Miracle-dz/UniFAR-FTUs huggingface dataset:
Elevated cerebrospinal fluid cytokine levels in tuberculous meningitis predict survival in response to dexamethasone

Significance Despite appropriate antibiotic treatment, tuberculous meningitis carries a high mortality ascribed to overexuberant inflammation. Genetic variations in the enzyme, LTA4H, alter inflammation, with individuals carrying the inflammation-associated LTA4H variant benefitting from antiinflammatory steroids administered alongside antibiotics. A prior study found poor correlation between LTA4H genotype and cerebrospinal fluid levels of cytokines, key mediators of inflammation. The study used “frequentist” statistical methods that can fail to detect true differences. Using Bayesian statistics, which can detect significant differences not found by frequentist methods, we found good correlation between LTA4H genotype and cytokine levels, and cytokine levels and outcome even independent of LTA4H genotype. These findings suggest that LTA4H and additional inflammation factors affect outcome and suggest tailoring steroid therapy to cytokine levels. Adjunctive treatment with antiinflammatory corticosteroids like dexamethasone increases survival in tuberculosis meningitis. Dexamethasone responsiveness associates with a C/T variant in Leukotriene A4 Hydrolase (LTA4H), which regulates expression of the proinflammatory mediator leukotriene B4 (LTB4). TT homozygotes, with increased expression of LTA4H, have the highest survival when treated with dexamethasone and the lowest survival without. While the T allele is present in only a minority of the world’s population, corticosteroids confer modest survival benefit worldwide. Using Bayesian methods, we examined how pretreatment levels of cerebrospinal fluid proinflammatory cytokines affect survival in dexamethasone-treated tuberculous meningitis. LTA4H TT homozygosity was associated with global cytokine increases, including tumor necrosis factor. Association between higher cytokine levels and survival extended to non-TT patients, suggesting that other genetic variants may also induce dexamethasone-responsive pathological inflammation. These findings warrant studies that tailor dexamethasone therapy to pretreatment cerebrospinal fluid cytokine concentrations, while searching for additional genetic loci shaping the inflammatory milieu.
The full model of the pMHC-TCR-CD3 complex: a structural and kinetics characterization

The machinery involved in cytotoxic T-cell activation requires three main characters such as: the major histocompatibility complex class I (MHC I) bound to the peptide (p), the T-cell receptor (TCR), and the CD3-complex which is a multidimer interfaced with the intracellular side. The pMHC:TCR interaction has been largely studied both in experimental and computational models, giving a contribution in understanding the complexity of the TCR triggering process. Nevertheless, a detailed study of the structural and dynamical characterization of the full complex (pMHC:TCR:CD3-complex) is still missing, due to insufficient data available on the CD3-chains arrangement around the TCR. The recent determination of the TCR:CD3-complex structure by means of Cryo-EM technique has given a chance to build the entire proteins system essential in the activation of T-cell, and thus in the adaptive immune response. Here, we present the first full model of the pMHC interacting with the TCR:CD3-complex, built in a lipid environment. To describe the conformational behaviour associated with the unbound and the bound states, all atoms Molecular Dynamics simulations were performed for the TCR:CD3-complex and for two pMHC:TCR:CD3-complex systems, bound to two different peptides. Our data point out that a conformational change affecting the TCR Constant β (Cβ) region occurs after the binding to the pMHC, revealing a key role of such a region in the propagation of the signal. Moreover, we found that the TCR reduces the flexibility of the MHC I binding groove, confirming our previous results.
Different contrast encoding in ON and OFF visual pathways

Subjective visual experience builds on sensory encoding of light reflected by different objects in our environment. Most retinal ganglion cells encode changes in light intensity, quantified as contrast, rather than the absolute intensity. Mathematically, contrast is often defined as a relative change in light intensity. Activity in the visual system and perceptual responses are usually explained with such definitions of contrast. Here, for the first time, we explicitly explored how contrast is actually represented in the visual system. Using mouse retina electrophysiology, we show that response strength of OFF retinal ganglion cells does not represent relative, but absolute changes in light intensity. ON RGC response strength is governed by a combination of absolute and relative change in light intensity. This is true for a wide range of ambient light levels, at least from scotopic to high mesopic regimes. Consequently, light decrements and increments are represented asymmetrically in the retina, which may explain the asymmetries in responses to negative and positive contrast observed throughout the visual system. These findings may help to more thoroughly design and interpret vision science studies where responses are driven by contrast of the visual stimuli.
Differential homeostatic regulation of glycinergic and GABAergic nanocolumns at mixed inhibitory synapses

Super-resolution imaging of synapses has revealed that key synaptic proteins are dynamically organized within sub-synaptic domains (SSDs). At mixed inhibitory synapses in spinal cord neurons, both GlyRs and GABAARs reside at the same post-synaptic density (PSD). To examine how the different inhibitory receptors are organized and regulated, we carried out dual-color direct stochastic optical reconstruction microscopy (dSTORM). We found that endogenous GlyRs and GABAARs as well as their common scaffold protein gephyrin form SSDs that align with pre-synaptic RIM1/2, thus forming trans-synaptic nanocolumns. Strikingly, GlyRs and GABAARs occupy different sub-synaptic spaces, exhibiting only a partial overlap at mixed inhibitory synapses. When network activity was increased by pharmacological treatment using the K+ channel blocker 4-aminopyridine (4-AP), the GABAAR copy numbers of as well as the number of GABAAR SSDs were reduced, while GlyRs remained largely unchanged. This differential regulation is likely the result of changes in gephyrin phosphorylation that preferentially occurred outside of the SSDs. The total gephyrin content was not altered by 4-AP application. The activity-dependent regulation of GABAARs versus GlyRs suggests that different signaling pathways control their respective sub-synaptic organization. Whereas gephyrin serves as a scaffold protein that upholds GlyR numbers at SSDs, it may act as a switch regulating GABAARs via its phosphorylation state. Taken together, our data reinforce the notion that the precise sub-synaptic organization of GlyRs, GABAARs and gephyrin has functional consequences for the homeostatic regulation of mixed inhibitory synapses. Highlights Alignment of sub-synaptic domains (SSDs) in trans-synaptic nanocolumns at inhibitory synapses Differential spatial organization of SSDs formed by GlyRs and GABAARs at mixed inhibitory synapses Activity-dependent regulation of GABAARs but not GlyRs at mixed inhibitory synapses Gephyrin phosphorylation is compartmentalized in SSDs within the synaptic scaffold
Bile acid excess impairs thermogenic function in brown adipose tissue

Bile acids (BAs) not only facilitate fat digestion but also protect against obesity. Here, we show that a genetic mouse model for BA overload (Farnesoid X receptor; Small heterodimer double knockout (DKO)) exhibits mitochondrial dysfunction resulting in a thermogenic defect. By housing DKO mice at thermoneutrality, the poor mitochondrial function in brown fat protects them from diet-induced obesity. Compared to control, we find higher adipose BA levels with excess accumulation of taurocholic acid in the DKO mice. We report that the expression of genes responsible for BA de novo synthesis, conjugation and transporters and accumulation of BAs are present in both brown and white adipocytes. We determine that BA overload is sufficient to cause adipocyte mitochondrial dysfunction and induce the expression of cellular senescence genes in vitro. Taken together, we uncover that BA levels within the adipose tissue may modulate its overall function. Highlights Mouse model of BA overload exhibits adipose defects, which is partially restored by housing at thermoneutrality. BAs are present in detectable concentrations in both BAT and WAT. Adipocytes express genes responsible for de novo synthesis, conjugation and transport of BAs, and accumulate BAs. Pathological accumulation of BAs impairs mitochondrial function leading to thermogenic defect.
Powder neutron diffraction study of the high temperature phase transitions in NaTaO3

Neutron powder diffraction has been used to examine the structural phase transitions in the perovskite-like NaTaO3, from room temperature to 933 K. The room temperature orthorhombic structure (Pbnm, a = 5.4768(1), b = 5.5212(1), c = 7.7890(2)) transforms to orthorhombic Cmcm at around 700 K, then to tetragonal P4/mbm at 835 K, and finally to cubic Pmm above 890 K. The structure in orthorhombic Cmcm is characterized by simultaneous tilting of the oxygen atom octahedron about two of its tetrad axes, the tilting of successive octahedra being out of phase along the b-axis, and in phase along the c-axis. The two tilt angles are comparable just above 700 K, but the out-of-phase tilt angle falls smoothly to zero as the transition to tetragonal is approached, in the manner suggestive of a tricritical transition. This results in an unusual variation of lattice parameters with temperature in the orthorhombic Cmcm phase. In the tetragonal phase the lattice parameters vary smoothly; however near the transition to cubic the in-phase tilt angle changes more rapidly with temperature than might be expected in a continuous phase transition.
Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage

Efficient peptide and protein identification from data-independent acquisition mass spectrometric (DIA-MS) data typically rely on an experiment-specific spectral library with a suitable size. Here, we report a computational strategy for optimizing the spectral library for a specific DIA dataset based on a comprehensive spectral library, which is accomplished by a priori analysis of the DIA dataset. This strategy achieved up to 44.7% increase in peptide identification and 38.1% increase in protein identification in the test dataset of six colorectal tumor samples compared with the comprehensive pan-human library strategy. We further applied this strategy to 389 carcinoma samples from 15 tumor datasets and observed up to 39.2% increase in peptide identification and 19.0% increase in protein identification. In summary, we present a computational strategy for spectral library size optimization to achieve deeper proteome coverage of DIA-MS data.
A Selective Projection from the Subthalamic Nucleus to Parvalbumin-Expressing Interneurons of the Striatum

Visual Abstract The striatum and subthalamic nucleus (STN) are considered to be the primary input nuclei of the basal ganglia. Projection neurons of both striatum and STN can extensively interact with other basal ganglia nuclei, and there is growing anatomic evidence of direct axonal connections from the STN to striatum. There remains, however, a pressing need to elucidate the organization and impact of these subthalamostriatal projections in the context of the diverse cell types constituting the striatum. To address this, we conducted monosynaptic retrograde tracing from genetically-defined populations of dorsal striatal neurons in adult male and female mice, quantifying the connectivity from STN neurons to spiny projection neurons, GABAergic interneurons, and cholinergic interneurons. In parallel, we used a combination of ex vivo electrophysiology and optogenetics to characterize the responses of a complementary range of dorsal striatal neuron types to activation of STN axons. Our tracing studies showed that the connectivity from STN neurons to striatal parvalbumin-expressing interneurons is significantly higher (∼4- to 8-fold) than that from STN to any of the four other striatal cell types examined. In agreement, our recording experiments showed that parvalbumin-expressing interneurons, but not the other cell types tested, commonly exhibited robust monosynaptic excitatory responses to subthalamostriatal inputs. Taken together, our data collectively demonstrate that the subthalamostriatal projection is highly selective for target cell type. We conclude that glutamatergic STN neurons are positioned to directly and powerfully influence striatal activity dynamics by virtue of their enriched innervation of GABAergic parvalbumin-expressing interneurons.
A dual-encoding system for dialect classification

In this paper we present the architecture, processing pipeline and results of the ensemble model developed for Romanian Dialect Identification task. The ensemble model consists of two TF-IDF encoders and a deep learning model aimed together at classifying input samples based on the writing patterns which are specific to each of the two dialects. Although the model performs well on the training set, its performance degrades heavily on the evaluation set. The drop in performance is due to the design decision which makes the model put too much weight on presence/lack of textual marks when determining the sample label.
Ovarian carcinosarcoma genomics and pre-clinical models highlight the N-MYC pathway as a key driver and susceptibility to EMT-targeting therapy

Ovarian carcinosarcoma (OCS) is an aggressive and rare tumour type with limited treatment options. OCS is hypothesised to develop via the combination theory from a single progenitor, resulting in carcinomatous and sarcomatous components, or alternatively via the conversion theory, with the sarcomatous component developing from the carcinomatous component through epithelial-to-mesenchymal transition (EMT). We show OCS from 18 women to be monoclonal through analysis of DNA variants from isolated carcinoma and sarcoma components. RNA sequencing indicated the carcinoma components were more mesenchymal when compared with pure ovarian carcinomas, supporting the conversion theory. We used pre-clinical OCS models to test the efficacy of microtubule-targeting drugs, including eribulin, which has been shown to reverse EMT characteristics. We demonstrated that microtubule inhibitors, vinorelbine and eribulin, were more effective than standard-of-care platinum-based chemotherapy. Eribulin reduced mesenchymal characteristics, N-MYC expression and cholesterol biosynthesis. Finally, eribulin induced a strong immune response, supporting immunotherapy combinations in the clinic.
Glycolic acid protects neurons against ischemia in vitro and in two animal models of stroke

Stroke is the second leading cause of death and disability worldwide. Current treatments, like pharmacological thrombolysis or mechanical thrombectomy, re-open occluded arteries but do not protect against ischemia-induced damage caused before reperfusion or ischemia/reperfusion-induced neuronal damage. It has been shown that knocking out djr-1.1 and djr-1.2 or glod-4 results in a decreased tolerance to anhydrobiosis in C elegans dauer larva and that Glycolic Acid (GA) can rescue this phenotype. During the process of desiccation/rehydration, a metabolic stop/start similar to the one observed during ischemia/reperfusion occurs. In this study we tested the protective effect of GA against ischemia in three different models (oxygen-glucose deprivation in vitro and Global cerebral ischemia as well as Middle Cerebral Artery Occlusion in vivo). Our results show that GA, given during reperfusion, strongly protects against ischemia-induced neuronal death, reduces the mortality in mice with large infarcts, significantly reduces the ischemic area in the brain and improves the functional outcome. The effect of GA is stronger when the substance is applied near the damaged tissue (i.e. directly to the neurons in vitro or intra-arterially via the internal carotid artery in vivo). These results suggest that GA treatment has the potential to dramatically reduce the mortality and disability caused by stroke in patients.
Medial frontal cortex activity predicts information sampling in economic choice

Decision-making not only requires agents to decide what to choose but also how much information to sample before committing to a choice. Previously established frameworks for economic choice argue for a deliberative process of evidence accumulation across time. These tacitly acknowledge a role of information sampling in that decisions are only made once sufficient evidence is acquired, yet few experiments have explicitly placed information sampling under the participant's control. Here, we use fMRI to investigate the neural basis of information sampling in economic choice by allowing participants (n = 30, sex not recorded) to actively sample information in a multistep decision task. We show that medial frontal cortex (MFC) activity is predictive of further information sampling before choice. Choice difficulty (inverse value difference, keeping sensory difficulty constant) was also encoded in MFC, but this effect was explained away by the inclusion of information sampling as a coregressor in the general linear model. A distributed network of regions across the prefrontal cortex encoded key features of the sampled information at the time it was presented. We propose that MFC is an important controller of the extent to which information is gathered before committing to an economic choice. This role may explain why MFC activity has been associated with evidence accumulation in previous studies in which information sampling was an implicit rather than explicit feature of the decision. SIGNIFICANCE STATEMENT The decisions we make are determined by the information we have sampled before committing to a choice. Accumulator frameworks of decision-making tacitly acknowledge the need to sample further information during the evidence accumulation process until a decision boundary is reached. However, relatively few studies explicitly place this decision to sample further information under the participant's control. In this fMRI study, we find that MFC activity is related to information sampling decisions in a multistep economic choice task. This suggests that an important role of evidence representations within MFC may be to guide adaptive sequential decisions to sample further information before committing to a final decision.
Differential Excitability of PV and SST Neurons Results in Distinct Functional Roles in Inhibition Stabilization of Up States

Up states are the best studied example of an emergent neural dynamic regime. Computational models based on a single class of inhibitory neurons indicate that Up states reflect bistable dynamic systems in which positive feedback is stabilized by strong inhibition and predict a paradoxical effect in which increased drive to inhibitory neurons results in decreased inhibitory activity. To date, however, computational models have not incorporated empirically defined properties of parvalbumin (PV) and somatostatin (SST) neurons. Here we first experimentally characterized the frequency–current (F–I) curves of pyramidal (Pyr), PV, and SST neurons from mice of either sex, and confirmed a sharp difference between the threshold and slopes of PV and SST neurons. The empirically defined F–I curves were incorporated into a three-population computational model that simulated the empirically derived firing rates of pyramidal, PV, and SST neurons. Simulations revealed that the intrinsic properties were sufficient to predict that PV neurons are primarily responsible for generating the nontrivial fixed points representing Up states. Simulations and analytical methods demonstrated that while the paradoxical effect is not obligatory in a model with two classes of inhibitory neurons, it is present in most regimes. Finally, experimental tests validated predictions of the model that the Pyr ↔ PV inhibitory loop is stronger than the Pyr ↔ SST loop. SIGNIFICANCE STATEMENT Many cortical computations, such as working memory, rely on the local recurrent excitatory connections that define cortical circuit motifs. Up states are among the best studied examples of neural dynamic regimes that rely on recurrent excitatory excitation. However, this positive feedback must be held in check by inhibition. To address the relative contribution of PV and SST neurons, we characterized the intrinsic input–output differences between these classes of inhibitory neurons and, using experimental and theoretical methods, show that the higher threshold and gain of PV leads to a dominant role in network stabilization.
Using seasonal genomic changes to understand historical adaptation: parallel selection on stickleback in highly-variable estuaries

Parallel evolution is considered strong evidence for natural selection. However, few studies have investigated the process of parallel selection as it plays out in real time. The common approach is to study historical signatures of selection in populations already well adapted to different environments. Here, to document selection in action under natural conditions, we study six populations of threespine stickleback (Gasterosteus aculeatus) inhabiting bar-built estuaries that undergo seasonal cycles of environmental changes. Estuaries are periodically isolated from the ocean due to sandbar formation during dry summer months, with concurrent environmental shifts that resemble the long-term changes associated with postglacial colonization of freshwater habitats by marine populations. We used pooled whole-genome sequencing (Pool-WGS) to track seasonal allele frequency changes in these populations and search for signatures of natural selection. We found consistent changes in allele frequency across estuaries, suggesting a potential role for parallel selection. Functional enrichment among candidate genes included transmembrane ion transport and calcium binding, which are important for osmoregulation and ion balance. The genomic changes that occur in threespine stickleback from bar-built estuaries could provide a glimpse into the early stages of adaptation that have occurred in many historical marine to freshwater transitions.
Leveraging WordNet Paths for Neural Hypernym Prediction

We formulate the problem of hypernym prediction as a sequence generation task, where the sequences are taxonomy paths in WordNet. Our experiments with encoder-decoder models show that training to generate taxonomy paths can improve the performance of direct hypernym prediction. As a simple but powerful model, the hypo2path model achieves state-of-the-art performance, outperforming the best benchmark by 4.11 points in hit-at-one (H@1).