Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-Cell Multiome Sequencing Clarifies Enteric Glial Cell Diversity and Identifies an Intraganglionic Population Poised for Neurogenesis

The enteric nervous system (ENS) consists of glial cells (EGCs) and neurons derived from neural crest precursors. EGCs retain capacity for large-scale neurogenesis in culture, and in vivo lineage tracing has identified neurons derived from glial cells in response to inflammation. We thus hypothesize that EGCs possess a chromatin structure poised for neurogenesis. We use single-cell multiome sequencing to assess EGCs undergoing spontaneous neurogenesis in culture, as well as freshly isolated small intestine myenteric plexus EGCs. Cultured EGCs maintain open chromatin at genomic loci accessible in neurons, and neurogenesis from EGCs involves dynamic chromatin rearrangements with a net decrease in accessible chromatin. Multiome analysis of freshly isolated EGCs reveals transcriptional diversity, with open chromatin at neuron-associated genomic elements. A subset of EGCs, highly enriched within the myenteric ganglia, has a gene expression program and chromatin state consistent with neurogenic potential.
Nontypeable Haemophilus influenzae redox recycling of protein thiols promotes resistance to oxidative killing and bacterial survival in biofilms in a smoke related infection model

Smoke exposure is a risk factor for community acquired pneumonia, which is typically caused by host adapted opportunists like nontypeable Haemophilus influenzae (NTHi). Genomic analyses of NTHi revealed homologs of enzymes involved in thiol metabolism, which can have key roles in oxidant resistance. Using a clinical NTHi isolate (NTHi 7P49H1), we generated isogenic mutant bacterial strains in which homologs of glutathione reductase (NTHI 0251), thiol peroxidase (NTHI 0361), thiol peroxidase (NTHI 0907), thioredoxin reductase (NTHI 1327) and glutaredoxin/peroxiredoxin (NTHI 0705) were inactivated. Bacterial protein analyses revealed significant increases in protein oxidation after oxidative stress for all the mutant strains. Similarly, each of these mutants were less resistant to oxidative killing compared with the parental strain; these phenotypes were reversed by genetic complementation. Quantitative confocal analysis of biofilms showed reducted biofilm thickness and density, and significant sensitization of bacteria within the biofilm structure to oxidative killing for thiol mutant strains. Smoke-exposed mice infected with NTHi 7P49H1 showed significantly increased lung bacterial load, as compared to control mice. Immunofluorescent staining of lung tissues showed NTHi communities on the lung mucosa, interspersed with host neutrophil extracellular traps; these bacteria had surface moieties associated with the Hi biofilm matrix, and transcript profiles consistent with NTHi biofilms. In contrast, infection with the panel of NTHi mutants showed significant decrease in lung bacterial load. Comparable results were observed in bactericidal assays with neutrophil extracellular traps in vitro. Thus, we conclude that thiol mediated redox homeostasis promotes persistence of NTHi within biofilm communities. Importance Chronic bacterial respiratory infections are a significant problem for smoke exposed individuals, especially those with chronic obstructive pulmonary disease (COPD). These infections often persist despite antibiotic use. Thus, the bacteria remain and contribute to the development of inflammation and other respiratory problems. Respiratory bacteria often form biofilms within the lungs, while growing in a biofilm their antibiotic and oxidative stress resistance is incredibly heightened. It is well documented that redox homeostasis genes are upregulated during this phase of growth. Many common respiratory pathogens such as NTHi and Streptococcus pneumoniae are reliant on scavenging from the host the necessary components they need to maintain these redox systems. This work here begins to lay down the foundation for exploiting this requirement and thiol redox homeostasis pathways of these bacteria as a therapeutic target for managing chronic respiratory bacterial infections, which are resistant to traditional antibiotic treatments alone.
An Intranasal OMV-Based Vaccine Induces High Mucosal and Systemic Protecting Immunity Against a SARS-CoV-2 Infection

The development of more effective, accessible and easy to administer COVID-19 vaccines next to the currently marketed mRNA, viral vector and whole inactivated vaccines, is essential to curtain the SARS-CoV-2 pandemic. A major concern is reduced vaccine-induced immune protection to emerging variants, and therefore booster vaccinations to broaden and strengthen the immune response might be required. Currently, all registered COVID-19 vaccines and the majority of COVID-19 vaccines in development are intramuscularly administered, targeting the induction of systemic immunity. Intranasal vaccines have the capacity to induce local mucosal immunity as well, thereby targeting the primary route of viral entry of SARS-CoV-2 with the potential of blocking transmission. Furthermore, intranasal vaccines offer greater practicality in terms of cost and ease of administration. Currently, only eight out of 112 vaccines in clinical development are administered intranasally. We developed an intranasal COVID-19 subunit vaccine, based on a recombinant, six proline stabilized, D614G spike protein (mC-Spike) of SARS-CoV-2 linked via the LPS-binding peptide sequence mCramp (mC) to Outer Membrane Vesicles (OMVs) from Neisseria meningitidis. The spike protein was produced in CHO cells and after linking to the OMVs, the OMV-mC-Spike vaccine was administered to mice and Syrian hamsters via intranasal or intramuscular prime-boost vaccinations. In all animals that received OMV-mC-Spike, serum neutralizing antibodies were induced upon vaccination. Importantly, high levels of spike-binding immunoglobulin G (IgG) and A (IgA) antibodies in the nose and lungs were only detected in intranasally vaccinated animals, whereas intramuscular vaccination only induced an IgG response in the serum. Two weeks after their second vaccination hamsters challenged with SARS-CoV-2 were protected from weight loss and viral replication in the lungs compared to the control groups vaccinated with OMV or spike alone. Histopathology showed no lesions in lungs seven days after challenge in OMV-mC-Spike vaccinated hamsters, whereas the control groups did show pathological lesions in the lung. The OMV-mC-Spike candidate vaccine data are very promising and support further development of this novel non-replicating, needle-free, subunit vaccine concept for clinical testing.
High temporal resolution RNA-seq time course data reveals mammalian lncRNA activation mirrors neighbouring protein-coding genes

Background The advent of next-generation sequencing revealed extensive transcription beyond protein-coding genes, identifying tens of thousands of long non-coding RNAs (lncRNAs). Selected functional examples raised the possibility that lncRNAs, as a class, may maintain broad regulatory roles. Compellingly, lncRNA expression is strongly linked with adjacent protein-coding gene expression, suggesting a potential cis-regulatory function. Evidence for these regulatory roles may be obtained through careful examination of the precise timing of lncRNA expression relative to adjacent protein-coding genes. Results Where causal cis-regulatory relationships exist, lncRNA activation is expected to precede changes in adjacent target gene expression. Using an RNA-seq time course of uniquely high temporal resolution, we profiled the expression dynamics of several thousand lncRNAs and protein-coding genes in synchronized, transitioning human cells. Our findings reveal lncRNAs are expressed synchronously with adjacent protein-coding genes. Analysis of lipopolysaccharide-activated mouse dendritic cells revealed the same temporal relationship observed in transitioning human cells. Conclusion Our findings suggest broad-scale cis-regulatory roles for lncRNAs are not common. The strong association between lncRNAs and adjacent genes may instead indicate an origin as transcriptional by-products from active protein-coding gene promoters and enhancers.
Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

Summary As the amount of three-dimensional chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix, an open-source C application to index and query Pairs files. Pairix (also available in Python and R) extends the functionalities of Tabix to paired coordinates data. We have also developed PairsQC, a collapsible HTML quality control report generator for Pairs files. Availability The format specification and source code are available at https://github.com/4dn-dcic/pairix, https://github.com/4dn-dcic/Rpairix and https://github.com/4dn-dcic/pairsqc. Contact peter_park@hms.harvard. edu or burak_alver@hms.harvard. edu
Impact of vitamin B12 on rhamnose metabolism, stress defense and in-vitro virulence of Listeria monocytogenes

Listeria monocytogenes is a facultative anaerobe which can cause a severe food-borne infection known as listeriosis. Rhamnose is a deoxyhexose sugar abundant in a range of environments, including the human intestine, and can be degraded by L. monocytogenes in aerobic and anaerobic conditions into lactate, acetate and 1,2-propanediol. Our previous study showed that addition of vitamin B12 stimulates anaerobic growth of L. monocytogenes on rhamnose due to the activation of bacterial microcompartment (BMC)-dependent 1,2-propanediol utilization with concomitant production of propionate and propanol. Notably, anaerobic propanediol metabolism has been linked to virulence of enteric pathogens including Salmonella spp. and L. monocytogenes. In this study we investigate the impact of B12 on aerobic and anerobic growth of L. monocytogenes on rhamnose, and observed growth stimulation and pdu BMC activation only in anaerobically grown cells with B12 added to the medium. Comparative Caco-2 virulence assays, showed that these pdu BMC induced cells have significantly higher translocation efficiency compared to aerobically grown cells (without and with added B12) and non-induced anaerobically grown cells, while adhesion and invasion capacity is similar for all cells. Comparative proteomics analysis showed specific and overlapping responses linked to metabolic shifts, activation of stress defense proteins and virulence factors, with RNA polymerase sigma factor SigL; teichoic acids export ATP-binding protein, TagH; DNA repair and protection proteins RadA and DPS; and glutathione synthase GshAB previously linked to activation of virulence response in L. monocytogenes, uniquely upregulated in anaerobically rhamnose grown pdu BMC induced cells. Our results shed new light into B12 impact on L. monocytogenes competitive fitness and virulence.
Dual signaling via interferon and DNA damage response elicits entrapment by giant PML nuclear bodies

PML nuclear bodies (PML-NBs) are dynamic interchromosomal macromolecular complexes implicated in epigenetic regulation as well as antiviral defense. During herpesvirus infection, PML-NBs induce epigenetic silencing of viral genomes, however, this defense is antagonized by viral regulatory proteins such as IE1 of human cytomegalovirus (HCMV). Here, we show that PML-NBs undergo a drastic rearrangement into highly enlarged PML cages upon infection with IE1-deficient HCMV. Importantly, our results demonstrate that dual signaling by interferon and DNA damage response is required to elicit giant PML-NBs. DNA labeling revealed that invading HCMV genomes are entrapped inside PML-NBs and remain stably associated with PML cages in a transcriptionally repressed state. Intriguingly, by correlative light and transmission electron microscopy (EM), we observed that PML cages also entrap newly assembled viral capsids demonstrating a second defense layer in cells with incomplete first line response. Further characterization by 3D EM showed that hundreds of viral capsids are tightly packed into several layers of fibrous PML. Overall, our data indicate that giant PML-NBs arise via combined interferon and DNA damage signaling which triggers entrapment of both nucleic acids and proteinaceous components. This represents a multilayered defense strategy to act in a cytoprotective manner and to combat viral infections.
Rhomboid protease RHBDL4/RHBDD1 cleaves SREBP-1c at ER monitoring and regulating fatty acids

The ER-embedded transcription factors, sterol-regulatory element-binding proteins (SREBPs), master regulators of lipid biosynthesis, are transported to Golgi for proteolytic activation to tune cellular cholesterol levels and regulate lipogenesis. However, mechanisms by which the cell responds to the levels of saturated or unsaturated fatty acids remain underexplored. Here we show that RHBDL4/RHBDD1, a rhomboid family protease, directly cleaves SREBP-1c at ER. The p97/VCP, AAA-ATPase complex then acts as an auxiliary segregase to extract the remaining ER-embedded fragment of SREBP-1c. Importantly, the enzymatic activity of RHBDL4 is enhanced by saturated fatty acids (SFAs), but inhibited by polyunsaturated fatty acids (PUFAs). Genetic deletion of RHBDL4 in mice fed on a Western diet enriched in SFAs and cholesterol prevented SREBP-1c from inducing genes for lipogenesis, particularly for synthesis and incorporation of PUFAs, and secretion of lipoproteins. The RHBDL4-SREBP-1c pathway reveals a regulatory system for monitoring fatty acid composition and maintaining cellular lipid homeostasis. Graphical Abstract
Enterohaemorrhagic E. coli utilizes an AND-OR logic gate to regulate expression of an outer membrane haem receptor

To sense the transition from environment to host, bacteria use a range of environmental cues to control expression of virulence genes. Iron is tightly sequestered in host tissues and in the human pathogen enterohaemorrhagic E. coli (EHEC) iron-limitation induces transcription of the outermembrane haem transporter encoded by chuAS. ChuA expression is post-transcriptionally activated at 37°C by a FourU RNA thermometer ensuring that the haem receptor is only expressed under low iron, high temperature conditions that indicate the host. Here we demonstrate that expression of chuA is also independently regulated by the cAMP-responsive sRNA CyaR and transcriptional terminator Rho. These results indicate that chuAS expression is regulated at the transcription initiation, transcript elongation, and translational level. The natural dependence of these processes creates a hierarchy of regulatory AND and OR logic gates that integrate information about the local environment. We show that the logic of the chuA regulatory circuit is activated under conditions that satisfy low iron AND (low glucose OR high temperature). We speculate that additional sensing of a gluconeogenic environment allows further precision in determining when EHEC is at the gastrointestinal epithelium of the host. With previous studies, it appears that the chuAS transcript is controlled by eight regulatory inputs that control expression through six different transcriptional and post-transcriptional mechanisms. The results highlight the ability of regulatory sRNAs to integrate multiple environmental signals into a conditional hierarchy of signal input.
Smooth Deep Reinforcement Learning for Power Control for Spectrum Sharing in Cognitive Radios

Spectrum sharing in a cognitive radio system involves a secondary user updating transmit power for sharing spectrum with a primary user. The deep <italic>Q</italic>-network in the framework of deep reinforcement learning achieves transmit power control by a deep neural network for learning a nonlinear mapping from states to <italic>Q</italic>-values. Since a deep neural network is confronted with noise susceptibility, the deep <italic>Q</italic>-network produces deteriorative network parameters and volatile <italic>Q</italic>-values in the presence of contaminated states. In view of the positive effect of kernel least mean square (KLMS) for signal smoothing, we combine KLMS with the deep <italic>Q</italic>-network for smoothing network-generated outputs. Since an inappropriate step size of KLMS causes under-smoothing or over-smoothing issues, a weighting procedure using past <italic>Q</italic>-values is proposed for cooperating with KLMS. We assess the incremental ratio of the success rate of the smooth deep <italic>Q</italic>-network to that of the deep <italic>Q</italic>-network (RSR) in cognitive radios. Simulations show that RSR has averaged almost over 30% at the early stage of power control. In particular, the maximum RSR reaches almost over 80% or 180% at different scenarios of power control for the primary user. In addition, the smooth deep <italic>Q</italic>-network achieves an improved success rate in comparison with other algorithms.
Hand Gesture Recognition System Using Computer Vision And Neural Networks

— A gesture can be recognized as a form of nonverbal communication in which certain bodily actions represent and communicate particular messages. These actions may be represented by facial features or by hand movement. The hand movements are conveniently deciphered to particular messages that are universal in nature. This research work presents a model system that allows the differently abled people to communicate with their counterparts effectively. It focuses on the problem of predicting the appropriate response to a particular hand sign gesture effectively. The system can be used as a support application to facilitate efficient communication in medical and other emergencies. In this regard, the human hand is segmented from the complicated background. Then, the area of hand gesture which has been detected in real time is recognized by convolutional neural network so as to realize the recognition of 26 alphabet digits. Experiments show 98.1% accuracy.
Prospective analysis of goal-directed fluid therapy vs conventional fluid therapy in perioperative outcome of composite resections of head and neck malignancy with free tissue transfer

Background and Aim: Head and neck cancer surgeries with free tissue transfer are complex procedures, and fluid management can grossly affect the microvascular anastomosis. We hypothesise that intra-operative goal-directed fluid therapy (GDFT) is the key to administer fluid individualised to a patient's requirement. The aim of this study was to observe the role of GDFT in perioperative flap outcome and length of hospital stay. Methods:A randomised prospective controlled study was performed in 106 patients undergoing composite resection of head and neck cancer with free tissue transfer. Patients in Group A received GDFT based on stroke volume variation whereas Group B received conventional fluid therapy intra-operatively. The endpoints of this study were total perioperative fluid, fluid boluses, vasopressor requirement, flap outcome and length of intensive care unit and hospital stay. Statistical analysis was done using Chi-square test. Results: The total intra-operative fluid given to both the groups was comparable but patients in Group A received more boluses and vasopressors compared to Group B during intra-operative period. The amount of fluid given in the first 24 hours post-operatively was significantly less in Group A (1807 + 476 ml) compared to Group B (2205 + 382 ml). Incidence of hypotension with tachycardia was observed in three patients in Group B and none in Group A. Poor flap outcome was observed in one patient in Group A versus four in Group B due to thrombosis. Conclusion: GDFT helps in early detection of fluid deficit and may avoid complications arising due to inadequate microvascular perfusion during the peri-operative period.
Development of polyelectrolyte sulphonated chitosan-alginate as an alternative methanol fuel cell membrane

The aim of this research is the development of biopolymers-based polyelectrolyte membranes (PEMs) for application in the fuel cell. The sulfonated chitosan derivatives and alginate base membranes are the parent biopolymer candidates used in this study to develop physically and chemically polyelectrolyte membranes fuel cell (PEMFC). The calcium alginate base membranes interact via ionic bonds with the sulfonated chitosan derivatives of different sulfonation degrees to have physically polyelectrolyte membranes. Activation of the calcium alginate base membranes with glutaraldehyde induced further covalent bonds in addition to the ionic ones during the reaction with the sulfonated chitosan derivatives of different sulfonation degrees to have chemically polyelectrolyte membranes. The developed PEMs were evaluated using Fourier-transform infrared spectroscopy, scanning electron microscopy, X-ray diffraction and thermal gravimetric analysis analyses. Moreover, their ion exchange capacity, methanol permeability, young modulus analysis, and water uptake characters were measured. The developed chemically PEMFC show superior characters regard the physical counterpart. Moreover, the developed chemically PEMFC show comparable characters to the Nafion 117 membrane which encourages nominating the finding formulations for further PEMs developments.
DESIGN OF TRIPLE BAND-NOTCHED UWB MIMO/DIVERSITY ANTENNA USING TRIPLE BANDGAP EBG STRUCTURE

This paper presents the design of a compact triple band-notched ultra-wideband (UWB) two element multiple-input multiple-output (MIMO) antenna. To validate the simulation results, the prototype of the design is fabricated and experimentally measured. From the experimental results, it is observed that the proposed design, operating in the frequency range 2.5–12 GHz, successfully rejects three interfering bands, i.e., the WiMAX band, WLAN band, and X-band satellite communication downlink channel, when a triple bandgap CSRR-loaded EBG structure is embedded close to the feedline of the UWB antenna. In the ground plane of the MIMO antenna, a rectangular slot and a mirrored pair of F-shaped stubs are added to minimize the mutual coupling between the UWB elements. The proposed MIMO antenna has good wideband isolation between the elements (> 20 dB), high diversity gain (10 dB), and low envelope correlation coefficient (< 0.02) over the entire UWB.
COMPACT ASYMMETRIC COPLANAR STRIP FED MIMO ANTENNA WITH BAND DISPENSION CHARACTERISTICS FOR UWB APPLICATIONS

A MIMO antenna with ACS-asymmetric coplanar strip feeding technique with compact size for UWB applications of band-notched features is presented. The proposed MIMO antenna contains two orthogonally placed rectangular-shaped radiating elements. The orthogonal mechanism of placement of radiating elements provides a good amount of isolation from 3.09GHz to 11.13GHz. The size of the antenna is 27× 27mm2. The isolation is more than 17 dB for most of the UWB range. The proposed MIMO antenna represents nearly omnidirectional radiation pattern and low value of envelope correlation coefficient. Because of the usage of ACS feeding techniques, the antenna size is reduced, and it is a uniplanar structure. The diversity performance of the MIMO antenna is explained in terms of ECCEnvelope Correlation Coefficient, DG-Diversity Gain, and TARC-Total Active Reflection coefficient.