黄亚明

Bio: 黄亚明 is an academic researcher. The author has an hindex of 1, co-authored 1 publications receiving 108 citations.

PubMed Central

Abstract: PubMed Central（PMC）是美国国立卫生研究院国立医学图书馆生物技术与信息中心开发和维护的生物医学与生命科学期刊文献免费数字文档库。其宗旨是承担起数字时代世界级图书馆的作用。它不是期刊出版商。出版商自愿加入PMC，并需满足一定的科研水平和编辑质量标准。

LINNAEUS: A species name identification system for biomedical literature

Abstract: The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles. In this paper we describe an open-source species name recognition and normalization software system, LINNAEUS, and evaluate its performance relative to several automatically generated biomedical corpora, as well as a novel corpus of full-text documents manually annotated for species mentions. LINNAEUS uses a dictionary-based approach (implemented as an efficient deterministic finite-state automaton) to identify species names and a set of heuristics to resolve ambiguous mentions. When compared against our manually annotated corpus, LINNAEUS performs with 94% recall and 97% precision at the mention level, and 98% recall and 90% precision at the document level. Our system successfully solves the problem of disambiguating uncertain species mentions, with 97% of all mentions in PubMed Central full-text documents resolved to unambiguous NCBI taxonomy identifiers. LINNAEUS is an open source, stand-alone software system capable of recognizing and normalizing species name mentions with speed and accuracy, and can therefore be integrated into a range of bioinformatics and text-mining applications. The software and manually annotated corpus can be downloaded freely at http://linnaeus.sourceforge.net/ .

NIH disease funding levels and burden of disease

Abstract: Background An analysis of NIH funding in 1996 found that the strongest predictor of funding, disability-adjusted life-years (DALYs), explained only 39% of the variance in funding. In 1998, Congress requested that the Institute of Medicine (IOM) evaluate priority-setting criteria for NIH funding; the IOM recommended greater consideration of disease burden. We examined whether the association between current burden and funding has changed since that time.

Local anaesthetics and regional anaesthesia for preventing chronic pain after surgery.

Abstract: Background Regional anaesthesia may reduce the rate of persistent (chronic) pain after surgery, a frequent and debilitating condition. Objectives To compare local anaesthetics and regional anaesthesia versus conventional analgesia for the prevention of persistent pain six or 12 months after surgery. Search methods We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2012, Issue 4), PubMed (1966 to April 2012), EMBASE (1966 to May 2012) and CINAHL (1966 to May 2012) without any language restriction. We used a combination of free text search and controlled vocabulary search. The results were limited to randomized controlled clinical trials (RCTs). We conducted a handsearch in reference lists of included trials, review articles and conference abstracts. Selection criteria We included RCTs comparing local anaesthetics or regional anaesthesia versus conventional analgesia with a pain outcome at six or 12 months after surgery. Data collection and analysis Two authors independently assessed trial quality and extracted data, including information on adverse events. We contacted study authors for additional information. Results are presented as pooled odds ratios (OR) with 95% confidence intervals (CI), based on random-effects models (inverse variance method). We grouped studies according to surgical interventions. We employed the Chi2 test and calculated the I2 statistic to investigate study heterogeneity. Main results We identified 23 RCTs studying local anaesthetics or regional anaesthesia for the prevention of persistent (chronic) pain after surgery. Data from a total of 1090 patients with outcomes at six months and of 441 patients with outcomes at 12 months were presented. No study included children. We pooled data from 250 participants after thoracotomy, with outcomes at six months. Data favoured regional anaesthesia for the prevention of chronic pain at six months after thoracotomy with an OR of 0.33 (95% CI 0.20 to 0.56). We pooled two studies on paravertebral block for breast cancer surgery; the pooled data of 89 participants with outcomes at five to six months favoured paravertebral block with an OR of 0.37 (95% CI 0.14 to 0.94).The methodological quality of the included studies was intermediate. Adverse effects were not studied systematically and were reported sparsely. Clinical heterogeneity, attrition and sparse outcome data hampered the assessment of effects, especially at 12 months. Authors' conclusions Epidural anaesthesia may reduce the risk of developing chronic pain after thoracotomy in about one patient out of every four patients treated. Paravertebral block may reduce the risk of chronic pain after breast cancer surgery in about one out of every five women treated. Our conclusions are significantly weakened by performance bias, shortcomings in allocation concealment, considerable attrition and incomplete outcome data. We caution that our evidence synthesis is based on only a few, small studies. More studies with high methodological quality, addressing various types of surgery and different age groups, including children, are needed.

Estimating Cost of Care for Patients With Acute Low Back Pain: A Retrospective Review of Patient Records

Abstract: Context Low back pain (LBP) has a major economic impact in the United States, with total costs related to this condition exceeding $100 billion per year. Objective: To estimate the cost of standard care compared to standard care plus osteopathic manipulative treatment (OMT) for acute LBP of less than 6 months' duration. Methods: A retrospective review of electronic medical records from patients who visited Florida Hospital East Orlando in Orlando. All patients had LBP of less than 6 months' duration and had received care between January 1,2002, and December 31,2005. The control group comprised patients who received standard care; the study group consisted of patients who received OMT in addition to standard care. Healthcare utilization (eg, radiologic scans, prescriptions) was determined by "episodes of care," and costs were averaged per patient. Results: A total of 1556 patients and 2030 episodes of care met inclusion criteria. Compared with subjects in the control group, individuals in the OMT group had an average of 0.5 more office visits per EOC, resulting in 38% more office visits. However, OMT patients had 18.5% fewer prescriptions written, 74.2% fewer radiographs, 76.9% fewer referrals, and 90% fewer magnetic resonance imaging scans. In the OMT group, total average costs were $38.26 lower (P=.02), and average prescription costs were $19.53 lower (P<.001). Patients in the OMT group also had $63.81 less average radiologic costs (P<.0001). Conclusion: Osteopathic manipulative treatment may reduce costs for the management of acute LBP. Further research in a prospective study is needed.

Scholarly context not found: one in five articles suffers from reference rot.

Abstract: The emergence of the web has fundamentally affected most aspects of information communication, including scholarly communication. The immediacy that characterizes publishing information to the web, as well as accessing it, allows for a dramatic increase in the speed of dissemination of scholarly knowledge. But, the transition from a paper-based to a web-based scholarly communication system also poses challenges. In this paper, we focus on reference rot, the combination of link rot and content drift to which references to web resources included in Science, Technology, and Medicine (STM) articles are subject. We investigate the extent to which reference rot impacts the ability to revisit the web context that surrounds STM articles some time after their publication. We do so on the basis of a vast collection of articles from three corpora that span publication years 1997 to 2012. For over one million references to web resources extracted from over 3.5 million articles, we determine whether the HTTP URI is still responsive on the live web and whether web archives contain an archived snapshot representative of the state the referenced resource had at the time it was referenced. We observe that the fraction of articles containing references to web resources is growing steadily over time. We find one out of five STM articles suffering from reference rot, meaning it is impossible to revisit the web context that surrounds them some time after their publication. When only considering STM articles that contain references to web resources, this fraction increases to seven out of ten. We suggest that, in order to safeguard the long-term integrity of the web-based scholarly record, robust solutions to combat the reference rot problem are required. In conclusion, we provide a brief insight into the directions that are explored with this regard in the context of the Hiberlink project.