bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthetic data-driven overlapped neural spikes sorting: decomposing hidden spikes from overlapping spikes
Authors: Kim Min-Ki , Kim Sung-Phil , Sohn Jeong-Woo 
Published: November 2024

AbstractSorting spikes from extracellular recordings, obtained by sensing neuronal activity around an electrode tip, is essential for unravelling the complexities of neural coding and its implications across diverse neuroscientific disciplines. However, the presence of overlapping spikes, originating from neurons firing simultaneously or within a short delay, has been overlooked because of the difficulty in identifying individual neurons due to the lack of ground truth. In this study, we propose a method to identify overlapping spikes in extracellular recordings and to recover hidden spikes by decomposing them. We initially estimate spike waveform templates through a series of steps, including discriminative subspace learning and the isolation forest algorithm. By leveraging these estimated templates, we generate synthetic spikes and train a classifier using their feature components to identify overlapping spikes from observed spike data. The identified overlapping spikes are then decomposed into individual hidden spikes using a particle swarm optimization. Results from the testing of the proposed approach, using the simulation dataset we generated, demonstrated that employing synthetic spikes in the overlapping spike classifier accurately identifies overlapping spikes among the detected ones (the maximum F1 score of 0.88). Additionally, the approach can infer the synchronization between hidden spikes by decomposing the overlapped spikes and reallocating them into distinct clusters. This study advances spike sorting by accurately identifying overlapping spikes, providing a more precise tool for neural activity analysis.
Tailoring glioblastoma treatment based on longitudinal analysis of post-surgical tumor microenvironment
Authors: Bastiancich Chiara , Snacel-Fazy Emmanuel , Fernandez Samantha , Robert Stéphane , Stacchini Roberta , Plantureux Léa , Boissonneau Sébastien , Testud Benoit , Guillet Benjamin , Debarbieux Franck , Luche Hervé , Figarella-Branger Dominique , Estève Marie-Anne , Tabouret Emeline , Tchoghandjian Aurélie 
Published: November 2024

AbstractGlioblastoma (GBM), an incurable primary brain tumor, typically requires surgical intervention followed by chemoradiation; however, recurrences remain fatal. Our previous work demonstrated that a nanomedicine hydrogel (GemC12-LNC) delays recurrence when administered post-surgery. However, tumor debulking also triggers time-dependent immune reactions that promote recurrence at the resection cavity borders. We hypothesized that combining the hydrogel with an immunomodulatory drug could enhance therapeutic outcomes. A thorough characterization of the post-surgical microenvironment (SMe) is crucial to guide combinatorial approaches.In this study, we performed cellular resolution imaging, flow cytometry and spatial hyperplexed immunofluorescence imaging to characterize the SMe in a syngeneic mouse model of tumor resection. Owing to our dynamic approach, we observed transient opening of the blood–brain barrier (BBB) during the first week after surgery. BBB permeability post-surgery was also confirmed in GBM patients. In our murine model, we also observed changes in immune cell morphology and spatial location post-surgery over time in resected animals as well as the accumulation of reactive microglia and anti-inflammatory macrophages in recurrences compared to unresected tumors since the first steps of recurrence growth. Therefore we investigated whether starting a systemic treatment with the SMAC mimetic small molecule (GDC-0152) directly after surgery would be beneficial for enhancing microglial anti-tumoral activity and decreasing the number of anti-inflammatory macrophages around the GemC12-LNC hydrogel-loaded tumor cavity. The immunomodulatory effects of this drug combination was firstly shown in patient-derived tumoroids. Its efficacy was confirmed in vivo by survival analysis and correlated with reversal of the immune profile as well as delayed tumor recurrence.This comprehensive study identified critical time frames and immune cellular targets within the SMe, aiding in the rational design of combination therapies to delay recurrence onset. Our findings suggest that post-surgical systemic injection of GDC-0152 in combination with GemC12-LNC local treatment is a promising and innovative approach for managing GBM recurrence, with potential for future translation to human patient.
Graphical Abstract
Intracranial hemorrhage in an infant leads to the diagnosis and treatment of severe hemophilia B: a case report
Authors: Lassandro Giuseppe , Palladino Valentina , Giordano Paola 
Published: November 2024

Abstract
Background
Hemophilia B is a rare bleeding disorder in males, characterized by a deficiency in coagulation factor IX (FIX). Replacement of FIX with a recombinant FIX (rFIX) fusion protein, to sustain therapeutic plasma levels, is recommended as both treatment and prophylaxis to prevent bleeding episodes, particularly intracranial hemorrhage (ICH).

Case presentation
This case report outlines the management of ICH in a 7-month-old infant with severe hemophilia B, following an accidental trauma-related event, resulting in a thin compound fracture of the left occiput. FIX levels were extremely low (˂1.0%) and large deletions of the coagulation F9 gene (including exons 1–6) were identified. Intensive treatment with a rFIX fusion protein conjugated to the immunoglobulin Fc fragment (rFIXFc) continued for 18 days before hospital discharge. A continuous regimen of weekly rFIXFc infusions was implemented. Thirty days after initiating rFIXFc therapy, neutralizing antibodies or FIX inhibitors (common in patients with large F9 gene deletions) were observed, causing a diffuse skin rash. Such allergic reactions typically indicate progression to potentially serious nephrotic syndrome. A unique immunotolerance regimen of oral oxatomide and intravenous hydrocortisone was started to proactively prevent allergic reactions in this patient during rFIXFc prophylaxis. Even though low titers of the inhibitor (0.6–1.0 Bethesda units) were observed occasionally during subsequent follow-up, there were no signs of further allergies or development of nephrotic syndrome.

Conclusion
This is an uncommon case in which rFIXFc was continued despite the appearance of an allergic reaction and the development of FIX inhibitors. Subsequent allergic reactions were prevented with a combination of oral oxatomide and intravenous hydrocortisone given prior to prophylactic rFIXFc. Further studies are recommended to determine the usefulness of this combination with rFIX therapy.
Impact of mesenchymal stem cell size and adhesion modulation on in vivo distribution: insights from quantitative PET imaging
Authors: Ji Xin , Wang Lizhen , Zhong Yudan , Xu Qian , Yan Junjie , Pan Donghui , Xu Yuping , Chen Chongyang , Wang Jing , Wang Guangji , Yang Min , Li Tiannv , Tang Lijun , Wang Xinyu 
Published: November 2024

Abstract
Background
Successful engraftment and localization of mesenchymal stem cells (MSCs) within target tissues are critical factors influencing their therapeutic efficacy for tissue repair and regeneration. However, the relative contributions of biophysical factors like cell size and adhesion capacity in regulating MSC distribution in vivo remain incompletely understood.

Methods
Cell adhesion peptides and hanging drop method were used to modify the adhesive capacity and size of MSCs. To quantitatively track the real-time biodistribution of transplanted MSCs with defined size and adhesion profiles in living mice and rats, the non-invasive positron emission tomography (PET) imaging was applied.

Results
Surface modification with integrin binding peptides like RGD, GFOGER, and HAVDI reduced MSC adhesion capacity in vitro by up to 43.5% without altering cell size, but did not significantly decrease lung entrapment in vivo. In contrast, culturing MSCs as 3D spheroids for 48 h reduced their cell diameter by 34.6% and markedly enhanced their ability to pass through the lungs and migrate to other organs like the liver after intravenous administration. This size-dependent effect on MSC distribution was more pronounced in rats compared to mice, likely due to differences in pulmonary microvessel diameters between species.

Conclusion
Our findings reveal that cell size is a predominant biophysical regulator of MSC localization in vivo compared to adhesion capacity, providing crucial insights to guide optimization of MSC delivery strategies for enhanced therapeutic efficacy.

Graphical abstract
cidalsDB: an AI-empowered platform for anti-pathogen therapeutics research
Authors: Harigua-Souiai Emna , Masmoudi Ons , Makni Samer , Oualha Rafeh , Abdelkrim Yosser Z. , Hamdi Sara , Souiai Oussama , Guizani Ikram 
Published: November 2024

AbstractComputer-aided drug discovery (CADD) is nurtured by late advances in big data analytics and Artificial Intelligence (AI) towards enhanced drug discovery (DD) outcomes. In this context, reliable datasets are of utmost importance. We herein present CidalsDB a novel web server for AI-assisted DD against infectious pathogens, namely Leishmania parasites and Coronaviruses. We performed a literature search on molecules with validated anti-pathogen effects. Then, we consolidated these data with bioassays from PubChem. Finally, we constructed a database to store these datasets and make them accessible and ready-to-use for the scientific community through CidalsDB, a web-based interface. In a second step, we implemented and optimized four machine learning (ML) and three deep learning (DL) algorithms that optimally predicted the biological activity of molecules. Random Forests (RF), Multi-Layer Perceptron (MLP) and ChemBERTa were the best classifiers of anti-Leishmania molecules, while Gradient Boosting (GB), Graph-Convolutional Network (GCN) and ChemBERTa achieved the best performances on the Coronaviruses dataset. All six models were optimized and deployed through CidalsDB as anti-pathogen activity prediction models.Scientific contributionCidalsDB is an open access web-based tool that allows browsing and access to ready-to-use datasets of anti-pathogen molecules, alongside best performing AI models for biological activity prediction. It offers a democratized no-code platform for AI-based CADD, which shall foster innovation and collaboration within the DD community. CidalsDB is accessible through https://cidalsdb.streamlit.app/.
Efficacy of restrictive versus liberal transfusion strategies in patients with traumatic brain injury: a systematic review and meta-analysis of randomized controlled trials
Authors: Yuan Xiang , Zhang Sen , Wan Jun , Chen Cheng , Wang Peng , Fan Shijie , Liu Yuyang , Yang Jingxian , Hou Jiayi , You Qiaoyu , Li Xiao , Li Kuilin , Xiang Ziyan , Rao Yang , Zhang Yu 
Published: November 2024

Abstract
Background
The effects of restrictive versus liberal transfusion strategies in critically ill patients with traumatic brain injury (TBI) and anemia, particularly in adult patients with moderate to severe TBI, remain inconclusive. Therefore, this systematic review and meta-analysis aim to evaluate the comparative impact of restrictive and liberal red blood cell transfusion strategies among critically ill adult patients with moderate to severe TBI.

Methods
We conducted a search of PubMed, EMBASE, and the Cochrane Central Register of Controlled Trials from their inception through October 20, 2024, to identify randomized controlled trials that compared restrictive (transfusions at a hemoglobin level of ≤ 7 g/dL) and liberal (transfusions at a hemoglobin level of ≤ 9–10 g/dL) transfusion strategies in adult patients with TBI. The primary outcome was mortality, with secondary outcomes including an unfavorable neurological outcome at six months, as determined by the Glasgow Outcome Scale (GOS < 4; or Glasgow Outcome Scale-Extended [GOSE] < 6), and the number of units of packed red blood cells (pRBCs) transfused.

Results
Five randomized controlled trials involving 1,528 patients were included in the analysis. The results showed that restrictive transfusion, compared to liberal transfusion, had no impact on mortality (RR 1.00, 95% CI 0.80 to 1.24, I2 = 0%) or unfavorable neurological outcome at 6 months (RR 1.06, 95% CI 0.94 to 1.20, I2 = 47%). Restrictive transfusion was associated with a reduction in the number of units of pRBCs transfused (MD -2.62, 95% CI -3.33 to -1.90, I2 = 63%).

Conclusion
In patients with TBI, a restrictive transfusion strategy did not reduce the risk of mortality or unfavorable neurological outcome compared with a liberal transfusion strategy.
Sociocultural attitudes towards appearance questionnaire-4-revised (SATAQ-4R): validation in a community sample of Norwegian adolescents
Authors: Lie Selma Øverland , Bastos Rafael Valdece Sousa , Sundgot-Borgen Christine , Wisting Line , Dahlgren Camilla Lindvall 
Published: November 2024

Abstract
Background
Negative body image and disordered eating are common among adolescents and young adults. The Sociocultural Attitudes Towards Appearance Questionnaire-4-Revised (SATAQ-4R) captures the internalization of societal appearance ideals and perceived pressures from others but has not been validated in a Norwegian adolescent population.

Methods
The current study explored the factor structure of SATAQ-4R in a sample of adolescent Norwegian males and females (n = 1558, mean age 17.04 ± 0.95) using confirmatory factor analysis (CFA) for a 6- and 7-factor structure in females, and a 7-factor structure in males. Correlations between subscales, internal consistency and reliability, and comparisons with convergent measures (disordered eating, body mass index, negative influence of social media) were explored.

Results
The CFA supported a 7-factor structure of the SATAQ-4R for both males and females. Internal consistency and reliability were acceptable. SATAQ-4R subscales largely correlated with disordered eating and additional convergent measures.

Conclusions
Results confirm the structure and reliability of the SATAQ-4R in a Norwegian adolescent population. The subscales showed good convergent validity, and high scores on internalization and societal pressures were related to higher levels of disordered eating and negative social media influence. The Norwegian version of the SATAQ-4R thus demonstrates good psychometric properties in adolescent males and females, and is well suited to capture internalization and sociocultural pressures that particularly affect adolescents. Results highlight the need to continue working towards reducing adverse internalization and improving body image among adolescents.
CardioAtlas: deciphering the single-cell transcriptome landscape in cardiovascular tissues and diseases
Authors: Jiang Tiantongfei , Jin Xiaoyan , Gao Yueying , Zhou Weiwei , Yu Jinyang , Li Yongsheng , Xu Juan , Cai Benzhi 
Published: November 2024

AbstractIncreasing scRNA-seq data in cardiovascular research have substantially improved our knowledge on the development of the cardiovascular system and the mechanisms underlying cardiovascular diseases. However, the single-cell transcriptome datasets were dispersed in literature and no resource for cardiovascular systems and diseases. Here, we constructed an organized resource CardioAtlas, which provides comprehensive analysis results for > 1,929,000 cells in 27 human data sets and > 1,088,000 cells in 39 mouse data sets. Through large-scale literature retrieval and manual annotation, we constructed 12 and 15 scRNA-seq reference atlas for common human and mouse cardiovascular systems and diseases, covering 43 and 39 cell types. In particular, CardioAtlas provides five analytic modules, including cell-type prediction, identification of marker genes, functional enrichment analysis, identification of cell-type-specific transcription regulons, and cell-cell communication analysis. In addition, users can upload scRNA-seq data for personalized analysis. CardioAtlas is available at http://bio-bigdata.hrbmu.edu.cn/CardioAtlas. CardioAtlas provides the first comprehensive and well-crafted reference atlas of cardiovascular systems and diseases and describes in detail previously unrecognized cell populations across a large number of humans and mice.
CT radiomics and human-machine hybrid system for differentiating mediastinal lymphomas from thymic epithelial tumors
Authors: Xia Han , Yu Jiahui , Nie Kehui , Yang Jun , Zhu Li , Zhang Shengjian 
Published: November 2024

Abstract
Background
It is difficult for radiologists, especially junior radiologists with limited experience to make differential diagnoses between mediastinal lymphomas and thymic epithelial tumors (TETs) due to the overlapping imaging features. The purpose of this study was to develop and validate a CT-based clinico-radiomics model for differentiating lymphomas from TETs and to investigate whether a human-machine hybrid system can assist junior radiologists in improving their diagnostic performance.

Methods
The patients who underwent contrast-enhanced chest CT and pathologically confirmed with lymphoma or TET at two centers from January 2011 to December 2019 and from January 2017 to December 2021 were retrospectively included and split as training/validation set and external test set, respectively. Clinical and radiomic signatures were pre-selected by elastic-net, and the models were established with the selected signatures using ensemble learning. Three radiologists independently reviewed CT images and assessed each case of the external test set with knowledge of the relevant clinical information. The diagnoses of reader 1, reader 2, and reader 3 were compared with those of the models in the external test set and further separately input to the model’s ensemble process as a human-machine system to make final decisions in the external test set. The improvement of diagnostic performance of radiologists by human-machine system was evaluated by the area under the receiver operating characteristic curve and increase rate.

Results
A total of 95 patients (51 with lymphomas and 44 with TETs) at Center 1 and 94 (52 with lymphomas and 42 with TETs) at Center 2 were enrolled and divided into training/validation sets and external test set, respectively. The diagnostic performance of the clinico-radiomics model has outperformed the junior radiologists and senior radiologist in AUC (clinico-radiomics model: 0.85 (0.76,0.92); reader 2: 0.70 (0.60,0.80); reader 3: 0.60 (0.49,0.71), reader 1: 0.76 (0.66,0.86), respectively) in the external test set. The human-machine hybrid system demonstrated significant increases in AUC (reader 1 + model: 0.87 (0.79,0.94), an increase of 14%; reader 2 + model: 0.86 (0.77,0.93), an increase of 23%; reader 3 + model: 0.84 (0.76,0.91), an increase of 40%), compared to the human performance alone.

Conclusions
The clinico-radiomics model outperformed three radiologists in differentiating lymphomas from TETs on CT. The use of the human-machine hybrid system significantly improved the performance of radiologists, especially junior radiologists. It provides a real-time decision tool to reduce bias and mistakes in radiologist diagnosis and enhances the diagnostic confidence of junior radiologists. This attempt may lead to more human-machine hybrid systems being explored in the diagnosis of different diseases to drive future clinical applications.
Analysis of factors related to anesthetic management affecting acute kidney injury occurring within 72 h after esophagectomy for esophageal cancer: a historical cohort study
Authors: Ishikawa Seiji , Hirashima Junko , Hiroyama Makiko , Ozato Shojiro , Watanabe Masayuki , Terajima Katsuyuki 
Published: November 2024

Abstract
Background
The effects of factors related to anesthetic management, including anesthesia methods and infusion volume, on acute kidney injury (AKI) after esophagectomy have not been thoroughly investigated.

Methods
A historical cohort study of patients who underwent esophagectomy between January 2008 and December 2022 was conducted. AKI was defined according to the Kidney Disease Improving Global Outcomes creatinine criteria within 72 h after esophagectomy. Logistic regression was used to model the association between perioperative factors, including factors related to anesthetic management, and postoperative AKI.

Results
Of 1005 patients, 48 patients (4.8%) had AKI (40 stage 1 and 8 stage 2). AKI patients were older (67.8 vs. 65.0 years, P = 0.046) and more likely to have hypertension (72.9 vs. 37.9%, P < 0.001), chronic kidney disease (39.6 vs. 14.3%, P < 0.0001), red blood cell (RBC) transfusions (12.5 vs. 3.4%, P = 0.0085), and longer duration of anesthesia (518 vs. 490 min, P = 0.0058) than non-AKI patients. AKI patients were less likely to have epidural anesthesia (72.9 vs. 91.5%, P < 0.001). The distribution of inhaled anesthetics chosen was not significantly different between AKI and non-AKI patients. On multivariable logistic regression analysis, AKI was associated with the Brinkman index (per 100 units, odds ratio (OR) = 1.06), hypertension (OR = 3.39), chronic kidney disease (OR = 2.58), duration of anesthesia (per 10 min, OR = 1.03), epidural anesthesia (OR = 0.35) and RBC transfusion (OR = 3.27).

Conclusions
Except for epidural anesthesia, no significant association was found between AKI and factors related to anesthetic management. Epidural anesthesia may protect against early postoperative AKI in patients undergoing esophagectomy.
Anti-oxidative, anti-AChE and neuroprotective effect of hydro-alcoholic extract of Sansevieria cylindrica leaves and Plumeria obtusa seed pods in Wistar rats
Authors: Shewale Sunil , Undale Vaishali , Bhalchim Vrushali , Kuchekar Mohini , Warude Bhagyashri , Mali Mayur 
Published: November 2024

Abstract
The rising incidence of neurodegenerative diseases represents a significant global health concern. The prognosis for such diseases is often unfavorable, and patients require supportive treatment to manage their condition effectively. The present study investigated the anti-oxidative, anti-acetylcholinesterase (anti-AChE) effect of hydro-alcoholic extract of Sansevieria cylindrica leaves and Plumeria obtusa seed pods in Wistar rats. Plants were authenticated followed by pharmacognostic evaluation. The antioxidant and anti-AChE activities were evaluated by scopolamine-induced oxidative stress and acetylcholine level alterations in Wistar rats. On the 0th, 7th, and 14th days during study period behavioral parameters were evaluated, including open field test, new object recognition test, and Morris water maze task. Different antioxidant enzymes were also evaluated in brain homogenate post 7 days treatment. AChE levels in rats’ brains were assessed post 14 days of treatment. Finally, histopathology of brains samples was performed. Correspondingly, in-vitro and in-silico studies were done to support the study findings.

Results
Sansevieria cylindrica and Plumeria obtusa exhibited strong antioxidant and anti-AChE activities due to secondary metabolites content. Rearing and, line crossing by rats showed substantial alteration (p < 0.05) by combination of both plants at high dose. The escape latency found to be reduced significantly (p < 0.05) by Sansevieria cylindrica individually and in combination with Plumeria obtusa at all doses. The lipid peroxidation level in brain was decreased significantly than standard at 1:1 combination of plants extracts. The levels of GSH, CAT and SOD were attenuated significantly by different concentration of extracts (p < 0.05 and p < 0.001, respectively). The reduction in AChE levels was around 34.62% and 31.10% in male and female rats, respectively in combination of both plants at high dose compared to disease control group. It was further evident in brain histopathology. All in-vivo results were supported by in-vitro free radicals scavenging effect and in-silico study.

Conclusion
The hydro-alcoholic extracts from Plumeria obtusa seed pods and Sansevieria cylindrica leaves showed a strong natural antioxidant, and acetylcholinesterase inhibitions which can aid in the treatment of neurodegerative diseases including Alzheimer.