bluuebunny/crossref_metadata_2025 huggingface dataset:
HTSinfer: Inferring metadata from bulk illumina RNA-Seq libraries
Authors: Balajti Máté , Kandari Rohan , Jurič Boris , Zavolan Mihaela , Kanitz Alexander
Published: February 2025

The Sequencing Read Archive is one of the largest and fastest-growing repositories of sequencing data, containing tens of petabytes of sequenced reads. Its data is used by a wide scientific community, often beyond the primary study that generated them. Such analyses rely on accurate metadata concerning the type of experiment and library, as well as the organism from which the sequenced reads were derived. These metadata are typically entered manually by contributors in an error-prone process, and are frequently incomplete. In addition, easy-to-use computational tools that verify the consistency and completeness of metadata describing the libraries to facilitate data reuse, are largely unavailable. Here we introduce HTSinfer, a Python-based tool to infer metadata directly and solely from bulk RNA-sequencing data generated on Illumina platforms. HTSinfer leverages genome sequence information and diagnostic genes to rapidly and accurately infer the library source and library type, as well as the relative read orientation, 3’ adapter sequence and read length statistics. HTSinfer is written in a modular manner, published under a permissible free and open-source license and encourages contributions by the community, enabling easy addition of new functionalities, for example for the inference of additional metrics, or the support of different experiment types or sequencing platforms.

Availability and implementation

HTSinfer is released under the Apache License 2.0. Latest code is available via GitHub at https://github.com/zavolanlab/htsinfer, while releases are published on Bioconda. A snapshot of the HTSinfer version described in this article was deposited at Zenodo at 10.5281/zenodo.13985958.
The small molecule inhibitor 3PO is a modulator of neutrophil metabolism, ROS production and NET release
Authors: Fresneda Alarcon Michele , Abdullah Genna Ali , Nolan Andy , Linford Christina , Meschis Maria Martina , Cross Andrew L , Sellin Andrew , Phelan Marie M , Wright Helen L
Published: February 2025

Neutrophils are key effector leukocytes of the innate immune system and play a pivotal role in defending the host against microbial infections. Recent studies have identified a crucial link between glycolysis and neutrophil cellular functions. Using human neutrophils, we have investigated the intricate relationship between glycolysis, extracellular glucose availability, and the enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3), in the regulation of reactive oxygen species (ROS) and neutrophil extracellular trap (NET) production. We have identified that PFKFB3 is elevated in rheumatoid arthritis (RA) neutrophils and that the small molecule PFKFB3 inhibitor 3PO is a key regulator of neutrophil ROS and NET production. 3PO blocked the production of ROS and NETs in a dose-dependent manner in both RA and healthy (HC) neutrophils (p<0.01), and RA neutrophils were more sensitive to lower concentrations of 3PO. Bacterial killing was only partially inhibited by 3PO, and the proportion of live neutrophils after 24h incubation was unchanged. Using NMR metabolomics, we identified that 3PO increases the concentration of lactate, phenylalanine and L-glutamine in neutrophils, as well as significantly decreasing intracellular glutathione (adj. p-value<0.05). We also demonstrated that RA neutrophils produce ROS and NETs in culture conditions which mimic the low glucose environments encountered in RA synovial joints. Our results also suggest 3PO may have molecular targets beyond PFKFB3. By dissecting the intricate interplay between metabolism and neutrophil effector functions, this study advances the understanding of the molecular mechanisms governing pro-inflammatory neutrophil responses and identifies 3PO as a potential therapeutic for conditions characterized by dysregulated neutrophil activation.
Difelikefalin for CKD-aP: real world evidence of efficacy and safety in Italian patients
Authors: Aucella Filippo , Zerbi Simona , Monaco Maria Pia , Bonomini Mario , Alberici Federico , Losappio Vincenzo , Tagliente Federica , Urciuolo Federica , Grandaliano Giuseppe , Aucella Francesco , Nardella Maria , Manenti Lucio
Published: February 2025

Introduction

Chronic Kidney Disease Associated Pruritus (CKD-aP), defined as moderate to severe itching directly related to kidney disease, affects about 1/3 of haemodialysis patients and has been associated with poor quality of life, poor sleep, depression and increased mortality. Difelikefalin (DFK) is the first-in-class therapy approved by FDA and EMA for this condition. The aim of the present study was to evaluate DFK efficacy and safety in a real-world setting in Italy.

Methods

We retrospectively collected data of 20 patients treated with DFK in a compassionate manner, before the drug was commercialized, after obtaining approval by the relevant Ethics Committee for each individual case. Mean age and dialysis vintage were 72±11 years and 54±44 months, respectively, basal WI-NRS score being 8.2 and 5D-ITCH 18.6. Scratching lesions were detected in 15/20 patients. DFK was administered IV with weight-based dosing at the end of each dialysis session.

Results

18/20 patients were treated for 12 weeks, 2 patients stopped treatment for dizziness (n.1) and discomfort (n.1). WI-NRS score improved >3 in 11/18 (61%) at week 4 and in 16/18 (88%) at week 12. 5D-ITCH decreased from basal 18,6 to 10,5 at week 12, while sleep quality at the same time points changed from 2,6 to 5,8; scratching lesions disappeared in 12/15 (80%). Except for the two early therapy breaks, no other side effects were reported.

Conclusions

In haemodialysis patients affected by CKD-aP, DFK is an effective and safe treatment that might clearly improve this distressing and overlooked condition.
Validating a variable-instar, climate-based phenology model for the Asian longhorned beetle (Coleoptera: Cerambycidae) using field data from South Carolina
Authors: Schmitt Lena R , Trotter R Talbot , Coyle David R
Published: February 2025

The Asian longhorned beetle, Anoplophora glabripennis (ALB, Coleoptera: Cerambycidae), is a federally regulated invasive species capable of infesting several different genera of hardwood trees. Accurate knowledge of ALB’s phenology is critical for the effective implementation of management and eradication plans. We updated the ALBLT prediction model and used empirical data collected in South Carolina, USA to validate ALBLT v. 2.0. The new model largely agreed with ALB life stages found in field collections, except for late instars and pupae. We also ran the model at 8 other potentially high-risk cities in the contiguous United States with latitudes ranging from 28°N (Tampa, FL) to 41°N (Chicago, IL) to predict how long a single ALB generation might take to develop in these environments. Model predictions ranged from a 2–3-yr lifecycle in Chicago to a potential life cycle of < 1 yr in Tampa. These predictions can help inform managers and invasive species specialists should ALB be found in new environments, and these data can aid in developing an adequate management and eradication plan.
Aortic valve reconstruction with Cardiocel: midterm results
Authors: Irimie Vadim P , Nasra Wasim , Atieh Alaa , Ahmidou Akram , Lehmkuhl³ Lukas , Urbanski Paul P
Published: February 2025

OBJECTIVES

The aim of the study was to evaluate the outcomes of aortic valve repair techniques using cusp patch-plasty with CardioCel.

METHODS

Between September 2014 and June 2021, a total of 167 patients underwent aortic valve reconstruction using cusp repair. In all patients CardioCel patch was used exclusively. An isolated cusp repair was performed in 117 patients (70%), while 50 patients with concomitant aortopathy needed a combined valve and root repair. Seventy-two patients (43%) presented with tricuspid valve. The mean age of the entire cohort was 54.3 ± 12.3 years , 143 patients being males.

RESULTS

Early (30-day/in-hospital) mortality was 0.6%. The survival at 2, 4, and 6 years was 98.8%, 96.8%, and 95.7%, respectively. During the mean follow-up of 4.2 ± 1.7 years (resulting in 697 patient-years), a relevant aortic insufficiency occurred in 10 patients (8 of them presenting with bicuspid valve). All the patients underwent a valve replacement, resulting in a 7.8 ± 2.5% cumulative risk of aortic valve reoperation and/or insufficiency ≥3+ at 6 years. The causes of reoperation were cusp tear at the suture line, progressive valve pathology, endocarditis, and unknown in 4, 4, 1, and 1, respectively. Degeneration and/or calcification of the CardioCel has not been observed.

CONCLUSIONS

The intermediate results of aortic cusp repair using CardioCel are good. Anatomo-pathology of the aortic valve and quality of the cusps seem to be main reason of repair failure. Further investigations are needed to assess the long-term durability of CardioCel patch-plasty as an alternative to biological valve replacement in specific aortic valve pathologies.
Non-invasive vagus nerve stimulation and exercise capacity in healthy volunteers: a randomized trial
Authors: Ackland Gareth L , Patel Amour B U , Miller Stuart , Gutierrez del Arroyo Ana , Thirugnanasambanthar Jeeveththaa , Ravindran Jeuela I , Schroth Johannes , Boot James , Caton Laura , Mein Chas A , Abbott Tom E F , Gourine Alexander V
Published: February 2025

Background and Aims

Vagal parasympathetic dysfunction is strongly associated with impaired exercise tolerance, indicating that coordinated autonomic control is essential for optimizing exercise performance. This study tested the hypothesis that autonomic neuromodulation by non-invasive transcutaneous vagus nerve stimulation (tVNS) can improve exercise capacity in humans.

Methods

This single-centre, randomized, double-blind, sham-controlled, crossover trial in 28 healthy volunteers evaluated the effect of bilateral transcutaneous stimulation of vagal auricular innervation, applied for 30 min daily for 7 days, on measures of cardiorespiratory fitness (peak oxygen consumption (VO2peak)) during progressive exercise to exhaustion. Secondary endpoints included peak work rate, cardiorespiratory measures, and the whole blood inflammatory response to lipopolysaccharide ex vivo.

Results

tVNS applied for 30 min daily over 7 consecutive days increased VO2peak by 1.04 mL/kg/min (95% CI: .34–1.73; P = .005), compared with no change after sham stimulation (−0.54 mL/kg/min; 95% CI: −1.52 to .45). No carry-over effect was observed following the 2-week washout period. tVNS increased work rate (by 6 W; 95% CI: 2–10; P = .006), heart rate (by 4 bpm; 95% CI: 1–7; P = .011), and respiratory rate (by 4 breaths/min; 95% CI: 2–6; P < .001) at peak exercise. Analysis of the whole blood transcriptomic response to lipopolysaccharide in serial samples obtained from five participants showed that tVNS reduced the inflammatory response.

Conclusions

Non-invasive vagal stimulation improves measures of cardiorespiratory fitness and attenuates inflammation, offering an inexpensive, safe, and scalable approach to improve exercise capacity.
Periodontitis-related myocardial fibrosis by expansion of collagen-producing SiglecF+ neutrophils
Authors: Wang Xuekui , Xu Yue , Yu Canqing , Deng Ruhua , Chen Yang , Jiang Kai , Liang Jiayi , Hu Congjiao , Yang Xingbo , Zhang Baowei , Yuan Xun , Pan Cancan , Wang Dandan , Sun Yao , Xiang Yaozu
Published: February 2025

Backgrounds and Aims

Patients with periodontitis (PD) are prone to developing myocardial infarction (MI), yet the prognosis and mechanisms remain unclear. Given the presumed close association of neutrophils with both conditions, this study aims to elucidate the roles of neutrophils in mediating the interaction between PD and MI.

Methods

Three prospective cohorts and PD + MI mouse model were investigated to assess the effects of PD on MI prognosis. Single-cell-RNA sequencing and genome-wide association study were employed to identify the neutrophil subtype involved. To characterize the function of SiglecF+ neutrophils, bone marrow transplantation, Edu-pulse chasing, lineage tracing, and collagen contraction assay were utilized. Adoptive neutrophil transfer, conditional Siglecf knockout and lipid nanoparticles facilitating local SiglecF+ neutrophils depletion was harnessed to explore the roles of SiglecF+ neutrophils in MI repair.

Results

Persisting but not short-term PD upset MI prognosis (cardiac fibrosis and function) in human and mice. Bone marrow neutrophils of PD were intrinsically skewed toward longer-lived SiglecF+ neutrophil differentiation, a subtype that was converted by GMCSF or TGFβ in PPARγ-dependent manner. SiglecF+ neutrophils were expanded in infarcted PD heart where they deposit collagen and activate fibroblasts to instigate excessive fibrosis. SiglecF+ neutrophil depletion was efficacious for mitigating fibrosis.

Conclusions

This study demonstrated that long-lasting PD-aggravated MI prognosis by expanding scar-associated SiglecF+ neutrophils into the heart and highlighted the clinical relevance of oral health examination for treating MI in a holistic fashion.
Oral semaglutide: an innovative paradigm in the management of cardiovascular risk in patients with Type 2 diabetes
Authors: Temporelli Pier Luigi
Published: February 2025

Cardiovascular (CV) diseases (CVDs) remain a leading global health issue, causing about one-third of all deaths worldwide. Among modifiable CV risk factors (systolic blood pressure, non-HDL cholesterol, diabetes, body mass index, and smoking), diabetes is a leading one, accounting for established CVDs in 34.8% of diabetic patients, with an increasing prevalence of disease. Glucagon-like peptide-1 receptor agonists (GLP-1 RAs), like exenatide, liraglutide, albiglutide, dulaglutide, and semaglutide, initially developed for treatment of Type 2 diabetes, have shown CV benefits, and international guidelines recommend now GLP-1 RAs as preferred drugs for CV prevention in diabetic patients regardless of baseline HbA1c or metformin use. Among GLP-1 RAs, subcutaneous semaglutide has demonstrated cardio-metabolic risk factors reduction and efficacy in CV prevention. Development of oral semaglutide represents the evolution of the molecule. The PIONEER study programme confirmed the efficacy of oral semaglutide in reducing HbA1c, body weight, and cardio-metabolic risk factors as well as CV safety. Notably, independently by route of administration, semaglutide showed early CV benefits, suggesting mechanisms beyond glycaemic control or weight reduction. Semaglutide, combining potent cardio-metabolic effects with oral route, emerges as a pivotal treatment for high-risk Type 2 diabetes patients, offering comprehensive CV protection independent of HbA1c levels.
Over 10 years of non-vitamin K antagonist oral anticoagulants: highlights, challenges, and future developments
Authors: De Caterina Raffaele , Chiusolo Simona
Published: February 2025

Over the past decade, non-vitamin K antagonist oral anticoagulants have revolutionized anticoagulation therapy, offering substantial benefits over traditional vitamin K antagonists. Non-vitamin K antagonist oral anticoagulants offer reduced bleeding risks, fixed dosing without frequent monitoring, and fewer drug and dietary interactions. Their effectiveness has been demonstrated in preventing stroke in atrial fibrillation, managing venous thromboembolism, and offering new options for patients with coronary artery disease and cancer-associated thrombosis. However, challenges remain, including bleeding risks, high costs, and limited efficacy in certain patient populations. Current research is focused on addressing these limitations, with Factor XI inhibitors emerging as a promising advancement for safer anticoagulation. This review provides an overview of the clinical highlights, challenges, and future directions of anticoagulation therapy.
Periodic breathing during exercise in heart failure: beyond the classic risk factors
Authors: Karsten Marlus , Salvioni Elisabetta , Palermo Pietro , Mattavelli Irene , Scatigna Marco , Mapelli Massimo , Grilli Giulia , Pezzuto Beatrice , Apostolo Anna , Ribeiro Gustavo dos Santos , Agostoni Piergiuseppe
Published: February 2025

Periodic breathing is a peculiar ventilatory pattern in patients with heart failure (HF), characterized by cyclic oscillations in minute ventilation. This phenomenon has been observed in awake patients, during sleep, and during exercise. Periodic breathing during exercise, also known as exercise oscillatory ventilation (EOV), is an important marker of clinical and functional status, morbidity, and mortality in HF patients. However, a clear understanding of the meaning, causes, and possible occurrence of different forms of EOV is still currently lacking. This review focuses on what is known, likely known, or unknown about EOV in HF, including topics such as the definition of EOV, pathophysiological mechanisms, EOV phenotypes, treatment modalities, and the prognostic role of EOV in patients with HF. Finally, some perspectives on research opportunities and clinical practice are presented, to increase the knowledge of EOV, and the application of tools for its assessment, which may improve the chances of identifying and treating EOV, with a positive impact on patients with HF.
Towards a phenotype profiling of the patients with heart failure and preserved ejection fraction
Authors: Bonfioli Giovanni Battista , Pagnesi Matteo , Calò Leonardo , Metra Marco
Published: February 2025

The prevalence of heart failure with preserved ejection fraction (HFpEF) is increasing and prognosis remains poor, with a high risk of mortality or hospitalizations for worsening heart failure events. Apart from sodium-glucose cotransporter-2 inhibitors and diuretics, the management of HFpEF is nowadays based on the different aetiologies and cardiovascular or non-cardiovascular comorbidities. A great heterogeneity of clinical profiles has been described in HFpEF, with several recent studies focused on the identification of different HFpEF phenotypes. In this review, we summarize available evidence on phenotype profiling in HFpEF, describing the different phenotypes with the relative therapeutic implications, and reporting other specific clinical conditions relevant for HFpEF differential diagnosis.
Pulsed field ablation in atrial fibrillation ablation: where are we and where are we going?
Authors: Schiavone Marco , Tondo Claudio
Published: February 2025

Pulsed field ablation (PFA) offers a novel approach to treating atrial fibrillation, demonstrating promising efficacy and safety. Unlike traditional thermal ablation techniques like radiofrequency or cryoablation, PFA uses non-thermal irreversible electroporation to selectively target myocardial tissue, minimizing damage to surrounding structures such as the oesophagus, phrenic nerve, and coronary arteries. Initial studies indicate that PFA is effective in achieving durable pulmonary vein isolation and posterior wall isolation, with a low incidence of serious complications. However, more long-term clinical data are needed to further confirm its efficacy.
The ‘Padua classification’ of cardiomyopathies into three groups: hypertrophic/restrictive, dilated/hypokinetic, and scarring/arrhythmogenic
Authors: Corrado Domenico , Graziano Francesca , Bauce Barbara , Bueno Marinas Maria , Calore Chiara , Celeghin Rudy , Cipriani Alberto , De Gaspari Monica , De Lazzari Manuel , Migliore Federico , Perazzolo Marra Martina , Pilichou Kalliopi , Rigato Ilaria , Rizzo Stefania , Angelini Annalisa , Zorzi Alessandro , Thiene Gaetano , Basso Cristina
Published: February 2025

The newly proposed classification of cardiomyopathies, referred to as ‘the Padua Classification’, is based on both pathobiological basis (genetics, molecular biology, and pathology) and clinical features (morpho-functional and structural ventricular remodelling as evidenced by cardiac magnetic resonance). Cardiomyopathies are grouped into tree main categories and characterized by a designation combining both ‘anatomical’ and ‘functional’ features: hypertrophic/restrictive, dilated/hypokinetic, and scarring/arrhythmogenic; each cardiomyopathy group includes either genetic or non-genetic aetiologic variants. This novel approach aims to enhance the diagnostic accuracy and to support ‘disease-specific’ therapeutic strategies, with the objective to improve patient management and outcome.
The clinical and pharmacoeconomic impact of established and novel heart failure therapies
Authors: Acquaro Mauro , Turco Annalisa , De Luca Leonardo
Published: February 2025

Chronic heart failure (HF) is a prevalent condition associated with significant morbidity, mortality, and economic burden worldwide. The pharmacological management of HF has evolved over time with various drug classes demonstrating efficacy in improving patient outcomes. This review examines the pharmacoeconomic aspects of these therapies, including common and newer HF therapies as angiotensin receptor-neprilysin inhibitors, sodium–glucose co-transporter-2 inhibitors, iron supplementation, and vericiguat, a novel soluble guanylate cyclase stimulator. By analysing cost-effectiveness studies and their implications on healthcare resource utilization, this paper aims to inform clinicians and policymakers on HF management optimization from both clinical and economic perspectives.
The role of functional assessment in the management of ischaemic heart disease
Authors: Prati Francesco , Albertucci Mario , Biccire’ Flavio Giuseppe , Gatto Laura
Published: February 2025

Over the past three decades, ischaemia research has been the cornerstone of the management and treatment of patients with atherosclerotic CAD. A robust body of evidence, including non-randomized and randomized trials, has supported the use of invasive and non-invasive coronary function tests to guide coronary revascularization. However, more recent data have questioned the clinical benefits of adopting this approach, especially in patients admitted with acute myocardial infarction. The increasing use of intracoronary imaging has identified the morphological features of plaques at higher risk of causing subsequent acute coronary events, despite the fact that they were not obstructive at the time of the index investigation. However, although functional assessment does not appear to have the same potential for identifying high-risk plaques as imaging modalities, it offers the simplicity and reproducibility of plaque assessment as a unique advantage. Furthermore, the ideal approach for the treatment of the so-called vulnerable plaques is still far from being identified, while a robust body of evidence supports the role of functionally guided revascularization, especially in stable patients. Overall, ischaemia research still provides non-negligible information that contributes to a personalized approach to improve patient outcomes.
Policy Strategies for Inclusion of Pregnant and Lactating Women in Vaccine Research
Authors: Serota Danielle E , Crooks Chelsea M , McGinty Emma E , Permar Sallie R , Riley Laura
Published: February 2025

Pregnant and lactating women (PLW) have historically been excluded from vaccine research, creating inequities in vaccine access and uptake for PLW. U.S. federal research policies create the framework for inclusion of diverse populations, including PLW, in research. We conducted a policy analysis and interviews (N=29) with experts in vaccine research for PLW to characterize the existing policy landscape and to identify policy strategies to promote inclusion of PLW in vaccine trials. We integrated policy analysis and interview results to inform five policy recommendations. Current federal policy does not require or incentivize the inclusion of PLW in vaccine trials. The Food and Drug Administration (FDA) guidance on inclusion of PLW in vaccine and other clinical research is nonbinding and lacks clarity. Extant policies do not adequately allay liability concerns among vaccine developers. To address these concerns, we recommend that the U.S. Congress pass legislation authorizing the FDA to require inclusion of PLW in vaccine research; incentivize sponsors to complete timely vaccine studies in PLW; create a national no-fault compensation program for clinical research participants, including PLW; remove pregnancy from the “vulnerable population” designation in FDA human subjects regulations and clarify existing federal regulations pertaining to clinical research with PLW.
Myocardial revascularization in patients with chronic kidney disease: a systematic review and metanalysis of surgical versus percutaneous coronary revascularization
Authors: Grazioli Valentina , Di Mauro Michele , Perocchio Giacomo , Gerometta Piersilvio , Agnino Alfonso , Pin Maurizio , Meani Paolo , Matteucci Matteo , Ronco Daniele , Massimi Giulio , Maessen Jos , Corradi Domenico , Gaudino Mario , Lorusso Roberto
Published: February 2025

OBJECTIVES

To compare outcomes of two different revascularization strategies in chronic kidney disease patients: coronary artery bypass grafting versus percutaneous coronary intervention.

METHODS

we conducted this metanalysis according to PRISMA guidelines and registered with PROSPERO (CRD42021238659), evaluated studies comparing CABG and PCI in patients with CAD and CKD (defined by KDIGO guidelines). Data were extracted from PubMed, EMBASE, and Cochrane from 2000 to 2023. The primary end-point was long-term MACCE rates, with secondary end-points including 30-day mortality, stroke, MI, and repeat revascularization. Statistical analyses included Kaplan–Meier estimations, Cox regression, and meta-regression to address heterogeneity. Publication bias was assessed via funnel plots. No funding was received, and the authors report no conflicts of interest.

RESULTS

We included 33 studies with 402,300 patients (eGFR <60 mL/min/1.73m2). The cohort comprised 132,314 coronary artery bypass graft and 269,986 percutaneous coronary intervention patients.

Over three years, coronary artery bypass group provided protection against major adverse cardiac and cerebrovascular events, myocardial infarction, and repeat revascularization compared to percutaneous coronary intervention. However, percutaneous coronary intervention showed better short-term outcomes, including lower 30-day mortality. Coronary artery bypass group was linked to a higher stroke risk over the 3-year follow-up.

CONCLUSIONS

Revascularization strategies for chronic kidney disease and coronary artery disease patients should balance percutaneous coronary intervention's short-term benefits with coronary artery bypass grafting's long-term advantages.
A novel semi-nested PCR assay with high sensitivity and robust specificity enables simultaneous detection of human and animal bocaviruses
Authors: Piewbang Chutchai , Zahro Aisyah Nikmatuz , Poonsin Panida , Puenpa Jiratchaya , Phupolphan Cherdpong , Kosoltanapiwat Nathamon , Ngamprasertwong Thongchai , Claude Julien , Lekchareonsuk Porntippa , Poovorawan Yong , Techangamsuwan Somporn
Published: February 2025

Background

Bocaviruses (BoVs), belonging to the Parvoviridae family, pose significant challenges in detection due to their genetic diversity and cross-species transmission capabilities. Efficient and broad-spectrum detection methods are essential for understanding BoV epidemiology and addressing potential zoonotic risks.

Methods

We developed a semi-nested PCR assay for simultaneous detection of diverse BoV species across human and animal hosts. Primers were designed by analyzing 765 BoV genome sequences, targeting conserved regions spanning the NP1 to VP2 genes. Sensitivity was determined through analytical tests, and specificity was evaluated against 39 non-BoV viruses. Validation was performed using spiked biological samples, and the method was applied to 552 clinical samples from 542 hosts, encompassing a broad range of mammalian species.

Results

The assay demonstrated high sensitivity, detecting BoVs at concentrations as low as 0.2 copies/µL. Specificity tests confirmed no cross-reactivity with other viral families. Validation using 37 strains representing 29 BoV species affirmed its broad efficacy. BoVs were identified across diverse hosts, including humans, bats, canines, porcines, rodents, and felines. Additionally, novel host associations were observed, such as Panthera uncia bocaparvovirus (PuBoV) in a tiger and serval cat, canine bocavirus 2 (CBoV-2) in raccoon dogs, and feline bocaviruses (FBoV) in murid rodents. Human bocaviruses were also detected in monkey samples, indicating potential pathogen spillover.

Conclusions

This semi-nested PCR method provides a sensitive and specific tool for BoV detection, enhancing surveillance in human and animal populations. It is instrumental in monitoring zoonotic risks and emerging infectious threats, offering critical insights into BoV epidemiology and cross-species transmission dynamics.
Spatio-temporal pattern evolution analysis of ecological networks based on the morphological spatial pattern analysis: A case study of Ningbo City, China
Authors: Zhang Jiyuan , Gao Xuehui , Liang Chaozhong , Zhang Maowen , Zhang Shuiming
Published: February 2025

The exponential expansion of urban areas has precipitated a concomitant deterioration in the natural environment. Constructing ecological networks is vital in improving landscape connectivity, protecting biodiversity, and maintaining regional sustainable development. Ningbo, China was set as the research area. The geographic information system (GIS) and the morphological spatial pattern analysis (MSPA) were employed to determine the ecological source area. Subsequently, the corridor design model Linkage Mapper was employed to ascertain and assess the linkages between the designated ecological source areas. The results showed that: (1) From 2000 to 2020, there was a large-scale change in land use type in Ningbo, with increasing complexity of patches and landscape fragmentation. The ecological sources of the three periods in Ningbo were primarily situated in the western, southern, and Hangzhou Bay coastal regions, exhibiting an uneven distribution in the eastern and western areas. (2) The number of primary ecological corridors in Ningbo underwent a significant reduction, from 26 to 17, between the years 2000 and 2020. In terms of the distribution of ecological corridors, the primary corridors were concentrated in the central, southern, and western regions of the study area in 2000. By 2020, however, the primary ecological corridors within the study region were distributed mainly in a southerly direction. The interaction between North and South ecological sources was weakened, which adversely affected the species spread and ecosystem stability. (3) After optimization, 12 ecological corridors, and 4 ecological nodes were incorporated into the Ningbo, 67 ecological breakpoints were identified, and 4 stepping stone patches were added. The study employed spatio-temporal change trends, including land use type and landscape pattern, to examine the ecological network of Ningbo. In conclusion, the proposed optimisation strategy is aligned with the current urban development context, offering a particularly pertinent reference point for Ningbo's ecological protection initiatives.
The elastic wave dispersion mechanism of different coal structures under room-dry condition
Authors: She Jiasheng , Zou Guangui , Peng Suping , Gong Fei , Zhao Tailang , Liu Yanhai , Li Bin , Yin Caiyun
Published: February 2025

The elastic characteristics of different coal structures (primary, cataclastic, granulated and mylonitized) are important for coalbed problems such as methane exploration and mining. However, due to various factors influencing coal elastic parameters, there is still little understanding about it. In this study, we selected four samples with different coal structures and measured their elastic parameters in seismic frequency band (4–300 Hz) under varying confining pressure (room pressure up to 20 MPa). The results show that coal elastic wave velocities are frequency dependent under room-dry condition. These results contrast with the previous understanding that rock dispersion phenomena are caused by fluids. The dispersion of elastic wave velocities decreases with increasing confining pressure and increases as the coal structure becomes more fragmented. Under room pressure, the P-wave velocity in primary coal and mylonitized coal exhibited 5.91% and 12.04% increases from 4 to 300 Hz, respectively. However, at 20 MPa, these increases were reduced to 2.78% and 4.75%. The fractal viscoelastic model, which is grounded in the staggered interlayer structure of coal matrix, effectively describes the dispersion characteristics of coal. That reveals the fractal structure of the coal may be used to describe the coal viscoelastic characteristics. We found that frictional dissipation and the viscoelastic components, such as clay and organic matter, caused the dispersion. The difference in compliant pore content is the primary reason for the different dispersion in various coal structures in this study. This research may provide a new basis for studying the elastic wave dispersion of different coal structures.
Variation in leaf construction cost and environmental drivers in China
Authors: Liu Yuhan , Zhao Yifei , Li Qiaosheng , Tan Zijun , Zhang Zugeng , Liu Yuxuan , Wang Jianming , Liu Congcong , Xiao Chunwang
Published: February 2025

Leaf construction cost (LCC), a proxy for the energetic investment plants make to construct leaf biomass, indicates carbon investment strategies of plants across diverse habitats. However, large-scale variations in LCC and their correlations with climate and soil factors have yet to be fully explored. Here, we compiled a dataset comprising 442 species-site combinations, spanning nearly all vegetation types in China, to address this knowledge gap. We found that LCC exhibited substantial variation, ranging from 0.72 g glucose g-1 to 1.93 g glucose g-1, with an average of 1.25 g glucose g-1. LCC was significantly higher in woody species compared to non-woody species; however, there was no significant difference in LCC between evergreen and deciduous plants. LCC decreased with latitude and longitude but increased with altitude. Among bivariate LCC-environment relationships, LCC was positively correlated with mean annual precipitation and temperature, but negatively correlated with temperature seasonality, precipitation seasonality, soil nitrogen content, and soil silt content. Collectively, climate and soil factors account for over 54% of the variance in LCC, with soil exerting a more significant influence than climate on LCC. This study offers an exhaustive analysis of the evident pattern of LCC over a large spatial scale, fostering a fresh perspective on functional biogeography and establishing the foundation for further research exploring the interplay between LCC, ecological functions, and macroevolutionary implications.
Systemic inflammation response index predicts overall survival in patients undergoing stereotactic radiosurgery for brain metastasis from non-small cell lung cancer
Authors: Matsuda Ryosuke , Tamamoto Tetsuro , Inooka Nobuyoshi , Hontsu Shigeto , Doi Akihiro , Maeoka Ryosuke , Nakazawa Tsutomu , Morimoto Takayuki , Yamaki Kaori , Miura Sachiko , Morisaki Yudai , Yokoyama Shohei , Kotsugi Masashi , Takeshima Yasuhiro , Isohashi Fumiaki , Nakagawa Ichiro
Published: February 2025

This study aimed to evaluate the prognostic value of pre-treatment blood cell counts in patients with brain metastasis (BM) from non-small cell lung cancer (NSCLC) who were treated using linear accelerator (linac)-based stereotactic radiosurgery (SRS) and fractionated stereotactic radiotherapy (fSRT) with a micro-multileaf collimator. Between January 2011 and November 2022, 271 consecutive patients underwent linac-based SRS/fSRT for BM from NSCLC. Thirty patients with insufficient blood test data during this period were excluded from this analysis. Thirty-five patients with steroid intake at the time point of the blood test and 18 patients with higher C-reactive protein were excluded. Thus, 188 patients were eventually enrolled in this study. The median follow-up period after SRS/fSRT was 21 months (range: 0–121 months), and the median survival time after SRS/fSRT was 19 months. Neutrophil–lymphocyte ratio ≥ 1.90, lymphocyte–monocyte ratio ≤ 1.67 and systemic inflammation response index (SIRI) ≥ 2.95 were unfavorable predictors of prognosis for patients who underwent SRS/fSRT for BM from NSCLC. Cox proportional-hazard multivariate analysis revealed that the SIRI was independent prognostic factors for increased risk of death. Thus, simple, less expensive, and routinely performed pre-treatment blood cell count measurements such as SIRI can predict the overall survival of patients treated with SRS/fSRT for BM from NSCLC.
A case of rapid rupture of a calcified amorphous tumor observed by echocardiography
Authors: Shirakura Kentaro , Ushioda Ryohei , Tsutsui Masahiro , Kunioka Shingo , Mochizuki Nobuhiro , Aonuma Tatsuya , Kawabata Naoko , Saitoh Erika , Nakagawa Naoki , Kamiya Hiroyuki
Published: February 2025

A calcified amorphous tumor (CAT) of the heart is a rare, non-neoplastic, intracavitary cardiac mass. Histological examination reveals the presence of calcified and amorphous fibrous material with underlying chronic inflammation. Some studies have reported that CAT typically exhibits rapid growth. However, we observed a case in which CAT unexpectedly ruptured within approximately two weeks. There was no cerebral infarction or significant valvular disease, therefore we were not sure about the indication for surgery; however considering the epidemiological possibility of CAT, we decided to operate and were able to treat the patient without complications.
Discovery of the variable optical counterpart of the redback pulsar PSR J2055+1545
Authors: Sen Marco Turchetta Bidisha , Simpson Jordan A , Linares Manuel , Breton Rene P , Casares Jorge , Kennedy Mark R , Shahbaz Tariq
Published: February 2025

We present the discovery of the variable optical counterpart to PSR J2055+1545, a redback millisecond pulsar, and the first radial velocity curve of its companion star. The multi-band optical light curves of this system show a 0.4–0.6 mag amplitude modulation with a single peak per orbit and variable colours, suggesting that the companion is mildly irradiated by the pulsar wind. We find that the flux maximum is asymmetric and occurs at orbital phase ≃ 0.4, anticipating the superior conjunction of the companion (where the optical emission of irradiated redback companions is typically brightest). We ascribe this asymmetry, well fit with a hot spot in our light curve modelling, to irradiation from the intrabinary shock between pulsar and companion winds. The optical spectra obtained with the Gran Telescopio Canarias reveal a G-dwarf companion star with temperatures of 5749 ± 34 K and 6106 ± 35 K at its inferior and superior orbital conjunctions, respectively, and a radial velocity semi-amplitude of 385 ± 3 km s−1. Our best-fit model yields a neutron star mass of $1.7^{+0.4}_{-0.1} \ \mathrm{M}_{\odot }$ and a companion mass of $0.29^{+0.07}_{-0.01} \ \mathrm{M}_{\odot }$. Based on the close similarity between the optical light curve of PSR J2055+1545 and those observed from PSR J1023+0038 and PSR J1227−4853 during their rotation-powered states, we suggest this system may develop an accretion disc in the future and manifest as a transitional millisecond pulsar.
Phase 1 dose-escalation trial using convection-enhanced delivery (CED) of radio-immunotheranostic 124I-Omburtamab for diffuse intrinsic pontine glioma (DIPG)
Authors: Souweidane Mark M , Bander Evan D , Zanzonico Pat , Reiner Anne S , Manino Nicole , Haque Sofia , Carrasquillo Jorge A , Lyashchenko Serge K , Thakur Sunitha B , Lewis Jason S , Donzelli Maria , Cheung Nai-Kong V , Larson Steven M , Kramer Kim , Pandit-Taskar Neeta , Dunkel Ira J
Published: February 2025

Background

Median survival for patients with Diffuse Intrinsic Pontine Glioma (DIPG) is 8-12 months.

Methods

A phase 1, open label, 3 + 3 dose escalation trial delivered radiolabeled 124I-Omburtamab, targeting B7-H3, using MR-guided stereotactic convection enhanced delivery (CED) into the brainstem of pediatric DIPG patients. CED was performed after completion of standard-of-care external-beam radiation therapy (EBRT). Fifty children were treated and evaluable. 124I-Omburtamab activity was escalated from 0.25-10.0 mCi (9.25-370 MBq) and volume escalated from 0.25 ml-10.0 ml with serial PET/MRI post-administration. Safety was the primary outcome. National Cancer Institute Common Terminology Criteria for Adverse Events were assessed for 30 days following CED of 124I-Omburtamab. Secondary outcomes included overall survival and lesion-to-whole-body absorbed dose ratio.

Results

The maximum tolerated activity per study protocol was determined to be 6mCi (222 MBq). The overall mean (±SD) total absorbed dose in the lesion per unit injected activity was 35.2 ± 18 cGy/MBq with a high lesion-to-whole-body absorbed dose ratio averaging 816, across all activity levels. Eleven patients had treatment-related grade 3 CNS toxicities with no grade-4 or -5 CNS toxicities. Five dose-limiting toxicity events occurred. Median survival was 15.29 months from diagnosis (95% CI: 12.20 – 16.83 months). Survival rate estimates at 1, 2, and 3 years were 65.4% (CI 53.3-80.1%), 18.4% (CI: 10.2-33.2%), and 11.7% (CI: 5.3-25.7%), respectively.

Conclusions

Administration of 124I-Omburtamab via CED is a safe treatment option for DIPG, with a maximum tolerated activity level identified. This study represents the first in-human theranostic use of a 124I radiopharmaceutical, simultaneously, as an imaging and therapeutic agent.
Content analysis of tobacco brands’ “Tagged” section on Instagram
Authors: Donaldson Scott I , La Capria Kathryn , DeJesus Amanda , Ganz Ollie , Allem Jon-Patrick
Published: February 2025

Introduction

Brands can be “tagged” in Instagram posts to communicate a partnership with a social media influencer. Little is known about the content of these communications in the tobacco-related literature. To address this gap, this study identified tagged posts on the official Instagram pages of tobacco brands and described the themes of such posts.

Methods

Six tobacco brands with official Instagram pages were identified. Each tagged section of the brand’s official Instagram page was examined to identify potential partnerships with social media influencers. Posts to the tagged section of the Instagram page were collected from November 2022 to February 2024. For each post, tobacco-related themes were coded.

Results

This study identified 594 tagged posts from 222 potential social media influencers. The most common theme among tagged posts was product presence (n=430, 72.4%), followed by branding (n=421, 70.9%). Young adults were identified in 40.4% (n=240) of posts. Among users who tagged a brand account, 96.1% (n=571) of their account profiles contained URL links to commercial websites, suggesting social media influencer status.

Conclusions

This study showed that the tagged section of tobacco brands’ Instagram pages contained posts suggestive of paid partnerships between the brand and social media influencers. These posts often featured tobacco use and young adults. Future research should examine whether the presence of (or accessibility to) URL links to commercial websites appearing on influencers’ pages increases an Instagram user’s purchase intentions and tobacco use initiation.

Implications

This study showed that the “tagged” sections of the official Instagram pages of six tobacco brands featured tobacco use, contained links to commercial websites, avoided content about addiction, and revealed that social media influencers inconsistently disclosed financial relationships with tobacco brands. In addition to enforcing and bolstering online marketing restrictions, prevention programs and interventions may focus on tobacco-related digital media literacy to help inoculate young adults against the pro-tobacco online environment.
Social Media Use and Exposure to E-Cigarette Content: A Comparison of Lesbian or Gay, Bisexual, and Questioning and Heterosexual Male and Female Young Adults in California
Authors: Ganz Ollie , Gonsalves Nishi , Talbot Eugene M , Donaldson Scott I , Jeong Michelle , Allem Jon-Patrick
Published: February 2025

Introduction

Given the rapidly changing media landscape and popularity of e-cigarettes among young adults who identify as lesbian or gay, bisexual, questioning, or something else (LGB+), timely data on media consumption and exposure to e-cigarette content across media channels is imperative for developing counter-messaging and public education campaigns for these individuals.

Methods

Using 2023 data from young adults in California, this study examined how social media use differed for heterosexual and LGB+ young adults, by sex. Exposure to e-cigarette content across media channels was also compared between heterosexual and LGB+ young adults, by sex.

Results

Findings from a non-probability representative sample of young adults in California showed that more LGB+ young adults reported using Tumblr and fewer reported using Facebook and Snapchat, compared with heterosexual young adults, among both males and females. Use of Reddit was more common among LGB+ versus heterosexual females, but there were no differences by sexual identity among males. Exposure to e-cigarette marketing was more common among LGB+ females compared with heterosexual females, but this was not the case for males. Exposure to user-generated e-cigarette content, and self-reported visits to e-cigarette websites, were more common among LGB+ females compared to heterosexual females.

Conclusions

These findings highlight the importance of treating LGB+ individuals as a heterogeneous group. As such, anti-tobacco campaigns targeting LGB+ individuals that leverage social media will want to consider which platforms are most used among their target audience to increase campaign reach.

Implications

This study builds upon the literature by providing timely data on how LGB+ young adults consume social media and are exposed to e-cigarette marketing. Findings have implications for tobacco education campaigns designed for LGB+ individuals that leverage social media.