bluuebunny/crossref_metadata_2025 huggingface dataset:
Valid and accepted novel bacterial taxa isolated from non-domestic animals and taxonomic revisions published in 2023
Authors: Munson Erik , Burbick Claire R. , Lawhon Sara D. , Krueger Trinity , Ruiz-Reyes Elena
Published: October 2024

Continued investigation into the bacteria associated with non-domestic animals provides important information for recognizing normal flora, assessing the health status of these unique species of animals, and identifying new or emerging pathogens of concern. In this summary of novel taxa and taxonomic revisions, considerable additions have been made toward understanding fecal and mucosal flora in multiple wild animal species. In addition, novel pathogenic bacteria are discussed, including multiple
Chlamydia
spp. causing disease in a hawk and crocodile, two
Corynebacterium
spp. causing oral lesions in penguins and a lesser-known genus,
Mergibacter
within Family
Pasteurellaceae
, causing disease in multiple wild bird species. Finally, a few revisions to bacteria isolated from normal non-domestic animal body sites are mentioned.
Galactosialidosis presenting as non-immune hydrops
Authors: Bajpai Shivani , Mandal Kausik , Naranje Kirti , Singh Anita
Published: October 2024

Hydrops fetalis is an abnormal accumulation of fluid in two or more foetal compartments which is easily detected using prenatal ultrasonography. It can be categorised into immune and non-immune. The non-immune hydrops can result from various aetiologies, including cardiovascular, respiratory, genitourinary infections, chromosomal anomalies and metabolic causes. The metabolic causes, including lysosomal storage disorders (LSD), are increasingly being recognised as the causes of non-immune hydrops. The hydrops fetalis associated with metabolic disorders is usually severe with huge ascites, hepatosplenomegaly, thick skin, renal abnormalities, increased nuchal translucency, renal abnormalities and skeletal deformities. In this report, we describe a case of LSD, that is, galactosialidosis presenting as non-immune hydrops and its diagnosis. In utero diagnosis of the disorder without an index case is challenging. The definitive diagnosis is important for planning and management of future conceptions.
Thiamine-responsive megaloblastic anaemia in a young adult with acute pancytopenia
Authors: Pascoe Michael Alan , Hall Alan M , Gray Adam
Published: October 2024

Thiamine-responsive megaloblastic anaemia (TRMA) is a rare autosomal recessive disorder characterised by the clinical triad of megaloblastic anaemia, sensorineural hearing loss and diabetes mellitus (DM) in young patients. We present a case of a young man with type 1 DM who presented with pancytopenia of unclear aetiology, initially attributed to a COVID-19 infection. After obtaining a bone marrow biopsy and pursuing genetic testing, two pathogenic variants of the SLC19A2 gene consistent with TRMA were discovered in this patient. Treatment with 100 mg of thiamine oral supplementation daily led to the complete resolution of his pancytopenia. It is important to consider a genetic cause of pancytopenia in a young person. Early recognition and diagnosis of TRMA can be life-altering given early treatment can reduce insulin requirements and resolve anaemia.
Bone cement implantation syndrome: the role of echocardiography and multidisciplinarity
Authors: Castro Pinto Tiago , Seabra Daniel , Castro Ana , Guedes Carolina
Published: October 2024

Bone cement implantation syndrome (BCIS) is a potentially serious complication after joint replacement surgery, resulting from bone marrow debris and cement embolisation, culminating in pulmonary and cardiovascular collapse. Echocardiography aids in diagnosis and management. We present a woman in her 80s with grade II BCIS. CT angiogram was inconclusive, but echocardiography revealed hyperechogenic material and right ventricular dysfunction, confirming the diagnosis. She received cardiovascular and respiratory support in a level II intensive care unit, showing full recovery of the right ventricle function when it was later reassessed. This potentially fatal condition is successfully managed if recognised early with adequate supportive care. Echocardiography might guide the diagnosis, consolidating supportive measures.
Treatment methods for oesophageal strictures in paediatric patients with epidermolysis bullosa: a systematic review
Authors: Khademian Majid , Saneian Hosein , Zare Narges , Famouri Fatemeh , Nasri Peiman , Moghadasi Mehri , Kelishadi Roya
Published: October 2024

Background

Epidermolysis bullosa (EB) is a collection of rare, inherited disorders that require treatment in specialised centres by multidisciplinary teams knowledgeable about the unique features and challenges of EB manifestations and complications.

A major gastrointestinal complication in patients with EB is oesophageal strictures. Effective management of oesophageal strictures can significantly improve patients’ quality of life. This study systematically reviews the current literature on treatment options for oesophageal strictures in paediatric patients with EB.

Methods

In September 2023, we conducted a systematic search for articles on the treatment of oesophageal stricture in patients with EB. We searched PubMed, Scopus, Embase and Ovid database without language or publication date restrictions. We screened 1042 articles, 15 of them were included in the current review. We extracted the following data from these studies: patient demographics, stricture characteristics, procedural details, clinical outcomes, complications and recurrences.

Results

Overall, in the reviewed papers, strictures were located mostly in cervical oesophagus followed by thoracic lesions. Moreover, in most of the cases only a single stricture was reported, but multiple strictures were not uncommon. Stricture treatment approaches included medical management, bougienage, as well as fluoroscopic and endoscopic balloon dilation or a combination of these methods. In most studies, fluoroscopic dilation was used as the primary treatment method in 756 procedures. They commonly used general anaesthesia for the procedure, only one study used sedation. Hospital stays were usually brief, with an average duration of 1 day, and in one study patients were discharged after just 4 hours. Most patients experienced symptom relief, could resume oral intake and gained weight soon after the procedure. However, recurrence rates had large variations from 12% to 83%. Studies reported median recurrence intervals ranging from 7 to 18 months. This review showed that complications such as perforation, fever and odynophagia were relatively uncommon, and were controlled by conservative treatment.

Conclusions

Both fluoroscopic and endoscopic balloon dilation are widely used methods for the management of oesophageal strictures in patients with EB. Each technique presents its own set of advantages and potential complications. Although the current evidence is notably limited, practical clinical decision-making may favour the fluoroscopic technique over endoscopic balloon dilation due to a comparatively reduced risk of procedural trauma. To ascertain the most effective approach, high-quality randomised controlled trials are imperative to delineate the superiority of one technique over the other.
Multicentre external validation of the Neonatal Healthcare-associated infectiOn Prediction (NeoHoP) score: a retrospective case–control study
Authors: Lloyd Lizel G , Dramowski Angela , Bekker Adrie , Ballot Daynia Elizabeth , Ferreyra Cecilia , Gleeson Birgitta , Nana Trusha , Sharland Michael , Velaphi Sithembiso Christopher , Wadula Jeannette , Whitelaw Andrew , van Weissenbruch Mirjam Maria
Published: October 2024

Background and objectives

Neonatal mortality due to severe bacterial infections is a pressing global issue, especially in low-middle-income countries (LMICs) with constrained healthcare resources. This study aims to validate the Neonatal Healthcare-associated infectiOn Prediction (NeoHoP) score, designed for LMICs, across diverse neonatal populations.

Methods

Prospective data from three South African neonatal units in the Neonatal Sepsis Observational (NeoOBS) study were analysed. The NeoHoP score, initially developed and validated internally in a South African hospital, was assessed using an external cohort of 573 sepsis episodes in 346 infants, focusing on different birth weight categories. Diagnostic metrics were evaluated, including sensitivity, specificity, positive predictive value and area under the receiver operating characteristic curve.

Results

The external validation cohort displayed higher median birth weight and gestational age compared with the internal validation cohort. A significant proportion were born before reaching healthcare facilities, resulting in increased sepsis evaluation, and diagnosed healthcare-associated infections (HAIs). Gram-negative infections predominated, with fungal infections more common in the external validation cohort.

The NeoHoP score demonstrated robust diagnostic performance, with 92% specificity, 65% sensitivity and a positive likelihood ratio of 7.73. Subgroup analysis for very low birth weight infants produced similar results. The score’s generalisability across diverse neonatal populations was evident, showing comparable performance across different birth weight categories.

Conclusion

This multicentre validation confirms the NeoHoP score as a reliable 'rule-in' test for HAI in neonates, regardless of birth weight. Its potential as a valuable diagnostic tool in LMIC neonatal units addresses a critical gap in neonatal care in low-resource settings.
p53 mutation biases squamocolumnar junction progenitor cells towards dysplasia rather than metaplasia in Barrett’s oesophagus
Authors: Lian Guodong , Malagola Ermanno , Wei Chengguo , Shi Qiongyu , Zhao Junfei , Hata Masahiro , Kobayashi Hiroki , Ochiai Yosuke , Zheng Biyun , Zhi Xiaofei , Wu Feijing , Tu Ruhong , Nápoles Osmel Companioni , Su Wenjing , Li Leping , Jing Changqing , Chen Man , Zamechek Leah , Friedman Richard , Nowicki-Osuch Karol , Quante Michael , Que Jianwen , Wang Timothy C
Published: October 2024

Background

While p53 mutations occur early in Barrett’s oesophagus (BE) progression to oesophageal adenocarcinoma (EAC), their role in gastric cardia stem cells remains unclear.

Objective

This study investigates the impact of p53 mutation on the fate and function of cardia progenitor cells in BE to EAC progression, particularly under the duress of chronic injury.

Design

We used a BE mouse model (L2-IL1β) harbouring a
Trp53
mutation (R172H) to study the effects of p53 on Cck2r
+
cardia progenitor cells. We employed lineage tracing, pathological analysis, organoid cultures, single-cell RNA sequencing (scRNA-seq) and computational analyses to investigate changes in progenitor cell behaviour, differentiation patterns and tumour progression. Additionally, we performed orthotopic transplantation of sorted metaplastic and mutant progenitor cells to assess their tumourigenic potential in vivo.

Results

The p53 mutation acts as a switch to expand progenitor cells and inhibit their differentiation towards metaplasia, but only amidst chronic injury. In L2-IL1β mice, p53 mutation increased progenitors expansion and lineage-tracing with a shift from metaplasia to dysplasia. scRNA-seq revealed dysplastic cells arise directly from mutant progenitors rather than progressing through metaplasia. In vitro, p53 mutation enhanced BE progenitors’ organoid-forming efficiency, growth, DNA damage resistance and progression to aneuploidy. Sorted metaplastic cells grew poorly with no progression to dysplasia, while mutant progenitors gave rise to dysplasia in orthotopic transplantation. Computational analyses indicated that p53 mutation inhibited stem cell differentiation through Notch activation.

Conclusions

p53 mutation contributes to BE progression by increasing expansion and fitness of undifferentiated cardia progenitors and preventing their differentiation towards metaplasia.
Long-term effects of left atrial appendage isolation in surgical ablation of atrial fibrillation based on lesion set: a multi-centre propensity-score weighted study
Authors: Pyo Won Kyung , Kim Joon Bum , Cho Yang Hyun , Je Hyoung-Gon , Kim Hee Jung , Lee Seung Hyun
Published: October 2024

Background

This present study aimed to investigate the impact of left atrial appendage (LAA) isolation on adverse clinical outcomes, with a further stratified analysis by biatrial (BA) and left atrial lesion sets, in patients with atrial fibrillation (AF) undergoing surgical ablation (SA) concurrent with mitral valve (MV) surgery.

Methods

We evaluated 875 patients (aged 65.1±12.0 years) who underwent SA of AF concomitant to MV surgery, excluding those with mechanical prostheses requiring lifelong anticoagulation, between 2005 and 2017 in five tertiary cardiac centres in South Korea. Of these, 458 had isolated the LAA, whereas the remainder (n=417) had the LAA preserved. Comparative risk of stroke, mortality and AF recurrence was assessed between the groups, considering death as a competing event. Inverse-probability treatment weighting was used for baseline adjustment.

Results

During the median follow-up of 57.4 months (IQR, 32.5–92.4 months), the adjusted risk of long-term stroke was significantly lower in the patients who underwent LAA isolation compared with those who preserved the LAA (subdistribution HR (SHR), 0.28; 95% CI 0.15 to 0.51; p<0.001). However, there were no significant differences in the adjusted risk of mortality (HR, 0.85; 95% CI 0.57 to 1.27; p=0.429) or AF recurrence (SHR, 0.92; 95% CI 0.78 to 1.08; p=0.291) between LAA isolation and preservation. In the subgroup of patients who underwent BA ablation, LAA isolation was associated with a lower long-term risk of stroke and AF recurrence (SHR, 0.77; 95% CI 0.61 to 0.94; p=0.029) compared with LAA preservation.

Conclusions

Concomitant LAA isolation during SA of AF in patients undergoing MV surgery was associated with a significantly lower risk of long-term stroke, but no survival benefit was observed.
Analysis of scalar fields with series convolution
Authors: Baysazan Emir , Birkandan Tolga , Ünver İsmail Eyüphan
Published: October 2024

Wave equations for some curved spacetimes may involve functions that prevent a solution in a closed form. In some cases, these functions can be eliminated by transformations and the solutions can be found analytically. In the cases where such transformations are not available, the infinite series expansions of these functions can be convoluted with the power series solution ansatz. We study such an example where the solution is based on a special function.
Efficient Modeling and Safety Analysis of Train–Track–Bridge Systems Using a Unified Double-Coordinate Model
Authors: Pan Jinhao , Gu Quan , Guo Wei , Liu Hanyun
Published: October 2024

Dynamic analysis of high-speed train–track–bridge (TTB) system presents engineering challenges, particularly under complex conditions like track irregularity and crosswinds. Achieving a balance between computational efficiency and accuracy using the traditional substructure method, i.e. modeling the train and track–bridge separately and possibly performing iterations between them, can be difficult. In this paper, a practical unified three-dimensional (3D) TTB model is presented by using two coordinate systems: a stationary system for the track–bridge, and a moving system for the high-speed train. A wheel–rail interaction (WRI) element model is further extended such that the wheel and rail nodes in WRI element belong to moving and stationary systems, respectively, so as to make the train and track–bridge models consistently combined into one unified model. The unified modeling method simplifies computations and improves efficiency and stability. The modeling method has been implemented into an open source finite element platform, i.e. OpenSees, and applied for dynamic response analysis of a train traveling at 50[Formula: see text]m/s over a seven-span simply supported bridge. Running safety assessments are performed using three criteria, i.e. the Nadal criterion, Prud’homme criterion and unloading criterion, considering track irregularities and crosswind loads. The analysis results provide practically useful references for engineering.
Post-Fire Stability Bearing Capacity of I-Shaped Aluminum Alloy Members Under Axial Compression
Authors: Guo Xiaonong , Chen Shaozhen , Luo Jinhui , Chen Chen
Published: October 2024

Compared to steel structures, aluminum alloy structures are more susceptible to fire damage. Accurately evaluating the residual bearing capacity of fire-damaged aluminum alloy members is crucial for effective post-disaster management. Therefore, this paper investigates the post-fire bearing capacity of I-shaped aluminum alloy members under axial compression. First, a post-fire test on 16 I-shaped aluminum alloy members under axial compression was carried out. The test results indicate that all specimens fail by the minor axis flexural buckling, and the bearing capacity of the specimens decreases with the increase of the slenderness ratio. Moreover, a trilinear relationship is found between bearing capacity and post-fire temperatures. Second, finite element (FE) models are established using ABAQUS and validated against the test results. Subsequently, numerical analysis is carried out, considering various aluminum alloy brands, post-fire temperatures, slenderness ratios, initial geometrical imperfections, and cross-section dimensions. Through the statistical regression technology and the introduction of strength and stability-bearing capacity reduction coefficients, the formulae for estimating the post-fire stability-bearing capacity of I-shaped aluminum alloy members under axial compression are derived. Finally, the proposed formulae are verified to be accurate through error analysis.
Structural Countermeasures Against Aerodynamic Torsional Divergence of a Suspension Bridge with a Main Span of 3000m
Authors: Zhang Zhitian , Yang Jiejun , Zeng Jiadong
Published: October 2024

Generalized structural and aerodynamic torsional stiffness of a suspension bridge with a main span length of 3[Formula: see text]000[Formula: see text]m are discussed first qualitatively in terms of analytical models. Two torsional divergence (TD) modes, symmetric and asymmetric, are compared in terms of the evolution of generalized torsional stiffness properties. It demonstrates that symmetric TD occurs prior to the asymmetric TD in a vast range of main span lengths. Numerical simulations of TD are then performed by the static finite element (FE) method. The results turn out a much lower critical wind speed of TD presented by the analytical model, due to stiffness degradation caused by main cable deformations. Finally, the effects of two types of countermeasures are examined. The replacement of the original deck section by a central slotted one can boost the critical wind speed of TD by 30%. Widening the main cable spacing enhances almost linearly the system’s critical wind speed. A combined countermeasure of a slotted bridge deck and widened main cable spacing stabilizes substantially the system’s aerodynamic static stability, resulting in a 45% increase in the critical wind speed of TD.
A Finite Integral Transform-Based Generalized Eigenvalue Formulation for Buckling of Orthotropic Rectangular Plates with Rotational Restraints
Authors: Chen Liang , Chen Yiming , Fu Yue , Xu Jie , An Dongqi , Li Jinbao , Ren Mingfa , Li Rui
Published: October 2024

Although the finite integral transform (FIT) method has been developed for buckling analysis of rectangular thin plates, the existing formulation involves solving complex nonlinear determinantal equations, leading to potentially questionable numerical results. To address this challenge, a new FIT-based formulation is established that transforms the solution of a complex nonlinear equation into that of a straightforward generalized eigenvalue problem. New analytical solutions for buckling of orthotropic rectangular thin plates with rotational restraints are obtained. The solution procedure is implemented via the following four steps: imposing the two-dimensional FIT on the governing equation; inputting deflection conditions of four edges, by which the relations between the transformed deflections and specific unknowns are provided; imposing the one-dimensional FIT on the elastic conditions to replace the unknowns with the transformed deflections, a generalized eigenvalue problem is constructed; determining the final analytical solutions by solving the generalized eigenvalue problem. Comprehensive highly accurate buckling load/mode solutions for typical rotationally restrained orthotropic plates are presented as benchmarks. The effects of boundary conditions, rotational fixity factors, and loading ratios on the buckling behaviors of orthotropic plates are expediently investigated adopting the present solutions.
Exploring Cross-Site User Modeling without Cross-Site User Identity Linkage: A Case Study of Content Preference Prediction
Authors: Zhou Qi , Zhang Peng , Gu Hansu , Lu Tun , Gu Ning
Published: October 2024

Performing user modeling on two or more social media platforms collaboratively and complementing each other (cross-site user modeling) has been a significant problem in the area of social media mining in recent years. The core of this problem is to get to know a person’s identities on multiple platforms and then train user models collaboratively among these platforms. However, for privacy protection, many people do not want their identities on different platforms to be linked and disclosed. For this problem, we set cross-site Content Preference Prediction as a task and propose a cross-site user modeling method without cross-site User Identity Linkage (UIL). The core thought borrowed from privacy-preserving recommender system research is to organize social media identities into groups to hide the identity linkage among platforms. Experiments on real-world datasets suggest that our method outperforms the existing cross-site user modeling methods with cross-site UIL regarding several metrics.
GCFExplainer: Global Counterfactual Explainer for Graph Neural Networks
Authors: Kosan Mert , Huang Zexi , Medya Sourav , Ranu Sayan , Singh Ambuj
Published: October 2024

Graph neural networks (GNNs) find applications in various domains such as computational biology, natural language processing, and computer security. Owing to their popularity, there is an increasing need to explain GNN predictions since GNNs are black-box machine learning models. One way to address this issue involves using
counterfactual
reasoning where the objective is to alter the GNN prediction by minimal changes in the input graph. Existing methods for counterfactual explanation of GNNs are limited to instance-specific
local
reasoning. This approach has two major limitations of not being able to offer global recourse policies and overloading human cognitive ability with too much information. In this work, we study the
global
explainability of GNNs through global counterfactual reasoning. Specifically, we want to find a
small
set of representative counterfactual graphs that explains
all
input graphs. Towards this goal, we propose GCF
Explainer
, a novel algorithm powered by
vertex-reinforced random walks
on an
edit map
of graphs with a
greedy summary
. Extensive experiments on real graph datasets show that the global explanation from GCF
Explainer
provides important high-level insights of the model behavior and achieves a
46.9%
gain in recourse coverage, a
9.5%
reduction in recourse cost compared to the state-of-the-art local counterfactual explainers. We also demonstrate that GCF
Explainer
generates explanations that are more consistent with input dataset characteristics, and is robust under adversarial attacks. In addition, K-GCF
Explainer
, which incorporates a graph clustering component into GCF
Explainer
, is introduced as a more competitive extension for datasets with a clustering structure, leading to superior performance in three out of four datasets in the experiments and better scalability.
Revisiting Conversation Discourse for Dialogue Disentanglement
Authors: Li Bobo , Fei Hao , Li Fei , Wu Shengqiong , Liao Lizi , Wei Yinwei , Chua Tat-seng , Ji Donghong
Published: October 2024

Dialogue disentanglement aims to detach the chronologically ordered utterances into several independent sessions. Conversation utterances are essentially organized and described by the underlying discourse, and thus dialogue disentanglement requires the full understanding and harnessing of the intrinsic discourse attribute. In this article, we propose enhancing dialogue disentanglement by taking full advantage of the dialogue discourse characteristics. First of all,
in feature encoding stage
, we construct the heterogeneous graph representations to model the various dialogue-specific discourse structural features, including the static speaker-role structures (i.e., speaker-utterance and speaker-mentioning structure) and the dynamic contextual structures (i.e., the utterance-distance and partial-replying structure). We then develop a structure-aware framework to integrate the rich structural features for better modeling the conversational semantic context. Second,
in model learning stage
, we perform optimization with a hierarchical ranking loss mechanism, which groups dialogue utterances into different discourse levels and carries training covering pairwise and session-wise levels hierarchically. Third,
in inference stage
, we devise an easy-first decoding algorithm, which performs utterance pairing under the easy-to-hard manner with a global context, breaking the constraint of traditional sequential decoding order. On two benchmark datasets, our overall system achieves new state-of-the-art performances on all evaluations. In-depth analyses further demonstrate the efficacy of each proposed idea and also reveal how our methods help advance the task. Our work has great potential to facilitate broader multi-party multi-thread dialogue applications.
“Together with Who?” Recognizing Partners during Collaborative Avatar Manipulation
Authors: Hashiura Kenta , Hagiwara Takayoshi , Barbareschi Giulia , Wakisaka Sohei , Minamizawa Kouta
Published: October 2024

The development of novel computer interfaces has led to the possibility of integrating inputs from multiple individuals into a single avatar, fostering collaboration by combining skills and sharing the cognitive load. However, the collaboration dynamic and its effectiveness may vary depending on the individuals involved. Particularly in scenarios where two individuals remotely control a robotic avatar without the possibility of direct communication, understanding each other’s characteristics can result in enhanced performance. To achieve this, it is essential to ascertain if individuals can discern their partner’s characteristics within the merged embodiment. This paper investigates the accuracy with which participants can distinguish between two different collaborating partners (one attempting to lead and one attempting to follow) when sharing control of a robot arm during a block pick-and-place task. The results suggested that participants who changed their roles according to the different roles of the two partners achieved the highest discrimination rates. Furthermore, participants changed their movements through the trials, adapting their actions to their preferred approach. This research provides insights into the factors determining individuals’ ability to understand partner characteristics during control of collaborative avatars.
Frequency Domain UWB Channel Characterization and Modeling in Indoor Static Environment
Authors: Pal Joydeep , Gupta Bhaskar
Published: October 2024

In this article, distance and frequency‐dependent indoor wireless channel characterization and modeling are presented in C, X, and Ku bands at the line of sight (LOS) and nonline of sight (nLOS) scenarios. Complex frequency responses of the indoor radio channel are measured using the frequency‐domain approach. The terminal and measurement setup dependencies of the propagation channel are deconvoluted using closed‐form expressions devised from a two‐port network model approach of the antenna transreceiver system. Subsequently, terminal independent frequency‐domain channel transfer functions (CTFs) and time‐domain channel impulse responses (CIRs) are derived for accurate statistical analysis of large‐ and small‐scale fading parameters of the propagation channel. A distance‐dependent statistical pathloss model is proposed. Successively, a frequency domain channel model using the fifth‐order autoregressive process is proposed. Subsequently, the existence of the multiple clusters in the environment is analyzed by the poles of the transfer functions of the model. Models are validated in both time and frequency domains by comparing the computer‐simulated synthetic model data with the empirical channel responses. The measurement data and the model data are seen to be in good agreement.
Aloperine Ameliorates Acetaminophen‐Induced Acute Liver Injury through HMGB1/TLR4/NF‐κB and NLRP3/Inflammasome Pathway
Authors: Chen Hui , Wang Shu , Chen Qiuyue , Yu Wen , Nie Hao , Liu Lian , Zheng Bing , Gong Quan
Published: October 2024

Purpose. Aloperine (ALO), an alkaloid isolated from Sophora alopecuroides L., possesses multiple pharmacological activities and holds a promise potential for the treatment of various clinical conditions, including skin hypersensitivity, cancer, and inflammatory disorders. The purpose of this study was to investigate the role of ALO in acetaminophen (N‐acetyl‐para‐aminophenol (APAP))‐induced acute liver injury and its underlying mechanisms. Materials and Methods. An animal model of acute liver injury was induced by intraperitoneal injection of APAP (150 mg/kg). Prior to APAP injection, ALO (40 mg/kg) was administered daily for 7 consecutive days. Serum alanine aminotransferase, aspartate aminotransferase, and lactate dehydrogenase levels were then measured using an automated chemical analyzer. Histopathological changes were evaluated using hematoxylin and eosin staining. Oxidative stress levels were measured by detecting superoxide dismutase (SOD), glutathione (GSH), and malondialdehyde (MDA). Pro‐inflammatory cytokines were detected in serum and liver tissues using ELISA and quantitative real‐time polymerase chain reaction (q‐PCR). The expression of members of the HMGB1/TLR4/NF‐κB signaling pathway and NLRP3 inflammasome were determined by Western blot and/or q‐PCR. In addition, the expression and location of NLRP3, cleaved caspase‐1, high‐mobility group box 1 (HMGB1), and phosphorylated p65 (p‐p65) were detected by immunofluorescence. Results. Pretreatment with ALO significantly protected mice from APAP‐induced acute liver injury, with decreased MDA content, and significantly increased GSH and SOD activities. Furthermore, ALO pretreatment reduced the release of pro‐inflammatory cytokines (IL‐1β and TNF‐α) and decreased the expression of caspase‐1, cleaved caspase‐1, and NLRP3. In addition, ALO pretreatment also inhibited the activation of the HMGB1/TLR4/NF‐κB signaling pathway. Conclusion. Taken together, ALO can ameliorate APAP‐induced acute liver injury by inhibiting oxidative stress, inflammation by inhibiting the HMGB1/TLR4/NF‐κB, and NLRP3/inflammasome pathway.
Comprehensive Application of Borehole Fine Detection Methods: A Case Study in Shantou Bay Subsea Tunnel
Authors: Wang Chengkun , Liu Zhengyu , Dong Zhao , Zhang Fengkai , Ma Chuanyi , Xu Xiaolin , Guo Qian
Published: October 2024

Water inrush disaster is one of the most severe problems during the construction of sea tunnels, primarily due to faults, karst, and weathered zones. Once a water inrush disaster occurs, it can lead to construction delays, traffic disruptions, and major economic losses, as well as potential consequences such as seawater intrusion, casualties, project suspension, and tunnel closure. Thus, advanced geological prediction is indispensable. During the construction of the Shantou Bay subsea tunnel, a sudden water inrush accident occurred in the sea–land transition section. To prevent such incidents and ensure safety, an integrated approach was employed. Firstly, the cross‐hole resistivity method was used to predict water content in front of the tunnel, as it is highly sensitive to water. Subsequently, borehole ground‐penetrating radar was applied to finely characterize the geological structure. By combining these two methods, the size, scale, location, water content, and spatial distribution of water‐bearing structures in front of the tunnel were identified. With the above measures, the Shantou Bay subsea tunnel passed through the detection section successfully. Herein, we present a case study and offer a valuable reference for similar projects concerning subsea tunnel construction.
Catalog of Endophytic Insects Associated with Rosinweeds (Silphium L., Heliantheae, Asteraceae) in North America
Authors: Nastasi Louis F. , Smith Cecil N. , Tooker John F. , Deans Andrew R.
Published: October 2024

Endophytic insects, including gall insects and leaf miners, are prominent in both natural and agricultural plant communities. We catalog the endophytic insect fauna in North America that are known to associate with rosinweeds (Silphium L., Heliantheae, Asteraceae). We provide details on host plant species, brief descriptions of insect associations, and known distributions of their association with Silphium species. We report associations with rosinweeds for 41 insect species from 18 families across four insect orders and detail the host plant tissue where these insects occur. The complex community we describe suggests that a further study of rosinweed endophytic insects could be useful to understanding evolution of host‐plant preferences and Silphium species boundaries.
Supplementary Data from Induced Pluripotent Stem Cells Facilitate the Development and Evaluation of Cancer Vaccines
Authors: Zhai Yuewen , Xu Xinyu , Fang Ji , He Fang , Li Siwen
Published: October 2024

Supplemental Material of CAN-24-0642-AT
Supplementary Table 3 from A Prime-Boost Vaccination Approach Induces Lung Resident Memory CD8+ T Cells Derived from Central Memory T Cells That Prevent Tumor Lung Metastasis
Authors: Xu Haoran , Yue Ming , Zhou Runhong , Wang Pui , Wong Michael Yik-Chun , Wang Jinlin , Huang Huarong , Chen Bohao , Mo Yufei , Tam Rachel Chun-Yee , Zhou Biao , Du Zhenglong , Huang Haode , Liu Li , Tan Zhiwu , Yuen Kwok-Yung , Song Youqiang , Chen Honglin , Chen Zhiwei
Published: October 2024

Lung tissue cell to CD8+ T cell communication ligand-receptor pairs in day 2 samples after Prime/boost vaccination
Supplementary Figure 11 from A Prime-Boost Vaccination Approach Induces Lung Resident Memory CD8+ T Cells Derived from Central Memory T Cells That Prevent Tumor Lung Metastasis
Authors: Xu Haoran , Yue Ming , Zhou Runhong , Wang Pui , Wong Michael Yik-Chun , Wang Jinlin , Huang Huarong , Chen Bohao , Mo Yufei , Tam Rachel Chun-Yee , Zhou Biao , Du Zhenglong , Huang Haode , Liu Li , Tan Zhiwu , Yuen Kwok-Yung , Song Youqiang , Chen Honglin , Chen Zhiwei
Published: October 2024

Effect of CXCR3 ligand-receptor interaction on TCM cell recruitment at day 14 post booster immunization
Supplementary Data from Therapeutic Targeting of the GLS1–c-Myc Positive Feedback Loop Suppresses Glutaminolysis and Inhibits Progression of Head and Neck Cancer
Authors: Yang Jianqiang , Chen Fanghui , Lang Liwei , Yang Fan , Fu Zhenzhen , Martinez Juan , Cho Amber , Saba Nabil F. , Teng Yong
Published: October 2024

Supplementary figures and tables
Table S5 from Proteomic Profiling of Serum Extracellular Vesicles Identifies Diagnostic Signatures and Therapeutic Targets in Breast Cancer
Authors: Xu Ganfei , Huang Rui , Wumaier Reziya , Lyu Jiacheng , Huang Minjing , Zhang Yaya , Chen Qingjian , Liu Wenting , Tao Mengyu , Li Junjian , Tao Zhonghua , Yu Bo , Xu Erxiang , Wang Lingfeng , Yu Guoying , Gires Olivier , Zhou Lei , Zhu Wei , Ding Chen , Wang Hongxia
Published: October 2024

Differentially expressed proteins between distant metastases and DCIS samples with >2-fold difference and two-way Student’s t-test p < 0.05. Related to Figure 5.
Table S4 from Proteomic Profiling of Serum Extracellular Vesicles Identifies Diagnostic Signatures and Therapeutic Targets in Breast Cancer
Authors: Xu Ganfei , Huang Rui , Wumaier Reziya , Lyu Jiacheng , Huang Minjing , Zhang Yaya , Chen Qingjian , Liu Wenting , Tao Mengyu , Li Junjian , Tao Zhonghua , Yu Bo , Xu Erxiang , Wang Lingfeng , Yu Guoying , Gires Olivier , Zhou Lei , Zhu Wei , Ding Chen , Wang Hongxia
Published: October 2024

Proteins with the highest predictive values in classifying BC-LN− and BC-LN+ samples by ExtraTrees. Related to Figure 4.
Figure S7 from Proteomic Profiling of Serum Extracellular Vesicles Identifies Diagnostic Signatures and Therapeutic Targets in Breast Cancer
Authors: Xu Ganfei , Huang Rui , Wumaier Reziya , Lyu Jiacheng , Huang Minjing , Zhang Yaya , Chen Qingjian , Liu Wenting , Tao Mengyu , Li Junjian , Tao Zhonghua , Yu Bo , Xu Erxiang , Wang Lingfeng , Yu Guoying , Gires Olivier , Zhou Lei , Zhu Wei , Ding Chen , Wang Hongxia
Published: October 2024

The EV proteome compared with serum proteome
Figure S4 from Proteomic Profiling of Serum Extracellular Vesicles Identifies Diagnostic Signatures and Therapeutic Targets in Breast Cancer
Authors: Xu Ganfei , Huang Rui , Wumaier Reziya , Lyu Jiacheng , Huang Minjing , Zhang Yaya , Chen Qingjian , Liu Wenting , Tao Mengyu , Li Junjian , Tao Zhonghua , Yu Bo , Xu Erxiang , Wang Lingfeng , Yu Guoying , Gires Olivier , Zhou Lei , Zhu Wei , Ding Chen , Wang Hongxia
Published: October 2024

Classification error matrix of the external validation cohorts for the 7 proteins using the XGBoost classifier, related to Figure 2
Table S2 from Hypoxic Memory Mediates Prolonged Tumor-Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression
Authors: Iriondo Oihana , Mecenas Desirea , Li Yilin , Chin Christopher R. , Thomas Amal , Moriarty Aidan , Marker Rebecca , Wang Yiru J. , Hendrick Haley , Amzaleg Yonatan , Ortiz Veronica , MacKay Matthew , Dickerson Amber , Lee Grace , Harotoonian Sevana , Benayoun Bérénice A. , Smith Andrew , Mason Christopher E. , Roussos Torres Evanthia T. , Klotz Remi , Yu Min
Published: October 2024

List of genes upregulated in BRx68 cells grown in hypoxia for 8 weeks
Figure S6 from Hypoxic Memory Mediates Prolonged Tumor-Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression
Authors: Iriondo Oihana , Mecenas Desirea , Li Yilin , Chin Christopher R. , Thomas Amal , Moriarty Aidan , Marker Rebecca , Wang Yiru J. , Hendrick Haley , Amzaleg Yonatan , Ortiz Veronica , MacKay Matthew , Dickerson Amber , Lee Grace , Harotoonian Sevana , Benayoun Bérénice A. , Smith Andrew , Mason Christopher E. , Roussos Torres Evanthia T. , Klotz Remi , Yu Min
Published: October 2024

Evaluation of epigenetic reasons for hypoxic downregulation of IFN/AP signal
Data from NAT10 Phase Separation Regulates YTHDF1 Splicing to Promote Gastric Cancer Progression
Authors: Liu Songyi , Lin Chunlin , Lin Xiang , Lin Penghang , He Ruofan , Pan Xiaoyu , Lin Yan , Ye Jianxin , Zhu Guangwei
Published: October 2024

Abstract
Gastric cancer is an aggressive malignancy with poor patient outcomes. N-Acetyltransferase 10 (NAT10) is an acetyltransferase that has been reported to contribute to gastric cancer progression. In-depth investigation into the underlying molecular mechanisms driven by NAT10 could help identify therapeutic targets to improve gastric cancer treatment. In this study, we found that NAT10 forms condensates to regulate RNA dynamics and promote gastric cancer progression. In samples of patients with gastric cancer, elevated NAT10 expression correlated with an unfavorable prognosis, advanced disease stage, and metastasis. NAT10 enhanced the proliferation, migration, and invasion of gastric cancer cells; supported the growth of patient-derived organoids; and accelerated tumor development. A C-terminal intrinsically disordered region-mediated liquid–liquid phase separation of NAT10 and was essential for its tumor-promoting function in gastric cancer. Moreover, NAT10 interacted with the splicing factor serine/arginine-rich splicing factor 2 (SRSF2), leading to its acetylation and increased stability. Acetylated SRSF2 directly bound to the pre-mRNA of the m6A reader YTHDF1, resulting in enhanced YTHDF1 exon 4 skipping and upregulation of a short YTHDF1 transcript that could stimulate gastric cancer cell proliferation and migration. Furthermore, YTHDF1 exon 4 skipping correlated with NAT10 and SRSF2 expression and was associated with a more aggressive phenotype in samples of patients with gastric cancer. Together, this study uncovers the role of NAT10 liquid–liquid phase separation in modulating YTHDF1 splicing through SRSF2 acetylation to drive gastric cancer progression, providing insights into the oncogenic mechanism of NAT10.

Significance: Phase separation of NAT10 enables acetylation of SRSF2 that enhances YTHDF1 exon 4 skipping, which is a tumor-promoting axis in gastric cancer that represents potential therapeutic targets and prognostic biomarkers.
Data from Hypoxic Memory Mediates Prolonged Tumor-Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression
Authors: Iriondo Oihana , Mecenas Desirea , Li Yilin , Chin Christopher R. , Thomas Amal , Moriarty Aidan , Marker Rebecca , Wang Yiru J. , Hendrick Haley , Amzaleg Yonatan , Ortiz Veronica , MacKay Matthew , Dickerson Amber , Lee Grace , Harotoonian Sevana , Benayoun Bérénice A. , Smith Andrew , Mason Christopher E. , Roussos Torres Evanthia T. , Klotz Remi , Yu Min
Published: October 2024

Abstract
Hypoxia is a common feature of many solid tumors due to aberrant proliferation and angiogenesis that is associated with tumor progression and metastasis. Most of the well-known hypoxia effects are mediated through hypoxia-inducible factors (HIF). Identification of the long-lasting effects of hypoxia beyond the immediate HIF-induced alterations could provide a better understanding of hypoxia-driven metastasis and potential strategies to circumvent it. Here, we uncovered a hypoxia-induced mechanism that exerts a prolonged effect to promote metastasis. In breast cancer patient-derived circulating tumor cell lines and common breast cancer cell lines, hypoxia downregulated tumor-intrinsic type I IFN signaling and its downstream antigen presentation (AP) machinery in luminal breast cancer cells, via both HIF-dependent and HIF-independent mechanisms. Hypoxia induced durable IFN/AP suppression in certain cell types that was sustained after returning to normoxic conditions, presenting a “hypoxic memory” phenotype. Hypoxic memory of IFN/AP downregulation was established by specific hypoxic priming, and cells with hypoxic memory had an enhanced ability for tumorigenesis and metastasis. Overexpression of IRF3 enhanced IFN signaling and reduced tumor growth in normoxic, but not hypoxic, conditions. The histone deacetylase inhibitor entinostat upregulated IFN targets and erased the hypoxic memory. These results point to a mechanism by which hypoxia facilitates tumor progression through a long-lasting memory that provides advantages for circulating tumor cells during the metastatic cascade.

Significance: Long-term cellular memory of hypoxia leads to sustained suppression of tumor-intrinsic type I IFN signaling and the antigen presentation pathway that facilitates tumorigenesis and metastasis.

See related commentary by Purdy and Ford, p. 3125
Supplementary Table S6 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Clinical features of the patients included in the OAK/POPLAR validation cohort and association with the KEAPness-dominant phenotype.
Supplementary Figure S9 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Supplementary Figure 9. Optimal cutoff of the KEAPness gene set.
Supplementary Figure S8 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Supplementary Figure 8. KEAPness and cancer-associated pathway signatures at the pan-cancer level (TCGA).
Supplementary Figure S2 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Supplementary Figure 2. Impact of KEAP1/NFE2L2 variants of uncertain significance (VUS) in differential gene expression
Supplementary Figure S15 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Supplementary Figure 15. KEAPness enrichment in relation to histology in the SU2C identification cohort and OAK/POPLAR validation cohort
Supplementary Figure S14 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Supplementary Figure 14. Impact of the KEAPness-dominant phenotype in advanced NSCLC treated with chemotherapy (docetaxel) in the OAK/POPLAR trials