The role of software in science: a knowledge graph-based analysis of software mentions in PubMed Central

Science across all disciplines has become increasingly data-driven, leading to additional needs with respect to software for collecting, processing and analysing data. Thus, transparency about software used as part of the scientific process is crucial to understand provenance of individual research data and insights, is a prerequisite for reproducibility and can enable macro-analysis of the evolution of scientific methods over time. However, missing rigor in software citation practices renders the automated detection and disambiguation of software mentions a challenging problem. In this work, we provide a large-scale analysis of software usage and citation practices facilitated through an unprecedented knowledge graph of software mentions and affiliated metadata generated through supervised information extraction models trained on a unique gold standard corpus and applied to more than 3 million scientific articles. Our information extraction approach distinguishes different types of software and mentions, disambiguates mentions and outperforms the state-of-the-art significantly, leading to the most comprehensive corpus of 11.8 M software mentions that are described through a knowledge graph consisting of more than 300 M triples. Our analysis provides insights into the evolution of software usage and citation patterns across various fields, ranks of journals, and impact of publications. Whereas, to the best of our knowledge, this is the most comprehensive analysis of software use and citation at the time, all data and models are shared publicly to facilitate further research into scientific use and citation of software.

The Genetic Polymorphism of TNF-α Associated with the Anti-TNF-α Therapy Used for COVID-19 Patients – Another Possible Approach

Objective: This work aimed of to review the implications of anti-TNF-α therapy in COVID-19 patients associated with the genetic polymorphism (TNF-α polymorphisms in the region-308) of this pertinent cytokine Methodology: Electronic searches were carried out on PUBMED Central, BVS/BIREME, Web of Science and The Cochrane Library with the aid of key-words. Results: Twenty-six articles were collected. Anti-TNF-α therapy was interpreted and evaluated. Conclusions: Although scarce information is available in the current literature, anti- TNF-α therapy seems to be a viable clinical approach for hospitalized COVID-19 patients who do not need oxygen supply. The genetic polymorphisms, although relevant, may be useful for further researched to assess the clinical response in different research groups.

Development Technologies for the Monitoring of Six-Minute Walk Test: A Systematic Review

In the pandemic time, the monitoring of the progression of some diseases is affected and rehabilitation is more complicated. Remote monitoring may help solve this problem using mobile devices that embed low-cost sensors, which can help measure different physical parameters. Many tests can be applied remotely, one of which is the six-minute walk test (6MWT). The 6MWT is a sub-maximal exercise test that assesses aerobic capacity and endurance, allowing early detection of emerging medical conditions with changes. This paper presents a systematic review of the use of sensors to measure the different physical parameters during the performance of 6MWT, focusing on various diseases, sensors, and implemented methodologies. It was performed with the PRISMA methodology, where the search was conducted in different databases, including IEEE Xplore, ACM Digital Library, ScienceDirect, and PubMed Central. After filtering the papers related to 6MWT and sensors, we selected 31 papers that were analyzed in more detail. Our analysis discovered that the measurements of 6MWT are primarily performed with inertial and magnetic sensors. Likewise, most research studies related to this test focus on multiple sclerosis and pulmonary diseases.

Importance of Osseoperception and Tactile Sensibility during Masticatory Function in Different Prosthetic Rehabilitations: A Review

Background and Objectives: Tactile sensibility is an important characteristic for evaluating the masticatory efficiency in different occlusal situations. When a tooth is extracted, relevant proprioceptors from the periodontal ligament get lost; and after the rehabilitation of this abscess by means of oral prosthesis, this sensibility decreases influencing masticatory function. Osseoperception is a sensitive phenomenon associated with dental implants that allows an increased tactile sensibility to those wearing implant prostheses. The purpose of this study was to determine the difference in tactile sensibility values between implant prosthesis, complete dentures, and natural teeth through a review of the available literature. Materials and Methods. In order to dissect the information, 24 articles from 2004 to 2021 were analyzed from MEDLINE, PubMed Central, and Web of Science databases. These articles were directly related to measuring tactile sensibility in different situations and demonstrating the influence of osseoperception in an improved masticatory function. Results: Tactile sensibility in implant prosthesis is slightly reduced compared with natural dentition but presents improved values with regard to complete dentures. Conclusions: Implant prosthesis are more effective during masticatory function than complete dentures, as they present an increased tactile sensibility, very similar to that present in natural dentition. This enhanced sensibility in implants is due to the osseoperception phenomenon.

LESÃO POR PRESSÃO EM PESSOAS IDOSAS: CARACTERIZAÇÃO DA PRODUÇÃO CIENTIFICA DE ENFERMAGEM

A LESÃO POR PRESSÃO OU DANO TISSULAR CONSISTE EM UM EVENTO ADVERSO DE ORIGEM MULTICAUSAL QUE ACOMETE PREDOMINANTEMENTE PESSOAS IDOSAS OU RESTRITAS AO LEITO, RESULTANDO EM MAIORES CUSTOS RELACIONADOS A ASSISTÊNCIA, BEM COMO DOR E DESCONFORTO AOS INDIVÍDUOS ACOMETIDOS. O CUIDADO DE ENFERMAGEM AO IDOSO REQUER CONHECIMENTOS CIENTÍFICOS ESPECÍFICOS PARA A ABORDAGEM AS PESSOAS COM LESÕES. ASSIM, OBJETIVOU-SE CARACTERIZAR A PRODUÇÃO CIENTÍFICA DE ENFERMAGEM SOBRE LESÃO POR PRESSÃO EM PESSOAS IDOSAS. ESTUDO DE REVISÃO DE LITERATURA REALIZADO NO MÊS DE AGOSTO DE 2020, NAS FONTES DE DADOS PERIÓDICOS DA CAPES, LILACS, SCIELO, SCOPUS E PUBMED CENTRAL. OS CRITÉRIOS DE SELEÇÃO ADOTADOS FORAM ARTIGOS PUBLICADOS ENTRE 2018 E 2020, DISPONÍVEIS GRATUITAMENTE E EM TEXTO COMPLETO, SEM RESTRIÇÃO DE IDIOMA. IDENTIFICOU-SE 8.666 ESTUDOS, APÓS A IMPLEMENTAÇÃO DOS CRITÉRIOS DE INCLUSÃO FORAM SELECIONADAS 317 PRODUÇÕES, DAS QUAIS 16 FORAM INCLUÍDAS PARA A SÍNTESE DOS RESULTADOS. A ORIGEM DOS ESTUDOS TEVE PREDOMINÂNCIA NO BRASIL, NAS REGIÕES SUL E NORDESTE. LEVANDO EM CONSIDERAÇÃO O CONTEXTO DA PRODUÇÃO CIENTÍFICA DE ENFERMAGEM, FOI OBSERVADO QUE AS PUBLICAÇÕES SE CONCENTRARAM EM ANOS MAIS RECENTES, EVIDENCIANDO MAIOR ATENÇÃO DOS PESQUISADORES NO QUE TANGE A SAÚDE, SEGURANÇA E BEM-ESTAR DA PESSOA IDOSA, COM ÊNFASE NO APRIMORAMENTO DA PRÁTICA ASSISTENCIAL DE ENFERMAGEM, PAUTADA NA ATENÇÃO SISTEMATIZADA E HUMANIZADA.

Mechanisms and substances involved in clastic activity of root resorptions – literature review

Aim: to research through literature review, the mechanisms involved in the establishment of root resorptions. Mediators such as interleukins, prostaglandins, nitric oxide and systemic calcium available were studied in this review. Methods: On line searches were accomplished by scrutinizing the database available from PUBMED Central, BVS/BIREME. Web of Science, Science Direct, Periodic Portal from CAPES, as well as The Cochrane Library and PROSPERO were also used. The inclusion criteria were articles that described osteoclastic activity involving the hard dental tissues (cement, dentin and enamel). The search acquired 35 articles and excluded other 30. The articles acquired ranged from 1976 up to 2017. Results: the results showed that the combination of the immunologic mediators researched above will be the determinant factors on the establishment of root resorptions. Conclusions: Prostaglandins, Interleukins as well as the systemic calcium available are some of the most important factors for the establishment of root resorptions. Their final outcome, however, depends directly on the quality of injury inflicted over the group of teeth, or single tooth, involved.

Efek Forest Bathing pada Kardiovaskular, Respon Inflamasi, Psikologi, dan Neurologi: Sebuah Tinjauan Sistematis

Terdapat hubungan antara manusia, lingkungan, dan kesehatan. Hidup dekat dengan alam mampu memberikan efek salutogenik pada kesehatan. Forest bathing memberikan kesempatan manusia untuk kembali hidup dekat dengan alam. Sejak dimulai pada tahun 1982, penelitian - penelitian terkait forest bathing banyak di lakukan di Jepang melaporkan berbagai efek fisiologis dan psikologis setelah terapi. Penelitian ini bertujuan untuk mengetahui pengaruh forest bathing pada berbagai sistem tubuh manusia. Tinjauan sistematis dilakukan dengan menggunakan kata kunci “forest bathing”, “forest theraphy”, dan “shinrin-yoku”. Pencarian ini digabungkan dengan operator Boolean AND/OR. Metode pencarian pada basis data elektronik yang dicari termasuk PubMed Central, PubMed, Cohrane Library dan Google Schoolar. Tinjauan sistematis ini melibatkan 23 studi eksperimental. Forest bathing memiliki pengaruh pada kardiovaskular, respon inflamasi, psikologi, dan neurologi. Forest bathing memiliki efek fisiologis dan psikologis sehingga dapat bermanfaat bagi kebutuhan penelitian di masa depan serta berpotensi sebagai terapi komplementer yang dapat di lakukan di Indonesia.

Examining the Effect of the Ratio of Biomedical Domain to General Domain Data in Corpus in Biomedical Literature Mining

Biomedical terms extracted using Word2vec, the most popular word embedding model in recent years, serve as the foundation for various natural language processing (NLP) applications, such as biomedical information retrieval, relation extraction, and recommendation systems. The objective of this study is to examine how changes in the ratio of the biomedical domain to general domain data in the corpus affect the extraction of similar biomedical terms using Word2vec. We downloaded abstracts of 214,892 articles from PubMed Central (PMC) and the 3.9 GB Billion Word (BW) benchmark corpus from the computer science community. The datasets were preprocessed and grouped into 11 corpora based on the ratio of BW to PMC, ranging from 0:10 to 10:0, and then Word2vec models were trained on these corpora. The cosine similarities between the biomedical terms obtained from the Word2vec models were then compared in each model. The results indicated that the models trained with both BW and PMC data outperformed the model trained only with medical data. The similarity between the biomedical terms extracted by the Word2vec model increased when the ratio of the biomedical domain to general domain data was 3:7 to 5:5. This study allows NLP researchers to apply Word2vec based on more information and increase the similarity of extracted biomedical terms to improve their effectiveness in NLP applications, such as biomedical information extraction.

Utilização da cirurgia de mohs no tratamento de neoplasias Malignas não melanocíticas da pele

Objetivo: Averiguar a efetividade da utilização da cirurgia de MOHS no manejo de tumores cutâneos tipo não melanoma em comparação a outros métodos de terapia. Métodos: O estudo consiste em uma revisão sistemática, cuja coleta de artigos ocorreu nas bases de dados MEDLINE, PubMed Central (PMC), LILACS e SciELO, utilizando os termos “Cirurgia de MOHS”, “Câncer de pele”, “Ensaio clínico”, excluindo “melanoma”. Resultados: Do total de 132 artigos identificados, foram considerados elegíveis 11. A análise dos artigos demonstrou que a CMM, comparada a outros métodos, apresentou resultados estéticos melhores, além de menor grau de complicações em tumores recorrentes e um custo/benefício variável com o país onde foi feita operação. A CMM também apresentou menores índices de recorrência em todos os estudos. Conclusão: No geral, a cirurgia de MOHS se mostrou um método terapêutico promissor. No entanto, existem ainda poucos estudos comparativos sobre a eficácia da CMM e os que existem se concentram em poucas regiões do mundo.

COVID-19 surveillance systems in 13 African countries

Background: Surveillance forms the basis for response to disease outbreaks, including COVID-19. Herein, we identified the COVID-19 surveillance systems and the associated challenges in 13 African countries. Methods: We conducted a comprehensive narrative review of peer-reviewed literature published between January 2020 and April 2021 in PubMed, Medline, PubMed Central, and Google Scholar using predetermined search terms. Relevant studies from the search and other data sources on COVID-19 surveillance strategies and associated challenges in 13 African countries (Mauritius, Algeria, Nigeria, Angola, Cote d’Ivoire, the Democratic Republic of the Congo, Ghana, Ethiopia, South Africa, Kenya, Zambia, Tanzania, and Uganda) were identified and reviewed. Results: Our findings revealed that the selected African countries have ramped up COVID-19 surveillance ranging from immediate case notification, virological surveillance, hospital-based surveillance to mortality surveillance among others. Despite this, there exist variations in the level of implementation of the surveillance systems across countries. Integrated Disease Surveillance and Response (IDSR) strategy is also being leveraged in some African countries, but the implementation across countries remains uneven. Our study also revealed various challenges facing surveillance which included shortage of skilled human resources resulting in poor data management, weak health systems, complexities of ethical considerations, diagnostic insufficiency, the burden of co-epidemic surveillance, and geographical barriers, among others. Conclusion: With the variations in the level of implementation of COVID-19 surveillance strategies seen across countries, it is pertinent to ensure proper coordination of the surveillance activities in the African countries and address all the challenges facing COVID-19 surveillance using tailored strategies.