An assessment of the frequency and cause of concentrated flow on agricultural fields in the Virginia Coastal Plain portion of the Chesapeake Bay watershed

Agricultural lands are the largest non-point source of nitrogen, phosphorous, and sediment that is delivered to Chesapeake Bay. There has been an increase in the amount of these nutrients and sediment being delivered to the Bay over the last century, which has caused extensive eutrophication and subsequent anoxic zones in the Bay. The Chesapeake Bay Act attempted to mitigate this problem by mandating 100-foot riparian buffer zones between agricultural fields and perennial streams in the Coastal Plain region of Virginia. Previous studies have shown that riparian buffers increase infiltration of runoff into the groundwater system, where nutrients and sediment can be removed from the water before it discharges into perennial streams. However, riparian buffers require flow to be widely disseminated throughout the buffer area in order for them to be effective. No declining trends have been noted in the amounts of nutrients and sediment being delivered to Chesapeake Bay since 1990, when buffers were required to be maintained in the Coastal Plain region of Virginia. I hypothesized that flow concentration, which can promote channel incision and allow agricultural runoff to bypass riparian buffers, is widespread in the Coastal Plain region of Virginia and may be one reason why reductions of nutrients and sediment in Bay waters have not been as great as expected. Geographic Information Systems (GIS) was used to determine flow accumulation patterns across 74 agricultural fields in the Coastal Plain region of Virginia. The percentage of each field drained by the 5 field margin points of greatest flow accumulation area was used as a proxy for measuring flow concentration. The cell size for points along each field margin was 3 m by 3 m. Further, 4 field indexes that related topographic and soil parameters on a field (wetness index, topographic index, water retention index, sediment transport index) were calculated for each field. These indexes were analyzed to determine if any were correlated with and could be used to easily predict places of flow concentration over a large geographic area, such as the Coastal Plain region of Virginia. Flow concentration occurred on all 74 study fields. On average, 70% of a field was drained through just 5 points along its field margin. The strongest field index relationship existed between the Wetness Index and flow concentration (R2 = 0.323). The field indexes were not good predictors of areas of high flow concentration because for any given value of an index, there was a large range of possible flow concentrations. Of the 6 topographic/soil property characteristics analyzed by these 4 field indexes (specific catchment area, runoff source area, slope, saturated hydraulic conductivity, depth to impermeable subsurface layer, and rainfall erosivity), the field slope showed the strongest relationship with flow concentration (R2 = 0.270). Principle component analysis on these 6 topographic/soil property characteristics had a first component that described 47% of the variance among these 6 variables and displayed the strongest relationship with flow concentration (R2 = 0.403). Rather than being attributable to characteristics of the topography or soil that vary from place to place, flow concentration seems to be a phenomenon that is of widespread occurrence in all areas of the Coastal Plain region of Virginia. I recommend requiring farmers to maintain riparian buffers on their land yearly. Future research should focus on determining how to reduce flow concentration through and increase the effectiveness of riparian buffers in the Coastal Plain region of Virginia

Navigating data governance associated with real-world data for public benefit: an overview in the UK and future considerations

Real-world data encompass data primarily captured for the provision or operation of services, for example, electronic health records for direct care purposes, but which may have secondary uses for informing research or commissioning. Public benefit is potentially forfeited by the underutilisation of real-world data for secondary uses, in part due to risk aversion when faced with the prospect of navigating necessary and important data governance processes. Such processes can be perceived as complex, daunting, time-consuming and exposing organisations to risk. By providing an overview description and discussion around the role of six key legal and information governance frameworks and their role regarding responsible data access, linkage and sharing, our intention is to make data governance a less daunting prospect and reduce the perception that it is a barrier to secondary uses, thus enabling public benefit

Learning Existing Social Conventions via Observationally Augmented Self-Play

In order for artificial agents to coordinate effectively with people, they must act consistently with existing conventions (e.g. how to navigate in traffic, which language to speak, or how to coordinate with teammates). A group's conventions can be viewed as a choice of equilibrium in a coordination game. We consider the problem of an agent learning a policy for a coordination game in a simulated environment and then using this policy when it enters an existing group. When there are multiple possible conventions we show that learning a policy via multi-agent reinforcement learning (MARL) is likely to find policies which achieve high payoffs at training time but fail to coordinate with the real group into which the agent enters. We assume access to a small number of samples of behavior from the true convention and show that we can augment the MARL objective to help it find policies consistent with the real group's convention. In three environments from the literature - traffic, communication, and team coordination - we observe that augmenting MARL with a small amount of imitation learning greatly increases the probability that the strategy found by MARL fits well with the existing social convention. We show that this works even in an environment where standard training methods very rarely find the true convention of the agent's partners.Comment: Published in AAAI-AIES2019 - Best Pape

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

Understanding the relationship between genetic and phenotypic variation is one of the great outstanding challenges in biology. To meet this challenge, comprehensive genomic variation maps of human as well as of model organism populations are required. Here, we present a nucleotide resolution catalog of single-nucleotide, multi-nucleotide, and structural variants in 39 Drosophila melanogaster Genetic Reference Panel inbred lines. Using an integrative, local assembly-based approach for variant discovery, we identify more than 3.6 million distinct variants, among which were more than 800,000 unique insertions, deletions (indels), and complex variants (1 to 6,000 bp). While the SNP density is higher near other variants, we find that variants themselves are not mutagenic, nor are regions with high variant density particularly mutation-prone. Rather, our data suggest that the elevated SNP density around variants is mainly due to population-level processes. We also provide insights into the regulatory architecture of gene expression variation in adult flies by mapping cis-expression quantitative trait loci (cis-eQTLs) for more than 2,000 genes. Indels comprise around 10% of all cis-eQTLs and show larger effects than SNP cis-eQTLs. In addition, we identified two-fold more gene associations in males as compared to females and found that most cis-eQTLs are sex-specific, revealing a partial decoupling of the genomic architecture between the sexes as well as the importance of genetic factors in mediating sex-biased gene expression. Finally, we performed RNA-seq-based allelic expression imbalance analyses in the offspring of crosses between sequenced lines, which revealed that the majority of strong cis-eQTLs can be validated in heterozygous individuals

Cancer Trajectories at the End of Life: is there an effect of age and gender?

<p>Abstract</p> <p>Background</p> <p>Few empirical data show the pattern of functional decline at the end of life for cancer patients, especially among older patients.</p> <p>Methods</p> <p>In a mortality follow-back survey (the Italian Survey of the Dying of Cancer – ISDOC) a random sample of 1,271 lay caregivers were interviewed, at a mean of 234 days after bereavement. The main outcome was number of days before death when the patient experienced a permanent functional decline.</p> <p>Results</p> <p>1,249 (98%) caregivers answered the question about patient's function. The probability to be free from a functional disability was high (94%) 52 weeks before death, but was lower for older age groups (15% for those aged 85 or more) and women (8%). It remained stable until 18 weeks before death, then fell to 63% at 12 weeks and 49% at 6 weeks before death (among those aged 85 or more the figures were 50% and 41%). The pattern was consistent across sub-groups, except for patients affected by Central Nervous System tumors who experienced a longer, slower functional decline.</p> <p>Conclusion</p> <p>This study provides empirical support for the declining trajectory in cancer, and suggests that the decline commences at around 12 weeks in all age groups, even among patients over 85 years.</p

Incarceration history and risk of HIV and hepatitis C virus acquisition among people who inject drugs: a systematic review and meta-analysis

Background People who inject drugs (PWID) experience a high prevalence of incarceration and might be at high risk of HIV and hepatitis C virus (HCV) infection during or after incarceration. We aimed to assess whether incarceration history elevates HIV or HCV acquisition risk among PWID. Methods In this systematic review and meta-analysis, we searched MEDLINE, Embase, and PsycINFO databases for studies in any language published from Jan 1, 2000 until June 13, 2017 assessing HIV or HCV incidence among PWID. We included studies that measured HIV or HCV incidence among community-recruited PWID. We included only studies reporting original results and excluded studies that evaluated incident infections by self-report. We contacted authors of cohort studies that met the inclusion or exclusion criteria, but that did not report on the outcomes of interest, to request data. We extracted and pooled data from the included studies using random-effects meta-analyses to quantify the associations between recent (past 3, 6, or 12 months or since last follow-up) or past incarceration and HIV or HCV acquisition (primary infection or reinfection) risk among PWID. We assessed the risk of bias of included studies using the Newcastle-Ottawa Scale. Between-study heterogeneity was evaluated using the I2 statistic and the P-value for heterogeneity. Findings We included published results from 20 studies and unpublished results from 21 studies. These studies originated from Australasia, western and eastern Europe, North and Latin America, and east and southeast Asia. Recent incarceration was associated with an 81% (relative risk [RR] 1·81, 95% CI 1·40–2·34) increase in HIV acquisition risk, with moderate heterogeneity between studies (I2=63·5%; p=0·001), and a 62% (RR 1·62, 95% CI 1·28–2·05) increase in HCV acquisition risk, also with moderate heterogeneity between studies (I2=57·3%; p=0·002). Past incarceration was associated with a 25% increase in HIV (RR 1·25, 95% CI 0·94–1·65) and a 21% increase in HCV (1·21, 1·02–1·43) acquisition risk. Interpretation Incarceration is associated with substantial short-term increases in HIV and HCV acquisition risk among PWID and could be a significant driver of HCV and HIV transmission among PWID. These findings support the need for developing novel interventions to minimise the risk of HCV and HIV acquisition, including addressing structural risks associated with drug laws and excessive incarceration of PWID

High platelet reactivity in patients with acute coronary syndromes undergoing percutaneous coronary intervention: Randomised controlled trial comparing prasugrel and clopidogrel

Background: Prasugrel is more effective than clopidogrel in reducing platelet aggregation in acute coronary syndromes. Data available on prasugrel reloading in clopidogrel treated patients with high residual platelet reactivity (HRPR) i.e. poor responders, is limited. Objectives: To determine the effects of prasugrel loading on platelet function in patients on clopidogrel and high platelet reactivity undergoing percutaneous coronary intervention for acute coronary syndrome (ACS). Patients: Patients with ACS on clopidogrel who were scheduled for PCI found to have a platelet reactivity ≥40 AUC with the Multiplate Analyzer, i.e. “poor responders” were randomised to prasugrel (60 mg loading and 10 mg maintenance dose) or clopidogrel (600 mg reloading and 150 mg maintenance dose). The primary outcome measure was proportion of patients with platelet reactivity <40 AUC 4 hours after loading with study medication, and also at one hour (secondary outcome). 44 patients were enrolled and the study was terminated early as clopidogrel use decreased sharply due to introduction of newer P2Y12 inhibitors. Results: At 4 hours after study medication 100% of patients treated with prasugrel compared to 91% of those treated with clopidogrel had platelet reactivity <40 AUC (p = 0.49), while at 1 hour the proportions were 95% and 64% respectively (p = 0.02). Mean platelet reactivity at 4 and 1 hours after study medication in prasugrel and clopidogrel groups respectively were 12 versus 22 (p = 0.005) and 19 versus 34 (p = 0.01) respectively. Conclusions: Routine platelet function testing identifies patients with high residual platelet reactivity (“poor responders”) on clopidogrel. A strategy of prasugrel rather than clopidogrel reloading results in earlier and more sustained suppression of platelet reactivity. Future trials need to identify if this translates into clinical benefit

Is There an Association between Advanced Paternal Age and Endophenotype Deficit Levels in Schizophrenia?

The children of older fathers have increased risks of developing schizophrenia spectrum disorders, and among those who develop these disorders, those with older fathers present with more severe clinical symptoms. However, the influence of advanced paternal age on other important domains related to schizophrenia, such as quantitative endophenotype deficit levels, remains unknown. This study investigated the associations between paternal age and level of endophenotypic impairment in a well-characterized family-based sample from the Consortium on the Genetics of Schizophrenia (COGS). All families included at least one affected subject and one unaffected sibling. Subjects met criteria for schizophrenia (probands; n = 293) or were unaffected first-degree siblings of those probands (n = 382). Paternal age at the time of subjects’ birth was documented. Subjects completed a comprehensive clinical assessment and a battery of tests that measured 16 endophenotypes. After controlling for covariates, potential paternal age–endophenotype associations were analyzed using one model that included probands alone and a second model that included both probands and unaffected siblings. Endophenotype deficits in the Identical Pairs version of the 4-digit Continuous Performance Test and in the Penn Computerized Neurocognitive Battery verbal memory test showed significant associations with paternal age. However, after correcting for multiple comparisons, no endophenotype was significantly associated with paternal age. These findings suggest that factors other than advanced paternal age at birth may account for endophenotypic deficit levels in schizophrenia

Exploiting Ligand-Protein Conjugates to Monitor Ligand-Receptor Interactions

We introduce three assays for analyzing ligand-receptor interactions based on the specific conjugation of ligands to SNAP-tag fusion proteins. Conjugation of ligands to different SNAP-tag fusions permits the validation of suspected interactions in cell extracts and fixed cells as well as the establishment of high-throughput assays. The different assays allow the analysis of strong and weak interactions. Conversion of ligands into SNAP-tag substrates thus provides access to a powerful toolbox for the analysis of their interactions with proteins