bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced optical conductivity and many-body effects in strongly-driven photo-excited semi-metallic graphite
Authors: Sidiropoulos T. P. H. , Di Palo N. , Rivas D. E. , Summers A. , Severino S. , Reduzzi M. , Biegert J. 
Published: November 2023

AbstractThe excitation of quasi-particles near the extrema of the electronic band structure is a gateway to electronic phase transitions in condensed matter. In a many-body system, quasi-particle dynamics are strongly influenced by the electronic single-particle structure and have been extensively studied in the weak optical excitation regime. Yet, under strong optical excitation, where light fields coherently drive carriers, the dynamics of many-body interactions that can lead to new quantum phases remain largely unresolved. Here, we induce such a highly non-equilibrium many-body state through strong optical excitation of charge carriers near the van Hove singularity in graphite. We investigate the system’s evolution into a strongly-driven photo-excited state with attosecond soft X-ray core-level spectroscopy. We find an enhancement of the optical conductivity of nearly ten times the quantum conductivity and pinpoint it to carrier excitations in flat bands. This interaction regime is robust against carrier-carrier interaction with coherent optical phonons acting as an attractive force reminiscent of superconductivity. The strongly-driven non-equilibrium state is markedly different from the single-particle structure and macroscopic conductivity and is a consequence of the non-adiabatic many-body state.
Fostering temporal crop diversification to reduce pesticide use
Authors: Guinet Maé , Adeux Guillaume , Cordeau Stéphane , Courson Emeric , Nandillon Romain , Zhang Yaoyun , Munier-Jolain Nicolas 
Published: November 2023

AbstractTemporal crop diversification could reduce pesticide use by increasing the proportion of crops with low pesticide use (dilution effects) or enhancing the regulation of pests, weeds and diseases (regulation effects). Here, we use the French National DEPHY Network to compare pesticide use between 16 main crops (dilution effect) and to assess whether temporal crop taxonomic and functional diversification, as implemented in commercial farms specialized in arable field crops, could explain variability in total pesticide use within 16 main crops (regulation effect). The analyses are based on 14,556 crop observations belonging to 1334 contrasted cropping systems spanning the diversity of French climatic regions. We find that cropping systems with high temporal crop diversity generally include crops with low pesticide use. For several crops, total pesticide use is reduced under higher temporal crop functional diversity, temporal crop taxonomic diversity, or both. Higher cover crop frequency increases total pesticide use through an increase in herbicide use. Further studies are required to identify crop sequences that maximize regulation and dilution effects while achieving other facets of cropping system multiperformance.
SND1 binds to ERG and promotes tumor growth in genetic mouse models of prostate cancer
Authors: Liao Sheng-You , Rudoy Dmytro , Frank Sander B. , Phan Luan T. , Klezovitch Olga , Kwan Julian , Coleman Ilsa , Haffner Michael C. , Li Dapei , Nelson Peter S. , Emili Andrew , Vasioukhin Valeri 
Published: November 2023

AbstractSND1 and MTDH are known to promote cancer and therapy resistance, but their mechanisms and interactions with other oncogenes remain unclear. Here, we show that oncoprotein ERG interacts with SND1/MTDH complex through SND1’s Tudor domain. ERG, an ETS-domain transcription factor, is overexpressed in many prostate cancers. Knocking down SND1 in human prostate epithelial cells, especially those overexpressing ERG, negatively impacts cell proliferation. Transcriptional analysis shows substantial overlap in genes regulated by ERG and SND1. Mechanistically, we show that ERG promotes nuclear localization of SND1/MTDH. Forced nuclear localization of SND1 prominently increases its growth promoting function irrespective of ERG expression. In mice, prostate-specific Snd1 deletion reduces cancer growth and tumor burden in a prostate cancer model (PB-Cre/Ptenflox/flox/ERG mice), Moreover, we find a significant overlap between prostate transcriptional signatures of ERG and SND1. These findings highlight SND1’s crucial role in prostate tumorigenesis, suggesting SND1 as a potential therapeutic target in prostate cancer.
Maternal vitamin B1 is a determinant for the fate of primordial follicle formation in offspring
Authors: Liu Wen-Xiang , Liu Hai-Ning , Weng Zhan-Ping , Geng Qi , Zhang Yue , Li Ya-Feng , Shen Wei , Zhou Yang , Zhang Teng 
Published: November 2023

AbstractThe mediation of maternal-embryonic cross-talk via nutrition and metabolism impacts greatly on offspring health. However, the underlying key interfaces remain elusive. Here, we determined that maternal high-fat diet during pregnancy in mice impaired preservation of the ovarian primordial follicle pool in female offspring, which was concomitant with mitochondrial dysfunction of germ cells. Furthermore, this occurred through a reduction in maternal gut microbiota-related vitamin B1 while the defects were restored via vitamin B1 supplementation. Intriguingly, vitamin B1 promoted acetyl-CoA metabolism in offspring ovaries, contributing to histone acetylation and chromatin accessibility at the promoters of cell cycle-related genes, enhancement of mitochondrial function, and improvement of granulosa cell proliferation. In humans, vitamin B1 is downregulated in the serum of women with gestational diabetes mellitus. In this work, these findings uncover the role of the non-gamete transmission of maternal high-fat diet in influencing offspring oogenic fate. Vitamin B1 could be a promising therapeutic approach for protecting offspring health.
Fate specification is spatially intermingled across planarian stem cells
Authors: Park Chanyoung , Owusu-Boaitey Kwadwo E. , Valdes Giselle M. , Reddien Peter W. 
Published: November 2023

AbstractRegeneration requires mechanisms for producing a wide array of cell types. Neoblasts are stem cells in the planarian Schmidtea mediterranea that undergo fate specification to produce over 125 adult cell types. Fate specification in neoblasts can be regulated through expression of fate-specific transcription factors. We utilize multiplexed error-robust fluorescence in situ hybridization (MERFISH) and whole-mount FISH to characterize fate choice distribution of stem cells within planarians. Fate choices are often made distant from target tissues and in a highly intermingled manner, with neighboring neoblasts frequently making divergent fate choices for tissues of different location and function. We propose that pattern formation is driven primarily by the migratory assortment of progenitors from mixed and spatially distributed fate-specified stem cells and that fate choice involves stem-cell intrinsic processes.
CELLULAR, A Cell Autophagy Imaging Dataset
Authors: Al Outa Amani , Hicks Steven , Thambawita Vajira , Andresen Siri , Enserink Jorrit M. , Halvorsen Pål , Riegler Michael A. , Knævelsrud Helene 
Published: November 2023

AbstractCells in living organisms are dynamic compartments that continuously respond to changes in their environment to maintain physiological homeostasis. While basal autophagy exists in cells to aid in the regular turnover of intracellular material, autophagy is also a critical cellular response to stress, such as nutritional depletion. Conversely, the deregulation of autophagy is linked to several diseases, such as cancer, and hence, autophagy constitutes a potential therapeutic target. Image analysis to follow autophagy in cells, especially on high-content screens, has proven to be a bottleneck. Machine learning (ML) algorithms have recently emerged as crucial in analyzing images to efficiently extract information, thus contributing to a better understanding of the questions at hand. This paper presents CELLULAR, an open dataset consisting of images of cells expressing the autophagy reporter mRFP-EGFP-Atg8a with cell-specific segmentation masks. Each cell is annotated into either basal autophagy, activated autophagy, or unknown. Furthermore, we introduce some preliminary experiments using the dataset that can be used as a baseline for future research.
Chromosome genome assembly and whole genome sequencing of 110 individuals of Conogethes punctiferalis (Guenée)
Authors: Gao Bojia , Peng Yan , Jin Minghui , Zhang Lei , Han Xiu , Wu Chao , Yuan He , Awawing Andongma , Zheng Fangqiang , Li Xiangdong , Xiao Yutao 
Published: November 2023

AbstractThe yellow peach moth, Conogethes punctiferalis, is a highly polyphagous pest widespread in eastern and southern Asia. It demonstrates a unique ability to adapt to rotten host fruits and displays resistance to pathogenic microorganisms, including fungi. However, the lack of available genomic resources presents a challenge in comprehensively understanding the evolution of its innate immune genes. Here, we report a high-quality chromosome-level reference genome for C. punctiferalis utilizing PacBio HiFi sequencing and Hi-C technology. The genome assembly was 494 Mb in length with a contig N50 of 3.25 Mb. We successfully anchored 1,226 contigs to 31 pseudochromosomes. Our BUSCO analysis further demonstrated a gene coverage completeness of 96.3% in the genome assembly. Approximately 43% repeat sequences and 21,663 protein-coding genes were identified. In addition, we resequenced 110 C. punctiferalis individuals from east China, achieving an average coverage of 18.4 × and identifying 5.8 million high-quality SNPs. This work provides a crucial resource for understanding the evolutionary mechanism of C. punctiferalis’ innate immune system and will help in developing new antibacterial drugs.
Canada Source Watershed Polygons (Can-SWaP): A dataset for the protection of Canada’s municipal water supply
Authors: Robinne François-Nicolas , Lamache Chloé , Thompson Daniel K. , Leach Jason A. , Bladon Kevin D. 
Published: November 2023

AbstractOver 80% of municipal (i.e., excluding industrial and agricultural) water use in Canada comes from streams, lakes, and reservoirs. These freshwater bodies and their catchments require adequate protection to secure drinking water supply for Canadians. Canada, like most countries, lacks a consolidated national dataset of municipal catchments, arguably due to gaps in data availability. Against this backdrop, we present the Canada Source Watershed Polygons dataset, or Can-SWaP. Can-SWaP was created using point locations of more than 3,300 municipal water licences defining rights to surface water withdrawal. Where possible, the resulting 1,574 catchments were assessed for accuracy in spatial coverage against provincial and local datasets. Each watershed in Can-SWaP has an estimated water volume used for municipal water purposes derived from licencing data, and several variables from RiverATLAS for investigating the integrity of surface drinking water sources in Canada. Furthermore, basing our method on the HydroSHEDS suite of global products offers a robust framework for the production of other national datasets following an established international standard.
Automating weighing of faces and voices based on cue saliency in trustworthiness impressions
Authors: Vives Marc-Lluís , Frances Candice , Baus Cristina 
Published: November 2023

AbstractWhen encountering people, their faces are usually paired with their voices. We know that if the face looks familiar, and the voice is high-pitched, the first impression will be positive and trustworthy. But, how do we integrate these two multisensory physical attributes? Here, we explore 1) the automaticity of audiovisual integration in shaping first impressions of trustworthiness, and 2) the relative contribution of each modality in the final judgment. We find that, even though participants can focus their attention on one modality to judge trustworthiness, they fail to completely filter out the other modality for both faces (Experiment 1a) and voices (Experiment 1b). When asked to judge the person as a whole, people rely more on voices (Experiment 2) or faces (Experiment 3). We link this change to the distinctiveness of each cue in the stimulus set rather than a general property of the modality. Overall, we find that people weigh faces and voices automatically based on cue saliency when forming trustworthiness impressions.
Just-in-time deep learning for real-time X-ray computed tomography
Authors: Graas Adriaan , Coban Sophia Bethany , Batenburg K. Joost , Lucka Felix 
Published: November 2023

AbstractReal-time X-ray tomography pipelines, such as implemented by RECAST3D, compute and visualize tomographic reconstructions in milliseconds, and enable the observation of dynamic experiments in synchrotron beamlines and laboratory scanners. For extending real-time reconstruction by image processing and analysis components, Deep Neural Networks (DNNs) are a promising technology, due to their strong performance and much faster run-times compared to conventional algorithms. DNNs may prevent experiment repetition by simplifying real-time steering and optimization of the ongoing experiment. The main challenge of integrating DNNs into real-time tomography pipelines, however, is that they need to learn their task from representative databeforethe start of the experiment. In scientific environments, such training data may not exist, and other uncertain and variable factors, such as the set-up configuration, reconstruction parameters, or user interaction, cannot easily be anticipated beforehand, either. To overcome these problems, we developedjust-in-time learning, an online DNN training strategy that takes advantage of the spatio-temporal continuity of consecutive reconstructions in the tomographic pipeline. This allows training and deploying comparatively small DNNs during the experiment. We provide software implementations, and study the feasibility and challenges of the approach by training the self-supervised Noise2Inverse denoising task with X-ray data replayed from real-world dynamic experiments.
Morphogenetic identification of a new record Deudorix livia (Lepidoptera: Lycaenidae) in Assiut Governorate of Northern Upper Egypt
Authors: Abdel-Galil Farouk A. , Mousa Sara E. , Abou-Elhagag Gaber H. , Ahmed Ahmed M. M. , Al-Farga Ammar , Allam Mohammad , Mahmoud Mervat A. B. 
Published: November 2023

AbstractDeudorix livia (Klug, 1834) (Lepidoptera: Lycaenidae) is one of the most serious lepidopteran insect pests attacking pomegranate fruit around the world, including Egypt (Assiut Governorate, Upper Egypt). To create an effective program (IPM) to control such harmful pests, accurate identification of the pest morphology and genetic structure is essential. Studies on the morphogenetics of this pest are scarce. So, the goal of this research is to identify it both morphologically and genetically. Pomegranate butterfly immature stages were collected from infested pomegranate fruits and reared in the laboratory until the adult's emergence. By using light and scanning electron microscopy, some morphological structures of males and females were studied. DNA was extracted from the legs of a pomegranate butterfly adult. Also, PCR was conducted by using the mitochondrial CO1 gene for sequencing and phylogenetic tests. The results show that the body scales are a mixture of dark and light gray on the dorsal side and white on the ventral side in both sexes. The average male body length (BL) was 11.674 ± 0.299 mm and was 11.458 ± 1.001 mm for the females. The wing venation is similar in both sexes. For the first time, a partial sequence of the mitochondrial CO1 gene in D. livia was deposited in GenBank (MW463927).
Hemokinin-1 is a mediator of chronic restraint stress-induced pain
Authors: Borbély Éva , Kecskés Angéla , Kun József , Kepe Eszter , Fülöp Barbara , Kovács-Rozmer Katalin , Scheich Bálint , Renner Éva , Palkovits Miklós , Helyes Zsuzsanna 
Published: November 2023

AbstractThe Tac4 gene-derived hemokinin-1 (HK-1) binds to the NK1 receptor, similarly to Substance P, and plays a role in acute stress reactions and pain transmission in mice. Here we investigated Tac4 mRNA expression in stress and pain-related regions and its involvement in chronic restraint stress-evoked behavioral changes and pain using Tac4 gene-deleted (Tac4-/-) mice compared to C57Bl/6 wildtypes (WT). Tac4 mRNA was detected by in situ hybridization RNAscope technique. Touch sensitivity was assessed by esthesiometry, cold tolerance by paw withdrawal latency from 0°C water. Anxiety was evaluated in the light–dark box (LDB) and open field test (OFT), depression-like behavior in the tail suspension test (TST). Adrenal and thymus weights were measured at the end of the experiment. We found abundant Tac4 expression in the hypothalamic–pituitary–adrenal axis, but Tac4 mRNA was also detected in the hippocampus, amygdala, somatosensory and piriform cortices in mice, and in the frontal regions and the amygdala in humans. In Tac4-/- mice of both sexes, stress-induced mechanical, but not cold hyperalgesia was significantly decreased compared to WTs. Stress-induced behavioral alterations were mild or absent in male WT animals, while significant changes of these parameters could be detected in females. Thymus weight decrease can be observed in both sexes. Higher baseline anxiety and depression-like behaviors were detected in male but not in female HK-1-deficient mice, highlighting the importance of investigating both sexes in preclinical studies. We provided the first evidence for the potent nociceptive and stress regulating effects of HK-1 in chronic restraint stress paradigm. Identification of its targets might open new perspectives for therapy of stress-induced pain.
Experimental and computational methods to highlight behavioural variations in TonB-dependent transporter expression in Pseudomonas aeruginosa versus siderophore concentration
Authors: Hubert Thibaut , Madec Morgan , Schalk Isabelle J. 
Published: November 2023

AbstractIron is a key nutrient for bacterial growth. The source can be either heme or siderophore-Fe complexes. Siderophores are small molecules synthesized by bacteria to scavenge iron from the bacterial environment. The pathogen Pseudomonas aeruginosa can express at least 15 different iron uptake pathways and all but one involve a TonB-dependent transporter (TBDT) for the uptake of iron across the outer membrane. Little is known about how bacteria modulate and adapt the expression of their different iron import pathways according to their environment. Here, we have developed fluorescent reporters between the promoter region of genes encoding a TBDT and the fluorescent reporter mCherry. With these constructs, we can follow the expression of TBDTs under different growth conditions. Mathematical modelling of the data obtained showed the transcription and expression of the gene encoding the TBDT PfeA to have a sigmoidal shape, whereas it was logarithmic for the TBDT gene foxA. Maximum transcription for pfeA was reached in the presence of 3 µM enterobactin, the siderophore recognized by PfeA, whereas the maximum was not reached for foxA with 100 µM nocardamine, the siderophore of FoxA.
Feasibility of resuscitative transesophageal echocardiography at out-of-hospital emergency scenes of cardiac arrest
Authors: Krammel Mario , Hamp Thomas , Hafner Christina , Magnet Ingrid , Poppe Michael , Marhofer Peter 
Published: November 2023

AbstractGuidelines recommend the use of ultrasound in cardiac arrest. Transthoracic echocardiography, has issues with image quality and by increasing hands-off times during resuscitation. We assessed the feasibility of transesophageal echocardiography (TEE), which does not have both problems, at out-of-hospital cardiac arrest (OHCA) emergency scenes. Included were 10 adults with non-traumatic OHCA in Vienna, Austria. An expert in emergency ultrasound was dispatched to the scenes in addition to the resuscitation team. Feasibility was defined as the ability to collect specific items of information by TEE within 10 min. Descriptive statistics were compiled and hands-off times were compared to a historical control group. TEE examinations were feasible in 9 of 10 cases and prompted changes in clinical management in 2 cases (cardiac tamponade: n = 1; right ventricular dilatation: n = 1). Their mean time requirement was 5.1 ± 1.7 (2.8–8.0) min, and image quality was invariably rated as excellent or good during both compressions and pauses. No TEE-related complications, or interferences with activities of advanced life support were observed. The hands-off times during resuscitation were comparable to a historical control group not involving ultrasound (P = 0.24). Given these feasibility results, we expect that TEE can be used routinely at OHCA emergency scenes.
Isothermal chemical denaturation assay for monitoring protein stability and inhibitor interactions
Authors: Mahran Randa , Vello Niklas , Komulainen Anita , Malakoutikhah Morteza , Härmä Harri , Kopra Kari 
Published: November 2023

AbstractThermal shift assay (TSA) with altered temperature has been the most widely used method for monitoring protein stability for drug research. However, there is a pressing need for isothermal techniques as alternatives. This urgent demand arises from the limitations of TSA, which can sometimes provide misleading ranking of protein stability and fail to accurately reflect protein stability under physiological conditions. Although differential scanning fluorimetry has significantly improved throughput in comparison to differential scanning calorimetry and differential static light scattering throughput, all these methods exhibit moderate sensitivity. In contrast, current isothermal chemical denaturation (ICD) techniques may not offer the same throughput capabilities as TSA, but it provides more precise information about protein stability and interactions. Unfortunately, ICD also suffers from limited sensitivity, typically in micromolar range. We have developed a novel method to overcome these challenges, namely throughput and sensitivity. The novel Förster Resonance Energy Transfer (FRET)-Probe as an external probe is highly applicable to isothermal protein stability monitoring but also to conventional TSA. We have investigated ICD for multiple proteins with focus on KRASG12C with covalent inhibitors and three chemical denaturants performed at nanomolar protein concentration. Data showed corresponding inhibitor-induced stabilization of KRASG12C to those reported by nucleotide exchange assay.
3D image scanning of gravel soil using in-situ X-ray computed tomography
Authors: Matsumura Satoshi , Kondo Akihiko , Nakamura Keita , Mizutani Takaaki , Kohama Eiji , Wada Kenji , Kobayashi Taizo , Roy Nimisha , Frost J. David 
Published: November 2023

AbstractA typical ground investigation for characterizing geotechnical properties of soil requires sampling soils to test in a laboratory. Laboratory X-ray computed tomography (CT) has been used to non-destructively observe soils and characterize their properties using image processing, numerical analysis, or three-dimensional (3D) printing techniques based on scanned images; however, if it becomes possible to scan the soils in the ground, it may enable the characterization without sampling them. In this study, an in-situ X-ray CT scanning system comprising a drilling machine with an integrated CT scanner was developed. A model test was conducted on gravel soil to verify if the equipment can drill and scan the soil underground. Moreover, image processing was performed on acquired 3D CT images to verify the image quality; the particle morphology (particle size and shape characteristics) was compared with the results obtained for projected particles captured in a two-dimensional (2D) manner by a digital camera. The equipment successfully drilled to a target depth of 800 mm, and the soil was scanned at depths of 700, 750, and 800 mm. Image processing results showed a reasonable agreement between the 3D and 2D particle morphology images, and confirmed the feasibility of the in-situ X-ray CT scanning system.