Effect of matrix-modulating enzymes on the cellular uptake of magnetic nanoparticles and on magnetic hyperthermia treatment of pancreatic cancer models in vivo

Magnetic hyperthermia can cause localized thermal eradication of several solid cancers. However, a localized and homogenous deposition of high concentrations of magnetic nanomaterials into the tumor stroma and tumor cells is mostly required. Poorly responsive cancers such as the pancreatic adenocarcinomas are hallmarked by a rigid stroma and poor perfusion to therapeutics and nanomaterials. Hence, approaches that enhance the infiltration of magnetic nanofluids into the tumor stroma convey potentials to improve thermal tumor therapy. We studied the influence of the matrix-modulating enzymes hyaluronidase and collagenase on the uptake of magnetic nanoparticles by pancreatic cancer cells and 3D spheroids thereof, and the overall impact on magnetic heating and cell death. Furthermore, we validated the effect of hyaluronidase on magnetic hyperthermia treatment of heterotopic pancreatic cancer models in mice. Treatment of cultured cells with the enzymes caused higher uptake of magnetic nanoparticles (MNP) as compared to nontreated cells. For example, hyaluronidase caused a 28% increase in iron deposits per cell. Consequently, the thermal doses (cumulative equivalent minutes at 43 ◦C, CEM43) increased by 15–23% as compared to heat dose achieved for cells treated with magnetic hyperthermia without using enzymes. Likewise, heatinduced cell death increased. In in vivo studies, hyaluronidase-enhanced infiltration and distribution of the nanoparticles in the tumors resulted in moderate heating levels (CEM43 of 128 min as compared to 479 min) and a slower, but persistent decrease in tumor volumes over time after treatment, as compared to comparable treatment without hyaluronidase. The results indicate that hyaluronidase, in particular, improves the infiltration of magnetic nanoparticles into pancreatic cancer models, impacts their thermal treatment and cell depletion, and hence, will contribute immensely in the fight against pancreatic and many other adenocarcinomas

An integrated tool-set for Control, Calibration and Characterization of quantum devices applied to superconducting qubits

Efforts to scale-up quantum computation have reached a point where the principal limiting factor is not the number of qubits, but the entangling gate infidelity. However, a highly detailed system characterization required to understand the underlying errors is an arduous process and impractical with increasing chip size. Open-loop optimal control techniques allow for the improvement of gates but are limited by the models they are based on. To rectify the situation, we provide a new integrated open-source tool-set for Control, Calibration and Characterization ($C^3$), capable of open-loop pulse optimization, model-free calibration, model fitting and refinement. We present a methodology to combine these tools to find a quantitatively accurate system model, high-fidelity gates and an approximate error budget, all based on a high-performance, feature-rich simulator. We illustrate our methods using fixed-frequency superconducting qubits for which we learn model parameters to an accuracy of $<1\%$ and derive a coherence limited cross-resonance (CR) gate that achieves $99.6\%$ fidelity without need for calibration.Comment: Source code available at http://q-optimize.org; added reference

Quantum optimal control in quantum technologies. Strategic report on current status, visions and goals for research in Europe

Quantum optimal control, a toolbox for devising and implementing the shapes of external fields that accomplish given tasks in the operation of a quantum device in the best way possible, has evolved into one of the cornerstones for enabling quantum technologies. The last few years have seen a rapid evolution and expansion of the field. We review here recent progress in our understanding of the controllability of open quantum systems and in the development and application of quantum control techniques to quantum technologies. We also address key challenges and sketch a roadmap for future developments.Comment: this is a living document - we welcome feedback and discussio

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

A community effort in SARS-CoV-2 drug discovery.

peer reviewedThe COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against Covid-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments.R-AGR-3826 - COVID19-14715687-CovScreen (01/06/2020 - 31/01/2021) - GLAAB Enric

Structural and functional characterization of Argonaute MID domains

Small RNAs associate with Argonaute (AGO) proteins and guide them to their target nucleic acids via sequence specific interactions. Most small RNAs are formed from a double-stranded precursor. It is critical that the correct strand of this duplex is chosen and associates with an appropriate AGO protein. These processes are referred to as 'strand selection' and 'small RNA sorting' (or 'Argonaute sorting') and they are strongly influenced by the identity of the nucleotide found at the small RNA 5' end. The AGO MID domain, which is the site of interaction with the 5' nucleotide, was proposed to have evolved to preferentially bind certain 5' nucleotides and discriminate others. Therefore, the MID domains are believed to direct small RNA sorting and strand selection via specific interactions with the 5' nucleotide.I have solved the crystal structures of the MID domain from human AGO2 (hAGO2) in complex with nucleoside monophosphates (NMPs), which mimic the 5' nucleotide. The structures identified specific contacts between a rigid loop in the protein, which we termed the 'nucleotide specificity loop', and the nucleotide base of U or A, but not C or G. Dissociation constants from NMR titration experiments are in agreement with the crystal structures and this bias we observed in the hAGO2 MID domain reflects the distribution of nucleotides at the 5' end of miRNAs, which are the main binding partners for this AGO protein. I then characterized nucleotide-specific interactions in the MID domains of Arabidopsis thaliana (at)AGO1, atAGO2, and atAGO5. NMR titration experiments confirmed that these proteins display a bias towards U, A, and C, respectively. Furthermore, crystal structures revealed that the nucleotide specificity loop adopts strikingly different conformations in each of these MID domains. Structures of the atAGO1 MID domain in complex with NMPs revealed the structural basis for specificity of interaction with U or C and not A or G. A number of studies had implicated the MID domain of hAGO2 in miRNA-mediated translational repression via direct interactions with the mRNA 5' cap structure. Using cap-analogues I demonstrated that the interaction is non-specific and not physiologically relevant since it is located in the 5' nucleotide binding site.Les petits ARNs s'associent aux protéines de la famille des Argonautes (AGO) et les guident vers les acides nucléiques ciblés par l'appariement de leurs séquences. La plupart des petits ARNs sont formés à partir d'ARN précurseurs à double brins. Il est critique que le bon brin de ce duplex soit choisi et qu'il s'associe à l'AGO approprié. Ces processus sont appelés 'sélection du brin' et 'triage du petit ARNs' (ou 'triage par l'Argonaute') et sont fortement influencés par l'identité du nucléotide se trouvant à l'extrémité 5' du petit ARN. Le domaine MID de l'AGO, étant le site de liaison avec le nucléotide 5', a été proposé d'avoir évolué afin d'interagir préférablement avec certains nucléotides 5' et de discriminer les autres. Ainsi, on croit que les domaines MID dirigent la sélection du brin et le triage du petit ARN en faisant appel à des interactions spécifiques avec le nucléotide 5'. J'ai résolu les structures cristallines du domaine MID de l'AGO2 humain (hAGO2) en complex avec des nucléosides monophosphates (NMPs), ces derniers imitant le nucléotide 5'. Les structures cristallines ont permis d'identifier des contacts spécifiques entre une boucle rigide de la protéine, appelée la 'boucle de spécificité au nucléotide', et la base des nucléotides U or A, mais pas C ou G. Les constantes de dissociation obtenues par des expériences de titration par RNM sont en accord avec les structures cristallines et la préférence observée chez le domaine MID d'hAGO2 reflète la distribution des nucléotides à l'extrémité 5' des micro (mi)ARNs, qui sont les principaux partenaires de liaison de cette protéine AGO. J'ai ensuite caractérisé les interactions spécifiques au nucléotide des domaines MID d'Arabidopsis thaliana (at)AGO1, atAGO2, et atAGO5. Des expériences de titration par RNM ont confirmé que ces protéines montrent une préférence pour U, A, et C, respectivement. De plus, les structures cristallines ont révélé que les boucles de spécificité au nucléotide adoptent des conformations considérablement différentes dans chacun de ces domaines MID. Les structures du domaine MID d'atAGO1 en complexe avec des NMPs ont révélé le fondement structural de la spécificité de l'interaction avec U ou C, et non A et G.Nombre d'études ont mêlé le domaine MID d'hAGO2 à la répression traductionnelle entremise par les miARNs par des interactions directes avec la coiffe à l'extrémité 5' de l'ARN messager. Par l'utilisation d'analogues de la coiffe, j'ai démontré que l'interaction est non-spécifique et n'est pas physiologiquement pertinente car elle est localisée dans le site de liaison avec le nucléotide 5'