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Introduction: Despite Tocilizumab is now recognized as a concrete therapeutic option in patients with severe SARS-CoV-2 related respiratory failure, literature lacks about factors influencing the response to it in this context. Therefore, the aim of our study was to provide evidence about predictors of poor outcome in Tocilizumab treated patients in the real-world practice., Materials and Methods: We retrospectively analyzed clinical, laboratory and chest computer tomography (CCT) data of patients firstly admitted in non Intensive Care Units (ICU) and suffering from severe respiratory failure, who were treated with the IL-6 antagonist Tocilizumab. We compared patients who died and/or required admission to ICU with oro-tracheal intubation (OTI) with those who did not., Results: Two hundreds and eighty-seven patients (29.9% females) with mean age ± SD 64.1 ± 12.6 years were the study population. In-hospital mortality was 18.8%, while the composite endpoint in-hospital mortality and/or ICU admission with OTI occurred in 23.7%. At univariate analysis, patients who died and/or were admitted to ICU with OTI were significantly older and co-morbid, had significantly higher values of creatinine, C-reactive protein (CRP) and procalcitonin and lower lymphocytes count, PaO2/FiO2 ratio (P/F) and room air pulsossimetry oxygen saturation (RAO 2 S) at hospital admission. Computed tomography ground glass opacities (CT-GGO) involving the pulmonary surface ≥ 50% were found in 55.4% of patients who died and/or were admitted to ICU with OTI and in 21.5% of patients who did not (p=0.0001). At multivariate analysis, age ≥ 65 years (OR 17.3, 95% CI: 3.7-81.0), procalcitonin ≥ 0.14 (OR 9.9, 95%CI: 1.7-56.1), RAO 2 S ≤ 90% (OR 4.6, 95%CI: 1.2-17.0) and CCT-GGO involvement ≥ 50% (OR 5.1, 95%CI: 1.2-21.0) were independent risk factors associated with death and/or ICU admission with OTI., Conclusion: Tocilizumab has shown to improve outcome in patients with severe respiratory failure associated to SARS-CoV-2 related pneumonia. In our multicentre study focusing on Tocilizumab treated severe COVID-19 patients, age ≥ 65 years, procalcitonin ≥ 0.14 ng/mL, RAO 2 S ≤ 90% and CCT-GGO involvement ≥ 50% were independent factors associated with poor outcome., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Although the success of molecular-replacement techniques requires the solution of a six-dimensional problem, this is often subdivided into two three-dimensional problems. REMO09 is one of the programs which have adopted this approach. It has been revisited in the light of a new probabilistic approach which is able to directly derive conditional distribution functions without passing through a previous calculation of the joint probability distributions. The conditional distributions take into account various types of prior information: in the rotation step the prior information may concern a non-oriented model molecule alone or together with one or more located model molecules. The formulae thus obtained are used to derive figures of merit for recognizing the correct orientation in the rotation step and the correct location in the translation step. The phases obtained by this new version of REMO09 are used as a starting point for a pipeline which in its first step extends and refines the molecular-replacement phases, and in its second step creates the final electron-density map which is automatically interpreted by CAB, an automatic model-building program for proteins and DNA/RNA structures., (open access.)

The program Buccaneer, a well known fast and efficient automatic model-building program, is also a tool for phase refinement: indeed, input phases are used to calculate electron-density maps that are interpreted in terms of a molecular model, from which new phase estimates may be obtained. This specific property is shared by all other automatic model-building programs and allows their cyclic use, as is usually performed in other phase-refinement methods (for example electron-density modification techniques). Buccaneer has been included in a cyclic procedure, called CAB, aimed at increasing the rate of success of Buccaneer and the quality of the molecular models provided. CAB has been tested on 81 protein structures that were solved via molecular-replacement, anomalous dispersion and ab initio methods. The corresponding phases were submitted to a phase-refinement process that synergically combines current phase-refinement techniques and out-of-mainstream refinement methods [Burla et al. (2017), Acta Cryst. D73, 877-888]. The phases thus obtained were used as input for CAB. The experimental results were compared with those obtained by the sole use of Buccaneer: it is shown that CAB improves the Buccaneer results, both in completeness and in accuracy.

Persons living with HIV should remain on antiretroviral therapy (ART) indefinitely; however, a switch in the drug regimen is often necessary. In order to investigate if reasons for switching ART changed over time, we retrospectively analyzed reasons for switching and characteristics of switches among patients at Santa Maria Annunziata Hospital (OSMA), Florence area, Tuscany, Italy, over two periods (November 2012-October 2013 and November 2014-October 2015). The reasons for switching were classified as: simplification; virologic failure; occurrence of co-morbidities; and drug tolerability/toxicity issues. In period 1 (2012-2013), 18% patients changed their regimen vs. 13.5% in period 2 (2014-2015) (p = 0.019). Among reasons for switching, switches for simplification significantly increased from 41% in period 1 to 53% in period 2 (p = 0.004), with an increasing use of single tablet regimens (p = 0.002); no other statistically significant differences were found in other reasons for switching in periods 1 and 2. Characteristics of patients and of switches were analyzed and described. According to our data, the main reason for switching is now simplification, reflecting the recent changes in recommendations aimed to enhance adherence and quality of life, and to minimize, at the same time, drug toxicity and side effects.

Crystallographic least-squares techniques, the main tool for crystal structure refinement of small and medium-size molecules, are for the first time used for ab initio phasing. It is shown that the chief obstacle to such use, the least-squares severe convergence limits, may be overcome by a multi-solution procedure able to progressively recognize and discard model atoms in false positions and to include in the current model new atoms sufficiently close to correct positions. The applications show that the least-squares procedure is able to solve many small structures without the use of important ancillary tools: e.g. no electron-density map is calculated as a support for the least-squares procedure.

Difference electron densities do not play a central role in modern phase refinement approaches, essentially because of the explosive success of the EDM (electron-density modification) techniques, mainly based on observed electron-density syntheses. Difference densities however have been recently rediscovered in connection with the VLD (Vive la Difference) approach, because they are a strong support for strengthening EDM approaches and for ab initio crystal structure solution. In this paper the properties of the most documented difference electron densities, here denoted as F - F p , mF - F p and mF - DF p syntheses, are studied. In addition, a fourth new difference synthesis, here denoted as {\overline F_q} synthesis, is proposed. It comes from the study of the same joint probability distribution function from which the VLD approach arose. The properties of the {\overline F_q} syntheses are studied and compared with those of the other three syntheses. The results suggest that the {\overline F_q} difference may be a useful tool for making modern phase refinement procedures more efficient.

Ab initio and non-ab initio phasing methods are often unable to provide phases of sufficient quality to allow the molecular interpretation of the resulting electron-density maps. Phase extension and refinement is therefore a necessary step: its success or failure can make the difference between solution and nonsolution of the crystal structure. Today phase refinement is trusted to electron-density modification (EDM) techniques, and in practice to dual-space methods which try, via suitable constraints in direct and in reciprocal space, to generate higher quality electron-density maps. The most popular EDM approaches, denoted here as mainstream methods, are usually part of packages which assist crystallographers in all of the structure-solution steps from initial phasing to the point where the molecular model perfectly fits the known features of protein chemistry. Other phase-refinement approaches that are based on different sources of information, denoted here as out-of-mainstream methods, are not frequently employed. This paper aims to show that mainstream and out-of-mainstream methods may be combined and may lead to dramatic advances in the present state of the art. The statement is confirmed by experimental tests using molecular-replacement, SAD-MAD and ab initio techniques.

This study clarifies why, in the phantom derivative (PhD) approach, randomly created structures can help in refining phases obtained by other methods. For this purpose the joint probability distribution of target, model, ancil and phantom derivative structure factors and its conditional distributions have been studied. Since PhD may use n phantom derivatives, with n ≥ 1, a more general distribution taking into account all the ancil and derivative structure factors has been considered, from which the conditional distribution of the target phase has been derived. The corresponding conclusive formula contains two components. The first is the classical Srinivasan & Ramachandran term, relating the phases of the target structure with the model phases. The second arises from the combination of two correlations: that between model and derivative (the first is a component of the second) and that between derivative and target. The second component mathematically codifies the information on the target phase arising from model and derivative electron-density maps. The result is new, and explains why a random structure, uncorrelated with the target structure, adds useful information on the target phases, provided a model structure is known. Some experimental tests aimed at checking if the second component really provides information on ϕ (the target phase) were performed; the favourable results confirm the correctness of the theoretical calculations and of the corresponding analysis.

The efficient multipurpose figure of merit MPF has been defined and characterized. It may be very helpful in phasing procedures. Indeed, it might be used for establishing the centric or acentric nature of an unknown structure, for identifying the presence of some pseudotranslational symmetry, for recognizing the correct solution in multisolution approaches and for estimating the quality of structure models as they become available during the phasing process. Thus, phase improvement or deterioration may be monitored and useless models may be discarded to save computing time. It is also shown that MPF may be applied in different phasing approaches, no matter if ab initio or non ab initio.

The Phantom Derivative (PhD) method [Giacovazzo (2015), Acta Cryst. A71, 483-512] has recently been described for ab initio and non-ab initio phasing. It is based on the random generation of structures with the same unit cell and the same space group as the target structure (called ancil structures), which are used to create derivatives devoid of experimental diffraction amplitudes. In this paper, the non-ab initio variant of the method was checked using phase sets obtained by molecular-replacement techniques as a starting point for phase extension and refinement. It has been shown that application of PhD is able to extend and refine phases in a way that is competitive with other electron-density modification techniques.

The difference electron density has recently been revisited via the method of joint probability distribution functions [Burla et al. (2010). Acta Cryst. A 66, 347-361]. New Fourier coefficients were devised which were the basis of a new ab initio method for the solution of the phase problem (i.e. VLD, vive la difference). In this paper we study the joint probability distribution functions P(F, F(p), F(Q)), where F(Q) is the structure factor corresponding to the ideal hybrid Fourier synthesis ρ(Q) = τρ - ωρ(p) and τ and ω are any pair of real numbers. New Fourier coefficients for the calculations of any hybrid synthesis are obtained, and the properties of the corresponding electron-density maps are discussed. The first applications show the correctness of our theoretical approach and suggest possible applications in phasing procedures., (© 2011 International Union of Crystallography)

The resolution parameter σ(A) is currently used for evaluating the degree of similarity between a model and the target structure. Here, quasi-Wilson distributions are used to represent the local statistics of the normalized amplitudes both for the target and for the model structure. The study uses the joint probability distribution approach to provide (i) a description of the statistical properties of the σ(A) parameter; (ii) a deeper insight into the role, for the σ(A) estimate, of the high-order moments of the target and of the model structure-factor distributions; and (iii) new statistical formulas for estimating σ(A). The theoretical results have been checked using test proteins.

The joint probability distribution function P(E, E(p)), where E and E(p) are the normalized structure factors of the target and of a model structure, respectively, is a fundamental tool in crystallographic methods devoted to crystal structure solution. It plays a central role in any attempt for improving phase estimates from a given structure model. More recently the difference electron density rho(q) = rho - rho(p) has been revisited and methods based on its modifications have started to play an important role in combination with electron density modification approaches. In this paper new coefficients for the difference electron density have been obtained by using the joint probability distribution function P(E, E(p), E(q)) and by taking into account both errors in the model and in measurements. The first applications show the correctness of our theoretical approach and the superiority of the new difference Fourier synthesis, particularly when the model is a rough approximation of the target structure. The new and the classic difference syntheses coincide when the model represents the target structure well.

The joint probability distribution function method is applied to multiple-wavelength anomalous dispersion (MAD) powder data. The distributions are calculated by assuming prior knowledge of the scattering intensities at two wavelengths and of the anomalous-scatterer substructure. The method leads to formulas estimating the full structure phases and their reliability. The procedure has been applied to two structures, one unknown and one known; the second was used as a control for the phasing procedure. In spite of the unavoidable peak overlapping in the diffraction pattern, the formulas proved to be very effective. Combined with a new algorithm for phase extension, they enabled the solution of both crystal structures.

Two algorithms are described for limiting data resolution and for predicting the most informative wavelength combinations in MAD techniques. Both have been successfully tested using experimental data from a large set of test structures.

New algorithms for solving ab initio protein crystal structures have been identified and implemented in a modified version of the program SIR2002. They succeed in solving numerous protein structures diffracting at atomic resolution; the solution was also attained when data were cut at 1.4 A resolution. The direct-space refinement procedure of SIR2003-N takes advantage of using the envelope of the protein, calculated during the phasing process from the current phases. The electron-density map is modified by assuming different weights for pixels within the envelope or out of it, so tentatively depleting the intensities of the false peaks. The map is then inverted and the resulting phase sets may improve their values. The new phasing strategy is also based on an optimal use of some figures of merit, one of which may be successfully applied in the early stages of the phasing process: only the most promising trials are submitted to the complete phasing procedure, so saving computing time. SIR2003-N has been successfully applied also in solving some protein structures diffracting at 1.4-1.5 A resolution.

The method of joint probability distribution functions is applied in order to estimate the structure-factor moduli of the anomalous scatterer substructure both in the SAD (single-wavelength anomalous dispersion) and in the MAD (multi-wavelength anomalous dispersion) cases. The experimental data |F(1)(+)|, |F(1)(-)|, ..., |F(n)(+)|, |F(n)(-)| measured at n wavelengths are used simultaneously to estimate the value of |F(oa)| arising from the normal scattering of the anomalous scatterers. A practical procedure is described that, when applied to the experimental diffraction data of several proteins, shows robustness and efficiency.

The [4 + 2] cycloadditions of (E)-2-aryl-1-cyano-1-nitroalkenes 1 with achiral and enantiopure vinyl ethers 2 and 3 carried out in sole water are reported. These reactions occur in a heterogeneous phase under mild conditions and are fast and highly stereoselective. By using (-)-N,N-dicyclohexyl-(1S)-isoborneol-10-sulfonamide as a chiral auxiliary, the cycloadditions are totally asymmetric. The face selectivity is discussed in terms of the shape of the chiral auxiliary and the reactive conformation of vinyl ether.

A new phasing procedure is described working both in direct and in reciprocal space. The procedure has been implemented into the program SIR2000, the heir to SIR99, and it is able routinely to solve ab initio crystal structures of proteins without any use of prior information and any user intervention. The moduli and the flow diagram of SIR2000 are also described and its efficiency tested on several protein diffraction data sets. Success has been attained for crystal structures with up to almost 2000 non-hydrogen atoms in the asymmetric unit and resolution higher than 1.2 A. The phasing process is analysed to provide a better insight into the role of the various steps of the procedure.

The moduli and flow diagram of the program SIR99 are described. New phasing algorithms are proposed working both in direct and in reciprocal space. Their cooperative work is able to solve the structures of both small and large molecules. In particular, small proteins can be solved ab initio without any use of prior information and any user intervention. The efficiency of the various algorithms employed by SIR99 has been tested, and the role of the tangent formula clarified. The user is also provided with some practical information concerning the computer power needed.

The X-ray structures of the isomorphous Mg2+, Ca2+, Mn2+ and Co2+ complexes of ATP have been determined. The metal ions are wrapped in hexa-coordination by the alpha, beta and gamma phosphate groups of two ATP molecules thus blocking the interaction of the metal ions with the adenine base. A second metal ion which is fully hydrated, M(H2O)2+(6), is engaged in a strong hydrogen bond with the gamma phosphate group of ATP and suggests a possible step in facilitating the cleavage between the beta and gamma phosphates in phosphoryl transfer reactions.