3D Conformation Research Articles

Conformal 3D Material Extrusion Additive Manufacturing for Large Moulds

Industrial engineering applications often require manufacturing large components in composite materials to obtain light structures; however, moulds are expensive, especially when manufacturing a limited batch of parts. On the one hand, when traditional approaches are carried out, moulds are milled from large slabs or laminated with composite materials on a model of the part to produce. In this case, the realisation of a mould leads to adding time-consuming operations to the manufacturing process. On the other hand, if a fully additively manufactured approach is chosen, the manufacturing time increases exponentially and does not match the market’s requirements. This research proposes a methodology to improve the production efficiency of large moulds using a hybrid technology by combining additive manufacturing and milling tools. A block of soft material such as foam is milled, and then the printing head of an additive manufacturing machine deposits several layers of plastic material or modelling clay using conformal three-dimensional paths. Finally, the mill can polish the surface, thus obtaining a mould of large dimensions quickly, with reduced cost and without needing trained personnel and handcraft polishing. A software tool has been developed to modify the G-code read by an additive manufacturing machine to obtain material deposition over the soft mould. The authors forced conventional machining instructions to match those of an AM machine. Thus, additive deposition of new material uses 3D conformal trajectories typical of CNC machines. Consequently, communication between two very different instruments using the same language is possible. At first, the code was tested on a modified Fused Filament Fabrication machine whose firmware has been adapted to manage a milling tool and a printing head. Then, the software was tested on a large machine suitable for producing moulds for the large parts typical of marine and aerospace engineering. The research demonstrates that AM technologies can integrate conventional machinery to support the composite materials industry when large parts are required.

Closed-loop controlled conformal 3D printing on moving objects via tool-localized object position sensing

The ability to functionalize and inspect moving objects is central to various emerging additive manufacturing (AM) applications, including in situ bioprinting and 3D printing in extreme conditions (e.g., space). This work provides a novel closed-loop controlled path planning method for planar and nonplanar microextrusion 3D printing on moving substrates and objects via real-time sensing of local object-tool offset that requires no description of the object's global geometry. Feedback control of the microextrusion nozzle z-axis position via real-time sensing of nozzle-surface offset using 1D laser displacement sensors enabled conformal 3D printing on moving substrates and objects. The method's utility was demonstrated by microextrusion 3D printing on planar substrates oscillating at the frequencies associated with tissue motion caused by human physiological processes, including respiration and the heartbeat. The method enabled conformal microextrusion 3D printing in the presence of substrate or object motion, including random vertical displacement (i.e., step changes) and continuous vibration (amplitude (A) = 0.8–6.7d, frequency (f) = 0.2, 0.4 and 1.3 Hz, where d is the nozzle diameter). The method was also validated by conformal microextrusion 3D printing on a human hand undergoing random vertical motion (A = 0–34.5d). This work advances closed-loop path planning for microextrusion 3D printing on moving substrates and objects. The created closed-loop path planning methodology and AM process may support various emerging AM applications, including in situ bioprinting and AM in mobile and extreme environments prone to mechanical disturbance, such as vehicles, vessels, aircraft, and spacecraft.

Characterization of the Response of 9L and U-251N Orthotopic Brain Tumors to 3D Conformal Radiation Therapy.

In a study employing MRI-guided stereotactic radiotherapy (SRS) in two orthotopic rodent brain tumor models, the radiation dose yielding 50% survival (the TCD50) was sought. Syngeneic 9L cells, or human U-251N cells, were implanted stereotactically in 136 Fischer 344 rats or 98 RNU athymic rats, respectively. At approximately 7 days after implantation for 9L, and 18 days for U-251N, rats were imaged with contrast-enhanced MRI (CE-MRI) and then irradiated using a Small Animal Radiation Research Platform (SARRP) operating at 220 kV and 13 mA with an effective energy of ∼70 keV and dose rate of ∼2.5 Gy per min. Radiation doses were delivered as single fractions. Cone-beam CT images were acquired before irradiation, and tumor volumes were defined using co-registered CE-MRI images. Treatment planning using MuriPlan software defined four non-coplanar arcs with an identical isocenter, subsequently accomplished by the SARRP. Thus, the treatment workflow emulated that of current clinical practice. The study endpoint was animal survival to 200 days. The TCD50 inferred from Kaplan-Meier survival estimation was approximately 25 Gy for 9L tumors and below 20 Gy, but within the 95% confidence interval in U-251N tumors. Cox proportional-hazards modeling did not suggest an effect of sex, with the caveat of wide confidence intervals. Having identified the radiation dose at which approximately half of a group of animals was cured, the biological parameters that accompany radiation response can be examined.

Deciphering an isolated lung phenotype of NKX2-1 frameshift pathogenic variant.

to perform a functional analysis of a new NK2 homeobox 1 (NKX2-1) variant (c.85_86del denominated NKX2-1DEL) identified in a family presenting with isolated respiratory disease, in comparison to another frameshift variant (c.254dup denominated NKX2-1DUP) identified in a subject with classical brain-lung-thyroid syndrome. pathogenic variants were introduced into the pcDNA3-1(+)-wt-TTF1 plasmid. The proteins obtained were analyzed by western blot assay. Subcellular localization was assessed by confocal microscopy in A549 and Nthy cells. Transactivation of SFTPA, SFTPB, SFTPC, and ABCA3 promoters was assessed in A549 cells. Thyroglobulin promoter activity was measured with the paired box gene 8 (PAX8) cofactor in Nthy cells. The two sequence variants were predicted to produce aberrant proteins identical from the 86th amino acid, with deletion of their functional homeodomain, including the nuclear localization signal. However, 3D conformation prediction of the conformation prediction of the mutant protein assumed the presence of a nuclear localization signal, a bipartite sequence, confirmed by confocal microscopy showing both mutant proteins localized in the nucleus and cytoplasm. Transcriptional activity with SFTPA, SFTPB, SFTPC, ABCA3 and thyroglobulin promoters was significantly decreased with both variants. However, with NKX2-1DEL, thyroglobulin transcriptional activity was maintained with the addition of PAX8. These results provide novel insights into understanding the molecular mechanism of phenotypes associated with NKX2-1 pathogenic variants.

Performance enhancement in thermally activated delayed fluorescence emitters by multi-fold layout

A series of thermally activated delayed fluorescence (TADF) materials, namely o-Ac2BBP, o-Px2BBP, D-BP-DMAC and D-BP-PXZ, were designed with double acridine (DMAC) or phenoxazine (PXZ) donors and double carbonyl acceptors. Phenylene and biphenylene were selected as the central bridges for these emitters, and each benzene ring on the central bridge was substituted at ortho-sites. The biphenylene bridge based D-BP-DMAC and D-BP-PXZ show 3D dimensional non-planar conformations and multi-fold layout, which result in multiple intramolecular interactions including C–H⋯O hydrogen bonds and C–H···π interactions and finally strongly stabilized and rigidified the whole molecular structures by locking the molecular geometry. As a result, the nonradiative transition rates (knr) were effectively suppressed by 5 times in comparison with the corresponding phenylene bridged analogues, and the photoluminescence quantum yields were increased to over 95%. The green and yellow OLEDs with D-BP-DMAC and D-BP-PXZ as doped emitters exhibited the maximum external quantum efficiencies (EQE) of 24.3% and 17.3%, which are almost double of the corresponding values (13.1% and 9.3%) of the phenylene bridged analogues o-Ac2BBP and o-Px2BBP. These results indicate that to increase molecular rigidity by multi-fold-layout is an effective design strategy to enhance the performance of TADF materials and OLEDs.

Advances in deep learning-based 3D molecular generative models

<p indent="0mm">Molecular generation, aiming at designing novel molecules with desired properties such as biological activity and drug metabolism and pharmacokinetic (DMPK) properties in a low-cost and high-efficient manner, is a fundamental problem in drug discovery. Recently, deep generative models have been widely used in drug discovery, along with numerous model architectures and optimization strategies being explored, most of which are developed to generate one-dimensional or two-dimensional molecular structures. Inspired by the rapid development of deep learning in processing geometric graph data, 3D generative models for molecular generation have also been proposed, gaining attention for their advantages and potential on direct 3D molecular conformation generation and structure-based drug discovery. This survey has offered a systematic summarization of existing research achievements of the domestic and foreign researchers in recent years in the aspects of 3D molecular generation. According to the input of 3D molecular generation algorithms, it is divided into latent variable-based generation, 2D graph-based generation and 3D geometry-based generation. Then, according to the output of 3D molecular generation algorithms, it is divided into goal-directed generation and non-goal-directed generation. Furthermore, the performance of different generative models on main public datasets is summarized, which proves the advantages and disadvantages of the various models. Finally, some promising research directions are proposed.

Clustering molecular dynamics conformations of the CC’-loop of the PD-1 immuno-checkpoint receptor

Molecular mechanisms within the checkpoint receptor PD-1 are essential for its activation by PD-L1 as well as for blocking such an activation via checkpoint inhibitors. We use molecular dynamics to scrutinize patterns of atomic motion in PD-1 without a ligand. Molecular dynamics is performed for the whole extracellular domain of PD-1, and the analysis focuses on its CC’-loop and some adjacent Cα-atoms. We extend previous work by applying common nearest neighbor clustering (Cnn) and compare the performance of this method with Daura clustering as well as UMAP dimension reduction and subsequent agglomerative linkage clustering. As compared to Daura clustering, we found Cnn less sensitive to cutoff selection and better able to return representative clusters for sets of different 3D atomic conformations. Interestingly, Cnn yields results quite similar to UMAP plus linkage clustering.

Ultra-selective, ultra-clean 1D rotating-frame Overhauser effect spectroscopy.

An ultra-selective 1D NMR experiment - GEMSTONE-ROESY - enables clear, unambiguous assignment of ROE signals in the not uncommon situation that traditional selective methods fail. Its usefulness is demonstrated in the analysis of the natural products cyclosporin and lacto-N-difucohexaose I, providing detailed insight into the structures and conformations of these molecules.

Multi-state modeling of antibody-antigen complexes with SAXS profiles and deep-learning models.

Antibodies are an established class of human therapeutics. Epitope characterization is an important part of therapeutic antibody discovery. However, structural characterization of antibody-antigen complexes remains challenging. On the one hand, X-ray crystallography or cryo-electron microscopy provide atomic resolution characterization of the epitope, but the data collection process is typically long and the success rate is low. On the other hand, computational methods for modeling antibody-antigen structures from the individual components frequently suffer from a high false positive rate, rarely resulting in a unique solution. Recent deep learning models for structure prediction are also successful in predicting protein-protein complexes. However, they do not perform well for antibody-antigen complexes. Small Angle X-ray Scattering (SAXS) is a reliable technique for rapid structural characterization of protein samples in solution albeit at low resolution. Here, we present an integrative approach for modeling antigen-antibody complexes using the antibody sequence, antigen structure, and experimentally determined SAXS profiles of the antibody, antigen, and the complex. The method models antibody structures using a novel deep-learning approach, NanoNet. The structures of the antibodies and antigens are represented using multiple 3D conformations to account for compositional and conformational heterogeneity of the protein samples that are used to collect the SAXS data. The complexes are predicted by integrating the SAXS profiles with scoring functions for protein-protein interfaces that are based on statistical potentials and antibody-specific deep-learning models. We validated the method via application to four Fab:EGFR and one Fab:PCSK9 antibody:antigen complexes with experimentally available SAXS datasets. The integrative approach returns accurate predictions (interface RMSD<4Å) in the top five predictions for four out of five complexes (respective interface RMSD values of 1.95, 2.18, 2.66 and 3.87Å), providing support for the utility of such a computational pipeline for epitope characterization during therapeutic antibody discovery.

3D Conformational Generative Models for Biological Structures Using Graph Information-Embedded Relative Coordinates.

Developing molecular generative models for directly generating 3D conformation has recently become a hot research area. Here, an autoencoder based generative model was proposed for molecular conformation generation. A unique feature of our method is that the graph information embedded relative coordinate (GIE-RC), satisfying translation and rotation invariance, was proposed as a novel way for encoding molecular three-dimensional structure. Compared with commonly used Cartesian coordinate and internal coordinate, GIE-RC is less sensitive on errors when decoding latent variables to 3D coordinates. By using this method, a complex 3D generation task can be turned into a graph node feature generation problem. Examples were shown that the GIE-RC based autoencoder model can be used for both ligand and peptide conformation generation. Additionally, this model was used as an efficient conformation sampling method to augment conformation data needed in the construction of neural network-based force field.

Three dimensions of thermolabile sex determination.

The molecular mechanism of temperature-dependent sex determination (TSD) is a long-standing mystery. How is the thermal signal sensed, captured and transduced to regulate key sex genes? Although there is compelling evidence for pathways via which cells capture the temperature signal, there is no known mechanism by which cells transduce those thermal signals to affect gene expression. Here we propose a novel hypothesis we call 3D-TSD (the three dimensions of thermolabile sex determination). We postulate that the genome has capacity to remodel in response to temperature by changing 3D chromatin conformation, perhaps via temperature-sensitive transcriptional condensates. This could rewire enhancer-promoter interactions to alter the expression of key sex-determining genes. This hypothesis can accommodate monogenic or multigenic thermolabile sex-determining systems, and could be combined with upstream thermal sensing and transduction to the epigenome to commit gonadal fate.

Roles of Polycomb Complexes in the Reconstruction of 3D Genome Architecture during Preimplantation Embryonic Development.

The appropriate deployment of developmental programs depends on complex genetic information encoded by genomic DNA sequences and their positioning and contacts in the three-dimensional (3D) space within the nucleus. Current studies using novel techniques including, but not limited to, Hi-C, ChIA-PET, and Hi-ChIP reveal that regulatory elements (Res), such as enhancers and promoters, may participate in the precise regulation of expression of tissue-specific genes important for both embryogenesis and organogenesis by recruiting Polycomb Group (PcG) complexes. PcG complexes usually poise the transcription of developmental genes by forming Polycomb bodies to compact poised enhancers and promoters marked by H3K27me3 in the 3D space. Additionally, recent studies have also uncovered their roles in transcriptional activation. To better understand the full complexities in the mechanisms of how PcG complexes regulate transcription and long-range 3D contacts of enhancers and promoters during developmental programs, we outline novel insights regarding PcG-associated dramatic changes in the 3D chromatin conformation in developmental programs of early embryos and naïve-ground-state transitions of pluripotent embryonic stem cells (ESCs), and highlight the distinct roles of unique and common subunits of canonical and non-canonical PcG complexes in shaping genome architectures and transcriptional programs.

Zeolite A/ZnCl2 nanoparticles as a catalyst for eco-friendly synthesis of pyrazole-1- carbothioamides with docking validation as Covid-19 main protease (MPRO) inhibitor

ABSTRACT. The synthesized Zeolite A/ZnCl2 nanoparticles via the hydrothermal route were characterized using FTIR, XRD, and SEM/EDAX techniques. The characterized catalyst was used for the eco-friendly synthesis of 4,5-dihydro-pyrazole-1-carbothioamide derivatives. Under solvent-free conditions, a multi-component reaction between hydrazine, isothiocyanate, and chalcone was done with a prepared nano-catalyst as an inexpensive, recyclable, easy-to-get, and nontoxic catalyst. The molecular docking study explained that dihydro-1-carbothioamide pyrazoles can be considered COVID-19 main protease (Mpro) inhibitors. In order to investigate the 3D conformation of the compounds that were synthesized, the density functional theory (DFT) was applied with a B3LYP hybrid functional and a 6-311++ G(d,p) basis set. This allowed us to investigate the compounds' electronic and charge transfer properties. In this series of compounds, the derivative 30d showed the lowest HOMO–LUMO energy gap.&#x0D; &#x0D; KEY WORDS: Zeolite A/ZnCl2 nanoparticles, Pyrazole-1-carbothioamides, Docking, XRD, SEM/EDX, HRTEM&#x0D; &#x0D; Bull. Chem. Soc. Ethiop. 2023, 37(2), 391-404. &#x0D; DOI: https://dx.doi.org/10.4314/bcse.v37i2.11

Interferon opens up: HIV-induced inflammation reconfigures 3D chromatin conformation and affects where HIV integrates

Plaza-Jennings etal. applied single-nucleus RNA-seq, sorted neuronal and microglia cells for HiC, and found that chronic HIV infection in the brain induces interferon stimulation in microglia, drives chromatin reconfiguration into a transcriptionally active environment, and changes HIV integration landscape.

Immunoinformatics design of multi-epitope peptide-based vaccine against Haemophilus influenzae strain using cell division protein.

Haemophilus influenzae is a pathogen that causes invasive bacterial infections in humans. The highest prevalence lies in both young children and adults. Generally, there are no vaccines available that target all the strains of Haemophilus influenzae. Hence, the purpose of this research is to employ bioinformatics and immunoinformatics approaches to design a Multi-Epitope Vaccine candidate employing the pathogenic cell division protein FtsN that specifically combat all the Haemophilus influenzae strains. The current research focuses on developing subunit vaccine in contrast to vaccines generated from the entire pathogen. This will be accomplished by combining multiple bioinformatics and immunoinformatics approaches. As a result, prospective T cells (helper T lymphocyte and cytotoxic T lymphocytes) and B cells epitopes were investigated. The human leukocyte antigen allele having strong associations with the antigenic and overlapping epitopes were chosen, with 70% of the total coverage of the world population. To construct a linked vaccine design, multiple linkers were used. To increase the immunogenic profile, an adjuvant was linked using EAAAK linker. The final vaccine construct with 149 amino acids was obtained after adjuvants and linkers were added. The developed Multi-Epitope Vaccine has a high antigenicity as well as viable physiochemical features. The 3D conformation was modeled and undergoes refinement and validation using bioinformatics methods. Furthermore, protein-protein molecular docking analysis was performed to predict the effective binding poses of Multi-Epitope Vaccine with the Toll-like receptor 4 protein. Besides, vaccine underwent the codon translational optimization and computational cloning to verify the reliability and proper Multi-Epitope Vaccine expression. In addition, it is necessary to conduct experiments and research in the laboratory to demonstrate that the vaccine that has been developed is immunogenic and protective.

GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources.

G protein-coupled receptors (GPCRs) are physiologically abundant signaling hubs routing hundreds of extracellular signal substances and drugs into intracellular pathways. The GPCR database, GPCRdb supports>5000 interdisciplinary researchers every month with reference data, analysis, visualization, experiment design and dissemination. Here, we present our fifth major GPCRdb release setting out with an overview of the many resources for receptor sequences, structures, and ligands. This includes recently published additions of class D generic residue numbers, a comparative structure analysis tool to identify functional determinants, trees clustering GPCR structures by 3D conformation, and mutations stabilizing inactive/active states. We provide new state-specific structure models of all human non-olfactory GPCRs built using AlphaFold2-MultiState. We also provide a new resource of endogenous ligands along with a larger number of surrogate ligands with bioactivity, vendor, and physiochemical descriptor data. The one-stop-shop ligand resources integrate ligands/data from the ChEMBL, Guide to Pharmacology, PDSP Kiand PubChem database. The GPCRdb is available at https://gpcrdb.org.

Dosimetric analysis of 3 dimensional conformal radiotherapy with volumetric modulated arc therapy in patients with carcinoma oesophagus – Prospective study

: To study the dosimetry and treatment plan of Volumetric Modulated Arc Therapy and 3 Dimensional Conformal Radiotherapy in patients with carcinoma oesophagus. : A prospective study was taken up in Department of Radiotherapy, from October 2017 to June 2019. A total 20 patients who achieved eligibility criteria was taken into study and both 3D CRT (3D Conformal Radiation Therapy)and VMAT(Volumetric Modulated Arc Therapy ) plans was done in all patients. Dosimetric comparison is done between these two techniques. Dose to spinal cord is significantly reduced with VMAT technique when compared to 3D CRT. VMAT plans in this study showed significantly reduced doses to heart, when compared to 3D CRT plans. VMAT plans decrease volume of lung receiving high dose(v20,dmean,v30,v40) compared to 3D CRT but at a cost of delivering low dose to more volume of lung (v5, v10, v15) resulting in serious complications like radiation pneumonitis. VMAT plans are advisable in carcinoma oesophagus patients to achieve reduced doses to OARs(Organs at Risk) like Spinal Cord, Heart &amp; Lung and better target coverage particularly in cervical esophagus where higher doses are planned.

Nucleotide Composition of Ultra-Conserved Elements Shows Excess of GpC and Depletion of GG and CC Dinucleotides.

The public UCNEbase database, comprising 4273 human ultra-conserved noncoding elements (UCNEs), was thoroughly investigated with the aim to find any nucleotide signals or motifs that have made these DNA sequences practically unchanged over three hundred million years of evolution. Each UCNE comprises over 200 nucleotides and has at least 95% identity between humans and chickens. A total of 31,046 SNPs were found within the UCNE database. We demonstrated that every human has over 300 mutations within 4273 UCNEs. No association of UCNEs with non-coding RNAs, nor preference of a particular meiotic recombination rate within them were found. No sequence motifs associated with UCNEs nor their flanking regions have been found. However, we demonstrated that UCNEs have strong nucleotide and dinucleotide sequence abnormalities compared to genome averages. Specifically, UCNEs are depleted for CC and GG dinucleotides, while GC dinucleotides are in excess of 28%. Importantly, GC dinucleotides have extraordinarily strong stacking free-energy inside the DNA helix and unique resistance to dissociation. Based on the adjacent nucleotide stacking abnormalities within UCNEs, we conjecture that peculiarities in dinucleotide distribution within UCNEs may create unique 3D conformation and specificity to bind proteins. We also discuss the strange dynamics of multiple SNPs inside UCNEs and reasons why these sequences are extraordinarily conserved.

Novel Insights on the Three-dimensional Shape of Microgels at Fluid Interfaces

Mechanically soft colloids (microgels) adsorbed at the interface between two fluids offer superior advantages over hard counterparts for a variety of applications ranging from foams/emulsion stabilization to the assembly of two-dimensional (2D) materials. Particle deformability and compressibility impart additional responses to microgel-laden interfaces that can be controlled on-demand by varying single-particle properties (e.g. crosslinking content and polymer density profile) and/or external parameters (e.g. interfacial compression and tension, temperature, oil polarity). In order to understand how single-particle softness influences the resulting material properties, a detailed quantification of the microgel’s 3D conformation when confined at the fluid interface is of utmost importance. This article describes how different methodologies can be used to visualize, and in some case quantify, the conformation of adsorbed microgels, putting particular emphasis on the multiple advantages offered by in situ atomic force microscopy imaging at the fluid interface. The influence of the internal particle architecture, as well as that of temperature, interfacial tension and solubility in the organic phase, will be discussed. Finally, some perspectives on how softness can be exploited to tune the structural and mechanical properties of microgel monolayers will be provided.

A Combined Hypofractionated Volumetric Modulated Arc Radiotherapy, Radio-Sensitising and Adjuvant Metronomic Chemotherapy Treatment for Canine Stage IV Nasal Tumours With Intracranial Extension

Radiation therapy has become the standard of care in the treatment of canine intranasal neoplasia, but because of the poor prognosis associated with stage IV nasal tumours and the proximity of the brain to the irradiation target, few data regarding the treatment of very advanced neoplasms are available. The aim of this pilot study was to evaluate the feasibility, safety and effectiveness of a combined treatment composed of definitive high-dose hypofractionated volumetric modulated arc radiotherapy on tumours with concurrent treatment of regional lymph nodes if positive or as prophylaxis, carboplatin radio-sensitising, and adjuvant metronomic chemotherapy for stage IV canine nasal tumours with intracranial extension.A pilot observational study was conducted in 7 dogs. Magnetic resonance imaging follow-up examinations revealed complete responses in 5 dogs and partial responses in 2. The median overall survival time, evaluated via Kaplan−Meier survival analysis, was 310 days with a 95% confidence interval of 210-400 days, whereas the median progression-free survival was 240 days with a 95% confidence interval of 190-290 days.Despite the proximity of highly sensitive organs at risk, no grade III or IV toxicities were observed, and volumetric modulated arc radiotherapy seemed to be a feasible treatment option for stage IV canine nasal tumours where conformal 3D radiotherapy has proven to give higher doses with severe damage to the surrounding unaffected tissues. Further studies are needed on the role of the sphenoid bone microscopic infiltration and regional lymph node involvement. The absence of severe toxicity could also lead to a dose escalation study and chemotherapy scheme.