bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Study on Three Autoencoder‐Based Deep Learning Algorithms for Geochemical Anomaly Identification
Authors: Feng Bin , Chen Lirong , Xu Yongyang , Zhang Yu 
Published: November 2022

AbstractDeep autoencoder (AE) networks show a powerful ability for geochemical anomaly identification. Because of little contribution to the AE network, small probability samples (again, please check this) having comparatively high reconstructed errors can be recognized by the trained model as anomalous samples. However, different autoencoder networks have different abilities for anomaly identification. To test these methods for geochemical anomaly identification, we based our study on stream sediment data of the Cu‐Zn‐Ag metallogenic area in southwest Fujian province as samples. Three unsupervised deep learning models: the autoencoder (AE), multi‐convolutional autoencoder (MCAE), and fusion convolutional autoencoder (FCAE), were used to extract the combined structural, spatial distribution, and mixed features of multiple‐elements. The results showed that the anomalous area delineated by the FCAE model had the best consistency with the known copper mineral occurrences, followed by the MCAE and AE models, with area under the curve values (AUC) of 0.80, 0.78, and 0.61, respectively. FCAE and AE were insensitive to changes in convolution window size, while MCAE extracted more spatial distribution or mixed features. Overall, FCAE focused more on structural distribution or mixed features, combining the advantages of both MCAE and AE. Therefore, FCAE performed best among the three deep learning methods. This study provides a practical basis for selecting and constructing geochemical anomaly recognition models based on deep learning algorithms.
Decoding the mechanism of hypertension through multiomics profiling
Authors: Adua Eric 
Published: November 2022

AbstractHypertension, characterised by a constant high blood pressure, is the primary risk factor for multiple cardiovascular events and a major cause of death in adults. Excitingly, innovations in high-throughput technologies have enabled the global exploration of the whole genome (genomics), revealing dysregulated genes that are linked to hypertension. Moreover, post-genomic biomarkers, from the emerging fields of transcriptomics, proteomics, glycomics and lipidomics, have provided new insights into the molecular underpinnings of hypertension. In this paper, we review the pathophysiology of hypertension, and highlight the multi-omics approaches for hypertension prediction and diagnosis.
Large-scale brain network dynamics in very preterm children and relationship with socio-emotional outcomes: an exploratory study
Authors: Siffredi Vanessa , Liverani Maria Chiara , Freitas Lorena G. A. , Tadros D. , Farouj Y. , Borradori Tolsa Cristina , Van De Ville Dimitri , Hüppi Petra Susan , Ha-Vinh Leuchter Russia 
Published: November 2022

AbstractBackgroundChildren born very preterm (VPT; <32 weeks’ gestation) are at high risk of neurodevelopmental and behavioural difficulties associated with atypical brain maturation, including socio-emotional difficulties. The analysis of large-scale brain network dynamics during rest allows us to investigate brain functional connectivity and its association with behavioural outcomes.MethodsDynamic functional connectivity was extracted by using the innovation-driven co-activation patterns framework in VPT and full-term children aged 6–9 to explore changes in spatial organisation, laterality and temporal dynamics of spontaneous large-scale brain activity (VPT,n = 28; full-term,n = 12). Multivariate analysis was used to explore potential biomarkers for socio-emotional difficulties in VPT children.ResultsThe spatial organisation of the 13 retrieved functional networks was comparable across groups. Dynamic features and lateralisation of network brain activity were also comparable for all brain networks. Multivariate analysis unveiled group differences in associations between dynamical functional connectivity parameters with socio-emotional abilities.ConclusionIn this exploratory study, the group differences observed might reflect reduced degrees of maturation of functional architecture in the VPT group in regard to socio-emotional abilities. Dynamic features of functional connectivity could represent relevant neuroimaging markers and inform on potential mechanisms through which preterm birth leads to neurodevelopmental and behavioural disorders.ImpactSpatial organisation of the retrieved resting-state networks was comparable between school-aged very preterm and full-term children.Dynamic features and lateralisation of network brain activity were also comparable across groups.Multivariate pattern analysis revealed different patterns of association between dynamical functional connectivity parameters and socio-emotional abilities in the very preterm and full-term groups.Findings suggest a reduced degree of maturation of the functional architecture in the very preterm group in association with socio-emotional abilities.
MARCH5 regulates mitotic apoptosis through MCL1-dependent and independent mechanisms
Authors: Wang Yang , Poon Randy Y. C. 
Published: November 2022

AbstractThe anti-apoptotic MCL1 is critical for delaying apoptosis during mitotic arrest. MCL1 is degraded progressively during mitotic arrest, removing its anti-apoptotic function. We found that knockout of components of ubiquitin ligases including APC/C, SCF complexes, and the mitochondrial ubiquitin ligase MARCH5 did not prevent mitotic degradation of MCL1. Nevertheless, MARCH5 determined the initial level of MCL1–NOXA network upon mitotic entry and hence the window of time during MCL1 was present during mitotic arrest. Paradoxically, although knockout of MARCH5 elevated mitotic MCL1, mitotic apoptosis was in fact enhanced in a BAK-dependent manner. Mitotic apoptosis was accelerated after MARCH5 was ablated in both the presence and absence of MCL1. Cell death was not altered after disrupting other MARCH5-regulated BCL2 family members including NOXA, BIM, and BID. Disruption of the mitochondrial fission factor DRP1, however, reduced mitotic apoptosis in MARCH5-disrupted cells. These data suggest that MARCH5 regulates mitotic apoptosis through MCL1-independent mechanisms including mitochondrial maintenance that can overcome the stabilization of MCL1.
von Willebrand factor links primary hemostasis to innate immunity
Authors: Drakeford Clive , Aguila Sonia , Roche Fiona , Hokamp Karsten , Fazavana Judicael , Cervantes Mariana P. , Curtis Annie M. , Hawerkamp Heike C. , Dhami Sukhraj Pal Singh , Charles-Messance Hugo , Hackett Emer E. , Chion Alain , Ward Soracha , Ahmad Azaz , Schoen Ingmar , Breen Eamon , Keane Joe , Murphy Ross , Preston Roger J. S. , O’Sullivan Jamie M. , Sheedy Frederick J. , Fallon Padraic , O’Donnell James S. 
Published: November 2022

AbstractThe plasma multimeric glycoprotein von Willebrand factor (VWF) plays a critical role in primary hemostasis by tethering platelets to exposed collagen at sites of vascular injury. Recent studies have identified additional biological roles for VWF, and in particular suggest that VWF may play an important role in regulating inflammatory responses. However, the molecular mechanisms through which VWF exerts its immuno-modulatory effects remain poorly understood. In this study, we report that VWF binding to macrophages triggers downstream MAP kinase signaling, NF-κB activation and production of pro-inflammatory cytokines and chemokines. In addition, VWF binding also drives macrophage M1 polarization and shifts macrophage metabolism towards glycolysis in a p38-dependent manner. Cumulatively, our findings define an important biological role for VWF in modulating macrophage function, and thereby establish a novel link between primary hemostasis and innate immunity.
The inner junction protein CFAP20 functions in motile and non-motile cilia and is critical for vision
Authors: Chrystal Paul W. , Lambacher Nils J. , Doucette Lance P. , Bellingham James , Schiff Elena R. , Noel Nicole C. L. , Li Chunmei , Tsiropoulou Sofia , Casey Geoffrey A. , Zhai Yi , Nadolski Nathan J. , Majumder Mohammed H. , Tagoe Julia , D’Esposito Fabiana , Cordeiro Maria Francesca , Downes Susan , Clayton-Smith Jill , Ellingford Jamie ,   Genomics England Research Consortium, Ambrose J. C. , Arumugam P. , Bevers R. , Bleda M. , Boardman-Pretty F. , Boustred C. R. , Brittain H. , Brown M. A. , Caulfield M. J. , Chan G. C. , Giess A. , Griffin J. N. , Hamblin A. , Henderson S. , Hubbard T. J. P. , Jackson R. , Jones L. J. , Kasperaviciute D. , Kayikci M. , Kousathanas A. , Lahnstein L. , Lakey A. , Leigh S. E. A. , Leong I. U. S. , Lopez F. J. , Maleady-Crowe F. , McEntagart M. , Minneci F. , Mitchell J. , Moutsianas L. , Mueller M. , Murugaesu N. , Need A. C. , O’Donovan P. , Odhams C. A. , Patch C. , Perez-Gil D. , Pereira M. B. , Pullinger J. , Rahim T. , Rendon A. , Rogers T. , Savage K. , Sawant K. , Scott R. H. , Siddiq A. , Sieghart A. , Smith S. C. , Sosinsky A. , Stuckey A. , Tanguy M. , Taylor Tavares A. L. , Thomas E. R. A. , Thompson S. R. , Tucci A. , Welland M. J. , Williams E. , Witkowska K. , Wood S. M. , Zarowiecki M. , Mahroo Omar A. , Hocking Jennifer C. , Cheetham Michael E. , Webster Andrew R. , Jansen Gert , Blacque Oliver E. , Allison W. Ted , Au Ping Yee Billie , MacDonald Ian M. , Arno Gavin , Leroux Michel R. 
Published: November 2022

AbstractMotile and non-motile cilia are associated with mutually-exclusive genetic disorders. Motile cilia propel sperm or extracellular fluids, and their dysfunction causes primary ciliary dyskinesia. Non-motile cilia serve as sensory/signalling antennae on most cell types, and their disruption causes single-organ ciliopathies such as retinopathies or multi-system syndromes. CFAP20 is a ciliopathy candidate known to modulate motile cilia in unicellular eukaryotes. We demonstrate that in zebrafish,cfap20is required for motile cilia function, and inC. elegans, CFAP-20 maintains the structural integrity of non-motile cilia inner junctions, influencing sensory-dependent signalling and development. Human patients and zebrafish withCFAP20mutations both exhibit retinal dystrophy. Hence, CFAP20 functions within a structural/functional hub centered on the inner junction that is shared between motile and non-motile cilia, and is distinct from other ciliopathy-associated domains or macromolecular complexes. Our findings suggest an uncharacterised pathomechanism for retinal dystrophy, and potentially for motile and non-motile ciliopathies in general.
Nanoscale heterogeneity of ultrafast many-body carrier dynamics in triple cation perovskites
Authors: Nishida Jun , Chang Peter T. S. , Ye Jiselle Y. , Sharma Prachi , Wharton Dylan M. , Johnson Samuel C. , Shaheen Sean E. , Raschke Markus B. 
Published: November 2022

AbstractIn high fluence applications of lead halide perovskites for light-emitting diodes and lasers, multi-polaron interactions and associated Auger recombination limit the device performance. However, the relationship of the ultrafast and strongly lattice coupled carrier dynamics to nanoscale heterogeneities has remained elusive. Here, in ultrafast visible-pump infrared-probe nano-imaging of the photoinduced carrier dynamics in triple cation perovskite films, a ~20 % variation in sub-ns relaxation dynamics with spatial disorder on tens to hundreds of nanometer is resolved. We attribute the non-uniform relaxation dynamics to the heterogeneous evolution of polaron delocalization and increasing scattering time. The initial high-density excitation results in faster relaxation due to strong many-body interactions, followed by extended carrier lifetimes at lower densities. These results point towards the missing link between the optoelectronic heterogeneity and associated carrier dynamics to guide synthesis and device engineering for improved perovskites device performance.
UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference
Authors: Gao Mingze , Qiao Chen , Huang Yuanhua 
Published: November 2022

AbstractThe recent breakthrough of single-cell RNA velocity methods brings attractive promises to reveal directed trajectory on cell differentiation, states transition and response to perturbations. However, the existing RNA velocity methods are often found to return erroneous results, partly due to model violation or lack of temporal regularization. Here, we present UniTVelo, a statistical framework of RNA velocity that models the dynamics of spliced and unspliced RNAs via flexible transcription activities. Uniquely, it also supports the inference of a unified latent time across the transcriptome. With ten datasets, we demonstrate that UniTVelo returns the expected trajectory in different biological systems, including hematopoietic differentiation and those even with weak kinetics or complex branches.
Alternate oscillations of Martian hydrogen and oxygen upper atmospheres during a major dust storm
Authors: Masunaga Kei , Terada Naoki , Yoshida Nao , Nakamura Yuki , Kuroda Takeshi , Yoshioka Kazuo , Suzuki Yudai , Nakagawa Hiromu , Kimura Tomoki , Tsuchiya Fuminori , Murakami Go , Yamazaki Atsushi , Usui Tomohiro , Yoshikawa Ichiro 
Published: November 2022

AbstractDust storms on Mars play a role in transporting water from its lower to upper atmosphere, seasonally enhancing hydrogen escape. However, it remains unclear how water is diurnally transported during a dust storm and how its elements, hydrogen and oxygen, are subsequently influenced in the upper atmosphere. Here, we use multi-spacecraft and space telescope observations obtained during a major dust storm in Mars Year 33 to show that hydrogen abundance in the upper atmosphere gradually increases because of water supply above an altitude of 60 km, while oxygen abundance temporarily decreases via water ice absorption, catalytic loss, or downward transportation. Additionally, atmospheric waves modulate dust and water transportations, causing alternate oscillations of hydrogen and oxygen abundances in the upper atmosphere. If dust- and wave-driven couplings of the Martian lower and upper atmospheres are common in dust storms, with increasing escape of hydrogen, oxygen will less efficiently escape from the upper atmosphere, leading to a more oxidized atmosphere. These findings provide insights regarding Mars’ water loss history and its redox state, which are crucial for understanding the Martian habitable environment.
In-sensor reservoir computing system for latent fingerprint recognition with deep ultraviolet photo-synapses and memristor array
Authors: Zhang Zhongfang , Zhao Xiaolong , Zhang Xumeng , Hou Xiaohu , Ma Xiaolan , Tang Shuangzhu , Zhang Ying , Xu Guangwei , Liu Qi , Long Shibing 
Published: November 2022

AbstractDetection and recognition of latent fingerprints play crucial roles in identification and security. However, the separation of sensor, memory, and processor in conventional ex-situ fingerprint recognition system seriously deteriorates the latency of decision-making and inevitably increases the overall computing power. In this work, a photoelectronic reservoir computing (RC) system, consisting of DUV photo-synapses and nonvolatile memristor array, is developed to detect and recognize the latent fingerprint with in-sensor and parallel in-memory computing. Through the Ga-rich design, we achieve amorphous GaOx (a-GaOx) photo-synapses with an enhanced persistent photoconductivity (PPC) effect. The PPC effect, which induces nonlinearly tunable conductivity, renders the a-GaOx photo-synapses an ideal deep ultraviolet (DUV) photoelectronic reservoir, thus mapping the complex input vector into a dimensionality-reduced output vector. Connecting the reservoirs and a memristor array, we further construct an in-sensor RC system for latent fingerprint identification. The system maintains over 90% recognition accuracy for latent fingerprint within 15% stochastic noise level via the proposed dual-feature strategy. This work provides a subversive prototype system of DUV in-sensor RC for highly efficient recognition of latent fingerprints.
Tuning instability of non-columnar neurons in the salt-and-pepper whisker map in somatosensory cortex
Authors: Wang Han Chin , LeMessurier Amy M. , Feldman Daniel E. 
Published: November 2022

AbstractRodent sensory cortex contains salt-and-pepper maps of sensory features, whose structure is not fully known. Here we investigated the structure of the salt-and-pepper whisker somatotopic map among L2/3 pyramidal neurons in somatosensory cortex, in awake mice performing one-vs-all whisker discrimination. Neurons tuned for columnar (CW) and non-columnar (non-CW) whiskers were spatially intermixed, with co-tuned neurons forming local (20 µm) clusters. Whisker tuning was markedly unstable in expert mice, with 35-46% of pyramidal cells significantly shifting tuning over 5-18 days. Tuning instability was highly concentrated in non-CW tuned neurons, and thus was structured in the map. Instability of non-CW neurons was unchanged during chronic whisker paralysis and when mice discriminated individual whiskers, suggesting it is an inherent feature. Thus, L2/3 combines two distinct components: a stable columnar framework of CW-tuned cells that may promote spatial perceptual stability, plus an intermixed, non-columnar surround with highly unstable tuning.
Spatially resolved phosphoproteomics reveals fibroblast growth factor receptor recycling-driven regulation of autophagy and survival
Authors: Watson Joanne , Ferguson Harriet R. , Brady Rosie M. , Ferguson Jennifer , Fullwood Paul , Mo Hanyi , Bexley Katherine H. , Knight David , Howell Gareth , Schwartz Jean-Marc , Smith Michael P. , Francavilla Chiara 
Published: November 2022

AbstractReceptor Tyrosine Kinase (RTK) endocytosis-dependent signalling drives cell proliferation and motility during development and adult homeostasis, but is dysregulated in diseases, including cancer. The recruitment of RTK signalling partners during endocytosis, specifically during recycling to the plasma membrane, is still unknown. Focusing on Fibroblast Growth Factor Receptor 2b (FGFR2b) recycling, we reveal FGFR signalling partners proximal to recycling endosomes by developing a Spatially Resolved Phosphoproteomics (SRP) approach based on APEX2-driven biotinylation followed by phosphorylated peptides enrichment. Combining this with traditional phosphoproteomics, bioinformatics, and targeted assays, we uncover that FGFR2b stimulated by its recycling ligand FGF10 activates mTOR-dependent signalling and ULK1 at the recycling endosomes, leading to autophagy suppression and cell survival. This adds to the growing importance of RTK recycling in orchestrating cell fate and suggests a therapeutically targetable vulnerability in ligand-responsive cancer cells. Integrating SRP with other systems biology approaches provides a powerful tool to spatially resolve cellular signalling.
Surface melting of a colloidal glass
Authors: Tian Li , Bechinger Clemens 
Published: November 2022

AbstractDespite their technological relevance, a full microscopic understanding of glasses is still lacking. This applies even more to their surfaces whose properties largely differ from that of the bulk material. Here, we experimentally investigate the surface of a two-dimensional glass as a function of the effective temperature. To yield a free surface, we use an attractive colloidal suspension of micron-sized particles interacting via tunable critical Casimir forces. Similar to crystals, we observe surface melting of the glass, i.e., the formation of a liquid film at the surface well below the glass temperature. Underneath, however, we find an unexpected region with bulk density but much faster particle dynamics. It results from connected clusters of highly mobile particles which are formed near the surface and deeply percolate into the underlying material. Because its thickness can reach several tens of particle diameters, this layer may elucidate the poorly understood properties of thin glassy films which find use in many technical applications.
Neural dynamics of phoneme sequences reveal position-invariant code for content and order
Authors: Gwilliams Laura , King Jean-Remi , Marantz Alec , Poeppel David 
Published: November 2022

AbstractSpeech consists of a continuously-varying acoustic signal. Yet human listeners experience it as sequences of discrete speech sounds, which are used to recognise discrete words. To examine how the human brain appropriately sequences the speech signal, we recorded two-hour magnetoencephalograms from 21 participants listening to short narratives. Our analyses show that the brain continuously encodes the three most recently heard speech sounds in parallel, and maintains this information long past its dissipation from the sensory input. Each speech sound representation evolves over time, jointly encoding both its phonetic features and the amount of time elapsed since onset. As a result, this dynamic neural pattern encodes both the relative order and phonetic content of the speech sequence. These representations are active earlier when phonemes are more predictable, and are sustained longer when lexical identity is uncertain. Our results show how phonetic sequences in natural speech are represented at the level of populations of neurons, providing insight into what intermediary representations exist between the sensory input and sub-lexical units. The flexibility in the dynamics of these representations paves the way for further understanding of how such sequences may be used to interface with higher order structure such as lexical identity.
Near-room-temperature martensitic actuation profited from one-dimensional hybrid perovskite structure
Authors: Liang Bei-Dou , Fan Chang-Chun , Liu Cheng-Dong , Chai Chao-Yang , Han Xiang-Bin , Zhang Wen 
Published: November 2022

AbstractMartensitic transformation, usually accompanied by ferroelastic and thermoelastic behaviors, is an interesting and useful mechanical-related property upon external stimuli. For molecular crystals, however, martensitic systems to show reversible stimuli-actuation behaviors are still limited because of a lack of designability and frequent crystal collapse due to large stress releases during the transformations. Here, a one-dimensional hybrid perovskite semiconductor (NMEA)PbI3 (NMEA = N-methylethylammonium) was prepared by following a dimensionality reduction design principle. The crystal undergoes reversible ferroelastic and thermoelastic martensitic transformations, which are attributed to weak intermolecular interactions among the chains that easily trigger the interchain shearing movement. The actuation behavior occurring during the phase transition is very close to room temperature and demonstrated to behave as a mechanical actuator for switching. This work provides an effective approach to designing molecular actuators with promising applications in next-generation intelligence devices.