bluuebunny/crossref_metadata_2025_split huggingface dataset:
A beginner’s guide on the use of brain organoids for neuroscientists: a systematic review
Authors: Mulder Lance A. , Depla Josse A. , Sridhar Adithya , Wolthers Katja , Pajkrt Dasja , Vieira de Sá Renata 
Published: April 2023

Abstract
Background
The first human brain organoid protocol was presented in the beginning of the previous decade, and since then, the field witnessed the development of many new brain region-specific models, and subsequent protocol adaptations and modifications. The vast amount of data available on brain organoid technology may be overwhelming for scientists new to the field and consequently decrease its accessibility. Here, we aimed at providing a practical guide for new researchers in the field by systematically reviewing human brain organoid publications.

Methods
Articles published between 2010 and 2020 were selected and categorised for brain organoid applications. Those describing neurodevelopmental studies or protocols for novel organoid models were further analysed for culture duration of the brain organoids, protocol comparisons of key aspects of organoid generation, and performed functional characterisation assays. We then summarised the approaches taken for different models and analysed the application of small molecules and growth factors used to achieve organoid regionalisation. Finally, we analysed articles for organoid cell type compositions, the reported time points per cell type, and for immunofluorescence markers used to characterise different cell types.

Results
Calcium imaging and patch clamp analysis were the most frequently used neuronal activity assays in brain organoids. Neural activity was shown in all analysed models, yet network activity was age, model, and assay dependent. Induction of dorsal forebrain organoids was primarily achieved through combined (dual) SMAD and Wnt signalling inhibition. Ventral forebrain organoid induction was performed with dual SMAD and Wnt signalling inhibition, together with additional activation of the Shh pathway. Cerebral organoids and dorsal forebrain model presented the most cell types between days 35 and 60. At 84 days, dorsal forebrain organoids contain astrocytes and potentially oligodendrocytes. Immunofluorescence analysis showed cell type-specific application of non-exclusive markers for multiple cell types.

Conclusions
We provide an easily accessible overview of human brain organoid cultures, which may help those working with brain organoids to define their choice of model, culture time, functional assay, differentiation, and characterisation strategies.
Tissue engineering modalities in skeletal muscles: focus on angiogenesis and immunomodulation properties
Authors: Namjoo Atieh Rezaei , Abrbekoh Fateme Nazary , Saghati Sepideh , Amini Hassan , Saadatlou Mohammad Ali Ebrahimi , Rahbarghazi Reza 
Published: April 2023

AbstractMuscular diseases and injuries are challenging issues in human medicine, resulting in physical disability. The advent of tissue engineering approaches has paved the way for the restoration and regeneration of injured muscle tissues along with available conventional therapies. Despite recent advances in the fabrication, synthesis, and application of hydrogels in terms of muscle tissue, there is a long way to find appropriate hydrogel types in patients with congenital and/or acquired musculoskeletal injuries. Regarding specific muscular tissue microenvironments, the applied hydrogels should provide a suitable platform for the activation of endogenous reparative mechanisms and concurrently deliver transplanting cells and therapeutics into the injured sites. Here, we aimed to highlight recent advances in muscle tissue engineering with a focus on recent strategies related to the regulation of vascularization and immune system response at the site of injury.
Overexpression of KCNJ2 enhances maturation of human-induced pluripotent stem cell-derived cardiomyocytes
Authors: Zhou Jingjun , Cui Baiping , Wang Xiaochen , Wang Hongkun , Zheng Junnan , Guo Fengfeng , Sun Yaxun , Fan Hangping , Shen Jiaxi , Su Jun , Wang Jue , Zhao Haige , Tang Yiquan , Gong Tingyu , Sun Ning , Liang Ping 
Published: April 2023

Abstract
Background
Although human-induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) are a promising cell resource for cardiovascular research, these cells exhibit an immature phenotype that hampers their potential applications. The inwardly rectifying potassium channel Kir2.1, encoded by the KCNJ2 gene, has been thought as an important target for promoting electrical maturation of iPSC-CMs. However, a comprehensive characterization of morphological and functional changes in iPSC-CMs overexpressing KCNJ2 (KCNJ2 OE) is still lacking.

Methods
iPSC-CMs were generated using a 2D in vitro monolayer differentiation protocol. Human KCNJ2 construct with green fluorescent protein (GFP) tag was created and overexpressed in iPSC-CMs via lentiviral transduction. The mixture of iPSC-CMs and mesenchymal cells was cocultured with decellularized natural heart matrix for generation of 3D human engineered heart tissues (EHTs).

Results
We showed that mRNA expression level of KCNJ2 in iPSC-CMs was dramatically lower than that in human left ventricular tissues. KCNJ2 OE iPSC-CMs yielded significantly increased protein expression of Kir2.1 and current density of Kir2.1-encoded IK1. The larger IK1 linked to a quiescent phenotype that required pacing to elicit action potentials in KCNJ2 OE iPSC-CMs, which can be reversed by IK1 blocker BaCl2. KCNJ2 OE also led to significantly hyperpolarized maximal diastolic potential (MDP), shortened action potential duration (APD) and increased maximal upstroke velocity. The enhanced electrophysiological maturation in KCNJ2 OE iPSC-CMs was accompanied by improvements in Ca2+ signaling, mitochondrial energy metabolism and transcriptomic profile. Notably, KCNJ2 OE iPSC-CMs exhibited enlarged cell size and more elongated and stretched shape, indicating a morphological phenotype toward structural maturation. Drug testing using hERG blocker E-4031 revealed that a more stable MDP in KCNJ2 OE iPSC-CMs allowed for obtaining significant drug response of APD prolongation in a concentration-dependent manner. Moreover, KCNJ2 OE iPSC-CMs formed more mature human EHTs with better tissue structure and cell junction.

Conclusions
Overexpression of KCNJ2 can robustly enhance maturation of iPSC-CMs in electrophysiology, Ca2+ signaling, metabolism, transcriptomic profile, cardiomyocyte structure and tissue engineering, thus providing more accurate cellular model for elucidating cellular and molecular mechanisms of cardiovascular diseases, screening drug-induced cardiotoxicity, and developing personalized and precision cardiovascular medicine.
Apoptotic vesicles resist oxidative damage in noise-induced hearing loss through activation of FOXO3a-SOD2 pathway
Authors: Huang Xiaotong , Kou Xiaoxing , Zhan Ting , Wei Guokun , He Feinan , Mao Xueli , Yang Haidi 
Published: April 2023

Abstract
Background
Mesenchymal stem cell (MSC) transplantation is a promising therapeutic approach for noise-induced hearing loss (NIHL). As the indispensable role of apoptosis in MSC transplantation was raised, the benefits of MSC-derived apoptotic vesicles (apoVs) in several disease models have been proved. However, whether apoVs benefit in NIHL have not been studied yet.

Methods
Female CBA/J mice and HEI-OC1 cells were used in this study. Flow cytometry, nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM) were used to characterize apoVs. Proteomic analysis was used to identify function proteins in apoVs. Immunofluorescence was used to reveal distribution pattern. Auditory brainstem response (ABR) test was used to measure the effect of apoVs treatment. DCFH-DA staining and MitoSOX staining were used to indicate oxidative damage. Western-blot and qRT-PCR were used to study the signaling pathways.

Results
We found that apoVs can be endocytosed by hair cells through systemic administration. Importantly, apoVs administration effectively attenuated NIHL and reduced hair cell loss by resisting oxidative damage in vivo. Further, apoVs application activated forkhead box o3 (FOXO3a)—mitochondrial superoxide dismutase 2(SOD2) pathway, which may relate to signal transduction and activators of transcription 3 (STAT3) in apoVs.

Conclusions
These findings uncovered the role of apoVs in preventing NIHL and resisting oxidative damage, indicating that apoVs is a promising way for inner ear delivery and a prospective cell-free therapy for NIHL.
Sex differences in the transcriptome of extracellular vesicles secreted by fetal neural stem cells and effects of chronic alcohol exposure
Authors: Chung Dae D. , Mahnke Amanda H. , Pinson Marisa R. , Salem Nihal A. , Lai Michael S. , Collins Natalie P. , Hillhouse Andrew E. , Miranda Rajesh C. 
Published: April 2023

Abstract
Background
Prenatal alcohol (ethanol) exposure (PAE) results in brain growth restriction, in part, by reprogramming self-renewal and maturation of fetal neural stem cells (NSCs) during neurogenesis. We recently showed that ethanol resulted in enrichment of both proteins and pro-maturation microRNAs in sub-200-nm-sized extracellular vesicles (EVs) secreted by fetal NSCs. Moreover, EVs secreted by ethanol-exposed NSCs exhibited diminished efficacy in controlling NSC metabolism and maturation. Here we tested the hypothesis that ethanol may also influence the packaging of RNAs into EVs from cell-of-origin NSCs.

Methods
Sex-specified fetal murine iso-cortical neuroepithelia from three separate pregnancies were maintained ex vivo, as neurosphere cultures to model the early neurogenic niche. EVs were isolated by ultracentrifugation from NSCs exposed to a dose range of ethanol. RNA from paired EV and cell-of-origin NSC samples was processed for ribosomal RNA-depleted RNA sequencing. Differential expression analysis and exploratory weighted gene co-expression network analysis (WGCNA) identified candidate genes and gene networks that were drivers of alterations to the transcriptome of EVs relative to cells.

Results
The RNA content of EVs differed significantly from cell-of-origin NSCs. Biological sex contributed to unique transcriptome variance in EV samples, where > 75% of the most variant transcripts were also sex-variant in EVs but not in cell-of-origin NSCs. WGCNA analysis also identified sex-dependent enrichment of pathways, including dopamine receptor binding and ectoderm formation in female EVs and cell-substrate adhesion in male EVs, with the top significant DEGs from differential analysis of overall individual gene expressions, i.e., Arhgap15, enriched in female EVs, and Cenpa, enriched in male EVs, also serving as WCGNA hub genes of sex-biased EV WGCNA clusters. In addition to the baseline RNA content differences, ethanol exposure resulted in a significant dose-dependent change in transcript expression in both EVs and cell-of-origin NSCs that predominantly altered sex-invariant RNAs. Moreover, at the highest dose, ~ 73% of significantly altered RNAs were enriched in EVs, but depleted in NSCs.

Conclusions
The EV transcriptome is distinctly different from, and more sex-variant than, the transcriptome of cell-of-origin NSCs. Ethanol, a common teratogen, results in dose-dependent sorting of RNA transcripts from NSCs to EVs which may reprogram the EV-mediated endocrine environment during neurogenesis.
Multiparametric dynamic whole-body PSMA PET/CT using [68Ga]Ga-PSMA-11 and [18F]PSMA-1007
Authors: Dias André H. , Jochumsen Mads R. , Zacho Helle D. , Munk Ole L. , Gormsen Lars C. 
Published: April 2023

Abstract
Background
Routine prostate-specific membrane antigen (PSMA) positron emission tomography (PET) performed for primary staging or restaging of prostate cancer patients is usually done as a single static image acquisition 60 min after tracer administration. In this study, we employ dynamic whole-body (D-WB) PET imaging to compare the pharmacokinetics of [68Ga]Ga-PSMA-11 and [18F]PSMA-1007 in various tissues and lesions, and to assess whether Patlak parametric images are quantitative and improve lesion detection and image readability.

Methods
Twenty male patients with prostate cancer were examined using a D-WB PSMA PET protocol. Ten patients were scanned with [68Ga]Ga-PSMA-11 and ten with [18F]PSMA-1007. Kinetic analyses were made using time-activity curves (TACs) extracted from organs (liver, spleen, bone, and muscle) and lesions. For each patient, three images were produced: SUV + Patlak parametric images (Ki and DV). All images were reviewed visually to compare lesion detection, image readability was quantified using target-to-background ratios (TBR), and Ki and DV values were compared.

Results
The two PSMA tracers exhibited markedly different pharmacokinetics in organs: reversible for [68Ga]Ga-PSMA-11 and irreversible for [18F]PSMA-1007. For both tracers, lesions kinetics were best described by an irreversible model. All parametric images were of good visual quality using both radiotracers. In general, Ki images were characterized by reduced vascular signal and increased lesion TBR compared with SUV images. No additional malignant lesions were identified on the parametric images.

Conclusion
D-WB PET/CT is feasible for both PSMA tracers allowing for direct reconstruction of parametric Ki images. The use of multiparametric PSMA images increased TBR but did not lead to the detection of more lesions. For quantitative whole-body Ki imaging, [18F]PSMA-1007 should be preferred over [68Ga]Ga-PSMA-11 due to its irreversible kinetics in organs and lesions.
Usefulness of machine learning softwares to screen titles of systematic reviews: a methodological study
Authors: dos Reis Ana Helena Salles , de Oliveira Ana Luiza Miranda , Fritsch Carolina , Zouch James , Ferreira Paulo , Polese Janaine Cunha 
Published: April 2023

Abstract
Objective
To investigate the usefulness and performance metrics of three freely-available softwares (Rayyan®, Abstrackr® and Colandr®) for title screening in systematic reviews.

Study design and setting
In this methodological study, the usefulness of softwares to screen titles in systematic reviews was investigated by the comparison between the number of titles identified by software-assisted screening and those by manual screening using a previously published systematic review. To test the performance metrics, sensitivity, specificity, false negative rate, proportion missed, workload and timing savings were calculated. A purposely built survey was used to evaluate the rater's experiences regarding the softwares’ performances.

Results
Rayyan® was the most sensitive software and raters correctly identified 78% of the true positives. All three softwares were specific and raters correctly identified 99% of the true negatives. They also had similar values for precision, proportion missed, workload and timing savings. Rayyan®, Abstrackr® and Colandr® had 21%, 39% and 34% of false negatives rates, respectively. Rayyan presented the best performance (35/40) according to the raters.

Conclusion
Rayyan®, Abstrackr® and Colandr® are useful tools and provided good metric performance results for systematic title screening. Rayyan® appears to be the best ranked on the quantitative and on the raters’ perspective evaluation. The most important finding of this study is that the use of software to screen titles does not remove any title that would meet the inclusion criteria for the final review, being valuable resources to facilitate the screening process.
Robust-PAC time-critical workflow offloading in edge-to-cloud continuum among heterogeneous resources
Authors: Liu Hongyun , Xin Ruyue , Chen Peng , Gao Hui , Grosso Paola , Zhao Zhiming 
Published: April 2023

AbstractEdge-to-cloud continuum connects and extends the calculation from edge side via network to cloud platforms, where diverse workflows go back and forth, getting executed on scheduled calculation resources. To better utilize the calculation resources from all sides, workflow offloading problems have been investigating lately. Most works focus on optimizing constraints like: latency requirements, resource utilization rate limits, and energy consumption bounds. However, the dynamics among the offloading environment have hardly been researched, which easily results in uncertain Quality of Service(QoS) on the user side. Any part of the workload change, resource availability change or network latency could incur dynamics in an offloading environment. In this work, we propose a robust PAC (probably approximately correct) offloading algorithm to address this dynamic issue together with optimization. We train an LSTM-based sequence-to-sequence neural network to learn how to offload workflows in edge-to-cloud continuum. Comprehensive implementations and corresponding comparison against state-of-the-art methods demonstrate the robustness of our proposed algorithm. More specifically, our algorithm achieves better offloading performance regarding dynamic heterogeneous offloading environment and faster adaptation to newly changed environments than fine-tuned state-of-the-art RL-based offloading methods.
User communities: from nice-to-have to must-have
Authors: Costa Joana , Amorim Inês , Reis João , Melão Nuno 
Published: April 2023

AbstractWith Industry 5.0 already on the horizon, firms need to adapt their strategies to better cater to an increasingly demanding and sustainability-conscious customer base. At the same time, the role of customers has shifted from being mere passive buyers to active users, who not only demand personalized products and services to suit their needs and preferences, but also actively engage other users and stakeholders, thereby grounding the Quadruple Helix model. The objective of this paper is to assess the role of user communities in fostering firms’ innovation in all types of innovation. Econometric estimations identified the user community as a driver of innovation propensity. Additionally, the relevance of these communities across all types of innovation (mainly for product and process innovation) was proven. Robustness analysis confirmed the results obtained in different dimensions and established a connection to human capital. This finding revealed that absorptive capacity serves not only as a facilitator of innovation, but also as a moderator. The empirical contributions point towards the urgency of policy actions that consistently involve these agents as vehicles of responsible innovation, which can fine-tune the innovation paths towards an eco-friendlier innovation ecosystem. Further testing the connection between human capital and the user community is required, as the establishment of efficient communication channels promoting the knowledge flows inside the firm will leverage innovation outputs in the different innovation types.
Hospital sanitary facilities on wards with high antibiotic exposure play an important role in maintaining a reservoir of resistant pathogens, even over many years
Authors: Neidhöfer Claudio , Sib Esther , Neuenhoff Marcel , Schwengers Oliver , Dummin Tobias , Buechler Christian , Klein Niklas , Balks Julian , Axtmann Katharina , Schwab Katjana , Holderried Tobias A. W. , Feldmann Georg , Brossart Peter , Engelhart Steffen , Mutters Nico T. , Bierbaum Gabriele , Parčina Marijo 
Published: April 2023

Abstract
Background
Hospitals with their high antimicrobial selection pressure represent the presumably most important reservoir of multidrug-resistant human pathogens. Antibiotics administered in the course of treatment are excreted and discharged into the wastewater system. Not only in patients, but also in the sewers, antimicrobial substances exert selection pressure on existing bacteria and promote the emergence and dissemination of multidrug-resistant clones. In previous studies, two main clusters were identified in all sections of the hospital wastewater network that was investigated, one K. pneumoniae ST147 cluster encoding NDM- and OXA-48 carbapenemases and one VIM-encoding P. aeruginosa ST823 cluster. In the current study, we investigated if NDM- and OXA-48-encoding K. pneumoniae and VIM-encoding P. aeruginosa isolates recovered between 2014 and 2021 from oncological patients belonged to those same clusters.

Methods
The 32 isolates were re-cultured, whole-genome sequenced, phenotypically tested for their antimicrobial susceptibility, and analyzed for clonality and resistance genes in silico.

Results
Among these strains, 25 belonged to the two clusters that had been predominant in the wastewater, while two others belonged to a sequence-type less prominently detected in the drains of the patient rooms.

Conclusion
Patients constantly exposed to antibiotics can, in interaction with their persistently antibiotic-exposed sanitary facilities, form a niche that might be supportive for the emergence, the development, the dissemination, and the maintenance of certain nosocomial pathogen populations in the hospital, due to antibiotic-induced selection pressure. Technical and infection control solutions might help preventing transmission of microorganisms from the wastewater system to the patient and vice versa, particularly concerning the shower and toilet drainage. However, a major driving force might also be antibiotic induced selection pressure and parallel antimicrobial stewardship efforts could be essential.
Mannan oligosaccharides alleviate oxidative injury in the head kidney and spleen in grass carp (Ctenopharyngodon idella) via the Nrf2 signaling pathway after Aeromonas hydrophila infection
Authors: Lu Zhiyuan , Feng Lin , Jiang Weidan , Wu Pei , Liu Yang , Jiang Jun , Kuang Shengyao , Tang Ling , Li Shuwei , Zhong Chengbo , Zhou Xiaoqiu 
Published: April 2023

Abstract
Background
Mannan oligosaccharides (MOS) are recommended as aquaculture additives owing to their excellent antioxidant properties. In the present study, we examined the effects of dietary MOS on the head kidney and spleen of grass carp (Ctenopharyngodon idella) with Aeromonas hydrophila infection.

Methods
A total of 540 grass carp were used for the study. They were administered six gradient dosages of the MOS diet (0, 200, 400, 600, 800, and 1,000 mg/kg) for 60 d. Subsequently, we performed a 14-day Aeromonas hydrophila challenge experiment. The antioxidant capacity of the head kidney and spleen were examined using spectrophotometry, DNA fragmentation, qRT-PCR, and Western blotting.

Results
After infection with Aeromonas hydrophila, 400–600 mg/kg MOS supplementation decreased the levels of reactive oxygen species, protein carbonyl, and malonaldehyde and increased the levels of anti-superoxide anion, anti-hydroxyl radical, and glutathione in the head kidney and spleen of grass carp. The activities of copper-zinc superoxide dismutase, manganese superoxide dismutase, catalase, glutathione S-transferase, glutathione reductase, and glutathione peroxidase were also enhanced by supplementation with 400–600 mg/kg MOS. Furthermore, the expression of most antioxidant enzymes and their corresponding genes increased significantly with supplementation of 200–800 mg/kg MOS. mRNA and protein levels of nuclear factor erythroid 2-related factor 2 also increased following supplementation with 400–600 mg/kg MOS. In addition, supplementation with 400–600 mg/kg MOS reduced excessive apoptosis by inhibiting the death receptor pathway and mitochondrial pathway processes.

Conclusions
Based on the quadratic regression analysis of the above biomarkers (reactive oxygen species, malondialdehyde, and protein carbonyl) of oxidative damage in the head kidney and spleen of on-growing grass carp, the recommended MOS supplementation is 575.21, 557.58, 531.86, 597.35, 570.16, and 553.80 mg/kg, respectively. Collectively, MOS supplementation could alleviate oxidative injury in the head kidney and spleen of grass carp infected with Aeromonas hydrophila.