Research

Teenage Migraine Researcher Uses Mobile Technology to Enhance Study

/ melissatelli / 1 Comment

A new clinical trial for adolescent migraine is underway, and it’s harnessing the power of consumer technology to collect better data and make study participation easier. The BRAiN-M Study, which is examining whether melatonin (a natural supplement) is effective in preventing teenage migraine, uses Fitbit devices and an online “headache diary” to collect data from study participants remotely.

Besides trying to figure out how to prevent teenage migraine, the study’s lead investigator, Dr. Amy Gelfand of UCSF, is looking to make pediatric migraine clinical trials more inclusive and accessible. Continue reading →

We’ve completed our NSF Grant! UCSF Profiles and its use by external partners

/ leslieyuan / 1 Comment

UCSF Profiles is an example of a Research networking system (RNS). These systems provide automated aggregation and mining of information to create profiles and networks of the people that make up an academic institution. RNS’s have in effect, become a new kind of ‘front door’ for the university, providing access to the university’s intellectual capital in a manner previously unattainable — i.e. one focused on expertise rather than schools or departments, thus intermingling experts regardless of where they’re officially housed. Against this backdrop, we wanted to understand how such a tool might enhance access to academic expertise by external partners, specifically industry, and improve UCSF’s response to industry interest. Continue reading →

UCSF dentistry co-authorships, internal vs. external (by institutions)

/ Anirvan Chatterjee

What does a typical UCSF publication look like, in terms of the number of internal co-authors vs. the number of external co-authoring institutions? Here’s a breakdown among dentistry-related publications by UCSF researchers published in 2013. (This is the same analysis as yesterday, but looking at the number of external institutions, vs. the number of external people.)

Again, I was surprised to see so many co-authorships between a single UCSF researcher and one or researchers from one or more external institutions (the very top row of results), which accounts for 52% of the papers we looked at.

UCSF vs External Co-Authoring InstitutionsView as PDF Continue reading →

UCSF dentistry co-authorships, internal vs. external

/ Anirvan Chatterjee

What does a typical UCSF publication look like, in terms of internal vs. external co-authors? Here’s a breakdown of each type of co-author, among dentistry-related publications by UCSF researchers published in 2013.

Three immediate take-aways:

  • I was surprised to see so many co-authorships between a single UCSF researcher and one or more external researchers — the very top row of results. By volume, this accounts for 52% of the papers we looked at.
  • When every author is internal to UCSF, there’s an average of 3.5 UCSF co-authors
  • When there’s an external collaboration, there’s an average of 2.0 UCSF co-authors

UCSF vs External Co-AuthorsView as PDF Continue reading →

UCSF dentistry collaborations, visualized

/ Anirvan Chatterjee

Looking at cross-institutional co-authorship networks is a useful way of seeing not only who we work with, but also where there may be gaps of interest.

I first looked at dentistry-related publications by UCSF researchers published in 2013, breaking out the institutions we co-authored with. And there we are, sitting pretty in the center of our universe, collaborating with major institutions in the US, Korea, Australia, Italy, Denmark, and more.

(Details: Institution node sizes indicate the total volume of dentistry-related articles published. Connecting line widths indicate the number of articles co-authored between two institutions. Distance between nodes indicates the tightness of co-authorship networks, and different sets of node colors help distinguish groups of institutions whose researchers frequently co-author together. Of 462 institutions that collaborated with UCSF researchers, we’re showing only 91 that had 10 or more cross-institutional articles in that time.)

View full-size visualization (PDF)

UCSF dentistry research co-authorships, Jan 1 - Dec 5 2013

Then I looked at the total universe of dentistry-related publications published in 2013 (see below). Notice a difference? I have to admit that it took me a while to find UCSF in the mess of dots. (If you look at the full-size view, we’re in the medium blue section, next to the pinks.) Of course this says more about the sheer volume of research being published by universities all over the world, than about any lack of cross-institutionally collaborative spirit on our part; in fact I hid over 80% of the institutions in the first image to keep it readable, which accounts for a a good chunk of the difference. But the sheer weight of institutions from Europe, East Asia, and Latin America in this second image that aren’t there in the first is intriguing, and something I’m going to try digging into.

(Details: Institution node sizes indicate the total volume of dentistry-related articles published. Connecting line widths indicate the number of articles co-authored between two institutions. Distance between nodes indicates the tightness of co-authorship networks, and different sets of node colors help distinguish groups of institutions whose researchers frequently co-author together. Of 2,575 institutions that we found, we’re showing only 374 that had 10 or more cross-institutional articles in that time.)

View full-size visualization (PDF)

Dentistry research co-authorships, Jan 1-Dec 5 2013

(And yes, I realize fully well that I’m probably looking at the wrong things here, privileging increasing the count of cross-institutional collaborations as an end in itself, avoiding any consideration of research quality, and giving greater visual weight to institutions that publish more, regardless of the size of the institution or the quality of work. Pretty pictures lie can hide lots of flaws. I hope you’ll bear with me as I publicly iterate through these topics, step by step, hopefully getting just a little bit less dumb every time.)

Additional uninteresting details: I searched Web of Science for dentistry-related articles published in 2013 (i.e. from January 1-December 5, 2013). I began by running a search for any articles published in 2013 matching a number of dentistry-related keywords (dental, dentistry, electrogalvanism, endodontics, jaw relation record, mouth rehabilitation, odontometry, oral, orthodontics, periodontics, prosthodontics, teeth, tooth), then filtered only those that matched the “DENTISTRY ORAL SURGERY MEDICINE” Web of Science category.

The 100 top researcher keywords at UCSF

/ Anirvan Chatterjee

I was looking to dig into some examples of collaboration patterns in different research areas, when I realized I didn’t even know the basics — what do UCSF researchers actually research?

UCSF Profiles uses PubMed data to extract MeSH keywords for every publication by every UCSF researcher in the system. We can use this to look at the most commonly used MeSH keywords across every researcher’s body of work. There are lots of caveats here (looking at all publications emphasizes past research interests over current ones; we’re not grouping related obscure MeSH terms with more popular ones; MeSH term assignment practices change over time; and this analysis ignores someone’s role as a first, middle, or last author). But this is certainly a start.

Here’s what I found, using the latest UCSF Profiles data:

  1. 98 researchers have HIV Infections in their top 5 MeSH keywords
  2. 53 researchers have Breast Neoplasms in their top 5 MeSH keywords
  3. 42 researchers have Magnetic Resonance Imaging in their top 5 MeSH keywords
  4. 39 researchers have Tomography, X-Ray Computed in their top 5 MeSH keywords
  5. 39 researchers have Brain Neoplasms in their top 5 MeSH keywords
  6. 37 researchers have Internship and Residency in their top 5 MeSH keywords
  7. 37 researchers have HIV-1 in their top 5 MeSH keywords
  8. 34 researchers have Alzheimer Disease in their top 5 MeSH keywords
  9. 33 researchers have Prostatic Neoplasms in their top 5 MeSH keywords
  10. 32 researchers have Saccharomyces cerevisiae in their top 5 MeSH keywords
  11. 31 researchers have Brain in their top 5 MeSH keywords
  12. 31 researchers have Anti-HIV Agents in their top 5 MeSH keywords
  13. 30 researchers have Neoplasms in their top 5 MeSH keywords
  14. 30 researchers have Smoking in their top 5 MeSH keywords
  15. 29 researchers have Diabetes Mellitus, Type 2 in their top 5 MeSH keywords
  16. 29 researchers have Asthma in their top 5 MeSH keywords
  17. 28 researchers have Stroke in their top 5 MeSH keywords
  18. 28 researchers have Sexual Behavior in their top 5 MeSH keywords
  19. 27 researchers have Myocardial Infarction in their top 5 MeSH keywords
  20. 27 researchers have Proteins in their top 5 MeSH keywords
  21. 26 researchers have Neurons in their top 5 MeSH keywords
  22. 26 researchers have Skin Neoplasms in their top 5 MeSH keywords
  23. 26 researchers have Antineoplastic Combined Chemotherapy Protocols in their top 5 MeSH keywords
  24. 25 researchers have Cognition Disorders in their top 5 MeSH keywords
  25. 25 researchers have Homosexuality, Male in their top 5 MeSH keywords
  26. 25 researchers have Emergency Service, Hospital in their top 5 MeSH keywords
  27. 25 researchers have Students, Medical in their top 5 MeSH keywords
  28. 24 researchers have Obesity in their top 5 MeSH keywords
  29. 24 researchers have Glioblastoma in their top 5 MeSH keywords
  30. 23 researchers have Epilepsy in their top 5 MeSH keywords
  31. 23 researchers have Pancreatic Neoplasms in their top 5 MeSH keywords
  32. 23 researchers have Dementia in their top 5 MeSH keywords
  33. 23 researchers have Liver Transplantation in their top 5 MeSH keywords
  34. 23 researchers have Hispanic Americans in their top 5 MeSH keywords
  35. 23 researchers have Education, Medical, Undergraduate in their top 5 MeSH keywords
  36. 22 researchers have Lung in their top 5 MeSH keywords
  37. 22 researchers have Genetic Predisposition to Disease in their top 5 MeSH keywords
  38. 22 researchers have Saccharomyces cerevisiae Proteins in their top 5 MeSH keywords
  39. 22 researchers have Lung Neoplasms in their top 5 MeSH keywords
  40. 22 researchers have Glioma in their top 5 MeSH keywords
  41. 21 researchers have Drosophila in their top 5 MeSH keywords
  42. 21 researchers have Mass Screening in their top 5 MeSH keywords
  43. 21 researchers have Heart Defects, Congenital in their top 5 MeSH keywords
  44. 21 researchers have Anti-Bacterial Agents in their top 5 MeSH keywords
  45. 21 researchers have Liver in their top 5 MeSH keywords
  46. 21 researchers have Polymorphism, Single Nucleotide in their top 5 MeSH keywords
  47. 21 researchers have Physician-Patient Relations in their top 5 MeSH keywords
  48. 21 researchers have Signal Transduction in their top 5 MeSH keywords
  49. 21 researchers have Primary Health Care in their top 5 MeSH keywords
  50. 21 researchers have Nerve Tissue Proteins in their top 5 MeSH keywords
  51. 21 researchers have Stem Cells in their top 5 MeSH keywords
  52. 21 researchers have Drosophila melanogaster in their top 5 MeSH keywords
  53. 20 researchers have Colorectal Neoplasms in their top 5 MeSH keywords
  54. 20 researchers have Stress Disorders, Post-Traumatic in their top 5 MeSH keywords
  55. 20 researchers have Calcium in their top 5 MeSH keywords
  56. 20 researchers have Health Services Accessibility in their top 5 MeSH keywords
  57. 20 researchers have Smoking Cessation in their top 5 MeSH keywords
  58. 20 researchers have Epithelial Cells in their top 5 MeSH keywords
  59. 20 researchers have Wounds and Injuries in their top 5 MeSH keywords
  60. 20 researchers have Drosophila Proteins in their top 5 MeSH keywords
  61. 20 researchers have Models, Molecular in their top 5 MeSH keywords
  62. 19 researchers have Magnetic Resonance Spectroscopy in their top 5 MeSH keywords
  63. 19 researchers have MicroRNAs in their top 5 MeSH keywords
  64. 19 researchers have Respiratory Distress Syndrome, Adult in their top 5 MeSH keywords
  65. 19 researchers have Curriculum in their top 5 MeSH keywords
  66. 19 researchers have Aging in their top 5 MeSH keywords
  67. 19 researchers have Embryonic Stem Cells in their top 5 MeSH keywords
  68. 19 researchers have Caenorhabditis elegans in their top 5 MeSH keywords
  69. 19 researchers have Kidney Transplantation in their top 5 MeSH keywords
  70. 18 researchers have Heart Failure in their top 5 MeSH keywords
  71. 18 researchers have Membrane Proteins in their top 5 MeSH keywords
  72. 18 researchers have Asian Americans in their top 5 MeSH keywords
  73. 18 researchers have DNA in their top 5 MeSH keywords
  74. 18 researchers have Tuberculosis in their top 5 MeSH keywords
  75. 18 researchers have Mental Disorders in their top 5 MeSH keywords
  76. 18 researchers have Transcription Factors in their top 5 MeSH keywords
  77. 18 researchers have Coronary Disease in their top 5 MeSH keywords
  78. 18 researchers have Gene Expression Profiling in their top 5 MeSH keywords
  79. 17 researchers have DNA-Binding Proteins in their top 5 MeSH keywords
  80. 17 researchers have CD8-Positive T-Lymphocytes in their top 5 MeSH keywords
  81. 17 researchers have Skin Diseases in their top 5 MeSH keywords
  82. 17 researchers have Bacterial Proteins in their top 5 MeSH keywords
  83. 17 researchers have Apoptosis in their top 5 MeSH keywords
  84. 17 researchers have Protein-Serine-Threonine Kinases in their top 5 MeSH keywords
  85. 17 researchers have Homeodomain Proteins in their top 5 MeSH keywords
  86. 17 researchers have Hypertension in their top 5 MeSH keywords
  87. 17 researchers have Stress, Psychological in their top 5 MeSH keywords
  88. 17 researchers have T-Lymphocytes in their top 5 MeSH keywords
  89. 17 researchers have Abortion, Induced in their top 5 MeSH keywords
  90. 17 researchers have Schizophrenia in their top 5 MeSH keywords
  91. 17 researchers have Antineoplastic Agents in their top 5 MeSH keywords
  92. 17 researchers have Proteomics in their top 5 MeSH keywords
  93. 17 researchers have Multiple Sclerosis in their top 5 MeSH keywords
  94. 17 researchers have Teaching in their top 5 MeSH keywords
  95. 17 researchers have Acquired Immunodeficiency Syndrome in their top 5 MeSH keywords
  96. 17 researchers have Hepatitis C in their top 5 MeSH keywords
  97. 17 researchers have Laparoscopy in their top 5 MeSH keywords
  98. 16 researchers have Muscle, Skeletal in their top 5 MeSH keywords
  99. 16 researchers have Amyloid beta-Peptides in their top 5 MeSH keywords
  100. 16 researchers have Ovarian Neoplasms in their top 5 MeSH keywords

Every researcher at UCSF — by department

/ Anirvan Chatterjee

Co-authorship networks can help us understand internal research collaboration patterns at UCSF. I used data from UCSF Profiles to create a visualization of (almost) every researcher currently at UCSF, and how their intra-UCSF co-authorship networks break out by department.

This visualization by department bears some more investigation than the previous one by school. Department of Medicine researchers are all over, collaborating with a wide variety of external departments. But an initial visual inspection suggests that almost all major departments have co-authorship relationships with members of other departments; some, like neurology, appear to form large standalone clusters, while others, like radiology, are more enmeshed in the work of others. This visualization flattens complex relationships into two dimensions, but it’s a starting point as we work to understand how UCSF collaborates.

View full-size visualization (PDF)

Every Researcher at UCSF, by department

Every researcher at UCSF — by school

/ Anirvan Chatterjee / 1 Comment

Co-authorship networks can help us understand internal research collaboration patterns at UCSF. I used data from UCSF Profiles to create a visualization of (almost) every researcher currently at UCSF, and how their intra-UCSF co-authorship networks break out by school.

Unsurprisingly, the School of Medicine takes up most of the space, and the visualization is probably most interesting in terms of what it might suggest about the smaller schools. Researchers from the Schools of Nursing and Dentistry form their own visible clusters, who often work with each other, but also have co-authorship relationships with researchers at the School of Medicine. But I was surprised by the School of Pharmacy, whose researchers form a main clusters in the bottom right, as well as additional clusters in the middle and top left, due to strong collaborative relationships with School of Medicine researchers.

View full-size visualization (PDF)

Every Researcher at UCSF, by school

Departmental BFFs: Which UCSF departments publish the most often together?

/ Anirvan Chatterjee

Batman and Robin smoking

Some UCSF departments work more closely together than others. I looked at co-authorship patterns in papers published between January 2012 and November 2013, based on data in UCSF Profiles, and pulled out the UCSF departments that collaborate the most frequently. The results aren’t necessarily surprising. The Department of Medicine is huge, and their cross-departmental collaborations make up 8 of the top 10 collaborations, measured by volume. On the flip side, smaller groups with research areas similar to others make up many of the most common collaborations, by percentage; for example, one-third of papers by researchers primarily affiliated with the Proctor Foundation for Research in Opthalmology are co-authored with researchers from the Department of Opthalmology. I wouldn’t have necessarily guessed, however, connections like that between nursing and psychiatry.

Top UCSF cross-departmental collaborations, by volume

  1. Epidemiology & Biostatistics + Medicine: 365 collaborative papers
  2. Medicine + Pediatrics: 139 collaborative papers
  3. Medicine + Psychiatry: 127 collaborative papers
  4. Neurological Surgery + Neurology: 115 collaborative papers
  5. Medicine + Pathology: 105 collaborative papers
  6. Laboratory Medicine + Medicine: 104 collaborative papers
  7. Medicine + Surgery: 99 collaborative papers
  8. Neurology + Radiology and Biomedical Imaging: 92 collaborative papers
  9. Medicine + Radiology and Biomedical Imaging: 90 collaborative papers
  10. Medicine + Neurology: 86 collaborative papers

Top UCSF cross-departmental collaborations, by percentage

  1. 64.8% of School of Nursing Dean’s Office papers are co-authored with Physiological Nursing
  2. 36.8% of Proctor Foundation papers are co-authored with Ophthalmology
  3. 33.8% of School of Nursing Dean’s Office papers are co-authored with Medicine
  4. 33.3% of Physiological Nursing papers are co-authored with School of Nursing Dean’s Office
  5. 33.3% of Institute for Neurodegenerative Disease papers are co-authored with Neurology
  6. 32.4% of School of Nursing Dean’s Office papers are co-authored with Psychiatry
  7. 29.8% of Physical Therapy & Rehab Sciences papers are co-authored with Radiology and Biomedical Imaging
  8. 27.5% of Physiological Nursing papers are co-authored with Medicine
  9. 25.0% of Epidemiology & Biostatistics papers are co-authored with Medicine
  10. 22.8% of Family & Community Medicine papers are co-authored with Medicine

Details: Data is drawn from UCSF Profiles, and is based on a list of all publications listed on PubMed published between Jan 2012–Nov 2013, focusing on those whose authors include groups of researchers that have primary affiliations to more than one UCSF department. We counted only those publications from researchers with a listed department, and for the purposes of counting top cross-departmental collaborations by percentage, only those collaborations that generated 10 or more papers during the time period. No attempt was made to account for the widely varying sizes and scopes of different departments, the fact that researchers may have multiple departmental affiliations, or the fact that some publications may have been authored before the researchers were affiliated with their current primary departments at UCSF.

Photo: “Glasgow’s own superheroes having a smoke outside the Counting House” by Stephen Fyfe/Flickr, under CC-BY-NC-ND