bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuronal activation sequences in lateral prefrontal cortex encode visuospatial working memory during virtual navigation
Authors: Busch Alexandra , Roussy Megan , Luna Rogelio , Leavitt Matthew L. , Mofrad Maryam H. , Gulli Roberto A. , Corrigan Benjamin , Mináč Ján , Sachs Adam J. , Palaniyappan Lena , Muller Lyle , Martinez-Trujillo Julio C. 
Published: May 2024

AbstractWorking memory (WM) is the ability to maintain and manipulate information ‘in mind’. The neural codes underlying WM have been a matter of debate. We simultaneously recorded the activity of hundreds of neurons in the lateral prefrontal cortex of male macaque monkeys during a visuospatial WM task that required navigation in a virtual 3D environment. Here, we demonstrate distinct neuronal activation sequences (NASs) that encode remembered target locations in the virtual environment. This NAS code outperformed the persistent firing code for remembered locations during the virtual reality task, but not during a classical WM task using stationary stimuli and constraining eye movements. Finally, blocking NMDA receptors using low doses of ketamine deteriorated the NAS code and behavioral performance selectively during the WM task. These results reveal the versatility and adaptability of neural codes supporting working memory function in the primate lateral prefrontal cortex.
Lipidome atlas of the adult human brain
Authors: Osetrova Maria , Tkachev Anna , Mair Waltraud , Guijarro Larraz Patricia , Efimova Olga , Kurochkin Ilia , Stekolshchikova Elena , Anikanov Nickolay , Foo Juat Chin , Cazenave-Gassiot Amaury , Mitina Aleksandra , Ogurtsova Polina , Guo Song , Potashnikova Daria M. , Gulin Alexander A. , Vasin Alexander A. , Sarycheva Anastasia , Vladimirov Gleb , Fedorova Maria , Kostyukevich Yury , Nikolaev Evgeny , Wenk Markus R. , Khrameeva Ekaterina E. , Khaitovich Philipp 
Published: May 2024

AbstractLipids are the most abundant but poorly explored components of the human brain. Here, we present a lipidome map of the human brain comprising 75 regions, including 52 neocortical ones. The lipidome composition varies greatly among the brain regions, affecting 93% of the 419 analyzed lipids. These differences reflect the brain’s structural characteristics, such as myelin content (345 lipids) and cell type composition (353 lipids), but also functional traits: functional connectivity (76 lipids) and information processing hierarchy (60 lipids). Combining lipid composition and mRNA expression data further enhances functional connectivity association. Biochemically, lipids linked with structural and functional brain features display distinct lipid class distribution, unsaturation extent, and prevalence of omega-3 and omega-6 fatty acid residues. We verified our conclusions by parallel analysis of three adult macaque brains, targeted analysis of 216 lipids, mass spectrometry imaging, and lipidome assessment of sorted murine neurons.
Above-room-temperature chiral skyrmion lattice and Dzyaloshinskii–Moriya interaction in a van der Waals ferromagnet Fe3−xGaTe2
Authors: Zhang Chenhui , Jiang Ze , Jiang Jiawei , He Wa , Zhang Junwei , Hu Fanrui , Zhao Shishun , Yang Dongsheng , Liu Yakun , Peng Yong , Yang Hongxin , Yang Hyunsoo 
Published: May 2024

AbstractSkyrmions in existing 2D van der Waals (vdW) materials have primarily been limited to cryogenic temperatures, and the underlying physical mechanism of the Dzyaloshinskii–Moriya interaction (DMI), a crucial ingredient for stabilizing chiral skyrmions, remains inadequately explored. Here, we report the observation of Néel-type skyrmions in a vdW ferromagnet Fe3−xGaTe2 above room temperature. Contrary to previous assumptions of centrosymmetry in Fe3−xGaTe2, the atomic-resolution scanning transmission electron microscopy reveals that the off-centered FeΙΙ atoms break the spatial inversion symmetry, rendering it a polar metal. First-principles calculations further elucidate that the DMI primarily stems from the Te sublayers through the Fert–Lévy mechanism. Remarkably, the chiral skyrmion lattice in Fe3−xGaTe2 can persist up to 330 K at zero magnetic field, demonstrating superior thermal stability compared to other known skyrmion vdW magnets. This work provides valuable insights into skyrmionics and presents promising prospects for 2D material-based skyrmion devices operating beyond room temperature.
A variational expectation-maximization framework for balanced multi-scale learning of protein and drug interactions
Authors: Rao Jiahua , Xie Jiancong , Yuan Qianmu , Liu Deqin , Wang Zhen , Lu Yutong , Zheng Shuangjia , Yang Yuedong 
Published: May 2024

AbstractProtein functions are characterized by interactions with proteins, drugs, and other biomolecules. Understanding these interactions is essential for deciphering the molecular mechanisms underlying biological processes and developing new therapeutic strategies. Current computational methods mostly predict interactions based on either molecular network or structural information, without integrating them within a unified multi-scale framework. While a few multi-view learning methods are devoted to fusing the multi-scale information, these methods tend to rely intensively on a single scale and under-fitting the others, likely attributed to the imbalanced nature and inherent greediness of multi-scale learning. To alleviate the optimization imbalance, we present MUSE, a multi-scale representation learning framework based on a variant expectation maximization to optimize different scales in an alternating procedure over multiple iterations. This strategy efficiently fuses multi-scale information between atomic structure and molecular network scale through mutual supervision and iterative optimization. MUSE outperforms the current state-of-the-art models not only in molecular interaction (protein-protein, drug-protein, and drug-drug) tasks but also in protein interface prediction at the atomic structure scale. More importantly, the multi-scale learning framework shows potential for extension to other scales of computational drug discovery.
Emergence of decadal linkage between Western Australian coast and Western–central tropical Pacific
Authors: Ding Yuewen , Lin Pengfei , Liu Hailong , Wu Bo , Li Yuanlong , Chen Lin , Zhang Lei , Hu Aixue , Wang Yiming , Yao Yiyun , Zhao Bowen , Bai Wenrong , Han Weiqing 
Published: May 2024

AbstractThe impact of interbasin linkage on the weather/climate and ecosystems is significantly broader and profounder than that of only appearing in an individual basin. Here, we reveal that a decadal linkage of sea surface temperature (SST) has emerged between western Australian coast and western–central tropical Pacific since 1985, associated with continuous intensification of decadal variabilities (8–16 years). The rapid SST changes in both tropical Indian Ocean and Indo-Pacific warm pool in association to greenhouse gases and volcanoes are emerging factors resulting in enhanced decadal co-variabilities between these two regions since 1985. These SST changes induce enhanced convection variability over the Maritime Continent, leading to stronger easterlies in the western–central tropical Pacific during the warm phase off western Australian coast. The above changes bring about cooling in the western–central tropical Pacific and strengthened Leeuwin Current and anomalous cyclonic wind off western Australian coast, and ultimately resulting in enhanced coupling between these two regions. Our results suggest that enhanced decadal interbasin connections can offer further understanding of decadal changes under future warmer conditions.
Widespread 2013-2020 decreases and reduction challenges of organic aerosol in China
Authors: Chen Qi , Miao Ruqian , Geng Guannan , Shrivastava Manish , Dao Xu , Xu Bingye , Sun Jiaqi , Zhang Xian , Liu Mingyuan , Tang Guigang , Tang Qian , Hu Hanwen , Huang Ru-Jin , Wang Hao , Zheng Yan , Qin Yue , Guo Song , Hu Min , Zhu Tong 
Published: May 2024

AbstractHigh concentrations of organic aerosol (OA) occur in Asian countries, leading to great health burdens. Clean air actions have resulted in significant emission reductions of air pollutants in China. However, long-term nation-wide trends in OA and their causes remain unknown. Here, we present both observational and model evidence demonstrating widespread decreases with a greater reduction in primary OA than in secondary OA (SOA) in China during the period of 2013 to 2020. Most of the decline is attributed to reduced residential fuel burning while the interannual variability in SOA may have been driven by meteorological variations. We find contrasting effects of reducing NOx and SO2 on SOA production which may have led to slight overall increases in SOA. Our findings highlight the importance of clean energy replacements in multiple sectors on achieving air-quality targets because of high OA precursor emissions and fluctuating chemical and meteorological conditions.
Metabolism of l-arabinose converges with virulence regulation to promote enteric pathogen fitness
Authors: Cottam Curtis , White Rhys T. , Beck Lauren C. , Stewart Christopher J. , Beatson Scott A. , Lowe Elisabeth C. , Grinter Rhys , Connolly James P. R. 
Published: May 2024

AbstractVirulence and metabolism are often interlinked to control the expression of essential colonisation factors in response to host-associated signals. Here, we identified an uncharacterised transporter of the dietary monosaccharide ʟ-arabinose that is widely encoded by the zoonotic pathogen enterohaemorrhagic Escherichia coli (EHEC), required for full competitive fitness in the mouse gut and highly expressed during human infection. Discovery of this transporter suggested that EHEC strains have an enhanced ability to scavenge ʟ-arabinose and therefore prompted us to investigate the impact of this nutrient on pathogenesis. Accordingly, we discovered that ʟ-arabinose enhances expression of the EHEC type 3 secretion system, increasing its ability to colonise host cells, and that the underlying mechanism is dependent on products of its catabolism rather than the sensing of ʟ-arabinose as a signal. Furthermore, using the murine pathogen Citrobacter rodentium, we show that ʟ-arabinose metabolism provides a fitness benefit during infection via virulence factor regulation, as opposed to supporting pathogen growth. Finally, we show that this mechanism is not restricted to ʟ-arabinose and extends to other pentose sugars with a similar metabolic fate. This work highlights the importance integrating central metabolism with virulence regulation in order to maximise competitive fitness of enteric pathogens within the host-niche.
Enantioselective nickel-catalyzed anodic oxidative dienylation and allylation reactions
Authors: Zhang Qinglin , Zhang Jiayin , Zhu Wangjie , Lu Ruimin , Guo Chang 
Published: May 2024

AbstractPrecision control of stereochemistry in radical reactions remains a formidable challenge due to the prevalence of incidental racemic background reactions resulting from undirected substrate oxidation in the absence of chiral induction. In this study, we devised an thoughtful approach—electricity-driven asymmetric Lewis acid catalysis—to circumvent this impediment. This methodology facilitates both asymmetric dienylation and allylation reactions, resulting in the formation of all-carbon quaternary stereocenters and demonstrating significant potential in the modular synthesis of functional and chiral benzoxazole-oxazoline (Boox) ligands. Notably, the involvement of chiral Lewis acids in both the electrochemical activation and stereoselectivity-defining radical stages offers innovative departures for designing single electron transfer-based reactions, significantly underscoring the relevance of this approach as a multifaceted and universally applicable strategy for various fields of study, including electrosynthesis, organic chemistry, and drug discovery.
The SPECTRAL Perfusion Arm Clamping dAtaset (SPECTRALPACA) for video-rate functional imaging of the skin
Authors: Ayala Leonardo , Mindroc-Filimon Diana , Rees Maike , Hübner Marco , Sellner Jan , Seidlitz Silvia , Tizabi Minu , Wirkert Sebastian , Seitel Alexander , Maier-Hein Lena 
Published: May 2024

AbstractSpectral imaging has the potential to become a key technique in interventional medicine as it unveils much richer optical information compared to conventional RBG (red, green, and blue)-based imaging. Thus allowing for high-resolution functional tissue analysis in real time. Its higher information density particularly shows promise for the development of powerful perfusion monitoring methods for clinical use. However, even though in vivo validation of such methods is crucial for their clinical translation, the biomedical field suffers from a lack of publicly available datasets for this purpose. Closing this gap, we generated the SPECTRAL Perfusion Arm Clamping dAtaset (SPECTRALPACA). It comprises ten spectral videos (∼20 Hz, approx. 20,000 frames each) systematically recorded of the hands of ten healthy human participants in different functional states. We paired each spectral video with concisely tracked regions of interest, and corresponding diffuse reflectance measurements recorded with a spectrometer. Providing the first openly accessible in human spectral video dataset for perfusion monitoring, our work facilitates the development and validation of new functional imaging methods.
The AusTraits plant dictionary
Authors: Wenk Elizabeth H. , Sauquet Hervé , Gallagher Rachael V. , Brownlee Rowan , Boettiger Carl , Coleman David , Yang Sophie , Auld Tony , Barrett Russell , Brodribb Timothy , Choat Brendan , Dun Lily , Ellsworth David , Gosper Carl , Guja Lydia , Jordan Gregory J. , Le Breton Tom , Leigh Andrea , Lu-Irving Patricia , Medlyn Belinda , Nolan Rachael , Ooi Mark , Sommerville Karen D. , Vesk Peter , White Matthew , Wright Ian J. , Falster Daniel S. 
Published: May 2024

AbstractTraits with intuitive names, a clear scope and explicit description are essential for all trait databases. The lack of unified, comprehensive, and machine-readable plant trait definitions limits the utility of trait databases, including reanalysis of data from a single database, or analyses that integrate data across multiple databases. Both can only occur if researchers are confident the trait concepts are consistent within and across sources. Here we describe the AusTraits Plant Dictionary (APD), a new data source of terms that extends the trait definitions included in a recent trait database, AusTraits. The development process of the APD included three steps: review and formalisation of the scope of each trait and the accompanying trait description; addition of trait metadata; and publication in both human and machine-readable forms. Trait definitions include keywords, references, and links to related trait concepts in other databases, enabling integration of AusTraits with other sources. The APD will both improve the usability of AusTraits and foster the integration of trait data across global and regional plant trait databases.
DCTPep, the data of cancer therapy peptides
Authors: Sun Xin , Liu Yanchao , Ma Tianyue , Zhu Ning , Lao Xingzhen , Zheng Heng 
Published: May 2024

AbstractWith the discovery of the therapeutic activity of peptides, they have emerged as a promising class of anti-cancer agents due to their specific targeting, low toxicity, and potential for high selectivity. In particular, as peptide-drug conjugates enter clinical, the coupling of targeted peptides with traditional chemotherapy drugs or cytotoxic agents will become a new direction in cancer treatment. To facilitate the drug development of cancer therapy peptides, we have constructed DCTPep, a novel, open, and comprehensive database for cancer therapy peptides. In addition to traditional anticancer peptides (ACPs), the peptide library also includes peptides related to cancer therapy. These data were collected manually from published research articles, patents, and other protein or peptide databases. Data on drug library include clinically investigated and/or approved peptide drugs related to cancer therapy, which mainly come from the portal websites of drug regulatory authorities and organisations in different countries and regions. DCTPep has a total of 6214 entries, we believe that DCTPep will contribute to the design and screening of future cancer therapy peptides.
Oropharyngeal swallowing hydrodynamics of thin and mildly thick liquids in an anatomically accurate throat-epiglottis model
Authors: Seifelnasr Amr , Ding Peng , Si Xiuhua , Biondi Andres , Xi Jinxiang 
Published: May 2024

AbstractUnderstanding the mechanisms underlying dysphagia is crucial in devising effective, etiology-centered interventions. However, current clinical assessment and treatment of dysphagia are still more symptom-focused due to our limited understanding of the sophisticated symptom-etiology associations causing swallowing disorders. This study aimed to elucidate the mechanisms giving rise to penetration flows into the laryngeal vestibule that results in aspirations with varying symptoms. Methods: Anatomically accurate, transparent throat models were prepared with a 45° down flapped epiglottis to simulate the instant of laryngeal closure during swallowing. Fluid bolus dynamics were visualized with fluorescent dye from lateral, rear, front, and endoscopic directions to capture key hydrodynamic features leading to aspiration. Three influencing factors, fluid consistency, liquid dispensing site, and dispensing speed, were systemically evaluated on their roles in liquid aspirations. Results: Three aspiration mechanisms were identified, with liquid bolus entering the airway through (a) the interarytenoid notch (notch overflow), (b) cuneiform tubercle recesses (recess overflow), and (c) off-edge flow underneath the epiglottis (off-edge capillary flow). Of the three factors considered, liquid viscosity has the most significant impact on aspiration rate, followed by the liquid dispensing site and the dispensing speed. Water had one order of magnitude higher aspiration risks than 1% w/v methyl cellulose solution, a mildly thick liquid. Anterior dispensing had higher chances for aspiration than posterior oropharyngeal dispensing for both liquids and dispensing speeds considered. The effects of dispending speed varied. A lower speed increased aspiration for anterior-dispensed liquids due to increased off-edge capillary flows, while it significantly reduced aspiration for posterior-dispensed liquids due to reduced notch overflows. Visualizing swallowing hydrodynamics from multiple orientations facilitates detailed site-specific inspections of aspiration mechanisms.
Integration of bioinformatics analysis, molecular docking and animal experiments to study the therapeutic mechanisms of berberine against allergic rhinitis
Authors: Luo Gaoqing , Gao Ming , Lin Qinghua 
Published: May 2024

AbstractAllergic rhinitis is a prevalent inflammatory condition that impacts individuals of all age groups. Despite reports indicating the potential of berberine in alleviating allergic rhinitis symptoms, the specific molecular mechanisms and therapeutic targets of berberine remain unclear. This research aims to explore the pharmacological mechanism of berberine in the treatment of allergic rhinitis through bioinformatic analyses and experimental validation. The research utilized public databases to identify potential targets of berberine. Furthermore, differentially expressed genes (DEGs) related to allergic rhinitis were pinpointed from the GSE52804 dataset. Through bioinformatics techniques, the primary targets were discovered and key KEGG and GO-BP pathways were established. To confirm the therapeutic mechanisms of berberine on allergic rhinitis, an OVA-induced allergic rhinitis model was developed using guinea pigs. We identified 32 key genes responsible for the effectiveness of berberine in treating allergic rhinitis. In addition, five central genes (Alb, Il6, Tlr4, Ptas2, and Il1b) were pinpointed. Further examination using KEGG and GO-BP pathways revealed that the main targets were primarily involved in pathways such as NF-kappa B, IL-17, TNF, and inflammatory response. Molecular docking analysis demonstrated that berberine exhibited strong affinity towards these five key targets. Furthermore, the expression levels of IL-6, TLR4, PTGS2, and IL-1β were significantly upregulated in the model group but downregulated following berberine treatment. This research has revealed the mechanism through which berberine combats allergic rhinitis and has identified its potential to regulate pathways linked to inflammation. These discoveries provide valuable insights for the development of novel medications for the treatment of allergic rhinitis.
An effective ensemble learning approach for classification of glioma grades based on novel MRI features
Authors: Hassan Mohammed Falih , Al-Zurfi Ahmed Naser , Abed Mohammed Hamzah , Ahmed Khandakar 
Published: May 2024

AbstractThe preoperative diagnosis of brain tumors is important for therapeutic planning as it contributes to the tumors’ prognosis. In the last few years, the development in the field of artificial intelligence and machine learning has contributed greatly to the medical area, especially the diagnosis of the grades of brain tumors through radiological images and magnetic resonance images. Due to the complexity of tumor descriptors in medical images, assessing the accurate grade of glioma is a major challenge for physicians. We have proposed a new classification system for glioma grading by integrating novel MRI features with an ensemble learning method, called Ensemble Learning based on Adaptive Power Mean Combiner (EL-APMC). We evaluate and compare the performance of the EL-APMC algorithm with twenty-one classifier models that represent state-of-the-art machine learning algorithms. Results show that the EL-APMC algorithm achieved the best performance in terms of classification accuracy (88.73%) and F1-score (93.12%) over the MRI Brain Tumor dataset called BRATS2015. In addition, we showed that the differences in classification results among twenty-two classifier models have statistical significance. We believe that the EL-APMC algorithm is an effective method for the classification in case of small-size datasets, which are common cases in medical fields. The proposed method provides an effective system for the classification of glioma with high reliability and accurate clinical findings.