Hyporheic Zone Microbiome Assembly Is Linked to Dynamic Water Mixing Patterns in Snowmelt-Dominated Headwater Catchments

Terrestrial and aquatic elemental cycles are tightly linked in upland fluvial networks. Biotic and abiotic mineral weathering, microbially mediated degradation of organic matter, and anthropogenic influences all result in the movement of solutes (e.g., carbon, metals, and nutrients) through these catchments, with implications for downstream water quality. Within the river channel, the region of hyporheic mixing represents a hot spot of microbial activity, exerting significant control over solute cycling. To investigate how snowmelt-driven seasonal changes in river discharge affect microbial community assembly and carbon biogeochemistry, depth-resolved pore water samples were recovered from multiple locations around a representative meander on the East River near Crested Butte, CO, USA. Vertical temperature sensor arrays were also installed in the streambed to enable seepage flux estimates. Snowmelt-driven high river discharge led to an expanding zone of vertical hyporheic mixing and introduced dissolved oxygen into the streambed that stimulated aerobic microbial respiration. These physicochemical processes contributed to microbial communities undergoing homogenizing selection, in contrast to other ecosystems where lower permeability may limit the extent of mixing. Conversely, lower river discharge conditions led to a greater influence of upwelling groundwater within the streambed and a decrease in microbial respiration rates. Associated with these processes, microbial communities throughout the streambed exhibited increasing dissimilarity between each other, suggesting that the earlier onset of snowmelt and longer periods of base flow may lead to changes in the composition (and associated function) of streambed microbiomes, with consequent implications for the processing and export of solutes from upland catchments

Adjusting a cancer mortality-prediction model for disease status-related eligibility criteria

<p>Abstract</p> <p>Background</p> <p>Volunteering participants in disease studies tend to be healthier than the general population partially due to specific enrollment criteria. Using modeling to accurately predict outcomes of cohort studies enrolling volunteers requires adjusting for the bias introduced in this way. Here we propose a new method to account for the effect of a specific form of healthy volunteer bias resulting from imposing disease status-related eligibility criteria, on disease-specific mortality, by explicitly modeling the length of the time interval between the moment when the subject becomes ineligible for the study, and the outcome.</p> <p>Methods</p> <p>Using survival time data from 1190 newly diagnosed lung cancer patients at MD Anderson Cancer Center, we model the time from clinical lung cancer diagnosis to death using an exponential distribution to approximate the length of this interval for a study where lung cancer death serves as the outcome. Incorporating this interval into our previously developed lung cancer risk model, we adjust for the effect of disease status-related eligibility criteria in predicting the number of lung cancer deaths in the control arm of CARET. The effect of the adjustment using the MD Anderson-derived approximation is compared to that based on SEER data.</p> <p>Results</p> <p>Using the adjustment developed in conjunction with our existing lung cancer model, we are able to accurately predict the number of lung cancer deaths observed in the control arm of CARET.</p> <p>Conclusions</p> <p>The resulting adjustment was accurate in predicting the lower rates of disease observed in the early years while still maintaining reasonable prediction ability in the later years of the trial. This method could be used to adjust for, or predict the duration and relative effect of any possible biases related to disease-specific eligibility criteria in modeling studies of volunteer-based cohorts.</p

Differential Dynamics of Transposable Elements during Long-Term Diploidization of Nicotiana Section Repandae (Solanaceae) Allopolyploid Genomes

PubMed ID: 23185607This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

The Primary Prevention of PTSD in Firefighters: Preliminary Results of an RCT with 12-Month Follow-Up

AIM: To develop and evaluate an evidence-based and theory driven program for the primary prevention of Post-traumatic Stress Disorder (PTSD). DESIGN: A pre-intervention / post-intervention / follow up control group design with clustered random allocation of participants to groups was used. The "control" group received "Training as Usual" (TAU). METHOD: Participants were 45 career recruits within the recruit school at the Department of Fire and Emergency Services (DFES) in Western Australia. The intervention group received a four-hour resilience training intervention (Mental Agility and Psychological Strength training) as part of their recruit training school curriculum. Data was collected at baseline and at 6- and 12-months post intervention. RESULTS: We found no evidence that the intervention was effective in the primary prevention of mental health issues, nor did we find any significant impact of MAPS training on social support or coping strategies. A significant difference across conditions in trauma knowledge is indicative of some impact of the MAPS program. CONCLUSION: While the key hypotheses were not supported, this study is the first randomised control trial investigating the primary prevention of PTSD. Practical barriers around the implementation of this program, including constraints within the recruit school, may inform the design and implementation of similar programs in the future. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (ANZCTR) ACTRN12615001362583

Towards a resolution of some outstanding issues in transitive research: an empirical test on middle childhood

Transitive Inference (deduce B > D from B > C and C > D) can help us to understand other areas of sociocognitive development. Across three experiments, learning, memory, and the validity of two transitive paradigms were investigated. In Experiment 1 (N = 121), 7-year-olds completed a three-term nontraining task or a five-term task requiring extensive-training. Performance was superior on the three-term task. Experiment 2 presented 5–10-year-olds with a new five-term task, increasing learning opportunities without lengthening training (N = 71). Inferences improved, suggesting children can learn five-term series rapidly. Regarding memory, the minor (CD) premise was the best predictor of BD-inferential performance in both task-types. However, tasks exhibited different profiles according to associations between the major (BC) premise and BD inference, correlations between the premises, and the role of age. Experiment 3 (N = 227) helped rule out the possible objection that the above findings simply stemmed from three-term tasks with real objects being easier to solve than computer-tasks. It also confirmed that, unlike for five-term task (Experiments 1 & 2), inferences on three-term tasks improve with age, whether the age range is wide (Experiment 3) or narrow (Experiment 2). I conclude that the tasks indexed different routes within a dual-process conception of transitive reasoning: The five-term tasks indexes Type 1 (associative) processing, and the three-term task indexes Type 2 (analytic) processing. As well as demonstrating that both tasks are perfectly valid, these findings open up opportunities to use transitive tasks for educability, to investigate the role of transitivity in other domains of reasoning, and potentially to benefit the lived experiences of persons with developmental issues

Methods to study splicing from high-throughput RNA Sequencing data

The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task. In the last few years, a plethora of tools have been developed, allowing researchers to process RNA-Seq data to study the expression of isoforms and splicing events, and their relative changes under different conditions. We provide an overview of the methods available to study splicing from short RNA-Seq data. We group the methods according to the different questions they address: 1) Assignment of the sequencing reads to their likely gene of origin. This is addressed by methods that map reads to the genome and/or to the available gene annotations. 2) Recovering the sequence of splicing events and isoforms. This is addressed by transcript reconstruction and de novo assembly methods. 3) Quantification of events and isoforms. Either after reconstructing transcripts or using an annotation, many methods estimate the expression level or the relative usage of isoforms and/or events. 4) Providing an isoform or event view of differential splicing or expression. These include methods that compare relative event/isoform abundance or isoform expression across two or more conditions. 5) Visualizing splicing regulation. Various tools facilitate the visualization of the RNA-Seq data in the context of alternative splicing. In this review, we do not describe the specific mathematical models behind each method. Our aim is rather to provide an overview that could serve as an entry point for users who need to decide on a suitable tool for a specific analysis. We also attempt to propose a classification of the tools according to the operations they do, to facilitate the comparison and choice of methods.Comment: 31 pages, 1 figure, 9 tables. Small corrections adde

Developing and Validating a Multivariable Prognostic-Predictive Classifier for Treatment Escalation of Oropharyngeal Squamous Cell Carcinoma: The PREDICTR-OPC Study.

PURPOSE: While there are several prognostic classifiers, to date, there are no validated predictive models that inform treatment selection for oropharyngeal squamous cell carcinoma (OPSCC).Our aim was to develop clinical and/or biomarker predictive models for patient outcome and treatment escalation for OPSCC. EXPERIMENTAL DESIGN: We retrospectively collated clinical data and samples from a consecutive cohort of OPSCC cases treated with curative intent at ten secondary care centers in United Kingdom and Poland between 1999 and 2012. We constructed tissue microarrays, which were stained and scored for 10 biomarkers. We then undertook multivariable regression of eight clinical parameters and 10 biomarkers on a development cohort of 600 patients. Models were validated on an independent, retrospectively collected, 385-patient cohort. RESULTS: A total of 985 subjects (median follow-up 5.03 years, range: 4.73-5.21 years) were included. The final biomarker classifier, comprising p16 and survivin immunohistochemistry, high-risk human papillomavirus (HPV) DNA in situ hybridization, and tumor-infiltrating lymphocytes, predicted benefit from combined surgery + adjuvant chemo/radiotherapy over primary chemoradiotherapy in the high-risk group [3-year overall survival (OS) 63.1% vs. 41.1%, respectively, HR = 0.32; 95% confidence interval (CI), 0.16-0.65; P = 0.002], but not in the low-risk group (HR = 0.4; 95% CI, 0.14-1.24; P = 0.114). On further adjustment by propensity scores, the adjusted HR in the high-risk group was 0.34, 95% CI = 0.17-0.67, P = 0.002, and in the low-risk group HR was 0.5, 95% CI = 0.1-2.38, P = 0.384. The concordance index was 0.73. CONCLUSIONS: We have developed a prognostic classifier, which also appears to demonstrate moderate predictive ability. External validation in a prospective setting is now underway to confirm this and prepare for clinical adoption

Insulin-Like Peptides and the Target of Rapamycin Pathway Coordinately Regulate Blood Digestion and Egg Maturation in the Mosquito Aedes aegypti

Mosquitoes are insects that vector many serious pathogens to humans and other vertebrates. Most mosquitoes must feed on the blood of a vertebrate host to produce eggs. In turn, multiple cycles of blood feeding promote frequent contacts with hosts and make mosquitoes ideal disease vectors. Both hormonal and nutritional factors are involved in regulating egg development in the mosquito, Aedes aegypti. However, the processes that regulate digestion of the blood meal remain unclear.Here we report that insulin peptide 3 (ILP3) directly stimulated late phase trypsin-like gene expression in blood fed females. In vivo knockdown of the mosquito insulin receptor (MIR) by RNA interference (RNAi) delayed but did not fully inhibit trypsin-like gene expression in the midgut, ecdysteroid (ECD) production by ovaries, and vitellogenin (Vg) expression by the fat body. In contrast, in vivo treatment with double-stranded MIR RNA and rapamycin completely blocked egg production. In vitro experiments showed that amino acids did not simulate late phase trypsin-like gene expression in the midgut or ECD production by the ovaries. However, amino acids did enhance ILP3-mediated stimulation of trypsin-like gene expression and ECD production.Overall, our results indicate that ILPs from the brain synchronize blood meal digestion and amino acid availability with ovarian ECD production to maximize Vg expression by the fat body. The activation of digestion by ILPs may also underlie the growth promoting effects of insulin and TOR signaling in other species

The Maternal Personhood of Cattle and Plants at a Hindu Center in the United States

Religious experiences with sacred nonhuman natural beings considered to be “persons” remain only vaguely understood. This essay provides a measure of clarification by engendering a dialogue between psychoanalytic self psychology on one side and, on the other, religious experiences of cattle and Tulsi plants as holy mothers at a Hindu cattle sanctuary in the United States. Ethnographic data from the Hindu center uncover experiences of sacred maternal natural beings that are tensive, liminal, and colored with affective themes of nurturance, respect, and intimacy, much like psychoanalytic maternal selfobjects. Devotees protect cattle and ritually venerate plants because these actions facilitate a limited experiential grounding of religiosity on what is perhaps the most fundamental of all relationships, the relationship with the mother, within a theological worldview that somewhat embraces nonhuman natural beings in both doctrine and practice

HMMSplicer: A Tool for Efficient and Sensitive Discovery of Known and Novel Splice Junctions in RNA-Seq Data

Background: High-throughput sequencing of an organism’s transcriptome, or RNA-Seq, is a valuable and versatile new strategy for capturing snapshots of gene expression. However, transcriptome sequencing creates a new class of alignment problem: mapping short reads that span exon-exon junctions back to the reference genome, especially in the case where a splice junction is previously unknown. Methodology/Principal Findings: Here we introduce HMMSplicer, an accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets. HMMSplicer identifies more splice junctions than currently available algorithms when tested on publicly available A. thaliana, P. falciparum, and H. sapiens datasets without a reduction in specificity. Conclusions/Significance: HMMSplicer was found to perform especially well in compact genomes and on genes with low expression levels, alternative splice isoforms, or non-canonical splice junctions. Because HHMSplicer does not rely on prebuilt gene models, the products of inexact splicing are also detected. For H. sapiens, we find 3.6 % of 39 splice sites and 1.4% of 59 splice sites are inexact, typically differing by 3 bases in either direction. In addition, HMMSplicer provides a score for every predicted junction allowing the user to set a threshold to tune false positive rates depending on the needs of the experiment. HMMSplicer is implemented in Python. Code and documentation are freely available a