Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales

DNA in marine sediment contains both fossil sequences and sequences from organisms that live in the sediment. The demarcation between these two pools and their respective rates of turnover are generally unknown. We address these issues by comparing the total extractable DNA pool to the fraction of sequenced chloroplast DNA (cpDNA) in sediment from two sites in the Bering Sea. We assume that cpDNA is a tracer of non-reproducing fossil DNA. Given \u3e150,000 sequence reads per sample, cpDNA is easily detectable in the shallowest samples but decays with depth, suggesting that sequencing-based richness assessments of communities in deep subseafloor sediment are relatively unaffected by fossil DNA. The initial decrease in cpDNA reads suggests that most cpDNA decays within 100–200 k.y. of deposition. However, cpDNA from a few phylotypes, including some that match fossil diatoms, are present throughout the cored sediment, ranging in age to 1.4 Ma. The relative fraction of sequences composed by cpDNA decreases non-linearly with increasing sediment age, suggesting that detectable cpDNA becomes more recalcitrant with age. This can be explained by biological activity decreasing with sediment age and/or by preferential long-term survival of only the most thoroughly protected DNA. The association of cpDNA reads with published records of siliceous microfossils, including diatom spores, at the same sites suggests that microfossils may help to preserve DNA. This DNA may be useful for studies of paleoenvironmental conditions and biological evolution on time scales that approach or exceed 1 m.y

Microbial Selection and Survival in Subseafloor Sediment

Many studies have examined relationships of microorganisms to geochemical zones in subseafloor sediment. However, responses to selective pressure and patterns of community succession with sediment depth have rarely been examined. Here we use 16S rDNA sequencing to examine the succession of microbial communities at sites in the Indian Ocean and the Bering Sea. The sediment ranges in depth from 0.16 to 332 m below seafloor and in age from 660 to 1,300,000 years. The majority of subseafloor taxonomic diversity is present in the shallowest depth sampled. The best predictor of sequence presence or absence in the oldest sediment is relative abundance in the near-seafloor sediment. This relationship suggests that perseverance of specific taxa into deep, old sediment is primarily controlled by the taxonomic abundance that existed when the sediment was near the seafloor. The operational taxonomic units that dominate at depth comprise a subset of the local seafloor community at each site, rather than a grown-in group of geographically widespread subseafloor specialists. At both sites, most taxa classified as abundant decrease in relative frequency with increasing sediment depth and age. Comparison of community composition to cell counts at the Bering Sea site indicates that the rise of the few dominant taxa in the deep subseafloor community does not require net replication, but might simply result from lower mortality relative to competing taxa on the long timescale of community burial

Implementation of a Nurse-Led Family Centered Engagement Intervention for Caregivers of Extremely Premature Infants in the Neonatal Intensive Care Unit

Objective: The objective of this feasibility study was to examine the implementation and usefulness of an intervention for extremely premature infant (EPI) caregivers. Results: One caregiver and five nurses provided feedback with a mean score of 4.4 out of 5 pertaining to helpfulness. Conclusions: Implementation of the Caregiver’s Guide was feasible and was positively received by NICU nurses and caregivers. We recommend implementing a revised version of this tool based on nurse and caregiver feedback. The delivery of education should be divided between dayshift and nightshift nurses so that one nurse is not responsible for providing all the information. The education should be categorized by gestational age and day of life and only given when it is pertinent to the care of the child. A section should be added to include a quick reference guide for the medical jargon used in the NICU

Assessment of the Perceived Role and Function of a Community Advisory Board in a NIH Center of Excellence: Lessons Learned

Background: The Community Advisory Board (CAB) was a vital component of the Center for Equal Health. The center addressed health disparities through community-based research and educational outreach initiatives. Objectives: To evaluate the perceived relationship of the CAB and Center, explore members’ perceptions of the CAB’s role, and elicit feedback on how to enhance the relationship between the Center and the CAB. Methods: Ten in-depth, semi-structured interviews were conducted. All interviews were transcribed verbatim and analyzed with a focus on predetermined codes. Results: Main themes focused on perception of CAB roles and need for utilization of board members; overall center challenges; and board member knowledge and communication within the center. Conclusions: Lessons learned mainly focused on clarification of CAB roles as necessary for more effective and efficient communication. Based on feedback, communication channels between the board and center were developed, orientation packets clarifying center roles were provided, and annual retreats were completed. Additional lessons learned for conducting community-academic partnerships are provided

Sexual violation of patients by physicians: A mixed-methods, exploratory analysis of 101 cases

A mixed-method, exploratory design was used to examine 101 cases of sexual violations in medicine. The study involved content analysis of cases to characterize the physicians, patient-victims, the practice setting, kinds of sexual violations, and consequences to the perpetrator. In each case, a criminal law framework was used to examine how motives, means, and opportunity combined to generate sexual misconduct. Finally, cross-case analysis was performed to identify clusters of causal factors that explain specific kinds of sexual misconduct. Most cases involved a combination of five factors: male physicians (100%), older than the age of 39 (92%), who were not board certified (70%), practicing in nonacademic settings (94%) where they always examined patients alone (85%). Only three factors (suspected antisocial personality, physician board certification, and vulnerable patients) differed significantly across the different kinds of sexual abuse: personality disorders were suspected most frequently in cases of rape, physicians were more frequently board certified in cases of consensual sex with patients, and patients were more commonly vulnerable in cases of child molestation. Drawing on study findings and past research, we offer a series of recommendations to medical schools, medical boards, chaperones, patients, and the national practitioners database

It\u27s way more than just writing a prescription : A qualitative study of preferences for integrated versus non-integrated treatment models among individuals with opioid use disorder

BACKGROUND: Increasingly, treatment for opioid use disorder (OUD) is offered in integrated treatment models addressing both substance use and other health conditions within the same system. This often includes offering medications for OUD in general medical settings. It remains uncertain whether integrated OUD treatment models are preferred to non-integrated models, where treatment is provided within a distinct treatment system. This study aimed to explore preferences for integrated versus non-integrated treatment models among people with OUD and examine what factors may influence preferences. METHODS: This qualitative study recruited participants (n = 40) through Craigslist advertisements and flyers posted in treatment programs across the United States. Participants were 18 years of age or older and scored a two or higher on the heroin or opioid pain reliever sections of the Tobacco, Alcohol, Prescription Medications, and Other Substances (TAPS) Tool. Each participant completed a demographic survey and a telephone interview. The interviews were coded and content analyzed. RESULTS: While some participants preferred receiving OUD treatment from an integrated model in a general medical setting, the majority preferred non-integrated models. Some participants preferred integrated models in theory but expressed concerns about stigma and a lack of psychosocial services. Tradeoffs between integrated and non-integrated models were centered around patient values (desire for anonymity and personalization, fear of consequences), the characteristics of the provider and setting (convenience, perceived treatment effectiveness, access to services), and the patient-provider relationship (disclosure, trust, comfort, stigma). CONCLUSIONS: Among this sample of primarily White adults, preferences for non-integrated versus integrated OUD treatment were mixed. Perceived benefits of integrated models included convenience, potential for treatment personalization, and opportunity to extend established relationships with medical providers. Recommendations to make integrated treatment more patient-centered include facilitating access to psychosocial services, educating patients on privacy, individualizing treatment, and prioritizing the patient-provider relationship. This sample included very few minorities and thus findings may not be fully generalizable to the larger population of persons with OUD. Nonetheless, results suggest a need for expansion of both OUD treatment in specialty and general medical settings to ensure access to preferred treatment for all

“It’s way more than just writing a prescription”: A qualitative study of preferences for integrated versus non-integrated treatment models among individuals with opioid use disorder

Background: Increasingly, treatment for opioid use disorder (OUD) is offered in integrated treatment models addressing both substance use and other health conditions within the same system. This often includes offering medications for OUD in general medical settings. It remains uncertain whether integrated OUD treatment models are preferred to non-integrated models, where treatment is provided within a distinct treatment system. This study aimed to explore preferences for integrated versus non-integrated treatment models among people with OUD and examine what factors may influence preferences. Methods: This qualitative study recruited participants (n = 40) through Craigslist advertisements and flyers posted in treatment programs across the United States. Participants were 18 years of age or older and scored a two or higher on the heroin or opioid pain reliever sections of the Tobacco, Alcohol, Prescription Medications, and Other Substances (TAPS) Tool. Each participant completed a demographic survey and a telephone interview. The interviews were coded and content analyzed. Results: While some participants preferred receiving OUD treatment from an integrated model in a general medical setting, the majority preferred non-integrated models. Some participants preferred integrated models in theory but expressed concerns about stigma and a lack of psychosocial services. Tradeoffs between integrated and non-integrated models were centered around patient values (desire for anonymity and personalization, fear of consequences), the characteristics of the provider and setting (convenience, perceived treatment effectiveness, access to services), and the patient-provider relationship (disclosure, trust, comfort, stigma). Conclusions: Among this sample of primarily White adults, preferences for non-integrated versus integrated OUD treatment were mixed. Perceived benefits of integrated models included convenience, potential for treatment personalization, and opportunity to extend established relationships with medical providers. Recommendations to make integrated treatment more patient-centered include facilitating access to psychosocial services, educating patients on privacy, individualizing treatment, and prioritizing the patient-provider relationship. This sample included very few minorities and thus findings may not be fully generalizable to the larger population of persons with OUD. Nonetheless, results suggest a need for expansion of both OUD treatment in specialty and general medical settings to ensure access to preferred treatment for all

Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Applied and Environmental Microbiology 82 (2016): 4994-4999, doi:10.1128/AEM.00809-16.Subseafloor sediment hosts a large, taxonomically rich and metabolically diverse microbial ecosystem. However, the factors that control microbial diversity in subseafloor sediment have rarely been explored. Here we show that bacterial richness varies with organic degradation rate and sediment age. At three open-ocean sites (in the Bering Sea and equatorial Pacific) and one continental margin site (Indian Ocean), richness decreases exponentially with increasing sediment depth. The rate of decrease in richness with depth varies from site to site. The vertical succession of predominant terminal electron acceptors correlates to abundance-weighted community composition, but does not drive the vertical decrease in richness. Vertical patterns of richness at the open-ocean sites closely match organic degradation rates; both properties are highest near the seafloor and decline together as sediment depth increases. This relationship suggests that (i) total catabolic activity and/or electron donor diversity exerts a primary influence on bacterial richness in marine sediment, and (ii) many bacterial taxa that are poorly adapted for subseafloor sedimentary conditions are degraded in the geologically young sediment where respiration rates are high. Richness consistently takes a few hundred thousand years to decline from near-seafloor values to much lower values in deep anoxic subseafloor sediment, regardless of sedimentation rate, predominant terminal electron acceptor, or oceanographic context.This work, including the efforts of Mitchell L. Sogin and Steven D’Hondt, was funded by Sloan Foundation (Census of Deep Life). This work, including the efforts of Steven D’Hondt, was funded by U.S. Science Support Program for IODP. This work, including the efforts of Steven D’Hondt, was funded by National Science Foundation (NSF) (OCE- 0752336 and OCE-0939564). The work of E. A. Walsh, J. B. Kirkpatrick, R. Pockalny, and J. Sauvage was funded by the grants to S. D’Hondt

Microbial Selection and Survival in Subseafloor Sediment

Many studies have examined relationships of microorganisms to geochemical zones in subseafloor sediment. However, responses to selective pressure and patterns of community succession with sediment depth have rarely been examined. Here we use 16S rDNA sequencing to examine the succession of microbial communities at sites in the Indian Ocean and the Bering Sea. The sediment ranges in depth from 0.16 to 332 m below seafloor and in age from 660 to 1,300,000 years. The majority of subseafloor taxonomic diversity is present in the shallowest depth sampled. The best predictor of sequence presence or absence in the oldest sediment is relative abundance in the near-seafloor sediment. This relationship suggests that perseverance of specific taxa into deep, old sediment is primarily controlled by the taxonomic abundance that existed when the sediment was near the seafloor. The operational taxonomic units that dominate at depth comprise a subset of the local seafloor community at each site, rather than a grown-in group of geographically widespread subseafloor specialists. At both sites, most taxa classified as abundant decrease in relative frequency with increasing sediment depth and age. Comparison of community composition to cell counts at the Bering Sea site indicates that the rise of the few dominant taxa in the deep subseafloor community does not require net replication, but might simply result from lower mortality relative to competing taxa on the long timescale of community burial