bluuebunny/crossref_metadata_2025_split huggingface dataset:
Secondary sclerosing cholangitis due to drug-induced liver injury: a retrospective cohort study
Authors: Chen Qiannan , Kong Derun , Liu Xiaochang 
Published: December 2024

Background
The main objective of our study was to assess the frequency of drug-induced liver injury (DILI) patients with coexisting secondary sclerosing cholangitis (SSC) within our center and then analyze clinical features of these patients. SSC has received limited attention in the context of DILI. These changes can be observed on magnetic resonance cholangiopancreatography (MRCP).

Methods
We conducted a single-center retrospective cohort study involving 185 consecutive patients diagnosed with DILI between January 2020 and August 2024. We reviewed MRCP images of 81 available patients.

Results
Among the 185 patients, 81 underwent MRCP and 14 patients (17.3%) were diagnosed with SSC. Nine (64.3%) of 14 were diagnosed with biliary strictures in extrahepatic bile ducts, and 11 of 14 patients (78.6%) displayed segmental distribution. The SSC group showed higher peak alkaline phosphatase (ALP) values (660 vs. 290 U/l, P = 0.015), longer resolution time (114 vs. 61 days, P = 0.038), and a higher frequency of chronic injury (35.7% vs. 10.4%, P = 0.016). Multivariate logistic regression analysis identified peak ALP values as a risk factor for SSC [odds ratio = 1.002 (1.000–1.005), P = 0.030].

Conclusion
The prevalence of drug-related SSC has noticeably increased in recent years. The higher peak ALP values potentially associated with an increased risk of drug-related SSC onset.
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.
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.
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

ABSTRACT
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.
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

AbstractMetagenomic 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

ABSTRACTMetagenome 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.IMPORTANCEThe 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

ABSTRACTDespite 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.