“Not Tied Up Neatly with a Bow”: Professionals’ Challenging Cases in Informed Consent for Genomic Sequencing

As the use of genomic technology has expanded in research and clinical settings, issues surrounding informed consent for genome and exome sequencing have surfaced. Despite the importance of informed consent, little is known about the specific challenges that professionals encounter when consenting patients or research participants for genomic sequencing. We interviewed 29 genetic counselors and research coordinators with considerable experience obtaining informed consent for genomic sequencing to understand their experiences and perspectives. As part of this interview, 24 interviewees discussed an informed consent case they found particularly memorable or challenging. We analyzed these case examples to determine the primary issue or challenge represented by each case. Challenges fell into two domains: participant understanding, and facilitating decisions about testing or research participation. Challenges related to participant understanding included varying levels of general and genomic literacy, difficulty managing participant expectations, and contextual factors that impeded participant understanding. Challenges related to facilitating decision-making included complicated family dynamics such as disagreement or coercion, situations in which it was unclear whether sequencing research would be a good use of participant time or resources, and situations in which the professional experienced disagreement or discomfort with participant decisions. The issues highlighted in these case examples are instructive in preparing genetics professionals to obtain informed consent for genomic sequencing

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Development and application of a pollen-based paleohydrologic reconstruction from the Lower Roanoke River Basin, North Carolina, USA

We used pollen assemblages to reconstruct late-Holocene paleohydrologic patterns in floodplain deposits from the lower Roanoke River basin (North Carolina, southeastern USA). Using 120 surface samples from 38 transects, we documented statistical relationships between pollen assemblages, vegetation, and landforms. Backswamp pollen assemblages (long hydroperiods) are dominated by Nyssa (tupelo) and Taxodium (cypress) and have high pollen concentrations. Sediments from elevated levees and seasonally flooded forests (shorter hydroperiods) are characterized by dominant Pinus (pine) pollen, variable abundance of hardwood taxa, and low pollen concentrations. We apply the calibration data set to interpret past vegetation and paleohydrology. Pollen from a radiocarbon-dated sediment core collected in a tupelo-cypress backswamp indicates centennial-scale fluctuations in forest composition during the last 2400 years. Backswamp vegetation has occupied the site since land clearance began ~300 years ago. Recent dam emplacement affected sedimentation rates, but vegetation changes are small compared with those caused by pre-Colonial climate variability. The occurrence of wetter conditions from ~2200 to 1800 cal. yr BP, ~1100 to 750 cal. yr BP, and ~400 to 250 cal. yr BP may indicate changes in cyclonic circulation patterns related to shifts in the position of the Bermuda High and jet stream

Colour Diffusion implementation in CP2K

Source code and an example for non-equilibrium molecular dynamics with CP2K, instructions for compiling the cod

Microscopic chaos in shear and elongational flows

The simulation of atoms and molecules under planar elongational flow in a nonequilibrium steady state for arbitrarily long times has recently been made possible by an appropriate implementation of nonequilibrium molecular dynamics (NEMD) with suitable periodic boundary conditions. We address some fundamental questions regarding the chaotic behaviour of this type of flow and compare its chaotic properties with the behaviour of fluids under planar shear flow. We analyse the spectra of Lyapunov exponents for a number of state points where the energy dissipation is the same for both flows, simulating a nonequilibrium steady state for isoenergetic and isokinetic constrained dynamics. We test the conjugate pairing rule and confirm its validity for planar elongation flow, as is expected from the Hamiltonian nature of the adiabatic equations of motion. Discussion about the chaoticity of the convective part of the flows, the link between Lyapunov exponents and viscosity and phase space contraction will also be presented

Appendix B. Sawgrass ridge pollen assemblages from core 02-05-21-2.

Sawgrass ridge pollen assemblages from core 02-05-21-2

Chaotic properties of planar elongational flow and planar shear flow

Abstract not available

Appendix E. Slough pollen assemblages from core 02-05-20-13.

Slough pollen assemblages from core 02-05-20-13