Searching chemical databases in the pre-history of cheminformatics.

This article highlights research from the last century that has provided the basis for the searching techniques that are used in present-day cheminformatics systems, and thus provides an acknowledgement of the contributions made by early pioneers in the field.

Scholarly communication between health informatics and information systems: A bibliometric study.

The challenges of IT adoption in the healthcare sector have generated much interest across a range of research communities, including Information Systems (IS) and Health Informatics (HI). Given their long-standing interest in IT design, development, implementation, and adoption to improve productivity and support organisational transformation, the IS and HI fields are highly correlated in their research interests. Nevertheless, the two fields serve different academic audiences, have different research foci, and theorise IT artifacts differently.

Senescence-induced immune remodeling facilitates metastatic adrenal cancer in a sex-dimorphic manner.

Aging markedly increases cancer risk, yet our mechanistic understanding of how aging influences cancer initiation is limited. Here we demonstrate that the loss of ZNRF3, an inhibitor of Wnt signaling that is frequently mutated in adrenocortical carcinoma, leads to the induction of cellular senescence that remodels the tissue microenvironment and ultimately permits metastatic adrenal cancer in old animals. The effects are sexually dimorphic, with males exhibiting earlier senescence activation and a greater innate immune response, driven in part by androgens, resulting in high myeloid cell accumulation and lower incidence of malignancy.

A bibliometric analysis of the Journal of Molecular Graphics and Modelling: An update.

This paper provides a bibliometric review of the articles published in the Journal of Molecular Graphics and Modelling (formerly the Journal of Molecular Graphics). The journal has grown rapidly since its establishment in 1983, with articles coming from countries throughout the world. It now primarily contains articles describing applications of molecular graphics and modelling in chemical and biological systems, rather than the underlying technology that was the focus of many of the early papers in the journal; however, it is these early, system-based papers that continue to attract by far the largest numbers of citations.

Commentary: the first twelve years of the Journal of chemoinformatics.

This commentary provides an overview of the publications in, and the citations to, the first twelve volumes of the Journal of Cheminformatics, covering the period 2009-2020. The analysis is based on the 622 articles that have appeared in the journal during that time and that have been indexed in the Clarivate Web of Science Core Collection database. It is clear that the journal has established itself as one of the most important publications in the field of cheminformatics: it attracts citations not only from other journals in its specialist field but also from biological and chemical journals more widely, and moreover from journals that are far removed in focus from it but that are still able to benefit from the articles that it publishes.

COVID-19 impact on global maritime mobility.

To prevent the outbreak of the Coronavirus disease (COVID-19), many countries around the world went into lockdown and imposed unprecedented containment measures. These restrictions progressively produced changes to social behavior and global mobility patterns, evidently disrupting social and economic activities. Here, using maritime traffic data collected via a global network of Automatic Identification System (AIS) receivers, we analyze the effects that the COVID-19 pandemic and containment measures had on the shipping industry, which accounts alone for more than 80% of the world trade.

Quickest Detection of COVID-19 Pandemic Onset.

This paper develops an easily-implementable version of Page's CUSUM quickest-detection test, designed to work in certain composite hypothesis scenarios with time-varying data statistics. The decision statistic can be cast in a recursive form and is particularly suited for on-line analysis. By back-testing our approach on publicly-available COVID-19 data we find reliable early warning of infection flare-ups, in fact sufficiently early that the tool may be of use to decision-makers on the timing of restrictive measures that may in the future need to be taken.

Decision support for the quickest detection of critical COVID-19 phases.

During the course of an epidemic, one of the most challenging tasks for authorities is to decide what kind of restrictive measures to introduce and when these should be enforced. In order to take informed decisions in a fully rational manner, the onset of a critical regime, characterized by an exponential growth of the contagion, must be identified as quickly as possible. Providing rigorous quantitative tools to detect such an onset represents an important contribution from the scientific community to proactively support the political decision makers.

The Literature of Chemoinformatics: 1978-2018.

This article presents a study of the literature of chemoinformatics, updating and building upon an analogous bibliometric investigation that was published in 2008. Data on outputs in the field, and citations to those outputs, were obtained by means of topic searches of the . The searches demonstrate that chemoinformatics is by now a well-defined sub-discipline of chemistry, and one that forms an essential part of the chemical educational curriculum.

Adaptive Bayesian Learning and Forecasting of Epidemic Evolution-Data Analysis of the COVID-19 Outbreak.

Since the beginning of 2020, the outbreak of a new strain of Coronavirus has caused hundreds of thousands of deaths and put under heavy pressure the world's most advanced healthcare systems. In order to slow down the spread of the disease, known as COVID-19, and reduce the stress on healthcare structures and intensive care units, many governments have taken drastic and unprecedented measures, such as closure of schools, shops and entire industries, and enforced drastic social distancing regulations, including local and national lockdowns. To effectively address such pandemics in a systematic and informed manner in the future, it is of fundamental importance to develop mathematical models and algorithms to predict the evolution of the spread of the disease to support policy and decision making at the governmental level.

Motivations, understandings, and experiences of open-access mega-journal authors: Results of a large-scale survey.

Open-access mega-journals (OAMJs) are characterized by their large scale, wide scope, open-access (OA) business model, and "soundness-only" peer review. The last of these controversially discounts the novelty, significance, and relevance of submitted articles and assesses only their "soundness." This article reports the results of an international survey of authors ( 11,883), comparing the responses of OAMJ authors with those of other OA and subscription journals, and drawing comparisons between different OAMJs.

Alternative Splicing of the Delta-Opioid Receptor Gene Suggests Existence of New Functional Isoforms.

The delta-opioid receptor (DOPr) participates in mediating the effects of opioid analgesics. However, no selective agonists have entered clinical care despite potential to ameliorate many neurological and psychiatric disorders. In an effort to address the drug development challenges, the functional contribution of receptor isoforms created by alternative splicing of the three-exonic coding gene, OPRD1, has been overlooked.

Cross-Classified Multilevel Modelling of the Effectiveness of Similarity-Based Virtual Screening.

The screening effectiveness of a chemical similarity search depends on a range of factors, including the bioactivity of interest, the types of similarity coefficient and fingerprint that comprise the similarity measure, and the nature of the reference structure that is being searched against a database. This study introduces the use of cross-classified multilevel modelling as a way to investigate the relative importance of these four factors when carrying out similarity searches on the ChEMBL database. Two principal conclusions can be drawn from the analyses: that the fingerprint plays a more important role than the similarity coefficient in determining the effectiveness of a similarity search, and that comparative studies of similarity measures should involve many more reference structures than has been the case in much previous work.

Comparison of Maximum Common Subgraph Isomorphism Algorithms for the Alignment of 2D Chemical Structures.

The identification of the largest substructure in common when two (or more) molecules are overlaid is important for several applications in chemoinformatics, and can be implemented using a maximum common subgraph (MCS) algorithm. Many such algorithms have been reported, and it is important to know which are likely to be the useful in operation. A detailed comparison was hence conducted of the efficiency (in terms of CPU time) and the effectiveness (in terms of the size of the MCS identified) of eleven MCS algorithms, some of which were exact and some of which were approximate in character.

Molecular similarity considerations in the licensing of orphan drugs.

The large costs associated with modern drug discovery mean that governments and regulatory bodies need to provide economic incentives to promote the development of orphan drugs (i.e., medicinal products that are designed to treat rare disease that affect only small numbers of patients).

Open-Access Mega-Journals: A Bibliometric Profile.

In this paper we present the first comprehensive bibliometric analysis of eleven open-access mega-journals (OAMJs). OAMJs are a relatively recent phenomenon, and have been characterised as having four key characteristics: large size; broad disciplinary scope; a Gold-OA business model; and a peer-review policy that seeks to determine only the scientific soundness of the research rather than evaluate the novelty or significance of the work. Our investigation focuses on four key modes of analysis: journal outputs (the number of articles published and changes in output over time); OAMJ author characteristics (nationalities and institutional affiliations); subject areas (the disciplinary scope of OAMJs, and variations in sub-disciplinary output); and citation profiles (the citation distributions of each OAMJ, and the impact of citing journals).

Chemoinformatics at the University of Sheffield 2002-2014.

This paper summarises work in chemoinformatics carried out in the Information School of the University of Sheffield during the period 2002-2014. Research studies are described on fingerprint-based similarity searching, data fusion, applications of reduced graphs and pharmacophore mapping, and on the School's teaching in chemoinformatics.

Special Issue: Chemoinformatics.

Chemoinformatics techniques were originally developed for the construction and searching of large archives of chemical structures but they were soon applied to problems in drug discovery and are now playing an increasingly important role in many additional areas of chemistry. This Special Issue contains seven original research articles and four review articles that provide an introduction to several aspects of this rapidly developing field.

Warm fresh whole blood and thoracic traumain iraq and afghanistan.

Background: Thoracic trauma occurred in 10% of the patients seen at US military treatment facilities in Iraq and Afghanistan and 52% of those patients were transfused. Among those transfused, 281 patients received warm fresh whole blood. A previous report documented improved survival with warm fresh whole blood in patients injured in combat without stratification by injury pattern.

Calculation of substructural analysis weights using a genetic algorithm.

This work describes a genetic algorithm for the calculation of substructural analysis for use in ligand-based virtual screening. The algorithm is simple in concept and effective in operation, with simulated virtual screening experiments using the MDDR and WOMBAT data sets showing it to be superior to substructural analysis weights based on a naive Bayesian classifier.

Maximum common substructure-based data fusion in similarity searching.

Data fusion has been shown to work very well when applied to fingerprint-based similarity searching, yet little is known of its application to maximum common substructure (MCS)-based similarity searching. Two similarity search applications of the MCS will be focused on here. Typically, the number of bonds in the MCS, as well as the bonds in the two molecules being compared, are used in a similarity coefficient.

Associations of medical comorbidity, psychosis, pain, and capacity with psychiatric hospital length of stay in geriatric inpatients with and without dementia.

Background: Geriatric psychiatry hospital beds are a limited resource. Our aim was to determine predictors of hospital length of stay (LOS) for geriatric patients with dementia admitted to inpatient psychiatric beds.

Methods: Admission and discharge data from a large urban mental health center, from 2005 to 2010 inclusive, were retrospectively analyzed.