bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated analysis of single-cell and bulk RNA sequencing data reveals a myeloid cell-related regulon predicting neoadjuvant immunotherapy response across cancers
Authors: Liu Hong , Sima Xiaoxian , Xiao Bijing , Gulizeba Haimiti , Zhao Shen , Zhou Ting , Huang Yan 
Published: May 2024

Abstract
Background
Immunotherapy has brought about a paradigm shift in the treatment of cancer. However, the majority of patients exhibit resistance or become refractory to immunotherapy, and the underlying mechanisms remain to be explored.

Methods
Sing-cell RNA sequencing (scRNA‑seq) datasets derived from 1 pretreatment and 1 posttreatment achieving pathological complete response (pCR) patient with lung adenocarcinoma (LUAD) who received neoadjuvant immunotherapy were collected, and pySCENIC was used to find the gene regulatory network (GRN) between cell types and immune checkpoint inhibitor (ICI) response. A regulon predicting ICI response was identified and validated using large‑scale pan-cancer data, including a colorectal cancer scRNA‑seq dataset, a breast cancer scRNA‑seq dataset, The Cancer Genome Atlas (TCGA) pan-cancer cohort, and 5 ICI transcriptomic cohorts. Symphony reference mapping was performed to construct the myeloid cell map.

Results
Thirteen major cluster cell types were identified by comparing pretreatment and posttreatment patients, and the fraction of myeloid cells was higher in the posttreatment group (19.0% vs. 11.8%). A PPARG regulon (containing 23 target genes) was associated with ICI response, and its function was validated by a colorectal cancer scRNA‑seq dataset, a breast cancer scRNA‑seq dataset, TCGA pan-cancer cohort, and 5 ICI transcriptomic cohorts. Additionally, a myeloid cell map was developed, and cluster I, II, and III myeloid cells with high expression of PPARG were identified. Moreover, we constructed a website called PPARG (https://pparg.online/PPARG/ or http://43.134.20.130:3838/PPARG/), which provides a powerful discovery tool and resource value for researchers.

Conclusions
The PPARG regulon is a predictor of ICI response. The myeloid cell map enables the identification of PPARG subclusters in public scRNA-seq datasets and provides a powerful discovery tool and resource value.
UBXN1 promotes liver tumorigenesis by regulating mitochondrial homeostasis
Authors: Jiao Kun , Xu Guiqin , Liu Yun , Yang Zhaojuan , Xiang Lvzhu , Chen Zehong , Xu Chen , Zuo You , Wu Zhibai , Zheng Ningqian , Xu Wangjie , Zhang Li , Liu Yongzhong 
Published: May 2024

Abstract
Background
The maintenance of mitochondrial homeostasis is critical for tumor initiation and malignant progression because it increases tumor cell survival and growth. The molecular events controlling mitochondrial integrity that facilitate the development of hepatocellular carcinoma (HCC) remain unclear. Here, we report that UBX domain-containing protein 1 (UBXN1) hyperactivation is essential for mitochondrial homeostasis and liver tumorigenesis.

Methods
Oncogene-induced mouse liver tumor models were generated with the Sleeping Beauty (SB) transposon delivery system. Assessment of HCC cell growth in vivo and in vitro, including tumour formation, colony formation, TUNEL and FACS assays, was conducted to determine the effects of UBXN1 on HCC cells, as well as the involvement of the UBXN1-prohibitin (PHB) interaction in mitochondrial function. Coimmunoprecipitation (Co-IP) was used to assess the interaction between UBXN1 and PHB. Liver hepatocellular carcinoma (LIHC) datasets and HCC patient samples were used to assess the expression of UBXN1.

Results
UBXN1 expression is commonly upregulated in human HCCs and mouse liver tumors and is associated with poor overall survival in HCC patients. UBXN1 facilitates the growth of human HCC cells and promotes mouse liver tumorigenesis driven by the NRas/c-Myc or c-Myc/shp53 combination. UBXN1 interacts with the inner mitochondrial membrane protein PHB and sustains PHB expression. UBXN1 inhibition triggers mitochondrial damage and liver tumor cell apoptosis.

Conclusions
UBXN1 interacts with PHB and promotes mitochondrial homeostasis during liver tumorigenesis.
Plasma-derived extracellular matrix for xenofree and cost-effective organoid modeling for hepatocellular carcinoma
Authors: El-Derby Azza M. , Khedr Mennatallah A. , Ghoneim Nehal I. , Gabr Mahmoud M. , Khater Sherry M. , El-Badri Nagwa 
Published: May 2024

Abstract
Background
Hepatocellular carcinoma (HCC) causes significant cancer mortality worldwide. Cancer organoids can serve as useful disease models by high costs, complexity, and contamination risks from animal-derived products and extracellular matrix (ECM) that limit its applications. On the other hand, synthetic ECM alternatives also have limitations in mimicking native biocomplexity. This study explores the development of a physiologically relevant HCC organoid model using plasma-derived extracellular matrix as a scaffold and nutritive biomatrix with different cellularity components to better mimic the heterogenous HCC microenvironment. Plasma-rich platelet is recognized for its elevated levels of growth factors, which can promote cell proliferation. By employing it as a biomatrix for organoid culture there is a potential to enhance the quality and functionality of organoid models for diverse applications in biomedical research and regenerative medicine and to better replicate the heterogeneous microenvironment of HCC.

Method
To generate the liver cancer organoids, HUH-7 hepatoma cells were cultured alone (homogenous model) or with human bone marrow-derived mesenchymal stromal cells and human umbilical vein endothelial cells (heterogeneous model) in plasma-rich platelet extracellular matrix (ECM). The organoids were grown for 14 days and analyzed for cancer properties including cell viability, invasion, stemness, and drug resistance.

Results
HCC organoids were developed comprising HUH-7 hepatoma cells with or without human mesenchymal stromal and endothelial cells in plasma ECM scaffolds. Both homogeneous (HUH-7 only) and heterogeneous (mixed cellularity) organoids displayed viability, cancer hallmarks, and chemoresistance. The heterogeneous organoids showed enhanced invasion potential, cancer stem cell populations, and late-stage HCC genetic signatures versus homogeneous counterparts.

Conclusion
The engineered HCC organoids system offers a clinically relevant and cost-effective model to study liver cancer pathogenesis, stromal interactions, and drug resistance. The plasma ECM-based culture technique could enable standardized and reproducible HCC modeling. It could also provide a promising option for organoid culture and scaling up.
Lactate facilitated mitochondrial fission-derived ROS to promote pulmonary fibrosis via ERK/DRP-1 signaling
Authors: Sun Zhiheng , Ji Zhihua , Meng Huiwen , He Wanyu , Li Bin , Pan Xiaoyue , Zhou Yanlin , Yu Guoying 
Published: May 2024

AbstractIdiopathic pulmonary fibrosis (IPF) is a chronic, progressive, fibrotic interstitial lung diseases, which mainly existed in middle-aged and elderly people. The accumulation of reactive oxygen species (ROS) is a common characteristic of IPF. Previous research also shown that lactate levels can be abnormally elevated in IPF patients. Emerging evidence suggested a relationship between lactate and ROS in IPF which needs further elucidation. In this article, we utilized a mouse model of BLM-induced pulmonary fibrosis to detect alterations in ROS levels and other indicators associated with fibrosis. Lactate could induce mitochondrial fragmentation by modulating expression and activity of DRP1 and ERK. Moreover, Increased ROS promoted P65 translocation into nucleus, leading to expression of lung fibrotic markers. Finally, Ulixertinib, Mdivi-1 and Mito-TEMPO, which were inhibitor activity of ERK, DRP1 and mtROS, respectively, could effectively prevented mitochondrial damage and production of ROS and eventually alleviate pulmonary fibrosis. Taken together, these findings suggested that lactate could promote lung fibrosis by increasing mitochondrial fission-derived ROS via ERK/DRP1 signaling, which may provide novel therapeutic solutions for IPF.
The advancement of artificial intelligence in biomedical research and health innovation: challenges and opportunities in emerging economies
Authors: da Silva Renan Gonçalves Leonel 
Published: May 2024

AbstractThe advancement of artificial intelligence (AI), algorithm optimization and high-throughput experiments has enabled scientists to accelerate the discovery of new chemicals and materials with unprecedented efficiency, resilience and precision. Over the recent years, the so-called autonomous experimentation (AE) systems are featured as key AI innovation to enhance and accelerate research and development (R&D). Also known as self-driving laboratories or materials acceleration platforms, AE systems are digital platforms capable of running a large number of experiments autonomously. Those systems are rapidly impacting biomedical research and clinical innovation, in areas such as drug discovery, nanomedicine, precision oncology, and others. As it is expected that AE will impact healthcare innovation from local to global levels, its implications for science and technology in emerging economies should be examined. By examining the increasing relevance of AE in contemporary R&D activities, this article aims to explore the advancement of artificial intelligence in biomedical research and health innovation, highlighting its implications, challenges and opportunities in emerging economies. AE presents an opportunity for stakeholders from emerging economies to co-produce the global knowledge landscape of AI in health. However, asymmetries in R&D capabilities should be acknowledged since emerging economies suffers from inadequacies and discontinuities in resources and funding. The establishment of decentralized AE infrastructures could support stakeholders to overcome local restrictions and opens venues for more culturally diverse, equitable, and trustworthy development of AI in health-related R&D through meaningful partnerships and engagement. Collaborations with innovators from emerging economies could facilitate anticipation of fiscal pressures in science and technology policies, obsolescence of knowledge infrastructures, ethical and regulatory policy lag, and other issues present in the Global South. Also, improving cultural and geographical representativeness of AE contributes to foster the diffusion and acceptance of AI in health-related R&D worldwide. Institutional preparedness is critical and could enable stakeholders to navigate opportunities of AI in biomedical research and health innovation in the coming years.
Massage for rehabilitation after total knee arthroplasty: a systematic review and meta-analysis of randomized controlled trials
Authors: Chen Ruinan , Jin Yaoyu , Jin Zhaokai , Gong Yichen , Chen Lei , Su Hai , Liu Xun 
Published: May 2024

Abstract
Objective
This study aimed to evaluate the effectiveness of massage for postoperative rehabilitation after total knee arthroplasty (TKA).

Data sources
The PubMed, Web of Science, EMBASE, Cochrane Library, and China National Knowledge Infrastructure (CNKI) databases were systematically searched from inception to May 2024.

Study selection
Any randomized controlled trials on the use of massage for postoperative TKA rehabilitation were included.

Data extraction
A meta-analysis of outcomes, including postoperative pain, knee range of motion (ROM), postoperative D-dimer levels, and length of hospital stay, was performed. The Cochrane Risk of Bias Assessment Tool was used to assess the risk of bias, and the data for each included study were extracted independently by two researchers.

Data synthesis
Eleven randomized controlled clinical trials with 940 subjects were included. The results showed that compared with the control group, the massage group experienced more significant pain relief on the 7th, 14th and 21st days after the operation. Moreover, the improvement in knee ROM was more pronounced on postoperative days 7 and 14. In addition, the massage group reported fewer adverse events. However, there was no statistically significant difference in the reduction in postoperative D-dimer levels between the patients and controls. Subgroup analysis revealed that massage shortened the length of hospital stay for postoperative patients in China but not significantly for patients in other regions. Nevertheless, the heterogeneity of the studies was large.

Conclusions
Increased massage treatment was more effective at alleviating pain and improving knee ROM in early post-TKA patients. However, massage did not perform better in reducing D-dimer levels in patients after TKA. Based on the current evidence, massage can be used as an adjunctive treatment for rehabilitation after TKA.
Natural L-type calcium channels antagonists from Chinese medicine
Authors: Xu Fangfang , Cai Wanna , Liu Bo , Qiu Zhenwen , Zhang Xiaoqi 
Published: May 2024

AbstractL-type calcium channels (LTCCs), the largest subfamily of voltage-gated calcium channels (VGCCs), are the main channels for Ca2+ influx during extracellular excitation. LTCCs are widely present in excitable cells, especially cardiac and cardiovascular smooth muscle cells, and participate in various Ca2+-dependent processes. LTCCs have been considered as worthy drug target for cardiovascular, neurological and psychological diseases for decades. Natural products from Traditional Chinese medicine (TCM) have shown the potential as new drugs for the treatment of LTCCs related diseases. In this review, the basic structure, function of LTCCs, and the related human diseases caused by structural or functional abnormalities of LTCCs, and the natural LTCCs antagonist and their potential usages were summarized.
Hereditary angioedema in Spain: medical care and patient journey
Authors: Caballero Teresa , Alonso Carmen , Baeza María Luisa , Baynova Krasimira , Cabeza José , Cortés Isabel , Escobar Oblitas Danilo , Guilarte Mar , Joral Alejandro , Jurado Palomo Jesús , Lara Jiménez María Ángeles , Martínez Virto Ana , Medrano Laura , Monte Boquet Emilio , Navarro Montserrat , Pérez Diego , Plá Martí María José , Smith Foltz Sara L. , Suero Coral , Zamora Carolina 
Published: May 2024

Abstract
Background
Hereditary angioedema due to C1 inhibitor deficiency (HAE-C1INH) is a genetic rare disease characterized by recurrent, transient and unpredictable episodes of cold, non-pruriginous oedema without associated urticaria. The characteristics of the disease have a considerable impact on the quality of life of patients. The aim of this study was to increase understanding of the patient journey of HAE in Spain.

Methods
A multidisciplinary committee of 16 HAE experts (allergy, immunology, emergency department, hospital pharmacy and nursing) and 3 representatives of the Spanish Hereditary Angioedema Patient Association (AEDAF) who were patients or caregivers participated in the study. A review of the publications on HAE treatment was performed. Semi-structured interviews were performed to HAE experts, patients, or caregivers. Three meetings with the experts, patients and caregivers were held to share, discuss, and validate data obtained from literature and interviews and to build the model.

Results
Throughout the project, the patient journey has been drawn up, dividing it into the stages of pre-diagnosis, diagnosis and treatment/follow-up. Some areas for improvement have been identified. Firstly, there is a need to enhance awareness and training on HAE among healthcare professionals, with a particular emphasis on primary care and emergency department personnel. Secondly, efforts should be made to minimize patient referral times to allergy/immunology specialists, ensuring timely access to appropriate care. Thirdly, it is crucial to encourage the study of the relatives of diagnosed patients to early identify potential cases. Fourthly, equitable access to self-administered treatments should be ensured, facilitated by systems that enable medication delivery at home and proper education and training for patients. Equitable access to long-term prophylactic treatment should also be prioritized for all patients in need. To standardize HAE management, the development of consensus guidelines that reduce variability in clinical practice is essential. Lastly, promoting research studies to enhance knowledge of the disease and align its treatment with new developments in the healthcare field should be encouraged.

Conclusions
The knowledge of the patient journey in HAE allowed us to identify improvement areas with the final aim to optimize the disease management.
Barriers to diverse clinical trial participation in Duchenne muscular dystrophy: Engaging Hispanic/Latina caregivers and health professionals
Authors: Crossnohere Norah L. , Campoamor Nicola B. , Camino Eric , Dresnick Erin , Martschenko Daphne Oluwaseun , Rodrigues Viana , Apkon Susan , Hazlett Alexis , Mittur Dhruv , Rodriguez Priscilla E. , Bridges John F. P. , Armstrong Niki 
Published: May 2024

Abstract
Background
Despite the increasing availability of clinical trials in Duchenne muscular dystrophy, racial/ethnic minorities and other populations facing health disparities remain underrepresented in clinical trials evaluating products for Duchenne. We sought to understand the barriers faced by Hispanic/Latino families specifically and underrepresented groups more generally to clinical trial participation in Duchenne.

Methods
We engaged two participant groups: Hispanic/Latino caregivers of children with Duchenne in the US, including Puerto Rico, and health professionals within the broader US Duchenne community. Caregiver interviews explored attitudes towards and experiences with clinical trials, while professional interviews explored barriers to clinical trial participation among socio-demographically underrepresented families (e.g., low income, rural, racial/ethnic minority, etc.). Interviews were analyzed aggregately and using a thematic analysis approach. An advisory group was engaged throughout the course of the study to inform design, conduct, and interpretation of findings generated from interviews.

Results
Thirty interviews were conducted, including with 12 Hispanic/Latina caregivers and 18 professionals. We identified barriers to clinical trial participation at various stages of the enrollment process. In the initial identification of patients, barriers included lack of awareness about trials and clinical trial locations at clinics that were less likely to serve diverse patients. In the prescreening process, barriers included ineligibility, anticipated non-compliance in clinical trial protocols, and language discrimination. In screening, barriers included concerns about characteristics of the trial, as well as mistrust/lack of trust. In consent and recruitment, barriers included lack of timely decision support, logistical factors (distance, time, money), and lack of translated study materials.

Conclusions
Numerous barriers hinder participation in Duchenne clinical trials for Hispanic/Latino families and other populations experiencing health disparities. Addressing these barriers necessitates interventions across multiple stages of the clinical trial enrollment process. Recommendations to enhance participation opportunities include developing clinical trial decision support tools, translating prominent clinical trials educational resources such as ClinicalTrials.gov, fostering trusting family-provider relationships, engaging families in clinical trial design, and establishing ethical guidelines for pre-screening potentially non-compliant patients.
Expiratory flow limitation during mechanical ventilation: real-time detection and physiological subtypes
Authors: Junhasavasdikul Detajin , Kasemchaiyanun Akarawut , Tassaneyasin Tanakorn , Petnak Tananchai , Bezerra Frank Silva , Mellado‐Artigas Ricard , Chen Lu , Sutherasan Yuda , Theerawit Pongdhep , Brochard Laurent ,   MAFAI VENT investigators
Published: May 2024

Abstract
Background
Tidal expiratory flow limitation (EFLT) complicates the delivery of mechanical ventilation but is only diagnosed by performing specific manoeuvres. Instantaneous analysis of expiratory resistance (Rex) can be an alternative way to detect EFLT without changing ventilatory settings. This study aimed to determine the agreement of EFLT detection by Rex analysis and the PEEP reduction manoeuvre using contingency table and agreement coefficient. The patterns of Rex were explored.

Methods
Medical patients ≥ 15-year-old receiving mechanical ventilation underwent a PEEP reduction manoeuvre from 5 cmH2O to zero for EFLT detection. Waveforms were recorded and analyzed off-line. The instantaneous Rex was calculated and was plotted against the volume axis, overlapped by the flow-volume loop for inspection. Lung mechanics, characteristics of the patients, and clinical outcomes were collected. The result of the Rex method was validated using a separate independent dataset.

Results
339 patients initially enrolled and underwent a PEEP reduction. The prevalence of EFLT was 16.5%. EFLT patients had higher adjusted hospital mortality than non-EFLT cases. The Rex method showed 20% prevalence of EFLT and the result was 90.3% in agreement with PEEP reduction manoeuvre. In the validation dataset, the Rex method had resulted in 91.4% agreement. Three patterns of Rex were identified: no EFLT, early EFLT, associated with airway disease, and late EFLT, associated with non-airway diseases, including obesity. In early EFLT, external PEEP was less likely to eliminate EFLT.

Conclusions
The Rex method shows an excellent agreement with the PEEP reduction manoeuvre and allows real-time detection of EFLT. Two subtypes of EFLT are identified by Rex analysis.
Trial registration: Clinical trial registered with www.thaiclinicaltrials.org (TCTR20190318003). The registration date was on 18 March 2019, and the first subject enrollment was performed on 26 March 2019.
Biologically informed NeuralODEs for genome-wide regulatory dynamics
Authors: Hossain Intekhab , Fanfani Viola , Fischer Jonas , Quackenbush John , Burkholz Rebekka 
Published: May 2024

Abstract
Background
Gene regulatory network (GRN) models that are formulated as ordinary differential equations (ODEs) can accurately explain temporal gene expression patterns and promise to yield new insights into important cellular processes, disease progression, and intervention design. Learning such gene regulatory ODEs is challenging, since we want to predict the evolution of gene expression in a way that accurately encodes the underlying GRN governing the dynamics and the nonlinear functional relationships between genes. Most widely used ODE estimation methods either impose too many parametric restrictions or are not guided by meaningful biological insights, both of which impede either scalability, explainability, or both.

Results
We developed PHOENIX, a modeling framework based on neural ordinary differential equations (NeuralODEs) and Hill-Langmuir kinetics, that overcomes limitations of other methods by flexibly incorporating prior domain knowledge and biological constraints to promote sparse, biologically interpretable representations of GRN ODEs. We tested the accuracy of PHOENIX in a series of in silico experiments, benchmarking it against several currently used tools. We demonstrated PHOENIX’s flexibility by modeling regulation of oscillating expression profiles obtained from synchronized yeast cells. We also assessed the scalability of PHOENIX by modeling genome-scale GRNs for breast cancer samples ordered in pseudotime and for B cells treated with Rituximab.

Conclusions
PHOENIX uses a combination of user-defined prior knowledge and functional forms from systems biology to encode biological “first principles” as soft constraints on the GRN allowing us to predict subsequent gene expression patterns in a biologically explainable manner.