bluuebunny/crossref_metadata_2025_split huggingface dataset:
Positive deviance/hearth intervention in collaboration between academia and NGOs: a realist evaluation
Authors: Putri Nuzulul Kusuma , Wardhani Leonika Pramudya , Ernawaty  
Published: December 2024

AbstractNumerous NGOs and donors from high-income countries (HICs) offer diverse funding to assist LMICs. A collaborative effort in nutrition programs in urban communities was conducted by an international NGO with a local university, representing the NGO’s first mode of partnership with academia. This study used realist evaluation to understand how and why Positive Deviance/Hearth intervention conducted by NGOs collaborated with university work or failed to work in urban population. We uncovered the underlying mechanisms that lead to certain outcomes in different situations of academia-NGO partnership. The initial program theory was formulated after discussions with main program officers from both NGO and academia. We conducted stakeholder interviews and FGD, along with validation and reviewing secondary data. The initial program theory underwent testing and refinement through a series of Focus Group Discussions (FGDs) involving program officers and local government health offices. We adhered to the RAMESES II reporting standards for realist evaluations when presenting the findings. Five Context Mechanism-Outcome (CMO) configurations are identified from three program theories. Our findings illustrate the importance of considering the local context of the population when implementing standardized international NGO interventions. All the CMOs indicate that at the very least, collaborative programs between academia and NGOs should involve more stakeholder involvement and build clearer expectations between stakeholders.
Evaluation of dentists’ clinical practices and antibiotic use in managing endodontic emergencies in Karachi, Pakistan: a cross-sectional survey
Authors: Yaqoob Hassan , Naved Nighat , Khan Shahrukh Ali , Jabeen Syeda Farah , Raza Syed Saqib , Khalid Taimur 
Published: December 2024

Abstract
Background
Endodontic emergencies, often presented as acute pain or swelling, constitute a substantial challenge in dental practice. While effective management emphasizes prompt intervention, antibiotics are typically indicated only when systemic signs and symptoms are present. There is limited research exists on evaluating the knowledge and clinical approach of dental practitioners in managing endodontic emergencies from our region of the world. Therefore, this study aims to evaluate dentists' knowledge, attitude, and practices regarding clinical management and the prescription of antibiotics in endodontic emergency cases.

Materials and methods
A web-based questionnaire was distributed to working dentists in secondary and tertiary care hospitals and clinics. Eligible participants included dental practitioners, postgraduate trainees, and consultants. The questionnaire included demographic information and inquiries about endodontic emergency treatment approaches, antibiotic prescribing habits, and awareness of guidelines. Statistical analysis was performed Stata software version 17 (StataCorp, College Station, Texas, USA), employing a χ2 test.

Results
Of the 527 dentists approached, 409 completed the survey (response rate: 77.6%). The majority of respondents were female (68%) and general dental practitioners (60.32%) with up to 5 years of experience (80.93%). Survey findings highlighted varied treatment approaches, favoring root canal treatment in multiple visits for cases of both irreversible pulpitis (73.59%) as well as with necrotic pulps/periapical lesions (79.95%). Similarly, 45.48% and 37.9% of the respondents favored pulpectomy combined with analgesics and antibiotics in managing irreversible pulpitis and acute apical periodontitis respectively. Moreover, antibiotics were frequently prescribed for acute apical abscess, with amoxicillin-clavulanate being the most common choice (83.6%). Most practitioners (69%) recommended a minimum of 5-day antibiotic course.

Conclusions
This study highlights Pakistani dentists' preferences in managing endodontic emergencies and prescribing antibiotics. Despite awareness of guidelines and the consequences of overuse, there's a tendency towards antibiotic overprescription, indicating a need for educational interventions to promote rational antibiotic use and mitigate antibiotic resistance.
Factors associated with patients’ demand for low-value care: a scoping review
Authors: Fraser Gillroy R. L. , Lambooij Mattijs S. , van Exel Job , Ostelo Raymond W. J. G. , van Harreveld Frenk , de Wit G. Ardine 
Published: December 2024

Abstract
Background
Low-value care is unnecessary care that contributes to inefficient use of health resources and constitutes a considerable proportion of healthcare expenditures worldwide. Factors contributing to patients’ demand for low-value care have often been overlooked and are dispersed in the literature. Therefore, the current study aimed to systematically summarize factors associated with patients’ demand for low-value care.

Methods
In this scoping review, scientific articles were identified based on a search query conducted in Embase and Scopus. We identified articles using search terms related to low-value care and demand-related factors, published in peer-reviewed journals, and written in English or Dutch. The titles, abstracts, results, and conclusions were inspected to only include articles that were deemed relevant for this topic. From these articles we extracted text fragments that contained factors associated with patients’ demand for low-value care. Hereafter, a thematic analysis was applied to openly, axially, and selectively code textual fragments to identify themes within the data.

Results
Forty-seven articles were included in this review. We identified eight core themes associated with patients’ demand for low-value care: cognitive biases, emotions, preferences and expectations, knowledge-related factors, socio-cultural factors, biomedical and care-related factors, economic factors, and factors related to the interaction with the healthcare provider. Within these core themes, thirty-three subthemes were identified. For example, risk aversion and anticipated regret aversion are sub-themes of cognitive biases, while consumerism and present and future income effects are sub-themes of economic factors.

Conclusions
Through this review we provide a systematic overview of factors associated with the demand for low-value care. We found that patients’ demand for low-value care could relate to a multitude of factors that were clustered into eight core themes and thirty-three subthemes. To understand the demand for low-value care from the patient’s perspective in greater detail, future research should focus on the interaction between and importance of these factors in different care contexts.
Economic evaluation of tenofovir disoproxil fumarate prophylaxis to prevent mother-to-child transmission of Hepatitis B virus infection: evidence from a lower-middle income country
Authors: Nguyen Ha T. , Chaikledkaew Usa , Hoang Minh V. , Tran Viet Q. , Thavorncharoensap Montarat , Praditsitthikorn Naiyana , Tran Quang D. , Thakkinstian Ammarin 
Published: December 2024

AbstractNo cost-effectiveness information of preventive strategies for mother-to-child transmission (MTCT) of hepatitis B virus (HBV) has existed for policy decision making. This study aimed to compare the cost-effectiveness of alternative strategies to prevent MTCT of HBV in Vietnam. Cost-utility analysis using a hybrid decision-tree and Markov model were performed from healthcare system and societal perspectives. Preventive strategies included HBV universal vaccination (S1), hepatitis B immunoglobulin (HBIG) for infants of mothers with HBeAg( +) (S2), HBIG for infants of mothers with HBsAg( +) (S3), tenofovir disoproxil fumarate (TDF) for mothers with high viral load (S4) and mothers with HBeAg( +) (S5), and the current practice (S6) with HBV vaccine in all infants and TDF for high viral load mothers. The current practice was dominant to all preventive strategies with interventions in only infants for both perspectives. In contrast, the strategies S4 and S5 were dominant to the current practice with incremental net monetary benefit varying from $33.94 to $70.64 under a healthcare system perspective and from $44.22 to $93.71 under a societal perspective. Addition of HBIG in infants born to mothers infected HBV and tenofovir prophylaxis for mothers with positive HBeAg was the most cost-effective strategy to prevent vertical transmission of HBV in Vietnam.
Aicardi-Goutières syndrome type 6: report of ADAR variant and clinical outcome after ruxolitinib treatment in the neonatal period
Authors: Gabaldon-Albero Alba , Martin-Grau Carla , Marti-Masanet Miguel , Lopez-Jimenez Alejandro , Llorens Roberto , Beseler-Soto Beatriz , Martin-Zamora Sergio , Lopez Berta , Calvo Inmaculada , Hernandez-Muela Sara , Rosello Monica , Orellana Carmen , Martinez Francisco 
Published: December 2024

Abstract
Background
Aicardi-Goutières Syndrome is a monogenic type 1 interferonopathy with infantile onset, characterized by a variable degree of neurological damage. Approximately 7% of Aicardi-Goutières Syndrome cases are caused by pathogenic variants in the ADAR gene and are classified as Aicardi-Goutières Syndrome type 6. Here, we present a new homozygous pathogenic variant in the ADAR gene. Currently, Janus Kinase inhibitors have been proposed to treat selected interferonopathies such as Aicardi-Goutières Syndrome, although limited information is available on its use and results in the neonatal presentation of this disease.

Case presentation
We present two siblings, a male neonate with congenital petechial rash, severe thrombopenia and generalized hypotonia and his deceased sister who had normal development until 5 months of age, when she suffered acute encephalopathy. We describe the clinical course, complementary examinations and follow-up with early treatment of the newborn with ruxolitinib. The homozygous variant c.2908G > A (p.Ala970Thr) in the ADAR gene was found in both siblings, parents were heterozygous carriers.

Conclusions
The homozygous variant c.2908G > A (p.Ala970Thr) in the ADAR gene causes Aicardi-Goutières Syndrome type 6. Intrafamilial phenotypic spectrum of the disease varies among individuals with the same pathogenic variant. Early initiation of ruxolitinib improved systemic signs but did not prevent the progression of neurological disease.
Definitions, epidemiology, and outcomes of persistent/chronic critical illness: a scoping review for translation to clinical practice
Authors: Ohbe Hiroyuki , Satoh Kasumi , Totoki Takaaki , Tanikawa Atsushi , Shirasaki Kasumi , Kuribayashi Yoshihide , Tamura Miku , Takatani Yudai , Ishikura Hiroyasu , Nakamura Kensuke ,   J-STAD (JAPAN Sepsis Treatment and Diagnosis) Study Group
Published: December 2024

Abstract
Background
Medical advances in intensive care units (ICUs) have resulted in the emergence of a new patient population—those who survive the initial acute phase of critical illness, but require prolonged ICU stays and develop chronic critical symptoms. This condition, often termed Persistent Critical Illness (PerCI) or Chronic Critical Illness (CCI), remains poorly understood and inconsistently reported across studies, resulting in a lack of clinical practice use. This scoping review aims to systematically review and synthesize the existing literature on PerCI/CCI, with a focus on definitions, epidemiology, and outcomes for its translation to clinical practice.

Methods
A scoping review was conducted using MEDLINE and Scopus, adhering to the PRISMA-ScR guidelines. Peer-reviewed original research articles published until May 31, 2024 that described adult PerCI/CCI in their definitions of patient populations, covariates, and outcomes were included. Data on definitions, epidemiology, and outcomes were extracted by a data charting process from eligible studies and synthesized.

Results
Ninety-nine studies met the inclusion criteria. Of these studies, 64 used the term CCI, 18 used PerCI, and 17 used other terms. CCI definitions showed greater variability, while PerCI definitions remained relatively consistent, with an ICU stay ≥ 14 days for CCI and ≥ 10 days for PerCI being the most common. A meta-analysis of the prevalence of PerCI/CCI among the denominators of “all ICU patients”, “sepsis”, “trauma”, and “COVID-19” showed 11% (95% confidence interval 10–12%), 28% (22–34%), 24% (15–33%), and 35% (20–50%), respectively. A meta-analysis of in-hospital mortality was 27% (26–29%) and that of one-year mortality was 45% (32–58%). Meta-analyses of the prevalence of CCI and PerCI showed 17% (16–18%) and 18% (16–20%), respectively, and those for in-hospital mortality were 28% (26–30%) and 26% (24–29%), respectively. Functional outcomes were generally poor, with many survivors requiring long-term care.

Conclusions
This scoping review synthesized many studies on PerCI/CCI, highlighting the serious impact of PerCI/CCI on patients’ long-term outcomes. The results obtained underscore the need for consistent terminology with high-quality research for PerCI/CCI. The results obtained provide important information to be used in discussions with patients and families regarding prognosis and care options.

Graphical abstract
A randomized trial of low-dose thrombolysis, ultrasound-assisted thrombolysis, or heparin for intermediate-high risk pulmonary embolism—the STRATIFY trial: design and statistical analysis plan
Authors: Kjærgaard Jesper , Carlsen Jørn , Sonne-Holm Emilie , Wiberg Sebastian , Holmvang Lene , Lassen Jens Flensted , Sørensen Rikke , Høfsten Dan , Ulriksen Peter Sommer , Jawad Samir , Palm Pernille , Thune Jens Jakob , Hassager Christian , Kristiansen Ole P. , Eskesen Kristian , Fanø Søren , Bang Lia E. 
Published: December 2024

Abstract
Background
Intermediate-high risk pulmonary embolism (PE) carries a significant risk of hemodynamic deterioration or death. Treatment should balance efficacy in reducing clot burden with the risk of complications, particularly bleeding. Previous studies on high-dose, short-term thrombolysis with alteplase (rtPA) showed a reduced risk of hemodynamic deterioration but no change in mortality and increased bleeding complications. Catheter-based techniques, including ultrasound-assisted thrombolysis (USAT), and low-dose thrombolysis may offer reasonable efficacy with lower risk. However, studies comparing these methods have been few. This trial aims to address this gap by randomizing patients to three treatment modalities.

Methods
Multicenter, randomized trial with 1:1:1 allocation of 210 patients with acute intermediate-high risk PE, excluding those with absolute contraindications to thrombolysis. Patients are eligible for inclusion if they are > 18 years of age, have had symptoms < 14 days, and are able to give informed consent. Patients are allocated 1:1:1 into three treatment strategies: (1) unfractionated heparin (UFH)/low molecular weight heparin (LMWH), (2) UFH/LMWH + 20 mg rtPA/6 h intravenously (IV), or (3) UFH + 20 mg rtPA/6 h via USAT. Co-primary outcomes include reduction in clot burden as assessed by refined Miller score from pre-treatment to follow-up (48–96 h) computed tomography pulmonary angiogram (CTPA) comparing low-dose rtPA (± USAT) groups to UFH/LMWH group (p < 0.01, N = 210) and reduction in refined Miller score on follow-up CT angiography comparing low-dose rtPA by USAT to intravenous rtPA, p < 0.04, N = 140). Secondary outcomes comprise bleeding complications, duration of index admission, FiO2, blood pressure, respiratory and heart rate at the time of follow-up CT angiography, mortality in the three groups, incidence of tricuspid regurgitation pressure gradient < 40 mmHg at 3 months follow-up echocardiography, 6-min walk test at 3 months comparing the three groups, and health-related quality of life at 3 months follow-up comparing the three groups.

Discussion
We hypothesize that in patients with intermediate-high risk PE (1) administration of 20 mg rtPA leads to a greater reduction in clot burden compared to heparins and (2) administration of 20 mg rtPA via USAT results in a greater reduction in clot burden compared to 20 mg rtPA intravenous.

Trial registration
ClinicalTrials.gov NCT04088292. Registered in September 2019 (retrospectively registered).
Morphological and molecular characterization of a Sarcocystis bovifelis-like sarcocyst in American beef
Authors: Gupta Aditya , de Araujo Larissa S. , Hemphill Andrew , Khan Asis , Rosenthal Benjamin M. , Dubey Jitender P. 
Published: December 2024

Abstract

Background
Parasites in the apicomplexan genus Sarcocystis infect cattle worldwide. Assessing the economic importance of each such parasite species requires proper diagnosis. Sarcocystis
cruzi, a thin-walled species, infects virtually all cattle. The prevalence of the other thin-walled parasite, Sarcocystis
heydorni, remains less well established. The remaining six species all have thick (> 3 µm) cyst walls (Sarcocystis
hirsuta,
S.
hominis,
S.
bovifelis,
S.
bovini,
S.
sigmoideus, and S.
rommeli). Thick-walled sarcocysts often induce inflammation in striated muscles (causing bovine eosinophilic myositis), leading to condemnation of carcasses at slaughter. One of these, S.
hirsuta, can be seen macroscopically and lead to condemnation of beef. Two Sarcocystis species, S.
hominis and S.
heydorni, are zoonotic. Although S.
hominis has been reported as prevalent in Europe, the occurrence of thick-walled species in the US remains poorly known. Here, for the first time to our knowldge, we characterize a thick-walled Sarcocystis species from a sample of beef from a local grocery store in Maryland. By morphological and genetic criteria, it closely, but not perfectly, resembles parasites previously ascribed to S.
bovifelis.

Methods
Beef samples were examined for Sarcocystis infection, using acid-pepsin digestion to search for bradyzoites, microscopically by compression between a glass slide and coverslip, by histology of paraffin embedded sections stained with hematoxylin and eosin, and by transmission electron microscopy (TEM). Molecular characterization was attempted employing genetic markers: 18S rRNA, 28S rRNA, cox1, ITS1, gapdh1, ron3, and rpoB.

Results
Molecular evaluation revealed 100% identity with S.
bovifelis-like sarcocysts from naturally infected cattle from Germany and Argentina; although the condition of the frozen material precludes complete characterization by TEM, we noted morphological features which differed from the S.
bovifelis originally described from experimentally infected cattle from Germany.

Conclusions
A novel Sarcocystis species is described from beef from the USA but not named until further evaluation.

Graphical Abstract
Metagenome-validated combined amplicon sequencing and text mining-based annotations for simultaneous profiling of bacteria and fungi: vaginal microbiota and mycobiota in healthy women
Authors: Virtanen Seppo , Saqib Schahzad , Kanerva Tinja , Ventin-Holmberg Rebecka , Nieminen Pekka , Holster Tiina , Kalliala Ilkka , Salonen Anne 
Published: December 2024

Abstract
Background
Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial communities. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene and ITS1 amplicons were pooled together for a single Illumina MiSeq or HiSeq run and analysed after primer-based segregation. Taxonomic assignments were performed with Blast in combination with an iterative text-extraction-based filtration approach, which uses extensive literature records from public databases to select the most probable hits that were further validated by shotgun metagenomic sequencing.

Results
Using 50 vaginal samples, we show that the combined run provides comparable results on bacterial composition and diversity to conventional 16S rRNA gene amplicon sequencing. The text-extraction-based taxonomic assignment-guided tool provided ecosystem-specific bacterial annotations that were confirmed by shotgun metagenomic sequencing (VIRGO, MetaPhlAn, Kraken2). Fungi were identified in 39/50 samples with ITS sequencing while in the metagenome data fungi largely remained undetected due to their low abundance and database issues. Co-abundance analysis of bacteria and fungi did not show strong between-kingdom correlations within the vaginal ecosystem of healthy women.

Conclusion
Combined amplicon sequencing for bacteria and fungi provides a simple and cost-effective method for simultaneous analysis of microbiota and mycobiota within the same samples. Conventional metagenomic sequencing does not provide sufficient fungal genome coverage for their reliable detection in vaginal samples. Text extraction-based annotation tool facilitates ecosystem-specific characterization and interpretation of microbial communities by coupling sequence homology to microbe metadata readily available through public databases.
Insights into genetic aberrations and signalling pathway interactions in chronic lymphocytic leukemia: from pathogenesis to treatment strategies
Authors: Sobczyńska-Konefał Anna , Jasek Monika , Karabon Lidia , Jaskuła Emilia 
Published: December 2024

AbstractChronic lymphocytic leukemia (CLL) is prevalent in adults and is characterized by the accumulation of mature B cells in the blood, bone marrow, lymph nodes, and spleens. Recent progress in therapy and the introduction of targeted treatments [inhibitors of Bruton's tyrosine kinase (BTKi) or inhibitor of anti-apoptotic B-cell lymphoma-2 (Bcl-2i) protein (venetoclax)] in place of chemoimmunotherapy have significantly improved the outcomes of patients with CLL. These advancements have shifted the importance of traditional predictive markers, leading to a greater focus on resistance genes and reducing the significance of mutations, such as TP53 and del(17p). Despite the significant progress in CLL treatment, some patients still experience disease relapse. This is due to the substantial heterogeneity of CLL as well as the interconnected genetic resistance mechanisms and pathway adaptive resistance mechanisms to targeted therapies in CLL. Although the knowledge of the pathomechanism of CLL has expanded significantly in recent years, the precise origins of CLL and the interplay between various genetic factors remain incompletely understood, necessitating further research. This review enhances the molecular understanding of CLL by describing how BCR signalling, NF-κB PI3K/AKT, and ROR1 pathways sustain CLL cell survival, proliferation, and resistance to apoptosis. It also presents genetic and pathway-adaptive resistance mechanisms in CLL. Identifying B-cell receptor (BCR) signalling as a pivotal driver of CLL progression, the findings advocate personalized treatment strategies based on molecular profiling, emphasizing the need for further research to unravel the complex interplay between BCR signalling and its associated pathways to improve patient outcomes.