Tech mining: a revisit and navigation.

This mini-review arrays the pertinent tools and purposes of "Tech Mining" - shorthand for empirical analyses of Science, Technology and Innovation (ST&I) data. The intent is to introduce the range of tools, and show how they can complement each other. Tech Mining aims to generate powerful intelligence to help manage R&D and innovation processes. We offer a 5-part array to help relate the analytical elements. An overview of a case study of Hybrid and Electric Vehicles illustrates the complexities involved and the potential to generate valuable "intel."

COVID-19 knowledge deconstruction and retrieval: an intelligent bibliometric solution.

COVID-19 has been an unprecedented challenge that disruptively reshaped societies and brought a massive amount of novel knowledge to the scientific community. However, as this knowledge flood continues surging, researchers have been disadvantaged by not having access to a platform that can quickly synthesize emerging information and link the new knowledge to the latent knowledge foundation. Aiming to fill this gap, we propose a research framework and develop a dashboard that can assist scientists in identifying, retrieving, and understanding COVID-19 knowledge from the ocean of scholarly articles. Incorporating principal component decomposition (PCD), a knowledge mode-based search approach, and hierarchical topic tree (HTT) analysis, the proposed framework profiles the COVID-19 research landscape, retrieves topic-specific latent knowledge foundation, and visualizes knowledge structures. The regularly updated dashboard presents our research results. Addressing 127,971 COVID-19 research papers from PubMed, the PCD topic analysis identifies 35 research hotspots, along with their inner correlations and fluctuating trends. The HTT result segments the global knowledge landscape of COVID-19 into clinical and public health branches and reveals the deeper exploration of those studies. To supplement this analysis, we additionally built a knowledge model from research papers on the topic of vaccination and fetched 92,286 pre-Covid publications as the latent knowledge foundation for reference. The HTT analysis results on the retrieved papers show multiple relevant biomedical disciplines and four future research topics: monoclonal antibody treatments, vaccinations in diabetic patients, vaccine immunity effectiveness and durability, and vaccination-related allergic sensitization.

The long COVID research literature.

While the COVID-19 pandemic morphs into less malignant forms, the virus has spawned a series of poorly understood, post-infection symptoms with staggering ramifications, i. e., long COVID (LC). This bibliometric study profiles the rapidly growing LC research domain [5,243 articles from PubMed and Web of Science (WoS)] to make its knowledge content more accessible. The article addresses What? Where? Who? and When? questions. A 13-topic Concept Grid presents bottom-up topic clusters. We break out those topics with other data fields, including disciplinary concentrations, topical details, and information on research "players" (countries, institutions, and authors) engaging in those topics. We provide access to results via a Dashboard website. We find a strongly growing, multidisciplinary LC research domain. That domain appears tightly connected based on shared research knowledge. However, we also observe notable concentrations of research activity in different disciplines. Data trends over 3 years of LC research suggest heightened attention to psychological and neurodegenerative symptoms, fatigue, and pulmonary involvement.

Modifiable contributing factors to COVID-19: A comprehensive review.

The devastating complications of coronavirus disease 2019 (COVID-19) result from an individual's dysfunctional immune response following the initial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Multiple toxic stressors and behaviors contribute to underlying immune system dysfunction. SARS-CoV-2 exploits the dysfunctional immune system to trigger a chain of events ultimately leading to COVID-19. The current study identifies eighty immune system dysfunction-enabling toxic stressors and behaviors (hereafter called modifiable contributing factors (CFs)) that also link directly to COVID-19. Each CF is assigned to one of the five categories in the CF taxonomy shown in Section 3.3.: Lifestyle (e.g., diet, substance abuse); Iatrogenic (e.g., drugs, surgery); Biotoxins (e.g., micro-organisms, mycotoxins); Occupational/Environmental (e.g., heavy metals, pesticides); Psychosocial/Socioeconomic (e.g., chronic stress, lower education). The current study shows how each modifiable factor contributes to decreased immune system capability, increased inflammation and coagulation, and increased neural damage and neurodegeneration. It is unclear how real progress can be made in combatting COVID-19 and other similar diseases caused by viral variants without addressing and eliminating these modifiable CFs.

"Big data" driven tech mining and ST&I management: an introduction.

Since the first Global Tech Mining (GTM) conference was held in Atlanta in 2011, the GTM conference has created a platform to connect tech mining researchers, exchange ideas and research progress, and promote collaborations. When it came to its 10th anniversary in 2020, COVID-19 forced the GTM conference into an online format. In tumultuous times for ST&I research activity, the GTM conference sought to focus on several issues: How to better collect and combine multiple "large data" sources? How to analyze these data effectively? And how to utilize these results more powerfully in ST&I management? In this collection, 15 papers are selected after evaluating by the science advisory committee, the guest editor team, and our peer review experts to address the following aspects regarding "tech mining": (1) DATA: Maximizing the potential of traditional and novel data; (2) METHODS: Advancing and integrating methods; (3) APPLICATIONS: Innovative analyses translating to usefulintelligence.

Contributing factors common to COVID­19 and gastrointestinal cancer.

The devastating complications of coronavirus disease 2019 (COVID­19) result from the dysfunctional immune response of an individual following the initial severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) infection. Multiple toxic stressors and behaviors contribute to underlying immune system dysfunction. SARS­CoV­2 exploits the dysfunctional immune system to trigger a chain of events, ultimately leading to COVID­19. The authors have previously identified a number of contributing factors (CFs) common to myriad chronic diseases. Based on these observations, it was hypothesized that there may be a significant overlap between CFs associated with COVID­19 and gastrointestinal cancer (GIC). Thus, in the present study, a streamlined dot­product approach was used initially to identify potential CFs that affect COVID­19 and GIC directly (i.e., the simultaneous occurrence of CFs and disease in the same article). The nascent character of the COVID­19 core literature (~1­year­old) did not allow sufficient time for the direct effects of numerous CFs on COVID­19 to emerge from laboratory experiments and epidemiological studies. Therefore, a literature­related discovery approach was used to augment the COVID­19 core literature­based 'direct impact' CFs with discovery­based 'indirect impact' CFs [CFs were identified in the non­COVID­19 biomedical literature that had the same biomarker impact pattern (e.g., hyperinflammation, hypercoagulation, hypoxia, etc.) as was shown in the COVID­19 literature]. Approximately 2,250 candidate direct impact CFs in common between GIC and COVID­19 were identified, albeit some being variants of the same concept. As commonality proof of concept, 75 potential CFs that appeared promising were selected, and 63 overlapping COVID­19/GIC potential/candidate CFs were validated with biological plausibility. In total, 42 of the 63 were overlapping direct impact COVID­19/GIC CFs, and the remaining 21 were candidate GIC CFs that overlapped with indirect impact COVID­19 CFs. On the whole, the present study demonstrates that COVID­19 and GIC share a number of common risk/CFs, including behaviors and toxic exposures, that impair immune function. A key component of immune system health is the removal of those factors that contribute to immune system dysfunction in the first place. This requires a paradigm shift from traditional Western medicine, which often focuses on treatment, rather than prevention.

Determination of Factors Driving the Genome Editing Field in the CRISPR Era Using Bibliometrics.

Over the past two decades, the discovery of CRISPR-Cas immune systems and the repurposing of their effector nucleases as biotechnological tools have revolutionized genome editing. The corresponding work has been captured by 90,000 authors representing 7,600 affiliations in 126 countries, who have published more than 19,000 papers spanning medicine, agriculture, and biotechnology. Here, we use tech mining and an integrated bibliometric and networks framework to investigate the CRISPR literature over three time periods. The analysis identified seminal papers, leading authors, influential journals, and rising applications and topics interconnected through collaborative networks. A core set of foundational topics gave rise to diverging avenues of research and applications, reflecting a bona fide disruptive emerging technology. This analysis illustrates how bibliometrics can identify key factors, decipher rising trends, and untangle emerging applications and technologies that dynamically shape a morphing field, and provides insights into the trajectory of genome editing.

Common contributing factors to COVID-19 and inflammatory bowel disease.

The devastating complications of coronavirus disease 2019 (COVID-19) result from an individual's dysfunctional immune response following the initial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Multiple toxic stressors and behaviors contribute to underlying immune system dysfunction. SARS-CoV-2 exploits the dysfunctional immune system to trigger a chain of events ultimately leading to COVID-19. We have previously identified many contributing factors (CFs) (representing toxic exposure, lifestyle factors and psychosocial stressors) common to myriad chronic diseases. We hypothesized significant overlap between CFs associated with COVID-19 and inflammatory bowel disease (IBD), because of the strong role immune dysfunction plays in each disease. A streamlined dot-product approach was used to identify potential CFs to COVID-19 and IBD. Of the fifty CFs to COVID-19 that were validated for demonstration purposes, approximately half had direct impact on COVID-19 (the CF and COVID-19 were mentioned in the same record; i.e., CF---→COVID-19), and the other half had indirect impact. The nascent character of the COVID-19 core literature (∼ one year old) did not allow sufficient time for the direct impacts of many CFs on COVID-19 to be identified. Therefore, an immune system dysfunction (ID) literature directly related to the COVID-19 core literature was used to augment the COVID-19 core literature and provide the remaining CFs that impacted COVID-19 indirectly (i.e., CF---→immune system dysfunction---→COVID-19). Approximately 13000 potential CFs for myriad diseases (obtained from government and university toxic substance lists) served as the starting point for the dot-product identification process. These phrases were intersected (dot-product) with phrases extracted from a PubMed-derived IBD core literature, a nascent COVID-19 core literature, and the COVID-19-related immune system dysfunction (ID) core literature to identify common ID/COVID-19 and IBD CFs. Approximately 3000 potential CFs common to both ID and IBD, almost 2300 potential CFs common to ID and COVID-19, and over 1900 potential CFs common to IBD and COVID-19 were identified. As proof of concept, we validated fifty of these ∼3000 overlapping ID/IBD candidate CFs with biologic plausibility. We further validated 24 of the fifty as common CFs in the IBD and nascent COVID-19 core literatures. This significant finding demonstrated that the CFs indirectly related to COVID-19 -- identified with use of the immune system dysfunction literature -- are strong candidates to emerge eventually as CFs directly related to COVID-19. As discussed in the main text, many more CFs common to all these core literatures could be identified and validated. ID and IBD share many common risk/contributing factors, including behaviors and toxic exposures that impair immune function. A key component to immune system health is removal of those factors that contribute to immune system dysfunction in the first place. This requires a paradigm shift from traditional Western medicine, which often focuses on treatment, rather than prevention.

Insecticide resistance management and industry: the origins and evolution of the Insecticide Resistance Action Committee (IRAC) and the mode of action classification scheme.

Insecticide resistance is a long-standing problem affecting the efficacy and utility of crop protection compounds. Insecticide resistance also impacts the ability and willingness of companies around the world to invest in new crop protection compounds and traits. The Insecticide Resistance Action Committee (IRAC) was formed in 1984 to provide a coordinated response by the crop protection industry to the problem of insecticide resistance. Since its inception, participation in IRAC has grown from a few agrochemical companies in Europe and the US to a much larger group of companies with global representation and an active presence (IRAC Country Groups) involving an even wider array of companies in more than 20 countries. The focus of IRAC has also evolved from that of defining and documenting cases of insecticide resistance to a pro-active role in addressing insecticide resistance management (IRM) providing an array of informational and educational tools (videos, posters, pamphlets) on insect pests, bioassay methods, insecticide mode of action and resistance management, all publicly available through its website (https://irac-online.org/). A key tool developed by IRAC is the Insecticide Mode of Action (MoA) Classification Scheme, which has evolved from a relatively simple acaricide classification started in 1998 to the far broader scheme that now includes biologics as well as insecticides and acaricides. A separate MoA Classification Scheme has also been recently developed for nematicides. The IRAC MoA Classification Scheme coupled with expanding use of MoA labeling on insecticide and acaricide product labels provides a straightforward means to implement IRM. An overview of the history of IRAC along with some of its notable accomplishments and future directions are reviewed. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

[Comment] COVID­19 vaccine safety.

In response to the SARS­CoV­2 outbreak, and the resulting COVID­19 pandemic, a global competition to develop an anti­COVID­19 vaccine has ensued. The targeted time frame for initial vaccine deployment is late 2020. The present article examines whether short­term, mid­term, and long­term vaccine safety can be achieved under such an accelerated schedule, given the myriad vaccine­induced mechanisms that have demonstrated adverse effects based on previous clinical trials and laboratory research. It presents scientific evidence of potential pitfalls associated with eliminating critical phase II and III clinical trials, and concludes that there is no substitute currently available for long­term human clinical trials to ensure long­term human safety.

Vaccine- and natural infection-induced mechanisms that could modulate vaccine safety.

A degraded/dysfunctional immune system appears to be the main determinant of serious/fatal reaction to viral infection (for COVID-19, SARS, and influenza alike). There are four major approaches being employed or considered presently to augment or strengthen the immune system, in order to reduce adverse effects of viral exposure. The three approaches that are focused mainly on augmenting the immune system are based on the concept that pandemics/outbreaks can be controlled/prevented while maintaining the immune-degrading lifestyles followed by much of the global population. The fourth approach is based on identifying and introducing measures aimed at strengthening the immune system intrinsically in order to minimize future pandemics/outbreaks. Specifically, the four measures are: 1) restricting exposure to virus; 2) providing reactive/tactical treatments to reduce viral load; 3) developing vaccines to prevent, or at least attenuate, the infection; 4) strengthening the immune system intrinsically, by a) identifying those factors that contribute to degrading the immune system, then eliminating/reducing them as comprehensively, thoroughly, and rapidly as possible, and b) replacing the eliminated factors with immune-strengthening factors. This paper focuses on vaccine safety. A future COVID-19 vaccine appears to be the treatment of choice at the national/international level. Vaccine development has been accelerated to achieve this goal in the relatively near-term, and questions have arisen whether vaccine safety has been/is being/will be compromised in pursuit of a shortened vaccine development time. There are myriad mechanisms related to vaccine-induced, and natural infection-induced, infections that could adversely impact vaccine effectiveness and safety. This paper summarizes many of those mechanisms.

The under-reported role of toxic substance exposures in the COVID-19 pandemic.

Coronavirus disease 2019 (COVID-19) and previous pandemics have been viewed almost exclusively as virology problems, with toxicology problems mostly being ignored. This perspective is not supported by the evolution of COVID-19, where the impact of real-life exposures to multiple toxic stressors degrading the immune system is followed by the SARS-CoV-2 virus exploiting the degraded immune system to trigger a chain of events ultimately leading to COVID-19. This immune system degradation from multiple toxic stressors (chemical, physical, biological, psychosocial stressors) means that attribution of serious consequences from COVID-19 should be made to the virus-toxic stressors nexus, not to any of the nexus constituents in isolation. The leading toxic stressors (identified in this study as contributing to COVID-19) are pervasive, contributing to myriad chronic diseases as well as immune system degradation. They increase the likelihood for comorbidities and mortality associated with COVID-19. For the short-term, tactical/reactive virology-focused treatments are of higher priority than strategic/proactive toxicology-focused treatments, although both could be implemented in parallel to reinforce each other. However, for long-term pandemic prevention, toxicology-based approaches should be given higher priority than virology-based approaches. Since current COVID-19 treatments globally ignore the toxicology component almost completely, only limited benefits can be expected from these treatments.

[Editorial] COVID­19: Post­lockdown guidelines.

Since March, 2020, in response to the COVID­19 pandemic, many countries have been on lockdown (at different levels of severity), restricting many activities and businesses that involve gatherings of large numbers of people in close proximity. Currently (early June, 2020), countries across the globe are in different stages of easing lockdown restrictions. Public policies for behaviors and actions during this transition period vary widely across countries and within country jurisdictions. The present editorial will address potential policies that could minimize resurgence of the present pandemic (the 'second­wave') and reduce the likelihood and severity of similar future pandemics.

Yoga practice in the UK: a cross-sectional survey of motivation, health benefits and behaviours.

OBJECTIVES: Despite the popularity of yoga and evidence of its positive effects on physical and mental health, little is known about yoga practice in the UK. This study investigated the characteristics of people who practise yoga, reasons for initiating and maintaining practice, and perceived impact of yoga on health and well-being. DESIGN, SETTING AND PARTICIPANTS: A cross-sectional online anonymous survey distributed through UK-based yoga organisations, studios and events, through email invites and flyers. 2434 yoga practitioners completed the survey, including 903 yoga teachers: 87% were women, 91% white and 71% degree educated; mean age was 48.7 years. MAIN OUTCOME MEASURES: Perceived impact of yoga on health conditions, health outcomes and injuries. Relationships between yoga practice and measures of health, lifestyle, stress and well-being. RESULTS: In comparison with national population norms, participants reported significantly higher well-being but also higher anxiety; lower perceived stress, body mass index and incidence of obesity, and higher rates of positive health behaviours. 47% reported changing their motivations to practise yoga, with general wellness and fitness key to initial uptake, and stress management and spirituality important to current practice. 16% of participants reported starting yoga to manage a physical or mental health condition. Respondents reported the value of yoga for a wide range of health conditions, most notably for musculoskeletal and mental health conditions. 20.7% reported at least one yoga-related injury over their lifetime. Controlling for demographic factors, frequency of yoga practice accounted for small but significant variance in health-related regression models (p<0.001). CONCLUSION: The findings of this first detailed UK survey were consistent with surveys in other Western countries. Yoga was perceived to have a positive impact on physical and mental health conditions and was linked to positive health behaviours. Further investigation of yoga's role in self-care could inform health-related challenges faced by many countries.

Tracking and Mining the COVID-19 Research Literature.

The unprecedented, explosive growth of the COVID-19 domain presents challenges to researchers to keep up with research knowledge within the domain. This article profiles this research to help make that knowledge more accessible via overviews and novel categorizations. We provide websites offering means for researchers to probe more deeply to address specific questions. We further probe and reassemble COVID-19 topical content to address research issues concerning topical evolution and emphases on tactical vs. strategic approaches to mitigate this pandemic and reduce future viral threats. Data suggest that heightened attention to strategic, immunological factors is warranted. Connecting with and transferring in research knowledge from outside the COVID-19 domain demand a viable COVID-19 knowledge model. This study provides complementary topical categorizations to facilitate such modeling to inform future Literature-Based Discovery endeavors.

Author Correction: Collaborative networks in gene editing.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Breast cancer diagnosis in a specialised breast clinic: Are cancers detected by ultrasound alone less aggressive?

INTRODUCTION: The aim of this study was to determine the relationship between the way breast cancer is diagnosed and its prognostic features. METHODS: We studied new primary invasive and non-invasive breast cancers (670) diagnosed between 2013 and 2015 where detection included at least clinical examination, mammography and breast ultrasound (BUS). The cancers were classified into six Diagnostic Groups according to the results of each modality. RESULTS: Overall, 79% of cancers were positive on mammography, but another 20% were diagnosed on BUS after a negative mammogram. The largest group (37.6% of cases), had all three modalities positive (Group 1). BUS was the only modality positive in 14.6% (Group 4). Mammography alone was positive in 21.2%, of which 73.9% were ductal carcinoma in situ (DCIS). Invasive lobular carcinoma comprised 9.6% of the groups where mammography was positive, but 16.5% of the groups where mammography was negative and BUS positive. Dense breast tissue was more common in the groups where mammography was negative and BUS positive. Invasive cancers comprised 82.7% of Group 4 and 95.2% of Group 1. For those in Group 4, the average size (10.2 mm) and the percentages with lymphovascular invasion (11.1%), lymph node involvement (17.3%) and poor differentiation (12.3%) were less than half the corresponding figures for Group 1 (27.3 mm, 35%, 44%, 44%). CONCLUSION: This study illustrates the complementary benefits of mammography and BUS, especially where breast density is high. Tumours diagnosed by BUS alone had better prognostic features in terms of size, lymphovascular invasion, lymph node status, differentiation and hormone receptors, compared with cancers where all three modalities were positive.

Mixed ductal-lobular carcinomas: evidence for progression from ductal to lobular morphology.

Mixed ductal-lobular carcinomas (MDLs) show both ductal and lobular morphology, and constitute an archetypal example of intratumoural morphological heterogeneity. The mechanisms underlying the coexistence of these different morphological entities are poorly understood, although theories include that these components either represent 'collision' of independent tumours or evolve from a common ancestor. We performed comprehensive clinicopathological analysis of a cohort of 82 MDLs, and found that: (1) MDLs more frequently coexist with ductal carcinoma in situ (DCIS) than with lobular carcinoma in situ (LCIS); (2) the E-cadherin-catenin complex was normal in the ductal component in 77.6% of tumours; and (3) in the lobular component, E-cadherin was almost always aberrantly located in the cytoplasm, in contrast to invasive lobular carcinoma (ILC), where E-cadherin is typically absent. Comparative genomic hybridization and multiregion whole exome sequencing of four representative cases revealed that all morphologically distinct components within an individual case were clonally related. The mutations identified varied between cases; those associated with a common clonal ancestry included BRCA2, TBX3, and TP53, whereas those associated with clonal divergence included CDH1 and ESR1. Together, these data support a model in which separate morphological components of MDLs arise from a common ancestor, and lobular morphology can arise via a ductal pathway of tumour progression. In MDLs that present with LCIS and DCIS, the clonal divergence probably occurs early, and is frequently associated with complete loss of E-cadherin expression, as in ILC, whereas, in the majority of MDLs, which present with DCIS but not LCIS, direct clonal divergence from the ductal to the lobular phenotype occurs late in tumour evolution, and is associated with aberrant expression of E-cadherin. The mechanisms driving the phenotypic change may involve E-cadherin-catenin complex deregulation, but are yet to be fully elucidated, as there is significant intertumoural heterogeneity, and each case may have a unique molecular mechanism. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.