bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk of Neurodevelopmental Disorders in Children Exposed to Human Immunodeficiency Virus and Antiretrovirals In Utero: A National Cohort Study in France
Authors: Collier Mathis , Chouchana Laurent , Frange Pierre , Sibiude Jeanne , Munnich Arnold , Treluyer Jean Marc , Blanche Stéphane
Published: February 2025

Background

The health of children exposed but uninfected by human immunodeficiency virus (HIV) requires long-term assessment, in particular in terms of neurological and cognitive development. Numerous confounding factors have hampered such assessment, and published data are contradictory.

Methods

Using data from the French National Health Data System from 2012 to 2022, we conducted a population-based matched cohort study on all live-born single children, including those born to mothers living with HIV, all prenatally exposed to antiretrovirals (ARVs). The primary outcome was the diagnosis of neurodevelopmental disorders according to the International Classification of Diseases, 10th Revision. The recourse to specialized consultations likely to indirectly reflect neurodevelopmental symptoms was also evaluated. Incidence was assessed using the Cox survival model.

Results

Of 6 667 363 live-born singletons, 9035 were born to mothers with HIV, all exposed to ARVs during pregnancy. Children were followed for up to 11 years (average, 5.5 years). Overall, the incidence of neurodevelopmental disorders among exposed children was higher than in the general population, even after matching for 5 sociodemographic criteria and gestational age (hazard ratio, 1.24 [95% confidence interval, 1.04–1.47]). It was not possible to dissect the respective role of maternal infection from that of maternal treatment, as all children were coexposed to HIV and ARVs. However, among those exposed to tenofovir-emtricitabine, the ritonavir-boosted darunavir–based combination was significantly associated with a higher combined incidence of neurodevelopmental disorders and related specialized consultations than other protease inhibitors (log-rank P < .001).

Conclusions

Children exposed to HIV and ARVs in utero have a higher risk of developing neurodevelopmental disorders of multifactorial origin.
Advancing periodontal diagnosis: Harnessing advanced artificial intelligence for patterns of periodontal bone loss in cone beam computed tomography
Authors: Kurt-Bayrakdar Sevda , Bayrakdar İbrahim Şevki , Kuran Alican , Çelik Özer , Orhan Kaan , Jagtap Rohan
Published: February 2025

Objectives

The current study aimed to automatically detect tooth presence, tooth numbering, and types of periodontal bone defects from CBCT images using a segmentation method with an advanced artificial intelligence (AI) algorithm.

Methods

This study utilized a dataset of CBCT volumes collected from 502 individual subjects. Initially, 250 CBCT volumes were used for automatic tooth segmentation and numbering. Subsequently, CBCT volumes from 251 patients diagnosed with periodontal disease were employed to train an AI system to identify various periodontal bone defects using a segmentation method in web-based labeling software. In the third stage, CBCT images from 251 periodontally healthy subjects were combined with images from 251 periodontally diseased subjects to develop an AI model capable of automatically classifying patients as either periodontally healthy or periodontally diseased. Statistical evaluation included ROC curve analysis and confusion matrix model.

Results

The AUC values for the models developed to segment teeth, total alveolar bone loss, supra-bony defects, infra-bony defects, perio-endo lesions, buccal defects, and furcation defects were 0.9594, 0.8499, 0.5052, 0.5613 (with cropping, AUC: 0.7488), 0.8893, 0.6780 (with cropping, AUC: 0.7592), and 0.6332 (with cropping, AUC: 0.8087), respectively. Additionally, the classification CNN model achieved an accuracy of 80% for healthy individuals and 76% for unhealthy individuals.

Conclusions

This study employed AI models on CBCT images to automatically detect tooth presence, numbering, and various periodontal bone defects, achieving high accuracy and demonstrating potential for enhancing dental diagnostics and patient care.
Characteristics analyses and tumor staging proposal for primary malignant melanoma of the esophagus: a retrospective study
Authors: Ye Weijie , Leng Changsen , Chen Junying , Mai Zihang , Liu Nianjin , Zhang Shuishen , Fu Jianhua , Liu Qianwen
Published: February 2025

Primary malignant melanoma of the esophagus (PMME) is a malignant tumor with a poor prognosis. This study aimed to conduct survival analysis for patients with PMME and propose a staging system for PMME. Data from 179 patients were compiled for survival analysis and to propose a staging system for PMME. Survival analysis was conducted using the Kaplan–Meier method, log-rank test, and Cox proportional hazards model. The median OS of the 179 patients with PMME was 20.0 months. The 1-, 3-, and 5-year survival rates were 67.0%, 35.0%, and 17.0%. In the pooled analysis of 179 patients, significant differences in OS were observed between patients with tumors invading the lamina propria or muscularis mucosae (T1a) and deeper layers (T1b, T2, T3, T4) (P < 0.001). Significant differences in OS were observed between patients with no regional lymph node metastasis and those with one or more regional lymph node metastases (P < 0.001). PD-1 inhibitors significantly improved 3-year OS for patients with the pT1b-4 N+ stage (P = 0.020). The proposed staging system for PMME is as follows: (1) Stage I: T1aN0M0 (2) Stage II: T1b-4N0M0 and T1N1M0; Stage III: T2-4N1M0 and TxNxM1(P < 0.001). The lower T-stage and no lymph node metastasis indicated better prognosis. Surgery could be considered an effective treatment for patients with early-stage PMME. The effectiveness of surgery as a treatment for advanced-stage patients remained unclear and required further research. However, PD-1 inhibitors might improve the 3-year OS for advanced-stage patients. Furthermore, the tumor, node, metastasis staging system for PMME was proposed, and could be valuable in guiding prognostic predictions.
A rare case of dual left anterior descending artery type 4 in inferior myocardial infarction patient: a case report
Authors: Isa W Yus Haniff W , Yusof Zurkurnai , Aziz Mohamad Fadini Abdul , Othman Mohd Khairi , Suliman Ayman
Published: February 2025

Background

This case highlights a type 4 dual left anterior descending coronary artery anomaly, identified incidentally during coronary angiography.

Case summary

A 51-year-old male patient presented with acute myocardial infarction, which was successfully treated with thrombolysis and percutaneous coronary intervention. Angiography revealed an anomalous origin of the left anterior descending artery (LAD) from the right coronary artery. Stenting was performed on the right coronary artery and the right posterior descending artery branch.

Discussion

Type 4 dual LAD is a rare coronary anomaly with potential clinical risks, including sudden cardiac death due to its course between major arteries. Variations in the structure of coronary arteries can present challenges for interventional cardiologists when conducting percutaneous coronary interventions. Accurate coronary anatomy assessment via angiography and computed tomography coronary angiography is crucial for successful percutaneous coronary intervention and surgical planning. Although uncommon, the dual LAD type 4 anomaly is a significant coronary artery variation that interventional cardiologists must consider due to its impact on prognosis and long-term treatment strategies.
Valve Thrombosis and Antithrombotic Therapy After Bioprosthetic Mitral Valve Replacement: A Systematic Review And Meta-Analysis
Authors: Zorman Mark J , Vibhishanan Jonathan , Dangas Katerina , Castle James , Li Ka Hou Christien , Coronelli Marco , Eastwick-Jones Kate , Swan Alexander , Johnson Nicky , Choksey Anurag , Yan Helen , Scott Sam G C , Henry Matthew , Cassar Mark Philip , Barnes Cara , Ferreira-Martins Joao , Newton James , Dawkins Sam , Alkhouli Mohamad , Rihal Charanjit , Eleid Mackram F , Pislaru Sorin V , Guerrero Mayra E , Ordonez-Mena Jose , Cahill Thomas J
Published: February 2025

Aims

Transcatheter mitral valve replacement (TMVR) has become a feasible alternative to surgical mitral valve replacement (SMVR) in selected patients at high surgical risk. The risk of valve thrombosis following SMVR and TMVR, and the optimal antithrombotic therapy following these procedures, remains uncertain. We aimed to compare the incidence of bioprosthetic mitral valve thrombosis (bMVT) after SMVR and TMVR, and the incidence of bMVT between patients on different antithrombotic regimens.

Methods and Results

A literature search of Medline, Embase and Cochrane Library was performed between January 2000 and August 2024. Random-effects models were used to derive pooled estimates of the incidence of bMVT in the absence of prior or active endocarditis and valve thrombosis. 47 studies (6170 patients, total follow-up 9541.8 patient-years) were eligible for inclusion. The overall incidence of bMVT was 5.05 (95%CI 3.18–8.01, I2 = 82%) per 100-patient-years. Subclinical bMVT was more common than clinically significant bMVT: incidence 19.11 vs 7.91 per 100-patient-years, adjusted incidence rate ratio (aIRR) 4.62 (95%CI 1.39–15.36), p = 0.012. bMVT was numerically more common after TMVR than SMVR, but the comparison was not statistically significant: incidence 7.03 vs 0.58 per 100-patient-years, aIRR 2.19 (95%CI 0.72–6.72), p = 0.170. Patients on vitamin-K antagonists (VKA) had a lower incidence of bMVT than patients on direct oral anticoagulants (DOAC; incidence 5.72 vs 17.08, aIRR 0.31, 95%CI 0.13–0.73, p = 0.007).

Conclusions

bMVT is not uncommon, with numerically higher incidence in transcatheter compared to surgical valves, but the comparison was not statistically significant. VKAs are associated with a lower incidence of bMVT compared to DOACs.
Application of omics technology in ecotoxicology of arthropod in farmland
Authors: Li Zhongyuan , Gao Cuimei , Wang Zhuoman , Huang Siqi , Jiang Zijian , Liu Jing , Yang Huilin
Published: February 2025

Arthropods, abundant in farmland, have unique biological traits that make them valuable for studying the ecotoxicological impacts of pollutants. Recent advancements in multi-omics technologies have enhanced their use in assessing pollution risks and understanding toxicity mechanisms. This paper reviews recent developments in applying omics technologies—genomics, transcriptomics, proteomics, metabolomics and meta-omics to ecotoxicological research on farmland arthropods. Agricultural arthropods manage genes and proteins like metallothioneins (MTs), antioxidant enzyme systems, heat shock proteins, cytochrome P450 (CYP450), carboxylesterases (CarEs), and glutathione S-transferases (GSTs), for detoxification and antioxidant purposes. They adjust amino acid, sugar, and lipid metabolism to counteract pollutant-induced energy drain and modify gut microbiota to aid in detoxification. This study advocates for enhanced analysis of compound pollution and emerging pollutants using multi-omics, especially meta-omics, to clarify the toxicological mechanisms underlying arthropod responses to these pollutants. Furthermore, it underscores the urgent need for subsequent gene function mining and validation to support biological control strategies and promote sustainable agricultural practices. The findings of this research provide significant insights into the toxicological impacts and mechanisms of pollutants within farmland ecosystems, thereby contributing to the preservation of arthropod diversity.
Prognostic relevance of baseline exercise stress test in RYR2-related CPVT
Authors: Kukavica Deni , Pili Gianluca , Trancuccio Alessandro , Giannini Gala , Pergola Valerio , Memmi Mirella , Gambelli Patrick , Marino Maira , Morini Massimo , Bloise Raffaella , Napolitano Carlo , Mazzanti Andrea , Priori Silvia G
Published: February 2025

Aims

Exercise stress test (EST) represents the gold standard for diagnosis of catecholaminergic polymorphic ventricular tachycardia (CPVT). We aimed to determine the relevance of exercise induced VT for the occurrence of LAE at follow-up.

Methods and results

In RYR2-related CPVT patients who underwent a baseline EST, we assessed the incidence and severity of ventricular arrhythmias (VA). Data were analysed using logistic regression models and Cox proportional hazards models. The primary outcome was the occurrence of life-threatening arrhythmic event (LAE; composite of sudden cardiac death, aborted cardiac arrest, or hemodynamically non-tolerated VT) at follow-up. In 102 RYR2-related CPVT patients (65 females; median age 16 years, IQR: 11–36 years), exercise-induced VT (bidirectional in 64% of cases) was elicited in 56% patients. VT could not be induced in pre-school children. Lower basal heart rate, early onset VA (within the first step of EST) and heart rate at the first minute of recovery were associated with exercise-induced VT. Cox analyses showed that early onset VA (HR 6.0, 95% CI: 1.3–27.9, P = 0.022) and exercise-induced VT (HR 6.6, 95% CI: 1.5–29.1, P = 0.012) at baseline EST were significantly associated with the occurrence of LAE at follow-up, and remained associated even after correction for symptoms.

Conclusion

Early onset VA and exercise-induced VT at baseline EST was associated with LAE at follow-up, allowing to identify a sub-set of patients at higher risk already at diagnosis.
Interactions within higher-order antibiotic combinations do not influence the rate of adaptation in bacteria
Authors: Lozano-Huntelman Natalie Ann , Cook Emoni , Bullivant Austin , Ida Nick , Zhou April , Boyd Sada , Yeh Pamela J
Published: February 2025

The prevalence and strength of antibiotic resistance has led to an ongoing battle between the development of new treatments and the evolution of resistance. Combining multiple drugs simultaneously is a potential solution for combating antibiotic resistance. However, this approach introduces new factors that must be considered, including the influence of drug interactions on the rate of resistance evolution. When antibiotics are used in combination, their effects can be additive, synergistic, or antagonistic. In this study, we investigated the effect of higher-order interactions involving three drugs on resistance evolution in Staphylococcus epidermidis. Previous studies have shown that synergistic interactions can increase the adaptation rate. However, the effects of higher-order interactions on rates of adaptation are unclear. We investigated the adaptation of Staphylococcus epidermidis to single-, two-, and three-drug environments to assess how interactions within drug combinations influence the rate of adaptation. We analyzed both the overall interaction and emergent interaction, the latter being a unique interaction that occurs in three-drug combinations due to the presence of all three drugs, rather than simply strong pairwise interactions. Our results show that neither the overall interactions nor the emergent interactions affect adaptation rates.
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

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

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

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

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

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

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

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

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 (>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

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 < 0.05). Plate counts of indigenous bacteria revealed that the outdoor-grown kale contained > 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

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

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

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

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

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

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

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.
Fundamental Breach and the CISG
Authors: Zeller Bruno
Published: February 2025

This chapter discusses the concept of fundamental breach. In brief, the United Nations Convention on Contracts for the International Sale of Goods (CISG) offers two different approaches to a breach of contract. If the breach is ‘minor’, the aggrieved party simply concludes the contract and asks for damages. If the breach is ‘major’, the contract can be avoided, or terminated, and remedies for breach of contract can be sought. Damages are among the most important remedies any legal system can award to restore financial equilibrium. However, in certain circumstances damages are not the remedy that is envisaged or practical. It should be noted that a breach of a contract gives rise to secondary rights and obligations. Fundamental breach is one of the secondary rights and must be read within the remedial framework of the CISG.
The UNIDROIT Principles and the CISG
Authors: Zeller Bruno
Published: February 2025

This chapter examines the interplay between the United Nations Convention on Contracts for the International Sale of Goods (CISG) and the UNIDROIT Principles of International Commercial Contracts (UNIDROIT Principles). The UNIDROIT Principles are a valuable tool in the interpretation of the CISG and can serve as terms in a contract. The optimum use of these international instruments would be to include the UNIDROIT Principles as terms into a contract, and the CISG would be the substantive law supplementing the contract. However, this would be asking the near-impossible, as far too many legal advisors still prefer to take shelter in domestic laws than to utilize international uniform laws. Nevertheless, it should be noted that the UNIDROIT Principles are already used in arbitral proceedings to resolve substantive issues.
Estimating the evolution and the content fractions of baryonic gas for Luminous Infrared Galaxies
Authors: Al Najm M N , Abdullah Ahmed H , Rashed Y E
Published: February 2025

Luminous Infrared Galaxies (LIRGs) play a crucial role in understanding of galaxy evolution. The present study examined 82 LIRGs, using data taken from the Sloan Digital Sky Survey (SDSS), NASA/IPAC Extragalactic Database (NED), and HyperLEDA to explore their gas fractions and optical properties. The analysis of data highlights the relationship between molecular-to-atomic mass of hydrogen gas ratio $M_{\text{H}_2}/M_{\rm{H {}{\small I}}}$ and morphological types, gas mass fractions, and galaxy characteristics such as color and luminosity. The results showed that the regressions between $M_{\text{dust}} - M^{*,V}$ and $M_{\text{dust}} - \text{SFR}$ are not quite flat (when correlation coefficient > 0.5), which indicates a decrease in the dust-to-stellar content ratio as the gas is consumed and transformed into stars, and also a relatively flat trend for $M_{\text{dust}} - M^{*,V}$ and $f_{\text{dust,bar}} - M^{*,V}$. Moreover, as the star’s mass declines, the total gas mass fraction ($f_{\text{gas}}$) increases quickly, with a high negative correlation coefficient of –0.7 and a regression of –0.85. Therefore, it can be inferred that galaxies with a high gas fraction ($f_{\text{gas}}$) are either accreting gas at a rate sufficient to meet their energy requirements for star formation or converting gas into stars less effectively. According to the findings, the gas exhaustion time in these galaxies quickly reduces as the stellar mass increases, with a significant negative correlation coefficient of –0.7 and a regression that is a nearly linear regression of –0.9. On the other hand, when the baryonic gas mass fraction grows, which makes up the majority of the baryonic gas, grows, the gas depletion time increases quickly.
Understanding the Mechanisms Behind the Distribution of Galactic Metals
Authors: Zhang Chuhan , Li Zefeng , Hu Zipeng , Krumholz Mark R
Published: February 2025

The evolution and distribution of metals within galaxies are critical for understanding galactic evolution and star formation processes, but the mechanisms responsible for shaping this distribution remain uncertain. In this study we carry out high-resolution simulations of an isolated Milky Way-like galaxy, including a star-by-star treatment of both feedback and element injection. We include seven key isotopes of observational and physical interest, and which are distributed across different nucleosynthetic channels—primarily AGB stars (N, Ba, Ce), supernovae (O, Mg, S), and Wolf-Rayet stars (C)show measurably different correlation statistics in space and time and their fluctuations. This difference arises from the distinct ejection mechanisms associated with each nucleosynthetic process. The large-scale properties ensure that different elements, despite having different nucleosynthetic origins, are highly correlated with one another (>0.85 for all, >0.99 for same origins), and their spatial correlations vary together in time. However small-scale variations naturally break elements into distinct nucleosynthetic familiars, with elements originating from the same channels correlating better with each other than with elements from different origins. Our findings suggest both challenges and opportunities for ongoing efforts to use chemical measurements of gas and stars to unravel the history and physics of galaxy assembly.
Timing and spectral analysis of GK Persei during the 2010 dwarf nova outburst
Authors: Pei Songpeng , Zhang Xiaowan , Li Qiang , Ou Ziwei , Yang Taozhi , Cai Yongzhi
Published: February 2025

GK Persei, an old nova and intermediate polar, exhibited a dwarf nova outburst in 2010. This outburst was extensively observed by the Neil Gehrels Swift Observatory, beginning 1.95 d after the eruption and continuing until 13.9 d before the maximum of the outburst in the optical. In this paper, we present timing and spectral analyses, comparing the results with those of other outbursts. We confirm the spin modulation in the 2–10 keV X-ray range with a period of $P_{\rm WD} = 351.325(9)$ s. Additionally, we detected spin modulation in the 0.3–2 keV band during the second half of the observations, a feature not seen in the 2015 and 2018 outbursts. This finding suggests that the soft X-ray emission in GK Persei may originate partly near the magnetic poles and partly from a wind or circumstellar material.
Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance and male germ cell survival
Authors: Munakata Yasuhisa , Hu Mengwen , Kitamura Yuka , Dani Raissa G , Bynder Adam L , Fritz Amelia S , Schultz Richard M , Namekawa Satoshi H
Published: February 2025

The ovarian reserve defines female reproductive lifespan, which in humans spans decades due to the maintenance of meiotic arrest in non-growing oocytes (NGOs) residing in primordial follicles. Unknown is how the chromatin state of NGOs is established to enable long-term maintenance of the ovarian reserve. Here, we show that a chromatin remodeler, CHD4, a member of the Nucleosome Remodeling and Deacetylase (NuRD) complex, establishes chromatin states required for formation and maintenance of the ovarian reserve. Conditional loss of CHD4 in perinatal mouse oocytes results in acute death of NGOs and depletion of the ovarian reserve. CHD4 establishes closed chromatin at regulatory elements of pro-apoptotic genes to prevent cell death and at specific genes required for meiotic prophase I to facilitate the transition from meiotic prophase I oocytes to meiotically-arrested NGOs. In male germ cells, CHD4 establishes closed chromatin at the regulatory elements of pro-apoptotic genes, allowing germ cell survival. These results demonstrate a role for CHD4 in defining a chromatin state that ensures germ cell survival, thereby enabling the long-term maintenance of both female and male germ cells.
zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters
Authors: Salamzade Rauf , Tran Patricia Q , Martin Cody , Manson Abigail L , Gilmore Michael S , Earl Ashlee M , Anantharaman Karthik , Kalan Lindsay R
Published: February 2025

Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements, such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of ortholog groups for individual protein-encoding genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of evolutionary statistics for each inferred ortholog group. Importantly, in comparison to tools for visual exploration of homologous relationships between gene clusters, zol can scale to handle thousands of gene cluster instances and produce detailed reports that are easy to digest. To showcase fai and zol, we apply them for: (i) longitudinal tracking of a virus in metagenomes, (ii) performing population genetic investigations of BGCs for a fungal species, and (iii) uncovering evolutionary trends for a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.