Miracle-dz/UniFAR-FTUs huggingface dataset:
Neural distinctiveness and reinstatement of hippocampal representations support unitization for associations

The medial temporal lobe (MTL) is critical to associative memory success. Yet not all types of associations may be processed in a similar manner within MTL subregions. In particular, work suggests that intra- and inter-item associations not only exhibit differences in overall rates of recollection, but also recruit different MTL subregions. Whereas intra-item associations, akin to unitization, take advantage of associations between within-item features, inter-item associations form links across discrete items. The current work aimed to examine the neural differences between these two types of associations using multivariate neural analyses. Specifically, the current study examined differences across face-occupation as a function of whether the pairing was viewed as a person performing the given job (intra-item binding) or a person saying that they knew someone who had a particular job (inter-item binding). The results show that at encoding, successfully recollected intra- and inter-item associations are discriminable from one another in the hippocampus, parahippocampal cortex, and perirhinal cortex. Additionally, the two trial types are reinstated distinctly such that inter-item trials have higher neural reinstatement from encoding to retrieval compared to intra-item trials in the hippocampus. We conclude that intra- and inter-associative pairs may utilize similar neural regions that represent patterns of activation differentially at encoding. However, in order to reinstate information to the same degree (i.e., subsequently successfully recollected) inter-item associations may act in a compensatory manner, while it is not necessary for intra-item associations to be reinstated to the same degree. This may indicate that intra-item associations promote more efficient reinstatement.
NudC regulated Lis1 stability is essential for maintenance of dynamic microtubule ends in the axon terminal

Axon terminal structure is critical for neuronal function. This cellular compartment houses synaptic terminals and is a site of high metabolic and functional demand. Axon terminals are also the site of a change in microtubule structure within the neuron. Microtubule stability is decreased relative to the axon shaft due to an enrichment of microtubule plus ends and increase in microtubule dynamics. These dynamic microtubule plus ends have many functions including serving as a docking site for the microtubule motor protein complex Cytoplasmic dynein. Here, we report an unexplored function of the dynein motor in axon terminals: regulation of microtubule stability. Using a forward genetic screen, we identified a mutant with abnormal axon terminal structure due to a loss of function mutation in the dynein interacting protein NudC. We show that the primary function of NudC in the axon terminal is as a chaperone for the protein Lis1. Loss of NudC results in decreased Lis1 protein in this neuronal compartment. Decreased Lis1 in nudc mutants causes dynein/dynactin accumulation and increased microtubule stability in axon terminals. Microtubules in the proximal axon are unaffected. Abnormal microtubule stability and structure can be suppressed by pharmacologically inhibiting dynein, implicating excess dynein motor activity as causal in the enhanced axon terminal microtubule stability. Together, our data support a model in which local NudC-Lis1 modulation of dynein motor activity is critical for regulation of microtubule stability in the axon terminal.
Phosphotungstic acid (PTA) preferentially binds to collagen-rich regions of porcine carotid arteries and human atherosclerotic plaques using 3D micro-computed tomography (CE-μCT)

Background and aims Atherosclerotic plaque rupture in the carotid artery can cause small emboli to travel to cerebral arteries, causing blockages and preventing blood flow leading to stroke. Contrast enhanced micro computed tomography (CEμCT) using a novel stain, phosphotungstic acid (PTA) can provide insights into the microstructure of the vessel wall and atherosclerotic plaque, and hence their likelihood to rupture. Furthermore, it has been suggested that collagen content and orientation can be related to mechanical integrity. This study aims to build on existing literature and establish a robust and reproducible staining and imaging technique to non-destructively quantify the collagen content within arteries and plaques as an alternative to routine histology. Methods Porcine carotid arteries and human atherosclerotic plaques were stained with a concentration of 1% PTA staining solution and imaged using MicroCT to establish the in-situ architecture of the tissue and measure collagen content. A histological assessment of the collagen content was also performed from picrosirius red (PSR) staining. Results PTA stained arterial samples highlight the reproducibility of the PTA staining and MicroCT imaging technique used with a quantitative analysis showing a positive correlation between the collagen content measured from CEμCT and histology. Furthermore, collagen-rich areas can be clearly visualised in both the vessel wall and atherosclerotic plaque. 3D reconstruction was also performed showing that different layers of the vessel wall and various atherosclerotic plaque components can be differentiated using Hounsfield Unit (HU) values. Conclusions The work presented here is unique as it offers a quantitative method of segmenting the vessel wall into its individual components and non-destructively quantifying the collagen content withing these tissues, whilst also delivering a visual representation of the fibrous structure using a single contrast agent. Graphical Abstract
Time-Dependent Maximum Entropy Model for Populations of Retinal Ganglion Cells†

The inverse Ising model is used in computational neuroscience to infer probability distributions of the synchronous activity of large neuronal populations. This method allows for finding the Boltzmann distribution with single neuron biases and pairwise interactions that maximizes the entropy and reproduces the empirical statistics of the recorded neuronal activity. Here we apply this strategy to large populations of retinal output neurons (ganglion cells) of different types, stimulated by multiple visual stimuli with their own statistics. The activity of retinal output neurons is driven by both the inputs from upstream neurons, which encode the visual information and reflect stimulus statistics, and the recurrent connections, which induce network effects. We first apply the standard inverse Ising model approach, and show that it accounts well for the system’s collective behavior when the input visual stimulus has short-ranged spatial correlations, but fails for long-ranged ones. This happens because stimuli with long-ranged spatial correlations synchronize the activity of neurons over long distances. This effect cannot be accounted for by pairwise interactions, and so by the pairwise Ising model. To solve this issue, we apply a previously proposed framework that includes a temporal dependence in the single neurons biases to model how neurons are driven in time by the stimulus. Thanks to this addition, the stimulus effects are taken into account by the biases, and the pairwise interactions allow for characterizing the network effect in the population activity and for reproducing the structure of the recurrent functional connections in the retinal architecture. In particular, the inferred interactions are strong and positive only for nearby neurons of the same type. Inter-type connections are instead small and slightly negative. Therefore, the retinal architecture splits into weakly interacting subpopulations composed of strongly interacting neurons. Overall, this temporal framework fixes the problems of the standard, static, inverse Ising model and accounts for the system’s collective behavior, for stimuli with either short or long-range correlations.
Molecular characterization of the intact muscle spindle using a multi-omics approach

The proprioceptive system is essential for the control of coordinated movement, posture and skeletal integrity. The sense of proprioception is produced in the brain using peripheral sensory input from receptors such as the muscle spindle, which detects changes in the length of skeletal muscles. Despite its importance, the molecular composition of the muscle spindle is largely unknown. In this study, we generated comprehensive transcriptomic and proteomic datasets of the entire muscle spindle. We then associated differentially expressed genes with the various tissues composing the spindle using bioinformatic analysis. Immunostaining verified these predictions, thus establishing new markers for the different spindle tissues. Utilizing these markers, we identified the differentiation stages the spindle capsule cells undergo during development. Together, these findings provide comprehensive molecular characterization of the intact spindle as well as new tools to study its development and function in health and disease.
Mechanisms of spontaneous Ca2+ release‐mediated arrhythmia in a novel 3D human atrial myocyte model: I. Transverse‐axial tubule variation

Intracellular calcium (Ca2+) cycling is tightly regulated in the healthy heart ensuring effective contraction. This is achieved by transverse (t)‐tubule membrane invaginations that facilitate close coupling of key Ca2+‐handling proteins such as the L‐type Ca2+ channel and Na+‐Ca2+ exchanger (NCX) on the cell surface with ryanodine receptors (RyRs) on the intracellular Ca2+ store. Although less abundant and regular than in the ventricle, t‐tubules also exist in atrial myocytes as a network of transverse invaginations with axial extensions known as the transverse‐axial tubule system (TATS). In heart failure and atrial fibrillation, there is TATS remodelling that is associated with aberrant Ca2+‐handling and Ca2+‐induced arrhythmic activity; however, the mechanism underlying this is not fully understood. To address this, we developed a novel 3D human atrial myocyte model that couples electrophysiology and Ca2+‐handling with variable TATS organization and density. We extensively parameterized and validated our model against experimental data to build a robust tool examining TATS regulation of subcellular Ca2+ release. We found that varying TATS density and thus the localization of key Ca2+‐handling proteins has profound effects on Ca2+ handling. Following TATS loss, there is reduced NCX that results in increased cleft Ca2+ concentration through decreased Ca2+ extrusion. This elevated Ca2+ increases RyR open probability causing spontaneous Ca2+ releases and the promotion of arrhythmogenic waves (especially in the cell interior) leading to voltage instabilities through delayed afterdepolarizations. In summary, the present study demonstrates a mechanistic link between TATS remodelling and Ca2+‐driven proarrhythmic behaviour that probably reflects the arrhythmogenic state observed in disease.
Macroscopic and microscopic study on floral biology and pollination of Cinnamomum verum Blume (Sri Lankan)

Cinnamomum verum Blume (syn Cinnamomum zeylanicum) commonly known as Ceylon cinnamon, has gained worldwide attention and well supported by experimental data. Maintaining the yield quality and quantity are essential, especially for high-end value-added products. Breeding superior varieties and producing good quality planting materials are critical for commercial cultivation efforts. However, limited literature is available on the floral development and biology of C. verum. We assessed the seasonal flowering, floral development and pollination of type A and type B varieties of C. verum. Both macroscopic and microscopic data were collected on floral biology, pollination, male and female floral organs before and after pollination. Cinnamomum verum is morpho-anatomically, structurally, and physiologically adapted for cross-pollination, possible between the two cultivars; type A (Sri Gemunu) and type B (Sri Wijaya) flowers; naturally evolved with Protogynous Dichogamy. It possesses a dry stigma, which changes its surface characteristics after pollination. During close-pollination, a higher percentage of pollen shrink and shrivel on stigma while it develops callose plugs to obstruct the growth of the pollen tube. However, during changes in environmental conditions, female and male stages in the same tree overlap for about 45-60 min suggesting possible close-pollination within the same plant. Moreover, 4-8% of the flowers formed fruits after natural close and hand pollination. pollen was found fully hydrated even after close-pollination. Although C. verum is adapted for cross-pollination, natural close-pollination is also possible. The data suggest the complex nature of the sexual reproduction of C. verum. Well-managed breeding attempts will develop superior C. verum varieties.
Inflammatory Signaling and Fibroblast-Cancer Cell Interactions Transfer from a Harmonized Human Single-cell RNA Sequencing Atlas of Pancreatic Ductal Adenocarcinoma to Organoid Co-Culture

Pancreatic ductal adenocarcinoma (PDAC) is a devastating malignancy driven by a heterogeneous tumor microenvironment enriched with cancer associated fibroblasts (CAFs) that influence its overall immunosuppressive composition. We examined inflammation in PDAC by leveraging our existing patient-derived organoid (PDO) model and a novel PDO-CAF co-culture. We first identified induction of major histocompatibility complex class II expression following treatment with interferon gamma. In parallel, we collated an atlas of 6 published single-cell RNA-sequencing datasets (174,394 cells) combining 61 PDAC (142,807 cells) and 16 non-malignant samples. By combining in silico modeling and in vitro PDO co-culture, we define a gene expression pattern of inflammatory processes in epithelial tumor cells. Following computational inferences, we examined interactions between epithelial tumor cells and CAFs, focusing on VEGF-A and ITGB1 pathways. This work, integrating computational and biological approaches, highlights the value of convergence to accelerate our understanding of key drivers of PDAC. Statement of Significance We established PDO-CAF co-cultures to model tumor cell interactions and validated discoveries using transfer learning into a single-cell RNA-seq atlas of PDAC tumors. This bidirectional approach from human to experimental systems facilitates interrogation of PDAC biology, including the role of inflammation associated with VEGF-A crosstalk between CAFs and tumor cells.
FtsK, a DNA Motor Protein, Coordinates the Genome Segregation and Early Cell Division Processes in Deinococcus radiodurans

Deinococcus radiodurans show extraordinary resistance to gamma radiation. It is polyploid and harbors a multipartite genome comprised of 2 chromosomes and 2 plasmids, packaged in a doughnut-shaped toroidal nucleoid. ABSTRACT Filament temperature-sensitive mutant K (FtsK)/SpoIIIE family proteins are DNA translocases known as the fastest DNA motor proteins that use ATP for their movement on DNA. Most of the studies in single chromosome-containing bacteria have established the role of FtsK in chromosome dimer resolution (CDR), connecting the bacterial chromosome segregation process with cell division. Only limited reports, however, are available on the interdependent regulation of genome segregation and cell division in multipartite genome harboring (MGH) bacteria. In this study, for the first time, we report the characterization of FtsK from the radioresistant MGH bacterium Deinococcus radiodurans R1 (drFtsK). drFtsK shows the activity characteristics of a typical FtsK/SpoIIIE/Tra family. It stimulates the site-specific recombination catalyzed by Escherichia coli tyrosine recombinases. drFtsK interacts with various cell division and genome segregation proteins of D. radiodurans. Microscopic examination of different domain deletion mutants of this protein reveals alterations in cellular membrane architecture and nucleoid morphology. In vivo localization studies of drFtsK-RFP show that it forms multiple foci on nucleoid as well as on the membrane with maximum density on the septum. drFtsK coordinates its movement with nucleoid separation. The alignment of its foci shifts from old to new septum indicating its cellular dynamics with the FtsZ ring during the cell division process. Nearly, similar positional dynamicity of FtsK was observed in cells recovering from gamma radiation exposure. These results suggest that FtsK forms a part of chromosome segregation, cell envelope, and cell division machinery in D. radiodurans. IMPORTANCE Deinococcus radiodurans show extraordinary resistance to gamma radiation. It is polyploid and harbors a multipartite genome comprised of 2 chromosomes and 2 plasmids, packaged in a doughnut-shaped toroidal nucleoid. Very little is known about how the tightly packed genome is accurately segregated and the next divisional plane is determined. Filament temperature-sensitive mutant K (FtsK), a multifunctional protein, helps in pumping the septum-trapped DNA in several bacteria. Here, we characterized FtsK of D. radiodurans R1 (drFtsK) for the first time and showed it to be an active protein. The absence of drFtsK causes many defects in morphology at both cellular and nucleoid levels. The compact packaging of the deinococcal genome and cell membrane formation is hindered in ftsK mutants. In vivo drFtsK is dynamic, forms foci on both nucleoid and septum, and coordinates with FtsZ for the next cell division. Thus, drFtsK role in maintaining the normal genome phenotype and cell division in D. radiodurans is suggested.
Specialized metabolism by trichome-preferentially-expressed Rubisco and fatty acid synthase components

Acylsugars, specialized metabolites with defense activities, are secreted by trichomes of many solanaceous plants. Several acylsugar metabolic genes (AMGs) remain unknown. We previously reported multiple candidate AMGs. Here, using multiple approaches, we characterized additional AMGs. First, we identified differentially expressed genes between high- and low-acylsugar-producing F2 plants derived from a cross between Solanum lycopersicum and S. pennellii, which produce acylsugars ∼1% and ∼20% of leaf dry weight, respectively. Expression levels of many known and candidate AMGs positively correlated with acylsugar amounts in F2 individuals. Next, we identified lycopersicum-pennellii putative orthologs with higher nonsynonymous to synonymous substitutions. These analyses identified four candidate genes, three of which showed enriched expression in stem trichomes compared to underlying tissues (shaved stems). Virus-induced gene silencing confirmed two candidates, Sopen05g009610 [beta-ketoacyl-(acyl-carrier-protein) reductase; fatty acid synthase component] and Sopen07g006810 (Rubisco small subunit), as AMGs. Phylogenetic analysis indicated that Sopen05g009610 is distinct from specialized metabolic cytosolic reductases, but closely related to two capsaicinoid biosynthetic reductases, suggesting evolutionary relationship between acylsugar and capsaicinoid biosynthesis. Additionally, data mining revealed that orthologs of Sopen05g009610 are preferentially expressed in trichomes of several acylsugar-producing solanaceous species. Similarly, orthologs of Sopen07g006810 were identified as trichome-preferentially-expressed members, which form a phylogenetic clade distinct from those of mesophyll-expressed “regular” Rubisco small subunits. Furthermore, δ13C analyses indicated recycling of metabolic CO2 into acylsugars by Sopen07g006810 and shed light on how trichomes support high levels of specialized metabolite production. These findings have implications for genetic manipulation of trichome specialized metabolism in solanaceous crops, including tomato, potato, and tobacco.
Noncovalent antibody catenation on a target surface drastically increases the antigen-binding avidity

Immunoglobulin G (IgG) antibodies are widely used for diagnosis and therapy. Given the unique dimeric structure of IgG, we hypothesized that, by genetically fusing a homodimeric protein (catenator) to the C-terminus of IgG, reversible catenation of antibody molecules could be induced on a surface where target antigen molecules are abundant, and that it could be an effective way to greatly enhance the antigen-binding avidity. A thermodynamic simulation shows that quite low homodimerization affinity of a catenator, e.g. dissociation constant of 100 μM, can enhance nanomolar antigen-binding avidity to a picomolar level, and that the fold enhancement sharply depends on the density of the antigen. In a proof-of-concept experiment where antigen molecules are immobilized on a biosensor tip, C-terminal fusion of a weakly homodimerizing protein to two different antibodies enhanced the antigen-binding avidity by at least 210 to 5,120 folds from the intrinsic binding avidity. Thus, the homodimerization-induced antibody catenation would be a simple, powerful and general approach to improve many antibody applications, including the detection of scarce biomarkers and targeted anticancer therapies.
Queueing network models for analysis of nonstationary manufacturing systems

Queueing and queueing network models have been extensively employed for the performance analysis of manufacturing systems. They have enjoyed successful applications in rapid modelling for system design and performance evaluation of operational plans. In this paper, we briefly review literature on significant queuing network models developed and applied to the analysis of manufacturing systems. Previous work has focused almost exclusively on static environments of various types including open and closed networks for serial and general systems with various attributes such as unreliable machines, general arrival and service distributions, finite buffers and controlled work-in-process levels. As many systems experience dynamic demand and time-dependent resource availability, we propose a framework for the analysis of manufacturing systems under dynamic conditions. Numerical validation of this framework against simulation estimates is performed for realistic sized flowshop and jobshop instances.
Multisite gating in tonic sensory circuits integrates multimodal context to control persistent behavioral states

Maintaining or shifting between behavioral states according to context is essential for animals to implement fitness-promoting strategies. How integration of internal state, past experience and sensory inputs orchestrate persistent multidimensional behavior changes remains poorly understood. Here, we show that C. elegans integrates food availability and environment temperature over different timescales to engage in persistent dwelling, scanning, global or glocal search strategies matching thermoregulatory and feeding needs. Transition between states, in each case, requires lifting multiple regulatory gates including AFD or FLP tonic sensory neurons activity, neuropeptide expression and downstream circuit responsiveness. State-specific FLP-6 or FLP-5 neuropeptide signaling acts on a distributed set of inhibitory receptors to promote scanning or glocal search, respectively, bypassing dopamine and glutamate-dependent behavioral state control. Multisite gating-dependent behavioral switch by GPCRs in tonic sensory circuits might represent a conserved regulatory logic for persistent behavioral state transitions enabling a flexible prioritization on the valance of multiple inputs.