Similar Microbial Communities Found on Two Distant Seafloor Basalts.

The oceanic crust forms two thirds of the Earth's surface and hosts a large phylogenetic and functional diversity of microorganisms. While advances have been made in the sedimentary realm, our understanding of the igneous rock portion as a microbial habitat has remained limited. We present the first comparative metagenomic microbial community analysis from ocean floor basalt environments at the Lō'ihi Seamount, Hawai'i, and the East Pacific Rise (EPR; 9°N). Phylogenetic analysis indicates the presence of a total of 43 bacterial and archaeal mono-phyletic groups, dominated by Alpha- and Gammaproteobacteria, as well as Thaumarchaeota. Functional gene analysis suggests that these Thaumarchaeota play an important role in ammonium oxidation on seafloor basalts. In addition to ammonium oxidation, the seafloor basalt habitat reveals a wide spectrum of other metabolic potentials, including CO2 fixation, denitrification, dissimilatory sulfate reduction, and sulfur oxidation. Basalt communities from Lō'ihi and the EPR show considerable metabolic and phylogenetic overlap down to the genus level despite geographic distance and slightly different seafloor basalt mineralogy

Using Developmental Frameworks to Implement Focus Groups in School-Aged Children

This poster describes the use of virtual focus groups with school-aged children in the development of a pediatric wellbeing picture scale to screen for mental health and wellbeing. Children\u27s opinions, creative ideas, and insights allow acquisition of new data and knowledge, but unfortunately, are frequently overlooked. When using developmentally-based principles, focus groups have been shown to be a successful and reliable method for collecting data from this age group and a novel way to better understand the child’s interactions and experiences. Focus groups have a number of advantages, allowing for in-depth exploration of discussion by the participants. Students in Nursing 499 conducted developmentally-based focus groups with children grades 3-5 to develop the Pediatric Well Being Picture Scale. Basing focus groups on theoretical frameworks of Piaget, Erikson, and Kohlberg creates an environment conducive to open discussion and expression of children’s ideas. These focus groups give children the opportunity to connect to one another and feel more comfortable in talking about items about emotional wellbeing. This allowed the researcher to gain an understanding of the children’s perspective for the items on the wellbeing scale. Limitations noted due to the virtual environment included maintaining the child’s attention, adequacy of technology, and assuring that each child had the opportunity to equally participate. Benefits include more openness and candor due a sense of anonymity from not being in the same location.https://orb.binghamton.edu/research_days_posters_2022/1066/thumbnail.jp

Identification of a transporter complex responsible for the cytosolic entry of nitrogen-containing bisphosphonates

Nitrogen-containing-bisphosphonates (N-BPs) are widely prescribed to treat osteoporosis and other bone-related diseases. Although previous studies established that N-BPs function by inhibiting the mevalonate pathway in osteoclasts, the mechanism by which N-BPs enter the cytosol from the extracellular space to reach their molecular target is not understood. Here we implemented a CRISPRi-mediated genome-wide screen and identified SLC37A3 (solute carrier family 37 member A3) as a gene required for the action of N-BPs in mammalian cells. We observed that SLC37A3 forms a complex with ATRAID (all-trans retinoic acid-induced differentiation factor), a previously identified genetic target of N-BPs. SLC37A3 and ATRAID localize to lysosomes and are required for releasing N-BP molecules that have trafficked to lysosomes through fluid-phase endocytosis into the cytosol. Our results elucidate the route by which N-BPs are delivered to their molecular target, addressing a key aspect of the mechanism of action of N-BPs that may have significant clinical relevance

Examiner seniority and experience are associated with bias when scoring communication, but not examination, skills in objective structured clinical examinations in Australia

Purpose The biases that may influence objective structured clinical examination (OSCE) scoring are well understood, and recent research has attempted to establish the magnitude of their impact. However, the influence of examiner experience, clinical seniority, and occupation on communication and physical examination scores in OSCEs has not yet been clearly established. Methods We compared the mean scores awarded for generic and clinical communication and physical examination skills in 2 undergraduate medicine OSCEs in relation to examiner characteristics (gender, examining experience, occupation, seniority, and speciality). The statistical significance of the differences was calculated using the 2-tailed independent t-test and analysis of variance. Results Five hundred and seventeen students were examined by 237 examiners at the University of New South Wales in 2014 and 2016. Examiner gender, occupation (academic, clinician, or clinical tutor), and job type (specialist or generalist) did not significantly impact scores. Junior doctors gave consistently higher scores than senior doctors in all domains, and this difference was statistically significant for generic and clinical communication scores. Examiner experience was significantly inversely correlated with generic communication scores. Conclusion We suggest that the assessment of examination skills may be less susceptible to bias because this process is fairly prescriptive, affording greater scoring objectivity. We recommend training to define the marking criteria, teaching curriculum, and expected level of performance in communication skills to reduce bias in OSCE assessment

Meter-Scale Early Diagenesis of Organic Matter Buried Within Deep-Sea Sediments Beneath the Amazon River Plume

Gravity cores and multi-cores were collected from the Demerara Abyssal plain to examine meter-scale downcore features of early diagenesis in the sediments and relate them to the location of the Amazon River plume in the North Atlantic Ocean. At all sites, the oxygen penetration depth, inferred from nitrate and dissolved manganese profiles, was ~10–20 cm and nitrate was depleted within ~50 cm. However, most of the cores also had a secondary nitrate maximum (4–13 μM) at ~50 cm, at a location where we observed changes in gradients of dissolved manganese, iron, and ammonium. Although there is spatial heterogeneity in the profile behavior across the study, we do find subtle diagenetic profile patterns that occur in sediments in relation to their position below the Amazon plume. Dissolved silica profiles show an initial increase downcore, but then all show a decrease to depths of 30–100 cm, thereafter concentrations increase. We suggest this zone of silica uptake is due to reverse weathering processes, possibly involving iron oxidation. A semi-lithified iron crust appeared at nearly all sites, and its position is relict, likely an indicator of the transition from glacial to interglacial sediments

Microsatellite Instability Is Associated with the Clinicopathologic Features of Gastric Cancer in Sporadic Gastric Cancer Patients

Purpose: Replication error is an important mechanism in carcinogenesis. The microsatellite instability (MSI-H) of colorectal cancers is associated with the development of multiple cancers. The influence of MSI-H on the development of multiple gastric cancers in sporadic gastric cancer patients has not been defined. This study was performed to reveal the association between the clinicopathologic features and MSI in sporadic gastric cancers. Materials and Methods: Between July 2004 and March 2009, the clinicopathologic characteristics, including MSI status, were evaluated in 128 consecutive patients with sporadic gastric cancers. None of the patients had hereditary non-polyposis colorectal cancer of familial gastric cancer. The markers that were recommended by the NCI to determine the MSI status for colorectal cancers were used. Results: MSI-H cancers were found in 10.9% of the patients (14/128). Synchronous gastric cancers were shown in 4 patients (3.1%). Synchronous cancers were found in 2 of 14 patients with MSI-H gastric cancer (14.3%) and 2 of 114 patients with MSS gastric cancer (1.8%; P=0.059, Fisher's exact test). Among the patients with synchronous cancer 50% (2/4) had MSI-H cancer, but 9.7% of the patients (12/124) without synchronous cancer had MSI-H cancer. MSI-H (RR, 24.7; 95% CI, 1.5~398.9; P=0.024) was related with to synchronous gastric cancer, but age, gender, family history, histologic type, location, gross morphology, size, and stage were not related to synchronous gastric cancer. Conclusions: MSI is associated with the intestinal-type gastric cancer and the presence of multiple gastric cancers in patients with sporadic gastric cancer. Special attention to the presence of synchronous and the development of metachronous multiple cancer in patients with MSI-H gastric cancer is needed. ?? 2010 by The Korean Gastric Cancer Association

Group-regularized individual prediction: theory and application to pain

Multivariate pattern analysis (MVPA) has become an important tool for identifying brain representations of psychological processes and clinical outcomes using fMRI and related methods. Such methods can be used to predict or ‘decode’ psychological states in individual subjects. Single-subject MVPA approaches, however, are limited by the amount and quality of individual-subject data. In spite of higher spatial resolution, predictive accuracy from single-subject data often does not exceed what can be accomplished using coarser, group-level maps, because single-subject patterns are trained on limited amounts of often-noisy data. Here, we present a method that combines population-level priors, in the form of biomarker patterns developed on prior samples, with single-subject MVPA maps to improve single-subject prediction. Theoretical results and simulations motivate a weighting based on the relative variances of biomarker-based prediction—based on population-level predictive maps from prior groups—and individual-subject, cross-validated prediction. Empirical results predicting pain using brain activity on a trial-by-trial basis (single-trial prediction) across 6 studies (N = 180 participants) confirm the theoretical predictions. Regularization based on a population-level biomarker—in this case, the Neurologic Pain Signature (NPS)—improved single-subject prediction accuracy compared with idiographic maps based on the individuals' data alone. The regularization scheme that we propose, which we term group-regularized individual prediction (GRIP), can be applied broadly to within-person MVPA-based prediction. We also show how GRIP can be used to evaluate data quality and provide benchmarks for the appropriateness of population-level maps like the NPS for a given individual or study