Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of neural communication dynamics in the Ventral Attention Network across distinct spatial and spatio-temporal scales

The Ventral Attention Network (VAN) is involved in reorienting attention from an ongoing task when a salient (pop-out) stimulus is detected in the environment. Previous neuroimaging studies have extensively evaluated the structural and functional connectivity of the VAN. However, directed effective connectivity within the network and the neural oscillations driving it still remain elusive. Functional magnetic resonance imaging (fMRI) studies have not been able to address this issue due to lack of appropriate temporal resolution required to capture the process of reorientation. In this study, we recorded scalp electroencephalography (EEG) and behavioural data from healthy human volunteers, obtained saliency-specific spectral changes, localized the sources underlying the spectral power modulations with individual-specific structural MRI scans, reconstructed the waveforms of the sources and investigated the causal relationships between the areas of the VAN using Granger causality (GC). Using a custom-designed experiment involving visual search on static images and a dynamic motion tracking task, we investigated the neural processing of salient distractors operating at very slow and very fast time scales, respectively. Our results revealed how a task-independent but context-specific VAN encompassing the right insula, the right lateral pre-frontal cortex, the anterior and the posterior right temporo-parietal junction communicating in the alpha frequency band (8-12 Hz) supports saliency processing.
Antibiotic-induced disturbances of the gut microbiota result in accelerated breast tumour growth via a mast cell-dependent pathway

The diverse community of commensal microbes that comprise the gut microbiota is known to play an integral role in human health, not least through its ability to regulate host immune responses and metabolic pathways. Alterations to the homeostasis of this community, including through the use of broad-spectrum antibiotics, have already been associated with the progression of several cancers, namely melanoma and liver. The aggressive nature of breast cancer (BrCa), largely due to its ability to metastasize early, has ranked the disease with the second highest mortality rate of all cancers globally. Yet the body of research into the complex relationship between the microbiota and BrCa is still limited. This study found that a depletion of the microbiota, through the administration of antibiotics, significantly increased the rate of primary tumour progression in mouse BrCa models. We show that antibiotic-induced microbiota disturbances lead to changes in behaviour of a relatively obscure tumour-immune cell population: mast cells. We observed increases in tumour stroma-associated mast cells in antibiotic treated animals. Moreover, inhibition of mast cell degranulation, via cromolyn, slowed tumour progression in antibiotic treated animals but not in control animals. Thus, it appears that a perturbed microbiota drives stroma-associated mast cell recruitment and activation, which in turn promotes primary tumour growth through an as yet unknown mechanism. One Sentence Summary: We show that breast cancer progression is accelerated through a unique/novel immune response involving mast cells as a result of an antibiotic induced perturbation of the gut microbiota in a mouse model.
Non-Toxic Virucidal Macromolecules Show High Efficacy Against Influenza Virus Ex Vivo and In Vivo

Influenza is one of the most widespread viral infections worldwide and represents a major public health problem. The risk that one of the next pandemics is caused by an influenza strain is very high. It is very important to develop broad-spectrum influenza antivirals to be ready for any possible vaccine shortcomings. Anti-influenza drugs are available but they are far from ideal. Arguably, an ideal antiviral should target conserved viral domains and be virucidal, i.e. irreversibly inhibit viral infectivity. Here, we describe a new class of broad-spectrum anti-influenza macromolecules that meets these criteria and displays exceedingly low toxicity. These compounds are based on a cyclodextrin core modified on its primary face with long hydrophobic linkers terminated in 6’sialyl-N-acetyllactosamine (6’SLN) or 3’SLN. SLN enables nanomolar inhibition of the viruses while the hydrophobic linkers confer irreversibility to the inhibition. The combination of these two properties allows for efficacy in vitro against several human or avian influenza strains, as well as against a 2009 pandemic influenza strain ex vivo. Importantly, we show that, in mice, the compounds provide therapeutic efficacy when administered 24h post-infection allowing 90% survival as opposed to no survival for the placebo and oseltamivir.
Fact retrieval or compacted procedures in arithmetic – a neurophysiological investigation of two hypotheses

There is broad consensus that adults solve single-digit multiplication problems almost exclusively by fact retrieval (i.e., retrieval of the solution from an arithmetic fact network). In contrast, there has been a long-standing debate on the cognitive processes involved in solving single-digit addition problems. This debate has evolved around two theoretical accounts. The fact-retrieval account postulates that these are solved through fact retrieval, just like multiplications, whereas the compacted-procedure account proposes that solving very small additions (i.e., problems with operands between 1 and 4) involves highly automatized and unconscious compacted procedures. In the present electroencephalography (EEG) study, we put these two accounts to the test by comparing neurophysiological correlates of solving very small additions and multiplications. A sample of 40 adults worked on an arithmetic production task involving all (non-tie) single-digit additions and multiplications. Afterwards, participants completed trial-by-trial strategy self-reports. In our EEG analyses, we focused on induced activity (event-related synchronization/desynchronization, ERS/ERD) in three frequency bands (theta, lower alpha, upper alpha). Across all frequency bands, we found higher evidential strength for similar rather than different neurophysiological processes accompanying the solution of very small addition and multiplication problems. This was also true when n + 1 and n × 1 problems were excluded from the analyses. In two additional analyses, we showed that ERS/ERD can differentiate between self-reported problem-solving strategies (retrieval vs. procedure) and even between n + 1 and n + m problems in very small additions, demonstrating its high sensitivity to cognitive processes in arithmetic. The present findings clearly support the fact-retrieval account, suggesting that both very small additions and multiplications are solved through fact retrieval. HIGHLIGHTS Neurophysiological test of fact retrieval and compacted procedures account Induced EEG data are sensitive to cognitive processes in arithmetic problem solving Both very small additions and multiplications are solved through fact retrieval
Structural basis for targeting human cancer antigen STEAP1 with antibodies

Six-transmembrane epithelial antigen of the prostate (STEAP1) is an integral membrane protein that is highly upregulated on the cell surface of several human cancers, making it a promising therapeutic target. It shares sequence homology with three enzymes (STEAP2-4) that catalyze the NADPH-dependent reduction of iron(III). However, STEAP1 lacks an intracellular NADPH-binding domain and does not exhibit cellular ferric-reductase activity. Thus, both the molecular function of STEAP1 and its role in cancer progression remain elusive. Here, we present a ~3.0 Å cryo-electron microscopy structure of trimeric human STEAP1 bound to three Fab-fragments of the clinically employed antibody mAb120.545. STEAP1 adopts a reductase-like conformation and interacts with the Fabs through its extracellular helices. Enzymatic assays in human cells reveal that STEAP1 promotes iron(III) reduction when fused to the intracellular NADPH-binding domain of its family member STEAP4, implicating STEAP1 as a functional ferric reductase in STEAP hetero-trimers. Our work provides a foundation for deciphering the molecular mechanisms of STEAP1 and will be instrumental in the design of new therapeutic strategies to target STEAP1 in cancer.
Evidence Supporting an Antimicrobial Origin of Targeting Peptides to Endosymbiotic Organelles

Mitochondria and chloroplasts emerged from primary endosymbiosis. Most proteins of the endosymbiont were subsequently expressed in the nucleo-cytosol of the host and organelle-targeted via the acquisition of N-terminal presequences, whose evolutionary origin remains enigmatic. Using a quantitative assessment of their physico-chemical properties, we show that organelle targeting peptides, which are distinct from signal peptides targeting other subcellular compartments, group with a subset of antimicrobial peptides. We demonstrate that extant antimicrobial peptides target a fluorescent reporter to either the mitochondria or the chloroplast in the green alga Chlamydomonas reinhardtii and, conversely, that extant targeting peptides still display antimicrobial activity. Thus, we provide strong computational and functional evidence for an evolutionary link between organelle-targeting and antimicrobial peptides. Our results support the view that resistance of bacterial progenitors of organelles to the attack of host antimicrobial peptides has been instrumental in eukaryogenesis and in emergence of photosynthetic eukaryotes.
Stimulus statistics and HCN current mediated resonance sets the scale of input-output mapping in Stellate cells of the Medial Entorhinal Cortex

The functional significance of the computations performed by Stellate cells of the Medial Entorhinal Cortex, proven time and again, makes them insightful, yet intriguing. The gradients of the intrinsic properties of these cells, aligned to the actual grid cell spacing gradients, have encouraged many thoughtful experiments. A long sought question in the stellate cell literature is thus the one seeking mechanistic implications for these correlates. The intrinsic dynamics of these cells have been tested previously in this light, primarily focusing on their spectral characteristics. However, the resonance phenomenon underlying these dynamics has not received the attention it deserves, and its potency under the in-vivo high conductance states to influence the input-output mapping remains to be estimated. In this light, we analyzed the signal gain of stellate cells in the presence of in-vivo like fluctuating conductance based synaptic inputs injected through the Dynamic clamp, in rat brain slices. We observed a consistent, HCN current sensitive, theta frequency peak in signal gain, indicating that the HCN current mediated resonance mechanisms are functional even under a heavy input barrage. Next, we tested the effects of an array of input statistics on this signal gain and observed it to be mostly unaffected by the input strength, but relatively susceptible to the input kinetics. Additionally, as a possible reflection of the underlying signal gain, we observed a significant theta modulation of inputs by HCN current, the extent of which was found to be influenced by the excitatory, but not inhibitory synaptic kinetics. Surprisingly, a corresponding modulation in the gamma frequencies was also observed for the firing rate response, wherein the signal gain in gamma frequencies was found to be higher in the presence of HCN, which also coincided with increased occurrence of bursts. A computational model with HCN-persistent sodium channels with similar simulated in vivo conditions could reproduce the experimental results, additionally suggesting the strength of inhibition and the kinetics of excitation as the input statistic based alternate resonance mechanisms which can operate independent of HCN. Our results thus suggest frequency dependent gain as an appropriate measure for analyzing the input-output mapping in the stellate cells, and point out the mechanisms via which the HCN currents and input statistics can interact and determine the scaling of responses in these cells.
Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks

Despite a common understanding that Gli TFs are utilized to reiterate a Hh morphogen gradient, genetic analyses suggest craniofacial development does not completely fit this paradigm. We demonstrated that rather than being driven by a Hh threshold, robust Gli3 transcriptional activity during skeletal and glossal development required interaction with the bHLH TF Hand2. Not only did genetic and expression data support a co-factorial relationship, but genomic analysis further revealed that Gli3 and Hand2 were enriched at regulatory elements for genes essential for mandibular patterning and development. Interestingly, motif analysis at sites co-occupied by Gli3 and Hand2 uncovered mandibular-specific, low-affinity, ‘divergent’ Gli binding motifs (dGBMs). Functional validation revealed these dGBMs conveyed synergistic activation of Gli targets essential for mandibular patterning and development. In summary, this work elucidates a novel, sequence-dependent mechanism for Gli transcriptional activity within the craniofacial complex that is independent of a graded Hh signal.
Scaling of organ masses in mammals and birds: phylogenetic signal and implications for metabolic rate scaling

Abstract The persistent enigma of why the whole-body metabolic rate increases hypoallometrically with body mass should be solved on both the ultimate and proximate levels. The proximate mechanism may involve hyperallometric scaling of metabolically inert tissue/organ masses, hypoallometric scaling of metabolically expensive organ masses, a decrease in mass-specific metabolic rates of organs or a combination of these three factors. Although there are literature data on the tissue/organ masses scaling, they do not consider phylogenetic information. Here, we analyse the scaling of tissue/organ masses in a sample of 100 mammalian and 22 bird species with a phylogenetically informed method (PGLS) to address two questions: the role of phylogenetic differences in organ/tissue size scaling and the potential role of organ/tissue mass scaling in interspecific metabolic rate scaling. Strong phylogenetic signal was found for the brain, kidney, spleen and stomach mass in mammals but only for the brain and leg muscle in birds. Metabolically relatively inert adipose tissue scales isometrically in both groups. The masses of energetically expensive visceral organs scale hypoallometrically in mammals, with the exception of lungs, with the lowest exponent for the brain. In contrast, only brain mass scales hypoallometrically in birds, whereas other tissues and organs scale isometrically or almost isometrically. Considering that the whole-body metabolic rate scales more steeply in mammals than in birds, the mass-specific metabolic rate of visceral organs must decrease with body mass much faster in birds than in mammals. In general, studying whole-body metabolic rate is not adequate for explaining its scaling, and measuring metabolic rates of organs, together with their contribution to body mass, is urgently required.
One-Day Construction Of Multiplex Arrays to Harness Natural CRISPR Systems

CRISPR-Cas systems are prokaryotic immune systems that have proliferated widely not only in bacteria and archaea, but also much more recently, in human biological research and applications. Much work to date has utilized synthetic sgRNAs along with the CRISPR nuclease Cas9, but the discovery of array-processing nucleases now allows the use of more compact, natural CRISPR arrays in heterologous hosts, in addition to organisms with endogenous systems. Unfortunately, the construction of multiplex natural CRISPR arrays remains technically challenging, expensive, and/or time-consuming. This limitation hampers research involving natural CRISPR arrays in both native and heterologous hosts. To address this problem, we present a method to assemble CRISPR arrays that is simple, rapid, affordable, and highly scalable – we assembled 9-spacer arrays with one day’s worth of work. We used this method to harness the endogenous CRISPR system of the highly competent bacterium Acinetobacter baylyi, showing that while single spacers are not always completely effective at blocking DNA acquisition through natural competence, multiplex natural CRISPR arrays enable both nearly complete DNA exclusion and genome editing, including with multiple targets for both. In addition to demonstrating a CRISPR array assembly method that will benefit a variety of applications, we also find a potential bet-hedging strategy for balancing CRISPR defense vs. DNA acquisition in naturally competent A. baylyi.
Kentrophoros magnus sp. nov. (Ciliophora, Karyorelictea), a new flagship species of marine interstitial ciliates

The karyorelictean ciliate Kentrophoros lacks a defined oral apparatus but has a dense coat of symbiotic bacteria that it consumes by phagocytosis. Body size, shape, and nuclear characters are variable in this genus. We formally describe a new species, K. magnus from Elba (Italy), which has unusual folding of its symbiont-bearing surface into pouch-like compartments, a body form that we term “pseudotrophosomal”. K. magnus cells are large (2100 ± 700 × 170 ± 23 μm in vivo), but contain only one micronucleus and two macronuclei, although these are much bigger than other Kentrophoros (widths 20 ± 2.5 and 31 ± 4.0 μm respectively in K. magnus). We also present morphological observations on a close relative from Twin Cayes (Belize), which also has relatively large nuclei (micronuclei 13 ± 1.5 μm, mature macronuclei 20 ± 2.8 μm), but unlike K. magnus, it has on average 22 nuclei per cell, with different developmental stages of the macronuclei present simultaneously, and lacks pouch-like folding. Nuclear number and arrangement are important characters for karyorelicts. We suggest the use of a “nuclear formula” to simplify descriptions. Our discovery of large and morphologically distinctive new species underlines the incompleteness of our knowledge about meiofaunal ciliates.
The periphery is the dominant site of B-cell deletion in a polyclonal repertoire

The concerted actions of multiple tolerance checkpoints limit the possibility of immune attack against self-antigens. For B cells, purging of autoreactivity from the developing repertoire has been almost exclusively studied using B-cell receptor transgenic models. Analyses have generally agreed that central and peripheral tolerance occurs in the form of deletion, receptor editing and anergy. However, when and where these processes occur in a normal polyclonal repertoire devoid of B-cell receptor engineering remain unclear. Here, employing sensitive tools that alleviate the need for B-cell receptor engineering, we track the development of self-reactive B cells and challenge whether deletion plays a meaningful role in B-cell tolerance. We find self-reactive B cells can mature unperturbed by ubiquitous self-antigen expression but, even in the presence of T-cell help, are robustly anergic in the periphery. These studies query the prominence attributed to central and peripheral deletion by most BCR transgenic studies and suggest that other mechanisms predominantly govern B cell tolerance.
Model-free or muddled models in the two-stage task?

1 Distinct model-free and model-based learning processes are thought to drive both typical and 2 dysfunctional behaviors. Data from two-stage decision tasks have seemingly shown that human 3 behavior is driven by both processes operating in parallel. In this study, however, we show that 4 more detailed task instructions lead participants to make primarily model-based choices that show 5 little, if any, model-free inﬂuence. We also demonstrate that the standard methods of analyzing 6 the two-stage task may falsely classify purely model-based agents that misunderstood the task as 7 hybrid model-based/model-free actors. Furthermore, we found evidence that many participants 8 do misunderstand the task in important ways. Overall, we argue that humans formulate a wide 9 variety of learning models. Consequently, the simple dichotomy of model-free versus model-based 10 learning is inadequate to explain behavior in the two-stage task and connections between reward 11 learning, habit formation, and compulsivity. 12
Lipid availability influences the metabolic maturation of human pluripotent stem cell-derived cardiomyocytes

Objectives Pluripotent stem cell-derived cardiomyocytes are phenotypically immature, which limits their utility in downstream applications. Metabolism is dramatically reprogramed during cardiac maturation in vivo and presents a potential avenue to drive in vitro maturation. We aimed to identify and address metabolic bottlenecks in the generation of human pluripotent stem cell (hPSC)-derived cardiomyocytes. Methods hPSCs were differentiated into cardiomyocytes using an established, chemically-defined differentiation protocol. We applied 13C metabolic flux analysis (MFA) and targeted transcriptomics to characterize cardiomyocyte metabolism in during differentiation in the presence or absence of exogenous lipids. Results hPSC-derived cardiomyocytes induced some cardiometabolic pathways (i.e. ketone body and branched-chain amino acid oxidation) but failed to effectively activate fatty acid oxidation. MFA studies indicated that lipid availability in cultures became limited during differentiation, suggesting potential issues with nutrient availability. Exogenous supplementation of lipids improved cardiomyocyte morphology, mitochondrial function, and promoted increased fatty acid oxidation in hPSC-derivatives. Conclusion hPSC-derived cardiomyocytes are dependent upon exogenous sources of lipids for metabolic maturation. Proper supplementation removes a potential roadblock in the generation of metabolically mature cardiomyocytes. These studies further highlight the importance of considering and exploiting metabolic phenotypes in the in vitro production and utilization of functional hPSC-derivatives.
DNMT inhibitors increase methylation at subset of CpGs in colon, bladder, lymphoma, breast, and ovarian, cancer genome

Background DNA methyltransferase inhibitors (DNMTi) decitabine and azacytidine are approved therapies for acute myeloid leukemia and myelodysplastic syndrome. Identification of CpGs violating demethylaion due to DNMTi treatment may help to understand their resistance mechanisms. Materials and Methods To identify such CpGs, we analysed publicly available 450K methylation data of multiple cancer type cell lines. Results We identified 637 CpGs corresponding to genes enriched for p53 and olfactory receptor pathways with a transient increase in methylation (median Δβ = 0.12) after decitabine treatment in HCT116 cells. Azacytidine treatment also increased methylation of identified CpGs in 9 colon, 9 ovarian, 3 breast, and 1 lymphoma cancer cell lines. Conclusion DNMTi treatment increases methylation of subset of CpGs in cancer genome.