Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of confidence in decision-making and its pupillary correlate during the interaction with a partner

Every decision we make is accompanied by a sense of confidence. Confidence mechanisms allow evaluating the evidence that supports our decisions such as the quality of our perceptual representations. Confidence is thought to play a critical role in guiding decision-making, but only a few empirical studies have actually investigated the function of confidence. To address this, we designed a perceptual task in which participants provided a confidence judgment on the accuracy of their perceptual decision. Then, they viewed the response of a machine or human partner, and they were instructed to decide whether to keep or change their initial response. We observed that confidence predicted participants’ decision to keep or change their initial responses more than task difficulty and perceptual accuracy. This suggests that confidence, as a subjective evaluation of uncertainty, enables us to weigh our decisions in order to adapt our decision-making behavior driving the interaction with a partner. Furthermore, confidence judgments could be predicted by eye pupil dynamics, suggesting that arousal changes are linked to confidence computations. This study contributes to our understanding of the function of confidence in decision-making and highlights the possibility of using pupil dynamics as a proxy of confidence.
Lattice relaxation at a metal surface

It is shown that all interatomic potentials of the classical type---Morse, Lennard-Jones, etc.,---yield, by their very nature, an expansion of the interlayer separation between the topmost surface layers. No such prediction can be made a priori for the oscillatory-type potentials. Using a simple procedure to compute the relaxations, we also show that Friedel's tight-binding model for transition metals yields contraction for the (100), (110), and (111) surfaces of a face-centered-cubic transition metal, a result in agreement with experiment.
Intraluminal neutrophils limit epithelium damage by reducing pathogen assault on intestinal epithelial cells during Salmonella gut infection

Recruitment of neutrophils into the gut epithelium is a cardinal feature of intestinal inflammation in response to enteric infections. Previous work using the model pathogen Salmonella Typhimurium (S. Tm) established that invasion of intestinal epithelial cells by S.Tm leads to recruitment of neutrophils into the gut lumen, where they can reduce pathogen loads transiently. Notably, a fraction of the pathogen population can survive this defense, re-grow to high density, and continue triggering enteropathy. However, the functions of intraluminal neutrophils in the defense against enteric pathogens and their effects on preventing or aggravating epithelial damage are still not fully understood. Here, we address this question via neutrophil depletion in different mouse models of Salmonella colitis, which differ in their degree of enteropathy. In an antibiotic pre-treated mouse model, neutrophil depletion by an anti-Ly6G antibody exacerbated epithelial damage. This could be linked to compromised neutrophil-mediated elimination and reduced physical blocking of the gut-luminal S.Tm population such that the pathogen density remained high near the epithelial surface throughout the infection. The removal of luminal S. Tm by gentamicin, an antibiotic restricted to the gut lumen, reversed the effect of neutrophil depletion on epithelial cell loss. Strikingly, when using germ-free mice and an S. Tm ssaV mutant capable of epithelium invasion, but attenuated for survival and growth within host tissues, neutrophil depletion caused exacerbated immune activation of the gut mucosa and a complete destruction of the epithelial barrier. Together, our data indicate that intraluminal neutrophils are central for maintaining epithelial barrier integrity during acute Salmonella-induced gut inflammation, by limiting the sustained pathogen assault on the epithelium in a critical window of the infection. Highlights ○ After the first wave of mucosal invasion (day 1 p.i.), S. Tm maintains the assault from the lumen, triggering the continued expulsion of epithelial cells in antibiotic pre-treated mice. ○ Neutrophil recruitment into the gut lumen is essential to limit this continued Salmonella attack on the epithelium. ○ In antibiotic pre-treated SPF mice, neutrophil depletion exacerbates S. Tm invasion, causing excessive epithelial cell loss, which compromises epithelial barrier integrity at later time points (day 2-3 p.i.). ○ In germ-free mice, neutrophil depletion exacerbates epithelial responses and epithelial barrier destruction even more strongly than in streptomycin pre-treated SPF mice. ○ Gentamicin treatment and ssaV mutant infections indicate that neutrophils prevent epithelial damage by eliminating and physically blocking gut-luminal pathogens.
Hippocampal engrams generate flexible behavioral responses and brain-wide network states

Memory engrams are both necessary and sufficient to mediate behavioral outputs. Defensive behaviors such as freezing and avoidance are commonly examined during hippocampal-mediated fear engram reactivation, yet how reactivation of these cellular populations across different contexts engages the brain to produce a variety of defensive behaviors is relatively unclear. To address this, we first optogenetically reactivated a tagged fear engram in the dentate gyrus (DG) subregion of the hippocampus across three distinct contexts. We found that there were differential amounts of light-induced freezing depending on the size of the context in which reactivation occurred: mice demonstrated robust light-induced freezing in the most spatially restricted of the three contexts but not in the largest. We then utilized graph theoretical analyses to identify brain-wide alterations in cFos co-activation during engram reactivation across the smallest and largest contexts. Our manipulations conferred greater positive cFos correlations and recruited regions spanning putative fear and defense systems as hubs in the respective networks. Moreover, reactivating DG-mediated engrams generated network topologies across experimental conditions, emphasizing both shared and distinct features. By identifying and manipulating the circuits supporting memory function, as well as their corresponding brain-wide activity patterns, it is thereby possible to resolve systems-level biological mechanisms mediating memory’s capacity to modulate behavioral states. SIGNIFICANCE STATEMENT Implementing appropriate defensive behaviors across disparate environments is essential for survival. Memories can be used to select these responses. Recent work identified and artificially manipulated cellular ensembles within the hippocampus that mediate fear memory recall, yet how these populations engage brain-wide pathways that mediate defensive behaviors under environmental contingencies is unclear. We demonstrated here that reactivation across environments of various sizes elicits different behavioral responses and corresponding brain-wide network dynamics. These findings establish the flexibility of memory-bearing ensembles in generating brain and behavior states.
Main Manuscript for Cell migration simulator-based biomarkers for glioblastoma

Glioblastoma is the most aggressive malignant brain tumor with poor survival due to its invasive nature driven by cell migration, with unclear linkage to transcriptomic information. Here, we applied a physics-based motor-clutch model, a cell migration simulator (CMS), to parameterize the migration of glioblastoma cells and define physical biomarkers on a patient-by-patient basis. We reduced the 11-dimensional parameter space of the CMS into 3D to identify three principal physical parameters that govern cell migration: motor number – describing myosin II activity, clutch number – describing adhesion level, and F-actin polymerization rate. Experimentally, we found that glioblastoma patient-derived (xenograft) (PD(X)) cell lines across mesenchymal (MES), proneural (PN), classical (CL) subtypes and two institutions (N=13 patients) had optimal motility and traction force on stiffnesses around 9.3kPa, with otherwise heterogeneous and uncorrelated motility, traction, and F-actin flow. By contrast, with the CMS parameterization, we found glioblastoma cells consistently had balanced motor/clutch ratios to enable effective migration, and that MES cells had higher actin polymerization rates resulting in higher motility. The CMS also predicted differential sensitivity to cytoskeletal drugs between patients. Finally, we identified 11 genes that correlated with the physical parameters, suggesting that transcriptomic data alone could potentially predict the mechanics and speed of glioblastoma cell migration. Overall, we describe a general physics-based framework for parameterizing individual glioblastoma patients and connecting to clinical transcriptomic data, that can potentially be used to develop patient-specific anti-migratory therapeutic strategies generally. Significance Statement Successful precision medicine requires biomarkers to define patient states and identify personalized treatments. While biomarkers are generally based on expression levels of protein and/or RNA, we ultimately seek to alter fundamental cell behaviors such as cell migration, which drives tumor invasion and metastasis. Our study defines a new approach for using biophysics-based models to define mechanical biomarkers that can be used to identify patient-specific anti-migratory therapeutic strategies.
A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don

Japanese cedar (Cryptomeria japonica D. Don) is the most important Japanese forest tree, occupying about 44% of artificial forests in Japan, and planted in East Asia, Azores Archipelago, and some islands in the Indian Ocean. Although the huge genome of the species (ca. 11 Gb) with abundant repeat elements might have been an obstacle for genetic analysis, the species is easily propagated by cutting, flowered by plant hormones like gibberellic acid, transformed by agrobacterium, and edited by CRISPR/Cas9. These characteristics of C. japonica are preferable to make the species a model conifer for which reference genome sequences are necessary. In this study, we report the first chromosome-level assembly for C. japonica (2n = 22) using a third generation selfed progeny with an estimated homozygosity of 0.96. Young leaf tissue was used to extract high-molecular-weight DNA (>50 kb) for HiFi PacBio long read sequencing and to construct Hi-C/Omni-C library for Illumina short read sequencing. Using the 29× and 26× genome coverage of HiFi and Illumina reads, respectively, de novo assembly resulted in 2,650 contigs (9.1 Gb in total) with N50 contig size of 12.0 Mb. The Hi-C analysis mapped 97% of the nucleotides on the 11 chromosomes. The assembly was verified by comparing with a consensus linkage map of 7,785 markers. The BUSCO analysis confirmed ~91% of conserved genes. Annotations of genes, repeat elements and synteny with other Cupressaceae and Pinaceae species were performed, providing fundamental resources for genomic research of conifers.
U1 AMO (antisense morpholino oligo) disrupts U1 snRNP structure to promote intronic premature cleavage and polyadenylation (PCPA)

Functional depletion of U1 snRNP with a 25 nt U1 AMO (antisense morpholino oligonucleotides) may lead to intronic premature cleavage and polyadenylation (PCPA) of thousands of genes, a phenomenon known as U1 snRNP telescripting; however, the underlying mechanism remains elusive. In this study, we demonstrated that U1 AMO could disrupt U1 snRNP structure both in vitro and in vivo, thereby affecting U1 snRNP/RNAP polymerase II (RNAPII) interaction. We further showed that U1 AMO treatment might promote RNAPII disassociation with pre-mRNA in an RNA pull-down assay. By performing ChIP-seq for phosphorylation of Ser2 (Ser2P) and Ser5 (Ser5P) of the C-terminal domain (CTD) of RNA polymerase II (RNAPII), we showed that transcription elongation was disturbed upon U1 AMO treatment, with a particular high Ser2P signal at intronic cryptic polyadenylation sites (PASs). In addition, we showed that core 3’ processing factors CPSF/CstF are involved in the processing of intronic cryptic PAS. Their recruitment accumulated toward cryptic PASs upon U1 AMO treatment, as indicated by ChIP-seq and iCLIP-seq analysis. Furthermore, we showed that most of these PCPAed transcripts could be exported to cytoplasm and have the potential to be translated. Conclusively, our data provide more insight into U1 snRNP telescripting, and suggest a common theme that modulation of transcription elongation may be an important mode for the regulation of mRNA polyadenylation.
Criticality supports cross-frequency cortical-thalamic information transfer during conscious states

Consciousness is thought to be regulated by bidirectional information transfer between the cortex and thalamus, but the nature of this bidirectional communication - and its possible disruption in unconsciousness - remains poorly understood. Here, we present two main findings elucidating mechanisms of corticothalamic information transfer during conscious states. First, we identify a highly preserved spectral channel of cortical-thalamic communication which is present during conscious states but which is diminished during the loss of consciousness and enhanced during psychedelic states. Specifically, we show that in humans, mice, and rats, information sent from either the cortex or thalamus via δ/θ/α waves (~1.5-13 Hz) is consistently encoded by the other brain region by high γ waves (~50-100 Hz); moroever, unconsciousness induced by propofol anesthesia or generalized spike-and-wave seizures diminishes this cross-frequency communication, whereas the psychedelic 5-methoxy-N,N/-dimethyltryptamine (5-MeO-DMT) enhances this interregional communication. Second, we leverage numerical simulations and neural electrophysiology recordings from the thalamus and cortex of human patients, rats, and mice to show that these changes in cross-frequency cortical-thalamic information transfer are mediated by excursions of low-frequency thalamocortical electrodynamics toward/away from edge-of-chaos criticality, or the phase transition from stability to chaos. Overall, our findings link thalamic-cortical communication to consciousness, and further offer a novel, mathematically well-defined framework to explain the disruption to thalamic-cortical information transfer during unconscious states.
Spectral and time domain OCT: a tool for optimal imaging of biological samples

Spectral and Time domain OCT (STdOCT) is a data analysis scheme proposed for sensitive Doppler imaging. In this work we show that it has an additional feature: when compared to those created using complex or amplitude averaging, tomograms prepared using STdOCT have the highest contrast to noise ratio and preserve high signal to noise ratio and image dynamic range. Images of uniformly scattering phantom as well as images of human retina in vivo prepared with three different techniques are shown.
High-Throughput Microfluidic Quantitative PCR Platform for the Simultaneous Quantification of Pathogens, Fecal Indicator Bacteria, and Microbial Source Tracking Markers.

Contamination of water with bacterial, viral, and protozoan pathogens can cause human diseases. Both humans and nonhumans can release these pathogens through their feces. To identify the sources of fecal contamination in the water environment, microbial source tracking (MST) approaches have been developed; however, the relationship between MST markers and pathogens is still not well understood most likely due to the lack of comprehensive datasets of pathogens and MST marker concentrations. In this study, we developed a novel microfluidic quantitative PCR (MFQPCR) platform for the simultaneous quantification of 37 previously validated MST markers, two fecal indicator bacteria (FIB), 22 bacterial, 11 viral, and five protozoan pathogens, and three internal amplification/process controls in many samples. The MFQPCR chip was applied to analyze pathogen removal rates during the wastewater treatment processes. In addition, multiple host-specific MST markers, FIB, and pathogens were successfully quantified in human and avian-impacted surface waters. While the genes for pathogens were relatively infrequently detected, positive correlations were observed between some potential pathogens such as Clostridium perfringens and Mycobacterium spp. , and human MST markers. The MFQPCR chips developed in this study, therefore, can provide useful information to monitor and improve water quality.
Peri-operative management of antiplatelet therapy in patients with coronary artery disease

Summary An increasing number of patients suffering from cardiovascular disease, especially coronary artery disease (CAD), are treated with aspirin and/or clopidogrel for the prevention of major adverse events. Unfortunately, there are no specific, widely accepted recommendations for the perioperative management of patients receiving antiplatelet therapy. Therefore, members of the Perioperative Haemostasis Group of the Society on Thrombosis and Haemostasis Research (GTH), the Perioperative Coagulation Group of the Austrian Society for Anesthesiology, Reanimation and Intensive Care (ÖGARI) and the Working Group Thrombosis of the European Society of Cardiology (ESC) have created this consensus position paper to provide clear recommendations on the perioperative use of antiplatelet agents (specifically with semi-urgent and urgent surgery), strongly supporting a multidisciplinary approach to optimize the treatment of individual patients with coronary artery disease who need major cardiac and non-cardiac surgery. With planned surgery, drug eluting stents (DES) should not be used unless surgery can be delayed for ≥12 months after DES implantation. If surgery cannot be delayed, surgical revascularisation, bare-metal stents or pure balloon angioplasty should be considered. During ongoing antiplatelet therapy, elective surgery should be delayed for the recommended duration of treatment. In patients with semi-urgent surgery, the decision to prematurely stop one or both antiplatelet agents (at least 5 days pre-operatively) has to be taken after multidisciplinary consultation, evaluating the individual thrombotic and bleeding risk. Urgently needed surgery has to take place under full antiplatelet therapy despite the increased bleeding risk. A multidisciplinary approach for optimal antithrombotic and haemostatic patient management is thus mandatory.
Average low-latitude meridional electric fields from DE 2 during solar maximum

Electric field data from the double probe vector electric field instrument (VEFI) on the DE 2 spacecraft have been analyzed to determine the average meridional electric field (zonal ion flow) patterns in the region between ±30° magnetic latitude during solar maximum conditions. Over 300 passes were used to compile the data set. Data were projected to a constant 300-km altitude and to the equatorial plane assuming that the electric field along the magnetic field was zero. The average data set displayed a rapid increase of the downward meridional electric field with local time near 1800 MLT with the higher latitudes seeing the change first. A secondary nighttime maximum of this electric field component was observed post midnight with the crossover to upward electric fields (westward ion flow) occurring between 0400 and 0500 MLT. A sharp return to near zero was observed between 1200 and 1300. Typical average amplitudes range between 3 and 6 mV/m. No consistent variations with magnetic activity were observed. Although the daily variation in the zonal ion flow is dominated by the diurnal term, a net superrotation is evident in the harmonic analysis. The superrotation is strongest near the equator and decreases with latitude, because of the disturbance dynamo. The higher order harmonics up through the quatrediurnal term are also of significant magnitude in the analysis of the shape of the daily variation. Close similarity is seen to the zonal neutral winds indicating that they form the principal driving force. The magnitudes of the electric field derived ion drift are somewhat higher than the average F region neutral wind values. This along with the higher order harmonic content argues for the need to develop fully coupled E and F region model depicting the ionosphere and thermosphere interactions in a self-consistent fashion.
Assessment of Bipedal and Quadrupedal Locomotion

Part I see this journal 1989; 2: 11-5 In a previous review article (1) the basic principles of biokinematical analysis of locomotion were presented. The present paper discusses technologies and methods for both biokinematical and biokinetical analyses of locomotion. The many noninvasive technologies available for locomotion analysis are generally similar for bipeds and quadrupeds and most have exploited recent advances in computer technology, sensor design and miniaturization of electronic circuitry (2, 3).
Resistive magnetohydrodynamic simulations of helicity-injected startup plasmas in National Spherical Torus eXperiment

The generation of helicity-injected startup plasmas in National Spherical Torus eXperiment (NSTX), including flux surface closure, is studied using resistive-magnetohydrodynamic simulations with plasma flows, currents, ohmic heating and anisotropic thermal conduction. An injection-voltage pulse shape is used that separates the injection and closure phases allowing elucidation of the physics. The formation of an X-point near the helicity-injection gap is triggered as the injector voltage drops to zero. Near the forming X-point, magnetic pressure due to toroidal field entrained in the E × B plasma flow from the helicity-injection gap drops, allowing resistive magnetic reconnection even though the total injected current is almost constant. Where appropriate, the simulations are compared with Transient Coaxial Helicity Injection experiments in the NSTX spherical tokamak, which have demonstrated the formation of a promising candidate for non-inductive startup plasmas [Raman et al., Phys. Rev. Lett. 90, 075005 (2003)].
A fast BiCG solver for the isotropic Poisson equation in the forward EIT problem in cylinder phantoms

We describe an efficient numerical method for solving the isotropic inhomogeneous 3D Poisson equation in cylindrical coordinates as applied to analysis of EIT phantom experimental systems. The proposed approach is based on the second order accuracy finite-difference scheme and the BiCG iterative method with the FFT preconditioner. Extensive validation, numerical examples and comparison with experimental results are given. The performance and accuracy of the proposed numerical method are investigated and compared with the similar BiCG method with the Jacoby preconditioner.