bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensing Optical Fibers for Earthquake Source Characterization Using Raw DAS Records
Authors: Strumia Claudio , Trabattoni Alister , Supino Mariano , Baillet Marie , Rivet Diane , Festa Gaetano 
Published: January 2024

AbstractDistributed Acoustic Sensing (DAS) is becoming a powerful tool for earthquake monitoring, providing continuous strain‐rate records of seismic events along fiber optic cables. However, the use of standard seismological techniques for earthquake source characterization requires the conversion of data in ground motion quantities. In this study we provide a new formulation for far‐field strain radiation emitted by a seismic rupture, which allows to directly analyze DAS data in their native physical quantity. This formulation naturally accounts for the complex directional sensitivity of the fiber to body waves and to the shallow layering beneath the cable. In this domain, we show that the spectral amplitude of the strain integral is related to the Fourier transform of the source time function, and its modeling allows to determine the source parameters. We demonstrate the validity of the technique on two case‐studies, where source parameters are consistent with estimates from standard seismic instruments in magnitude range 2.0–4.3. When analyzing events from a 1‐month DAS survey in Chile, moment‐corner frequency distribution shows scale invariant stress drop estimates, with an average of Δσ = (0.8 ± 0.6) MPa. Analysis of DAS data acquired in the Southern Apennines shows a dominance of the local attenuation that masks the effective corner frequency of the events. After estimating the local attenuation coefficient, we were able to retrieve the corner frequencies for the largest magnitude events in the catalog. Overall, this approach shows the capability of DAS technology to depict the characteristic scales of seismic sources and the released moment.
The Impact of Single Group Flashes on Geostationary Lightning Mapper Data
Authors: Mach Douglas M. , Bateman Monte G. 
Published: January 2024

AbstractThe Geostationary Lightning Mapper (GLM) is an instrument on the NOAA Geostationary Operational Environmental Satellites‐R (GOES‐R) Series. The GLM data are processed by the Lightning Cluster Filter Algorithm which filters the GLM data and clusters it into a series of events, groups, and flashes. One of the current filters in the GLM algorithm (as of June 2023) removes all flashes that have only a single group. Combining the flashes (including the flashes with only single group) from two of the GLMs (the GLM on GOES‐16 and the GLM on GOES‐17) in the region where they overlap produces a unique data set of coincident flashes (detected by both GLMs) and non‐coincident flashes (detected by only one GLM). Coincident flashes detected by both GLMs are very unlikely to be from noise sources. This data set allows us to estimate the impact of the single group flashes on the Detection Efficiency (DE) and the False Alarm Rate (FAR). We find that the single group flash filter does greatly improve the FAR but does slightly decrease the DE. Subsequent analysis shows that some of the removed flashes with single groups are from true lightning. A simple modification to the single group flash filter to only remove flashes with a single event increases the FAR without a corresponding improvement in DE. A more complex algorithm is needed to recover the single group flashes that are likely from lightning without adding back single group flashes that are from noise sources.
Local Controls on Near‐Surface Glacier Cooling Under Warm Atmospheric Conditions
Authors: Shaw Thomas E. , Buri Pascal , McCarthy Michael , Miles Evan S. , Pellicciotti Francesca 
Published: January 2024

AbstractThe near‐surface boundary layer can mediate the response of mountain glaciers to external climate, cooling the overlying air and promoting a density‐driven glacier wind. The fundamental processes are conceptually well understood, though the magnitudes of cooling and presence of glacier winds are poorly quantified in space and time, increasing the forcing uncertainty for melt models. We utilize a new data set of on‐glacier meteorological measurements on three neighboring glaciers in the Swiss Alps to explore their distinct response to regional climate under the extreme 2022 summer. We find that synoptic wind origins and local terrain modifications, not only glacier size, play an important role in the ability of a glacier to cool the near‐surface air. Warm air intrusions from valley or synoptically‐driven winds onto the glacier can occur between ∼19% and 64% of the time and contribute between 3% and 81% of the total sensible heat flux to the surface during warm afternoon hours, depending on the fetch of the glacier flowline and its susceptibility to boundary layer erosion. In the context of extreme summer warmth, indicative of future conditions, the boundary layer cooling (up to 6.5°C cooler than its surroundings) and resultant katabatic wind flow are highly heterogeneous between the study glaciers, highlighting the complex and likely non‐linear response of glaciers to an uncertain future.
TrkB-dependent regulation of molecular signaling across septal cell types
Authors: Rodriguez Lionel A. , Tran Matthew Nguyen , Garcia-Flores Renee , Oh Seyun , Phillips Robert A. , Pattie Elizabeth A. , Divecha Heena R. , Kim Sun Hong , Shin Joo Heon , Lee Yong Kyu , Montoya Carly , Jaffe Andrew E. , Collado-Torres Leonardo , Page Stephanie C. , Martinowich Keri 
Published: January 2024

AbstractThe lateral septum (LS), a GABAergic structure located in the basal forebrain, is implicated in social behavior, learning, and memory. We previously demonstrated that expression of tropomyosin kinase receptor B (TrkB) in LS neurons is required for social novelty recognition. To better understand molecular mechanisms by which TrkB signaling controls behavior, we locally knocked down TrkB in LS and used bulk RNA-sequencing to identify changes in gene expression downstream of TrkB. TrkB knockdown induces upregulation of genes associated with inflammation and immune responses, and downregulation of genes associated with synaptic signaling and plasticity. Next, we generated one of the first atlases of molecular profiles for LS cell types using single nucleus RNA-sequencing (snRNA-seq). We identified markers for the septum broadly, and the LS specifically, as well as for all neuronal cell types. We then investigated whether the differentially expressed genes (DEGs) induced by TrkB knockdown map to specific LS cell types. Enrichment testing identified that downregulated DEGs are broadly expressed across neuronal clusters. Enrichment analyses of these DEGs demonstrated that downregulated genes are uniquely expressed in the LS, and associated with either synaptic plasticity or neurodevelopmental disorders. Upregulated genes are enriched in LS microglia, associated with immune response and inflammation, and linked to both neurodegenerative disease and neuropsychiatric disorders. In addition, many of these genes are implicated in regulating social behaviors. In summary, the findings implicate TrkB signaling in the LS as a critical regulator of gene networks associated with psychiatric disorders that display social deficits, including schizophrenia and autism, and with neurodegenerative diseases, including Alzheimer’s.
Dysregulated immune and metabolic pathways are associated with poor survival in adult acute myeloid leukemia with CEBPA bZIP in-frame mutations
Authors: Tien Feng-Ming , Yao Chi-Yuan , Tsai Xavier Cheng-Hong , Lo Min-Yen , Chen Chien-Yuan , Lee Wan-Hsuan , Lin Chien-Chin , Kuo Yuan-Yeh , Peng Yen-Ling , Tseng Mei-Hsuan , Wu Yu-Sin , Liu Ming-Chih , Lin Liang-In , Chuang Ming-Kai , Ko Bor-Sheng , Yao Ming , Tang Jih-Luh , Chou Wen-Chien , Hou Hsin-An , Tien Hwei-Fang 
Published: January 2024

AbstractAcute myeloid leukemia (AML) with CEBPA bZIP in-frame mutations (CEBPAbZIP-inf) is classified within the favorable-risk group by the 2022 European LeukemiaNet (ELN-2022). However, heterogeneous clinical outcomes are still observed in these patients. In this study, we aimed to investigate the mutation profiles and transcriptomic patterns associated with poor outcomes in patients with CEBPAbZIP-inf. One hundred and thirteen CEBPAbZIP-inf patients were identified in a cohort of 887 AML patients homogeneously treated with intensive chemotherapy. Concurrent WT1 or DNMT3A mutations significantly predicted worse survival in AML patients with CEBPAbZIP-inf. RNA-sequencing analysis revealed an enrichment of interferon (IFN) signaling and metabolic pathways in those with a shorter event-free survival (EFS). CEBPAbZIP-inf patients with a shorter EFS had higher expression of IFN-stimulated genes (IRF2, IRF5, OAS2, and IFI35). Genes in mitochondrial complexes I (NDUFA12 and NDUFB6) and V (ATP5PB and ATP5IF1) were overexpressed and were associated with poorer survival, and the results were independently validated in the TARGET AML cohort. In conclusion, concurrent WT1 or DNMT3A mutations and a dysregulated immune and metabolic state were correlated with poor survival in patients with CEBPAbZIP-inf, and upfront allogeneic transplantation may be indicated for better long-term disease control.
Exogenous carbon monoxide promotes GPX4-dependent ferroptosis through ROS/GSK3β axis in non-small cell lung cancer
Authors: Cao Wei , Sun Mingyu , Yu K. N. , Zhao Lele , Feng Yue , Tan Chunhua , Yang Miaomiao , Wang Ying , Zhu Fengqin , Chen Lianjun , Nie Lili , Zhao Ye , Chen Guodong , Han Wei 
Published: January 2024

AbstractThe gas therapy is drawing increasing attention in the treatment of many diseases including cancer. As one of gas signaling molecules, carbon monoxide (CO) has been proved to exert anti-cancer effects via triggering multiple cell death types, such as autophagy, apoptosis and necrosis. Here, we showed that low concentration CO delivered from CO-releasing molecule 3 (CORM-3) effectively induced ferroptosis, known as a novel proinflammatory programmed cell death, in vitro and in vivo. Mechanistically, we found that CO triggered ferroptosis by modulating the ROS/GSK3β/GPX4 signaling pathway, resulting in the accumulation of lipid hydroperoxides and the occurrence of ferroptosis. We think our findings provide novel insights into the anti-cancer mechanisms of CO, and suggest that CO could potentially be exploited as a novel ferroptosis inducer for cancer treatment in the future.
Non-alcoholic fatty liver disease promotes liver metastasis of colorectal cancer via fatty acid synthase dependent EGFR palmitoylation
Authors: Zhang Chi , Zhang Yue , Dong Yan , Zi Ruiyang , Wang Yijie , Chen Yanrong , Liu Chengxiang , Wang Junyi , Wang Xuesong , Li Jianjun , Liang Houjie , Ou Juanjuan 
Published: January 2024

AbstractLiver metastasis is the major reason for most of colorectal cancer (CRC) related deaths. Accumulating evidence indicates that CRC patients with non-alcoholic fatty liver disease (NAFLD) are at a greater risk of developing liver metastasis. With the growing prevalence of NAFLD, a better understanding of the molecular mechanism in NAFLD-driven CRC liver metastasis is needed. In this study, we demonstrated that NAFLD facilitated CRC liver metastasis as a metabolic disorder and promoted the stemness of metastatic CRC cells for their colonization and outgrowth in hepatic niches. Metabolically, the lipid-rich microenvironment in NAFLD activated de novo palmitate biosynthesis in metastatic CRC cells via upregulating fatty acid synthase (FASN). Moreover, increased intracellular palmitate bioavailability promoted EGFR palmitoylation to enhance its protein stability and plasma membrane localization. Furthermore, we demonstrated that the FDA-approved FASN inhibitor orlistat could reduce NAFLD-activated endogenous palmitate production, thus inhibiting palmitoylation of EGFR to suppress CRC cell stemness and restrict liver metastasis in synergy with conventional chemotherapy. These findings reveal that the NAFLD metabolic microenvironment boosts endogenous palmitate biosynthesis in metastatic CRC cells and promotes cell stemness via EGFR palmitoylation, and FASN inhibitor orlistat could be a candidate adjuvant drug to suppress liver metastasis in CRC patients with NAFLD.
A dynamic knowledge graph approach to distributed self-driving laboratories
Authors: Bai Jiaru , Mosbach Sebastian , Taylor Connor J. , Karan Dogancan , Lee Kok Foong , Rihm Simon D. , Akroyd Jethro , Lapkin Alexei A. , Kraft Markus 
Published: January 2024

AbstractThe ability to integrate resources and share knowledge across organisations empowers scientists to expedite the scientific discovery process. This is especially crucial in addressing emerging global challenges that require global solutions. In this work, we develop an architecture for distributed self-driving laboratories within The World Avatar project, which seeks to create an all-encompassing digital twin based on a dynamic knowledge graph. We employ ontologies to capture data and material flows in design-make-test-analyse cycles, utilising autonomous agents as executable knowledge components to carry out the experimentation workflow. Data provenance is recorded to ensure its findability, accessibility, interoperability, and reusability. We demonstrate the practical application of our framework by linking two robots in Cambridge and Singapore for a collaborative closed-loop optimisation for a pharmaceutically-relevant aldol condensation reaction in real-time. The knowledge graph autonomously evolves toward the scientist’s research goals, with the two robots effectively generating a Pareto front for cost-yield optimisation in three days.
Miniaturized spectrometer with intrinsic long-term image memory
Authors: Wu Gang , Abid Mohamed , Zerara Mohamed , Cho Jiung , Choi Miri , Ó Coileáin Cormac , Hung Kuan-Ming , Chang Ching-Ray , Shvets Igor V. , Wu Han-Chun 
Published: January 2024

AbstractMiniaturized spectrometers have great potential for use in portable optoelectronics and wearable sensors. However, current strategies for miniaturization rely on von Neumann architectures, which separate the spectral sensing, storage, and processing modules spatially, resulting in high energy consumption and limited processing speeds due to the storage-wall problem. Here, we present a miniaturized spectrometer that utilizes a single SnS2/ReSe2 van der Waals heterostructure, providing photodetection, spectrum reconstruction, spectral imaging, long-term image memory, and signal processing capabilities. Interface trap states are found to induce a gate-tunable and wavelength-dependent photogating effect and a non-volatile optoelectronic memory effect. Our approach achieves a footprint of 19 μm, a bandwidth from 400 to 800 nm, a spectral resolution of 5 nm, and a > 104 s long-term image memory. Our single-detector computational spectrometer represents a path beyond von Neumann architectures.
Total syntheses of Tetrodotoxin and 9-epiTetrodotoxin
Authors: Chen Peihao , Wang Jing , Zhang Shuangfeng , Wang Yan , Sun Yuze , Bai Songlin , Wu Qingcui , Cheng Xinyu , Cao Peng , Qi Xiangbing 
Published: January 2024

AbstractTetrodotoxin and congeners are specific voltage-gated sodium channel blockers that exhibit remarkable anesthetic and analgesic effects. Here, we present a scalable asymmetric syntheses of Tetrodotoxin and 9-epiTetrodotoxin from the abundant chemical feedstock furfuryl alcohol. The optically pure cyclohexane skeleton is assembled via a stereoselective Diels-Alder reaction. The dense heteroatom substituents are established sequentially by a series of functional group interconversions on highly oxygenated cyclohexane frameworks, including a chemoselective cyclic anhydride opening, and a decarboxylative hydroxylation. An innovative SmI2-mediated concurrent fragmentation, an oxo-bridge ring opening and ester reduction followed by an Upjohn dihydroxylation deliver the highly oxidized skeleton. Ruthenium-catalyzed oxidative alkyne cleavage and formation of the hemiaminal and orthoester under acidic conditions enable the rapid assembly of Tetrodotoxin, anhydro-Tetrodotoxin, 9-epiTetrodotoxin, and 9-epi lactone-Tetrodotoxin.
Manually annotated and curated Dataset of diverse Weed Species in Maize and Sorghum for Computer Vision
Authors: Genze Nikita , Vahl Wouter K. , Groth Jennifer , Wirth Maximilian , Grieb Michael , Grimm Dominik G. 
Published: January 2024

AbstractSustainable weed management strategies are critical to feeding the world’s population while preserving ecosystems and biodiversity. Therefore, site-specific weed control strategies based on automation are needed to reduce the additional time and effort required for weeding. Machine vision-based methods appear to be a promising approach for weed detection, but require high quality data on the species in a specific agricultural area. Here we present a dataset, the Moving Fields Weed Dataset (MFWD), which captures the growth of 28 weed species commonly found in sorghum and maize fields in Germany. A total of 94,321 images were acquired in a fully automated, high-throughput phenotyping facility to track over 5,000 individual plants at high spatial and temporal resolution. A rich set of manually curated ground truth information is also provided, which can be used not only for plant species classification, object detection and instance segmentation tasks, but also for multiple object tracking.
Antirepressor specificity is shaped by highly efficient dimerization of the staphylococcal pathogenicity island regulating repressors: Stl repressor dimerization perturbed by dUTPases
Authors: Nyíri Kinga , Gál Enikő , Laczkovich Máté , Vértessy Beáta G. 
Published: January 2024

AbstractThe excision and replication, thus the life cycle of pathogenicity islands in staphylococci are regulated by Stl master repressors that form strong dimers. It has been recently shown that SaPIbov1-Stl dimers are separated during the activation of the Staphylococcus aureus pathogenicity island (SaPI) transcription via helper phage proteins. To understand the mechanism of this regulation, a quantitative analysis of the dimerization characteristics is required. Due to the highly efficient dimerization process, such an analysis has to involve specific solutions that permit relevant experiments to be performed. In the present work, we focused on two staphylococcal Stls associated with high biomedical interest, namely Stl proteins of Staphylococcus aureus bov1 and Staphylococcus hominis ShoCI794_SEPI pathogenicity islands. Exploiting the interactions of these two Stl proteins with their antirepressor-mimicking interaction partners allowed precise determination of the Stl dimerization constant in the subnanomolar range.
Task design for crowdsourced glioma cell annotation in microscopy images
Authors: Schwarze Svea , Schaadt Nadine S. , Sobotta Viktor M. G. , Spicher Nicolai , Skripuletz Thomas , Esmaeilzadeh Majid , Krauss Joachim K. , Hartmann Christian , Deserno Thomas M. , Feuerhake Friedrich 
Published: January 2024

AbstractCrowdsourcing has been used in computational pathology to generate cell and cell nuclei annotations for machine learning. Herein, we broaden its scope to the previously unsolved challenging task of glioma cell detection. This requires multiplexed immunofluorescence microscopy due to diffuse invasiveness and exceptional similarity between glioma cells and reactive astrocytes. In four pilot experiments, we iteratively developed a task design enabling high-quality annotations by crowdworkers on Amazon Mechanical Turk. We applied majority or weighted vote and validated them against ground truth in the final setting. On the base of a YOLO convolutional neural network architecture, we used these consensus labels for training with different image representations regarding colors, intensities, and immmunohistochemical marker combinations. A crowd of 712 workers defined aggregated point annotations in 235 images with an average$$F_1$$F1score of 0.627 for majority vote. The networks resulted in acceptable$$F_1$$F1scores up to 0.69 for YOLOv8 on average and indicated first evidence for transferability to images lacking tumor markers, especially in IDH-wildtype glioblastoma. Our work confirms feasibility of crowdsourcing to generate labels suitable for training of machine learning tools in the challenging and clinically relevant use case of glioma microenvironment.
CRP, IL-1α, IL-1β, and IL-6 levels and the risk of breast cancer: a two-sample Mendelian randomization study
Authors: Cui Yongjia , Cui Shasha , Lu Wenping , Wang Ya’nan , Zhuo Zhili , Wang Ruipeng , Zhang Dongni , Wu Xiaoqing , Chang Lei , Zuo Xi , Zhang Weixuan , Mei Heting , Zhang Mengfan 
Published: January 2024

AbstractEpidemiological studies have reported a positive association between chronic inflammation and cancer risk. However, the causal association between chronic inflammation and breast cancer (BC) risk remains unclear. Here, we performed a Mendelian randomization study to investigate the etiological role of chronic inflammation in BC risk. We acquired data regarding C-reactive protein (CRP), interleukin (IL)-1a, IL-1b, and IL-6 expression and BC related to single nucleotide polymorphisms (SNPs) from two larger consortia (the genome-wide association studies and the Breast Cancer Association Consortium). Next, we conducted the two-sample Mendelian randomization study to investigate the relationship of the abovementioned inflammatory factors with the incidence of BC. We found that genetically predicted CRP, IL-6, and IL-1a levels did not increase BC incidence (odds ratio (OR)CRP 1.06, 95% confidence interval (CI) 0.98–1.12, P = 0.2059, ORIL-6 1.05, 95% CI 0.95–1.16, P = 0.3297 and ORIL-1a 1.01, 95% CI 0.99–1.03, P = 0.2167). However, in subgroup analysis, genetically predicted IL-1b levels increased ER + BC incidence (OR 1.15, 95% CI 1.03–1.27, P = 0.0088). Our study suggested that genetically predicted IL-1b levels were found to increase ER + BC susceptibility. However, due to the support of only one SNP, heterogeneity and pleiotropy tests cannot be performed, which deserves further research.
Impaired motor inhibition during perceptual inhibition in older, but not younger adults: a psychophysiological study
Authors: Healey Rebecca , Goldsworthy Megan , Salomoni Sauro , Weber Simon , Kemp Sarah , Hinder Mark R. , St George Rebecca J. 
Published: January 2024

AbstractThe prefrontal cortex (PFC) governs the ability to rapidly cancel planned movements when no longer appropriate (motor inhibition) and ignore distracting stimuli (perceptual inhibition). It is unclear to what extent these processes interact, and how they are impacted by age. The interplay between perceptual and motor inhibition was investigated using a Flanker Task, a Stop Signal Task and a combined Stop Signal Flanker Task in healthy young (n = 33, Mean = 24 years) and older adults (n = 32, Mean = 71 years). PFC activity was measured with functional near-infrared spectroscopy (fNIRS), while electromyography (EMG) measured muscle activity in the fingers used to respond to the visual cues. Perceptual inhibition (the degree to which incongruent flankers slowed response time to a central cue) and motor inhibition (the speed of cancellation of EMG activation following stop cues) independently declined with age. When both processes were engaged together, PFC activity increased for both age groups, however only older adults exhibited slower motor inhibition. The results indicate that cortical upregulation was sufficient to compensate for the increased task demands in younger but not older adults, suggesting potential resource sharing and neural limitations particularly in older adults.