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Monday, April 1, 2019

PubMed

From Wikipedia, the free encyclopedia

US-NLM-PubMed-Logo.svg
Contact
Research centerUnited States National Library of Medicine (NLM)
Release dateJanuary 1996
Access
Websitewww.ncbi.nlm.nih.gov/pubmed/

PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval.

From 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home- and office-based MEDLINE searching. The PubMed system was offered free to the public starting in June 1997.

Content

In addition to MEDLINE, PubMed provides access to:
  • older references from the print version of Index Medicus, back to 1951 and earlier
  • references to some journals before they were indexed in Index Medicus and MEDLINE, for instance Science, BMJ, and Annals of Surgery
  • very recent entries to records for an article before it is indexed with Medical Subject Headings (MeSH) and added to MEDLINE
  • a collection of books available full-text and other subsets of NLM records
  • PMC citations
  • NCBI Bookshelf
Many PubMed records contain links to full text articles, some of which are freely available, often in PubMed Central and local mirrors such as UK PubMed Central.

Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog.

As of 6 December 2018, PubMed has more than 29.1 million records going back to 1966, selectively to the year 1865, and very selectively to 1809; about 500,000 new records are added each year. As of the same date, 13.1 million of PubMed's records are listed with their abstracts, and 14.2 million articles have links to full-text (of which 3.8 million articles are available, full-text for free for any user). Approximately 12% of the records in PubMed correspond to cancer-related entries, which have grown from 6% in the 1950s to 16% in 2016. Other significant proportion of records correspond to "chemistry" (8.69%), "therapy" (8.39%), and "infection" (5%).

In 2016, NLM changed the indexing system so that publishers will be able to directly correct typos and errors in PubMed indexed articles.

Characteristics

Standard searches

Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMed's search window.

PubMed translates this initial search formulation and automatically adds field names, relevant MeSH (Medical Subject Headings) terms, synonyms, Boolean operators, and 'nests' the resulting terms appropriately, enhancing the search formulation significantly, in particular by routinely combining (using the OR operator) textwords and MeSH terms. 

The examples given in a PubMed tutorial demonstrate how this automatic process works:
Causes Sleep Walking is translated as ("etiology"[Subheading] OR "etiology"[All Fields] OR "causes"[All Fields] OR "causality"[MeSH Terms] OR "causality"[All Fields]) AND ("somnambulism"[MeSH Terms] OR "somnambulism"[All Fields] OR ("sleep"[All Fields] AND "walking"[All Fields]) OR "sleep walking"[All Fields])
Likewise,
soft
Attack Aspirin Prevention is translated as ("myocardial infarction"[MeSH Terms] OR ("myocardial"[All Fields] AND "infarction"[All Fields]) OR "myocardial infarction"[All Fields] OR ("heart"[All Fields] AND "attack"[All Fields]) OR "heart attack"[All Fields]) AND ("aspirin"[MeSH Terms] OR "aspirin"[All Fields]) AND ("prevention and control"[Subheading] OR ("prevention"[All Fields] AND "control"[All Fields]) OR "prevention and control"[All Fields] OR "prevention"[All Fields])
A new PubMed interface was launched in October 2009 and encouraged the use of such quick, Google-like search formulations; they have also been described as 'telegram' searches. By default the results are sorted by Most Recent, but this can be changed to Best Match, Publication Date, First Author, Last Author, Journal, or Title.

Comprehensive searches

For optimal searches in PubMed, it is necessary to understand its core component, MEDLINE, and especially of the MeSH (Medical Subject Headings) controlled vocabulary used to index MEDLINE articles. They may also require complex search strategies, use of field names (tags), proper use of limits and other features; reference librarians and search specialists offer search services.

Journal article parameters

When a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are: Article Type (MeSH terms, e.g., "Clinical Trial"), Secondary identifiers, (MeSH terms), Language, Country of the Journal or publication history (e-publication date, print journal publication date).

Publication Type: Clinical queries/systematic reviews

Publication type parameter allows searching by the type of publication, including reports of various kinds of clinical research.

Secondary ID

Since July 2005, the MEDLINE article indexing process extracts identifiers from the article abstract and puts those in a field called Secondary Identifier (SI). The secondary identifier field is to store accession numbers to various databases of molecular sequence data, gene expression or chemical compounds and clinical trial IDs. For clinical trials, PubMed extracts trial IDs for the two largest trial registries: ClinicalTrials.gov (NCT identifier) and the International Standard Randomized Controlled Trial Number Register (IRCTN identifier).

See also

A reference which is judged particularly relevant can be marked and "related articles" can be identified. If relevant, several studies can be selected and related articles to all of them can be generated (on PubMed or any of the other NCBI Entrez databases) using the 'Find related data' option. The related articles are then listed in order of "relatedness". To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The 'related articles' function has been judged to be so precise that the authors of a paper suggested it can be used instead of a full search.

Mapping to MeSH

PubMed automatically links to MeSH terms and subheadings. Examples would be: "bad breath" links to (and includes in the search) "halitosis", "heart attack" to "myocardial infarction", "breast cancer" to "breast neoplasms". Where appropriate, these MeSH terms are automatically "expanded", that is, include more specific terms. Terms like "nursing" are automatically linked to "Nursing [MeSH]" or "Nursing [Subheading]". This feature is called Auto Term Mapping and is enacted, by default, in free text searching but not exact phrase searching (i.e. enclosing the search query with double quotes). This feature makes PubMed searches more sensitive and avoids false-negative (missed) hits by compensating for the diversity of medical terminology.

My NCBI

The PubMed optional facility "My NCBI" (with free registration) provides tools for
  • saving searches
  • filtering search results
  • setting up automatic updates sent by e-mail
  • saving sets of references retrieved as part of a PubMed search
  • configuring display formats or highlighting search terms
and a wide range of other options. The "My NCBI" area can be accessed from any computer with web-access. An earlier version of "My NCBI" was called "PubMed Cubby".

LinkOut

LinkOut, a NLM facility to link (and make available full-text) local journal holdings. Some 3,200 sites (mainly academic institutions) participate in this NLM facility (as of March 2010), from Aalborg University in Denmark to ZymoGenetics in Seattle. Users at these institutions see their institution's logo within the PubMed search result (if the journal is held at that institution) and can access the full-text. Link out is being consolodated with Outside Tool as of the major platform update coming in the Summer of 2019. 

PubMed Commons

In 2016, PubMed allows authors of articles to comment on articles indexed by PubMed. This feature was initially tested in a pilot mode (since 2013) and was made permanent in 2016. In February 2018, PubMed Commons was discontinued due to the fact that "usage has remained minimal".

PubMed for handhelds/mobiles

PubMed/MEDLINE can be accessed via handheld devices, using for instance the "PICO" option (for focused clinical questions) created by the NLM. A "PubMed Mobile" option, providing access to a mobile friendly, simplified PubMed version, is also available.

askMEDLINE

askMEDLINE, a free-text, natural language query tool for MEDLINE/PubMed, developed by the NLM, also suitable for handhelds.

PubMed identifier

A PMID (PubMed identifier or PubMed unique identifier) is a unique integer value, starting at 1, assigned to each PubMed record. A PMID is not the same as a PMCID which is the identifier for all works published in the free-to-access PubMed Central.

The assignment of a PMID or PMCID to a publication tells the reader nothing about the type or quality of the content. PMIDs are assigned to letters to the editor, editorial opinions, op-ed columns, and any other piece that the editor chooses to include in the journal, as well as peer-reviewed papers. The existence of the identification number is also not proof that the papers have not been retracted for fraud, incompetence, or misconduct. The announcement about any corrections to original papers may be assigned a PMID.

Alternative interfaces

MEDLINE is one of the databases which are accessible via PubMed. Several companies provide access to MEDLINE through their platforms.
 
The National Library of Medicine leases the MEDLINE information to a number of private vendors such as Embase, Ovid, Dialog, EBSCO, Knowledge Finder and many other commercial, non-commercial, and academic providers. As of October 2008, more than 500 licenses had been issued, more than 200 of them to providers outside the United States. As licenses to use MEDLINE data are available for free, the NLM in effect provides a free testing ground for a wide range of alternative interfaces and 3rd party additions to PubMed, one of a very few large, professionally curated databases which offers this option. 

Lu identifies a sample of 28 current and free Web-based PubMed versions, requiring no installation or registration, which are grouped into four categories:
  1. Ranking search results, for instance: eTBLAST; MedlineRanker; MiSearch;
  2. Clustering results by topics, authors, journals etc., for instance: Anne O'Tate; ClusterMed;
  3. Enhancing semantics and visualization, for instance: EBIMed; MedEvi.
  4. Improved search interface and retrieval experience, for instance, askMEDLINE BabelMeSH; and PubCrawler.
As most of these and other alternatives rely essentially on PubMed/MEDLINE data leased under license from the NLM/PubMed, the term "PubMed derivatives" has been suggested. Without the need to store about 90 GB of original PubMed Datasets, anybody can write PubMed applications using the eutils-application program interface as described in "The E-utilities In-Depth: Parameters, Syntax and More", by Eric Sayers, PhD. Various citation format generators, taking PMID numbers as input, are examples of web applications making use of the eutils-application program interface. Sample web pages include Citation Generator - Mick Schroeder, Pubmed Citation Generator - Ultrasound of the Week, PMID2cite, and Cite this for me.

Data mining of PubMed

Alternative methods to mine the data in PubMed use programming environments such as Matlab, Python or R. In these cases, queries of PubMed are written as lines of code and passed to PubMed and the response is then processed directly in the programming environment. Code can be automated to systematically queries with different keywords such as disease, year, organs, etc. A recent publication (2017) found that the proportion of cancer-related entries in PubMed has risen from 6% in the 1950s to 16% in 2016.

The data accessible by PubMed can be mirrored locally using an unofficial tool such as MEDOC.

National Institutes of Health

From Wikipedia, the free encyclopedia

NIH Master Logo Vertical 2Color.png
National Institutes of Health logo
NIH Clinical Research Center aerial.jpg
Aerial photo of the NIH Mark O. Hatfield Clinical Research Center, Bethesda, Maryland
Agency overview
Formed1887
Preceding agency
  • Hygienic Laboratory
HeadquartersBethesda, Maryland, U.S.
Employees20,262
Annual budgetIncrease US$37 billion (as of 2018)
Agency executive
Parent agencyDepartment of Health & Human Services
Child agencies
Websitewww.nih.gov

The National Institutes of Health (NIH) is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late 1870s and is now part of the United States Department of Health and Human Services. The majority of NIH facilities are located in Bethesda, Maryland. The NIH conducts its own scientific research through its Intramural Research Program (IRP) and provides major biomedical research funding to non-NIH research facilities through its Extramural Research Program.

As of 2013, the IRP had 1,200 principal investigators and more than 4,000 postdoctoral fellows in basic, translational, and clinical research, being the largest biomedical research institution in the world, while, as of 2003, the extramural arm provided 28% of biomedical research funding spent annually in the U.S., or about US$26.4 billion.

The NIH comprises 27 separate institutes and centers of different biomedical disciplines and is responsible for many scientific accomplishments, including the discovery of fluoride to prevent tooth decay, the use of lithium to manage bipolar disorder, and the creation of vaccines against hepatitis, Haemophilus influenzae (HIB), and human papillomavirus (HPV).

History

The Laboratory of Hygiene in 1887
 
Ida A. Bengtson, a bacteriologist who in 1916 was the first woman hired to work in the Hygienic Laboratory.
 
Dedication of first six NIH buildings by President Franklin D. Roosevelt in 1940
 
NIH campus in Bethesda, Maryland, in 1945
 
NIH's roots extend back to the Marine Hospital Service in the late 1790s that provided medical relief to sick and disabled men in the U.S. Navy. By 1870, a network of marine hospitals had developed and was placed under the charge of a medical officer within the Bureau of the Treasury Department. In the late 1870s, Congress allocated funds to investigate the causes of epidemics like cholera and yellow fever, and it created the National Board of Health, making medical research an official government initiative.

In 1887, a laboratory for the study of bacteria, the Hygienic Laboratory, was established at the Marine Hospital in New York. In the early 1900s, Congress began appropriating funds for the Marine Hospital Service. By 1922, this organization changed its name to Public Health Services and established a Special Cancer Investigations laboratory at Harvard Medical School. This marked the beginning of a partnership with universities. In 1930, the Hygienic Laboratory was re-designated as the National Institute of Health by the Ransdell Act, and was given $750,000 to construct two NIH buildings. Over the next few decades, Congress would increase funding tremendously to the NIH, and various institutes and centers within the NIH were created for specific research programs. In 1944, the Public Health Service Act was approved, and the National Cancer Institute became a division of NIH. In 1948, the name changed from National Institute of Health to National Institutes of Health. 

In the 1960s, virologist and cancer researcher Chester M. Southam injected HeLa cancer cells into patients at the Jewish Chronic Disease Hospital. When three doctors resigned after refusing to inject patients without their consent, the experiment gained considerable media attention. The NIH was a major source of funding for Southam's research and had required all research involving human subjects to obtain their consent prior to any experimentation. Upon investigating all of their grantee institutions, the NIH discovered that the majority of them did not protect the rights of human subjects. From then on, the NIH has required all grantee institutions to approve any research proposals involving human experimentation with review boards.

In 1967, the Division of Regional Medical Programs was created to administer grants for research for heart disease, cancer, and strokes. That same year, the NIH director lobbied the White House for increased federal funding in order to increase research and the speed with which health benefits could be brought to the people. An advisory committee was formed to oversee further development of the NIH and its research programs. By 1971 cancer research was in full force and President Nixon signed the National Cancer Act, initiating a National Cancer Program, President's Cancer Panel, National Cancer Advisory Board, and 15 new research, training, and demonstration centers.

Funding for the NIH has often been a source of contention in Congress, serving as a proxy for the political currents of the time. In 1992, the NIH encompassed nearly 1 percent of the federal government's operating budget and controlled more than 50 percent of all funding for health research, and 85 percent of all funding for health studies in universities. While government funding for research in other disciplines has been increasing at a rate similar to inflation since the 1970s, research funding for the NIH nearly tripled through the 1990s and early 2000s, but has remained relatively stagnant since then.

By the 1990s, the NIH committee focus had shifted to DNA research, and launched the Human Genome Project.

Directors

The NIH Office of the Director is the central office responsible for setting policy for NIH, and for planning, managing and coordinating the programs and activities of all NIH components. The NIH Director plays an active role in shaping the agency's activities and outlook. The Director is responsible for providing leadership to the Institutes and Centers by identifying needs and opportunities, especially in efforts involving multiple Institutes. Within this Office is the Division of Program Coordination, Planning and Strategic Initiatives with 12 divisions including:
Previous directors:

Locations and campuses

Intramural research is primarily conducted at the main campus in Bethesda, Maryland and Rockville, Maryland, and the surrounding communities. 

The Bayview Campus in Baltimore, Maryland houses the research programs of the National Institute on Aging, National Institute on Drug Abuse, and National Human Genome Research Institute with nearly 1,000 scientists and support staff. The Frederick National Laboratory in Frederick, MD and the nearby Riverside Research Park, houses many components of the National Cancer Institute, including the Center for Cancer Research, Office of Scientific Operations, Management Operations Support Branch, the division of Cancer Epidemiology and Genetics and the division of Cancer Treatment and Diagnosis.


Other ICs have satellite locations in addition to operations at the main campus. The National Institute of Allergy and Infectious Diseases maintains its Rocky Mountain Labs in Hamilton, Montana, with an emphasis on BSL3 and BSL4 laboratory work. NIDKK operates the Phoenix Epidemiology and Clinical Research Branch in Phoenix, AZ.

Research

Clinical Center – Building 10
 
As of 2017, 153 scientists receiving financial support from the NIH have been awarded a Nobel Prize and 195 have been awarded a Lasker Award.

Intramural research

NIH devotes 10% of its funding to research within its own facilities (intramural research). The institution gives 80% of its funding in research grants to extramural (outside) researchers. Of this extramural funding, a certain percentage (2.8% in 2014) must be granted to small businesses under the SBIR/STTR program. The extramural funding consists of about 50,000 grants to more than 325,000 researchers at more than 3000 institutions. In FY 2010, NIH spent US$10.7bn (not including temporary funding from the American Recovery and Reinvestment Act of 2009) on clinical research, US$7.4bn on genetics-related research, US$6.0bn on prevention research, US$5.8bn on cancer, and US$5.7bn on biotechnology.

Public Access Policy

In 2008 a Congressional mandate called for investigators funded by the NIH to submit an electronic version of their final manuscripts to the National Library of Medicine's research repository, PubMed Central (PMC), no later than 12 months after the official date of publication. The NIH Public Access Policy was the first public access mandate for a U.S. public funding agency.

NIH Interagency Pain Research Coordinating Committee

On February 13, 2012, the National Institutes of Health (NIH) announced a new group of individuals assigned to research pain. This committee is composed of researchers from different organizations and will focus to "coordinate pain research activities across the federal government with the goals of stimulating pain research collaboration… and providing an important avenue for public involvement" ("Members of new," 2012). With a committee such as this research will not be conducted by each individual organization or person but instead a collaborating group which will increase the information available. With this hopefully more pain management will be available including techniques for arthritis sufferers.

Economic return

In 2000, the Joint Economic Committee of Congress reported NIH research, which was funded at $16 billion a year in 2000, that some econometric studies had given a rate of return of 25 to 40 percent per year by reducing the economic cost of illness in the US. It found that of the 21 drugs with the highest therapeutic impact on society introduced between 1965 and 1992, public funding was "instrumental" for 15. As of 2011 NIH-supported research helped to discover 153 new FDA-approved drugs, vaccines, and new indications for drugs in the 40 years prior. One study found NIH funding aided either directly or indirectly in developing the drugs or drug targets for all of the 210 FDA-approved drugs from 2010 to 2016. In 2015, Pierre Azoulay et al. estimated $10 million invested in research generated two to three new patents.

Notable discoveries and developments

Since its inception, the NIH intramural research program has been a source of many pivotal scientific and medical discoveries. Some of these include:
  • 1908 – George W. McCoy's discovery that rodents were a reservoir of bubonic plague.
  • 1911 – George W. McCoy, Charles W. Chapin, William B. Wherry, and B. H. Lamb described the previously-unknown tularemia.
  • 1924 – Roscoe R. Spencer and Ralph R. Parker developed a vaccine against Rocky Mountain spotted fever.
  • 1930 – Sanford M. Rosenthal developed a treatment for mercury poisoning used widely before the development of dimercaptoethanol.
  • 1943 – Wilton R. Earle pioneered the cell culture process and published a paper describing the production of malignancy in vitro, Katherine K. Sanford developed the first clone from an isolated cancer cell, and Virginia J. Evans devised a medium that supported growth of cells in vitro.
  • 1940s-50s – Bernard Horecker and colleagues described the pentose phosphate pathway.
  • 1950s – Julius Axelrod discovered a new class of enzymes, cytochrome P450 monooxygenases, a fundamental of drug metabolism.
  • 1950 – Earl Stadtman discovered phosphotransacetylose, elucidating the role of acetyl CoA in fatty acid metabolism.
  • 1960s – Discovered the first human slow virus disease, kuru, which is a degenerative, fatal infection of the central nervous system. This discovery of a new mechanism for infectious diseases revolutionized thinking in microbiology and neurology.
  • 1960s – Defined the mechanisms that regulate noradrenaline, one of the most important neurotransmitters in the brain.
  • 1960s – Developed the first licensed rubella vaccine and the first test for rubella antibodies for large scale testing.
  • 1960s – Developed an effective combination drug regimen for Hodgkin's lymphoma.
  • 1960s – Discovery that tooth decay is caused by bacteria.
  • 1970s – Developed the assay for human chorionic gonadotropin that evolved into the home pregnancy tests.
  • 1970s – Described the hormonal cycle involved in menstruation.
  • 1980s – Determined the complete structure of the IgE receptor that is involved in allergic reactions.
  • 1990s – First trial of gene therapy in humans.

NIH Toolbox

In September 2006, the NIH Blueprint for Neuroscience Research started a contract for the NIH Toolbox for the Assessment of Neurological and Behavioral Function to develop a set of state-of-the-art measurement tools to enhance collection of data in large cohort studies. Scientists from more than 100 institutions nationwide contributed. In September 2012, the NIH Toolbox was rolled out to the research community. NIH Toolbox assessments are based, where possible, on Item Response Theory and adapted for testing by computer.

Funding

Budget and politics

Historical NIH budget
Year Budget (millions)
1938 0.5
1940 0.7
1945 2.8
1950 52.7
1955 81.2
1960 399.4
1965 959.2
1970 1,061.0
1975 2,092.9
1980 3,428.9
1985 5,149.5
1990 7,567.4
1995 11,299.5
2000 17,840.5
2005 28,594.4
2010 31,238.0
2015 30,311.4
2016 32,311.4
2017 34,300.9
2018 37,311.3

To allocate funds, the NIH must first obtain its budget from Congress. This process begins with institute and center (IC) leaders collaborating with scientists to determine the most important and promising research areas within their fields. IC leaders discuss research areas with NIH management who then develops a budget request for continuing projects, new research proposals, and new initiatives from the Director. NIH submits its budget request to the Department of Health and Human Services (HHS), and the HHS considers this request as a portion of its budget. Many adjustments and appeals occur between NIH and HHS before the agency submits NIH's budget request to the Office of Management and Budget (OMB). OMB determines what amounts and research areas are approved for incorporation into the President's final budget. The President then sends NIH's budget request to Congress in February for the next fiscal year's allocations. The House and Senate Appropriations Subcommittees deliberate and by fall, Congress usually appropriates funding. This process takes approximately 18 months before the NIH can allocate any actual funds.

Historical funding

Over the last century, the responsibility to allocate funding has shifted from the OD and Advisory Committee to the individual ICs and Congress increasingly set apart funding for particular causes. In the 1970s, Congress began to earmark funds specifically for cancer research, and in the 1980s there was a significant amount allocated for AIDS/HIV research.

Funding for the NIH has often been a source of contention in Congress, serving as a proxy for the political currents of the time. During the 1980s, President Reagan repeatedly tried to cut funding for research, only to see Congress partly restore funding. The political contention over NIH funding slowed the nation's response to the AIDS epidemic; while AIDS was reported in newspaper articles from 1981, no funding was provided for research on the disease. In 1984 National Cancer Institute scientists found implications that "variants of a human cancer virus called HTLV-III are the primary cause of acquired immunodeficiency syndrome (AIDS)," a new epidemic that gripped the nation.

In 1992, the NIH encompassed nearly 1 percent of the federal government's operating budget and controlled more than 50 percent of all funding for health research and 85 percent of all funding for health studies in universities. From 1993 to 2001 the NIH budget doubled. Since then, funding essentially remained flat, and during the decade following the financial crisis, the NIH budget struggled to keep up with inflation.

In 1999 Congress increased the NIH's budget by $2.3 billion to $17.2 billion in 2000. In 2009 Congress again increased the NIH budget to $31 billion in 2010. In 2017 and 2018, despite President Trump's proposals to cut the NIH budget, Congress passed laws with bipartisan support that substantially increasing appropriations for NIH, which was 37.3 billion dollars annually in FY2018.

Extramural research

Researchers at universities or other institutions outside of NIH can apply for research project grants (RPGs) from the NIH. There are numerous funding mechanisms for different project types (e.g., basic research, clinical research etc.) and career stages (e.g., early career, postdoc fellowships etc.). The NIH regularly issues "requests for applications" (RFAs), e.g., on specific programmatic priorities or timely medical problems (such as Zika virus research in early 2016). In addition, researchers can apply for "investigator-initiated grants" whose subject is determined by the scientist. 

The total number of applicants has increased substantially, from about 60,000 investigators who had applied during the period from 1999 to 2003 to slightly less than 90,000 in who had applied during the period from 2011 to 2015. Due to this, the "cumulative investigator rate," that is, the likelihood that unique investigators are funded over a 5-year window, has declined from 43% to 31%.

R01 grants are the most common funding mechanism and include investigator-initiated projects. The roughly 27,000 to 29,000 R01 applications had a funding success of 17-19% during 2012 though 2014. Similarly, the 13,000 to 14,000 R21 applications had a funding success of 13-14% during the same period. In FY 2016, the total number of grant applications received by the NIH was 54,220, with approximately 19% being awarded funding. Institutes have varying funding rates. The National Cancer Institute awarded funding to 12% of applicants, while the National Institute for General Medical Science awarded funding to 30% of applicants.

Funding criteria

NIH employs five broad decision criteria in its funding policy. First, ensure the highest quality of scientific research by employing an arduous peer review process. Second, seize opportunities that have the greatest potential to yield new knowledge and that will lead to better prevention and treatment of disease. Third, maintain a diverse research portfolio in order to capitalize on major discoveries in a variety of fields such as cell biology, genetics, physics, engineering, and computer science. Fourth, address public health needs according to the disease burden (e.g., prevalence and mortality). And fifth, construct and support the scientific infrastructure (e.g., well-equipped laboratories and safe research facilities) necessary to conduct research.

Advisory committee members advise the Institute on policy and procedures affecting the external research programs and provide a second level of review for all grant and cooperative agreement applications considered by the Institute for funding.

Gender and sex bias

In 2014, it was announced that the NIH is directing scientists to perform their experiments with both female and male animals, or cells derived from females as well as males if they are studying cell cultures, and that the NIH would take the balance of each study design into consideration when awarding grants. The announcement also stated that this rule would probably not apply when studying sex-specific diseases (for example, ovarian or testicular cancer).

Government shutdown

When a government shutdown occurs, the NIH continues to treat people who are already enrolled in clinical trials, but does not start any new clinical trials and does not admit new patients who are not already enrolled in a clinical trial, except for the most critically ill, as determined by the NIH Director.

Stakeholders

General public

One of the goals of the NIH is to "expand the base in medical and associated sciences in order to ensure a continued high return on the public investment in research." Taxpayer dollars funding NIH are from the taxpayers, making them the primary beneficiaries of advances in research. Thus, the general public is a key stakeholder in the decisions resulting from the NIH funding policy. However, some in the general public do not feel their interests are being represented, and individuals have formed patient advocacy groups to represent their own interests.

Extramural researchers and scientists

Important stakeholders of the NIH funding policy include researchers and scientists. Extramural researchers differ from intramural researchers in that they are not employed by the NIH but may apply for funding. Throughout the history of the NIH, the amount of funding received has increased, but the proportion to each IC remains relatively constant. The individual ICs then decide who will receive the grant money and how much will be allotted. 

Policy changes on who receives funding significantly affects researchers. For example, the NIH has recently attempted to approve more first-time NIH R01 applicants, or the research grant applications of young scientists. To encourage the participation of young scientists, the application process has been shortened and made easier. In addition, first-time applicants are being offered more funding for their research grants than those who have received grants in the past.

Commercial partnerships

In 2011 and 2012, the Department of Health and Human Services Office of Inspector General published a series of audit reports revealing that throughout the fiscal years 2000–2010, institutes under the aegis of the NIH did not comply with the time and amount requirements specified in appropriations statutes, in awarding federal contracts to commercial partners, committing the federal government to tens of millions of dollars of expenditure ahead of appropriation of funds from Congress.

Institutes and centers

The NIH is composed of 27 separate institutes and centers (ICs) that conduct and coordinate research across different disciplines of biomedical science. These are: 





In addition, the National Center for Research Resources operated from April 13, 1962 to December 23, 2011.

Research

From Wikipedia, the free encyclopedia

Basrelief sculpture "Research holding the torch of knowledge" (1896) by Olin Levi Warner. Library of Congress, Thomas Jefferson Building, in Washington, D.C.

Research comprises "creative and systematic work undertaken to increase the stock of knowledge, including knowledge of humans, culture and society, and the use of this stock of knowledge to devise new applications." It is used to establish or confirm facts, reaffirm the results of previous work, solve new or existing problems, support theorems, or develop new theories. A research project may also be an expansion on past work in the field. Research projects can be used to develop further knowledge on a topic, or in the example of a school research project, they can be used to further a student's research prowess to prepare them for future jobs or reports. To test the validity of instruments, procedures, or experiments, research may replicate elements of prior projects or the project as a whole. The primary purposes of basic research (as opposed to applied research) are documentation, discovery, interpretation, or the research and development (R&D) of methods and systems for the advancement of human knowledge. Approaches to research depend on epistemologies, which vary considerably both within and between humanities and sciences. There are several forms of research: scientific, humanities, artistic, economic, social, business, marketing, practitioner research, life, technological, etc.

Etymology

Aristotle, (384–322 BC), one of the early figures in the development of the scientific method.
 
The word research is derived from the Middle French "recherche", which means "to go about seeking", the term itself being derived from the Old French term "recerchier" a compound word from "re-" + "cerchier", or "sercher", meaning 'search'. The earliest recorded use of the term was in 1577.

Definitions

Research has been defined in a number of different ways, and while there are similarities, there does not appear to be a single, all-encompassing definition that is embraced by all who engage in it. 

One definition of research is used by the OECD, "Any creative systematic activity undertaken in order to increase the stock of knowledge, including knowledge of man, culture and society, and the use of this knowledge to devise new applications."

Another definition of research is given by John W. Creswell, who states that "research is a process of steps used to collect and analyze information to increase our understanding of a topic or issue". It consists of three steps: pose a question, collect data to answer the question, and present an answer to the question.

The Merriam-Webster Online Dictionary defines research in more detail as "studious inquiry or examination; especially : investigation or experimentation aimed at the discovery and interpretation of facts, revision of accepted theories or laws in the light of new facts, or practical application of such new or revised theories or laws"

Forms of research

Original research is research that is not exclusively based on a summary, review or synthesis of earlier publications on the subject of research. This material is of a primary source character. The purpose of the original research is to produce new knowledge, rather than to present the existing knowledge in a new form (e.g., summarized or classified).

Original research can take a number of forms, depending on the discipline it pertains to. In experimental work, it typically involves direct or indirect observation of the researched subject(s), e.g., in the laboratory or in the field, documents the methodology, results, and conclusions of an experiment or set of experiments, or offers a novel interpretation of previous results. In analytical work, there are typically some new (for example) mathematical results produced, or a new way of approaching an existing problem. In some subjects which do not typically carry out experimentation or analysis of this kind, the originality is in the particular way existing understanding is changed or re-interpreted based on the outcome of the work of the researcher.

The degree of originality of the research is among major criteria for articles to be published in academic journals and usually established by means of peer review. Graduate students are commonly required to perform original research as part of a dissertation.

Scientific research is a systematic way of gathering data and harnessing curiosity. This research provides scientific information and theories for the explanation of the nature and the properties of the world. It makes practical applications possible. Scientific research is funded by public authorities, by charitable organizations and by private groups, including many companies. Scientific research can be subdivided into different classifications according to their academic and application disciplines. Scientific research is a widely used criterion for judging the standing of an academic institution, but some argue that such is an inaccurate assessment of the institution, because the quality of research does not tell about the quality of teaching (these do not necessarily correlate).

Research in the humanities involves different methods such as for example hermeneutics and semiotics. Humanities scholars usually do not search for the ultimate correct answer to a question, but instead, explore the issues and details that surround it. Context is always important, and context can be social, historical, political, cultural, or ethnic. An example of research in the humanities is historical research, which is embodied in historical method. Historians use primary sources and other evidence to systematically investigate a topic, and then to write histories in the form of accounts of the past. Other studies aim to merely examine the occurrence of behaviours in societies and communities, without particularly looking for reasons or motivations to explain these. These studies may be qualitative or quantitative, and can use a variety of approaches, such as queer theory or feminist theory.

Artistic research, also seen as 'practice-based research', can take form when creative works are considered both the research and the object of research itself. It is the debatable body of thought which offers an alternative to purely scientific methods in research in its search for knowledge and truth.

Scientific research

Primary scientific research being carried out at the Microscopy Laboratory of the Idaho National Laboratory.
 
Scientific research equipment at MIT.
 
Generally, research is understood to follow a certain structural process. Though step order may vary depending on the subject matter and researcher, the following steps are usually part of most formal research, both basic and applied:
  1. Observations and formation of the topic: Consists of the subject area of one's interest and following that subject area to conduct subject related research. The subject area should not be randomly chosen since it requires reading a vast amount of literature on the topic to determine the gap in the literature the researcher intends to narrow. A keen interest in the chosen subject area is advisable. The research will have to be justified by linking its importance to already existing knowledge about the topic.
  2. Hypothesis: A testable prediction which designates the relationship between two or more variables.
  3. Conceptual definition: Description of a concept by relating it to other concepts.
  4. Operational definition: Details in regards to defining the variables and how they will be measured/assessed in the study.
  5. Gathering of data: Consists of identifying a population and selecting samples, gathering information from or about these samples by using specific research instruments. The instruments used for data collection must be valid and reliable.
  6. Analysis of data: Involves breaking down the individual pieces of data to draw conclusions about it.
  7. Data Interpretation: This can be represented through tables, figures, and pictures, and then described in words.
  8. Test, revising of hypothesis
  9. Conclusion, reiteration if necessary
A common misconception is that a hypothesis will be proven (see, rather, null hypothesis). Generally, a hypothesis is used to make predictions that can be tested by observing the outcome of an experiment. If the outcome is inconsistent with the hypothesis, then the hypothesis is rejected (see falsifiability). However, if the outcome is consistent with the hypothesis, the experiment is said to support the hypothesis. This careful language is used because researchers recognize that alternative hypotheses may also be consistent with the observations. In this sense, a hypothesis can never be proven, but rather only supported by surviving rounds of scientific testing and, eventually, becoming widely thought of as true. 

A useful hypothesis allows prediction and within the accuracy of observation of the time, the prediction will be verified. As the accuracy of observation improves with time, the hypothesis may no longer provide an accurate prediction. In this case, a new hypothesis will arise to challenge the old, and to the extent that the new hypothesis makes more accurate predictions than the old, the new will supplant it. Researchers can also use a null hypothesis, which states no relationship or difference between the independent or dependent variables.

Historical research

German historian Leopold von Ranke (1795–1886), considered to be one of the founders of modern source-based history.
 
The historical method comprises the techniques and guidelines by which historians use historical sources and other evidence to research and then to write history. There are various history guidelines that are commonly used by historians in their work, under the headings of external criticism, internal criticism, and synthesis. This includes lower criticism and sensual criticism. Though items may vary depending on the subject matter and researcher, the following concepts are part of most formal historical research:

Artistic research

The controversial trend of artistic teaching becoming more academics-oriented is leading to artistic research being accepted as the primary mode of enquiry in art as in the case of other disciplines. One of the characteristics of artistic research is that it must accept subjectivity as opposed to the classical scientific methods. As such, it is similar to the social sciences in using qualitative research and intersubjectivity as tools to apply measurement and critical analysis.

Artistic research has been defined by the University of Dance and Circus (Dans och Cirkushögskolan, DOCH), Stockholm in the following manner - "Artistic research is to investigate and test with the purpose of gaining knowledge within and for our artistic disciplines. It is based on artistic practices, methods, and criticality. Through presented documentation, the insights gained shall be placed in a context." Artistic research aims to enhance knowledge and understanding with presentation of the arts. A more simple understanding by Julian Klein defines Artistic Research as any kind of research employing the artistic mode of perception. For a survey of the central problematics of today's Artistic Research, see Giaco Schiesser.

According to artist Hakan Topal, in artistic research, "perhaps more so than other disciplines, intuition is utilized as a method to identify a wide range of new and unexpected productive modalities". Most writers, whether of fiction or non-fiction books, also have to do research to support their creative work. This may be factual, historical, or background research. Background research could include, for example, geographical or procedural research.

The Society for Artistic Research (SAR) publishes the triannual Journal for Artistic Research (JAR), an international, online, open access, and peer-reviewed journal for the identification, publication, and dissemination of artistic research and its methodologies, from all arts disciplines and it runs the Research Catalogue (RC), a searchable, documentary database of artistic research, to which anyone can contribute. 

Patricia Leavy addresses eight arts-based research (ABR) genres: narrative inquiry, fiction-based research, poetry, music, dance, theatre, film, and visual art.

In 2016 ELIA (European League of the Institutes of the Arts) launched The Florence Principles' on the Doctorate in the Arts. The Florence Principles relating to the Salzburg Principles and the Salzburg Recommendations of EUA (European University Association) name seven points of attention to specify the Doctorate / PhD in the Arts compared to a scientific doctorate / PhD The Florence Principles have been endorsed and are supported also by AEC, CILECT, CUMULUS and SAR.

Steps in conducting research

Research is often conducted using the hourglass model structure of research. The hourglass model starts with a broad spectrum for research, focusing in on the required information through the method of the project (like the neck of the hourglass), then expands the research in the form of discussion and results. The major steps in conducting research are:
  • Identification of research problem;
  • Literature review;
  • Specifying the purpose of research;
  • Determining specific research questions;
  • Specification of a conceptual framework, sometimes including a set of hypotheses;
  • Choice of a methodology (for data collection);
  • Data collection;
  • Verifying data;
  • Analyzing and interpreting the data;
  • Reporting and evaluating research;
  • Communicating the research findings and, possibly, recommendations.
The steps generally represent the overall process; however, they should be viewed as an ever-changing iterative process rather than a fixed set of steps. Most research begins with a general statement of the problem, or rather, the purpose for engaging in the study. The literature review identifies flaws or holes in previous research which provides justification for the study. Often, a literature review is conducted in a given subject area before a research question is identified. A gap in the current literature, as identified by a researcher, then engenders a research question. The research question may be parallel to the hypothesis. The hypothesis is the supposition to be tested. The researcher(s) collects data to test the hypothesis. The researcher(s) then analyzes and interprets the data via a variety of statistical methods, engaging in what is known as empirical research. The results of the data analysis in rejecting or failing to reject the null hypothesis are then reported and evaluated. At the end, the researcher may discuss avenues for further research. However, some researchers advocate for the reverse approach: starting with articulating findings and discussion of them, moving "up" to identification of a research problem that emerges in the findings and literature review. The reverse approach is justified by the transactional nature of the research endeavor where research inquiry, research questions, research method, relevant research literature, and so on are not fully known until the findings have fully emerged and been interpreted.

Rudolph Rummel says, "... no researcher should accept any one or two tests as definitive. It is only when a range of tests are consistent over many kinds of data, researchers, and methods can one have confidence in the results."

Plato in Meno talks about an inherent difficulty, if not a paradox, of doing research that can be paraphrased in the following way, "If you know what you're searching for, why do you search for it?! [i.e., you have already found it] If you don't know what you're searching for, what are you searching for?!"

Research methods

The research room at the New York Public Library, an example of secondary research in progress.
 
Maurice Hilleman is credited with saving more lives than any other scientist of the 20th century.
 
The goal of the research process is to produce new knowledge or deepen understanding of a topic or issue. This process takes three main forms (although, as previously discussed, the boundaries between them may be obscure):
There are two major types of empirical research design: qualitative research and quantitative research. Researchers choose qualitative or quantitative methods according to the nature of the research topic they want to investigate and the research questions they aim to answer:
Qualitative research
This involves understanding human behavior and the reasons that govern such behavior, by asking a broad question, collecting data in the form of words, images, video etc that is analyzed, and searching for themes. This type of research aims to investigate a question without attempting to quantifiably measure variables or look to potential relationships between variables. It is viewed as more restrictive in testing hypotheses because it can be expensive and time-consuming and typically limited to a single set of research subjects. Qualitative research is often used as a method of exploratory research as a basis for later quantitative research hypotheses. Qualitative research is linked with the philosophical and theoretical stance of social constructionism.
Social media posts are used for qualitative research.
Quantitative research
This involves systematic empirical investigation of quantitative properties and phenomena and their relationships, by asking a narrow question and collecting numerical data to analyze it utilizing statistical methods. The quantitative research designs are experimental, correlational, and survey (or descriptive). Statistics derived from quantitative research can be used to establish the existence of associative or causal relationships between variables. Quantitative research is linked with the philosophical and theoretical stance of positivism.
The quantitative data collection methods rely on random sampling and structured data collection instruments that fit diverse experiences into predetermined response categories. These methods produce results that are easy to summarize, compare, and generalize. Quantitative research is concerned with testing hypotheses derived from theory or being able to estimate the size of a phenomenon of interest.

If the research question is about people, participants may be randomly assigned to different treatments (this is the only way that a quantitative study can be considered a true experiment). If this is not feasible, the researcher may collect data on participant and situational characteristics to statistically control for their influence on the dependent, or outcome, variable. If the intent is to generalize from the research participants to a larger population, the researcher will employ probability sampling to select participants.

In either qualitative or quantitative research, the researcher(s) may collect primary or secondary data. Primary data is data collected specifically for the research, such as through interviews or questionnaires. Secondary data is data that already exists, such as census data, which can be re-used for the research. It is good ethical research practice to use secondary data wherever possible.

Mixed-method research, i.e. research that includes qualitative and quantitative elements, using both primary and secondary data, is becoming more common. This method has benefits that using one method alone cannot offer. For example, a researcher may choose to conduct a qualitative study and follow it up with a quantitative study to gain additional insights.

Big data has brought big impacts on research methods so that now many researchers do not put much effort into data collection; furthermore, methods to analyze easily available huge amounts of data have also been developed.
Non-empirical research
Non-empirical (theoretical) research is an approach that involves the development of theory as opposed to using observation and experimentation. As such, non-empirical research seeks solutions to problems using existing knowledge as its source. This, however, does not mean that new ideas and innovations cannot be found within the pool of existing and established knowledge. Non-empirical research is not an absolute alternative to empirical research because they may be used together to strengthen a research approach. Neither one is less effective than the other since they have their particular purpose in science. Typically empirical research produces observations that need to be explained; then theoretical research tries to explain them, and in so doing generates empirically testable hypotheses; these hypotheses are then tested empirically, giving more observations that may need further explanation; and so on.

A simple example of a non-empirical task is the prototyping of a new drug using a differentiated application of existing knowledge; another is the development of a business process in the form of a flow chart and texts where all the ingredients are from established knowledge. Much of cosmological research is theoretical in nature. Mathematics research does not rely on externally available data; rather, it seeks to prove theorems about mathematical objects.

Research ethics

Research ethics involves the application of fundamental ethical principles to a variety of topics involving research, including scientific research. These principles include deontology, consequentialism, virtue ethics and value (ethics). Ethical issues may arise in the design and implementation of research involving human experimentation or animal experimentation, such as: various aspects of academic scandal, including scientific misconduct (such as fraud, fabrication of data and plagiarism), whistleblowing; regulation of research, etc. Research ethics is most developed as a concept in medical research. The key agreement here is the 1964 Declaration of Helsinki. The Nuremberg Code is a former agreement, but with many still important notes. Research in the social sciences presents a different set of issues than those in medical research and can involve issues of researcher and participant safety, empowerment and access to justice.

When research involves human subjects, obtaining informed consent from them is essential.

Problems in research

Methods of research

In many disciplines, Western methods of conducting research are predominant. Researchers are overwhelmingly taught Western methods of data collection and study. The increasing participation of indigenous peoples as researchers has brought increased attention to the lacuna in culturally-sensitive methods of data collection. Non-Western methods of data collection may not be the most accurate or relevant for research on non-Western societies. For example, "Hua Oranga" was created as a criterion for psychological evaluation in Māori populations, and is based on dimensions of mental health important to the Māori people – "taha wairua (the spiritual dimension), taha hinengaro (the mental dimension), taha tinana (the physical dimension), and taha whanau (the family dimension)".

Linguicism

Periphery scholars face the challenges of exclusion and linguicism in research and academic publication. As the great majority of mainstream academic journals are written in English, multilingual periphery scholars often must translate their work to be accepted to elite Western-dominated journals. Multilingual scholars' influences from their native communicative styles can be assumed to be incompetence instead of difference.

Publication peer review

Peer review is a form of self-regulation by qualified members of a profession within the relevant field. Peer review methods are employed to maintain standards of quality, improve performance, and provide credibility. In academia, scholarly peer review is often used to determine an academic paper's suitability for publication. Usually, the peer review process involves experts in the same field who are consulted by editors to give a review of the scholarly works produced by a colleague of theirs from an unbiased and impartial point of view, and this is usually done free of charge. The tradition of peer reviews being done for free has however brought many pitfalls which are also indicative of why most peer reviewers decline many invitations to review. It was observed that publications from periphery countries rarely rise to the same elite status as those of North America and Europe, because limitations on the availability of resources including high-quality paper and sophisticated image-rendering software and printing tools render these publications less able to satisfy standards currently carrying formal or informal authority in the publishing industry. These limitations in turn result in the under-representation of scholars from periphery nations among the set of publications holding prestige status relative to the quantity and quality of those scholars' research efforts, and this under-representation in turn results in disproportionately reduced acceptance of the results of their efforts as contributions to the body of knowledge available worldwide.

Influence of the open-access movement

The open access movement assumes that all information generally deemed useful should be free and belongs to a "public domain", that of "humanity". This idea gained prevalence as a result of Western colonial history and ignores alternative conceptions of knowledge circulation. For instance, most indigenous communities consider that access to certain information proper to the group should be determined by relationships.

There is alleged to be a double standard in the Western knowledge system. On the one hand, "digital right management" used to restrict access to personal information on social networking platforms is celebrated as a protection of privacy, while simultaneously when similar functions are used by cultural groups (i.e. indigenous communities) this is denounced as "access control" and reprehended as censorship.

Future perspectives

Even though Western dominance seems to be prominent in research, some scholars, such as Simon Marginson, argue for "the need [for] a plural university world". Marginson argues that the East Asian Confucian model could take over the Western model. 

This could be due to changes in funding for research both in the East and the West. Focussed on emphasizing educational achievement, East Asian cultures, mainly in China and South Korea, have encouraged the increase of funding for research expansion. In contrast, in the Western academic world, notably in the United Kingdom as well as in some state governments in the United States, funding cuts for university research have occurred, which some say may lead to the future decline of Western dominance in research.

Professionalisation

In several national and private academic systems, the professionalisation of research has resulted in formal job titles.

In Russia

In present-day Russia, the former Soviet Union and in some post-Soviet states the term researcher (Russian: Научный сотрудник, nauchny sotrudnik) is both a generic term for a person who carried out scientific research, as well as a job position within the frameworks of the USSR Academy of Sciences, Soviet universities, and in other research-oriented establishments. 

The following ranks are known:
  • Junior Researcher (Junior Research Associate);
  • Researcher (Research Associate);
  • Senior Researcher (Senior Research Associate);
  • Leading Researcher (Leading Research Associate);
  • Chief Researcher (Chief Research Associate).

Publishing

Cover of the first issue of Nature, 4 November 1869.
 
Academic publishing is a system that is necessary for academic scholars to peer review the work and make it available for a wider audience. The system varies widely by field and is also always changing, if often slowly. Most academic work is published in journal article or book form. There is also a large body of research that exists in either a thesis or dissertation form. These forms of research can be found in databases explicitly for theses and dissertations. In publishing, STM publishing is an abbreviation for academic publications in science, technology, and medicine. Most established academic fields have their own scientific journals and other outlets for publication, though many academic journals are somewhat interdisciplinary, and publish work from several distinct fields or subfields. The kinds of publications that are accepted as contributions of knowledge or research vary greatly between fields, from the print to the electronic format. A study suggests that researchers should not give great consideration to findings that are not replicated frequently. It has also been suggested that all published studies should be subjected to some measure for assessing the validity or reliability of its procedures to prevent the publication of unproven findings. Business models are different in the electronic environment. Since about the early 1990s, licensing of electronic resources, particularly journals, has been very common. Presently, a major trend, particularly with respect to scholarly journals, is open access. There are two main forms of open access: open access publishing, in which the articles or the whole journal is freely available from the time of publication, and self-archiving, where the author makes a copy of their own work freely available on the web.

Research funding

Most funding for scientific research comes from three major sources: corporate research and development departments; private foundations, for example, the Bill and Melinda Gates Foundation; and government research councils such as the National Institutes of Health in the USA and the Medical Research Council in the UK. These are managed primarily through universities and in some cases through military contractors. Many senior researchers (such as group leaders) spend a significant amount of their time applying for grants for research funds. These grants are necessary not only for researchers to carry out their research but also as a source of merit. The Social Psychology Network provides a comprehensive list of U.S. Government and private foundation funding sources.

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