Choice of anesthesia technique is associated with earlier hospital discharge and reduced costs after transcatheter transfemoral aortic valve implantation

Background

Transcatheter aortic valve implantation (TAVI) has become a viable alternative to palliation in patients with severe aortic stenosis. We compared general anesthesia to conscious sedation for TAVI procedures with respect to post operative morbidity, hospital length of stay, and financial burden.

Methods

We conducted a retrospective review of prospectively collected data in patients undergoing transfemoral TAVI procedures from 2012 to 2017. Patients were matched based on age and sex and classed into either general anesthesia or conscious sedation groups respectively. Conscious sedation was provided with a dexmedetomidine infusion, and patients in general anesthesia group received a standard induction, tracheal intubation, and maintenance with sevoflurane. The hospital case costs were compared between the two groups before and after adjustment for inflation.

Results

We matched 124 pairs for a total of 248 patients. Both groups were similar with respect to demographic data, past medical history, medications, and intraoperative characteristics. There was no difference in postoperative morbidity and mortality between the two groups. The median hospital length of stay was 5 [interquartile range (IQR): 3, 10] and 7 (IQR: 4, 12) days, P=0.01, and after adjustment for inflation, the total hospital case costs were $48,984 (IQR: $44,802, $61,438) Canadian (CAD) vs. $55,333 (IQR: $46,832, $68,702) CAD, P=0.01, in the conscious sedation and general anesthesia groups, respectively.

Conclusions

Advancements in TAVI technologies, conscious sedation and a collaborative, multidisciplinary team approach reduces overall length of hospital stay and procedure costs.

Impact of pregnancy vaccine uptake and socio-demographic determinants on subsequent childhood Measles, Mumps and Rubella vaccine uptake: A UK birth cohort study

BACKGROUND

We examined the association between socio-demographic determinants and uptake of childhood Measles, Mumps & Rubella (MMR) vaccines and the association between pregnant women's pertussis vaccine uptake and their children's MMR vaccine uptake.

METHODS

We used nationally-representative linked mother-baby electronic records from the United Kingdom's Clinical-Practice-Research-Datalink. We created a birth cohort of children born between 01.01.2000 and 12.12.2020. We estimated the proportion vaccinated with first MMR vaccine by age 2 years and first and second MMR vaccines by age 5 years. We used survival-analysis and Cox proportional hazard models to examine the association between deprivation, ethnicity and maternal age and pertussis vaccination in pregnancy and children's MMR uptake.

RESULTS

Overall, 89.4 % (710,797/795,497) of children had first MMR by age 2 years and 92.6 % (736,495/795,497) by age 5 years. Among children still in the cohort when second MMR was due, 85.9 % (478,480/557,050) had two MMRs by age 5 years. Children from the most-deprived areas, children of Black ethnicity and children of mothers aged < 20 years had increased risk of being unvaccinated compared with children from the least-deprived areas, White children and children of mothers aged 31-40 years: first MMR by 5 years, adjusted Hazard Ratios (HR):0.86 (CI:0.85-0.87), HR:0.87 (CI:0.85-0.88) & HR:0.89 (CI:0.88-0.90) respectively. Deprivation was the determinant associated with the greatest risk of missed second MMR: adjusted HR:0.82 (CI:0.81-0.83). Children of mothers vaccinated in pregnancy were more likely than children of unvaccinated mothers to have MMR vaccines after adjusting for ethnicity, deprivation, and maternal age (First and Second MMRs adjusted HRs:1.43 (CI:1.41-1.45), 1.49 (CI:1.45-1.53).

CONCLUSION

Children from most-deprived areas are less likely to have MMR vaccines compared with children from least-deprived areas. Mothers who take up pregnancy vaccines are more likely to have their children vaccinated with MMR. Healthcare services should promote and facilitate access to both maternal and childhood vaccines during pregnancy.

Impact of COVID-19 on electroconvulsive therapy practice across Canadian provinces during the first wave of the pandemic

BACKGROUND

Electroconvulsive therapy (ECT) is a procedural treatment that is potentially life-saving for some patients with severe psychiatric illness. At the start of the global coronavirus disease 2019 (COVID-19) pandemic, ECT practice was remarkably disrupted, putting vulnerable individuals at increased risk of symptom exacerbation and death by suicide. This study aimed to capture the self-reported experiences of psychiatrists based at healthcare facilities across Canadian provinces who were delivering ECT treatments during the first phase of the COVID-19 pandemic (i.e., from mid-March 2020 to mid-May 2020).

METHODS

A multidisciplinary team of experts developed a survey focusing on five domains: ECT unit operations, decision-making, hospital resources, ECT procedure, and mitigating patient impact. Responses were collected from psychiatrists providing ECT at 67 ECT centres in Canada, grouped by four geographical regions (Ontario, Quebec, Atlantic Canada, and Western Canada).

RESULTS

Clinical operations of ECT programs were disrupted across all four regions - however, centres in Atlantic Canada were able to best preserve outpatient and maintenance care, while centres in Western Canada were able to best preserve inpatient and acute care. Similarly, Atlantic and Western Canada demonstrated the best decision-making practices of involving the ECT team and clinical ethicists in the development of pandemic-related guidelines. Across all four regions, ECT practice was affected by the redeployment of professionals, the shortage of personal protective equipment, and the need to enforce social distancing. Attempts to introduce modifications to the ECT delivery room and minimize bag-valve-mask ventilation were consistently reported. All four regions developed a new patient prioritization framework, and Western Canada, notably, aimed to provide ECT to only the most severe cases.

CONCLUSIONS

The results suggest that ECT provision was disproportionately affected across different parts of Canada. Possible factors that could explain these interregional differences include population, distribution of urban vs. rural areas, pre-pandemic barriers in access to ECT, number of cases, ability to control the spread of infection, and the general reduction in physicians' activities across different areas of health care. Studying these factors in the future will inform how medical centres should respond to public health emergencies and pandemic-related circumstances in the context of procedural treatments.

Examining ACCURE's Nurse Navigation Through an Antiracist Lens: Transparency and Accountability in Cancer Care

There are persistent disparities in the delivery of cancer treatment, with Black patients receiving fewer of the recommended cancer treatment cycles than their White counterparts on average. To enhance racial equity in cancer care, innovative methods that apply antiracist principles to health promotion interventions are needed. The parent study for the current analysis, the Accountability for Cancer Care through Undoing Racism and Equity (ACCURE) intervention, was a system-change intervention that successfully eliminated the Black-White disparity in cancer treatment completion among patients with early-stage breast and lung cancer. The intervention included specially trained nurse navigators who leveraged real-time data to follow-up with patients during their treatment journeys. Community and academic research partners conducted thematic analysis on all clinical notes (n = 3,251) written by ACCURE navigators after each contact with patients in the specialized navigation arm (n = 162). Analysis was informed by transparency and accountability, principles adapted from the antiracist resource Undoing Racism and determined as barriers to treatment completion through prior research that informed ACCURE. We identified six themes in the navigator notes that demonstrated enhanced accountability of the care system to patient needs. Underlying these themes was a process of enhanced data transparency that allowed navigators to provide tailored patient support. Themes include (1) patient-centered advocacy, (2) addressing system barriers to care, (3) connection to resources, (4) re-engaging patients after lapsed treatment, (5) addressing symptoms and side effects, and (6) emotional support. Future interventions should incorporate transparency and accountability mechanisms and examine the impact on racial equity in cancer care.

Electroconvulsive Therapy in Canada During the First Wave of COVID-19: Results of the "What Happened" National Survey

OBJECTIVES

The COVID-19 pandemic has disrupted the provision of essential and potentially life-saving procedural treatments such as electroconvulsive therapy (ECT). We surveyed ECT providers across Canada to understand how the first wave of the pandemic affected ECT delivery between mid-March 2020 and mid-May 2020.

METHODS

The survey was administered to ECT team members and decision makers at 107 Canadian health care centers with a focus on 5 domains: operations, decision-making, hospital resources, ECT procedure, and patient impact. Responses were obtained from 72 institutions, and collected answers were used to derive representative responses reflecting the situation at each ECT center. For specific domains, responses were split into 2 databases representing the perspective of psychiatrists (n = 67 centers) and anesthesiologists (n = 24 centers).

RESULTS

Provision of ECT decreased in 64% centers and was completely suspended in 27% of centers after the onset of the pandemic. Outpatient and maintenance ECT were more affected than inpatient and acute ECT. Programs reported a high level of collaboration between psychiatry and hospital leadership (59%) but a limited input from clinical ethicists (18%). Decisions were mostly made ad hoc leading to variability across institutions in adopted resource allocation, physical location of ECT delivery, and triaging frameworks. The majority of centers considered ECT to be aerosol-generating and incorporated changes to airway management.

CONCLUSIONS

Electroconvulsive therapy services in Canada were markedly disrupted by the COVID-19 pandemic. The variability in decision-making across centers warrants the development of a rational approach toward offering ECT in pandemic contexts.

A core outcome set for school-based physical activity interventions: an international consensus

Background

Studies of school-based physical activity interventions vary in the outcomes they measure. This prevents comparisons of results to establish impacts. We aimed to develop a core outcome set agreed by key stakeholders for future studies of school-based physical activity interventions.

Methods

We used a modified-Delphi consensus method. First, we conducted a systematic review to identify outcomes measured in relevant studies and listed these in a Delphi survey. Next, we recruited key stakeholders to complete 2 survey rounds: Round 1 was to rate each outcome from ‘not important' to ‘critical', and Round 2 was to re-rate the outcomes based on feedback from Round 1. Outcomes rated ‘critical' by 70% of stakeholders (i.e., reaching consensus) were highlighted. Then, using the full list of outcomes, we conducted a children's workshop to include their views. Finally, we held a stakeholder meeting to discuss results and agree consensus.

Results

We identified 50 outcomes from the systematic review. Sixty-five stakeholders (16 educators, 13 health professionals, 12 parents, 24 researchers) representing 9 countries completed both survey rounds; 13/50 outcomes reached consensus. Children (n = 16) identified 8 outcomes of importance; 3 were consistent with the survey results. Stakeholders attending the meeting (n = 13) reached consensus on 14 outcomes to be included in the core outcome set: fitness, physical activity intensity, energy, sleep, diet, happiness, stress, depression, anxiety, wellbeing, self-esteem, enjoyment, concentration, and focus. These core outcomes were reviewed and agreed by all 65 stakeholders.

Conclusions

Our core outcome set agreed by international stakeholders includes physical and mental health, and cognitive function. We recommend its use in future studies of school-based physical activity interventions. Findings from future studies can be compared and combined which will be relevant to public health policy makers and educators.

Key messages

School-based physical activity interventions should measure physical and mental health, and cognitive function. Wide use of this core outcome set will enable findings to be compared and combined.

Artificial intelligence in radiation oncology: A review of its current status and potential application for the radiotherapy workforce

OBJECTIVE

Radiation oncology is a continually evolving speciality. With the development of new imaging modalities and advanced imaging processing techniques, there is an increasing amount of data available to practitioners. In this narrative review, Artificial Intelligence (AI) is used as a reference to machine learning, and its potential, along with current problems in the field of radiation oncology, are considered from a technical position.

KEY FINDINGS

AI has the potential to harness the availability of data for improving patient outcomes, reducing toxicity, and easing clinical burdens. However, problems including the requirement of complexity of data, undefined core outcomes and limited generalisability are apparent.

CONCLUSION

This original review highlights considerations for the radiotherapy workforce, particularly therapeutic radiographers, as there will be an increasing requirement for their familiarity with AI due to their unique position as the interface between imaging technology and patients.

IMPLICATIONS FOR PRACTICE

Collaboration between AI experts and the radiotherapy workforce are required to overcome current issues before clinical adoption. The development of educational resources and standardised reporting of AI studies may help facilitate this.

A Proactive Nurse Driven Systematic Approach for Covid-19 Screening for Patients Undergoing Aerosol Generating Procedures

Background Information

Objectives of Project

Process of Implementation

Statement of Successful Practice

Implication for Advancing the Practice of Perianesthesia nursing

'It's like you don't have a roadmap really': using an antiracism framework to analyze patients' encounters in the cancer system

Background: Cancer patients can experience healthcare system-related challenges during the course of their treatment. Yet, little is known about how these challenges might affect the quality and completion of cancer treatment for all patients, and particularly for patients of color. Accountability for Cancer Care through Undoing Racism and Equity is a multi-component, community-based participatory research intervention to reduce Black-White cancer care disparities. This formative work aimed to understand patients' cancer center experiences, explore racial differences in experiences, and inform systems-level interventions.Methods: Twenty-seven breast and lung cancer patients at two cancer centers participated in focus groups, grouped by race and cancer type. Participants were asked about what they found empowering and disempowering regarding their cancer care experiences. The community-guided analysis used a racial equity approach to identify racial differences in care experiences.Results: For Black and White patients, fear, uncertainty, and incomplete knowledge were disempowering; trust in providers and a sense of control were empowering. Although participants denied differential treatment due to race, analysis revealed implicit Black-White differences in care.Conclusions: Most of the challenges participants faced were related to lack of transparency, such that improvements in communication, particularly two-way communication could greatly improve patients' interaction with the system. Pathways for accountability can also be built into a system that allows patients to find solutions for their problems with the system itself. Participants' insights suggest the need for patient-centered, systems-level interventions to improve care experiences and reduce disparities.

Impact of school-based physical activity interventions in primary schools: measuring what matters

Background

A growing number of small studies suggest that school-based physical activity initiatives can help children achieve the recommended 60 minutes of physical activity per day. However, the heterogeneity of outcomes and measures used in small studies prevents pooling of results to demonstrate whether short-term health benefits are sustained. Qualitative studies suggest many benefits that are not represented by outcomes in trials to date. The aim of this study was to generate a list of outcomes that have been studied to develop a core outcome set (COS) acceptable to key stakeholders for future studies evaluating school-based physical activity initiatives.

Methods

We searched six databases (MEDLINE, EMBASE, PsycINFO, CINAHL, CENTRAL and Cochrane Database of Systematic Reviews) systematically for reviews of school-based physical activity interventions, and extracted relevant studies to identify the outcomes and measures used in each paper. A long list was generated from the literature and a previous workshop with stakeholders. This study is registered with COMET (#1322), and with PROSPERO (CRD42019146621).

Results

75/121 cited studies drawn from 53/2409 reviews met our inclusion criteria. We grouped 65 outcomes into 3 domains: (i) physical activity and health (ii) social and emotional health, and (iii) educational attainment. We will conduct two Delphi survey rounds with four stakeholder groups (health professionals, researchers, educators and parents) to rate the importance of each outcome. A core outcome set will be generated from a consensus process.

Conclusions

There is currently a large variation of outcomes and measures studied that precludes evidence synthesis of the impact of school-based physical activity interventions. Consensus methods are needed to focus research on the outcomes that matter the most to key stakeholders and to provide tools for future studies to assess long-term impact.

Key messages

Variations in outcomes studied precludes evidence synthesis of SBPA intervention impacts. A core outcome set is needed to ensure future SBPA interventions measure outcomes that matter the most.

The role of changing temperature in microbial metabolic processes during permafrost thaw

Approximately one fourth of the Earth's Northern Hemisphere is underlain by permafrost, earth materials (soil, organic matter, or bedrock), that has been continuously frozen for at least two consecutive years. Numerous studies point to evidence of accelerated climate warming in the Arctic and sub-Arctic where permafrost is located. Changes to permafrost biochemical processes may critically impact ecosystem processes at the landscape scale. Here, we sought to understand how the permafrost metabolome responds to thaw and how this response differs based on location (i.e. chronosequence of permafrost formation constituting diverse permafrost types). We analyzed metabolites from microbial cells originating from Alaskan permafrost. Overall, permafrost thaw induced a shift in microbial metabolic processes. Of note were the dissimilarities in biochemical structure between frozen and thawed samples. The thawed permafrost metabolomes from different locations were highly similar. In the intact permafrost, several metabolites with antagonist properties were identified, illustrating the competitive survival strategy required to survive a frozen state. Interestingly, the intensity of these antagonistic metabolites decreased with warmer temperature, indicating a shift in ecological strategies in thawed permafrost. These findings illustrate the impact of change in temperature and spatial variability as permafrost undergoes thaw, knowledge that will become crucial for predicting permafrost biogeochemical dynamics as the Arctic and Antarctic landscapes continue to warm.

Establishing New Community-Based Participatory Research Partnerships using the Community-Based Participatory Research Charrette Model: Lessons from the Cancer Health Accountability for Managing Pain and Symptoms Study

BACKGROUND

Community-based participatory research (CBPR) is a collaborative and equitable approach to research inquiry; however, the process of establishing and maintaining CBPR partnerships can be challenging. There is an ongoing need for innovative strategies that foster partnership development and long-term sustainability. In 2010, the University of North Carolina at Chapel Hill developed a CBPR charrette model to facilitate stakeholder engagement in translational research.

OBJECTIVE

To describe how the Cancer Health Accountability for Managing Pain and Symptoms (CHAMPS) Study leveraged the CBPR charrette process to develop and strengthen its CBPR partnership and successfully implement research objectives.

METHODS

Fourteen CHAMPS community, academic, and medical partners participated in the CBPR charrette. Two co-facilitators guided the charrette application process and in-person discussion of partnership strengths, needs, and challenges. Community experts (CEs) and academic experts (AEs) with extensive experience in CBPR and health disparities provided technical assistance and recommendations during the in-person charrette.

CONCLUSIONS

Overall, the CHAMPS partnership benefited significantly from the charrette process. Specifically, the charrette process engendered greater transparency, accountability, and trust among CHAMPS partners by encouraging collective negotiation of project goals and implementation, roles and responsibilities, and compensation and communication structures. The process also allowed for the exploration of newly identified challenges and potential solutions with support from CEs and AEs. Furthermore, the charrette also functioned as a catalyst for capacity building among CHAMPS community, academic, and medical partners. Future studies should compare the impact of the CBPR charrette, relative to other approaches, on partnership development and process evaluation outcomes.

Innovating Qualitative Framing Analysis for Purposes of Media Analysis Within Public Health Inquiry

Public health is said to lack methodological diversity and creativity in media analysis. Although the framing paradigm offers important conceptual and operational insights for undertaking media analysis in public health research, frames are described as "elusive" to measure with their analysis a "methodological black box." With this article, we aim to foster creative thinking around media analysis in public health and to make the "black box" of framing analysis more transparent, by illustrating the innovation and application of a qualitative framing analysis technique in original public health research. We provide a "how to" guide for this framing analysis method and use data to illustrate methodological challenges encountered during the research. The findings drawn from this method are contrasted with findings gained from thematic analysis applied to the same data. The article concludes by considering the benefits of this type of framing analysis within public health scholarship.

Hemodialysis-Associated Febrile Episodes: Surveillance before and after Major Alteration in the Water Treatment System

Surveillance for bacteremic or pyrogenic episodes associated with hemodialysis was undertaken before and after the reconstruction of the water treatment system at our University medical center. The new water system included a holding tank with iodination treatment. The water delivered to individual dialysis stations had only occasional positive bacterial cultures (3 of 21 samples before completion of construction, 2 of 16 samples afterwards) and intermittent detection of endotoxin (6 of 21 samples before completion of construction, 9 of 16 samples afterwards) at monthly sampling. Among 51 individual dialysis treatments (25 patients) before reconstruction and 56 treatments (29 patients), after, only 2 and 3 febrile events were identified, respectively. All of these were associated with underlying infectious illness and not with the hemodialysis procedure itself. Overall, we conclude that pyrogenic episodes associated directly with hemodialysis treatment are infrequent, and that the addition of a water storage tank with iodination treatment does not appear to increase the risk of bacteremia or pyrogenic episodes.

Equity in patient-provider communication regarding treatment-related symptoms and health-related quality of life (HRQOL) among breast cancer survivors

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Background: Compared with white breast cancer patients, black patients more often report inadequate symptom control and decrements in health-related quality of life (HRQOL). Racial differences in patient-provider communication (PPC) are well-documented and linked to worse health outcomes for minorities; however, less is known about inequities in symptom and HRQOL discussions among cancer patients and providers. As part of an NCI-funded systems change intervention to improve racial equity in treatment completion among Black and White cancer patients, we assessed racial differences in PPC regarding treatment-related symptoms, HRQOL issues (e.g., physical, psychosocial, financial, and spiritual well-being), and symptom management among breast cancer survivors (BCS). Methods: We conducted 6 focus groups (FGs) and semi-structured interviews with 22 stage 1-3 BCS (3 black FGs; 3 white FGs) from 2 cancer centers. Guided by a community-based participatory research approach, our diverse community-academic-medical team facilitated FGs and conducted qualitative analyses. Results: Although both black and white BCS reported multiple treatment-related symptoms and changes in HRQOL, perspectives on PPC differed. Some black and white BCS described positive aspects of PPC, including providers’ thorough explanations of treatment side effects and responsiveness to symptom concerns. However, white BCS expressed greater satisfaction with PPC, while black BCS more often described concerns regarding providers’ verbal (e.g., nondisclosure, dismissiveness) and non-verbal communication (e.g., unapproachability, poor eye contact) skills in the context of symptom management. Most BCS, regardless of race, indicated that providers typically discussed physical symptoms/HRQOL issues, but often failed to mention non-physical side effects of treatment (e.g., social isolation, financial toxicity). Conclusions: Racial differences in PPC exist among BCS and may contribute to inequities in symptom management and HRQOL. Inadequate communication regarding non-physical symptoms likely represents a critical missed opportunity for improving the quality and equity of palliative care.

Removal of Exogenous Materials from the Outer Portion of Frozen Cores to Investigate the Ancient Biological Communities Harbored Inside

The cryosphere offers access to preserved organisms that persisted under past environmental conditions. In fact, these frozen materials could reflect conditions over vast time periods and investigation of biological materials harbored inside could provide insight of ancient environments. To appropriately analyze these ecosystems and extract meaningful biological information from frozen soils and ice, proper collection and processing of the frozen samples is necessary. This is especially critical for microbial and DNA analyses since the communities present may be so uniquely different from modern ones. Here, a protocol is presented to successfully collect and decontaminate frozen cores. Both the absence of the colonies used to dope the outer surface and exogenous DNA suggest that we successfully decontaminated the frozen cores and that the microorganisms detected were from the material, rather than contamination from drilling or processing the cores.

Genetic diversity, virulence and fitness evolution in an obligate fungal parasite of bees

Within-host competition is predicted to drive the evolution of virulence in parasites, but the precise outcomes of such interactions are often unpredictable due to many factors including the biology of the host and the parasite, stochastic events and co-evolutionary interactions. Here, we use a serial passage experiment (SPE) with three strains of a heterothallic fungal parasite (Ascosphaera apis) of the Honey bee (Apis mellifera) to assess how evolving under increasing competitive pressure affects parasite virulence and fitness evolution. The results show an increase in virulence after successive generations of selection and consequently faster production of spores. This faster sporulation, however, did not translate into more spores being produced during this longer window of sporulation; rather, it appeared to induce a loss of fitness in terms of total spore production. There was no evidence to suggest that a greater diversity of competing strains was a driver of this increased virulence and subsequent fitness cost, but rather that strain-specific competitive interactions influenced the evolutionary outcomes of mixed infections. It is possible that the parasite may have evolved to avoid competition with multiple strains because of its heterothallic mode of reproduction, which highlights the importance of understanding parasite biology when predicting disease dynamics.

The relationship between serum urea levels and outcome in acute epistaxis

OBJECTIVES

To establish whether, for the patient presenting with epistaxis, there is a relationship between clinical outcome and serum urea levels measured on initial attendance at the accident and emergency (A&E) department.

METHODOLOGY

Records were reviewed from all patients attending a single teaching hospital A&E department between 1st January 2010 and 11st February 2011 with a diagnosis of epistaxis. Patients were analysed according to their admission serum urea and creatinine levels and then grouped according to clinical outcome.

RESULTS

We identified 278 patients (145 males, 133 females), 82 of which required hospital admission. Eleven required blood transfusion, and five required surgical arrest of the haemorrhage. No patients died. Serum urea and creatinine levels were measured in 119/278 patients. The mean serum urea level was significantly higher in patients admitted for further management of epistaxis than in patients who were discharged from the A&E department (9.35 mmol/l vs. 6.74 mmol/l, respectively; p = 0.003). There was no significant difference in mean serum urea levels between patients who were transfused and patients who were not, or between patients who went to the operating theatre and patients who did not.

CONCLUSIONS

Elevated serum urea levels on hospital admission are related to more severe clinical outcome in epistaxis.

Network portal: a database for storage, analysis and visualization of biological networks

The ease of generating high-throughput data has enabled investigations into organismal complexity at the systems level through the inference of networks of interactions among the various cellular components (genes, RNAs, proteins and metabolites). The wider scientific community, however, currently has limited access to tools for network inference, visualization and analysis because these tasks often require advanced computational knowledge and expensive computing resources. We have designed the network portal (http://networks.systemsbiology.net) to serve as a modular database for the integration of user uploaded and public data, with inference algorithms and tools for the storage, visualization and analysis of biological networks. The portal is fully integrated into the Gaggle framework to seamlessly exchange data with desktop and web applications and to allow the user to create, save and modify workspaces, and it includes social networking capabilities for collaborative projects. While the current release of the database contains networks for 13 prokaryotic organisms from diverse phylogenetic clades (4678 co-regulated gene modules, 3466 regulators and 9291 cis-regulatory motifs), it will be rapidly populated with prokaryotic and eukaryotic organisms as relevant data become available in public repositories and through user input. The modular architecture, simple data formats and open API support community development of the portal.

Bacterial endophyte communities of two wheatgrass varieties following propagation in different growing media

Bacterial endophyte communities of two wheatgrass varieties currently being used in the revegetation of military training ranges were studied. Culturable and direct 16S rDNA PCR amplification techniques were used to describe bacterial communities present in Siberian and slender wheatgrass seeds, leaf tissues, and root tissues following propagation in either sand or a peat-based growing mix. Our hypothesis was that the resulting plant endophytic communities would be distinct, showing not only the presence of endophytes originating from the seed but also the characteristics of growth in the two different growing media. Both culture and culture-independent assays showed the likely translocation of Actinobacteria, Firmicutes, and Gammaproteobacteria from seed to mature plant tissues as well as subsequent colonization by exogenous organisms. Statistical analysis of 16S terminal restriction fragment profiles identified growing media as having a greater significant effect on the formation of the endpoint endophytic communities than either plant tissue or wheatgrass variety. In silico digests of the ribosomal database produced putative identifications indicating an increase in overall species diversity and increased relative abundances of Firmicutes and Cyanobacteria following propagation in sand and Betaproteobacteria following propagation in the peat-based growing mix. Results indicated a substantial translocation of endophytes from seed to mature plant tissues for both growing media and that growing medium was a dominant determinant of the final taxonomy of the endpoint plant endophytic communities.

P1-09-03: Prevalence of Germline TP53 Mutations in Young Women with HER2−Positive Breast Cancer

Background: Li Fraumeni syndrome is a rare inherited cancer susceptibility condition associated with germline mutations in the TP53 gene, in which breast cancer (BC) is the most frequent tumor. The prevalence of TP53 mutations in population-based series of very young onset BC (&lt;30 years at diagnosis) ranges from &lt;1% to approximately 7%1-4. Recent data show that BC in patients carrying a germline TP53 mutation are commonly HER2 amplified (63-83%)5-7. In this study, we assessed the prevalence of germline TP53 mutations in women with HER2 positive BC diagnosed age ≤ 50 years.

Material & Methods: We identified 347 women with invasive HER2 positive BC diagnosed at age ≤ 50 years using the Clinical Operations and Research Information System (CORIS) at the Dana Farber Cancer Institute. Information on age at diagnosis, histology, hormone receptor and HER2 status as well as personal and family cancer history was confirmed from medical records. 129 patients were excluded for various reasons, including a cancer diagnosis prior to the BC and a documented BRCA1/2 mutation. A combination of Exon Grouping Analysis (EGAN) and Sanger sequencing for detection of TP53 mutations in exons 2–11 including surrounding intronic sequence was performed on 218 germline DNA samples. Multiplex Ligation-dependent Probe Amplification (MLPA) analysis for the detection of TP53 deletions or duplications is ongoing.

Results: A germline TP53 mutation was identified in 4 women diagnosed at age ≤ 50 years (1.8%, 95%CI 0.5−4.6). At BC diagnosis, they were 23, 32, 44 and 50 years. Two BC were ER+/PR+, HER2+ and 2 were ER-/PR-, HER2+. Estimate of prevalence of germline TP53 mutations by age at BC diagnosis are: age ≤ 35, 2/41 (4.9%, 95%CI 0.6−16.6), and age ≤ 45 3/168 (1.8%, 95%CI 0.4−5.1). Among the women with germline TP53 mutations, 2 met the Chompret criteria8 and none the classic LFS criteria.

Discussion: TP53 mutations were identified in a cohort of women with HER2+ BC at young age. As expected, the frequency is higher in younger women, but mutations were seen in all age groups that were evaluated. None of these women met classic LFS criteria by family history. Consideration of TP53 testing should be given to women diagnosed below age 35 who are negative for BRCA1/2 mutations regardless of family history. Analysis of other series will be helpful in reaching more stable estimates of the prevalence of mutation carriers among patients with HER2+ BC at young age.

1. Sidransky D et al. Cancer Res. 1992; 52:2984–2986.

2. Borresen AL et al. Cancer Res.1992; 52:3234–3236.

3. Lalloo F et al. Lancet 2003; 361:1101–02

4. Gonzalez KD et al. J Clin Oncol 2009;27(8):1250–6

5. Wilson JR et al. J Med Genet 2010;47(11):771–774.

6. Melhem-Bertrandt A et al: San Antonio Breast Cancer Symposium 2010: P3-12-01.

7. Masciari S et al: J Clin Oncol 29: 2011 (suppl; abstr 1519)

8. Tinat J et al. J Clin Oncol. 2009;27(26):e108–9

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-09-03.

EFFECT OF JOB SKILLS TRAINING ON EMPLOYMENT AND JOB SEEKING BEHAVIORS IN AN AMERICAN INDIAN SUBSTANCE ABUSE TREATMENT SAMPLE

Employment difficulties are common among American Indian individuals in substance abuse treatment. To address this problem, the Southwest Node of NIDA's Clinical Trials Network conducted a single-site adaptation of its national Job Seekers Workshop study in an American Indian treatment program, Na'Nizhoozhi Center (NCI). 102 (80% men, 100% American Indian) participants who were in residential treatment and currently unemployed were randomized to (1) a three session, manualized program (Job seekers workshop: JSW) or (2) a 40-minute Job Interviewing Video: JIV). Outcomes were assessed at 3-month follow up: 1) number of days to a new taxed job or enrollment in a job-training program, and 2) total hours working or enrolled in a job-training program. No significant differences were found between the two groups for time to a new taxed job or enrollment in a job-training program. There were no significant differences between groups in substance use frequency at 3-month follow-up. These results do not support the use of the costly and time-consuming JSW intervention in this population and setting. Despite of the lack of a demonstrable treatment effect, this study established the feasibility of including a rural American Indian site in a rigorous CTN trial through a community-based participatory research approach.

Utility of lipid biomarkers in support of bioremediation efforts at army sites

Lipid biomarker analysis has proven valuable in testing the hypothesis that attributes of the extant microbiota can directly reflect the occurrence of contaminant biodegradation. Two past research efforts have demonstrated this utility and are described here. A 4.5 m vertical core was obtained from a diesel fuel oil contamination plume. Core material was assayed for total petroleum hydrocarbons (TPH) and bacterial membrane phospholipids (PLFA) via a single solvent extraction. Microbial viable biomass and the relative abundance of Gram-negative bacterial PLFA biomarkers were found to be significantly correlated with TPH concentration. The core TPH profile also revealed two distinct areas where the average TPH level of 3,000 microg g(-1) fell to near detection limits. Both areas were characterized by a three-fold decrease in the hexadecane/pristane ratio, indicating alkane biodegradation, and a distinct PLFA profile that showed a close similarity to the uncontaminated surface soil. Low-order, incomplete detonations can deposit hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) into training range surface soils. Since surface soils are exposed to temporal and diurnal moisture cycles, we investigated the effect two very different soil moisture tensions had on the in situ microbiota and RDX biodegradation. Saturated soils were characterized by rapid RDX biodegradation, 4 day half-life, a decrease in number of species detected and increase in PLFA biomarkers for Gram-negative proteobacteria (n16:1omega7c, n18:1omega9c, and n18:1omega7c) and Gram-positive firmicutes (i15:0 and a15:0). Terminal restriction fragment length polymorphism (T-RFLP) profiles of endpoint microbial communities indicated a shift from 18 to 36% firmicutes, the loss of gamma-proteobacteria and the emergence of alpha-proteobacteria. These two past research efforts demonstrated the utility of the lipid biomarker analysis in identifying microbial community characteristics that were associated with two very different soil contaminants. Lipid biomarkers defined areas of TPH biodegradation and identified community shifts as a result of soil conditions that affected explosives fate. Information like this can be used to enhance the predictive power of ecological models such as the Army Training and Testing Area Carrying Capacity for munitions model [ATTACC].

Human metabolism of [(14)C]indisulam following i.v. infusion in cancer patients

Indisulam is a new anticancer drug with a unique mechanism of action, arresting the cell cycle at the G1/S transition. The major excretory pathway of indisulam is via the urine, accounting for 63% of the radioactive dose ([(14)C]indisulam) administered in a human mass balance study. Radiochromatographic profiling of urine samples resulted in the detection of several radioactive peaks. The purpose of the present investigation was to elucidate the chemical structures of these observed indisulam metabolites. We collected fractions after chromatographic separation of the urine samples. These fractions were analysed using tandem mass spectrometry. We propose the chemical structure of 15 indisulam metabolites in urine. The metabolism of indisulam is very complex, consisting of oxidative dechlorination, hydroxylation, hydrolysis, acetylation, sulphation and glucuronidation. The clinical relevance of the observed indisulam metabolites needs further investigation.

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

Accurate determinations of alpha(s) from realistic lattice QCD

We obtain a new value for the QCD coupling constant by combining lattice QCD simulations with experimental data for hadron masses. Our lattice analysis is the first to (1) include vacuum polarization effects from all three light-quark flavors (using MILC configurations), (2) include third-order terms in perturbation theory, (3) systematically estimate fourth and higher-order terms, (4) use an unambiguous lattice spacing, and (5) use an [symbol: see text](a2)-accurate QCD action. We use 28 different (but related) short-distance quantities to obtain alpha((5)/(MS))(M(Z)) = 0.1170(12).

A community-based clinical selective in end-of-life care

There is a widespread recognition among medical educators and accreditation organizations that medical students and young physicians lack the competency necessary to care for persons near the end of life. This article describes the institutional and attitudinal barriers to innovation in curriculum design. It then presents and evaluates a 1-month selective for fourth year students that focuses on providing end-of-life care to immigrant populations in community-based home hospice. The selective joined biomedical training in pain management and palliative care, a clinical rotation in home hospice care with an analysis of the way that social and ethnic factors inform and influence end-of-life care.

Quantitative determination of the novel anticancer drug E7070 (indisulam) and its metabolite (1,4-benzenedisulphonamide) in human plasma, urine and faeces by high-performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry

E7070 (indisulam) is a novel anticancer drug currently undergoing clinical investigation. We present a sensitive and specific method for the quantitative determination of E7070 and its metabolite M1 (1,4-benzenedisulphonamide) in human plasma, urine and faeces. The analytes and their tetra-deuterated analogues, which were used as internal standards, were isolated from the biological matrix by solid-phase extraction with OASIS cartridges (0.5 mL plasma or 1 mL urine) and by liquid-liquid extraction with ethyl acetate at pH 5 (1 mL faecal homogenate). The analytes were separated on a C8 reversed-phase chromatographic column and analyzed using electrospray ionization and tandem mass spectrometric detection in the negative ion mode. The validated concentration ranges in plasma were 0.1-20 microg/mL for E7070 and 0.01-2 microg/mL for M1. In urine and faecal homogenate, a concentration range from 0.05-10 microg/mL or microg/g, respectively, was validated for both analytes. Validation of the plasma assay was performed according to the most recent FDA guidelines. The assay fulfilled all generally accepted requirements for linearity (r > 0.99, residuals between -8 and 10%), accuracy (-13.5 to 1.4%) and precision (all less than 11%) in the tested matrices. We investigated recovery, stability (working solutions at -20 degrees C and at room temperature, biological matrices at -20 degrees C, room temperature and after 3 freeze/thaw cycles; final extracts at room temperature) and robustness. All these parameters were found acceptable. This method is suited for mass balance studies or therapeutic drug monitoring, as demonstrated by a case example showing plasma concentrations and cumulative excretion of E7070 and M1 in urine and faeces. Furthermore, we show the presence of E7070 metabolites in patient urine.