Temporal and size-based patterns in juvenile sablefish energy allocation and diet

Thesis (M.S.) University of Alaska Fairbanks, 2020A recent marine heatwave in the Gulf of Alaska caused depressed growth, poor body condition, and low survival in many fish species, but juvenile sablefish (Anoplopoma fimbria) thrived. These fast-growing piscivores are the target of a valuable commercial fishery in Alaska as adults and have historically shown high variability in recruitment. The first winter is a period of nutritional stress and high mortality for many fish species and first winter survival may dictate year class strength, but the importance of the first winter for juvenile sablefish is understudied. We examined juvenile sablefish energy storage, growth, and diet during their first two years of life, specifically as newly settled juveniles in their first autumn, in late winter, and during their second summer and autumn. Sablefish grew rapidly in autumn and growth slowed but continued through winter. Mean energy density (kJ g⁻¹) declined over the winter but total energy (kJ individual⁻¹) increased significantly between October and March. Slopes of energy density and total energy versus length regressions were atypical for high latitude marine fish in that they were steepest in March. This indicates that large fish grew during winter with minimal energy depletion while small fish grew but depleted their energy stores. Stable isotope results revealed that larger fish were enriched in [delta]¹³C and [delta]⁻¹⁵N in March relative to smaller fish, suggesting diet differences may contribute to size-specific energy storage patterns during winter. Pacific herring (Clupea pallasii) dominated diets but consumption of herring and other prey varied seasonally and annually. Relative stomach content weights were highest in autumn 2018, which was a period of rapid growth. Results of this study show advantages for sablefish achieving large size prior to winter and broadly support the hypothesis that first winter is a life history bottleneck for juvenile sablefish. The generalist feeding strategy of sablefish and rapid growth early in life may provide the ability to adapt to a wide range of environmental conditions.North Pacific Research Board (project 1703 under primary award NA15NMF4720173), Rasmuson FoundationChapter 1: First winter energy allocation in juvenile sablefish Anoplopoma fimbria, a fast growing marine piscivore -- Chapter 2: Temporal and size-based variation in diet composition and quality for juvenile Sablefish: Inferences from stomach contents and stable isotopes -- General conclusion -- Appendix

DNA Persistence in Predator Saliva from Multiple Species and Methods for Optimal Recovery from Depredated Carcasses

Molecular forensics is an important component of wildlife research and management. Using DNA from noninvasive samples collected at predation sites, we can identify predator species and obtain individual genotypes, improving our understanding of predator–prey dynamics and impacts of predators on livestock and endangered species. To improve sample collection strategies, we tested two sample collection methods and estimated degradation rates of predator DNA on the carcasses of multiple prey species. We fed carcasses of calves (Bos taurus) and lambs (Ovis aires) to three captive predator species: wolves (Canis lupus), coyotes (C. latrans), and mountain lions (Puma concolor). We swabbed the carcass in the field, as well as removed a piece of hide from the carcasses and then swabbed it in the laboratory. We swabbed all tissue samples through time and attempted to identify the predator involved in the depredation using salivary DNA. We found the most successful approach for yielding viable salivary DNA was removing hide from the prey and swabbing it in the laboratory. As expected, genotyping error increased through time and our ability to obtain complete genotypes decreased over time, the latter falling below 50% after 24 h. We provide guidelines for sampling salivary DNA from tissues of depredated carcasses for maximum probability of detection

Association of community sanitation usage with soil-transmitted helminth infections among school-aged children in Amhara Region, Ethiopia.

BACKGROUND: Globally, in 2010, approximately 1.5 billion people were infected with at least one species of soil-transmitted helminth (STH), Ascaris lumbricoides, Trichuris trichiura, hookworm (Ancylostoma duodenale and Necator americanus). Infection occurs through ingestion or contact (hookworm) with eggs or larvae in the environment from fecal contamination. To control these infections, the World Health Organization recommends periodic mass treatment of at-risk populations with deworming drugs. Prevention of these infections typically relies on improved excreta containment and disposal. Most evidence of the relationship between sanitation and STH has focused on household-level access or usage, rather than community-level sanitation usage. We examined the association between the proportion of households in a community with latrines in use and prevalence of STH infections among school-aged children. METHODS: Data on STH prevalence and household latrine usage were obtained during four population-based, cross-sectional surveys conducted between 2011 and 2014 in Amhara, Ethiopia. Multilevel regression was used to estimate the association between the proportion of households in the community with latrines in use and presence of STH infection, indicated by > 0 eggs in stool samples from children 6-15 years old. RESULTS: Prevalence of STH infection was estimated as 22% (95% CI: 20-24%), 14% (95% CI: 13-16%), and 4% (95% CI: 4-5%) for hookworm, A. lumbricoides, and T. trichiura, respectively. Adjusting for individual, household, and community characteristics, hookworm prevalence was not associated with community sanitation usage. Trichuris trichuria prevalence was higher in communities with sanitation usage ≥ 60% versus sanitation usage < 20%. Association of community sanitation usage with A. lumbricoides prevalence depended on household sanitation. Community sanitation usage was not associated with A. lumbricoides prevalence among households with latrines in use. Among households without latrines in use, A. lumbricoides prevalence was higher comparing communities with sanitation usage ≥ 60% versus < 20%. Households with a latrine in use had lower prevalence of A. lumbricoides compared to households without latrines in use only in communities where sanitation usage was ≥ 80%. CONCLUSIONS: We found no evidence of a protective association between community sanitation usage and STH infection. The relationship between STH infection and community sanitation usage may be complex and requires further study

Pre-operative trichiatic eyelash pattern predicts post-operative trachomatous trichiasis.

IMPORTANCE: Trichiasis surgery programs globally have faced high rates of poor surgical outcomes. Identifying correctable risk factors for improving long-term outcomes is essential for countries targeting elimination of trachoma as a public health problem. OBJECTIVE: To determine whether the location of trichiatic eyelashes prior to surgery influences development of post-operative trichiasis (PTT) within two years after surgery. DESIGN: Secondary data analysis of four randomized clinical trials evaluating methods to improve trichiasis surgery outcomes. These include the Surgery for Trichiasis, Antibiotics for Recurrence (STAR) trial, Partnership for Rapid Elimination of Trachoma (PRET-Surgery), absorbable versus silk sutures trial, and epilation versus surgery for minor trichiasis trial. SETTING: Primary trials were conducted in rural areas of Ethiopia and Tanzania. INTERVENTIONS OR EXPOSURES: Trichiasis surgery performed with either the bilamellar tarsal rotation procedure or posterior lamellar rotation procedure. MAIN OUTCOMES: Prevalence of PTT within two years after surgery, location of trichiatic eyelashes pre-operatively and post-operatively. RESULTS: 6,747 eyelids that underwent first-time trichiasis surgery were included. PTT rates varied by study, ranging from 10-40%. PTT was less severe (based on number of trichiatic eyelashes) than initial trichiasis for 72% of those developing PTT, and only 2% of eyelids were worse at follow up than pre-operatively. Eyelids with central only-trichiasis pre-operatively had lower rates of PTT than eyelids with peripheral only trichiasis in each of the three trials that included severe TT cases. 10% of eyelids with peripheral trichiasis pre-operatively that develop PTT have central TT post-operatively. CONCLUSIONS AND RELEVANCE: Pre-operative central trichiasis is less likely than peripheral trichiasis to be associated with subsequent PTT. Regardless of type of surgery, surgeon skill levels, or pre-operative trichiasis severity, the presence of peripheral trichiasis pre-operatively is associated with higher rates of PTT. Making an incision that extends the length of the eyelid and adequately rotating the nasal and temporal aspects of the eyelid when suturing may help to minimize the chance of developing peripheral PTT. TRIAL REGISTRATION: ClinicalTrials.gov PRET: NCT00886015; Suture: NCT005228560; Epilation: NCT00522912

Paths Explored, Paths Omitted, Paths Obscured: Decision Points & Selective Reporting in End-to-End Data Analysis

Drawing reliable inferences from data involves many, sometimes arbitrary, decisions across phases of data collection, wrangling, and modeling. As different choices can lead to diverging conclusions, understanding how researchers make analytic decisions is important for supporting robust and replicable analysis. In this study, we pore over nine published research studies and conduct semi-structured interviews with their authors. We observe that researchers often base their decisions on methodological or theoretical concerns, but subject to constraints arising from the data, expertise, or perceived interpretability. We confirm that researchers may experiment with choices in search of desirable results, but also identify other reasons why researchers explore alternatives yet omit findings. In concert with our interviews, we also contribute visualizations for communicating decision processes throughout an analysis. Based on our results, we identify design opportunities for strengthening end-to-end analysis, for instance via tracking and meta-analysis of multiple decision paths

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie

Pathogenesis of progressive scarring trachoma in Ethiopia and Tanzania and its implications for disease control: two cohort studies.

BACKGROUND: Trachoma causes blindness through a conjunctival scarring process initiated by ocular Chlamydia trachomatis infection; however, the rates, drivers and pathophysiological determinants are poorly understood. We investigated progressive scarring and its relationship to conjunctival infection, inflammation and transcript levels of cytokines and fibrogenic factors. METHODOLOGY/PRINCIPAL FINDINGS: We recruited two cohorts, one each in Ethiopia and Tanzania, of individuals with established trachomatous conjunctival scarring. They were followed six-monthly for two years, with clinical examinations and conjunctival swab sample collection. Progressive scarring cases were identified by comparing baseline and two-year photographs, and compared to individuals without progression. Samples were tested for C. trachomatis by PCR and transcript levels of S100A7, IL1B, IL13, IL17A, CXCL5, CTGF, SPARCL1, CEACAM5, MMP7, MMP9 and CD83 were estimated by quantitative RT-PCR. Progressive scarring was found in 135/585 (23.1%) of Ethiopian participants and 173/577 (30.0%) of Tanzanian participants. There was a strong relationship between progressive scarring and increasing inflammatory episodes (Ethiopia: OR 5.93, 95%CI 3.31-10.6, p<0.0001. Tanzania: OR 5.76, 95%CI 2.60-12.7, p<0.0001). No episodes of C. trachomatis infection were detected in the Ethiopian cohort and only 5 episodes in the Tanzanian cohort. Clinical inflammation, but not scarring progression, was associated with increased expression of S100A7, IL1B, IL17A, CXCL5, CTGF, CEACAM5, MMP7, CD83 and reduced SPARCL1. CONCLUSIONS/SIGNIFICANCE: Scarring progressed in the absence of detectable C. trachomatis, which raises uncertainty about the primary drivers of late-stage trachoma. Chronic conjunctival inflammation appears to be central and is associated with enriched expression of pro-inflammatory factors and altered expression of extracellular matrix regulators. Host determinants of scarring progression appear more complex and subtle than the features of inflammation. Overall this indicates a potential role for anti-inflammatory interventions to interrupt progression and the need for trichiasis disease surveillance and surgery long after chlamydial infection has been controlled at community level

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

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research