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1.
IUCrJ ; 10(Pt 1): 6-15, 2023 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-36598498

RESUMEN

The Cambridge Structural Database (CSD) is a collection of over one million experimental three-dimensional structures obtained through crystallographic analyses. These structures are determined by crystallographers worldwide and undergo curation and enhancement by scientists at the Cambridge Crystallographic Data Centre (CCDC) prior to their addition to the database. Though the CSD is substantial and contains widespread chemical diversity across organic and metal-organic compounds, it is estimated that a significant proportion of crystal structures determined are not published or shared through the peer-reviewed journal mechanism. To help overcome this, scientists can publish structures directly through the database as CSD Communications and these structural datasets are made publicly available alongside structures associated with scientific articles. CSD Communications contribute to the collective crystallographic knowledge as nearly two thirds are novel structures that are not otherwise available in the scientific literature. The primary benefits of sharing data through CSD Communications include the long-term preservation of scientific data, the strengthening of a widely data-mined world repository (the CSD), and the opportunity for scientists to receive recognition for their work through a formal and citable data publication. All CSD Communications are assigned unique digital object identifiers (DOIs). Contributions as CSD Communications currently comprise about 3.89% of the total CSD entries. Each individual CSD Communication is free to view and retrieve from the CCDC website.


Asunto(s)
Comunicación , Bases de Datos Factuales , Cristalografía
2.
PLoS One ; 18(1): e0272473, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36662691

RESUMEN

The dramatic increase in the number of microbe descriptions in databases, reports, and papers presents a two-fold challenge for accessing the information: integration of heterogeneous data in a standard ontology-based representation and normalization of the textual descriptions by semantic analysis. Recent text mining methods offer powerful ways to extract textual information and generate ontology-based representation. This paper describes the design of the Omnicrobe application that gathers comprehensive information on habitats, phenotypes, and usages of microbes from scientific sources of high interest to the microbiology community. The Omnicrobe database contains around 1 million descriptions of microbe properties. These descriptions are created by analyzing and combining six information sources of various kinds, i.e. biological resource catalogs, sequence databases and scientific literature. The microbe properties are indexed by the Ontobiotope ontology and their taxa are indexed by an extended version of the taxonomy maintained by the National Center for Biotechnology Information. The Omnicrobe application covers all domains of microbiology. With simple or rich ontology-based queries, it provides easy-to-use support in the resolution of scientific questions related to the habitats, phenotypes, and uses of microbes. We illustrate the potential of Omnicrobe with a use case from the food innovation domain.


Asunto(s)
Minería de Datos , Ecosistema , Minería de Datos/métodos , Bases de Datos Factuales , Publicaciones , Fenotipo
3.
PLoS One ; 18(1): e0280597, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36662761

RESUMEN

INTRODUCTION: Hypoglycemia is one of the most frequent metabolic conditions in neonates. Clinical practice guidelines (CPGs) influence clinical practice as high-quality CPGs facilitate the use of evidence in practice. This proposed study aims to systematically identify and appraise CPGs and CPG recommendations (CPGRs) for treating neonatal hypoglycemia (NH). METHODS AND ANALYSIS: We will conduct searches in MEDLINE, EMBASE, CINAHL, Cochrane Library, LILACS (Latin American & Caribbean Health Sciences Literature), and Epistemonikos. Authors will search CPGs-specific databases and grey literature. Two reviewers will independently perform the titles and abstract screening, full-text review, and data extraction. Two appraisers will assess the quality of the CPGs and their recommendations using AGREE II (Appraisal of Guidelines Research and Evaluation) and AGREE-REX (Appraisal of Guidelines Research and Evaluation-Recommendations Excellence) instruments. Scores of ≥ 60% in the rigour of development domain will be considered for defining high-quality with AGREE II tool. CPGRs with scores >60% in the three domains will be used to determine high quality with the AGREE REX tool. We will perform a synthesis of the CPGRs to identify the consistency among the CPGRs and the methodological quality of primary studies that support them. ETHICS AND DISSEMINATION: The results will help us to identify the methodological and quality gaps in the existing CPGs for the treatment of NH. Our findings will be submitted to peer-review journals and presented at academic conferences. Based on the study design, approval from the institutional ethics board is not required for this project. TRIAL REGISTRATIONS: Systematic Review Registration Number (PROSPERO): CRD 42021239921.


Asunto(s)
Proyectos de Investigación , Recién Nacido , Humanos , Bases de Datos Factuales , Región del Caribe , Revisiones Sistemáticas como Asunto
4.
BMC Cancer ; 23(1): 69, 2023 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-36670431

RESUMEN

BACKGROUND: The initial management of patients with sarcoma is a critical issue. We used the nationwide French National Cancer Institute-funded prospective sarcoma database NETSARC to report the management and oncologic outcomes in adolescents and young adults (AYAs) patients with sarcoma at the national level. PATIENTS AND METHODS: NETSARC database gathers regularly monitored and updated data from patients with sarcoma. NETSARC was queried for patients (15-30 years) with sarcoma diagnosed from 2010 to 2017 for whom tumor resection had been performed. We reported management, locoregional recurrence-free survival (LRFS), progression-free survival (PFS), and overall survival (OS) in AYA treated in French reference sarcoma centers (RSC) and outside RSC (non-RSC) and conducted multivariable survival analyses adjusted for classical prognostic factors. RESULTS: Among 3,227 patients aged 15-30 years with sarcoma diagnosed between 2010 and 2017, the study included 2,227 patients with surgery data available, among whom 1,290 AYAs had been operated in RSC, and 937 AYAs in non-RSC. Significant differences in compliance to guidelines were observed including pre-treatment biopsy (RSC: 85.9%; non-RSC 48.1%), pre-treatment imaging (RSC: 86.8%; non-RSC: 56.5%) and R0 margins (RSC 57.6%; non-RSC: 20.2%) (p < 0.001). 3y-OS rates were 81.1% (95%CI 78.3-83.6) in AYA in RSC and 82.7% (95%CI 79.4-85.5) in AYA in non-RSC, respectively. Whereas no significant differences in OS was observed in AYAs treated in RSC and in non-RSC, LRFS and PFS were improved in AYAs treated in RSC compared to AYAs treated in non-RSC (Hazard Ratios (HR): 0.58 and 0.83, respectively). CONCLUSIONS: This study highlights the importance for AYA patients with sarcoma to be managed in national sarcoma reference centers involving multidisciplinary medical teams with paediatric and adult oncologists.


Asunto(s)
Sarcoma , Neoplasias de los Tejidos Blandos , Humanos , Adolescente , Adulto Joven , Niño , Estudios Prospectivos , Sarcoma/diagnóstico , Sarcoma/cirugía , Neoplasias de los Tejidos Blandos/cirugía , Bases de Datos Factuales , Supervivencia sin Progresión
5.
Nucleic Acids Res ; 51(D1): D621-D628, 2023 01 06.
Artículo en Inglés | MEDLINE | ID: mdl-36624664

RESUMEN

Quantitative activity and species source data of natural products (NPs) are important for drug discovery, medicinal plant research, and microbial investigations. Activity values of NPs against specific targets are useful for discovering targeted therapeutic agents and investigating the mechanism of medicinal plants. Composition/concentration values of NPs in individual species facilitate the assessments and investigations of the therapeutic quality of herbs and phenotypes of microbes. Here, we describe an update of the NPASS natural product activity and species source database previously featured in NAR. This update includes: (i) new data of ∼95 000 records of the composition/concentration values of ∼1 490 NPs/NP clusters in ∼390 species, (ii) extended data of activity values of ∼43 200 NPs against ∼7 700 targets (∼40% and ∼32% increase, respectively), (iii) extended data of ∼31 600 species sources of ∼94 400 NPs (∼26% and ∼32% increase, respectively), (iv) new species types of ∼440 co-cultured microbes and ∼420 engineered microbes, (v) new data of ∼66 600 NPs without experimental activity values but with estimated activity profiles from the established chemical similarity tool Chemical Checker, (vi) new data of the computed drug-likeness properties and the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties for all NPs. NPASS update version is freely accessible at http://bidd.group/NPASS.


Asunto(s)
Productos Biológicos , Investigación Biomédica , Bases de Datos Factuales , Descubrimiento de Drogas , Preparaciones Farmacéuticas/aislamiento & purificación
6.
BMC Infect Dis ; 23(1): 51, 2023 Jan 24.
Artículo en Inglés | MEDLINE | ID: mdl-36694131

RESUMEN

BACKGROUND: Around the world, policymakers have clearly communicated that COVID-19 vaccination programs need to be accepted by a large proportion of the population to allow life return to normal. However, according to the Center for Disease Control, about 31% of the United States population had not completed the primary vaccination series as of November 2022. AIMS: The primary aim of this work is to identify the factors associated by American citizens with the decision to be vaccinated against COVID-19. In addition, the proportion of fatal events from COVID-19 vaccinations was estimated and compared with the data in the VAERS database. METHODS: An online survey of COVID-19 health experiences was conducted. Information was collected regarding reasons for and against COVID-19 inoculations, experiences with COVID-19 illness and COVID-19 inoculations by survey respondents and their social circles. Logit regression analyses were carried out to identify factors influencing the likelihood of being vaccinated. RESULTS: A total of 2840 participants completed the survey between December 18 and 23, 2021. 51% (1383 of 2840) of the participants were female and the mean age was 47 (95% CI 46.36-47.64) years. Those who knew someone who experienced a health problem from COVID-19 were more likely to be vaccinated (OR: 1.309, 95% CI 1.094-1.566), while those who knew someone who experienced a health problem following vaccination were less likely to be vaccinated (OR: 0.567, 95% CI 0.461-0.698). 34% (959 of 2840) reported that they knew at least one person who had experienced a significant health problem due to the COVID-19 illness. Similarly, 22% (612 of 2840) of respondents indicated that they knew at least one person who had experienced a severe health problem following COVID-19 vaccination. With these survey data, the total number of fatalities due to COVID-19 inoculation may be as high as 278,000 (95% CI 217,330-332,608) when fatalities that may have occurred regardless of inoculation are removed. CONCLUSION: Knowing someone who reported serious health issues either from COVID-19 or from COVID-19 vaccination are important factors for the decision to get vaccinated. The large difference in the possible number of fatalities due to COVID-19 vaccination that emerges from this survey and the available governmental data should be further investigated.


Asunto(s)
COVID-19 , Humanos , Femenino , Persona de Mediana Edad , Masculino , COVID-19/epidemiología , COVID-19/prevención & control , Vacunas contra la COVID-19 , Vacunación , Bases de Datos Factuales , Gobierno
7.
J Chem Inf Model ; 63(2): 507-521, 2023 Jan 23.
Artículo en Inglés | MEDLINE | ID: mdl-36594600

RESUMEN

Electrophilicity (E) is one of the most important parameters to understand the reactivity of an organic molecule. Although the theoretical electrophilicity index (ω) has been associated with E in a small homologous series, the use of w to predict E in a structurally heterogeneous set of compounds is not a trivial task. In this study, a robust ensemble model is created using Mayr's database of reactivity parameters. A combination of topological and quantum mechanical descriptors and different machine learning algorithms are employed for the model's development. The predictability of the model is assessed using different statistical parameters, and its validation is examined, including a training/test partition, an applicability domain, and a y-scrambling test. The global ensemble model presents a Q5-fold2 of 0.909 and a Qext2 of 0.912, demonstrating an excellent predictability performance of E values and showing that w is not a good descriptor for the prediction of E, especially for the case of neutral compounds. ElectroPredictor, a noncommercial Python application (https://github.com/mmoreno1/ElectroPredictor), is developed to predict E. QM9, a well-known large dataset containing 133885 neutral molecules, is used to perform a virtual screening (94.0% coverage). Finally, the 10 most electrophilic molecules are analyzed as possible new Mayr's electrophiles, which have not yet been experimentally tested. This study confirms the necessity to build an ensemble model using nonlinear machine learning algorithms, topographic descriptors, and separating molecules into charged and neutral compounds to predict E with precision.


Asunto(s)
Algoritmos , Aprendizaje Automático , Bases de Datos Factuales
8.
PLoS One ; 18(1): e0280016, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36696394

RESUMEN

The aim of this study is to reveal a robust correlation between the amount of attention international journalism devotes to scientific papers and the amount of attention scientific journals devote to the respective topics. Using a Mainstream-Media-Score (MSM) ≥ 100 (which we regard as an indicator for news media attention) from the altmetrics provider Altmetric, we link 983 research articles with 185,166 thematically similar articles from the PubMed database (which we use to operationalize attention from scientific journals). The method we use is to test whether there is a concomitant increase in scientific attention after a research article has received popular media coverage. To do so, we compare the quotient of the number of thematically similar articles published in scientific journals during the period before and after the publication of an MSM ≥ 100 article. Our main result shows that in 59 percent of cases, more thematically similar articles were published in scientific journals after a scientific paper received noteworthy news media coverage than before (p < 0.01). In this context, we neither found significant differences between various types of scientific journal (p = 0.3) nor between scientific papers that were originally published in renowned opinion-leading journals or in less renowned, non-opinion-leading journals (p = 0.1). Our findings indicate a robust correlation between the choice of topics in the mass media and in research. However, our study cannot clarify whether this correlation occurs because researchers and/or scientific journals are oriented towards public relevance (publicity effect) or whether the correlation is due to the parallelism of relevance attributions in quality journalism and research (earmark hypothesis). We infer that topics of social relevance are (more) likely to be picked up by popular media as well as by scientific journals. Altogether, our study contributes new empirical findings to the relationship between topic selection in journalism and in research.


Asunto(s)
Publicaciones Periódicas como Asunto , Medios de Comunicación Sociales , Factor de Impacto de la Revista , Bibliometría , Medios de Comunicación de Masas , Bases de Datos Factuales
9.
Anticancer Res ; 43(2): 883-891, 2023 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-36697083

RESUMEN

BACKGROUND/AIM: Anemia is one of the dose-limiting toxicities of olaparib. A global randomized controlled trial confirmed that anemia occurrence in Japanese was relatively high. The factors related to anemia in different nationalities remain unknown. Therefore, this study investigated the factors of olaparib-related anemia in real-world settings using an adverse event reporting system database. PATIENTS AND METHODS: We used data from FDA Adverse Events Reporting System (FAERS) and Japanese Adverse Drug Event Report database (JADER) between 2018 and 2021. FAERS reports from Japan were collected to conduct subgroup analysis, which was defined as FAERS-Japan. The endpoint was the occurrence of olaparib-related anemia. Disproportionality analysis was conducted to calculate reporting odds ratio (ROR), with a confidence interval of 95%. Adjusted ROR (aROR) was calculated to control for sex differences. RESULTS: In FAERS and JADER, the daily olaparib dose per body weight (DPBW) ≥12 mg/kg was associated with anemia occurrence [aROR; FAERS, 4.483 (3.009-6.680), p<0.001, FAERS-Japan, 1.834 (1.091-3.063), p=0.009, and JADER, 1.628 (1.039-2.551), p=0.034]. Furthermore, FAERS reports confirmed that females with body weight <50 kg, reports from Japan, concomitant use of drugs causing vitamin B12 deficiency, and previous platinum treatment history were associated with olaparib-related anemia. FAERS-Japan also showed that body weight <50 kg and previous platinum treatment history were associated with anemia occurrence. CONCLUSION: High DPBW constitutes a significant risk of olaparib-related anemia. In addition, information on co-administration of drugs causing vitamin B12 deficiency and previous platinum treatment history is also important for the evaluation of the risk of olaparib-related anemia.


Asunto(s)
Anemia , Efectos Colaterales y Reacciones Adversas Relacionados con Medicamentos , Humanos , Masculino , Femenino , Estados Unidos , Platino (Metal) , Piperazinas/efectos adversos , Bases de Datos Factuales , Anemia/inducido químicamente , Anemia/epidemiología
10.
BMJ Open ; 13(1): e068127, 2023 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-36669842

RESUMEN

OBJECTIVE: Cardiac therapy drugs are widely used in the treatment of heart disease. However, the concern regarding adverse events (AEs) of cardiac therapy drugs have been rising. This study aimed to analyse cardiac therapy drug-related AEs using the Jinan adverse event reporting system (JAERS) database mining and conduct a comprehensive evaluation to provide safe medication information for patients. DESIGN: Retrospective observational study. SETTING: In this study, cardiac therapy drug-related AEs were detected using the JAERS database from January 2000 to March 2022. METHODS: Reports of cardiac therapy drug-related AEs were extracted from JAERS database, and the basic information of patients, reports and common AEs were analysed. Four disproportionality analysis methods, proportional reporting ratio (PRR), reporting odds ratio (ROR), Bayesian Confidence Propagation Neural Network (BCPNN), Medicines and Healthcare products Regulatory Agency (MHRA), were used to detect cardiac therapy drug-related signals. We further checked whether the detected signals exist on drug labels in China and two developed countries, the USA and Japan. RESULTS: In total, 168 314 AEs were reported, of which 4788 were associated with cardiac therapy drugs. Using the PRR, ROR, MHRA and BCPNN method, we detected 52 signals, 52 signals, 33 signals and 43 signals, respectively. Among the 52 signals, 14 were not included on the drug labels of China. One (isosorbide mononitrate-head bilges) was not included on the drug labels of the three countries. CONCLUSION: We identified 14 new cardiac therapy drug signals that did not appear on drug labels in China and 1 new signal that did not appear on drug labels in 3 counties. A causal link between cardiac therapy drugs and AEs should be evaluated in further studies.


Asunto(s)
Sistemas de Registro de Reacción Adversa a Medicamentos , Efectos Colaterales y Reacciones Adversas Relacionados con Medicamentos , Humanos , Estados Unidos , Estudios Retrospectivos , Teorema de Bayes , Efectos Colaterales y Reacciones Adversas Relacionados con Medicamentos/diagnóstico , Efectos Colaterales y Reacciones Adversas Relacionados con Medicamentos/epidemiología , Minería de Datos , Bases de Datos Factuales , United States Food and Drug Administration
11.
PLoS One ; 18(1): e0279847, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36602984

RESUMEN

INTRODUCTION: In the quest to improve the understanding of climate change impacts on elements of the atmospheric, physical, and life systems, scientists are challenged by the scarcity and uneven distribution of grounded data. Through their long history of interaction with the environment, Indigenous Peoples and local communities have developed complex knowledge systems that allow them to detect impacts of climate change in the local environment. The study protocol presented here is designed 1) to inventory climate change impacts on the atmospheric, physical, and life systems based on local knowledge and 2) to test hypotheses on the global spatial, socioeconomic, and demographic distribution of reported impacts. The protocol has been developed within the framework of a project aiming to bring insights from Indigenous and local knowledge systems to climate research (https://licci.eu). METHODS: Data collection uses a mixed-method approach and relies on the collaboration of a team of 50 trained partners working in sites where people's livelihood directly depend on nature. The data collection protocol consists of two steps. Step 1 includes the collection of secondary data (e.g., spatial and meteorological data) and site contextual information (e.g., village infrastructure, services). Step 1 also includes the use of 1) semi-structured interviews (n = 20-30/site) to document observations of environmental change and their drivers and 2) focus group discussions to identify consensus in the information gathered. Step 2 consist in the application of a household (n from 75 to 125) and individual survey (n from 125 to 175) using a standardized but locally adapted instrument. The survey includes information on 1) individual and household socio-demographic characteristics, 2) direct dependence on nature, 3) household's vulnerability, and 4) individual perceptions of climate change impacts. Survey data are entered in a specifically designed database. EXPECTED RESULTS: This protocol allows the systematic documentation and analysis of the patterned distribution of local indicators of climate change impacts across climate types and livelihood activities. Data collected with this protocol helps fill important gaps on local climate change impacts research and can provide tangible outcomes for local people who will be able to better reflect on how climate change impacts them.


Asunto(s)
Cambio Climático , Pueblos Indígenas , Humanos , Encuestas y Cuestionarios , Grupos de Población , Bases de Datos Factuales
12.
Math Biosci Eng ; 20(1): 76-92, 2023 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-36650758

RESUMEN

BACKGROUND: Non-chromosomal structure maintenance protein condensin complex I subunit H (NCAPH) has been reported to play a regulatory role in a variety of cancers and is associated with tumor poor prognosis. This study aims to explore the potential role of NCAPH with a view to providing insights on pathologic mechanisms. METHODS: The expression of NCAPH in different tumors was explored by The Cancer Genome Atlas (TCGA) and Genotype Tissue Expression (GTEx). The prognostic value of NCAPH was retrieved through GEPIA and Kaplan-Meier Plotter databases. Tumor Immunity Estimation Resource (TIMER) and Single-Sample Gene Set Enrichment Analysis (GSEA) to search for the association of NCAPH with tumor immune infiltration. The cBioPortal and PhosphoSite Plus databases showed NCAPH phosphorylation status in tumors. Gene set enrichment analysis (GSEA) was performed using bioinformatics. RESULTS: Our findings revealed that NCAPH showed high expression levels in a wide range of tumor types, and was strongly correlated with the prognosis of patients. Moreover, a higher phosphorylation level at S59, S67, S76, S190, S222 and T38 site was discovered in head and neck squamous cell carcinoma (HNSC). NCAPH overexpression was positively correlated with the infiltration level of CD8+T cells and myeloid dendritic infiltration in breast cancer and thymoma. CONCLUSIONS: The up-regulation of NCAPH was significantly correlated with the poor prognosis and immune infiltration in pan-cancer, and NCAPH could be served as a potential immunotherapeutic target for cancers.


Asunto(s)
Proteínas de Ciclo Celular , Neoplasias , Proteínas Nucleares , Humanos , Linfocitos T CD8-positivos , Biología Computacional , Bases de Datos Factuales
13.
Brief Bioinform ; 24(1)2023 Jan 19.
Artículo en Inglés | MEDLINE | ID: mdl-36617187

RESUMEN

Differential abundance analysis (DAA) is one central statistical task in microbiome data analysis. A robust and powerful DAA tool can help identify highly confident microbial candidates for further biological validation. Current microbiome studies frequently generate correlated samples from different microbiome sampling schemes such as spatial and temporal sampling. In the past decade, a number of DAA tools for correlated microbiome data (DAA-c) have been proposed. Disturbingly, different DAA-c tools could sometimes produce quite discordant results. To recommend the best practice to the field, we performed the first comprehensive evaluation of existing DAA-c tools using real data-based simulations. Overall, the linear model-based methods LinDA, MaAsLin2 and LDM are more robust than methods based on generalized linear models. The LinDA method is the only method that maintains reasonable performance in the presence of strong compositional effects.


Asunto(s)
Benchmarking , Microbiota , Antivirales , Microbiota/genética , Modelos Lineales , Bases de Datos Factuales , Metagenómica/métodos
14.
J Tradit Chin Med ; 43(1): 14-26, 2023 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-36639991

RESUMEN

OBJECTIVE: To evaluate the available evidence from randomized controlled trials (RCTs) of moxibustion alone for lumbar disc herniation (LDH) treatment. METHODS: A systematic search of 10 databases (until August 30, 2021) was used to identify studies that reported the response rate, visual analogue scale (VAS) score, Japanese Orthopedic Association (JOA) score, and Oswestry Disability Index (ODI) score. Study selection and data extraction were independently performed by two reviewers. Cochrane criteria for risk of bias were used to assess the methodological quality of the trials. The Grading of Recommendations Assessment, Development, and Evaluation Methodology (GRADE) were also used to test the quality of the result evidence. RESULTS: Nineteen RCTs, including 1888 patients, met the inclusion criteria. Five studies showed no difference between moxibustion and acupuncture on response rate [risk ratio () = 1.07, 95%(0.98, 1.16), = 0.11]. Meanwhile, six studies suggested that there is no significant difference between moxibustion and acupuncture on VAS score [mean difference () = -0.43, 95% (-0.91, 0.05), = 0.08]. Eight studies implied that there is no significant difference between moxibustion and acupuncture on JOA score [ = 0.84, 95% (-1.27, 2.96), = 0.44]. Two studies indicated that moxibustion may have equivalent effects for treating LDH in the VAS score in comparison with drug therapy [ = -1.16, 95% (-2.63, 0.31), = 0.12]. The evidence level of results was determined to be very low to low. CONCLUSIONS: Based on the existing evidence, moxibustion may not be suitable for treating LDH alone, but it may be applied as an adjuvant treatment. Furthermore, welldesigned RCTs with high quality and larger samples are still needed to evaluate the efficacy and safety of moxibustion alone for LDH treatment.


Asunto(s)
Desplazamiento del Disco Intervertebral , Moxibustión , Humanos , Terapia por Acupuntura/métodos , Bases de Datos Factuales , Desplazamiento del Disco Intervertebral/terapia , Moxibustión/métodos , Ensayos Clínicos Controlados Aleatorios como Asunto , Vértebras Lumbares
15.
Brief Bioinform ; 24(1)2023 Jan 19.
Artículo en Inglés | MEDLINE | ID: mdl-36642412

RESUMEN

Machine learning-based scoring functions (MLSFs) have become a very favorable alternative to classical scoring functions because of their potential superior screening performance. However, the information of negative data used to construct MLSFs was rarely reported in the literature, and meanwhile the putative inactive molecules recorded in existing databases usually have obvious bias from active molecules. Here we proposed an easy-to-use method named AMLSF that combines active learning using negative molecular selection strategies with MLSF, which can iteratively improve the quality of inactive sets and thus reduce the false positive rate of virtual screening. We chose energy auxiliary terms learning as the MLSF and validated our method on eight targets in the diverse subset of DUD-E. For each target, we screened the IterBioScreen database by AMLSF and compared the screening results with those of the four control models. The results illustrate that the number of active molecules in the top 1000 molecules identified by AMLSF was significantly higher than those identified by the control models. In addition, the free energy calculation results for the top 10 molecules screened out by the AMLSF, null model and control models based on DUD-E also proved that more active molecules can be identified, and the false positive rate can be reduced by AMLSF.


Asunto(s)
Proteínas , Proteínas/metabolismo , Bases de Datos Factuales , Ligandos , Simulación del Acoplamiento Molecular , Unión Proteica
16.
Sci Rep ; 13(1): 1095, 2023 Jan 19.
Artículo en Inglés | MEDLINE | ID: mdl-36658254

RESUMEN

Several challenges prevent extracting knowledge from biomedical resources, including data heterogeneity and the difficulty to obtain and collaborate on data and annotations by medical doctors. Therefore, flexibility in their representation and interconnection is required; it is also essential to be able to interact easily with such data. In recent years, semantic tools have been developed: semantic wikis are collections of wiki pages that can be annotated with properties and so combine flexibility and expressiveness, two desirable aspects when modeling databases, especially in the dynamic biomedical domain. However, semantics and collaborative analysis of biomedical data is still an unsolved challenge. The aim of this work is to create a tool for easing the design and the setup of semantic databases and to give the possibility to enrich them with biostatistical applications. As a side effect, this will also make them reproducible, fostering their application by other research groups. A command-line software has been developed for creating all structures required by Semantic MediaWiki. Besides, a way to expose statistical analyses as R Shiny applications in the interface is provided, along with a facility to export Prolog predicates for reasoning with external tools. The developed software allowed to create a set of biomedical databases for the Neuroscience Department of the University of Padova in a more automated way. They can be extended with additional qualitative and statistical analyses of data, including for instance regressions, geographical distribution of diseases, and clustering. The software is released as open source-code and published under the GPL-3 license at https://github.com/mfalda/tsv2swm .


Asunto(s)
Semántica , Programas Informáticos , Bases de Datos Factuales
17.
J Immunol Res ; 2023: 2975581, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36660246

RESUMEN

Background: Endometriosis is an inflammatory gynecological disease leading to deep pelvic pain, dyspareunia, and infertility. The pathophysiology of endometriosis is complex and depends on a variety of biological processes and pathways. Therefore, there is an urgent need to identify reliable biomarkers for early detection and accurate diagnosis to predict clinical outcomes and aid in the early intervention of endometriosis. We screened transcription factor- (TF-) immune-related gene (IRG) regulatory networks as potential biomarkers to reveal new molecular subgroups for the early diagnosis of endometriosis. Methods: To explore potential therapeutic targets for endometriosis, the Gene Expression Omnibus (GEO), Immunology Database and Analysis Portal (ImmPort), and TF databases were used to obtain data related to the recognition of differentially expressed genes (DEGs), differentially expressed IRGs (DEIRGs), and differentially expressed TFs (DETFs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the DETFs and DEIRGs. Then, DETFs and DEIRGs were further validated in the external datasets of GSE51981 and GSE1230103. Then, we used quantitative real-time polymerase chain reaction (qRT-PCR) to verify the hub genes. Simultaneously, the Pearson correlation analysis and protein-protein interaction (PPI) analyses were used to indicate the potential mechanisms of TF-IRGs at the molecular level and obtain hub IRGs. Finally, the receiver operating characteristic (ROC) curve analysis was used to assess the diagnostic value of the hub IRGs. Results: We screened a total of 94 DETFs and 121 DEIRGs in endometriosis. Most downregulated DETFs showed decreased expression in the endometria of moderate/severe endometriosis patients. The top-ranked upregulated DEIRGs were upregulated in the endometra of infertile women. Functional analysis showed that DETFs and DEIRGs may be involved in the biological behaviors and pathways of endometriosis. The TF-IRG PPI network was successfully constructed. Compared with the control group, high C3, VCAM1, ITGB2, and C3AR1 expression had statistical significance in endometriosis among the hub DEIRGs. They also showed higher sensitivity and specificity by ROC analysis for the diagnosis of endometriosis. Finally, compared with controls, C3 and VCAM1 were highly expressed in endometriosis tissue samples. In addition, they also showed high specificity and sensitivity for diagnosing endometriosis. Conclusion: Overall, we discovered the TF-IRG regulatory network and analyzed 4 hub IRGs that were closely related to endometriosis, which contributes to the diagnosis of endometriosis. Additionally, we verified that DETFs or DEIRGs were associated with the clinicopathological features of endometriosis, and external datasets also confirmed the hub IRGs. Finally, C3 and VCAM1 were highly expressed in endometriosis tissue samples compared with controls and may be potential biomarkers of endometriosis, which are helpful for the early diagnosis of endometriosis.


Asunto(s)
Endometriosis , Infertilidad Femenina , Femenino , Humanos , Endometriosis/diagnóstico , Endometriosis/genética , Biomarcadores , Bases de Datos Factuales , Endometrio
18.
Sensors (Basel) ; 23(2)2023 Jan 04.
Artículo en Inglés | MEDLINE | ID: mdl-36679394

RESUMEN

As one of the most remarkable indicators of physiological health, heart rate (HR) has become an unfailing investigation for researchers. Unlike many existing methods, this article proposes an approach to implement short-time HR estimation from electrocardiography in time series missing patterns. Benefiting from the rapid development of deep learning, we adopted a bidirectional long short-term memory model (Bi-LSTM) and temporal convolution network (TCN) to recover complete heartbeat signals from those with durations are less than one cardiac cycle, and the estimated HR from recovered segment combining the input and the predicted output. We also compared the performance of Bi-LSTM and TCN in PhysioNet dataset. Validating the method over a resting heart rate range of 60-120 bpm in the database without significant arrhythmias and a corresponding range of 30-150 bpm in the database with arrhythmias, we found that networks provide an estimated approach for incomplete signals in a fixed format. These results are consistent with real heartbeats in the normal heartbeat dataset (γ > 0.7, RMSE < 10) and in the arrhythmia database (γ > 0.6, RMSE < 30), verifying that HR could be estimated by models in advance. We also discussed the short-time limits for the predictive model. It could be used for physiological purposes such as mobile sensing in time-constrained scenarios, and providing useful insights for better time series analyses in missing data patterns.


Asunto(s)
Arritmias Cardíacas , Procesamiento de Señales Asistido por Computador , Humanos , Frecuencia Cardíaca/fisiología , Arritmias Cardíacas/diagnóstico , Electrocardiografía/métodos , Bases de Datos Factuales , Algoritmos
19.
Sensors (Basel) ; 23(2)2023 Jan 09.
Artículo en Inglés | MEDLINE | ID: mdl-36679535

RESUMEN

The ripeness of bananas is the most significant factor affecting nutrient composition and demand. Conventionally, cutting and ripeness analysis requires expert knowledge and substantial human intervention, and different studies have been conducted to automate and substantially reduce human effort. Using the Preferred Reporting Items for the Systematic Reviews approach, 1548 studies were extracted from journals and conferences, using different research databases, and 35 were included in the final review for key parameters. These studies suggest the dominance of banana fingers as input data, a sensor camera as the preferred capturing device, and appropriate features, such as color, that can provide better detection. Among six stages of ripeness, the studies employing the four mentioned stages performed better in terms of accuracy and coefficient of determination value. Among all the works for detecting ripeness stages prediction, convolutional neural networks were found to perform sufficiently well with large datasets, whereas conventional artificial neural networks and support vector machines attained better performance for sensor-related data. However, insufficient information on the dataset and capturing device, limited data availability, and exploitation of data augmentation techniques are limitations in existing studies. Thus, effectively addressing these shortcomings and close collaboration with experts to predict the ripeness stages should be pursued.


Asunto(s)
Aprendizaje Profundo , Musa , Humanos , Redes Neurales de la Computación , Bases de Datos Factuales , Nutrientes
20.
PLoS One ; 18(1): e0280718, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36689421

RESUMEN

Heart rate variability (HRV) is a non-invasive measure of autonomic function. The relationship between unselected long-term traumatic injury (TI) and HRV has not been investigated. This systematic review examines the impact of non-acute TI (>7 days post-injury) on standard HRV indices in adults. Four electronic databases (CINAHL, Medline, Scopus, and Web of Science) were searched. The quality of studies, risk of bias (RoB), and quality of evidence (QoE) were assessed using Axis, RoBANS and GRADE, respectively. Using the random-effects model, mean difference (MD) for root mean square of successive differences (RMSSD) and standard deviation of NN-intervals (SDNN), and standardized mean difference (SMD) for Low-frequency (LF): High-Frequency (HF) were pooled in RevMan guided by the heterogeneity score (I2). 2152 records were screened followed by full-text retrieval of 72 studies. 31 studies were assessed on the inclusion and exclusion criteria. Only four studies met the inclusion criteria. Three studies demonstrated a high RoB (mean RoBANS score 14.5±3.31) with a low QoE. TI was associated with a significantly higher resting heart rate. Meta-analysis of three cross-sectional studies demonstrated a statistically significant reduction in RMSSD (MD -8.45ms, 95%CI-12.78, -4.12, p<0.0001) and SDNN (MD -9.93ms, 95%CI-14.82, -5.03, p<0.0001) (low QoE) in participants with TI relative to the uninjured control. The pooled analysis of four studies showed a higher LF: HF ratio among injured versus uninjured (SMD 0.20, 95%CI 0.01-0.39, p<0.04) (very low QoE). Albeit low QoE, non-acute TI is associated with attenuated HRV indicating autonomic imbalance. The findings might explain greater cardiovascular risk following TI. Trial registration PROSPERO registration number: CRD: CRD42021298530.


Asunto(s)
Enfermedades del Sistema Nervioso Autónomo , Enfermedades Vasculares , Humanos , Adulto , Frecuencia Cardíaca/fisiología , Estudios Transversales , Bases de Datos Factuales
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