SARS-CoV-2 Mpro responds to oxidation by forming disulfide and NOS/SONOS bonds.

The main protease (Mpro) of SARS-CoV-2 is critical for viral function and a key drug target. Mpro is only active when reduced; turnover ceases upon oxidation but is restored by re-reduction. This suggests the system has evolved to survive periods in an oxidative environment, but the mechanism of this protection has not been confirmed. Here, we report a crystal structure of oxidized Mpro showing a disulfide bond between the active site cysteine, C145, and a distal cysteine, C117. Previous work proposed this disulfide provides the mechanism of protection from irreversible oxidation. Mpro forms an obligate homodimer, and the C117-C145 structure shows disruption of interactions bridging the dimer interface, implying a correlation between oxidation and dimerization. We confirm dimer stability is weakened in solution upon oxidation. Finally, we observe the protein's crystallization behavior is linked to its redox state. Oxidized Mpro spontaneously forms a distinct, more loosely packed lattice. Seeding with crystals of this lattice yields a structure with an oxidation pattern incorporating one cysteine-lysine-cysteine (SONOS) and two lysine-cysteine (NOS) bridges. These structures further our understanding of the oxidative regulation of Mpro and the crystallization conditions necessary to study this structurally.

Enhancing combinatorial optimization with classical and quantum generative models.

Devising an efficient exploration of the search space is one of the key challenges in the design of combinatorial optimization algorithms. Here, we introduce the Generator-Enhanced Optimization (GEO) strategy: a framework that leverages any generative model (classical, quantum, or quantum-inspired) to solve optimization problems. We focus on a quantum-inspired version of GEO relying on tensor-network Born machines, and referred to hereafter as TN-GEO. To illustrate our results, we run these benchmarks in the context of the canonical cardinality-constrained portfolio optimization problem by constructing instances from the S&P 500 and several other financial stock indexes, and demonstrate how the generalization capabilities of these quantum-inspired generative models can provide real value in the context of an industrial application. We also comprehensively compare state-of-the-art algorithms and show that TN-GEO is among the best; a remarkable outcome given the solvers used in the comparison have been fine-tuned for decades in this real-world industrial application. Also, a promising step toward a practical advantage with quantum-inspired models and, subsequently, with quantum generative models.

Correlation between rs1800871, rs1800872 and rs1800896 Polymorphisms at IL-10 Gene and Lung Cancer Risk.

BACKGROUND: The tumorigenesis of lung cancer is complicated, and genetic factor may have the role in the malignant transformation of lung cells. IL-10 gene polymorphisms have been evaluated for their potential roles in lung cancer. However, those studies results are controversial. To clarify the effects of IL-10 rs1800871, rs1800872 and rs1800896 polymorphisms on the risk of lung cancer, a meta-analysis was performed with eligible individual studies. METHODS: Eligible publications were gathered by retrieving PubMed, Web of Science, Embase, Wan Fang, and CNKI up to September 01, 2023. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of such association. RESULTS: A total of 23 studies, including 5950 patients with lung cancer and 8046 healthy controls, were identified in this meta-analysis.  Overall, there was no a significant association between the rs1800871, rs1800872 and rs1800896 polymorphisms at IL-10 gene and susceptibility to lung cancer globally when all studies in the pooled into this meta-analysis. Stratified analysis by ethnicity showed that rs1800872 polymorphism was associated with lung cancer among Asians and Caucasians. However, no significant association was identified between the rs1800871 and rs1800896 and risk of lung cancer. CONCLUSIONS: Pooled data showed that  IL-10 rs1800871, rs1800872 and rs1800896 polymorphisms were not associated with lung cancer globally. Future well-designed large case-control studies with different ethnicities are recommended.

Light-induced Trpin/Metout Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC.

The understanding of signal transduction mechanisms in photoreceptor proteins is essential for elucidating how living organisms respond to light as environmental stimuli. In this study, we investigated the ATP binding, photoactivation and signal transduction process in the photoactivatable adenylate cyclase from Oscillatoria acuminata (OaPAC) upon blue light excitation. Structural models with ATP bound in the active site of native OaPAC at cryogenic as well as room temperature are presented. ATP is found in one conformation at cryogenic- and in two conformations at ambient-temperature, and is bound in an energetically unfavorable conformation for the conversion to cAMP. However, FTIR spectroscopic experiments confirm that this conformation is the native binding mode in dark state OaPAC and that transition to a productive conformation for ATP turnover only occurs after light activation. A combination of time-resolved crystallography experiments at synchrotron and X-ray Free Electron Lasers sheds light on the early events around the Flavin Adenine Dinucleotide (FAD) chromophore in the light-sensitive BLUF domain of OaPAC. Early changes involve the highly conserved amino acids Tyr6, Gln48 and Met92. Crucially, the Gln48 side chain performs a 180° rotation during activation, leading to the stabilization of the FAD chromophore. Cryo-trapping experiments allowed us to investigate a late light-activated state of the reaction and revealed significant conformational changes in the BLUF domain around the FAD chromophore. In particular, a Trpin/Metout transition upon illumination is observed for the first time in the BLUF domain and its role in signal transmission via α-helix 3 and 4 in the linker region between sensor and effector domain is discussed.

A comparison of adsorption capacity of several synthesis methods of cellulose-based absorbent towards Pb(II) removal: Optimization with response surface methodology.

The effects of various synthesis methods of a novel biodegradable magnetically recyclable cellulose-based adsorbent (a magnetized modified silica aerogel) on Pb(II) removal efficiency were studied. QSM (quince seed mucilage) was modified via hydrothermal and ultrasonic modes. Oven-drying and freeze-drying procedures were then used to obtain the final adsorbents. The adsorbents were named A1 to A4 and B1 to B4, depending on the synthesis and drying techniques. XRD, FTIR, BET, and SEM are characterization techniques for identifying the adsorbents. Average crystallite sizes of 15.5, 8.3, 10.9, and 2.7 nm were obtained for A1, A2, A3, and A4 samples (Scherrer formula). SEM image confirmed a Sticky bullets-like morphology. The pHpzc values of 3.4, 6.0, and 4.1 were also determined for Fe-silica aerogel, Fe-QSM, and Fe-silica aerogel-QSM samples. The highest adsorption efficiency of the A2 adsorbent towards Pb(II) cations was followed via the experimental design by the RSM (response surface methodology) approach. ANOVA results showed model F value 185 (>F0.05, 14, 15 = 2.42) and LOF F-value of 0.3831 (

Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography.

Time-resolved crystallography enables the visualization of protein molecular motion during a reaction. Although light is often used to initiate reactions in time-resolved crystallography, only a small number of proteins can be activated by light. However, many biological reactions can be triggered by the interaction between proteins and ligands. The sample delivery method presented here uses a mix-and-extrude approach based on 3D-printed microchannels in conjunction with a micronozzle. The diffusive mixing enables the study of the dynamics of samples in viscous media. The device design allows mixing of the ligands and protein crystals in 2 to 20 s. The device characterization using a model system (fluorescence quenching of iq-mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within lipidic cubic phase, can be mixed efficiently. The potential of this approach for time-resolved membrane protein crystallography to support the development of new drugs is discussed.

Effect of a comprehensive nutrition education program on nutritional behavior and food security of female-headed households who receive welfare support in Zanjan Province, Iran.

BACKGROUND: In recent years, the food security and dietary quality of many Iranian families have deteriorated due to unprecedented inflation. Nutrition education programs can be an effective and inexpensive method to improve food quality and security. The present study aimed to investigate the effect of a comprehensive nutrition education program for low-income women who are heads of households and are covered by the Zanjan province's welfare. METHODS: The food security of 2600 female-headed households covered by the Welfare of Zanjan province was evaluated using a standard 6-item questionnaire. A total of 600 women with the highest food insecurity scores were selected for the comprehensive nutrition education program. The participants received six sessions of 1.5 h of courses about how to improve the quality of their diets and manage their budgets and be physically active. At the beginning of the study and one month after the completion of the intervention, the participants were asked to complete a questionnaire designed and validated by the investigators. The scores of each section before and after the intervention were compared using paired t-test method and p values ​​of < 0.05 were considered statistically significant. RESULTS: The prevalence of severe food insecurity among female-headed households who receive welfare support in Abhar, Khodabandeh, and Zanjan cities was 59.5%, 75%, and 62%, respectively. A total of 505 participants successfully completed the courses. After completion of the educational intervention, diet quality, physical activity, budgeting, and food safety scores of the participants increased by 6%, 4%, 4%, and 5%, respectively, which were statistically significant (p < 0.001). However, no significant difference was observed in the food insecurity scores. CONCLUSION: The comprehensive nutrition education program without financial or nutritional support can have a small but significant impact on the improvement of the nutritional behaviors and dietary quality of low-income people.

XFEL Microcrystallography of Self-Assembling Silver n-Alkanethiolates.

New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd-even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd-even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd-even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. We conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.

Salivary anti-cyclic citrullinated peptide as a screening tool for rheumatoid arthritis.

Objectives: This study aims to evaluate the sensitivity and specificity of salivary anti-cyclic citrullinated peptide 3 (anti-CCP3) for the early diagnosis of rheumatoid arthritis. Patients and methods: Between June 2017 and April 2019, a total of 63 patients with rheumatoid arthritis (10 males, 53 females; mean age: 50.4±9.5 years; range, 27 to 74 years) and 49 healthy controls (8 males, 41 females; mean age: 49.3±9.3 years; range 27 to 67 years) were included. Salivary samples were collected by passive drooling. Anti-cyclic citrullinated peptide analyses of salivary and serum samples were performed. Results: The mean polyclonal immunoglobulin (Ig)G-IgA anti-CCP3 salivary levels were significantly different in patients (149.2±134.2) compared to healthy controls (28.5±23.9). The mean polyclonal IgG-IgA anti-CCP3 serum levels were measured as 254.0±169.5 in patients and 3.8±3.6 in healthy individuals. The diagnostic accuracy analysis of salivary IgG-IgA anti-CCP3 results in an area under the curve (AUC) of 0.818, as well as 91.84% specificity and 61.90% sensitivity. Conclusion: Salivary anti-CCP3 may be considered as an additional screening test for rheumatoid arthritis.

Tautomerism of pyridinylbutane-1,3-diones: An NMR and DFT study.

The three possible 1-(n-pyridinyl)butane-1,3-diones (nPM) have been synthesized. Structures, tautomerism, and conformations are investigated by means of DFT calculations. 1 H and 13 C NMR spectra are assigned, and deuterium isotope effects on 13 C chemical shifts have been measured. Analysis of the isotope effects leads to the equilibrium constants of the keto-enol tautomers. Some interesting differences are seen between the three compounds and the phenyl analogs. The isotope effects can also rank the hydrogen bonds of the compounds, with the one with nitrogen in the three positions of the pyridine ring as the weakest. Structures, conformers, energies, and NMR nuclear shieldings are calculated using DFT calculations at the B3LYP/6-311++G(d,p) level.

Electronic transport on the two state "ON-OFF" of 1,3,3-trimethylindolino-6'-nitrobenzopyrylospiran as a light-driven molecular optical switch: A first-principle study.

Here, the electronic transport characteristics of the 1,3,3-trimethylindolino-6'-nitrobenzopyrylospiran were studied by using NEGF and DFT methods. By being exposed to UV or visible light, this molecule can change from its MC to SP states. The titled structure was optimized at B3LYP/6-311++G(d,p) level of theory. To obtain conductivity results, the electrons of metal and organic atoms were approached by the single-plus polarization (SZP) for single-zeta and double-plus polarization (DZP) for double zeta basis sets, respectively. We examined some factors in this study, including various molecule geometries, the type of surface materials (Platinum, gold, and silver), the switching ratio, the gap between HOMO and LUMO levels, and the transmission spectra, at different bias voltages. The outcomes show that conductivity transforms from an off-state (high resistance) to an on-state as the molecule switches from MC to SP form (low resistance).

Automatic bad-pixel mask maker for X-ray pixel detectors with application to serial crystallography.

X-ray crystallography has witnessed a massive development over the past decade, driven by large increases in the intensity and brightness of X-ray sources and enabled by employing high-frame-rate X-ray detectors. The analysis of large data sets is done via automatic algorithms that are vulnerable to imperfections in the detector and noise inherent with the detection process. By improving the model of the behaviour of the detector, data can be analysed more reliably and data storage costs can be significantly reduced. One major requirement is a software mask that identifies defective pixels in diffraction frames. This paper introduces a methodology and program based upon concepts of machine learning, called robust mask maker (RMM), for the generation of bad-pixel masks for large-area X-ray pixel detectors based on modern robust statistics. It is proposed to discriminate normally behaving pixels from abnormal pixels by analysing routine measurements made with and without X-ray illumination. Analysis software typically uses a Bragg peak finder to detect Bragg peaks and an indexing method to detect crystal lattices among those peaks. Without proper masking of the bad pixels, peak finding methods often confuse the abnormal values of bad pixels in a pattern with true Bragg peaks and flag such patterns as useful regardless, leading to storage of enormous uninformative data sets. Also, it is computationally very expensive for indexing methods to search for crystal lattices among false peaks and the solution may be biased. This paper shows how RMM vastly improves peak finders and prevents them from labelling bad pixels as Bragg peaks, by demonstrating its effectiveness on several serial crystallography data sets.

Structural and vibrational investigation of Cis-Trans isomers of potent insecticide allethrin.

In this research, the optimised structural and vibrational properties of cis-trans isomers of powerful insecticide allethrin were theoretically studied in gas phase and in aqueous and ethanol solutions by using hybrid B3LYP/6-311 + + g(d,p) level of theory. The results revealed that the permittivity of solvent has influence on the properties of both isomers, thus, higher dipole moments and solvation energies are observed in water, a solvent of higher permittivity (78.355) than ethanol. Complete vibrational assignments of both isomers were done by combining the experimental IR spectrum of allethrin with the scaled quantum mechanical force field (SQMFF) methodology and the determination of corresponding scaled force constants in gas phase and aqueous solution are reported. Different signs of dihedral O2C10C6C4 angles of both isomers (negative in cis and positive in trans) support the differences in the vibrational assignments. Natural bond orbital (NBO) calculations suggest that both isomers are highly stable in gas phase and aqueous solution and that the side chains and five member's rings are involved in the n → σ* interactions. However, atoms in molecules (AIM) studies reveal a higher stability of form cis in both media than the trans one. Merz-Kollman (MK), Mulliken and natural population atomic (NPA) charges for both isomers support the higher hydration of trans isomer in aqueous media and, hence, the higher solvation energy in water (ΔGC/ZPVE = - 80.29 kJ/mol). Changes in the bond orders of O and C atoms of side chain are observed in water as a consequence of hydration. The higher stability of the cis form in the above solutions could be explained by the lower solvation energy in water, as supported by AIM calculations. The studies of frontier orbital reveal that the cis form in both media is sligthly more reactive than the trans form.

Towards real-time analysis of liquid jet alignment in serial femtosecond crystallography.

Liquid sample delivery systems are used extensively for serial femtosecond crystallography at X-ray free-electron lasers (XFELs). However, misalignment of the liquid jet and the XFEL beam leads to the X-rays either partially or completely missing the sample, resulting in sample wastage and a loss of experiment time. Implemented here is an algorithm to analyse optical images using machine vision to determine whether there is overlap of the X-ray beam and liquid jet. The long-term goal is to use the output from this algorithm to implement an automated feedback mechanism to maintain constant alignment of the X-ray beam and liquid jet. The key elements of this jet alignment algorithm are discussed and its performance is characterized by comparing the results with a manual analysis of the optical image data. The success rate of the algorithm for correctly identifying hits is quantified via a similarity metric, the Dice coefficient. In total four different nozzle designs were used in this study, yielding an overall Dice coefficient of 0.98.

Prevalence of Molar-incisor hypomineralization in Iranian children - A systematic review and narrative synthesis.

INTRODUCTION: Molar-incisor hypomineralization is a developmental defect of enamel with clinical features vary from demarcated opacities to severe tissue breakdown which calls for considerable preventive and interceptive measures. The aim of this article was to systematically review the literature on the prevalence of MIH in Iran and highlight the condition in Iranian children. MATERIALS AND METHODS: A systematic search of literature was conducted in Scopus, Pubmed, Ovid, Embase, Web of Science, and Google-Scholar as well as national Iranian database and digital archives of dental schools from the beginning of 2000 to the end of 2021 for published and unpublished studies. Data from cross-sectional, cohort, and case-control studies on prevalence of molar-incisor hypomineralization among 6-13-year-old children was gathered, using the following MeSH terms and keywords and their Persian equivalents: Prevalence, Hypomineralisation, Hypomineralization, MIH, "molar incisor", "molar-incisor", "cheese molars", "Hypomineralised first permanent molars", "Hypomineralized first permanent molars", "developmental defects of enamel", "enamel developmental defects", Iran*. Methodological quality and the risk of bias of quantitative studies was assessed using a modified version of Newcastle-Ottawa Scale. Due to the considerable clinical and statistical heterogeneity of the included studies, pooling of data through meta-analysis was not possible. Therefore, a descriptive synthesis of data was performed. RESULTS: Fifteen cross-sectional studies with a total number of 12011 participants were included in the systematic review. The prevalence of MIH ranged from 5.1% to 25.6%. All of the included studies were at a moderate risk of bias (NOS of 4-6). The lowest prevalence of MIH was reported in Kerman (5.14%) and the highest in Tehran (25.6%). Substantial methodological, clinical and statistical heterogeneity was observed. CONCLUSION: This is the first study to systematically review the available literature on MIH prevalence in Iran. However, the present review has some limitations such as limited number of included studies, large heterogeneity of the research, and moderate quality of included studies. Further high-quality research is warranted.

Molecular insights into the crystalline nanocellulose and human lysozyme interactions: An experimental and theoretical research.

In the present research, we performed a combination of detailed computational and spectroscopic methods to determine the effect of crystalline nanocellulose (CNC) on the structure and dynamics of human lysozyme (hLyz). Fluorescence spectroscopy revealed static quenching as the major mechanism in forming a stable CNC-hLyz complex, and the binding was energetically favorable. The obtained values of the thermodynamic parameters (∆G, ∆H, and ∆S) proposed that the complex formation between the enzyme and cellulose nanocrystals is driven by electrostatic interactions, which were also confirmed by molecular dynamics (MD) simulation. Additionally, the MD simulation analysis displays that the enzyme's structural elements and tertiary structure were primarily maintained, and only loops regions were affected in the presence of cellulose nanocrystals. At the same time, circular dichroism (CD) outcomes highlighted that higher cellulose nanocrystals concentration caused a reduction in the secondary structure of hLyz. Our observations proved that low cellulose nanocrystals concentrations have no considerable effect on the human lysozyme structure. The current research results provide a valuable opportunity to elucidate the molecular interactions between protein and nanocelluloses, guiding further investigations of CNC-based material for biomedical, pharmaceutical, and food industry applications.

Live demonstration versus multimedia: A comparison of two educational methods of orthodontic dental cast trimming.

Introduction: The aim of this study was to compare the effect of two educational methods: live practical and multimedia demonstrations of dental cast trimming. Methods: In this quasi-experimental study, all 44 dental students from Zanjan University Dental School who were studying in the 8th semester entered the study. Using simple randomization, we assigned them to two groups. Multimedia and live demonstrations were used in the intervention (n=21) and control (n=23) groups, respectively. Knowledge of students was assessed using pre-test and post-test. Practical skills were compared using the students' final semester scores. The Individual Development and Educational Assessment questionnaire was used to assess the students' reaction to instruction. For data analysis, mean and standard deviation, and independent and paired t-tests were used. Statistical analysis was performed using SPSS software. Results: In terms of knowledge, the pre-test scores of the intervention and control groups were not significantly different (p-value= 0.457), and the post-test scores of the two intervention and control groups had no significant difference (p-value= 0.053); however, in both intervention and control groups there was a significant difference between the scores before and after the test, and the scores of both groups increased after training (p-value= 0.001, p-value= 0.001). In terms of practical skills, no significant difference was observed in the mean and standard deviation of the scores in the two groups (p-value=0.902). There was no significant difference in terms of the students' reaction to instruction. Conclusion: All students passed this course successfully. Further, their knowledge and skills were improved in both groups. Similar to the live practical demonstration, that of the multimedia led to a positive reaction to instruction in students. Therefore, multimedia education can be used well with the traditional method and even replaces it.

A multi-million image Serial Femtosecond Crystallography dataset collected at the European XFEL.

Serial femtosecond crystallography is a rapidly developing method for determining the structure of biomolecules for samples which have proven challenging with conventional X-ray crystallography, such as for membrane proteins and microcrystals, or for time-resolved studies. The European XFEL, the first high repetition rate hard X-ray free electron laser, provides the ability to record diffraction data at more than an order of magnitude faster than previously achievable, putting increased demand on sample delivery and data processing. This work describes a publicly available serial femtosecond crystallography dataset collected at the SPB/SFX instrument at the European XFEL. This dataset contains information suitable for algorithmic development for detector calibration, image classification and structure determination, as well as testing and training for future users of the European XFEL and other XFELs.

3D printed devices and infrastructure for liquid sample delivery at the European XFEL.

The Sample Environment and Characterization (SEC) group of the European X-ray Free-Electron Laser (EuXFEL) develops sample delivery systems for the various scientific instruments, including systems for the injection of liquid samples that enable serial femtosecond X-ray crystallography (SFX) and single-particle imaging (SPI) experiments, among others. For rapid prototyping of various device types and materials, sub-micrometre precision 3D printers are used to address the specific experimental conditions of SFX and SPI by providing a large number of devices with reliable performance. This work presents the current pool of 3D printed liquid sample delivery devices, based on the two-photon polymerization (2PP) technique. These devices encompass gas dynamic virtual nozzles (GDVNs), mixing-GDVNs, high-viscosity extruders (HVEs) and electrospray conical capillary tips (CCTs) with highly reproducible geometric features that are suitable for time-resolved SFX and SPI experiments at XFEL facilities. Liquid sample injection setups and infrastructure on the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument are described, this being the instrument which is designated for biological structure determination at the EuXFEL.