tbuckley/cabot-search huggingface dataset:
A dynamic nomogram for predicting intraoperative brain bulge during decompressive craniectomy in patients with traumatic brain injury: a retrospective study
Authors: Dongzhou Zhuang, Tian Li, Huan Xie, Jiangtao Sheng, Xiaoxuan Chen, Xiaoning Li, Kangsheng Li, Weiqiang Chen, Shousen Wang
Journal: International Journal of Surgery (2023)

Objective: The aim of this paper is to investigate the risk factors associated with intraoperative brain bulge, especially the CT value of the diseased lateral transverse sinus, and to develop a reliable predictive model to alert neurosurgeons to the possibility of intraoperative brain bulge. Methods: A retrospective analysis was performed on 937 patients undergoing traumatic decompressive craniectomy. A total of 644 patients from Fuzong Clinical Medical College of Fujian Medical University were included in the development cohort and 293 patients from the First Affiliated Hospital of Shantou University Medical College were included in the external validation cohort. Univariate and multifactorial logistic regression analyses identified independent risk factors associated with intraoperative brain bulge. The logistic regression models consisted of independent risk factors, and receiver operating characteristic curve, calibration, and decision curve analyses were used to assess the performance of the models. Various machine learning models were used to compare with the logistic regression model and analyze the importance of the factors, which were eventually jointly developed into a dynamic nomogram for predicting intraoperative brain bulge and published online in the form of a simple calculator. Results: Intraoperative brain expansion occurred in 93/644 (14.4%) patients in the developmental cohort, and 47/293 (16.0%) in the validation cohort. Univariate and multifactorial regression analyses showed that age, subdural hematoma, contralateral fracture, brain contusion, and CT value of the diseased lateral transverse sinus were associated with intraoperative brain bulge. A logistic regression model (full model) consisting of the above risk factors had excellent predictive power in both the development cohort (AUC=0.930) and the validation cohort (AUC=0.913). Among the four machine learning models, the Adaboost model showed the best predictive value (AUC=0.998). Factors in the Adaboost model were ranked by importance and combined with the full model to create a dynamic nomogram for clinical application, which was published online as a practical and easy-to-use calculator. Conclusions: The CT value of the diseased lateral transverse is an independent risk factor and a reliable predictor of intraoperative brain bulge. The online dynamic nomogram formed by combining logistic regression analysis models and machine learning models can more accurately predict the possibility of intraoperative brain bulge in patients undergoing traumatic decompressive craniectomy.
Diagnosis of cystic lung diseases: a position statement from the UK Cystic Lung Disease Rare Disease Collaborative Network
Authors: Simon R Johnson, Dominick E Shaw, Michael Avoseh, Irshad Soomro, Kate S Pointon, Maria Kokosi, Andrew G Nicholson, Sujal R Desai, Peter M George
Journal: Thorax (2024)

Background Rare cystic lung diseases are increasingly recognised due the wider application of CT scanning making cystic lung disease management a growing part of respiratory care. Cystic lung diseases tend to have extrapulmonary features that can both be diagnostic but also require surveillance and treatment in their own right. As some of these diseases now have specific treatments, making a precise diagnosis is crucial. While Langerhans cell histiocytosis, Birt-Hogg-Dubé syndrome, lymphoid interstitial pneumonia and lymphangioleiomyomatosis are becoming relatively well-known diseases to respiratory physicians, a targeted and thorough workup improves diagnostic accuracy and may suggest other ultrarare diseases such as light chain deposition disease, cystic pulmonary amyloidosis, low-grade metastatic neoplasms or infections. In many cases, diagnostic information is overlooked leaving uncertainty over the disease course and treatments. Aims This position statement from the Rare Disease Collaborative Network for cystic lung diseases will review how clinical, radiological and physiological features can be used to differentiate between these diseases. Narrative We highlight that in many cases a multidisciplinary diagnosis can be made without the need for lung biopsy and discuss where tissue sampling is necessary when non-invasive methods leave diagnostic doubt. We suggest an initial workup focusing on points in the history which identify key disease features, underlying systemic and familial diseases and a clinical examination to search for connective tissue disease and features of genetic causes of lung cysts. All patients should have a CT of the thorax and abdomen to characterise the pattern and burden of lung cysts and extrapulmonary features and also spirometry, gas transfer and a 6 min walk test. Discussion with a rare cystic lung disease centre is suggested before a surgical biopsy is undertaken. Conclusions We suggest that this focused workup should be performed in all people with multiple lung cysts and would streamline referral pathways, help guide early treatment, management decisions, improve patient experience and reduce overall care costs. It could also potentially catalyse a national research database to describe these less well-understood and unidentified diseases, categorise disease phenotypes and outcomes, potentially leading to better prognostic data and generating a stronger platform to understand specific disease biology.
Modafinil for Severe Fatigue in Inflammatory Bowel Disease: A Prospective Case Series
Authors: Calum D. Moulton, Allan H. Young, Ailsa L. Hart
Journal: Clinical Gastroenterology and Hepatology (2024)

Fatigue is highly prevalent in patients with IBD, affecting 72% of patients with active inflammatory bowel disease (IBD) and 47% in remission, and is associated with poor quality of life and significantly wider costs.
Near-infrared light-activatable, analgesic nanocomposite delivery system for comprehensive therapy of diabetic wounds in rats
Authors: Sufang Chen, Haixia Wang, Jingyi Du, Zhendong Ding, Tienan Wang, Linan Zhang, Jing Yang, Yu Guan, Chaojin Chen, Mingqiang Li, Ziqing Hei, Yu Tao, Weifeng Yao
Journal: Biomaterials (2024)
Inhibition of 15‐hydroxyprostaglandin dehydrogenase protects neurons from ferroptosis in ischemic stroke
Authors: Yunfei Xu, Kexin Li, Yao Zhao, Lin Zhou, Nina He, Haoduo Qiao, Qing Xu, Huali Zhang, Ying Liu, Jie Zhao
Journal: MedComm (2024)

Ischemic stroke is an acute serious cerebrovascular disease with high mortality and disability. Ferroptosis is an important regulated cell death (RCD) in ischemic stroke. 15-Hydroxyprostaglandin dehydrogenase (15-PGDH), a degrading enzyme of prostaglandin E2 (PGE2), is shown to regulate RCD such as autophagy and apoptosis. The study aimed to determine whether 15-PGDH regulates ferroptosis and ischemic stroke, and further the exact mechanism. We demonstrated that overexpression of 15-PGDH in the brain tissues or primary cultured neurons significantly aggravated cerebral injury and neural ferroptosis in ischemic stroke. While inhibition of 15-PGDH significantly protected against cerebral injury and neural ferroptosis, which benefits arise from the activation of the PGE2/PGE2 receptor 4 (EP4) axis. While the impact of 15-PGDH was abolished with glutathione peroxidase 4 (GPX4) deficiency. Then, 15-PGDH inhibitor was found to promote the activation of cAMP-response element-binding protein (CREB) and nuclear factor kappa-B (NF-κB) via the PGE2/EP4 axis, subsequently transcriptionally upregulate the expression of GPX4. In summary, our study indicates that inhibition of 15-PGDH promotes the activation PGE2/EP4 axis, subsequently transcriptionally upregulates the expression of GPX4 via CREB and NF-κB, and then protects neurons from ferroptosis and alleviates the ischemic stroke. Therefore, 15-PGDH may be a potential therapeutic target for ischemic stroke.
Mitochondrial phospholipid transport: Role of contact sites and lipid transport proteins
Authors: Vijay Aditya Mavuduru, Lavanya Vadupu, Krishna Kanta Ghosh, Sabyasachi Chakrabortty, Balázs Gulyás, Parasuraman Padmanabhan, Writoban Basu Ball
Journal: Progress in Lipid Research (2024)
Top 10 research priorities for basal cell carcinoma: results of the Skin Investigation Network of Canada Priority Setting Initiative
Authors: Ilya Shoimer, Omer Kleiner, Rachael Manion, Jan Dutz, Anie Philip, An-Wen Chan, Yuka Asai, Kathleen Barnard, Rienk De Vries, Ryan DeCoste, Jeanne DesBrisay, Aaron M Drucker, Julie Fradette, Lucie Germain, Robert Gniadecki, Omar Hasan Ali, Melanie Laurin, Ivan V Litvinov, Elizabeth Leach, Sarvesh Logsetty, Barbara Lokach, Jillian Macdonald, Marilynne Madigan, Morris F Manolson, P Régine Mydlarski, Brandon Pearsell, Patricia Pearsell, Vincent Piguet, Girish Shah, Michael Stevens, Debbie Ward, Lin Xing, Youwen Zhou
Journal: British Journal of Dermatology (2023)

The Skin Investigation Network of Canada (SkIN Canada) completed a national priority setting initiative to identify the top 10 knowledge uncertainties for BCC based on the James Lind Alliance principles. Overall, 91 patients, clinicians and researchers provided input in two survey rounds and one workshop. The top 10 list of research priorities will help the skin research community, funders and policymakers to address key knowledge uncertainties for the benefit of patients with BCC.
Ferroptosis boosted oral cancer photodynamic therapy by carrier-free Sorafenib-Ce6 self-assembly nanoparticles
Authors: Yingying Xu, Liu Yang, Chengyan Wang, Weiming Sun, Yijing Zheng, Beiwei Ou, Lixian Wu, Leilei Shi, Xi Lin, Wei Chen
Journal: Journal of Controlled Release (2024)
Use of inhaled corticosteroids and the risk of hospitalisation for pneumonia in children with asthma: a nationwide cohort study
Authors: Karl-Hermann Sielinou Kamgang, Samuel Arthur Rhedin, Catarina Almqvist, Viktor Wintzell
Journal: Thorax (2024)

Background The potential association between the use of inhaled corticosteroids (ICS) and the risk of pneumonia among adults is disputed and paediatric-specific evidence is scarce. Aim To assess the potential association between ICS, use and the risk of hospitalisation for pneumonia among children (age 2–17 years) with asthma. Methods This was a cohort study based on nationwide data from routine clinical practice in Sweden (January 2007 to November 2021). From 425 965 children with confirmed asthma, episodes of new ICS use and no use were identified using records of dispensed drugs. We adjusted for potential confounders with propensity score overlap weighting and the risk of a hospitalisation with pneumonia as primary diagnosis was estimated. Multiple subgroup and sensitivity analyses were also performed. Results We identified 249 351 ICS (mean follow-up of 0.9 years) and 214 840 no-use (mean follow-up of 0.7 years) episodes. During follow-up, 369 and 181 events of hospitalisation for pneumonia were observed in the ICS and no-use episodes, respectively. The weighted incidence rates of hospitalisation for pneumonia was 14.5 per 10 000 patient-years for ICS use episodes and 14.6 for no-use episodes. The weighted HR for hospitalisation for pneumonia associated with ICS use was 1.06 (95% CI 0.88 to 1.28) and the absolute rate difference was −0.06 (95% CI −2.83 to 2.72) events per 10 000 patient-years, compared with no use. Conclusions In this nationwide cohort study, we found no evidence of an association between ICS use and the risk of hospitalisation for pneumonia among children with asthma, as compared with no use.
Hierarchical-unlocking virus-esque NanoCRISPR precisely disrupts autocrine and paracrine pathway of VEGF for tumor inhibition and antiangiogenesis
Authors: Shuang Ma, Yingjie Li, Furong Liu, Xinxin Wang, Zeyi Qin, Li Wang, Jin Yang, Li Wang, Wen Yang, Ning Wang, Yanjie You, Qinjie Wu, Changyang Gong
Journal: Journal of Controlled Release (2024)
Ferrous/Ferric Ions Crosslinked Type II Collagen Multifunctional Hydrogel for Advanced Osteoarthritis Treatment
Authors: Lili Wang, Xian Chen, Shenghong Wang, Jianrui Ma, Xiaxia Yang, Hongli Chen, Jianxi Xiao
Journal: Advanced Healthcare Materials (2024)

Abstract Osteoarthritis (OA) is a highly prevalent and intricate degenerative joint disease affecting an estimated 500 million individuals worldwide. Collagen‐based hydrogels have sparked immense interest in cartilage tissue engineering, but substantial challenges persist in developing biocompatible and robust crosslinking strategies, as well as improving their effectiveness against the multifaceted nature of OA. Herein, a novel discovery wherein the simple incorporation of ferrous/ferric ions enables efficient dynamic crosslinking of type II collagen, leading to the development of injectable, self‐healing hydrogels with 3D interconnected porous nanostructures, is unveiled. The ferrous/ferric ions crosslinked type II collagen hydrogels demonstrate exceptional physical properties, such as significantly enhanced mechanical strength, minimal swelling ratios, and remarkable resistance to degradation, while also exhibiting extraordinary biocompatibility and bioactivity, effectively promoting cell proliferation, adhesion, and chondrogenic differentiation. Additionally, the hydrogels reveal potent anti‐inflammatory effects by upregulating anti‐inflammatory cytokines while downregulating pro‐inflammatory cytokines. In a rat model of cartilage defects, these hydrogels exhibit impressive efficacy, substantially accelerating cartilage tissue regeneration through enhanced collagen deposition and increased proteoglycan secretion. The innovative discovery of the multifunctional role of ferrous/ferric ions in endowing type II collagen hydrogels with a myriad of beneficial properties presents exciting prospects for developing advanced biomaterials with potential applications in OA.
Rare copy-number variants as modulators of common disease susceptibility
Authors: Chiara Auwerx, Maarja Jõeloo, Marie C. Sadler, Nicolò Tesio, Sven Ojavee, Charlie J. Clark, Reedik Mägi, Tõnu Esko, Andres Metspalu, Lili Milani, Mari Nelis, Alexandre Reymond, Zoltán Kutalik
Journal: Genome Medicine (2024)

Copy-number variations (CNVs) have been associated with rare and debilitating genomic disorders (GDs) but their impact on health later in life in the general population remains poorly described.
Comparison of immunoassay- with mass spectrometry-derived p-tau quantification for the detection of Alzheimer’s disease pathology
Authors: Joseph Therriault, Marcel S. Woo, Gemma Salvadó, Johan Gobom, Thomas K. Karikari, Shorena Janelidze, Stijn Servaes, Nesrine Rahmouni, Cécile Tissot, Nicholas J. Ashton, Andréa Lessa Benedet, Laia Montoliu-Gaya, Arthur C. Macedo, Firoza Z. Lussier, Jenna Stevenson, Paolo Vitali, Manuel A. Friese, Gassan Massarweh, Jean-Paul Soucy, Tharick A. Pascoal, Erik Stomrud, Sebastian Palmqvist, Niklas Mattsson-Carlgren, Serge Gauthier, Henrik Zetterberg, Oskar Hansson, Kaj Blennow, Pedro Rosa-Neto
Journal: Molecular Neurodegeneration (2024)

Abstract Background Antibody-based immunoassays have enabled quantification of very low concentrations of phosphorylated tau (p-tau) protein forms in cerebrospinal fluid (CSF), aiding in the diagnosis of AD. Mass spectrometry enables absolute quantification of multiple p-tau variants within a single run. The goal of this study was to compare the performance of mass spectrometry assessments of p-tau 181 , p-tau 217 and p-tau 231 with established immunoassay techniques. Methods We measured p-tau 181 , p-tau 217 and p-tau 231 concentrations in CSF from 173 participants from the TRIAD cohort and 394 participants from the BioFINDER-2 cohort using both mass spectrometry and immunoassay methods. All subjects were clinically evaluated by dementia specialists and had amyloid-PET and tau-PET assessments. Bland–Altman analyses evaluated the agreement between immunoassay and mass spectrometry p-tau 181 , p-tau 217 and p-tau 231 . P-tau associations with amyloid-PET and tau-PET uptake were also compared. Receiver Operating Characteristic (ROC) analyses compared the performance of mass spectrometry and immunoassays p-tau concentrations to identify amyloid-PET positivity. Results Mass spectrometry and immunoassays of p-tau 217 were highly comparable in terms of diagnostic performance, between-group effect sizes and associations with PET biomarkers. In contrast, p-tau 181 and p-tau 231 concentrations measured using antibody-free mass spectrometry had lower performance compared with immunoassays. Conclusions Our results suggest that while similar overall, immunoassay-based p-tau biomarkers are slightly superior to antibody-free mass spectrometry-based p-tau biomarkers. Future work is needed to determine whether the potential to evaluate multiple biomarkers within a single run offsets the slightly lower performance of antibody-free mass spectrometry-based p-tau quantification.
MAGPIE: accurate pathogenic prediction for multiple variant types using machine learning approach
Authors: Yicheng Liu, Tianyun Zhang, Ningyuan You, Sai Wu, Ning Shen
Journal: Genome Medicine (2024)

Abstract Identifying pathogenic variants from the vast majority of nucleotide variation remains a challenge. We present a method named Multimodal Annotation Generated Pathogenic Impact Evaluator (MAGPIE) that predicts the pathogenicity of multi-type variants. MAGPIE uses the ClinVar dataset for training and demonstrates superior performance in both the independent test set and multiple orthogonal validation datasets, accurately predicting variant pathogenicity. Notably, MAGPIE performs best in predicting the pathogenicity of rare variants and highly imbalanced datasets. Overall, results underline the robustness of MAGPIE as a valuable tool for predicting pathogenicity in various types of human genome variations. MAGPIE is available at https://github.com/shenlab-genomics/magpie .
Bone marrow graft versus peripheral blood graft in haploidentical hematopoietic stem cells transplantation: a retrospective analysis in1344 patients of SFGM-TC registry
Authors: Claire Lacan, Jérôme Lambert, Edouard Forcade, Marie Robin, Patrice Chevallier, Sandrine Loron, Claude-Éric Bulabois, Corentin Orvain, Patrice Ceballos, Etienne Daguindau, Amandine Charbonnier, Yves Chalandon, Marc Bernard, Célestine Simand, Marie-Thérèse Rubio, Pascal Turlure, Johan Maertens, Anne Huynh, Michael Loschi, Jacques-Olivier Bay, Gaëlle Guillerm, Mustafa Alani, Cristina Castilla-Llorente, Xavier Poiré, Sylvain Chantepie, Natacha Maillard, Yves Beguin, Ambroise Marçais, Jérôme Cornillon, Jean-Valère Malfuson, Sébastien Maury, Nathalie Meuleman, Alban Villate, Mohammed-Amine Bekadja, Anouk Walter-Petrich, Nathalie Jacque, Micha Srour, Raynier Devillier, Stéphanie Nguyen
Journal: Journal of Hematology & Oncology (2024)

Abstract The use of peripheral blood (PB) or bone marrow (BM) stem cells graft in haploidentical hematopoietic stem cell transplantation with post-transplant cyclophosphamide (PTCy) for graft-versus-host disease (GVHD) prophylaxis remains controversial. Moreover, the value of adding anti-thymoglobulin (ATG) to PTCy is unknown. A total of 1344 adult patients received an unmanipulated haploidentical transplant at 37 centers from 2012 to 2019 for hematologic malignancy. We compared the outcomes of patients according to the type of graft, using a propensity score analysis. In total population, grade II–IV and III–IV acute GVHD (aGVHD) were lower with BM than with PB. Grade III–IV aGVHD was lower with BM than with PB + ATG. All outcomes were similar in PB and PB + ATG groups. Then, in total population, adding ATG does not benefit the procedure. In acute leukemia, myelodysplastic syndrome and myeloproliferative syndrome (AL-MDS-MPS) subgroup receiving non-myeloablative conditioning, risk of relapse was twice greater with BM than with PB (51 vs. 22%, respectively). Conversely, risk of aGVHD was greater with PB (38% for aGVHD II–IV; 16% for aGVHD III–IV) than with BM (28% for aGVHD II–IV; 8% for aGVHD III–IV). In this subgroup with intensified conditioning regimen, risk of relapse became similar with PB and BM but risk of aGVHD III–IV remained higher with PB than with BM graft (HR = 2.0; range [1.17–3.43], p = 0.012).
Efficacy, safety, and pharmacokinetics of capsid assembly modulator linvencorvir plus standard of care in chronic hepatitis B patients
Authors: Jinlin Hou, Edward Gane, Rozalina Balabanska, Wenhong Zhang, Jiming Zhang, Tien Huey Lim, Qing Xie, Chau-Ting Yeh, Sheng-Shun Yang, Xieer Liang, Piyawat Komolmit, Apinya Leerapun, Zenghui Xue, Ethan Chen, Yuchen Zhang, Qiaoqiao Xie, Ting-Tsung Chang, Tsung-Hui Hu, Seng Gee Lim, Wan-Long Chuang, Barbara Leggett, Qingyan Bo, Xue Zhou, Miriam Triyatni, Wen Zhang, Man-Fung Yuen
Journal: Clinical and Molecular Hepatology (2024)

Four-week treatment of linvencorvir (RO7049389) was generally safe and well tolerated, and showed anti-viral activity in chronic hepatitis B (CHB) patients. This study evaluated the efficacy, safety, and pharmacokinetics of 48-week treatment with linvencorvir plus standard of care (SoC) in CHB patients.
COP28 reflections
Authors: None The Lancet Planetary Health
Journal: The Lancet Planetary Health (2024)

Despite its short fallings, the United Nations Framework Convention on Climate Change (UNFCCC) is the central pillar of international climate policy. Each year the conference of the parties convenes world leaders ostensibly to work together to tackle climate change. This year the 28th such convening (COP28) was hosted in UAE and presided over by Dr Sultan Al Jaber, who was a controversial choice for president given his role as the head of the UAE's state-owned oil company, the Abu Dhabi National Oil Company (ADNOC).
Expiratory Muscle Activity Counteracts Positive End-Expiratory Pressure and Is Associated with Fentanyl Dose in Patients with Acute Respiratory Distress Syndrome
Authors: Glauco M. Plens, Maddalena T. Droghi, Glasiele C. Alcala, Sérgio M. Pereira, Iuri C. Wawrzeniak, Josué A. Victorino, Chiara Crivellari, Alice Grassi, Emanuele Rezoagli, Giuseppe Foti, Eduardo L. V. Costa, Marcelo B. P. Amato, Giacomo Bellani
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

Rationale: Hypoxemia during mechanical ventilation might be worsened by expiratory muscle activity, which reduces end-expiratory lung volume through lung collapse. A proposed mechanism of benefit from neuromuscular blockade (NMBA) in acute respiratory distress syndrome (ARDS) is abolition of expiratory efforts. This may contribute to restoration of lung volumes. The prevalence of this phenomenon, however, is unknown. Objectives: To investigate the incidence and amount of end-expiratory lung impedance (EELI) increase after NMBA, clinical factors associated with this phenomenon, its impact on regional lung ventilation, and association with changes in pleural pressure. Methods: We included mechanically ventilated ARDS patients monitored with electrical impedance tomography (EIT) who received NMBA in two centers. We measured changes in EELI, a surrogate for end-expiratory lung volume, before and after NMBA. In additional 10 patients, we investigated characteristic signatures of expiratory muscle activity depicted by EIT and esophageal catheters simultaneously. Clinical factors associated with EELI changes were assessed. Measurements and Main Results: We included 46 patients, half of whom increased EELI by more than 10% of the corresponding tidal volume (46.2% [23.9–60.9%]). Degree of EELI increase correlated positively with fentanyl dosage and negatively with changes in end-expiratory pleural pressures. This suggests expiratory muscle activity might exert strong counter-effects against PEEP, which are possibly aggravated by fentanyl. Conclusions: Administration of NMBA during EIT monitoring disclosed activity of expiratory muscles in half of ARDS patients. The resultant increase in EELI had a dose-response relationship with fentanyl dosage. This suggests a potential side-effect of fentanyl during protective ventilation.