Analysis of the fecal metagenome in long-term survivors of pancreas cancer.

BACKGROUND: The 5-year overall survival of pancreas adenocarcinoma (PCa) remains less than 10%. Clinical and tumor genomic characteristics have not differentiated PCa long-term survivors (LTSs) from unselected patients. Preclinical studies using fecal transplant experiments from LTSs of PCa have revealed delayed tumor growth through unknown mechanisms involving the fecal microbiota. However, features of the fecal microbiome in patients with long-term survival are not well described. METHODS: In this cross-sectional study, comprehensive shotgun metagenomics was performed on stool from PCa patients with long-term survival (n = 16). LTS was defined as >4 years from pancreatectomy and all therapy without recurrence. LTSs were compared to control patients with PCa who completed pancreatectomy and chemotherapy (n = 8). Stool was sequenced using an Illumina NextSeq500. Statistical analyses were performed in R with MicrobiomeSeq and Phyloseq for comparison of LTSs and controls. RESULTS: All patients underwent pancreatectomy and chemotherapy before sample donation. The median time from pancreatectomy of 6 years (4-14 years) for LTSs without evidence of disease compared to a median disease-free survival of 1.8 years from pancreatectomy in the control group. No differences were observed in overall microbial diversity for LTSs and controls using Shannon/Simpson indexes. Significant enrichment of species relative abundance was observed in LTSs for the Ruminococacceae family specifically Faecalibacterium prausnitzii species as well as Akkermansia muciniphila species. CONCLUSIONS: Stool from patients cured from PCa has more relative abundance of Faecalibacterium prausnitzii and Akkermansia muciniphila. Additional studies are needed to explore potential mechanisms by which the fecal microbiota may influence survival in PCa. PLAIN LANGUAGE SUMMARY: Although pancreatic cancer treatments have improved, the number of long-term survivors has remained stagnant with a 5-year overall survival estimate of 9%. Emerging evidence suggests that microbes within the gastrointestinal tract can influence cancer response through activation of the immune system. In this study, we profiled the stool microbiome in long-term survivors of pancreas cancer and controls. Several enriched species previously associated with enhanced tumor immune response were observed including Faecalibacterium prausnitzii and Akkermansia muciniphila. These findings warrant additional study assessing mechanisms by which the fecal microbiota may enhance pancreatic cancer immune response.

Robotic approach mitigates the effect of major complications on survival after pancreaticoduodenectomy for periampullary cancer.

BACKGROUND: Major complications (MCs) after pancreaticoduodenectomy (PD) are a known independent predictor of worse oncologic outcomes. There are limited data on the effect of major complications on long-term outcomes after robotic PD (RPD). The aim of this study is to compare the effect of MC on overall (OS) and disease-free survival (DFS) after RPD and open PD (OPD). METHODS: This is a single-center, retrospective review of a prospectively maintained database of all patients undergoing PD for periampullary cancer including ampullary adenocarcinoma, distal cholangiocarcinoma, and duodenal carcinoma. Univariate analysis was performed on all clinical, pathologic, and treatment factors. MCs were defined as Clavien-Dindo ≥ grade 3. Kaplan-Maier survival analysis was performed with log-rank test for group comparison. Multivariable Cox regression analysis was used to identify factors associated with overall survival (OS) in both the OPD and RPD groups. RESULTS: A total of 190 patients with ampullary carcinoma (n = 98), cholangiocarcinoma (n = 55), and duodenal adenocarcinoma (n = 37) were examined over the study period with 61.1% (n = 116) undergoing RPD and 38.9% (n = 74) undergoing OPD. There was no significant difference in patient demographics between the RPD and OPD cohorts. Furthermore, R0 resection rates, tumor size, and lymph node involvement were similar between the RPD and OPD cohorts. OPD had higher rate of MC (40.5% vs 28.3% in RPD, p = 0.011) including clinically relevant pancreatic fistula (25.7% vs 8.6%, p = 0.001) and wound infection (34.5% vs 13.8%, p < 0.001). MCs were associated with a lower OS in the OPD cohort (HR = 2.18, 95%CI 1.0-4.55, p = 0.038). MCs were not associated with OS in the RPD cohort (HR = 1.55, 95%CI 0.87-2.76, p = 0.14). CONCLUSION: MCs are associated with worse patient outcomes after OPD but not after RPD. Robotic approach mitigates and possibly abrogates the negative effects of MCs on patient outcomes after PD for malignancy and is associated with improved adjuvant chemotherapy completion rates.

Ceramide levels in blood plasma correlate with major depressive disorder severity and its neutralization abrogates depressive behavior in mice.

Major depressive disorder (MDD) is a severe disease of unknown pathogenesis that will affect ∼10% of people during their lifetime. Therapy for MDD requires prolonged treatment and often fails, predicating a need for novel treatment strategies. Here, we report increased ceramide levels in the blood plasma of MDD patients and in murine stress-induced models of MDD. These blood plasma ceramide levels correlated with the severity of MDD in human patients and were independent of age, sex, or body mass index. In addition, intravenous injection of anti-ceramide antibodies or neutral ceramidase rapidly abrogated stress-induced MDD, and intravenous injection of blood plasma from mice with MDD induced depression-like behavior in untreated mice, which was abrogated by ex vivo preincubation of the plasma with anti-ceramide antibodies or ceramidase. Mechanistically, we demonstrate that ceramide accumulated in endothelial cells of the hippocampus of stressed mice, evidenced by the quantitative measurement of ceramide in purified hippocampus endothelial cells. We found ceramide inhibited the activity of phospholipase D (PLD) in endothelial cells in vitro and in the hippocampus in vivo and thereby decreased phosphatidic acid in the hippocampus. Finally, we show intravenous injection of PLD or phosphatidic acid abrogated MDD, indicating the significance of this pathway in MDD pathogenesis. Our data indicate that ceramide controls PLD activity and phosphatidic acid formation in hippocampal endothelial cells and thereby mediates MDD. We propose that neutralization of plasma ceramide could represent a rapid-acting targeted treatment for MDD.

The volume-outcomes relationship in donation after circulatory death liver transplantation.

BACKGROUND: Donation after circulatory death (DCD) liver transplantation (LT) has become an effective mechanism for expanding the donor pool and decreasing waitlist mortality. However, it is unclear if low-volume DCD centers can achieve comparable outcomes to high-volume centers. METHODS: From 2011 to 2019 utilizing the United Network for Organ Sharing (UNOS) database, liver transplant centers were categorized into tertiles based on their annual volume of DCD LTs. Donor selection, recipient selection, and survival outcomes were compared between very-low volume (VLV, n = 1-2 DCD LTs per year), low-volume (LV, n = 3-5), and high-volume (HV, n > 5) centers. RESULTS: One hundred and ten centers performed 3273 DCD LTs. VLV-centers performed 339 (10.4%), LV-centers performed 627 (19.2%), and HV-centers performed 2307 (70.4%) LTs. 30-day, 90-day, and 1-year patient and graft survival were significantly increased at HV-centers (all P < .05). Recipients at HV-centers had shorter waitlist durations (P < .01) and shorter hospital lengths of stay (P < .01). On multivariable regression, undergoing DCD LT at a VLV-center or LV-center was associated with increased 1-year patient mortality (VLV-OR:1.73, 1.12-2.69) (LV-OR: 1.42, 1.01-2.00) and 1-year graft failure (VLV-OR: 1.79, 1.24-2.58) (LV-OR: 1.28, .95-1.72). DISCUSSION: Increased annual DCD liver transplant volume is associated with improved patient and graft survival.

Ten quick tips for making things findable.

The distribution of scholarly content today happens in the context of an immense deluge of information found on the internet. As a result, researchers face serious challenges when archiving and finding information that relates to their work. Library science principles provide a framework for navigating information ecosystems in order to help researchers improve findability of their professional output. Here, we describe the information ecosystem which consists of users, context, and content, all 3 of which must be addressed to make information findable and usable. We provide a set of tips that can help researchers evaluate who their users are, how to archive their research outputs to encourage findability, and how to leverage structural elements of software to make it easier to find information within and beyond their publications. As scholars evaluate their research communication strategies, they can use these steps to improve how their research is discovered and reused.

Ten quick tips for delivering programming lessons.

Teaching well is a craft like any other, and success often comes from an accumulation of small improvements rather than from any single large change. This paper describes 10 practices you can use when teaching programming (and other subjects). All are easy to adopt and have proven their value in institutional classrooms, intensive workshops, and other settings.

Managing Genetic Diversity and Extinction Risk for a Rare Plains Bison (Bison bison bison) Population.

Unfenced plains bison are rare and only occur in a small number of locations throughout Canada and the United States. We examined management guidelines for maintenance of genetic health and population persistence for a small and isolated population of plains bison that occupy the interface between a protected national park and private agricultural lands. To address genetic health concerns, we measured genetic diversity relative to other populations and assessed the potential effects of genetic augmentation. We then used individual-based population viability analyses (PVA) to determine the minimum abundance likely to prevent genetic diversity declines. We assessed this minimum relative to a proposed maximum social carrying capacity related to bison use of human agricultural lands. We also used the PVA to assess the probability of population persistence given the limiting factors of predation, hunting, and disease. Our results indicate that genetic augmentation will likely be required to achieve genetic diversity similar to that of other plains bison populations. We also found that a minimum population of 420 bison yields low probability of additional genetic loss while staying within society-based maxima. Population estimates based on aerial surveys indicated that the population has been below this minimum since 2007. Our PVA simulations indicate that current hunting practices will result in undesirable levels of population extinction risk and further declines in genetic variability. Our study demonstrates that PVA can be used to evaluate potential management scenarios as they relate to long-term genetic conservation and population persistence for rare species.

Ten quick tips for creating an effective lesson.

We present 10 tips for building effective lessons that are grounded in empirical research on pedagogy and cognitive psychology and that we have found to be practically useful in both classroom and free-range settings.

Investing in Gulfport: Development of an Academic-Community Partnership to Address Health Disparities.

BACKGROUND: Invest Health, a collaboration between the Robert Wood Johnson Foundation and The Reinvestment Fund, selected 50 midsized cities to participate in a health initiative that encourages cross-sector alliances to think creatively about mechanisms that address barriers to reducing health disparities among low-income populations. Gulfport, Mississippi, was 1 of 50 teams chosen to participate. OBJECTIVE: To develop an academic-community partnership among the University of Southern Mississippi, Coastal Family Health Center (CFHC), Mercy Housing and Human Development (MHHD), the Mississippi State Department of Health Office of Health Disparity Elimination, and Gulfport residents to create the Healthy Gulfport Initiative, and, ultimately, the Gulf Coast Healthy Communities Collaborative (GCHCC). METHODS: A Gulfport City team was developed per Invest Health guidelines and included five individuals who represented the public sector, community development, and an academic or health-related anchor institution in the community. Several data sources were used to develop city-wide priority health outcomes. A priority neighborhood experiencing health disparities related to the priority health outcomes was identified. A community-engaged needs assessment was conducted in the priority neighborhood. Residents were engaged in prioritizing the health, education, and activity needs of their community via a participatory nominal group process and survey data collection. RESULTS: Residents in the priority neighborhood lack access to health care and healthy food options owing to transportation difficulties and proximity to resources. CONCLUSIONS: The GCHCC will be established to act as a "backbone organization," so that a common agenda can be created with an emphasis on potential for collective impact.

Good enough practices in scientific computing.

Computers are now essential in all branches of science, but most researchers are never taught the equivalent of basic lab skills for research computing. As a result, data can get lost, analyses can take much longer than necessary, and researchers are limited in how effectively they can work with software and data. Computing workflows need to follow the same practices as lab projects and notebooks, with organized data, documented steps, and the project structured for reproducibility, but researchers new to computing often don't know where to start. This paper presents a set of good computing practices that every researcher can adopt, regardless of their current level of computational skill. These practices, which encompass data management, programming, collaborating with colleagues, organizing projects, tracking work, and writing manuscripts, are drawn from a wide variety of published sources from our daily lives and from our work with volunteer organizations that have delivered workshops to over 11,000 people since 2010.