Tuesday, September 16, 2014

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Article References for September 2014 San Francisco Medicine

References cited in Our Bodies’ Best Buddies by Elisabeth M. Bik

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  4. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J; MetaHIT Consortium, Bork P, Ehrlich SD, Wang J. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010; 464(7285):59-65. DOI: 10.1038/nature08821.
  5. Ridaura VK1, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013; 341(6150):1241214. DOI: 10.1126/science.1241214.
  6. David L, Materna AC, Friedman J, Campos-Baptista MI, Blackburn MC, Perrotta A, Erdman SE, and Alm EJ. Host lifestyle affects human microbiota on daily timescales. Genome Biology. 2014; 15:R89. DOI: 10.1186/gb-2014-15-7-r89.
  7. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA. 2011; 108 Suppl 1: 4554-61. DOI: 10.1073/pnas.1000087107. 
  8. Seekatz AM, Young VB. Clostridium difficile and the microbiota. J Clin Invest. 2014. DOI:10.1172/JCI72336.
  9. Blaser ML. Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. Henry Holt and Co., Publ. 2014. ISBN-10: 0805098100. 
  10. Vaz LE, Kleinman KP, Raebel MA, Nordin JD, Lakoma MD, Dutta-Linn MM, Finkelstein JA. Recent trends in outpatient antibiotic use in children. Pediatrics. 2014; 133(3):375-85. DOI: 10.1542/peds.2013-2903. 

References cited in The "Second Genome" and Women's Health by Linda C. Giudice, MD, PhD

  1. Bajzer M, Seeley RJ. The intestinal bacteria in obese humans and mice differ from those in lean individuals. Are these bacteria involved in how we regulate body weight, and are they a factor in the obesity epidemic? Nature. 2006; 444:1009-1010.
  2. Round JL, Sarkis K. The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews Immunology. 2009; 9:313-323. 
  3. Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI. Human nutrition, the gut microbiome and the immune system. Nature 2011;474:327-336.
  4. Markle JGM et al. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science. 2013: 339;1084-1088.
  5. Witkin SS, Linhares IM, Giraldo P. Bacterial flora of the female genital tract: Function and immune regulation. Best Pract Res Clin Obstet Gynaecol. 2007; 21(3):347-54. 
  6. Zhou X, Bent SJ, Schneider MG, Davis CC, Islam MR, Forney LJ. Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods. Microbiology. 2004; 150(Pt 8):2565-73. 
  7. Verhelst R, Verstraelen H, Claeys G, Verschraegen G, Delanghe J, Van Simaey L, De Ganck C, Temmerman M, Vaneechoutte M. Cloning of 16S rRNA genes amplified from normal and disturbed vaginal microflora suggests a strong association between Atopobium vaginae, Gardnerella vaginalis and bacterial vaginosis. BMC Microbiol. 2004; 4:16.
  8. Hyman RW, Fukushima M, Diamond L, Kumm J, Giudice LC, Davis RW. Microbes on the human vaginal epithelium. Proc Natl Acad Sci USA. 2005; 102(22):7952-7. 
  9. Human Microbiome Project Consortium Collaborators (248). Structure, function and diversity of the healthy human microbiome. Nature. 2012; 13:486(7402):207-14. 
  10. Fredricks DN, Fiedler TL, Marrazzo JM. Molecular identification of bacteria associated with bacterial vaginosis. N Engl J Med. 2005; 353(18):1899-911. 
  11. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci USA. 2011; 15:108 Suppl 1:4680-7. 
  12. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magda Magris M, Glida Hidalgo G, Robert N. Baldassano RN, Andrey P. Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. Human gut microbiome viewed across age and geography. Nature. 2012; 486:222-228.
  13. Verstraelen H, Verhelst R, Claeys G, De Backer E, Temmerman M, Vaneechoutte M. Longitudinal analysis of the vaginal microflora in pregnancy suggests that L. crispatus promotes the stability of the normal vaginal microflora and that L. gasseri and/or L. iners are more conducive to the occurrence of abnormal vaginal microflora. BMC Microbiol. 2009; 9:116. DOI: 10.1186/1471-2180-9-116. 
  14. Gajer P, Brotman RM, Bai G, Sakamoto J, Schütte UME, Zhong X, Koenig SSK, Fu L, Ma Z, Zhou X, Abdo Z, Forney LJ, Ravel J. Temporal dynamics of the human vaginal microbiota. Sci. Transl. Med. 2012; 4:132ra52.
  15. Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, Gevers D, Huttenhower C, Petrosino J, Versalovic J. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLOS ONE. 2012; 7(6):e36466. 
  16. Hyman RW, Fukushima M, Jiang H, Fung E, Rand L, Johnson B, Vo KC, Caughey AB, Hilton J F, Davis R W, Giudice LC. Diversity of the vaginal microbiome correlates with preterm birth. Reproductive Sciences. 2014; 21: 32-40.
  17. Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Backhed HK, Gonzalez A, Werner JJ, Angenent LT, Knight R, Backhed F, Isolauri E, Salminen S, Ley RE. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell. 2012; 150:470-480.
  18. Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J. The placenta harbors a unique microbiome. Sci. Transl. Med. 2014; 6:237ra65.
  19. Muglia LJ, Katz M. The enigma of spontaneous preterm birth. N Engl J Med. 2010; 362(6):529-35. 
  20. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA. 2010; 107:11971-11975.
  21. Bergstrom A, Skov TH, Bahl MI, Roager HM, Christensen LB, Eilerskov KT, Molgaard C, Michaelsen KF, Licht TR. Establishment of intestinal microbiota during early life: A longitudinal, explorative study of a large cohort of Danish infants. Appl Environ Microbiol. 2014; 80:2889-2900.
  22. Siddiqui H, Nederbragt AJ, Lagesen K, JeanssonSL Jakobsen KS. Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiology. 2011; 11:244-251.
  23. Alan J, Wolfe AJ, Toh E, Shibata N, Bong B, Kenton K, FitzGerald MP, Mueller ER, Schreckenberger P, Dong Q, Nelson DE, Brubaker L. Evidence of uncultivated bacteria in the adult female bladder. J Clin Microbiol. 2012; 50:1376-1383.
  24. Lewis DA, Brown R, Williams J, White P, Jacobson SK, Marchesi JR, Drake MJ. The human urinary microbiome: Bacterial DNA in voided urine of asymptomatic adults. Front Cell Infect Microbiol. 2013; 3:41.
  25. Brubaker L. Annual Meeting of the Ammerican UroGynecologic Society 2013.
  26. Pearce MM, Hilt EE, Rosenfeld AB, Zilliox MJ, Thomas-White K, Fok C, Kliethermes S, Schreckenberger PC, Brubaker L, Gai X, Wolfe AJ. The female urinary microbiome: A comparison of women with and without urgency urinary incontinence. mBio. 2014; 5(4):e01283-14.
  27. Siddiqui H, Lagesen K, Nederbragt AJ, Jeansson SL, Jakobsen KS. Alterations of microbiota in urine from women with interstitial cystitis. BMC Microbiology. 2012; 12:205-211-215.
  28. Fouts DE, Pieper R, Szpakowski S, Pohl H, Knoclach S, Suh M-H, Huang S-T, Ljungberg I, Sprague BM, Lucas SK, Torralba M, Nelson KE, Groah. Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury. J Transl Med. 2012; 10:174.
  29. Imirzalioglu C, Hain T, Chakraborty T, Domann E. Hidden pathogens uncovered: Metagenomic analysis of urinary tract infections. Andrologia. 2008; 4066-71.

References cited in Pre- and Probiotic Foods for a Healthy Gut by Jo Ann T. Hattner, MPH RDN and Susan Anderes, MLIS 

  1. Pollan M. Some of my best friends are germs. New York Times Magazine. May 15, 2013.
  2. Food and Agriculture Organization of the United Nations, World Health Organization. Probiotics in food: Health and nutritional properties and guidelines for evaluation. Rome: Food and Agriculture Organization of the United Nations: World Health Organization. 2006; viii:50.
  3. Hattner JAT, Anderes S. Gut Insight: Probiotics and Prebiotics for Digestive Health and Well-Being. San Francisco: Hattner Nutrition. 2009. www.gutinsight.com.
  4. German JB. The future of yogurt: Scientific and regulatory needs. Am J Clin Nutr. 2014; 99(5 Suppl):1271S-8S. DOI: 10.3945/ajcn.113.076844. PubMed PMID: 24695899; PubMed Central PMCID: PMC3985222.
  5. Hertzler SR, Clancy SM. Kefir improves lactose digestion and tolerance in adults with lactose maldigestion. J Am Diet Assoc. 2003; 103(5):582-7. DOI: 10.1053/jada.2003.50111. PubMed PMID: 12728216.
  6. Farnworth ER, Mainville I, Desjardins MP, Gardner N, Fliss I, Champagne C. Growth of probiotic bacteria and bifidobacteria in a soy yogurt formulation. Int J Food Microbiol. 2007; 116(1):174-81. DOI: 10.1016/j.ijfoodmicro.2006.12.015. PubMed PMID: 17292991.
  7. Moshfegh AJ, Friday JE, Goldman JP, Ahuja JK. Presence of inulin and oligofructose in the diets of Americans. J Nutr. 1999; 129(7 Suppl):1407S-11S. Epub 1999/07/08. PubMed PMID: 10395608.
  8. Saavedra JM, Dattilo A. Microbiota of the intestine. Encyclopedia of Human Nutrition: Elsevier. 2013.
  9. van Loo J, Coussement P, de Leenheer L, Hoebregs H, Smits G. On the presence of inulin and oligofructose as natural ingredients in the western diet. Crit Rev Food Sci Nutr. 1995; 35(6):525-52. DOI: 10.1080/10408399509527714. PubMed PMID: 8777017.

References cited in The NIH Human Microbiome Project by Erica Goode, MD

  1. www.commonfund.nih.gov/hmp/initiatives#elucidation
  2. www.microbemaggazias.org/index.php?option=com
  3. Huttenhower C. Functional analysis of the human microbiome, metagenomes, metatranscriptions, and multi-omics. Broad Institute, Raes Lab, VUV-KU Leuwens lecture. July 24, 2013.
  4. Morgan. TiG 2012. Huttenhower, ibid.
  5. Tan P. The neonatal microbiome and NEC. Washington University, St. Louis, collaborative study, NIH HMP. 2014.
  6. Turnbaugh P, Gordon J et al. Washington University, St. Louis. microbemagazine.org. 2013.
  7. Huenemann R. U.C. Berkeley, School of Public Health. Communication, 1968.
  8. Clement K. Bariatric surgery, adipose tissue, and gut microbiota. Int’l. J. of Obesity. 2011;  35:S7-15.
  9. Kong LC et al. Gut microbiota after gastric bypass in human obesity: Increased richness and associations of bacterial genera with adipose tissue genes. Am. J. Clinical Nutrition. 2013; 98:(1), 16-24.
  10. Turnbaugh, ibid.
  11. Aroth T, Sharma R et al. Fermentation potential of the gut micro biome: Implications for energy homeostasis and weight management. Nutr. Rev. 2012; 69:(2), 99-106.

References cited in Why the Microbiome Matters: One Primary Care Physician's Journey toward Understanding Its Significance by Payal Bhandari, MD

  1. Hattner JA. www.gutinsight.com. 2013.
  2. Dong TL, MD. Healthy at Home: Get Well and Stay Well Without Prescriptions.  2014. Published by National Geographic Society.
  3. Robinson, J. Eating on the Wild Side. 2013. Published by Little & Brown.
  4. Metchnikoff E. Essais optimistes; The Prolongation of Life: Optimistic studies. Translated and edited by P. Chalmers Mitchell. 1907. London: Heinemann.
  5. Pesticide Action Network. http://www.panna.org.
  6. Flight I, Clifton P. Cereal grains and legumes in the prevention of coronary heart disease and stroke: A review of the Lliterature. European Journal of Clinical Nutrition. 2006; 60:1145-59. 
  7. USDA Economic Research Service. Loss-adjusted food availability: Spreadsheets. Fresh vegetable consumption. 2008.8 Lad V, MA. The Complete Book of Ayurvedic Home Remedies. 1998. Published by Three Rivers Press. 

Vote No on Proposition 46

Originally published on SFgate.com on September 12, 2014

By Michael H. Rokeach, MD

As an emergency-room doctor in San Francisco for more than 30 years, I see some of the city’s most critical patients — people suffering heart attacks, life-threatening infections, gunshot wounds and more. Proposition 46, which seeks to increase the limit on the amount of medical malpractice lawsuit awards, is a critical threat to the health care of all Californians. The thoughtful response is to oppose it.

The initiative is a complicated, costly measure — written and funded by trial attorneys — which makes sweeping changes to California’s health system without any input from health care experts or medical practitioners.

It’s also deceptive. It uses alcohol and drug testing of doctors (whether they are on or off duty — unprecedented in the U.S.) to disguise the real intent, which is to lift the cap on the medical malpractice lawsuit awards to $1.1 million from $250,000, thereby raising attorney fees, while increasing costs for everybody else.

But, worst of all, it’s bad for health care and health access for low-income communities. It will cost the state and local governments hundreds of millions of dollars and it will make it harder for community clinics such as Planned Parenthood to provide specialty services.

With millions of newly insured patients looking for quality care under the Affordable Care Act, I can’t think of a worse possible time to increase cost and decrease access to trusted health providers. Vote NO on Prop. 46.

Michael H. Rokeach is an emergency-room physician and past president of the San Francisco Medical Society.

SFMS Member Appointed Newest San Francisco Health Commissioner

David Pating, MD, an SFMS board member and chief of addiction medicine at Kaiser San Francisco, was appointed and sworn in as a member of the San Francisco Health Commission by Mayor Ed Lee.

The Health Commission oversees all activities of the health services of the City and County of San Francisco, including the Department of Public Health and San Francisco General Hospital. Dr. Pating joins SFMS past-President Edward Chow, MD, Commission President, and his nomination was strongly endorsed by the SFMS.

Dr. Pating, an Assistant Clinical Professor in Psychiatry at UCSF and vice-chair of the California Mental Health Services Oversight and Accountability Commission, has been a guest editor of the SFMS journal San Francisco Medicine, and president of the California Society of Addiction Medicine, among many other positions and contributions.

New CMS Rule Changes Meaningful Use Timeline

The Centers for Medicare and Medicaid Services (CMS) published a new final rule that would provide eligible professionals participating in the Medicare and Medi-Cal electronic health record (EHR) incentive program an additional year to upgrade their certified electronic health record technology (CEHRT) and revises the meaningful use timeline. The rule will go into effect on October 1, 2014.

The final rule would allow eligible professionals to use 2011 Edition CEHRT or a combination of 2011 and 2014 Edition CEHRT for the 2014 EHR reporting period to demonstrate meaningful use. Eligible professionals that were scheduled to begin Stage 2 in 2014 will not be required to begin Stage 2 until 2015 if they attest that they could not fully implement 2014 Edition CEHRT due to delays in availability of 2014 Edition CEHRT for the 2014 reporting period. The final rule would also revise the meaningful use timeline for Stage 3 to begin in 2017 for eligible professionals.


CMS, however, emphasizes that beginning in 2015, all providers will be required to report using 2014 Edition CEHRT to successfully demonstrate meaningful use.

SFMS members can access detailed information on the federal EHR incentive program and meaningful use via CAM’s On-Call Documents #4301 “Electronic Health Records: Federal Incentive Program,” #4302 “Meaningful Use of Electronic Health Records,” and #4305 “EHR Meaningful Use: Stage 2.” These and other resources are complimentary to SFMS members and at $2/page to non-members.

California County Medical Societies Oppose Prop 45, Flawed Measure Giving Too Much Power to One Politician Over Health Care

Across the state, county medical societies are opposing Proposition 45, a November ballot measure that would give the state Insurance Commissioner sweeping new power over health care benefits and rates.

“Proposition 45 gives one politician too much power over health care benefits and treatment options, which can have a significant impact on patient care,” said Dr. Man-Kit Leung, Board Member of the San Francisco Medical Society. “Treatment decisions should be made by doctors and patients—not by someone with a political agenda.”

30 county medical societies and dozens of statewide groups—representing more than 40,000 doctors—joined the growing coalition opposed to Prop 45. 
“We all want to reduce the cost of health care and strive every day to enhance its quality, but our health care system is too complex to make major changes through a ballot measure pushed by one special interest group,” said Dr. Pedram Salimpour, President of the Los Angeles County Medical Association. “If we are going to make major changes, patients, doctors, nurses, clinics and hospitals should all be part of the solution.”
Prop 45 was drafted and filed in 2011, prior to the implementation of the President’s historic Affordable Care Act, and failed to qualify for the 2012 ballot, forcing it to this year’s November ballot.

Academics and health care experts, including Covered California board members, have raised serious concerns about Prop 45 creating obstacles for those who need health insurance through the state’s exchange, largely due to the initiative allowing outside groups and individuals to file lengthy legal challenges against Covered California plans.

At the August Covered California board meeting, board members expressed their opposition to the measure, saying that it could have “significant detrimental impacts” to the exchange’s operations.

County medical societies that have announced their opposition to Prop 45 include:

  • Alameda-Contra Costa Medical Association
  • Butte-Glenn Medical Society
  • Humboldt-Del Norte County Medical County
  • Imperial County Medical Society
  • Los Angeles County Medical Association
  • Kern County Medical Society
  • Kings County Medical Society
  • Marin Medical Society
  • Merced-Mariposa County Medical Society
  • Mendocino-Lake County Medical Society
  • Monterey County Medical Society
  • Napa County Medical Society
  • North Valley Medical Association
  • Orange County Medical Association
  • Placer-Nevada County Medical Society
  • Riverside County Medical Association
  • San Bernardino County Medical Society
  • San Diego County Medical Society
  • San Francisco Medical Society
  • San Joaquin County Medical Society
  • San Mateo County Medical Association
  • Santa Barbara County Medical Society
  • Santa Clara County Medical Association
  • Sierra Sacramento Valley Medical Society
  • Solano County Medical Society
  • Sonoma County Medical Association
  • Tulare County Medical Society
  • Ventura County Medical Association
  • Yuba Sutter Colusa County Medical Society

Click here for more information on Prop 45.

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