Pitfalls in measurements of R1 relaxation rates of protein backbone 15N nuclei.

The dynamics of the backbone and side-chains of protein are routinely studied by interpreting experimentally determined 15N spin relaxation rates. R1(15N), the longitudinal relaxation rate, reports on fast motions and encodes, together with the transverse relaxation R2, structural information about the shape of the molecule and the orientation of the amide bond vectors in the internal diffusion frame. Determining error-free 15N longitudinal relaxation rates remains a challenge for small, disordered, and medium-sized proteins. Here, we show that mono-exponential fitting is sufficient, with no statistical preference for bi-exponential fitting up to 800 MHz. A detailed comparison of the TROSY and HSQC techniques at medium and high fields showed no statistically significant differences. The least error-prone DD/CSA interference removal technique is the selective inversion of amide signals while avoiding water resonance. The exchange of amide with solvent deuterons appears to affect the rate R1 of solvent-exposed amides in all fields tested and in each DD/CSA interference removal technique in a statistically significant manner. In summary, the most accurate R1(15N) rates in proteins are achieved by selective amide inversion, without the addition of D2O. Importantly, at high magnetic fields stronger than 800 MHz, when non-mono-exponential decay is involved, it is advisable to consider elimination of the shortest delays (typically up to 0.32 s) or bi-exponential fitting.

Combined Machine Learning and Molecular Modelling Workflow for the Recognition of Potentially Novel Fungicides.

Novel machine learning and molecular modelling filtering procedures for drug repurposing have been carried out for the recognition of the novel fungicide targets of Cyp51 and Erg2. Classification and regression approaches on molecular descriptors have been performed using stepwise multilinear regression (FS-MLR), uninformative-variable elimination partial-least square regression, and a non-linear method called Forward Stepwise Limited Correlation Random Forest (FS-LM-RF). Altogether, 112 prediction models from two different approaches have been built for the descriptor recognition of fungicide hit compounds. Aiming at the fungal targets of sterol biosynthesis in membranes, antifungal hit compounds have been selected for docking experiments from the Drugbank database using the Autodock4 molecular docking program. The results were verified by Gold Protein-Ligand Docking Software. The best-docked conformation, for each high-scored ligand considered, was submitted to quantum mechanics/molecular mechanics (QM/MM) gradient optimization with final single point calculations taking into account both the basis set superposition error and thermal corrections (with frequency calculations). Finally, seven Drugbank lead compounds were selected based on their high QM/MM scores for the Cyp51 target, and three were selected for the Erg2 target. These lead compounds could be recommended for further in vitro studies.

The FRS nomination of Sir Prafulla C. Ray and the correspondence of N. R. Dhar.

Sir Prafulla Chandra Ray (1861-1944) was the first Indian chemist to achieve high international reputation. Originally trained at the University of Edinburgh, he worked for many years at Presidency College in Calcutta and then at Calcutta University. He built up a remarkable school of chemical research by attracting many outstanding students to work with him and published about 150 papers-many of them in leading British and German journals. Ray was highly respected by his British peers and was the first Indian of that era to be nominated for FRS, in 1913. At the time when his nomination was being considered by the Royal Society, Ray's favourite student, Nil Ratan Dhar (1892-1986), who was to become the second Indian chemist to achieve high international reputation, worked in London and Paris for a few years. Even when Dhar was merely a 24-year-old student, he lobbied with several leading British chemists for the election of Ray and kept Ray informed in a series of fascinating letters-giving us a rare glimpse of what election to the Royal Society meant for Indian scientists of that era. During this time, Ray received a knighthood for his contributions to chemistry, and Nature published a front-page article on Ray's 'life-work'. Many British chemists felt strongly that Ray should be elected FRS and were willing to discuss Ray's case with the young Dhar quite openly. But, rather mysteriously, Ray never got elected.

Structure binding relationship of human surfactant protein D and various lipopolysaccharide inner core structures.

As a major player of the innate immune system, surfactant protein D (SP-D) recognizes and promotes elimination of various pathogens such as Gram-negative bacteria. SP-D binds to l-glycero-d-manno-heptose (Hep), a constituent of the partially conserved lipopolysaccharide (LPS) inner core of many Gram-negative bacteria. Binding and affinity of trimeric human SP-D to Hep in distinct LPS inner core glycans differing in linkages and adjacent residues was elucidated using glycan array and surface plasmon resonance measurements that were compared to in silico interaction studies. The combination of in vitro assays using defined glycans and molecular docking and dynamic simulation approaches provides insights into the interaction of trimeric SP-D with those glycan ligands. Trimeric SP-D wildtype recognized larger LPS inner core oligosaccharides with slightly enhanced affinity than smaller compounds suggesting the involvement of stabilizing secondary interactions. A trimeric human SP-D mutant D324N+D325N+R343K resembling rat SP-D bound to various LPS inner core structures in a similar pattern as observed for the wildtype but with higher affinity. The selective mutation of SP-D promotes targeting of LPS inner core oligosaccharides on Gram-negative bacteria to develop novel therapeutic agents.

Redox mediators boost NOx reduction via trade-off electron charges using a cube-shaped (cMn@rGO) catalyst; mechanism and electrochemical study.

Gaseous pollutants like sulfur dioxide and nitrogen oxide(s) (SO2, NOx) have been increasing exponentially for the last two decades, which have had adverse effects on human health, aquatic life, and the environment. Recently, for air pollution taming, manganese/oxide (Mn/MnO) has become a very promising heterogeneous catalyst due to its environment-friendly, low-price, and remarkable catalytic abilities for toxic gases. In this work, cube-shaped Mn nanoparticles (cMn NPs) were decorated on the surface of reduced graphene oxide (rGO) by the solvothermal method. The resulting cMn@rGO composite was employed for electrochemical NOx reduction. However, the microscopic (TEM/HRTEM) and structural analysis were utilised to investigate the morphology and characteristics of the cMn@rGO composite. This electrochemical-based treatment for NOx reduction is employed by using electron shuttle or redox mediators. Here, four distinct redox mediators are used to address electrochemical obstacles, which effectively facilitate electron transportation and promoted NOx reduction on the electrode surface. These mediators not only significantly enhanced the NOx conversion into valuable products, i.e., N2 and N2O, but also made the process smooth with high performance. Among these mediators, neutral red (N.R) exhibited extraordinary potential in enhancing NOx reduction. The obtained results indicated that the remarkable catalytic performance (∼93%) of the cMn@rGO can be attributed to several factors, including the catalyst's three-dimensional architecture structure and abundant active sites. The designed catalyst (cMn@rGO) is not only cost-effective and sustainable but also exhibits excellent potential in effectively reducing NOx, which could be beneficial for large-scale NOx abatement.

Real-World Effectiveness of Nirmatrelvir/Ritonavir and Dexamethasone Among Hospitalized Patients with COVID-19: A Prospective Cohort Study.

Purpose: Anti-viral and anti-inflammatory therapies were effective in altering virus repletion and immune dysregulation in Coronavirus Disease 2019 (COVID-19) patients. This study aimed to explore the effect of combination therapy on disease progression in a real-world setting. Patients and Methods: A total of 836 patients confirmed with SARS-CoV-2 infection participated in the study from 15 November to 25 December 2022 at Beijing Youan Hospital, Capital Medical University. A prospective cohort study was implemented to investigate the prognostic effect of the combination therapy on virus shedding and clinical recovery. Results: About 78% of patients used nirmatrelvir/ritonavir (N/R, Paxlovid®, Pfizer) negatively, 16% of patients were prescribed nirmatrelvir/ritonavir beyond five days of symptom onset, 4% of patients received N/R monotherapy within five days of symptom onset and 2% of patients received N/R combined with dexamethasone. Compared with untreated patients, N/R monotherapy reduced the median time to 10.0 days from 12.0 days according to the negative conversion of nucleic acid amplification test (NAAT), and combination therapy reduced the time to 7.0 days, and increased to a 1.99 (95% CI 0.92, 4.32) and 14.23-fold (95% CI 4.50, 44.95) probability of negative NAAT, respectively. N/R monotherapy reduced the clinical recovery time to 10.0 days from 13.0 days. Single-use and combined-use non-significantly increased the recovery probability by 61% and 69%, respectively. In mild and moderate patients, the HRs for clinical recovery increased to 1.69 (95% CI 0.73, 3.94) and 2.18 (95% CI 0.29, 16.62), respectively. Conclusion: Combination therapy of N/R and dexamethasone increased negative conversion of NAAT and was associated with a non-significant improvement in clinical recovery. Further studies are warranted to confirm this efficacy.

Impact of the SARS-CoV-2 nucleocapsid 203K/204R mutations on the inflammatory immune response in COVID-19 severity.

BACKGROUND: The excessive inflammatory responses provoked by SARS-CoV-2 infection are critical factors affecting the severity and mortality of COVID-19. Previous work found that two adjacent co-occurring mutations R203K and G204R (KR) on the nucleocapsid (N) protein correlate with increased disease severity in COVID-19 patients. However, links with the host immune response remain unclear. METHODS: Here, we grouped nasopharyngeal swab samples of COVID-19 patients into two cohorts based on the presence and absence of SARS-CoV-2 nucleocapsid KR mutations. We performed nasopharyngeal transcriptome analysis of age, gender, and ethnicity-matched COVID-19 patients infected with either SARS-CoV-2 with KR mutations in the N protein (KR patients n = 39) or with the wild-type N protein (RG patients n = 39) and compared to healthy controls (n = 34). The impact of KR mutation on immune response was further characterized experimentally by transcriptomic and proteomic profiling of virus-like-particle (VLP) incubated cells. RESULTS: We observed markedly elevated expression of proinflammatory cytokines, chemokines, and interferon-stimulated (ISGs) genes in the KR patients compared to RG patients. Using nasopharyngeal transcriptome data, we found significantly higher levels of neutrophils and neutrophil-to-lymphocyte (NLR) ratio in KR patients than in the RG patients. Furthermore, transcriptomic and proteomic profiling of VLP incubated cells confirmed a similar hyper-inflammatory response mediated by the KR variant. CONCLUSIONS: Our data demonstrate an unforeseen connection between nucleocapsid KR mutations and augmented inflammatory immune response in severe COVID-19 patients. These findings provide insights into how mutations in SARS-CoV-2 modulate host immune output and pathogenesis and may contribute to more efficient therapeutics and vaccine development.

National and international guidelines on the replacement of missing teeth with dentures for head and neck cancer patients post-radiotherapy: A rapid review.

Background: Replacement of missing teeth is not a straightforward task in head and neck cancer (HNC) patients post-radiotherapy. There is debate regarding the best way to care for these patients as it has been reported that using dentures by HNC patients after receiving treatment with radiotherapy might initiate the development of osteoradionecrosis. Aim: This rapid review aimed to collate and compare the national and international guidelines for the use of dentures following radiotherapy for HNC patients. Materials and methods: Three steps were included in data collection of this rapid review (first step; identification of dental and relevant non-dental associations/societies, second step, identification of national and international guidelines regarding the dental management of HNC patients, and third step; identification of recommendations about the replacement of missing teeth in HNC patients). Results: In the 193 countries recognized by the United Nations, there were 238 relevant societies found, from those 175 confirmed that they do not have clear guidelines. Only 32 associations/societies (all in either Europe and North America) recommend guidelines for their dentists (N = 12 guidelines) about the dental management of HNC patients and show their position regarding the use of dentures for HNC patients after receiving treatment with radiotherapy. Conclusions: There are very few guidelines and those that do exist differ, lack detail, and rarely go beyond routine advice. Accordingly, clear, detailed, and evidence-based guidelines are required to inform the management of patients with missing teeth following radiotherapy for HNC patients.

Frequency control of nuclear-renewable hybrid energy systems using optimal PID and FOPID controllers.

This paper investigates the applications of Proportional-Integrator-Derivative (PID) and Fractional Order PID (FOPID) controllers in Nuclear-Renewable Hybrid Energy Systems (N-R HESs). The N-R HES is a recent technology in the area of decarbonized energy systems. N-R HESs are expected to contribute immensely to providing carbon-free and sustainable energy infrastructure in the upcoming days. It is also anticipated that system resiliency will be the primary concern when nuclear reactors are incorporated with intermittent renewable energy resources. Therefore, in this research, the authors intend to evaluate the compatibility of two classical controllers, PID and FOPID, to ensure the stability of N-R HESs. The N-R HES of this paper consists of different energy sources, such as solar, wind, nuclear, fuel cell systems, Battery Energy Storage Systems (BESS), and Flywheel Energy Storage Systems (FESS). To encounter system performance requirements, the PID and FOPID controller parameters are adjusted using a metaheuristic algorithm, namely Artificial-Bee-Colony (ABC) optimization algorithm. Metaheuristic optimization algorithms always do not guarantee global maxima/minima. Hence, another metaheuristic optimization algorithm, Teaching-Learning-based Optimization (TLBO), is used to validate the results. The results clearly show that the optimal PID and FOPID controllers can handle the system frequency and maintain the stability of the studied N-R HES.

Bandwidth Enhancement and Generation of CP of Yagi-Uda-Shape Feed on a Rectangular DRA for 5G Applications.

A wideband circularly polarized rectangular dielectric resonator antenna (DRA) fed by a single feeding mechanism has been studied theoretically and experimentally. The purpose of the study is to determine how adding a parasitic strip next to the flat surface metallic feed would affect various far- and near-field antenna characteristics. Initially, the basic antenna design, i.e., the T-shape feed known as antenna A, produced a 4.81% impedance matching bandwidth (|S11| -10 dB). Due to the narrow and undesirable results of the initial antenna design, antenna-A was updated to the antenna-B design, i.e., Yagi-Uda. The antenna-B produced a decent result (7.89% S11) as compared to antenna-A but still needed the bandwidth widened, for this, a parasitic patch was introduced next to the Yagi-Uda antenna on the rectangular DRA at an optimized location to further improve the results. This arrangement produced circular polarization (CP) waves spanning a broad bandwidth of 28.21% (3.59-3.44 GHz) and a broad impedance |S11| bandwidth of around 29.74% (3.71-3.62 GHz). These findings show that, in addition to producing CP, parasite patches also cause the return loss to rise by a factor of almost three times when compared to results obtained with the Yagi-Uda-shape feed alone. Computer simulation technology was used for the simulation (CST-2017). The planned antenna geometry prototype was fabricated and measured. Performance indicators show that the suggested antenna is a good fit for 5G applications. The simulated outcomes and measurements match up reasonably.

Clinical efficacies, underlying mechanisms and molecular targets of Chinese medicines for diabetic nephropathy treatment and management.

Diabetic nephropathy (DN) has been recognized as a severe complication of diabetes mellitus and a dominant pathogeny of end-stage kidney disease, which causes serious health problems and great financial burden to human society worldwide. Conventional strategies, such as renin-angiotensin-aldosterone system blockade, blood glucose level control, and bodyweight reduction, may not achieve satisfactory outcomes in many clinical practices for DN management. Notably, due to the multi-target function, Chinese medicine possesses promising clinical benefits as primary or alternative therapies for DN treatment. Increasing studies have emphasized identifying bioactive compounds and molecular mechanisms of reno-protective effects of Chinese medicines. Signaling pathways involved in glucose/lipid metabolism regulation, antioxidation, anti-inflammation, anti-fibrosis, and podocyte protection have been identified as crucial mechanisms of action. Herein, we summarize the clinical efficacies of Chinese medicines and their bioactive components in treating and managing DN after reviewing the results demonstrated in clinical trials, systematic reviews, and meta-analyses, with a thorough discussion on the relative underlying mechanisms and molecular targets reported in animal and cellular experiments. We aim to provide comprehensive insights into the protective effects of Chinese medicines against DN.

Triterpene saponins from the roots of Ilex pubescens.

Five new triterpene saponins, Ilexpublesnins N-R (1-5), along with seven known analogs were isolated from the root of Ilex pubescens. Their structures were elucidated on the basis of extensive spectroscopic analysis, including 1D and 2D NMR experiments. Ilexpublesnin N (1) possessed a rare 20-hydroxyursolic acid scaffold from natural resource. These compounds were evaluated in vitro for their cytotoxic effects on human cancer cell lines HepG2, HLE, BEL7402, BEL7403, BEL7405, MCF-7, HeLa. Among them, only compounds 5 and 10 showed cytotoxic potentiality against BEl-7403 and HEL cell lines [inhibition (%): 35.38 and 45.12, respectively].

Comparison of LILT and STEP procedures in children with short bowel syndrome -- a systematic review of the literature.

PURPOSE: To compare LILT and STEP, the two principal procedures to lengthen the native bowel in children with a short bowel syndrome (SBS), by discussing the indications and presenting the outcome from published data. METHODS: A review of literature was performed. N=39 publications were reviewed. RESULTS: For LILT and STEP, failure to achieve intestinal autonomy by conservative therapy represents the main indication, and end-stage liver disease the main contraindication. A sufficiently dilated intestinal segment is a common anatomical precondition for both procedures. STEP can be performed on shorter intestinal segments and on intricate segments such as the duodenum, which is technically not feasible for LILT. Both procedures have a similar extent of intestinal lengthening (approximately 70%) and result in improvement of enteral nutrition and reversal of complications of parenteral nutrition. STEP seems to have a lower mortality and overall progression to transplantation. CONCLUSIONS: STEP and LILT are both accepted procedures for non-transplant surgical management of SBS in children. The outcome after STEP seems to be more favourable, but larger series are needed to further assess accurate selection of eligible patients and to estimate effectiveness of procedures. A considerably higher number of cases for evaluation might be accomplished through the widespread use of a centralised registry.

Efficacy of different antimicrobials on inhibition of Listeria monocytogenes growth in laboratory medium and on cold-smoked salmon.

Listeria monocytogenes is of particular concern in cold-smoked fish products as it can survive curing and cold-smoking, and can subsequently grow from low numbers to potentially hazardous levels during refrigerated storage. The purpose of this study was to (i) quantify the effects of organic acids, nisin, and their combinations on controlling L. monocytogenes growth on cold-smoked salmon at refrigeration temperatures, (ii) identify synergistic interactions of binary combinations of these antimicrobials, and (iii) determine if results from laboratory growth media can predict antimicrobial efficacy on cold-smoked salmon. Strains representing the genetic diversity of L. monocytogenes lineages I and II were grown in brain heart infusion (BHI) broth as well as on the surface of commercially produced wet-cured, cold-smoked salmon slices at 7°C. BHI broth and cold-smoked salmon were supplemented with sodium diacetate (SDA, 0.14% water phase (w.p.)), potassium lactate (PL, 2% w.p.), nisin (NI, 50ppm), and binary combinations of inhibitors at the same levels. Cell densities of L. monocytogenes were measured over time and used to calculate growth parameters, including initial cell density (N0), lag phase (λ), maximum growth rate (µmax), and maximum cell density (Nmax) for each antimicrobial treatment. N0 was significantly lowered by addition of NI with a similar average reduction on salmon (2.02±0.99 log(CFU/g)) and in BHI (1.51±0.83 log(CFU/ml)). Among all antimicrobial treatments, the combination of PL and SDA led to the greatest increase in λ both on salmon (7.1±3.6days) and in BHI (9.7±3.8days) when compared to the controls. The combination of PL and SDA had synergistic effects on increasing λ and lowering Nmax both in BHI and on salmon. Among all the treatments tested, the combination of NI and PL led to the greatest reductions in Nmax on salmon. We observed positive correlations between the growth parameters obtained from BHI broth and cold-smoked salmon, indicating that growth of L. monocytogenes in broth, to some extent, qualitatively reflected characteristics of growth on cold-smoked salmon under antimicrobial stresses. Results from BHI could quantitatively predict the variability of growth parameters obtained from salmon for lineage II strains, but not for lineage I strains. Although results from laboratory growth medium may not provide exact predictions of antimicrobial efficacy on cold-smoked salmon, they could be used to rapidly identify effective combinations for further examination on cold-smoked salmon.

Synthesis and Anticancer Activity of 2-(Alkyl-, Alkaryl-, Aryl-, Hetaryl-)-[1,2,4]triazolo[1,5-c]quinazolines.

The combinatorial library of novel potential anticancer agents, namely, 2-(alkyl-, alkaryl-, aryl-, hetaryl-)[1,2,4]triazolo[1,5-c]quinazolines, was synthesized by the heterocyclization of the alkyl-, alkaryl-, aryl-, hetarylcarboxylic acid (3H-quinazoline-4-ylidene)hydrazides by oxidative heterocyclization of the 4-(arylidenehydrazino)quinazolines using bromine, and by the heterocyclization of N-(2-cyanophenyl)formimidic acid ethyl ester. The optimal method for synthesis of the s-triazolo[1,5-c]quinazolines appeared to be cyclocondensation of the corresponding carboxylic acid (3H-quinazoline-4-ylidene)hydrazides. The compounds' structures were established by (1)H, (13)C NMR, LC- and EI-MS analysis. The in vitro screening of anticancer activity determined the most active compound to be 3,4,5-trimethoxy-N'-[quinazolin-4(3H)-ylidene]benzohydrazide (3.20) in micromolar concentrations with the GI50 level (MG_MID, GI50 is 2.29). Thus, the cancer cell lines whose growth is greatly inhibited by compound 3.20 are: non-small cell lung cancer (NCI-H522, GI50=0.34), CNS (SF-295, GI50=0.95), ovarian (OVCAR-3, GI50=0.33), prostate (PC-3, GI50=0.56), and breast cancer (MCF7, GI50=0.52), leukemia (K-562, GI50=0.41; SR, GI50=0.29), and melanoma (MDA-MB-435, GI50=0.31; SK-MEL-5, GI50=0.74; UACC-62, GI50=0.32). SAR-analysis is also discussed.

Mapping biological behaviors by application of longer-lived positron emitting radionuclides.

With the technological development of positron emission tomography (PET) and the advent of novel antibody-directed drug delivery systems, longer-lived positron-emitting radionuclides are moving to the forefront to take important roles in tracking the distribution of biotherapeutics such as antibodies, and for monitoring biological processes and responses. Longer half-life radionuclides possess advantages of convenient on-site preparation procedures for both clinical and non-clinical applications. The suitability of the long half-life radionuclides for imaging intact monoclonal antibodies (mAbs) and their respective fragments, which have inherently long biological half-lives, has attracted increased interest in recent years. In this review, we provide a survey of the recent literature as it applies to the development of nine-selected longer-lived positron emitters with half-lives of 9-140h (e.g., (124)I, (64)Cu, (86)Y and (89)Zr), and describe the biological behaviors of radionuclide-labeled mAbs with respect to distribution and targeting characteristics, potential toxicities, biological applications, and clinical translation potentials.