The next-generation Open Targets Platform: reimagined, redesigned, rebuilt.

The Open Targets Platform (https://platform.opentargets.org/) is an open source resource to systematically assist drug target identification and prioritisation using publicly available data. Since our last update, we have reimagined, redesigned, and rebuilt the Platform in order to streamline data integration and harmonisation, expand the ways in which users can explore the data, and improve the user experience. The gene-disease causal evidence has been enhanced and expanded to better capture disease causality across rare, common, and somatic diseases. For target and drug annotations, we have incorporated new features that help assess target safety and tractability, including genetic constraint, PROTACtability assessments, and AlphaFold structure predictions. We have also introduced new machine learning applications for knowledge extraction from the published literature, clinical trial information, and drug labels. The new technologies and frameworks introduced since the last update will ease the introduction of new features and the creation of separate instances of the Platform adapted to user requirements. Our new Community forum, expanded training materials, and outreach programme support our users in a range of use cases.

Open Targets Platform: supporting systematic drug-target identification and prioritisation.

The Open Targets Platform (https://www.targetvalidation.org/) provides users with a queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery based upon underlying evidence. It is publicly available and the underlying code is open source. Since our last update two years ago, we have had 10 releases to maintain and continuously improve evidence for target-disease relationships from 20 different data sources. In addition, we have integrated new evidence from key datasets, including prioritised targets identified from genome-wide CRISPR knockout screens in 300 cancer models (Project Score), and GWAS/UK BioBank statistical genetic analysis evidence from the Open Targets Genetics Portal. We have evolved our evidence scoring framework to improve target identification. To aid the prioritisation of targets and inform on the potential impact of modulating a given target, we have added evaluation of post-marketing adverse drug reactions and new curated information on target tractability and safety. We have also developed the user interface and backend technologies to improve performance and usability. In this article, we describe the latest enhancements to the Platform, to address the fundamental challenge that developing effective and safe drugs is difficult and expensive.

Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics.

Open Targets Genetics (https://genetics.opentargets.org) is an open-access integrative resource that aggregates human GWAS and functional genomics data including gene expression, protein abundance, chromatin interaction and conformation data from a wide range of cell types and tissues to make robust connections between GWAS-associated loci, variants and likely causal genes. This enables systematic identification and prioritisation of likely causal variants and genes across all published trait-associated loci. In this paper, we describe the public resources we aggregate, the technology and analyses we use, and the functionality that the portal offers. Open Targets Genetics can be searched by variant, gene or study/phenotype. It offers tools that enable users to prioritise causal variants and genes at disease-associated loci and access systematic cross-disease and disease-molecular trait colocalization analysis across 92 cell types and tissues including the eQTL Catalogue. Data visualizations such as Manhattan-like plots, regional plots, credible sets overlap between studies and PheWAS plots enable users to explore GWAS signals in depth. The integrated data is made available through the web portal, for bulk download and via a GraphQL API, and the software is open source. Applications of this integrated data include identification of novel targets for drug discovery and drug repurposing.

Open Targets Platform: new developments and updates two years on.

The Open Targets Platform integrates evidence from genetics, genomics, transcriptomics, drugs, animal models and scientific literature to score and rank target-disease associations for drug target identification. The associations are displayed in an intuitive user interface (https://www.targetvalidation.org), and are available through a REST-API (https://api.opentargets.io/v3/platform/docs/swagger-ui) and a bulk download (https://www.targetvalidation.org/downloads/data). In addition to target-disease associations, we also aggregate and display data at the target and disease levels to aid target prioritisation. Since our first publication two years ago, we have made eight releases, added new data sources for target-disease associations, started including causal genetic variants from non genome-wide targeted arrays, added new target and disease annotations, launched new visualisations and improved existing ones and released a new web tool for batch search of up to 200 targets. We have a new URL for the Open Targets Platform REST-API, new REST endpoints and also removed the need for authorisation for API fair use. Here, we present the latest developments of the Open Targets Platform, expanding the evidence and target-disease associations with new and improved data sources, refining data quality, enhancing website usability, and increasing our user base with our training workshops, user support, social media and bioinformatics forum engagement.

LED Wristbands for Cell-Based Crowd Evacuation: An Adaptive Exit-Choice Guidance System Architecture.

Cell-based crowd evacuation systems provide adaptive or static exit-choice indications that favor a coordinated group dynamic, improving evacuation time and safety. While a great effort has been made to modeling its control logic by assuming an ideal communication and positioning infrastructure, the architectural dimension and the influence of pedestrian positioning uncertainty have been largely overlooked. In our previous research, a cell-based crowd evacuation system (CellEVAC) was proposed that dynamically allocates exit gates to pedestrians in a cell-based pedestrian positioning infrastructure. This system provides optimal exit-choice indications through color-based indications and a control logic module built upon an optimized discrete-choice model. Here, we investigate how location-aware technologies and wearable devices can be used for a realistic deployment of CellEVAC. We consider a simulated real evacuation scenario (Madrid Arena) and propose a system architecture for CellEVAC that includes: a controller node, a radio-controlled light-emitting diode (LED) wristband subsystem, and a cell-node network equipped with active Radio Frequency Identification (RFID) devices. These subsystems coordinate to provide control, display, and positioning capabilities. We quantitatively study the sensitivity of evacuation time and safety to uncertainty in the positioning system. Results showed that CellEVAC was operational within a limited range of positioning uncertainty. Further analyses revealed that reprogramming the control logic module through a simulation optimization process, simulating the positioning system's expected uncertainty level, improved the CellEVAC performance in scenarios with poor positioning systems.

MuTraff: A Smart-City Multi-Map Traffic Routing Framework.

Urban traffic routing is deemed to be a significant challenge in intelligent transportation systems. Existing implementations suffer from several intrinsic issues such as scalability in centralized systems, unnecessary complexity of mechanisms and communication in distributed systems, and lack of privacy. These imply force intensive computational tasks in the traffic control center, continuous communication in real-time with involved stakeholders which require drivers to reveal their location, origin, and destination of their trips. In this paper we present an innovative urban traffic routing framework and reference architecture (multimap traffic control architecture, MuTraff), which is based on the strategical generation and distribution of a set of traffic network maps (traffic weighted multimaps, TWM) to vehicle categories or fleets. Each map in a TWM map set has the same topology but a different distribution of link weights, which are computed by considering policies and constraints that may apply to different vehicle groups. MuTraff delivers a traffic management system (TMS), where a traffic control center generates and distributes maps, while routing computation is performed at the vehicles. We show how this balance between generation, distribution, and routing computation improves scalability, eases communication complexities, and solves former privacy issues. Our study presents case studies in a real city environment for (a) global congestion management using random maps; (b) congestion control on road incidents; and c) emergency fleets routing. We show that MuTraff is a promising foundation framework that is easy to deploy, and is compatible with other existing TMS frameworks.

Evaluation of three-year neurodevelopmental outcomes in infants prenatally exposed to substance use.

INTRODUCTION: Prenatal exposure to substance use is associated with long-term deficits in the neurodevelopment of children. The objective was to investigate the association between cognitive, motor, and language neurodevelopment at three years of age in infants prenatally exposed to substance use. MATERIAL AND METHODS: A prospective matched case-control study was conducted. Biomarkers of fetal exposure were measured in meconium samples. The Bayley Scales of Infant and Toddler Development (BSID-III) were used to calculate neurodevelopment scores. RESULTS: 32 non-exposed and 32 exposed infants were evaluated, of which 16 were exposed to cannabis, 8 to ethanol, 2 to cocaine and 6 to more than one substance. Normal BSID-III scores ≥85 in all domains, were detected in 23 exposed infants to any substance and 29 infants non-exposed. Neurodevelopmental delay was detected in the language domain, specifically in male infants exposed to cannabis. Two infants exposed to cannabis had a severe developmental delay (score<70). Infants exposed to any substance obtained significantly lower total scores than control infants in all domains. Infants exposed to cannabis obtained significantly lower composite scores in the cognitive and motor domains. Infants exposed to more than one substance had lower scores in motor skills. By gender, only males exposed obtained significantly lower composite scores than non-exposed males in the cognitive domain. CONCLUSIONS: The most common and severe neurodevelopmental delay at 36 months was detected in the domain of language in male infants prenatally exposed to cannabis. Neurodevelopmental disorders detected can enable an early intervention and plan therapeutic strategies.

Base-free two-step synthesis of 1,3-diketones and ß-ketoesters from α-diazocarbonyl compounds, trialkylboranes, and aromatic aldehydes.

We describe a convergent, base-free two-step synthesis of 1,3-diketones and ß-ketoesters from α-diazocarbonyl compounds, trialkylboranes, and aromatic aldehydes in a three-component process. The synthetic potential of this protocol was underscored by the synthesis of several symmetrical 1,3,5-triaryl-4-alkyl and 1,3,4,5-tetraryl substituted pyrazoles in a three-step sequence.

An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci.

Genome-wide association studies (GWASs) have identified many variants associated with complex traits, but identifying the causal gene(s) is a major challenge. In the present study, we present an open resource that provides systematic fine mapping and gene prioritization across 133,441 published human GWAS loci. We integrate genetics (GWAS Catalog and UK Biobank) with transcriptomic, proteomic and epigenomic data, including systematic disease-disease and disease-molecular trait colocalization results across 92 cell types and tissues. We identify 729 loci fine mapped to a single-coding causal variant and colocalized with a single gene. We trained a machine-learning model using the fine-mapped genetics and functional genomics data and 445 gold-standard curated GWAS loci to distinguish causal genes from neighboring genes, outperforming a naive distance-based model. Our prioritized genes were enriched for known approved drug targets (odds ratio = 8.1, 95% confidence interval = 5.7, 11.5). These results are publicly available through a web portal ( http://genetics.opentargets.org ), enabling users to easily prioritize genes at disease-associated loci and assess their potential as drug targets.

A proteome-wide genetic investigation identifies several SARS-CoV-2-exploited host targets of clinical relevance.

Background: The virus SARS-CoV-2 can exploit biological vulnerabilities (e.g. host proteins) in susceptible hosts that predispose to the development of severe COVID-19. Methods: To identify host proteins that may contribute to the risk of severe COVID-19, we undertook proteome-wide genetic colocalisation tests, and polygenic (pan) and cis-Mendelian randomisation analyses leveraging publicly available protein and COVID-19 datasets. Results: Our analytic approach identified several known targets (e.g. ABO, OAS1), but also nominated new proteins such as soluble Fas (colocalisation probability >0.9, p=1 × 10-4), implicating Fas-mediated apoptosis as a potential target for COVID-19 risk. The polygenic (pan) and cis-Mendelian randomisation analyses showed consistent associations of genetically predicted ABO protein with several COVID-19 phenotypes. The ABO signal is highly pleiotropic, and a look-up of proteins associated with the ABO signal revealed that the strongest association was with soluble CD209. We demonstrated experimentally that CD209 directly interacts with the spike protein of SARS-CoV-2, suggesting a mechanism that could explain the ABO association with COVID-19. Conclusions: Our work provides a prioritised list of host targets potentially exploited by SARS-CoV-2 and is a precursor for further research on CD209 and FAS as therapeutically tractable targets for COVID-19. Funding: MAK, JSc, JH, AB, DO, MC, EMM, MG, ID were funded by Open Targets. J.Z. and T.R.G were funded by the UK Medical Research Council Integrative Epidemiology Unit (MC_UU_00011/4). JSh and GJW were funded by the Wellcome Trust Grant 206194. This research was funded in part by the Wellcome Trust [Grant 206194]. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.

Individuals who become infected with the virus that causes COVID-19 can experience a wide variety of symptoms. These can range from no symptoms or minor symptoms to severe illness and death. Key demographic factors, such as age, gender and race, are known to affect how susceptible an individual is to infection. However, molecular factors, such as unique gene mutations and gene expression levels can also have a major impact on patient responses by affecting the levels of proteins in the body. Proteins that are too abundant or too scarce may mean the difference between dying from or surviving COVID-19. Identifying the molecular factors in a host that affect how viruses can infect individuals, evade immune defences or trigger severe illness, could provide new ways to treat patients with COVID-19. Such factors are likely to remain constant, even when the virus mutates into new strains. Hence, insights would likely apply across all virus strains, including current strains, such as alpha and delta, and any new strains that may emerge in the future. Using such a 'natural experiment' approach, Karim et al. compared the genetic profiles of over 30,000 COVID-19 patients and a million healthy individuals. Nine proteins were found to have an impact on COVID-19 infection and disease severity. Four proteins were ranked as top priorities for potential treatment targets. One protein, called CD209 (also known as DC-SIGN), is involved in how the virus enters the host cells, and had one of the strongest associations with COVID-19. Two proteins, called IL-6R and FAS, were involved in the immune response and could be responsible for the immune over-activation often seen in severe COVID-19. Finally, one protein, called OAS1, formed part of the body's innate antiviral defence system and appeared to reduce susceptibility to COVID-19. Knowing more about the proteins that influence the severity of COVID-19 opens up new ways to predict, protect and treat patients who may have severe or fatal reactions to infection. Indeed, one of the identified proteins (IL-6R) had already been targeted in recent clinical trials with some encouraging results. Considering CD209 as a potential receptor for the virus could provide another avenue for therapeutics, similar to previously successful approaches to block the virus' known interaction with a receptor protein. Ultimately, this research could supply an entirely new set of treatment options to help combat the COVID-19 pandemic.

Using RFID to enhance security in off-site data storage.

Off-site data storage is one of the most widely used strategies in enterprises of all sizes to improve business continuity. In medium-to-large size enterprises, the off-site data storage processes are usually outsourced to specialized providers. However, outsourcing the storage of critical business information assets raises serious security considerations, some of which are usually either disregarded or incorrectly addressed by service providers. This article reviews these security considerations and presents a radio frequency identification (RFID)-based, off-site, data storage management system specifically designed to address security issues. The system relies on a set of security mechanisms or controls that are arranged in security layers or tiers to balance security requirements with usability and costs. The system has been successfully implemented, deployed and put into production. In addition, an experimental comparison with classical bar-code-based systems is provided, demonstrating the system's benefits in terms of efficiency and failure prevention.

Crystal structure of trans-N,N'-bis-(3,5-di-tert-butyl-2-hy-droxy-phen-yl)oxamide methanol monosolvate.

The here crystallized oxamide was previously characterized as an unsolvated species [Jímenez-Pérez et al. (2000 ▸). J. Organomet. Chem. 614-615, 283-293], and is now reported with methanol as a solvent of crystallization, C30H44N2O4·CH3OH, in a different space group. The introduction of the solvent influences neither the mol-ecular symmetry of the oxamide, which remains centrosymmetric, nor the mol-ecular conformation. However, the unsolvated mol-ecule crystallized as an ordered system, while many parts of the solvated crystal are disordered. The hy-droxy group in the oxamide is disordered over two chemically equivalent positions, with occupancies 0.696 (4):0.304 (4); one tert-butyl group is disordered by rotation about the C-C bond, and was modelled with three sites for each methyl group, each one with occupancy 1/3. Finally, the methanol solvent, which lies on a twofold axis, is disordered by symmetry. The disorder affecting hy-droxy groups and the solvent of crystallization allows the formation of numerous supra-molecular motifs using four hydrogen bonds, with N-H and O-H groups as donors and the oxamide and methanol mol-ecule as acceptors.

Sarcoma de Kaposi en conjuntiva bulbar / Kaposi´s sarcoma in bulbar conjunctiva

Paciente masculino de 29 años de edad, raza blanca, soltero, profesor universitario, con antecedentes de padecer crisis de epilepsia tratado con fenitoína y actualmente controlado, menciona que desde hace aproximadamente 4 semanas comenzó con ojo rojo y molestias oculares del ojo derecho, por lo cual acudió a su área de salud donde fue tratado como cuadro de conjuntivitis. No mostró mejoría alguna, sino empeoramiento del cuadro clínico, y observó un enrojecimiento ocular intenso en el ángulo interno de dicho ojo que se fue extendiendo, acompañado de ligera fotofobia. Por la tórpida evolución del cuadro decidió acudir a nuestra institución por lo cual fue remitido a la Consulta de Oculoplastia. También refirió que desde hacía dos meses había presentado anorexia, dificultad al comer, así como pérdida de peso, por lo cual se decidió comenzar estudio y tratamiento. Se decidió realizar la resección de la masa tumoral en conjuntiva bulbar y se envió para estudio anatomopatológico. El resultado fue compatible con un sarcoma de Kaposi(AU)

A twenty-nine years-old male Caucasian patient, single and university professor, with a history of epilepsy treated with fenitoin and managed at present. He stated that 4 weeks ago approximately, he began feeling ocular discomfort in addition to reddened eye, so he went to his health area where he was treated as a conjunctivitis case. No improvement occurred, the clinical picture worsened and there was intensive ocular reddening in the internal angle of the eye that extended and mild photofobia. Because of the rapid profession of the clinical picture, he decided to go to our institution where he was referred to the Oculoplasty Service. He also said that he had been suffering anorexia, difficulties to eating and weight loss two months ago. It was then decided to start the study and treatment of this case. First, the tumor mass from the bulbar conjunctiva was resected and then sent to anatomical pathological study service. The result was compatible with Kaposi´s sarcoma diagnosis(AU)

3,5-Dimethyl and 3,5-di-tert-butylpyrazolato complexes with alkali metals: monomeric, dimeric, cluster, and 1D chain structures.

The pyrazolato complexes [(Me(2)pz)(THF)Li] (1), [((t)Bu(2)pz)Li](4) (2), [((t)Bu(2)pzH)((t)()Bu(2)pz)Li](2) (2a), [(Me(2)pz)Na] (3), [((t)Bu(2)pz)Na](4), [((t)Bu(2)pz)(6)(OH)Na(7)] (4a), [((t)Bu(2)pz)(18-crown-6)Na] (4b), and [((t)Bu(2)pz)K] (5) were synthesized by metalation reactions between R(2)pzH (R = Me, (t)()Bu) and alkyllithium, elemental sodium, or potassium. All the complexes were characterized by spectroscopic methods and microanalysis, and in addition, the crystal structures of 2, 2a, 3, 4a, 4b, and 5 were obtained by single-crystal X-ray diffraction. They show monomeric, dimeric, cluster, and 1D chain structures in the solid state. Ab initio calculations on the structure and stabilities of the monomeric pzM complexes were performed at the MP2 level of theory showing good agreement with the coordination preferences of the pyrazolato ligand to a particular alkali ion.