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The μ-opioid receptor (μOR), a prototypical G protein-coupled receptor (GPCR), is the target of opioid analgesics such as morphine and fentanyl. Due to the severe side effects of current opioid drugs, there is considerable interest in developing novel modulators of μOR function. Most GPCR ligands today are small molecules, however biologics, including antibodies and nanobodies, represent alternative therapeutics with clear advantages such as affinity and target selectivity. Here, we describe the nanobody NbE, which selectively binds to the μOR and acts as an antagonist. We functionally characterize NbE as an extracellular and genetically encoded μOR ligand and uncover the molecular basis for μOR antagonism by determining the cryo-EM structure of the NbE-μOR complex. NbE displays a unique ligand binding mode and achieves μOR selectivity by interactions with the orthosteric pocket and extracellular receptor loops. Based on a β-hairpin loop formed by NbE that deeply protrudes into the μOR, we design linear and cyclic peptide analogs that recapitulate NbEs antagonism. The work illustrates the potential of nanobodies to uniquely engage with GPCRs and describes lower molecular weight μOR ligands that can serve as a basis for therapeutic developments.

The rapid evolution of viruses generates proteins that are essential for infectivity and replication but with unknown functions, due to extreme sequence divergence1. Here, using a database of 67,715 newly predicted protein structures from 4,463 eukaryotic viral species, we found that 62% of viral proteins are structurally distinct and lack homologues in the AlphaFold database2,3. Among the remaining 38% of viral proteins, many have non-viral structural analogues that revealed surprising similarities between human pathogens and their eukaryotic hosts. Structural comparisons suggested putative functions for up to 25% of unannotated viral proteins, including those with roles in the evasion of innate immunity. In particular, RNA ligase T-like phosphodiesterases were found to resemble phage-encoded proteins that hydrolyse the host immune-activating cyclic dinucleotides 3',3'- and 2',3'-cyclic GMP-AMP (cGAMP). Experimental analysis showed that RNA ligase T homologues encoded by avian poxviruses similarly hydrolyse cGAMP, showing that RNA ligase T-mediated targeting of cGAMP is an evolutionarily conserved mechanism of immune evasion that is present in both bacteriophage and eukaryotic viruses. Together, the viral protein structural database and analyses presented here afford new opportunities to identify mechanisms of virus-host interactions that are common across the virome.

This paper introduces the Cyclic Production Routing Problem (CPRP). The CPRP is an extension of the well-known NP-hard Production Routing Problem (PRP), which is a hard-to-solve combinatorial optimisation problem with numerous practical applications in the field of freight transportation, logistics and supply chain management. Under the PRP setting, a manufacturer is responsible for determining production decisions, as well as the timing and quantity of replenishment services offered to a set of geographically dispersed customers over a multi-period time horizon. The problem calls for jointly optimising the production, inventory, distribution and routing decisions. In this paper, the basic PRP model is modified to generate repeatable cyclic production and delivery schedules. A two-commodity flow formulation is proposed along with valid inequalities. Extensive comparisons between the basic PRP and the proposed cyclic variant on well-known benchmark instances are provided. The new variant is significantly harder to solve, especially when the vehicle fleet is limited. From a managerial perspective, the generation of cyclic production-routing schedules significantly increases all costs, whereas the number of vehicle routes required to implement a cyclic schedule is higher. [ABSTRACT FROM AUTHOR]

The proteasome degrades proteins, which is essential for cellular homeostasis. Ubiquitin independent proteolysis degrades highly disordered and misfolded proteins. A decline of proteasomal activity has been associated with multiple neurodegenerative diseases due to the accumulation of misfolded proteins. In this work, cyclic peptide proteasome stimulators (CyPPSs) that enhance the clearance of misfolded proteins were discovered. In the initial screen of predicted natural products (pNPs), several cyclic peptides were found to stimulate the 20S core particle (20S CP). Development of a robust structural activity relationship led to the identification of potent, cell permeable CyPPSs. In vitro assays revealed that CyPPSs stimulate degradation of highly disordered and misfolded proteins without affecting ordered proteins. Furthermore, using a novel flow-based assay for proteasome activity, several CyPPSs were found to stimulate the 20S CP in cellulo. Overall, this work describes the development of CyPPSs as chemical tools capable of stimulating the proteasome and provides strong support for proteasome stimulation as a therapeutic strategy for neurodegenerative diseases.

The mechanisms associated with the transitions of strong El Niño (EN) events and their implications for the South American precipitation were investigated for the 1950–2023 period. Strong EN events exhibit cyclic or episodic characteristics in their transitions. Cyclic EN events are both preceded and followed by La Niña (LN) conditions, whereas episodic EN events are preceded by neutral conditions, with a more uncertain transition following. For cyclic EN, tropical Pacific mechanisms initiates and peak warming in the eastern tropical Pacific from austral winter to early summer. In contrast, for episodic EN, coupled subtropical and tropical Pacific mechanisms, respectively, initiate and peak warming in the central tropical Pacific from autumn to late summer. The Pacific Decadal Oscillation (PDO) mean state modulates EN's decay stage. During the +PDO mean state, cyclones in the eastern subtropical Pacific of both hemispheres sustain the warming of episodic EN, whereas during the −PDO mean state, anticyclones in the eastern subtropical Pacific accelerate the decay of cyclic EN, favouring its transition to an LN. These mechanisms explain why episodic EN initiates earlier, peaks later, is more intense and decays more slowly than cyclic EN. During an episodic EN summer, the strengthened atmospheric circulation maintains the Atlantic Intertropical Convergence Zone (ITCZ) north of the equator, causing persistent negative precipitation anomalies in north–northeastern South America (SA) until the following winter, while positive precipitation anomalies in southeastern SA are driven by south–southeastward moisture transport from equatorial Atlantic. Conversely, during a cyclic EN summer, negative (positive) precipitation anomalies impact north–northwestern (southeastern) SA; however, the anomalous atmospheric circulation and precipitation in SA quickly return to normal conditions in the autumn, and positive precipitation anomalies appear in northern SA in the following winter. Understanding these mechanisms is crucial for predicting EN's future changes and, consequently, their potential socio‐economic impacts globally. [ABSTRACT FROM AUTHOR]

This paper introduces an innovative heuristic optimization approach, referred to as Optimization Approach-Single Hoist Cyclic Scheduling Problem (OA-SHCSP), which aims to minimize the cycle time of the Single Hoist Scheduling Problem (SHCSP). The effectiveness of this proposed heuristic is compared with a previously established heuristic, the Earliest Starting Time (EST). The comparison results reveal that the proposed OA-SHCSP heuristic consistently outperforms the EST heuristic in minimizing cycle time, particularly when more than two products are produced simultaneously. Moreover, as the number of part tasks soaked during a cycle increases, OA-SHCSP demonstrates significantly improved computational efficiency over the EST heuristic. The reduction in average cycle time achieved by OA-SHCSP ranges from 28.73% to 60.29%, underscoring its effectiveness and potential for application in high-volume production environments. [ABSTRACT FROM AUTHOR]

Humanity's efforts are manifested in the creation of novel solutions to complex problems in diverse fields. Traditional mathematical methods fail to solve real-world problems due to their complexity. Researchers have come up with new mathematical theories like fuzzy set theory and rough set theory to help them figure out how to model the uncertainty in these fields. Soft set theory is a novel approach to real-world problem solving that does not require the membership function to be specified. This aids in the resolution of a wide range of issues, and significant progress has recently been made. After Jun et al. came up with a hybrid system that combined fuzzy and soft set concepts, many people came up with hybrid ideas in different algebraic structures. In this paper, we introduce the concepts of subsystem and strong subsystem of a hybrid finite state machine (HFSM) and investigate a portion of their significant properties. We also provide an example that shows that every subsystem does not need to be a strong subsystem. Additionally, we study the cyclic subsystem of HFSMs and also obtain their equivalent results and examples. Finally, we define the notions of homomorphism of subsystems and strong subsystems of HFSMs. [ABSTRACT FROM AUTHOR]

Reinforced concrete (RC) bridge columns often encounter complex combinations of loads, including flexural, axial, shear, and torsional forces, during seismic events, especially in the presence of geometric irregularities such as skewed or curved bridges, unequal spans, or varying column heights. Corrosion-related deterioration in RC structures spurred the adoption of glass fiber-reinforced polymer (GFRP) as a promising alternative to steel reinforcement. This study experimentally investigates the performance of GFRP-RC circular columns under cyclic loading, including torsion with different torsion-to-bending moment ratios (tm and longitudinal reinforcement ratios. The results showed that, with the same reinforcement ratios, the addition of torsion to cyclic bending and shear significantly altered the behavior of the GFRP-RC column in terms of mode of failure, load resistance, drift capacity, and energy dissipation. The inelastic deformability hinge shifted upward with increased tm. Higher tm accelerated stiffness degradation, while increasing the longitudinal reinforcement ratio enhanced lateral load, drift, and twist capacities. [ABSTRACT FROM AUTHOR]

Cyclic-oligonucleotide-based anti-phage signaling system (CBASS) is a common immune system that uses cyclic oligonucleotide signals to limit phage replication. In turn, phages encode anti-CBASS (Acb) proteins such as Acb2, which can sequester some cyclic dinucleotides (CDNs) and limit downstream effector activation. Here, we identified that Acb2 sequesters many CDNs produced by CBASS systems and inhibits stimulator of interferon genes (STING) activity in human cells. Surprisingly, the Acb2 hexamer also binds with high affinity to CBASS cyclic trinucleotides (CTNs) 333-cyclic AMP-AMP-AMP and 333-cAAG at a distinct site from CDNs. One Acb2 hexamer can simultaneously bind two CTNs and three CDNs. Phage-encoded Acb2 provides protection from type III-C CBASS that uses cA3 signaling molecules. Moreover, phylogenetic analysis of >2,000 Acb2 homologs encoded by diverse phages and prophages revealed that most are expected to bind both CTNs and CDNs. Altogether, Acb2 sequesters nearly all known CBASS signaling molecules through two distinct binding pockets and therefore serves as a broad-spectrum inhibitor of cGAS-based immunity.

Various testing methods have been proposed and conducted on cable bolt pull out in the last century. Large and small scale tests have both provided valuable information about the behaviour of the cable bolts. This study compares large scale and small scale pull out experiments with similar cables, bonding agents (grout and resin), and loading paths (monotonic and cyclic) to juxtapose the unique characteristics of each test. The results suggested that small scale tests in grout tend to have lower repeatability compared to large scale test while large scale test typically provide a stiffer behaviour with higher initial peak loads. In cyclic loading, large scale testing tended to have most of their cycles in the first 5 mm whereas small scale test loading and unloading cycles were more spread. In resin cases, bulbed cables had similar behaviour whereas the unbulbed cables had various load values suggesting the presence of bulbs overshadows other characteristics. [ABSTRACT FROM AUTHOR]

Cushing’s syndrome, a clinical condition characterized by hypercortisolemia, exhibits distinct clinical signs and is associated with cyclic cortisol secretion in some patients. The clinical presentation of cyclic Cushing’s syndrome can be ambiguous and its diagnosis is often challenging. We experienced a 72-year-old woman with cyclic ACTH-dependent Cushing’s syndrome caused by a pulmonary carcinoid tumor. Diagnosis was challenging because of the extended trough periods, and the responsible lesion was initially unidentified. A subsequent follow-up computed tomography revealed a pulmonary lesion, and ectopic ACTH secretion from this lesion was confirmed by pulmonary artery sampling. Despite the short peak secretion period of ACTH (approximately one week), immunostaining of the surgically removed tumor confirmed ACTH positivity. Interestingly, stored plasma chromogranin A levels were elevated during both peak and trough periods. The experience in evaluating this patient prompted us to investigate the potential use of plasma chromogranin A as a diagnostic marker of ACTH-dependent Cushing’s syndrome. A retrospective study was conducted to determine the efficacy of plasma chromogranin A in three patients with ectopic ACTH syndrome (EAS), including the present case, and six patients with Cushing’s disease (CD) who visited our hospital between 2018 and 2021. Notably, plasma chromogranin A levels were higher in patients with EAS than in those with CD. Additionally, a chromogranin A level in the present case during the trough phase was lower than that in the peak phase, and was similar to those in CD patients. The measurement of plasma chromogranin A levels could aid in differentiating EAS from CD.

Climate change has resulted in increasing attention being paid to the effects of temperature and humidity on vegetated soil. However, existing constitutive models rarely investigate the thermo-mechanical behaviour, such as the accumulation of plastic strain under non-isothermal conditions, of unsaturated vegetated soil. To address this issue, this study developed a comprehensive constitutive model by adopting state-dependent dilatancy in conjugation with loading, memory, and bounding surfaces. Moreover, root-induced hardening due to pore occupancy and internal bonding is modelled with dependence on the root volume ratio. The performance of this newly developed constitutive model is then evaluated using previous laboratory element tests. Comparisons between the computed and measured results reveal that the model is capable of capturing variations in soil state at a range of temperatures, suctions, and root volume ratios. The shearing behaviour of vegetated soil, especially its volumetric response, is well predicted by the model, as confirmed by comparing it with triaxial compression test results. Moreover, the model predicts that the accumulated volumetric strain of unsaturated vegetated soil (0.2%) is significantly less than saturated bare soil (1.1%) after four thermal cycles. These computed results imply that vegetation can mitigate the effects of climate change on soil through both transpiration-induced suction and mechanical reinforcement. [ABSTRACT FROM AUTHOR]

In the present study, the undrained cyclic behaviour of biotreated sands using microbial and enzyme-induced carbonate precipitation was investigated for a wide range of initial void ratio after consolidation ( e 0 ), initial effective normal stress ( σ N 0 ′ ) and calcium carbonate content (CC) under direct simple shear (DSS) testing conditions. The critical state soil mechanics framework for untreated sand was first established using a series of drained and undrained (constant volume) tests, which served as a benchmark for evaluating the undrained cyclic liquefaction behaviour of untreated and biotreated sands. The results indicated that the modified initial state parameter ( ψ m 0 ) in DSS condition showed a good correlation with instability states and phase transformation under monotonic shearing. In undrained cyclic DSS loading condition, samples displayed cyclic mobility indicated by an abrupt accumulation of large strain or σ N 0 ′ transiently reaching zero or a sudden build-up of excess pore water pressure. The linkage between static and cyclic liquefaction was established for untreated and biotreated sand specimens based on the equivalence of characteristic soil states. The number of cycles before liquefaction (NL) for the biotreated sand specimens was mainly controlled by the cyclic stress ratio, e 0 , σ N 0 ′ and CC. For a similar initial state prior to undrained cyclic loading, the biotreated specimens required a larger NL compared to the untreated sand. The cyclic resistance ratio at NL = 15 (CRR15) increased with decreasing ψ m 0 for the untreated sand, while the CRR15 for biotreated sand increased with increasing CC and decreasing σ N 0 ′ . [ABSTRACT FROM AUTHOR]

This study investigates the cyclic loading behaviour of a two-layered unpaved road model reinforced with untreated/treated woven and non-woven coir geotextiles over 10,000 cycles. In this study, research efforts were made to develop artificial-neural-network (ANN)-based prediction models for the plastic deformation of untreated/treated coir geotextile-reinforced unpaved road models. Pearson's coefficient of correlation (R2) and the root mean square error (RMSE) was utilized to evaluate the predictive accuracy of the predictive models. Key discoveries include a substantial reduction in plastic deformation for the reinforced two-layered unpaved road models (Types W1, W2, NW1, and NW2), showcasing decreases of 69%, 74%, 58%, and 66%, respectively, compared to the unreinforced model, particularly in unsoaked conditions. The results demonstrated reduction in the plastic deformation in treated coir geotextiles reinforced models. The study reveals an escalation in plastic deformation at 60% cyclic load as opposed to 30%, evident in both unsoaked and soaked conditions. The selected neural network model exhibits high accuracy, with R2 values exceeding 0.95 and RMSE values below 1, indicating precise prediction of plastic deformation of untreated/treated coir geotextile-reinforced unpaved road model. [ABSTRACT FROM AUTHOR]

The proton affinity (PA) and gas phase basicity values of previously reported cyclic allene series are investigated using high-level quantum chemical calculations. Some of the studied structures possessed more than one protonation site. All protonation types were explored for each structure and the compounds with PA value more than ≈1030 kJ mol−1 were considered superbasic structures. Cyclic allene's basicity strength was affected by ring size, adjacent heteroatom's presence and resonance existence in protonated form. [ABSTRACT FROM AUTHOR]

Macrocyclic peptides have become increasingly important in the pharmaceutical industry. We present a detailed computational investigation of the reaction mechanism of the recently developed CyClick chemistry to selectively form imidazolidinone cyclic peptides from linear peptide aldehydes, without using catalysts or directing groups (Angew. Chem. Int. Ed. 2019, 58, 19073-19080). We conducted computational mechanistic to investigate the effects of intramolecular hydrogen bonds (IMHBs) in promoting a kinetically facile zwitterionic mechanism in CyClick of pentapeptide aldehyde AFGPA. Our DFT calculations highlighted the importance of IMHB in pre-organization of the resting state, stabilization of the zwitterion intermediate, and the control of the product stereoselectivity. Furthermore, we have also identified that the low ring strain energy promotes the CyClick of hexapeptide aldehyde AAGPFA to form a thermodynamically more stable 15+5 imidazolidinone cyclic peptide product. In contrast, large ring strain energy suppresses CyClick reactivity of tetra peptide aldehyde AFPA from forming the 9+5 imidazolidinone cyclic peptide product.

Naturally occurring peptides with high membrane permeability often have ester bonds on their backbones. However, the impact of amide-to-ester substitutions on the membrane permeability of peptides has not been directly evaluated. Here we report the effect of amide-to-ester substitutions on the membrane permeability and conformational ensemble of cyclic peptides related to membrane permeation. Amide-to-ester substitutions are shown to improve the membrane permeability of dipeptides and a model cyclic hexapeptide. NMR-based conformational analysis and enhanced sampling molecular dynamics simulations suggest that the conformational transition of the cyclic hexapeptide upon membrane permeation is differently influenced by an amide-to-ester substitution and an amide N-methylation. The effect of amide-to-ester substitution on membrane permeability of other cyclic hexapeptides, cyclic octapeptides, and a cyclic nonapeptide is also investigated to examine the scope of the substitution. Appropriate utilization of amide-to-ester substitution based on our results will facilitate the development of membrane-permeable peptides.

Background: Genetic syndromes of hyperkinetic movement disorders associated with epileptic encephalopathy and intellectual disability are becoming increasingly recognized. Recently, a de novo heterozygous NACC1 (nucleus accumbens‐associated 1) missense variant was described in a patient cohort including one patient with a combined mitochondrial oxidative phosphorylation (OXPHOS) deficiency. Objectives: The objective is to characterize the movement disorder in affected patients with the recurrent c.892C>T NACC1 variant and study the NACC1 protein and mitochondrial function at the cellular level. Methods: The movement disorder was analyzed on four patients with the NACC1 c.892C>T (p.Arg298Trp) variant. Studies on NACC1 protein and mitochondrial function were performed on patient‐derived fibroblasts. Results: All patients had a generalized hyperkinetic movement disorder with chorea and dystonia, which occurred cyclically and during sleep. Complex I was found altered, whereas the other OXPHOS enzymes and the mitochondria network seemed intact in one patient. Conclusions: The movement disorder is a prominent feature of NACC1‐related disease. [ABSTRACT FROM AUTHOR]

Reinforced concrete (RC) columns with short lap splices built in the early 1970s or before are known to have deficient seismic strength and ductility. These short lap splices are poorly confined and located right above the foundation level, where it is known that the inelastic demands are high under seismic loading. In this study, a numerical model for estimating the lateral strength and deformation of RC columns with short lap splices is introduced. The latter model is based on local bond–slip analytical models derived from isolated anchored bars through the closed-form solution of the differential equation of bond. The proposed model is correlated to experimental data from cyclic loading tests on RC columns with deficient lap splices. It can be seen that the strength of short lap splices, the failure mode, and the column's lateral resistance and deformation are in good agreement with the experimental results both under monotonic and cyclic seismic analyses. [ABSTRACT FROM AUTHOR]

We explore the role of monomer geometry on the structural, dynamic, and thermodynamic properties of polyolefis by employing all‐atom molecular dynamic simulations. Specifically, we compare properties of atactic polyolefins in the molten state including polypropylene (aPP), a short‐chain branched polymer: poy(1‐hexene) (aPH), and a polymer having cyclic olefins: poly(vinyl cyclobutane) (aPVCB). We find polymers having the same chain mass and atom composition (hydrocarbon‐based molecules), but having different monomer architecture differ strongly in material properties. In particular, the polymer glass transition (Tg) and bulk modulus (B) show higher values for aPVCB in comparison to aPP and aPH. This increase is caused by having the carbon atoms in a cyclic structure, making aPVCB achieve higher mass and energy densities. By contrast, adding linear short side chains to polymer backbones causes a reduction in Tg and B, since side chains make backbones displace each other reducing their packing and thus their mass and energy densities. More broadly, our numerical results suggest that the incorporation of VCB monomers to linear polyolefins will enhance their properties, opening the possibility for designing a new set of materials. [ABSTRACT FROM AUTHOR]

We extend the notion of convex-cyclicity for matrices to that of convex-cyclicity for abelian semigroups of matrices on K n . We say that an abelian semigroup G of matrices on K n is convex-cyclic if there exists x ∈ K n such that the convex hull of the orbit G(x) of x under G is dense in K n . We provide an effective method for checking that a given abelian semigroup is convex-cyclic. In particular we give a spectral characterization of convex-cyclicity for finitely generated abelian semigroups of diagonalizable matrices. We also obtain an example of a convex-cyclic abelian semigroup which does not contain a convex-cyclic matrix. We prove that there exists an abelian semigroup of matrices on K n which is somewhere convex-cyclic but not convex-cyclic. This solves two questions of Rezaei in (Linear Algebra Appl 438:4190–4203, 2013) and Feldman and McGuire in (Oper Matrices 12(2):465–492, 2017) respectively. On the other hand, we provide the link between ε -hypercyclicity and convex-cyclicity for abelian semigroups of matrices on K n for every 0 < ε < 1 . [ABSTRACT FROM AUTHOR]

Cyclic thrombocytopenia (CTP) is a rare disease characterized by the oscillations seen in the platelet count of the patients. The pathomechanism of the disease is poorly understood, several pathological processes have been implied in the background of CTP. In our current study, we aimed to thoroughly investigate the case of a 41-year-old female patient with a 22-year history of CTP. Wide-ranging laboratory testing, histological analyses and genetic investigations were carried out to investigate all the defects and alterations of physiological pathways described in the background of CTP to date. Bone marrow biopsy showed normal hemopoiesis with the abundance of megakaryocytes, some of which displayed hypolobulated nuclei. T-cell receptor rearrangement studies showed a polyclonal pattern with no indication of a monoclonal cell population. Flow cytometric assessment of the platelets revealed large number of immature platelets and decreased expression of glycoprotein IIb and IIIa at platelet zenith. Increased expression of glycoprotein IIb, IIIa and glycoprotein Ib-IX complex was observed at the nadir of the cycle. Whole exome sequencing revealed a heterozygous missense variant of uncertain significance in the SERPINC1 gene, which has been associated with hereditary antithrombin deficiency. The screening of autoantibodies did not reveal signs of autoreactive processes, and no thyroid dysfunction was found. Furthermore, synchronization with the menstrual cycle could not be concluded based on our patient’s case. With our results we contribute to the very limited data known about the long-term course of the disease and provide valuable insights into the genetic architecture of CTP.

As one of the first families of marine natural products to undergo clinical trials, the didemnin depsipeptides have played a significant role in inspiring the discovery of marine drugs. Originally developed as anticancer therapeutics, the recent re-evaluation of these compounds including synthetically derived dehydrodidemnin B or Aplidine, has led to their advancement towards antiviral applications. While conventionally associated with production in colonial tunicates of the family Didemnidae, recent studies have identified their biosynthetic gene clusters from the marine-derived bacteria Tistrella mobilis. While these studies confirm the production of didemnin X/Y, the low titer and general lack of understanding of their biosynthesis in Tistrella currently prevents the development of effective microbial or synthetic biological approaches for their production. To this end, we conducted a survey of known species of Tistrella and report on their ability to produce the didemnin depsipeptides. These data were used to develop conditions to produce didemnin B at titers over 15 mg/L.

Ternatin-family cyclic peptides inhibit protein synthesis by targeting the eukaryotic elongation factor-1α. A potentially related cytotoxic natural product ('A3') was isolated from Aspergillus, but only 4 of its 11 stereocentres could be assigned. Here, we synthesized SR-A3 and SS-A3-two out of 128 possible A3 epimers-and discovered that synthetic SR-A3 is indistinguishable from naturally derived A3. Relative to SS-A3, SR-A3 exhibits an enhanced residence time and rebinding kinetics, as revealed by single-molecule fluorescence imaging of elongation reactions catalysed by eukaryotic elongation factor-1α in vitro. An increased residence time-stereospecifically conferred by the unique β-hydroxyl in SR-A3-was also observed in cells. Consistent with its prolonged duration of action, thrice-weekly dosing with SR-A3 led to a reduced tumour burden and increased survival in an aggressive Myc-driven mouse lymphoma model. Our results demonstrate the potential of SR-A3 as a cancer therapeutic and exemplify an evolutionary mechanism for enhancing cyclic peptide binding kinetics via stereospecific side-chain hydroxylation.

Reinforced concrete (RC) columns with short lap splices built in the early 1970s or before are known to have deficient seismic strength and ductility. These short lap splices are poorly confined and located right above the foundation level, where it is known that the inelastic demands are high under seismic loading. In this study, a numerical model for estimating the lateral strength and deformation of RC columns with short lap splices is introduced. The latter model is based on local bond–slip analytical models derived from isolated anchored bars through the closed-form solution of the differential equation of bond. The proposed model is correlated to experimental data from cyclic loading tests on RC columns with deficient lap splices. It can be seen that the strength of short lap splices, the failure mode, and the column’s lateral resistance and deformation are in good agreement with the experimental results both under monotonic and cyclic seismic analyses.

Retinal cyclic nucleotide-gated (CNG) channels consist of two protein subunits (CNGA1 and CNGB1). Calmodulin (CaM) binds to two separate sites within the cytosolic region of CNGB1: CaM binding to an N-terminal site (human CNGB1 residues 565-587, called CaM1) decreases the open probability of CNG channels at elevated Ca2+ levels in dark-adapted photoreceptors, whereas CaM binding to a separate C-terminal site (CNGB1 residues 1120-1147, called CaM2) may increase channel open probability in light activated photoreceptors. We recently reported NMR chemical shift assignments of Ca2+-saturated CaM bound to the CaM1 site of CNGB1 (BMRB no. 51222). Here, we report complete NMR chemical shift assignments of Ca2+-saturated CaM bound to the C-terminal CaM2 site of CNGB1 (BMRB no. 51447).

Retinal cyclic nucleotide-gated (CNG) channels (composed of three CNGA1 and one CNGB1 subunits) exhibit a Ca2+-induced reduction in channel open probability mediated by calmodulin (CaM). Defects in the Ca2+-dependent regulation of CNG channels may be linked to autosomal recessive retinitis pigmentosa and other inherited forms of blindness. Here, we report the NMR structure and binding analysis of CaM bound to two separate sites within CNGB1 (CaM1: residues 565-589 and CaM2: residues 1120-1147). Our binding studies reveal that CaM1 binds to the Ca2+-bound CaM N-lobe with at least fivefold higher affinity than it binds to the CaM C-lobe. By contrast, the CaM2 site binds to the Ca2+-bound CaM C-lobe with higher affinity than it binds to the N-lobe. CaM1 and CaM2 both exhibited very weak binding to Ca2+-free CaM. We present separate NMR structures of Ca2+-saturated CaM bound to CaM1 and CaM2 that define key intermolecular contacts: CaM1 residue F575 interacts with the CaM N-lobe while CaM2 residues L1129, L1132, and L1136 each make close contact with the CaM C-lobe. The CNGB1 mutation F575E abolishes CaM1 binding to the CaM N-lobe while L1132E and L1136E each abolish CaM2 binding to the CaM C-lobe. Thus, a single CaM can bind to both sites in CNGB1 in which the CaM N-lobe binds to CaM1 and the CaM C-lobe binds to CaM2. We propose a Ca2+-dependent conformational switch in the CNG channel caused by CaM binding, which may serve to attenuate cGMP binding to CNG channels at high cytosolic Ca2+ levels in dark-adapted photoreceptors.

Cyclic and linear siloxanes are compounds synthesized from silicon consisting of alternating atoms of silicone and oxygen [Si-O] units with organic side chains. The most common cyclic siloxanes are octamethylcyclotetrasiloxane (D4), decamethylcyclopentasiloxane (D5), and dodecamethylcyclohexasiloxane (D6), while the most common linear siloxanes are high molecular weight polydimethylsiloxanes (PDMS) and low molecular weight volatile linear siloxanes known as hexamethyldisiloxane (L2), octamethyltrisiloxane (L3), decamethyltetrasiloxane (L4), dodecamethylpentasiloxane (L5). These compounds (1) exhibit low dermal toxicity, (2) are generally inert and non-reactive, and (3) are compatible with a wide range of chemicals offering beneficial chemical properties which include the following: wash-off or transfer resistance from the skin, sun protection factor (SPF) enhancement, emolliency in cleaning products). Because of these properties, these compounds are incorporated into multiple consumer products for use on the skin, such as cosmetics and health-care products, with over 300,000 tons annually sold into the personal care and consumer products sector. Because of their widespread use in consumer products and potential for human dermal exposure, a comprehensive understanding of the dermal absorption and overall fate of siloxanes following dermal exposure is important. This review summarizes available data associated with the dermal absorption/penetration as well as fate of the most commonly used siloxane substances. [ABSTRACT FROM AUTHOR]

Axle shafts, which are an important part of the vehicle's powertrain system, transfer the torque to the wheels and enable the vehicle to move. In this respect, the design of the axle shaft to be used in a new vehicle is of great importance for vehicle manufacturers. When a cylindrical shaft is torsionally loaded, the shear stress is highest at the surface of component and zero at the center. Therefore, these axle shafts are exposed to an induction hardening process that enables only this superficial case to have its properties changed, remaining the core zone with its material original characteristics. Current study presents the results of a project aimed at developing and evaluating the fatigue life of axle shaft that belongs to a commercial vehicle. Developments were made on the existing axle and the results were examined using experimental tests and finite element analysis method. In line with the improvements made, the developed axle shaft has 331.7% more fatigue life than the existing axle, while the cost is 24% lower. According to these results, more attention must be paid to material selection, induction hardening process, stress concentration and surface condition of axle shaft in the design. This study involves many disciplines such as design, manufacturing, analysis, testing, etc. It is very important to ensure communication between all these disciplines in the production of the product. The output obtained from one discipline becomes the input of another discipline. In the cumulative sum of all these inputs, the optimum level of parts is obtained. For this reason, this study, which processes all these disciplines together, is very valuable. [ABSTRACT FROM AUTHOR]

Context: We have performed a detailed MM and DFT investigation of neutral water clusters (H2O)n (n = 3–12). Our results show the trend of interaction energies in these clusters as a function of the size of the cluster. They show that the H-bond strength increases with cluster size and that the model of water is better described if two different partial charges are used on the hydrogen, depending on whether hydrogen is H-bonded or not. The average binding enthalpy change due to the formation of H-bonds between water molecules is found to be − 25.9 kJ mol−1 at B3LYP/aug-cc-pVDZ level of theory. We observe the formation of cyclic H-bonded networks through the analysis of frontier orbitals and IR vibrational frequencies spectra. For the water cluster with n = 11, we observe an unusual reduction of the bandgap indicative of a cyclic H-bonded network. Methods: Calculations were performed with the MMFF94 force field and the B3LYP method using various large basis sets. Molecular orbital diagrams and population analysis were done using standard tools in Gaussian. [ABSTRACT FROM AUTHOR]

Precast segmental bridge piers attract engineers due to the strengths of accelerated construction, reduced traffic disturbance and enhanced quality control. However, their widely applications in high-seismicity areas are hindered, for the insufficient capacities of energy dissipation. In this study, precast segmental piers' seismic behaviors were investigated, focusing on the connection of 'grouted sleeves/bonded tendons'. To this end, four piers were cyclically loaded, of one cast-in-place pier, one precast segmental pier, and two prestressed precast segmental piers. Among them, Benefits of bonded tendons were evidenced, in terms of lateral strength, ductility, energy dissipation capacity and residual drift. Of particular, bonded tendons prevented the shear-induced slip between the shaft and footing segments. Enlightened from observations, cyclic dowel-friction effect is proposed and implemented within a zero-thickness sliding spring in the finite element model, capable of capturing the shear-induced joint slip. Furthermore, seismic vulnerability assessments of the bridge piers are obtained in terms of fragility curves, by performing incremental dynamic analyses. In addition, the effects of bonded or unbounded tendons are also discussed. Two criteria are adopted to define the limit states, namely displacement ductility and residual drift. It is suggested that bonded tendons could significantly ameliorate the fragility curves of precast segmental piers. Four bridge piers were cyclically loaded, with various prestressing levels. A reliable fiber-based model was constructed, considering shear-induced slip at the segmental joint for the first time. Seismic vulnerability assessments were performed to quantify the piers' behaviors. [ABSTRACT FROM AUTHOR]

The lap-spliced crosstie is formed by lapping two J-shaped reinforcing bars with a 180° hook at one end and a straight line at the other end, which can address the difficulty and poor construction quality of conventional crossties. This study conducted cyclic lateral load testing of four large reinforced concrete (RC) columns to explore the seismic performance of RC columns with lap-spliced crossties under cyclic axial force. The results are as follows: (1) Under the action of cyclic axial force, all the specimens basically fulfilled the requirements of earthquake-resistant structures under axial compression. The flexural ductility of the specimen with crossties of 180-deg hooks was the best, followed by the specimens using lap-spliced crossties. The specimen with conventional crossties performed the worst. (2) The seismic performance for all the specimens in enduring axial tension was more satisfactory than that for axial compression. (3) When an inner column endures only axial compression during an earthquake with a column axial force ratio of greater than 30%, the use of lap-spliced crossties both meets specification requirements and can facilitate the construction process. (4) When an outer column is subjected to cyclic axial compression and tension during earthquakes, the column axial force ratio is generally less than 30%. Therefore, lap-spliced crossties can be used to replace conventional crossties. (5) For columns that withstand only axial compression, when the column axial force ratio is less than 30%, lap-spliced crossties can be used instead of conventional crossties. (6) RC columns with lap-spliced crossties enclosing lapped longitudinal reinforcements as well as the rectangular column section and intermediate longitudinal reinforcements merit further research and clarification. [ABSTRACT FROM AUTHOR]

Cyclic dinucleotides (CDN) and Toll-like receptor (TLR) ligands mobilize antitumor responses by natural killer (NK) cells and T cells, potentially serving as complementary therapies to immune checkpoint therapy. In the clinic thus far, however, CDN therapy targeting stimulator of interferon genes (STING) protein has yielded mixed results, perhaps because it initiates responses potently but does not provide signals to sustain activation and proliferation of activated cytotoxic lymphocytes. To improve efficacy, we combined CDN with a half life-extended interleukin-2 (IL-2) superkine, H9-MSA (mouse serum albumin). CDN/H9-MSA therapy induced dramatic long-term remissions of the most difficult to treat major histocompatibility complex class I (MHC I)–deficient and MHC I+ tumor transplant models. H9-MSA combined with CpG oligonucleotide also induced potent responses. Mechanistically, tumor elimination required CD8 T cells and not NK cells in the case of MHC I+ tumors and NK cells but not CD8 T cells in the case of MHC-deficient tumors. Furthermore, combination therapy resulted in more prolonged and more intense NK cell activation, cytotoxicity, and expression of cytotoxic effector molecules in comparison with monotherapy. Remarkably, in a primary autochthonous sarcoma model that is refractory to PD-1 checkpoint therapy, the combination of CDN/H9-MSA with checkpoint therapy yielded long-term remissions in the majority of the animals, mediated by T cells and NK cells. This combination therapy has the potential to activate responses in tumors resistant to current therapies and prevent MHC I loss accompanying acquired resistance of tumors to checkpoint therapy.

Signal integration of converging neural circuits is poorly understood. One example is in the retina where the integration of rod and cone signaling is responsible for the large dynamic range of vision. The relative contribution of rods versus cones is dictated by a complex function involving background light intensity and stimulus temporal frequency. One understudied mechanism involved in coordinating rod and cone signaling onto the shared retinal circuit is the hyperpolarization activated current (Ih) mediated by hyperpolarization-activated cyclic nucleotide-gated 1 (HCN1) channels expressed in rods and cones. Ih opposes membrane hyperpolarization driven by activation of the phototransduction cascade and modulates the strength and kinetics of the photoreceptor voltage response. We examined conditional knock-out (KO) of HCN1 from mouse rods using electroretinography (ERG). In the absence of HCN1, rod responses are prolonged in dim light which altered the response to slow modulation of light intensity both at the level of retinal signaling and behavior. Under brighter intensities, cone-driven signaling was suppressed. To our surprise, conditional KO of HCN1 from mouse cones had no effect on cone-mediated signaling. We propose that Ih is dispensable in cones because of the high level of temporal control of cone phototransduction. Thus, HCN1 is required for cone-driven retinal signaling only indirectly by modulating the voltage response of rods to limit their output.SIGNIFICANCE STATEMENT Hyperpolarization gated hyperpolarization-activated cyclic nucleotide-gated 1 (HCN1) channels carry a feedback current that helps to reset light-activated photoreceptors. Using conditional HCN1 knock-out (KO) mice we show that ablating HCN1 from rods allows rods to signal in bright light when they are normally shut down. Instead of enhancing vision this results in suppressing cone signaling. Conversely, ablating HCN1 from cones was of no consequence. This work provides novel insights into the integration of rod and cone signaling in the retina and challenges our assumptions about the role of HCN1 in cones.

Plitidepsin, a marine-derived cyclic-peptide, inhibits SARS-CoV-2 replication at nanomolar concentrations by targeting the host protein eukaryotic translation elongation factor 1A. Here, we show that plitidepsin distributes preferentially to lung over plasma, with similar potency against across several SARS-CoV-2 variants in preclinical studies. Simultaneously, in this randomized, parallel, open-label, proof-of-concept study (NCT04382066) conducted in 10 Spanish hospitals between May and November 2020, 46 adult hospitalized patients with confirmed SARS-CoV-2 infection received either 1.5 mg (n = 15), 2.0 mg (n = 16), or 2.5 mg (n = 15) plitidepsin once daily for 3 d. The primary objective was safety; viral load kinetics, mortality, need for increased respiratory support, and dose selection were secondary end points. One patient withdrew consent before starting procedures; 45 initiated treatment; one withdrew because of hypersensitivity. Two Grade 3 treatment-related adverse events were observed (hypersensitivity and diarrhea). Treatment-related adverse events affecting more than 5% of patients were nausea (42.2%), vomiting (15.6%), and diarrhea (6.7%). Mean viral load reductions from baseline were 1.35, 2.35, 3.25, and 3.85 log10 at days 4, 7, 15, and 31. Nonmechanical invasive ventilation was required in 8 of 44 evaluable patients (16.0%); six patients required intensive care support (13.6%), and three patients (6.7%) died (COVID-19-related). Plitidepsin has a favorable safety profile in patients with COVID-19.

Rod cyclic nucleotide-gated (CNG) channels are formed by two protein subunits (CNGA1 and CNGB1). Calmodulin (CaM) binds to the cytosolic regulatory domain of CNGB1 and decreases the open probability of CNGA1/CNGB1 channels. The CaM binding site within bovine CNGB1 (residues 679-702) binds tightly to Ca2+-bound CaM, which promotes Ca2+-induced inactivation of CNGA1/CNGB1 channels in retinal rods. We report complete NMR chemical shift assignments of Ca2+-saturated CaM bound to the CaM-binding domain of CNGB1 (BMRB no. 51222).

Voltage-gated sodium channel (VGSC) activators promote neurite outgrowth by augmenting intracellular Na+ concentration ([Na+]i) and upregulating N-methyl-d-aspartate receptor (NMDAR) function. NMDAR activation stimulates calcium (Ca2+) influx and increases brain-derived neurotrophic factor (BDNF) release and activation of tropomyosin receptor kinase B (TrkB) signaling. The BDNF-TrkB pathway has been implicated in activity-dependent neuronal development. We have previously shown that antillatoxin (ATX), a novel lipopeptide isolated from the cyanobacterium Moorea producens, is a VGSC activator that produces an elevation of [Na+]i. Here we address the effect of ATX on the synthesis and release of BDNF and determine the signaling mechanisms by which ATX enhances neurite outgrowth in immature cerebrocortical neurons. ATX treatment produced a concentration-dependent release of BDNF. Acute treatment with ATX also resulted in increased synthesis of BDNF. ATX stimulation of neurite outgrowth was prevented by pretreatment with a TrkB inhibitor or transfection with a dominant-negative Trk-B. The ATX activation of TrkB and Akt was blocked by both a NMDAR antagonist (MK-801) and a VGSC blocker (tetrodotoxin). These results suggest that VGSC activators such as the structurally novel ATX may represent a new pharmacological strategy to promote neuronal plasticity through a NMDAR-BDNF-TrkB-dependent mechanism.

Despite the notoriously poor membrane permeability of peptides, many cyclic peptide natural products show high passive membrane permeability and potently inhibit a variety of "undruggable" intracellular targets. A major impediment to the design of cyclic peptides with good permeability is the high desolvation energy associated with the peptide backbone amide NH groups. While several strategies have been proposed to mitigate this deleterious effect, only few studies have used polar side chains to sequester backbone NH groups. We investigated the ability of N,N-pyrrolidinylglutamine (Pye), whose side chain contains a powerful hydrogen-bond-accepting C═O amide group but no hydrogen-bond donors, to sequester exposed backbone NH groups in a series of cyclic hexapeptide diastereomers. Analyses revealed that specific Leu-to-Pye substitutions conferred dramatic improvements in aqueous solubility and permeability in a scaffold- and position-dependent manner. Therefore, this approach offers a complementary tool for improving membrane permeability and solubility in cyclic peptides.

The natural product himastatin has an unusual homodimeric structure that presents a substantial synthetic challenge. We report the concise total synthesis of himastatin from readily accessible precursors, incorporating a final-stage dimerization strategy that was inspired by a detailed consideration of the compound's biogenesis. Combining this approach with a modular synthesis enabled expedient access to more than a dozen designed derivatives of himastatin, including synthetic probes that provide insight into its antibiotic activity.

Retinal cyclic nucleotide-gated (CNG) ion channels bind to intracellular cGMP and mediate visual phototransduction in photoreceptor rod and cone cells. Retinal rod CNG channels form hetero-tetramers comprised of three CNGA1 and one CNGB1 protein subunits. Cone CNG channels are similar tetramers consisting of three CNGA3 and one CNGB3 subunits. Calmodulin (CaM) binds to two distinct sites (CaM1: residues 565-587 and CaM2: residues 1120-1147) within the cytosolic domains of rod CNGB1. The binding of Ca2+-bound CaM to CNGB1 promotes the Ca2+-induced desensitization of CNG channels in retinal rods that may be important for photoreceptor light adaptation. Mutations that affect Ca2+-dependent CNG channel function are responsible for inherited forms of blindness. In this review, we propose structural models of the rod CNG channel bound to CaM that suggest how CaM might cause channel desensitization and how dysregulation of the channel may lead to retinal disease.

Woodward and Hoffmann, in their treatise on orbital symmetry in 1969, stated "Violations. There are none!" Prinzbach reported in 1978 that the electrocyclization of vinylogous sesquifulvalene occurs exclusively through the Woodward-Hoffmann orbital-symmetry-forbidden 14π-electron conrotatory pathway, despite the availability of a variety of orbital-symmetry-allowed processes. Prinzbach later demonstrated that an 18π-electron homologue exhibits the same forbidden behavior. And yet, the analogous vinylogous pentafulvalene and heptafulvalene both follow the orbital symmetry rules, each proceeding through its allowed conrotatory 12π and 16π process, respectively. We report the investigation of these reactions with ωB97X-D DFT. The physical origins of the flagrant Prinzbach violations of the Woodward-Hoffmann orbital symmetry selection rules have now been elucidated by these calculations in conjunction with extensive analyses and comparisons to electrocyclizations that obey the Woodward-Hoffmann rules. This remarkable reversal of the Rules (the 14π-electron-forbidden process is found to be 11 kcal/mol more energetically facile than the allowed process) occurs due to the high degree of polarization of this hydrocarbon, such that conrotatory electrocyclization of vinylogous sesquifulvalene behaves like a cyclopentadienide combining with a tropylium. These results are compared to other forbidden pericyclic processes driven by steric constraints and strain release or by diradical character of the reactants that facilitates the formation of diradical transition states for symmetry-forbidden reactions. We predict how strong donor-acceptor substitution can modify nodal properties to level the difference between allowed and forbidden electrocyclic reaction barriers, and we provide computational predictions of two such cases.