Retrieving taxa names from large biodiversity data collections using a flexible matching workflow

In the domain of biological classification there are several taxon name matching services that can search for a species scientific name in a large collection of taxonomic names. Many of these services are available online, and many others run on computers of individual scientists. While these systems may work very well, most suffer from the fact that the list of names used as a reference, and the criteria to decide on a match, are hard-coded in the engine that performs the name matching. In this paper we present BiOnym, a taxon name matching system that separates reference namelists, search criteria and matching engine. The user is offered a choice of several taxonomic reference lists, including the option to upload his/her own list onto the system. Furthermore, BiOnym is a flexible workflow, which embeds and combines techniques using lexical matching algorithms as well as expert knowledge. It is also an open platform allowing developers to contribute with new techniques. In this paper we demonstrate the benefits brought by this approach in terms of the efficiency and effectiveness of the information retrieval process with respect to other solutions.     

Medicaid and the Mainstream: Reassessment in the Context of the Taxpayer Revolt

California''s Medicaid program—Medi-Cal—attempted to implement the ideal of mainstream medical care for the poor by giving program beneficiaries a “credit card” for use in the private health care marketplace. This exposed the program to the perverse economic incentives of the fee-for-service, costplus health care system, and contributed to a high rate of increase in program costs. Attempts to control costs have been equally perverse, resulting in low payment rates, the second-guessing of physician professional judgments, the probing of medical and fiscal records, and the use of computerized surveillance systems.Attempts to shift to the use of more efficient delivery systems have had small success. Attempts to attain cost containment through restructuring the Medi-Cal program have been rejected in the name of the mainstream ideal. Costs have continued to escalate, with annual increases as high as 20 percent in some years. Medi-Cal now costs $4 billion per year, the largest single program in California state government.The taxpayer revolt in California is creating a fiscal crisis that will force rethinking of the premises of publicly funded health care for the poor, and a restructuring of strategies for reaching that objective. In the short run, it appears that the issue may not be whether the indigent will have access to mainstream medical care, but whether they will have access to any medical care. In the longer run, the crisis should represent an opportunity for building a system of health care that can serve the financially disadvantaged at a cost tolerable to our society.     

Translation is not enough. Interpreting in a medical setting.

Unique obstacles must be overcome when providing medical care to patients who have an incomplete command of the English language. Serious barriers to effective communication may arise at the exact point where our health care system must succeed or fail. Miscommunication, differences in attitudes about health care, and various other misunderstandings interfere with or frustrate good health care for these patients and their families. Such difficulties are best overcome by the use of a professional interpreter who can ensure good communication between patients and health care professionals. My daily experiences as a professional medical interpreter and translator in Spanish provide insights into the complexities of bilingual and bicultural communication in the hospital setting. Although the examples given relate to Hispanic patients, the lessons learned can be extended to other foreign language patients as well.     

Gene name ambiguity of eukaryotic nomenclatures

MOTIVATION: With more and more scientific literature published online, the effective management and reuse of this knowledge has become problematic. Natural language processing (NLP) may be a potential solution by extracting, structuring and organizing biomedical information in online literature in a timely manner. One essential task is to recognize and identify genomic entities in text. 'Recognition' can be accomplished using pattern matching and machine learning. But for 'identification' these techniques are not adequate. In order to identify genomic entities, NLP needs a comprehensive resource that specifies and classifies genomic entities as they occur in text and that associates them with normalized terms and also unique identifiers so that the extracted entities are well defined. Online organism databases are an excellent resource to create such a lexical resource. However, gene name ambiguity is a serious problem because it affects the appropriate identification of gene entities. In this paper, we explore the extent of the problem and suggest ways to address it. RESULTS: We obtained gene information from 21 organisms and quantified naming ambiguities within species, across species, with English words and with medical terms. When the case (of letters) was retained, official symbols displayed negligible intra-species ambiguity (0.02%) and modest ambiguities with general English words (0.57%) and medical terms (1.01%). In contrast, the across-species ambiguity was high (14.20%). The inclusion of gene synonyms increased intra-species ambiguity substantially and full names contributed greatly to gene-medical-term ambiguity. A comprehensive lexical resource that covers gene information for the 21 organisms was then created and used to identify gene names by using a straightforward string matching program to process 45,000 abstracts associated with the mouse model organism while ignoring case and gene names that were also English words. We found that 85.1% of correctly retrieved mouse genes were ambiguous with other gene names. When gene names that were also English words were included, 233% additional 'gene' instances were retrieved, most of which were false positives. We also found that authors prefer to use synonyms (74.7%) to official symbols (17.7%) or full names (7.6%) in their publications. CONTACT: lifeng.chen@dbmi.columbia.edu     

Land Tenure and Naming Systems in Aboriginal Australia

Naming systems play a prominent role in discussions of land tenure by Aboriginal people. Reference to one area of land and its owners is most commonly in terms of name ‘X’, whereas reference to another area of land and its owners is most commonly made in terms of name ‘Y’. Much of the analytical literature examines how these names refer to groups of people. There is considerable dispute as to whether the reference of these names suffices to determine disjoint groupings of owners that can be described by the term ‘clan’. This paper proposes that the analysis of linkages between names and areas of land should have priority over the analysis of linkages between names and groups of people. The evidence shows that the attachment of names to areas of land is more stable and consistent than their attachment to groups of people. There are differences in the ways that names attach to the landscape, and these differences are significant—they determine whether or not more than one name from the same system may be attached to an area of land. This paper focuses on two areas of Australia: the northern Kakadu‐Oenpelli area and the Timber Creek area (both in the Northern Territory). It shows that naming systems identify disjunctive areas of land as the targets for claims of primary ownership in both areas. These disjunctive areas may reasonably be described with the translation term ‘estates’. In the northern Kakadu‐Oenpelli area, corresponding to these estates, there are disjunctive groupings of owners, which may be termed ‘clans’. However, groupings of owners are not clearly disjunctive in the Timber Creek area, and there is little motivation for using the term ‘clan’. This paper proposes that this difference reflects a general pattern in Aboriginal Australia, with naming systems stably and consistently identifying ‘estates’ across much of the continent. They do not identify ‘clans’ with equivalent stability and consistency.     

Shiftwork, age and well-being: recent developments and future perspectives

The working population is aging fast in most European countries and in the USA. The health and well-being of an elderly shift worker depends on the interaction of several individual, medical, psychosocial and job-related factors. These factors are related to the biological ageing process, but also to changes in one's individual life situation and the needs of the ageing shift worker. The evidence of good age-specific solutions in working hours is limited, but the few published intervention studies support the use of individual flexibility, rapid forward rotating shift systems, and earlier shift start-end times in three-shift work. In addition to the development of shift schedules, the counter-measures to improve the health and well-being of ageing shift workers should be focused on the improvement of occupational health care and the promotion of appropriate coping mechanisms for the aging.     

Iconicity in English and Spanish and Its Relation to Lexical Category and Age of Acquisition

Signed languages exhibit iconicity (resemblance between form and meaning) across their vocabulary, and many non-Indo-European spoken languages feature sizable classes of iconic words known as ideophones. In comparison, Indo-European languages like English and Spanish are believed to be arbitrary outside of a small number of onomatopoeic words. In three experiments with English and two with Spanish, we asked native speakers to rate the iconicity of ~600 words from the English and Spanish MacArthur-Bates Communicative Developmental Inventories. We found that iconicity in the words of both languages varied in a theoretically meaningful way with lexical category. In both languages, adjectives were rated as more iconic than nouns and function words, and corresponding to typological differences between English and Spanish in verb semantics, English verbs were rated as relatively iconic compared to Spanish verbs. We also found that both languages exhibited a negative relationship between iconicity ratings and age of acquisition. Words learned earlier tended to be more iconic, suggesting that iconicity in early vocabulary may aid word learning. Altogether these findings show that iconicity is a graded quality that pervades vocabularies of even the most “arbitrary” spoken languages. The findings provide compelling evidence that iconicity is an important property of all languages, signed and spoken, including Indo-European languages.     

Drugs Versus Diets: Disillusions with Dutch Health Care

Biology incorporated into other disciplines is often distorted, alarmingly so in some areas of medicine. Together with other forms of bias, this may have detrimental effects for patients depending on medical research for their health. A case study concerning omeprazole (Losec), one of the acid-suppressive drugs against gastric ulcers, and NSAIDs, non-steroid anti-inflammatory drugs, confirms that distorted biology together with biased health care policies foster disasters in current biomedicine and medical practice. In our country, The Netherlands, omeprazole is presumably the most commonly used medication. NSAIDs are also used in large quantities, increasingly since they have become available as analgesic over-the-counter drugs. Unofficial and official sources tend to inform the general public that the drugs promote human health. We argue that their being used on a massive scale is actually a medical disaster. The health of many patients would be served better if the drugs they take were replaced by proper forms of diet, but the pharmaceutical industry, the most potent force affecting medication policies, appears to prevent a shift in the balance from over-medicalization towards healthy life styles. The shift should come from government agencies responsible for regulation in the medication market. Policies of these agencies are now a dismal failure.     

我国医患纠纷处理的几种尝试及思考

现阶段我国的医患纠纷日益增多,医患矛盾尖锐。寻求合理的医患纠纷处理方式具有重要现实意义。对于医患纠纷的处理,世界各国均有较多尝试,美国、德国、日本、中国台湾地区等也出现了诸多处理方式。通过对这些处理方式的比较与分析,旨在吸取经验,为改善医患关系,提高医疗服务质量抛砖引玉。     

县乡村三级卫生人力资源的构成与分布特征研究

目的 通过分析县乡村三级人力资源配置的内部构成及各级机构间的分布差异情况,为农村卫生人力资源的纵向整合和三级医疗预防保健网的建设提供依据。 方法 用EXCEL2010分析各级医疗机构的人口学特征及内部构成比,用SPSS20.0进行卡方检验分析不同级别,不同地域类型的医疗机构卫生人员的构成与分布是否存在差异。结果 总体上男性医务人员多于女性医务人员,但由于村卫生室以乡村医生为主,所以医务人员的内部构成比例和性别分布情况与县乡两级机构不同。60岁及以上人员在县级医疗机构为2.69%,在村卫生室的比例达27.51%（P<0.05）。与2014年相比,2015年该市乡镇卫生院人员引进了15人,流失了27人,而县级医院引进了50人,流失了24人。结论 分级诊疗相关政策影响农村卫生人力资源的配置和床日负担水平,县乡村三级医疗机构医务人员的性别年龄分布均有差异,不同地域类型乡镇卫生院均需对高学历医务工作者给予针对性的激励措施。     

Building Large Collections of Chinese and English Medical Terms from Semi-Structured and Encyclopedia Websites

To build large collections of medical terms from semi-structured information sources (e.g. tables, lists, etc.) and encyclopedia sites on the web. The terms are classified into the three semantic categories, Medical Problems, Medications, and Medical Tests, which were used in i2b2 challenge tasks. We developed two systems, one for Chinese and another for English terms. The two systems share the same methodology and use the same software with minimum language dependent parts. We produced large collections of terms by exploiting billions of semi-structured information sources and encyclopedia sites on the Web. The standard performance metric of recall (R) is extended to three different types of Recall to take the surface variability of terms into consideration. They are Surface Recall (), Object Recall (), and Surface Head recall (). We use two test sets for Chinese. For English, we use a collection of terms in the 2010 i2b2 text. Two collections of terms, one for English and the other for Chinese, have been created. The terms in these collections are classified as either of Medical Problems, Medications, or Medical Tests in the i2b2 challenge tasks. The English collection contains 49,249 (Problems), 89,591 (Medications) and 25,107 (Tests) terms, while the Chinese one contains 66,780 (Problems), 101,025 (Medications), and 15,032 (Tests) terms. The proposed method of constructing a large collection of medical terms is both efficient and effective, and, most of all, independent of language. The collections will be made publicly available.     

Quantifying your body: A how-to guide from a systems biology perspective

During the coming decade we will see an accelerated digital transformation of healthcare. Leading this change within the institutional medical community are both the move to digital medical records and the use of digital biomedical measurement devices. In addition to this institutional evolution, there is a non-institutional, bottom-up, unorganized, highly idiosyncratic movement by early adopters to "quantify" their own bodies. In this article, I share my decade-long personal experience of tracking many blood and stool biomarkers, which provide insight into the health or disease of major subsystems of my body. These results are interpreted in the context of the genetics of my human DNA and that of the microbes in my gut. Even though I am a computer scientist and not a medical professional, by using commercially available tests and a systems biology integrative approach, I have become an early example of Leroy Hood's vision of the emergence of predictive, preventive, personalized, and participatory (P4) medicine. It is an individual's story illustrating how each of us can contribute to realizing this paradigm shift.     

Ethnicity determination by names among the Aymara of Chile and Bolivia

The importance of surnames in genetic studies has been recognized for a century or so. While the ethnic affiliations of individuals are ordinarily established in genetic studies by admixture analysis based on gene frequencies, often there are implicit assumptions in these attempts that are difficult to validate in the absence of detailed ethnohistories. In northern Chile and western Bolivia, where genetic admixture has been known to occur among the Aymara Indians and Spanish Caucasoids, the naming pattern (parental patriand matrinyms) allowed us to classify individuals on the basis of the frequency of Aymara names into 9 'ethnic' groups. From a sample of 2525 individuals it is shown that admixture occurred in lineages nonrandomly, implying assortative mating of surnames. Admixture and genetic distance analysis on the basis of 31 genetic markers on approximately 1700 of these individuals reveals that there is a reasonable agreement of ethnic classification of individuals by name and phenotype data on genetic markers. The Aymara-named groups are shown to be predominantly Amerindian (89%) in their genetic profiles. Individuals whose current naming pattern is basically Spanish also exhibit a substantial fraction of genes of Amerindian origin (67%). Presence of some rare alleles not found in Amerindian or Spanish Caucasoids in the admixed groups suggest infiltration of Negroid genes in the past.     

氢气与肠道菌群的关系研究进展

目前,氢气已被证实在多种疾病中具有显著的医学效应,然而其发挥效应的分子机制并不清楚。肠道菌群被人们看作人体的一个重要“器官”,与人类健康的关系密不可分。研究表明,人类肠道菌群中存在着大量能够进行氢气代谢的菌群,这些菌群的变化可能与多种疾病的发生发展密切相关。此外,研究还发现外源氢气干预可能通过重塑肠道菌群改善炎症性肠病、脂肪性肝病等。综述了肠道菌群的氢气代谢及其与疾病发生发展的关系以及外源氢气干预通过调节肠道菌群影响疾病进展的相关研究,希望能为致力于从肠道菌群角度研究氢气医学效应的科研工作者提供帮助。     

公立医疗机构政府补偿与监管机制的研究框架

在补偿机制扭曲、政府监管滞后的背景下,科学设定公立医疗机构政府补偿标准和方式,改进政府监管手段和能力对保障公立医疗机构公益性具有重要意义。上海市闵行区开展了基于公益性绩效的政府补偿机制改革和基于信息平台的政府监管机制改革。文章以新公共行政理论为指导,总结闵行区政府补偿和监管机制的特点,评价改革的效果,并且探索分析补偿和监管机制改革对医疗机构运行绩效的影响,为深化公立医院改革提供决策参考。     

A Critical Note on the Scientific Name of the Leguminous Plant“Lü Tou”

The Chinese name for the vegetable leguminous plant “LüTOU “or English,Green Gram is identified with the scientific name Phaseolus radiatus Linn.     

Pattern, process and the evolution of meaning: species and units of selection

Many of the fundamental concepts of biology lack consensual, precise definitions. Partly, this is due to a contrast between our discrete language and the continuous character of nature. Some debates over these concepts are confounded by the use of the same terms with different specific meanings, indicating a possible need for an expanded scientific lexicon. Words have their own histories, and frequently scientific terms with a vernacular origin retain associated vestigial meanings. Even terms newly coined within science have histories and changing meanings, which can lead to confusion among debaters. Debates over concepts are further confounded when the same terms are used in different fields of biology, with distinct (even conflicting) objectives, and by biologists with different approaches and perspectives. I illustrate these issues by considering the debate over the concept of species and the unit of selection.