bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiology and genotypes analysis of human papillomavirus infection in Beijing, China
Authors: Wang Jiao , Li Haotian , Zhang Jieqiong , Wang Hui , Li Ying , Liu Zhaohui , Liu Hongtu 
Published: January 2024

Abstract
Background
This study aimed to investigate the epidemiology of high-risk human papillomavirus (HPV) in the female population in Beijing, China, and identify the relationship between HPV genotypes and host factors.

Methods
HPV testing was performed on women aged 15–89 (mean age 38.0 ± 10.9 years) from Beijing in 2020. High-risk HPV genotyping real-time polymerase chain reaction was used to determine HPV genotypes. The overall prevalence, age-specific prevalence, genotype distribution, and the correlation between HPV genotypes and cervical cytology were analyzed.

Results
Among the 25,344 study participants, the single and double infection rates were 18.8% (4,777/25,344) and 4.2% (1,072/25,344), respectively. A total of 6,119 HPV-positive individuals were found to have 91.6% negative results for intraepithelial lesion or malignancy (NILM), 5.8% atypical squamous cells of undetermined significance (ASC-US), 0.9% low-grade squamous intraepithelial lesion (LSIL), and 1.7% high-grade squamous intraepithelial lesion (HSIL). In single HPV infections, the HPV16 genotype was highly associated with cervical cytology severity (χ2 trend = 172.487, P < 0.001). Additionally, HPV infection rates increased gradually with age, and statistical differences were observed across age groups (χ2 = 180.575; P < 0.001). High-risk HPV genotypes were highly prevalent in women below 25 years of age and those aged 55–59 years. Cluster analysis revealed that the 13 HPV genotypes could be roughly divided into two groups in a single infection; however, patterns of infection consistent with biological characteristics were not observed.

Conclusion
High-risk HPV was found in 24.1% of outpatients, with HPV52, HPV58, HPV16, HPV39, and HPV51 being the most common high-risk genotypes. Single high-risk HPV infection was predominant. HPV16, HPV39, HPV51, and HPV52 were associated with cervical lesion progression. HPV16 infection was especially worrying since it aggravates cervical lesions. Because the infection rates of the 13 HPV genotypes differed by age, the peak HPV infection rate should not guide vaccination, screening, and prevention programs. Instead, these initiatives should be tailored based on the regional HPV distribution characteristics. Moreover, it was determined that Beijing’s populace needed to receive treatment for HPV39 infection.
Clinical efficacy of percutaneous endoscopic posterior lumbar interbody fusion and modified posterior lumbar interbody fusion in the treatment of lumbar degenerative disease
Authors: Liu Zhengping , Wang Siyu , Li Tao , Chen Si , Li Ying , Xie Wei , Tang Jin 
Published: January 2024

Abstract
Background
To compare the early clinical efficacy of percutaneous endoscopic posterior lumbar interbody fusion (PE-PLIF) and modified posterior lumbar interbody fusion (MPLIF) in the treatment of lumbar degenerative disease (LDD).

Methods
A total of 37 patients who underwent PE-PLIF and 58 patients who underwent MPLIF from March 2019 to January 2022 were retrospectively reviewed. The operation time, intraoperative blood loss, post-operative hospitalization time, and post-operative bedrest time were recorded. The visual analogue scale (VAS) scores of leg pain and low back pain, Japanese Orthopaedic Association (JOA) scores, and the Oswestry Disability Index (ODI) scores were evaluated and compared before the operation, 3 days after the operation, 1 week after the operation, 1 month after the operation, 6 months after the operation and at the last follow-up. The modified MacNab’s criteria were applied at the last follow-up. The fusion rate and surgical-related complications during follow-up were recorded.

Results
The average operation time in the PE-PLIF group was highly significant longer than that in the MPLIF group (P < 0.01). The intraoperative blood loss, post-operative hospitalization time, and post-operative bedrest time were significantly less in the PE-PLIF group than those in the MPLIF group (P < 0.01). There were highly significant differences in VAS scores of leg pain, VAS scores of low back pain, JOA scores, ODI scores at the last follow-up compared with those before the operation in the two groups (P < 0.01). Three days after the operation and 1 week after the operation, the VAS scores for low back pain and ODI were highly significant less in the PE-PLIF group than that in the MPLIF group (P < 0.01). Three days after the operation, the JOA scores were highly significant higher in the PE-PLIF group than that in the MPLIF group (P < 0.01). All patients showed intervertebral fusion at 6 months after the operation. Two patients (5.4%) in the PE-PLIF group experienced complications.

Conclusion
Both PE-PLIF and MPLIF surgery were clinically effective and safe for patients with single-segment LDD. PE-PLIF surgery is a promising technique that can be used as an alternative treatment for single-segment LDD.
Multimodal epigenetic sequencing analysis (MESA) of cell-free DNA for non-invasive colorectal cancer detection
Authors: Li Yumei , Xu Jianfeng , Chen Chaorong , Lu Zhenhai , Wan Desen , Li Diange , Li Jason S. , Sorg Allison J. , Roberts Curt C. , Mahajan Shivani , Gallant Maxime A. , Pinkoviezky Itai , Cui Ya , Taggart David J. , Li Wei 
Published: January 2024

Abstract
Background
Detecting human cancers through cell-free DNA (cfDNA) in blood is a sensitive and non-invasive option. However, capturing multiple forms of epigenetic information remains a technical and financial challenge.

Methods
To address this, we developed multimodal epigenetic sequencing analysis (MESA), a flexible and sensitive approach to capturing and integrating a diverse range of epigenetic features in cfDNA using a single experimental assay, i.e., non-disruptive bisulfite-free methylation sequencing, such as Enzymatic Methyl-seq. MESA enables simultaneous inference of four epigenetic modalities: cfDNA methylation, nucleosome occupancy, nucleosome fuzziness, and windowed protection score for regions surrounding gene promoters and polyadenylation sites.

Results
When applied to 690 cfDNA samples from 3 colorectal cancer clinical cohorts, MESA’s novel modalities, which include nucleosome fuzziness, and genomic features, including polyadenylation sites, improve cancer detection beyond the traditional epigenetic markers of promoter DNA methylation.

Conclusions
Together, MESA stands as a major advancement in the field by utilizing comprehensive and complementary epigenetic profiles of cfDNA for effective non-invasive cancer detection.
The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young
Authors: Puckelwartz Megan J. , Pesce Lorenzo L. , Hernandez Edgar J. , Webster Gregory , Dellefave-Castillo Lisa M. , Russell Mark W. , Geisler Sarah S. , Kearns Samuel D. , Karthik Felix , Etheridge Susan P. , Monroe Tanner O. , Pottinger Tess D. , Kannankeril Prince J. , Shoemaker M. Benjamin , Fountain Darlene , Roden Dan M. , Faulkner Meghan , MacLeod Heather M. , Burns Kristin M. , Yandell Mark , Tristani-Firouzi Martin , George Alfred L. , McNally Elizabeth M. 
Published: January 2024

Abstract
Background
Sudden unexpected death in children is a tragic event. Understanding the genetics of sudden death in the young (SDY) enables family counseling and cascade screening. The objective of this study was to characterize genetic variation in an SDY cohort using whole genome sequencing.

Methods
The SDY Case Registry is a National Institutes of Health/Centers for Disease Control and Prevention surveillance effort to discern the prevalence, causes, and risk factors for SDY. The SDY Case Registry prospectively collected clinical data and DNA biospecimens from SDY cases < 20 years of age. SDY cases were collected from medical examiner and coroner offices spanning 13 US jurisdictions from 2015 to 2019. The cohort included 211 children (median age 0.33 year; range 0–20 years), determined to have died suddenly and unexpectedly and from whom DNA biospecimens for DNA extractions and next-of-kin consent were ascertained. A control cohort consisted of 211 randomly sampled, sex- and ancestry-matched individuals from the 1000 Genomes Project. Genetic variation was evaluated in epilepsy, cardiomyopathy, and arrhythmia genes in the SDY and control cohorts. American College of Medical Genetics/Genomics guidelines were used to classify variants as pathogenic or likely pathogenic. Additionally, pathogenic and likely pathogenic genetic variation was identified using a Bayesian-based artificial intelligence (AI) tool.

Results
The SDY cohort was 43% European, 29% African, 3% Asian, 16% Hispanic, and 9% with mixed ancestries and 39% female. Six percent of the cohort was found to harbor a pathogenic or likely pathogenic genetic variant in an epilepsy, cardiomyopathy, or arrhythmia gene. The genomes of SDY cases, but not controls, were enriched for rare, potentially damaging variants in epilepsy, cardiomyopathy, and arrhythmia-related genes. A greater number of rare epilepsy genetic variants correlated with younger age at death.

Conclusions
While damaging cardiomyopathy and arrhythmia genes are recognized contributors to SDY, we also observed an enrichment in epilepsy-related genes in the SDY cohort and a correlation between rare epilepsy variation and younger age at death. These findings emphasize the importance of considering epilepsy genes when evaluating SDY.
Agenesis of the right lobe of the liver: a case report
Authors: Feleke Ashenafi Amsalu , Birhanu Friehiwot Amsalu , Tirfe Fraol Worku , Molla Yohannis Derbew 
Published: January 2024

Abstract
Introduction
Agenesis of the right hepatic lobe is a rare congenital anomaly. Developmental anomalies of the right lobe of the liver were first reported in 1870 by Heller [6]. Anatomical variations of the liver are common, occur during the normal development of the organ, and correspond to variations in the distribution of liver territories. Agenesis of the right lobe of the liver is an incidental finding revealed by the popularization of ultrasonography, computed tomography, or magnetic resonance imaging due to the condition being asymptomatic.

Case presentation
A 35-year-old Ethiopian female patient presented to the outpatient clinic with a complaint of right upper abdominal pain for 1 year, along with symptoms of fatty meal intolerance and long-standing epigastric burning pain. Her examination was unremarkable, and imaging investigations were suggestive of right hepatic lobe agenesis with multiple gallstones. Therefore, the patient was operated on and discharged with no perioperative complications.

Conclusion
Surgical understanding of such anatomical anomalies is necessary for surgical planning, the appropriate interpretation of intraoperative surgical findings, and the design of postoperative therapy. Here we report a case of right hepatic lobe agenesis with cholelithiasis and cholidocholithiasis and a brief review of right lobe agenesis in the literature.
Mechanical ventilation as a major driver of COVID-19 hospitalization costs: a costing study in a German setting
Authors: Zwerwer Leslie R. , Kloka Jan , van der Pol Simon , Postma Maarten J. , Zacharowski Kai , van Asselt Antoinette D. I. , Friedrichson Benjamin 
Published: January 2024

Abstract
Background
While COVID-19 hospitalization costs are essential for policymakers to make informed health care resource decisions, little is known about these costs in western Europe. The aim of the current study is to analyze these costs for a German setting, track the development of these costs over time and analyze the daily costs.

Methods
Administrative costing data was analyzed for 598 non-Intensive Care Unit (ICU) patients and 510 ICU patients diagnosed with COVID-19 at the Frankfurt University hospital. Descriptive statistics of total per patient hospitalization costs were obtained and assessed over time. Propensity scores were estimated for length of stay (LOS) at the general ward and mechanical ventilation (MV) duration, using covariate balancing propensity score for continuous treatment. Costs for each additional day in the general ward and each additional day in the ICU with and without MV were estimated by regressing the total hospitalization costs on the LOS and the presence or absence of several treatments using generalized linear models, while controlling for patient characteristics, comorbidities, and complications.

Results
Median total per patient hospitalization costs were €3,010 (Q1 – Q3: €2,224—€5,273), €5,887 (Q1 – Q3: €3,054—€10,879) and €21,536 (Q1 – Q3: €7,504—€43,480), respectively, for non-ICU patients, non-MV and MV ICU patients. Total per patient hospitalization costs for non-ICU patients showed a slight increase over time, while total per patient hospitalization costs for ICU patients decreased over time. Each additional day in the general ward for non-ICU COVID-19 patients costed €463.66 (SE: 15.89). Costs for each additional day in the general ward and ICU without and with mechanical ventilation for ICU patients were estimated at €414.20 (SE: 22.17), €927.45 (SE: 45.52) and €2,224.84 (SE: 70.24).

Conclusions
This is, to our knowledge, the first study examining the costs of COVID-19 hospitalizations in Germany. Estimated costs were overall in agreement with costs found in literature for non-COVID-19 patients, except for higher estimated costs for mechanical ventilation. These estimated costs can potentially improve the precision of COVID-19 cost effectiveness studies in Germany and will thereby allow health care policymakers to provide better informed health care resource decisions in the future.
Epigenetic reshaping through damage: promoting cell fate transition by BrdU and IdU incorporation
Authors: Li Chuang , Xu Xiaoduo , Chen Shuyan , Xu Anchun , Guan Tongxing , Wu Haokaifeng , Pei Duanqing , Liu Jing 
Published: January 2024

Abstract
Background
Thymidine analogs have long been recognized for their ability to randomly incorporate into DNA. However, the precise mechanisms through which thymidine analogs facilitate cell fate transition remains unclear.

Results
Here, we discovered a strong correlation between the dosage dependence of thymidine analogs and their ability to overcome reprogramming barrier. The extraembryonic endoderm (XEN) state seems to be a cell's selective response to DNA damage repair (DDR), offering a shortcut to overcome reprogramming barriers. Meanwhile, we found that homologous recombination repair (HRR) pathway causes an overall epigenetic reshaping of cells and enabling them to overcome greater barriers. This response leads to the creation of a hypomethylated environment, which facilitates the transition of cell fate in various reprogramming systems. We term this mechanism as Epigenetic Reshaping through Damage (ERD).

Conclusion
Overall, our study finds that BrdU/IdU can activate the DNA damage repair pathway (HRR), leading to increased histone acetylation and genome-wide DNA demethylation, regulating somatic cell reprogramming. This offers valuable insights into mechanisms underlying cell fate transition.

Graphical Abstract
RETRACTED ARTICLE: Future of low back pain: unravelling IVD components and MSCs’ potential
Authors: Leão Monteiro Raquel 
Published: January 2024

AbstractLow back pain (LBP) mainly emerges from intervertebral disc (IVD) degeneration. However, the failing mechanism of IVD ́s components, like the annulus fibrosus (AF) and nucleus pulposus (NP), leading to IVD degeneration/herniation is still poorly understood. Moreover, the specific role of cellular populations and molecular pathways involved in the inflammatory process associated with IVD herniation remains to be highlighted. The limited knowledge of inflammation associated with the initial steps of herniation and the lack of suitable models to mimic human IVD ́s complexity are some of the reasons for that. It has become essential to enhance the knowledge of cellular and molecular key players for AF and NP cells during inflammatory-driven degeneration. Due to unique properties of immunomodulation and pluripotency, mesenchymal stem cells (MSCs) have attained diverse recognition in this field of bone and cartilage regeneration. MSCs therapy has been particularly valuable in facilitating repair of damaged tissues and may benefit in mitigating inflammation’ degenerative events. Therefore, this review article conducts comprehensive research to further understand the intertwine between the mechanisms of action of IVD components and therapeutic potential of MSCs, exploring their characteristics, how to optimize their use and establish them safely in distinct settings for LPB treatment.
Support interventions to promote health and wellbeing among women with health-related consequences following traumatic experiences linked to armed conflicts and forced migration: a scoping review
Authors: Jolof Linda , Rocca Patricia , Carlsson Tommy 
Published: January 2024

Abstract
Background
Women exposed to armed conflicts and forced migration face significant health-related risks and consequences. Consequently, there is a need to identify and develop effective interventions that provide tailored support for them. The aim of this scoping review was to examine research evaluating support interventions promoting the health and well-being among women with traumatic experiences linked to armed conflict and/or forced migration.

Methods
A scoping review of empirical studies evaluating non-pharmacologic/non-surgical interventions promoting health and well-being among adult women with traumatic experiences linked to armed, torture, and/or forced migration, identified through systematic searches in February 2022 within five databases (AMED, CINAHL, Cochrane Library, PsycINFO, and PubMed). Methodological characteristics and results were extracted and analyzed with narrative analysis using tabulations, descriptive statistics, text-based summaries, and thematization.

Results
Assessment of 16 748 records resulted in 13 included reports. The methodological approaches were quantitative (n = 9), qualitative (n = 2), and mixed methods (n = 2), with most reports being feasibility/pilot studies (n = 5) and/or randomized controlled trials (n = 4). The most common recruitment strategy was non-probability sampling (n = 8). Most interventions were conducted in North America (n = 4), Asia (n = 3) or Middle East (n = 3). Thirteen intra-intervention techniques and five categories of components utilized within the interventions were identified, the most common being skill building (n = 12). Ten developed the interventions through theoretical frameworks or manuals/therapy, while five developed interventions through public or stakeholder involvement. Eleven studies evaluated outcomes related to psychological health, disorders, or distress. A large proportion of the investigated outcomes showed post-exposure improvements and improvements when compared with controls. Qualitative findings highlighted improved mental and physical health, empowerment and stigma reduction, and enhanced knowledge.

Conclusion
Few studies have developed and evaluated tailored support interventions for this population, containing a range of components and intra-intervention techniques. No clear focus was identified regarding outcome measures, and most studies used non-probability sampling. Few developed interventions through public contribution in collaboration with women. While limited studies show promising effects on women’s mental health, more empirical intervention research that closely corresponds to women’s needs are needed.
Epigenetic characterization of sarcopenia-associated genes based on machine learning and network screening
Authors: Chen Yong , Zhang Zhenyu , Hu Xiaolan , Zhang Yang 
Published: January 2024

AbstractTo screen characteristic genes related to sarcopenia by bioinformatics and machine learning, and to verify the accuracy of characteristic genes in the diagnosis of sarcopenia. Download myopia-related data sets from geo public database, find the differential genes through R language limma package after merging, STRING database to build protein interaction network, and do Go analysis and GSEA analysis to understand the functions and molecular signal pathways that may be affected by the differential genes. Further screen the characteristic genes through LASSO and SVM-RFE machine algorithms, make the ROC curve of the characteristic genes, and obtain the AUC value. 10 differential genes were obtained from the data set, including 7 upregulated genes and 3 downregulated genes. Eight characteristic genes were screened by a machine learning algorithm, and the AUC value of characteristic genes exceeded 0.7. In patients with sarcopenia, the expression of TPPP3, C1QA, LGR5, MYH8, and CDKN1A genes are upregulated, and the expression of SLC38A1, SERPINA5, and HOXB2 genes are downregulated. The above genes have high accuracy in the diagnosis of sarcopenia. The research results provide new ideas for the diagnosis and mechanism research of sarcopenia.
The future of organic certification: potential impacts of the inclusion of Participatory Guarantee Systems in the European organic regulation
Authors: Sacchi Giovanna , Romanello Lavinia , Canavari Maurizio 
Published: January 2024

AbstractThird-party certification (TPC) is the standard approach to quality assurance for organic production, but its administrative burden and cost make it difficult for smallholders to access it. Internal Control Systems (ICS) and Participatory Guarantee Systems (PGS) are possible alternative approaches because they are more accessible and less costly. Regulation (EU) 2018/848 on organic production allows ICS for small farmers. However, PGS are not included, despite being promoted by the International Federation of Organic Agriculture Movements (IFOAM) and officially recognised by several countries worldwide. This study aims to evaluate the possible future inclusion of PGS at the European level. Twenty-eight experts participated in a Delphi exercise, and both optimistic and pessimistic views were agreed upon amongst them. In the pessimistic view, bureaucratic excess and standardisation requirements needed in the process of PGS institutionalisation could emerge, resulting in even more rigid practices compared to the current ones. In the optimistic view, recognising PGS as a legitimate approach to guarantee the quality of organic products could foster the inclusion of smallholders by lowering certification costs, increasing cohesion and competencies amongst rural development actors and increasing the reputation of PGS-certified local products.