COVID-19 and Airborne Transmission: Science Rejected, Lives Lost. Can Society Do Better?

This is an account that should be heard of an important struggle: the struggle of a large group of experts who came together at the beginning of the Covid-19 pandemic to warn the world about the risk of airborne transmission and the consequences of ignoring it. We alerted the World Health Organization (WHO) about the potential significance of the airborne transmission of SARS-CoV-2 and the urgent need to control it, but our concerns were dismissed. Here we describe how this happened and the consequences. We hope that by reporting this story, we can raise awareness of the importance of interdisciplinary collaboration and the need to be open to new evidence, and to prevent it from happening again. Acknowledgement of an issue and the emergence of new evidence related to it, is the first necessary step towards finding effective mitigation solutions.

Ventilation strategies to reduce airborne transmission of viruses in classrooms: A systematic review of scientific literature

The recent pandemic due to SARS-CoV-2 has brought to light the need for strategies to mitigate contagion between human beings. Apart from hygiene measures and social distancing, air ventilation highly prevents airborne transmission within enclosed spaces. Among others, educational environments become critical in strategic planning to control the spread of pathogens and viruses amongst the population, mainly in cold conditions. In the event of a virus outbreak - such as COVID or influenza - many school classrooms still lack the means to guarantee secure and healthy environments. The present review examines school contexts that implement air ventilation strategies to reduce the risk of contagion between students. The analysed articles present past experiences that use either natural or mechanical systems assessed through mathematical models, numerical models, or full-scale experiments. For naturally ventilated classrooms, the studies highlight the importance of the architectural design of educational spaces and propose strategies for aeration control such as CO₂-based control and risk-infection control. When it comes to implementing mechanical ventilation in classrooms, different systems with different airflow patterns are assessed based on their ability to remove airborne pathogens considering parameters like the age of air and the generation of airflow streamlines. Moreover, studies report that programmed mechanical ventilation systems can reduce risk-infection during pandemic events. In addition to providing a systematic picture of scientific studies in the field, the findings of this review can be a valuable reference for school administrators and policymakers to implement the best strategies in their classroom settings towards reducing infection risks.

Quantifying geographical accessibility to cancer clinical trials in different income landscapes

Background

Clinical trials are increasingly perceived as a therapeutic opportunity for cancer patients. Favoring their concentration in few high-expertise academic centers maximizes quality of data collection but poses an issue of access equality. Analytical tools to quantify trial accessibility are needed to rationalize resources.

Materials and methods

We constructed a distance-based accessibility index (dAI) using publicly available data on demographics, cancer incidence and trials. Multiple strategies were applied to mitigate or quantify clear sources of bias: reporting biases by text mining multiple registries; reliability of simple geographical distance by comparison with high-quality travel cost data for Italy; index inflation due to highly heterogeneous cancer incidence by log-transformation. We studied inequalities by Gini index and time trend significance by Mann–Kendall test. We simulated different resource allocation models in representative countries and identified locations where new studies would maximally improve the national index.

Results

The dAI approximated well a more realistic but not widely applicable travel cost-based index. Accessibility was unevenly distributed across and within countries (Gini index ∼0.75), with maximal inequalities in high- and upper-middle-income countries (China, United States, Russian Federation). Over time, accessibility increased but less than the total number of trials, most evidently in upper-middle-income countries. Simulations in representative countries (Italy and Serbia) identified ideal locations able to maximally raise the national index.

Conclusions

Access to clinical trials is highly uneven across and within countries and is not mitigated by simple increase in the number of trials; a rational algorithmic approach can be used to mitigate inequalities.

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Accessibility to cancer clinical trials grew less than total number of trials over time in upper-middle-income countries.

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Accessibility is unevenly distributed, with maximal inequalities in high- and upper-middle-income countries.

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Simulation of resource allocation can identify ideal locations able to raise the national accessibility index.

Combining immunotherapy with an epidrug in squamous cell carcinomas of different locations: rationale and design of the PEVO basket trial

Squamous cell carcinomas (SCCs) are among the most frequent solid tumors in humans. SCCs, related or not to the human papillomavirus, share common molecular features. Immunotherapies, and specifically immune checkpoint inhibitors, have been shown to improve overall survival in multiple cancer types, including SCCs. However, only a minority of patients experience a durable response with immunotherapy. Epigenetic modulation plays a major role in escaping tumor immunosurveillance and confers resistance to immune checkpoint inhibitors. Preclinical evidence suggests that modulating the epigenome might improve the efficacy of immunotherapy. We herein review the preclinical and the clinical rationale for combining immunotherapy with an epidrug, and detail the design of PEVOsq, a basket clinical trial combining pembrolizumab with vorinostat, a histone deacetylase inhibitor, in patients with SCCs of different locations. Sequential blood and tumor sampling will be collected in order to identify predictive and pharmacodynamics biomarkers of efficacy of the combination. We also present how clinical and biological data will be managed with the aim to enable the development of a prospective integrative platform to allow secure and controlled access to the project data as well as further exploitations.

How can airborne transmission of COVID-19 indoors be minimised?

During the rapid rise in COVID-19 illnesses and deaths globally, and notwithstanding recommended precautions, questions are voiced about routes of transmission for this pandemic disease. Inhaling small airborne droplets is probable as a third route of infection, in addition to more widely recognized transmission via larger respiratory droplets and direct contact with infected people or contaminated surfaces. While uncertainties remain regarding the relative contributions of the different transmission pathways, we argue that existing evidence is sufficiently strong to warrant engineering controls targeting airborne transmission as part of an overall strategy to limit infection risk indoors. Appropriate building engineering controls include sufficient and effective ventilation, possibly enhanced by particle filtration and air disinfection, avoiding air recirculation and avoiding overcrowding. Often, such measures can be easily implemented and without much cost, but if only they are recognised as significant in contributing to infection control goals. We believe that the use of engineering controls in public buildings, including hospitals, shops, offices, schools, kindergartens, libraries, restaurants, cruise ships, elevators, conference rooms or public transport, in parallel with effective application of other controls (including isolation and quarantine, social distancing and hand hygiene), would be an additional important measure globally to reduce the likelihood of transmission and thereby protect healthcare workers, patients and the general public.

Data on energy consumption and Nearly zero energy buildings (NZEBs) in Europe

This data article refers to the paper "What is a Nearly zero energy building? Overview, implementation and comparison of definitions" (D׳Agostino and Mazzarella, 2019). Data linked with this article allow an overview of the European status in relation to energy consumption and energy savings in buildings. Further data are available in relation to Nearly zero energy buildings (NZEBs).

Data relate to primary and final energy consumption, detailing electricity, gas, oil, coal, heat, and wood consumption from 1994 to 2014 in different countries. Data also relate to the stock of constructions of total, single-family, and multi-family dwellings in Europe. Energy consumption per different energy carriers is also given for the residential sector in European and non-European countries. Energy consumption and savings trends can be visualized. In relation to NZEBs, selected retrofit case studies in Europe are presented. Data include energy consumption, saving percentages, costs, payback period, implemented efficiency measures and renewables. Further data is available about building geometry, costs, envelope, lighting, appliances and systems.

Histological and Ultrastructural Study of the «Cortico-medullary Perivenular Lymphoid Sheaths» of the Mouse Thymus

The present study is concerned with morphological investigations on some special vascular structures of the mouse thymus pertinent to the problem of «cellular traffic» in this organ. Thymuses from 20 normal mice of C3Hf/Gs and C57BL strains, ranging in age from 30 to 50 days, were examined by both light and electron microscopy. At the cortico-medullary junction wide post-capillary venules are present, running parallel to the border between cortex and medulla. They receive at right angles narrow capillaries coming especially from the cortex. The wall of these venules is formed of flattened endothelium, its basement membrane and epithelial reticular cells arranged as adventitial cells. The basement membrane of the endothelium is more or less regularly split in two layers (the inner «vascular» layer and the outer «parenchymal» layer) thus delineating a perivascular space containing one or more rows of lymphoid cells. This space, which has on the whole the character of a cylindrical perivascular channel, accompanies the cortico-medullary venules, although not necessarily along their entire course, and it is recognizable even around the cortical capillaries draining into them. The two layers of the basement membrane are lined on the inner side by the laminar cytoplasm of epithelial reticular cells, often interconnected by desmosomes. The ultrastructural characteristics of the perivascular space do not support the hypothesis of its lymphatic nature, as maintained by other authors. Lymphocytes were found in the process of migrating through either the «parenchymal» or «vascular» layer of the basement membrane. Although the direction of migration cannot be determined by static pictures, some morphological data seem to suggest that lymphocytes, at the level of the cortico-medullary venules, move from the thymic parenchyma towards the perivascular space and from there into the circulating blood stream. It is suggested that the perivascular apparatus be termed «cortico-medullary perivenular lymphoid sheath».

Ultrastructural Characteristics of Kaposi's Sarcoma

The uncertainty which exists on the histogenesis of Kaposi's sarcoma is emphasized and the pertinent literature is briefly reviewed, with particular reference to electron microscopic studies. The results of an investigation on the fine structure in 6 cases of the disease are presented and the characteristic features of the two principal types of cellular elements, endothelial-like and spindle cells, are described. The relevant aspects observed were a clearly outlined basement membrane, vesicles due to pinocytosis, dense granules presumably due to erythrophagocytosis and, most interesting because it had never been recognized before, the presence of cytoplasmic filaments 90–110 Å thick, which show considerable variation in number, distribution, course and direction. These filaments appear to be similar to those that have been shown in endothelial cells and seem structurally identical to leiomyofilaments. In discussing the significance of these findings, a correlation is made with the results of previously reported electron microscopic studies and the hypothesis is postulated that the tissue of Kaposi's sarcoma originates from mesenchymatous elements which may develop into cells either of the endothelial-like and of the leiomuscular-like type.

Cytotoxic drugs for patients with breast cancer in the era of targeted treatment: back to the future?

BACKGROUND

Despite current trend of targeted therapy development, cytotoxic agents are a mainstay of treatment of patients with breast cancer. We reviewed recent advances in cytotoxic therapy for patients with metastatic breast cancer (MBC).

MATERIALS AND METHODS

Medline searches were conducted for English language studies using the term 'MBC' and 'cytotoxic drugs'. The data search was restricted to the period 2000-2011.

RESULTS

Several novel cytotoxic compounds, all microtubule inhibitors, have been approved for clinical use in MBC: (i) nab-paclitaxel, reported to improve tumour response and decrease hypersensitivity reactions in comparison with other taxanes; (ii) ixabepilone, shown to have clinical benefit in taxane- and anthracycline-resistant disease and (iii) eribulin, shown to improve overall survival in heavily pre-treated patients, when compared with best available standard treatment. Agents, such as larotaxel, vinflunine, trabectidin and formulations, including cationic liposomal paclitaxel or paclitaxel poliglumex, are currently under evaluation in phase II/III trials.

CONCLUSION

Toxicity and chemotherapy resistance are still major limitations in the treatment of patients with MBC. Further research into new cytotoxic compounds is needed in order to maximise benefit, whilst minimising toxicity.

Bovine seminal ribonuclease: structure at 1.9 A resolution

The crystal structure of bovine seminal ribonuclease, a homodimeric enzyme closely related to pancreatic ribonuclease, has been refined at a nominal resolution of 1.9 A employing data collected on an electronic area detector. The final model consists of two chains containing 1990 non-H atoms, seven sulfate anions and 113 water molecules per asymmetric unit. The unit-cell parameters are a = 36.5 (1), b = 66.7 (1) and c = 107.5 (2) A, space group P22(1)2(1). The R factor is 0.177 for 16 492 reflections in the resolution range 6.0-1.9 A and the deviations from ideal values of bond lengths and bond angles are 0.020 A and 3.7 degrees, respectively. The molecule is formed by two pancreatic like chains, which have their N-terminal segments interchanged so that each active site is formed by residues from both subunits. The two chains are related by a non-crystallographic twofold symmetry and are covalently linked by two consecutive disulfide bridges, which form an unusual sixteen-membered ring across the dimer interface. The deviations from the molecular symmetry, the hydration shell and the sulfate-binding sites are also discussed in relation to the known structure of the pancreatic enzyme.

Crystal structure of the dimeric unswapped form of bovine seminal ribonuclease

Bovine seminal ribonuclease is a unique case of protein dimorphism, since it exists in two dimeric forms, with different biological and kinetic behavior, which interconvert into one another through three-dimensional swapping. Here we report the crystal structure, at 2.2 A resolution, of the unswapped form of bovine seminal ribonuclease. Besides completing the structural definition of bovine seminal ribonuclease conformational dimorphism, this study provides the structural basis to explain the dependence of the enzyme cooperative effects on its swapping state.

Atomic resolution structures of ribonuclease A at six pH values

The diffraction pattern of protein crystals extending to atomic resolution guarantees a very accurate picture of the molecular structure and enables the study of subtle phenomena related to protein functionality. Six structures of bovine pancreatic ribonuclease at the pH* values 5.2, 5.9, 6.3, 7.1, 8.0 and 8.8 and at resolution limits in the range 1.05-1.15A have been refined. An overall description of the six structures and several aspects, mainly regarding pH-triggered conformational changes, are described here. Since subtle variations were expected, a thorough validation assessment of the six refined models was first carried out. Some stereochemical parameters, such as the N[bond]C(alpha)[bond]C angle and the pyramidalization at the carbonyl C atoms, indicate that the standard target values and their weights typically used in refinement may need revision. A detailed comparison of the six structures has provided experimental evidence on the role of Lys41 in catalysis. Furthermore, insights are given into the structural effects related to the pH-dependent binding of a sulfate anion, which mimics the phosphate group of RNA, in the active site. Finally, the results support a number of thermodynamic and kinetic experimental data concerning the role of the disulfide bridge between Cys65 and Cys72 in the folding of RNase A.

Crystal structure of a collagen-like polypeptide with repeating sequence Pro-Hyp-Gly at 1.4 A resolution: implications for collagen hydration

The use of polypeptide models has proved to be a valuable tool to obtain accurate information on the collagen triple helix. Here we report the high resolution crystal structure of a collagen-like polypeptide with repeating sequence Pro-Hyp-Gly. The structure has been refined to an R(factor) of 0.137 and an R(free) of 0.163 using synchrotron diffraction data extending up to 1.4 A resolution. The polypeptide triple-helical structure binds a large number of water molecules, in contrast with a previous structure determination at lower resolution. The highly hydrated nature of this polypeptide confirms a number of previous studies conducted both in solution and in the crystal state. In addition, neighboring polypeptide triple helices are directly bound in the crystal through Hyp-Hyp hydrogen-bonding interactions. This finding supports the idea that Hyp residues may be important for the assembly of the triple helices in the collagen fibrils and may stabilize the fibrils by mediating direct contacts between neighboring molecules.

Cinchoninium L-tartrate tetrahydrate

The title compound, (3R,4S,8R,9S)-cinchoninium (2R,3R)-tartrate tetrahydrate, C19H23N2O+*C4H5O6-*4H2O, is a hydrated salt of cinchonine. In the cinchoninium cation, the geometry around the quinuclidinic N atom is typical of a protonated N atom, and the bond lengths and angles in the tartrate moiety clearly indicate the mono-ionized form. The relative orientation of the quinoline and quinuclidine systems is that most frequently observed in structures of cinchona salts and corresponds to one of the energy minima calculated for this type of molecule in the gas phase. An extended network of intermolecular hydrogen bonds spreads parallel to the bc plane separating apolar layers.

Preferred proline puckerings in cis and trans peptide groups: implications for collagen stability

The interplay between side-chain and main-chain conformations is a distinctive characteristic of proline residues. Here we report the results of a statistical analysis of proline conformations using a large protein database. In particular, we found that proline residues with the preceding peptide bond in the cis state preferentially adopt a down puckering. Indeed, out of 178 cis proline residues, as many as 145 (81%) are down. By analyzing the 1-4 and 1-5 nonbonding distances between backbone atoms, we provide a structural explanation for the observed trend. The observed correlation between proline puckering and peptide bond conformation suggests a new mechanism to explain the reported shift of the cis-trans equilibrium in proline derivatives. The implications of these results for the current models of collagen stability are also discussed.

Liganded and unliganded forms of Antarctic fish haemoglobins in polyethylene glycol: crystallization of an R-state haemichrome intermediate

Liganded and unliganded forms of two Antarctic fish haemoglobins, from Trematomus newnesi and T. bernacchii, have been crystallized in low-salt media using polyethylene glycol as precipitant. In particular, crystals of air-exposed T. newnesi carbomonoxy haemoglobin were found to be isomorphous to the crystals grown in high-salt media. Preliminary X-ray analysis of the diffraction data revealed that the beta-haem iron of this haemoglobin is in the haemichrome state, with both the proximal and distal histidyl residues linked to the iron. This is the first crystallization of a haemichrome intermediate of a vertebrate haemoglobin.

Experimental evidence for the correlation of bond distances in peptide groups detected in ultrahigh-resolution protein structures

The structural analysis of a deamidated derivative of ribonuclease A, determined at 0.87 A resolution, reveals a highly significant negative correlation between CN and CO bond distances in peptide groups. This trend, i.e. the CO bond lengthens when the CN bond shortens, is also found in seven out of eight protein structures, determined at ultrahigh resolution (<0.95 A). In five of them the linear correlation is statistically significant at the 95% confidence level. The present findings are consistent with the traditional view of amide resonance and, although already found in small peptide structures, they represent a new and important result. In fact, in a protein structure the fine details of the peptide geometry are only marginally affected by the crystal field and they are mostly produced by intramolecular and solvent interactions. The analysis of very high-resolution protein structures can reveal subtle information about local electronic features of proteins which may be critical to folding, function or ligand binding.

Effect of deamidation on folding of ribonuclease A

The folding of ribonuclease A (RNase A) has been extensively studied by characterizing the disulfide containing intermediates using different experimental conditions and analytical techniques. So far, some aspects still remain unclear such as the role of the loop 65-72 in the folding pathway. We have studied the oxidative folding of a RNase A derivative containing at position 67 the substitution Asn --> isoAsp where the local structure of the loop 65-72 has been modified keeping intact the C65-C72 disulfide bond. By comparing the folding behavior of this mutant to that of the wild-type protein, we found that the deamidation significantly decreases the folding rate and alters the folding pathway of RNase A. Results presented here shed light on the role of the 65-72 region in the folding process of RNase A and also clarifies the effect of the deamidation on the folding/unfolding processes. On a more general ground, this study represents the first characterization of the intermediates produced along the folding of a deamidated protein.

Pyramidalization of backbone carbonyl carbon atoms in proteins

The high accuracy of X-ray analyses at atomic resolution is now able to display subtle deformations from standard geometry of building blocks in proteins. From the analysis of nine ultra-high resolution protein structures, we derived the first experimental evidence that a significant pyramidalization at the main-chain carbonyl carbon atom occurs in proteins. Our findings also show that this pyramidalization is related to the main-chain psi torsion angle. The carbonyl carbon atoms of residues that adopt alphaR and extended conformations show a clear preference for positive and negative pyramidalization, respectively. The agreement between our data and those previously obtained from small molecule structures demonstrates that carbon pyramidalization is an intrinsic property of the peptide structure. Although small in magnitude, the pyramidalization is well preserved in the complex folded state of a macromolecular structure that results from the interplay of many different forces. In addition, this property of the peptide group may have interesting implications for the enzymatic reactions involving the carbonyl carbon atoms.

Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2',5')guanosine

Guanine-containing mono- and dinucleotides bind to the active site of ribonuclease A in a nonproductive mode (retro-binding) (Aguilar CF, Thomas PJ, Mills A, Moss DS, Palmer RA. 1992. J Mol Biol 224:265-267). Guanine binds to the highly specific pyrimidine site by forming hydrogen bonds with Thr45 and with the sulfate anion located in the P1 site. To investigate the influence of the anion present in the P1 site on retro-binding, we determined the structure of two new complexes of RNase A with uridylyl(2',5')guanosine obtained by soaking two different forms of pre-grown RNase A crystals. In one case, RNase A was crystallized without removing the sulfate anion strongly bound to the active site; in the other, the protein was first equilibrated with a basic solution to displace the anion from the P1 site. The X-ray structures of the complexes with and without sulfate in P1 were refined using diffraction data up to 1.8 A (R-factor 0.192) and 2.0 A (R-factor 0.178), respectively. The binding mode of the substrate analogue to the protein differs markedly in the two complexes. When the sulfate is located in P1, we observe retro-binding; whereas when the anion is removed from the active site, the uridine is productively bound at the B1 site. In the productive complex, the electron density is very well defined for the uridine moiety, whereas the downstream guanine is disordered. This finding indicates that the interactions of guanine in the B2 site are rather weak and that this site is essentially adenine preferring. In this crystal form, there are two molecules per asymmetric unit, and due to crystal packing, only the active site of one molecule is accessible to the ligand. Thus, in the same crystal we have a ligand-bound and a ligand-free RNase A molecule. The comparison of these two structures furnishes a detailed and reliable picture of the structural alterations induced by the binding of the substrate. These results provide structural information to support the hypotheses on the role of RNase A active site residues that have recently emerged from site-directed mutagenesis studies.