Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic attention signaling in V4: relation to excitatory/inhibitory cell class and population coupling

Neurons have different roles in attention processing. These roles are determined by a neuron’s firing properties, neurotransmitter expression, and functional connectivity. Neurons in the visual cortical area, V4, are reliably engaged by selective attention but exhibit differences in firing rate and correlated variability. It remains unclear what specific neuronal properties shape these attention effects. We identified neurons as fast-spiking (FS) (putative inhibitory) and regular-spiking (RS) (putative excitatory) and investigated their role in anticipatory attention and how this related to their functional connectivity. V4 neurons exhibited a continuum of time-varying attention effects ranging from “restless-weak” neurons at one extreme to “quiet-strong” neurons at another. We found an interdependence between neural attention effects (e.g., restless-weak or quiet-strong), neuron type (FS, RS), and functional connectivity. In particular, we found neurons with restless-weak attention effects were more likely to be RS and have greater population coupling, compared to neurons with other types of attention effects. Also, quiet-strong neurons were more likely to be FS and these FS neurons exhibited higher spike synchrony. From this we propose that time-varying attention effects in a neuronal population depends on the relative involvement of neurons that drive stimulus processing and those that are engaged by intrinsic population activity. These results add important information to our understanding of visual attention circuits at the cellular level.
Three-Phase PFC Rectifier and High-Voltage Generator for X-Ray Systems

Medical X-ray systems have been under steady development since the discovery of X-rays by Röngten in 1895. However, the principle of X-ray generation has remained the same. Electrons are accelerated within an evacuated tube by a high-voltage difference from the cathode towards the anode. X-rays are emitted when electrons hits the anode. However, most of the energy of the electrons is dissipated by the anode in form of heat. Therefore, an X-ray power supply needs to provide not only voltages up to 150 kV but also a peak power of up to 100 kW. Since the cooling capability of the vacuum tube is typically only in the range of 1 kW, the power supply has to deliver high peak but only low average power. In the development of X-ray systems there are three major trends affecting the high-voltage generator. First, nowadays X-ray systems use passive three-phase rectifiers which limit the application with weak power grids, emit low-frequency current harmonics and usually require adaption transformers for use with different nominal mains voltages. It is desired to use an active rectifier instead in order to provide a wide input voltage range that allows world-wide use of the device without modifications to the hardware. Second, currently available high-voltage generators typically provide riseand fall-times of the tube voltage in the range of 500 μs. In pulsed fluoroscopy applications short riseand fall-times of the tube voltage would eliminate the need for the cathode control grid which is necessary to keep the patient dose at a minimum. In dual energy computer tomography shorter falland rise-times could replace nowadays systems using two X-ray tubes at two different voltage levels by a single tube which is alternating between two voltage levels. Finally, the additional features should be achieved in a cost effective manner in order to make the technology affordable for all patients. In order to achieve cost reductions the design of the inductive components is of particular importance. The high peak power but low average power of the application allows to reduce the volume and material cost of inductors and transformers substantially without exceeding the thermal limit. One basic element for the design of inductive components is the winding loss model which needs to take into account skin effect and proximity effect losses within the winding. An easy to use winding loss model is presented based on asymptotic approximations of the exact analytic equations for skin effect and proximity effect. Using appropriate asymptotic solutions for the low-frequency v
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors

Vaccines and drugs have helped reduce disease severity and blunt the spread of SARS-CoV-2. However, ongoing virus transmission, continuous evolution, and increasing selective pressures have the potential to yield viral variants capable of resisting these interventions. Here, we investigate the susceptibility of natural variants of the main protease (Mpro/3CLpro) of SARS-CoV-2 to protease inhibitors. Multiple single amino acid changes in Mpro confer resistance to nirmatrelvir (the active component of Paxlovid). An additional clinical-stage inhibitor, ensitrelvir (Xocova), shows a different resistance mutation profile. Importantly, phylogenetic analyses indicate that several of these resistant variants have pre-existed the introduction of these drugs into the human population and are capable of spreading. These results encourage the monitoring of resistance variants and the development of additional protease inhibitors and other antiviral drugs with different mechanisms of action and resistance profiles for combinatorial therapy. One Sentence Summary Resistance to protease inhibitor drugs, nirmatrelvir (Paxlovid) and ensitrelvir (Xocova), exists in SARS-CoV-2 variants in the human population.
Distributed cortical regions for the recall of people, places and objects

Human medial parietal cortex (MPC) is recruited during multiple cognitive processes. Previously, we demonstrated regions specific to recall of people or places and proposed that the functional organization of MPC mirrors the category selectivity defining the medial-lateral axis of ventral temporal cortex (VTC). However, prior work considered recall of people and places only and VTC also shows object-selectivity sandwiched between face- and scene-selective regions. Here, we tested a strong prediction of our proposal: like VTC, MPC should show a region specifically recruited during object recall, and its relative cortical position should mirror the one of VTC. While responses during people and place recall showed a striking replication of prior findings, we did not observe any evidence for object-recall effects within MPC, which differentiates it from the spatial organization in VTC. Importantly, beyond MPC, robust recall-effects were observed for people, places, and objects on the lateral surface of the brain. Place-recall effects were present in the angular gyrus, frontal eye fields and peripheral portions of early visual cortex, whereas people-recall selectively drove response in the right posterior superior temporal sulcus. Object-recall effects were largely restricted to a region posterior to left somatosensory cortex, in the vicinity of the supramarginal gyrus. Taken together, these data demonstrate that while there are distributed regions active during recall of people, places and objects, the functional organization of MPC does not mirror the medial-lateral axis of VTC but reflects only the most salient features of that axis - namely representations of people and places. Significance statement Human medial parietal cortex (MPC) is recruited during multiple cognitive. Recently, we proposed a framework for interpreting the functional organization of MPC by suggesting that it reflects the categorical preferences for people and places that is evident also in ventral temporal cortex (VTC). Because VTC also exhibits selectivity for objects, we here extend this framework to test whether MPC also shows object selectivity during recall. Robust people and place recall effects were evident in MPC, but we found no evidence for object-recall within MPC, suggesting that MPC and VTC are not mirror-copies of each other. Together, these data suggest that the functional organization of MPC reflects the most salient categorical representations within VTC for people and places.
Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributions

Transcriptional rates are often estimated by fitting the distribution of mature mRNA numbers measured using smFISH (single molecule fluorescence in situ hybridization) with the distribution predicted by the telegraph model of gene expression, which defines two promoter states of activity and inactivity. However, fluctuations in mature mRNA numbers are strongly affected by processes downstream of transcription. In addition, the telegraph model assumes one gene copy, but in experiments cells may have two gene copies as cells replicate their genome during the cell cycle. Whilst it is often presumed that post-transcriptional noise and gene copy number variation affect transcriptional parameter estimation, the size of the error introduced remains unclear. To address this issue, here we measure both mature and nascent mRNA distributions of GAL10 in yeast cells using smFISH and classify each cell according to its cell cycle phase. We infer transcriptional parameters from mature and nascent mRNA distributions, with and without accounting for cell cycle phase and compare the results to live-cell transcription measurements of the same gene. We find that: (i) correcting for cell cycle dynamics decreases the promoter switching rates and the initiation rate, and increases the fraction of time spent in the active state, as well as the burst size; (ii) additional correction for post-transcriptional noise leads to further increases in the burst size and to a large reduction in the errors in parameter estimation. Furthermore, we outline how to correctly adjust for measurement noise in smFISH due to uncertainty in transcription site localisation when introns cannot be labelled. Simulations with parameters estimated from nascent smFISH data, which is corrected for cell cycle phases and measurement noise, leads to autocorrelation functions that agree with those obtained from live-cell imaging.
Multi-modal haptic image recognition based on deep learning

Purpose This paper aims to improve the diversity and richness of haptic perception by recognizing multi-modal haptic images. Design/methodology/approach First, the multi-modal haptic data collected by BioTac sensors from different objects are pre-processed, and then combined into haptic images. Second, a multi-class and multi-label deep learning model is designed, which can simultaneously learn four haptic features (hardness, thermal conductivity, roughness and texture) from the haptic images, and recognize objects based on these features. The haptic images with different dimensions and modalities are provided for testing the recognition performance of this model. Findings The results imply that multi-modal data fusion has a better performance than single-modal data on tactile understanding, and the haptic images with larger dimension are conducive to more accurate haptic measurement. Practical implications The proposed method has important potential application in unknown environment perception, dexterous grasping manipulation and other intelligent robotics domains. Originality/value This paper proposes a new deep learning model for extracting multiple haptic features and recognizing objects from multi-modal haptic images.
Different modality-specific mechanisms mediate perceptual history effects in vision and audition

Perceptual history plays an important role in sensory processing and decision making, shaping how we perceive and judge external objects and events. Indeed, past stimuli can bias what we are currently seeing in an attractive fashion, making a current stimulus to appear more similar to its preceding one than it actually is. Such attractive effects across successive stimuli appear to be ubiquitous, affecting almost every aspect of perception – from very basic visual attributes (i.e., orientation) to more complex features (i.e., face identity) – suggesting that they may reflect a fundamental principle of brain processing. However, it is unclear whether the ubiquitous nature of these effects is due to an underlying centralised mechanism mediating all of them, or by the existence of separate mechanisms implemented independently in different perceptual pathways. Here we address this question by assessing the behavioural and neural signature of perceptual history in audition and vision, in the context of time perception. Our results first show a double dissociation between the two modalities, whereby the behavioural effect of perceptual history shows opposite patterns of selectivity for the features and position of the stimuli. Electroencephalography results further support a difference between audition and vision, demonstrating that the signature of perceptual history unfolds according to different dynamics in the two modalities and show different relations with the behavioural effect. Overall, our results suggest that the effect of perceptual history may be mediated by different and at least partially independent mechanisms based on the same computational principle, implemented in different sensory pathways. SIGNIFICANCE STATEMENT The recent history of stimulation, or perceptual history, plays a fundamental role in perception, shaping what we see according to what we saw in the past. The brain mechanisms mediating the integration of past and present perceptual information are however still unclear. In this study we asked whether perceptual history operates via a centralized mechanism shared across sensory modalities, or via distinct modality-specific mechanisms. Our findings show a double dissociation in attractive perceptual history effects across vision and audition, while EEG data show neural signatures of perceptual history with distinct dynamics and properties. Overall, we thus demonstrate that perceptual history affects sensory processing starting from the earliest level of processing, within distinct modality-specific sensory pathways.
Subfunctionalization and constrained size of the immunoglobulin loci in Ambystoma mexicanum

Background The axolotl, Ambystoma mexicanum is a unique biological model for complete tissue regeneration. Is a neotenic endangered species and is highly susceptible to environmental stress, including infectious disease. In contrast to other amphibians, the axolotl is particularly vulnerable to certain viral infections. Like other salamanders, the axolotl genome is one of the largest (32 Gb) and the impact of genome size on Ig loci architecture is unknown. To better understand the immune response in axolotl, we aimed to characterize the immunoglobulin loci of A. mexicanum and compare it with other model tetrapods. Methods The most recently published genome sequence of A. mexicanum (V6) was used for alignment-based annotation and manual curation using previously described axolotl Ig sequences or reference sequences from other tetrapods. Gene models were further curated using A. mexicanum spleen RNA-seq data. Human reference genomes, Xenopus tropicalis, and Danio rerio (zebrafish) were used for comparison. Results Canonical A. mexicanum Heavy chain (IGH), lambda (IGL), sigma (IGS) and Surrogate light chain (SLC) loci were identified. No kappa locus was found. More than half of the IGHV genes and the IGHF gene are pseudogenes, there are no clan I IGHV genes and CDRH3 diversity is restricted. Although the IGH locus size is proportional to genome size, we found local size restriction in the IGHM gene and in the V gene intergenic distances. In addition, there were V genes with abnormally large V-intron sizes, which correlated with loss of gene functionality. Conclusion The A. mexicanum immunoglobulin loci share the same general genome architecture as most studied tetrapods. Consistent with its large genome, Ig loci are larger; however, local size restrictions indicate evolutionary constraints likely to be imposed by high transcriptional demand of certain Ig genes, as well as the V(D)J recombination over very long genomic distance ranges. The A. mexicanum has undergone an extensive process of pseudogenization which partially explains a reduced potential repertoire diversity that may contribute to its impaired antibody response.
Clarifying the role of an unavailable distractor in human multiattribute choice

Decisions between two economic goods can be swayed by a third unavailable ‘decoy’ alternative, which does not compete for choice, notoriously violating the principles of rational choice theory. Although decoy effects typically depend on the decoy’s position in a multiattribute choice space, recent studies using risky prospects (i.e., varying in reward and probability) reported a novel ‘positive’ decoy effect operating on a single ‘value’ dimension: the higher the ‘expected value’ of an unavailable (distractor) prospect was, the easier the discrimination between two available target prospects became, especially when their expected-value difference was small. Here we show that this unidimensional distractor effect affords alternative interpretations: it occurred because the distractor’s expected value covaried positively with the subjective utility difference between the two targets. Looking beyond this covariation, we report a modest ‘negative’ distractor effect operating on subjective utility, as well as classic multiattribute decoy effects. A normatively meaningful model (selective integration), in which subjective utilities are shaped by ‘intra-attribute’ information distortion, reproduces the multiattribute decoy effects, and as an epiphenomenon, the negative unidimensional distractor effect. These findings clarify the modulatory role of an unavailable distracting option, shedding fresh light on the mechanisms that govern multiattribute decisions.
Persistent effects of acute trauma on Pavlovian-to-instrumental transfer

In humans, an acutely traumatic experience can lead to post-traumatic stress disorder (PTSD), which is often characterized by changes in anxiety and motivation months after trauma. There are few demonstrations of the persistent motivational effects of an acute stressor in rodent approaches to PTSD. In two experiments, we evaluated the persistent effects of a battery of footshocks in one context on appetitive Pavlovian conditioning, instrumental learning, and Pavlovian-to-instrumental transfer (PIT) in a different context. A battery of footshocks before appetitive training caused deficits in single-outcome PIT in male Long Evans rats. The same battery of footshocks after appetitive training, but before testing had little effect on single-outcome PIT, but there were some qualitative deficits. Although males showed more generalized fear from the aversive to the appetitive context compared to females, there were no effects of shock on sensory-specific PIT in male or female rats. In general females showed less evidence for sensory-specific PIT compared to males, who showed robust sensory-specific PIT, with clear extinction and spontaneous recovery of the sensory-specific PIT effect across test sessions. These findings show that (a) an acute trauma can have persistent effects on general motivational processes and (b) sensory-specific PIT is a useful approach for exploring sex differences in strategies for instrumental learning. We discuss implications for current approaches to stress and motivation in preclinical and clinical studies.
Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components

The establishment of cellular identity is driven by transcriptional and epigenetic regulation exerted by the components of the chromatin proteome - the chromatome. However, chromatome composition and its dynamics in functional phases of pluripotency have not been comprehensively analyzed thus limiting our understanding of these processes. To address this problem, we developed an accurate mass spectrometry (MS)-based proteomic method called Chromatin Aggregation Capture (ChAC) followed by Data-Independent Acquisition (DIA) to analyze chromatome reorganizations during the transition from ground to formative and primed pluripotency states. This allowed us to generate a comprehensive atlas of proteomes, chromatomes, and chromatin affinities for the three pluripotency phases, revealing the specific binding and rearrangement of regulatory complexes. The technical advances, the comprehensive chromatome atlas, and the extensive analysis reported here provide a foundation for an in-depth understanding of mechanisms that govern the phased progression of pluripotency and changes of cellular identities in development and disease.
Establishment of the body condition score for adult female Xenopus laevis

The assessment of animals’ health and nutritional status using a Body Condition Score (BCS) has become a common and reliable tool in lab-animal science. It enables a simple, semi-objective, and non-invasive assessment (palpation of osteal prominences and subcutaneous fat tissue) in routine examination of an animal. In mammals, the BCS classification contains 5 levels: A low score describes a poor nutritional condition (BCS 1-2). A BCS of 3 to 4 is considered optimum, whereas a high score (BCS=5) is associated with obesity. While BCS are published for most common laboratory mammals, these assessment criteria are not directly applicable to clawed frogs (Xenopus laevis) due to their intracoelomic fat body instead of subcutaneous fat tissue. Therefore this assessment tool is still missing for Xenopus laevis. The present study aimed to establish a species-specific BCS for clawed frogs in terms of experimental refinement. Accordingly, 62 adult female Xenopus laevis were weighed and sized. Further, the body contour was defined, classified, and assigned to BCS groups. A BCS 5 was associated with a mean body weight of 193.3 g (± 27.6 g), whereas a BCS 4 ranged at 163.1 g (±16.0 g). Animals with a BCS=3 had an average body weight of 114.7 g (±16.7 g). A BCS=2 was determined in 3 animals (103 g, 110 g, and 111 g). One animal had a BCS=1 (83 g), which would be equivalent to a humane endpoint. In conclusion, individual examination using the presented visual BCS provides a quick and easy assessment of nutritional status and overall health of adult female Xenopus laevis. Due to their ectothermic nature and the associated special metabolic situation, it can be assumed that a BCS ≥3 is to be preferred for female Xenopus laevis. In addition, BCS assessment may indicate underlying subclinical health problems that require further diagnostic investigation.