bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mental navigation and telekinesis with a hippocampal map-based brain-machine interface
Authors: Lai Chongxi , Tanaka Shinsuke , Harris Timothy D. , Lee Albert K. 
Published: April 2023

AbstractThe hippocampus is critical for recollecting and imagining experiences. This is believed to involve voluntarily drawing from hippocampal memory representations of people, events, and places, including the hippocampus’ map-like representations of familiar environments. However, whether the representations in such “cognitive maps” can be volitionally and selectively accessed is unknown. We developed a brain-machine interface to test if rats could control their hippocampal activity in a flexible, goal-directed, model-based manner. We show that rats can efficiently navigate or direct objects to arbitrary goal locations within a virtual reality arena solely by activating and sustaining appropriate hippocampal representations of remote places. This should provide insight into the mechanisms underlying episodic memory recall, mental simulation/planning, and imagination, and open up possibilities for high-level neural prosthetics utilizing hippocampal representations.
A cross-sectional study of the association between COVID-19 infection and psychological distress in Japanese workers
Authors: Tesen Hirofumi , Konno Yusuke , Tateishi Seiichiro , Mafune Kosuke , Tsuji Mayumi , Ogami Akira , Nagata Tomohisa , Matsugaki Ryutaro , Yoshimura Reiji , Fujino Yoshihisa ,   the CORoNaWork Project
Published: April 2023

AbstractThe COVID-19 pandemic infected many people worldwide with SARS-CoV2. Psychological distress is one of the sequelae reported to occur in many of those infected (Choutka et al., 2022). We investigated the association between personal experience of COVID-19 infection and psychological distress in Japan. A total of 18,560 persons participated in the original survey, conducted in December 2020. After excluding unreliable responses, data from 14,901 persons who participated in a follow-up survey in December 2022-were included in the analysis. Odds ratios (ORs) were estimated by univariate and multiple logistic regression analysis with history of COVID-19 infection as the independent variable and presence of psychological distress as the dependent variable.This results showed that the experience of COVID-19 infection is associated with psychological distress. Moreover, most cases of mental distress among those who experienced COVID-19 infection can be at least partly explained by a perception of unfair treatment.
A self-renewing biomimetic skeletal muscle construct engineered using induced myogenic progenitor cells
Authors: Kim Inseon , Lee Seunghun S. , Ghosh Adhideb , Ferguson Stephen J. , Bar-Nur Ori 
Published: April 2023

AbstractSkeletal muscle is a highly organized and regenerative tissue that maintains its homeostasis primarily by activation and differentiation of muscle stem cells. Mimicking anin vitroskeletal muscle differentiation program that contains self-renewing adult muscle stem cells and aligned myotubes has been challenging. Here, we set out to engineer a biomimetic skeletal muscle construct that can self-regenerate and produce aligned myotubes using induced myogenic progenitor cells (iMPCs), a heterogeneous culture consisting of skeletal muscle stem, progenitor and differentiated cells. Utilizing electrospinning, we fabricated polycaprolactone (PCL) substrates that enabled iMPC-differentiation into aligned myotubes by controlling PCL fiber orientation. Newly-conceived constructs contained highly organized multinucleated myotubes in conjunction with self-renewing muscle stem cells, whose differentiation capacity was augmented by Matrigel supplementation. Additionally, we demonstrate using single cell RNA-sequencing (scRNA-seq) that iMPC-derived constructs faithfully recapitulate a step-wise myogenic differentiation program. Notably, when the constructs were subjected to a damaging myonecrotic agent, self-renewing muscle stem cells rapidly differentiated into aligned myotubes, akin to skeletal muscle repairin vivo. Taken together, we report on a novelin vitrosystem that mirrors myogenic regeneration and muscle fiber alignment, and can serve as a platform to study myogenesis, model muscular dystrophies or perform drug screens.
Interdependence patterns of multi-frequency oscillations predict visuomotor behavior
Authors: Bahuguna Jyotika , Schwey Antoine , Battaglia Demian , Malfait Nicole 
Published: April 2023

AbstractWe show that sensorimotor behavior can be reliably predicted from single-trial EEG oscillations fluctuating in a coordinated manner across brain regions, frequency bands and movement time epochs. We define high-dimensionaloscillatory portraitsto capture the interdependence between basicoscillatory elements, quantifying oscillations occurring in single-trials at specific frequencies, locations and time epochs. We find that the general structure of the element-interdependence networks (effective connectivity) remains stable across task conditions, reflecting an intrinsic coordination architecture and responds to changes in task constraints by subtle but consistently distinct topological reorganizations. Trial categories are reliably and significantly better separated using oscillatory portraits, than from the information contained in individual oscillatory elements, suggesting an inter-element coordination-based encoding. Furthermore, single-trial oscillatory portrait fluctuations are predictive of fine trial-to-trial variations in movement kinematics. Remarkably, movement accuracy appears to be reflected in the capacity of the oscillatory coordination architecture to flexibly update as an effect of movement-error integration.
PMIpred: A physics-informed web server for quantitative Protein-Membrane Interaction prediction
Authors: van Hilten Niek , Verwei Nino , Methorst Jeroen , Nase Carsten , Bernatavicius Andrius , Risselada Herre Jelger 
Published: April 2023

AbstractMotivationMany membrane peripheral proteins have evolved to transiently interact with the surface of (curved) lipid bilayers. Currently, methods toquantitativelypredict sensing and binding free energies for protein sequences or structures are lacking, and such tools could greatly benefit the discovery of membrane-interacting motifs, as well as theirde novodesign.ResultsHere, we trained a transformer neural network model on molecular dynamics data for>50,000 peptides that is able to accurately predict the (relative) membrane-binding free energy for any given amino acid sequence. Using this information, our physics-informed model is able to classify a peptide’s membrane-associative activity as either non-binding, curvature sensing, or membrane binding. Moreover, this method can be applied to detect membraneinteraction regions in a wide variety of proteins, with comparable predictive performance as state-of-the-art data-driven tools like DREAMM, PPM3, and MODA, but with a wider applicability regarding protein diversity, and the added feature to distinguish curvature sensing from general membrane binding.AvailabilityWe made these tools available as a web server, coined Protein-Membrane Interaction predictor (PMIpred), which can be accessed athttps://pmipred.fkt.physik.tu-dortmund.de.
Probe capture enrichment sequencing ofamoAgenes discloses diverse ammonia-oxidizing archaeal and bacterial populations
Authors: Hiraoka Satoshi , Ijichi Minoru , Takeshima Hirohiko , Kumagai Yohei , Yang Ching-Chia , Makabe-Kobayashi Yoko , Fukuda Hideki , Yoshizawa Susumu , Iwasaki Wataru , Kogure Kazuhiro , Shiozaki Takuhei 
Published: April 2023

AbstractThe ammonia monooxygenase subunit A (amoA) gene has been used to investigate the phylogenetic diversity, spatial distribution, and activity of ammonia-oxidizing archaeal (AOA) and bacterial (AOB), which contribute significantly to the nitrogen cycle in various ecosystems. Amplicon sequencing ofamoAis a widely used method; however, it produces inaccurate results owing to the lack of a ‘universal’ primer set. Moreover, currently available primer sets suffer from amplification biases, which can lead to severe misinterpretation. Although shotgun metagenomic and metatranscriptomic analyses are alternative approaches without amplification bias, the low concentration of target genes in heterogeneous environmental DNA restricts a comprehensive analysis to a realizable sequencing depth. In this study, we developed a method foramoAenrichment sequencing using a hybridization capture technique. Using metagenomic mock community samples, our approach effectively enrichedamoAgenes with low compositional changes, outperforming amplification and meta-omics sequencing analyses. Following the analysis of metatranscriptomic marine samples, we predicted 80 operational taxonomic units (OTUs) assigned to either AOA or AOB, of which 30 OTUs were unidentified using simple metatranscriptomic oramoAgene amplicon sequencing. Mapped read ratios to all the detected OTUs were significantly higher for the capture samples (50.4 ± 27.2%) than for non-capture samples (0.05 ± 0.02%), demonstrating the high enrichment efficiency of the method. The analysis also revealed the spatial diversity of AOA ecotypes with high sensitivity and phylogenetic resolution, which are difficult to examine using conventional approaches.
Title: Toleration of Frameshift Mutations in mRNA Sequences Encoding the N-terminal Peptides of Bacterial Type III Effectors
Authors: Yang Jielin , Lu Moyang , Yu Mingyang , Wang Xinlong , Zhao Ziyi , Luo Lijun , Cai Xuxia , Chen Runhong , Hu Yueming , Wang Yejun 
Published: April 2023

AbstractGram-negative bacteria deliver effector proteins into eukaryotic host cells through type III and type IV secretion systems, causing infections and diseases. It remains unclear about the signals guiding the specific secretion of the effectors. Here, we adopted anin silicoapproach to analyze the mRNA sequences encoding the putative peptides essential for effective secretion and translocation of type III and IV effectors. A surprisingly high proportion of type III effectors showed tolerance on frameshift mutations in signal-encoding mRNA sequences, and in contrast, very low percentage of type IV effectors showed the similar frameshift tolerance. The type III effectors with frameshift tolerance of secretion signals were widely distributed in effector or signal families and bacterial species. Natural frameshifts could be identified in type III effector genes, which were often remedied in time by nearby paired insertions or deletions. Frameshift-derived peptide sequences also retained the common properties present in the signal peptides of raw type III effectors. Natural language processing models were adopted to represent the common features in the mRNA sequences encoding N-terminal peptides of type III effectors or C-terminal peptides of type IV effectors, with which transfer learning models could well predict the effectors, especially type IV effectors. The observations in the study would facilitate us understand the nature and evolution of secretion signals of type III and IV effectors.SignificanceIt has been a debate on the nature of signals for translocation of type III secreted effectors for a long time. Meanwhile, there has been no examination on the possibility of mRNA being as translocation signals for type IV or other types of secreted effectors. By computational simulation, the study demonstrated the protein nature of translocation signals for both type IV effectors and most type III effectors. Despite wide frameshift tolerance and atypical common features in mRNA sequences encoding the putative N-terminal signal sequences of type III effectors, more typical common physicochemical and amino acid composition properties between the mutation-derived and raw peptides, and the frequent self-correction phenomenon for naturally happening frameshifts supported the translocation signals at protein level of type III effectors. The common features in mRNA sequences encoding the translocation signal peptides of type III and IV effectors could also be combined in models for better prediction of the effectors respectively.
Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs
Authors: Ashwood Brennan , Jones Michael S. , Radakovic Aleksandar , Khanna Smayan , Lee Yumin , Sachleben Joseph R. , Szostak Jack W. , Ferguson Andrew L. , Tokmakoff Andrei 
Published: April 2023

AbstractHybridization of short nucleic acid segments (<4 nucleotides) to single-strand templates occurs as a critical intermediate in processes such as non-enzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood due to experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy. Our results suggest that dinucleotide binding is stabilized through coaxial stacking interactions with the adjacent duplex segments as well as from potential non-canonical base pairing configurations and structural dynamics of gap and overhang templates revealed using molecular dynamics simulations. We measure timescales for dissociation ranging from 0.2 to 40 µs depending on the template and temperature. Dinucleotide hybridization and dehybridization involves a significant free energy barrier with characteristics resembling that of canonical oligonucleotides. Together, our work provides an initial step for predicting the stability and kinetics of hybridization between short nucleic acid segments and various templates.
Hormonal coordination of peripheral motor output and corollary discharge in a communication system
Authors: Fukutomi Matasaburo , Carlson Bruce A. 
Published: April 2023

AbstractSteroid hormones remodel neural networks to induce developmental or seasonal changes in animal behavior, but little is known about hormonal modulation of sensorimotor integration. Here, we investigate hormonal effects on a predictive motor signal, termed corollary discharge, that modulates sensory processing in weakly electric mormyrid fish. In the electrosensory pathway mediating communication behavior, inhibition activated by a corollary discharge precisely blocks sensory responses to self-generated electric pulses, allowing the downstream circuit to selectively analyze communication signals from nearby fish. These electric pulses are elongated by increasing testosterone levels in males during the breeding season. Using systematic testosterone treatment, we induced electric-pulse elongation in fish and found that the timing of electroreceptor spiking responses to self-generated pulses (reafference) was delayed as electric pulse duration increased. Recording evoked potentials from a midbrain electrosensory nucleus revealed that the timing of corollary discharge inhibition was delayed and elongated by testosterone. Further, this shift in corollary discharge timing was precisely matched to the shift in timing of the reafferent spikes. We then asked whether the shift in inhibition timing was caused by direct action of testosterone on the corollary discharge circuit or plasticity of the circuit through altered sensory feedback. We surgically silenced the electric organs of fish and found similar hormonal modulation of corollary discharge timing between intact and silent fish, suggesting that sensory feedback was not required for this shift. These results demonstrate that testosterone directly and independently modulates peripheral motor output and a predictive motor signal in a coordinated manner.SignificanceSelf-other discrimination is essential for animals. Internal predictive motor signals, or corollary discharge, provide motor information to sensory areas so that animals can perceive self- and other-generated stimuli differently. As behavior and associated sensory feedback change with development, corollary discharge must adjust accordingly. Using weakly electric mormyrid fish, we show that the steroid hormone testosterone alters electric signaling behavior and the resulting sensory feedback, as well as the timing of corollary discharge, to precisely match the altered sensory feedback. We also found that the altered sensory feedback itself is not necessary to drive this corollary discharge modulation. Our findings demonstrate that testosterone directly and independently regulates peripheral motor output and corollary discharge in a coordinated manner.
Fully-primed slowly-recovering vesicles mediate presynaptic LTP at neocortical neurons
Authors: Weichard Iron , Taschenberger Holger , Gsell Felix , Bornschein Grit , Ritzau-Jost Andreas , Schmidt Hartmut , Kittel Robert J. , Eilers Jens , Neher Erwin , Hallermann Stefan , Nerlich Jana 
Published: April 2023

AbstractPre- and postsynaptic forms of long-term potentiation (LTP) are candidate synaptic mechanisms underlying learning and memory. At layer 5 pyramidal neurons LTP increases the initial synaptic strength but also short-term depression during high-frequency transmission. This classical form of presynaptic LTP has been referred to as redistribution of synaptic efficacy. However, the underlying mechanisms remain unclear. We therefore performed whole-cell recordings from layer 5 pyramidal neurons in acute cortical slices of rats and analyzed presynaptic function before and after LTP induction by paired pre- and postsynaptic neuronal activity. LTP was successfully induced in about half of the synaptic connections tested and resulted in increased synaptic depression during high-frequency transmission and a decelerated recovery from depression due to an increased occurrence of a slow recovery component. Analysis with a recently established sequential two-step vesicle priming model indicates an increase in the abundance of fully-primed and slowly-recovering vesicles. A systematic analysis of short-term plasticity and synapse-to-synapse variability of synaptic strength at various types of synapses revealed that stronger synapses generally recover more slowly from synaptic depression. Finally, pharmacological stimulation of the cyclic adenosine monophosphate (cAMP) and diacylglycerol (DAG) signaling pathways, which are both known to promote synaptic vesicle priming mimicked electrically-induced LTP and slowed the recovery from depression. Our data thus demonstrate that LTP at layer 5 pyramidal neurons increases synaptic strength primarily by enlarging a subpool of fully-primed slowly-recovering vesicles.
Cholinergic Modulation is Necessary for Upward Firing Rate Homeostasis in Rodent Visual Cortex
Authors: Bottorff Juliet , Padgett Sydney , Turrigiano Gina G. 
Published: April 2023

ABSTRACTBidirectional homeostatic plasticity allows neurons and circuits to maintain stable firing in the face of developmental or learning-induced perturbations. In primary visual cortex (V1), upward firing rate homeostasis (FRH) only occurs during active wake (AW) and downward during sleep, but how this behavioral state-dependent gating is accomplished is unknown. Here we focus on how AW enables upward FRH in V1 of juvenile Long Evans rats. A major difference between quiet wake (QW) when upward FRH is absent, and AW when it is present, is increased cholinergic (ACh) tone; we therefore chemogenetically inhibited V1-projecting basal forebrain cholinergic (BF ACh) neurons while inducing upward FRH using visual deprivation, and found that upward FRH was completely abolished. Next, we examined the impact on synaptic scaling and intrinsic excitability, two important cellular targets of homeostatic regulation. BF ACh inhibition impaired synaptic scaling up, and dramatically decreased the intrinsic excitability of activity-deprived V1 pyramidal neurons, consistent with the block of upward FRH. Interestingly, knock down of the highly abundant M1 ACh receptor in V1 failed to phenocopy the effects of decreased BF ACh activity on intrinsic excitability, suggesting either that BF ACh activity acts through a different receptor within V1, or acts indirectly via other brain regions or cell types. Together, our results show that BF ACh modulation is a key enabler of upward homeostatic plasticity, and more broadly suggest that neuromodulatory tone is a critical factor that segregates upward and downward homeostatic plasticity into distinct behavioral states.SIGNIFICANCE STATEMENTHebbian, positive feedback-based and homeostatic, negative feedback-based plasticity mechanisms are necessary to maintain the functionality of flexible yet stable complex neuronal circuits. Growing evidence suggests a role for behavioral state in temporally segregating these opposing plasticity mechanisms, but how behavioral states enact this gating remains unknown. Here, we tested the role of acetylcholine (ACh), a widespread neuromodulator largely released during active wake, in the regulation of upward homeostatic plasticity. We found that ACh modulation is indeed necessary for the expression of active wake-gated upward firing rate homeostasis, likely due to its role in maintaining intrinsic excitability of cortical pyramidal neurons. Our results suggest potential mechanisms by which neuromodulatory tone may enable behavioral state gating of homeostatic plasticity.