bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton
Authors: Lampe Robert H. , Coale Tyler H. , Forsch Kiefer O. , Jabre Loay J. , Kekuewa Samuel , Bertrand Erin M. , Horák Aleš , Oborník Miroslav , Rabines Ariel J. , Rowland Elden , Zheng Hong , Andersson Andreas J. , Barbeau Katherine A. , Allen Andrew E. 
Published: November 2023

AbstractCoastal upwelling regions are among the most productive marine ecosystems but may be threatened by amplified ocean acidification. Increased acidification is hypothesized to reduce iron bioavailability for phytoplankton thereby expanding iron limitation and impacting primary production. Here we show from community to molecular levels that phytoplankton in an upwelling region respond to short-term acidification exposure with iron uptake pathways and strategies that reduce cellular iron demand. A combined physiological and multi-omics approach was applied to trace metal clean incubations that introduced 1200 ppm CO2for up to four days.Although variable, molecular-level responses indicate a prioritization of iron uptake pathways that are less hindered by acidification and reductions in iron utilization. Growth, nutrient uptake, and community compositions remained largely unaffected suggesting that these mechanisms may confer short-term resistance to acidification; however, we speculate that cellular iron demand is only temporarily satisfied, and longer-term acidification exposure without increased iron inputs may result in increased iron stress.
Determining zebrafish dorsal organizer size by a negative feedback loop between canonical/non-canonical Wnts and Tlr4/NFκB
Authors: Zou Juqi , Anai Satoshi , Ota Satoshi , Ishitani Shizuka , Oginuma Masayuki , Ishitani Tohru 
Published: November 2023

AbstractIn vertebrate embryos, the canonical Wnt ligand primes the formation of dorsal organizers that govern dorsal-ventral patterns by secreting BMP antagonists. In contrast, inDrosophilaembryos, Toll-like receptor (Tlr)-mediated NFκB activation initiates dorsal-ventral patterning, wherein Wnt-mediated negative feedback regulation of Tlr/NFκB generates a BMP antagonist-secreting signalling centre to control the dorsal-ventral pattern. Although both Wnt and BMP antagonist are conserved among species, the involvement of Tlr/NFκB and feedback regulation in vertebrate organizer formation remains unclear. By imaging and genetic modification, we reveal that a negative feedback loop between canonical and non-canonical Wnts and Tlr4/NFκB determines the size of zebrafish organizer, and that Tlr/NFκB and Wnts switch initial cue and feedback mediator roles betweenDrosophilaand zebrafish. Here, we show that canonical Wnt signalling stimulates the expression of the non-canonical Wnt5b ligand, activating the Tlr4 receptor to stimulate NFκB-mediated transcription of the Wnt antagonist frzb, restricting Wnt-dependent dorsal organizer formation.
Speos: an ensemble graph representation learning framework to predict core gene candidates for complex diseases
Authors: Ratajczak Florin , Joblin Mitchell , Hildebrandt Marcel , Ringsquandl Martin , Falter-Braun Pascal , Heinig Matthias 
Published: November 2023

AbstractUnderstanding phenotype-to-genotype relationships is a grand challenge of 21st century biology with translational implications. The recently proposed “omnigenic” model postulates that effects of genetic variation on traits are mediated bycore-genes and -proteins whose activities mechanistically influence the phenotype, whereasperipheralgenes encode a regulatory network that indirectly affects phenotypes via core gene products. Here, we develop a positive-unlabeled graph representation-learning ensemble-approach based on a nested cross-validation to predict core-like genes for diverse diseases using Mendelian disorder genes for training. Employing mouse knockout phenotypes for external validations, we demonstrate that core-like genes display several key properties of core genes: Mouse knockouts of genes corresponding to our most confident predictions give rise to relevant mouse phenotypes at rates on par with the Mendelian disorder genes, and all candidates exhibit core gene properties like transcriptional deregulation in disease and loss-of-function intolerance. Moreover, as predicted for core genes, our candidates are enriched for drug targets and druggable proteins. In contrast to Mendelian disorder genes the new core-like genes are enriched for druggable yet untargeted gene products, which are therefore attractive targets for drug development. Interpretation of the underlying deep learning model suggests plausible explanations for our core gene predictions in form of molecular mechanisms and physical interactions. Our results demonstrate the potential of graph representation learning for the interpretation of biological complexity and pave the way for studying core gene properties and future drug development.
Spatial transcriptomics uncover sucrose post-phloem transport during maize kernel development
Authors: Fu Yuxin , Xiao Wenxin , Tian Lang , Guo Liangxing , Ma Guangjin , Ji Chen , Huang Yongcai , Wang Haihai , Wu Xingguo , Yang Tao , Wang Jiechen , Wang Jirui , Wu Yongrui , Wang Wenqin 
Published: November 2023

AbstractMaize kernels are complex biological systems composed of three genetic sources, namely maternal tissues, progeny embryos, and progeny endosperms. The lack of gene expression profiles with spatial information has limited the understanding of the specific functions of each cell population, and hindered the exploration of superior genes in kernels. In our study, we conduct microscopic sectioning and spatial transcriptomics analysis during the grain filling stage of maize kernels. This enables us to visualize the expression patterns of all genes through electronical RNA in situ hybridization, and identify 11 cell populations and 332 molecular marker genes. Furthermore, we systematically elucidate the spatial storage mechanisms of the three major substances in maize kernels: starch, protein, and oil. These findings provide valuable insights into the functional genes that control agronomic traits in maize kernels.
Daily fluctuation of colonic microbiome in response to nutrient substrates in a pig model
Authors: Wang Hongyu , Xu Rongying , Li Qiuke , Su Yong , Zhu Weiyun 
Published: November 2023

AbstractStudies on rodents indicate the daily oscillations of the gut microbiota have biological implications for host. However, the responses of fluctuating gut microbes to the dynamic nutrient substrates are not fully clear. In the study, we found that the feed intake, nutrient substrates, microbiota and metabolites in the colon underwent asynchronous oscillation within a day. Short-chain fatty acids (SCFAs) including acetate, propionate, butyrate and valerate peaked during T24 ~ T27 (Timepoint 24, 12:00 pm, T27, 03:00 am) whereas branched SCFAs isobutyrate and isovalerate peaked during T09 ~ T12. Further extended local similarity analysis (eLSA) revealed that the fluctuation of feed intake dynamically correlated with the colonic carbon substrates which further influenced the oscillation of sugar metabolites and acetate, propionate, butyrate and valerate with a certain time shift. The relative abundance of primary degrader Ruminococcaceae taxa was highly related to the dynamics of the carbon substrates whereas the fluctuations of secondary degraders Lactobacillaceae and Streptococcaceae taxa were highly correlated with the sugar metabolites. Meanwhile, colonic nitrogen substrates were correlated with branched amino acids and the branched SCFAs. Furthermore, we validated the evolution of gut microbes under different carbohydrate and protein combinations by using an in vitro fermentation experiment. The study pictured the dynamics of the micro-ecological environment within a day which highlights the implications of the temporal dimension in studies related to the gut microbiota. Feed intake, more precisely substrate intake, is highly correlated with microbial evolution, which makes it possible to develop chronotherapies targeting the gut microbiota through nutrition intervention.
Prediction models for hormone receptor status in female breast cancer do not extend to males: further evidence of sex-based disparity in breast cancer
Authors: Chatterji Subarnarekha , Niehues Jan Moritz , van Treeck Marko , Loeffler Chiara Maria Lavinia , Saldanha Oliver Lester , Veldhuizen Gregory Patrick , Cifci Didem , Carrero Zunamys Itzell , Abu-Eid Rasha , Speirs Valerie , Kather Jakob Nikolas 
Published: November 2023

AbstractBreast cancer prognosis and management for both men and women are reliant upon estrogen receptor alpha (ERα) and progesterone receptor (PR) expression to inform therapy. Previous studies have shown that there are sex-specific binding characteristics of ERα and PR in breast cancer and, counterintuitively, ERα expression is more common in male than female breast cancer. We hypothesized that these differences could have morphological manifestations that are undetectable to human observers but could be elucidated computationally. To investigate this, we trained attention-based multiple instance learning prediction models for ERα and PR using H&E-stained images of female breast cancer from the Cancer Genome Atlas (TCGA) (n = 1085) and deployed them on external female (n = 192) and male breast cancer images (n = 245). Both targets were predicted in the internal (AUROC for ERα prediction: 0.86 ± 0.02, p < 0.001; AUROC for PR prediction = 0.76 ± 0.03, p < 0.001) and external female cohorts (AUROC for ERα prediction: 0.78 ± 0.03, p < 0.001; AUROC for PR prediction = 0.80 ± 0.04, p < 0.001) but not the male cohort (AUROC for ERα prediction: 0.66 ± 0.14, p = 0.43; AUROC for PR prediction = 0.63 ± 0.04, p = 0.05). This suggests that subtle morphological differences invisible upon visual inspection may exist between the sexes, supporting previous immunohistochemical, genomic, and transcriptomic analyses.
DOES - A multimodal dataset for supervised and unsupervised analysis of steel scrap
Authors: Schäfer Michael , Faltings Ulrike , Glaser Björn 
Published: November 2023

AbstractDOES- Dataset of European scrap classes. Today, scrap is already an important raw material for industry. Due to the transformation to green steel, the secondary raw material scrap will become increasingly important in the coming years. WithDOESa free dataset is presented, which represents common non-alloyed European scrap classes. Two important points were considered in this dataset. First, scrap oxidizes under normal external conditions and the visual appearance changes, which plays an important role in visual inspections. Therefore,DOESincludes scrap images of different degrees of corrosion attack. Second, images of scrap metal (mostly scrap piles) usually have no intrinsic order. For this reason, a technique to extract many overlapping rectangles from raw images was used, which can be used to train deep learning algorithms without any disadvantage. This dataset is very suitable to develop industrial applications or to research classification algorithms. The dataset was validated by experts and through machine learning models.
Daylong acoustic recordings of grazing and rumination activities in dairy cows
Authors: Martinez-Rau Luciano S. , Chelotti José O. , Ferrero Mariano , Utsumi Santiago A. , Planisich Alejandra M. , Vignolo Leandro D. , Giovanini Leonardo L. , Rufiner H. Leonardo , Galli Julio R. 
Published: November 2023

AbstractMonitoring livestock feeding behavior may help assess animal welfare and nutritional status, and to optimize pasture management. The need for continuous and sustained monitoring requires the use of automatic techniques based on the acquisition and analysis of sensor data. This work describes an open dataset of acoustic recordings of the foraging behavior of dairy cows. The dataset includes 708 h of daily records obtained using unobtrusive and non-invasive instrumentation mounted on five lactating multiparous Holstein cows continuously monitored for six non-consecutive days in pasture and barn. Labeled recordings precisely delimiting grazing and rumination bouts are provided for a total of 392 h and for over 6,200 ingestive and rumination jaw movements. Companion information on the audio recording quality and expert-generated labels is also provided to facilitate data interpretation and analysis. This comprehensive dataset is a useful resource for studies aimed at exploring new tools and solutions for precision livestock farming.
MultiXC-QM9: Large dataset of molecular and reaction energies from multi-level quantum chemical methods
Authors: Nandi Surajit , Vegge Tejs , Bhowmik Arghya 
Published: November 2023

AbstractWell curated extensive datasets have helped spur intense molecular machine learning (ML) method development activities over the last few years, encouraging nonchemists to be part of the effort as well. QM9 dataset is one of the benchmark databases for small molecules with molecular energies based on B3LYP functional. G4MP2 based energies of these molecules were published later. To enable a wide variety of ML tasks like transfer learning, delta learning, multitask learning, etc. with QM9 molecules, in this article, we introduce a new dataset with QM9 molecule energies estimated with 76 different DFT functionals and three different basis sets (228 energy numbers for each molecule). We additionally enumerated all possible A ↔ B monomolecular interconversions within the QM9 dataset and provided the reaction energies based on these 76 functionals, and basis sets. Lastly, we also provide the bond changes for all the 162 million reactions with the dataset to enable structure- and bond-based reaction energy prediction tools based on ML.
FIKElectricity: A Electricity Consumption Dataset from Three Restaurant Kitchens in Portugal
Authors: Pereira Lucas , Aguiar Vitor , Vasconcelos Fábio , Martins Ricardo , Garcês Toni , Morais Hugo 
Published: November 2023

AbstractIndustrial Kitchens are very energy-intensive businesses, consuming between five and seven times more energy per square meter than other commercial spaces like office spaces and retail stores. Still, very little research has been carried out on improving the energy efficiency of this industry. This paper presents the FIKElectricity dataset, a collection of electricity data from three Portuguese restaurant kitchens during their daily operation. The duration of the datasets spans three to four weeks in each industrial kitchen and comprises aggregated and individual appliance consumption, collected at 1 Hz and $$\frac{1}{5}$$

1

5

Hz, respectively. The public release of FIKElectricity is expected to draw more attention from the research community to this overlooked industrial sector. The data collection and post-processing methods are thoroughly described in this paper, as well as the dataset organization. Examples showing the dataset’s quality and instructions for its reuse are also provided.
Toll-like receptor 9-positive plasmacytoid dendritic cells promote Th17 immune responses in oral lichen planus stimulated by epithelium-derived cathepsin K
Authors: Miyahara Yuka , Chen Hu , Moriyama Masafumi , Mochizuki Keita , Kaneko Naoki , Haque A. S. M. Rafiul , Chinju Akira , Kai Kazuki , Sakamoto Mizuki , Kakizoe-Ishiguro Noriko , Yamauchi Masaki , Ogata Kenichi , Kiyoshima Tamotsu , Kawano Shintaro , Nakamura Seiji 
Published: November 2023

AbstractOral lichen planus (OLP) is a chronic inflammatory disease associated with T cell infiltration. The crosstalk between oral epithelium and mucosal T cells was considered to be crucial in the pathogenesis of OLP. Here, we selectively extracted the normal epithelium (NE) and lesional epithelium (LE) of buccal mucosa specimens from three patients with OLP by laser capture microdissection due to identify the pathogenic factors. Cathepsin K (CTSK) was identified as one of common upregulated genes in the LE by DNA microarray. Immunohistochemically, CTSK was distinctly detected in and around the LE, while it was rarely seen in the NE. Recent studies showed that CTSK enhanced Toll-like receptor 9 (TLR9) signaling in antigen-presenting cells, leading to Th17 cell differentiation. TLR9 expression mainly co-localized with CD123+ plasmacytoid dendritic cells (pDCs). The number of RORγt-positive cells correlated with that of CTSK-positive cells in OLP tissues. CD123+ pDCs induced the production of Th17-related cytokines (IL-6, IL-23, and TGF-β) upon stimulation with TLR9 agonist CpG DNA. Moreover, single cell RNA-sequencing analysis revealed that TLR9-positive pDCs enhanced in genes associated with Th17 cell differentiation in comparison with TLR9-negative pDCs. CTSK could induce Th17-related production of CD123+ pDCs via TLR9 signaling to promote the pathogenesis of OLP.
Analytical study of the spherical hydrostatic bearing dynamics through a unique technique
Authors: Elescandarany Ahmad Waguih 
Published: November 2023

AbstractBecause of their self-alignment property and design simplicity, the spherical hydrostatic bearings have the advantage over the other bearing configurations. Their static and dynamic performances have been intensively studied. Focusing on the bearing dynamic performance, it could be realized that the researchers used to mechanically excite the bearing in the experimental studies and perturb the rotor (spatial finite displacement) in the theoretical studies, observing its behavior and expressing it by dynamic stiffness and damping coefficient. Owing to a lack of information on bearing oscillation, this study adopts a new method to analyze this bearing behavior theoretically and grasp its nature. Unusually, the bearing vibration is studied hydro-dynamically rather than mechanically, showing the effect of eccentricity, inertia, restrictor type, seat configuration, and the supply pressure on the performance. New and unique formulas have been derived to predict the frequency, stiffness, and dampness, explaining how these parameters create the bearing self-alignment property. Some thrust bearings, designed with different techniques, have been examined where the results show vibration even in the bearing’s stationary state. Also, the newly derived formulas could precisely predict the rotation and rotational speed of the Kugel ball (recently proved and designed as a spherical hydrostatic bearing).
Microcracking of strawberry fruit cuticles: mechanism and factors
Authors: Hurtado Grecia , Knoche Moritz 
Published: November 2023

AbstractMicroscopic cracks in the cuticle (microcracks) are the first symptom of the strawberry fruit disorder ‘water soaking’ in which the fruit surface appears watery, translucent, and pale. Water soaking severely impacts fruit quality. The objective was to investigate the factors and mechanisms of cuticular microcracking in strawberry. Fluorescence microscopy revealed numerous microcracks in the achene depressions, on the rims between depressions and at the bases of trichomes. Microcracks in the achene depressions and on the rims were either parallel or transversely oriented relative to a radius drawn from the rim to the point of attachment of the achene. In the achene depression, the frequency of microcracks with parallel orientation decreased from the calyx end of the fruit, towards the fruit tip, while the frequency of those with transverse orientation remained constant. Most microcracks occurred above the periclinal cell walls of the epidermal cells. The long axes of the epidermal cells were primarily parallel-oriented. Microcracking increased during fruit development. Cuticle mass per fruit remained constant as fruit surface area increased but cuticle thickness decreased. When fruit developed under high relative humidity (RH) conditions, the cuticle had more microcracks than under low RH conditions. Exposing the fruit surface to increasing RHs, increased microcracking, especially above 75% RH. Liquid-phase water on the fruit surface was markedly more effective in inducing microcracking than high vapor-phase water (high RH). The results demonstrate that a combination of surface area growth strain and water exposure is causal in inducing microcracking of the strawberry cuticle.
Low extracellular magnesium induces phenotypic and metabolic alterations in C2C12-derived myotubes
Authors: Zocchi Monica , Bartolini Marco , Maier Jeanette A. , Castiglioni Sara 
Published: November 2023

AbstractMagnesium (Mg) has a pivotal role in upholding skeletal muscle health and optimizing performance. Its deficiency decreases muscle strength, and an association has been reported between Mg intake and sarcopenia. To gain a comprehensive understanding of the repercussions arising from low Mg concentrations on muscle behavior, we employed an in vitro model utilizing C2C12-derived myotubes. Myotubes cultured in low Mg show a significant reduction of thickness and a concomitant down-regulation of myosin heavy chain (MyHC), Myog and Myomixer. In parallel, myotubes shape their metabolism. Glycolysis is inhibited and beta-oxidation increases. These metabolic changes are consistent with the increase of MyHC I (slow) vs. MyHC II (fast) expression. We identified an essential player in these changes, namely nitric oxide (NO), as the increase in NO production appeared to orchestrate the observed modifications in myotube behavior and metabolism under low Mg conditions. Understanding these underlying mechanisms may pave the way for targeted interventions to ameliorate muscle-related conditions associated with Mg deficiency and contribute to enhancing overall muscle health and function.
Vortex clustering in trapped Bose-Einstein condensates
Authors: Easton Thomas , Kokmotos Marios , Barontini Giovanni 
Published: November 2023

AbstractWe numerically study the formation of vortex clusters in trapped Bose-Einstein condensates where vortices are initially imprinted in a line. We show that such a system exhibits a rich phenomenology depending on the distance at which the vortices are imprinted and their number. In particular we observe that it is possible to obtain systems of twin vortex clusters, twin vortex clusters with orbiting satellite vortices, and triplets of clusters. By using a clustering algorithm we are able to quantitatively describe the formation and dynamics of the clusters. We finally utilise an analytical model to determine the range of parameters for which the clustering occurs. Our work sets the stage for possible experimental implementations where the formation of vortex clusters and more exotic bound states of vortices could be observed.
Handwritten digit recognition by spin waves in a Skyrmion reservoir
Authors: Lee Mu-Kun , Mochizuki Masahito 
Published: November 2023

AbstractBy performing numerical simulations for the handwritten digit recognition task, we demonstrate that a magnetic skyrmion lattice confined in a thin-plate magnet possesses high capability of reservoir computing. We obtain a high recognition rate of more than 88%, higher by about 10% than a baseline taken as the echo state network model. We find that this excellent performance arises from enhanced nonlinearity in the transformation which maps the input data onto an information space with higher dimensions, carried by interferences of spin waves in the skyrmion lattice. Because the skyrmions require only application of static magnetic field instead of nanofabrication for their creation in contrast to other spintronics reservoirs, our result consolidates the high potential of skyrmions for application to reservoir computing devices.