bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell invasion during competitive growth of polycrystalline solidification patterns
Authors: Song Younggil , Mota Fatima L. , Tourret Damien , Ji Kaihua , Billia Bernard , Trivedi Rohit , Bergeon Nathalie , Karma Alain 
Published: April 2023

AbstractSpatially extended cellular and dendritic array structures forming during solidification processes such as casting, welding, or additive manufacturing are generally polycrystalline. Both the array structure within each grain and the larger scale grain structure determine the performance of many structural alloys. How those two structures coevolve during solidification remains poorly understood. By in situ observations of microgravity alloy solidification experiments onboard the International Space Station, we have discovered that individual cells from one grain can unexpectedly invade a nearby grain of different misorientation, either as a solitary cell or as rows of cells. This invasion process causes grains to interpenetrate each other and hence grain boundaries to adopt highly convoluted shapes. Those observations are reproduced by phase-field simulations further demonstrating that invasion occurs for a wide range of misorientations. Those results fundamentally change the traditional conceptualization of grains as distinct regions embedded in three-dimensional space.
Direct correction of haemoglobin E β-thalassaemia using base editors
Authors: Badat Mohsin , Ejaz Ayesha , Hua Peng , Rice Siobhan , Zhang Weijiao , Hentges Lance D. , Fisher Christopher A. , Denny Nicholas , Schwessinger Ron , Yasara Nirmani , Roy Noemi B. A. , Issa Fadi , Roy Andi , Telfer Paul , Hughes Jim , Mettananda Sachith , Higgs Douglas R. , Davies James O. J. 
Published: April 2023

AbstractHaemoglobin E (HbE) β-thalassaemia causes approximately 50% of all severe thalassaemia worldwide; equating to around 30,000 births per year. HbE β-thalassaemia is due to a point mutation in codon 26 of the human HBB gene on one allele (GAG; glutamatic acid → AAG; lysine, E26K), and any mutation causing severe β-thalassaemia on the other. When inherited together in compound heterozygosity these mutations can cause a severe thalassaemic phenotype. However, if only one allele is mutated individuals are carriers for the respective mutation and have an asymptomatic phenotype (β-thalassaemia trait). Here we describe a base editing strategy which corrects the HbE mutation either to wildtype (WT) or a normal variant haemoglobin (E26G) known as Hb Aubenas and thereby recreates the asymptomatic trait phenotype. We have achieved editing efficiencies in excess of 90% in primary human CD34 + cells. We demonstrate editing of long-term repopulating haematopoietic stem cells (LT-HSCs) using serial xenotransplantation in NSG mice. We have profiled the off-target effects using a combination of circularization for in vitro reporting of cleavage effects by sequencing (CIRCLE-seq) and deep targeted capture and have developed machine-learning based methods to predict functional effects of candidate off-target mutations.
Mapping genomic regulation of kidney disease and traits through high-resolution and interpretable eQTLs
Authors: Han Seong Kyu , McNulty Michelle T. , Benway Christopher J. , Wen Pei , Greenberg Anya , Onuchic-Whitford Ana C. ,   Nephrotic Syndrome Study Network (NEPTUNE), Jang Dongkeun , Flannick Jason , Burtt Noël P. , Wilson Parker C. , Humphreys Benjamin D. , Wen Xiaoquan , Han Zhe , Lee Dongwon , Sampson Matthew G. 
Published: April 2023

AbstractExpression quantitative trait locus (eQTL) studies illuminate genomic variants that regulate specific genes and contribute to fine-mapped loci discovered via genome-wide association studies (GWAS). Efforts to maximize their accuracy are ongoing. Using 240 glomerular (GLOM) and 311 tubulointerstitial (TUBE) micro-dissected samples from human kidney biopsies, we discovered 5371 GLOM and 9787 TUBE genes with at least one variant significantly associated with expression (eGene) by incorporating kidney single-nucleus open chromatin data and transcription start site distance as an “integrative prior” for Bayesian statistical fine-mapping. The use of an integrative prior resulted in higher resolution eQTLs illustrated by (1) smaller numbers of variants in credible sets with greater confidence, (2) increased enrichment of partitioned heritability for GWAS of two kidney traits, (3) an increased number of variants colocalized with the GWAS loci, and (4) enrichment of computationally predicted functional regulatory variants. A subset of variants and genes were validated experimentally in vitro and using a Drosophila nephrocyte model. More broadly, this study demonstrates that tissue-specific eQTL maps informed by single-nucleus open chromatin data have enhanced utility for diverse downstream analyses.
The microbial food revolution
Authors: Graham Alicia E. , Ledesma-Amaro Rodrigo 
Published: April 2023

AbstractOur current food system relies on unsustainable practices, which often fail to provide healthy diets to a growing population. Therefore, there is an urgent demand for new sustainable nutrition sources and processes. Microorganisms have gained attention as a new food source solution, due to their low carbon footprint, low reliance on land, water and seasonal variations coupled with a favourable nutritional profile. Furthermore, with the emergence and use of new tools, specifically in synthetic biology, the uses of microorganisms have expanded showing great potential to fulfil many of our dietary needs. In this review, we look at the different applications of microorganisms in food, and examine the history, state-of-the-art and potential to disrupt current foods systems. We cover both the use of microbes to produce whole foods out of their biomass and as cell factories to make highly functional and nutritional ingredients. The technical, economical, and societal limitations are also discussed together with the current and future perspectives.
Allosteric role of the citrate synthase homology domain of ATP citrate lyase
Authors: Wei Xuepeng , Schultz Kollin , Pepper Hannah L. , Megill Emily , Vogt Austin , Snyder Nathaniel W. , Marmorstein Ronen 
Published: April 2023

AbstractATP citrate lyase (ACLY) is the predominant nucleocytosolic source of acetyl-CoA and is aberrantly regulated in many diseases making it an attractive therapeutic target. Structural studies of ACLY reveal a central homotetrameric core citrate synthase homology (CSH) module flanked by acyl-CoA synthetase homology (ASH) domains, with ATP and citrate binding the ASH domain and CoA binding the ASH-CSH interface to produce acetyl-CoA and oxaloacetate products. The specific catalytic role of the CSH module and an essential D1026A residue contained within it has been a matter of debate. Here, we report biochemical and structural analysis of an ACLY-D1026A mutant demonstrating that this mutant traps a (3S)-citryl-CoA intermediate in the ASH domain in a configuration that is incompatible with the formation of acetyl-CoA, is able to convert acetyl-CoA and OAA to (3S)-citryl-CoA in the ASH domain, and can load CoA and unload acetyl-CoA in the CSH module. Together, this data support an allosteric role for the CSH module in ACLY catalysis.
Formation of calcareous deposits in the tidal zone and its effect on cathodic protection
Authors: Yao Caiqi , Wang Xinru , Zhang Wei , Xia Wenting , Chen Zhiwei , Han Bing 
Published: April 2023

AbstractUsing the wire beam electrode technique, electrochemical impedance spectroscopy, energy-dispersive X-ray spectroscopy, the formation of calcareous deposits in a tidal zone and its effects on the corrosion and protection of Q235 steel under cathodic protection were studied. Results showed that the production of aragonite CaCO3 crystals significantly reduced from the immersion zone to the high-tide zone, the protective performance of the deposited layer weakened, and the corrosion of the metal intensified. In the immersion zone, the cathodic protection current density decreased, and the potential shifted negatively, indicating that the protection performance of the deposited layer was enhanced and the metal was effectively protected. In the tidal zone, the deposited layer was stratified, and the porosity of the deposited layer increased by dry-wet cycling. During flood tide, the cathodic reaction is accelerated near the waterline, which promotes the corrosion of the metal and the loss of the sacrificial anode under water.
Molecular dynamic study of radiation-moisture aging effects on the interface properties of nano-silica/silicone rubber composites
Authors: Lou Weitao , Xie Chaoyang , Guan Xuefei 
Published: April 2023

AbstractThe influence of radiation-moisture aging on the thermodynamic and interface properties of nano-silica/silicone rubber (PDMS) composites was investigated using molecular dynamics simulation. The deterioration of polymer matrix was incorporated into the PDMS-silica interface models based on the hydrolysis products and the dominant role of cross-linking over chain scission. The results indicate that the long-chain structure with the higher molecular weight and the stronger intermolecular interactions are formed by incorporating multi-chain cross-linking and more hydroxyl groups. The coupling effects of the long-chain structure and stronger intermolecular interactions enhance the binding strength between the silica and PDMS matrix owing to the formation of more hydrogen bonds, and restrict the diffusion mobility of PDMS chains and water molecules. The aging of the PDMS matrix facilitates water molecules to adsorb on the surface of the silica and the PDMS matrix to form hydrogen bonds, and eventually weakens the bonding strength of the silica-PDMS interface.
Ultrafiltration separation of Am(VI)-polyoxometalate from lanthanides
Authors: Zhang Hailong , Li Ao , Li Kai , Wang Zhipeng , Xu Xiaocheng , Wang Yaxing , Sheridan Matthew V. , Hu Han-Shi , Xu Chao , Alekseev Evgeny V. , Zhang Zhenyi , Yan Pu , Cao Kecheng , Chai Zhifang , Albrecht-Schönzart Thomas E. , Wang Shuao 
Published: April 2023

AbstractPartitioning of americium from lanthanides (Ln) present in used nuclear fuel plays a key role in the sustainable development of nuclear energy1–3. This task is extremely challenging because thermodynamically stable Am(III) and Ln(III) ions have nearly identical ionic radii and coordination chemistry. Oxidization of Am(III) to Am(VI) produces AmO22+ ions distinct with Ln(III) ions, which has the potential to facilitate separations in principle. However, the rapid reduction of Am(VI) back to Am(III) by radiolysis products and organic reagents required for the traditional separation protocols including solvent and solid extractions hampers practical redox-based separations. Herein, we report a nanoscale polyoxometalate (POM) cluster with a vacancy site compatible with the selective coordination of hexavalent actinides (238U, 237Np, 242Pu and 243Am) over trivalent lanthanides in nitric acid media. To our knowledge, this cluster is the most stable Am(VI) species in aqueous media observed so far. Ultrafiltration-based separation of nanoscale Am(VI)-POM clusters from hydrated lanthanide ions by commercially available, fine-pored membranes enables the development of a once-through americium/lanthanide separation strategy that is highly efficient and rapid, does not involve any organic components and requires minimal energy input.
Dedifferentiation maintains melanocyte stem cells in a dynamic niche
Authors: Sun Qi , Lee Wendy , Hu Hai , Ogawa Tatsuya , De Leon Sophie , Katehis Ioanna , Lim Chae Ho , Takeo Makoto , Cammer Michael , Taketo M. Mark , Gay Denise L. , Millar Sarah E. , Ito Mayumi 
Published: April 2023

AbstractFor unknow reasons, the melanocyte stem cell (McSC) system fails earlier than other adult stem cell populations1, which leads to hair greying in most humans and mice2,3. Current dogma states that McSCs are reserved in an undifferentiated state in the hair follicle niche, physically segregated from differentiated progeny that migrate away following cues of regenerative stimuli4–8. Here we show that most McSCs toggle between transit-amplifying and stem cell states for both self-renewal and generation of mature progeny, a mechanism fundamentally distinct from those of other self-renewing systems. Live imaging and single-cell RNA sequencing revealed that McSCs are mobile, translocating between hair follicle stem cell and transit-amplifying compartments where they reversibly enter distinct differentiation states governed by local microenvironmental cues (for example, WNT). Long-term lineage tracing demonstrated that the McSC system is maintained by reverted McSCs rather than by reserved stem cells inherently exempt from reversible changes. During ageing, there is accumulation of stranded McSCs that do not contribute to the regeneration of melanocyte progeny. These results identify a new model whereby dedifferentiation is integral to homeostatic stem cell maintenance and suggest that modulating McSC mobility may represent a new approach for the prevention of hair greying.
The BlueBio project’s database: web-mapping cooperation to create value for the Blue Bioeconomy
Authors: Tassetti Anna Nora , Ferrà Carmen , Manarini Tania , Moro Fabrizio , Pinat Massimiliano , Pulcinella Jacopo , Punzo Elisa , Salvalaggio Vera , Scarpini Paolo , Spagnolo Alessandra , Thorud Kristin Elisabeth , Fabi Gianna 
Published: April 2023

AbstractFunding innovation requires knowledge on previous/on-going research and identification of gaps and synergies among actors, networks and projects, but targeted databases remain scattered, incomplete and scarcely searchable. Here we present the BlueBio database: a first comprehensive and robust compilation of internationally and nationally funded research projects active in the years 2003–2019 in Fisheries, Aquaculture, Seafood Processing and Marine Biotechnology. Based on the previous research projects’ database realized in the framework of the COFASP ERA-NET, it was implemented within the ERA-NET Cofund BlueBio project through a 4-years data collection including 4 surveys and a wide data retrieval. After being integrated, data were harmonised, shared as open and disseminated through a WebGIS that was key for data entry, update and validation. The database consists of 3,254 “georeferenced” projects, described by 22 parameters that are clustered into textual and spatial, some directly collected while others deduced. The database is a living archive to inform actors of the Blue Bioeconomy sector in a period of rapid transformations and research needs and is freely available at: https://doi.org/10.6084/m9.figshare.21507837.v3.
Shared cross-cultural principles underlie human prosocial behavior at the smallest scale
Authors: Rossi Giovanni , Dingemanse Mark , Floyd Simeon , Baranova Julija , Blythe Joe , Kendrick Kobin H. , Zinken Jörg , Enfield N. J. 
Published: April 2023

AbstractProsociality and cooperation are key to what makes us human. But different cultural norms can shape our evolved capacities for interaction, leading to differences in social relations. How people share resources has been found to vary across cultures, particularly when stakes are high and when interactions are anonymous. Here we examine prosocial behavior among familiars (both kin and non-kin) in eight cultures on five continents, using video recordings of spontaneous requests for immediate, low-cost assistance (e.g., to pass a utensil). We find that, at the smallest scale of human interaction, prosocial behavior follows cross-culturally shared principles: requests for assistance are very frequent and mostly successful; and when people decline to give help, they normally give a reason. Although there are differences in the rates at which such requests are ignored, or require verbal acceptance, cultural variation is limited, pointing to a common foundation for everyday cooperation around the world.
Fronto-central resting-state 15-29 Hz transient beta events change with therapeutic transcranial magnetic stimulation for posttraumatic stress disorder and major depressive disorder
Authors: Morris Alexander T. , Temereanca Simona , Zandvakili Amin , Thorpe Ryan , Sliva Danielle D. , Greenberg Benjamin D. , Carpenter Linda L. , Philip Noah S. , Jones Stephanie R. 
Published: April 2023

AbstractRepetitive transcranial magnetic stimulation (rTMS) is an established treatment for major depressive disorder (MDD) and shows promise for posttraumatic stress disorder (PTSD), yet effectiveness varies. Electroencephalography (EEG) can identify rTMS-associated brain changes. EEG oscillations are often examined using averaging approaches that mask finer time-scale dynamics. Recent advances show some brain oscillations emerge as transient increases in power, a phenomenon termed “Spectral Events,” and that event characteristics correspond with cognitive functions. We applied Spectral Event analyses to identify potential EEG biomarkers of effective rTMS treatment. Resting 8-electrode EEG was collected from 23 patients with MDD and PTSD before and after 5 Hz rTMS targeting the left dorsolateral prefrontal cortex. Using an open-source toolbox (https://github.com/jonescompneurolab/SpectralEvents), we quantified event features and tested for treatment associated changes. Spectral Events in delta/theta (1–6 Hz), alpha (7–14 Hz), and beta (15–29 Hz) bands occurred in all patients. rTMS-induced improvement in comorbid MDD PTSD were associated with pre- to post-treatment changes in fronto-central electrode beta event features, including frontal beta event frequency spans and durations, and central beta event maxima power. Furthermore, frontal pre-treatment beta event duration correlated negatively with MDD symptom improvement. Beta events may provide new biomarkers of clinical response and advance the understanding of rTMS.
Adaptive data-driven selection of sequences of biological and cognitive markers in pre-clinical diagnosis of dementia
Authors: Wyss Patric , Ginsbourger David , Shou Haochang , Davatzikos Christos , Klöppel Stefan , Abdulkadir Ahmed 
Published: April 2023

AbstractEffective clinical decision procedures must balance multiple competing objectives such as time-to-decision, acquisition costs, and accuracy. We describe and evaluate POSEIDON, a data-driven method for PrOspective SEquentIal DiagnOsis with Neutral zones to individualize clinical classifications. We evaluated the framework with an application in which the algorithm sequentially proposes to include cognitive, imaging, or molecular markers if a sufficiently more accurate prognosis of clinical decline to manifest Alzheimer’s disease is expected. Over a wide range of cost parameter data-driven tuning lead to quantitatively lower total cost compared to ad hoc fixed sets of measurements. The classification accuracy based on all longitudinal data from participants that was acquired over 4.8 years on average was 0.89. The sequential algorithm selected 14 percent of available measurements and concluded after an average follow-up time of 0.74 years at the expense of 0.05 lower accuracy. Sequential classifiers were competitive from a multi-objective perspective since they could dominate fixed sets of measurements by making fewer errors using less resources. Nevertheless, the trade-off of competing objectives depends on inherently subjective prescribed cost parameters. Thus, despite the effectiveness of the method, the implementation into consequential clinical applications will remain controversial and evolve around the choice of cost parameters.
Cognitive impairment in young adults with post COVID-19 syndrome
Authors: Herrera Elena , Pérez-Sánchez María del Carmen , San Miguel-Abella Romina , Barrenechea Arrate , Blanco Claudia , Solares Lucía , González Lucía , Iza Clara , Castro Isabel , Nicolás Elena , Sierra Damián , Suárez Paula , González-Nosti María 
Published: April 2023

AbstractIn this study, we aimed to examine different cognitive domains in a large sample of patients with post COVID-19 syndrome. Two hundred and fourteen patients, 85.04% women, ranged 26 to 64 years (mean = 47.48 years) took part in this investigation. Patients’ processing speed, attention, executive functions and various language modalities were examined online using a comprehensive task protocol designed for this research. Alteration in some of the tasks was observed in 85% of the participants, being the attention and executive functions tests the ones that show the highest percentage of patients with severe impairment. Positive correlations were observed between the age of the participants in almost all the tasks assessed, implying better performance and milder impairment with increasing age. In the comparisons of patients according to age, the oldest patients were found to maintain their cognitive functions relatively preserved, with only a mild impairment in attention and speed processing, while the youngest showed the most marked and heterogeneous cognitive impairment. These results confirm the subjective complaints in patients with post COVID-19 syndrome and, thanks to the large sample size, allow us to observe the effect of patient age on performance, an effect never reported before in patients with these characteristics.
Application of various machine learning techniques to predict obstructive sleep apnea syndrome severity
Authors: Han Hyewon , Oh Junhyoung 
Published: April 2023

AbstractAs the incidence of obstructive sleep apnea syndrome (OSAS) increases worldwide, the need for a new screening method that can compensate for the shortcomings of the traditional diagnostic method, polysomnography (PSG), is emerging. In this study, data from 4014 patients were used, and both supervised and unsupervised learning methods were used. Clustering was conducted with hierarchical agglomerative clustering, K-means, bisecting K-means algorithm, Gaussian mixture model, and feature engineering was carried out using both medically researched methods and machine learning techniques. For classification, we used gradient boost-based models such as XGBoost, LightGBM, CatBoost, and Random Forest to predict the severity of OSAS. The developed model showed high performance with 88%, 88%, and 91% of classification accuracy for three thresholds for the severity of OSAS: Apnea-Hypopnea Index (AHI) $$\ge $$
≥
5, AHI $$\ge $$
≥
15, and AHI $$\ge $$
≥
30, respectively. The results of this study demonstrate significant evidence of sufficient potential to utilize machine learning in predicting OSAS severity.
Excessive flexed position of the femoral component causes abnormal kinematics and joint contact/ ligament forces in total knee arthroplasty
Authors: Nishitani Kohei , Kuriyama Shinichi , Nakamura Shinichiro , Song Young Dong , Morita Yugo , Ito Hiromu , Matsuda Shuichi 
Published: April 2023

AbstractPoor clinical outcomes are reported in excessive flexion of the femoral component in total knee arthroplasty (TKA), but their mechanisms have not yet been elucidated. This study aimed to investigate the biomechanical effect of flexion of the femoral component. Cruciate-substituting (CS) and posterior-stabilised (PS) TKA were reproduced in a computer simulation. The femoral component was then flexed from 0° to 10° with anterior reference, keeping the implant size and the extension gap. Knee kinematics, joint contact, and ligament forces were evaluated in deep-knee-bend activity. When the femoral component was flexed 10° in CS TKA, paradoxical anterior translation of the medial compartment was observed at mid-flexion. The PS implant was best stabilised with a 4° flexion model in mid-flexion range. The medial compartment contact force and the medial collateral ligament (MCL) force increased with the flexion of the implant. There were no remarkable changes in the patellofemoral contact force or quadriceps in either implant. In conclusions, excessive flexion of the femoral component yielded abnormal kinematics and contact/ligament forces. Avoiding excessive flexion and maintaining mild flexion of the femoral component would provide better kinematics and biomechanical effects in CS and PS TKA.