Miracle-dz/UniFAR-FTUs huggingface dataset:
A Pharmacophore Model for SARS-CoV-2 3CLpro Small Molecule Inhibitors and in Vitro Experimental Validation of Computationally Screened Inhibitors

Among the biomedical efforts in response to the current coronavirus (COVID-19) pandemic, pharmacological strategies to reduce viral load in patients with severe forms of the disease are being studied intensively. One of the main drug target proteins proposed so far is the SARS-CoV-2 viral protease 3CLpro (also called Mpro), an essential component for viral replication. Ongoing ligand- and receptor-based computational screening efforts would be facilitated by an improved understanding of the electrostatic, hydrophobic and steric features that characterize small molecule inhibitors binding stably to 3CLpro, as well as by an extended collection of known binders. Here, we present combined virtual screening, molecular dynamics simulation, machine learning and in vitro experimental validation analyses which have led to the identification of small molecule inhibitors of 3CLpro with micromolar activity, and to a pharmacophore model that describes functional chemical groups associated with the molecular recognition of ligands by the 3CLpro binding pocket. Experimentally validated inhibitors using a ligand activity assay include natural compounds with available prior knowledge on safety and bioavailability properties, such as the natural compound rottlerin (IC50 = 37 µM), and synthetic compounds previously not characterized (e.g. compound CID 46897844, IC50 = 31 µM). In combination with the developed pharmacophore model, these and other confirmed 3CLpro inhibitors may provide a basis for further similarity-based screening in independent compound databases and structural design optimization efforts, to identify 3CLpro ligands with improved potency and selectivity. Overall, this study suggests that the integration of virtual screening, molecular dynamics simulations and machine learning can facilitate 3CLpro-targeted small molecule screening investigations. Different receptor-, ligand- and machine learning-based screening strategies provided complementary information, helping to increase the number and diversity of identified active compounds. Finally, the resulting pharmacophore model and experimentally validated small molecule inhibitors for 3CLpro provide resources to support follow-up computational screening efforts for this drug target.
Handcuffing intrinsically disordered regions in Mlh1–Pms1 disrupts mismatch repair

The DNA mismatch repair (MMR) factor Mlh1-Pms1 contains long intrinsically disordered regions (IDRs). While essential for MMR, their exact functions remain elusive. We performed cross-linking mass spectrometry to identify the major interactions within the Mlh1-Pms1 heterodimer and used this information to insert FRB and FKBP dimerization domains into the IDRs of Mlh1 and Pms1. Yeast bearing these constructs were grown with rapamycin to induce dimerization. Strains containing FRB and FKBP domains in the Mlh1 IDR displayed complete MMR defects when grown with rapamycin, but removing rapamycin restored MMR functions. Furthermore, linking the Mlh1 and Pms1 IDRs through FRB-FKBP dimerization disrupted Mlh1-Pms1 binding to DNA, inappropriately activated Mlh1-Pms1, and caused MMR defects in vivo. We conclude that dynamic and coordinated rearrangements of the MLH IDRs regulate how the complex clamps DNA to catalyze MMR. The application of the FRB-FKBP dimerization system to interrogate in vivo functions of a critical repair complex will be useful for probing IDRs in diverse enzymes and to probe transient loss of MMR on demand.
A Cultured Sensorimotor Organoid Model Forms Human Neuromuscular Junctions

Human induced pluripotent stem cells (iPSCs) hold promise for modeling diseases in individual human genetic backgrounds and thus for developing precision medicine. Here, we generate sensorimotor organoids containing physiologically functional neuromuscular junctions (NMJs) within a cultured organoid system and apply the model to different subgroups of amyotrophic lateral sclerosis (ALS). Using a range of molecular, genomic, and physiological techniques, we identify and characterize motor neurons and skeletal muscle, along with sensory neurons, astrocytes, microglia, and vasculature. Organoid cultures derived from ALS subject iPSC lines and isogenic lines edited to harbor familial ALS mutations all show impairment at the level of the NMJ, as detected by both contraction and immunocytochemical measurements. The physiological resolution of the human NMJ synapse, combined with the generation of major cellular cohorts exerting autonomous and non-cell autonomous effects in motor and sensory diseases, may prove valuable for more comprehensive disease modeling.
Mutation Profiles, Glycosylation Site Distribution and Codon Usage Bias of HPV16

Human papillomavirus type 16 (HPV16) is the most prevalent HPV type causing cervical cancers. Herein, using 1,597 full genomes of HPV16, we systemically investigated the mutation profiles, surface protein glycosylation sites and the codon usage bias of the eight open reading frames (ORFs) of HPV16 genomes from different lineages and sublineages. Multiple lineage- or sublineage-specific mutation sites were identified. Glycosylation analysis showed that HPV16 lineage D contained the highest number of unique potential glycosylation site in both L1 and L2 capsid protein, which might lead to their antigenic distances from other HPV16 lineages. Nucleotide composition of HPV16 showed that the overall AT content was higher than GC content at the 3rd codon position. Relatively high ENC values suggested that the HPV16 ORFs didn’t have strong codon usage bias. Most of the HPV16 ORFs were mainly governed by natural selection pressure such as translational pressure, except for L2. HPV16 only shared some of the preferred codons with human, which might help reduce competition in translational resources. These findings may help increase our understanding of the heterogeneity between HPV16 lineages and sublineages, and the adaptation mechanism of HPV in human cells, which might facilitate HPV classification and improve vaccine development and application.
Targeting Biofilm of MDR Providencia stuartii by Phages Using a Catheter Model

Providencia spp. are emerging pathogens mainly in nosocomial infections. Providencia stuartii in particular is involved in urinary tract infections and contributes significantly to the high incidence of biofilm-formation in catheterized patients. Furthermore, recent reports suggested a role for multiple drug resistant (MDR) P. stuartii in hospital-associated outbreaks which leads to excessive complications resulting in challenging treatments. Phage therapy is currently one of the most promising solutions to combat antibiotic-resistant infections. However, the number of available phages targeting Providencia spp. is extremely limited, restricting the use of phage therapy in such cases. In the present study, we describe the isolation and characterization of 17 lytic and lysogenic bacteriophages targeting clinical isolates of Providencia spp. as part of the Israeli Phage Bank (IPB). These phages, isolated from sewage samples, were evaluated for host range activity and effectively eradicated 95% of the tested bacterial strains isolated from different geographic locations and displaying a wide range of antibiotic resistance. Their lytic activity is demonstrated on agar plates, planktonic cultures, and biofilm formed in a catheter model. The results suggest that these bacteriophages can potentially be used for treatment of antibiotic-resistant Providencia spp. infections in general and of urinary tract infections in particular.
Discovery and validation of novel human genomic safe harbor sites for gene and cell therapies

Existing approaches for the integration and expression of genes of interest in a desired human cellular context are marred by the safety concerns related to either the random nature of viral-mediated integration or unpredictable pattern of gene expression in currently employed targeted genomic integration sites. Disadvantages of these methods lead to their limited use in clinical practice, thus encouraging future research in identifying novel human genomic sites that allow for predictable and safe expression of genes of interest. We conducted a bioinformatic search followed by experimental validation of novel genomic sites and identified two that demonstrated stable expression of integrated reporter and therapeutic genes without detrimental changes to cellular transcriptome. The cell-type agnostic criteria used in our bioinformatic search suggest wide-scale applicability of our sites for engineering of a diverse range of tissues for therapeutic as well as enhancement purposes, including modified T-cells for cancer therapy and engineered skin to ameliorate inherited diseases and aging. Additionally, the stable and robust levels of gene expression from identified sites allow for their use in industry-scale biomanufacturing of desired proteins in human cells.
An IPI based immune prognostic model for diffuse large B-cell lymphoma

Background International Prognostic Index (IPI) was widely used to better discriminate prognosis of patients with diffuse large B-cell lymphoma (DLBCL). However, there is a significant need to identify novel valuable biomarkers in the context of targeted therapies, such as immune checkpoint blockade (ICB) therapy. Methods Gene expression data and clinical information of DLBCL were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. 371 immune-related hub genes in DLBCL patients with different IPI levels were identified by weighted gene co-expression network analysis (WGCNA), and 8 genes were selected to construct an IPI-based immune prognostic model (IPI-IPM). Afterward, the genetic, somatic mutational and molecular profiles of IPI-IPM subgroups were analyzed, as well as the potential clinical response of ICB in different IPI-IPM subgroups. Results The IPI-IPM was constructed based on the expression of CMBL, TLCD3B, SYNDIG1, ESM1, EPHA3, HUNK, PTX3 and IL12A, where high-risk patients had shorter overall survival (OS) than low-risk patients, consistent with the results in the GEO cohorts. The comprehensive results showed that high IPI-IPM risk scores were correlated with immune-related signaling pathways, high KMT2D and CD79B mutation rates, as well as up-regulation of inhibitory immune checkpoints including PD-L1, BTLA and SIGLEC7, indicating more potential response to ICB therapy. Conclusion The IPI-IPM has independent prognostic significance for DLBCL patients, which provides an immunological perspective to elucidate the mechanisms on tumor progression, also sheds a light on developing immunotherapy for DLBCL.
Nemertean, brachiopod and phoronid neuropeptidomics reveals ancestral spiralian signalling systems

Neuropeptides are diverse signalling molecules in animals commonly acting through G-protein coupled receptors (GPCRs). Neuropeptides and their receptors underwent extensive diversification in bilaterians and the relationships of many peptide-receptor systems have been clarified. However, we lack a detailed picture of neuropeptide evolution in lophotrochozoans as in-depth studies only exist for molluscs and annelids. Here we analyse peptidergic systems in Nemertea, Brachiopoda and Phoronida. We screened transcriptomes from thirteen nemertean, six brachiopod and four phoronid species for proneuropeptides and neuropeptide GPCRs. With mass spectrometry from the nemertean Lineus longissimus, we validated several predicted peptides and identified novel ones. Molecular phylogeny combined with peptide-sequence and gene-structure comparisons allowed us to comprehensively map spiralian neuropeptide evolution. We found most mollusc and annelid peptidergic systems also in nemerteans, brachiopods and phoronids. We uncovered previously hidden relationships including the orthologies of spiralian CCWamides to arthropod agatoxin-like peptides and of mollusc APGWamides to RGWamides from annelids, with orthologues systems in nemerteans, brachiopods and phoronids. We found that pleurin neuropeptides previously only found in molluscs are also present in nemerteans and brachiopods. We also identified cases of gene family duplications and losses. These include a protostome-specific expansion of RFamide/Wamide signalling, a spiralian expansion of GnRH-related peptides, and duplications of vasopressin/oxytocin before the divergence of brachiopods, phoronids and nemerteans. This analysis expands our knowledge of peptidergic signalling in spiralians and protostomes. Our annotated dataset of nearly 1,300 proneuropeptide sequences and 600 GPCRs presents a useful resource for further studies of neuropeptide signalling in protostomes.
Synthesis of ultra-fine porous tin oxide fibres and its process characterization

Porous rutile-structured SnO2 fibres, with their length of several millimetres, diameter from 100 nm to 40 µm and potentials for sensor applications, were synthesized from a precursor solution of poly(ethylene oxide) (PEO), chloroform (CHCl3) and dimethyldineodecanoate tin (C22H44O4Sn) using electrospinning and metal–organic decomposition techniques. Fourier-transform infrared spectroscopy, thermogravimetric and differential thermal analysis and x-ray diffraction were used to characterize the synthesized fibres so as to reveal the series of physical and chemical changes occurring from the starting chemicals to the final product of ultra-fine SnO2 fibres: the solvent CHCl3 evaporates during the electrospinning; the organic groups in PEO and C22H44O4Sn decompose, with Sn–C bond in C22H44O4Sn replaced by Sn–O between 220 and 300 °C, and the atomic arrangement transforms into the genesis of a rutile-type lattice between 300 and 380 °C; the incipient lattice finally develops into the rutile structure during heat treatment at higher temperatures up to 600 °C.
Identification of gene products involved in plant colonization by Pantoea sp. YR343 using a diguanylate cyclase expressed in the presence of plants

Microbial colonization of plant roots is a highly complex process that requires the coordination and regulation of many gene networks, yet the functions of many of these gene products remain poorly understood. Pantoea sp. YR343, a gamma-proteobacterium isolated from the rhizosphere of Populus deltoides, forms robust biofilms along the root surfaces of Populus and possesses plant growth-promoting characteristics. The mechanisms governing biofilm formation along plant roots by bacteria, including Pantoea sp. YR343, are not fully understood and many genes involved in this process have yet to be discovered. In this work, we identified three diguanylate cyclases in the plant-associated microbe Pantoea sp. YR343 that are expressed in the presence of plant roots, One of these diguanylate cyclases, DGC2884 localizes to discrete sites in the cells and its overexpression results in reduced motility and increased EPS production and biofilm formation. We then performed a genetic screen by expressing this diguanylate cyclase from an inducible promoter in order to identify candidate downstream effectors of c-di-GMP signaling which may be involved in root colonization by Pantoea sp. YR343. Further, we demonstrate the importance of other domains in DGC2884 to its activity, which in combination with the genes identified by transposon mutagenesis, may yield insights into activity and regulation of homologous enzymes in medically and agriculturally relevant microbes.
The NADPH oxidase NOX2 is a marker of adverse prognosis involved in chemoresistance of acute myeloid leukemias

Resistance to chemotherapeutic drugs is a major cause of treatment failure in Acute Myeloid Leukemias (AML). To better characterize the mechanisms of chemoresistance, we first identified genes whose expression is dysregulated in AML cells resistant to daunorubicin (DNR) or cytarabine (Ara-C), the main drugs used for the induction therapy. The genes found activated are mostly linked to immune signaling and inflammation. Among them, we identified a strong up-regulation of the NOX2 NAPDH oxidase subunit genes (CYBB, CYBA, NCF1, NCF2, NCF4 and RAC2). The ensuing increase in NADPH oxidase activity, which is particularly strong in DNR-resistant cells, participates in the acquisition and/or maintenance of resistance to DNR. In addition, analyzing gp91phox (CYBB-encoded Nox2 catalytic sub-unit) expression at the surface of leukemic blasts from 74 patients at diagnosis showed that NOX2 is generally more expressed and active in leukemic cells from the FAB M4/M5 subtypes compared to FAB M0-M2 ones. Using a gene expression-based score we demonstrate that high NOX2 subunit genes expression is a marker of adverse prognosis, independent of the cytogenetic-based risk classification, in AML patients.
A Framework of Quantum Strong Exponential-Time Hypotheses

The strong exponential-time hypothesis (SETH) is a commonly used conjecture in the field of complexity theory. It essentially states that determining whether a CNF formula is satisfiable can not be done faster than exhaustive search over all possible assignments. This hypothesis and its variants gave rise to a fruitful field of research, fine-grained complexity, obtaining (mostly tight) lower bounds for many problems in P whose unconditional lower bounds are very likely beyond current techniques. In this work, we introduce an extensive framework of Quantum Strong Exponential-Time Hypotheses, as quantum analogues to what SETH is for classical computation. Using the QSETH framework, we are able to translate quantum query lower bounds on black-box problems to conditional quantum time lower bounds for many problems in P . As an example, we provide a conditional quantum time lower bound of Ω( n 1 . 5 ) for the Longest Common Subsequence and Edit Distance problems. We also show that the n 2 SETH-based lower bound for a recent scheme for Proofs of Useful Work carries over to the quantum setting using our framework, maintaining a quadratic gap between verifier and prover. Lastly, we show that the assumptions in our framework can not be simplified further with relativizing proof techniques, as they are false in relativized worlds.
Plasma Amination of Low-Density Polyethylene by DBD Afterglows at Atmospheric Pressure

Surfaces of LDPE can be functionalized with primary amino groups using the afterglows from dielectric barrier discharges in N 2 , N 2 + H 2 , and N 2 + NH 3 mixtures at atmospheric pressure. Quantitative analysis by a recently developed ATR FT-IR spectroscopic method allows calculation of the number of NH 2 groups generated per unit area. Treatment in N 2 + H 2 afterglows was found to be most efficient in terms of area densities of primary amines achieved (more than is nm -2 ), but appreciable quantities of -NH 2 , up to about 3 nm -2 , are also obtained in pure N 2 . Possible mechanisms of the amination reaction and the roles of gas additives are discussed.
The Adsorption of Dioxan by Porous Silicas

Volumetric adsorption of nitrogen and gravimetric adsorption of dioxan is reported for nonporous, mesoporous, and microporous silicas. Adsorption on the microporous material is governed by pore volume and dimensions. Adsorption on the nonporous silica and the mesoporous silica at up to monolayer coverages is governed by specific hydrogen bonding interactions between surface silanol groups and dioxan molecules. Different silanol group distributions for different silicas after standard treatment coupled with different possible modes of adsorption casts doubt on the use of nonporous silica as a standard for the study of interactions between porous silicas and H-bond acceptor molecules.
Shape Memory Alloy (SMA) Actuator With Embedded Liquid Metal Curvature Sensor for Closed-Loop Control

We introduce a soft robot actuator composed of a pre-stressed elastomer film embedded with shape memory alloy (SMA) and a liquid metal (LM) curvature sensor. SMA-based actuators are commonly used as electrically-powered limbs to enable walking, crawling, and swimming of soft robots. However, they are susceptible to overheating and long-term degradation if they are electrically stimulated before they have time to mechanically recover from their previous activation cycle. Here, we address this by embedding the soft actuator with a capacitive LM sensor capable of measuring bending curvature. The soft sensor is thin and elastic and can track curvature changes without significantly altering the natural mechanical properties of the soft actuator. We show that the sensor can be incorporated into a closed-loop “bang-bang” controller to ensure that the actuator fully relaxes to its natural curvature before the next activation cycle. In this way, the activation frequency of the actuator can be dynamically adapted for continuous, cyclic actuation. Moreover, in the special case of slower, low power actuation, we can use the embedded curvature sensor as feedback for achieving partial actuation and limiting the amount of curvature change.
The Complex World of Regulation of Pituitary Growth Hormone Secretion: The Role of Ghrelin, Klotho, and Nesfatins in It

The classic concept of how pituitary GH is regulated by somatostatin and GHRH has changed in recent years, following the discovery of peripheral hormones involved in the regulation of energy homeostasis and mineral homeostasis. These hormones are ghrelin, nesfatins, and klotho. Ghrelin is an orexigenic hormone, released primarily by the gastric mucosa, although it is widely expressed in many different tissues, including the central nervous system and the pituitary. To be active, ghrelin must bind to an n-octanoyl group (n = 8, generally) on serine 3, forming acyl ghrelin which can then bind and activate a G-protein-coupled receptor leading to phospholipase C activation that induces the formation of inositol 1,4,5-triphosphate and diacylglycerol that produce an increase in cytosolic calcium that allows the release of GH. In addition to its direct action on somatotrophs, ghrelin co-localizes with GHRH in several neurons, facilitating its release by inhibiting somatostatin, and acts synergistically with GHRH stimulating the synthesis and secretion of pituitary GH. Gastric ghrelin production declines with age, as does GH. Klotho is an anti-aging agent, produced mainly in the kidneys, whose soluble circulating form directly induces GH secretion through the activation of ERK1/2 and inhibits the inhibitory effect that IGF-I exerts on GH. Children and adults with untreated GH-deficiency show reduced plasma levels of klotho, but treatment with GH restores them to normal values. Deletions or mutations of the Klotho gene affect GH production. Nesfatins 1 and 2 are satiety hormones, they inhibit food intake. They have been found in GH3 cell cultures where they significantly reduce the expression of gh mRNA and that of pituitary-specific positive transcription factor 1, consequently acting as inhibitors of GH production. This is a consequence of the down-regulation of the cAMP/PKA/CREB signaling pathway. Interestingly, nesfatins eliminate the strong positive effect that ghrelin has on GH synthesis and secretion. Throughout this review, we will attempt to broadly analyze the role of these hormones in the complex world of GH regulation, a world in which these hormones already play a very important role.