This collection was launched with the mission to share knowledge about lab organization and scientific management. Each Perspective article represents an interview with a Principal Investigator, who shares his or her experience of running a lab by discussing selected topics in an informal and personal style. By creating this collection at PLOS Computational Biology, a journal committed to open knowledge, the collection editors hope to create a dialog through which we all can learn from each other.
Public Library of Science Applied Science Data and Primary Sources
Public Library of Science Applied Science Data and Primary Sources Collection Resources (45)
Without reliable methods to evaluate how the mucosal immune system responds to an experimental HIV vaccine, important information about how well that vaccine worked is missed. The HIV Mucosal Immunology Group (MIG) was established to address the challenge of assessing the impact of potential HIV vaccines on the mucosal immune system. The MIG comprises of expert scientists who are coordinating their efforts to improve mucosal sampling, specimen storage and assay technologies. This collection reports the results of those efforts, providing important, practical details on studying immune responses in the genital and rectal mucosa.
The PLOS Medicine series on Big Food aims to examine and stimulate debate about the activities and influence of the food industry in global health. We define Big Food as the multinational food and beverage industry with huge and concentrated market power. The series adopts a multi-disciplinary approach and includes critical perspectives from around the world. It represents one of first times such issues have been examined in the general medical literature.
Bioinformatics is being introduced into the school curriculum earlier and earlier as the field matures. PLOS Computational Biology's Education section introduces a new collection, Bioinformatics: Starting Early, which is devoted to teaching bioinformatics in secondary schools.
'Blue marble health' is a recent concept that recognizes a paradoxical disease burden among poor people living in G20 and other wealthier countries. Socioeconomic disparities caused by income, ethnicity and relative poverty constitute a major and growing determinant of health to at-risk populations regardless of the average income of their country of residence. Neglected Tropical Diseases found among poor people in wealthy countries contribute substantially to health disparities, whilst non-communicable diseases, such as diabetes and coronary artery disease, urgently require action as increasingly prevalent causes of illness and death in lower-and middle-income countries.
Millennium Development Goal 4 calls for a reduction of two-thirds in the under-5 mortality rate between 1990 and 2015. Reliable estimates of child mortality are critical to the monitoring of progress toward this important goal. The UN Inter-agency Group for Child Mortality Estimation (IGME) annually reports on country, regional and global trends in child mortality. In this collection of research articles and reviews the independent Technical Advisory Group (TAG) to the UN IGME introduces the group's methodological innovations in estimating child mortality.The Collection is produced with support from UNICEF and the TAG of the UN IGME.
In this collection PLOS NTDs highlights the contributions of Indian authors, labs, and institutions to the global fight against neglected tropical diseases. It includes over 40 primary research articles reporting significant advances in the fields of epidemiology, diagnosis, treatment, vaccine development and applications, and vector control.
In response to the 2014 Ebola outbreak in West Africa, PLOS editors curated content from across the journals, PLOS Currents and the PLOS Blogs Network into a rapidly evolving collection of research. Like all our content, these papers are freely and openly available to download, use and reuse. Incidents such as the Ebola outbreak reinforce the importance of rapid, Open Access publishing to ensure that the latest critical data and research is accessible to those who most need it without restriction.
Recognizing the need for training and education in bioinformatics and computational biology specifically targeted to biologists, PLOS Computational Biology launched its Education section in January 2006. The goals are to provide practical tutorials and background information on important computational methods used to investigate key biological questions as well as resources for training scientists at all stages of their careers.
With exciting new research opportunities comes the much needed consideration of ethical challenges. This Focus Feature, led by Philip E. Bourne, addresses the ethical challenges that accompany the use of big data in biology and medicine. PLOS Computational Biology "Focus Features" are a resource to encourage community engagement and discussion on a focussed topic. A Focus Feature is directed by the editors with a view to shape the debate on a topic of interest to the computational biology community. By consisting of a small number of articles, each Focus Feature may draw on the new and old research in order to further the conversation.
The burden of HIV is heavily disproportionate in sex workers, where the high rates of partner change and their vulnerability increase the likelihood of sexual transmitted infections. This collection presents analyses of the influence of direct and indirect intervention programs aimed at interrupting this high-incidence of infection. Calls are made for a rapid scale-up of combination prevention programs and HIV care and treatment in order to improve conditions for sex workers. Publication of the collection was made possible by the generous financial support of World Bank, The Bill & Melinda Gates Foundation and the President's Emergency Plan for AIDS Relief (PEPFAR) through USAID; Linkages Across the Continuum of HIV Services for Key Populations Affected by HIV (LINKAGES) project cooperative agreement; and Research to Prevention (R2P) Project and Supporting Operational AIDS Research (SOAR).
The January 2012 issue of PLOS Neglected Tropical Diseases presented an Editorial, a Viewpoint, and two accompanying Expert Commentaries that focussed on the application of genetically modified (GM) insects for control of animal and plant diseases. These articles describe the technological advances these tools represent, the regulatory framework, and the societal dialogue that is necessary for their wide-scale application for disease control. Here, we have assembled a collection of articles published in the PLOS journals that describe the technical and applied aspects of GM insects. We also included articles that are not strictly GM, but aim to modify the disease transmission traits of insects through the use of symbiotic microbes.
This collection of essays, perspectives, and reviews from six PLOS journals provides insights into how genomics can revolutionize our understanding of emerging infectious disease. Produced with support from Google
Noncommunicable diseases (NCDs) are responsible for two-thirds of the world's deaths, one-fourth of which occur before the age of 60. Nearly 80% of NCD deaths occur in low- and middle-income countries, where they are also increasing most rapidly. With these global needs and disparities in mind, PLOS Medicine launched a collection of research and commentary on NCDs directed toward improving population health and reducing health disparities.
Estimates of global health indicators - which give insight into death and disease rates, document advances in development, and help policymakers monitor progress - are absolutely essential for improving global health. Estimates, however, are always imperfect and are sometimes fiercely debated. Recently, new players from academia have entered the game of global health estimation, once the chief domain of United Nations agencies such as WHO. In November 2010, PLOS Medicine published a collection articles from a series of experts that provide insights and opinion on what estimates mean for global health and how to move forward with better data, measurement, coordination, and leadership. The collection includes the perspectives of WHO, the Institute for Health Metrics and Evaluation, and stakeholders from low- and middle-income countries.
In this PLOS Collection, global health leaders chart the path to a dramatic reduction in the global burden of disease by 2035. This ambitious convergence in global health will require strategic investments in research and development as well as an aggressive scale-up of health-care delivery systems to ensure that existing health tools and services reach those who need them. Grand Convergence: Aligning Technologies and Realities in Global Health describes how to reduce avertable infectious, maternal, and child deaths down to universally low levels within a generation by aggressively scaling up health tools and continuing to invest in the tools of tomorrow.
In order to revisit the health consequences of the Asian tsunami of December 2004 six months on, PLOS Medicinecommissioned a collection of Magazine articles that were published in April 2005. We later updated this collection to include a new research article and an additional essay of relevance.
The healthy adult body hosts ten times as many microbial cells as human cells.The metagenome carried collectively by these microbial communities dwarfs the human genome in size, and their influences on normal development, diet and obesity, immunity, and disease are under active research. Funded by the National Institutes of Health Common Fund, the Human Microbiome Project (HMP) was established to provide a comprehensive baseline of the microbial diversity at 18 different human body sites.These data join resources generated by computational tool development for analysis of the microbiome, research on the ethical, legal, and social implications of the microbiota, technology development for investigating these microbial communities, and a range of disease-focused microbiome demonstration projects.
The HIV Modelling Consortium aims to strengthen the support that mathematical modelling and related quantitative disciplines can provide to global decision-making in HIV. In November 2011 the HIV Modelling Consortium held a meeting in South Africa to focus on the cross-cutting issues of the impact of new scientific findings about HIV treatment preventing new infections. The group considered the feasibility of interventions, potential epidemiological impact, affordability, and new scientific observational studies and community trials. The nine reviews and one research article which comprise this collection arose from that meeting and provide insights into the factors which will support evidence-based decision-making in HIV prevention, with a focus on the use of antiretroviral treatment to prevent HIV transmission.
Drug research in malaria often focuses on blood stage parasites because they are responsible for the symptoms of the disease and are easier to manipulate in the laboratory.This collection describes multiple parasite and host processes engaged in infection in blood, the blocking of which could stop human illness. However, control and eradication of malaria will also require the development of drugs against stages responsible for mosquito transmission and those that remain latent in the liver, also summarized in the collection. Although these selected papers represent significant research at the highest levels, they are only a fraction of the malaria drug discovery literature. The collection highlights PLOS authors contribution to basic drug discovery research.
This collection presents innovative assessments of the validity of measuring population coverage for interventions in this field. Coverage indicators are widely used to assess whether interventions are reaching women and children in low- and middle-income countries, particularly through population-based household surveys. The collection shows that while some indicators can be measured accurately, others may not provide valid results and therefore need further investigation and development. It explores issues around measurement using household surveys, assessment of health inequalities, consideration of survey error, and the generation of indicators for global monitoring, and presents recommendations for transforming the findings of these and previous studies into better measurement, reporting and interpretation of coverage estimates.
Between October 2009 and February 2010 PLOS Medicine published a seven part series of articles proposing "packages of care" for mental, neurological, and substance-use disorders in low- and middle-income countries. In the introduction to the series, Guest Editors Vikram Patel and Graham Thornicroft explain that a large mental health "treatment gap" exists, in which 90% of people with these mental health disorders in the developing world go untreated.
In May and June 2011, PLOS Medicine published a commissioned six-part series on migration and health. If internal and international migrants comprised a nation, it would be the third most populous country in the world, just after China and India. Thus, there can be little doubt that population mobility is among the leading policy issues of the 21st century. However, policies to protect migrants and global health have so far been hampered by inadequate policy attention and poor international coordination. More coordination is needed across borders and policy sectors. In an editorial published at the end of the series, the PLOS Medicine Editors highlight one particularly troubling aspect of migration - sex trafficking - and what needs to be done to address it.
This collection presents a global framework for monitoring progress towards Universal Health Coverage (UHC) conducted by the World Health Organisation and the World Bank Group. UHC is defined as the desired outcome of health system performance whereby all people who need health services promotion, prevention, treatment, rehabilitation and palliation receive them without undue financial hardship. These articles demonstrate the essential and interlinked components, explaining how UHC monitoring can be fully integrated into the overall monitoring of health system performance. The technical reviews provide insight into current international consensus around UHC and address issues related to the measurement of financial protection, service coverage, effective coverage, and equity. The case studies each discuss progress towards UHC in the featured countries as written by national experts.
Mycetoma is a serious and debilitating condition that meets all of the criteria we ordinarily attribute to a neglected tropical disease (NTD). Classically, it is a destructive fungal or bacterial infection of the foot (although other body parts can be affected) that results in disfigurement and social stigma. It overwhelmingly occurs in impoverished areas of a mycetoma belt that extends across the globe, roughly between the Equator and the Tropic of Cancer, with most of the cases reported from India, Mexico, Sudan, several countries in Africas Sahel (including Chad, Mali, and Mauritania), and Somalia and Yemen.
The Society for Brain Mapping and Therapeutics(SBMT)is a non-profit organization that encourages scientists in areas of brain mapping, engineering, stem cells, nanotechnology, imaging, and medical devices to improve the diagnosis, treatment and rehabilitation of patients with neurological disorders. One challenge of the twenty-first century is to catalyze the development of medical advances from basic science. To help accelerate diagnostic and therapeutic discoveries, SBMT brings together clinicians, scientists, engineers, and policy makers from multiple disciplines who share this aspiration of improving patient care. The organization believes this strategy is essential to bring about advances in neurosurgery, radiology, neurology, and clinical psychiatry. This collection contains a selection of PLOS ONE articles that are representative of the aims of the SBMT.
To coincide with the meeting of the American Association for Cancer Research (AACR), to be held in Philadelphia from April 18 to 22, 2015, PLOS Medicine launches this open access collection of recently published articles representing the full spectrum of clinically relevant cancer research and commentary, from translational to clinical to epidemiological. To expand this collection, and to support the mission we share with the AACR to conquer cancer through research and education, PLOS Medicine issues a call to the clinical genomics and cancer research community for papers that provide novel insights into cancer heterogeneity, progression, translational and clinical medicine, with strong potential to advance patient care, public policy or clinical research agendas.
PLOS Pathogens presents an Open Access compendium of "lessons-that-last." This living collection of short, educational, and highly useful articles addresses topics of relevance and importance within the wide-ranging field of pathogens research, with insights for trainees and scientists at all career stages.
In a commitment to increasing the evidence base for improving child health, PLOS journals publish high-quality, Open Access research and commentary on Pediatric Medicine. Open Access publication ensures this crucial evidence is freely available to read and use throughout the world without restriction. In 2014, PLOS Medicine celebrated a decade of publishing. PLOS Medicine marked the journal's tenth anniversary with a call for research papers on the health and well-being of pre-adolescent children, including 10-year-olds, from around the world. The papers that resulted from this call are included below.
The Council of Science Editors organized a Global Theme Issue on Poverty and Human Development in October 2007. More than 200 science and health journals, including PLOS Medicine, PLOS Biology, and PLOS Neglected Tropical Diseases, participated by publishing new articles.
In several recent PLOS Neglected Tropical Diseases papers on rabies marking the third anniversary of World Rabies Day scientists describe the situation of canine rabies control in developing countries, as well as various recent advances in the development of vaccines and treatments that will contribute to the elimination of human deaths from rabies.
In most low-income countries, Ministries of Health and their partners must rely on periodic household surveys as their primary population-level source of vital statistics. Recent initiatives around the Millennium Development Goals have directed the attention of the scientific, policy, and practice communities towards the limited progress over the last 60 years in improving vital statistics systems in low-income countries, leading to increased demands by public health officials for the measurement of short-term changes in under-five mortality. Few studies have examined the accuracy of real-time mortality measurement in low resource settings, and the potential for such approaches to be strengthened and scaled up. This new PLOS Collection brings together the results of a five-year program of research focused on improving the measurement of short-term changes in neonatal and child mortality in low-resource settings.
More than half of the world's population is at risk of helminthiases, and millions of people are currently infected with one or more helminth species. Consequences of infection include suffering, stigmatization, morbidity, and premature death. These infections are associated with low work productivity, poor cognitive performance, and slow socioeconomic development, thereby contributing to accentuate poverty and inequality.The Disease Reference Group on Helminth Infections (DRG4) put forward a series of reviews that, taken together, outline a compelling research and development (R&D) agenda for the control and elimination of helminth diseases of humans.
This collection of essays from prominent workers in the field of bioinformatics relates how selected scientific, technological, economic, and even cultural threads came to influence the development of the field we know today. Collection Editor: David B. Searls is an Independent Consultant based in Philadelphia, Pennsylvania, United States of America.
In the February 2011 issue of PLOS Neglected Tropical Diseases (PLOS NTDs), Simarro and colleagues report in "The Human African Trypanosomiasis Control and Surveillance Programme of the World Health Organization 2000-2009: The Way Forward" that new cases of human African trypanosomiasis (HAT), more familiarly known as sleeping sickness, fell below 10,000 in 2009, perhaps signaling the end to this epidemic cycle. Deputy Editor-in-Chief Serap Aksoy elaborates on this finding in her editorial, titled "Sleeping Sickness Elimination in Sight: Time to Celebrate, Reflect but not Relax." To highlight the existing literature PLOS NTDs authors have contributed to the field, Dr. Aksoy combed the archives to find those articles on HAT that we have published with potential applications for disease control.
The PLOS Computational Biology Software Section was launched in 2011 and has been steadily gathering momentum since its beginnings. Handled by our Software Editors, Software articles highlight and describe outstanding open source software of exceptional importance that has been shown to provide new biological insights, either as a part of the Software article, or published elsewhere.
This collection of articles represents the output of a group of international research institutions (informally referred to as EUMOOD) who collaborated around the causal link between stress exposure and depression vulnerability. Within the collection, preclinical and clinical research papers present an integrated experimental effort, employing a variety of methods and concepts from different disciplines such as biological psychiatry, neuroscience, and neuroendocrinology. Editorial oversight, and coordination of the peer-review was provided by Bernhard Baune, PLOS ONE Section Editor for Neuroscience and Psychiatry.
When global policymakers address the health and economic impact of the soil-transmitted helminth infections, they generally refer to the "unholy trinity" of ascariasis, hookworm infection, and trichuriasis. However, increasing information suggests that strongyloidiasis is an important fourth soil-transmitted helminthiasis. There are many reasons for the global neglect of strongyloidiasis, not the least of which is the inconvenient truth that there are little or no global burden of disease data for this infection, nor even any accurate accounting for the actual number of people infected. We also know very little about the true geographic distribution of strongyloidiasis. This special collection will help to highlight this somewhat mysterious yet very important neglected tropical disease, its enormous potential global impact on human health, and the urgent need for basic and applied research.
Across all realms of the sciences, the rapid growth in the number of works published digitally presents new challenges and opportunities for making sense of this wealth of textual information. The maturing field of Text Mining aims to solve problems concerning the retrieval, extraction and analysis of unstructured information in digital text, and revolutionize how scientists access and interpret data that might otherwise remain buried in the literature. PLOS acknowledges the growing body of work in the area of Text Mining by bringing together reviews and research studies to create the PLOS Text Mining Collection. It is no coincidence that research in Text Mining is burgeoning: the widespread uptake of the Open Access publishing model developed by PLOS and other publishers now makes it easier than ever to obtain, mine and redistribute data from published texts.
This collection aims to increase the coverage of computational biology topics in Wikipedia by rewarding authors with a citable, PubMed-indexed static version of the living document on Wikipedia. All Topic Pages undergo a fully open peer-review process on the Topic Pages wiki, with the reviews and responses posted to both the static article and Wikipedia talk page on publication. The Collection Editors are Daniel Mietchen and Shoshana J. Wodak.