bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uni-Fold Symmetry: Harnessing Symmetry in Folding Large Protein Complexes
Authors: Li Ziyao , Yang Shuwen , Liu Xuyang , Chen Weijie , Wen Han , Shen Fan , Ke Guolin , Zhang Linfeng 
Published: August 2022

AbstractDeep folding models have revolutionized the conventional methods of protein complex prediction. However, applying them to large protein oligomers is not easy. These models generally require copying the sequences of identical subunits to capture the in-between relationships. Accordingly, the scales of target protein complexes are strictly limited due to the cubic complexity of these models. To address this issue, we propose UF-Symmetry (Uni-Fold Symmetry), which is extricated from the need of sequence copying via harnessing the intrinsic symmetry of large protein oligomers. Taking the sequences of the asymmetric unit (AU) and a pre-specified symmetry group, UF-Symmetry learns to fold the AU and to assemble the complex structure in an end-to-end manner. By reducing the input scales from entire assemblies to AUs, UF-Symmetry allows to predict much larger assemblies with significant acceleration: for a complex of 4-fold cyclic symmetry (C4) and AU size of 512, UF-Symmetry achieves approximately 20 times acceleration to current methods. On a benchmark of recently released PDB multimers, UF-Symmetry approximately halves the failure rate of current methods and achieves approaching accuracy on commonly successful cases.
A Parcellation Scheme of Mouse Isocortex Based on Reversals in Connectivity Gradients
Authors: Reimann Michael W , Guyonnet-Hencke Timothé 
Published: August 2022

AbstractThe brain is composed of several anatomically clearly separated structures. This parcellation is often extended into the isocortex, based on anatomical, physiological or functional differences. Here, we derive a parcellation scheme based purely on the spatial structure of long-range synaptic connections within the cortex. To that end, we analyzed a publicly available dataset of average mouse brain connectivity, and split the isocortex into disjunct regions. Instead of clustering connectivity based on modularity, our scheme is inspired by methods that split sensory cortices into subregions where gradients of neuronal response properties, such as the location of the receptive field, reverse. We calculated comparable gradients from voxelized brain connectivity data and automatically detected reversals in them. This approach better respects the known presence of functional gradients within brain regions than clustering-based approaches. Placing borders at the reversals resulted in a parcellation into 41 subregions that differs significantly from an established scheme in nonrandom ways, but is comparable in terms of the modularity of connectivity between regions. It reveals unexpected trends of connectivity, such as a tripartite split of somatomotor regions along an anterior to posterior gradient. The method can be readily adapted to other organisms and data sources, such as human functional connectivity.
Monosynaptic trans-collicular pathways link mouse whisker circuits to integrate somatosensory and motor cortical signals
Authors: Martín-Cortecero Jesús , Isaías-Camacho Emilio Ulises , Boztepe Berin , Ziegler Katharina , Mease Rebecca Audrey , Groh Alexander 
Published: August 2022

AbstractThe superior colliculus (SC), a conserved midbrain-node with extensive long-range connectivity throughout the brain, is a key structure for innate behaviors. Descending cortical pathways are increasingly recognized as central control points for SC-mediated behaviors, but how cortico-collicular pathways coordinate SC activity at the cellular level is poorly understood. Moreover, despite the known role of the SC as a multisensory integrator, the involvement of the SC in the somatosensory system is largely unexplored in comparison to its involvement in the visual and auditory systems. Here, we mapped the connectivity of the whisker-sensitive region of the SC in mice with trans-synaptic and intersectional tracing tools and in vivo electrophysiology. The results reveal a novel trans-collicular connectivity motif in which neurons in motor- and somatosensory cortices impinge onto the brainstem-SC-brainstem sensory-motor arc and onto SC-midbrain output pathways via only one synapse in the SC. Intersectional approaches and optogenetically assisted connectivity quantificationsin vivoreveal convergence of motor and somatosensory cortical input on individual SC neurons, providing a new framework for sensory-motor integration in the SC. More than a third of the cortical recipient neurons in the whisker SC are GABAergic neurons, which include a hitherto unknown population of GABAergic projection neurons targeting thalamic nuclei and the zona incerta. These results pinpoint a whisker region in the SC of mice as a node for the integration of somatosensory and motor cortical signals via parallel excitatory and inhibitory trans-collicular pathways which link cortical and subcortical whisker circuits for somato-motor integration.
Transcription Factor Localization Dynamics and DNA Binding Drive Distinct Promoter Interpretations
Authors: Sweeney Kieran , McClean Megan N. 
Published: August 2022

SUMMARYEnvironmental information may be encoded in the temporal dynamics of transcription factor (TF) activation and subsequently decoded by gene promoters to enact stimulus-specific gene expression programs. Previous studies of this behavior focused on the encoding and decoding of information in TF nuclear localization dynamics, yet cells control the activity of TFs in myriad ways, including by regulating their ability to bind DNA. Here, we use light-controlled mutants of the yeast TF Msn2 as a model system to investigate how promoter decoding of TF localization dynamics is affected by changes in the ability of the TF to bind DNA. We find that yeast promoters directly decode the light-controlled localization dynamics of Msn2 and that the effects of changing Msn2 affinity on that decoding behavior are highly promoter dependent, illustrating how cells could potentially regulate TF localization dynamics and DNA binding in concert for improved control of gene expression.
The condensin II/TOP-2 axis silences transcription during germline specification inC. elegans
Authors: Belew Mezmur D. , Chien Emilie , Wong Matthew , Michael W. Matthew 
Published: August 2022

AbstractInC. elegans, the germline is specified via a preformation mechanism that relies on the PIE-1 protein’s ability to globally silence mRNA transcription in germline precursor cells, also known as the P-lineage. Recent work from our group has identified additional genome silencing events inC. elegansduring oogenesis and in starved L1 larvae, and these require the condensin II complex, topoisomerase II (TOP-2), and components of the H3K9me/heterochromatin pathway. Interestingly, silencing in oocytes also requires PIE-1, but this is not the case in starved L1s. Here, we ask if additional genome silencing components besides PIE-1 are required to repress gene expression in the P-lineage of early embryos, and we find that condensin II and TOP-2 are required and the H3K9me/heterochromatin pathway is not. We show that depletion of condensin II/TOP-2 activates the normally suppressed RNA polymerase II to inappropriately transcribe somatic genes in the P-lineage. We also present evidence that while both PIE-1 and condensin II/TOP-2 are required for genome silencing in the P-lineage, PIE-1 can silence transcription independently of condensin II/TOP-2 when misexpressed in somatic cells. Thus, in oocytes, all three genome silencing systems (TOP-2/condensin II, H3K9me, and PIE-1) are operational while in both early embryos and starved L1s two of the three are active (TOP- 2/condensin II and PIE-1 for early embryos, TOP-2/condensin II and H3K9me for starved L1s). Our data show that multiple, redundantly acting genome silencing mechanisms act in a mix and match manner to repress transcription at different developmental stages in theC. elegansgermline.
A paralog of Pcc1 is the fifth core subunit of KEOPS complex in Archaea
Authors: Daugeron Marie-Claire , Missoury Sophia , Da Cunha Violette , Lazar Noureddine , Collinet Bruno , van Tilbeurgh Herman , Basta Tamara 
Published: August 2022

ABSTRACTIn Archaea and Eukaryotes, the synthesis of a universal tRNA modification, t6A, is catalyzed by the KEOPS complex composed of Kae1, Bud32, Cgi121 and Pcc1. A fifth subunit, Gon7, is found only in Fungi and Metazoa. Mutations in all five genes encoding human KEOPS subunits leads to Galloway-Mowat syndrome, a severe genetic disease causing childhood lethality. Here, we describe the discovery and biochemical characterization of the archaeal fifth KEOPS subunit. This protein, dubbed Pcc2, is a paralog of Pcc1 and is widely conserved in Archaea. Pcc1 and Pcc2 form a heterodimer in solution, show modest sequence conservation but very high structural similarity. The 5-subunit KEOPS lost its capacity to form dimers but its tRNA binding and t6A synthetic activity remained robust. Pcc2 can substitute Pcc1 but the resulting KEOPS complex is inactive suggesting a distinct function for the two paralogs. Comparative sequence and structure analyses point to a possible evolutionary link between archaeal Pcc2 and eukaryotic Gon7 proteins. Our work thus reveals that Pcc2 has evolved to regulate the oligomeric state of KEOPS complex thus adding another layer of complexity to the biosynthesis of t6A that seems to be conserved from Archaea to Eukaryotes.
Biosynthesis of the Fungal Nonribosomal Peptide Penilumamide A and Biochemical Characterization of a Pterin-Specific Adenylation Domain
Authors: Heard Stephanie C. , Winter Jaclyn M. 
Published: August 2022

ABSTRACTWe report the characterization of the penilumamide A biosynthetic gene cluster from the marine-derived fungus Aspergillus flavipes CNL-338. In vitro reconstitution studies demonstrated that three Plm nonribosomal peptide synthetases encoding four modules are required for constructing the lumazine-containing tripeptide. Further investigations using dissected adenylation domains determined substrate specificity for methionine and anthranilic acid and led to the first biochemical characterization of an adenylation domain with selectivity for a pterin-derived building block.
Diffusive lensing as a mechanism of intracellular transport and compartmentalization
Authors: Venkatesh Achuthan Raja , Le Kathy H. , Weld David M. , Brandman Onn 
Published: August 2022

AbstractWhile inhomogeneous diffusivity has been identified as a ubiquitous feature of the cellular interior, its implications for particle mobility and concentration at different length scales remain largely unexplored. In this work, we use agent-based simulations of diffusion to investigate how heterogeneous diffusivity affects movement and concentration of diffusing particles. We propose that a nonequilibrium mode of membraneless compartmentalization arising from the convergence of diffusive trajectories into low-diffusive sinks, which we call “diffusive lensing,” is relevant for living systems. Our work highlights the phenomenon of diffusive lensing as a potentially key driver of mesoscale dynamics in the cytoplasm, with possible far-reaching implications for biochemical processes.
Noninvasive method for monitoring breathing patterns in monkeys
Authors: Kunimatsu Jun , Akiyama Yusuke , Toyoshima Osamu , Matsumoto Masayuki 
Published: August 2022

AbstractRespiration is strongly linked to internal states such as arousal, emotion, and even cognitive processes and provides objective biological information to estimate these states in humans and animals. However, the measurement of respiration has not been established in macaque monkeys that have been widely used as model animals for understanding various higher brain functions. In the present study, we developed a method to monitor the respiration of behaving monkeys. We first measured the temperature of their nasal breathing, which changes between inspiration and expiration phases, in an anesthetized condition and estimated the respiration pattern. We compared the estimated pattern with that obtained by a conventional chest band method that has been used in humans and applies to anesthetized, but not behaving, monkeys. These respiration patterns matched well, suggesting that the measurement of nasal air temperature can be used to monitor the respiration of monkeys. Furthermore, we confirmed that the respiration frequency in behaving monkeys monitored by the measurement of nasal air temperature was not affected by the orofacial movement of licking to obtain the liquid reward. We next examined the frequency of respiration when they listened to music or white noise. The respiratory frequency was higher when the monkeys listened to music than the noise. This result is consistent with a phenomenon in humans and indicates the accuracy of our monitoring method. These data suggest that the measurement of nasal air temperature enables us to monitor the respiration of behaving monkeys and thereby estimate their internal states.Significance StatementWhile respiration is linked with internal processing, such as emotional and cognitive states, methods have not been established for physiological research on monkeys. We developed a novel method that obtained respiration signals by measuring the nasal air temperatures of behaving monkeys. Our method was able to continuously track the respiration pattern without distortions evoked by orofacial movements to lick the liquid reward. The respiratory frequency increased while listening to music than when listening to white noise for all monkeys. These results demonstrate that nasal air temperature measurements can be used to monitor the respiration patterns of aroused monkeys, allowing us to understand their internal state. This will be useful for investigating the underlying neuronal mechanism of neuropsychiatric disorders using monkeys.
Lipotype acquisition during neural developmentin vivois not recapitulated in stem cell-derived neurons
Authors: Gopalan Anusha B. , van Uden Lisa , Sprenger Richard R. , Marx Nadine Fernandez-Novel , Bogetofte Helle , Neveu Pierre , Meyer Morten , Noh Kyung-Min , Diz-Muñoz Alba , Ejsing Christer S. 
Published: August 2022

AbstractDuring development, different tissues acquire distinct lipotypes that are coupled to tissue function and homeostasis. In the brain, where complex membrane trafficking systems are required for neural function, specific glycerophospholipids, sphingolipids, and cholesterol are highly abundant, and defective lipid metabolism is associated with abnormal neural development and neurodegenerative disease. Notably, the production of tissue-specific lipotypes requires appropriate programming of the underlying lipid metabolic machinery, but when and how this occurs is unclear. To address this, we used high-resolution mass spectrometry-based (MSALL) lipidomics to perform a quantitative and comprehensive analysis of mouse brain development covering early embryonic and postnatal stages. We discovered a distinct bifurcation in the establishment of the neural lipotype, whereby the canonical brain lipid biomarkers 22:6-glycerophospholipids and 18:0-sphingolipids begin to be producedin utero, whereas cholesterol attains its characteristic high levels after birth. In contrast, when profiling rodent and human stem cell-derived neurons, we observed that these do not acquire a brain lipotypeper se. However, upon probing the lipid metabolic wiring by supplementing brain lipid precursors, we found that the stem cell-derived neurons were partially able to establish a brain-like lipotype, demonstrating that the cells are partially metabolically committed. Altogether, our report provides an extensive lipidomic resource for brain development and highlights a potential challenge in using stem cell-derived neurons for mechanistic studies of lipid biochemistry, membrane biology and biophysics that can be mitigated by further optimizingin vitrodifferentiation protocols.Significance StatementWe report an extensive time-resolved resource of lipid molecule abundances across mouse brain development, starting as early as 10 days post-fertilization. The resource reveals a bifurcation in the establishment of the neural lipotype where the canonical 22:6-glycerophospholipid and 18:0-sphingolipid biomarkers are attainedin utero, whereas cholesterol is attained after birth. Furthermore, we uncover that the neural lipotype is not established in rodent and human stem cell-derived neuronsin vitro.
Female projectionists on the move: Exhibiting socialist gender equality in rural China (1949–1966)
Authors: Guo Yanping 
Published: August 2022

AbstractThe gender discourse in Maoist China can be summed up in Mao's famous motto ‘men and women are the same’. Images of women operating various technologies were massively propagated in the 1950s and 1960s, illustrating that men and women were not only equal in political status but also in physical strength with the help of technology. In reality, however, women working in technical jobs were not on the same footing as their male counterparts. Taking female projectionists as the research subject, this article investigates how new professional women, assigned by the state, overcame gender bias in rural areas where a patriarchal culture prevailed. By examining the inconsistency between the Chinese Communist Party's gender policies that encouraged women's public participation and the rural culture that derided women in public space, this article contends that female projectionists’ experiences of performing screening techniques played a significant role in opening up new spaces for women's repositioning in the patriarchal society. While operating technology did not naturally give women the same social status as men, it was through female projectionists’ bodily practices that the socialist ideas of gender equality were disseminated in rural areas.
Can curiosity spark the fire of innovation? An investigation in China
Authors: Li Rui , Tian Jingyuan , Zhang Junhong , Wu Shaobo 
Published: August 2022

AbstractCuriosity has been seen as an important driver of individual innovation. However, empirical evidence regarding the relationship between curiosity and innovation is equivocal. We draw on the situational strength perspective to develop and test a contingency model that focuses on the contextual boundary conditions of this relationship among Chinese employees. In a controlled experiment with 191 part‐time MBA students, in which curiosity was examined as a state, we found that (1) the main effect of curiosity on innovative behavioral intention was insignificant; (2) authoritarian leadership and job autonomy moderated the association of curiosity with innovative behavioral intention, such that this association was positively significant under circumstances of low authoritarian leadership or high job autonomy but not under circumstances of high authoritarian leadership or low job autonomy; and (3) job autonomy functioned as a mediator for the moderating effect of authoritarian leadership. These findings were constructively replicated in a field study of 206 subordinate–supervisor dyads in which curiosity was examined as a trait and innovative behavior was rated by supervisors. Theoretical and practical implications of our findings and directions for future research are discussed.
Relative performance of Bayesian morphological clock and parsimony methods for phylogenetic reconstructions: Insights from the case of Myomiminae and Dryomyinae glirid rodents
Authors: Dalmasso Andrea , Peláez‐Campomanes Pablo , López‐Antoñanzas Raquel 
Published: August 2022

AbstractExtinct organisms provide crucial information about the origin and time of origination of extant groups. The importance of morphological phylogenetics for rigorously dating the tree of life is now widely recognized and has been revitalized by methodological developments such as the application of tip‐dating Bayesian approaches. Traditionally, molecular clocks have been node calibrated. However, node calibrations are often unsatisfactory because they do not allow the fossil age to inform about phylogenetic hypothesis. The introduction of tip calibrations allow fossil species to be included alongside their living relatives, and the absence of molecular sequence data for these taxa to be remedied by supplementing the sequence alignments for living taxa with phenotype character matrices for both living and fossil taxa. Therefore, only phylogenetic analyses that take into account morphological characters can incorporate both fossil and extant species. Herein we present an unprecedented morphological dataset for a vast group of glirid rodents, to which different phylogenetic methodologies have been applied. We have compared the tree topologies resulting from traditional parsimony and Bayesian phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip‐dated clock methods seem to outperform parsimony with our dataset. The strict consensus tree recovered by tip dating invalidates the classic classification and allows dates to be proposed for the divergence and origin of the different clades.
Validation of machine learning approaches for estimating wheel fatigue loads at the front suspension of a race car during track driving
Authors: Cortivo Davide , Campagnolo Alberto , Meneghetti Giovanni 
Published: August 2022

AbstractThe wheel loads of a race car have been estimated in view of structural durability assessments. First, the front left double‐wishbone suspension of a rear‐wheel‐drive race vehicle has been instrumented; then, wheel loads have been estimated by means of four approaches: (i) a geometric matrix (GM) method, (ii) a feedforward neural network (FNN) approach applied to the fully instrumented suspension (FIS), (iii) a FNN approach involving a reduced number of sensors (the partially instrumented suspension (PIS)) and an inertial measurement unit (IMU), and (iv) a linear modeling approach (LM). After having trained the FNNs by using suspension signals acquired in a racetrack as inputs and related tire forces measured with the GM method as targets, the FNN‐based methods have been validated on three different racetracks by comparing the estimated loads with those estimated by means of the GM method. According to the results achieved, the FNN approaches are effective for the estimation of the wheel forces.
Constraining China's land carbon sink from emerging satellite CO2 observations: Progress and challenges
Authors: Wang Yilong , Tian Xiangjun , Chevallier Frédéric , Johnson Matthew S. , Philip Sajeev , Baker David F. , Schuh Andrew E. , Deng Feng , Zhang Xingying , Zhang Lu , Zhu Dan , Wang Xuhui 
Published: August 2022

AbstractLand carbon sink is a vital component for the achievement of China's ambitious carbon neutrality goal, but its magnitude is poorly known. Atmospheric observations and inverse models are valuable tools to constrain the China's land carbon sink. Space‐based CO2 measurements from satellites form an emerging data stream for application of such atmospheric inversions. Here, we reviewed the satellite missions that is dedicated to the monitoring of CO2, and the recent progresses on the inversion of China's land carbon sink using satellite CO2 measurements. We summarized the limitations and challenges in current space platforms, retrieval algorithms, and the inverse modeling. It is shown that there are large uncertainties of contemporary satellite‐based estimates of China's land carbon sink. We discussed future opportunities of continuous improvements in three aspects to better constrain China's land carbon sink with space‐based CO2 measurements.