A retrospective cohort study of structured abstracts in MEDLINE, 1992-2006.
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ABSTRACT:
SUBMITTER: Ripple AM
PROVIDER: S-EPMC3066587 | biostudies-literature | 2011 Apr
REPOSITORIES: biostudies-literature
Publications
A retrospective cohort study of structured abstracts in MEDLINE, 1992-2006.
Ripple Anna M AM Mork James G JG Knecht Lou S LS Humphreys Betsy L BL
Journal of the Medical Library Association : JMLA 20110401 2
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Project description:Cholera is still a major public health concern in many African countries. In Angola, after a decade of absence, cholera reemerged in 1987, spreading throughout the country until 1996, with outbreaks recurring in a seasonal pattern. In 2006 Angola was hit by one of the most severe outbreaks of the last decade, with ca. 240,000 cases reported. We analyzed 21 clinical strains isolated between 1992 and 2006 from several provinces throughout the country: Benguela, Bengo, Luanda, Cuando Cubango, and Cabinda. We used two multiplex PCR assays to investigate discriminatory mobile genetic elements (MGE) [Integrative Conjugative Elements (ICEs), VSP-II, GI12, GI14, GI15, K, and TLC phages] and we compared the profiles obtained with those of different reference V. cholerae O1 variants (prototypical, altered, and hybrid), responsible for the ongoing 7th pandemic. We also tested the strains for the presence of specific VSP-II variants and for the presence of a genomic island (GI) (WASA-1), correlated with the transmission of seventh pandemic cholera from Africa to South America. Based on the presence/absence of the analyzed genetic elements, five novel profiles were detected in the epidemic strains circulating in the 1990s. The most frequent profiles, F and G, were characterized by the absence of ICEs and the three GIs tested, and the presence of GI WASA-1 and the WASA variant of the VSP-II island. Our results identified unexpected variability within the 1990s epidemic, showing different rearrangements in a dynamic part of the genome not present in the prototypical V. cholerae O1 N16961. Moreover the 2006 strains differed from the current pandemic V. cholerae O1 strain. Taken together, our results highlight the role of horizontal gene transfer (HGT) in diversifying the genetic background of V. cholerae within a single epidemic.
| S-EPMC3842873 | biostudies-literature
Project description:BACKGROUND: Time delays are important factors that are often neglected in gene regulatory network (GRN) inference models. Validating time delays from knowledge bases is a challenge since the vast majority of biological databases do not record temporal information of gene regulations. Biological knowledge and facts on gene regulations are typically extracted from bio-literature with specialized methods that depend on the regulation task. In this paper, we mine evidences for time delays related to the transcriptional regulation of yeast from the PubMed abstracts. RESULTS: Since the vast majority of abstracts lack quantitative time information, we can only collect qualitative evidences of time delays. Specifically, the speed-up or delay in transcriptional regulation rate can provide evidences for time delays (shorter or longer) in GRN. Thus, we focus on deriving events related to rate changes in transcriptional regulation. A corpus of yeast regulation related abstracts was manually labeled with such events. In order to capture these events automatically, we create an ontology of sub-processes that are likely to result in transcription rate changes by combining textual patterns and biological knowledge. We also propose effective feature extraction methods based on the created ontology to identify the direct evidences with specific details of these events. Our ontologies outperform existing state-of-the-art gene regulation ontologies in the automatic rule learning method applied to our corpus. The proposed deterministic ontology rule-based method can achieve comparable performance to the automatic rule learning method based on decision trees. This demonstrates the effectiveness of our ontology in identifying rate-changing events. We also tested the effectiveness of the proposed feature mining methods on detecting direct evidence of events. Experimental results show that the machine learning method on these features achieves an F1-score of 71.43%. CONCLUSIONS: The manually labeled corpus of events relating to rate changes in transcriptional regulation for yeast is available in https://sites.google.com/site/wentingntu/data. The created ontologies summarized both biological causes of rate changes in transcriptional regulation and corresponding positive and negative textual patterns from the corpus. They are demonstrated to be effective in identifying rate-changing events, which shows the benefits of combining textual patterns and biological knowledge on extracting complex biological events.
| S-EPMC4015878 | biostudies-literature
Project description:Chemicals interact with genes in the process of disease development and treatment. Although much biomedical research has been performed to understand relationships among genes, chemicals, and diseases, which have been reported in biomedical articles in Medline, there are few studies that extract disease-gene-chemical relationships from biomedical literature at a PubMed scale. In this study, we propose a deep learning model based on bidirectional long short-term memory to identify the evidence sentences of relationships among genes, chemicals, and diseases from Medline abstracts. Then, we develop the search engine DigChem to enable disease-gene-chemical relationship searches for 35,124 genes, 56,382 chemicals, and 5,675 diseases. We show that the identified relationships are reliable by comparing them with manual curation and existing databases. DigChem is available at http://gcancer.org/digchem.
| S-EPMC6519793 | biostudies-literature
Project description:Diseases are developed by abnormal behavior of genes in biological events such as gene regulation, mutation, phosphorylation, and epigenetics and post-translational modification. Many studies of text mining attempted to identify the relationship between gene and disease by mining the literature, but they did not consider the biological events in which genes show abnormal behaviour in response to diseases. In this study, we propose to identify disease-related genes that are involved in the development of disease through biological events from Medline abstracts. We identified associations between 13,054 genes and 4,494 disease types, which cover more disease-related genes than manually curated databases for all disease types (e.g., Online Mendelian Inheritance in Man) and also than those for specific diseases (e.g., Alzheimer's disease and hypertension). We show that the text mining findings are reliable, as per the PubMed scale, in that the disease-disease relationships inferred from the literature-wide findings are similar to those inferred from manually curated databases in a well-known study. In addition, literature-wide distribution of biological events across disease types reveals different characteristics of disease types.
| S-EPMC5215527 | biostudies-literature
Project description:BackgroundAbomasitis is a syndrome affecting young milk-fed calves. The current veterinary literature describes mainly its necropsy findings.ObjectivesTo describe the clinical presentation, complementary tests, treatments, and case-fatality rate of calves with a clinical diagnosis of abomasitis and to identify potential factors associated with outcome.MethodsObservational retrospective cohort study (2006-2016). Review of the medical records of calves <3 months of age presented with abdominal and abomasal distension for <7 days that were clinically diagnosed with abomasitis at the Faculty of Veterinary Medicine of the Université de Montréal. A follow-up examination was conducted by telephone interview.AnimalsTwenty-three calves clinically diagnosed with abomasitis.ResultsMedian age of presentation was 3 days (range, 0-62 days). The typical duration of the clinical course was <24 hours (15/23). On admission, the 2 most common clinical signs were anorexia (13/14) and positive succussion (13/14). Hyper-l-lactatemia (15/16) and increased γ-glutamyl-transferase activity (13/14) were the most common laboratory abnormalities. Hypoproteinemia (19/22) and a left shift (15/18) of the neutrophils also were observed. The short-term case-fatality rate was 52% (12/23). The clinical diagnosis was confirmed on all necropsied calves. Clostridium spp. and Escherichia coli were the most frequently isolated bacteria. Based on univariate statistical analysis, the surviving calves were significantly (P < .05) less hypothermic, less acidemic, less hyper-l-lactatemic, and had lower serum creatinine concentrations on admission than did the deceased calves.Conclusions and clinical importanceIn our study, abomasitis was associated with a guarded prognosis.
| S-EPMC7096666 | biostudies-literature
Project description:BackgroundCycling is an increasingly important mode of transport for environmental and health reasons. Cycling fatalities in London were previously investigated in 1994 using routinely collected data. Since then, there have been shifts in the modes of transport used, and in transport policies. We sought to replicate the previous work using data on cyclist deaths in London between 1992 and 2006, specifically investigating whether heavy goods vehicles continued to pose a threat.MethodsObservational study based on analysis of time series of police road casualties data, 1992 to 2006, in London, UK. The main outcome measures were cyclists killed in road traffic collisions. Poisson regression and chi-squared test for homogeneity were used to assess time effects. Travel flow data was then used to estimate annual fatality rates per 100,000 cyclists per kilometre.ResultsFrom 1992 to 2006 there was a mean of 16 cycling fatalities per year (range 8-21). 146 deaths (60%) were in inner London and 96 in outer London. There was no evidence for a decline over time (p = 0.7) other than a pronounced dip in 2004 when there were 8 fatalities. Freight vehicles were involved in 103 of 242 (43%) of all incidents and the vehicle was making a left turn in over half of these (53%). The fatality rate ranged from 20.5 deaths in 1992 to 11.1 deaths in 2006 per 100,000 estimated cyclists per kilometre (rate ratio 0.54, 95% confidence interval 0.28 to 1.03).ConclusionsThere is little evidence fatality rates have fallen. Freight vehicles over 3.5 tonnes continue to present a disproportionate threat; they should be removed from urban roads and more appropriate means of delivery of essential goods found.
| S-EPMC2992064 | biostudies-literature
Project description:BackgroundThe objective of this study was to determine the epidemiology of hospitalized pediatric sepsis in Brazil (1992-2006) and to compare mortality caused by sepsis to that caused by other major childhood diseases.Methods and findingsWe performed a retrospective descriptive study of hospital admissions using a government database of all hospital affiliated with the Brazilian health system. We studied all hospitalizations in children from 28 days through 19 years with diagnosis of bacterial sepsis defined by the criteria of the International Classification of Diseases (ICD), (Appendix S1). Based on the data studied from 1992 through 2006, the pediatric hospital mortality rate was 1.23% and there were 556,073 pediatric admissions with bacterial sepsis with a mean mortality rate of 19.9%. There was a case reduction of 67% over 1992-2006 (p<0.001); however, the mortality rate remained unchanged (from 1992-1996, 20.5%; and from 2002-2006, 19.7%). Sepsis-hospital mortality rate was substantially higher than pneumonia (0.5%), HIV (3.3%), diarrhea (0.3%), undernutrition (2.3%), malaria (0.2%) and measles (0.7%). The human development index (HDI) and mortality rates (MR) by region were: North region 0.76 and 21.7%; Northeast region 0.72 and 27.1%; Central-West 0.81 and 23.5%; South region 0.83 and 12.2% and Southeast region 0.82 and 14.8%, respectively.ConclusionsWe concluded that sepsis remains an important health problem in children in Brazil. The institution of universal primary care programs has been associated with substantially reduced sepsis incidence and therefore deaths; however, hospital mortality rates in children with sepsis remain unchanged. Implementation of additional health initiatives to reduce sepsis mortality in hospitalized patients could have great impact on childhood mortality rates in Brazil.
| S-EPMC3108592 | biostudies-literature
Project description:BackgroundRecent evidence indicated that gender disparity in child health is minimal and narrowed over time in India. However, considering the geographical and socio-cultural diversity in India, the gender gap may persist across disaggregated socioeconomic context which may be masked by average level. This study examines the dynamics of gender disparity in childhood immunization across regions, residence, wealth, caste and religion in India during 1992-2006.MethodWe used multi-waves of the cross-sectional data of National Family Health Survey conducted in India between 1992-93 and 2005-06. Gender disparity ratio was used to measure the gender gap in childhood immunization across the selected socioeconomic characteristics. Multinomial regression analysis was used to examine the gender gap after accounting for other covariates.ResultResults indicate that, at aggregate level, gender disparity in full immunization is minimal and has stagnated during the study period. However, gender disparity--disfavouring female children--becomes apparent across the regions, poor households, and religion--particularly among Muslims. Adjusted gender disparity ratio indicates that, full immunization is lower among female than male children of the western region, poor household and among Muslims. Between 1992-93 and 2005-06, the disparity in full immunization had narrowed in the northern region whereas it had, astonishingly, increased in some of the western and southern states of the country.ConclusionOur findings emphasize the need to integrate gender issues in the ongoing immunization programme in India, with particular attention to urban areas, developed states, and to the Muslim community.
| S-EPMC4134226 | biostudies-literature
Project description:BackgroundFor years, Uniform Resource Locator (URL) decay or "link rot" has been a growing concern in the field of biomedical sciences. This paper addresses this issue by examining the status of the URLs published in MEDLINE abstracts, establishing current availability and estimating URL decay in these records from 1994 to 2006. We also reviewed the information provided by the URL to determine if the context that the author cited in writing the paper is the same information presently available in the URL. Lastly, with all the documented recommended methods to preserve URL links, we determined which among them have gained acceptance among authors and publishers.MethodsMEDLINE records from 1994 to 2006 from the National Library of Medicine in Extensible Mark-up Language (XML) format were processed yielding 10,208 URL addresses. These were accessed once daily at random times for 30 days. Titles and abstracts were also searched for the presence of archival tools such as WebCite, Persistent URL (PURL) and Digital Object Identifier (DOI).ResultsResults showed that the average URL length ranged from 13 to 425 characters with a mean length of 35 characters [Standard Deviation (SD) = 13.51; 95% confidence interval (CI) 13.25 to 13.77]. The most common top-level domains were ".org" and ".edu", each with 34%. About 81% of the URL pool was available 90% to 100% of the time, but only 78% of these contained the actual information mentioned in the MEDLINE record. "Dead" URLs constituted 16% of the total. Finally, a survey of archival tool usage showed that since its introduction in 1998, only 519 of all abstracts reviewed had incorporated DOI addresses in their MEDLINE abstracts.ConclusionURL persistence parallels previous studies which showed approximately 81% general availability during the 1-month study period. As peer-reviewed literature remains to be the main source of information in biomedicine, we need to ensure the accuracy and preservation of these links.
| S-EPMC2435527 | biostudies-literature
Project description:In this study, we developed and evaluated a novel text-mining approach, using non-negative tensor factorization (NTF), to simultaneously extract and functionally annotate transcriptional modules consisting of sets of genes, transcription factors (TFs), and terms from MEDLINE abstracts. A sparse 3-mode term × gene × TF tensor was constructed that contained weighted frequencies of 106,895 terms in 26,781 abstracts shared among 7,695 genes and 994 TFs. The tensor was decomposed into sub-tensors using non-negative tensor factorization (NTF) across 16 different approximation ranks. Dominant entries of each of 2,861 sub-tensors were extracted to form term-gene-TF annotated transcriptional modules (ATMs). More than 94% of the ATMs were found to be enriched in at least one KEGG pathway or GO category, suggesting that the ATMs are functionally relevant. One advantage of this method is that it can discover potentially new gene-TF associations from the literature. Using a set of microarray and ChIP-Seq datasets as gold standard, we show that the precision of our method for predicting gene-TF associations is significantly higher than chance. In addition, we demonstrate that the terms in each ATM can be used to suggest new GO classifications to genes and TFs. Taken together, our results indicate that NTF is useful for simultaneous extraction and functional annotation of transcriptional regulatory networks from unstructured text, as well as for literature based discovery. A web tool called Transcriptional Regulatory Modules Extracted from Literature (TREMEL), available at http://binf1.memphis.edu/tremel, was built to enable browsing and searching of ATMs.
| S-EPMC5581332 | biostudies-literature