San Francisco Research Articles

Poly- and perfluoroalkyl substances in wastewater: Significance of unknown precursors, manufacturing shifts, and likely AFFF impacts

In late 2014, wastewater effluent samples were collected from eight treatment plants that discharge to San Francisco (SF) Bay in order to assess poly- and perfluoroalkyl substances (PFASs) currently released from municipal and industrial sources. In addition to direct measurement of twenty specific PFAS analytes, the total concentration of perfluoroalkyl acid (PFAA) precursors was also indirectly measured by adapting a previously developed oxidation assay. Effluent from six municipal treatment plants contained similar amounts of total PFASs, with highest median concentrations of PFHxA (24 ng/L), followed by PFOA (23 ng/L), PFBA (19 ng/L), and PFOS (15 ng/L). Compared to SF Bay municipal wastewater samples collected in 2009, the short chain perfluorinated carboxylates PFBA and PFHxA rose significantly in concentration. Effluent samples from two treatment plants contained much higher levels of PFASs: over two samplings, wastewater from one municipal plant contained an average of 420 ng/L PFOS and wastewater from an airport industrial treatment plant contained 560 ng/L PFOS, 390 ng/L 6:2 FtS, 570 ng/L PFPeA, and 500 ng/L PFHxA. The elevated levels observed in effluent samples from these two plants are likely related to aqueous film forming foam (AFFF) sources impacting their influent; PFASs attributable to both current use and discontinued AFFF formulations were observed. Indirectly measured PFAA precursor compounds accounted for 33%–63% of the total molar concentration of PFASs across all effluent samples and the PFAA precursors indicated by the oxidation assay were predominately short-chained. PFAS levels in SF Bay effluent samples reflect the manufacturing shifts towards shorter chained PFASs while also demonstrating significant impacts from localized usage of AFFF.

Transcultural San Francisco

Andrew Furuseth and Olaf Tveitmoe, both immigrants from Norway, were two of the most powerful labor leaders on the West Coast in the early twentieth century. Their perspectives and experiences as Scandinavians, as immigrants, and as San Franciscans helped to forge an approach to political activism that has long been overshadowed by the far more famous events of the 1960s and 1970s. Working with innovative methods in the field of transcultural biography, this article argues that the contradictory, transcultural nature of each man’s career, which included both anti-Asian racism and a profound opposition to war and militarism, had a major impact on San Francisco’s political consciousness that is still felt today.

Data-Driven Modeling and Prediction of the Process for Selecting Runway Configurations

Runway configuration is a key driver of airport capacity at any time. Several factors, such as wind speed and direction, visibility, traffic demand, air traffic controller workload, and the coordination of flows with neighboring airports, influence the selection of the runway configuration. This paper infers the utility functions of the nominal decision-making process of air traffic personnel by using a discrete choice modeling approach. Given operational and weather conditions that have already been reported, such as ceiling and visibility, traffic demand, and current runway configuration, the model produces a probabilistic forecast of the runway configuration on a 15-min horizon. The prediction is then extended to a more realistic 3-h planning horizon. Case studies for San Francisco (SFO), California; LaGuardia (LGA), New York; and Newark (EWR), New Jersey, airports were completed by using this approach. Given the weather and airport arrival demand, the model predicts the correct runway configuration at SFO, LGA, and EWR on a 3-h horizon with accuracies of 81.2%, 81.3%, and 77.8%, respectively.

Selection of gas turbines for energy recovery at san francisco’s southeast treatment plant

Selection of gas turbines for energy recovery at san francisco’s southeast treatment plant

Are Clade Specific HIV Vaccines a Necessity? An Analysis Based on Mathematical Models

As HIV-1 envelope immune responses are critical to vaccine related protection, most candidate HIV vaccines entering efficacy trials are based upon a clade specific design. This need for clade specific vaccine prototypes markedly reduces the implementation of potentially effective HIV vaccines. We utilized a mathematical model to determine the effectiveness of immediate roll-out of a non-clade matched vaccine with reduced efficacy compared to constructing clade specific vaccines, which would take considerable time to manufacture and test in safety and efficacy trials. We simulated the HIV epidemic in San Francisco (SF) and South Africa (SA) and projected effectiveness of three vaccination strategies: i) immediate intervention with a 20–40% vaccine efficacy (VE) non-matched vaccine, ii) delayed intervention by developing a 50% VE clade-specific vaccine, and iii) immediate intervention with a non-matched vaccine replaced by a clade-specific vaccine when developed. Immediate vaccination with a non-clade matched vaccine, even with reduced efficacy, would prevent thousands of new infections in SF and millions in SA over 30years. Vaccination with 50% VE delayed for five years needs six and 12years in SA to break-even with immediate 20 and 30% VE vaccination, respectively, while not able to surpass the impact of immediate 40% VE vaccination over 30years. Replacing a 30% VE with a 50% VE vaccine after 5years reduces the HIV acquisition by 5% compared to delayed vaccination. The immediate use of an HIV vaccine with reduced VE in high risk communities appears desirable over a short time line but higher VE should be the pursued to achieve strong long-term impact. Our analysis illustrates the importance of developing surrogate markers (correlates of protection) to allow bridging types of immunogenicity studies to support more rapid assessment of clade specific vaccines.

Structure Without Hierarchy

Structure Without Hierarchy

If you are not counted, you don't count: Estimating the number of African-American Men who have Sex with Men in San Francisco.

International Journal of Epidemiology, 2015, Vol. 44, Supplement 1 i39 Risky Behaviors: Free Papers Abstract #: 2474 If you are not counted, you don’t count: Estimating the number of African-American Men who have Sex with Men in San Francisco. P. D. Wesson, BA 1 , M. S. Handcock, PhD 2 , W. McFarland, PhD 3,4 and H. F. Raymond, DrPH 3,4 University of California, Berkeley, Berkeley, CA, USA, 2 University of California, Los Angeles, Los Angeles, CA, USA, 3 University of California, San Francisco, San Francisco, CA, USA, 4 San Francisco Department of Public Health, San Francisco, CA, USA Downloaded from http://ije.oxfordjournals.org/ by guest on October 25, 2016 INTRODUCTION: The HIV epidemic has disproportionately affected African-American (AA) men who have sex with men (MSM). Resource allocation for programs targeting key populations such as AA MSM require reliable estimates of their numbers. Current population size estimation (PSE) methods rely on assump- tions that are difficult to meet, potentially producing large biases. METHODS: We applied a new method to estimate the number of AA MSM in San Francisco (SF) using a respondent-driven sampling (RDS) survey. The approach uses respondents’ self-reported network size (i.e. the number of other AA MSM known to them in SF), along with a specification of the prior knowledge about the population size, to model the total size of the target population based on their proba- bility of recruitment. A Bayesian approach is used to quantify the amount of information on population size available in the survey. The plausibility of the resulting estimate was corroborated against an inde- pendent estimate of all MSM in SF and HIV case reporting data. RESULTS: 259 AA MSM were recruited in the RDS survey. The method calculated a median of 6,230 AA MSM living in SF (95% CI 1,984–35,545). The prevalence of diagnosed HIV in the survey (17.3%) projects 1,078 known HIV cases among AA MSM, compa- rable to the 1,170 actually reported to city’s surveillance system. A previous independent survey estimating 66,487 total MSM in SF, 6.1% AA, estimates 4055 AA MSM. CONCLUSIONS: The new method produced a robust, plausible, and consistent population size estimate for AA MSM. Given that RDS surveys are frequently done in many hidden populations world- wide, the method provides a simple, appealing tool to rapidly pro- duce estimates of the size of high risk populations – a fundamental public health measure that has been scarce for much of the HIV epi- demic. It is a useful complement to existing methods, especially when only RDS data are available.

P09.15 Time to clearance for molecular test-of-cure among men treated for urethral, pharyngeal, or rectal gonorrhoea in san francisco, 2013–2014

Introduction Due to the potential emergence of cephalosporin-resistant Neisseria gonorrhoeae (NG), some public health agencies recommend a test of cure (TOC) using nucleic acid amplification tests (NAATs). NAATs can remain positive after the infection has been effectively eradicated; the optimal time to obtain a TOC is unclear. To inform TOC recommendations, we conducted NAATs for 21 days following treatment for men who have sex with men (MSM) NG-infected at the urethra, rectum or pharynx. Methods MSM with untreated urethral, rectal or pharyngeal gonorrhoea were eligible. At enrollment, prior to provision of antibiotics, infection-site specimens were collected by a clinician for culture and NAAT testing. Participants whose enrollment-day specimens were negative were excluded. Participants self-collected daily infection-site specimens (rectal or pharyngeal swabs or urine) for 3 weeks and returned on days 7, 14, and 21 to submit their self-collected specimens for NAAT testing and provide clinician-collected specimens for culture and NAAT testing. We planned to follow at least 10 participants for at least 7 days in each of the urethral (U), rectal (R), and pharyngeal (P) study arms. Results We enrolled 46 MSM. Eleven participants had negative enrollment-day specimens, and 4 did not return after enrollment. Of the 31 included in the analysis (11U, 11R, 9P), 22 (71%) provided all 21 days of specimens; another 6 provided nearly all study specimens. The majority (94%) were negative on Day 7 (11U, 11R, 7P), though 4 (2U, 1R, 1P) had subsequent positive results. Conclusion A high proportion of participants had a negative NAAT before antibiotics, despite a prior positive result, indicating either an original false positive result or natural clearance of infection. Additional analyses will determine the effectiveness of other TOC time-points, including median time to: first negative result, 3 consecutive negative results, and clearance (consistently negative results through follow-up); and clearance at Days 14 and 21. Disclosure of interest statement No pharmaceutical grants were received in the development of this study.

Difference in Survival between Housed and Homeless individuals with HIV, San Francisco, 2002-2011.

San Francisco (SF), a city with large HIV-infected and homeless populations, expanded supportive housing for HIV-infected people in 2007. We used the SF HIV/AIDS registry to compare survival between people who were homeless and who were housed at time of HIV diagnosis from 2002 through 2011. Housing status was obtained from medical records and deaths from local, state, and national vital registration. Survival was estimated using the Kaplan-Meier product-limit method. Ten percent of the 5,474 cases were homeless. Among people diagnosed between 2002 and 2006, the five-year survival was worse for people who were homeless at HIV diagnosis than for housed individuals (79% vs. 92%, p<.0001), but not for those diagnosed between 2007 and 2011 (92% vs. 93%, p=.3938). The improved survival among HIV-infected homeless people occurred during the time of increased supportive housing for this population. Our findings support including housing as an essential component of HIV care.

Between Mao and McCarthy: Chinese American politics in the Cold War years

During the Cold War, Chinese Americans struggled to gain political influence in the United States. Considered potentially sympathetic to communism, their communities attracted substantial public and government scrutiny, particularly in San Francisco and New York. Between Mao and McCarthy looks at the divergent ways that Chinese Americans in these two cities balanced domestic and international pressures during the tense Cold War era. On both coasts, Chinese Americans sought to gain political power and defend their civil rights, yet only the San Franciscans succeeded. Forging multiracial coalitions and encouraging voting and moderate activism, they avoided the deep divisions and factionalism that consumed their counterparts in New York. Drawing on extensive research in both Chinese- and English-language sources, Charlotte Brooks uncovers the complex, diverse, and surprisingly vibrant politics of an ethnic group trying to find its voice and flex its political muscle in Cold War America.

Redefining boundaries at the 2015 Paleoanthropology Society and Society for American Archaeology (SAA) meeting in San Francisco.

Redefining boundaries at the 2015 Paleoanthropology Society and Society for American Archaeology (SAA) meeting in San Francisco.

Fluoroquinolone resistance in Neisseria gonorrhoeae after cessation of ciprofloxacin usage in San Francisco: using molecular typing to investigate strain turnover.

Ciprofloxacin resistance (CipR) among gonococcal strains in San Francisco (SF) increased between 2001 and 2006 and decreased between 2007 and 2009. Molecular typing of isolates obtained from 2005 to 2009 was performed to elucidate changes in CipR prevalence. A total of 2526 samples were collected at the SF City Clinic between 2001 and 2009. Minimum inhibitory concentrations to ciprofloxacin were obtained by agar dilution. Prevalences of CipR strains were determined, with corresponding confidence intervals (CIs). Between 2005 and 2009, 460 isolates were selected for molecular typing using Neisseria gonorrhoeae multiantigen sequence typing. Between 2001 and 2006, the prevalence of CipR increased from 3.4% (95% CI, 1.3%-5.4%) to 44% (95% CI, 39%-50%). However, in 2007 prevalence began to decrease, reaching 9.6% (95% CI, 6.0%-13%) by 2009. Of the 203 strain types identified between 2005 and 2009, 126 genogroups of closely related strain types were formed (varying by ≤1% at both target loci). Levels of CipR within the data set correlate with the prevalence of 3 major genogroups (G): G437, G1407, and G3112. Molecular typing reveals that CipR within the tested population is maintained by strain turnover between resistant genogroups. Despite early recommendation in 2002 to stop ciprofloxacin use in California, CipR in SF increased through 2006. The subsequent decrease in CipR corresponds with the 2007 national recommendation to cease ciprofloxacin treatment of gonorrhea, which suggests that national recommendations are potentially more effective at reducing CipR than regional recommendations in areas with high strain turnover.

Opera as Politics

This article describes the troubled, politically fraught path to the realization of San Francisco's War Memorial Opera House, the first municipally owned operatic performance venue in the nation. Although envisioned prior to the 1906 earthquake (in which the two most important opera houses in the city were destroyed), the realization of an innovative concept in which the people of the city would found and maintain an opera house took a quarter century to materialize. Supporters of the idea ascribed to the common sentiment of the time that classical music had an “elevating” and “ennobling” potential to “uplift” the poor and create a more responsible citizenry, but opera's historic association with wealth and elitism counteracted these arguments and blocked progress on the building until at last, in the 1920s, San Franciscans raised $2 million in direct contributions and voted for a $4 million bond issue.

Empress San Francisco: The Pacific Rim, the Great West and California at the Panama-Pacific International Exposition by Abigail M. Markwyn (review)

Reviewed by: Empress San Francisco: The Pacific Rim, the Great West and California at the Panama-Pacific International Exposition by Abigail M. Markwyn Sherry L. Smith EMPRESS SAN FRANCISCO: The Pacific Rim, the Great West and California at the Panama-Pacific International Exposition. By Abigail M. Markwyn. Lincoln: University of Nebraska Press. 2014. The 1915 Panama-Pacific International Expedition (PPIE) was very much a creature of its time. The same can be said for Abigail Markwyn’s account of the fair. Celebrating completion of the Panama Canal and its consequent boon for the West Coast, exposition organizers championed muscular imperialism, Anglo and male dominance, technological achievement, and a dynamic city’s remarkable ability to recover from the devastation of earthquake and fire. These themes now typify our understanding of the early twentieth century’s dominant moods. Markwyn’s book, however, challenges that single dimension “narrative” and convincingly argues that San Francisco’s elite businessmen, who created the exposition, could not solely control its meaning. Rather, numerous interests, nations, races, and ethnicities, plus women, contested the PPIE’s official message and asserted their own views upon the exposition. The fair became a contested space where various groups jockeyed for social, political, and explanatory power. Rather than an escape from Progressive era politics—a place simply to have fun—it became in Markwyn’s rendering yet another landscape where Americans fought over meaning. Her emphasis on power, particularly regarding issues of race, class and gender, typifies today’s social history. It is a valuable and viable approach. But if one wants to know more about the actual experience of attending the exposition, what it meant to most people who attended, or any one of a number of alternative ways of looking at the event, one must look elsewhere. To be sure, much of the fairground’s art and architecture trumpeted American expansion across the continent, the technological wonder of the Panama Canal, and the nation’s presumed destiny to dominate the Pacific in the future as primarily masculine and white accomplishments. Markwyn has the good sense to probe beyond the outward appearances, however. She quickly uncovers the “others” who insisted on having a voice, as well. Most notably were white women who, among other things, created a Woman’s Board, since the official board was completely male. They did not particularly push for women’s rights, but they insisted on a prominently displayed pioneer mother statue—a nod to white women’s roles in American expansion. Hawaiian women, daughters of [End Page 115] white and nonwhite parents, donned shirtwaists and visibly challenged the supposed divide between the civilized and the primitive. The Congressional Union for Women established a booth, produced pageants and parades, and proselytized for a federal woman suffrage amendment. Over the course of the fair’s first seven months, they acquired 500,000 signatures on a petition demanding such an amendment and organized the very first national convention of women voters. Ten thousand men and women attended the convention pageant on the Court of the Universe grounds. African Americans asserted their position as equal citizens of the Bay Area by creating floats and participating in the Alameda County Day parade while refusing to sanction a racist and segregationist Negro Day. Local Catholics, Chinese, and Irish—objects of discrimination in everyday life—visited, worked and performed at the fair on their own terms as well. Latin American nations used the exposition to define themselves and to pursue their own economic interests, particularly hoping to attract investment capital to their shores. Of course, it is difficult to assess how successful any of these groups or interests were in shaping others’ perceptions of them. The larger point, however, is that they tried. Markwyn’s evidence is compelling, the research impressive, and the writing clear. Perhaps it comes as no surprise, one-hundred years later, that anything intending to speak for all of San Francisco would be contested. This close study of a fleeting but significant event underscores the diversity, vitality, and complexity of not only a city on the cusp of the continent and the century, but also the foundation upon which it, and the nation itself, continues to wrestle with fundamental questions...

Designing a learning health organization for collective impact.

In May 2014, the Public Health Leadership Forum published “The High Achieving Governmental Health Department in 2020 as the Community Chief Health Strategist.”1 This groundbreaking paper started with the following statement: Local and state health departments need to adapt and evolve if governmental public health is to address emerging health demands, minimize current as well as looming pitfalls, and take advantage of new and promising opportunities. To succeed requires a view into the future. In November 2011, the San Francisco Department of Public Health (SFDPH), Population Health Division embarked on this journey to reorganize the public health division into a high-achieving governmental health department for the future. We used public health accreditation as the catalyst to reorganize, and the new organization structure launched on July 1, 2013. For the staff in the SFDPH, public health accreditation is about the humble and passionate pursuit of results, equity, and accountability for improving community health. This inspired us to call our framework for public health accreditation and improvement REACH (Results, Equity and Accountability for Community Health). Staff are focused on achieving results (impacts, goals, and outcomes); integrating equity into quality improvement efforts; designing accountability into our activities, including community-based evidence (local voice, wisdom, and knowledge) with science- and practice-based evidence; and protecting and promoting population health. REACH was developed after the SFDPH leadership embraced the idea that public health accreditation could be used as a vehicle to protect and promote the health of all San Franciscans. The San Francisco Health Commission—the governing health body—passed a resolution declaring public health accreditation a top strategic health priority for San Francisco. With this support, the SFDPH embarked on an extensive reorganization of its public health services into a new Population Health Division. The overarching goal was to design a community-centered, responsive, and agile health organization that could adapt quickly to current and emerging public health challenges and opportunities. Strategic objectives included the following: provide leadership in health protection, health promotion, disease and injury prevention, and disaster preparedness; expand our focus to community wellness, beyond disease events; promote healthy and sustainable environments; integrate health equity into quality improvement efforts; strengthen service excellence to communities, clients, and providers; ensure a culture of trust and innovation; strengthen our culture of finding, translating, and implementing science-based solutions to problems; and achieve and maintain public health accreditation. An organization design team consisting of leaders, managers, and staff was convened. Because there is limited collective knowledge and funding for developing organizational structures in local health departments, a new structure was designed using existing local experience and published resources. The design team members reviewed public health accreditation domains and standards, population health models,2,3 the Baldrige Criteria for Performance Excellence (CPE),4 key public health texts,5,6 and modern organization design books.7,8 The design team actively engaged the staff, the affected community, and other stakeholders to bring in and build connections of trust and understanding. By pulling together all those sources of input, the design team developed a strategic map and then created an organization design framework and staffing chart. With that foundation, the REACH framework evolved after reviewing and testing several quality improvement models.9–16 Finally, the SFDPH was able to leverage funding and technical assistance from the Centers for Disease Control and Prevention and the National Association of County & City Health Officials, which supported preparation for public health accreditation and funding for program collaboration and service integration.17 The purpose of this commentary is to review how the SFDPH used organization design concepts and continuous improvement frameworks to reorganize from autonomous, categorical silos of public health services to an integrated, community-centered Population Health Division. We believe that these concepts and methods can be adapted to many health organizations.

Mark Twain in Washington, D.C.: The Adventures of a Capital Correspondent

Mark Twain in Washington, D.C.: The Adventures of a Capital Correspondent

The story of serratia marcescens: pathologic risk factors in breast implant surgery.

Serratia marcescens (S. marcescens) emerged as an opportunist in the setting of immunodeficiency in the 1970s, when serious infections occurred in San Francisco hospitals after USA. Navy experiments had aerosolized the bacteria to study biologic warfare. We investigate the risks of S. marcescens in San Franciscans who undergo mastectomy with implant reconstruction. From 2007 to 2011, the senior author took breast capsule cultures for all patients at the time of tissue expander exchange/explant. Of the 142 women who had reconstruction, 23 had positive cultures. Only the two patients who were positive for S. marcescens developed clinical infections that required explantation. Both had postoperative chemotherapy with transient neutropenia, and both had close ties to San Francisco. Clinical signs of infection emerged for both patients months after initial surgery, despite having previously well healed incisions. Other patients were culture positive for Pseudomonas, Proteus, Enterococcus and MRSA and did not develop require explant. While the link between San Francisco and S. marcescens is controversial, a patient's geography is a simple screening tool when considering postoperative risks, especially in the immunocompromised. Closer monitoring for neutropenia during chemotherapy, and a lower threshold to administer S. marcescens targeted antibiotics may be warranted in these patients.

Intensive Care Unit Palliative Care Shortens Hospital Stays

Intensive Care Unit Palliative Care Shortens Hospital Stays

Insights From the San Francisco Match Rank List Data

For many years, the independent plastic surgery match has been regarded as a competitive process. Applicants expend significant time and resources applying to, and interviewing with, many programs to increase their chance for success. Public data from the San Francisco (SF) Match provide no predictors of success in the Match. Previous survey-based studies have provided some data, but suffer from recall and sampling bias. The purpose of this study was to provide match participants with objective primary-source data that can aid them in making informed decisions with regard to planning their interviews. Four years of fully deidentified individual-level and program-level data from the SF Match (2010-2013) were analyzed. Data included number of programs applied to, interview offers, and length of rank lists. For applicants who matched, data included the applicant's rank of program and the program's rank of applicant. During the 4 match years, 434 (86.3%) of 503 applicants received at least 1 interview offer. Of these candidates, 355 (82%) matched. Match rate increased with number of interviews, reaching 96% for those with 5 or more interview offers; 95% of applicants matched within their top 7 choices. On average, applicants matched at number 2.9 on their rank lists. Number of interview invitations is a strong predictor of success in the independent plastic surgery match, with the "magic number" being 5. Applicants rarely match to programs below number 7 on their rank lists. These data can aid applicants wishing to maximize their potential while minimizing unnecessary expenditures.

The lung microbiome of Ugandan HIV-infected pneumonia patients is compositionally and functionally distinct from that of San Franciscan patients.

Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome was significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population.