Effects on Campostoma oligolepis Digestive Morphology and Gut Microbiota Composition across a Gradient of Urbanization

Campostoma oligolepis, the Largescale Stoneroller, is a species of minnow native to northwest Georgia. This study investigated the impacts of urbanization on gut length and gut microbiota community composition in C. oligolepis from four small watersheds within the Etowah River drainage basin with different levels of impervious surface coverage (ISC). Individuals were collected from each sample site in the summer of 2016 between late July and early September. A second round of sampling was conducted in the fall between mid-October and mid-November. The gut length to total length ratio was calculated for each individual to allow for an unbiased comparison of gut lengths between individuals of varying sizes. Additionally, gut microbiota communities from summer individuals’ fore- and hindguts were identified using 16S metagenomic sequencing on an Ion Torrent platform. Summer individuals from watersheds with lower ISC had significantly longer gut lengths than individuals from watersheds with higher ISC. However, no significant difference in relative gut length was found between sample sites for the individuals collected in fall. A significant decrease in relative gut length of individuals from sites with lower ISC was observed from summer to fall. Sequence data from the summer individuals revealed the presence of 36 bacterial phyla and 1,008 genera in Campostoma gut contents. Overall, Proteobacteria and Firmicutes accounted for the greatest percentage of the attributable reads. Pseudoalteromonas, Acinetobacter, and Blautia were the three most prevalent genera across sites and between gut regions. Nonmetric multi-dimensional scaling analysis using the 22 bacterial genera that accounted for the highest proportion of sequences across all sites revealed some grouping of samples based on site. However, distinct patterns in bacterial composition according to gut region or ISC by site were not apparent. These findings suggest that Campostoma may not rely on symbiotic bacteria to aid in digestion

Potential Spawning Strategy and Fecundity of Alabama Shad (Alosa alabamae) from the Apalachicola River, Florida

Alabama shad (Alosa alabamae), classified as a Species of Concern by the National Marine Fisheries Service, are native to the northern Gulf of Mexico drainages. Our study estimated the fecundity of 39 female Alabama shad from the Apalachicola River, Florida. Individuals ranged in age from 2-4 years with an average weight of 729 g. Samples (1 g) were cut from the center of each ovary, and oocytes present were counted. Diameters of 50 randomly-sampled oocytes were measured per sample. Oocyte diameters ranged from 0.3-2.7 mm, with a mode of 1.5 mm. The unimodal oocyte diameter percent frequency distribution suggests that Alabama shad spawn multiple times in a spawning season. Total mean ovary weight was 67.88 ± 25.90 (s.d.) g/individual, with average annual fecundity estimated to be 79,420 ± 26,896 (s.d.) oocytes/individual. Our results were consistent with previous Alabama shad fecundity studies out of the Apalachicola River

Late Permian–Early Triassic environmental changes recorded by multi-isotope (Re-Os-N-Hg) data and trace metal distribution from the Hovea-3 section, Western Australia

The temporal coincidence between the Late Permian mass extinction (LPME) and the emplacement of Siberian Trap basalts suggests a causal link between the two events. Here, we discuss stratigraphic changes of organic and inorganic (including isotopic) geochemical properties of marine sediments across the Permian–Triassic boundary (PTB) in the Hovea-3 core, Western Australia, a key PTB section in the southern Neo-Tethys ocean. These data are compared with published data from the Meishan section, southern China, and from the Opal Creek section in western Canada, providing a view of Tethys and Panthalassa changes at the PTB. Trace metal and N-isotopic data, together with organic matter properties suggest that anoxic conditions were established prior to the LPME, intensified close to the LPME, and continued with photic-zone euxinia into the Early Triassic. For the Hovea-3 section, Re-Os ages confirm Changhsingian (253.5 ± 1.4 Ma) deposition of the dated interval sampled immediately below the stratigraphic level characterized by major lithological and isotopic changes. Evaluation of Re-Os, N, and Hg elemental and isotopic data for Hovea-3 suggests that anoxic conditions in the latest Permian were generally unrelated to direct magmatic contributions. A major increase in the initial Os isotopic ratio of Lower Triassic shales suggest an ~8× increase in the Early Triassic continental runoff, based on moderately conservative assumptions for end-members contributing Os to the Permian–Triassic ocean. Comparison to other PTB sections confirms a global signal of increasing Re/Os ratios in the Late Permian, and major and long-lived changes in the isotopic composition of the post-extinction ocean. A distinct peak in Hg concentrations carrying a volcanic isotopic signature, also identified in other PTB sections, likely represents a major pulse of Siberian Trap volcanism. This Hg peak in the Hovea-3 section, however, is detected above the stratigraphic level containing multiple other widely recognized and more permanent geochemical changes. Therefore, direct volcanic inputs to the Permian–Triassic Ocean likely post-date the LPME in this Western Australian section

Ontogeny vs. phylogeny in Primate/Canid comparisons: a meta-analysis of the object choice task

The Object Choice Task (OCT) is a widely used paradigm with which researchers measure the ability of a subject to comprehend deictic (directional) cues, such as pointing gestures and eye gaze. There is a widespread belief that nonhuman primates evince only a weak capacity to use deictic cues; in contrast, domestic dogs (Canis familiaris) tend to demonstrate high success rates. This pattern of canid superiority has been taken to support the Domestication Hypothesis, which posits enhancing effects of artificial selection on the sociocognitive abilities of dogs and humans. Here we review nearly two decades of published findings, using variants of the OCT. We find systematic confounds with species classification in task-relevant preparation of the subjects, in the imposition of a barrier between reward and subject, and in the specific deictic cues used to indicate the location of hidden objects. Thus, the widespread belief that dogs outperform primates on OCTs is undermined by the systematic procedural differences in the assessments of these skills, differences that are confounded with taxonomic classification

Chapter 9 Outdoor air pollutants sources, characteristics, and impact on human health and the environment

In this chapter, sources and characteristics of outdoor air pollutants are presented along with their effects on human health and the environment. In addition, emphasis is given to air pollutant monitoring by exploring the type of monitoring programs, sampling methods, and emission standards and by presenting the case of air pollution monitoring in the United Arab Emirates. Finally, the chapter explores the case of climate change by looking into its causes and economic and environmental impacts

Circulating microRNAs in sera correlate with soluble biomarkers of immune activation but do not predict mortality in ART treated individuals with HIV-1 infection: A case control study

Introduction: The use of anti-retroviral therapy (ART) has dramatically reduced HIV-1 associated morbidity and mortality. However, HIV-1 infected individuals have increased rates of morbidity and mortality compared to the non-HIV-1 infected population and this appears to be related to end-organ diseases collectively referred to as Serious Non-AIDS Events (SNAEs). Circulating miRNAs are reported as promising biomarkers for a number of human disease conditions including those that constitute SNAEs. Our study sought to investigate the potential of selected miRNAs in predicting mortality in HIV-1 infected ART treated individuals. Materials and Methods: A set of miRNAs was chosen based on published associations with human disease conditions that constitute SNAEs. This case: control study compared 126 cases (individuals who died whilst on therapy), and 247 matched controls (individuals who remained alive). Cases and controls were ART treated participants of two pivotal HIV-1 trials. The relative abundance of each miRNA in serum was measured, by RTqPCR. Associations with mortality (all-cause, cardiovascular and malignancy) were assessed by logistic regression analysis. Correlations between miRNAs and CD4+ T cell count, hs-CRP, IL-6 and D-dimer were also assessed. Results: None of the selected miRNAs was associated with all-cause, cardiovascular or malignancy mortality. The levels of three miRNAs (miRs -21, -122 and -200a) correlated with IL-6 while miR-21 also correlated with D-dimer. Additionally, the abundance of miRs -31, -150 and -223, correlated with baseline CD4+ T cell count while the same three miRNAs plus miR- 145 correlated with nadir CD4+ T cell count. Discussion: No associations with mortality were found with any circulating miRNA studied. These results cast doubt onto the effectiveness of circulating miRNA as early predictors of mortality or the major underlying diseases that contribute to mortality in participants treated for HIV-1 infection

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 Validation of a Risk Score for Chronic Kidney Disease in HIV Infection Using Prospective Cohort Data from the D:A:D Study

Ristola M. on työryhmien DAD Study Grp ; Royal Free Hosp Clin Cohort ; INSIGHT Study Grp ; SMART Study Grp ; ESPRIT Study Grp jäsen.Background Chronic kidney disease (CKD) is a major health issue for HIV-positive individuals, associated with increased morbidity and mortality. Development and implementation of a risk score model for CKD would allow comparison of the risks and benefits of adding potentially nephrotoxic antiretrovirals to a treatment regimen and would identify those at greatest risk of CKD. The aims of this study were to develop a simple, externally validated, and widely applicable long-term risk score model for CKD in HIV-positive individuals that can guide decision making in clinical practice. Methods and Findings A total of 17,954 HIV-positive individuals from the Data Collection on Adverse Events of Anti-HIV Drugs (D:A:D) study with >= 3 estimated glomerular filtration rate (eGFR) values after 1 January 2004 were included. Baseline was defined as the first eGFR > 60 ml/min/1.73 m2 after 1 January 2004; individuals with exposure to tenofovir, atazanavir, atazanavir/ritonavir, lopinavir/ritonavir, other boosted protease inhibitors before baseline were excluded. CKD was defined as confirmed (>3 mo apart) eGFR In the D:A:D study, 641 individuals developed CKD during 103,185 person-years of follow-up (PYFU; incidence 6.2/1,000 PYFU, 95% CI 5.7-6.7; median follow-up 6.1 y, range 0.3-9.1 y). Older age, intravenous drug use, hepatitis C coinfection, lower baseline eGFR, female gender, lower CD4 count nadir, hypertension, diabetes, and cardiovascular disease (CVD) predicted CKD. The adjusted incidence rate ratios of these nine categorical variables were scaled and summed to create the risk score. The median risk score at baseline was -2 (interquartile range -4 to 2). There was a 1: 393 chance of developing CKD in the next 5 y in the low risk group (risk score = 5, 505 events), respectively. Number needed to harm (NNTH) at 5 y when starting unboosted atazanavir or lopinavir/ritonavir among those with a low risk score was 1,702 (95% CI 1,166-3,367); NNTH was 202 (95% CI 159-278) and 21 (95% CI 19-23), respectively, for those with a medium and high risk score. NNTH was 739 (95% CI 506-1462), 88 (95% CI 69-121), and 9 (95% CI 8-10) for those with a low, medium, and high risk score, respectively, starting tenofovir, atazanavir/ritonavir, or another boosted protease inhibitor. The Royal Free Hospital Clinic Cohort included 2,548 individuals, of whom 94 individuals developed CKD (3.7%) during 18,376 PYFU (median follow-up 7.4 y, range 0.3-12.7 y). Of 2,013 individuals included from the SMART/ESPRIT control arms, 32 individuals developed CKD (1.6%) during 8,452 PYFU (median follow-up 4.1 y, range 0.6-8.1 y). External validation showed that the risk score predicted well in these cohorts. Limitations of this study included limited data on race and no information on proteinuria. Conclusions Both traditional and HIV-related risk factors were predictive of CKD. These factors were used to develop a risk score for CKD in HIV infection, externally validated, that has direct clinical relevance for patients and clinicians to weigh the benefits of certain antiretrovirals against the risk of CKD and to identify those at greatest risk of CKD.Peer reviewe