bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual-Alpha: a large EEG study for dual-frequency SSVEP brain–computer interface
Authors: Sun Yike , Liang Liyan , Li Yuhan , Chen Xiaogang , Gao Xiaorong 
Published: August 2024

Abstract

Background
The domain of brain–computer interface (BCI) technology has experienced significant expansion in recent years. However, the field continues to face a pivotal challenge due to the dearth of high-quality datasets. This lack of robust datasets serves as a bottleneck, constraining the progression of algorithmic innovations and, by extension, the maturation of the BCI field.

Findings
This study details the acquisition and compilation of electroencephalogram data across 3 distinct dual-frequency steady-state visual evoked potential (SSVEP) paradigms, encompassing over 100 participants. Each experimental condition featured 40 individual targets with 5 repetitions per target, culminating in a comprehensive dataset consisting of 21,000 trials of dual-frequency SSVEP recordings. We performed an exhaustive validation of the dataset through signal-to-noise ratio analyses and task-related component analysis, thereby substantiating its reliability and effectiveness for classification tasks.

Conclusions
The extensive dataset presented is set to be a catalyst for the accelerated development of BCI technologies. Its significance extends beyond the BCI sphere and holds considerable promise for propelling research in psychology and neuroscience. The dataset is particularly invaluable for discerning the complex dynamics of binocular visual resource distribution.
Efficient phylogenetic tree inference for massive taxonomic datasets: harnessing the power of a server to analyze 1 million taxa
Authors: Piñeiro César , Pichel Juan C 
Published: August 2024

Abstract

Background
Phylogenies play a crucial role in biological research. Unfortunately, the search for the optimal phylogenetic tree incurs significant computational costs, and most of the existing state-of-the-art tools cannot deal with extremely large datasets in reasonable times.

Results
In this work, we introduce the new VeryFastTree code (version 4.0), which is able to construct a tree on 1 server using single-precision arithmetic from a massive 1 million alignment dataset in only 36 hours, which is 3 times and 3.2 times faster than its previous version and FastTree-2, respectively. This new version further boosts performance by parallelizing all tree traversal operations during the tree construction process, including subtree pruning and regrafting moves. Additionally, it introduces significant new features such as support for new and compressed file formats, enhanced compatibility across a broader range of operating systems, and the integration of disk computing functionality. The latter feature is particularly advantageous for users without access to high-end servers, as it allows them to manage very large datasets, albeit with an increase in computing time.

Conclusions
Experimental results establish VeryFastTree as the fastest tool in the state-of-the-art for maximum likelihood phylogeny estimation. It is publicly available at https://github.com/citiususc/veryfasttree. In addition, VeryFastTree is included as a package in Bioconda, MacPorts, and all Debian-based Linux distributions.
LacdiNAc to LacNAc: remodelling of bovine α-lactalbumin N-glycosylation during the transition from colostrum to mature milk
Authors: Gazi Inge , Reiding Karli R , Groeneveld André , Bastiaans Jan , Huppertz Thom , Heck Albert J R 
Published: August 2024

Abstract
α -Lactalbumin, an abundant protein present in the milk of most mammals, is associated with biological, nutritional and technological functionality. Its sequence presents N-glycosylation motifs, the occupancy of which is species-specific, ranging from no to full occupancy. Here, we investigated the N-glycosylation of bovine α-lactalbumin in colostrum and milk sampled from four individual cows, each at 9 time points starting from the day of calving up to 28.0 d post-partum. Using a glycopeptide-centric mass spectrometry-based glycoproteomics approach, we identified N-glycosylation at both Asn residues found in the canonical Asn-Xxx-Ser/Thr motif, i.e. Asn45 and Asn74 of the secreted protein. We found similar glycan profiles in all four cows, with partial site occupancies, averaging at 35% and 4% for Asn45 and Asn74, respectively. No substantial changes in occupancy occurred over lactation at either site. Fucosylation, sialylation, primarily with N-acetylneuraminic acid (Neu5Ac), and a high ratio of N,N′-diacetyllactosamine (LacdiNAc)/N-acetyllactosamine (LacNAc) motifs were characteristic features of the identified N-glycans. While no substantial changes occurred in site occupancy at either site during lactation, the glycoproteoform (i.e. glycosylated form of the protein) profile revealed dynamic changes; the maturation of the α-lactalbumin glycoproteoform repertoire from colostrum to mature milk was marked by substantial increases in neutral glycans and the number of LacNAc motifs per glycan, at the expense of LacdiNAc motifs. While the implications of α-lactalbumin N-glycosylation on functionality are still unclear, we speculate that N-glycosylation at Asn74 results in a structurally and functionally different protein, due to competition with the formation of its two intra-molecular disulphide bridges.
ABIOTIC STRESS GENE 1 mediates aroma volatiles accumulation by activating MdLOX1a in apple
Authors: Zhang Jing , Wang Yongxu , Zhang Susu , Zhang Shuhui , Liu Wenjun , Wang Nan , Fang Hongcheng , Zhang Zongying , Chen Xuesen 
Published: August 2024

Abstract
Fruit aroma is an important organoleptic quality, which influences consumer preference and market competitiveness. Aroma compound synthesis pathways in plants have been widely identified, among the lipoxygenase pathway is crucial for fatty acid catabolism to form esters in apple. However, the regulatory mechanism of this pathway remains elusive. In this study, linear regression analysis and transgene verification revealed that the lipoxygenase MdLOX1a is involved in ester biosynthesis. Yeast one-hybrid library screening indicated that a protein, MdASG1 (ABIOTIC STRESS GENE 1), was a positive regulator of MdLOX1a and ester production based on yeast one-hybrid and dual-luciferase assays, as well as correlation analysis among eight different apple cultivars. Overexpression of MdASG1 in apple and tomato stimulated the lipoxygenase pathway and increased the fatty acid-derived volatile content, whereas the latter was decreased by MdASG1 silencing and CRISPR/Cas9 knockout. Furthermore, MdASG1 overexpression enhanced the salt-stress tolerance of tomato and apple ‘Orin’ calli accompanied by a higher content of fatty acid-derived volatiles compared to that of non-stressed transgenic tomato fruit, while MdASG1-Cas9 knockdown calli do not respond to salt stress and promote the biosynthesis of fatty acid-derived volatiles. Collectively, these findings indicate that MdASG1 activates MdLOX1a expression and participates in the lipoxygenase pathway, subsequently increasing the accumulation of aroma compounds, especially under moderate salt stress treatment. The results also provide insight into the theory for improving fruit aroma quality in adversity.
A Comparison of the Mitochondrial Performance between Migratory and Sedentary Mimid Thrushes
Authors: Rhodes Emma M , Yap Kang Nian , Hill Geoffrey E , Hood Wendy R 
Published: August 2024

Synopsis
Birds exhibit a variety of migration strategies. Because sustained flapping flight requires the production of elevated levels of energy compared to typical daily activities, migratory birds are well-documented to have several physiological adaptations to support the energy demands of migration. However, even though mitochondria are the source of ATP that powers flight, the respiratory performance of the mitochondria is almost unstudied in the context of migration. We hypothesized that migratory species would have higher mitochondrial respiratory performance during migration compared to species that do not migrate. To test this hypothesis, we compared variables related to mitochondrial respiratory function between two confamilial bird species—the migratory Gray Catbird (Dumetella carolinensis) and the non-migratory Northern Mockingbird (Mimus polyglottos). Birds were captured at the same location along the Alabama Gulf Coast, where we assumed that Gray Catbirds were migrants and where resident Northern Mockingbirds live year-round. We found a trend in citrate synthase activity, which suggests that Gray Catbirds have a greater mitochondrial volume in their pectoralis muscle, but we observed no other differences in mitochondrial respiration or complex enzymatic activities between individuals from the migrant vs. the non-migrant species. However, when we assessed the catbirds included in our study using well-established indicators of migratory physiology, birds fell into two groups: a group with physiological parameters indicating a physiology of birds engaged in migration and a group with the physiology of birds not migrating. Thus, our comparison included catbirds that appeared to be outside of migratory condition. When we compared the mitochondrial performance of these three groups, we found that the mitochondrial respiratory capacity of migrating catbirds was very similar to that of Northern Mockingbirds, while the catbirds judged to be not migrating were lowest. One explanation for these observations is these species display very different daily flight behaviors. While the mockingbirds we sampled were not breeding nor migrating, they are highly active birds, living in the open and engaging in flapping flights throughout each day. In contrast, Gray Catbirds live in shrubs and fly infrequently when not migrating. Such differences in baseline energy needs likely confounded our attempt to study adaptations to migration.
Early left atrial reverse remodelling in patients with hypertrophic obstructive cardiomyopathy receiving transapical beating-heart septal myectomy
Authors: Lu Shirui , Zhang Jun , Zhu Ying , Zhou Wei , Cheng Xueqing , Wang Hui , Chen Yue , Wei Xiang , Liu Yani 
Published: August 2024

Abstract

OBJECTIVES
This study aims to investigate the short-term effects of transapical beating-heart septal myectomy (TA-BSM) on left atrial (LA) anatomy and function and its association with clinical indicators in patients with hypertrophic obstructive cardiomyopathy (HOCM).

METHODS
A total of 105 HOCM patients who received TA-BSM were included. Clinical and comprehensive echocardiographic data were obtained before surgery, at discharge, and 3 months after myectomy. LA reverse remodelling was defined as LA maximum volume index (LAVI) ≤34 ml/m2 and a change of ≥10%.

RESULTS
At 3 months after TA-BSM, New York Heart Association (NYHA) functional class and 6-min walking test were significantly improved, N-terminal pro–B-type natriuretic peptide (NT-proBNP) decreased, left ventricular outflow tract (LVOT) peak gradient and mitral regurgitation were significantly reduced. LAVI decreased in 76%, with a median change of 20%, and the criteria for LA reverse remodelling were met in 48%. LA strain parameters were improved at 3 months after TA-BSM. Moreover, left ventricular (LV) diastolic function was significantly improved, but LV global longitudinal strain was not significantly changed at 3 months after operation. Improvement in LVOT peak gradient, LAVI, LA reservoir strain (LASr) and conduit strain (LAScd) were associated with reduction in NT-proBNP.

CONCLUSIONS
Along with effectively relieving the obstruction of the LVOT and mitral regurgitation, TA-BSM could significantly improve LA size and function during the short-term follow-up for HOCM patients. The indicators of LA reverse remodelling were associated with reduction in a biomarker of myocardial wall stress, indicating the early recovery of LV relaxation and clinical status for patients.
Large attachment organelle mediates interaction between Nanobdellota archaeon YN1 and its host
Authors: Johnson Matthew D , Sakai Hiroyuki D , Paul Bindusmita , Nunoura Takuro , Dalvi Somavally , Mudaliyar Manasi , Shepherd Doulin C , Shimizu Michiru , Udupa Shubha , Ohkuma Moriya , Kurosawa Norio , Ghosal Debnath 
Published: August 2024

Abstract
DPANN archaea are an enigmatic superphylum that are difficult to isolate and culture in the laboratory due to their specific culture conditions and apparent ectosymbiotic lifestyle. Here, we successfully isolated and cultivated a coculture system of a novel Nanobdellota archaeon YN1 and its host Sulfurisphaera ohwakuensis YN1HA. We characterized the coculture system by complementary methods, including metagenomics and metabolic pathway analysis, fluorescence microscopy, and high-resolution electron cryo-tomography (cryoET). We show that YN1 is deficient in essential metabolic processes and requires host resources to proliferate. CryoET imaging revealed an enormous attachment organelle present in the YN1 envelope that forms a direct interaction with the host cytoplasm, bridging the two cells. Together, our results unravel the molecular and structural basis of ectosymbiotic relationship between YN1 and YN1HA. This research broadens our understanding of DPANN biology and the versatile nature of their ectosymbiotic relationships.
Long-Term Outcomes of a Cultured Autologous Dermo-Epidermal Skin Substitute in Children: 5-Year Results of a Phase I Clinical Trial
Authors: Schiestl Clemens , Neuhaus Kathrin , Meuli Martin , Farkas Melinda , Hartmann-Fritsch Fabienne , Elrod Julia , Bressan Jenny , Reichmann Ernst , Böttcher-Haberzeth Sophie 
Published: August 2024

Abstract
Limited donor sites and poor long-term outcomes with standard treatment for large skin defects remain a huge problem. An autologous, bilayered, laboratory-grown skin substitute (denovoSkin) was developed to overcome this problem and has shown to be safe in 10 pediatric patients in a Phase I clinical trial after transplantation. The goal of this article was to report on 48-month long-term results. The pediatric participants of the phase I clinical trial were followed up at yearly visits up to 5 years after transplantation. Safety parameters, including the occurrence of adverse events, possible deviations of vital signs, and changes in concomitant therapy as well as additional parameters regarding skin stability, scar quality, and tumor formation, were assessed. Furthermore, scar maturation was photographically documented. Of the 10 patients treated with denovoSkin in this phase I clinical trial, 7 completed the 5-year follow-up period. Skin substitutes continued to be deemed safe, remained stable, and practically unchanged, with no sign of fragility and no tumor formation at clinical examination. Scar quality, captured using the Patient and Observer Scar Assessment Scale, was evaluated as close to normal skin. Transplantation of this laboratory-grown skin substitute in children is to date considered safe and shows encouraging functional and aesthetical long-term results close to normal skin. These results are promising and highlight the potential of a life-saving therapy for large skin defects. A multicentre, prospective, randomized, phase II clinical trial is currently ongoing to further evaluate the safety and efficacy of this novel skin substitute. Clinicaltrials.gov identifier NCT02145130.
Java Coffee, French Sardines and Malaga Raisins: Marketing Place in Colonial Australian Food Culture
Authors: Moran Frieda 
Published: August 2024

Abstract
In nineteenth-century colonial Australian newspapers, foods were commonly identified by their place of origin. Advertisements spoke of global networks and exchanges, listing Scotch herring, Mauritius sugar, Ceylon coffee, Valencia raisins, and so forth. Disparate places were connected in newspaper advertisements and on the plates of Australian colonists. There is a substantial body of literature concerned with place of origin advertising, yet the historical roots of this phenomena have received less attention, particularly in relation to colonial food chains. Place of origin advertising was a semiotic device, a trustmark, communicating culturally contingent meanings of food safety and quality. Trustmarks were shortcuts that helped to make sense of complex food systems. Burgeoning global and industrialized food chains fed Australia in the nineteenth century, circulating goods and ideas through and beyond the networks of empire; place marketing inferred transparency and connectivity of supply chains. Using case studies of fish, coffee, and dried fruits, this article demonstrates how place labeling spoke to Australians about potential concerns around labor, class, race, culinary hierarchies, and new technologies. Discursive sources shaped “imaginative geographies,” which, accurately or not, likely informed ideas of food quality. Places attached to foods meant something to the nineteenth-century consumer, and by examining potential meanings, we can better understand how ideas of places and people informed Australian food choices.
Combined transcriptome and metabolome analysis identifies triterpenoid-induced defense responses in Myzus persicae Sülzer-infested peach
Authors: Pan Lei , Huang Rui , Lu Zhenhua , Duan Wenyi , Sun Shihang , Yan Lele , Cui Guochao , Niu Liang , Wang Zhiqiang , Zeng Wenfang 
Published: August 2024

Abstract
Piercing/sucking insects such as green peach aphid (GPA) (Myzus persicae) cause direct damage by obtaining phloem nutrients and indirect damage by spreading plant viruses. To investigate the response of peach trees (Prunus persica) to aphids, the leaf transcriptome and metabolome of two genotypes with different sensitivities to GPA were studied. The gene expression of aphid-susceptible plants infested with aphids was similar to that of control plants, whereas the gene expression of aphid-resistant plants infested with aphids showed strong induced changes in gene expression compared with control plants. Furthermore, gene transcripts in defense-related pathways, including plant–pathogen interaction, MAPK signaling, and several metabolic pathways, were strongly enriched upon aphid infestation. Untargeted secondary metabolite profiling confirmed that aphid infestation induced larger changes in aphid-resistant than in aphid-susceptible peaches. Consistent with transcriptomic alterations, nine triterpenoids showed highly significant GPA-induced accumulation in aphid-resistant peaches, whereas triterpenoid abundance remained predominantly unchanged or undetected in aphid-susceptible peaches. Furthermore, some types of transcription factors (including WRKYs, ERFs, and NACs) were strongly induced upon GPA infestation in aphid-resistant, but not in aphid-susceptible peaches. These results suggested that the accumulation of specialized triterpenoids and the corresponding pathway transcripts may play a key role in peach GPA resistance.
FNet II: spectral classification of quasars, galaxies, stars, and broad absorption line (BAL) quasars
Authors: Moradi R , Rastegarnia F , Wang Y , Mirtorabi M T 
Published: August 2024

ABSTRACT
In this work, we enhance the FNet, a 1D convolutional neural network (CNN) with a residual neural network (ResNet) architecture, to perform spectral classification of quasars, galaxies, stars, and broad absorption line (BAL)-quasars in the SDSS-IV catalogue from DR17 of eBOSS. Leveraging its convolutional layers and the ResNet structure with different kernel sizes, FNet autonomously identifies various patterns within the entire sample of spectra. Since FNet does not require the intermediate step of identifying specific lines, a simple modification enabled our current network to classify all SDSS spectra. This modification involves changing the final output layer from a single value (redshift) to multiple values (probabilities of all classes), and accordingly adjusting the loss function from mean squared error to cross-entropy. FNet achieves a completeness of 99.00 per cent $\pm$ 0.20 for galaxies, 98.50 per cent $\pm$ 0.30 for quasars, 99.00 per cent $\pm$ 0.18 for BAL-quasars, and 98.80 per cent $\pm$ 0.20 for stars. These results are comparable to those obtained using QuasarNET, a standard CNN employed in the SDSS routine, comprises convolutional layers without the ResNet structure with equal kernel sizes, and is utilized for redshift measurement and classification by identifying seven emission lines. QuasarNET, in order to overcome the problem of finding a C iv emission line with broad absorption which is slightly more challenging than that of detecting emission lines requires to add BAL C iv line to the list of lines that the network learns to identify. However, this procedure is not necessary in FNet as it learns the features through a self-learning procedure.
Galaxy mergers in UNIONS – I. A simulation-driven hybrid deep learning ensemble for pure galaxy merger classification
Authors: Ferreira Leonardo , Bickley Robert W , Ellison Sara L , Patton David R , Byrne-Mamahit Shoshannah , Wilkinson Scott , Bottrell Connor , Fabbro Sébastien , Gwyn Stephen D J , McConnachie Alan 
Published: August 2024

ABSTRACT
Merging and interactions can radically transform galaxies. However, identifying these events based solely on structure is challenging as the status of observed mergers is not easily accessible. Fortunately, cosmological simulations are now able to produce more realistic galaxy morphologies, allowing us to directly trace galaxy transformation throughout the merger sequence. To advance the potential of observational analysis closer to what is possible in simulations, we introduce a supervised deep learning convolutional neural network and vision transformer hybrid framework, Mummi (MUlti Model Merger Identifier). Mummi is trained on realism-added synthetic data from IllustrisTNG100-1, and is comprised of a multistep ensemble of models to identify mergers and non-mergers, and to subsequently classify the mergers as interacting pairs or post-mergers. To train this ensemble of models, we generate a large imaging data set of 6.4 million images targeting UNIONS with RealSimCFIS. We show that Mummi offers a significant improvement over many previous machine learning classifiers, achieving 95 per cent pure classifications even at Gyr long time-scales when using a jury-based decision-making process, mitigating class imbalance issues that arise when identifying real galaxy mergers from $z=0$ to 0.3. Additionally, we can divide the identified mergers into pairs and post-mergers at 96 per cent success rate. We drastically decrease the false positive rate in galaxy merger samples by 75 per cent. By applying Mummi to the UNIONS DR5-SDSS DR7 overlap, we report a catalogue of 13 448 high-confidence galaxy merger candidates. Finally, we demonstrate that Mummi produces powerful representations solely using supervised learning, which can be used to bridge galaxy morphologies in simulations and observations.