The SYNOP Experiment: Inverted Echo Sounder Data Report for Jun 1989 to Sep 1990

The SYNoptic Ocean Prediction experiment (SYNOP) was undertaken with the goal that increased understanding of the Gulf Stream obtained through coordinated observations could be integrated with numerical models, including predictive models of the Gulf Stream. Our moored experiment, which began in the fall of 1987, consists of two separate arrays in the Gulf Stream as part of the SYNOP program. The Inlet array of inverted echo sounders (IES) and deep current meters measures key parameters that that describe the variability of the Gulf Stream and the deep western boundary current (DWBC) near Cape Hatteras. In this region the Gulf Stream first flows into deeper water and crosses over the DWBC. The Central array of IESs, in a 350 km square centered on the Gulf Stream near 68 o W, monitors the thermocline structure of the Gulf Stream in the region of large meanders and frequent interactions with rings. The array also contained thirteen tall current meter moorings, that reached into the Gulf Stream core. Additionally most of the IESs in the interior of the array are outfitted with bottom pressure recorders (PIES). IES data recovered during the summer of 1990, from the Year 3 deployment period, are documented here by plots and tables of basic statistics and pertinent deployment information. Altogether 32 IES records are presented, plus pressure records at 12 sites. he echo sounders were recovered during a cruise aboard the R/V Endeavor, EN216 (4 August 1990 to 5 September 1990). The IESs had been deployed the previous summer during cruises on the R/V Oceanus, OC207 (26 May 1989 to 21 June 1989) and OC210 (8 August 1989 to 1 September 1989). One IES was exchanged in mid-October 1989 using the R/V Cape Henlopen. The plots are time series of measured travel time, pressure, temperature; the residual pressure; and low-pass filtered records of residual pressure, thermocline depth, and temperature. A brief description of the experiment is given; the standard steps of data processing are discussed along with special processing for several IES records that had different problems

Inverted Echo Sounder Data Processing Report

The Inverted Echo Sounder (IES) is an instrument that acoustically monitors the depth of the main thermocline from a moored position one meter above the ocean floor. Additionally, the IESs can be equipped to measure both pressure and temperature. The standard steps for processing IES data are documented here. The effect and purpose of each step are discussed followed by a description of how to apply the computer programs that constitute the step. The FORTRAN and MATLAB codes are also supplied

Ray Tracing on Topographic Rossby Waves

Topographic Rossby Waves (TRWs) have been identified with the largest variability in deep current meter records along the continental slope in the Mid-Atlantic Bight (MAB). Ray tracing theory is applied to TRWs using the real bottom topography of the MAB and the observed stratification. The dispersion relation for TRWs is derived and various wavenumber limits are discussed. A computational method for tracing the waves is presented, including the necessity of smoothing the bathymetry. In the examples shown, TRW with periods of 24-48 days generally propagate southwestward, changing their wavelengths from 400 to 100 kilometers in response to the change in bottom slope. TRW paths are shown that connect from the SYNOP Central Array near 68oW to the SYNOP Inlet Array near Cape Hatteras

Mapping systematic errors in helium abundance determinations using Markov Chain Monte Carlo

Monte Carlo techniques have been used to evaluate the statistical and systematic uncertainties in the helium abundances derived from extragalactic H~II regions. The helium abundance is sensitive to several physical parameters associated with the H~II region. In this work, we introduce Markov Chain Monte Carlo (MCMC) methods to efficiently explore the parameter space and determine the helium abundance, the physical parameters, and the uncertainties derived from observations of metal poor nebulae. Experiments with synthetic data show that the MCMC method is superior to previous implementations (based on flux perturbation) in that it is not affected by biases due to non-physical parameter space. The MCMC analysis allows a detailed exploration of degeneracies, and, in particular, a false minimum that occurs at large values of optical depth in the He~I emission lines. We demonstrate that introducing the electron temperature derived from the [O~III] emission lines as a prior, in a very conservative manner, produces negligible bias and effectively eliminates the false minima occurring at large optical depth. We perform a frequentist analysis on data from several "high quality" systems. Likelihood plots illustrate degeneracies, asymmetries, and limits of the determination. In agreement with previous work, we find relatively large systematic errors, limiting the precision of the primordial helium abundance for currently available spectra.Comment: 25 pages, 11 figure

Standardizing Evaluation of Patient-Specific 3D Printed Models in Surgical Planning: Development of a Cross-Disciplinary Survey Tool for Physician and Trainee Feedback

Background: 3D printed models are becoming increasingly popular in healthcare as visual and tactile tools to enhance understanding of anatomy and pathology in medical trainee education, provide procedural simulation training, and guide surgical procedures. Patient-specific 3D models are currently being used preoperatively for trainee medical education in planning surgical approaches and intraoperatively to guide decision-making in several specialties. Our study group utilized a modified Delphi process to create a standardized assessment for trainees using patient-specific 3D models as a tool in medical education during pre-surgical planning. Methods: A literature review was conducted to identify survey questions administered to clinicians in published surgical planning studies regarding the use of patient-specific 3D models. A core study team reviewed these questions, removed duplicates, categorized them, mapped them to overarching themes, and, where applicable, modified individual questions into a form generalizable across surgical specialties. The core study panel included a physician, physician-scientist, social scientist, engineer/medical student, and 3D printing lab manager. A modified Delphi process was then used to solicit feedback on the clarity and relevance of the individual questions from an expert panel consisting of 12 physicians from specialties including anesthesiology, emergency medicine, radiology, urology, otolaryngology, and obstetrics/gynecology. When the Radiological Society of North America (RSNA)/American College of Radiology (ACR) 3D Printing Registry Data Dictionary was released, additional survey questions were reviewed. A final cross-disciplinary survey of the utility of 3D printed models in surgical planning medical education was developed. Results: The literature review identified 100 questions previously published in surveys assessing patient-specific 3D models for surgical planning. Following the review, generalization, and mapping of survey questions from these studies, a list of 24 questions was generated for review by the expert study team. Five additional questions were identified in the RSNA/ACR 3D Printing Registry Data Dictionary and included for review. A final questionnaire consisting of 20 questions was developed. Conclusions: As 3D printed models become more common in medical education, the need for standardized assessment is increasingly essential. The standardized questionnaire developed in this study reflects the interests of a variety of stakeholders in patient-specific 3D models across disciplines

EXPORTS North Atlantic eddy tracking

The EXPORTS North Atlantic field campaign (EXPORTS-NA) of May 2021 used a diverse array of ship-based and autonomous platforms to measure and quantify processes leading to carbon export in the open ocean. The success of this field program relied heavily on the ability to make measurements following a Lagrangian trajectory within a coherent, retentive eddy (Sections 1, 2). Identifying an eddy that would remain coherent and retentive over the course of a monthlong deployment was a significant challenge that the EXPORTS team faced. This report details the processes and procedures used by the primarily shore-based eddy tracking team to locate, track, and sample with autonomous assets such an eddy before and during EXPORTS-NA.This field deployment was funded by the NASA Ocean Biology and Biogeochemistry program and the National Science Foundation Biological and Chemical Oceanography programs. Initial gliders deployments were performed by the RRS Discovery and the authors thank the Porcupine Abyssal Plain – Sustained Observatory of the Natural Environment Research Council (NERC, UK), which is principally funded through the Climate Linked Atlantic Sector Science (CLASS) project supported by NERC National Capability funding (NE/R015953/1) and by IFADO (Innovation in the Framework of the Atlantic Deep Ocean) EAPA_165/2016. Technical assistance with glider deployment was provided by Marine Autonomous Robotic Systems (NOC). The authors thank Inia Soto Ramos for assistance in publishing this manuscript through the NASA Technical Memorandum series. This is PMEL contribution number 5372

Analysis of Gene Targeting Techniques for Huntington’s Disease and Gene Expression in Human Cells

Gemstone Team CHANGEHuntington’s disease (HD) is an inherited neurodegenerative disorder that is caused by a CAG trinucleotide repeat expansion in the huntingtin (HTT) gene. Our team performed a literature analysis to investigate the current state of research for treating HD and identified a new technology called prime editing that could be applied to HD in combination with single nucleotide polymorphisms (SNPs). We found that at least 729 SNPs within the HTT gene are compatible with our proposed approach. Experimentally, we performed preliminary studies using Western Blots and RT-qPCR to examine the differences in expression of HTT in a variety of cell lines. Our literature-based work suggests that prime editing is a promising tool for addressing the basis of a variety of genetic disorders. Our experimental-based work confirms that human fibroblast cells express HTT and therefore may be used in proof of concept studies of gene targeting techniques to address HD

Applying genetic technologies to combat infectious diseases in aquaculture

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies—sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/ parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.publishedVersio

Gene Targeting Techniques for Huntington's Disease

Huntington’s disease (HD) is an autosomal neurodegenerative disorder caused by extended trinucleotide CAG repetition in the HTT gene. Although this mutation in the HTT gene is mostly associated with neurological and physical symptoms that HD typically exhibits, wild-type Huntingtin protein (HTT) is involved in a variety of cellular functions such as vesicle transportation, cell division, transcription regulation, autophagy, and tissue maintenance. The main cause of HD symptoms is due to aggregation and accumulation of mutant HTT (mHTT) proteins in neurons. In this review, we discuss multiple approaches targeting DNA and RNA to reduce mHTT expression. These approaches are categorized into non-allele-specific silencing and allele-specific-silencing using SNPs and haplogroup analysis, and the possible limitations of targeting mHTT is also discussed. Additionally, this review discusses am potential appliction of recent CRISPR prime editing technology in treating HD