The unseen world: environmental microbial sequencing and identification methods for ecologists

Archaea, bacteria, microeukaryotes, and the viruses that infect them (collectively “microorganisms”) are foundational components of all ecosystems, inhabiting almost every imaginable environment and comprising the majority of the planet’s organismal and evolutionary diversity. Microorganisms play integral roles in ecosystem functioning; are important in the biogeochemical cycling of carbon (C), nitrogen (N), sulfur (S), phosphorus (P), and various metals (eg Barnard et al. 2005); and may be vital to ecosystem responses to large-scale climatic change (Mackelprang et al. 2011). Rarely found alone, microorganisms often form complex communities that are dynamic in space and time (Martiny et al. 2006). For these and other reasons, ecologists and environmental scientists have become increasingly interested in understanding microbial dynamics in ecosystems. Ecological studies of microbes in the environment generally focus on determining which organisms are present and what functional roles they are playing or could play. Rapid advances in molecular and bioinformatic approaches over the past decade have dramatically reduced the difficulty and cost of addressing such questions (Figure 1; WebTable 1). Yet the range of methodologies currently in use and the rapid pace of their ongoing development can be daunting for researchers unaccustomed to these technologies

Effect of analytical conditions in wavelength dispersive electron microprobe analysis on the measurement of strontium-to-calcium (Sr/Ca) ratios in otoliths of anadromous salmonids

The use of strontium-to-calcium (Sr/Ca) ratios in otoliths is becoming a standard method to describe life history type and the chronology of migrations between freshwater and seawater habitats in teleosts (e.g. Kalish, 1990; Radtke et al., 1990; Secor, 1992; Rieman et al., 1994; Radtke, 1995; Limburg, 1995; Tzeng et al. 1997; Volk et al., 2000; Zimmerman, 2000; Zimmerman and Reeves, 2000, 2002). This method provides critical information concerning the relationship and ecology of species exhibiting phenotypic variation in migratory behavior (Kalish, 1990; Secor, 1999). Methods and procedures, however, vary among laboratories because a standard method or protocol for measurement of Sr in otoliths does not exist. In this note, we examine the variations in analytical conditions in an effort to increase precision of Sr/Ca measurements. From these findings we argue that precision can be maximized with higher beam current (although there is specimen damage) than previously recommended by Gunn et al. (1992)

A method of mounting multiple otoliths for beam-based microchemical analyses

Beam-based analytical methods are widely used to measure the concentrations of elements and isotopes in otoliths. These methods usually require that otoliths be individually mounted and prepared to properly expose the desired growth region to the analytical beam. Most analytical instruments, such as LA-ICPMS and ion and electron microprobes, have sample holders that will accept only one to six slides or mounts at a time. We describe a method of mounting otoliths that allows for easy transfer of many otoliths to a single mount after they have been prepared. Such an approach increases the number of otoliths that can be analyzed in a single session by reducing the need open the sample chamber to exchange slides—a particularly time consuming step on instruments that operate under vacuum. For ion and electron microprobes, the method also greatly reduces the number of slides that must be coated with an electrical conductor prior to analysis. In this method, a narrow strip of cover glass is first glued at one end to a standard microscope slide. The otolith is then mounted in thermoplastic resin on the opposite, free end of the strip. The otolith can then be ground and flipped, if needed, by reheating the mounting medium. After otolith preparation is complete, the cover glass is cut with a scribe to free the otolith and up to 20 small otoliths can be arranged on a single petrographic slide

Beam Test Results of the BTeV Silicon Pixel Detector

The results of the BTeV silicon pixel detector beam test carried out at Fermilab in 1999-2000 are reported. The pixel detector spatial resolution has been studied as a function of track inclination, sensor bias, and readout threshold.Comment: 8 pages of text, 8 figures, Proceedings paper of Pixel 2000: International Workshop on Semiconductor Pixel Detectors for Particles and X-Rays, Genova, June 5-8, 200

Ecological relation of sympatric steelhead and resident rainbow trout in the Deschutes River, Oregon

Sympatric steelhead and resident rainbow trout (Oncorhynchus mykiss) are known to exist in many rivers throughout the Pacific Rim. Whether sympatric steelhead and resident rainbow trout are polymorphisms within a single gene pool or two reproductively isolated populations has significant implications concerning the study and conservation of this polytypic species. I examined population structure and use of spawning and rearing habitats by steelhead and resident rainbow trout in the Deschutes River, Oregon. I used otolith microchemistry to determine the maternal origin (steelhead verses resident) of adult steelhead and resident rainbow trout based on Sr/Ca ratios in primordia and freshwater growth regions of otoliths. Only steelhead of steelhead origin and resident rainbow trout of resident origin were encountered. In the Babine River of British Columbia, however, steelhead of resident origin and resident rainbow trout of steelhead origin were present. Temporal and spatial segregation of spawning habitat served to limit breeding between steelhead and resident rainbow trout in the mainstem Deschutes River. The timing of 50% spawning by steelhead occurred 9 to 10 weeks earlier than by resident rainbow trout. Steelhead spawning sites were deeper and of larger substrate than those used by resident rainbow trout. There was an overlap in the timing of emergence by steelhead and resident rainbow trout fry in the mainstem Deschutes River, but higher levels of aggression and territoriality characterize newly emerged steelhead fry. Determination of maternal origin based on otolith microchemistry indicated that young-of- year 0. mykiss in small hydrologically unstable tributaries to the Deschutes River were exclusively the progeny of steelhead. Progeny of resident rainbow trout numerically dominated mainstem-rearing habitats. Based on the degree of segregation between steelhead and resident rainbow trout, the two life history forms act as two separate species in the Deschutes River. This relationship has significant implications concerning the restoration and conservation of steelhead and resident rainbow trout. Where steelhead and resident rainbow trout constitute reproductively isolated populations, conservation of both life history forms within the species cannot be achieved unless both populations are maintained

Population structure of coastal cutthroat trout (Oncorhynchus clarki clarki) in the Muck Creek Basin, Washington

The relationship of coastal cutthroat trout (Oncorhynchus clarki clarki) populations in the Muck Creek basin, a 238 km² southern Puget Sound stream basin in western Washington, was examined using starch gel electrophoresis and meristic analysis. Coastal cutthroat trout were collected from six sites throughout the basin including tributaries, portions of the mainstem, and a lake. Four sites contained only resident trout, the lower mainstem contained resident and anadromous trout, and the lake contained only mature anadromous trout based on size and appearance. Patterns of allelic and meristic variation suggest a significant structuring and separation of coastal cutthroat trout populations in the basin. The lake population was distinguished from the other populations by significant differences in allele frequencies and meristic characters. The other sites grouped more closely together with significant variation among and between sites meristically and at several loci

The economic trade-offs of large language models: A case study

Contacting customer service via chat is a common practice. Because employing customer service agents is expensive, many companies are turning to NLP that assists human agents by auto-generating responses that can be used directly or with modifications. Large Language Models (LLMs) are a natural fit for this use case; however, their efficacy must be balanced with the cost of training and serving them. This paper assesses the practical cost and impact of LLMs for the enterprise as a function of the usefulness of the responses that they generate. We present a cost framework for evaluating an NLP model's utility for this use case and apply it to a single brand as a case study in the context of an existing agent assistance product. We compare three strategies for specializing an LLM - prompt engineering, fine-tuning, and knowledge distillation - using feedback from the brand's customer service agents. We find that the usability of a model's responses can make up for a large difference in inference cost for our case study brand, and we extrapolate our findings to the broader enterprise space.Comment: Paper to be published at the Association for Computational Linguistics in the Industry Track 202

Telemedicine Facilitates CHF Home Health Care for Those with Systolic Dysfunction

An estimated 5 million Americans have congestive heart failure (CHF) and one in five over the age of 40 will develop CHF. There are numerous examples of CHF patients living beyond the years normally expected for people with the disease, usually attributed to taking an active role in disease management. A relatively new alternative for CHF outpatient care is telemedicine and e-health. We investigated the effects of a 6-week in-home telemedicine education and monitoring program for those with systolic dysfunction on the utilization of health care resources. We also measured the effects of the unit 4.5 months after its removal (a total of 6 months post introduction of the unit into the home). Concurrently, we assessed participants' perceptions of the value of having a telemedicine unit. Participants in the telemedicine group reported weighing more times a week with less variability than did the control group. Telemedicine led to a reduction in physician and emergency department visits and those in the experimental group reported the unit facilitating self-care, though this was not significantly different from the control group (possibly due to small sample size). These findings suggest a possibility for improvement in control of CHF when telemedicine is implemented. Our review of the literature also supports the role of telemedicine in facilitating home health care and self-management for CHF patients. There are many challenges still to be addressed before this potential can be reached and further research is needed to identify opportunities in telemedicine

Circular holonomy in the Taub-NUT spacetime

Parallel transport around closed circular orbits in the equatorial plane of the Taub-NUT spacetime is analyzed to reveal the effect of the gravitomagnetic monopole parameter on circular holonomy transformations. Investigating the boost/rotation decomposition of the connection 1-form matrix evaluated along these orbits, one finds a situation that reflects the behavior of the general orthogonally transitive stationary axisymmetric case and indeed along Killing trajectories in general.Comment: 9 pages, LaTeX iopart class, no figure

Improving Follow-Up Skeletal Survey Compliance in Suspected Nonaccidental Trauma Patients: What\u27s the FUSS About?

Introduction: Nonaccidental trauma (NAT) victims account for a significant percentage of our pediatric trauma population. The skeletal survey (SS) and follow-up skeletal survey (FUSS) are essential in the evaluation of selected NAT patients. We identified that our clinically indicated FUSS completion rate was suboptimal. We hypothesized that implementing an intervention of postdischarge follow-up in our pediatric surgery clinic would improve FUSS completion rates. Methods: A follow-up clinic for NAT patients was established in July 2013. A retrospective review was performed of all suspected NAT cases younger than 2 years old seen at Kentucky Children’s Hospital between November 2012 and February 2014. The study population was divided into pre (Group 1) and postintervention (Group 2). Bivariate analysis was performed. Results: Group 1 consisted of 50 patients (58% male; median age, 9 months). Forty-7 (94%) had an SS; fractures were identified in 37 (74%) patients. Only 20 patients (40%) had FUSS; of those, 4 had newly identified fractures. Group 2 consisted of 52 patients (54% male; median age, 7 months). All 52 children (100%) had an SS; fractures were identified in 35 (67%) patients. Forty-seven patients (90%) had FUSS. Of those, 6 had new radiographic findings. Thirty-five patients (67%) were seen in our clinic. This improvement in FUSS (40% versus 90%) was statistically significant, P \u3c 0.001. Conclusion: The decision to follow NAT patients in our clinic had significantly increased our rates of FUSS completion. This additional clinic follow-up also provided more evidence for NAT evaluation