The new FLYA automated resonance assignment algorithm determines NMR chemical shift assignments on the basis of peak lists from any combination of multidimensional through-bond or through-space NMR ...experiments for proteins. Backbone and side-chain assignments can be determined. All experimental data are used simultaneously, thereby exploiting optimally the redundancy present in the input peak lists and circumventing potential pitfalls of assignment strategies in which results obtained in a given step remain fixed input data for subsequent steps. Instead of prescribing a specific assignment strategy, the FLYA resonance assignment algorithm requires only experimental peak lists and the primary structure of the protein, from which the peaks expected in a given spectrum can be generated by applying a set of rules, defined in a straightforward way by specifying through-bond or through-space magnetization transfer pathways. The algorithm determines the resonance assignment by finding an optimal mapping between the set of expected peaks that are assigned by definition but have unknown positions and the set of measured peaks in the input peak lists that are initially unassigned but have a known position in the spectrum. Using peak lists obtained by purely automated peak picking from the experimental spectra of three proteins, FLYA assigned correctly 96–99% of the backbone and 90–91% of all resonances that could be assigned manually. Systematic studies quantified the impact of various factors on the assignment accuracy, namely the extent of missing real peaks and the amount of additional artifact peaks in the input peak lists, as well as the accuracy of the peak positions. Comparing the resonance assignments from FLYA with those obtained from two other existing algorithms showed that using identical experimental input data these other algorithms yielded significantly (40–142%) more erroneous assignments than FLYA. The FLYA resonance assignment algorithm thus has the reliability and flexibility to replace most manual and semi-automatic assignment procedures for NMR studies of proteins.
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Corruption in Higher Education: Global Challenges and Responses discusses the magnitude of this phenomenon, its complexity, and the actions that are needed to mitigate it.
Conspectus In this Account, we briefly discuss the recently discovered and rapidly developing superbase-promoted self-organization reactions of several equivalents of acetylenes and ketones to afford ...complex compounds that represent promising synthetic building blocks common in natural products. Notably, acetylenes play a special role in these reactions because of their dual (acting as an electrophile and a nucleophile) and flexible reactivity. These unique properties of acetylenes are elegantly expressed in superbasic media, where acetylenes are more deprotonated and their electrophilicity increases as a result of complexation with alkali metal cations, with simultaneous enhancement of the nucleophilic reactants due to desolvation. Under these conditions, acetylenes behave as a driving and organizing force toward other reactants. Various combinations of nucleophilic addition to the triple bond and acetylene deprotonation in the presence of other reactants with dual reactivity (e.g., ketones) enables the self-organization of complex molecular architectures that are inaccessible by conventional reactions. Herein we analyze recent achievements in this area concerning the reactions of acetylenes with ketones in superbasic KOH/DMSO-type systems that selectively afford synthetically and pharmaceutically valuable carbo- and heterocycles. Most of the reactions are triggered by the nucleophilic addition of deprotonated ketones (enolate anions) to acetylenes (superbase-catalyzed C-vinylation of ketones with acetylenes, which was recently introduced by our group into a toolkit of organic chemistry). The β,γ-ethylenic ketones thus formed can then take part in cascade processes with ketones and acetylenes to afford either carbocycles (e.g., hexahydroazulenones, acyl terphenyls, functionalized and cyclopentenols) or heterocycles (e.g., furans, benzoxepines, dioxabicyclo3.2.1octanes, and dioxadispiro5.1.5.2pentadecanes), depending on the structure of the reactants and the reaction conditions. Most of these compounds are selectively built from several equivalents of ketones and acetylenes in different combinations, and despite the presence of two or more asymmetric carbons in the products, they are generated as single diastereomers. When other nucleophiles (hydroxylamine, hydrazines, guanidine, and oximes) and ketones are involved in these self-organization processes, the intermediate β,γ-ethylenic ketones allow the formation of diverse heterocyclic systems (pyrroles, isoxazolines, pyrazolines, aminopyrimidines, and azabicyclo3.1.0hexanes). The discovered unique chemical transformations do not require transition metal catalysts and proceed under mild and operationally simple conditions. Most of these syntheses involve cascade addition reactions and therefore represent pot-, atom-, step-, and energy-saving processes that meet the requirements of green chemistry. The significance of the approach discussed herein is that it represents a viable alternative to existing classic and modern transition-metal-based catalytic syntheses of some fundamental carbo- and heterocycles. This is demonstrated by its employment of readily available, inexpensive starting materials like acetylenes and ketones and simple, widely accessible superbasic systems such as KOH/DMSO, which serves as a highly active universal catalyst and auxiliary. As shown in this Account, as this approach has developed, the number of preparatively attractive methods for the synthesis of diverse and potentially useful compounds has rapidly ballooned. The impressive experimental results presented in this Account will hopefully draw the attention of large circles of organic chemists involved in the design of rational and ecologically sound synthetic procedures and thus increase the application of these techniques in medicinal chemistry and materials science.
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Despite significant evidence around barriers hindering timely access to cataract surgery in low- and middle-income countries (LMICs), little is known about the strategies necessary to overcome them ...and the factors associated with improved access. Despite significant evidence that certain groups, women for example, experience disproportionate difficulties in access, little is known about how to improve the situation for them. Two reviews were conducted recently: Ramke et al., 2018 reported experimental and quasi-experimental evaluations of interventions to improve access of cataract surgical services, and Mercer et al., 2019 investigated interventions to improve gender equity. The aim of this systematic review was to collate, appraise and synthesise evidence from studies on factors associated with uptake of cataract surgery and strategies to improve the uptake in LMICs. We performed a literature search of five electronic databases, google scholar and a detailed reference review. The review identified several strategies that have been suggested to improve uptake of cataract surgery including surgical awareness campaigns; use of successfully operated persons as champions; removal of patient direct and indirect costs; regular community outreach; and ensuring high quality surgeries. Our findings provide the basis for the development of a targeted combination of interventions to improve access and ensure interventions which address barriers are included in planning cataract surgical services. Future research should seek to examine the effectiveness of these strategies and identify other relevant factors associated with intervention effects.
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The reaction of 5‐hydroxy‐1‐pyrrolines with arenes in TfOH at room temperature for 1 h afford 5‐aryl‐1‐pyrrolines in 55–98 % yields. 5‐Hydroxy‐1‐pyrrolines in TfOH or H2SO4 at room temperature for ...0.5–1 h undergo dehydration with the formation of N‐protonated forms of 3H‐pyrroles, which were characterized by NMR. Upon hydrolysis, the N‐protonated species give quantitatively the corresponding 3H‐pyrroles. The intermediate cationic species derived from the protonation of 5‐hydroxy‐1‐pyrrolines in Brønsted acids have been studied by means of NMR and DFT calculations. Plausible reaction mechanisms are discussed.
Reaction of 5‐hydroxy‐1‐pyrrolines with arenes in TfOH result in the formation of 5‐aryl‐1‐pyrrolines in yields up to 98 %. These pyrrolines in TfOH or H2SO4 without arenes are quantitatively transformed into 3H‐pyrroles. Intermediate cationic species of these reactions were studied by NMR and DFT calculations.
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Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely ...give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available.
Increasing brown adipose tissue (BAT) thermogenesis in mice and humans improves metabolic health and understanding BAT function is of interest for novel approaches to counteract obesity. The role of ...long noncoding RNAs (lncRNAs) in these processes remains elusive. We observed maternally expressed, imprinted lncRNA H19 increased upon cold-activation and decreased in obesity in BAT. Inverse correlations of H19 with BMI were also observed in humans. H19 overexpression promoted, while silencing of H19 impaired adipogenesis, oxidative metabolism and mitochondrial respiration in brown but not white adipocytes. In vivo, H19 overexpression protected against DIO, improved insulin sensitivity and mitochondrial biogenesis, whereas fat H19 loss sensitized towards HFD weight gains. Strikingly, paternally expressed genes (PEG) were largely absent from BAT and we demonstrated that H19 recruits PEG-inactivating H19-MBD1 complexes and acts as BAT-selective PEG gatekeeper. This has implications for our understanding how monoallelic gene expression affects metabolism in rodents and, potentially, humans.
A number of neglected tropical diseases are targeted for elimination or eradication. An effective surveillance system is critical to determine if these goals have been achieved and maintained. ...Trachoma has two related but morphologically different presentations that are monitored for elimination, the active infectious form of trachoma and trachomatous trichiasis (TT), the progression of the disease. There are a number of lessons learnt from the Guinea worm surveillance system that are particularly compatible for TT surveillance and the onchocerciasis surveillance system which can provide insights for surveillance of the infectious form of trachoma.
A literature search of peer-reviewed published papers and grey literature was conducted using PUBMED and Google Scholar for articles relating to dracunculiasis or Guinea worm, onchocerciasis and trachoma, along with surveillance or elimination or eradication. The abstracts of relevant papers were read and inclusion was determined based on specified inclusion and exclusion criteria. The credibility and bias of relevant papers were also critically assessed using published criteria. A total of 41 papers were identified that were eligible for inclusion into the review. The Guinea worm programme is designed around a surveillance-containment strategy and combines both active and passive surveillance approaches, with a focus on village-based surveillance and reporting. Although rumour reporting and a monetary incentive for the identification of confirmed Guinea worm cases have been reported as successful for identifying previously unknown transmission there is little unbiased evidence to support this conclusion. More rigorous evidence through a randomised controlled trial, influenced by motivational factors identified through formative research, would be necessary in order to consider applicability for TT case finding in an elimination setting. The onchocerciasis surveillance strategy focuses on active surveillance through sentinel surveillance of villages and breeding sites. It relies on an entomological component, monitoring infectivity rates of black flies and an epidemiological component, tracking exposure to infection in humans. Challenges have included the introduction of relatively complex diagnostics that are not readily available in onchocerciasis endemic countries and target thresholds, which are practically unattainable with current diagnostic tests. Although there is utility in monitoring for infection and serological markers in trachoma surveillance, it is important that adequate considerations are made to ensure evidence-based and achievable guidelines for their utility are put in place.
The experiences of both the Guinea worm and onchocerciasis surveillance strategies have very useful lessons for trachoma surveillance, pre- and post-validation. The use of a monetary reward for identification of TT cases and further exploration into the use of infection and serological indicators particularly in a post-validation setting to assist in identifying recrudescence would be of particular relevance. The next step would be a real-world evaluation of their relative applicability for trachoma surveillance.
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Aggregation of organic dyes often has consequences on their spectroscopic properties in materials. Here, we study a new sterically hindered boron-dipyrromethene (BODIPY), with adamantyl moieties ...grafted for the first time on the BODIPY core. Its aggregation behavior was investigated in poly(methyl methacrylate) (PMMA) and on drop-casted films by monitoring absorption, fluorescence emission, relative quantum yield (ΦFluo,Rel), lifetime and time-resolved anisotropy. Aggregates only appear from 0.067 mol·L–1. A multicomponent analysis demonstrated that the aggregation process can be described by three distinguishable components which correspond to a monomer species (M) and J and H aggregates. The results also indicated a concentration frontier: when the dye concentration increased up to 0.29 mol·L–1, the concentration of M decreased in favor of the aggregates. ΦFluo,Rel is yet only divided by 5 compared to the dye in solution. Above 0.29 mol·L–1, an equilibrium between M and the J aggregates is established, showing meanwhile a steady ΦFluo,Rel. The J aggregates are found to be dimers, whereas the aggregation number is varying for the H aggregates. Analysis of fluorescence and anisotropy decays showed that the excitation energy was transferred from M to the J dimers, and very probably trapped by H aggregates.
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