy in HPO term assignment, bypassing the limitations of baseline models while avoiding the time and resource intensive process of fine-tuning. RAG-HPO integrates a dynamic vector database, allowing real-time retrieval and contextual matching.

Methods

The high-dimensional vector database utilized by RAG-HPO includes >54,000 phenotypic phrases mapped to HPO IDs, derived from the HPO database and supplemented with additional validated phrases. The RAG-HPO workflow uses an LLM to first extract phenotypic phrases that are then matched via semantic similarity to entries within a vector database before providing best term matches back to the LLM as context for final HPO term assignment. A benchmarking dataset of 120 published case reports with 1,792 manually-assigned HPO terms was developed, and the performance of RAG-HPO measured against existing published tools Doc2HPO, ClinPhen, and FastHPOCR.

Results

In evaluations, RAG-HPO, powered by Llama-3 70B and applied to a set of 120 case reports, achieved a mean precision of 0.84, recall of 0.78, and an F1 score of 0.80—significantly surpassing conventional tools (p<0.00001). False positive HPO term identification occurred for 15.8% (256/1,624) of terms, of which only 2.7% (7/256) represented hallucinations, and 33.6% (86/256) unrelated terms; the remainder of false positives (63.7%, 163/256) were relative terms of the target term.

Conclusions

RAG-HPO is a user-friendly, adaptable tool designed for secure evaluation of clinical text and outperforms standard HPO-matching tools in precision, recall, and F1. Its enhanced precision and recall represent a substantial advancement in phenotypic analysis, accelerating the identification of genetic mechanisms underlying rare diseases and driving progress in genetic research and clinical genomics.
Extreme MetaboHealth scores in three cohort studies associate with plasma protein markers for inflammation and cholesterol transport
Authors: Bizzarri D. , van den Akker E.B. , Reinders M.J.T. , Pool R. , Beekman M. , Lakenberg N. , Drouin N. , Stecker K.E. , Heck A.J.R. , Knol E.F. , Vergeer J.M. , Ikram M.A. , Ghanbari M. , van Gool A.J. ,   BBMRI-NL, Boomsma D.I. , Slagboom P.E.
Published: December 2024

The MetaboHealth score is a highly informative health indicator in ageing studies and yet contains only a small number of metabolites. Here we estimate the heritability of the score in 726 monozygotic (MZ) and 450 dizygotic (DZ) twin pairs, and test for association with plasma proteins by comparing extreme scoring individuals selected from two large population cohorts -the Leiden Longevity Study (LLS) and the Rotterdam Study (RS) and discordant monozygotic twin pairs from the Netherlands Twin Register (NTR).

The heritability for the MetaboHealth score was estimated at 40%. In 50 high and 50 low scoring MetaboHealth groups from LLS and RS, we uncovered significant differences in plasma proteins, notably in 3 (out of 15) cytokines (GDF15, IL6, and MIG), and 106 proteins (out of 289) as determined by Mass Spectrometry based proteomics analysis. A high MetaboHealth score associated with an increased level for 42 serum proteins, predominantly linked to inflammation and immune response, including CRP and HPT. A low score associated with decreased levels of 71 proteins enriched in high-density lipoprotein (HDL) remodeling and cholesterol transport pathways, featuring proteins such as APOA1, APOA2, APOA4, and TETN.

In MZ twins selected for maximal discordance within a pair we found 68 serum proteins associated with the MetaboHealth score indicating that a minor part of the associations observed in LLS and RS is likely explained by genetic influences. Taken together, our study sheds light on the intricate interplay between MetaboHealth, plasma proteins, cytokines, and genetic influences, paving the way for future investigations aimed at optimizing this mortality risk indicator.
Detection of Pneumonia in Children through Chest Radiographs using Artificial Intelligence in a Low-Resource Setting: A Pilot Study
Authors: Togunwa Taofeeq Oluwatosin , Babatunde Abdulhammed Opeyemi , Fatade Oluwatosin Ebunoluwa , Olatunji Richard , Ogbole Godwin , Falade Adegoke
Published: December 2024

Pneumonia is a leading cause of death among children under 5 years in low-and-middle-income-countries (LMICs), causing an estimated 700,000 deaths annually. This burden is compounded by limited diagnostic imaging expertise. Artificial intelligence (AI) has potential to improve pneumonia diagnosis from chest radiographs (CXRs) through enhanced accuracy and faster diagnostic time. However, most AI models lack validation on prospective clinical data from LMICs, limiting their real-world applicability. This study aims to develop and validate an AI model for childhood pneumonia detection using Nigerian CXR data. In a multi-center cross-sectional study in Ibadan, Nigeria, CXRs were prospectively collected from University College Hospital (a tertiary hospital) and Rainbow-Scans (a private diagnostic center) radiology departments via cluster sampling (November 2023–August 2024). An AI model was developed on open-source paediatric CXR dataset from the USA, to classify the local prospective CXRs as either normal or pneumonia. Two blinded radiologists provided consensus classification as the reference standard. The model's accuracy, precision, recall, F1-score, and area-under-the-curve (AUC) were evaluated. The AI model was developed on 5,232 open-source paediatric CXRs, divided into training (1,349 normal, 3,883 pneumonia) and internal test (234 normal, 390 pneumonia) sets, and externally tested on 190 radiologist-labeled Nigerian CXRs (93 normal, 97 pneumonia). The model achieved 86% accuracy, 0.83 precision, 0.98 recall, 0.79 F1-score, and 0.93 AUC on the internal test, and 58% accuracy, 0.62 precision, 0.48 recall, 0.68 F1-score, and 0.65 AUC on the external test. This study illustrates AI’s potential for childhood pneumonia diagnosis but reveals challenges when applied across diverse healthcare environments, as revealed by discrepancies between internal and external evaluations. This performance gap likely stems from differences in imaging protocols/equipment between LMICs and high-income settings. Hence, public health priority should be developing robust, locally relevant datasets in Africa to facilitate sustainable and independent AI development within African healthcare.