Urban health and pharmaceutical consumption in Delhi, India

This paper interrogates the routine and unproblematic use of terms such as 'self-medication' in biomedical and anthropological discourse. A typical depiction of the social factors that explain the practice of 'self-medication' in India is to put together the supply side factors (such as protection offered by the government for the production of generic drugs, especially in the small scale sector, and expansion of the number of drug store outlets), with the increasing demand for allopathic drugs. The paper provides an ethnographic account of the intricate connections between households and biomedical practitioners in urban neighbourhoods in Delhi. It breaks away from the conventional opposition drawn between the practices of physicians and the beliefs of their patients, and suggests that what constitutes the medical environments of these neighbourhoods is the product of medical practices, household economies and concepts of disease. Thus pharmaceutical use is determined as much by practices of dispensation and by how practitioners understand what constitutes therapy as by household understanding of the normal and the pathological. This paper uses both quantitative data and narrative interviews to provide an in-depth understanding of the circulation of pharmaceuticals within the life worlds of the urban poor.     

Immunology for the next generation

Immunologists need to establish a vibrant dialogue with young people. This is not only important for the continuation and progress of biomedical research, but it can also contribute to the fight against diseases such as HIV/AIDS and can help young people to make informed decisions about lifestyle, medical treatment and ethical issues. Good communication skills are crucial to any scientific career, and the lessons learned from talking with non-scientists can also be useful when writing scientific papers and grants. This article is a personal account of one scientist's experience of communicating biomedical science to young people.     

Introduction

Abstrat

In this paper we discuss genetic discourses and practices in stem cell science. We report on how biomedical scientists, in both the UK and the USA, view the scientific literature and their own experimental research in the emerging field of human embryonic stem (hES) cells. We focus on the genetic manipulation of stem cells to make specialized (beta) cells as a potential cure for diabetes. We draw on Gieryn's notion of boundary work as an analytical motif, and suggest this is a productive way to theorize boundary crossings in the shifting landscapes of expectations in the field of new medical technologies. We argue that initial expectations of a revolution in regenerative medicine have been damped down by the difficulties of making insulin producing pancreatic beta cells from stem cells. We contend the consequent shifts in expectations have led to the emergence of other more radical experimental strategies (such as using oncogenes) in the search for potential cures for Type 1 diabetes. In conclusion, we argue that regenerative medicine is a fruitful example of the shaping of contested biomedical landscapes and we contend that embryonic stem cells are a productive case study of the interactions between genetics, science and society.     

A web service for biomedical term look-up

Recent years have seen a huge increase in the amount of biomedical information that is available in electronic format. Consequently, for biomedical researchers wishing to relate their experimental results to relevant data lurking somewhere within this expanding universe of on-line information, the ability to access and navigate biomedical information sources in an efficient manner has become increasingly important. Natural language and text processing techniques can facilitate this task by making the information contained in textual resources such as MEDLINE more readily accessible and amenable to computational processing. Names of biological entities such as genes and proteins provide critical links between different biomedical information sources and researchers' experimental data. Therefore, automatic identification and classification of these terms in text is an essential capability of any natural language processing system aimed at managing the wealth of biomedical information that is available electronically. To support term recognition in the biomedical domain, we have developed Termino, a large-scale terminological resource for text processing applications, which has two main components: first, a database into which very large numbers of terms can be loaded from resources such as UMLS, and stored together with various kinds of relevant information; second, a finite state recognizer, for fast and efficient identification and mark-up of terms within text. Since many biomedical applications require this functionality, we have made Termino available to the community as a web service, which allows for its integration into larger applications as a remotely located component, accessed through a standardized interface over the web.     

MaSTerClass: a case-based reasoning system for the classification of biomedical terms

MOTIVATION: The sheer volume of textually described biomedical knowledge exerts the need for natural language processing (NLP) applications in order to allow flexible and efficient access to relevant information. Specialized semantic networks (such as biomedical ontologies, terminologies or semantic lexicons) can significantly enhance these applications by supplying the necessary terminological information in a machine-readable form. With the explosive growth of bio-literature, new terms (representing newly identified concepts or variations of the existing terms) may not be explicitly described within the network and hence cannot be fully exploited by NLP applications. Linguistic and statistical clues can be used to extract many new terms from free text. The extracted terms still need to be correctly positioned relative to other terms in the network. Classification as a means of semantic typing represents the first step in updating a semantic network with new terms. RESULTS: The MaSTerClass system implements the case-based reasoning methodology for the classification of biomedical terms.     

Identification of key concepts in biomedical literature using a modified Markov heuristic

MOTIVATION: The recent explosion of interest in mining the biomedical literature for associations between defined entities such as genes, diseases and drugs has made apparent the need for robust methods of identifying occurrences of these entities in biomedical text. Such concept-based indexing is strongly dependent on the availability of a comprehensive ontology or lexicon of biomedical terms. However, such ontologies are very difficult and expensive to construct, and often require extensive manual curation to render them suitable for use by automatic indexing programs. Furthermore, the use of statistically salient noun phrases as surrogates for curated terminology is not without difficulties, due to the lack of high-quality part-of-speech taggers specific to medical nomenclature. RESULTS: We describe a method of improving the quality of automatically extracted noun phrases by employing prior knowledge during the HMM training procedure for the tagger. This enhancement, when combined with appropriate training data, can greatly improve the quality and relevance of the extracted phrases, thereby enabling greater accuracy in downstream literature mining tasks.     

The fundamentals of clinical discovery

There is a widespread view that clinical research is failing to advance appropriately, particularly in comparison with other aspects of biomedical science. I argue that this is due in part to an inadequate understanding of how medical advance occurs. The common usage of such terms as basic or fundamental, or the uncritical use of the term model is unhelpful--unhelpful, in that such terms tend to presuppose a certain model of clinical advance that is unusual, and furthermore, because they tend to exaggerate the importance of research in subjects such as biochemistry and genetics at the expense of other areas. I suggest that much medical research is best viewed as a form of engineering rather than science, and that the knowledge base and research funding for the amelioration of disease needs to be much more broadly based than at present.     

Can flies help humans treat neurodegenerative diseases?

Neurodegenerative diseases are becoming increasingly common as life expectancy increases. Recent years have seen tremendous progress in the identification of genes that cause these diseases. While mutations have been found and cellular processes defined that are altered in the disease state, the identification of treatments and cures has proven more elusive. The process of finding drugs and therapies to treat human diseases can be slow, expensive and frustrating. Can model organisms such as Drosophila speed the process of finding cures and treatments for human neurodegenerative diseases? We pose three questions, (1) can one mimic the essential features of human diseases in an organism like Drosophila, (2) can one cure a model organisms of human disease and (3) will these efforts accelerate the identification of useful therapies for testing in mice and ultimately humans? Here we focus on the use of Drosophila to identify potential treatments for neurodegenerative diseases such as Huntington's and we discuss how well these therapies translate into mammalian systems. BioEssays 26:485–496, 2004. © 2004 Wiley Periodicals, Inc.     

Public engagement with science? Local understandings of a vaccine trial in the Gambia

This paper considers how parents engage with a large, internationally supported childhood pneumococcal vaccine trial in The Gambia. Current analysis and professional reflection on public engagement is strongly shaped by the imperatives of public health and research institutions, and is thus couched in terms of acceptance and refusal, and 'informed consent'. In contrast Gambian parents' perspectives on the trial are couched in conceptual and experiential terms that are linked to their wider dilemmas of raising infants amidst the hazards of globally connected village life. Ethnographic research reveals how for most parents, longer-term experiences of the organization managing the research (the UK Medical Research Council Laboratories in The Gambia) as a health-providing institution override their reflection on trial-specific aims. A decision to participate in the trial involves a perceived balance of benefit and danger -- in the extreme, of free medical treatment, versus one's child being drained of blood for sale to Europe. Social relations (especially gender relations) shape this calculus and study participation. This case suggests how the idea of 'public engagement with science' in a globalized context might be recast, with implications for debates in biomedical ethics, and the sustainability of public participation in medical research.     

Hæwenhnydele: an Anglo-Saxon Medicinal Plant

Summary

The Old English plant-name, hæwenhnydele, occurs in herbal and medical texts and in glossaries containing translated Latin plant-names. Where it is linked with a Latin name, that name is always Herba Britannica, a cure for scurvy. Some scholars, rather naively assuming that the two names must refer to the same plant, have thought the identity of hæwenhnydele almost obvious, whereas others, knowing the frequently garbled accounts of herbal cures inherited by the Anglo-Saxons, have despaired of ever identifying it. An Anglo-Saxon translator, working on the Old English version of the Latin Pseudo-Apuleius, inherited an account of Herba Britannica which was a confusion of two different plants, compiled from several sources. The information available to him is discussed, in an effort to understand how he made an identification. Evidence such as the synonyms attached to the plant entry, the etymology of hæwenhnydele, and the illustration of the plant is presented. There is also a brief discussion of the two recorded occurrences of the rural plant-name, hawdod, from the 16th and 18th centuries, and whether this name could be cognate with hæwenhnydele. In the Durham Glossary, another name, vihtmeresvyrt, is linked with Herba Britannica and hæwenhnydele. This name is discussed, and found to denote a well-known source of Vitamin C, the cure for scurvy. This paper demonstrates that the attempts of the Anglo-Saxons to identify Herba Britannica, and to link their guesses with real herbal cures, are an impressive rationalisation of an almost nonsensical Latin plant record.     

Low temperature cure of a male killing agent in Drosophila melanogaster

Environmental factors can affect transmission or phenotype expression of selfish cytoplasmic endosymbionts such as embryonic male killers. Temperature is one factor that usually affects the transmission rate of selfish cytoplasmic endosymbionts. Heat cures have been described for several host-parasite systems, cold cures, however, are rare. We report a temperature cure of the Drosophila melanogaster male-killing agent, which occurs when flies are raised at 16.5 degrees C. Flies grown at 20, 24, and 28 degrees C maintained an extremely female biased sexual proportion.     

Learning to extract relations for protein annotation

MOTIVATION: Protein annotation is a task that describes protein X in terms of topic Y. Usually, this is constructed using information from the biomedical literature. Until now, most of literature-based protein annotation work has been done manually by human annotators. However, as the number of biomedical papers grows ever more rapidly, manual annotation becomes more difficult, and there is increasing need to automate the process. Recently, information extraction (IE) has been used to address this problem. Typically, IE requires pre-defined relations and hand-crafted IE rules or annotated corpora, and these requirements are difficult to satisfy in real-world scenarios such as in the biomedical domain. In this article, we describe an IE system that requires only sentences labelled according to their relevance or not to a given topic by domain experts. RESULTS: We applied our system to meet the annotation needs of a well-known protein family database; the results show that our IE system can annotate proteins with a set of extracted relations by learning relations and IE rules for disease, function and structure from only relevant and irrelevant sentences.     

流感疫情中的医学信息学

在应对当前甲型流感暴发的疾病控制过程中,医学信息学发挥着不可替代的重要作用．本文结合多种信息学数据库来源的最新资料,在介绍甲型流感病毒的生物学知识和生物信息学分析手段的同时,对本次甲型流感病毒的来源、进化、传播和预防等一系列重要问题,结合信息学分析的结果做了深入的分析和探讨．并且突出介绍和评论了医学信息学在疾病控制中的前景和潜力,希望能有助于多种相关学科的生物医学研究人员．     

A clinical-parasitological monotherapy cure in the treatment of experimental infection by a highly virulent strain ofToxoplasma gondii

Toxoplasmic encephalitis in patients with the acquired immunodeficiency syndrome (AIDS) is treated classically with pyrimethamine plus sulfadiazine. Unfortunately, up to 40% of these patients are unable to complete, the course of therapy because of adverse reactions to sulfonamides. This study considers the possible usefulness of monotherapies in the treatment of acute toxoplasmosis, producing parasitological cures 2–3 months after the date of infection. With this therapy, the main adverse effects are suppressed. Groups of mice infected with the RH strain ofToxoplasma gondii were treated with pyrimethamine alone, sulfadiazine alone, and pyrimethamine plus sulfadiazine for 7 d. Treatment with pyrimethamine plus sulfadiazine produced clinical cures in 100% of the infected mice 1 month after infection. Treatment with pyrimethamine gave a 60% survival rate (clinical cure), at 1 month postinfection. Finally, treatment with sulfadiazine produced a 60% survival rate at 1 month postinfection. Although the antitoxoplasmic regimen with pyrimethamine plus sulfadiazine has proven to be effective in intensive treatment of toxoplasmic encephalitis, relapses occur in more than 80% of cases after cessation of antitoxoplasmic therapy, making secondary prophylaxis mandatory. In this study the efficacy of treatment was also evaluated in terms of parasitological cure. None of the three therapies showed parasitological cure after 1 month of treatment. When the intervals were extended to a 3-month observation, monotherapy with pyrimethamine and sulfadiazine alone produced a parasitological cure.     

Can Andean medicine coexist with biomedical healthcare? A comparison of two rural communities in Peru and Bolivia

ABSTRACT: BACKGROUND: It is commonly assumed that indigenous medical systems are strong in developing countries because biomedicine is physically inaccessible or financially not affordable. This paper compares the health-seeking behavior of households from rural Andean communities at a Peruvian and a Bolivian study site. The main research question was whether the increased presence of biomedicine led to a displacement of Andean indigenous medical practices or to coexistence of the two healing traditions. Methodology: Interviews were conducted between June 2006 and December 2008 with 18 households at each study site. Qualitative identification and analysis of households' therapeutic strategies and use of remedies was complemented by quantitative assessment of the incidence of culture-bound illnesses in local ethnobiological inventories. RESULTS: Our findings indicate that the health-seeking behavior of Andean households is independent of the degree of availability of biomedical facilities in terms of quality of services provided, physical accessibility, and financial affordability, except for specific practices such as childbirth. Preference for natural remedies over pharmaceuticals coexisted with biomedical healthcare that was both accessible and affordable. Furthermore, our results show that greater access to biomedicine does not lead to less prevalence of Andean indigenous medical knowledge, as represented by the levels of knowledge about culture-bound illnesses. CONCLUSIONS: The take-home lesson for health policy-makers from this study is that the main obstacle to improved use of biomedicine in resource-poor rural areas might not be infrastructural or economic alone. Rather, it may lie in lack of sufficient recognition by biomedical practitioners of the value and importance of indigenous medical systems. We propose that the implementation of health care in indigenous communities be designed as a process of joint development of complementary knowledge and practices from indigenous and biomedical health traditions.     

Bioie: retargetable information extraction and ontological annotation of biological interactions from the literature

The need for extracting general biological interactions of arbitrary types from the rapidly growing volume of the biomedical literature is drawing increased attention, while the need for this much diversity also requires both a robust treatment of complex linguistic phenomena and a method to consistently characterize the results. We present a biomedical information extraction system, BioIE, to address both of these needs by utilizing a full-fledged English grammar formalism, or a combinatory categorial grammar, and by annotating the results with the terms of Gene Ontology, which provides a common and controlled vocabulary. BioIE deals with complex linguistic phenomena such as coordination, relative structures, acronyms, appositive structures, and anaphoric expressions. In order to deal with real-world syntactic variations of ontological terms, BioIE utilizes the syntactic dependencies between words in sentences as well, based on the observation that the component words in an ontological term usually appear in a sentence with known patterns of syntactic dependencies.     

Recent Advances in CRISPR‐Cas9 Genome Editing Technology for Biological and Biomedical Investigations

The Type II CRISPR‐Cas9 system is a simple, efficient, and versatile tool for targeted genome editing in a wide range of organisms and cell types. It continues to gain more scientific interest and has established itself as an extremely powerful technology within our synthetic biology toolkit. It works upon a targeted site and generates a double strand breaks that become repaired by either the NHEJ or the HDR pathway, modifying or permanently replacing the genomic target sequences of interest. These can include viral targets, single‐mutation genetic diseases, and multiple‐site corrections for wide scale disease states, offering the potential to manage and cure some of mankind's most persistent biomedical menaces. Here, we present the developing progress and future potential of CRISPR‐Cas9 in biological and biomedical investigations, toward numerous therapeutic, biomedical, and biotechnological applications, as well as some of the challenges within. J. Cell. Biochem. 119: 81–94, 2018. © 2017 Wiley Periodicals, Inc.     

Evolution and medicine in undergraduate education: a prescription for all biology students

The interface between evolutionary biology and the biomedical sciences promises to advance understanding of the origins of genetic and infectious diseases in humans, potentially leading to improved medical diagnostics, therapies, and public health practices. The biomedical sciences also provide unparalleled examples for evolutionary biologists to explore. However, gaps persist between evolution and medicine, for historical reasons and because they are often perceived as having disparate goals. Evolutionary biologists have a role in building a bridge between the disciplines by presenting evolutionary biology in the context of human health and medical practice to undergraduates, including premedical and preprofessional students. We suggest that students will find medical examples of evolution engaging. By making the connections between evolution and medicine clear at the undergraduate level, the stage is set for future health providers and biomedical scientists to work productively in this synthetic area. Here, we frame key evolutionary concepts in terms of human health, so that biomedical examples may be more easily incorporated into evolution courses or more specialized courses on evolutionary medicine. Our goal is to aid in building the scientific foundation in evolutionary biology for all students, and to encourage evolutionary biologists to join in the integration of evolution and medicine.     

Non-canonical aging model systems and why we need them

Aging is one of the greatest challenges for biomedical research in the developed world. The continuing increase in lifespan without accompanying increases in health span has extreme economic and societal implications for an aging society. The majority of adult-onset diseases such as cancer, cardiovascular disease, and Alzheimer's are a direct consequence of aging, and with changing demographics, more and more people are afflicted. If we knew how to slow down the negative effects of aging, we could delay or prevent all of these diseases at once. We therefore need to understand the underlying molecular mechanisms of aging and longevity so as to develop applications that ultimately improve health span.