bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous genetic transformation and genome editing of mixed lines in soybean (Glycine max) and maize (Zea mays)
Authors: Valentine Michelle , Butruille David , Achard Frederic , Beach Steven , Brower-Toland Brent , Cargill Edward , Hassebrock Megan , Rinehart Jennifer , Ream Thomas , Chen Yurong 
Published: June 2024

AbstractRobust genome editing technologies are becoming part of the crop breeding toolbox. Currently, genome editing is usually conducted either at a single locus, or multiple loci, in a variety at one time. Massively parallel genomics platforms, multifaceted genome editing capabilities, and flexible transformation systems enable targeted variation at nearly any locus, across the spectrum of genotypes within a species. We demonstrate here the simultaneous transformation and editing of many genotypes, by targeting mixed seed embryo explants with genome editing machinery, followed by re-identification through genotyping after plant regeneration. Transformation and Editing of Mixed Lines (TREDMIL) produced transformed individuals representing 101 of 104 (97%) mixed elite genotypes in soybean; and 22 of 40 (55%) and 9 of 36 (25%) mixed maize female and male elite inbred genotypes, respectively. Characterization of edited genotypes for the regenerated individuals identified over 800 distinct edits at the Determinate1 (Dt1) locus in samples from 101 soybean genotypes and 95 distinct Brown midrib3 (Bm3) edits in samples from 17 maize genotypes. These results illustrate how TREDMIL can help accelerate the development and deployment of customized crop varieties for future precision breeding.
Emerging Challenges for Cleaner Production Networks – The decline of the Global Resource Efficient and Cleaner Production Network (RECPnet)
Authors: Muzamwese Tawanda Collins 
Published: June 2024

AbstractCleaner production has been channelled through National Cleaner Production Centres (NCPCs) across the world since the year 1994. In order to strengthen the scaling up and replication of Resource Efficient and Cleaner Production (RECP) in developing and transition countries, the Global Resource Efficient and Cleaner Production Network (RECPnet) was formed as a platform for networking, knowledge exchange and information transfer. However, the success of such networks can become short-lived if there is no funding strategy beyond project financing and if individual network members fail to take ownership of the network. This research assesses the role of the Global RECPnet in promoting cleaner production and analyses the challenges that the network faced in ensuring its continuity beyond project finance. The research further identifies barriers in the advancement of the Global RECPnet and its goals. A Case Study methodology was used and within the case study, interviews were undertaken with key industry experts in the field of Resource Efficient and Cleaner Production (RECP). Questionnaires were also send to selected members of the network. Content analysis was undertaken on publicly available Global RECPnet documents and evaluation reports. We conclude that networks such as Global RECPnet are effective drivers of cleaner production, but require a plan for network survival beyond patron agencies. However, without patron agencies and international funders, the network proved not to be viable, as most of the members could not finance their own subscriptions. We propose for a hybrid mechanism of network financing and dealing with dependencies on development support.
Fusing multi-source social media data and street view imagery to inform urban space quality: a study of user perceptions at Kampong Glam and Haji Lane
Authors: Wang Yue 
Published: June 2024

AbstractThis study proposes a novel approach to urban perception studies by integrating street view imagery and multi-source social media data to infer user perceptions and preferences of urban spaces, thereby informing placemaking strategies. With advanced pre-trained Google Cloud Vision AI, this study regards street view imagery as a baseline to compare with user-generated content from social media platforms, namely, Flickr, TripAdvisor, and X (formerly Twitter), together revealing spatial elements perceived by users and diverse demands across users groups. The research evaluates urban space qualities at two spatial levels through a case study at Kampong Glam district and Haji Lane, focusing on Uniqueness, Vitality, and Liveability derived from classic urban theories. The transition in user focus from spatial and transport features in Google Street View to activities and decorations in Flickr imagery emphasizes the spatial features that contribute to Uniqueness and Vitality. In addition, textual data from Twitter and TripAdvisor differentiate residents' and tourists' perceptions of Liveability, encompassing aspects like History, Religion, Space, and Activity. The findings articulate alignments of users' perceptions from street to district levels and diverse preferences on spatial features contributing to Uniqueness, Vitality, and Liveability, offering valuable insights for user-centric placemaking and urban planning.
Prediction of the mechanical performance of polyethylene fiber-based engineered cementitious composite (PE-ECC)
Authors: Hossain Shameem , Uddin Md Nasir , Yan Kangtai , Hossain Md Minaz , Golder Md Sabbir Hossen , Hoque Md Ahatasamul 
Published: June 2024

AbstractIn recent years, extensive research has focused on applying machine learning (ML) techniques to predict the properties of engineered cementitious composites (ECCs). ECCs exhibit crucial characteristics such as compressive strength (CS), tensile strength (TS), and tensile strain (TSt). Accurate forecasting of these critical properties can reduce material waste, lower construction expenses, and expedite project timelines for engineers and designers. This study investigates mixture design components and corresponding strengths of ECCs based on only polyethylene fiber drawing from existing literatures. Artificial neural network (ANN) models are developed to predict CS, TS, and TSt using a dataset of 339 experimental results with twelve input variables. The ANN models, implemented in MATLAB, consider various hidden layers and neurons to optimize accuracy and validation metrics demonstrate the model's high accuracy. Sensitivity analysis explores individual parameter impacts. Drawing inspiration from this study, it would be advantageous to enhance the predictive modeling toolkit by leveraging the progress made in existing technologies, thereby driving the green and low-carbon development of civil engineering. This approach not only improves the efficiency and sustainability of construction practices but also aligns with global environmental goals by reducing the carbon footprint associated with civil engineering projects.
UK pediatric critical care society research priorities revisited following the COVID-19 pandemic
Authors: Mustafa Khurram , Menzies Julie , Ray Samiran , Ramnarayan Padmanabhan , Tume Lyvonne N. ,   Paediatric Critical Care Society Study Group (PCCS-SG)
Published: June 2024

Abstract
Purpose
A research prioritisation exercise was undertaken by the UK Paediatric Critical Care Society Study Group in 2018. Since then, the COVID-19 pandemic occurred and several multi-centre studies have been, or are being, conducted to address topics prioritised by healthcare professionals and parents. We aimed to determine how these priorities had changed in five years and post COVID-19 pandemic and compare these to international PICU priorities.

Methods
A modified three-round e-Delphi study was conducted in 2022 with surveys sent to all members of the Paediatric Critical Care Society. Following this, the top 20 topics were ranked and voted on using the Hanlon method in an online consensus webinar.

Results
247 research topics were submitted by 85 respondents in Round one. 135 of these were categorised into 12 domains and put forward into Round two, and were scored by 112 participants. 45 highest scoring topics were included in Round three and these were re-scored by 67 participants. Following this, the top 20 topics were voted on (using the Hanlon method) in an online consensus webinar in November 2022, to generate a top 10 list of priority research topics for pediatric critical care in 2023. The top research priorities related to complex decision-making in relation to withdrawing/withholding critical care, antimicrobial therapy and rapid diagnostics, intravenous fluid restriction, long-term outcomes, staffing and retention, implementation science and the role of artificial intelligence.

Conclusion
Some of the research priorities for pediatric critical care in the UK have changed over the last five years and there are similar priorities in other high-income countries with a potential for multi-national collaborations to address these key areas.
The research landscape of renal cancer ablation
Authors: Mahmood Hassan , Deshwal Avinash , Khalid Aleena 
Published: June 2024

Abstract
Background
Renal ablation has emerged as a minimally invasive treatment option for kidney cancer. This systematic review uses bibliometric analysis to identify the influential publications, authors, institutions, and countries in the field of renal cancer ablation.

Methods
A comprehensive search was conducted using the Web of Science database, and data on authors, publications, citations, affiliations, and keywords were collected. Statistical analysis was performed using several software tools, including Bibliometrix, Microsoft Excel, Tableau, VoxViewer, and R.

Results
A total of 285 documents were detected, with a significant positive correlation between the year of publication and number of articles. The majority of papers were on “Radiofrequency Ablation” (n = 145) with significant less literature on other forms of renal ablation. The top 10 most prolific journals published 48% of all articles. The United States was the most prolific contributor (n = 113), with Harvard being the most productive (n = 33) and cited institution (2231 citations). Liang P. was the most prolific author (n = 18), Mueller, P.R. was the most cited (1493 citations) and Gervais, D.A. the most collaborative. The three most frequently used author keywords were “renal cell carcinoma,” “radiofrequency ablation,” and “microwave ablation.”

Discussion
This study offers a comprehensive overview of the knowledge base surrounding renal cancer ablation, providing insight into the most influential publications, authors, institutions, countries, and emerging topics. While the majority of the current literature is on RFA, our analysis suggests a growing interest and focus on alternative ablation techniques such as microwave and cryoablation in recent years.
Sulfide Copper‐Iron Isotopic Fractionation During Formation of the Kalatongke Magmatic Cu‐Ni Sulfide Deposit in the Central Asian Orogenic Belt
Authors: Tang Dongmei , Qin Kezhang , Evans Noreen J. , Wang Haoru 
Published: June 2024

AbstractCopper and iron isotopic signatures in sulfide and silicate minerals are important genetic indicators in magmatic sulfide deposits. Kalatongke is a large‐scale magmatic Cu‐Ni sulfide deposit in the Central Asian Orogenic Belt, and one that experienced multiple stages of magmatism and contamination. It is an ideal deposit in which to study Cu‐Fe isotopic fractionation during multiple stages of magmatism and sulfide mineralization processes. The Kalatongke sulfide orebodies are hosted by three small mafic intrusions in which pyroxene and sulfides (pyrrhotite, pentlandite, and chalcopyrite) are the most common Fe‐rich minerals, and chalcopyrite is the dominant Cu‐rich mineral. Sulfide liquid and silicate melt ▵56FeSul‐Sil (0.03–0.19‰) and ▵65CuCcp‐Sil (−0.78–0.74‰) values are indicative of non‐equilibrium fractionation. Most of the Cu isotope compositions in the sulfide ores at Kalatongke can be modeled as subduction‐ metasomatized, oxidized mantle source‐derived silicate melt (initial δ57Fe = 0.15‰, δ65Cu = −0.07‰) that underwent lower crustal contamination, and then reacted with silicate melt, having an R factor of 100–1,000. Rapid silicate melt and sulfide liquid Fe isotope exchange and re‐equilibration between chalcopyrite and pyrrhotite in the massive ores is reflected in the similarity of their δ56Fe values. Sulfide in disseminated ores shows a range of Fe isotope ratios, influenced by the proportions of monosulfide solid solution (MSS) and intermediate solid solution (ISS) formed. Copper isotopes can be utilized to characterize crustal contamination and silicate melt‐sulfide liquid interaction, while the Fe isotope ratios of sulfide minerals record sulfide liquid segregation and evolution in magmatic sulfide deposits.
ENSO‐Related Precursor Pathways of Interannual Thermal Anomalies Identified Using a Transformer‐Based Deep Learning Model in the Tropical Pacific
Authors: Zhou Lu , Zhang Rong‐Hua 
Published: June 2024

AbstractRecent studies have demonstrated great values of deep‐learning (DL) methods for improving El Niño‐Southern Oscillation (ENSO) predictions. However, the black‐box nature of DL makes it challenging to physically interpret mechanisms responsible for successful ENSO predictions. Here, we demonstrate an interpretable method by performing perturbation experiments to predictors and quantifying input‐output relationships in predictions by using a transformer‐based model; ENSO‐related thermal precursors serving as initial conditions during multi‐month time intervals (TIs) are identified in the equatorial‐northern Pacific, acting to precondition input predictors to provide for long‐lead ENSO predictability. Results reveal the existence of upper‐ocean temperature anomaly pathways and consistent phase propagations of thermal precursors around the tropical Pacific. It is illustrated that three‐dimensional thermal fields and their basinwide evolution during long TIs act to enhance long‐lead prediction skills of ENSO. These physically explainable results indicate that neural networks can adequately represent predictable precursors in the input predictors for successful ENSO predictions.
Sequestosome-1 (SQSTM1/p62) as a target in dopamine catabolite-mediated cellular dyshomeostasis
Authors: Masato Anna , Andolfo Annapaola , Favetta Giulia , Bellini Edoardo Niccolò , Cogo Susanna , Dalla Valle Luisa , Boassa Daniela , Greggio Elisa , Plotegher Nicoletta , Bubacco Luigi 
Published: June 2024

AbstractAlterations in the dopamine catabolic pathway are known to contribute to the degeneration of nigrostriatal neurons in Parkinson’s disease (PD). The progressive cellular buildup of the highly reactive intermediate 3,4-dihydroxyphenylacetaldehye (DOPAL) generates protein cross-linking, oligomerization of the PD-linked αSynuclein (αSyn) and imbalance in protein quality control. In this scenario, the autophagic cargo sequestome-1 (SQSTM1/p62) emerges as a target of DOPAL-dependent oligomerization and accumulation in cytosolic clusters. Although DOPAL-induced oxidative stress and activation of the Nrf2 pathway promote p62 expression, p62 oligomerization rather seems to be a consequence of direct DOPAL modification. DOPAL-induced p62 clusters are positive for ubiquitin and accumulate within lysosomal-related structures, likely affecting the autophagy-lysosomal functionality. Finally, p62 oligomerization and clustering is synergistically augmented by DOPAL-induced αSyn buildup. Hence, the substantial impact on p62 proteostasis caused by DOPAL appears of relevance for dopaminergic neurodegeneration, in which the progressive failure of degradative pathways and the deposition of proteins like αSyn, ubiquitin and p62 in inclusion bodies represent a major trait of PD pathology.
TauP301L disengages from the proteosome core complex and neurogranin coincident with enhanced neuronal network excitability
Authors: Hole Katriona L. , Zhu Bangfu , Huggon Laura , Brown Jon T. , Mason Jody M. , Williams Robert J. 
Published: June 2024

AbstractTauopathies are characterised by the pathological accumulation of misfolded tau. The emerging view is that toxic tau species drive synaptic dysfunction and potentially tau propagation before measurable neurodegeneration is evident, but the underlying molecular events are not well defined. Human non-mutated 0N4R tau (tauWT) and P301L mutant 0N4R tau (tauP301L) were expressed in mouse primary cortical neurons using adeno-associated viruses to monitor early molecular changes and synaptic function before the onset of neuronal loss. In this model tauP301L was differentially phosphorylated relative to tauwt with a notable increase in phosphorylation at ser262. Affinity purification - mass spectrometry combined with tandem mass tagging was used to quantitatively compare the tauWT and tauP301L interactomes. This revealed an enrichment of tauP301L with ribosomal proteins but a decreased interaction with the proteasome core complex and reduced tauP301L degradation. Differences in the interaction of tauP301L with members of a key synaptic calcium-calmodulin signalling pathway were also identified, most notably, increased association with CaMKII but reduced association with calcineurin and the candidate AD biomarker neurogranin. Decreased association of neurogranin to tauP301L corresponded with the appearance of enhanced levels of extracellular neurogranin suggestive of potential release or leakage from synapses. Finally, analysis of neuronal network activity using micro-electrode arrays showed that overexpression of tauP301L promoted basal hyperexcitability coincident with these changes in the tau interactome and implicating tau in specific early alterations in synaptic function.
APR-246 as a radiosensitization strategy for mutant p53 cancers treated with alpha-particles-based radiotherapy
Authors: Michaeli Or , Luz Ishai , Vatarescu Maayan , Manko Tal , Weizman Noam , Korotinsky Yevgeniya , Tsitrina Alexandra , Braiman Alex , Arazi Lior , Cooks Tomer 
Published: June 2024

AbstractRadiation therapy (RT) remains a common treatment for cancer patients worldwide, despite the development of targeted biological compounds and immunotherapeutic drugs. The challenge in RT lies in delivering a lethal dose to the cancerous site while sparing the surrounding healthy tissues. Low linear energy transfer (low-LET) and high linear energy transfer (high-LET) radiations have distinct effects on cells. High-LET radiation, such as alpha particles, induces clustered DNA double-strand breaks (DSBs), potentially inducing cell death more effectively. However, due to limited range, alpha-particle therapies have been restricted. In human cancer, mutations in TP53 (encoding for the p53 tumor suppressor) are the most common genetic alteration. It was previously reported that cells carrying wild-type (WT) p53 exhibit accelerated senescence and significant rates of apoptosis in response to RT, whereas cells harboring mutant p53 (mutp53) do not. This study investigated the combination of the alpha-emitting atoms RT based on internal Radium-224 (224Ra) sources and systemic APR-246 (a p53 reactivating compound) to treat tumors with mutant p53. Cellular models of colorectal cancer (CRC) or pancreatic ductal adenocarcinoma (PDAC) harboring mutant p53, were exposed to alpha particles, and tumor xenografts with mutant p53 were treated using224Ra source and APR-246. Effects on cell survival and tumor growth, were assessed. The spread of alpha emitters in tumors was also evaluated as well as the spatial distribution of apoptosis within the treated tumors. We show that mutant p53 cancer cells exhibit radio-sensitivity to alpha particles in vitro and to alpha-particles-based RT in vivo. APR-246 treatment enhanced sensitivity to alpha radiation, leading to reduced tumor growth and increased rates of tumor eradication. Combining alpha-particles-based RT with p53 restoration via APR-246 triggered cell death, resulting in improved therapeutic outcomes. Further preclinical and clinical studies are needed to provide a promising approach for improving treatment outcomes in patients with mutant p53 tumors.
Siglec-6 as a therapeutic target for cell migration and adhesion in chronic lymphocytic leukemia
Authors: Nunes Jessica , Tafesse Rakeb , Mao Charlene , Purcell Matthew , Mo Xiaokui , Zhang Liwen , Long Meixiao , Cyr Matthew G. , Rader Christoph , Muthusamy Natarajan 
Published: June 2024

AbstractSiglec-6 is a lectin receptor with restricted expression in the placenta, mast cells and memory B-cells. Although Siglec-6 is expressed in patients with chronic lymphocytic leukemia (CLL), its pathophysiological role has not been elucidated. We describe here a role for Siglec-6 in migration and adhesion of CLL B cells to CLL- bone marrow stromal cells (BMSCs) in vitro and compromised migration to bone marrow and spleen in vivo. Mass spectrometry analysis revealed interaction of Siglec-6 with DOCK8, a guanine nucleotide exchange factor. Stimulation of MEC1-002 CLL cells with a Siglec-6 ligand, sTn, results in Cdc42 activation, WASP protein recruitment and F-actin polymerization, which are all associated with cell migration. Therapeutically, a Siglec-6/CD3-bispecific T-cell-recruiting antibody (T-biAb) improves overall survival in an immunocompetent mouse model and eliminates CLL cells in a patient derived xenograft model. Our findings thus reveal a migratory role for Siglec-6 in CLL, which can be therapeutically targeted using a Siglec-6 specific T-biAb.
Reconstructing higher-order interactions in coupled dynamical systems
Authors: Malizia Federico , Corso Alessandra , Gambuzza Lucia Valentina , Russo Giovanni , Latora Vito , Frasca Mattia 
Published: June 2024

AbstractHigher-order interactions play a key role for the operation and function of a complex system. However, how to identify them is still an open problem. Here, we propose a method to fully reconstruct the structural connectivity of a system of coupled dynamical units, identifying both pairwise and higher-order interactions from the system time evolution. Our method works for any dynamics, and allows the reconstruction of both hypergraphs and simplicial complexes, either undirected or directed, unweighted or weighted. With two concrete applications, we show how the method can help understanding the complexity of bacterial systems, or the microscopic mechanisms of interaction underlying coupled chaotic oscillators.
Characterization and regulation of cell cycle-independent noncanonical gene targeting
Authors: Saito Shinta , Adachi Noritaka 
Published: June 2024

AbstractHomology-dependent targeted DNA integration, generally referred to as gene targeting, provides a powerful tool for precise genome modification; however, its fundamental mechanisms remain poorly understood in human cells. Here we reveal a noncanonical gene targeting mechanism that does not rely on the homologous recombination (HR) protein Rad51. This mechanism is suppressed by Rad52 inhibition, suggesting the involvement of single-strand annealing (SSA). The SSA-mediated gene targeting becomes prominent when DSB repair by HR or end-joining pathways is defective and does not require isogenic DNA, permitting 5% sequence divergence. Intriguingly, loss of Msh2, loss of BLM, and induction of a target-site DNA break all significantly and synergistically enhance SSA-mediated targeted integration. Most notably, SSA-mediated integration is cell cycle-independent, occurring in the G1 phase as well. Our findings provide unequivocal evidence for Rad51-independent targeted integration and unveil multiple mechanisms to regulate SSA-mediated targeted as well as random integration.