bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of mp-tNGS in Bronchoalveolar Lavage Fluid for the Diagnosis of Invasive Pulmonary Aspergillosis in Nonneutropenic Patients
Authors: Wang Hansheng , Chen Xiao , You Hui , Wang Yunyun , Xia Xianru , Tang Yijun , Ren Tao , Wang Meifang 
Published: January 2025

Abstract

Background
Multiplex polymerase chain reaction (PCR)-based targeted next-generation sequencing (tNGS) is a promising tool for distinguishing lower respiratory tract infections in clinical practice, and its detectable pathogen spectrum can cover more than 95% of clinical cases, but there is limited information on systematic evaluation of the clinical use of multiplex PCR-based tNGS (mp-tNGS) in invasive pulmonary aspergillosis (IPA) cases. We aim to assess mp-tNGS in bronchoalveolar lavage fluid (BALF) for Aspergillus detection in patients with suspected IPA to provide a reliable basis for initiating antifungal therapy without microbiological or histopathological evidence.

Methods
We prospectively enrolled a cohort of consecutive patients with suspected IPA; all had undergone serum/BALF galactomannan antigen (GM), BALF mp-tNGS, and traditional tests (direct smear and culture of respiratory specimens). EORTC/MSG and FUDICU criteria or clinical compound diagnosis were used for IPA diagnosis.

Results
Thirty-two patients were diagnosed with IPA and 42 with non-IPA. Compared with the final diagnosis, the sensitivity of BALF mp-tNGS was 87.5%, while the sensitivities of traditional tests, serum GM, and BALF GM assay were 43.8%, 21.9%, and 62.5%, respectively. The specificity of BALF mp-tNGS was 90.5%, which was similar to traditional tests. The average turnaround time for Aspergillus detection by BALF mp-tNGS was 22.10 hours (SD 2.49 hours), which was significantly faster than traditional tests.

Conclusions
BALF mp-tNGS showed good performance in identification of Aspergillus in nonneutropenic IPA patients. Importantly, positive mp-tNGS in BALF can provide a basis for early antifungal therapy before microbiological evidence is available.
Prophage-encoded chitinase gene supports growth of its bacterial host isolated from deep-sea sediments
Authors: Middelboe Mathias , Traving Sachia J , Castillo Daniel , Kalatzis Panos G , Glud Ronnie N 
Published: January 2025

Abstract
Auxiliary metabolic genes encoded by bacteriophages can influence host metabolic function during infection. In temperate phages, auxiliary metabolic genes (AMGs) may increase host fitness when integrated as prophages into the host genome. However, little is known about the contribution of prophage-encoded AMGs to host metabolic properties. In this study, we examined a temperate bacteriophage, and its piezotolerant Pseudomonas sp. host obtained from sediment samples collected from the Kermadec Trench at ~10 000 m water depth. Both the phage and host were present throughout the sediment profiles from the surface to 30 cm into the sediment, covering large gradients of environmental conditions. The host and phage each carried one chitinase gene, which differed from each other, suggesting that chitin degradation plays a role in their substrate supply. We demonstrated that prophage-encoded chitinase supported host chitin degradation and growth in the presence of chitin. Furthermore, prophage induction dynamics were strongly substrate-dependent, suggesting that the host controls the lysis-lysogeny switch in response to the presence of chitin, thus optimizing the trade-off between the loss of cells from prophage induction and prophage enhancement of host performance. Overall, the results demonstrate prophage-encoded AMGs as collaborative goods for their hosts and emphasize the potential role of phage-host interactions in benthic biogeochemical cycling, as well as for the capability of deep-sea bacteria to efficiently adapt and thrive at a wide range of environmental conditions.
The no-hair theorems at work in M87*
Authors: Iorio Lorenzo 
Published: January 2025

ABSTRACT
Recently, a perturbative calculation to the first post-Newtonian order has shown that the analytically worked out Lense–Thirring precession of the orbital angular momentum of a test particle following a circular path around a massive spinning primary is able to explain the measured features of the jet precession of the supermassive black hole at the centre of the giant elliptical galaxy M87. It is shown that also the hole’s mass quadrupole moment $Q_2$, as given by the no-hair theorems, has a dynamical effect, which cannot be neglected, as, instead, done so far in the literature. New allowed regions for the hole’s dimensionless spin parameter $a^\ast$ and the effective radius $r_0$ of the accretion disc, assumed tightly coupled with the jet, are obtained by including both the Lense–Thirring and the quadrupole effects in the dynamics of the effective test particle modelling the accretion disc. One obtains that, by numerically integrating the resulting averaged equations for the rates of change of the angles $\eta$ and $\phi$ characterizing the orientation of the orbital angular momentum with $a^\ast = +0.98$ and $r_0=14.1$ gravitational radii, it is possible to reproduce, both quantitatively and qualitatively, the time series for them recently measured with the Very Long Baseline Interferometry technique. Instead, the resulting time series produced with $a^\ast = -0.95$ and $r_0=16$ gravitational radii turn out to be out of phase with respect to the observationally determined ones, while maintaining the same amplitudes.
AI-guided virtual biopsy: Automated differentiation of cerebral gliomas from other benign and malignant MRI findings using deep learning
Authors: Holtkamp Mathias , Parmar Vicky , Hosch René , Salhöfer Luca , Styczen Hanna , Li Yan , Opitz Marcel , Glas Martin , Guberina Nika , Wrede Karsten , Deuschl Cornelius , Forsting Michael , Nensa Felix , Umutlu Lale , Haubold Johannes 
Published: January 2025

Abstract

Background
This study aimed to develop an automated algorithm to noninvasively distinguish gliomas from other intracranial pathologies, preventing misdiagnosis and ensuring accurate analysis before further glioma assessment.

Methods
A cohort of 1280 patients with a variety of intracranial pathologies was included. It comprised 218 gliomas (mean age 54.76 ± 13.74 years; 136 males, 82 females), 514 patients with brain metastases (mean age 59.28 ± 12.36 years; 228 males, 286 females), 366 patients with inflammatory lesions (mean age 41.94 ± 14.57 years; 142 males, 224 females), 99 intracerebral hemorrhages (mean age 62.68 ± 16.64 years; 56 males, 43 females), and 83 meningiomas (mean age 63.99 ± 13.31 years; 25 males, 58 females). Radiomic features were extracted from fluid-attenuated inversion recovery (FLAIR), contrast-enhanced, and noncontrast T1-weighted MR sequences. Subcohorts, with 80% for training and 20% for testing, were established for model validation. Machine learning models, primarily XGBoost, were trained to distinguish gliomas from other pathologies.

Results
The study demonstrated promising results in distinguishing gliomas from various intracranial pathologies. The best-performing model consistently achieved high area-under-the-curve (AUC) values, indicating strong discriminatory power across multiple distinctions, including gliomas versus metastases (AUC = 0.96), gliomas versus inflammatory lesions (AUC = 1.0), gliomas versus intracerebral hemorrhages (AUC = 0.99), gliomas versus meningiomas (AUC = 0.98). Additionally, across all these entities, gliomas had an AUC of 0.94.

Conclusions
The study presents an automated approach that effectively distinguishes gliomas from common intracranial pathologies. This can serve as a quality control upstream to further artificial-intelligence-based genetic analysis of cerebral gliomas.
Effects of Infant Formula Supplemented With Prebiotics on the Gut Microbiome, Gut Environment, Growth Parameters, and Safety and Tolerance: A Systematic Review and Meta-Analysis
Authors: Kebbe Maryam , Leung Kennedy , Perrett Ben , Reimer Raylene A , Adamo Kristi , Redman Leanne M 
Published: January 2025

Abstract

Context
Prebiotics are often added to infant formulas to mimic the benefits of oligosaccharides found in human milk.

Objective
This systematic review and meta-analysis evaluated the effects of prebiotic-supplemented cow’s milk–based formula on the gut microbiota, gut environment, growth parameters, and safety and tolerance in infants ≤6 months old, compared with a standard formula or human milk comparator.

Data Sources
Searches were performed in the PubMed, Embase, Cochrane Central Register of Controlled Trials, and ProQuest Dissertations & Theses databases. Articles were included that reported on randomized controlled trials, were published from inception until April 2024, and met prespecified inclusion and exclusion criteria.

Data Extraction
Outcomes included gut microbiota (eg, diversity; taxa at phylum, family, genus and species levels), gut environment (eg, pH, secretory immunoglobulin A, fecal calprotectin, fecal metabolites), growth parameters (eg, z scores), and safety and tolerance. Fixed or random effects models were used and mean differences (MDs) with 95% CIs were calculated to assess pooled effects. Risk of bias was assessed using the Cochrane Collaboration Tool (RoB 2).

Data Analysis
A total of 30 articles met inclusion criteria, with 5290 infants included. Whereas effects on Lactobacillus were inconsistent, prebiotic formula supplementation increased Bifidobacterium counts (k = 7 [MD: 0.49; 95% CI, 0.27-0.71]; I2 = 13%; P &lt; .00001) and decreased fecal pH (k = 7 [MD: –0.39; 95% CI, –0.57 to –0.20]; I2 = 0%; P &lt; .0001) compared with standard formula. Prebiotic formula supplementation increased total bacteria compared with human milk (MD: 0.41 [95% CI, 0.17-0.65]; I2 = 8%; P = .0006). In terms of growth parameters, weight-for-age z scores favored the prebiotic formula group compared with the human milk group (k = 2 [MD: 0.23; 95% CI, 0.04-0.42]; I2 = 7%; P = .02).

Conclusions
Prebiotic supplementation in infant formula can positively alter the gut microbiota, particularly Bifidobacterium, without negative impacts on growth. Standardized, high-quality research is needed to confirm the study findings and inform guidelines for prebiotic use in infant nutrition.

Systematic Review Registration
PROSPERO registration no. CRD42021253589.
Machine learning models for predicting postoperative peritoneal metastasis after hepatocellular carcinoma rupture: a multicenter cohort study in China
Authors: Xia Feng , Chen Qian , Liu Zhicheng , Zhang Qiao , Guo Bin , Fan Feimu , Huang Zhiyuan , Zheng Jun , Gao Hengyi , Xia Guobing , Ren Li , Mei Hongliang , Chen Xiaoping , Cheng Qi , Zhang Bixiang , Zhu Peng 
Published: January 2025

Abstract

Background
Peritoneal metastasis (PM) after the rupture of hepatocellular carcinoma (HCC) is a critical issue that negatively affects patient prognosis. Machine learning models have shown great potential in predicting clinical outcomes; however, the optimal model for this specific problem remains unclear.

Methods
Clinical data were collected and analyzed from 522 patients with ruptured HCC who underwent surgery at 7 different medical centers. Patients were assigned to the training, validation, and test groups in a random manner, with a distribution ratio of 7:1.5:1.5. Overall, 78 (14.9%) patients experienced postoperative PM. Five different types of models, including logistic regression, support vector machines, classification trees, random forests, and deep learning (DL) models, were trained using these data and evaluated based on their receiver operating characteristic curve and area under the curve (AUC) values and F1 scores.

Results
The DL models achieved the highest AUC values (10-fold training cohort: 0.943, validation set: 0.928, and test set: 0.892) and F1 scores (10-fold training set: 0.917, validation cohort: 0.908, and test set:0.899) The results of the analysis indicate that tumor size, timing of hepatectomy, alpha-fetoprotein levels, and microvascular invasion are the most important predictive factors closely associated with the incidence of postoperative PM.

Conclusion
The DL model outperformed all other machine learning models in predicting postoperative PM after the rupture of HCC based on clinical data. This model provides valuable information for clinicians to formulate individualized treatment plans that can improve patient outcomes.
Radiotherapy and surgery: can this combination be further optimized for patients with metastatic spine disease?
Authors: Amelink Jantijn J G J , Bindels Bas J J , Kasperts Nicolien , MacDonald Shannon M , Tobert Daniel G , Verlaan Jorrit-Jan 
Published: January 2025

Abstract
This narrative review provides a comprehensive overview of the current status, recent advancements, and future directions in the management of metastatic spine disease using both radiotherapy and surgery. Emphasis has been put on the integrated use of radiotherapy and surgery, incorporating recent developments such as separation surgery, active dose sparing of the surgical field, and the implementation of carbon fiber-reinforced polymer implants. Future studies should explore the effects of minimizing the time between radiotherapy and surgery and investigate the potential of vertebral re-ossification after radiotherapy to obviate the need for stabilization surgery. Concerted efforts should be directed toward fostering multidisciplinary collaboration among radiation oncologists, spine surgeons, and medical oncologists.
Phototherapy in lymphoproliferative and inflammatory diseases associated with human T-lymphotropic virus
Authors: de Lima Lobato Brena Andrade , de Brito João Augusto Gomes de Souza Monteiro , Abreu Junior José Maria de Castro , de Sousa Maísa Silva , Silva Carlos Augusto Moreira , Carneiro Thiago Xavier , Sousa Rita Catarina Medeiros , Xavier Marília Brasil 
Published: January 2025

Abstract

Background
Dermatological manifestations affect 5% of patients with human T-lymphotropic virus (HTLV).

Methods
Thirteen patients with inflammatory or lymphoproliferative dermatological diseases, both HTLV-positive and HTLV-negative, were selected for treatment with ultraviolet B narrowband (UVB-NB) phototherapy. Clinical and histopathological evaluations were conducted before and after 120 d of phototherapy.

Results
All seven HTLV-positive patients evaluated were type 1. Clinical evaluation showed improvement in all 13 patients. In the histopathological examination, all patients with lymphoproliferative diseases and five with inflammatory diseases showed regression in most of the assessed parameters.

Conclusions
The present research suggests that UVB-NB phototherapy is a promising treatment for lymphoproliferative and inflammatory skin diseases in HTLV-1 patients.
Anemonin suppresses sepsis‐induced acute lung injury by inactivation of nuclear factor‐kappa B and activation of nuclear factor erythroid 2‐related factor‐2/heme oxygenase‐1 pathway
Authors: Xia Qingping , Liu Guohao , Zhang Liangqing , Xie Baodong , Deng Li 
Published: January 2025

AbstractSepsis‐induced acute lung injury (ALI) is a common acute and severe reason of death in the intensive care unit. Although the pathogenesis is complicated and multifactorial, elevated inflammation and oxidative stress are considered as fundamental mechanisms for the progression of ALI. Anemonin is a natural compound with diverse biological properties including anti‐inflammatory and anti‐oxidative effects. To identify whether anemonin has protective effects on sepsis‐induced ALI, a mouse sepsis‐induced ALI model and cellular models using the mouse alveolar macrophage MH‐S cells and mouse lung epithelial MLE‐12 cells were established. Our results showed that anemonin reduced lipopolysaccharide (LPS)‐induced mortality, and improved sepsis‐induced ALI in the mouse model, as shown by improved histopathological changes, decreased lung wet/dry weight ratio, and myeloperoxidase activity. Anemonin alleviated LPS‐induced secretion of tumor necrosis factor‐α (TNF‐α), interleukin‐1β (IL‐1β), and interleukin‐6 (IL‐6) in bronchoalveolar lavage fluid samples, as well as reversed the LPS‐caused increase in malondialdehyde (MDA) content and decrease in activities of the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT) in lung tissues. In the cellular model, anemonin inhibited the LPS‐induced inflammatory responses and oxidative stress in MH‐S and MLE‐12 cells. In addition, anemonin inhibited LPS‐induced nuclear factor‐kappa B (NF‐κB) pathway, while enhancing the activation of nuclear factor erythroid 2‐related factor‐2 (Nrf2) in lung tissues, MH‐S, and MLE‐12 cells. NF‐κB inhibition enhanced the anti‐inflammatory and anti‐oxidative effects of anemonin, while Nrf2 knockdown attenuated these effects of anemonin, implying the critical roles of NF‐κB and Nrf2. These results indicated that anemonin suppressed sepsis‐induced acute lung injury by inhibition of NF‐κB and activation of Nrf2/heme oxygenase‐1 pathway, suggesting that anemonin might be developed as a new therapeutic agent for the treatment of sepsis‐induced ALI.
Spontaneous ruptured solid pseudopapillary tumor of pancreas: a rare condition identified in a patient presenting with features of shock
Authors: Devkota Shishir , Acharya Kshitiz , Poudel Navin , Shrestha Aron , Bhattarai Abhishek , Kansakar Prasan B.S. 
Published: January 2025

Introduction:
Solid pseudopapillary tumor of pancreas are rare benign tumors of pancreas, that typically affects the young women. They are usually asymptomatic or minimally symptomatic, and are usually diagnosed by different imaging modalities.

Case presentation:
We herein present a case of solid pseudopapillary tumor of pancreas in an 18-year-old female patient who presented to our emergency department with features of shock following its spontaneous rupture. Imaging showed features suggestive of solid pseudopapillary tumor of pancreas, and she was managed by exploratory laparotomy following initial resuscitation.

Discussion:
Solid pseudopapillary tumors of pancreas are one of the rare exocrine pancreatic tumors. Their origin is not exactly clear, the most accepted theory states that these tumors originate from the multipotent primordial cells. Preoperative diagnosis can be made showing features distinct from other pancreatic solid/cystic neoplasms. Surgical management is the preferred treatment modality in these tumors.

Conclusion:
These are rare entities of pancreas, and may present with vague abdominal symptoms. Sometimes, these tumors may undergo spontaneous rupture, presenting with features of shock.
Lutembacher syndrome with congenital atrial septal defect in an 18-year-old female: a rare case report
Authors: Astanbouli Sara Mohamed , Othman Abdulrahman Ahmad , Takkem Saleh , Al Aboud Mohammad Yassin , Yousef Hamza , Yousef Haidar , AlRhman Judy Alabd , Abbas Mahmoud Mustafa , Alhasan Mahmoud Mohamad Khair , Jaamour Khaled Taysir , Buz Ahmad Ibraheem , Sleiay Bilal 
Published: January 2025

Introduction:
Lutembacher syndrome (LS) is a rare condition with congenital atrial septal defect (ASD) and mitral stenosis (MS), often post-rheumatic illness. Diagnosis uses Doppler echocardiography, and treatment may involve surgery or percutaneous options.

Case presentation:
An 18-year-old female presented with worsening dyspnea, orthopnea, and potential undiagnosed rheumatic fever. Chest X-ray showed cardiomegaly. An echocardiogram revealed left atrial dilation and mitral stenosis with regurgitation, aortic valve showed thickening without stenosis, and the right ventricle was mildly dilated; an interatrial shunt was present. Mitral stenosis worsened left-to-right shunt.

Discussion:
LS results from the balance of ASD and MS. Factors influencing prognosis include pulmonary resistance, ASD size, and mitral stenosis severity. Echocardiography is essential for diagnosis, which revealed left atrial dilation, normal left ventricular function, severe mitral stenosis, and pulmonary valve changes. ECG indicated right ventricular hypertrophy. CXR showed left atrial enlargement and right ventricle enlargement. Treatment included an open heart surgery which replaced the mitral valve and closed the ASD.

Conclusion:
Lutembacher syndrome, a rare condition combining ASD and mitral stenosis, can cause cardiac failure and pulmonary hypertension if untreated. Given the patient’s stable condition in the early stages of the disease, early surgical or percutaneous intervention is advisable.
Whole genome sequencing-based analysis of genetic predisposition to adult glioblastoma
Authors: van Opijnen Mark P. , van Valkengoed Devin R. , de Ligt Joep , de Vos Filip Y.F. , Broekman Marike L.D. , Cuppen Edwin , Koster Roelof 
Published: January 2025

AbstractBackgroundGlioblastoma is most commonly reported in the second (pediatric form) and seventh (adult form) decade of life. Pathogenic germline variants (PGVs) and its association to late onset glioblastoma remains unclear. This study aimed to investigate the genetic predisposition to adult glioblastoma.MethodsWe performed an in-depth analysis of whole genome sequencing (WGS) data of tumor-normal tissue pairs of 98 glioma WHO grade 4 patients for potential presence of PGVs, in a comprehensive set of 170 genes associated with cancer predisposition. All candidate pathogenic events were also assessed for second-hit somatic events.ResultsIn 11 patients (11%), PGVs were observed that were considered relevant by clinical experts in the context of glioblastoma. In these patients, 13 PGVs were found in genes known for a strong association with familial glioblastoma (MSH6(3x),PMS2(5x),MSH2,TP53,NF1andBRCA1) or with medulloblastoma (SUFU). In eight of these patients (73%) causality was supported by a second (somatic) event and/or a matching genome-wide mutational signature.ConclusionsGermline predisposition does also play a role in the development of adult glioblastoma, with mismatch repair deficiency being the main mechanism. Our results do illustrate benefits of tumor-normal WGS for glioblastoma patients and their relatives beyond the identification of potentially actionable mutations for therapy guidance.Key pointsPathogenic germline variants occur in more than 10% of adult glioblastomaMismatch repair deficiency is the main predisposition mechanismPathogenic germline variants could be used for (targeted) treatment selectionImportance of the StudyThe hereditary of adult glioblastoma is still largely unexplored. With the option of broad molecular testing, it is crucial that clinicians are aware of the a priori probability of finding germline predisposition in a glioblastoma patient. Here, we studied the genetic predisposition to adult glioblastoma in an unselected, average cohort. We observed that pathogenic germline variants occurred in about 1 out of 10 patients, with mismatch repair deficiency being the main predisposition mechanism. This information should be kept in mind when broad molecular testing, like WGS, is discussed with the patient. Clinicians and patients should discuss the probability of finding evidence of heredity of the tumor and potential consequences for relatives.