bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biofilm destruction activity of α-tocopherol against Staphylococcus aureus, Proteus mirabilis and Pseudomonas aeruginosa
Authors: Leong Pui Yee , Tan Wei Qi , Choo Wee Sim 
Published: February 2025

Abstract
Antibiotic resistance and the persistence of sessile cells within biofilms complicate the eradication of biofilm-related infections using conventional antibiotics. This highlights the necessity for alternate therapy methods. The objective of this study was to investigate the biofilm destruction activity of α-tocopherol against Staphylococcus aureus, Proteus mirabilis and Pseudomonas aeruginosa on polystyrene. α-Tocopherol showed significant biofilm destruction activity on the pre-formed biofilms of S. aureus (45–46%), Pr. mirabilis (42–54%) and Ps. aeruginosa (28%). Resazurin assay showed that α-tocopherol disrupted all bacteria biofilms without interfering with their cell viability. Scanning electron microscope images showed lower bacterial cell count and less compacted cell aggregates on polystyrene surfaces after treatment with alpha-tocopherol. This study demonstrated the biofilm destruction activity of alpha-tocopherol against S. aureus, Pr. mirabilis and Ps. aeruginosa. α-Tocopherol could potentially be used to decrease biofilm-associated infections of these bacteria.
Forensic comparison analysis of smokeless powders by gel permeation chromatography and likelihood ratio evaluation methods
Authors: Guo Hongling , Wang Ping , Hu Can , Mei Hongcheng , Li Yajun , Zhu Jun 
Published: February 2025

Abstract
In China, the use of smokeless powders for making homemade ammunition and bombs is an incipient criminal practice. One of the key tasks of analyzing smokeless powders in forensic sciences is to make comparisons between them, providing information about their source or establishing a link between two different smokeless powders seized at different locations. The main component of smokeless is nitrocellulose (NC) no matter what type of the smokeless powder is. As a kind of polymer, NC may have different molecular weights and polydispersity index (PDI) values, which could help the identification and differentiation of the smokeless powders. In this study, weight-average molecular weights (Mw), number-average molecular weights (Mn), and PDI value of 79 propellants samples from different sources were measured by gel permeation chromatography, and likelihood ratio evaluation method was applied to facilitate interpretation of the data. The possibility of using these methods to make comparisons between smokeless powders was explored instead of depending on analysis of target compounds with trace amounts in them.
Measuring linkage disequilibrium and improvement of pruning and clumping in structured populations
Authors: Bercovich Ulises , Rasmussen Malthe Sebro , Li Zilong , Wiuf Carsten , Albrechtsen Anders 
Published: February 2025

Abstract
Standard measures of linkage disequilibrium (LD) are affected by admixture and population structure, such that loci that are not in LD within each ancestral population appear linked when considered jointly across the populations. The influence of population structure on LD can cause problems for downstream analysis methods, in particular those that rely on LD pruning or clumping. To address this issue, we propose a measure of LD that accommodates population structure using the top inferred principal components. We estimate LD from the correlation of genotype residuals and prove that this LD measure remains unaffected by population structure when analyzing multiple populations jointly, even with admixed individuals. Based on this adjusted measure of LD, we can perform LD pruning to remove the correlation between markers for downstream analysis. Traditional LD pruning is more likely to remove markers with high differences in allele frequencies between populations, which biases measures for genetic differentiation and removes markers that are not in LD in the ancestral populations. Using data from moderately differentiated human populations and highly differentiated giraffe populations we show that traditional LD pruning biases FST and principal component analysis (PCA), which can be alleviated with the adjusted LD measure. In addition, we show that the adjusted LD leads to better PCA when pruning and that LD clumping retains more sites with the retained sites having stronger associations.
Telomere-to-telomere genome assembly and 3D chromatin architecture of Centella asiatica insight into evolution and genetic basis of triterpenoid saponin biosynthesis
Authors: Song Wan-ling , Chen Bao-zheng , Feng Lei , Chen Geng , He Si-mei , Hao Bing , Zhang Guang-hui , Dong Yang , Yang Sheng-chao 
Published: February 2025

Abstract
Centella asiatica is renowned for its medicinal properties, particularly due to its triterpenoid saponins, such as asiaticoside and madecassoside, which are in excess demand for the cosmetic industry. However, comprehensive genomic resources for this species are lacking, which impedes the understanding of its biosynthetic pathways. Here, we report a telomere-to-telomere (T2T) C. asiatica genome. The genome size is 438.12 Mb with a contig N50 length of 54.12 Mb. The genome comprises 258.87 Mb of repetitive sequences and 25,200 protein-coding genes. Comparative genomic analyses revealed that C. asiatica as early diverging genus within the Apiaceae family with a single whole-genome duplication (WGD, Apiaceae-ω) event following the ancient γ-triplication, contrasting with Apiaceae species that exhibit two WGD events (Apiaceae-α and Apiaceae-ω). We further constructed 3D chromatin structures, A/B compartments and topologically associated domains (TAD) in C. asiatica leaves, elucidating the influence of chromatin organization on expression WGD-derived genes. Additionally, gene family and functional characterization analysis highlight the key role of CasiOSC03 in α-amyrin production while also revealing significant expansion and high expression of CYP716, CYP714, and UGT73 families involved in asiaticoside biosynthesis compared to other Apiaceae species. Notably, a unique and large UGT73 gene cluster, located within the same TAD, is potentially pivotal for enhancing triterpenoid saponin. Weighted gene co-expression network analysis (WGCNA) further highlighted the pathways modulated in response to MeJA, offering insights into the regulatory networks governing saponin biosynthesis. This work not only provides a valuable genomic resource for C. asiatica but also sheds light on the molecular mechanisms driving the biosynthesis of pharmacologically important metabolites.
Impact of Psychosocial and Neurodevelopmental Disorders on Pediatric Ulcerative Colitis: A Single-Center, Retrospective, Observational Study
Authors: Nakamura Akio , Jimbo Keisuke , Suzuki Mitsuyoshi , Hibio Musashi , Nagata Masumi , Arai Nobuyasu , Miyata Eri , Kudo Takahiro , Hoshino Eri , Shoji Hiromichi 
Published: February 2025

Abstract

Background
This study aimed to evaluate the effects of psychosocial and neurodevelopmental disorders on pediatric ulcerative colitis management. Specifically, the relationships between these disorders and disease severity, as well as treatment strategies, were assessed through a single-center, retrospective, observational study.

Methods
The study included pediatric patients with ulcerative colitis (UC) under 15 years of age diagnosed by colonoscopy and histological evaluation between January 2022 and May 2024. Data on comorbid functional gastrointestinal disorders and neurodevelopmental disorders were obtained from patients’ electronic medical records, and their effects on disease severity and treatment choices were analyzed.

Results
Of the 166 patients with UC, 21.4% had neurodevelopmental disorders, and 17.5% had functional gastrointestinal disorders. Patients with these comorbidities had significantly lower Pediatric Ulcerative Colitis Activity Index scores, with notable differences in parameters such as abdominal pain and stool consistency. In addition, these patients had more extensive disease and higher rates of immunomodulator (66.1%) and biologic use (46.4%) than those without these complications. The prevalence of functional gastrointestinal disorders was higher in patients with autism spectrum disorder, and specialized care at a developmental outpatient clinic was required in 23.2% of cases.

Conclusions
Psychosocial and neurodevelopmental disorders are prevalent in children with UC and significantly affect both disease severity and therapeutic approaches. The findings suggest that comprehensive management involving psychosocial interventions and multidisciplinary support is crucial for effectively treating these patients.
A commentary: what do Rebecca Cheptegei and Gisèle Pelicot have in common?
Authors: Shah Safieh 
Published: February 2025

Abstract
This commentary accompanies a study that focuses on the profound impact of intimate partner violence (IPV) on women's health in Ethiopia. The study highlights the dose–response relationship between IPV and antenatal care uptake, emphasizing the need for nuanced, context-specific interventions. The commentary highlights the need for new, sustainable and reliable ways of collecting IPV data across countries over time to effectively monitor Sustainable Development Goal 5. It advocates for a multilayered approach, combining healthcare, legal reforms and community-based strategies, to address the social causes of IPV, thereby aiming to critically appraise previously established ways of seeing information and ideas.
Rumen DNA virome in beef cattle reveals an unexplored diverse community with potential links to carcass traits
Authors: Sato Yoshiaki 
Published: February 2025

Abstract
Rumen DNA viruses that infect and replicate within bacteria and archaea are key modulators of the prokaryotic community. These viruses influence prokaryotic community abundance, composition, and function impacting host productivity and methane production. In this study, viral genomes were assembled from the rumen of 37 Japanese Black cattle using virus-like particle metagenome sequencing, providing insights into viral diversity, functional potential, and virus-host interactions. The relationship between the rumen DNA virome and carcass traits, particularly carcass weight and marbling, was also investigated. A total of 22 942 viral operational taxonomic units of medium-quality or higher (≥5 kb length and ≥ 50% completeness), referred to as Japanese Black Rumen Viral genomes, were reconstructed. Among these, 5973 putative novel genera were identified, significantly expanding the catalog of rumen viral genomes. Hosts were predicted for 2364 viral operational taxonomic units, including carbohydrate-degrading bacteria and methanogens. Additionally, 27 auxiliary metabolic genes were categorized as glycosyl hydrolases which are responsible for the degradation of cellulose, hemicellulose, and oligosaccharides, suggesting that rumen viruses may enhance the breakdown of complex carbohydrates during infection. Furthermore, the rumen virome differed considerably between high versus low carcass weight cattle and high versus low marbling cattle. Viruses associated with Methanobrevibacter were linked to higher carcass weight. This database and the insights from this study provide primary information for the development and improvement of beef production.
Active bacteria driving N2O mitigation and dissimilatory nitrate reduction to ammonium in ammonia recovery bioreactors
Authors: Phan Hop V , Yasuda Shohei , Oba Kohei , Tsukamoto Hiroki , Hori Tomoyuki , Kuroiwa Megumi , Terada Akihiko 
Published: February 2025

Abstract
Shifting from ammonia removal to recovery is the current strategy in wastewater treatment management. We recently developed a microaerophilic activated sludge system for retaining ammonia whereas removing organic carbon with minimal N2O emissions. A comprehensive understanding of nitrogen metabolisms in the system is essential to optimize system performance. Here, we employed metagenomics and metatranscriptomics analyses to characterize the microbial community structure and activity during the transition from a microoxic to an oxic condition. A hybrid approach combining high-quality short reads and Nanopore long reads reconstructed 98 medium- to high-quality non-redundant metagenome-assembled genomes from the communities. The suppressed bacterial ammonia monooxygenase (amoA) expression was upregulated after shifting from a microoxic to an oxic condition. Seventy-three reconstructed metagenome-assembled genomes (&gt;74% of the total) from 11 bacterial phyla harbored genes encoding proteins involved in nitrate respiration; 39 (~53%) carried N2O reductase (nosZ) genes with the predominance of clade II nosZ (31 metagenome-assembled genomes), and 24 (~33%) possessed nitrite reductase (ammonia-forming) genes (nrfA). Clade II nosZ and nrfA genes exhibited the highest and second-highest expressions among nitrogen metabolism genes, indicating robust N2O consumption and ammonification. Non-denitrifying clade II nosZ bacteria, Cloacibacterium spp., in the most abundant and active phylum Bacteroioda, were likely major N2O sinks. Elevated dissolved oxygen concentration inhibited clade II nosZ expression but not nrfA expression, potentially switching phenotypes from N2O reduction to ammonification. Collectively, the multi-omics analysis illuminated bacteria responsible for N2O reduction and ammonification in microoxic and oxic conditions, facilitating high-performance ammonia recovery.
Reduced Growth of Salmonella enterica and Listeria monocytogenes on Outdoor- Vs. Indoor-Grown Kale (Brassica oleracea var. acephala)
Authors: Tran Thao D , Lee SangIn , Hnasko Robert , McGarvey Jeffery A 
Published: February 2025

Abstract

Aim
To compare the abilities of Salmonella enterica and Listeria monocytogenes to grow on kale (Brassica oleracea var. acephala) grown in an indoor vertical hydroponic system (IVHS) or outdoors.

Methods and Results
IVHS- and outdoor-grown kale was inoculated with L. monocytogenes and incubated at 4°C for 9 days or with S. enterica and incubated at 20°C for 24 h. L. monocytogenes showed significant growth on the IVHS-grown kale after 6 days but was unable to grow on the outdoor-grown kale. S. enterica grew on both types of kale but to significantly greater numbers on the IVHS-grown kale (P &lt; 0.05). Plate counts of indigenous bacteria revealed that the outdoor-grown kale contained &gt; 2 log more culturable bacteria g−1 than the IVHS-grown kale. Analysis of 16S rRNA gene sequence libraries derived from the IVHS- and outdoor-grown kale revealed no significant differences in alpha diversity or community composition.

Conclusion
The ability of the pathogens to grow on outdoor- or IVHS-grown kale do not appear to be related to the microbial population structures but to the levels of indigenous bacteria. We propose that the reduced bacterial cell density on the IVHS-grown kale is the result of reduced bacterial community productivity that supplies the pathogens with space and nutrients for growth.
The skeletal abnormalities and their clinical challenges in SATB2-Associated Syndrome
Authors: Kuo Bryan , Bolster Marcy B , Fan WuQiang 
Published: February 2025

Abstract
SATB2-Associated Syndrome (SAS) is an autosomal dominant genetic disorder caused by pathogenic variations in the special AT-rich sequence-binding protein 2 (SATB2) gene. In addition to neurodevelopmental and craniofacial defects, over 90% of patients with SAS manifest biochemical and/or radiographic skeletal abnormalities, and around one third of patients report clinical and/or radiographic fractures. SATB2 protein is a potent transcription factor that promotes osteoblast differentiation and maturation; loss-of-function pathogenic variations of the SATB2 gene result in a wide spectrum of skeletal abnormalities ranging from gross skeletal anomalies to abnormal bone turnover markers, low bone mineral density, and recurrent fractures. There is at present no known effective treatment for bone health in patients with SAS. We present an adult patient with SAS who has recurrent fractures despite long-term treatment with antiresorptive agents. We propose an alternative pharmacotherapy approach utilizing a PTH analogue to stimulate osteoblasts, hence addressing the underlying pathophysiology of bone disease in patients with SAS.
A two-step approximation for quantifying the effects of geographical location, environment and stand on tree allometry
Authors: Huang Yao , Lu Fei 
Published: February 2025

Abstract
Tree allometric models based on height (H) and diameter (D) are the most commonly used method to estimate forest biomass. Environments and stand characteristics are recognized to affect tree allometries. However, few studies have focused on how to incorporate these effects into allometric models, which restricts the use of these models in a wide domain. Adopting the power-law function Y=aGb as a basic model where Y is either tree height or biomass and the corresponding G is tree diameter D at breast height or D2H, we developed a two-step approximation procedure to quantify the effects of environments and stand characteristics on allometric coefficients a and b for Cunninghamia lanceolata and Pinus forest in China. Results show that most of the allometric coefficients are dependent on stand characteristics for C. lanceolata forest, and on mean annual temperature, stand age and latitude for Pinus forest. The allometric models via the two-step approximation Y=fα+αjxjGfβ+βixi (xj or xi are key drivers associated with environments and stand characteristics. α, αj, β and βi are regression coefficients) considerably improved the accuracy of tree height and biomass estimation. Compared to the basic model, the second approximation models significantly reduced the mean absolute bias between the observed and computed values by 25–34% for C. lanceolata and by 21–26% for Pinus forest, respectively. Our results highlight the necessity of incorporating environments and stand characteristics into the allometric models and provide a universal method to accurately estimate H-D-based tree biomass across a wider domain.
Microsurgical treatment of spinal dural arteriovenous fistula with subarachnoid hemorrhage: a case report
Authors: Huang Yunfan , Wang Ya , Sun Chunming , Lu Xiaocheng 
Published: February 2025

Abstract
A rare spinal vascular malformation, the spinal dural arteriovenous fistula (sDAVF), is characterized by subtle clinical signs that make diagnosis and treatment of it highly challenging. In this case, we report a 70-year-old male who presented with subarachnoid hemorrhage, an unusual initial symptom of sDAVF. This report emphasizes the diagnostic complexities and highlights a successful management approach utilizing intraoperative indocyanine green angiography. Early identification and precise localization via advanced imaging techniques were pivotal in achieving a favorable outcome.
Multidisciplinary marvel: surgical management of aggressive giant cell tumor around the knee in pregnancy: a case report
Authors: Ali A , Sahito B , Irfan S A , Farooq Z , Ali S , Iqbal J 
Published: February 2025

Abstract
Giant cell tumors (GCTs) are rare, representing 4–5% of all bone tumors. Although uncommon in pregnancy, the literature showed the accelerated progression and recurrence of GCT in pregnancy; however, the tumor growth in pregnancy has not been clarified. We report a case of a 28-year-old woman in her first trimester presenting with an aggressive GCT, significantly affecting the patient’s quality of life due to the debilitating nature of her symptoms. Considering the significant functional impairment and aggressive nature of the tumor, a multidisciplinary team opted for surgical intervention, entailing marginal resection and mega-prosthesis implantation. A multidisciplinary approach tailored to the patient’s needs enabled successful surgical intervention and positive maternal and fetal outcomes. This case paves the way for the possibility that surgical management of GCTs can be safely performed during pregnancy, highlighting the challenges and critical importance of multidisciplinary care in rare tumor management during pregnancy through timely intervention.
Synchronous cervical lymph node involvement with a papillary thyroid carcinoma and small lymphocytic lymphoma: a case report
Authors: Ben Rejeb Sarra , Sakly Safia , Hachicha Amani , Dridi Kalthoum , Turki Senda 
Published: February 2025

Abstract
The occurrence of multiple malignancies in the same lymph node is rare, and even more so when these malignancies include both papillary thyroid carcinoma (PTC) metastasis and small lymphocytic lymphoma (SLL). We present a unique case of a 58-year-old male with a history of stable, indolent SLL, who developed metastatic PTC within a lymph node previously involved by lymphoma. Despite initial treatment with total thyroidectomy and cervical lymphadenectomy, post-operative surveillance showed elevated thyroglobulin levels and suspicious lymphadenopathy, prompting further investigation. Fine needle aspiration of the lymph node revealed SLL, but the thyroglobulin level in the aspirate was elevated, suggesting metastasis. A subsequent lymph node dissection confirmed PTC metastasis within the lymphomatous background. This case emphasizes the diagnostic challenges in patients with multiple malignancies, particularly when the presence of an indolent lymphoma complicates the assessment of lymphadenopathy.
Management and outcomes of rib fractures in the UK: a national service evaluation
Authors: Bradley Rebecca Anne , Baker Edward , Caponi Noemi , Cole Elaine , Marsden Max , Melia Georgia , Naeem Salman , Vulliamy Paul , Battle Ceri 
Published: February 2025

Abstract
Rib fractures are a common but challenging presentation with global variations in management and outcomes. Rib fractures are often associated with intra-thoracic organ injury and pulmonary complications, even in patients with a good respiratory functional baseline. In the UK, the delivery of care to patients with rib fractures is challenging due to a lack of national current national guidelines or care pathways. Management and Outcomes of Rib Fractures in the UK (MORK-UK) is a national, multi-centre service evaluation of the current management and outcomes of rib fractures in the UK. The aim of MORF-UK is to evaluate the processes of care and variation in clinical practice for adult patients presenting with rib fractures at a national level. The project will be overseen by the National Trauma Research and Innovation Collaborative (NaTRIC). Patient and public involvement representatives have been involved in project development. The prospective, multi-centre service evaluation will include adult patients with radiologically identified rib fractures (non-pathological and non-historical). Participating centres will be identified through pre-existing trauma networks. De-identified data will be collected from eligible patients over a distinct, consecutive 30-day period (January to June 2025). Data will be collected until discharge, death, or 30 days post-index admission, whichever comes first. This data will be used to drive national quality improvement and guideline development in chest injuries across the UK.
The Methodology for Interpretation of the CISG
Authors: Zeller Bruno 
Published: February 2025

Abstract
This chapter discusses the methodology for interpreting the United Nations Convention on Contracts for the International Sale of Goods (CISG). Before any attempt is made to comment on and interpret the method of awarding damages under the CISG, the general interpretive methodology must be understood. The CISG, in Article 7, makes it clear that interpretation must be within the ‘four corners’ of the convention, without recourse to domestic law; that is, interpretation cannot rely on methods or processes that are not contained within the CISG. Thus, Article 7 regulates the method by which the CISG is applied internationally. It is the reason domestic courts are interpreting the CISG uniformly and without recourse to domestic law and its methodology.